Unprecedented staining of polar lipids by a luminescent rhenium complex revealed by FTIR microspectroscopy in adipocytes.

PubMed

Bader, C A; Carter, E A; Safitri, A; Simpson, P V; Wright, P; Stagni, S; Massi, M; Lay, P A; Brooks, D A; Plush, S E

2016-06-21

Fourier transform infrared (FTIR) microspectroscopy and confocal imaging have been used to demonstrate that the neutral rhenium(i) tricarbonyl 1,10-phenanthroline complex bound to 4-cyanophenyltetrazolate as the ancillary ligand is able to localise in regions with high concentrations of polar lipids such as phosphatidylethanolamine (PE), sphingomyelin, sphingosphine and lysophosphatidic acid (LPA) in mammalian adipocytes.

A Stylistic Study on the Linguistic Deviations in E. E. Cummings' Poetry

ERIC Educational Resources Information Center

Li, Xin; Shi, Mengchen

2015-01-01

Regarded as the pioneer of experimental poetry, E. E. Cummings' unconventional treatment of poetic language has reached an unprecedented acme, which has intrigued and baffled numerous scholars, researchers and readers alike. Nevertheless, the very existence of poetry, like other types of literary texts, demonstrates the significance and value of…

A series of three-dimensional lanthanide coordination polymers with rutile and unprecedented rutile-related topologies.

PubMed

Qin, Chao; Wang, Xin-Long; Wang, En-Bo; Su, Zhong-Min

2005-10-03

The complexes of formulas Ln(pydc)(Hpydc) (Ln = Sm (1), Eu (2), Gd (3); H2pydc = pyridine-2,5-dicarboxylic acid) and Ln(pydc)(bc)(H2O) (Ln = Sm (4), Gd (5); Hbc = benzenecarboxylic acid) have been synthesized under hydrothermal conditions and characterized by elemental analysis, IR, TG analysis, and single-crystal X-ray diffraction. Compounds 1-3 are isomorphous and crystallize in the orthorhombic system, space group Pbcn. Their final three-dimensional racemic frameworks can be considered as being constructed by helix-linked scalelike sheets. Compounds 4 and 5 are isostructural and crystallize in the monoclinic system, space group P2(1)/c. pydc ligands bridge dinuclear lanthanide centers to form the three-dimensional frameworks featuring hexagonal channels along the a-axis that are occupied by one-end-coordinated bc ligands. From the topological point of view, the five three-dimensional nets are binodal with six- and three-connected nodes, the former of which exhibit a rutile-related (4.6(2))(2)(4(2).6(9).8(4)) topology that is unprecedented within coordination frames, and the latter two species display a distorted rutile (4.6(2))(2)(4(2).6(10).8(3)) topology. Furthermore, the luminescent properties of 2 were studied.

DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information.

PubMed

Neri, Dario; Lerner, Richard A

2018-06-20

The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice. This review provides a historical account of important milestones in the development of DNA-encoded chemical libraries, a survey of relevant ongoing research activities, and a glimpse into the future.

Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands.

PubMed

Phipps, M Lisa; Lillo, Antoinetta M; Shou, Yulin; Schmidt, Emily N; Paavola, Chad D; Naranjo, Leslie; Bemdich, Sara; Swanson, Basil I; Bradbury, Andrew R M; Martinez, Jennifer S

2016-01-01

Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The "helper cell" packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report on the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.

Ligand combination strategy for the preparation of novel low-dimensional and open-framework metal cluster materials

NASA Astrophysics Data System (ADS)

Anokhina, Ekaterina V.

Low-dimensional and open-framework materials containing transition metals have a wide range of applications in redox catalysis, solid-state batteries, and electronic and magnetic devices. This dissertation reports on research carried out with the goal to develop a strategy for the preparation of low-dimensional and open-framework materials using octahedral metal clusters as building blocks. Our approach takes its roots from crystal engineering principles where the desired framework topologies are achieved through building block design. The key idea of this work is to induce directional bonding preferences in the cluster units using a combination of ligands with a large difference in charge density. This investigation led to the preparation and characterization of a new family of niobium oxychloride cluster compounds with original structure types exhibiting 1ow-dimensional or open-framework character. Most of these materials have framework topologies unprecedented in compounds containing octahedral clusters. Comparative analysis of their structural features indicates that the novel cluster connectivity patterns in these systems are the result of complex interplay between the effects of anisotropic ligand arrangement in the cluster unit and optimization of ligand-counterion electrostatic interactions. The important role played by these factors sets niobium oxychloride systems apart from cluster compounds with one ligand type or statistical ligand distribution where the main structure-determining factor is the total number of ligands. These results provide a blueprint for expanding the ligand combination strategy to other transition metal cluster systems and for the future rational design of cluster-based materials.

Copper-catalyzed asymmetric conjugate addition of Grignard reagents to trisubstituted enones. Construction of all-carbon quaternary chiral centers.

PubMed

Martin, David; Kehrli, Stefan; d'Augustin, Magali; Clavier, Hervé; Mauduit, Marc; Alexakis, Alexandre

2006-07-05

The copper-catalyzed asymmetric conjugate addition of Grignard reagents to trisubstituted cyclic enones affords enantioenriched all-carbon quaternary centers with up to 96% ee. The chiral ligand is a diaminocarbene, directly generated in situ. The combination of Grignard reagent and diaminocarbene is unprecedented in conjugate addition, and the additon of the phenyl group, on such enones, cannot be done by other conjugate addition methods.

One-Bead-Two-Compound Thioether Bridged Macrocyclic γ-AApeptide Screening Library against EphA2.

PubMed

Shi, Yan; Challa, Sridevi; Sang, Peng; She, Fengyu; Li, Chunpu; Gray, Geoffrey M; Nimmagadda, Alekhya; Teng, Peng; Odom, Timothy; Wang, Yan; van der Vaart, Arjan; Li, Qi; Cai, Jianfeng

2017-11-22

Identification of molecular ligands that recognize peptides or proteins is significant but poses a fundamental challenge in chemical biology and biomedical sciences. Development of cyclic peptidomimetic library is scarce, and thus discovery of cyclic peptidomimetic ligands for protein targets is rare. Herein we report the unprecedented one-bead-two-compound (OBTC) combinatorial library based on a novel class of the macrocyclic peptidomimetics γ-AApeptides. In the library, we utilized the coding peptide tags synthesized with Dde-protected α-amino acids, which were orthogonal to solid phase synthesis of γ-AApeptides. Employing the thioether linkage, the desired macrocyclic γ-AApeptides were found to be effective for ligand identification. Screening the library against the receptor tyrosine kinase EphA2 led to the discovery of one lead compound that tightly bound to EphA2 (K d = 81 nM) and potently antagonized EphA2-mediated signaling. This new approach of macrocyclic peptidomimetic library may lead to a novel platform for biomacromolecular surface recognition and function modulation.

Reactivity of the Donor-Stabilized Silylenes [iPrNC(Ph)NiPr]2 Si and [iPrNC(NiPr2 )NiPr]2 Si: Activation of CO2 and CS2.

PubMed

Mück, Felix M; Baus, Johannes A; Nutz, Marco; Burschka, Christian; Poater, Jordi; Bickelhaupt, F Matthias; Tacke, Reinhold

2015-11-09

Activation of CO2 by the bis(amidinato)silylene 1 and the analogous bis(guanidinato)silylene 2 leads to the structurally analogous six-coordinate silicon(IV) complexes 4 (previous work) and 8, respectively, the first silicon compounds with a chelating carbonato ligand. Likewise, CS2 activation by silylene 1 affords the analogous six-coordinate silicon(IV) complex 10, the first silicon compound with a chelating trithiocarbonato ligand. CS2 activation by silylene 2, however, yields the five-coordinate silicon(IV) complex 13 with a carbon-bound CS2 (2-) ligand, which also represents an unprecedented coordination mode in silicon coordination chemistry. Treatment of the dinuclear silicon(IV) complexes 5 and 6 with CO2 also affords the six-coordinate carbonatosilicon(IV) complexes 4 and 8, respectively. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

DOE PAGES

Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

2015-04-02

The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K 1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO 2 2+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K 1 values are significantly overestimated. Accurate predictions of the absolute log K 1 values (root mean square deviation from experiment < 1.0 for logmore » K 1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.« less

Monodisperse hexagonal silver nanoprisms: synthesis via thiolate-protected cluster precursors and chiral, ligand-imprinted self-assembly.

PubMed

Cathcart, Nicole; Kitaev, Vladimir

2011-09-27

Silver nanoprisms of a predominantly hexagonal shape have been prepared using a ligand combination of a strongly binding thiol, captopril, and charge-stabilizing citrate together with hydrogen peroxide as an oxidative etching agent and a strong base that triggered nanoprism formation. The role of the reagents and their interplay in the nanoprism synthesis is discussed in detail. The beneficial role of chloride ions to attain a high degree of reproducibility and monodispersity of the nanoprisms is elucidated. Control over the nanoprism width, thickness, and, consequently, plasmon resonance in the system has been demonstrated. One of the crucial factors in the nanoprism synthesis was the slow, controlled aggregation of thiolate-stabilized silver nanoclusters as the intermediates. The resulting superior monodispersity (better than ca. 10% standard deviation in lateral size and ca. 15% standard deviation in thickness (<1 nm variation)) and charge stabilization of the produced silver nanoprisms enabled the exploration of the rich diversity of the self-assembled morphologies in the system. Regular columnar assemblies of the self-assembled nanoprisms spanning 2-3 μm in length have been observed. Notably, the helicity of the columnar phases was evident, which can be attributed to the chirality of the strongly binding thiol ligand. Finally, the enhancement of Raman scattering has been observed after oxidative removal of thiolate ligands from the AgNPR surface. © 2011 American Chemical Society

Beyond helper phage: Using "helper cells" to select peptide affinity ligands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phipps, Mary Lisa; Lillo, Antoinetta M.; Shou, Yulin

Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The “helper cell” packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report onmore » the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Here, based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.« less

Beyond helper phage: Using "helper cells" to select peptide affinity ligands

DOE PAGES

Phipps, Mary Lisa; Lillo, Antoinetta M.; Shou, Yulin; ...

2016-09-14

Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The “helper cell” packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report onmore » the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Here, based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.« less

Homochiral 3D Metal-Organic Frameworks from Chiral 1D Rods: 6 – Way Helical Packing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, Sung M.; Moon, Dohyun; Jeong, Kyung S.

2011-07-20

The chiral 3D MOFs resulted from the packing of chiral 1D SBBs were studied. It was demonstrated that the final packing pattern is dependent on the dimension of SBB's. In addition, we were able to identify a new plywood-like network from ligand 2H2 exhibiting an unprecedented six-way chiral helical packing motif, which can be added on the list of invariant rod packings.

Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data

PubMed Central

2017-01-01

Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide–MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is, in general, challenging due to the polyspecificity nature of the data. We here outline a general pipeline for dealing with this challenge and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in silico models. We illustrate the approach here in the context of MHC-I molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T-cell epitopes. The prediction model is freely available at http://www.cbs.dtu.dk/services/NetMHCpan/NetBoLApan. The approach has here been applied to the BoLA-I system, but the pipeline is readily applicable to MHC systems in other species. PMID:29115832

Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data.

PubMed

Nielsen, Morten; Connelley, Tim; Ternette, Nicola

2018-01-05

Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide-MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is, in general, challenging due to the polyspecificity nature of the data. We here outline a general pipeline for dealing with this challenge and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in silico models. We illustrate the approach here in the context of MHC-I molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T-cell epitopes. The prediction model is freely available at http://www.cbs.dtu.dk/services/NetMHCpan/NetBoLApan . The approach has here been applied to the BoLA-I system, but the pipeline is readily applicable to MHC systems in other species.

A molecular dynamics study of the three-dimensional model of human synovial fluid phospholipase A2--transition state mimic complexes.

PubMed

Hariprasad, V; Kulkarni, V M

1996-01-01

Different modes of binding of transition state mimics: amide, phosphonate and difluoro ketone, to human synovial fluid phospholipase A2 (HSF PLA2) are studies by molecular dynamics simulations computed in solvent. The results are analysed in the light of primary binding sites. Hydrogen bonding interaction plays an important role for amino acids such as Gly32, Val30, and Glu55, apart from the well known active site residues viz Asp48, Gly25, Gly29, Gly31, His27, His47, Lys62, Phe23, Asn114 and Tyr112. In addition, the hydrogen bonding interaction between Sn-1 tetrahedral phosphonate group of amide and difluoro ketone inhibitors and crystallographic water molecules (H2O 523, H2O 524 and H2O 401) seems to have a significant role. Many of the active site charged residues display considerable movement upon ligand binding. The structural effects of ligand binding were analyzed from RMS deviations of C alpha in the resulting energy-minimized average structures of the receptor-ligand complexes. The values of the RMS deviations differ among the HSF PLA2s, in a pattern that is not the same for the three complexes. This suggests that ligands with different pharmacological efficacies induce different types of conformational changes of the receptor. Our active-orientation model is, at least qualitatively, consistent with experimental data and should be useful for the rational design of more potent inhibitors.

Protein stability and dynamics influenced by ligands in extremophilic complexes - a molecular dynamics investigation.

PubMed

Khan, Sara; Farooq, Umar; Kurnikova, Maria

2017-08-22

In this study, we explore the structural and dynamic adaptations of the Tryptophan synthase α-subunit in a ligand bound state in psychrophilic, mesophilic and hyperthermophilic organisms at different temperatures by MD simulations. We quantify the global and local fluctuations in the 40 ns time scale by analyzing the root mean square deviation/fluctuations. The distinct behavior of the active site and loop 6 is observed with the elevation of temperature. Protein stability relies more on electrostatic interactions, and these interactions might be responsible for the stability of varying temperature evolved proteins. The paper also focuses on the effect of temperature on protein dynamics and stability governed by the distinct behavior of the ligand associated with its retention, binding and dissociation over the course of time. The integration of principle component analysis and a free energy landscape was useful in identifying the conformational space accessible to ligand bound homologues and how the presence of the ligand alters the conformational and dynamic properties of the protein.

Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures.

PubMed

Rühmann, Eggert H; Rupp, Melinda; Betz, Michael; Heine, Andreas; Klebe, Gerhard

2016-02-04

Structural preorganization to fix bioactive conformations at protein binding sites is a popular strategy to enhance binding affinity during late-stage optimization. The rationale for this enhancement relates to entropic advantages assigned to rigidified versus flexible ligands. We analyzed a narrow series of peptidomimetics binding to thrombin. The individual ligands exhibit at P2 a conformationally flexible glycine, more restricted alanine, N-methylglycine, N-methylhomoalanine, and largely rigidified proline moiety. Overall, affinity was found to increase by a factor of 1000, explained partly by an entropic advantage. All ligands adopt the same binding mode with small deviations. The residual mobility of the bound ligands is decreased across the series, and a protein side chain differs in its order/disorder behavior along with changes in the surface-water network pattern established across the newly generated protein-ligand surfaces. The enthalpy/entropy inventory displays a rather complex picture and emphasizes that thermodynamics can only be compared in terms of relative differences within a structurally similar ligand series. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Uranium and thorium complexes of the phosphaethynolate ion

DOE PAGES

Camp, Clément; Settineri, Nicholas; Lefèvre, Julia; ...

2015-06-20

New tris-amidinate actinide (Th, U) complexes containing a rare O-bound terminal phosphaethynolate (OCP⁻) ligand were synthesized and fully characterized. The cyanate (OCN⁻) and thiocyanate (SCN⁻) analogs were prepared for comparison and feature a preferential N-coordination to the actinide metals. The Th(amid) 3(OCP) complex reacts with Ni(COD) 2 to yield the heterobimetallic adduct (amid) 3Th(μ-η 1(O):η 2(C,P)-OCP)Ni(COD) featuring an unprecedented reduced (OCP⁻) bent fragment bridging the two metals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sinha, Shashi B.; Shopov, Dimitar Y.; Sharninghausen, Liam S.

We describe facial and meridional isomers of [RhIII(pyalk)3], as well as meridional [RhIV(pyalk)3]+ {pyalk =2-(2-pyridyl)-2-propanoate}, the first coordination complex in an N,O-donor environment to show a clean, reversible RhIII/IV redox couple and to have a stable Rh(IV) form, which we characterize by EPR and UV–visible spectroscopy as well as X-ray crystallography. The unprecedented stability of the Rh(IV) species is ascribed to the exceptional donor strength of the ligands, their oxidation resistance, and the meridional coordination geometry.

What should be impossible: resolution of the mononuclear gallium coordination complex, Tris(benzohydroxamato)gallium(III).

PubMed

Brumaghim, Julia L; Raymond, Kenneth N

2003-10-08

Complexes of Ga3+, a d10 metal ion which lacks ligand-field-stabilization energy, are considered labile. In fact, hexaaquagallium(III) has a ligand exchange rate of 403 s-1, 2.5 times that of the analagous Fe3+ complex (Hugi-Cleary, D.; Helm, L.; Merbach, A. E. J. Am. Chem. Soc. 1987, 109, 4444-4450). Given this lability, resolution of Ga3+ complexes should be impossible. Despite this, we report the resolution of the Lambda and Delta isomers of tris(benzohydroxamate)gallium (III) (1), the first resolution of a mononuclear gallium complex. Not only is resolution possible, but these resolved complexes show remarkable resistance to racemization in aprotic solvents. The unprecedented stability of Lambda- and Delta-1 is a surprise, and as such, alters our understanding of classical coordination chemistry.

Bis-lactam-1,10-phenanthroline (BLPhen), a New Type of Preorganized Mixed N,O-Donor Ligand That Separates Am(III) over Eu(III) with Exceptionally High Efficiency

DOE PAGES

Jansone-Popova, Santa; Ivanov, Alexander S.; Bryantsev, Vyacheslav S.; ...

2017-05-04

Here, we report a new family of preorganized bislactam- 1,10-phenanthroline (BLPhen) complexants that possess both hard and soft donor atoms within a convergent cavity and show unprecedented extraction strength for the trivalent fblock metal ions. BLPhen ligands with saturated and unsaturated δ-lactam rings have notable differences in their affinity and selectivity for Am(III) over Eu(III), with the latter being the most selective mixed N,O-donor extractant of Am(III) reported to date. Saturated BLPhen was crystallized with five Ln(III) nitrates to form charge-neutral 1:1 complexes in the solid state. DFT calculations further elaborate on the variety of effects that dictate the performancemore » of these preorganized compounds.« less

A unique fluoride nanocontainer: porous molecular capsules can accommodate an unusually high number of "rather labile" fluoride anions.

PubMed

Garai, Somenath; Rubčić, Mirta; Bögge, Hartmut; Haupt, Erhard T K; Gouzerh, Pierre; Müller, Achim

2015-05-11

The present work refers to the challenging issue of fluoride anion recognition/binding in water by taking advantage of the unique possibilities offered by the porous molecular nanocontainers of the {Mo132} Keplerate type allowing the study of a variety of new phenomena. Reaction of the highly reactive carbonate-type capsule with aqueous HF results in the release of carbon dioxide and integration of an unprecedentedly large number of fluoride anions--partly as coordinated ligands at both the pentagonal units and the linkers, partly as a disordered water/fluoride assembly inside the cavity. The internal assembly and some of the fluoride ligands are easily released, which provides interesting options for future studies regarding coordination chemistry and catalysis under confined conditions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular assembly and magnetic dynamics of two novel Dy6 and Dy8 aggregates.

PubMed

Guo, Yun-Nan; Chen, Xiao-Hua; Xue, Shufang; Tang, Jinkui

2012-04-02

Complexation of dysprosium(III) with the heterodonor chelating ligand o-vanillin picolinoylhydrazone (H(2)ovph) in the presence of a carbonato ligand affords two novel Dy(6) and Dy(8) clusters, namely, [Dy(6)(ovph)(4)(Hpvph)(2)Cl(4)(H(2)O)(2)(CO(3))(2)]·CH(3)OH·H(2)O·CH(3)CN (2) and [Dy(8)(ovph)(8)(CO(3))(4)(H(2)O)(8)]·12CH(3)CN·6H(2)O (3). Compound 2 is composed of three petals of the Dy(2) units linked by two carbonato ligands, forming a triangular prism arrangement, while compound 3 possesses an octanuclear core with an unprecedented tub conformation, in which Dy(ovph) fragments are attached to the sides of the carbonato core. The static and dynamic magnetic properties are reported and discussed. In the Dy(6) aggregate, three Dy(2) "skeletons", having been well preserved (see the scheme), contribute to the single-molecule-magnet behavior with a relatively slow tunneling rate, while the Dy(8) cluster only exhibits a rather small relaxation barrier.

Dynamics of ligand substitution in labile cobalt complexes resolved by ultrafast T-jump

PubMed Central

Ma, Hairong; Wan, Chaozhi; Zewail, Ahmed H.

2008-01-01

Ligand exchange of hydrated metal complexes is common in chemical and biological systems. Using the ultrafast T-jump, we examined this process, specifically the transformation of aqua cobalt (II) complexes to their fully halogenated species. The results reveal a stepwise mechanism with time scales varying from hundreds of picoseconds to nanoseconds. The dynamics are significantly faster when the structure is retained but becomes rate-limited when the octahedral-to-tetrahedral structural change bottlenecks the transformation. Evidence is presented, from bimolecular kinetics and energetics (enthalpic and entropic), for a reaction in which the ligand assists the displacement of water molecules, with the retention of the entering ligand in the activated state. The reaction time scale deviates by one to two orders of magnitude from that of ionic diffusion, suggesting the involvement of a collisional barrier between the ion and the much larger complex. PMID:18725628

Ligand reorganization and activation energies in nonadiabatic electron transfer reactions

NASA Astrophysics Data System (ADS)

Zhu, Jianjun; Wang, Jianji; Stell, George

2006-10-01

The activation energy and ligand reorganization energy for nonadiabatic electron transfer reactions in chemical and biological systems are investigated in this paper. The free energy surfaces and the activation energy are derived exactly in the general case in which the ligand vibration frequencies are not equal. The activation energy is derived by free energy minimization at the transition state. Our formulation leads to the Marcus-Hush [J. Chem. Phys. 24, 979 (1956); 98, 7170 (1994); 28, 962 (1958)] results in the equal-frequency limit and also generalizes the Marcus-Sumi [J. Chem. Phys. 84, 4894 (1986)] model in the context of studying the solvent dynamic effect on electron transfer reactions. It is found that when the ligand vibration frequencies are different, the activation energy derived from the Marcus-Hush formula deviates by 5%-10% from the exact value. If the reduced reorganization energy approximation is introduced in the Marcus-Hush formula, the result is almost exact.

Prediction of kinase-inhibitor binding affinity using energetic parameters

PubMed Central

Usha, Singaravelu; Selvaraj, Samuel

2016-01-01

The combination of physicochemical properties and energetic parameters derived from protein-ligand complexes play a vital role in determining the biological activity of a molecule. In the present work, protein-ligand interaction energy along with logP values was used to predict the experimental log (IC50) values of 25 different kinase-inhibitors using multiple regressions which gave a correlation coefficient of 0.93. The regression equation obtained was tested on 93 kinase-inhibitor complexes and an average deviation of 0.92 from the experimental log IC50 values was shown. The same set of descriptors was used to predict binding affinities for a test set of five individual kinase families, with correlation values > 0.9. We show that the protein-ligand interaction energies and partition coefficient values form the major deterministic factors for binding affinity of the ligand for its receptor. PMID:28149052

Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules.

PubMed

Teunis, Meghan B; Nagaraju, Mulpuri; Dutta, Poulami; Pu, Jingzhi; Muhoberac, Barry B; Sardar, Rajesh; Agarwal, Mangilal

2017-09-28

This article describes the mechanisms underlying electronic interactions between surface passivating ligands and (CdSe) 34 semiconductor cluster molecules (SCMs) that facilitate band-gap engineering through the delocalization of hole wave functions without altering their inorganic core. We show here both experimentally and through density functional theory calculations that the expansion of the hole wave function beyond the SCM boundary into the ligand monolayer depends not only on the pre-binding energetic alignment of interfacial orbitals between the SCM and surface passivating ligands but is also strongly influenced by definable ligand structural parameters such as the extent of their π-conjugation [π-delocalization energy; pyrene (Py), anthracene (Anth), naphthalene (Naph), and phenyl (Ph)], binding mode [dithiocarbamate (DTC, -NH-CS 2 - ), carboxylate (-COO - ), and amine (-NH 2 )], and binding head group [-SH, -SeH, and -TeH]. We observe an unprecedentedly large ∼650 meV red-shift in the lowest energy optical absorption band of (CdSe) 34 SCMs upon passivating their surface with Py-DTC ligands and the trend is found to be Ph- < Naph- < Anth- < Py-DTC. This shift is reversible upon removal of Py-DTC by triethylphosphine gold(i) chloride treatment at room temperature. Furthermore, we performed temperature-dependent (80-300 K) photoluminescence lifetime measurements, which show longer lifetime at lower temperature, suggesting a strong influence of hole wave function delocalization rather than carrier trapping and/or phonon-mediated relaxation. Taken together, knowledge of how ligands electronically interact with the SCM surface is crucial to semiconductor nanomaterial research in general because it allows the tuning of electronic properties of nanomaterials for better charge separation and enhanced charge transfer, which in turn will increase optoelectronic device and photocatalytic efficiencies.

Accuracy of binding mode prediction with a cascadic stochastic tunneling method.

PubMed

Fischer, Bernhard; Basili, Serena; Merlitz, Holger; Wenzel, Wolfgang

2007-07-01

We investigate the accuracy of the binding modes predicted for 83 complexes of the high-resolution subset of the ASTEX/CCDC receptor-ligand database using the atomistic FlexScreen approach with a simple forcefield-based scoring function. The median RMS deviation between experimental and predicted binding mode was just 0.83 A. Over 80% of the ligands dock within 2 A of the experimental binding mode, for 60 complexes the docking protocol locates the correct binding mode in all of ten independent simulations. Most docking failures arise because (a) the experimental structure clashed in our forcefield and is thus unattainable in the docking process or (b) because the ligand is stabilized by crystal water. 2007 Wiley-Liss, Inc.

DNA aptamer affinity ligands for highly selective purification of human plasma-related proteins from multiple sources.

PubMed

Forier, Cynthia; Boschetti, Egisto; Ouhammouch, Mohamed; Cibiel, Agnès; Ducongé, Frédéric; Nogré, Michel; Tellier, Michel; Bataille, Damien; Bihoreau, Nicolas; Santambien, Patrick; Chtourou, Sami; Perret, Gérald

2017-03-17

Nucleic acid aptamers are promising ligands for analytical and preparative-scale affinity chromatography applications. However, a full industrial exploitation requires that aptamer-grafted chromatography media provide a number of high technical standards that remained largely untested. Ideally, they should exhibit relatively high binding capacity associated to a very high degree of specificity. In addition, they must be highly resistant to harsh cleaning/sanitization conditions, as well as to prolonged and repeated exposure to biological environment. Here, we present practical examples of aptamer affinity chromatography for the purification of three human therapeutic proteins from various sources: Factor VII, Factor H and Factor IX. In a single chromatographic step, three DNA aptamer ligands enabled the efficient purification of their target protein, with an unprecedented degree of selectivity (from 0.5% to 98% of purity in one step). Furthermore, these aptamers demonstrated a high stability under harsh sanitization conditions (100h soaking in 1M NaOH). These results pave the way toward a wider adoption of aptamer-based affinity ligands in the industrial-scale purification of not only plasma-derived proteins but also of any other protein in general. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.

PubMed

Wang, Lingle; Wu, Yujie; Deng, Yuqing; Kim, Byungchan; Pierce, Levi; Krilov, Goran; Lupyan, Dmitry; Robinson, Shaughnessy; Dahlgren, Markus K; Greenwood, Jeremy; Romero, Donna L; Masse, Craig; Knight, Jennifer L; Steinbrecher, Thomas; Beuming, Thijs; Damm, Wolfgang; Harder, Ed; Sherman, Woody; Brewer, Mark; Wester, Ron; Murcko, Mark; Frye, Leah; Farid, Ramy; Lin, Teng; Mobley, David L; Jorgensen, William L; Berne, Bruce J; Friesner, Richard A; Abel, Robert

2015-02-25

Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over the past few decades, free-energy calculations have benefited from improved force fields and sampling algorithms, as well as the advent of low-cost parallel computing. However, it has proven to be challenging to reliably achieve the level of accuracy that would be needed to guide lead optimization (∼5× in binding affinity) for a wide range of ligands and protein targets. Not surprisingly, widespread commercial application of free-energy simulations has been limited due to the lack of large-scale validation coupled with the technical challenges traditionally associated with running these types of calculations. Here, we report an approach that achieves an unprecedented level of accuracy across a broad range of target classes and ligands, with retrospective results encompassing 200 ligands and a wide variety of chemical perturbations, many of which involve significant changes in ligand chemical structures. In addition, we have applied the method in prospective drug discovery projects and found a significant improvement in the quality of the compounds synthesized that have been predicted to be potent. Compounds predicted to be potent by this approach have a substantial reduction in false positives relative to compounds synthesized on the basis of other computational or medicinal chemistry approaches. Furthermore, the results are consistent with those obtained from our retrospective studies, demonstrating the robustness and broad range of applicability of this approach, which can be used to drive decisions in lead optimization.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibson, John K.; de Jong, Wibe A.; van Stipdonk, Michael J.

In uranyl coordination complexes, UO 2(L) n 2+, uranium in the formally dipositive [O=U=O] 2+ moiety is coordinated by n neutral organic electron donor ligands, L. The extent of ligand electron donation, which results in partial reduction of uranyl and weakening of the U=O bonds, is revealed by the magnitude of the red-shift of the uranyl asymmetric stretch frequency, ν 3 . This phenomenon appears in gas-phase complexes in which uranyl is coordinated by electron donor ligands: the ν 3 red-shift increases as the number of ligands and their proton affinity (PA) increases. Because PA is a measure of themore » enthalpy change associated with a proton-ligand interaction, which is much stronger and of a different nature than metal ion-ligand bonding, it is not necessarily expected that ligand PAs should reliably predict uranyl-ligand bonding and the resulting ν 3 red-shift. In this study, ν 3 was measured for uranyl coordinated by ligands with a relatively broad range of PAs, revealing a surprisingly good correlation between PA and ν 3 frequency. From computed ν 3 frequencies for bare UO 2 cations and neutrals, it is inferred that the effective charge of uranyl in UO 2(L) n 2+ complexes can be reduced to near zero upon ligation by sufficiently strong charge-donor ligands. The basis for the correlation between ν 3 and ligand PAs, as well as limitations and deviations from it, are considered. It is demonstrated that the correlation evidently extends to a ligand that exhibits polydentate metal ion coordination.« less

Exploring Molecular Mechanisms of Ligand Recognition by Opioid Receptors with Metadynamics†

PubMed Central

Provasi, Davide; Bortolato, Andrea; Filizola, Marta

2009-01-01

Opioid receptors are G protein-coupled receptors (GPCRs) of utmost significance in the development of potent analgesic drugs for the treatment of severe pain. An accurate evaluation at the molecular level of the ligand binding pathways into these receptors may play a key role in the design of new molecules with more desirable properties and reduced side effects. The recent characterization of high-resolution X-ray crystal structures of non-rhodopsin GPCRs for diffusible hormones and neurotransmitters presents an unprecedented opportunity to build improved homology models of opioid receptors, and to study in more detail their molecular mechanisms of ligand recognition. In this study, possible entry pathways of the non-selective antagonist naloxone (NLX) from the water environment into the well-accepted alkaloid binding pocket of a delta opioid receptor (DOR) molecular model based on the β2-adrenergic receptor crystal structure are explored using microsecond-scale well-tempered metadynamics simulations. Using as collective variables distances that account for the position of NLX and of the receptor extracellular loop 2 in relation to the DOR binding pocket, we were able to distinguish between the different states visited by the ligand (i.e., docked, undocked, and metastable bound intermediates), and to predict a free energy of binding close to experimental values after correcting for possible drawbacks of the sampling approach. The strategy employed herein holds promise for its application to the docking of diverse ligands to the opioid receptors as well as to other GPCRs. PMID:19785461

Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics.

PubMed

Provasi, Davide; Bortolato, Andrea; Filizola, Marta

2009-10-27

Opioid receptors are G protein-coupled receptors (GPCRs) of utmost significance in the development of potent analgesic drugs for the treatment of severe pain. An accurate evaluation at the molecular level of the ligand binding pathways into these receptors may play a key role in the design of new molecules with more desirable properties and reduced side effects. The recent characterization of high-resolution X-ray crystal structures of non-rhodopsin GPCRs for diffusible hormones and neurotransmitters presents an unprecedented opportunity to build improved homology models of opioid receptors, and to study in more detail their molecular mechanisms of ligand recognition. In this study, possible pathways for entry of the nonselective antagonist naloxone (NLX) from the water environment into the well-accepted alkaloid binding pocket of a delta opioid receptor (DOR) molecular model based on the beta2-adrenergic receptor crystal structure are explored using microsecond-scale well-tempered metadynamics simulations. Using as collective variables distances that account for the position of NLX and of the receptor extracellular loop 2 in relation to the DOR binding pocket, we were able to distinguish between the different states visited by the ligand (i.e., docked, undocked, and metastable bound intermediates) and to predict a free energy of binding close to experimental values after correcting for possible drawbacks of the sampling approach. The strategy employed herein holds promise for its application to the docking of diverse ligands to the opioid receptors as well as to other GPCRs.

Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein-Ligand Binding: Binding Site Variability

PubMed Central

Raman, E. Prabhu; MacKerell, Alexander D.

2015-01-01

The thermodynamic driving forces behind small molecule-protein binding are still not well understood, including the variability of those forces associated with different types of ligands in different binding pockets. To better understand these phenomena we calculate spatially resolved thermodynamic contributions of the different molecular degrees of freedom for the binding of propane and methanol to multiple pockets on the proteins Factor Xa and p38 MAP kinase. Binding thermodynamics are computed using a statistical thermodynamics based end-point method applied on a canonical ensemble comprising the protein-ligand complexes and the corresponding free states in an explicit solvent environment. Energetic and entropic contributions of water and ligand degrees of freedom computed from the configurational ensemble provides an unprecedented level of detail into the mechanisms of binding. Direct protein-ligand interaction energies play a significant role in both non-polar and polar binding, which is comparable to water reorganization energy. Loss of interactions with water upon binding strongly compensates these contributions leading to relatively small binding enthalpies. For both solutes, the entropy of water reorganization is found to favor binding in agreement with the classical view of the “hydrophobic effect”. Depending on the specifics of the binding pocket, both energy-entropy compensation and reinforcement mechanisms are observed. Notable is the ability to visualize the spatial distribution of the thermodynamic contributions to binding at atomic resolution showing significant differences in the thermodynamic contributions of water to the binding of propane versus methanol. PMID:25625202

A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity

PubMed Central

Hayik, Seth A.; Dunbrack, Roland; Merz, Kenneth M.

2010-01-01

Computational methods for predicting protein-ligand binding free energy continue to be popular as a potential cost-cutting method in the drug discovery process. However, accurate predictions are often difficult to make as estimates must be made for certain electronic and entropic terms in conventional force field based scoring functions. Mixed quantum mechanics/molecular mechanics (QM/MM) methods allow electronic effects for a small region of the protein to be calculated, treating the remaining atoms as a fixed charge background for the active site. Such a semi-empirical QM/MM scoring function has been implemented in AMBER using DivCon and tested on a set of 23 metalloprotein-ligand complexes, where QM/MM methods provide a particular advantage in the modeling of the metal ion. The binding affinity of this set of proteins can be calculated with an R2 of 0.64 and a standard deviation of 1.88 kcal/mol without fitting and 0.71 and a standard deviation of 1.69 kcal/mol with fitted weighting of the individual scoring terms. In this study we explore using various methods to calculate terms in the binding free energy equation, including entropy estimates and minimization standards. From these studies we found that using the rotational bond estimate to ligand entropy results in a reasonable R2 of 0.63 without fitting. We also found that using the ESCF energy of the proteins without minimization resulted in an R2 of 0.57, when using the rotatable bond entropy estimate. PMID:21221417

Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.

PubMed

Erickson, Jon A; Jalaie, Mehran; Robertson, Daniel H; Lewis, Richard A; Vieth, Michal

2004-01-01

The key to success for computational tools used in structure-based drug design is the ability to accurately place or "dock" a ligand in the binding pocket of the target of interest. In this report we examine the effect of several factors on docking accuracy, including ligand and protein flexibility. To examine ligand flexibility in an unbiased fashion, a test set of 41 ligand-protein cocomplex X-ray structures were assembled that represent a diversity of size, flexibility, and polarity with respect to the ligands. Four docking algorithms, DOCK, FlexX, GOLD, and CDOCKER, were applied to the test set, and the results were examined in terms of the ability to reproduce X-ray ligand positions within 2.0A heavy atom root-mean-square deviation. Overall, each method performed well (>50% accuracy) but for all methods it was found that docking accuracy decreased substantially for ligands with eight or more rotatable bonds. Only CDOCKER was able to accurately dock most of those ligands with eight or more rotatable bonds (71% accuracy rate). A second test set of structures was gathered to examine how protein flexibility influences docking accuracy. CDOCKER was applied to X-ray structures of trypsin, thrombin, and HIV-1-protease, using protein structures bound to several ligands and also the unbound (apo) form. Docking experiments of each ligand to one "average" structure and to the apo form were carried out, and the results were compared to docking each ligand back to its originating structure. The results show that docking accuracy falls off dramatically if one uses an average or apo structure. In fact, it is shown that the drop in docking accuracy mirrors the degree to which the protein moves upon ligand binding.

Equatorial coordination of uranyl: Correlating ligand charge donation with the O yl-U-O yl asymmetric stretch frequency

DOE PAGES

Gibson, John K.; de Jong, Wibe A.; van Stipdonk, Michael J.; ...

2017-10-14

In uranyl coordination complexes, UO 2(L) n 2+, uranium in the formally dipositive [O=U=O] 2+ moiety is coordinated by n neutral organic electron donor ligands, L. The extent of ligand electron donation, which results in partial reduction of uranyl and weakening of the U=O bonds, is revealed by the magnitude of the red-shift of the uranyl asymmetric stretch frequency, ν 3 . This phenomenon appears in gas-phase complexes in which uranyl is coordinated by electron donor ligands: the ν 3 red-shift increases as the number of ligands and their proton affinity (PA) increases. Because PA is a measure of themore » enthalpy change associated with a proton-ligand interaction, which is much stronger and of a different nature than metal ion-ligand bonding, it is not necessarily expected that ligand PAs should reliably predict uranyl-ligand bonding and the resulting ν 3 red-shift. In this study, ν 3 was measured for uranyl coordinated by ligands with a relatively broad range of PAs, revealing a surprisingly good correlation between PA and ν 3 frequency. From computed ν 3 frequencies for bare UO 2 cations and neutrals, it is inferred that the effective charge of uranyl in UO 2(L) n 2+ complexes can be reduced to near zero upon ligation by sufficiently strong charge-donor ligands. The basis for the correlation between ν 3 and ligand PAs, as well as limitations and deviations from it, are considered. It is demonstrated that the correlation evidently extends to a ligand that exhibits polydentate metal ion coordination.« less

Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A As Revealed by Neutron Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerlits, Oksana O.; Coates, Leighton; Woods, Robert J.

Plant lectins are carbohydrate-binding proteins with various biomedical applications. Concanavalin A (Con A) holds promise in treating cancerous tumors. To better understand the Con A carbohydrate binding specificity, we obtained a room-temperature neutron structure of this legume lectin in complex with a disaccharide Manα1–2Man, mannobiose. The neutron structure afforded direct visualization of the hydrogen bonding between the protein and ligand, showing that the ligand is able to alter both protonation states and interactions for residues located close to and distant from the binding site. An unprecedented low-barrier hydrogen bond was observed forming between the carboxylic side chains of Asp28 andmore » Glu8, with the D atom positioned equidistant from the oxygen atoms having an O···D···O angle of 101.5°.« less

Controlling Second Coordination Sphere Effects in Luminescent Ruthenium Complexes by Means of External Pressure.

PubMed

Pannwitz, Andrea; Poirier, Stéphanie; Bélanger-Desmarais, Nicolas; Prescimone, Alessandro; Wenger, Oliver S; Reber, Christian

2018-06-04

Two luminescent heteroleptic Ru II complexes with a 2,2'-biimidazole (biimH 2 ) ligand form doubly hydrogen-bonded salt bridges to 4-sulfobenzoate anions in single crystals. The structure of one of these cation-anion adducts shows that the biimH 2 ligand is deprotonated. Its 3 MLCT luminescence band does not shift significantly under the influence of an external hydrostatic pressure, a behavior typical for these electronic transitions. In contrast, hydrostatic pressure on the other crystalline cation-anion adduct induces a shift of proton density from the peripheral N-H groups of biimH 2 towards benzoate, leading to a pronounced redshift of the 3 MLCT luminescence band. Such a significant and pressure-tunable influence from an interaction in the second coordination sphere is unprecedented in artificial small-molecule-based systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Endogenous vs Exogenous Allosteric Modulators in GPCRs: A dispute for shuttling CB1 among different membrane microenvironments

NASA Astrophysics Data System (ADS)

Stornaiuolo, Mariano; Bruno, Agostino; Botta, Lorenzo; Regina, Giuseppe La; Cosconati, Sandro; Silvestri, Romano; Marinelli, Luciana; Novellino, Ettore

2015-10-01

A Cannabinoid Receptor 1 (CB1) binding site for the selective allosteric modulator ORG27569 is here identified through an integrate approach of consensus pocket prediction, mutagenesis studies and Mass Spectrometry. This unprecedented ORG27569 pocket presents the structural features of a Cholesterol Consensus Motif, a cholesterol interacting region already found in other GPCRs. ORG27569 and cholesterol affects oppositely CB1 affinity for orthosteric ligands. Moreover, the rise in cholesterol intracellular level results in CB1 trafficking to the axonal region of neuronal cells, while, on the contrary, ORG27568 binding induces CB1 enrichment at the soma. This control of receptor migration among functionally different membrane regions of the cell further contributes to downstream signalling and adds a previously unknown mechanism underpinning CB1 modulation by ORG27569 , that goes beyond a mere control of receptor affinity for orthosteric ligands.

A python-based docking program utilizing a receptor bound ligand shape: PythDock.

PubMed

Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

2011-09-01

PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design.

Crystal structure of fac-[2-(4-methyl-5-phenyl-pyridin-2-yl)phenyl-κ2C1,N]bis-[2-(pyridin-2-yl)phenyl-κ2C1,N]iridium(III).

PubMed

Lee, Chi-Heon; Moon, Suk-Hee; Park, Ki-Min; Kang, Youngjin

2016-12-01

In the title compound, [Ir(C 11 H 8 N) 2 (C 18 H 14 N)], the Ir III ion adopts a distorted octa-hedral coordination environment defined by three C , N -chelating ligands, one stemming from a 2-(4-phenyl-5-methyl-pyridin-2-yl)phenyl ligand and two from 2-(pyridin-2-yl)phenyl ligands, arranged in a facial manner. The Ir III ion lies almost in the equatorial plane [deviation = 0.0069 (15) Å]. In the crystal, inter-molecular π-π stacking inter-actions, as well as inter-molecular C-H⋯π inter-actions, are present, leading to a three-dimensional network.

Ligand reorganization and activation energies in nonadiabatic electron transfer reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu Jianjun; Wang Jianji; Stell, George

2006-10-28

The activation energy and ligand reorganization energy for nonadiabatic electron transfer reactions in chemical and biological systems are investigated in this paper. The free energy surfaces and the activation energy are derived exactly in the general case in which the ligand vibration frequencies are not equal. The activation energy is derived by free energy minimization at the transition state. Our formulation leads to the Marcus-Hush [J. Chem. Phys. 24, 979 (1956); 98, 7170 (1994); 28, 962 (1958)] results in the equal-frequency limit and also generalizes the Marcus-Sumi [J. Chem. Phys. 84, 4894 (1986)] model in the context of studying themore » solvent dynamic effect on electron transfer reactions. It is found that when the ligand vibration frequencies are different, the activation energy derived from the Marcus-Hush formula deviates by 5%-10% from the exact value. If the reduced reorganization energy approximation is introduced in the Marcus-Hush formula, the result is almost exact.« less

Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets.

PubMed

Cerisier, Natacha; Regad, Leslie; Triki, Dhoha; Camproux, Anne-Claude; Petitjean, Michel

2017-11-01

We analyzed 78 binding pockets of the human urokinase plasminogen activator (uPA) catalytic domain extracted from a data set of crystallized uPA-ligand complexes. These binding pockets were computed with an original geometric method that does NOT involve any arbitrary parameter, such as cutoff distances, angles, and so on. We measured the deviation from convexity of each pocket shape with the pocket convexity index (PCI). We defined a new pocket descriptor called distributional sphericity coefficient (DISC), which indicates to which extent the protein atoms of a given pocket lie on the surface of a sphere. The DISC values were computed with the freeware PCI. The pocket descriptors and their high correspondences with ligand descriptors are crucial for polypharmacology prediction. We found that the protein heavy atoms lining the urokinases binding pockets are either located on the surface of their convex hull or lie close to this surface. We also found that the radii of the urokinases binding pockets and the radii of their ligands are highly correlated (r = 0.9).

'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

PubMed

Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M

2014-04-09

The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins.

Siderocalin-mediated recognition, sensitization, and cellular uptake of actinides.

PubMed

Allred, Benjamin E; Rupert, Peter B; Gauny, Stacey S; An, Dahlia D; Ralston, Corie Y; Sturzbecher-Hoehne, Manuel; Strong, Roland K; Abergel, Rebecca J

2015-08-18

Synthetic radionuclides, such as the transuranic actinides plutonium, americium, and curium, present severe health threats as contaminants, and understanding the scope of the biochemical interactions involved in actinide transport is instrumental in managing human contamination. Here we show that siderocalin, a mammalian siderophore-binding protein from the lipocalin family, specifically binds lanthanide and actinide complexes through molecular recognition of the ligands chelating the metal ions. Using crystallography, we structurally characterized the resulting siderocalin-transuranic actinide complexes, providing unprecedented insights into the biological coordination of heavy radioelements. In controlled in vitro assays, we found that intracellular plutonium uptake can occur through siderocalin-mediated endocytosis. We also demonstrated that siderocalin can act as a synergistic antenna to sensitize the luminescence of trivalent lanthanide and actinide ions in ternary protein-ligand complexes, dramatically increasing the brightness and efficiency of intramolecular energy transfer processes that give rise to metal luminescence. Our results identify siderocalin as a potential player in the biological trafficking of f elements, but through a secondary ligand-based metal sequestration mechanism. Beyond elucidating contamination pathways, this work is a starting point for the design of two-stage biomimetic platforms for photoluminescence, separation, and transport applications.

Structure and magnetism of a new hydrogen-bonded layered cobalt(II) network, constructed by the unprecedented carboxylate-phosphinate ligand [O2(C6H5)PCH2CO2]2-.

PubMed

Midollini, Stefano; Orlandini, Annabella; Rosa, Patrick; Sorace, Lorenzo

2005-03-21

By hydrothermal reaction of CoCl2 x 6H2O with K2pcc (H2pcc = phenyl(carboxymethyl) phosphinic acid) at 423 K, a novel hybrid material of formula [Co2(pcc)2 (H2O)2] x H2O has been obtained. The compound, which is the first pcc/metal complex reported, exhibits a polymeric arrangement, where cobalt metal ions, linked together by bridging carboxylate and phosphinate oxygens, form infinite chains of edge-shared CoO6 octahedra. The cobalt chains are in turn linked together through important hydrogen-bonding interactions, which create an infinite 2D architecture. The two crystallographically independent cobalt centers, both displaying distorted octahedral coordination, present different environments as one is surrounded by six ligand oxygens and the other by four ligand oxygens and by two water oxygens. Careful magnetic studies performed by a home-built alternating current susceptometer reveal that the system undergoes an antiferromagnetic transition below 2.0 K leading to a canted structure. Field-dependent studies further indicate the occurrence of a metamagnetic transition at a critical field of 650 +/- 50 G.

Four unprecedented cobalt(II) and cadmium(II) metal-organic frameworks based on a rigid tricarboxylate ligand: Synthesis, crystal structures, magnetic and fluorescence properties

NASA Astrophysics Data System (ADS)

Liu, Yaru; Liu, Lan; Zhang, Xiao; Wu, Jie

2018-03-01

A Co(II) MOF {[Co3(L)2(H2O)4](DMF)2}n (1) and three Cd(II) MOFs [Cd3(L)2(H2O)7]n (2), [Cd3(L)2(H2O)11]n (3) and [Cd3(L)2(DMF)2(H2O)]n (4) are synthesized based on the promising multifunctional tricarboxylate ligand 6-(3, 5-dicarboxyl phenyl) nicotinic acid (H3L). 1 exhibits a 3D framework with 1D channels which contains opposite-handedness helical chains based on the trinuclear Co(II) clusters. 2-4 are obtained depend on different reaction conditions. 2 displays a 3D framework, which is composed of two kinds of 2D layers linked with each other. 3 shows a rare tongue-and-groove-type bilayer structure. And 4 is an interesting 3D framework containing infinite 1D inorganic Cdsbnd Osbnd Cd chains. In these MOFs, the H3L ligand shows the versatile coordination modes and strong coordination ability. Furthermore, the magnetic and solid-state luminescent properties of the MOFs have been investigated.

Siderocalin-mediated recognition, sensitization, and cellular uptake of actinides

PubMed Central

Allred, Benjamin E.; Rupert, Peter B.; Gauny, Stacey S.; An, Dahlia D.; Ralston, Corie Y.; Sturzbecher-Hoehne, Manuel; Strong, Roland K.; Abergel, Rebecca J.

2015-01-01

Synthetic radionuclides, such as the transuranic actinides plutonium, americium, and curium, present severe health threats as contaminants, and understanding the scope of the biochemical interactions involved in actinide transport is instrumental in managing human contamination. Here we show that siderocalin, a mammalian siderophore-binding protein from the lipocalin family, specifically binds lanthanide and actinide complexes through molecular recognition of the ligands chelating the metal ions. Using crystallography, we structurally characterized the resulting siderocalin–transuranic actinide complexes, providing unprecedented insights into the biological coordination of heavy radioelements. In controlled in vitro assays, we found that intracellular plutonium uptake can occur through siderocalin-mediated endocytosis. We also demonstrated that siderocalin can act as a synergistic antenna to sensitize the luminescence of trivalent lanthanide and actinide ions in ternary protein–ligand complexes, dramatically increasing the brightness and efficiency of intramolecular energy transfer processes that give rise to metal luminescence. Our results identify siderocalin as a potential player in the biological trafficking of f elements, but through a secondary ligand-based metal sequestration mechanism. Beyond elucidating contamination pathways, this work is a starting point for the design of two-stage biomimetic platforms for photoluminescence, separation, and transport applications. PMID:26240330

Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme

PubMed Central

Ahalawat, Navjeet; Pandit, Subhendu; Kay, Lewis E.

2018-01-01

Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (T4L L99A) that rapidly binds benzene (~106 M-1s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound T4L L99A are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive. The current work, using extensive molecular dynamics simulation, achieves this by capturing the complete process of spontaneous recognition of benzene by T4L L99A at atomistic resolution. A series of multi-microsecond unbiased molecular dynamics simulation trajectories unequivocally reveal how benzene, starting in bulk solvent, diffuses to the protein and spontaneously reaches the solvent inaccessible cavity of T4L L99A. The simulated and high-resolution X-ray derived bound structures are in excellent agreement. A robust four-state Markov model, developed using cumulative 60 μs trajectories, identifies and quantifies multiple ligand binding pathways with low activation barriers. Interestingly, none of these identified binding pathways required large conformational changes for ligand access to the buried cavity. Rather, these involve transient but crucial opening of a channel to the cavity via subtle displacements in the positions of key helices (helix4/helix6, helix7/helix9) leading to rapid binding. Free energy simulations further elucidate that these channel-opening events would have been unfavorable in wild type T4L. Taken together and via integrating with results from experiments, these simulations provide unprecedented mechanistic insights into the complete ligand recognition process in a buried cavity. By illustrating the power of subtle helix movements in opening up multiple pathways for ligand access, this work offers an alternate view of ligand recognition in a solvent-inaccessible cavity, contrary to the common perception of a single dominant pathway for ligand binding. PMID:29775455

Solid-to-solid oxidation of a vanadium(IV) to a vanadium(V) compound: chemisty of a sulfur-containing siderophore.

PubMed

Chatterjee, Pabitra B; Crans, Debbie C

2012-09-03

Visible light facilitates a solid-to-solid photochemical aerobic oxidation of a hunter-green microcrystalline oxidovanadium(IV) compound (1) to form a black powder of cis-dioxidovanadium(V) (2) at ambient temperature. The siderophore ligand pyridine-2,6-bis(thiocarboxylic acid), H(2)L, is secreted by a microorganism from the Pseudomonas genus. This irreversible transformation of a metal monooxo to a metal dioxo complex in the solid state in the absence of solvent is unprecedented. It serves as a proof-of-concept reaction for green chemistry occurring in solid matrixes.

An unprecedented up-field shift in the 13C NMR spectrum of the carboxyl carbons of the lantern-type dinuclear complex TBA[Ru2(O2CCH3)4Cl2] (TBA+ = tetra(n-butyl)ammonium cation).

PubMed

Hiraoka, Yuya; Ikeue, Takahisa; Sakiyama, Hiroshi; Guégan, Frédéric; Luneau, Dominique; Gillon, Béatrice; Hiromitsu, Ichiro; Yoshioka, Daisuke; Mikuriya, Masahiro; Kataoka, Yusuke; Handa, Makoto

2015-08-14

A large up-field shift (-763 ppm) has been observed for the carboxyl carbons of the dichlorido complex TBA[Ru(2)(O(2)CCH(3))(4)Cl(2)] (TBA(+) = tetra(n-butyl)ammonium cation) in the (13)C NMR spectrum (CD(2)Cl(2) at 25 °C). The DFT calculations showed spin delocalization from the paramagnetic Ru(2)(5+) core to the ligands, in agreement with the large up-field shift.

Rhodium-Catalyzed Asymmetric N-H Functionalization of Quinazolinones with Allenes and Allylic Carbonates: The First Enantioselective Formal Total Synthesis of (-)-Chaetominine.

PubMed

Zhou, Yirong; Breit, Bernhard

2017-12-22

An unprecedented asymmetric N-H functionalization of quinazolinones with allenes and allylic carbonates was successfully achieved by rhodium catalysis with the assistance of chiral bidentate diphosphine ligands. The high efficiency and practicality of this method was demonstrated by a low catalyst loading of 1 mol % as well as excellent chemo-, regio-, and enantioselectivities with broad functional group compatibility. Furthermore, this newly developed strategy was applied as key step in the first enantioselective formal total synthesis of (-)-chaetominine. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking

NASA Astrophysics Data System (ADS)

Olsson, Martin A.; García-Sosa, Alfonso T.; Ryde, Ulf

2018-01-01

We have studied the binding of 102 ligands to the farnesoid X receptor within the D3R Grand Challenge 2016 blind-prediction competition. First, we employed docking with five different docking software and scoring functions. The selected docked poses gave an average root-mean-squared deviation of 4.2 Å. Consensus scoring gave decent results with a Kendall's τ of 0.26 ± 0.06 and a Spearman's ρ of 0.41 ± 0.08. For a subset of 33 ligands, we calculated relative binding free energies with free-energy perturbation. Five transformations between the ligands involved a change of the net charge and we implemented and benchmarked a semi-analytic correction (Rocklin et al., J Chem Phys 139:184103, 2013) for artifacts caused by the periodic boundary conditions and Ewald summation. The results gave a mean absolute deviation of 7.5 kJ/mol compared to the experimental estimates and a correlation coefficient of R 2 = 0.1. These results were among the four best in this competition out of 22 submissions. The charge corrections were significant (7-8 kJ/mol) and always improved the results. By employing 23 intermediate states in the free-energy perturbation, there was a proper overlap between all states and the precision was 0.1-0.7 kJ/mol. However, thermodynamic cycles indicate that the sampling was insufficient in some of the perturbations.

Water oxidation by Ruthenium complexes incorporating multifunctional biipyridyl diphosphonate ligands

DOE PAGES

Xie, Yan; Shaffer, David W.; Lewandowska-Andralojc, Anna; ...

2016-05-11

Here, we describe herein the synthesis and characterization of ruthenium complexes with multifunctional bipyridyl diphosphonate ligands as well as initial water oxidation studies. In these complexes, the phosphonate groups provide redox-potential leveling through charge compensation and σ donation to allow facile access to high oxidation states. These complexes display unique pH-dependent electrochemistry associated with deprotonation of the phosphonic acid groups. The position of these groups allows them to shuttle protons in and out of the catalytic site and reduce activation barriers. A mechanism for water oxidation by these catalysts is proposed on the basis of experimental results and DFT calculations.more » The unprecedented attack of water at a neutral six-coordinate [Ru IV] center to yield an anionic seven-coordinate [Ru IV–OH] – intermediate is one of the key steps of a single-site mechanism in which all species are anionic or neutral. These complexes are among the fastest single-site catalysts reported to date.« less

A novel extended architecture with 4 6·6 4 topology based on mixed-valence Wells-Dawson arsenotungstate and mixed-ligand Cu(I) units

NASA Astrophysics Data System (ADS)

Tong, Ruizhan; Ren, Xiaoyu; Li, Zuoxi; Liu, Bin; Hu, Huaiming; Xue, Ganglin; Fu, Feng; Wang, Jiwu

2010-09-01

A novel inorganic-organic hybrid compound based on mixed-valence Wells-Dawson arsenotungstate and mixed-ligand Cu(I) units, Cu 8I(imi) 4(bpy) 6(H 2O)[As 2VW 2VW 16VlO 62]·2H 2O ( 1) (bpy=4,4'-bipydine; imi=imidazole), has been hydrothermally synthesized and characterized by elemental analysis, IR spectroscopy, thermal gravimetric analysis, luminescent spectrum and single crystal X-ray diffraction. Single-crystal X-ray diffraction revealed that four terminal and three bridging oxygen atoms of the Wells-Dawson cluster are coordinated to Cu(I) ions and form an unprecedented hepta-supporting polyoxometalate. The functionalized arsenotungstates are further connected by two kinds of tridentate linkers, Imi-Cu-(bpy)-Cu-(bpy)-Cu-(bpy)-Cu-Imi and Imi-Cu-(bpy)-Cu-(bpy)-Cu-H 2O, to construct a 3D framework with 4 6·6 4 topology. The hybrid material has an intense emission at about 397 nm.

Switch in Site of Inhibition: A Strategy for Structure-Based Discovery of Human Topoisomerase IIα Catalytic Inhibitors

PubMed Central

2015-01-01

A study of structure-based modulation of known ligands of hTopoIIα, an important enzyme involved in DNA processes, coupled with synthesis and in vitro assays led to the establishment of a strategy of rational switch in mode of inhibition of the enzyme’s catalytic cycle. 6-Arylated derivatives of known imidazopyridine ligands were found to be selective inhibitors of hTopoIIα, while not showing TopoI inhibition and DNA binding. Interestingly, while the parent imidazopyridines acted as ATP-competitive inhibitors, arylated derivatives inhibited DNA cleavage similar to merbarone, indicating a switch in mode of inhibition from ATP-hydrolysis to the DNA-cleavage stage of catalytic cycle of the enzyme. The 6-aryl-imidazopyridines were relatively more cytotoxic than etoposide in cancer cells and less toxic to normal cells. Such unprecedented strategy will encourage research on “choice-based change” in target-specific mode of action for rapid drug discovery. PMID:25941559

Modulation of Correlated Segment Fluctuations in IDPs upon Complex Formation as an Allosteric Regulatory Mechanism.

PubMed

Beier, Andreas; Schwarz, Thomas C; Kurzbach, Dennis; Platzer, Gerald; Tribuzio, Francesca; Konrat, Robert

2018-05-05

Molecular recognition of and by intrinsically disordered proteins (IDPs) is an intriguing and still largely elusive phenomenon. Typically, protein recognition involving IDPs requires either folding upon binding or, alternatively, the formation of "fuzzy complexes." Here we show via correlation analyses of paramagnetic relaxation enhancement data unprecedented and striking alterations of the concerted fluctuations within the conformational ensemble of IDPs upon ligand binding. We study the binding of α-synuclein to calmodulin, a ubiquitous calcium-binding protein, and the binding of the extracellular matrix IDP osteopontin to heparin, a mimic of the extracellular matrix ligand hyaluronic acid. In both cases, binding leads to reduction of correlated long-range motions in these two IDPs and thus indicates a loosening of structural compaction upon binding. Most importantly, however, the simultaneous presence of correlated and anti-correlated fluctuations in IDPs suggests the prevalence of "energetic frustration" and provides an explanation for the puzzling observation of disordered allostery in IDPs. Copyright © 2018. Published by Elsevier Ltd.

Efficient hydrogenation of organic carbonates, carbamates and formates indicates alternative routes to methanol based on CO2 and CO

NASA Astrophysics Data System (ADS)

Balaraman, Ekambaram; Gunanathan, Chidambaram; Zhang, Jing; Shimon, Linda J. W.; Milstein, David

2011-08-01

Catalytic hydrogenation of organic carbonates, carbamates and formates is of significant interest both conceptually and practically, because these compounds can be produced from CO2 and CO, and their mild hydrogenation can provide alternative, mild approaches to the indirect hydrogenation of CO2 and CO to methanol, an important fuel and synthetic building block. Here, we report for the first time catalytic hydrogenation of organic carbonates to alcohols, and carbamates to alcohols and amines. Unprecedented homogeneously catalysed hydrogenation of organic formates to methanol has also been accomplished. The reactions are efficiently catalysed by dearomatized PNN Ru(II) pincer complexes derived from pyridine- and bipyridine-based tridentate ligands. These atom-economical reactions proceed under neutral, homogeneous conditions, at mild temperatures and under mild hydrogen pressures, and can operate in the absence of solvent with no generation of waste, representing the ultimate ‘green’ reactions. A possible mechanism involves metal-ligand cooperation by aromatization-dearomatization of the heteroaromatic pincer core.

New coordination features; A bridging pyridine and the forced shortest non-covalent distance between two CO 3 2- species

DOE PAGES

Velasco, V.; Aguilà, D.; Barrios, L. A.; ...

2014-09-29

The aerobic reaction of the multidentate ligand 2,6-bis-(3-oxo-3-(2-hydroxyphenyl)-propionyl)-pyridine, H 4L, with Co (II) salts in strong basic conditions produces the clusters [Co 4(L) 2(OH)(py) 7]NO 3 (1) and [Co 8Na 4(L) 4(OH) 2(CO 3) 2(py) 10](BF 4) 2 (2). Analysis of their structure unveils unusual coordination features including a very rare bridging pyridine ligand or two trapped carbonate anions within one coordination cage, forced to stay at an extremely close distance (d O···O = 1.946 Å). This unprecedented non-bonding proximity represents a meeting point between long covalent interactions and “intermolecular” contacts. These original motifs have been analysed here through DFTmore » calculations, which have yielded interaction energies and the reduced repulsion energy experimented by both CO 3 2- anions when located in close proximity inside the coordination cage.« less

Reversing Conventional Reactivity of Mixed Oxo/Alkyl Rare-Earth Complexes: Non-Redox Oxygen Atom Transfer.

PubMed

Hong, Jianquan; Tian, Haiwen; Zhang, Lixin; Zhou, Xigeng; Del Rosal, Iker; Weng, Linhong; Maron, Laurent

2018-01-22

The preferential substitution of oxo ligands over alkyl ones of rare-earth complexes is commonly considered as "impossible" due to the high oxophilicity of metal centers. Now, it has been shown that simply assembling mixed methyl/oxo rare-earth complexes to a rigid trinuclear cluster framework cannot only enhance the activity of the Ln-oxo bond, but also protect the highly reactive Ln-alkyl bond, thus providing a previously unrecognized opportunity to selectively manipulate the oxo ligand in the presence of numerous reactive functionalities. Such trimetallic cluster has proved to be a suitable platform for developing the unprecedented non-redox rare-earth-mediated oxygen atom transfer from ketones to CS 2 and PhNCS. Controlled experiments and computational studies shed light on the driving force for these reactions, emphasizing the importance of the sterical accessibility and multimetallic effect of the cluster framework in promoting reversal of reactivity of rare-earth oxo complexes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Uranium azide photolysis results in C-H bond activation and provides evidence for a terminal uranium nitride

NASA Astrophysics Data System (ADS)

Thomson, Robert K.; Cantat, Thibault; Scott, Brian L.; Morris, David E.; Batista, Enrique R.; Kiplinger, Jaqueline L.

2010-09-01

Uranium nitride [U≡N]x is an alternative nuclear fuel that has great potential in the expanding future of nuclear power; however, very little is known about the U≡N functionality. We show, for the first time, that a terminal uranium nitride complex can be generated by photolysis of an azide (U-N=N=N) precursor. The transient U≡N fragment is reactive and undergoes insertion into a ligand C-H bond to generate new N-H and N-C bonds. The mechanism of this unprecedented reaction has been evaluated through computational and spectroscopic studies, which reveal that the photochemical azide activation pathway can be shut down through coordination of the terminal azide ligand to the Lewis acid B(C6F5)3. These studies demonstrate that photochemistry can be a powerful tool for inducing redox transformations for organometallic actinide complexes, and that the terminal uranium nitride fragment is reactive, cleaving strong C-H bonds.

Efficient hydrogenation of organic carbonates, carbamates and formates indicates alternative routes to methanol based on CO2 and CO.

PubMed

Balaraman, Ekambaram; Gunanathan, Chidambaram; Zhang, Jing; Shimon, Linda J W; Milstein, David

2011-07-22

Catalytic hydrogenation of organic carbonates, carbamates and formates is of significant interest both conceptually and practically, because these compounds can be produced from CO2 and CO, and their mild hydrogenation can provide alternative, mild approaches to the indirect hydrogenation of CO2 and CO to methanol, an important fuel and synthetic building block. Here, we report for the first time catalytic hydrogenation of organic carbonates to alcohols, and carbamates to alcohols and amines. Unprecedented homogeneously catalysed hydrogenation of organic formates to methanol has also been accomplished. The reactions are efficiently catalysed by dearomatized PNN Ru(II) pincer complexes derived from pyridine- and bipyridine-based tridentate ligands. These atom-economical reactions proceed under neutral, homogeneous conditions, at mild temperatures and under mild hydrogen pressures, and can operate in the absence of solvent with no generation of waste, representing the ultimate 'green' reactions. A possible mechanism involves metal-ligand cooperation by aromatization-dearomatization of the heteroaromatic pincer core.

Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.

PubMed

Kim, Jungwook; Xiao, Hui; Bonanno, Jeffrey B; Kalyanaraman, Chakrapani; Brown, Shoshana; Tang, Xiangying; Al-Obaidi, Nawar F; Patskovsky, Yury; Babbitt, Patricia C; Jacobson, Matthew P; Lee, Young-Sam; Almo, Steven C

2013-06-06

The identification of novel metabolites and the characterization of their biological functions are major challenges in biology. X-ray crystallography can reveal unanticipated ligands that persist through purification and crystallization. These adventitious protein-ligand complexes provide insights into new activities, pathways and regulatory mechanisms. We describe a new metabolite, carboxy-S-adenosyl-l-methionine (Cx-SAM), its biosynthetic pathway and its role in transfer RNA modification. The structure of CmoA, a member of the SAM-dependent methyltransferase superfamily, revealed a ligand consistent with Cx-SAM in the catalytic site. Mechanistic analyses showed an unprecedented role for prephenate as the carboxyl donor and the involvement of a unique ylide intermediate as the carboxyl acceptor in the CmoA-mediated conversion of SAM to Cx-SAM. A second member of the SAM-dependent methyltransferase superfamily, CmoB, recognizes Cx-SAM and acts as a carboxymethyltransferase to convert 5-hydroxyuridine into 5-oxyacetyl uridine at the wobble position of multiple tRNAs in Gram-negative bacteria, resulting in expanded codon-recognition properties. CmoA and CmoB represent the first documented synthase and transferase for Cx-SAM. These findings reveal new functional diversity in the SAM-dependent methyltransferase superfamily and expand the metabolic and biological contributions of SAM-based biochemistry. These discoveries highlight the value of structural genomics approaches in identifying ligands within the context of their physiologically relevant macromolecular binding partners, and in revealing their functions.

Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deka, Ranjit K.; Brautigam, Chad A.; Goldberg, Martin

2012-05-25

Treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite ATP-independent periplasmic transporter (TRAP-T). TRAP-Ts typically employ a periplasmic substrate-binding protein (SBP) to deliver the cognate ligand to the transmembrane symporter. Herein, we demonstrate that the genes encoding the putative TRAP-T components from T. pallidum, tp0957 (the SBP), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. We determined the crystal structure of recombinant Tp0956; the protein is trimeric and perforated by a pore. Part of Tp0956 forms an assembly similar to those of 'tetratricopeptide repeat' (TPR) motifs. The crystal structure ofmore » recombinant Tp0957 was also determined; like the SBPs of other TRAP-Ts, there are two lobes separated by a cleft. In these other SBPs, the cleft binds a negatively charged ligand. However, the cleft of Tp0957 has a strikingly hydrophobic chemical composition, indicating that its ligand may be substantially different and likely hydrophobic. Analytical ultracentrifugation of the recombinant versions of Tp0956 and Tp0957 established that these proteins associate avidly. This unprecedented interaction was confirmed for the native molecules using in vivo cross-linking experiments. Finally, bioinformatic analyses suggested that this transporter exemplifies a new subfamily of TPATs (TPR-protein-associated TRAP-Ts) that require the action of a TPR-containing accessory protein for the periplasmic transport of a potentially hydrophobic ligand(s).« less

Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets

PubMed Central

Cerisier, Natacha; Regad, Leslie; Triki, Dhoha; Camproux, Anne-Claude

2017-01-01

Abstract We analyzed 78 binding pockets of the human urokinase plasminogen activator (uPA) catalytic domain extracted from a data set of crystallized uPA–ligand complexes. These binding pockets were computed with an original geometric method that does NOT involve any arbitrary parameter, such as cutoff distances, angles, and so on. We measured the deviation from convexity of each pocket shape with the pocket convexity index (PCI). We defined a new pocket descriptor called distributional sphericity coefficient (DISC), which indicates to which extent the protein atoms of a given pocket lie on the surface of a sphere. The DISC values were computed with the freeware PCI. The pocket descriptors and their high correspondences with ligand descriptors are crucial for polypharmacology prediction. We found that the protein heavy atoms lining the urokinases binding pockets are either located on the surface of their convex hull or lie close to this surface. We also found that the radii of the urokinases binding pockets and the radii of their ligands are highly correlated (r = 0.9). PMID:28570103

5D-QSAR for spirocyclic sigma1 receptor ligands by Quasar receptor surface modeling.

PubMed

Oberdorf, Christoph; Schmidt, Thomas J; Wünsch, Bernhard

2010-07-01

Based on a contiguous and structurally as well as biologically diverse set of 87 sigma(1) ligands, a 5D-QSAR study was conducted in which a quasi-atomistic receptor surface modeling approach (program package Quasar) was applied. The superposition of the ligands was performed with the tool Pharmacophore Elucidation (MOE-package), which takes all conformations of the ligands into account. This procedure led to four pharmacophoric structural elements with aromatic, hydrophobic, cationic and H-bond acceptor properties. Using the aligned structures a 3D-model of the ligand binding site of the sigma(1) receptor was obtained, whose general features are in good agreement with previous assumptions on the receptor structure, but revealed some novel insights since it represents the receptor surface in more detail. Thus, e.g., our model indicates the presence of an H-bond acceptor moiety in the binding site as counterpart to the ligands' cationic ammonium center, rather than a negatively charged carboxylate group. The presented QSAR model is statistically valid and represents the biological data of all tested compounds, including a test set of 21 ligands not used in the modeling process, with very good to excellent accuracy [q(2) (training set, n=66; leave 1/3 out) = 0.84, p(2) (test set, n=21)=0.64]. Moreover, the binding affinities of 13 further spirocyclic sigma(1) ligands were predicted with reasonable accuracy (mean deviation in pK(i) approximately 0.8). Thus, in addition to novel insights into the requirements for binding of spirocyclic piperidines to the sigma(1) receptor, the presented model can be used successfully in the rational design of new sigma(1) ligands. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Le Coq, Johanne; Ghosh, Partho

2012-06-19

Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein,more » TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd ({approx}16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10{sup 20} potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.« less

Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

PubMed Central

Le Coq, Johanne; Ghosh, Partho

2011-01-01

Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd (∼16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 1020 potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation. PMID:21873231

Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement.

PubMed

Le Coq, Johanne; Ghosh, Partho

2011-08-30

Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd (∼16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10(20) potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.

Understanding the molecular differential recognition of muramyl peptide ligands by LRR domains of human NOD receptors.

PubMed

Vijayrajratnam, Sukhithasri; Pushkaran, Anju Choorakottayil; Balakrishnan, Aathira; Vasudevan, Anil Kumar; Biswas, Raja; Mohan, Chethampadi Gopi

2017-07-27

Human nucleotide-binding oligomerization domain proteins, hNOD1 and hNOD2, are host intracellular receptors with C-terminal leucine-rich repeat (LRR) domains, which recognize specific bacterial peptidoglycan (PG) fragments as their ligands. The specificity of this recognition is dependent on the third amino acid of the stem peptide of the PG ligand, which is usually meso -diaminopimelic acid ( meso DAP) or l-lysine (l-Lys). Since the LRR domains of hNOD receptors had been experimentally shown to confer the PG ligand-sensing specificity, we developed three-dimensional structures of hNOD1-LRR and the hNOD2-LRR to understand the mechanism of differential recognition of muramyl peptide ligands by hNOD receptors. The hNOD1-LRR and hNOD2-LRR receptor models exhibited right-handed curved solenoid shape. The hot-spot residues experimentally proved to be critical for ligand recognition were located in the concavity of the NOD-LRR and formed the recognition site. Our molecular docking analyses and molecular electrostatic potential mapping studies explain the activation of hNOD-LRRs, in response to effective molecular interactions of PG ligands at the recognition site; and conversely, the inability of certain PG ligands to activate hNOD-LRRs, by deviations from the recognition site. Based on molecular docking studies using PG ligands, we propose few residues - G825, D826 and N850 in hNOD1-LRR and L904, G905, W931, L932 and S933 in hNOD2-LRR, evolutionarily conserved across different host species, which may play a major role in ligand recognition. Thus, our integrated experimental and computational approach elucidates the molecular basis underlying the differential recognition of PG ligands by hNOD receptors. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015

NASA Astrophysics Data System (ADS)

Kumar, Ashutosh; Zhang, Kam Y. J.

2016-09-01

Evaluation of ligand three-dimensional (3D) shape similarity is one of the commonly used approaches to identify ligands similar to one or more known active compounds from a library of small molecules. Apart from using ligand shape similarity as a virtual screening tool, its role in pose prediction and pose scoring has also been reported. We have recently developed a method that utilizes ligand 3D shape similarity with known crystallographic ligands to predict binding poses of query ligands. Here, we report the prospective evaluation of our pose prediction method through the participation in drug design data resource (D3R) Grand Challenge 2015. Our pose prediction method was used to predict binding poses of heat shock protein 90 (HSP90) and mitogen activated protein kinase kinase kinase kinase (MAP4K4) ligands and it was able to predict the pose within 2 Å root mean square deviation (RMSD) either as the top pose or among the best of five poses in a majority of cases. Specifically for HSP90 protein, a median RMSD of 0.73 and 0.68 Å was obtained for the top and the best of five predictions respectively. For MAP4K4 target, although the median RMSD for our top prediction was only 2.87 Å but the median RMSD of 1.67 Å for the best of five predictions was well within the limit for successful prediction. Furthermore, the performance of our pose prediction method for HSP90 and MAP4K4 ligands was always among the top five groups. Particularly, for MAP4K4 protein our pose prediction method was ranked number one both in terms of mean and median RMSD when the best of five predictions were considered. Overall, our D3R Grand Challenge 2015 results demonstrated that ligand 3D shape similarity with the crystal ligand is sufficient to predict binding poses of new ligands with acceptable accuracy.

A novel gene from the takeout family involved in termite trail-following behavior.

PubMed

Schwinghammer, Margaret A; Zhou, Xuguo; Kambhampati, Srinivas; Bennett, Gary W; Scharf, Michael E

2011-03-15

This study investigated physiological and behavioral functions of a novel gene identified from the termite Reticulitermes flavipes. The gene, named deviate, encodes an apparent ligand binding protein from the takeout-homologous family. Initial studies were conducted to investigate deviate mRNA expression among termite castes and body regions, and changes in response to light-dark conditions, starvation, temperature, and juvenile hormone (JH). Deviate has ubiquitous caste and tissue expression, including antennal expression. Consistent with characteristics of other takeout family members, deviate expression is responsive to photophase conditions (p<0.1), and feeding, temperature, and JH (p<0.05). Using RNA-interference (RNAi) techniques, short-interfering RNAs (siRNAs) homologous to the deviate gene were synthesized and injected into worker termites, which were then subjected to bioassays designed to (1) induce caste differentiation or (2) measure various behavioral aspects of foraging and trail following. No impacts on JH-dependent caste differentiation were observable. However, trail following accuracy was significantly reduced in termites that received deviate siRNA injections, and this pattern generally mirrored deviate mRNA attenuation and recovery after RNAi. In a subsequent distance foraging bioassay, deviate-silenced termites exhibited equal feeding levels to controls, suggesting the deviate gene is not linked to general vigor or the ability/motivation of termites to move and forage. These findings are among the first linking the expression of a termite gene with eusocial behavior; they illustrate the connection between deviate expression and trailing behavior, which is a key evolutionary adaptation vital to subterranean social insects such as termites and ants. Copyright © 2010 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yi, Xiu-Chun; Xi, Fu-Gui; Wang, Kun

From a new dicarboxylate ligand, 9H-carbazole-2,7-dicarboxylic acid (2,7-H{sub 2}CDC), three Zn(II) metal-organic frameworks were synthesized in the absence or presence of ditopic N-donor ligands. They are formulated as [Zn{sub 5}(μ{sub 3}-OH){sub 2}(2,7-CDC){sub 4}(DEF){sub 2}] (1) (DEF=N,N-diethylformamide), [Zn{sub 2}(2,7-CDC){sub 2}(DABCO)(H{sub 2}O)]·5DMF·H{sub 2}O (2) (DABCO=1-diaza-bicyclo[2.2.2]octane, DMF=N,N-dimethylformamide), and [Zn{sub 2}(2,7-CDC){sub 2}(bpea)]·3DMA·2 H{sub 2}O (3) (bpea=1,2-bis(4-pyridyl)ethylane, DMA=N,N-dimethylacetamide). Compounds 1 and 3 display the 3D pcu frameworks. In 1 the unusual pentanuclear [Zn{sub 5}(μ{sub 3}-OH){sub 2}(COO){sub 8}] secondary building units (SBUs) are linked by dicarboxylate ligands. Differently, in 3 the well-known paddle–wheel [Zn{sub 2}(COO){sub 4}] SBUs are linked by dicarboxylate and dipyridyl ligands. Compound 2more » shows the rare self-catenated 3D alb-3,6-C2/c net topology based on the dinuclear paddle–wheel SBU and a mononuclear unit. The stability and fluorescent properties of the compounds have been studied. - Graphical abstract: A new dicarboxylate ligand, 9H-carbazole-2,7-dicarboxylic acid, was used to construct Zn(II) metal-organic frameworks, including a novel self-catenated network with the rare 3D alb-3,6-C2/c net and two pcu-type networks based on an unprecedented pentanuclear clusters and the common paddle–wheel units. The compounds show blue fluorescent properties. Display Omitted - Highlights: • MOFs with a new carbazole-based dicarboxylate ligand. • New pentanuclear [Zn{sub 5}(μ{sub 3}-OH){sub 2}(COO){sub 8}] secondary building unit. • The rare self-catenated 3D alb-3,6-C2/c net.« less

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins.

PubMed

Andersen, Ole Juul; Grouleff, Julie; Needham, Perri; Walker, Ross C; Jensen, Frank

2015-11-19

Current enhanced sampling molecular dynamics methods for studying large conformational changes in proteins suffer from certain limitations. These include, among others, the need for user defined collective variables, the prerequisite of both start and end point structures of the conformational change, and the need for a priori knowledge of the amount by which to boost specific parts of the potential. In this paper, a framework is proposed for a molecular dynamics method for studying ligand-induced conformational changes, in which the nonbonded interactions between the ligand and the protein are used to calculate a biasing force. The method requires only a single input structure, and does not entail the use of collective variables. We provide a proof-of-concept for accelerating conformational changes in three simple test molecules, as well as promising results for two proteins known to undergo domain closure upon ligand binding. For the ribose-binding protein, backbone root-mean-square deviations as low as 0.75 Å compared to the crystal structure of the closed conformation are obtained within 50 ns simulations, whereas no domain closures are observed in unbiased simulations. A skewed closed structure is obtained for the glutamine-binding protein at high bias values, indicating that specific protein-ligand interactions might suppress important protein-protein interactions.

Biologically active ligands for yersinia outer protein H (YopH): feature based pharmacophore screening, docking and molecular dynamics studies.

PubMed

Tamilvanan, Thangaraju; Hopper, Waheeta

2014-01-01

Yersinia pestis, a Gram negative bacillus, spreads via lymphatic to lymph nodes and to all organs through the bloodstream, causing plague. Yersinia outer protein H (YopH) is one of the important effector proteins, which paralyzes lymphocytes and macrophages by dephosphorylating critical tyrosine kinases and signal transduction molecules. The purpose of the study is to generate a three-dimensional (3D) pharmacophore model by using diverse sets of YopH inhibitors, which would be useful for designing of potential antitoxin. In this study, we have selected 60 biologically active inhibitors of YopH to perform Ligand based pharmacophore study to elucidate the important structural features responsible for biological activity. Pharmacophore model demonstrated the importance of two acceptors, one hydrophobic and two aromatic features toward the biological activity. Based on these features, different databases were screened to identify novel compounds and these ligands were subjected for docking, ADME properties and Binding energy prediction. Post docking validation was performed using molecular dynamics simulation for selected ligands to calculate the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF). The ligands, ASN03270114, Mol_252138, Mol_31073 and ZINC04237078 may act as inhibitors against YopH of Y. pestis.

A 920-kilometer optical fiber link for frequency metrology at the 19th decimal place.

PubMed

Predehl, K; Grosche, G; Raupach, S M F; Droste, S; Terra, O; Alnis, J; Legero, Th; Hänsch, T W; Udem, Th; Holzwarth, R; Schnatz, H

2012-04-27

Optical clocks show unprecedented accuracy, surpassing that of previously available clock systems by more than one order of magnitude. Precise intercomparisons will enable a variety of experiments, including tests of fundamental quantum physics and cosmology and applications in geodesy and navigation. Well-established, satellite-based techniques for microwave dissemination are not adequate to compare optical clocks. Here, we present phase-stabilized distribution of an optical frequency over 920 kilometers of telecommunication fiber. We used two antiparallel fiber links to determine their fractional frequency instability (modified Allan deviation) to 5 × 10(-15) in a 1-second integration time, reaching 10(-18) in less than 1000 seconds. For long integration times τ, the deviation from the expected frequency value has been constrained to within 4 × 10(-19). The link may serve as part of a Europe-wide optical frequency dissemination network.

Molecular dynamics simulation studies of novel β-lactamase inhibitor.

PubMed

Ul Haq, Farhan; Abro, Asma; Raza, Saad; Liedl, Klaus R; Azam, Syed Sikander

2017-06-01

New Delhi Metallo-β-Lactamase-1 (NDM-1) has drawn great attention due to its diverse antibiotic resistant activity. It can hydrolyze almost all clinically available β-lactam antibiotics. To inhibit the activity of NDM-1 a new strategy is proposed using computational methods. Molecular dynamics (MD) simulations are used to analyze the molecular interactions between selected inhibitor candidates and NDM-1 structure. The enzyme-ligand complex is subject to binding free energy calculations using MM(PB/GB)SA methods. The role of each residue of the active site contributing in ligand binding affinity is explored using energy decomposition analysis. Furthermore, a hydrogen bonding network between ligand and enzyme active site is observed and key residues are identified ensuring that the ligand stays inside the active site and maintains its movement towards the active site pocket. A production run of 150ns is carried out and results are analyzed using root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) to explain the stability of enzyme ligand complex. Important active site residue e.g. PHE70, VAL73, TRP93, HIS122, GLN123, ASP124, HIS189, LYS216, CYS208, LYS211, ALA215, HIS250, and SER251 were observed to be involved in ligand attachemet inside the active site pocket, hence depicting its inhibitor potential. Hydrogen bonds involved in structural stability are analyzed through radial distribution function (RDF) and contribution of important residues involved in ligand movement is explained using a novel analytical tool, axial frequency distribution (AFD) to observe the role of important hydrogen bonding partners between ligand atoms and active site residues. Copyright © 2017 Elsevier Inc. All rights reserved.

Infrared Multiphoton Dissociation Spectroscopy of a Gas-Phase Complex of Uranyl and 3-Oxa-Glutaramide: An Extreme Red-Shift of the [O=U=O]²⁺ Asymmetric Stretch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibson, John K.; Hu, Hanshi; Van Stipdonk, Michael J.

2015-04-09

The gas-phase complex UO₂(TMOGA)₂²⁺ (TMOGA = tetramethyl-3-oxa-glutaramide) prepared by electrospray ionization was characterized by infrared multiphoton dissociation (IRMPD) spectroscopy. The IRMPD spectrum from 700–1800 cm⁻¹ was interpreted using a computational study based on density functional theory. The predicted vibrational frequencies are in good agreement with the measured values, with an average deviation of only 8 cm⁻¹ (<1%) and a maximum deviation of 21 cm⁻¹ (<2%). The only IR peak assigned to the linear uranyl moiety was the asymmetric ν₃ mode, which appeared at 965 cm⁻¹ and was predicted by DFT as 953 cm⁻¹. This ν₃ frequency is red-shifted relative tomore » bare uranyl, UO₂²⁺, by ca. 150 cm⁻¹ due to electron donation from the TMOGA ligands. Based on the degree of red-shifting, it is inferred that two TMOGA oxygen-donor ligands have a greater effective gas basicity than the four monodentate acetone ligands in UO₂(acetone)₄²⁺. The uranyl ν₃ frequency was also computed for uranyl coordinated by two TMGA ligands, in which the central Oether of TMOGA has been replaced by CH₂. The computed ν₃ for UO₂(TMGA)₂²⁺, 950 cm⁻¹, is essentially the same as that for UO₂(TMOGA)₂²⁺, suggesting that electron donation to uranyl from the Oether of TMOGA is minor. The computed ν₃ asymmetric stretching frequencies for the three actinyl complexes, UO₂(TMOGA)₂²⁺, NpO₂(TMOGA)₂²⁺ and PuO₂(TMOGA)₂²⁺, are comparable. This similarity is discussed in the context of the relationship between ν₃ and intrinsic actinide-oxygen bond energies in actinyl complexes.« less

MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.

PubMed

Sharma, Monika; Bulusu, Gopalakrishnan; Mitra, Abhijit

2009-09-01

Riboswitches are structural cis-acting genetic regulatory elements in 5' UTRs of mRNAs, consisting of an aptamer domain that regulates the behavior of an expression platform in response to its recognition of, and binding to, specific ligands. While our understanding of the ligand-bound structure of the aptamer domain of the adenine riboswitches is based on crystal structure data and is well characterized, understanding of the structure and dynamics of the ligand-free aptamer is limited to indirect inferences from physicochemical probing experiments. Here we report the results of 15-nsec-long explicit-solvent molecular dynamics simulations of the add A-riboswitch crystal structure (1Y26), both in the adenine-bound (CLOSED) state and in the adenine-free (OPEN) state. Root-mean-square deviation, root-mean-square fluctuation, dynamic cross-correlation, and backbone torsion angle analyses are carried out on the two trajectories. These, along with solvent accessible surface area analysis of the two average structures, are benchmarked against available experimental data and are shown to constitute the basis for obtaining reliable insights into the molecular level details of the binding and switching mechanism. Our analysis reveals the interaction network responsible for, and conformational changes associated with, the communication between the binding pocket and the expression platform. It further highlights the significance of a, hitherto unreported, noncanonical W:H trans base pairing between A73 and A24, in the OPEN state, and also helps us to propose a possibly crucial role of U51 in the context of ligand binding and ligand discrimination.

Ligand Binding Pathways and Conformational Transitions of the HIV Protease.

PubMed

Miao, Yinglong; Huang, Yu-Ming M; Walker, Ross C; McCammon, J Andrew; Chang, Chia-En A

2018-03-06

It is important to determine the binding pathways and mechanisms of ligand molecules to target proteins to effectively design therapeutic drugs. Molecular dynamics (MD) is a promising computational tool that allows us to simulate protein-drug binding at an atomistic level. However, the gap between the time scales of current simulations and those of many drug binding processes has limited the usage of conventional MD, which has been reflected in studies of the HIV protease. Here, we have applied a robust enhanced simulation method, Gaussian accelerated molecular dynamics (GaMD), to sample binding pathways of the XK263 ligand and associated protein conformational changes in the HIV protease. During two of 10 independent GaMD simulations performed over 500-2500 ns, the ligand was observed to successfully bind to the protein active site. Although GaMD-derived free energy profiles were not fully converged because of insufficient sampling of the complex system, the simulations still allowed us to identify relatively low-energy intermediate conformational states during binding of the ligand to the HIV protease. Relative to the X-ray crystal structure, the XK263 ligand reached a minimum root-mean-square deviation (RMSD) of 2.26 Å during 2.5 μs of GaMD simulation. In comparison, the ligand RMSD reached a minimum of only ∼5.73 Å during an earlier 14 μs conventional MD simulation. This work highlights the enhanced sampling power of the GaMD approach and demonstrates its wide applicability to studies of drug-receptor interactions for the HIV protease and by extension many other target proteins.

Structure, Bonding, and Stability of Mercury Complexes with Thiolate and Thioether Ligands from High-Resolution XANES Spectroscopy and First-Principles Calculations.

PubMed

Manceau, Alain; Lemouchi, Cyprien; Rovezzi, Mauro; Lanson, Martine; Glatzel, Pieter; Nagy, Kathryn L; Gautier-Luneau, Isabelle; Joly, Yves; Enescu, Mironel

2015-12-21

We present results obtained from high energy-resolution L3-edge XANES spectroscopy and first-principles calculations for the structure, bonding, and stability of mercury(II) complexes with thiolate and thioether ligands in crystalline compounds, aqueous solution, and macromolecular natural organic matter (NOM). Core-to-valence XANES features that vary in intensity differentiate with unprecedented sensitivity the number and identity of Hg ligands and the geometry of the ligand environment. Post-Hartree-Fock XANES calculations, coupled with natural population analysis, performed on MP2-optimized Hg[(SR)2···(RSR)n] complexes show that the shape, position, and number of electronic transitions observed at high energy-resolution are directly correlated to the Hg and S (l,m)-projected empty densities of states and occupations of the hybridized Hg 6s and 5d valence orbitals. Linear two-coordination, the most common coordination geometry in mercury chemistry, yields a sharp 2p to 6s + 5d electronic transition. This transition varies in intensity for Hg bonded to thiol groups in macromolecular NOM. The intensity variation is explained by contributions from next-nearest, low-charge, thioether-type RSR ligands at 3.0-3.3 Å from Hg. Thus, Hg in NOM has two strong bonds to thiol S and k additional weak Hg···S contacts, or 2 + k coordination. The calculated stabilization energy is -5 kcal/mol per RSR ligand. Detection of distant ligands beyond the first coordination shell requires precise measurement of, and comparison to, spectra of reference compounds as well as accurate calculation of spectra for representative molecular models. The combined experimental and theoretical approaches described here for Hg can be applied to other closed-shell atoms, such as Ag(I) and Au(I). To facilitate further calculation of XANES spectra, experimental data, a new crystallographic structure of a key mercury thioether complex, Cartesian coordinates of the computed models, and examples of input files are provided as Supporting Information .

Tailor-made Molecular Cobalt Catalyst System for the Selective Transformation of Carbon Dioxide to Dialkoxymethane Ethers.

PubMed

Schieweck, Benjamin G; Klankermayer, Jürgen

2017-08-28

Herein a non-precious transition-metal catalyst system for the selective synthesis of dialkoxymethane ethers from carbon dioxide and molecular hydrogen is presented. The development of a tailored catalyst system based on cobalt salts in combination with selected Triphos ligands and acidic co-catalysts enabled a synthetic pathway, avoiding the oxidation of methanol to attain the formaldehyde level of the central CH 2 unit. This unprecedented productivity based on the molecular cobalt catalyst is the first example of a non-precious transition-metal system for this transformation utilizing renewable carbon dioxide sources. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unusual centrosymmetric structure of [M(18-crown-6)](+) (M = Rb, Cs and NH4) complexes stabilized in an environment of hexachloridoantimonate(V) anions.

PubMed

Ponomarova, Vira V; Rusanova, Julia A; Rusanov, Eduard B; Domasevitch, Konstantin V

2015-10-01

In (1,4,7,10,13,16-hexaoxacyclooctadecane)rubidium hexachloridoantimonate(V), [Rb(C12H24O6)][SbCl6], (1), and its isomorphous caesium {(1,4,7,10,13,16-hexaoxacyclooctadecane)caesium hexachloridoantimonate(V), [Cs(C12H24O6)][SbCl6]}, (2), and ammonium {ammonium hexachloridoantimonate(V)-1,4,7,10,13,16-hexaoxacyclooctadecane (1/1), (NH4)[SbCl6]·C12H24O6}, (3), analogues, the hexachloridoantimonate(V) anions and 18-crown-6 molecules reside across -3 axes passing through the Sb atoms and the centroids of the 18-crown-6 groups, both of which coincide with centres of inversion. The Rb(+) [in (1)], Cs(+) [in (2)] and NH4(+) [in (3)] cations are situated inside the cavity of the 18-crown-6 ring; they are situated on -3 axes and are equally disordered about centres of inversion, deviating from the centroid of the 18-crown-6 molecule by 0.4808 (13), 0.9344 (7) and 0.515 (8) Å, respectively. Interaction of the ammonium cation and the 18-crown-6 group is supported by three equivalent hydrogen bonds [N...O = 2.928 (3) Å and N-H...O = 162°]. The centrosymmetric structure of [Cs(18-crown-6)](+), with the large Cs(+) cation approaching the centre of the ligand cavity, is unprecedented and accompanied by unusually short Cs-O bonds [2.939 (2) and 3.091 (2) Å]. For all three compounds, the [M(18-crown-6)](+) cations and [SbCl6](-) anions afford linear stacks along the c axis, with the cationic complexes embedded between pairs of inversion-related anions.

How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

PubMed

Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

2015-06-09

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the ligands. This improved the root-mean-square error (RMSE) for the predicted binding free energy from 1.9 kcal/mol with the original partial charges to 1.3 kcal/mol with the corrected partial charges.

How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

PubMed Central

2016-01-01

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the ligands. This improved the root-mean-square error (RMSE) for the predicted binding free energy from 1.9 kcal/mol with the original partial charges to 1.3 kcal/mol with the corrected partial charges. PMID:26085821

Dispersed metal cluster catalysts by design. Synthesis, characterization, structure, and performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arslan, Ilke; Dixon, David A.; Gates, Bruce C.

2015-09-30

To understand the class of metal cluster catalysts better and to lay a foundation for the prediction of properties leading to improved catalysts, we have synthesized metal catalysts with well-defined structures and varied the cluster structures and compositions systematically—including the ligands bonded to the metals. These ligands include supports and bulky organics that are being tuned to control both the electron transfer to or from the metal and the accessibility of reactants to influence catalytic properties. We have developed novel syntheses to prepare these well-defined catalysts with atomic-scale control the environment by choice and placement of ligands and applied state-of-themore » art spectroscopic, microscopic, and computational methods to determine their structures, reactivities, and catalytic properties. The ligands range from nearly flat MgO surfaces to enveloping zeolites to bulky calixarenes to provide controlled coverages of the metal clusters, while also enforcing unprecedented degrees of coordinative unsaturation at the metal site—thereby facilitating bonding and catalysis events at exposed metal atoms. With this wide range of ligand properties and our arsenal of characterization tools, we worked to achieve a deep, fundamental understanding of how to synthesize robust supported and ligand-modified metal clusters with controlled catalytic properties, thereby bridging the gap between active site structure and function in unsupported and supported metal catalysts. We used methods of organometallic and inorganic chemistry combined with surface chemistry for the precise synthesis of metal clusters and nanoparticles, characterizing them at various stages of preparation and under various conditions (including catalytic reaction conditions) and determining their structures and reactivities and how their catalytic properties depend on their compositions and structures. Key characterization methods included IR, NMR, and EXAFS spectroscopies to identify ligands on the metals and their reactions; EXAFS spectroscopy and high-resolution STEM to determine cluster framework structures and changes resulting from reactant treatment and locations of metal atoms on support surfaces; X-ray diffraction crystallography to determine full structures of cluster-ligand combinations in the absence of a support, and TEM with tomographic methods to observe individual metal atoms and determine three-dimensional structures of catalysts. Electronic structure calculations were used to verify and interpret spectra and extend the understanding of reactivity beyond what is measurable experimentally.« less

Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

PubMed Central

Frimurer, Thomas M.; Meiler, Jens

2013-01-01

The rapidly increasing number of high-resolution X-ray structures of G-protein coupled receptors (GPCRs) creates a unique opportunity to employ comparative modeling and docking to provide valuable insight into the function and ligand binding determinants of novel receptors, to assist in virtual screening and to design and optimize drug candidates. However, low sequence identity between receptors, conformational flexibility, and chemical diversity of ligands present an enormous challenge to molecular modeling approaches. It is our hypothesis that rapid Monte-Carlo sampling of protein backbone and side-chain conformational space with Rosetta can be leveraged to meet this challenge. This study performs unbiased comparative modeling and docking methodologies using 14 distinct high-resolution GPCRs and proposes knowledge-based filtering methods for improvement of sampling performance and identification of correct ligand-receptor interactions. On average, top ranked receptor models built on template structures over 50% sequence identity are within 2.9 Å of the experimental structure, with an average root mean square deviation (RMSD) of 2.2 Å for the transmembrane region and 5 Å for the second extracellular loop. Furthermore, these models are consistently correlated with low Rosetta energy score. To predict their binding modes, ligand conformers of the 14 ligands co-crystalized with the GPCRs were docked against the top ranked comparative models. In contrast to the comparative models themselves, however, it remains difficult to unambiguously identify correct binding modes by score alone. On average, sampling performance was improved by 103 fold over random using knowledge-based and energy-based filters. In assessing the applicability of experimental constraints, we found that sampling performance is increased by one order of magnitude for every 10 residues known to contact the ligand. Additionally, in the case of DOR, knowledge of a single specific ligand-protein contact improved sampling efficiency 7 fold. These findings offer specific guidelines which may lead to increased success in determining receptor-ligand complexes. PMID:23844000

On the structural features of hairpin triloops in rRNA: from nucleotide to global conformational change upon ligand binding.

PubMed

Mitrasinovic, Petar M

2006-03-01

RNA structure can be viewed as both a construct composed of various structural motifs and a flexible polymer that is substantially influenced by its environment. In this light, the present paper represents an attempt to reconcile the two standpoints. By using the 3D structures both of four (16S and 23S) portions of unbound 50S, H50S, and T30S ribosomal subunits and of 38 large ribonucleoligand complexes as the starting point, the behavior, which is induced by ligand binding, of 73 hairpin triloops with closing g-c and c-g base pairs was investigated using root-mean-square deviation (RMSD) approach and pseudotorsional (eta,theta) convention at the nucleotide-by-nucleotide level. Triloops were annotated in accordance with a recent proposal of geometric nomenclature. A simple measure for the determination of the strain of a triloop is introduced. It is believed that a possible classification of the interior triloops, based on the 2D eta-theta unique path, will aid to conceive their local behavior upon ligand binding. All rRNA residues in contact with ligands as well as regions of considerable conformational changes upon complex formation were identified. The analysis offers the answer to: how proximal to and how far from the actual ligand-binding sites the structural changes occur?

Coordination Structure and Fragmentation Chemistry of the Tripositive Lanthanide-Thio-Diglycolamide Complexes.

PubMed

Chen, Xiuting; Li, Qingnuan; Gong, Yu

2017-12-14

Tripositive Ln(TMTDA) 3 3+ complexes (Ln = La-Lu except Pm, TMTDA = tetramethyl 3-thio-diglycolamide) were observed in the gas phase by electrospray ionization of LnCl 3 and TMTDA mixtures. Collision-induced dissociation (CID) was employed to investigate their fragmentation chemistry, which revealed the influence of metal center as well as ligand on the ligated complexes. Ln(TMTDA) 2 (TMTDA-45) 3+ resulting from C carbonyl -N bond cleavage of TMTDA and hydrogen transfer was the major CID product for all Ln(TMTDA) 3 3+ except Eu(TMTDA) 3 3+ , which predominantly formed charge-reducing product Eu II (TMTDA) 2 2+ via electron transfer from TMTDA to Eu 3+ . Density functional theory calculations on the structure of La(TMTDA) 3 3+ and Lu(TMTDA) 3 3+ revealed that Ln 3+ was coordinated by six O carbonyl atoms from three neutral TMTDA ligands, and both complexes possessed C 3h symmetry. The S ether atom deviating from the ligand plane was not coordinated to the metal center. On the basis of the CID results of Ln(TMTDA) 3 3+ , Ln(TMGA) 3 3+ , and Ln(TMOGA) 3 3+ , the fragmentation chemistry associated with the ligand depends on the coordination mode, while the redox chemistry of these tripositive ions is related to the nature of both metal centers and diamide ligands.

Homoleptic Ce(III) and Ce(IV) Nitroxide Complexes: Significant Stabilization of the 4+ Oxidation State

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bogart, Justin A.; Lewis, Andrew J.; Medling, Scott A.

2014-06-25

Electrochemical experiments performed on the complex Ce-IV[2-((BuNO)-Bu-t)py](4), where [2-((BuNO)-Bu-t)py](-) = N-tert-butyl-N-2-pyridylnitroxide, indicate a 2.51 V stabilization of the 4+ oxidation state of Ce compared to [(Bu4N)-Bu-n](2)[Ce(NO3)(6)] in acetonitrile and a 2.95 V stabilization compared to the standard potential for the ion under aqueous conditions. Density functional theory calculations suggest that this preference for the higher oxidation state is a result of the tetrakis(nitroxide) ligand framework at the Ce cation, which allows for effective electron donation into, and partial covalent overlap with, vacant 4f orbitals with delta symmetry. The results speak to the behavior of CeO2 and related solid solutions inmore » oxygen uptake and transport applications, in particular an inherent local character of bonding that stabilizes the 4+ oxidation state. The results indicate a cerium(IV) complex that has been stabilized to an unprecedented degree through tuning of its ligand-field environment.« less

Axial iron coordination and spin state change in a heme c upon electrostatic protein-SAM interaction.

PubMed

Di Rocco, Giulia; Ranieri, Antonio; Bortolotti, Carlo Augusto; Battistuzzi, Gianantonio; Bonifacio, Alois; Sergo, Valter; Borsari, Marco; Sola, Marco

2013-08-28

A bacterial di-heme cytochrome c binds electrostatically to a gold electrode surface coated with a negatively charged COOH-terminated SAM adopting a sort of 'perpendicular' orientation. Cyclic voltammetry, Resonance Raman and SERRS spectroscopies indicate that the high-potential C-terminal heme center proximal to the SAM's surface undergoes an adsorption-induced swapping of one axial His ligand with a water molecule, which is probably lost in the reduced form, and a low- to high-spin transition. This coordination change for a bis-His ligated heme center upon an electrostatically-driven molecular recognition is as yet unprecedented, as well as the resulting increase in reduction potential. We discuss it in comparison with the known methionine ligand lability in monoheme cytochromes c occurring upon interaction with charged molecular patches. One possible implication of this finding in biological ET is that mobile redox partners do not behave as rigid and invariant bodies, but in the ET complex are subjected to molecular changes and structural fluctuations that affect in a complex way the thermodynamics and the kinetics of the process.

An Icosidodecahedral Supramolecule Based on Pentaphosphaferrocene: From a Disordered Average Structure to Individual Isomers

PubMed Central

Heindl, Claudia; Peresypkina, Eugenia; Virovets, Alexander V.; Bushmarinov, Ivan S.; Medvedev, Michael G.; Krämer, Barbara; Dittrich, Birger

2017-01-01

Abstract Pentaphosphaferrocenes [CpRFe(η5‐P5)] (1) and CuI halides are excellent building blocks for the formation of discrete supramolecules. Herein, we demonstrate the potential of Cu(CF3SO3) for the construction of the novel 2D polymer [{Cp*Fe(μ4,η5:1:1:1‐P5)}{Cu(CF3SO3)}]n (2) and the unprecedented nanosphere (CH2Cl2)1.4@[{CpBnFe(η5‐P5)}12{Cu(CF3SO3)}19.6] (3). The supramolecule 3 has a unique scaffold beyond the fullerene topology, with 20 copper atoms statistically distributed over the 30 vertices of an icosidodecahedron. Combinatorics was used to interpret the average disordered structure of the supramolecules. In this case, only two pairs of enantiomers with D5 and D2 symmetry are possible for bidentate bridging coordination of the triflate ligands. DFT calculations showed that differences in the energies of the isomers are negligible. The benzyl ligands enhance the solubility of 3, enabling NMR‐spectroscopic and mass‐spectrometric investigations. PMID:28793182

Silylene-Nickel Promoted Cleavage of B-O Bonds: From Catechol Borane to the Hydroborylene Ligand.

PubMed

Hadlington, Terrance J; Szilvási, Tibor; Driess, Matthias

2017-06-19

The first 16 valence electron [bis(NHC)](silylene)Ni 0 complex 1, [( TMS L)ClSi:→Ni(NHC) 2 ], bearing the acyclic amido-chlorosilylene ( TMS L)ClSi: ( TMS L=N(SiMe 3 )Dipp; Dipp=2,6-Pr i 2 C 6 H 4 ) and two NHC ligands (N-heterocyclic carbene=:C[(Pr i )NC(Me)] 2 ) was synthesized in high yield and structurally characterized. Compound 1 is capable of facile dihydrogen activation under ambient conditions to give the corresponding HSi-NiH complex 2. Most notably, 1 reacts with catechol borane to afford the unprecedented hydroborylene-coordinated (chloro)(silyl)nickel(II) complex 3, {[cat( TMS L)Si](Cl)Ni←:BH(NHC) 2 }, via the cleavage of two B-O bonds and simultaneous formation of two Si-O bonds. The mechanism for the formation of 3 was rationalized by means of DFT calculations, which highlight the powerful synergistic effects of the Si:→Ni moiety in the breaking of incredibly strong B-O bonds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Controlling Thermal Expansion: A Metal–Organic Frameworks Route

PubMed Central

2016-01-01

Controlling thermal expansion is an important, not yet resolved, and challenging problem in materials research. A conceptual design is introduced here, for the first time, for the use of metal–organic frameworks (MOFs) as platforms for controlling thermal expansion devices that can operate in the negative, zero, and positive expansion regimes. A detailed computer simulation study, based on molecular dynamics, is presented to support the targeted application. MOF-5 has been selected as model material, along with three molecules of similar size and known differences in terms of the nature of host–guest interactions. It has been shown that adsorbate molecules can control, in a colligative way, the thermal expansion of the solid, so that changing the adsorbate molecules induces the solid to display positive, zero, or negative thermal expansion. We analyze in depth the distortion mechanisms, beyond the ligand metal junction, to cover the ligand distortions, and the energetic and entropic effect on the thermo-structural behavior. We provide an unprecedented atomistic insight on the effect of adsorbates on the thermal expansion of MOFs as a basic tool toward controlling the thermal expansion. PMID:28190918

Evolving nucleotide binding surfaces

NASA Technical Reports Server (NTRS)

Kieber-Emmons, T.; Rein, R.

1981-01-01

An analysis is presented of the stability and nature of binding of a nucleotide to several known dehydrogenases. The employed approach includes calculation of hydrophobic stabilization of the binding motif and its intermolecular interaction with the ligand. The evolutionary changes of the binding motif are studied by calculating the Euclidean deviation of the respective dehydrogenases. Attention is given to the possible structural elements involved in the origin of nucleotide recognition by non-coded primordial polypeptides.

Nonlinear Meridional Moisture Advection and the ENSO-Southern China Rainfall Teleconnection

NASA Astrophysics Data System (ADS)

Wang, Qiang; Cai, Wenju; Zeng, Lili; Wang, Dongxiao

2018-05-01

In the boreal cooler months of 2015, southern China (SC) experienced the largest rainfall since 1950, exceeding 4 times the standard deviation of SC rainfall. Although an El Niño typically induces a positive SC rainfall anomaly during these months, the unprecedented rainfall increase cannot be explained by the strong El Niño of 2015/2016, and the dynamics is unclear. Here we show that a nonlinear meridional moisture advection contributes substantially to the unprecedented rainfall increase. During cooler months of 2015, the meridional flow anomaly over the South China Sea region, which acts on an El Niño-induced anomalous meridional moisture gradient, is particularly large and is supported by an anomalous zonal sea surface temperature gradient over the northwestern Pacific, which recorded its largest value in 2015 since 1950. Our study highlights, for the first time, the importance of the nonlinear process associated with the combined impact of a regional sea surface temperature gradient and large-scale El Niño anomalies in forcing El Niño rainfall teleconnection.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jansone-Popova, Santa; Ivanov, Alexander S.; Bryantsev, Vyacheslav S.

Here, we report a new family of preorganized bislactam- 1,10-phenanthroline (BLPhen) complexants that possess both hard and soft donor atoms within a convergent cavity and show unprecedented extraction strength for the trivalent fblock metal ions. BLPhen ligands with saturated and unsaturated δ-lactam rings have notable differences in their affinity and selectivity for Am(III) over Eu(III), with the latter being the most selective mixed N,O-donor extractant of Am(III) reported to date. Saturated BLPhen was crystallized with five Ln(III) nitrates to form charge-neutral 1:1 complexes in the solid state. DFT calculations further elaborate on the variety of effects that dictate the performancemore » of these preorganized compounds.« less

Au99(SPh)42 nanomolecules: aromatic thiolate ligand induced conversion of Au144(SCH2CH2Ph)60.

PubMed

Nimmala, Praneeth Reddy; Dass, Amala

2014-12-10

A new aromatic thiolate protected gold nanomolecule Au99(SPh)42 has been synthesized by reacting the highly stable Au144(SCH2CH2Ph)60 with thiophenol, HSPh. The ubiquitous Au144(SR)60 is known for its high stability even at elevated temperature and in the presence of excess thiol. This report demonstrates for the first time the reactivity of the Au144(SCH2CH2Ph)60 with thiophenol to form a different 99-Au atom species. The resulting Au99(SPh)42 compound, however, is unreactive and highly stable in the presence of excess aromatic thiol. The molecular formula of the title compound is determined by high resolution electrospray mass spectrometry (ESI-MS) and confirmed by the preparation of the 99-atom nanomolecule using two ligands, namely, Au99(SPh)42 and Au99(SPh-OMe)42. This mass spectrometry study is an unprecedented advance in nanoparticle reaction monitoring, in studying the 144-atom to 99-atom size evolution at such high m/z (∼12k) and resolution. The optical and electrochemical properties of Au99(SPh)42 are reported. Other substituents on the phenyl group, HS-Ph-X, where X = -F, -CH3, -OCH3, also show the Au144 to Au99 core size conversion, suggesting minimal electronic effects for these substituents. Control experiments were conducted by reacting Au144(SCH2CH2Ph)60 with HS-(CH2)n-Ph (where n = 1 and 2), bulky ligands like adamantanethiol and cyclohexanethiol. It was observed that conversion of Au144 to Au99 occurs only when the phenyl group is directly attached to the thiol, suggesting that the formation of a 99-atom species is largely influenced by aromaticity of the ligand and less so on the bulkiness of the ligand.

Global and local curvature in density functional theory.

PubMed

Zhao, Qing; Ioannidis, Efthymios I; Kulik, Heather J

2016-08-07

Piecewise linearity of the energy with respect to fractional electron removal or addition is a requirement of an electronic structure method that necessitates the presence of a derivative discontinuity at integer electron occupation. Semi-local exchange-correlation (xc) approximations within density functional theory (DFT) fail to reproduce this behavior, giving rise to deviations from linearity with a convex global curvature that is evidence of many-electron, self-interaction error and electron delocalization. Popular functional tuning strategies focus on reproducing piecewise linearity, especially to improve predictions of optical properties. In a divergent approach, Hubbard U-augmented DFT (i.e., DFT+U) treats self-interaction errors by reducing the local curvature of the energy with respect to electron removal or addition from one localized subshell to the surrounding system. Although it has been suggested that DFT+U should simultaneously alleviate global and local curvature in the atomic limit, no detailed study on real systems has been carried out to probe the validity of this statement. In this work, we show when DFT+U should minimize deviations from linearity and demonstrate that a "+U" correction will never worsen the deviation from linearity of the underlying xc approximation. However, we explain varying degrees of efficiency of the approach over 27 octahedral transition metal complexes with respect to transition metal (Sc-Cu) and ligand strength (CO, NH3, and H2O) and investigate select pathological cases where the delocalization error is invisible to DFT+U within an atomic projection framework. Finally, we demonstrate that the global and local curvatures represent different quantities that show opposing behavior with increasing ligand field strength, and we identify where these two may still coincide.

Hurricane-induced ocean waves and stokes drift and their impacts on surface transport and dispersion in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Curcic, Milan; Chen, Shuyi S.; Özgökmen, Tamay M.

2016-03-01

Hurricane Isaac induced large surface waves and a significant change in upper ocean circulation in the Gulf of Mexico before making landfall at the Louisiana coast on 29 August 2012. Isaac was observed by 194 surface drifters during the Grand Lagrangian Deployment (GLAD). A coupled atmosphere-wave-ocean model was used to forecast hurricane impacts during GLAD. The coupled model and drifter observations provide an unprecedented opportunity to study the impacts of hurricane-induced Stokes drift on ocean surface currents. The Stokes drift induced a cyclonic (anticyclonic) rotational flow on the left (right) side of the hurricane and accounted for up to 20% of the average Lagrangian velocity. In a significant deviation from drifter measurements prior to Isaac, the scale-dependent relative diffusivity is estimated to be 6 times larger during the hurricane, which represents a deviation from Okubo's (1971) canonical results for lateral dispersion in nonhurricane conditions at the ocean surface.

Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data?

PubMed

Ramírez, David; Caballero, Julio

2018-04-28

Molecular docking is the most frequently used computational method for studying the interactions between organic molecules and biological macromolecules. In this context, docking allows predicting the preferred pose of a ligand inside a receptor binding site. However, the selection of the “best” solution is not a trivial task, despite the widely accepted selection criterion that the best pose corresponds to the best energy score. Here, several rigid-target docking methods were evaluated on the same dataset with respect to their ability to reproduce crystallographic binding orientations, to test if the best energy score is a reliable criterion for selecting the best solution. For this, two experiments were performed: (A) to reconstruct the ligand-receptor complex by performing docking of the ligand in its own crystal structure receptor (defined as self-docking), and (B) to reconstruct the ligand-receptor complex by performing docking of the ligand in a crystal structure receptor that contains other ligand (defined as cross-docking). Root-mean square deviation (RMSD) was used to evaluate how different the obtained docking orientation is from the corresponding co-crystallized pose of the same ligand molecule. We found that docking score function is capable of predicting crystallographic binding orientations, but the best ranked solution according to the docking energy is not always the pose that reproduces the experimental binding orientation. This happened when self-docking was achieved, but it was critical in cross-docking. Taking into account that docking is typically used with predictive purposes, during cross-docking experiments, our results indicate that the best energy score is not a reliable criterion to select the best solution in common docking applications. It is strongly recommended to choose the best docking solution according to the scoring function along with additional structural criteria described for analogue ligands to assure the selection of a correct docking solution.

Femtomole-Scale High-Throughput Screening of Protein Ligands with Droplet-Based Thermal Shift Assay.

PubMed

Liu, Wen-Wen; Zhu, Ying; Fang, Qun

2017-06-20

There is a great demand to measure protein-ligand interactions in rapid and low cost way. Here, we developed a microfluidic droplet-based thermal shift assay (dTSA) system for high-throughput screening of small-molecule protein ligands. The system is composed of a nanoliter droplet array chip, a microfluidic droplet robot, and a real-time fluorescence detection system. Total 324 assays could be performed in parallel in a single chip with an 18 × 18 droplet array. The consumption of dTSA for each protein or ligand sample was only 5 nL (femtomole scale), which is significantly reduced by over 3 orders of magnitude compared with those in 96- or 384-well plate-based systems. We also observed the implementation of TSA in nanoliter droplet format could substantially improve assay precision with relative standard deviation (RSD) of 0.2% (n = 50), which can be ascribed to the enhanced thermal conduction in small volume reactors. The dTSA system was optimized by studying the effect of droplet volumes, as well as protein and fluorescent dye (SYPRO Orange) concentrations. To demonstrate its potential in drug discovery, we applied the dTSA system in screening inhibitors of human thrombin with a commercial library containing 100 different small molecule compounds, and two inhibitors were successfully identified and confirmed.

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters

PubMed Central

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.

2013-01-01

Binding free energy calculations offer a thermodynamically rigorous method to compute protein-ligand binding, and they depend on empirical force fields with hundreds of parameters. We examined the sensitivity of computed binding free energies to the ligand’s electrostatic and van der Waals parameters. Dielectric screening and cancellation of effects between ligand-protein and ligand-solvent interactions reduce the parameter sensitivity of binding affinity by 65%, compared with interaction strengths computed in the gas-phase. However, multiple changes to parameters combine additively on average, which can lead to large changes in overall affinity from many small changes to parameters. Using these results, we estimate that random, uncorrelated errors in force field nonbonded parameters must be smaller than 0.02 e per charge, 0.06 Å per radius, and 0.01 kcal/mol per well depth in order to obtain 68% (one standard deviation) confidence that a computed affinity for a moderately-sized lead compound will fall within 1 kcal/mol of the true affinity, if these are the only sources of error considered. PMID:24015114

Threshold concentration in the nonlinear absorbance law.

PubMed

Tolbin, Alexander Yu; Pushkarev, Victor E; Tomilova, Larisa G; Zefirov, Nikolay S

2017-05-24

A new nonlinear relationship of the absorption coefficient with the concentration was proposed, allowing the calculation of the threshold concentration, which shows that there is a deviation from the Beer-Lambert law. The nonlinear model was successfully tested on a stable dimeric phthalocyanine ligand of J-type in solvents with different polarity. It was shown that deviation from the linearity is connected with a specific association of the macrocyclic molecules, which, in the case of non-polar solvents, leads to the formation of H-aggregates composed of J-type dimeric molecules. The aggregation number was estimated to be less than 1.5, which has allowed us to conduct a series of analytical experiments in a wide range of concentrations (1 × 10 -6 -5 × 10 -4 mol L -1 ).

Dependence of cancer cell adhesion kinetics on integrin ligand surface density measured by a high-throughput label-free resonant waveguide grating biosensor.

PubMed

Orgovan, Norbert; Peter, Beatrix; Bősze, Szilvia; Ramsden, Jeremy J; Szabó, Bálint; Horvath, Robert

2014-02-07

A novel high-throughput label-free resonant waveguide grating (RWG) imager biosensor, the Epic® BenchTop (BT), was utilized to determine the dependence of cell spreading kinetics on the average surface density (v(RGD)) of integrin ligand RGD-motifs. v(RGD) was tuned over four orders of magnitude by co-adsorbing the biologically inactive PLL-g-PEG and the RGD-functionalized PLL-g-PEG-RGD synthetic copolymers from their mixed solutions onto the sensor surface. Using highly adherent human cervical tumor (HeLa) cells as a model system, cell adhesion kinetic data of unprecedented quality were obtained. Spreading kinetics were fitted with the logistic equation to obtain the spreading rate constant (r) and the maximum biosensor response (Δλmax), which is assumed to be directly proportional to the maximum spread contact area (Amax). r was found to be independent of the surface density of integrin ligands. In contrast, Δλmax increased with increasing RGD surface density until saturation at high densities. Interpreting the latter behavior with a simple kinetic mass action model, a 2D dissociation constant of 1753 ± 243 μm(-2) (corresponding to a 3D dissociation constant of ~30 μM) was obtained for the binding between RGD-specific integrins embedded in the cell membrane and PLL-g-PEG-RGD. All of these results were obtained completely noninvasively without using any labels.

Deflection of the Interstellar Neutral Hydrogen Flow Across the Heliospheric Interface: an Interstellar Magnetic Compass

NASA Astrophysics Data System (ADS)

Lallement, R.; Eric, Q.; Jean-Loup, B.; Dimitra, K.; Risto, P.

2005-05-01

Analyses of SOHO-SWAN observations show that the interstellar neutral H flow direction differs by about 4 degrees from the neutral He flow direction recently derived with an unprecedented accuracy using combined data sets (Mobius et al, 2004). The most likely explanation is a distortion of the heliospheric interface under the action of an inclined interstellar magnetic field, with imprints of the distorsion on the neutral H flow due to charge-transfer reactions between H atoms and ions. The direction of the ambient interstellar magnetic field and the heliospheric shape can be derived from the observed deviation. Implications for Voyager trajectories are discussed.

Structure of zirconocene complexes relevant for olefin catalysis: infrared fingerprint of the Zr(C(5)H(5))(2)(OH)(CH(3)CN)(+) cation in the gas phase.

PubMed

Lagutschenkov, Anita; Springer, Andreas; Lorenz, Ulrich Joseph; Maitre, Philippe; Dopfer, Otto

2010-02-11

Cationic zirconocene complexes are active species in Ziegler-Natta catalysis for olefin polymerization. Their structure and metal-ligand bond strength strongly influence their activity. In the present work, the infrared multiphoton dissociation (IRMPD) spectrum of mass selected Zr(C(5)H(5))(2)(OH)(CH(3)CN)(+) cations was obtained in the 300-1500 cm(-1) fingerprint range by coupling a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization (ESI) source and the infrared free electron laser (IR-FEL) at the Centre Laser Infrarouge d'Orsay (CLIO). The experimental efforts are complemented by quantum chemical calculations at the MP2 and B3LYP levels using the 6-311G* basis set. Vibrational assignments of transitions observed in the IRMPD spectra to modes of the Zr-O-H, C(5)H(5), and CH(3)CN moieties are based on comparison to calculated linear absorption spectra. Both the experimental data and the calculations provide unprecedented information about structure, metal-ligand bonding, charge distribution, and binding energy of the complex.

Dioxygenase-like reactivity of an isolable superoxo-nickel(II) complex.

PubMed

Company, Anna; Yao, Shenglai; Ray, Kallol; Driess, Matthias

2010-08-16

Although O(2) activation by metals such as iron and copper has been a matter of intensive research in the last decades, this type of chemistry for nickel systems is still in its infancy. Moreover, studies regarding the oxidizing ability of the resulting "Ni(n)-O(2)" species towards exogenous substrates are scarce. In this work, we report on the reactivity of an isolable and thermally stable mononuclear superoxo-nickel compound [Ni(II)(beta-diketiminato)(O(2))] (1) towards different types of organic substrates. In addition, we have been able to prove that the beta-diketiminato ligand can undergo partial intramolecular oxidation due to close proximity between the isopropyl groups of the beta-diketiminato-aryl and the superoxo subunits. Compound 1 performs hydrogen-atom abstraction from O-H and N-H groups and most importantly it shows an unprecedented dioxygenase-like reactivity in the oxidation of 2,4,6-tri-tert-butylphenol. The latter reaction most likely occurs through the mediation of a putative [Ni(III)-oxo] intermediate, affording an unprecedented oxidation product of the phenol that incorporates two oxygen atoms from a single O(2) subunit. Results presented herein provide evidence of the striking oxidizing ability of dioxygen-nickel species and further support the viability to use such systems as oxidation catalysts analogous to its heavy metal congener, palladium.

Optoelectronic properties and structural effects of the incremental addition of pyridyl moieties on a rhodium dimer.

PubMed

Chartrand, Daniel; Hanan, Garry S

2014-11-13

The synthesis and characterization of five C-C coupling products obtained from the reaction of a paddlewheel tetrakis 4-bromo-N,N'-diphenylbenzamidinate dirhodium dimer with 4-pyridineboronic acid pinacol ester are reported. The coupling reactions occur on one to four amidinate ligands, leading to rhodium dimers containing [tetrakis, tris, cis-bis, trans-bis, or mono]-N,N'-diphenyl-4-(pyridin-4-yl)benzamidinate ligands, effectively creating new binding sites on the metal complexes. The new compounds were isolated by column chromatography, and the exact conformations were verified by X-ray crystallography. Redox processes showed only a small variation within the coupling products and included two oxidations (1.30 ± 0.02 V, 0.27 ± 0.01 V vs SCE) and one reduction (-1.55 ± 0.02 V vs SCE), all centered on the Rh-Rh core. Time-dependent density functional theory (TD-DFT) was used to analyze this series with four other fully characterized N,N'-diphenyl-aryl-amidinate rhodium dimers that were found in the literature. The two main absorption bands of these nine rhodium dimers were compared to TD-DFT calculations, both giving excellent correlation. The first, a metal-to-metal (MM) transition around 11800 cm(-1) (845 nm) was blue-shifted in the calculation, with an average difference of 1378 cm(-1) but had only a 15 cm(-1) standard deviation, showing a strong correlation despite the energy difference. The second, a metal-to-ligand charge transfer (MLCT) transition around 18900 cm(-1) (530 nm) was a near perfect match with only a 64 cm(-1) average difference and a 35 cm(-1) standard deviation. The electronic transition, redox potentials, and HOMO and LUMO energies of all dimers were plotted versus the Hammett parameter (σ) of the aryl group and Taft's model with 2 components: field effects (σF) and resonance (σR). The properties involving only the Rh-Rh core (MM band, all oxidation potentials, HOMO and LUMO) were fit with a single set of σF and σR contributions (73% and 27%), with a goodness-of-fit (R(2)) value ranging from 90% to 99.7%. The metal-dimer to ligand charge-transfer band, involving the amidinate ligand, displayed different values of contribution with 45% and 55% for the σF and σR, respectively, with a fit of 94.8%. The accuracy of these fits enables the designed modification of amidinate-based dirhodium complexes to achieve desirable redox and spectroscopic properties.

Bottom-up approach to fabricate nanostructured thin films from colloidal nanocrystal precursors

NASA Astrophysics Data System (ADS)

Shaw, Santosh

Control over microstructures at the nanoscale (<100nm) still seems challenging due to, among other things, the stochastic nature of nucleation in the bulk phase. The densification of assemblies of ligand-capped nanocrystals (colloidal nanocrystal assemblies, CNAs) could bypass this challenge that limits our control over the nanostructure and, therefore, the properties of materials. However, the removal of the ligands and the cracking that follows it are the two critical hurdles that have been stymieing this approach. We show that low-pressure plasma processing can effectively remove ligands from CNAs (down to 0.6 at.% of carbon which can be accounted for adventitious carbon) without harming the properties of the inorganic cores of the nanoparticles and the structure of CNAs. The cracking of CNAs is correlated with the structure of the CNAs, which can be controlled and easily predicted by Hansen solubility parameters of solvent in which the nanoparticles are dispersed. While a fully solvated ligand shell leads to the formation of close-packed ordered CNAs - which cracked after self-assembly or ligand removal - a partially solvated one results in interdigitation of the ligand shell yielding disordered CNAs, which remained crack-free after ligand removal and sintering up to a critical cracking thickness of 440nm. The process is demonstrated with particles of different compositions, ligands, sizes, shapes, as well as with binary systems. These findings allowed for the fabrication of cm2 crack-free, phase-pure polycrystalline films with tunable, near-monodisperse grain sizes using CNAs as precursors. We observed electrical conductivities of PbS films produced by this approach over 1 cm to be 1.370 S/cm which is comparable to those of bulk crystal. This conductivity value is remarkable considering the fact that the typical porosity in fully processed CNAs is around 40%. We simultaneously answered the fundamental question that how microstructure of CNAs evolves during ligand removal and studied its effect on microstructure related physical properties, e.g., mechanical properties. We further demonstrated that our bottom-up approach can control the grain boundary composition in the final materials by controlling the chemical structure and composition of the ligands and the characteristics of the plasma. We show that with our unprecedented control on grain boundary composition, we can selectively modify grain growth mechanisms, control phase transitions, and affect mechanical properties. By understanding the interaction of plasma species with CNAs and the mass transport in the system, we were able to accelerate the plasma etching rate by more than an order of magnitude. Finally, we demonstrate the applicability of our approach in developing an optics-free lithography in which CNAs are used as resist and as an active material. By selectively masking the interaction of plasma with CNAs with a hard mask we could change the solubility of the exposed regions. This patterning technology can pattern materials which are hard to pattern by traditional inorganic etching based pattern transfer (example, copper, gold).

How Does Amino Acid Ligand Modulate Au Core Structure and Characteristics in Peptide Coated Au Nanocluster?

PubMed

Li, Nan; Li, Xu; Zhao, Hongkang; Zhao, Lina

2018-03-01

The atomic structures and the corresponding physicochemical properties of peptide coated Au nanoclusters determine their distinctive biological targeting applications. To learn the modulation of amino acid ligand on the atomic structure and electronic characteristics of coated Au core is the fundamental knowledge for peptide coated Au nanocluster design and construction. Based on our recent coated Au nanocluster configuration study (Nanoscale, 2016, 8, 11454), we built the typically simplified Au13(Cys-Au-Cys) system to more clearly learn the basic modulation information of amino acid ligand on Au core by the density functional theory (DFT) calculations. There are two isomers as ligand adjacent bonding (Iso1) and diagonal bonding (Iso2) to Au13 cores. The geometry optimizations indicate the adjacent bonding Iso1 is more stable than Iso2. More important, the Au13 core of Iso1 distorts much more significantly than that of Iso2 by Cys-Au-Cys bonding through the root-mean-square deviation (RMSD) analysis, which modulate their electronic characteristics in different ways. In addition, the frontier molecular orbital results of Au13(Cys-Au-Cys) isomers confirm that the Au cores mainly determine the blue shifts of Au13(Cys-Au-Cys) systems versus the original Au13 core in their UV-visible absorption spectrum studies. The configuration of Au13 core performs deformation under Cys-Au-Cys ligand modulation to reach new stability with distinct atomic structure and electronic properties, which could be the theory basis for peptide coated AuNCs design and construction.

Binding Site and Potency Prediction of Teixobactin and other Lipid II Ligands by Statistical Base Scoring of Conformational Space Maps.

PubMed

Lungu, Claudiu N; Diudea, Mircea V

2018-01-01

Lipid II, a peptidoglycan, is a precursor in bacterial cell synthesis. It has both hydrophilic and lipophilic properties. The molecule translocates a bacterial membrane to deliver and incorporate "building blocks" from disaccharide-pentapeptide into the peptidoglican wall. Lipid II is a valid antibiotic target. A receptor binding pocket may be occupied by a ligand in various plausible conformations, among which only few ones are energetically related to a biological activity in the physiological efficiency domain. This paper reports the mapping of the conformational space of Lipid II in its interaction with Teixobactin and other Lipid II ligands. In order to study computationally the complex between Lipid II and ligands, a docking study was first carried on. Docking site was retrieved form literature. After docking, 5 ligand conformations and further 5 complexes (denoted 00 to 04) for each molecule were taken into account. For each structure, conformational studies were performed. Statistical analysis, conformational analysis and molecular dynamics based clustering were used to predict the potency of these compounds. A score for potency prediction was developed. Appling lipid II classification according to Lipid II conformational energy, a conformation of Teixobactin proved to be energetically favorable, followed by Oritravicin, Dalbavycin, Telvanicin, Teicoplamin and Vancomycin, respectively. Scoring of molecules according to cluster band and PCA produced the same result. Molecules classified according to standard deviations showed Dalbavycin as the most favorable conformation, followed by Teicoplamin, Telvanicin, Teixobactin, Oritravicin and Vancomycin, respectively. Total score showing best energetic efficiency of complex formation shows Teixobactin to have the best conformation (a score of 15 points) followed by Dalbavycin (14 points), Oritravicin (12v points), Telvanicin (10 points), Teicoplamin (9 points), Vancomycin (3 points). Statistical analysis of conformations can be used to predict the efficiency of ligand - target interaction and consecutively to find insight regarding ligand potency and postulate about favorable conformation of ligand and binding site. In this study it was shown that Teixobactin is more efficient in binding with Lipid II compared to Vancomycin, results confirmed by experimental data reported in literature. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Ligand Structural Influences upon Electrochemical Reactivity: Organic Substituent Effects upon Carboxylatopentaamminecobalt(III) Reductions at Mercury and Gold Electrodes.

DTIC Science & Technology

1985-01-01

surface interactions, substituent effects, nonaqueous medi\\ ZO’ ST RA T (Continue an rev roe . d f nroomy aidje e i a bloc nube) .tne e-ectroreducton...seen for the 2+ . Ru(NH3 6 reduction kinetics in aqueous solution. * . .,:. *.**f: % *% *. ** % ** * * * * *% **% - ........... <. . . -W ! -- .... d ...accordance with Eq. (1) has been found for a number of systems, substantial deviations have also been observed. b d 2b Of particular interest are the rate

NO binding kinetics in myoglobin investigated by picosecond Fe K-edge absorption spectroscopy

PubMed Central

Silatani, Mahsa; Lima, Frederico A.; Penfold, Thomas J.; Rittmann, Jochen; Reinhard, Marco E.; Rittmann-Frank, Hannelore M.; Borca, Camelia; Grolimund, Daniel; Milne, Christopher J.; Chergui, Majed

2015-01-01

Diatomic ligands in hemoproteins and the way they bind to the active center are central to the protein’s function. Using picosecond Fe K-edge X-ray absorption spectroscopy, we probe the NO-heme recombination kinetics with direct sensitivity to the Fe-NO binding after 532-nm photoexcitation of nitrosylmyoglobin (MbNO) in physiological solutions. The transients at 70 and 300 ps are identical, but they deviate from the difference between the static spectra of deoxymyoglobin and MbNO, showing the formation of an intermediate species. We propose the latter to be a six-coordinated domed species that is populated on a timescale of ∼200 ps by recombination with NO ligands. This work shows the feasibility of ultrafast pump–probe X-ray spectroscopic studies of proteins in physiological media, delivering insight into the electronic and geometric structure of the active center. PMID:26438842

Comparison of computational methods to model DNA minor groove binders.

PubMed

Srivastava, Hemant Kumar; Chourasia, Mukesh; Kumar, Devesh; Sastry, G Narahari

2011-03-28

There has been a profound interest in designing small molecules that interact in sequence-selective fashion with DNA minor grooves. However, most in silico approaches have not been parametrized for DNA ligand interaction. In this regard, a systematic computational analysis of 57 available PDB structures of noncovalent DNA minor groove binders has been undertaken. The study starts with a rigorous benchmarking of GOLD, GLIDE, CDOCKER, and AUTODOCK docking protocols followed by developing QSSR models and finally molecular dynamics simulations. In GOLD and GLIDE, the orientation of the best score pose is closer to the lowest rmsd pose, and the deviation in the conformation of various poses is also smaller compared to other docking protocols. Efficient QSSR models were developed with constitutional, topological, and quantum chemical descriptors on the basis of B3LYP/6-31G* optimized geometries, and with this ΔT(m) values of 46 ligands were predicted. Molecular dynamics simulations of the 14 DNA-ligand complexes with Amber 8.0 show that the complexes are stable in aqueous conditions and do not undergo noticeable fluctuations during the 5 ns production run, with respect to their initial placement in the minor groove region.

Social media fingerprints of unemployment.

PubMed

Llorente, Alejandro; Garcia-Herranz, Manuel; Cebrian, Manuel; Moro, Esteban

2015-01-01

Recent widespread adoption of electronic and pervasive technologies has enabled the study of human behavior at an unprecedented level, uncovering universal patterns underlying human activity, mobility, and interpersonal communication. In the present work, we investigate whether deviations from these universal patterns may reveal information about the socio-economical status of geographical regions. We quantify the extent to which deviations in diurnal rhythm, mobility patterns, and communication styles across regions relate to their unemployment incidence. For this we examine a country-scale publicly articulated social media dataset, where we quantify individual behavioral features from over 19 million geo-located messages distributed among more than 340 different Spanish economic regions, inferred by computing communities of cohesive mobility fluxes. We find that regions exhibiting more diverse mobility fluxes, earlier diurnal rhythms, and more correct grammatical styles display lower unemployment rates. As a result, we provide a simple model able to produce accurate, easily interpretable reconstruction of regional unemployment incidence from their social-media digital fingerprints alone. Our results show that cost-effective economical indicators can be built based on publicly-available social media datasets.

Social Media Fingerprints of Unemployment

PubMed Central

Llorente, Alejandro; Garcia-Herranz, Manuel; Cebrian, Manuel; Moro, Esteban

2015-01-01

Recent widespread adoption of electronic and pervasive technologies has enabled the study of human behavior at an unprecedented level, uncovering universal patterns underlying human activity, mobility, and interpersonal communication. In the present work, we investigate whether deviations from these universal patterns may reveal information about the socio-economical status of geographical regions. We quantify the extent to which deviations in diurnal rhythm, mobility patterns, and communication styles across regions relate to their unemployment incidence. For this we examine a country-scale publicly articulated social media dataset, where we quantify individual behavioral features from over 19 million geo-located messages distributed among more than 340 different Spanish economic regions, inferred by computing communities of cohesive mobility fluxes. We find that regions exhibiting more diverse mobility fluxes, earlier diurnal rhythms, and more correct grammatical styles display lower unemployment rates. As a result, we provide a simple model able to produce accurate, easily interpretable reconstruction of regional unemployment incidence from their social-media digital fingerprints alone. Our results show that cost-effective economical indicators can be built based on publicly-available social media datasets. PMID:26020628

Sulfated steroids as natural ligands of mouse pheromone-sensing neurons.

PubMed

Nodari, Francesco; Hsu, Fong-Fu; Fu, Xiaoyan; Holekamp, Terrence F; Kao, Lung-Fa; Turk, John; Holy, Timothy E

2008-06-18

Among mice, pheromones and other social odor cues convey information about sex, social status, and identity; however, the molecular nature of these cues is essentially unknown. To identify these cues, we screened chromatographic fractions of female mouse urine for their ability to cause reproducible firing rate increases in the pheromone-detecting vomeronasal sensory neurons (VSNs) using multielectrode array (MEA) recording. Active compounds were found to be remarkably homogenous in their basic properties, with most being of low molecular weight, moderate hydrophobicity, low volatility, and possessing a negative electric charge. Purification and structural analysis of active compounds revealed multiple sulfated steroids, of which two were identified as sulfated glucocorticoids, including corticosterone 21-sulfate. Sulfatase-treated urine extracts lost >80% of their activity, indicating that sulfated compounds are the predominant VSN ligands in female mouse urine. As measured by MEA recording, a collection of 31 synthetic sulfated steroids triggered responses 30-fold more frequently than did a similarly sized stimulus set containing the majority of all previously reported VSN ligands. Collectively, VSNs detected all major classes of sulfated steroids, but individual neurons were sensitive to small variations in chemical structure. VSNs from both males and females detected sulfated steroids, but knock-outs for the sensory transduction channel TRPC2 did not detect these compounds. Urine concentrations of the two sulfated glucocorticoids increased many fold in stressed animals, indicating that information about physiological status is encoded by the urine concentration of particular sulfated steroids. These results provide an unprecedented characterization of the signals available for chemical communication among mice.

Sulfated steroids as natural ligands of mouse pheromone-sensing neurons

PubMed Central

Nodari, Francesco; Hsu, Fong-Fu; Fu, Xiaoyan; Holekamp, Terrence F.; Kao, Lung-Fa; Turk, John; Holy, Timothy E.

2009-01-01

Among mice, pheromones and other social odor cues convey information about sex, social status, and identity; however, the molecular nature of these cues is largely unknown. To identify these cues, we screened chromatographic fractions of female mouse urine for their ability to cause reproducible firing rate increases in the pheromone-detecting vomeronasal sensory neurons (VSNs) using multielectrode array (MEA) recording. Active compounds were found to be remarkably homogenous in their basic properties, with most being of low molecular weight, moderate hydrophobicity, low volatility, and possessing a negative electric charge. Purification and structural analysis of active compounds revealed multiple sulfated steroids, of which two were identified as sulfated glucocorticoids, including corticosterone 21-sulfate. Sulfatase-treated urine extracts lost more than 80% of their activity, indicating that sulfated compounds are the predominant VSN ligands in female mouse urine. As measured by MEA recording, a collection of 31 synthetic sulfated steroids triggered responses 30-fold more frequently than did a similarly-sized stimulus set containing the majority of all previously-reported VSN ligands. Collectively, VSNs detected all major classes of sulfated steroids, but individual neurons were sensitive to small variations in chemical structure. VSNs from both males and females detected sulfated steroids, but knockouts for the sensory transduction channel TRPC2 did not detect these compounds. Urine concentrations of the two sulfated glucocorticoids increased many-fold in stressed animals, indicating that information about physiological status is encoded by the urine concentration of particular sulfated steroids. These results provide an unprecedented characterization of the signals available for chemical communication among mice. PMID:18562612

Pure white-light emitting ultrasmall organic-inorganic hybrid perovskite nanoclusters.

PubMed

Teunis, Meghan B; Lawrence, Katie N; Dutta, Poulami; Siegel, Amanda P; Sardar, Rajesh

2016-10-14

Organic-inorganic hybrid perovskites, direct band-gap semiconductors, have shown tremendous promise for optoelectronic device fabrication. We report the first colloidal synthetic approach to prepare ultrasmall (∼1.5 nm diameter), white-light emitting, organic-inorganic hybrid perovskite nanoclusters. The nearly pure white-light emitting ultrasmall nanoclusters were obtained by selectively manipulating the surface chemistry (passivating ligands and surface trap-states) and controlled substitution of halide ions. The nanoclusters displayed a combination of band-edge and broadband photoluminescence properties, covering a major part of the visible region of the solar spectrum with unprecedentedly large quantum yields of ∼12% and photoluminescence lifetime of ∼20 ns. The intrinsic white-light emission of perovskite nanoclusters makes them ideal and low cost hybrid nanomaterials for solid-state lighting applications.

A New Domain of Reactivity for High-Valent Dinuclear [M(μ-O)2 M'] Complexes in Oxidation Reactions.

PubMed

Engelmann, Xenia; Yao, Shenglai; Farquhar, Erik R; Szilvási, Tibor; Kuhlmann, Uwe; Hildebrandt, Peter; Driess, Matthias; Ray, Kallol

2017-01-02

The strikingly different reactivity of a series of homo- and heterodinuclear [(M III )(μ-O) 2 (M III )'] 2+ (M=Ni; M'=Fe, Co, Ni and M=M'=Co) complexes with β-diketiminate ligands in electrophilic and nucleophilic oxidation reactions is reported, and can be correlated to the spectroscopic features of the [(M III )(μ-O) 2 (M III )'] 2+ core. In particular, the unprecedented nucleophilic reactivity of the symmetric [Ni III (μ-O) 2 Ni III ] 2+ complex and the decay of the asymmetric [Ni III (μ-O) 2 Co III ] 2+ core through aromatic hydroxylation reactions represent a new domain for high-valent bis(μ-oxido)dimetal reactivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

In this issue--engineering the immune system to fight cancer and infections.

PubMed

Bot, Adrian

2011-01-01

As the immune system essentially evolved to fight off or keep at bay life-threatening infectious agents rather than cancer, the question remains as to how to best redeploy it for the treatment of a broader range of diseases. This is reflected by an unprecedented diversification of platform technologies in development, facilitated by rapid progress in biotechnology. In this issue, we host several contributions outlining major efforts in developing novel immune interventions spanning antigen-specific vaccination, non-antigen-targeted immune intervention, genetically engineered lymphocytes, and ultraspecific antigen-targeted ligands. In addition, the journal is hosting in this issue, two reviews discussing the complex matter and dynamic balance between immunity and viral infections, as the concept of fine modulation of that balance still carries the promise of yielding novel therapies.

Crystal structure of tetra­aqua­(5,5′-dimethyl-2,2′-bipyridyl-κ2 N,N′)iron(II) sulfate

PubMed Central

Belamri, Yamine; Setifi, Fatima; Francuski, Bojana M.; Novaković, Sladjana B.; Zouaoui, Setifi

2014-01-01

In the title compound, [Fe(C12H12N2)(H2O)4]SO4, the central FeII ion is coordinated by two N atoms from the 5,5′-dimethyl-2,2′-bi­pyridine ligand and four water O atoms in a distorted octa­hedral geometry. The Fe—O coordination bond lengths vary from 2.080 (3) to 2.110 (3) Å, while the two Fe—N coordination bonds have practically identical lengths [2.175 (3) and 2.177 (3) Å]. The chelating N—Fe—N angle of 75.6 (1)° shows the largest deviation from an ideal octa­hedral geometry; the other coordination angles deviate from ideal values by 0.1 (1) to 9.1 (1)°. O—H⋯O hydrogen bonding between the four aqua ligands of the cationic complex and four O-atom acceptors of the anion leads to the formation of layers parallel to the ab plane. Neighbouring layers further inter­act by means of C—H⋯O and π–π inter­actions involving the laterally positioned bi­pyridine rings. The perpen­dicular distance between π–π inter­acting rings is 3.365 (2) Å, with a centroid–centroid distance of 3.702 (3) Å. PMID:25552988

Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions.

PubMed

Ruvinsky, Anatoly M

2007-06-01

We present results of testing the ability of eleven popular scoring functions to predict native docked positions using a recently developed method (Ruvinsky and Kozintsev, J Comput Chem 2005, 26, 1089) for estimation the entropy contributions of relative motions to protein-ligand binding affinity. The method is based on the integration of the configurational integral over clusters obtained from multiple docked positions. We use a test set of 100 PDB protein-ligand complexes and ensembles of 101 docked positions generated by (Wang et al. J Med Chem 2003, 46, 2287) for each ligand in the test set. To test the suggested method we compared the averaged root-mean square deviations (RMSD) of the top-scored ligand docked positions, accounting and not accounting for entropy contributions, relative to the experimentally determined positions. We demonstrate that the method increases docking accuracy by 10-21% when used in conjunction with the AutoDock scoring function, by 2-25% with G-Score, by 7-41% with D-Score, by 0-8% with LigScore, by 1-6% with PLP, by 0-12% with LUDI, by 2-8% with F-Score, by 7-29% with ChemScore, by 0-9% with X-Score, by 2-19% with PMF, and by 1-7% with DrugScore. We also compared the performance of the suggested method with the method based on ranking by cluster occupancy only. We analyze how the choice of a clustering-RMSD and a low bound of dense clusters impacts on docking accuracy of the scoring methods. We derive optimal intervals of the clustering-RMSD for 11 scoring functions.

Physiologic distribution of PSMA-ligand in salivary glands and seromucous glands of the head and neck on PET/CT.

PubMed

Klein Nulent, Thomas J W; Valstar, Matthijs H; de Keizer, Bart; Willems, Stefan M; Smit, Laura A; Al-Mamgani, Abrahim; Smeele, Ludwig E; van Es, Robert J J; de Bree, Remco; Vogel, Wouter V

2018-05-01

Prostate-specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT) is used for detection and (re)staging of prostate cancer. However, healthy salivary, seromucous, and lacrimal glands also have high PSMA-ligand uptake. This study aimed to describe physiologic PSMA-ligand uptake distribution characteristics in the head and neck to aid in PSMA PET/CT interpretation and to identify possible new clinical applications for PSMA-ligand imaging. Thirty consecutive patients who underwent PSMA PET/CT for prostate cancer were evaluated. Tracer maximum standardized uptake values (SUV max ) in the salivary, seromucous, and lacrimal glands were determined visually and quantitatively. Overall and intraindividual variations were reported. All gland locations had increased tracer uptake. The mean SUV max  ± standard deviation varied: parotid 12.3 ± 3.9; submandibular 11.7 ± 3.5; sublingual 4.5 ± 1.9; soft palate 2.4 ± 0.5; pharyngeal wall 4.3 ± 1.3; nasal mucosa 3.4 ± 0.9; supraglottic larynx 2.7 ± 0.7; and lacrimal 6.2 ± 2.2. The parotid had the largest overall variation in SUV max (5.2-22.9), and the sublingual glands had the largest mean intraindividual difference (18.1%). Major and minor salivary and seromucous glands consistently have high PSMA-ligand uptake. Minor gland locations can be selectively visualized by this technique for the first time. This provides potential new applications such as quantification of present salivary gland tissues and individualization of radiotherapy for head and neck cancer or lutetium-177-PSMA radionuclide treatment. Copyright © 2018 Elsevier Inc. All rights reserved.

Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins.

PubMed

Ashtawy, Hossam M; Mahapatra, Nihar R

2015-01-01

Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable binding pose of a ligand, when bound to a receptor protein, from among a large set of candidate poses. Despite intense efforts in developing conventional SFs, which are either force-field based, knowledge-based, or empirical, their limited docking power (or ability to successfully identify the correct pose) has been a major impediment to cost-effective drug discovery. Therefore, in this work, we explore a range of novel SFs employing different machine-learning (ML) approaches in conjunction with physicochemical and geometrical features characterizing protein-ligand complexes to predict the native or near-native pose of a ligand docked to a receptor protein's binding site. We assess the docking accuracies of these new ML SFs as well as those of conventional SFs in the context of the 2007 PDBbind benchmark dataset on both diverse and homogeneous (protein-family-specific) test sets. Further, we perform a systematic analysis of the performance of the proposed SFs in identifying native poses of ligands that are docked to novel protein targets. We find that the best performing ML SF has a success rate of 80% in identifying poses that are within 1 Å root-mean-square deviation from the native poses of 65 different protein families. This is in comparison to a success rate of only 70% achieved by the best conventional SF, ASP, employed in the commercial docking software GOLD. In addition, the proposed ML SFs perform better on novel proteins that they were never trained on before. We also observed steady gains in the performance of these scoring functions as the training set size and number of features were increased by considering more protein-ligand complexes and/or more computationally-generated poses for each complex.

Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins

PubMed Central

2015-01-01

Background Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable binding pose of a ligand, when bound to a receptor protein, from among a large set of candidate poses. Despite intense efforts in developing conventional SFs, which are either force-field based, knowledge-based, or empirical, their limited docking power (or ability to successfully identify the correct pose) has been a major impediment to cost-effective drug discovery. Therefore, in this work, we explore a range of novel SFs employing different machine-learning (ML) approaches in conjunction with physicochemical and geometrical features characterizing protein-ligand complexes to predict the native or near-native pose of a ligand docked to a receptor protein's binding site. We assess the docking accuracies of these new ML SFs as well as those of conventional SFs in the context of the 2007 PDBbind benchmark dataset on both diverse and homogeneous (protein-family-specific) test sets. Further, we perform a systematic analysis of the performance of the proposed SFs in identifying native poses of ligands that are docked to novel protein targets. Results and conclusion We find that the best performing ML SF has a success rate of 80% in identifying poses that are within 1 Å root-mean-square deviation from the native poses of 65 different protein families. This is in comparison to a success rate of only 70% achieved by the best conventional SF, ASP, employed in the commercial docking software GOLD. In addition, the proposed ML SFs perform better on novel proteins that they were never trained on before. We also observed steady gains in the performance of these scoring functions as the training set size and number of features were increased by considering more protein-ligand complexes and/or more computationally-generated poses for each complex. PMID:25916860

A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures.

PubMed

Schellman, J A

1990-08-31

The properties of a simple model for solvation in mixed solvents are explored in this paper. The model is based on the supposition that solvent replacement is a simple one-for-one substitution reaction at macromolecular sites which are independent of one another. This leads to a new form for the binding polynomial in which all terms are associated with ligand interchange rather than ligand addition. The principal solvent acts as one of the ligands. Thermodynamic analysis then shows that thermodynamic binding (i.e., selective interaction) depends on the properties of K'-1, whereas stoichiometric binding (site occupation) depends on K'. K' is a 'practical' interchange equilibrium constant given by (f3/f1)K, where K is the true equilibrium constant for the interchange of components 3 and 1 on the site and f3 and f4 denote their respective activity coefficients on the mole fraction scale. Values of K' less than unity lead to negative selective interaction. It is selective interaction and not occupation number which determines the thermodynamic effects of solvation. When K' greater than 100 on the mole fraction scale or K' greater than 2 on the molality scale (in water), the differences between stoichiometric binding and selective interaction become less than 1%. The theory of this paper is therefore necessary only for very weak binding constants. When K'-1 is small, large concentrations of the added solvent component are required to produce a thermodynamic effect. Under these circumstances the isotherms for the selective interaction and for the excess (or transfer) free energy are strongly dependent on the behavior of the activity coefficients of both solvent components. Two classes of behavior are described depending on whether the components display positive or negative deviations from Raoult's law. Examples which are discussed are aqueous solutions of urea and guanidinium chloride for positive deviations and of sucrose and glucose for negative deviations. Examination of the few studies which have been reported in the literature shows that most of the qualitative features of the stabilization of proteins by sugars and their destabilization by urea and guanidinium chloride are faithfully represented with the model. This includes maxima in the free energy of stabilization and destabilization, decreased and zero selective interaction at high concentrations, etc. These phenomena had no prior explanation. Deficiencies in the model as a representation of solvation in aqueous solution are discussed in the appendix.

High Harmonic Generation XUV Spectroscopy for Studying Ultrafast Photophysics of Coordination Complexes

NASA Astrophysics Data System (ADS)

Ryland, Elizabeth S.; Lin, Ming-Fu; Benke, Kristin; Verkamp, Max A.; Zhang, Kaili; Vura-Weis, Josh

2017-06-01

Extreme ultraviolet (XUV) spectroscopy is an inner shell technique that probes the M_{2,3}-edge excitation of atoms. Absorption of the XUV photon causes a 3p→3d transition, the energy and shape of which is directly related to the element and ligand environment. This technique is thus element-, oxidation state-, spin state-, and ligand field specific. A process called high-harmonic generation (HHG) enables the production of ultrashort (˜20fs) pulses of collimated XUV photons in a tabletop instrument. This allows transient XUV spectroscopy to be conducted as an in-lab experiment, where it was previously only possible at accelerator-based light sources. Additionally, ultrashort pulses provide the capability for unprecedented time resolution (˜50fs IRF). This technique has the capacity to serve a pivotal role in the study of electron and energy transfer processes in materials and chemical biology. I will present the XUV transient absorption instrument we have built, along with ultrafast transient M_{2,3}-edge absorption data of a series of small inorganic molecules in order to demonstrate the high specificity and time resolution of this tabletop technique as well as how our group is applying it to the study of ultrafast electronic dynamics of coordination complexes.

NMR Chemical Exchange as a Probe for Ligand-Binding Kinetics in a Theophylline-Binding RNA Aptamer

PubMed Central

Latham, Michael P.; Zimmermann, Grant R.; Pardi, Arthur

2009-01-01

The apparent on- and off-rate constants for theophylline binding to its RNA aptamer in the absence of Mg2+ were determined here by 2D 1H-1H NMR ZZ-exchange spectroscopy. Analysis of the build-up rate of the exchange cross peaks for several base-paired imino protons in the RNA yielded an apparent kon of 600 M-1 s-1. This small apparent kon results from the free RNA existing as a dynamic equilibrium of inactive states rapidly interconverting with a low population of active species. The data here indicate that the RNA aptamer employs a conformational selection mechanism for binding theophylline in the absence of Mg2+. The kinetic data here also explain a very unusual property of this RNA-theophylline system, slow exchange on the NMR chemical shift timescale for a weak-binding complex. To our knowledge, it is unprecedented to have such a weak binding complex (Kd ≈ 3.0 mM at 15 °C) show slow exchange on the NMR chemical shift timescale, but the results clearly demonstrate that slow exchange and weak binding are readily rationalized by a small kon. Comparisons with other ligand-receptor interactions are presented. PMID:19317486

Whole cell quenched flow analysis.

PubMed

Chiang, Ya-Yu; Haeri, Sina; Gizewski, Carsten; Stewart, Joanna D; Ehrhard, Peter; Shrimpton, John; Janasek, Dirk; West, Jonathan

2013-12-03

This paper describes a microfluidic quenched flow platform for the investigation of ligand-mediated cell surface processes with unprecedented temporal resolution. A roll-slip behavior caused by cell-wall-fluid coupling was documented and acts to minimize the compression and shear stresses experienced by the cell. This feature enables high-velocity (100-400 mm/s) operation without impacting the integrity of the cell membrane. In addition, rotation generates localized convection paths. This cell-driven micromixing effect causes the cell to become rapidly enveloped with ligands to saturate the surface receptors. High-speed imaging of the transport of a Janus particle and fictitious domain numerical simulations were used to predict millisecond-scale biochemical switching times. Dispersion in the incubation channel was characterized by microparticle image velocimetry and minimized by using a horizontal Hele-Shaw velocity profile in combination with vertical hydrodynamic focusing to achieve highly reproducible incubation times (CV = 3.6%). Microfluidic quenched flow was used to investigate the pY1131 autophosphorylation transition in the type I insulin-like growth factor receptor (IGF-1R). This predimerized receptor undergoes autophosphorylation within 100 ms of stimulation. Beyond this demonstration, the extreme temporal resolution can be used to gain new insights into the mechanisms underpinning a tremendous variety of important cell surface events.

New coordination features; a bridging pyridine and the forced shortest non-covalent distance between two CO3 2– species† †Electronic supplementary information (ESI) available: Mass Spectrometry and BVS analysis CCDC 996546–996548. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc02491e Click here for additional data file. Click here for additional data file.

PubMed Central

Velasco, V.; Aguilà, D.; Barrios, L. A.; Borilovic, I.; Roubeau, O.; Ribas-Ariño, J.; Fumanal, M.; Teat, S. J.

2015-01-01

The aerobic reaction of the multidentate ligand 2,6-bis-(3-oxo-3-(2-hydroxyphenyl)-propionyl)-pyridine, H4L, with Co(ii) salts in strong basic conditions produces the clusters [Co4(L)2(OH)(py)7]NO3 (1) and [Co8Na4(L)4(OH)2(CO3)2(py)10](BF4)2 (2). Analysis of their structure unveils unusual coordination features including a very rare bridging pyridine ligand or two trapped carbonate anions within one coordination cage, forced to stay at an extremely close distance (d O···O = 1.946 Å). This unprecedented non-bonding proximity represents a meeting point between long covalent interactions and “intermolecular” contacts. These original motifs have been analysed here through DFT calculations, which have yielded interaction energies and the reduced repulsion energy experimented by both CO3 2– anions when located in close proximity inside the coordination cage. PMID:28616127

Selective androgen receptor modulators as function promoting therapies.

PubMed

Bhasin, Shalender; Jasuja, Ravi

2009-05-01

The past decade has witnessed an unprecedented discovery effort to develop selective androgen receptor modulators (SARMs) that improve physical function and bone health without adversely affecting the prostate and cardiovascular outcomes. This review describes the historical evolution, the rationale for SARM development, and the mechanisms of testosterone action and SARM selectivity. Although steroidal SARMs have been around since the 1940s, a number of nonsteroidal SARMs that do not serve as substrates for CYP19 aromatase or 5alpha-reductase, act as full agonists in muscle and bone and as partial agonists in prostate are in development. The differing interactions of steroidal and nonsteroidal compounds with androgen receptor (AR) contribute to their unique pharmacologic actions. Ligand binding induces specific conformational changes in the ligand-binding domain, which could modulate surface topology and protein-protein interactions between AR and coregulators, resulting in tissue-specific gene regulation. Preclinical studies have demonstrated the ability of SARMs to increase muscle and bone mass in preclinical rodent models with varying degree of prostate sparing. Phase I trials of SARMs in humans have reported modest increments in fat-free mass. SARMs hold promise as a new class of function promoting anabolic therapies for a number of clinical indications, including functional limitations associated with aging and chronic disease, frailty, cancer cachexia, and osteoporosis.

Selective Androgen Receptor Modulators (SARMs) as Function Promoting Therapies

PubMed Central

Bhasin, Shalender; Jasuja, Ravi

2010-01-01

Purpose of review The last decade has witnessed unprecedented discovery effort to develop selective androgen receptor modulators (SARMs) that improve physical function and bone health without adversely affecting the prostate and cardiovascular outcomes. This review describes the historical evolution, the rationale for SARM development, and the mechanisms of testosterone action and SARM selectivity. Recent Findings While steroidal SARMs have been around since the 1940s, a number of nonsteroidal SARMs that do not serve as substrates for CYP19 aromatase or 5α-reductase, act as full agonists in muscle and bone and as partial agonists in prostate are in development. The differing interactions of steroidal and nonsteroidal compounds with AR contribute to their unique pharmacologic actions. Ligand binding induces specific conformational changes in the ligand binding domain, which could modulate surface topology and protein-protein interactions between AR and coregulators, resulting in tissue-specific gene regulation. Preclinical studies have demonstrated the ability of SARMs to increase muscle and bone mass in preclinical rodent models with varying degree of prostate sparing. Phase I trials of SARMs in humans have reported modest increments in fat-free mass. Summary SARMs hold promise as a new class of function promoting anabolic therapies for a number of clinical indications, including functional limitations associated with aging and chronic disease, frailty, cancer cachexia, and osteoporosis. PMID:19357508

A New Model for Allosteric Regulation of Phenylalanine Hydroxylase: Implications for Disease and Therapeutics

PubMed Central

Stith, Linda; Lawrence, Sarah H.; Andrake, Mark; Dunbrack, Roland L.

2013-01-01

The structural basis for allosteric regulation of phenylalanine hydroxylase (PAH), whose dysfunction causes phenylketonuria (PKU), is poorly understood. A new morpheein model for PAH allostery is proposed to consist of a dissociative equilibrium between two architecturally different tetramers whose interconversion requires a ~90° rotation between the PAH catalytic and regulatory domains, the latter of which contains an ACT domain. This unprecedented model is supported by in vitro data on purified full length rat and human PAH. The conformational change is both predicted to and shown to render the tetramers chromatographically separable using ion exchange methods. One novel aspect of the activated tetramer model is an allosteric phenylalanine binding site at the inter-subunit interface of ACT domains. Amino acid ligand-stabilized ACT domain dimerization follows the multimerization and ligand binding behavior of ACT domains present in other proteins in the PDB. Spectroscopic, chromatographic, and electrophoretic methods demonstrate a PAH equilibrium consisting of two architecturally distinct tetramers as well as dimers. We postulate that PKU-associated mutations may shift the PAH quaternary structure equilibrium in favor of the low activity assemblies. Pharmacological chaperones that stabilize the ACT:ACT interface can potentially provide PKU patients with a novel small molecule therapeutic. PMID:23296088

A microwave satellite water vapour column retrieval for polar winter conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perro, Christopher; Lesins, Glen; Duck, Thomas J.

A new microwave satellite water vapour retrieval for the polar winter atmosphere is presented. The retrieval builds on the work of Miao et al. (2001) and Melsheimer and Heygster (2008), employing auxiliary information for atmospheric conditions and numerical optimization. It was tested using simulated and actual measurements from the Microwave Humidity Sounder (MHS) satellite instruments. Ground truth was provided by the G-band vapour radiometer (GVR) at Barrow, Alaska. For water vapour columns less than 6 kg m -2, comparisons between the retrieval and GVR result in a root mean square (RMS) deviation of 0.39 kg m -2 and a systematic bias of 0.08 kg m -2. These results aremore » compared with RMS deviations and biases at Barrow for the retrieval of Melsheimer and Heygster (2008), the AIRS and MIRS satellite data products, and the ERA-Interim, NCEP, JRA-55, and ASR reanalyses. When applied to MHS measurements, the new retrieval produces a smaller RMS deviation and bias than for the earlier retrieval and satellite data products. The RMS deviations for the new retrieval were comparable to those for the ERA-Interim, JRA-55, and ASR reanalyses; however, the MHS retrievals have much finer horizontal resolution (15 km at nadir) and reveal more structure. The new retrieval can be used to obtain pan-Arctic maps of water vapour columns of unprecedented quality. It may also be applied to measurements from the Special Sensor Microwave/Temperature 2 (SSM/T2), Advanced Microwave Sounding Unit B (AMSU-B), Special Sensor Microwave Imager/Sounder (SSMIS), Advanced Technology Microwave Sounder (ATMS), and Chinese MicroWave Humidity Sounder (MWHS) instruments.« less

New fluorescent azo-Schiff base Cu(II) and Zn(II) metal chelates; spectral, structural, electrochemical, photoluminescence and computational studies

NASA Astrophysics Data System (ADS)

Purtas, Fatih; Sayin, Koray; Ceyhan, Gokhan; Kose, Muhammet; Kurtoglu, Mukerrem

2017-06-01

A new Schiff base containing azo chromophore group obtained by condensation of 2-hydroxy-4-[(E)-phenyldiazenyl]benzaldehyde with 3,4-dimethylaniline (HL) are used for the syntheses of new copper(II) and zinc(II) chelates, [Cu(L)2], and [Zn(L)2], and characterized by physico-chemical and spectroscopic methods such as 1H and 13C NMR, IR, UV.-Vis. and elemental analyses. The solid state structure of the ligand was characterized by single crystal X-ray diffraction study. X-ray diffraction data was then used to calculate the harmonic oscillator model of aromaticity (HOMA) indexes for the rings so as to investigate of enol-imine and keto-amine tautomeric forms in the solid state. The phenol ring C10-C15 shows a considerable deviation from the aromaticity with HOMA value of 0.837 suggesting the shift towards the keto-amine tautomeric form in the solid state. The analytical data show that the metal to ligand ratio in the chelates was found to be 1:2. Theoretical calculations of the possible isomers of the ligand and two metal complexes are performed by using B3LYP method. Electrochemical and photoluminescence properties of the synthesized azo-Schiff bases were also investigated.

A Prediction Method of Binding Free Energy of Protein and Ligand

NASA Astrophysics Data System (ADS)

Yang, Kun; Wang, Xicheng

2010-05-01

Predicting the binding free energy is an important problem in bimolecular simulation. Such prediction would be great benefit in understanding protein functions, and may be useful for computational prediction of ligand binding strengths, e.g., in discovering pharmaceutical drugs. Free energy perturbation (FEP)/thermodynamics integration (TI) is a classical method to explicitly predict free energy. However, this method need plenty of time to collect datum, and that attempts to deal with some simple systems and small changes of molecular structures. Another one for estimating ligand binding affinities is linear interaction energy (LIE) method. This method employs averages of interaction potential energy terms from molecular dynamics simulations or other thermal conformational sampling techniques. Incorporation of systematic deviations from electrostatic linear response, derived from free energy perturbation studies, into the absolute binding free energy expression significantly enhances the accuracy of the approach. However, it also is time-consuming work. In this paper, a new prediction method based on steered molecular dynamics (SMD) with direction optimization is developed to compute binding free energy. Jarzynski's equality is used to derive the PMF or free-energy. The results for two numerical examples are presented, showing that the method has good accuracy and efficiency. The novel method can also simulate whole binding proceeding and give some important structural information about development of new drugs.

Structural properties of platinum(II) biphenyl complexes containing 1,10-phenanthroline derivatives

NASA Astrophysics Data System (ADS)

Rillema, D. Paul; Cruz, Arvin J.; Tasset, Brandon J.; Moore, Curtis; Siam, Khamis; Huang, Wei

2013-06-01

Seven platinum(II) complexes formulated as Pt(bph)L, where bph is the 2,2'-biphenyl dianion and L = 4-methyl-1,10-phenanthroline (4-Mephen), 5-methyl-1,10-phenanthroline (5-Mephen), 5-chloro-1,10-phenanthroline (5-Clphen), 5,6-dimethyl-1,10-phenanthroline (5,6-Me2phen), 4,7-dimethyl-1,10-phenanthroline (4,7-Me2phen), 4,7-diphenyl-1,10-phenanthroline (4,7-Ph2phen) and 3,4,7,8-tetramethyl-1,10-phenanthroline (3,4,7,8-Me4phen) are reported. Protons attached to the phen ligand resonate downfield from those attached to the bph ligand and two proton signals are split by interaction with 195Pt. Pt(bph)(3,4,7,8-Me4phen), Pt(bph)(4,7-Me2phen), Pt(bph)(5,6-Me2phen), Pt(bph)(4,7-Ph2phen) and Pt(bph)(5-Mephen) crystallize in the space groups Pna21, P21/n, P21/c, P - 1 and Pca21, respectively. The structures of the complexes deviate from true planarity and divide themselves into two groups where the bph and phen ligands cross in an X configuration or bow out in a butterfly (B) configuration. Circular dichroism revealed two different spectra with respect to the X and B configurations.

Bottom-up construction of a superstructure in a porous uranium-organic crystal

NASA Astrophysics Data System (ADS)

Li, Peng; Vermeulen, Nicolaas A.; Malliakas, Christos D.; Gómez-Gualdrón, Diego A.; Howarth, Ashlee J.; Mehdi, B. Layla; Dohnalkova, Alice; Browning, Nigel D.; O'Keeffe, Michael; Farha, Omar K.

2017-05-01

Bottom-up construction of highly intricate structures from simple building blocks remains one of the most difficult challenges in chemistry. We report a structurally complex, mesoporous uranium-based metal-organic framework (MOF) made from simple starting components. The structure comprises 10 uranium nodes and seven tricarboxylate ligands (both crystallographically nonequivalent), resulting in a 173.3-angstrom cubic unit cell enclosing 816 uranium nodes and 816 organic linkers—the largest unit cell found to date for any nonbiological material. The cuboctahedra organize into pentagonal and hexagonal prismatic secondary structures, which then form tetrahedral and diamond quaternary topologies with unprecedented complexity. This packing results in the formation of colossal icosidodecahedral and rectified hexakaidecahedral cavities with internal diameters of 5.0 nanometers and 6.2 nanometers, respectively—ultimately giving rise to the lowest-density MOF reported to date.

Biosynthetic inorganic chemistry.

PubMed

Lu, Yi

2006-08-25

Inorganic chemistry and biology can benefit greatly from each other. Although synthetic and physical inorganic chemistry have been greatly successful in clarifying the role of metal ions in biological systems, the time may now be right to utilize biological systems to advance coordination chemistry. One such example is the use of small, stable, easy-to-make, and well-characterized proteins as ligands to synthesize novel inorganic compounds. This biosynthetic inorganic chemistry is possible thanks to a number of developments in biology. This review summarizes the progress in the synthesis of close models of complex metalloproteins, followed by a description of recent advances in using the approach for making novel compounds that are unprecedented in either inorganic chemistry or biology. The focus is mainly on synthetic "tricks" learned from biology, as well as novel structures and insights obtained. The advantages and disadvantages of this biosynthetic approach are discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Chunying; Lu, Jialin; Han, Jingyu

Polymeric lanthanide complexes with thiostannate and polyamine mixed ligands, [Ln(peha)(μ–SnS{sub 4}H)]{sub n} [Ln=La (1a), Nd (1b)] and [(Ln(tepa)(μ–OH)){sub 2}(μ–Sn{sub 2}S{sub 6})]{sub n}nH{sub 2}O [Ln=Nd (2a), Sm (2b), Gd (2c), Dy (2d)] (peha=pentaethylenehexamine, tepa=tetraethylenepentamine) were respectively prepared in peha and tepa coordinative solvents by the solvothermal methods. In 1a and 1b, the Ln{sup 3+} ions are coordinated by a hexadentate peha ligand forming [Ln(peha)]{sup 3+} units. The [SnS{sub 4}H]{sup 3−} anion chelates a [Ln(peha)]{sup 3+} unit via two S atoms and coordinates to another [Ln(peha)]{sup 3+} unit via the third S atom. As a result, the [Ln(peha)]{sup 3+} units are connectedmore » into coordination polymers [Ln(peha)(μ–SnS{sub 4}H)]{sub n} by an unprecedented tridentate μ–η{sup 1},η{sup 2}–SnS{sub 4}H bridging ligands. In 2a–2d, the Ln{sup 3+} ions are coordinated by a pentadentate tepa ligand, and two [Ln(tepa)]{sup 3+} units are joined by two μ–OH bridges to form a binuclear [(Ln(tepa)(μ–OH)){sub 2}]{sup 4+} unit. Behaving as a bidentate μ–η{sup 1}, η{sup 1}–Sn{sub 2}S{sub 6} bridging ligand, the Sn{sub 2}S{sub 6} unit connects [(Ln(tepa)(μ–OH)){sub 2}]{sup 4+} units into a neutral coordination polymer [(Ln(tepa)(μ–OH)){sub 2}(μ–Sn{sub 2}S{sub 6})]{sub n} via the trans S atoms. The Ln{sup 3+} ions are in distorted monocapped square antiprismatic and bicapped trigonal prismatic environments in [(Ln(peha)(μ–SnS{sub 4}H)]{sub n} and [(Ln(tepa)(μ–OH)){sub 2}(μ–Sn{sub 2}S{sub 6})]{sub n}, respectively. The denticities of ethylene polyamine play an important role on the formation and complexation of the thiostannate in the presence of lanthanide ions. Compounds 1a–2d show well-defined absorption edges with band gaps between 2.81 and 3.15 eV. - Graphical abstract: Lanthanide coordination polymers concerning thiostannate ligands were prepared by the solvothermal methods, and μ{sub 3}–SnS{sub 4}H and μ–Sn{sub 2}S{sub 6} ligands to Ln(III) centers were obtained. - Highlights: • Lanthanide coordination polymers were prepared in polyamines with higher denticity. • The μ–η{sup 1},η{sup 2}–SnS{sub 4}H and μ–η{sup 1},η{sup 1}–Sn{sub 2}S{sub 6} ligands to Ln(III) centers were obtained. • Effect of amine on the complexation of Ln(III) with thiostannate is observed.« less

Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked with solanesol as an anti-cancer agent

PubMed Central

Daneial, Betty; Joseph, Jacob Paul Vazhappilly; Ramakrishna, Guruprasad

2017-01-01

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds). Hence, ligand-protein docking was completed using AutoDock with a modified contact based scoring function. The FAK-solanesol complex model was further energy minimized and simulated in GROMOS96 (53a6) force field followed by post simulation analysis such as Root mean square deviation (RMSD), root mean square fluctuations (RMSF) and solvent accessible surface area (SASA) calculations to explain solanesol-FAK binding. PMID:29081606

Visual detection and sequential injection determination of aluminium using a cinnamoyl derivative.

PubMed

Elečková, Lenka; Alexovič, Michal; Kuchár, Juraj; Balogh, Ioseph S; Andruch, Vasil

2015-02-01

A cinnamoyl derivative, 3-[4-(dimethylamino)cinnamoyl]-4-hydroxy-6-methyl-3,4-2H-pyran-2-one, was used as a ligand for the determination of aluminium. Upon the addition of an acetonitrile solution of the ligand to an aqueous solution containing Al(III) and a buffer solution at pH 8, a marked change in colour from yellow to orange is observed. The colour intensity is proportional to the concentration of Al(III); thus, the 'naked-eye' detection of aluminium is possible. The reaction is also applied for sequential injection determination of aluminium. Beer׳s law is obeyed in the range from 0.055 to 0.66 mg L(-1) of Al(III). The limit of detection, calculated as three times the standard deviation of the blank test (n=10), was found to be 4 μg L(-1) for Al(III). The method was applied for the determination of aluminium in spiked water samples and pharmaceutical preparations. Copyright © 2014 Elsevier B.V. All rights reserved.

Crystal structure of cis-tetra-aqua-dichlorido-cobalt(II) sulfolane disolvate.

PubMed

Boudraa, Mhamed; Bouacida, Sofiane; Bouchareb, Hasna; Merazig, Hocine; Chtoun, El Hossain

2015-02-01

In the title compound, [CoCl2(H2O)4]·2C4H8SO2, the Co(II) cation is located on the twofold rotation axis and is coordinated by four water mol-ecules and two adjacent chloride ligands in a slightly distorted octa-hedral coordination environment. The cisoid angles are in the range 83.27 (5)-99.66 (2)°. The three transoid angles deviate significantly from the ideal linear angle. The crystal packing can be described as a linear arrangement of complex units along c formed by bifurcated O-H⋯Cl hydrogen bonds between two water mol-ecules from one complex unit towards one chloride ligand of the neighbouring complex. Two solvent mol-ecules per complex are attached to this infinite chain via O-H⋯O hydrogen bonds in which water mol-ecules act as the hydrogen-bond donor and sulfolane O atoms as the hydrogen-bond acceptor sites.

Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked with solanesol as an anti-cancer agent.

PubMed

Daneial, Betty; Joseph, Jacob Paul Vazhappilly; Ramakrishna, Guruprasad

2017-01-01

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds). Hence, ligand-protein docking was completed using AutoDock with a modified contact based scoring function. The FAK-solanesol complex model was further energy minimized and simulated in GROMOS96 (53a6) force field followed by post simulation analysis such as Root mean square deviation (RMSD), root mean square fluctuations (RMSF) and solvent accessible surface area (SASA) calculations to explain solanesol-FAK binding.

The Slow Controls System of the New Muon g-2 Experiment at Fermilab

NASA Astrophysics Data System (ADS)

Eads, Michael; New Muon g-2 Collaboration

2015-04-01

The goal of the new muon g-2 experiment (E-989), currently under construction at Fermi National Accelerator Laboratory, is to measure the anomalous gyromagnetic ratio of the muon with unprecedented precision. The uncertainty goal of the experiment, 0.14ppm, represents a four-fold improvement over the current best measurement of this value and has the potential to increase the current three standard deviation disagreement with the predicted standard model value to five standard deviations. Measuring the operating conditions of the experiment will be essential to achieving these uncertainty goals. This talk will describe the design and the current status of E-989's slow controls system. This system, based on the MIDAS Slow Control Bus, will be used to measure and record currents, voltages, temperatures, humidities, pressures, flows, and other data which is collected asynchronously with the injection of the muon beam. The system consists of a variety of sensors and front-end electronics which interface to back-end data acquisition, data storage, and data monitoring systems. Parts of the system are all already operational and the full system will be completed before beam commissioning begins in 2017.

Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme

PubMed Central

Leong, Max K.; Syu, Ren-Guei; Ding, Yi-Lung; Weng, Ching-Feng

2017-01-01

The glycine-binding site of the N-methyl-D-aspartate receptor (NMDAR) subunit GluN1 is a potential pharmacological target for neurodegenerative disorders. A novel combinatorial ensemble docking scheme using ligand and protein conformation ensembles and customized support vector machine (SVM)-based models to select the docked pose and to predict the docking score was generated for predicting the NMDAR GluN1-ligand binding affinity. The predicted root mean square deviation (RMSD) values in pose by SVM-Pose models were found to be in good agreement with the observed values (n = 30, r2 = 0.928–0.988,  = 0.894–0.954, RMSE = 0.002–0.412, s = 0.001–0.214), and the predicted pKi values by SVM-Score were found to be in good agreement with the observed values for the training samples (n = 24, r2 = 0.967,  = 0.899, RMSE = 0.295, s = 0.170) and test samples (n = 13, q2 = 0.894, RMSE = 0.437, s = 0.202). When subjected to various statistical validations, the developed SVM-Pose and SVM-Score models consistently met the most stringent criteria. A mock test asserted the predictivity of this novel docking scheme. Collectively, this accurate novel combinatorial ensemble docking scheme can be used to predict the NMDAR GluN1-ligand binding affinity for facilitating drug discovery. PMID:28059133

Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme.

PubMed

Leong, Max K; Syu, Ren-Guei; Ding, Yi-Lung; Weng, Ching-Feng

2017-01-06

The glycine-binding site of the N-methyl-D-aspartate receptor (NMDAR) subunit GluN1 is a potential pharmacological target for neurodegenerative disorders. A novel combinatorial ensemble docking scheme using ligand and protein conformation ensembles and customized support vector machine (SVM)-based models to select the docked pose and to predict the docking score was generated for predicting the NMDAR GluN1-ligand binding affinity. The predicted root mean square deviation (RMSD) values in pose by SVM-Pose models were found to be in good agreement with the observed values (n = 30, r 2  = 0.928-0.988,  = 0.894-0.954, RMSE = 0.002-0.412, s = 0.001-0.214), and the predicted pK i values by SVM-Score were found to be in good agreement with the observed values for the training samples (n = 24, r 2  = 0.967,  = 0.899, RMSE = 0.295, s = 0.170) and test samples (n = 13, q 2  = 0.894, RMSE = 0.437, s = 0.202). When subjected to various statistical validations, the developed SVM-Pose and SVM-Score models consistently met the most stringent criteria. A mock test asserted the predictivity of this novel docking scheme. Collectively, this accurate novel combinatorial ensemble docking scheme can be used to predict the NMDAR GluN1-ligand binding affinity for facilitating drug discovery.

Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme

NASA Astrophysics Data System (ADS)

Leong, Max K.; Syu, Ren-Guei; Ding, Yi-Lung; Weng, Ching-Feng

2017-01-01

The glycine-binding site of the N-methyl-D-aspartate receptor (NMDAR) subunit GluN1 is a potential pharmacological target for neurodegenerative disorders. A novel combinatorial ensemble docking scheme using ligand and protein conformation ensembles and customized support vector machine (SVM)-based models to select the docked pose and to predict the docking score was generated for predicting the NMDAR GluN1-ligand binding affinity. The predicted root mean square deviation (RMSD) values in pose by SVM-Pose models were found to be in good agreement with the observed values (n = 30, r2 = 0.928-0.988,  = 0.894-0.954, RMSE = 0.002-0.412, s = 0.001-0.214), and the predicted pKi values by SVM-Score were found to be in good agreement with the observed values for the training samples (n = 24, r2 = 0.967,  = 0.899, RMSE = 0.295, s = 0.170) and test samples (n = 13, q2 = 0.894, RMSE = 0.437, s = 0.202). When subjected to various statistical validations, the developed SVM-Pose and SVM-Score models consistently met the most stringent criteria. A mock test asserted the predictivity of this novel docking scheme. Collectively, this accurate novel combinatorial ensemble docking scheme can be used to predict the NMDAR GluN1-ligand binding affinity for facilitating drug discovery.

Concentration, Complexation and Chemical Speciation of Zinc and Cadmium in the Western North Pacific Ocean : Exploring Sources and Transport of Trace Metals and Complexing Ligands.

NASA Astrophysics Data System (ADS)

Carrasco, G. G.; Morton, P. L.; Donat, J. R.

2008-12-01

We determined Zn and Cd total dissolved (0.45 µm-filtered) concentrations, organic complexation and chemical speciation in surface water samples collected along the transect of the 2002 IOC Baseline Contaminant Survey expedition in the Western North Pacific and in vertical profile water samples at nine stations. The goals of this work were (1) to compare and contrast various trace metal sources, including both natural and anthropogenic atmospheric deposition, upwelling, marginal seas and others; (2) to study the organic ligand sources, generally thought to be phytoplankton; and (3) to investigate metal and ligand transport mechanisms, residence times and eventual upwelling in the Eastern North Pacific. Total dissolved (TD) Zn and Cd values were obtained using a combination of differential pulse stripping anodic voltammetry (DPASV), preconcentration with 8-HQ or APDC/DDC and quantification at ICPMS or AA. Organic complexation and chemical speciation of Zn and Cd were determined simultaneously using DPASV at a thin-mercury-film, glassy-carbon-disk-electrode. Surface transect TDZn and TDCd concentrations were low in the Subtropical Gyre (STG), in contrast with high values in the Western Subarctic Gyre (WSG). Zn and Cd were organically complexed in most surface samples: at least one ligand class was detected for Zn and Cd, whose conditional stability constants (log K') averaged 10.2 and 10.5, respectively. These ligands were found in excess of the total dissolved metal throughout the region of study except in the WSG for Cd. Vertical distributions of TDZn and TDCd exhibited nutrient-type profiles for all the STG stations. While constant Zn/Si and Cd/P values were observed throughout the water column in the WSG, some deviations were observed within the STG. In addition, the mode and intermediate water masses of the STG displayed very high concentrations of a Zn-complexing ligand (log K' 10.0) in excess of TDZn. As these water masses moved eastward, we observed that the ligand concentrations decreased. In contrast to the STG, the upper 1000m of the WSG showed elevated concentrations of both metals. Despite elevated surface (0-200m) Zn concentrations (~2nM), a Zn-complexing ligand (log K' 9.8) was found in excess of TDZn; below the photic layer, even higher TDZn concentrations might have saturated the ligand. A ligand for Cd was present in lower-than-TDCd concentrations in the same surface waters; below them, organic complexation of Cd was observed rarely in both STG and WSG regions. By studying the geographic distribution of the total dissolved metals and ligands, along with other dissolved and particulate tracers, possible sources and transport mechanisms can be contrasted and evaluated. Furthermore, the influence of these sources and transport mechanisms on the distribution of Zn and Cd chemical species and, ultimately, the bioavailability of these micronutrient metals can be studied.

Conversion of (η(5)-C2B9H10R)TaX3 (X = Me, NMe2) to (η(6)-C2B9H10R)TaX' (X' = NMe2, azaallyl) in the absence of a reducing agent: synthesis and structure of tantallacarboranes incorporating an arachno-η(6)-C2B9(4-) ligand.

PubMed

Xiang, Li; Xie, Zuowei

2014-08-04

Heating a benzene solution of [η(5)-(Me2NCH2CH2)C2B9H10] Ta(NMe2)3 (1) in the presence of pyridine gave an unprecedented complex [η(1):η(6)-(Me2NCH2CH2)C2B9H10]Ta (NMe2)(NC5H5) (2). On the other hand, reaction of (η(5)-C2B9H11)TaMe3 with adamantly isonitrile (AdNC) in dimethoxyethane (DME) at room temperature afforded another unexpected complex (η(6)-C2B9H11)Ta[η(3)-C,C,N-CH2C(CH3)NAd](DME) (4). These results show that pyridine and DME are essential for the formation of 2 and 4, respectively. It is suggested that the nido-η(5)-C2B9H10R(2−) ligand in tantallacarboranes takes up two electrons released by reductive elimination to form an arachno-η(6)-C2B9H10R(4−) fragment via the cage C–C bond cleavage.

Designing Hybrids of Graphene Oxide and Gold Nanoparticles for Nonlinear Optical Response

NASA Astrophysics Data System (ADS)

Yadav, Rajesh Kumar; Aneesh, J.; Sharma, Rituraj; Abhiramnath, P.; Maji, Tuhin Kumar; Omar, Ganesh Ji; Mishra, A. K.; Karmakar, Debjani; Adarsh, K. V.

2018-04-01

Nonlinear optical absorption of light by materials is weak due to its perturbative nature, although a strong nonlinear response is of crucial importance to applications in optical limiting and switching. Here we demonstrate experimentally and theoretically an extremely efficient scheme of excited-state absorption by charge transfer between donor and acceptor materials as a method to enhance the nonlinear absorption by orders of magnitude. With this idea, we demonstrate a strong excited-state absorption (ESA) in reduced graphene oxide that otherwise shows an increased transparency at high fluence and enhancement of ESA by one order of magnitude in graphene oxide by attaching gold nanoparticles (Au NP) in the tandem configuration that acts as an efficient charge-transfer pair when excited at the plasmonic wavelength. To explain the unprecedented enhancement, we develop a five-level rate-equation model based on the charge transfer between the two materials and numerically simulate the results. To understand the correlation of interfacial charge transfer with the concentration and type of the functional ligands attached to the graphene oxide sheet, we investigate the Au-NP—graphene oxide interface with various possible ligand configurations from first-principles calculations. By using the strong ESA of our hybrid materials, we fabricate liquid cell-based high-performance optical limiters with important device parameters better than that of the benchmark optical limiters.

Phosphinodi(benzylsilane) PhP{(o-C6H4CH2)SiMe2H}2: a versatile "PSi2Hx" pincer-type ligand at ruthenium.

PubMed

Montiel-Palma, Virginia; Muñoz-Hernández, Miguel A; Cuevas-Chávez, Cynthia A; Vendier, Laure; Grellier, Mary; Sabo-Etienne, Sylviane

2013-09-03

The synthesis of the new phosphinodi(benzylsilane) compound PhP{(o-C6H4CH2)SiMe2H}2 (1) is achieved in a one-pot reaction from the corresponding phenylbis(o-tolylphosphine). Compound 1 acts as a pincer-type ligand capable of adopting different coordination modes at Ru through different extents of Si-H bond activation as demonstrated by a combination of X-ray diffraction analysis, density functional theory calculations, and multinuclear NMR spectroscopy. Reaction of 1 with RuH2(H2)2(PCy3)2 (2) yields quantitatively [RuH2{[η(2)-(HSiMe2)-CH2-o-C6H4]2PPh}(PCy3)] (3), a complex stabilized by two rare high order ε-agostic Si-H bonds and involved in terminal hydride/η(2)-Si-H exchange processes. A small free energy of reaction (ΔrG298 = +16.9 kJ mol(-1)) was computed for dihydrogen loss from 3 with concomitant formation of the 16-electron species [RuH{[η(2)-(HSiMe2)-CH2-o-C6H4]PPh[CH2-o-C6H4SiMe2]}(PCy3)] (4). Complex 4 features an unprecedented (29)Si NMR decoalescence process. The dehydrogenation process is fully reversible under standard conditions (1 bar, 298 K).

Using the Deep Space Atomic Clock for Navigation and Science.

PubMed

Ely, Todd A; Burt, Eric A; Prestage, John D; Seubert, Jill M; Tjoelker, Robert L

2018-06-01

Routine use of one-way radiometric tracking for deep space navigation and radio science is not possible today because spacecraft frequency and time references that use state-of-the-art ultrastable oscillators introduce errors from their intrinsic drift and instability on timescales past 100 s. The Deep Space Atomic Clock (DSAC), currently under development as a NASA Technology Demonstration Mission, is an advanced prototype of a space-flight suitable, mercury-ion atomic clock that can provide an unprecedented frequency and time stability in a space-qualified clock. Indeed, the ground-based results of the DSAC space demonstration unit have already achieved an Allan deviation of at one day; space performance on this order will enable the use of one-way radiometric signals for deep space navigation and radio science.

Directional amorphization of boron carbide subjected to laser shock compression.

PubMed

Zhao, Shiteng; Kad, Bimal; Remington, Bruce A; LaSalvia, Jerry C; Wehrenberg, Christopher E; Behler, Kristopher D; Meyers, Marc A

2016-10-25

Solid-state shock-wave propagation is strongly nonequilibrium in nature and hence rate dependent. Using high-power pulsed-laser-driven shock compression, unprecedented high strain rates can be achieved; here we report the directional amorphization in boron carbide polycrystals. At a shock pressure of 45∼50 GPa, multiple planar faults, slightly deviated from maximum shear direction, occur a few hundred nanometers below the shock surface. High-resolution transmission electron microscopy reveals that these planar faults are precursors of directional amorphization. It is proposed that the shear stresses cause the amorphization and that pressure assists the process by ensuring the integrity of the specimen. Thermal energy conversion calculations including heat transfer suggest that amorphization is a solid-state process. Such a phenomenon has significant effect on the ballistic performance of B 4 C.

U(SMes*)n, (n = 3, 4) and Ln(SMes*)3 (Ln = La, Ce, Pr, Nd): lanthanide(III)/actinide(III) differentiation in agostic interactions and an unprecedented eta3 ligation mode of the arylthiolate ligand, from X-ray diffraction and DFT analysis.

PubMed

Roger, Mathieu; Barros, Noémi; Arliguie, Thérèse; Thuéry, Pierre; Maron, Laurent; Ephritikhine, Michel

2006-07-12

Reaction of U(NEt(2))(4) with HS-2,4,6-(t)Bu(3)C(6)H(2) (HSMes) gave U(SMes)(3)(NEt(2))(py) (1), whereas similar treatment of U[N(SiMe(3))SiMe(2)CH(2)][N(SiMe(3))(2)](2) afforded U(SMes)[N(SiMe(3))(2)](3) (2) and U(SMes)(3)[N(SiMe(3))(2)]. The first neutral homoleptic uranium(IV) thiolate to have been crystallographically characterized, U(SMes)(4) (4), was isolated from the reaction of U(BH(4))(4) and KSMes. The first homoleptic thiolate complex of uranium(III), U(SMes)(3) (5), was synthesized by protonolysis of U[N(SiMe(3))(2)](3) with HSMes in cyclohexane. The crystal structure of 5 exhibits the novel eta(3) ligation mode for the arylthiolate ligand. Comparison of the crystal structure of 5 with those of the isomorphous lanthanide congeners Ln(SMes)(3) (Ln = La, Ce, Pr, and Nd) indicates that the U-S, U-C(ipso)(), and U-C(ortho)() bond lengths are shorter than the corresponding ones in the 4f-element analogues, when taking into account the variation in the ionic radii of the metals. The distance between the uranium and the carbon atoms involved in the U...H-C epsilon agostic interaction of each thiolate ligand is shorter, by approximately 0.05 A, than that expected from a purely ionic bonding model. The lanthanide(III)/actinide(III) differentiation was analyzed by density functional theory (DFT). The nature of the M-S bond is shown to be ionic strongly polarized at the sulfur for M = U and iono-covalent (i.e. strongly ionic with low orbital interaction), for M = Ln. The strength of the U...H-C epsilon agostic interaction is proposed to be controlled by the maximization of the interaction between U(+) and S(-) under steric constraints. The eta(3) ligation mode of the arylthiolate ligand is also obtained from DFT.

Cocaine Inhibits Store-Operated Ca2+ Entry in Brain Microvascular Endothelial Cells: Critical Role for Sigma-1 Receptors

PubMed Central

Brailoiu, G. Cristina; Deliu, Elena; Console-Bram, Linda M; Soboloff, Jonathan; Abood, Mary E; Unterwald, Ellen M; Brailoiu, Eugen

2015-01-01

Sigma-1 receptor (Sig-1R) is an intracellular chaperone protein with many ligands, located at the endoplasmic reticulum. Binding of cocaine to Sig-1R has previously been found to modulate endothelial functions. In the present study, we show that cocaine dramatically inhibits store-operated Ca2+ entry (SOCE), a Ca2+ influx mechanism promoted by depletion of intracellular Ca2+ stores, in rat brain microvascular endothelial cells. Using either Sig-1R shRNA or pharmacological inhibition with the unrelated Sig-1R antagonists BD-1063 and NE-100, we show that cocaine-induced SOCE inhibition is dependent on Sig-1R. In addition to revealing new insight into fundamental mechanisms of cocaine-induced changes in endothelial function, these studies provide an unprecedented role for Sig-1R as a SOCE inhibitor. PMID:26467159

Structural characterization of a non-heme iron active site in zeolites that hydroxylates methane

DOE PAGES

Snyder, Benjamin E. R.; Bottger, Lars H.; Bols, Max L.; ...

2018-04-02

Iron-containing zeolites exhibit unprecedented reactivity in the low-temperature hydroxylation of methane to form methanol. Reactivity occurs at a mononuclear ferrous active site, α-Fe(II), that is activated by N 2O to form the reactive intermediate α-O. This has been defined as an Fe(IV)=O species. Using nuclear resonance vibrational spectroscopy coupled to X-ray absorption spectroscopy, we probe the bonding interaction between the iron center, its zeolite lattice-derived ligands, and the reactive oxygen. α-O is found to contain an unusually strong Fe(IV)=O bond resulting from a constrained coordination geometry enforced by the zeolite lattice. As a result, density functional theory calculations clarify howmore » the experimentally determined geometric structure of the active site leads to an electronic structure that is highly activated to perform H-atom abstraction.« less

Structural characterization of a non-heme iron active site in zeolites that hydroxylates methane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snyder, Benjamin E. R.; Bottger, Lars H.; Bols, Max L.

Iron-containing zeolites exhibit unprecedented reactivity in the low-temperature hydroxylation of methane to form methanol. Reactivity occurs at a mononuclear ferrous active site, α-Fe(II), that is activated by N 2O to form the reactive intermediate α-O. This has been defined as an Fe(IV)=O species. Using nuclear resonance vibrational spectroscopy coupled to X-ray absorption spectroscopy, we probe the bonding interaction between the iron center, its zeolite lattice-derived ligands, and the reactive oxygen. α-O is found to contain an unusually strong Fe(IV)=O bond resulting from a constrained coordination geometry enforced by the zeolite lattice. As a result, density functional theory calculations clarify howmore » the experimentally determined geometric structure of the active site leads to an electronic structure that is highly activated to perform H-atom abstraction.« less

Ferrocenyl-functionalised terpyridines and their transition-metal complexes: syntheses, structures and spectroscopic and electrochemical properties.

PubMed

Siemeling, Ulrich; Vor der Brüggen, Jens; Vorfeld, Udo; Neumann, Beate; Stammler, Anja; Stammler, Hans-George; Brockhinke, Andreas; Plessow, Regina; Zanello, Piero; Laschi, Franco; Fabrizi de Biani, Fabrizia; Fontani, Marco; Steenken, Steen; Stapper, Marion; Gurzadyan, Gagik

2003-06-16

Terpyridine ligands of the type Fc'-X-tpy (Fc'=ferrocenyl or octamethylferrocenyl, X=rigid spacer, tpy'=4'-substituted 2,2':6',2''-terpyridine) were prepared, crystallographically characterised and used for the synthesis of di- and trinuclear bis(terpyridine) complexes of RuII, FeII and ZnII. Donor-sensitiser dyads and triads based on RuII were thoroughly investigated by (spectro)electrochemistry, UV/Vis, transient absorption and luminescence spectroscopy, and an energy level scheme was derived on the basis of the data collected. Intramolecular quenching of the photoexcited RuII complexes by the redox-active Fc' groups can occur reductively and by energy transfer. Both the redox potential of the donor Fc' and the nature of the spacer X have a decisive influence on excited-state lifetimes and emission properties of the complexes. Some of the compounds show room-temperature luminescence, which is unprecedented for ferrocenyl-functionalised compounds of this kind.

Covalent inhibitors: an opportunity for rational target selectivity.

PubMed

Lagoutte, Roman; Patouret, Remi; Winssinger, Nicolas

2017-08-01

There is a resurging interest in compounds that engage their target through covalent interactions. Cysteine's thiol is endowed with enhanced reactivity, making it the nucleophile of choice for covalent engagement with a ligand aligning an electrophilic trap with a cysteine residue in a target of interest. The paucity of cysteine in the proteome coupled to the fact that closely related proteins do not necessarily share a given cysteine residue enable a level of unprecedented rational target selectivity. The recent demonstration that a lysine's amine can also be engaged covalently with a mild electrophile extends the potential of covalent inhibitors. The growing database of protein structures facilitates the discovery of covalent inhibitors while the advent of proteomic technologies enables a finer resolution in the selectivity of covalently engaged proteins. Here, we discuss recent examples of discovery and design of covalent inhibitors. Copyright © 2017 Elsevier Ltd. All rights reserved.

Giant Rugby Ball [{CpBnFe(η5-P5)}24Cu96Br96] Derived from Pentaphosphaferrocene and CuBr2

PubMed Central

2015-01-01

The self-assembly of [CpBnFe(η5-P5)] (CpBn = η5-C5(CH2Ph)5) with CuBr2 leads to the formation of an unprecedented rugby ball-shaped supramolecule consisting of 24 units of the pentaphosphaferrocene and an extended CuBr framework, which does not follow the fullerene topology. The resulting scaffold of 312 noncarbon atoms reveals three different coordination modes of the cyclo-P5 ligand including a novel π-coordination. The outer dimensions of 3.7 × 4.6 nm of the sphere approach the range of the size of proteins. With a value of 32.1 nm3, it is 62 times larger in volume than a C60 molecule. Surprisingly, this giant rugby ball is also slightly soluble in CH2Cl2. PMID:26280785

Bottom-up construction of a superstructure in a porous uranium-organic crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Peng; Vermeulen, Nicolaas A.; Malliakas, Christos D.

Bottom-up construction of highly intricate structures from simple building blocks remains one of the most difficult challenges in chemistry. We report a structurally complex, mesoporous uranium-based metal-organic framework (MOF) made from simple starting components. The structure comprises 10 uranium nodes and seven tricarboxylate ligands (both crystallographically nonequivalent), resulting in a 173.3-angstrom cubic unit cell enclosing 816 uranium nodes and 816 organic linkers—the largest unit cell found to date for any nonbiological material. The cuboctahedra organize into pentagonal and hexagonal prismatic secondary structures, which then form tetrahedral and diamond quaternary topologies with unprecedented complexity. This packing results in the formation ofmore » colossal icosidodecahedral and rectified hexakaidecahedral cavities with internal diameters of 5.0 nanometers and 6.2 nanometers, respectively—ultimately giving rise to the lowest-density MOF reported to date.« less

Plant synthetic biology for molecular engineering of signalling and development.

PubMed

Nemhauser, Jennifer L; Torii, Keiko U

2016-03-02

Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.

Ordered microporous layered lanthanide 1,3,5-benzenetriphosphonates pillared with cationic organic molecules.

PubMed

Araki, Takahiro; Kondo, Atsushi; Maeda, Kazuyuki

2015-04-13

Novel isomorphous pillared-layer-type crystalline lanthanide 1,3,5-benzenetriphosphonates were prepared with bpy and dbo as organic pillars (LnBP-bpy and LnBP-dbo; Ln: Ce, Pr, and Nd). Ab initio crystal structure solution using synchrotron X-ray powder diffraction data revealed that the organic pillars do not exist as neutral coordinating ligands but as cationic molecules. Especially the LnBP-dbo phases have ordered interlayer space filled with water molecules between the dbo pillars, and the interlayer water is successfully removed by heating under vacuum with slightly distorted but basically retained pillared layer structures. Microporosity of the materials is confirmed by adsorption of nitrogen, carbon dioxide, and hydrogen gases. Such microporous layered metal phosphonates pillared with cationic molecules should be unprecedented and should offer new strategies to design ordered microporous materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single-molecule magnet behavior in an octanuclear dysprosium(iii) aggregate inherited from helical triangular Dy3 SMM-building blocks.

PubMed

Zhang, Li; Zhang, Peng; Zhao, Lang; Wu, Jianfeng; Guo, Mei; Tang, Jinkui

2016-06-28

An unprecedented octanuclear dysprosium(iii) cluster with the formula [Dy8L6(μ3-OH)4(μ2-CH3O)2(CH3OH)6(H2O)2]·6H2O·10CH3OH·2CH3CN () based on a nonlinearly tritopic aroylhydrazone ligand H3L has been isolated, realizing the successful linking of pairwise interesting triangular Dy3 SMMs. It is noteworthy that two enantiomers (Λ and Δ configurations) individually behaving as a coordination-induced chirality presented in the Dy3 helicate are connected in the meso Dy8 cluster. Remarkably, alternating-current magnetic susceptibility measurements revealed that the Dy8 cluster shows typical SMM behavior inherited from its Dy3 helical precursor. It is one of the rare polynuclear Lnn SMMs (n > 7) under zero dc field.

Elucidating photophysical attributes of alpha,alpha'-diimine ligands, rhodium(III) dicyano-bis (alpha,alpha'-diimine) and tris(alpha,alpha'-diimine) complexes via ab inition and density-functional calculations

NASA Astrophysics Data System (ADS)

Matz, Phillip Daniel

Based on crystal structure data, the recently developed density functional PBE1PBE predicts ground state equilibrium geometries in good agreement with experiments. Bond length and angle alpha,alpha'-diimine ligand Mean Absolute Deviation (MAD) values of 0.0077 A and 0.63° are obtained with the low-cost model chemistry PBE1PBE/6-21G. Theoretical trends, specifically the gs → 1pipi* absorption energies and 3pipi* → gs phosphorescence emission energies of the ligands also agree well with experiment. Computations on [Ru(II)(1,10-phenanthroline)3]2+ indicate that the Stuttgart ECP ECP28MWB is capable of reproducing adequately the geometries and photophysical characteristics of transition-metal complexes when paired with the DFT hybrid functional PBE1PBE and the Pople-style split-valence 6-21G basis set describing the ligands. Examination shows that the predicted photophysical properties of both [Rh(III)(s-NN)3](PF6) 3 and [Rh(III)(CN)2(s-NN)2](PF6) complexes agree with experimental evidence in many, but not all aspects. The experimentally observed spectroscopic trend for the gs → 1pipi* absorption energies is reproduced, namely the absorption bands of phenanthroline complexes containing progressively more methyl substituents are monotonically red-shifted relative to the parent phenanthroline in the following energy order: phen > 4-Mephen > 4,7-Me2phen > 3,4,7,8-Me4phen >> 5,6-Me 2phen. Also, the trend of the experimental 3pipi* → gs phosphorescence emission energies is reproduced by the calculations. Experimentally, the activation barriers for the onset of photochemistry in glycerol matrices are reported to be around 2500 cm-1 and 2000 cm-1 for the [Rh(III)(s-NN)3](PF 6)3 and [Rh(III)(CN)2(s-NN)2](PF 6) complexes, respectively. Calculations of the energy gap between the lowest 3pipi* states and the ligand-field states locate the ligand-field states ˜5000cm-1 above the 3pipi* manifolds in the [Rh(III)(s-NN)3](PF6) 3 complexes, far exceeding the experimentally observed values. Analogous calculations on [Rh(III)(CN)2(s-NN)2](PF6) complexes predict an energy gap closer to the experimentally observed activation barriers (˜2500 cm-1) and correctly reproduce the observed trend of increasing activation energy with increasing methyl-substitution, but the ligand field states are shown to possess substantial ligand-centered character.

Robust scoring functions for protein-ligand interactions with quantum chemical charge models.

PubMed

Wang, Jui-Chih; Lin, Jung-Hsin; Chen, Chung-Ming; Perryman, Alex L; Olson, Arthur J

2011-10-24

Ordinary least-squares (OLS) regression has been used widely for constructing the scoring functions for protein-ligand interactions. However, OLS is very sensitive to the existence of outliers, and models constructed using it are easily affected by the outliers or even the choice of the data set. On the other hand, determination of atomic charges is regarded as of central importance, because the electrostatic interaction is known to be a key contributing factor for biomolecular association. In the development of the AutoDock4 scoring function, only OLS was conducted, and the simple Gasteiger method was adopted. It is therefore of considerable interest to see whether more rigorous charge models could improve the statistical performance of the AutoDock4 scoring function. In this study, we have employed two well-established quantum chemical approaches, namely the restrained electrostatic potential (RESP) and the Austin-model 1-bond charge correction (AM1-BCC) methods, to obtain atomic partial charges, and we have compared how different charge models affect the performance of AutoDock4 scoring functions. In combination with robust regression analysis and outlier exclusion, our new protein-ligand free energy regression model with AM1-BCC charges for ligands and Amber99SB charges for proteins achieve lowest root-mean-squared error of 1.637 kcal/mol for the training set of 147 complexes and 2.176 kcal/mol for the external test set of 1427 complexes. The assessment for binding pose prediction with the 100 external decoy sets indicates very high success rate of 87% with the criteria of predicted root-mean-squared deviation of less than 2 Å. The success rates and statistical performance of our robust scoring functions are only weakly class-dependent (hydrophobic, hydrophilic, or mixed).

Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O2 pathways and escape routes in T-state deoxyhemoglobin.

PubMed

Shadrina, Maria S; English, Ann M; Peslherbe, Gilles H

2012-07-11

The diffusion of small gases to special binding sites within polypeptide matrices pivotally defines the biochemical specificity and reactivity of proteins. We investigate here explicit O(2) diffusion in adult human hemoglobin (HbA) as a case study employing the recently developed temperature-controlled locally enhanced sampling (TLES) method and vary the parameters to greatly increase the simulation efficiency. The method is carefully validated against standard molecular dynamics (MD) simulations and available experimental structural and kinetic data on ligand diffusion in T-state deoxyHbA. The methodology provides a viable alternative approach to traditional MD simulations and/or potential of mean force calculations for: (i) characterizing kinetically accessible diffusion tunnels and escape routes for light ligands in porous proteins; (ii) very large systems when realistic simulations require the inclusion of multiple subunits of a protein; and (iii) proteins that access short-lived conformations relative to the simulation time. In the case of T-state deoxyHbA, we find distinct ligand diffusion tunnels consistent with the experimentally observed disparate Xe cavities in the α- and β-subunits. We identify two distal barriers including the distal histidine (E7) that control access to the heme. The multiple escape routes uncovered by our simulations call for a review of the current popular hypothesis on ligand escape from hemoglobin. Larger deviations from the crystal structure during simulated diffusion in isolated α- and β-subunits highlight the dampening effects of subunit interactions and the importance of including all subunits of multisubunit proteins to map realistic kinetically accessible diffusion tunnels and escape routes.

Metal-organic and supramolecular architectures based on mechanically interlocked molecules

NASA Astrophysics Data System (ADS)

Fernando, Isurika Rosini

The focus of this work is on mechanically interlocked molecules (MIMs), which have unusual physicochemical and mechanical properties with potential applications in nano-scale/molecular devices and high strength materials. Rotaxanes, for example, consist of an axle-like molecule threaded through a wheel-like molecule, with bulky groups at the two ends of the axle preventing the wheel from dissociating. The position of the wheel along the axle can be switched in a controllable and reversible manner by applying external stimuli, a feature that might lead to the next generation of computers. Molecularly woven materials (MWMs), another example of molecules with mechanically interlocked features, are predicted to be unprecedentedly strong while being lightweight and flexible. With the ultimate goal of achieving control over the functioning of molecular devices in the solid state, a variety of pseudorotaxane building blocks were prepared and characterized, including a novel, rare blue-colored motif. The temperature-dependent assembly/disassembly of pseudorotaxanes was exploited for the construction of single-wavelength colorimetric temperature sensors over a 100 °C window. Pseudorotaxanes based on aromatic crown ether wheels and disubstituted 4,4'-bipyridinium axles were converted into rotaxanes upon binding to metal complexes (zinc, cadmium, mercury, copper, cobalt), and the formation of ordered crystalline arrays was studied in the solid state. The columnar organization of pseudorotaxanes by Hg2X6 2-- complexes (X = Cl, Br, I), leading to unprecedented dichroic (blue/red) rotaxane crystals, was demonstrated for the first time. From the crystal structures studied it became apparent that negatively charged metal complexes are needed for successful assembly with the positively charged pseudorotaxane units. To be able to use the more common, positively charged metal ions for rotaxane framework construction, neutral and negatively charged pseudorotaxanes were synthesized, by attaching anionic substituents (carboxylates, sulfonates) to either the wheel or the axle component. It was found that pseudorotaxane formation also enabled resolution of two sulfonated crown ether isomers, which were inseparable by conventional methods. Organic ligands for MWM precursors were designed and synthesized according to multi-step schemes. Helical metal-complexes based on these ligands were prepared and characterized. Chromatography, Nuclear Magnetic Resonance and UV-Visible spectroscopy, Mass spectrometry, Electrochemistry, Thermogravimetric Analysis and X-ray crystallography were used in identification, purification and characterization of the compounds involved.

Empirical scoring functions for advanced protein-ligand docking with PLANTS.

PubMed

Korb, Oliver; Stützle, Thomas; Exner, Thomas E

2009-01-01

In this paper we present two empirical scoring functions, PLANTS(CHEMPLP) and PLANTS(PLP), designed for our docking algorithm PLANTS (Protein-Ligand ANT System), which is based on ant colony optimization (ACO). They are related, regarding their functional form, to parts of already published scoring functions and force fields. The parametrization procedure described here was able to identify several parameter settings showing an excellent performance for the task of pose prediction on two test sets comprising 298 complexes in total. Up to 87% of the complexes of the Astex diverse set and 77% of the CCDC/Astex clean listnc (noncovalently bound complexes of the clean list) could be reproduced with root-mean-square deviations of less than 2 A with respect to the experimentally determined structures. A comparison with the state-of-the-art docking tool GOLD clearly shows that this is, especially for the druglike Astex diverse set, an improvement in pose prediction performance. Additionally, optimized parameter settings for the search algorithm were identified, which can be used to balance pose prediction reliability and search speed.

Autogrid-based clustering of kinases: selection of representative conformations for docking purposes.

PubMed

Marzaro, Giovanni; Ferrarese, Alessandro; Chilin, Adriana

2014-08-01

The selection of the most appropriate protein conformation is a crucial aspect in molecular docking experiments. In order to reduce the errors arising from the use of a single protein conformation, several authors suggest the use of several tridimensional structures for the target. However, the selection of the most appropriate protein conformations still remains a challenging goal. The protein 3D-structures selection is mainly performed based on pairwise root-mean-square-deviation (RMSD) values computation, followed by hierarchical clustering. Herein we report an alternative strategy, based on the computation of only two atom affinity map for each protein conformation, followed by multivariate analysis and hierarchical clustering. This methodology was applied on seven different kinases of pharmaceutical interest. The comparison with the classical RMSD-based strategy was based on cross-docking of co-crystallized ligands. In the case of epidermal growth factor receptor kinase, also the docking performance on 220 known ligands were evaluated, followed by 3D-QSAR studies. In all the cases, the herein proposed methodology outperformed the RMSD-based one.

Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design

PubMed Central

2015-01-01

False negative docking outcomes for highly symmetric molecules are a barrier to the accurate evaluation of docking programs, scoring functions, and protocols. This work describes an implementation of a symmetry-corrected root-mean-square deviation (RMSD) method into the program DOCK based on the Hungarian algorithm for solving the minimum assignment problem, which dynamically assigns atom correspondence in molecules with symmetry. The algorithm adds only a trivial amount of computation time to the RMSD calculations and is shown to increase the reported overall docking success rate by approximately 5% when tested over 1043 receptor–ligand systems. For some families of protein systems the results are even more dramatic, with success rate increases up to 16.7%. Several additional applications of the method are also presented including as a pairwise similarity metric to compare molecules during de novo design, as a scoring function to rank-order virtual screening results, and for the analysis of trajectories from molecular dynamics simulation. The new method, including source code, is available to registered users of DOCK6 (http://dock.compbio.ucsf.edu). PMID:24410429

Directional amorphization of boron carbide subjected to laser shock compression

PubMed Central

Zhao, Shiteng; Kad, Bimal; Remington, Bruce A.; LaSalvia, Jerry C.; Wehrenberg, Christopher E.; Behler, Kristopher D.; Meyers, Marc A.

2016-01-01

Solid-state shock-wave propagation is strongly nonequilibrium in nature and hence rate dependent. Using high-power pulsed-laser-driven shock compression, unprecedented high strain rates can be achieved; here we report the directional amorphization in boron carbide polycrystals. At a shock pressure of 45∼50 GPa, multiple planar faults, slightly deviated from maximum shear direction, occur a few hundred nanometers below the shock surface. High-resolution transmission electron microscopy reveals that these planar faults are precursors of directional amorphization. It is proposed that the shear stresses cause the amorphization and that pressure assists the process by ensuring the integrity of the specimen. Thermal energy conversion calculations including heat transfer suggest that amorphization is a solid-state process. Such a phenomenon has significant effect on the ballistic performance of B4C. PMID:27733513

Directional amorphization of boron carbide subjected to laser shock compression

DOE PAGES

Zhao, Shiteng; Kad, Bimal; Remington, Bruce A.; ...

2016-10-12

Solid-state shock-wave propagation is strongly nonequilibrium in nature and hence rate dependent. When using high-power pulsed-laser-driven shock compression, an unprecedented high strain rates can be achieved; we report the directional amorphization in boron carbide polycrystals. At a shock pressure of 45~50 GPa, multiple planar faults, slightly deviated from maximum shear direction, occur a few hundred nanometers below the shock surface. High-resolution transmission electron microscopy reveals that these planar faults are precursors of directional amorphization. We also propose that the shear stresses cause the amorphization and that pressure assists the process by ensuring the integrity of the specimen. Thermal energy conversionmore » calculations including heat transfer suggest that amorphization is a solid-state process. Such a phenomenon has significant effect on the ballistic performance of B 4C.« less

Hg(ii) and Pd(ii) complexes with a new selenoether bridged biscarbene ligand: efficient mono- and bis-arylation of methyl acrylate with a pincer biscarbene Pd(ii) precatalyst.

PubMed

Rishu; Prashanth, Billa; Bawari, Deependra; Mandal, Ushnish; Verma, Aditya; Choudhury, Angshuman Roy; Singh, Sanjay

2017-05-16

Two equivalents of 1-benzyl-3-bromoethylbenzimidazolium bromide couple with Na 2 Se to produce the first selenoether bridged bis-benzimidazolium salt (LH 2 )Br 2 . The nitrate (LH 2 )(NO 3 ) 2 and tetrafluoroborate (LH 2 )(BF 4 ) 2 salts were also synthesized from (LH 2 )Br 2 . The reaction of Hg(OAc) 2 with (LH 2 )Br 2 gave the first pseudo pincer carbene mercury complex, [Hg(L-κ 2 C)][HgBr 4 ] (C1). Different complexes of Pd(ii) with selenoether bridged carbene were obtained using (LH 2 )Br 2 and (LH 2 )(NO 3 ) 2 . Syntheses of these complexes were dependent on the counter anion and the temperature. Thus, the pincer type ionic complex [PdBr(L-κ 3 CSeC)]Br (C2) was isolated at 80 °C and the pseudo pincer type neutral complex cis-[PdBr 2 (L-κ 2 C)] (C3) was isolated at room temperature from (LH 2 )Br 2 and Pd(OAc) 2 in DMSO. The nitrate precursor (LH 2 )(NO 3 ) 2 on palladation with Pd(OAc) 2 afforded [Pd(L-κ 4 C Bz CSeC)]NO 3 (C4) showing an unprecedented intramolecular metallation at the ortho position of the benzyl wingtip of the benzimidazole moiety. The ligand salts and metal complexes have been characterized using HRMS, heteronuclear NMR and IR spectroscopy. Single crystal X-ray structures of the ligand salts (LH 2 )Br 2 and (LH 2 )(BF 4 ) 2 and complexes C1-C4 have also been elucidated. Complex C2 showed good activity for C-C coupling in the mono-Heck reaction of methyl acrylate and arylbromides. Interestingly, the less common bis-arylation was also observed with deactivated arylbromides as the result of double-Heck coupling.

Probing the Impact of Solvation on Photoexcited Spin Crossover Complexes with High-Precision X-ray Transient Absorption Spectroscopy

DOE PAGES

Liu, Cunming; Zhang, Jianxin; Lawson Daku, Latevi M.; ...

2017-11-10

Investigating the photoinduced electronic and structural response of bistable molecular building blocks incorporating transition metals in solution phase constitutes a necessary stepping stone for steering their properties towards applications and perfomance optimizations. Here, this paper presents a detailed X-ray transient absorption (XTA) spectroscopy study of a prototypical spin crossover (SCO) complex [Fe II(mbpy) 3] 2+ (where mbpy=4,4’-dimethyl-2,2’-bipyridine) with a [Fe IIN 6] first coordination shell in water (H 2O) and acetonitrile (CH 3CN). The unprecedented data quality of the XTA spectra together with the direct fitting of the difference spectra in k space using a large number of scattering pathsmore » enables resolving the subtle difference in the photoexcited structures of an Fe II complex in two solvents for the first time. Also, compared to the low spin (LS) 1A 1 state, the average Fe-N bond elongations for the photoinduced high spin (HS) 5T 2 state are found to be 0.181 ± 0.003 Å in H 2O and 0.199 ± 0.003 Å in CH 3CN. This difference in structural response is attributed to ligand-solvent interactions that are stronger in H 2O than in CH 3CN for the HS excited state. Our studies demonstrate that, although the metal center of [Fe II(mbpy) 3] 2+ could have been expected to be rather shielded by the three bidentate ligands with quasi-octahedral-coordination, the ligand field strength in the HS excited state is nevertheless indirectly affected by solvation that modifies the charge distribution within the Fe-N covalent bonds. More generally, this work highlights the importance of including solvation effects in order to develop a generalized understanding of the spin-state switching at the atomic level.« less

Design of stereoelectronically promoted super lewis acids and unprecedented chemistry of their complexes.

PubMed

Foroutan-Nejad, Cina; Vicha, Jan; Marek, Radek

2014-09-01

A new family of stereoelectronically promoted aluminum and scandium super Lewis acids is introduced on the basis of state-of-the-art computations. Structures of these molecules are designed to minimize resonance electron donation to central metal atoms in the Lewis acids. Acidity of these species is evaluated on the basis of their fluoride-ion affinities relative to the antimony pentafluoride reference system. It is demonstrated that introduced changes in the stereochemistry of the designed ligands increase acidity considerably relative to Al and Sc complexes with analogous monodentate ligands. The high stability of fluoride complexes of these species makes them ideal candidates to be used as weakly coordinating anions in combination with highly reactive cations instead of conventional Lewis acid-fluoride complexes. Further, the interaction of all designed molecules with methane is investigated. All studied acids form stable pentavalent-carbon complexes with methane. In addition, interactions of the strongest acid of this family with very weak bases, namely, H2, N2, carbon oxides, and noble gases were investigated; it is demonstrated that this compound can form considerably stable complexes with the aforementioned molecules. To the best of our knowledge, carbonyl and nitrogen complexes of this species are the first hypothetical four-coordinated carbonyl and nitrogen complexes of aluminum. The nature of bonding in these systems is studied in detail by various bonding analysis approaches. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Eu(III) Complex with DO3A-amino-phosphonate Ligand as a Concentration-Independent pH-Responsive Contrast Agent for Magnetic Resonance Spectroscopy (MRS).

PubMed

Krchová, Tereza; Herynek, Vít; Gálisová, Andrea; Blahut, Jan; Hermann, Petr; Kotek, Jan

2017-02-20

A new DOTA-like ligand H 5 do3aNP with a 2-[amino(methylphosphonic acid)]ethyl-coordinating pendant arm was prepared, and its coordinating properties were studied by NMR spectroscopy and potentiometry. The study revealed a rare slow exchange (on the 1 H and 31 P NMR time scale) between protonated and unprotonated complex species with a corresponding acidity constant pK A ∼ 8.0. This unusually slow time scale associated with protonation is caused by a significant geometric change from square-antiprismatic (SA) arrangement observed for protonated complex SA-[Eu(Hdo3aNP)] - to twisted-square-antiprismatic (TSA) arrangement found for deprotonated complex TSA-[Eu(do3aNP)] 2- . This behavior results in simultaneous occurrence of the signals of both species in the 31 P NMR spectra at approximately -118 and +70 ppm, respectively. Such an unprecedented difference in the chemical shifts between species differing by a proton is caused by a significant movement of the principal magnetic axis and by a change of phosphorus atom position in the coordination sphere of the central Eu(III) ion (i.e., by relative movement of the phosphorus atom with respect to the principal magnetic axis). It changes the sign of the paramagnetic contribution to the 31 P NMR chemical shift. The properties discovered can be employed in the measurement of pH by MRS techniques as presented by proof-of-principle experiments on phantoms.

Deviation from the trans -Effect in Ligand-Exchange Reactions of Zeise’s Ions PtCl 3(C 2H 4) - with Heavier Halides (Br –, I - )

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Gao-Lei; Govind, Niranjan; Xantheas, Sotiris S.

Four new Zeise’s family ions with mixed-halide ligands, i.e., PtCl nX 3-n(C 2H 4) - (X = Br, I; n = 1, 2), were synthesized via ligand-exchange reactions of KX salts with KPtCl 3(C 2H 4) in aqueous solutions, and were detected in vacuum via electrospray ionization mass spectrometry. Their photoelectron spectra reveal a series of well-resolved spectral peaks with their electron binding energies (EBEs) decreasing with increasing halide size, with I having a much stronger effect than Br, i.e., 4.57 (–Cl 3) > 4.56 (–Cl 2Br) > 4.53 (–ClBr 2) > 4.34 (–Cl 2I) > 4.30 eV (–ClI 2).more » Ab initio electronic structure calculations including spin-orbit coupling (SOC) predict that the cis- and trans-isomers are nearly isoenergetic with the cis-isomer for –Cl 2X, and the trans-isomer for –ClX 2 slightly favored, respectively. Excited-state spectra calculated with time-dependent density functional theory (TDDFT), and their comparison with the observed ones, suggest that for each species, both the cis- and trans-configurations coexist in the experiments and contribute to the observed spectra, a fact that clearly violates the prediction of the widely accepted trans-effect, which suggests that only one isomer would have formed.« less

FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols.

PubMed

Bohari, Mohammed H; Sastry, G Narahari

2012-09-01

Efficient drug discovery programs can be designed by utilizing existing pools of knowledge from the already approved drugs. This can be achieved in one way by repositioning of drugs approved for some indications to newer indications. Complex of drug to its target gives fundamental insight into molecular recognition and a clear understanding of putative binding site. Five popular docking protocols, Glide, Gold, FlexX, Cdocker and LigandFit have been evaluated on a dataset of 199 FDA approved drug-target complexes for their accuracy in predicting the experimental pose. Performance for all the protocols is assessed at default settings, with root mean square deviation (RMSD) between the experimental ligand pose and the docked pose of less than 2.0 Å as the success criteria in predicting the pose. Glide (38.7 %) is found to be the most accurate in top ranked pose and Cdocker (58.8 %) in top RMSD pose. Ligand flexibility is a major bottleneck in failure of docking protocols to correctly predict the pose. Resolution of the crystal structure shows an inverse relationship with the performance of docking protocol. All the protocols perform optimally when a balanced type of hydrophilic and hydrophobic interaction or dominant hydrophilic interaction exists. Overall in 16 different target classes, hydrophobic interactions dominate in the binding site and maximum success is achieved for all the docking protocols in nuclear hormone receptor class while performance for the rest of the classes varied based on individual protocol.

Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions.

PubMed

Vosmeer, C Ruben; Kooi, Derk P; Capoferri, Luigi; Terpstra, Margreet M; Vermeulen, Nico P E; Geerke, Daan P

2016-01-01

Recently an iterative method was proposed to enhance the accuracy and efficiency of ligand-protein binding affinity prediction through linear interaction energy (LIE) theory. For ligand binding to flexible Cytochrome P450s (CYPs), this method was shown to decrease the root-mean-square error and standard deviation of error prediction by combining interaction energies of simulations starting from different conformations. Thereby, different parts of protein-ligand conformational space are sampled in parallel simulations. The iterative LIE framework relies on the assumption that separate simulations explore different local parts of phase space, and do not show transitions to other parts of configurational space that are already covered in parallel simulations. In this work, a method is proposed to (automatically) detect such transitions during the simulations that are performed to construct LIE models and to predict binding affinities. Using noise-canceling techniques and splines to fit time series of the raw data for the interaction energies, transitions during simulation between different parts of phase space are identified. Boolean selection criteria are then applied to determine which parts of the interaction energy trajectories are to be used as input for the LIE calculations. Here we show that this filtering approach benefits the predictive quality of our previous CYP 2D6-aryloxypropanolamine LIE model. In addition, an analysis is performed of the gain in computational efficiency that can be obtained from monitoring simulations using the proposed filtering method and by prematurely terminating simulations accordingly.

Growth hormone receptor deficiency in Ecuador: clinical and biochemical phenotype in two populations.

PubMed

Guevara-Aguirre, J; Rosenbloom, A L; Fielder, P J; Diamond, F B; Rosenfeld, R G

1993-02-01

We have identified 56 patients with GH receptor deficiency (Laron syndrome) from two provinces in southern Ecuador, one group of 26 (Loja province) with a 4:1 female predominance and 30 patients from neighboring El Oro province with a normal sex ratio. There were no significant differences between the Loja and El Oro populations in stature (-5.3 to -11.5 standard deviation score), other auxologic measures, or in biochemical measures. GH binding protein, the circulating extracellular domain of the GH receptor, was measured by ligand immunofunction assay and found to be comparably low in children and adults. Levels of insulin-like growth factor (IGF)-I and -II and the GH-dependent IGF binding protein-3 (measured by RIA) were significantly greater, and GH and IGF binding protein-2 levels significantly lower in adults than children. Levels of IGF-I (adults) and IGF binding protein-3 (children and adults) correlated inversely with statural deviation from normal (P < 0.01). School performance was at an exceptionally high level, 41 out of 47 who had attended school being in the top 3 in classes of 15-50 persons.

mRAISE: an alternative algorithmic approach to ligand-based virtual screening

NASA Astrophysics Data System (ADS)

von Behren, Mathias M.; Bietz, Stefan; Nittinger, Eva; Rarey, Matthias

2016-08-01

Ligand-based virtual screening is a well established method to find new lead molecules in todays drug discovery process. In order to be applicable in day to day practice, such methods have to face multiple challenges. The most important part is the reliability of the results, which can be shown and compared in retrospective studies. Furthermore, in the case of 3D methods, they need to provide biologically relevant molecular alignments of the ligands, that can be further investigated by a medicinal chemist. Last but not least, they have to be able to screen large databases in reasonable time. Many algorithms for ligand-based virtual screening have been proposed in the past, most of them based on pairwise comparisons. Here, a new method is introduced called mRAISE. Based on structural alignments, it uses a descriptor-based bitmap search engine (RAISE) to achieve efficiency. Alignments created on the fly by the search engine get evaluated with an independent shape-based scoring function also used for ranking of compounds. The correct ranking as well as the alignment quality of the method are evaluated and compared to other state of the art methods. On the commonly used Directory of Useful Decoys dataset mRAISE achieves an average area under the ROC curve of 0.76, an average enrichment factor at 1 % of 20.2 and an average hit rate at 1 % of 55.5. With these results, mRAISE is always among the top performing methods with available data for comparison. To access the quality of the alignments calculated by ligand-based virtual screening methods, we introduce a new dataset containing 180 prealigned ligands for 11 diverse targets. Within the top ten ranked conformations, the alignment closest to X-ray structure calculated with mRAISE has a root-mean-square deviation of less than 2.0 Å for 80.8 % of alignment pairs and achieves a median of less than 2.0 Å for eight of the 11 cases. The dataset used to rate the quality of the calculated alignments is freely available at http://www.zbh.uni-hamburg.de/mraise-dataset.html. The table of all PDB codes contained in the ensembles can be found in the supplementary material. The software tool mRAISE is freely available for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise).

Reactivity of cyclopentadienyl molybdenum compounds towards formic acid: Structural characterization of CpMo(PMe 3)(CO) 2H, CpMo(PMe 3) 2(CO)H, [CpMo(μ-O)(μ-O 2CH)] 2, and [Cp*Mo(μ-O)(μ-O 2CH)] 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neary, Michelle C.; Parkin, Gerard

Here, the molecular structures of CpMo(PMe 3)(CO) 2H and CpMo(PMe 3) 2(CO)H have been determined by X-ray diffraction, thereby revealing four-legged piano-stool structures in which the hydride ligand is trans to CO. However, in view of the different nature of the four basal ligands, the geometries of CpMo(PMe 3)(CO) 2H and CpMo(PMe 3) 2(CO)H deviate from that of an idealized four-legged piano stool, such that the two ligands that are orthogonal to the trans H–Mo–CO moiety are displaced towards the hydride ligand. While CpRMo(PMe 3) 3–x(CO) xH (Cp R = Cp, Cp*; x = 1, 2, 3) are catalysts formore » the release of H 2 from formic acid, the carbonyl derivatives, CpRMo(CO)3H, are also observed to form dinuclear formate compounds, namely, [Cp RMo(μ-O)(μ-O 2CH)] 2. The nature of the Mo···Mo interactions in [CpMo(μ-O)(μ-O 2CH)] 2 and [Cp*Mo(μ-O)(μ-O 2CH)] 2 have been addressed computationally. In this regard, the two highest occupied molecular orbitals of [CpMo(μ-O)(μ-O 2CH)] 2 correspond to metal-based δ* (HOMO) and σ (HOMO–1) orbitals. The σ 2δ *2 configuration thus corresponds to a formal direct Mo–Mo bond order of zero. The preferential occupation of the δ* orbital rather than the δ orbital is a consequence of the interaction of the latter orbital with p orbitals of the bridging oxo ligands. In essence, lone-pair donation from oxygen increases the electron count so that the molybdenum centers can achieve an 18-electron configuration without the existence of a Mo–Mo bond, whereas a Mo=Mo double bond is required in the absence of lone-pair donation.« less

Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods.

PubMed

Antony, Jens; Grimme, Stefan; Liakos, Dimitrios G; Neese, Frank

2011-10-20

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.

Reactivity of cyclopentadienyl molybdenum compounds towards formic acid: Structural characterization of CpMo(PMe 3)(CO) 2H, CpMo(PMe 3) 2(CO)H, [CpMo(μ-O)(μ-O 2CH)] 2, and [Cp*Mo(μ-O)(μ-O 2CH)] 2

DOE PAGES

Neary, Michelle C.; Parkin, Gerard

2017-01-19

Here, the molecular structures of CpMo(PMe 3)(CO) 2H and CpMo(PMe 3) 2(CO)H have been determined by X-ray diffraction, thereby revealing four-legged piano-stool structures in which the hydride ligand is trans to CO. However, in view of the different nature of the four basal ligands, the geometries of CpMo(PMe 3)(CO) 2H and CpMo(PMe 3) 2(CO)H deviate from that of an idealized four-legged piano stool, such that the two ligands that are orthogonal to the trans H–Mo–CO moiety are displaced towards the hydride ligand. While CpRMo(PMe 3) 3–x(CO) xH (Cp R = Cp, Cp*; x = 1, 2, 3) are catalysts formore » the release of H 2 from formic acid, the carbonyl derivatives, CpRMo(CO)3H, are also observed to form dinuclear formate compounds, namely, [Cp RMo(μ-O)(μ-O 2CH)] 2. The nature of the Mo···Mo interactions in [CpMo(μ-O)(μ-O 2CH)] 2 and [Cp*Mo(μ-O)(μ-O 2CH)] 2 have been addressed computationally. In this regard, the two highest occupied molecular orbitals of [CpMo(μ-O)(μ-O 2CH)] 2 correspond to metal-based δ* (HOMO) and σ (HOMO–1) orbitals. The σ 2δ *2 configuration thus corresponds to a formal direct Mo–Mo bond order of zero. The preferential occupation of the δ* orbital rather than the δ orbital is a consequence of the interaction of the latter orbital with p orbitals of the bridging oxo ligands. In essence, lone-pair donation from oxygen increases the electron count so that the molybdenum centers can achieve an 18-electron configuration without the existence of a Mo–Mo bond, whereas a Mo=Mo double bond is required in the absence of lone-pair donation.« less

Reactivity of Cyclopentadienyl Molybdenum Compounds towards Formic Acid: Structural Characterization of CpMo(PMe3)(CO)2H, CpMo(PMe3)2(CO)H, [CpMo(μ-O)(μ-O2CH)]2, and [Cp*Mo(μ-O)(μ-O2CH)]2.

PubMed

Neary, Michelle C; Parkin, Gerard

2017-02-06

The molecular structures of CpMo(PMe 3 )(CO) 2 H and CpMo(PMe 3 ) 2 (CO)H have been determined by X-ray diffraction, thereby revealing four-legged piano-stool structures in which the hydride ligand is trans to CO. However, in view of the different nature of the four basal ligands, the geometries of CpMo(PMe 3 )(CO) 2 H and CpMo(PMe 3 ) 2 (CO)H deviate from that of an idealized four-legged piano stool, such that the two ligands that are orthogonal to the trans H-Mo-CO moiety are displaced towards the hydride ligand. While Cp R Mo(PMe 3 ) 3-x (CO) x H (Cp R = Cp, Cp*; x = 1, 2, 3) are catalysts for the release of H 2 from formic acid, the carbonyl derivatives, Cp R Mo(CO) 3 H, are also observed to form dinuclear formate compounds, namely, [Cp R Mo(μ-O)(μ-O 2 CH)] 2 . The nature of the Mo···Mo interactions in [CpMo(μ-O)(μ-O 2 CH)] 2 and [Cp*Mo(μ-O)(μ-O 2 CH)] 2 have been addressed computationally. In this regard, the two highest occupied molecular orbitals of [CpMo(μ-O)(μ-O 2 CH)] 2 correspond to metal-based δ* (HOMO) and σ (HOMO-1) orbitals. The σ 2 δ* 2 configuration thus corresponds to a formal direct Mo-Mo bond order of zero. The preferential occupation of the δ* orbital rather than the δ orbital is a consequence of the interaction of the latter orbital with p orbitals of the bridging oxo ligands. In essence, lone-pair donation from oxygen increases the electron count so that the molybdenum centers can achieve an 18-electron configuration without the existence of a Mo-Mo bond, whereas a Mo═Mo double bond is required in the absence of lone-pair donation.

Empirical electronic polarizabilities: deviations from the additivity rule. I. M2+SO4·nH2O, blödite Na2M2+(SO4)2·4H2O, and kieserite-related minerals with sterically strained structures

NASA Astrophysics Data System (ADS)

Gagné, Olivier; Hawthorne, Frank; Shannon, Robert D.; Fischer, Reinhard X.

2017-09-01

Empirical electronic polarizabilities allow the prediction of total mineral polarizabilities and mean refractive indices of the vast majority of minerals and synthetic oxides. However, deviations from the valence-sum rule at cations in some minerals are associated with large deviations of observed from calculated total polarizabilities. We have identified several groups of minerals and compounds where deviations from the valence-sum rule at cations lead to polarizability deviations of 2-5%: M(SO4)·nH2O, n = 1-6, blödite-group minerals [Na2M2+(SO4)2·4H2O], and the kieserite-related minerals: isokite, panasqueiraite and tilasite. In these minerals, the environment of the M ions contains both O and H2O: Mg[O4(H2O)2] in kieserite, szmikite, and szomolnokite; Mg[O2(H2O)4] in starkeyite, ilesite, and rozenite, and Mg[(H2O)6] in hexahydrite. In compounds where the ligands are only H2O, deviations from the valence-sum rule at the M(H2O)6 groups are not accompanied by significant polarizability deviations. This is the case for epsomite, MgSO4·7H2O; bieberite, CoSO4·7H2O; goslarite, ZnSO4·7H2O, six silicofluorides, MSiF6·6H2O; eighteen Tutton's salts, M2M'(SO4)2·6H2O, where M = K, Rb, Cs and M' = Mg, Mn, Fe, Co, Ni, Cu, and Zn; and eleven MM'(SO4)2·12H2O alums, where M = Na, K, Rb and Cs, and M' = Al, Cr, Ga and In. This is also the case for the sulfates alunogen, Al2(SO4)3·17H2O and halotrichite, FeAl2(SO4)4·22H2O; three hydrated nitrates; one phosphate; three antimonates and two hydrated perchlorates. A possible explanation for this different behavior is that the bond-valence model treats O and H separately, whereas polarizability calculations treat the polarizability of the entire H2O molecule.

Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn–Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Xuefei; Zhang, Wenjing; Tang, Mingsheng

2015-05-12

Coupled-cluster (CC) methods have been extensively used as the high-level approach in quantum electronic structure theory to predict various properties of molecules when experimental results are unavailable. It is often assumed that CC methods, if they include at least up to connected-triple-excitation quasiperturbative corrections to a full treatment of single and double excitations (in particular, CCSD(T)), and a very large basis set, are more accurate than Kohn–Sham (KS) density functional theory (DFT). In the present work, we tested and compared the performance of standard CC and KS methods on bond energy calculations of 20 3d transition metal-containing diatomic molecules againstmore » the most reliable experimental data available, as collected in a database called 3dMLBE20. It is found that, although the CCSD(T) and higher levels CC methods have mean unsigned deviations from experiment that are smaller than most exchange-correlation functionals for metal–ligand bond energies of transition metals, the improvement is less than one standard deviation of the mean unsigned deviation. Furthermore, on average, almost half of the 42 exchange-correlation functionals that we tested are closer to experiment than CCSD(T) with the same extended basis set for the same molecule. The results show that, when both relativistic and core–valence correlation effects are considered, even the very high-level (expensive) CC method with single, double, triple, and perturbative quadruple cluster operators, namely, CCSDT(2)Q, averaged over 20 bond energies, gives a mean unsigned deviation (MUD(20) = 4.7 kcal/mol when one correlates only valence, 3p, and 3s electrons of transition metals and only valence electrons of ligands, or 4.6 kcal/mol when one correlates all core electrons except for 1s shells of transition metals, S, and Cl); and that is similar to some good xc functionals (e.g., B97-1 (MUD(20) = 4.5 kcal/mol) and PW6B95 (MUD(20) = 4.9 kcal/mol)) when the same basis set is used. We found that, for both coupled cluster calculations and KS calculations, the T1 diagnostics correlate the errors better than either the M diagnostics or the B1 DFT-based diagnostics. The potential use of practical standard CC methods as a benchmark theory is further confounded by the finding that CC and DFT methods usually have different signs of the error. We conclude that the available experimental data do not provide a justification for using conventional single-reference CC theory calculations to validate or test xc functionals for systems involving 3d transition metals.« less

Performance Characterization of Dye-Sensitized Photovoltaics under Indoor Lighting.

PubMed

Chen, Chia-Yuan; Jian, Zih-Hong; Huang, Shih-Han; Lee, Kun-Mu; Kao, Ming-Hsuan; Shen, Chang-Hong; Shieh, Jia-Min; Wang, Chin-Li; Chang, Chiung-Wen; Lin, Bo-Zhi; Lin, Ching-Yao; Chang, Ting-Kuang; Chi, Yun; Chi, Cheng-Yu; Wang, Wei-Ting; Tai, Yian; Lu, Ming-De; Tung, Yung-Liang; Chou, Po-Ting; Wu, Wen-Ti; Chow, Tahsin J; Chen, Peter; Luo, Xiang-Hao; Lee, Yuh-Lang; Wu, Chih-Chung; Chen, Chih-Ming; Yeh, Chen-Yu; Fan, Miao-Syuan; Peng, Jia-De; Ho, Kuo-Chuan; Liu, Yu-Nan; Lee, Hsiao-Yi; Chen, Chien-Yu; Lin, Hao-Wu; Yen, Chia-Te; Huang, Yu-Ching; Tsao, Cheng-Si; Ting, Yu-Chien; Wei, Tzu-Chien; Wu, Chun-Guey

2017-04-20

Indoor utilization of emerging photovoltaics is promising; however, efficiency characterization under room lighting is challenging. We report the first round-robin interlaboratory study of performance measurement for dye-sensitized photovoltaics (cells and mini-modules) and one silicon solar cell under a fluorescent dim light. Among 15 research groups, the relative deviation in power conversion efficiency (PCE) of the samples reaches an unprecedented 152%. On the basis of the comprehensive results, the gap between photometry and radiometry measurements and the response of devices to the dim illumination are identified as critical obstacles to the correct PCE. Therefore, we use an illuminometer as a prime standard with a spectroradiometer to quantify the intensity of indoor lighting and adopt the reverse-biased current-voltage (I-V) characteristics as an indicator to qualify the I-V sampling time for dye-sensitized photovoltaics. The recommendations can brighten the prospects of emerging photovoltaics for indoor applications.

Probing short-range protein Brownian motion in the cytoplasm of living cells.

PubMed

Di Rienzo, Carmine; Piazza, Vincenzo; Gratton, Enrico; Beltram, Fabio; Cardarelli, Francesco

2014-12-23

The translational motion of molecules in cells deviates from what is observed in dilute solutions. Theoretical models provide explanations for this effect but with predictions that drastically depend on the nanoscale organization assumed for macromolecular crowding agents. A conclusive test of the nature of the translational motion in cells is missing owing to the lack of techniques capable of probing crowding with the required temporal and spatial resolution. Here we show that fluorescence-fluctuation analysis of raster scans at variable timescales can provide this information. By using green fluorescent proteins in cells, we measure protein motion at the unprecedented timescale of 1 μs, unveiling unobstructed Brownian motion from 25 to 100 nm, and partially suppressed diffusion above 100 nm. Furthermore, experiments on model systems attribute this effect to the presence of relatively immobile structures rather than to diffusing crowding agents. We discuss the implications of these results for intracellular processes.

Coherent Structures and Extreme Events in Rotating Multiphase Turbulent Flows

NASA Astrophysics Data System (ADS)

Biferale, L.; Bonaccorso, F.; Mazzitelli, I. M.; van Hinsberg, M. A. T.; Lanotte, A. S.; Musacchio, S.; Perlekar, P.; Toschi, F.

2016-10-01

By using direct numerical simulations (DNS) at unprecedented resolution, we study turbulence under rotation in the presence of simultaneous direct and inverse cascades. The accumulation of energy at large scale leads to the formation of vertical coherent regions with high vorticity oriented along the rotation axis. By seeding the flow with millions of inertial particles, we quantify—for the first time—the effects of those coherent vertical structures on the preferential concentration of light and heavy particles. Furthermore, we quantitatively show that extreme fluctuations, leading to deviations from a normal-distributed statistics, result from the entangled interaction of the vertical structures with the turbulent background. Finally, we present the first-ever measurement of the relative importance between Stokes drag, Coriolis force, and centripetal force along the trajectories of inertial particles. We discover that vortical coherent structures lead to unexpected diffusion properties for heavy and light particles in the directions parallel and perpendicular to the rotation axis.

High-resolution Statistics of Solar Wind Turbulence at Kinetic Scales Using the Magnetospheric Multiscale Mission

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chasapis, Alexandros; Matthaeus, W. H.; Parashar, T. N.

Using data from the Magnetospheric Multiscale (MMS) and Cluster missions obtained in the solar wind, we examine second-order and fourth-order structure functions at varying spatial lags normalized to ion inertial scales. The analysis includes direct two-spacecraft results and single-spacecraft results employing the familiar Taylor frozen-in flow approximation. Several familiar statistical results, including the spectral distribution of energy, and the sale-dependent kurtosis, are extended down to unprecedented spatial scales of ∼6 km, approaching electron scales. The Taylor approximation is also confirmed at those small scales, although small deviations are present in the kinetic range. The kurtosis is seen to attain verymore » high values at sub-proton scales, supporting the previously reported suggestion that monofractal behavior may be due to high-frequency plasma waves at kinetic scales.« less

Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Huanchen; Falck, J.R.; Hall, Traci M. Tanaka

2012-01-11

Inositol pyrophosphates (such as IP7 and IP8) are multifunctional signaling molecules that regulate diverse cellular activities. Inositol pyrophosphates have 'high-energy' phosphoanhydride bonds, so their enzymatic synthesis requires that a substantial energy barrier to the transition state be overcome. Additionally, inositol pyrophosphate kinases can show stringent ligand specificity, despite the need to accommodate the steric bulk and intense electronegativity of nature's most concentrated three-dimensional array of phosphate groups. Here we examine how these catalytic challenges are met by describing the structure and reaction cycle of an inositol pyrophosphate kinase at the atomic level. We obtained crystal structures of the kinase domainmore » of human PPIP5K2 complexed with nucleotide cofactors and either substrates, product or a MgF{sub 3}{sup -} transition-state mimic. We describe the enzyme's conformational dynamics, its unprecedented topological presentation of nucleotide and inositol phosphate, and the charge balance that facilitates partly associative in-line phosphoryl transfer.« less

Structure-based drug design targeting the cell membrane receptor GPBAR1: exploiting the bile acid scaffold towards selective agonism

NASA Astrophysics Data System (ADS)

di Leva, Francesco Saverio; Festa, Carmen; Renga, Barbara; Sepe, Valentina; Novellino, Ettore; Fiorucci, Stefano; Zampella, Angela; Limongelli, Vittorio

2015-11-01

Bile acids can regulate nutrient metabolism through the activation of the cell membrane receptor GPBAR1 and the nuclear receptor FXR. Developing an exogenous control over these receptors represents an attractive strategy for the treatment of enterohepatic and metabolic disorders. A number of dual GPBAR1/FXR agonists are known, however their therapeutic use is limited by multiple unwanted effects due to activation of the diverse downstream signals controlled by the two receptors. On the other hand, designing selective GPBAR1 and FXR agonists is challenging since the two proteins share similar structural requisites for ligand binding. Here, taking advantage of our knowledge of the two targets, we have identified through a rational drug design study a series of amine lithocholic acid derivatives as selective GPBAR1 agonists. The presence of the 3α-NH2 group on the steroidal scaffold is responsible for the selectivity over FXR unveiling unprecedented structural insights into bile acid receptors activity modulation.

Evidence for photosensitised hydrogen production from water in the absence of precious metals, redox-mediators and co-catalysts.

PubMed

Salzl, S; Ertl, M; Knör, G

2017-03-22

The water-soluble zinc porphyrin complex Zn(TPPS) 4- with TPPS = tetrakis-(4-sulfonatophenyl)porphyrin surprisingly was found to produce significant amounts of hydrogen from aqueous sulfite or amine solutions under visible-light exposure without requiring any other components such as electron relays or additional proton reduction catalysts. Although the production rates and total amounts of chemically stored fuel obtained under these conditions are still much too low to be relevant for practical applications, the background of this unprecedented observation was further studied in its own right. Since the central metal zinc is unlikely to be involved in proton-coupled electron transfer steps upon long-wavelength irradiation and the process does not seem to be much affected by variations of the electron donor added, the mechanism of photocatalytic H 2 release is suggested to involve previously neglected redox features of the in situ generated hydroporphyrin ligand system in aqueous solution.

Cancer-selective, single agent chemoradiosensitising gold nanoparticles

PubMed Central

Grellet, Sophie; Tzelepi, Konstantina; Roskamp, Meike; Williams, Phil; Sharif, Aquila; Slade-Carter, Richard; Goldie, Peter; Whilde, Nicky; Śmiałek, Małgorzata A.; Mason, Nigel J.

2017-01-01

Two nanometre gold nanoparticles (AuNPs), bearing sugar moieties and/or thiol-polyethylene glycol-amine (PEG-amine), were synthesised and evaluated for their in vitro toxicity and ability to radiosensitise cells with 220 kV and 6 MV X-rays, using four cell lines representing normal and cancerous skin and breast tissues. Acute 3 h exposure of cells to AuNPs, bearing PEG-amine only or a 50:50 ratio of alpha-galactose derivative and PEG-amine resulted in selective uptake and toxicity towards cancer cells at unprecedentedly low nanomolar concentrations. Chemotoxicity was prevented by co-administration of N-acetyl cysteine antioxidant, or partially prevented by the caspase inhibitor Z-VAD-FMK. In addition to their intrinsic cancer-selective chemotoxicity, these AuNPs acted as radiosensitisers in combination with 220 kV or 6 MV X-rays. The ability of AuNPs bearing simple ligands to act as cancer-selective chemoradiosensitisers at low concentrations is a novel discovery that holds great promise in developing low-cost cancer nanotherapeutics. PMID:28700660

Solvothermal synthesis and structural characterization of a three-dimensional metal organic polymer [NaZn(1,2,4-BTC)] (1,2,4-BTC=1,2,4-benzenetricarboxylate)

NASA Astrophysics Data System (ADS)

Wang, Lei; Shi, Zhan; Li, Guanghua; Fan, Yong; Fu, Wensheng; Feng, Shouhua

2004-01-01

A new three-dimensional metal-organic polymer, [NaZn(1,2,4-BTC)] (where 1,2,4-BTC=1,2,4-benzenetricarboxylate), has been prepared under solvothermal conditions and characterized by single crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2 1/ c, with cell parameters: a=9.7706(4) Å, b=12.3549(5) Å, c=6.8897(3) Å, β=91.640(2)°, V=831.35(6) Å 3 and Z=4. In the three-dimensional structure of the compound, each Zn atom is five-coordinated in distorted trigonal bipyramidal geometry, while the sixfold coordination of Na corresponds to a slightly distorted triangular prism. The organic ligand, 1,2,4-BTC, shows a novel and unprecedented coordination mode: 11 bonds to 10 metals with each carboxylate function exhibiting different linkages. It remains stable when desolvated and when heated up to 410 °C.

Formation of unprecedented actinidecarbon triple bonds in uranium methylidyne molecules

PubMed Central

Lyon, Jonathan T.; Hu, Han-Shi; Andrews, Lester; Li, Jun

2007-01-01

Chemistry of the actinide elements represents a challenging yet vital scientific frontier. Development of actinide chemistry requires fundamental understanding of the relative roles of actinide valence-region orbitals and the nature of their chemical bonding. We report here an experimental and theoretical investigation of the uranium methylidyne molecules X3UCH (X = F, Cl, Br), F2ClUCH, and F3UCF formed through reactions of laser-ablated uranium atoms and trihalomethanes or carbon tetrafluoride in excess argon. By using matrix infrared spectroscopy and relativistic quantum chemistry calculations, we have shown that these actinide complexes possess relatively strong UC triple bonds between the U 6d-5f hybrid orbitals and carbon 2s-2p orbitals. Electron-withdrawing ligands are critical in stabilizing the U(VI) oxidation state and sustaining the formation of uranium multiple bonds. These unique UC-bearing molecules are examples of the long-sought actinide-alkylidynes. This discovery opens the door to the rational synthesis of triple-bonded actinidecarbon compounds. PMID:18024591

Losses and depolarization of ultracold neutrons on neutron guide and storage materials

NASA Astrophysics Data System (ADS)

Bondar, V.; Chesnevskaya, S.; Daum, M.; Franke, B.; Geltenbort, P.; Göltl, L.; Gutsmiedl, E.; Karch, J.; Kasprzak, M.; Kessler, G.; Kirch, K.; Koch, H.-C.; Kraft, A.; Lauer, T.; Lauss, B.; Pierre, E.; Pignol, G.; Reggiani, D.; Schmidt-Wellenburg, P.; Sobolev, Yu.; Zechlau, T.; Zsigmond, G.

2017-09-01

At Institut Laue-Langevin (ILL) and Paul Scherrer Institute (PSI), we have measured the losses and depolarization probabilities of ultracold neutrons on various materials: (i) nickel-molybdenum alloys with weight percentages of 82/18, 85/15, 88/12, 91/9, and 94/6 and natural nickel Ni100, (ii) nickel-vanadium NiV93/7, (iii) copper, and (iv) deuterated polystyrene (dPS). For the different samples, storage-time constants up to ˜460 s were obtained at room temperature. The corresponding loss parameters for ultracold neutrons, η , varied between 1.0 ×10-4 and 2.2 ×10-4 . All η values are in agreement with theory except for dPS, where anomalous losses at room temperature were established with four standard deviations. The depolarization probabilities per wall collision β measured with unprecedented sensitivity varied between 0.7 ×10-6 and 9.0 ×10-6 . Our depolarization result for copper differs from other experiments by 4.4 and 15.8 standard deviations. The β values of the paramagnetic NiMo alloys over molybdenum content show an increase of β with increasing Mo content. This is in disagreement with expectations from literature. Finally, ferromagnetic behavior of NiMo alloys at room temperature was found for molybdenum contents of 6.5 at.% or less and paramagnetic behavior for more than 8.7 at.%. This may contribute to solving an ambiguity in literature.

Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance.

PubMed

van Oene, Maarten M; Ha, Seungkyu; Jager, Tessa; Lee, Mina; Pedaci, Francesco; Lipfert, Jan; Dekker, Nynke H

2018-04-24

Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and several different implementations of magnetic (torque) tweezers. Although systematic analyses of the position and force precision of single-molecule techniques have attracted considerable attention, their angle and torque precision have been treated in much less detail. Here, we propose Allan deviation as a tool to systematically quantitate angle and torque precision in single-molecule measurements. We apply the Allan variance method to experimental data from our implementations of (electro)magnetic torque tweezers and an OTW and find that both approaches can achieve a torque precision better than 1 pN · nm. The OTW, capable of measuring torque on (sub)millisecond timescales, provides the best torque precision for measurement times ≲10 s, after which drift becomes a limiting factor. For longer measurement times, magnetic torque tweezers with their superior stability provide the best torque precision. Use of the Allan deviation enables critical assessments of the torque precision as a function of measurement time across different measurement modalities and provides a tool to optimize measurement protocols for a given instrument and application. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Structure and organization of heteromeric AMPA-type glutamate receptors.

PubMed

Herguedas, Beatriz; García-Nafría, Javier; Cais, Ondrej; Fernández-Leiro, Rafael; Krieger, James; Ho, Hinze; Greger, Ingo H

2016-04-29

AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we report the first AMPAR heteromer structures, which deviate substantially from existing GluA2 homomer structures. Crystal structures of the GluA2/3 and GluA2/4 N-terminal domains reveal a novel compact conformation with an alternating arrangement of the four subunits around a central axis. This organization is confirmed by cysteine cross-linking in full-length receptors, and it permitted us to determine the structure of an intact GluA2/3 receptor by cryogenic electron microscopy. Two models in the ligand-free state, at resolutions of 8.25 and 10.3 angstroms, exhibit substantial vertical compression and close associations between domain layers, reminiscent of N-methyl-D-aspartate receptors. Model 1 resembles a resting state and model 2 a desensitized state, thus providing snapshots of gating transitions in the nominal absence of ligand. Our data reveal organizational features of heteromeric AMPARs and provide a framework to decipher AMPAR architecture and signaling. Copyright © 2016, American Association for the Advancement of Science.

Evaluations of the conformational search accuracy of CAMDAS using experimental three-dimensional structures of protein-ligand complexes

NASA Astrophysics Data System (ADS)

Oda, A.; Yamaotsu, N.; Hirono, S.; Takano, Y.; Fukuyoshi, S.; Nakagaki, R.; Takahashi, O.

2013-08-01

CAMDAS is a conformational search program, through which high temperature molecular dynamics (MD) calculations are carried out. In this study, the conformational search ability of CAMDAS was evaluated using structurally known 281 protein-ligand complexes as a test set. For the test, the influences of initial settings and initial conformations on search results were validated. By using the CAMDAS program, reasonable conformations whose root mean square deviations (RMSDs) in comparison with crystal structures were less than 2.0 Å could be obtained from 96% of the test set even though the worst initial settings were used. The success rate was comparable to those of OMEGA, and the errors of CAMDAS were less than those of OMEGA. Based on the results obtained using CAMDAS, the worst RMSD was around 2.5 Å, although the worst value obtained was around 4.0 Å using OMEGA. The results indicated that CAMDAS is a robust and versatile conformational search method and that it can be used for a wide variety of small molecules. In addition, the accuracy of a conformational search in relation to this study was improved by longer MD calculations and multiple MD simulations.

An improvement to the ligand optimisation method (LOM) for measuring the apparent dissociation constant and ligand purity in Ca2+ and Mg2+ buffer solutions.

PubMed

McGuigan, John A S; Kay, James W; Elder, Hugh Y

2014-01-01

In Ca(2+)/Mg(2+) buffers the calculated ionised concentrations ([X(2+)]) can vary by up to a factor of seven. Since there are no defined standards it is impossible to check calculated [X(2+)], making measurement essential. The ligand optimisation method (LOM) is an accurate method to measure [X(2+)] in Ca(2+)/Mg(2+) buffers; independent estimation of ligand purity extends the method to pK(/) < 4. To simplify calculation, Excel programs ALE and AEC were compiled for LOM and its extension. This paper demonstrates that the slope of the electrode in the pX range 2.000-3.301 deviates from Nernstian behaviour as it depends on the value of the lumped interference, Σ. ALE was modified to include this effect; this modified program SALE, and the programs ALE and AEC were used on simulated data for Ca(2+)-EGTA and Mg(2+)-ATP buffers, to calculate electrode and buffer characteristics as a function of Σ. Ca(2+)-electrodes have a Σ < 10(-6) mol/l and there was no difference amongst the three methods. The Σ for Mg(2+)-electrodes lies between 10(-5) and 1.5 (∗) 10(-5) mol/l and calculated [Mg(2+)] with ALE were around 3% less than the true value. SALE and AEC correctly predicted [Mg(2+)]. SALE was used to recalculate K(/) and pK(/) on measured data for Ca(2+)-EGTA and Mg(2+)-EDTA buffers. These results demonstrated that it is pK(/) that is normally distributed. Until defined standards are available, [X(2+)] in Ca(2+)/Mg(2+) buffers have to be measured. The most appropriate method is to use Ca(2+)/Mg(2) electrodes combined with the Excel programs SALE or AEC. Copyright © 2014 Elsevier Ltd. All rights reserved.

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics.

PubMed

Krokhotin, Andrey; Niemi, Antti J; Peng, Xubiao

2013-05-07

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

NASA Astrophysics Data System (ADS)

Krokhotin, Andrey; Niemi, Antti J.; Peng, Xubiao

2013-05-01

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

Oxoiron(IV) Complex of the Ethylene-Bridged Dialkylcyclam Ligand Me2EBC.

PubMed

England, Jason; Prakash, Jai; Cranswick, Matthew A; Mandal, Debasish; Guo, Yisong; Münck, Eckard; Shaik, Sason; Que, Lawrence

2015-08-17

We report herein the first example of an oxoiron(IV) complex of an ethylene-bridged dialkylcyclam ligand, [Fe(IV)(O)(Me2EBC)(NCMe)](2+) (2; Me2EBC = 4,11-dimethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane). Complex 2 has been characterized by UV-vis, (1)H NMR, resonance Raman, Mössbauer, and X-ray absorption spectroscopy as well as electrospray ionization mass spectrometry, and its properties have been compared with those of the closely related [Fe(IV)(O)(TMC)(NCMe)](2+) (3; TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), the intensively studied prototypical oxoiron(IV) complex of the macrocyclic tetramethylcyclam ligand. Me2EBC has an N4 donor set nearly identical with that of TMC but possesses an ethylene bridge in place of the 1- and 8-methyl groups of TMC. As a consequence, Me2EBC is forced to deviate from the trans-I configuration typically found for Fe(IV)(O)(TMC) complexes and instead adopts a folded cis-V stereochemistry that requires the MeCN ligand to coordinate cis to the Fe(IV)═O unit in 2 rather than in the trans arrangement found in 3. However, switching from the trans geometry of 3 to the cis geometry of 2 did not significantly affect their ground-state electronic structures, although a decrease in ν(Fe═O) was observed for 2. Remarkably, despite having comparable Fe(IV/III) reduction potentials, 2 was found to be significantly more reactive than 3 in both oxygen-atom-transfer (OAT) and hydrogen-atom-transfer (HAT) reactions. A careful analysis of density functional theory calculations on the HAT reactivity of 2 and 3 revealed the root cause to be the higher oxyl character of 2, leading to a stronger O---H bond specifically in the quintet transition state.

A flexible docking scheme to explore the binding selectivity of PDZ domains

PubMed Central

Gerek, Z Nevin; Ozkan, S Banu

2010-01-01

Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using RosettaLigand, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 Å. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately. PMID:20196074

Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza-decaline scaffold.

PubMed

Teruya, Kenta; Hattori, Yasunao; Shimamoto, Yasuhiro; Kobayashi, Kazuya; Sanjoh, Akira; Nakagawa, Atsushi; Yamashita, Eiki; Akaji, Kenichi

2016-11-04

Design of inhibitors against severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro) ) is a potentially important approach to fight against SARS. We have developed several synthetic inhibitors by structure-based drug design. In this report, we reveal two crystal structures of SARS 3CL(pro) complexed with two new inhibitors based on our previous work. These structures combined with six crystal structures complexed with a series of related ligands reported by us are collectively analyzed. To these eight complexes, the structural basis for inhibitor binding was analyzed by the COMBINE method, which is a chemometrical analysis optimized for the protein-ligand complex. The analysis revealed that the first two latent variables gave a cumulative contribution ratio of r(2)  = 0.971. Interestingly, scores using the second latent variables for each complex were strongly correlated with root mean square deviations (RMSDs) of side-chain heavy atoms of Met(49) from those of the intact crystal structure of SARS-3CL(pro) (r = 0.77) enlarging the S2 pocket. The substantial contribution of this side chain (∼10%) for the explanation of pIC50 s was dependent on stereochemistry and the chemical structure of the ligand adapted to the S2 pocket of the protease. Thus, starting from a substrate mimic inhibitor, a design for a central scaffold for a low molecular weight inhibitor was evaluated to develop a further potent inhibitor. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 391-403, 2016. © 2015 Wiley Periodicals, Inc.

Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ecale Zhou, C L; Zemla, A T; Roe, D

2005-01-29

Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set ofmore » ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket in close proximity (but not overlapping) the active site that is suitable for bi-dentate ligand development. These methods are generally applicable to identification of surface epitopes and binding pockets for development of diagnostic reagents, therapeutics, and vaccines.« less

Auto-assembly of nanometer thick, water soluble layers of plasmid DNA complexed with diamines and basic amino acids on graphite: Greatest DNA protection is obtained with arginine.

PubMed

Khalil, T T; Boulanouar, O; Heintz, O; Fromm, M

2017-02-01

We have investigated the ability of diamines as well as basic amino acids to condense DNA onto highly ordered pyrolytic graphite with minimum damage after re-dissolution in water. Based on a bibliographic survey we briefly summarize DNA binding properties with diamines as compared to basic amino acids. Thus, solutions of DNA complexed with these linkers were drop-cast in order to deposit ultra-thin layers on the surface of HOPG in the absence or presence of Tris buffer. Atomic Force Microscopy analyses showed that, at a fixed ligand-DNA mixing ratio of 16, the mean thickness of the layers can be statistically predicted to lie in the range 0-50nm with a maximum standard deviation ±6nm, using a simple linear law depending on the DNA concentration. The morphology of the layers appears to be ligand-dependent. While the layers containing diamines present holes, those formed in the presence of basic amino acids, except for lysine, are much more compact and dense. X-ray Photoelectron Spectroscopy measurements provide compositional information indicating that, compared to the maximum number of DNA sites to which the ligands may bind, the basic amino acids Arg and His are present in large excess. Conservation of the supercoiled topology of the DNA plasmids was studied after recovery of the complex layers in water. Remarkably, arginine has the best protection capabilities whether Tris was present or not in the initial solution. Copyright © 2016 Elsevier B.V. All rights reserved.

Structure and magnetic properties of an unprecedented syn-anti μ-nitrito-1κO:2κO' bridged Mn(III)-salen complex and its isoelectronic and isostructural formate analogue.

PubMed

Kar, Paramita; Biswas, Rituparna; Drew, Michael G B; Ida, Yumi; Ishida, Takayuki; Ghosh, Ashutosh

2011-04-07

The preparation, crystal structures and magnetic properties of two new isoelectronic and isomorphous formate- and nitrite-bridged 1D chains of Mn(III)-salen complexes, [Mn(salen)(HCOO)](n) (1) and [Mn(salen)(NO(2))](n) (2), where salen is the dianion of N,N'-bis(salicylidene)-1,2-diaminoethane, are presented. The structures show that the salen ligand coordinates to the four equatorial sites of the metal ion and the formate or nitrite ions coordinate to the axial positions to bridge the Mn(III)-salen units through a syn-antiμ-1κO:2κO' coordination mode. Such a bridging mode is unprecedented in Mn(III) for formate and in any transition metal ion for nitrite. Variable-temperature magnetic susceptibility measurements of complexes 1 and 2 indicate the presence of ferromagnetic exchange interactions with J values of 0.0607 cm(-1) (for 1) and 0.0883 cm(-1) (for 2). The ac measurements indicate negligible frequency dependence for 1 whereas compound 2 exhibits a decrease of χ(ac)' and a concomitant increase of χ(ac)'' on elevating frequency around 2 K. This finding is an indication of slow magnetization reversal characteristic of single-chain magnets or spin-glasses. The μ-nitrito-1κO:2κO' bridge seems to be a potentially superior magnetic coupler to the formate bridge for the construction of single-molecule/-chain magnets as its coupling constant is greater and the χ(ac)' and χ(ac)'' show frequency dependence. © The Royal Society of Chemistry 2011

Four unprecedented 2D trinuclear Mn(II)-complexes with adenine nucleobase controlled by solvent or co-ligand: Hydrothermal synthesis, crystal structure and magnetic behaviour

NASA Astrophysics Data System (ADS)

Zhao, Hongkun; He, Hongming; Wang, Xiuguang; Liu, Zhongyi; Ding, Bo; Yang, Hanwen

2018-03-01

Four unique infinite 2D Mn(II) aggregates, [Mn3(μ3-ade)2(OAc)4X]n (X = DMF for 1, DMA for 2 and C2H5O- for 3), [Mn3(μ3-ade)2(ap)2DMF]n (4) (Hade = adenine; DMF = N,N-dimethylformamide; DMA = N,N-dimethylacetamide, OAc- = acetate ion, H2ap = adipic acid) with trinuclear Mn(II) as secondary building units (SBUs), have been successfully synthesized by the assembly of Hade nucleobase and manganese acetate under solvothermal conditions. The resultant complexes can be applied to explore the influence of solvent or co-ligands on the self-assembly and properties of metal complexes based on adenine. The Hade represent tridentate μ3-N3, N7, N9 bridging coordination modes. The acetate anions exhibit μ2-η1:η1 bidentate, μ2-η1:η2 tridentate mode, and μ2-η0:η2 bidentate mode. The adipate anions in complex 4 adopt two coordination modes: one is μ4-η2:η1:η1:η1 pentadentate mode, the other one is μ3-η1:η2:η2:η1 hexadentate mode. Their magnetic behaviors exhibit interesting variations, in which the local net magnetization at low temperature increases from 1 to 3. The MnII3 SBUs in 1-3 are symmetric with an inversion center, whereas that in 4 has three crystallographically independent MnII atoms. Thus, the magnetic behaviors of 4 are different from complex 1-3.

Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ito, Tasuku; Saikawa, Kyo; Kim, Seonah

2014-04-25

Graphical abstract: - Highlights: • HypBA1 β-L-arabinofuranosidase belongs to glycoside hydrolase family 127. • Crystal structure of HypBA1 was determined. • HypBA1 consists of a catalytic barrel and two additional β-sandwich domains. • The active site contains a Zn{sup 2+} coordinated by glutamate and three cysteines. • A possible reaction mechanism involving cysteine as the nucleophile is proposed. - Abstract: Enzymes acting on β-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of β-L-arabinofuranosyl oligosaccharides in plant cells. Recently, a β-L-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system ofmore » hydroxyproline-linked β-L-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and β-L-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional β-sandwich domains, with one β-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn{sup 2+} coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the β-L-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.« less

Spontaneous chiral resolution of a rare 3D self-penetration coordination polymer for sensitive aqueous-phase detection of picric acid.

PubMed

Song, Bai-Qiao; Qin, Chao; Zhang, Yu-Teng; Wu, Xue-Song; Yang, Liu; Shao, Kui-Zhan; Su, Zhong-Min

2015-11-14

Two unprecedented homochiral enantiomers based on two different kinds of rigid ligands, namely [Cd(NDC)L]2·H2O (1R and 1L), have been synthesized under hydrothermal conditions through spontaneous resolution. Their structures were determined by single-crystal X-ray diffraction analysis and further characterized by elemental analysis, IR, and thermogravimetric (TG) analysis. The resulting framework 1, constructed by four kinds of homo-handed helical chains represents the first 3D self-penetrating framework formed by decoration of single (10,3)-a net with helical chains. The single (10,3)-a net in 1 formed by three kinds of different homo-handed helical chains is different from the standard one, which should be ascribed to the usage of V-shaped ligand L. A unique self-penetration motif can be discovered in 1 where one helical chain alternately passes through 10-membered shortest circuits linked to each other and in contrary, the corresponding circuits are bound to the helical chain. Interestingly, 1 exhibits fluorescent emission in both the solid and solution phase. The uncoordinated nitrogen atom and amino group from the triazole core on the crystal surface make it suitable to detect picric acid in water. The luminescence intensity of 1 in water can be efficiently quenched by the addition of picric acid (PA). The sensitive detection of PA can be continuously performed for at least five cycles without diminishing the fluorescence intensity and destroying the framework structure of 1. The possible quenching mechanisms for PA are also investigated.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

PubMed Central

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

2013-01-01

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol−1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol−1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning. PMID:24320250

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.

PubMed

Rocklin, Gabriel J; Mobley, David L; Dill, Ken A; Hünenberger, Philippe H

2013-11-14

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol(-1)) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

Redox routes to substitution of aluminum(III): synthesis and characterization of (IP-)2AlX (IP = α-iminopyridine, X = Cl, Me, SMe, S2CNMe2, C≡CPh, N3, SPh, NHPh).

PubMed

Myers, Thomas W; Holmes, Alexandra L; Berben, Louise A

2012-08-20

Redox active ligands are shown to facilitate a variety of group transfer reactions at redox inert aluminum(III). Disulfides can be used as a two-electron group transfer reagent, and we show that (IP(-))(2)AlSR can be formed by reaction of [(THF)(6)Na][(IP(2-))(2)Al] (1c) with disulfides RSSR (where X = C(S)NMe(2), 4; SMe, 5). In a more general redox route to substitution of aluminum bis(iminopyridine) complexes, we report zinc(II) salts as a group transfer reagent. Reaction of [((R)IP(2-))(2)Al](-) (R = H, 1c; Me, 1d) with ZnX(2) affords ((R)IP(-))(2)AlX (where IP = iminopyridine, R = H, and X = Cl, 2; CCPh, 6; N(3), 7; SPh, 8; or R = Me and X = NHPh, 9). Single crystal X-ray diffraction analysis of the complexes reveal that each of the five coordinate complexes reported here has a trigonal bipyramidal geometry with τ = 0.668 - 0.858. We observed a correlation between the greatest deviations from ideal trigonal bipyramidal symmetry (lowest τ values), the bond lengths consistent with smallest degree of ligand reduction, and the least polarizable X ligand in (IP(-))(2)AlX. Complex 4 is six-coordinate and is best described as distorted octahedral. Variable temperature magnetic susceptibility measurements indicate that each of the complexes 3-9 has a biradical electronic structure similar to previously reported 2. Magnetic exchange coupling constants in the range J = -94 to -212 cm(-1) were fit to the data for 2-9 to describe the energy of antiferromagnetic interaction between ligand radicals assuming a spin Hamiltonian of the form Ĥ = -2JŜ(L(1))·Ŝ(L(2)). The strongest coupling occurs when the angle between the ligand planes is smallest, presumably to afford good overlap with the Al-X σ* orbital. Electrochemical properties of the complexes were probed using cyclic voltammetry and each of 3-9 displayed a reversible two-electron reduction and two quasi-reversible one-electron oxidation processes. The energy of the ligand based redox processes for 2-9 differ by about 150 mV over all complexes and show a correlation with the degree of IP(-) reduction observed crystallographically; more reduced IP(-) ligands require higher potentials for further reduction. Comproportionation constants that describe the equilibrium for the reaction (IP(-))(2)AlX + (IP)(2)AlX ↔ (IP(-))(IP)AlX fall in the range of K(c) = 10(5.7) to 10(7.9) for 3-9.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

NASA Astrophysics Data System (ADS)

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

2013-11-01

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol-1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol-1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

The impact trajectory of asteroid 2008 TC3

NASA Astrophysics Data System (ADS)

Farnocchia, Davide; Jenniskens, Peter; Robertson, Darrel K.; Chesley, Steven R.; Dimare, Linda; Chodas, Paul W.

2017-09-01

The impact of asteroid 2008 TC3 was an unprecedented event-the first ever predicted impact of a near-Earth object. When it was first detected about 20 h before impact, 2008 TC3 was still farther away than the Moon. Once it was recognized as an impactor and announced as such, 2008 TC3 began to receive considerable attention from astronomical observers. Using the unprecedented dataset of nearly 900 astrometric observations and the latest observation debiasing and weighting techniques, we estimate the precise trajectory of 2008 TC3 and its impact ground track. At the entry point into the atmosphere, the 3-σ formal uncertainty in predicted position is an ellipse only 1.4 km × 0.15 km in size. The locations of the many meteorites recovered from the desert floor mark the asteroid's actual ground track and provide a unique opportunity to validate trajectory models. We find that the second-order zonal harmonics of the Earth gravity field moves the ground track by more than 1 km and the location along the ground track by more than 2 km, while non-zonal and higher order harmonics change the impact prediction by less than 20 m. The contribution of atmospheric drag to the trajectory of 2008 TC3 is similar to the numerical integration error level, a few meters, down to an altitude of 50 km. Integrating forward to lower altitudes and ignoring the break-up of 2008 TC3, atmospheric drag causes an along-track deviation that can be as large as a few kilometers at sea level.

Bis(2,1,3-benzoselenadiazole-κN)dibromidocopper(II)

PubMed Central

Fun, Hoong-Kun; Goh, Jia Hao; Maity, Annada C.; Goswami, Shyamaprosad

2011-01-01

In the title complex, [CuBr2(C6H4N2Se)2], the CuII ion is tetra­coordinated by two bromide anions and two N atoms in a distorted square-planar geometry. The two essentially planar 2,1,3-benzoselenadiazole ligands [maximum deviations = 0.012 (2) and 0.030 (2) Å] are approximately coplanar [dihedral angle = 6.14 (6)°]. In the crystal, short inter­molecular Se⋯Br, Se⋯N and N⋯N inter­actions are observed. These short inter­actions and inter­molecular C—H⋯Br hydrogen bonds link the complex mol­ecules into two-dimensional arrays parallel to the ac plane. PMID:21522854

High temperature extended x-ray absorption fine structure study of multiferroic BiFeO3

NASA Astrophysics Data System (ADS)

Raghavendra Reddy, V.; Meneghini, Carlo; Kothari, Deepti; Gupta, Ajay; Aquilanti, Giuliana

2012-08-01

Local atomic structure modifications around Fe atoms in polycrystalline multiferroic BiFeO3 are studied by Fe K edge x-ray absorption spectroscopy as a function of temperature across the Néel temperature (TN = 643 K) in order to reveal local structure modifications related to the magnetic transition. This work demonstrates that on crossing TN the local structure around Fe shows peculiar changes: the Fe-O bond lengths get shorter, the ligand symmetry increases and the Fe-O bond length disorder (σ2) deviates from Debye behaviour. These results suggest that the structural transition at the ferroelectric Curie temperature (TC = 1103 K) is anticipated by early local rearrangement of the structure starting already at TN.

Several novel N-donor tridentate ligands formed in chemical studies of new fac-Re(CO)3 complexes relevant to fac-99mTc(CO)3 radiopharmaceuticals: attack of a terminal amine on coordinated acetonitrile.

PubMed

Perera, Theshini; Marzilli, Patricia A; Fronczek, Frank R; Marzilli, Luigi G

2010-03-01

To evaluate syntheses of fac-[Re(CO)(3)L](+) complexes in organic solvents, we treated fac-[Re(CO)(3)(CH(3)CN)(3)]PF(6)/BF(4) in acetonitrile with triamine ligands (L). When L had two primary or two tertiary terminal amine groups, the expected fac-[Re(CO)(3)L](+) complexes formed. In contrast, N,N-dimethyldiethylenetriamine (N,N-Me(2)dien) formed an unusual compound, fac-[Re(CO)(3)(DAE)]BF(4) {DAE = (Z)-N'-(2-(2-(dimethylamino)ethylamino)ethyl)acetimidamide = (Me(2)NCH(2)CH(2))NH(CH(2)CH(2)N=C(NH(2))Me)}. DAE is formed by addition of acetonitrile to the N,N-Me(2)dien terminal primary amine, converting this sp(3) nitrogen to an sp(2) nitrogen with a double bond to the original acetonitrile sp carbon. The three Ns bound to Re derive from N,N-Me(2)dien. The pathway to fac-[Re(CO)(3)(DAE)]BF(4) is suggested by a second unusual compound, fac-[Re(CO)(3)(MAE)]PF(6) {MAE = N-methyl-N-(2-(methyl-(2-(methylamino)ethyl)amino)ethyl)acetimidamide = MeN(H)-CH(2)CH(2)-N(Me)-CH(2)CH(2)-N(Me)-C(Me)=NH}, isolated after treating fac-[Re(CO)(3)(CH(3)CN)(3)]PF(6) with N,N',N''-trimethyldiethylenetriamine (N,N',N''-Me(3)dien). MAE chelates via a terminal and a central sp(3) N from N,N',N''-Me(3)dien and via one sp(2) NH in a C(Me)=NH group. This group is derived from acetonitrile by addition of the other N,N',N''-Me(3)dien terminal amine to the nitrile carbon. This addition creates an endocyclic NMe group within a seven-membered chelate ring. The structure and other properties of fac-[Re(CO)(3)(MAE)]PF(6) allow us to propose a reaction scheme for the formation of the unprecedented DAE ligand. The new compounds advance our understanding of the spectral and structural properties of Re analogues of (99m)Tc radiopharmaceuticals.

Diverse reactivity of a tricoordinate organoboron L2PhB: (L = oxazol-2-ylidene) towards alkali metal, group 9 metal, and coinage metal precursors† †Electronic supplementary information (ESI) available: Experimental and calculation details, and crystallographic information for 2, 3, 4, 6, 8. CCDC 1038665, 1038666, 1038667, 1011534, and 1011533. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc00404g Click here for additional data file. Click here for additional data file.

PubMed Central

Kong, Lingbing; Ganguly, Rakesh; Li, Yongxin

2015-01-01

The reactivity of a tricoordinate organoboron L2PhB: (L = oxazol-2-ylidene) 1 towards metal precursors and its coordination chemistry were comprehensively studied. While the boron center in 1 is reluctant to coordinate to the alkali metals in their trifluoromethanesulfonate salts (MOTf) (M = Li, Na, K), the unprecedented compound 2 containing two L2PhB: units linked by a cyclic Li(OTf)2Li spacer was obtained from the reaction of 1 with LiOTf. Treatment of 1 with group 9 metal complexes [MCl(COD)]2 (M = Rh, Ir) afforded the first zwitterionic rhodium(i)–boronium complex 3 and the iridium(iii)–borane complex 4, respectively. The reaction pathway may involve C–H activation followed by proton migration from the metals to the boron center, demonstrating the first example of the deprotonation of metal hydrides by a basic boron. In the reactions with coinage metals, 1 could act as a two-electron reducing agent towards the metal chlorides MCl (M = Cu, Ag, Au). Meanwhile, the reaction of 1 with gold chloride supported by a N-heterocyclic carbene (NHC) produced a heteroleptic cationic gold complex [(L2PhB)Au(NHC)]Cl (6) featuring both carbene and L2PhB: ligands on the gold atom. In contrast, an isolable gold chloride complex (L2PhB)AuCl (8) was obtained by direct complexation between 1 and triphenylphosphine-gold chloride via ligand exchange. X-ray diffraction analysis and computational studies revealed the nature of the B:→Au bonding interaction in complexes 6 and 8. Natural Population Analysis (NPA) and Natural Bond Orbital (NBO) analysis support the strong σ-donating property of the L2PhB: ligand. Moreover, preliminary studies showed that complex 8 can serve as an efficient precatalyst for the addition of X–H (X = N, O, C) to alkynes under ambient conditions, demonstrating the first application of a metal complex featuring a neutral boron-based ligand in catalysis. PMID:29308167

Thermalization of Heavy Ions in the Solar Wind

NASA Astrophysics Data System (ADS)

Tracy, Patrick J.; Kasper, Justin C.; Zurbuchen, Thomas H.; Raines, Jim M.; Shearer, Paul; Gilbert, Jason

2015-10-01

Observations of velocity distribution functions from the Advanced Composition Explorer/Solar Wind Ion Composition Spectrometer heavy ion composition instrument are used to calculate ratios of kinetic temperature and Coulomb collisional interactions of an unprecedented 50 ion species in the solar wind. These ions cover a mass per charge range of 1-5.5 amu/e and were collected in the time range of 1998-2011. We report the first calculation of the Coulomb thermalization rate between each of the heavy ion (A > 4 amu) species present in the solar wind along with protons (H+) and alpha particles (He2+). From these rates, we find that protons are the dominant source of Coulomb collisional thermalization for heavy ions in the solar wind and use this fact to calculate a collisional age for those heavy ion populations. The heavy ion thermal properties are well organized by this collisional age, but we find that the temperature of all heavy ions does not simply approach that of protons as Coulomb collisions become more important. We show that He2+ and C6+ follow a monotonic decay toward equal temperatures with protons with increasing collisional age, but O6+ shows a noted deviation from this monotonic decay. Furthermore, we show that the deviation from monotonic decay for O6+ occurs in solar wind of all origins, as determined by its Fe/O ratio. The observed differences in heavy ion temperature behavior point toward a local heating mechanism that favors ions depending on their charge and mass.

Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii.

PubMed

Ahmad, Sajjad; Raza, Saad; Uddin, Reaz; Azam, Syed Sikander

2017-10-01

MurF ligase catalyzes the final cytoplasmic step of bacterial peptidoglycan biosynthesis and, as such, is a validated target for therapeutic intervention. Herein, we performed molecular docking to identify putative inhibitors of Acinetobacter baumannii MurF (AbMurF). Based on comparative docking analysis, compound 114 (ethyl pyridine substituted 3-cyanothiophene) was predicted to potentially be the most active ligand. Computational pharmacokinetic characterization of drug-likeness of the compound showed it to fulfil all the parameters of Muegge and the MDDR rule. A molecular dynamic simulation of 114 indicated the complex to be stable on the basis of an average root mean square deviation (RMSD) value of 2.09Å for the ligand. The stability of the complex was further supported by root mean square fluctuation (RMSF), beta factor and radius of gyration values. Analyzing the complex using radial distribution function (RDF) and a novel analytical tool termed the axial frequency distribution (AFD) illustrated that after simulation the ligand is positioned in close vicinity of the protein active site where Thr42 and Asp43 participate in hydrogen bonding and stabilization of the complex. Binding free energy calculations based on the Poisson-Boltzmann or Generalized-Born Surface Area Continuum Solvation (MM(PB/GB)SA) method indicated the van der Waals contribution to the overall binding energy of the complex to be dominant along with electrostatic contributions involving the hot spot amino acids from the protein active site. The present results indicate that the screened compound 114 may act as a parent structure for designing potent derivatives against AbMurF in specific and MurF of other bacterial pathogens in general. Copyright © 2017 Elsevier Inc. All rights reserved.

Temperature controlled ionic liquid-based dispersive micro-extraction using two ligands, for determination of aluminium in scalp hair samples of Alzheimer's patients: A multivariate study

NASA Astrophysics Data System (ADS)

Arain, Mariam S.; Arain, Salma A.; Kazi, Tasneem G.; Afridi, Hassan I.; Ali, Jamshaid; Naeemulllah; Arain, Sadaf S.; Brahman, Kapil Dev; Mughal, Moina Akhtar

2015-02-01

A green and sensitive temperature controlled dispersive liquid-liquid microextraction (TIL-DLLME) methodology based on the application of ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, [C4mim][PF6], as an extractant solvent was proposed for the preconcentration of trace levels of aluminium (Al3+) in scalp hair samples of Alzheimer's (AD) patients, prior to analyzing by flame atomic absorption spectrometry (FAAS). The Al3+ was complexed with 8-hydrooxyquinoline (oxine) (L1) and 3,5,7,2‧-4‧ pentahydroxy flavone (morin) (L2) separately and then extracted by IL at temperature (50 ± 2.0 °C). Some effective factors that influence the TIL-DLLME efficiency such as pH, ligands concentrations, volume of IL, ionic strength, and incubation time were investigated and optimized by multivariate analysis. In the optimum experimental conditions, the limit of detection (3 s) and enhancement factor were 0.56 μg L-1, 0.64 μg L-1 and 85, 73 for both ligands, respectively. The relative standard deviation (RSD) for six replicate determinations of 100 μg L-1 Al3+ complexed with oxine and morin were found to be 3.88% and 4.74%, respectively. The developed method was validated by the analysis of certified reference material of human hair (NCSZC81002).and applied satisfactorily to the determination of Al3+ in acid digested scalp hair samples of AD patients and healthy controls. The resulted data shows significant higher level in scalp hair samples of AD male patients with related to referents of same age and socioeconomic status.

Photophysical Properties of Pt(II) Polypyridines with Five- versus Six-Membered Chelate Rings: Trade-Offs in Angle Strain.

PubMed

Natoli, Sean N; Hight, Lauren M; Zeller, Matthias; McMillin, David R

2018-06-04

This report describes the synthesis and characterization of a series of eight [Pt(NNN)X] + complexes where the tridentate NNN ligand is (2,2'-bipyrid-6-yl)(pyrid-2-yl)sulfide (btp) or methyl(2,2'-bipyrid-6-yl)(pyrid-2-yl)amine (bmap) and X is OMe, Cl, phenylethynyl (C 2 Ph), or cyclohexylethynyl (C 2 Cy). The expectation was that inserting a heteroatom into the backbone of 2,2':6',2″-terpyridine (trpy) would expand the overall intraligand bite angle, introduce ILCT character into the excited states, and improve the photophysical properties. Crystal structures of [Pt(bmap)C 2 Ph] + and [Pt(btp)Cl] + reveal that atom insertion into the trpy backbone successfully expands the bite angle of the ligand by 8-10°. However, the impact on the photophysics is minimal. Indeed, of the eight systems investigated, only the [Pt(bmap)C 2 Ph] + and [Pt(btp)C 2 Ph] + complexes display appreciable emission in fluid solution, and they exhibit shorter emission lifetimes than [Pt(trpy)C 2 Ph] + . One reason is that the bond angle preferences of platinum and the inserted heteroatom induce the six-membered rings to deviate from planarity and adopt a boat-like conformation, impairing charge delocalization within the ligand. In addition, angle strain induces the donor atoms about platinum to assume a pseudotetrahedral arrangement, which offsets any benefit due to the increase in overall bite angle by promoting deactivation via d-d excited states. The results reveal that, in order to improve the luminescence of a [Pt(NNN)X] + system, one must take care to avoid trading one kind of angle strain for another.

Functional selectivity of G-protein-coupled receptors: from recombinant systems to native human cells.

PubMed

Seifert, Roland

2013-10-01

In the mid 1990s, it was assumed that a two-state model, postulating an inactive (R) state and an active (R*) state provides the molecular basis for GPCR activation. However, it became clear that this model could not accommodate many experimental observations. Accordingly, the two-state model was superseded by a multi-state model according to which any given ligand stabilizes a unique receptor conformation with distinct capabilities of activating down-stream G-proteins and β-arrestin. Much of this research was conducted with the β2-adrenoceptor in recombinant systems. At the molecular level, there is now no doubt anymore that ligand-specific receptor conformations, also referred to as functional selectivity, exist. This concept holds great potential for drug discovery in terms of developing drugs with higher selectivity for specific cells and/or cell functions and fewer side effects. A major challenge is the analysis for functional selectivity in native cells. Here, I discuss our current knowledge on functional selectivity of three representative GPCRs, the β2-adrenoceptor and the histamine H2- and H4-receptors, in recombinant systems and native human cells. Studies with human neutrophils and eosinophils support the concept of functional selectivity. A major strategy for the analysis of functional selectivity in native cells is to generate complete concentration/response curves with a large set of structurally diverse ligands for multiple parameters. Next, correlations of potencies and efficacies are analyzed, and deviations of the correlations from linearity are indicative for functional selectivity. Additionally, pharmacological inhibitors are used to dissect cell functions from each other. Copyright © 2013 Elsevier Inc. All rights reserved.

Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method.

PubMed

Guo, Meiyuan; Sørensen, Lasse Kragh; Delcey, Mickaël G; Pinjari, Rahul V; Lundberg, Marcus

2016-01-28

The intensities and relative energies of metal K pre-edge features are sensitive to both geometric and electronic structures. With the possibility to collect high-resolution spectral data it is important to find theoretical methods that include all important spectral effects: ligand-field splitting, multiplet structures, 3d-4p orbital hybridization, and charge-transfer excitations. Here the restricted active space (RAS) method is used for the first time to calculate metal K pre-edge spectra of open-shell systems, and its performance is tested against on six iron complexes: [FeCl6](n-), [FeCl4](n-), and [Fe(CN)6](n-) in ferrous and ferric oxidation states. The method gives good descriptions of the spectral shapes for all six systems. The mean absolute deviation for the relative energies of different peaks is only 0.1 eV. For the two systems that lack centrosymmetry [FeCl4](2-/1-), the ratios between dipole and quadrupole intensity contributions are reproduced with an error of 10%, which leads to good descriptions of the integrated pre-edge intensities. To gain further chemical insight, the origins of the pre-edge features have been analyzed with a chemically intuitive molecular orbital picture that serves as a bridge between the spectra and the electronic structures. The pre-edges contain information about both ligand-field strengths and orbital covalencies, which can be understood by analyzing the RAS wavefunction. The RAS method can thus be used to predict and rationalize the effects of changes in both the oxidation state and ligand environment in a number of hard X-ray studies of small and medium-sized molecular systems.

Crystal structure of tetra­aqua­[2-(pyridin-2-yl)-1H-imidazole-κ2 N 2,N 3]iron(II) sulfate

PubMed Central

Setifi, Zouaoui; Setifi, Fatima; Francuski, Bojana M.; Novaković, Sladjana B.; Merazig, Hocine

2015-01-01

In the title compound, [Fe(C8H7N3)(H2O)4]SO4, the central FeII ion is octa­hedrally coordinated by two N atoms from the bidentate 2-(pyridin-2-yl)-1H-imidazole ligand and by four O atoms of the aqua ligands. The largest deviation from the ideal octa­hedral geometry is reflected by the small N—Fe—N bite angle of 76.0 (1)°. The Fe—N coordination bonds have markedly different lengths [2.1361 (17) and 2.243 (2) Å], with the shorter one to the pyrimidine N atom. The four Fe—O coordination bond lengths vary from 2.1191 (18) to 2.1340 (17) Å. In the crystal, the cations and anions are arranged by means of medium-strength O—H⋯O hydrogen bonds into layers parallel to the ab plane. Neighbouring layers further inter­connect by N—H⋯O hydrogen bonds involving the imidazole fragment as donor group to one sulfate O atom as an acceptor. The resulting three-dimensional network is consolidated by C—H⋯O, C—H⋯π and π–π inter­actions. PMID:26029386

Benchmarking Commercial Conformer Ensemble Generators.

PubMed

Friedrich, Nils-Ole; de Bruyn Kops, Christina; Flachsenberg, Florian; Sommer, Kai; Rarey, Matthias; Kirchmair, Johannes

2017-11-27

We assess and compare the performance of eight commercial conformer ensemble generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE Conformation Import, and OMEGA) and one leading free algorithm, the distance geometry algorithm implemented in RDKit. The comparative study is based on a new version of the Platinum Diverse Dataset, a high-quality benchmarking dataset of 2859 protein-bound ligand conformations extracted from the PDB. Differences in the performance of commercial algorithms are much smaller than those observed for free algorithms in our previous study (J. Chem. Inf. 2017, 57, 529-539). For commercial algorithms, the median minimum root-mean-square deviations measured between protein-bound ligand conformations and ensembles of a maximum of 250 conformers are between 0.46 and 0.61 Å. Commercial conformer ensemble generators are characterized by their high robustness, with at least 99% of all input molecules successfully processed and few or even no substantial geometrical errors detectable in their output conformations. The RDKit distance geometry algorithm (with minimization enabled) appears to be a good free alternative since its performance is comparable to that of the midranked commercial algorithms. Based on a statistical analysis, we elaborate on which algorithms to use and how to parametrize them for best performance in different application scenarios.

Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains.

PubMed

Teyra, Joan; Sidhu, Sachdev S; Kim, Philip M

2012-08-14

Peptide-binding domains play a critical role in regulation of cellular processes by mediating protein interactions involved in signalling. In recent years, the development of large-scale technologies has enabled exhaustive studies on the peptide recognition preferences for a number of peptide-binding domain families. These efforts have provided significant insights into the binding specificities of these modular domains. Many research groups have taken advantage of this unprecedented volume of specificity data and have developed a variety of new algorithms for the prediction of binding specificities of peptide-binding domains and for the prediction of their natural binding targets. This knowledge has also been applied to the design of synthetic peptide-binding domains in order to rewire protein-protein interaction networks. Here, we describe how these experimental technologies have impacted on our understanding of peptide-binding domain specificities and on the elucidation of their natural ligands. We discuss SH3 and PDZ domains as well characterized examples, and we explore the feasibility of expanding high-throughput experiments to other peptide-binding domains. Copyright © 2012. Published by Elsevier B.V.

Bioorthogonal Diversification of Peptides through Selective Ruthenium(II)-Catalyzed C-H Activation.

PubMed

Schischko, Alexandra; Ren, Hongjun; Kaplaneris, Nikolaos; Ackermann, Lutz

2017-02-01

Methods for the chemoselective modification of amino acids and peptides are powerful techniques in biomolecular chemistry. Among other applications, they enable the total synthesis of artificial peptides. In recent years, significant momentum has been gained by exploiting palladium-catalyzed cross-coupling for peptide modification. Despite major advances, the prefunctionalization elements on the coupling partners translate into undesired byproduct formation and lengthy synthetic operations. In sharp contrast, we herein illustrate the unprecedented use of versatile ruthenium(II)carboxylate catalysis for the step-economical late-stage diversification of α- and β-amino acids, as well as peptides, through chemo-selective C-H arylation under racemization-free reaction conditions. The ligand-accelerated C-H activation strategy proved water-tolerant and set the stage for direct fluorescence labelling as well as various modes of peptide ligation with excellent levels of positional selectivity in a bioorthogonal fashion. The synthetic utility of our approach is further demonstrated by twofold C-H arylations for the complexity-increasing assembly of artificial peptides within a multicatalytic C-H activation manifold. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Amorfrutins are potent antidiabetic dietary natural products

PubMed Central

Weidner, Christopher; de Groot, Jens C.; Prasad, Aman; Freiwald, Anja; Quedenau, Claudia; Kliem, Magdalena; Witzke, Annabell; Kodelja, Vitam; Han, Chung-Ting; Giegold, Sascha; Baumann, Matthias; Klebl, Bert; Siems, Karsten; Müller-Kuhrt, Lutz; Schürmann, Annette; Schüler, Rita; Pfeiffer, Andreas F. H.; Schroeder, Frank C.; Büssow, Konrad; Sauer, Sascha

2012-01-01

Given worldwide increases in the incidence of obesity and type 2 diabetes, new strategies for preventing and treating metabolic diseases are needed. The nuclear receptor PPARγ (peroxisome proliferator-activated receptor gamma) plays a central role in lipid and glucose metabolism; however, current PPARγ-targeting drugs are characterized by undesirable side effects. Natural products from edible biomaterial provide a structurally diverse resource to alleviate complex disorders via tailored nutritional intervention. We identified a family of natural products, the amorfrutins, from edible parts of two legumes, Glycyrrhiza foetida and Amorpha fruticosa, as structurally new and powerful antidiabetics with unprecedented effects for a dietary molecule. Amorfrutins bind to and activate PPARγ, which results in selective gene expression and physiological profiles markedly different from activation by current synthetic PPARγ drugs. In diet-induced obese and db/db mice, amorfrutin treatment strongly improves insulin resistance and other metabolic and inflammatory parameters without concomitant increase of fat storage or other unwanted side effects such as hepatoxicity. These results show that selective PPARγ-activation by diet-derived ligands may constitute a promising approach to combat metabolic disease. PMID:22509006

Self-assembly of five 8-hydroxyquinolinate-based complexes: tunable core, supramolecular structure, and photoluminescence properties.

PubMed

Yuan, Guozan; Shan, Weilong; Qiao, Xuelong; Ma, Li; Huo, Yanping

2014-07-01

Five new Zn(II) complexes, namely [Zn(3)(L)(6)] (1), [Zn(2)(Cl)(2)(L)(2) (py)(2)] (2), [Zn(2)(Br)(2) (L)(2)(py)(2)] (3), [Zn(L)(2)(py)] (4), and [Zn(2)(OAc)(2)(L)(2)(py)(2)] (5), were prepared by the solvothermal reaction of ZnX(2) (X(-) =Cl(-), Br(-), F(-), and OAc(-)) salts with a 8-hydroxyquinolinate ligand (HL) that contained a trifluorophenyl group. All of the complexes were characterized by elemental analysis, IR spectroscopy, and powder and single-crystal X-ray crystallography. The building blocks exhibited unprecedented structural diversification and their self-assembly afforded one mononuclear, three binuclear, and one trinuclear Zn(II) structures in response to different anions and solvent systems. Complexes 1-5 featured four types of supramolecular network controlled by non-covalent interactions, such as π⋅⋅⋅π-stacking, C-H⋅⋅⋅π, hydrogen-bonding, and halogen-related interactions. Investigation of their photoluminescence properties exhibited disparate emission wavelengths, lifetimes, and quantum yields in the solid state. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gravitational geons in asymptotically anti-de Sitter spacetimes

NASA Astrophysics Data System (ADS)

Martinon, Grégoire; Fodor, Gyula; Grandclément, Philippe; Forgács, Peter

2017-06-01

We report on numerical constructions of fully non-linear geons in asymptotically anti-de Sitter (AdS) spacetimes in four dimensions. Our approach is based on 3  +  1 formalism and spectral methods in a gauge combining maximal slicing and spatial harmonic coordinates. We are able to construct several families of geons seeded by different families of spherical harmonics. We can reach unprecedentedly high amplitudes, with mass of order  ∼1/2 of the AdS length, and with deviations of the order of 50% compared to third order perturbative approaches. The consistency of our results with numerical resolution is carefully checked and we give extensive precision monitoring techniques. All global quantities, such as mass and angular momentum, are computed using two independent frameworks that agree with each other at the 0.1% level. We also provide strong evidence for the existence of ‘excited’ (i.e. with one radial node) geon solutions of Einstein equations in asymptotically AdS spacetimes by constructing them numerically.

Offset-frequency locking of extended-cavity diode lasers for precision spectroscopy of water at 1.38 μm.

PubMed

Gianfrani, Livio; Castrillo, Antonio; Fasci, Eugenio; Galzerano, Gianluca; Casa, Giovanni; Laporta, Paolo

2010-10-11

We describe a continuous-wave diode laser spectrometer for water-vapour precision spectroscopy at 1.38 μm. The spectrometer is based upon the use of a simple scheme for offset-frequency locking of a pair of extended-cavity diode lasers that allows to achieve unprecedented accuracy and reproducibility levels in measuring molecular absorption. When locked to the master laser with an offset frequency of 1.5 GHz, the slave laser exhibits residual frequency fluctuations of 1 kHz over a time interval of 25 minutes, for a 1-s integration time. The slave laser could be continuously tuned up to 3 GHz, the scan showing relative deviations from linearity below the 10{-6} level. Simultaneously, a capture range of the order of 1 GHz was obtained. Quantitative spectroscopy was also demonstrated by accurately determining relevant spectroscopic parameters for the 22,1→22,0line of the H2(18)O v1+v3 band at 1384.6008 nm.

Probing short-range protein Brownian motion in the cytoplasm of living cells

PubMed Central

Di Rienzo, Carmine; Piazza, Vincenzo; Gratton, Enrico; Beltram, Fabio; Cardarelli, Francesco

2014-01-01

The translational motion of molecules in cells deviates from what is observed in dilute solutions. Theoretical models provide explanations for this effect but with predictions that drastically depend on the nanoscale organization assumed for macromolecular crowding agents. A conclusive test of the nature of the translational motion in cells is missing owing to the lack of techniques capable of probing crowding with the required temporal and spatial resolution. Here we show that fluorescence-fluctuation analysis of raster scans at variable timescales can provide this information. By using green fluorescent proteins in cells, we measure protein motion at the unprecedented timescale of 1 μs, unveiling unobstructed Brownian motion from 25 to 100 nm, and partially suppressed diffusion above 100 nm. Furthermore, experiments on model systems attribute this effect to the presence of relatively immobile structures rather than to diffusing crowding agents. We discuss the implications of these results for intracellular processes. PMID:25532887

Measurement of light and charge yield of low-energy electronic recoils in liquid xenon

NASA Astrophysics Data System (ADS)

Goetzke, L. W.; Aprile, E.; Anthony, M.; Plante, G.; Weber, M.

2017-11-01

The dependence of the light and charge yield of liquid xenon on the applied electric field and recoil energy is important for dark matter detectors using liquid xenon time projections chambers. Few measurements have been made of this field dependence at recoil energies less than 10 keV. In this paper, we present results of such measurements using a specialized detector. Recoil energies are determined via the Compton coincidence technique at four drift fields relevant for liquid xenon dark matter detectors: 0.19, 0.48, 1.02, and 2.32 kV /cm . Mean recoil energies down to 1 keV were measured with unprecedented precision. We find that the charge and light yield are anticorrelated above ˜3 keV and that the field dependence becomes negligible below ˜6 keV . However, below 3 keV, we find a charge yield significantly higher than expectation and a reconstructed energy deviating from linearity.

Ab Initio Quantum Monte Carlo Simulation of the Warm Dense Electron Gas in the Thermodynamic Limit

DOE PAGES

Dornheim, Tobias; Groth, Simon; Sjostrom, Travis; ...

2016-10-07

Here we perform ab initio quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with the linear response theory, we are able to remove finite-size errors from the potential energy over the substantial parts of the warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)]. Extensive new QMC results for up to N = 1000 electrons enable us to compute the potential energy V and the exchange-correlation free energy F xc of the macroscopic electron gas withmore » an unprecedented accuracy of | Δ V | / | V | , | Δ F xc | / | F | xc ~ 10 $-$3. Finally, a comparison of our new data to the recent parametrization of F xc by Karasiev et al. [Phys. Rev. Lett. 112, 076403 (2014)] reveals significant deviations to the latter.« less

Tests of gravity with future space-based experiments

NASA Astrophysics Data System (ADS)

Sakstein, Jeremy

2018-03-01

Future space-based tests of relativistic gravitation—laser ranging to Phobos, accelerometers in orbit, and optical networks surrounding Earth—will constrain the theory of gravity with unprecedented precision by testing the inverse-square law, the strong and weak equivalence principles, and the deflection and time delay of light by massive bodies. In this paper, we estimate the bounds that could be obtained on alternative gravity theories that use screening mechanisms to suppress deviations from general relativity in the Solar System: chameleon, symmetron, and Galileon models. We find that space-based tests of the parametrized post-Newtonian parameter γ will constrain chameleon and symmetron theories to new levels, and that tests of the inverse-square law using laser ranging to Phobos will provide the most stringent constraints on Galileon theories to date. We end by discussing the potential for constraining these theories using upcoming tests of the weak equivalence principle, and conclude that further theoretical modeling is required in order to fully utilize the data.

Millisecond coherence time in a tunable molecular electronic spin qubit [An unprecedented coherence time in a tunable molecular V(IV) electronic spin qubit

DOE PAGES

Zadrozny, Joseph M.; Niklas, Jens; Poluektov, Oleg G.; ...

2015-12-02

Here, quantum information processing (QIP) could revolutionize areas ranging from chemical modeling to cryptography. One key figure of merit for the smallest unit for QIP, the qubit, is the coherence time ( T 2), which establishes the lifetime for the qubit. Transition metal complexes offer tremendous potential as tunable qubits, yet their development is hampered by the absence of synthetic design principles to achieve a long T 2. We harnessed molecular design to create a series of qubits, (Ph 4P) 2[V(C 8S 8) 3] (1), (Ph 4P) 2[V(β-C 3S 5) 3] (2), (Ph 4P) 2[V(α-C 3S 5) 3] (3), andmore » (Ph 4P) 2[V(C 3S 4O) 3] (4), with T 2s of 1–4 μs at 80 K in protiated and deuterated environments. Crucially, through chemical tuning of nuclear spin content in the vanadium(IV) environment we realized a T 2 of ~1 ms for the species ( d 20-Ph 4P) 2[V(C 8S 8) 3] in CS 2, a value that surpasses the coordination complex record by an order of magnitude. This value even eclipses some prominent solid-state qubits. Electrochemical and continuous wave electron paramagnetic resonance (EPR) data reveal variation in the electronic influence of the ligands on the metal ion across 1–4. However, pulsed measurements indicate that the most important influence on decoherence is nuclear spins in the protiated and deuterated solvents utilized herein. Our results illuminate a path forward in synthetic design principles, which should unite CS 2 solubility with nuclear spin free ligand fields to develop a new generation of molecular qubits.« less

Electroregulated Metal-Binding with a Crown Ether Tetrathiafulvalene Derivative: Toward Electrochemically Addressed Metal Cation Sponges.

PubMed

Le Derf, Franck; Mazari, Miloud; Mercier, Nicolas; Levillain, Eric; Richomme, Pascal; Becher, Jan; Garín, Javier; Orduna, Jesus; Gorgues, Alain; Sallé, Marc

1999-12-27

A redox responsive ligand incorporating the tetrathiafulvalene unit has been synthesized. The crystal structure of the free ligand (Z)-1 (C(20)H(30)O(5)S(8), triclinic P&onemacr;, Z = 2, a = 9.087(6) Å, b = 11.637(7) Å, c = 14.370(8) Å, alpha = 65.54(3) degrees, beta = 82.32(5) degrees, gamma = 84.18(6) degrees, V = 1368 Å(3)) shows the redox-active tetrathiafulvalene core to be essentially planar, which allows observation of two reversible one-electron processes upon electrochemical oxidation. The efficiency of this system in the control of the reversible complexation/expulsion sequence of a metallic cation (i.e., Ba(2+)) has been made possible thanks to a combination of (a) an unprecedented high coordination ability among tetrathiafulvalene-based macrocycles as determined by LSI mass spectrometry (log K degrees = 3.5, NBA-matrix) as well as by solution investigations ((1)H NMR and cyclic voltammetry titration studies), which remarkably converge to similar binding constant values (i.e., log K degrees = 4.2-4.3), and (b) reversible metal cation expulsion upon electrochemical oxidation to the dicationic state. A channel-like solid-state structure is observed for the Ba(2+) complex (C(20)H(30)O(5)S(8), Ba(2+)(CF(3)SO(3))(2)(2-), (H(2)O)(2), CD(3)CN, monoclinic C2/c, Z = 8, a = 45.66(1) Å, b = 8.897(5) Å, c = 23.124(8) Å, beta = 105.54(4) degrees, V = 9050 Å(3)), which results from the segregated stacking mode of the crown ether and the redox-active tetrathiafulvalene subunits, respectively.

Network dimensionality and ligand flexibility in lanthanide terephthalate hydrates

NASA Astrophysics Data System (ADS)

Zehnder, Ralph A.; Renn, Robert A.; Pippin, Ethan; Zeller, Matthias; Wheeler, Kraig A.; Carr, Jason A.; Fontaine, Nick; McMullen, Nathan C.

2011-01-01

Various lanthanide open framework materials incorporating the terephthalate (TP) entity were prepared using hydrothermal synthesis methods at a moderate temperature of 170 °C. The compounds Nd 2(TP) 3(H 2O) 4( 1), Er 2(TP) 3(H 2O) 4( 2), Yb 2(TP) 3(H 2O) 2( 3), Yb 2(TP) 3(H 2O) 6( 4), and Yb 2(TP) 3(H 2O) 8·2H 2O ( 5), were characterized by single crystal structural analysis and FT-IR spectroscopy. While compounds 1 and 2 have been reported before on the basis of powder X-ray diffraction, the structural characterization of any ytterbium terephthalate species is unprecedented. Compounds 1- 5 crystallize in triclinic settings with space group P-1. The compounds are compared with their previously reported Er and Tb-counterparts and the reduction of the dimensionality of the resulting networks from 3D over 2D to 1D with increasing level of hydration is discussed. Compounds 1, 2, and 3 with the lowest water content assemble in three-dimensional network lattices. Compounds 4 and 5, however, form 2D layered systems and 1D rod like chains, respectively, which are held together by hydrogen bonds originating from coordinating H 2O. The crystal lattices of the 3D networks experience higher levels of tension as can be seen by increasing out-of-plane torsion with regard to the terephthalate carboxylate groups. Moreover, there seems to be a correlation between the level of strain on the aromatic ligands and the reduction of the number of carboxylate oxygen atoms that are part of the coordination polyhedra.

Targeted endothelial nanomedicine for common acute pathological conditions

PubMed Central

Shuvaev, Vladimir V.; Brenner, Jacob S.; Muzykantov, Vladimir R.

2017-01-01

Endothelium, a thin monolayer of specialized cells lining the lumen of blood vessels is the key regulatory interface between blood and tissues. Endothelial abnormalities are implicated in many diseases, including common acute conditions with high morbidity and mortality lacking therapy, in part because drugs and drug carriers have no natural endothelial affinity. Precise endothelial drug delivery may improve management of these conditions. Using ligands of molecules exposed to the bloodstream on the endothelial surface enables design of diverse targeted endothelial nanomedicine agents. Target molecules and binding epitopes must be accessible to drug carriers, carriers must be free of harmful effects, and targeting should provide desirable sub-cellular addressing of the drug cargo. The roster of current candidate target molecules for endothelial nanomedicine includes peptidases and other enzymes, cell adhesion molecules and integrins, localized in different domains of the endothelial plasmalemma and differentially distributed throughout the vasculature. Endowing carriers with an affinity to specific endothelial epitopes enables an unprecedented level of precision of control of drug delivery: binding to selected endothelial cell phenotypes, cellular addressing and duration of therapeutic effects. Features of nanocarrier design such as choice of epitope and ligand control delivery and effect of targeted endothelial nanomedicine agents. Pathological factors modulate endothelial targeting and uptake of nanocarriers. Selection of optimal binding sites and design features of nanocarriers are key controllable factors that can be iteratively engineered based on their performance from in vitro to pre-clinical in vivo experimental models. Targeted endothelial nanomedicine agents provide antioxidant, anti-inflammatory and other therapeutic effects unattainable by non-targeted counterparts in animal models of common acute severe human disease conditions. The results of animal studies provide the basis for the challenging translation endothelial nanomedicine into the clinical domain. PMID:26435455

Synthesis and first use of pyridine-2,6-diylbis(pyrazine-2-ylmethanone) in metal cluster chemistry: a {Mn(III)3Na2} complex with an ideal trigonal bipyramidal geometry.

PubMed

Giannopoulos, Dimosthenis P; Wilson-Konderka, Cody; Gagnon, Kevin J; Teat, Simon J; Escuer, Albert; Metallinos, Costa; Stamatatos, Theocharis C

2015-03-07

The successful organic synthesis of a new dipyrazole/pyridine-dicarbonyl organic molecule, namely pyridine-2,6-diylbis(pyrazine-2-ylmethanone) [(pz)CO(py)CO(pz)], followed by its employment in Mn coordination chemistry has yielded the neutral cluster compound [Mn3Na2O(N3)3(L)3] (1), where L(2-) is the (pz)C(CH2COCH3)(O(-))(py)C(CH2COCH3)(O(-))(pz) dianion. The latter group was formed in situ, presumably by the nucleophilic attack of the carbanion (-)CH2COCH3 to the carbonyl carbon atoms of (pz)CO(py)CO(pz), in the presence of Mn(n+) ions under basic conditions and in solvent Me2CO. Complex 1 possesses an almost ideal trigonal bipyramidal topology, with the two Na(I) ions occupying the apical positions and the three Mn(III) ions residing in the equatorial trigonal plane. The bridging ligation about the metal ions is provided by a μ3-O(2-) ion and six μ-OR(-) groups from the L(2-) ligand, while peripheral ligation is completed by three terminal azido groups and the pyridine N and carbonyl O atoms of L(2-). Magnetic susceptibility studies revealed the presence of predominant antiferromagnetic exchange interactions between the paramagnetic Mn(III) centres; the use of an anisotropic, equilateral Mn(III)3 triangle model allowed us to fit the magnetic data and obtain the best-fit parameters: J = -10.8 cm(-1), D = -5.3 cm(-1), and g = 1.99. The combined results demonstrate the rich chemical reactivity of carbonyl groups and the ability of poly-ketone ligands to stabilize cluster compounds with unprecedented structural motifs and interesting architectures.

Modular synthesis of amphiphilic Janus glycodendrimers and their self-assembly into glycodendrimersomes and other complex architectures with bioactivity to biomedically relevant lectins.

PubMed

Percec, Virgil; Leowanawat, Pawaret; Sun, Hao-Jan; Kulikov, Oleg; Nusbaum, Christopher D; Tran, Tam M; Bertin, Annabelle; Wilson, Daniela A; Peterca, Mihai; Zhang, Shaodong; Kamat, Neha P; Vargo, Kevin; Moock, Diana; Johnston, Eric D; Hammer, Daniel A; Pochan, Darrin J; Chen, Yingchao; Chabre, Yoann M; Shiao, Tze C; Bergeron-Brlek, Milan; André, Sabine; Roy, René; Gabius, Hans-J; Heiney, Paul A

2013-06-19

The modular synthesis of 7 libraries containing 51 self-assembling amphiphilic Janus dendrimers with the monosaccharides D-mannose and D-galactose and the disaccharide D-lactose in their hydrophilic part is reported. These unprecedented sugar-containing dendrimers are named amphiphilic Janus glycodendrimers. Their self-assembly by simple injection of THF or ethanol solution into water or buffer and by hydration was analyzed by a combination of methods including dynamic light scattering, confocal microscopy, cryogenic transmission electron microscopy, Fourier transform analysis, and micropipet-aspiration experiments to assess mechanical properties. These libraries revealed a diversity of hard and soft assemblies, including unilamellar spherical, polygonal, and tubular vesicles denoted glycodendrimersomes, aggregates of Janus glycodendrimers and rodlike micelles named glycodendrimer aggregates and glycodendrimermicelles, cubosomes denoted glycodendrimercubosomes, and solid lamellae. These assemblies are stable over time in water and in buffer, exhibit narrow molecular-weight distribution, and display dimensions that are programmable by the concentration of the solution from which they are injected. This study elaborated the molecular principles leading to single-type soft glycodendrimersomes assembled from amphiphilic Janus glycodendrimers. The multivalency of glycodendrimersomes with different sizes and their ligand bioactivity were demonstrated by selective agglutination with a diversity of sugar-binding protein receptors such as the plant lectins concanavalin A and the highly toxic mistletoe Viscum album L. agglutinin, the bacterial lectin PA-IL from Pseudomonas aeruginosa, and, of special biomedical relevance, human adhesion/growth-regulatory galectin-3 and galectin-4. These results demonstrated the candidacy of glycodendrimersomes as new mimics of biological membranes with programmable glycan ligand presentations, as supramolecular lectin blockers, vaccines, and targeted delivery devices.

Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains.

PubMed

Li, Shan; Zhang, Li; Yao, Qing; Li, Lin; Dong, Na; Rong, Jie; Gao, Wenqing; Ding, Xiaojun; Sun, Liming; Chen, Xing; Chen, She; Shao, Feng

2013-09-12

The tumour necrosis factor (TNF) family is crucial for immune homeostasis, cell death and inflammation. These cytokines are recognized by members of the TNF receptor (TNFR) family of death receptors, including TNFR1 and TNFR2, and FAS and TNF-related apoptosis-inducing ligand (TRAIL) receptors. Death receptor signalling requires death-domain-mediated homotypic/heterotypic interactions between the receptor and its downstream adaptors, including TNFR1-associated death domain protein (TRADD) and FAS-associated death domain protein (FADD). Here we discover that death domains in several proteins, including TRADD, FADD, RIPK1 and TNFR1, were directly inactivated by NleB, an enteropathogenic Escherichia coli (EPEC) type III secretion system effector known to inhibit host nuclear factor-κB (NF-κB) signalling. NleB contained an unprecedented N-acetylglucosamine (GlcNAc) transferase activity that specifically modified a conserved arginine in these death domains (Arg 235 in the TRADD death domain). NleB GlcNAcylation (the addition of GlcNAc onto a protein side chain) of death domains blocked homotypic/heterotypic death domain interactions and assembly of the oligomeric TNFR1 complex, thereby disrupting TNF signalling in EPEC-infected cells, including NF-κB signalling, apoptosis and necroptosis. Type-III-delivered NleB also blocked FAS ligand and TRAIL-induced cell death by preventing formation of a FADD-mediated death-inducing signalling complex (DISC). The arginine GlcNAc transferase activity of NleB was required for bacterial colonization in the mouse model of EPEC infection. The mechanism of action of NleB represents a new model by which bacteria counteract host defences, and also a previously unappreciated post-translational modification.

Crystal Structure of Faradaurate-279: Au279(SPh-tBu)84 Plasmonic Nanocrystal Molecules.

PubMed

Sakthivel, Naga Arjun; Theivendran, Shevanuja; Ganeshraj, Vigneshraja; Oliver, Allen G; Dass, Amala

2017-11-01

We report the discovery of an unprecedentedly large, 2.2 nm diameter, thiolate protected gold nanocrystal characterized by single crystal X-ray crystallography (sc-XRD), Au 279 (SPh-tBu) 84 named Faradaurate-279 (F-279) in honor of Michael Faraday's (1857) pioneering work on nanoparticles. F-279 nanocrystal has a core-shell structure containing a truncated octahedral core with bulk face-centered cubic-like arrangement, yet a nanomolecule with a precise number of metal atoms and thiolate ligands. The Au 279 S 84 geometry was established from a low-temperature 120 K sc-XRD study at 0.90 Å resolution. The atom counts in core-shell structure of Au 279 follows the mathematical formula for magic number shells: Au@Au 12 @Au 42 @Au 92 @Au 54 , which is further protected by a final shell of Au 48 . Au 249 core is protected by three types of staple motifs, namely: 30 bridging, 18 monomeric, and 6 dimeric staple motifs. Despite the presence of such diverse staple motifs, Au 279 S 84 structure has a chiral pseudo-D 3 symmetry. The core-shell structure can be viewed as nested, concentric polyhedra, containing a total of five forms of Archimedean solids. A comparison between the Au 279 and Au 309 cuboctahedral superatom model in shell-wise growth is illustrated. F-279 can be synthesized and isolated in high purity in milligram quantities using size exclusion chromatography, as evidenced by mass spectrometry. Electrospray ionization-mass spectrometry independently verifies the X-ray diffraction study based heavy atoms formula, Au 279 S 84 , and establishes the molecular formula with the complete ligands, namely, Au 279 (SPh-tBu) 84 . It is also the smallest gold nanocrystal to exhibit metallic behavior, with a surface plasmon resonance band around 510 nm.

Innovative Opioid Peptides and Biased Agonism: Novel Avenues for More Effective and Safer Analgesics to Treat Chronic Pain.

PubMed

Bedini, Andrea; Spampinato, Santi Mario

2017-02-15

Chronic pain is a clinically relevant and yet unsolved conditions that is poorly treated with the currently available drugs, thus highlighting the urgent need of innovative analgesics. Although opiates are not very effective in the treatment of inflammatory and neuropathic pain, developing novel opioid receptor peptide agonists, as well as modulating the opioid receptor-mediated responses in a ligand-specific fashion, may represent an innovative and promising strategy to identify more efficacious and safer antalgic drugs. In this review, novel analogues of endomorphin 1 (a mu opioid receptor selective agonist able to induce analgesia in different animal models of pain - including neuropathic pain) and dermorphin (one of the most potent opioid peptide existing in nature) will be discussed as they are emerging as a promising starting point to develop novel opioid agonists: endomorphin 1 analogues, in fact, may determine antinociception in different models of neuropathic pain with reduced side effects as compared to classic opiates as morphine; dermorphin analogues may elicit analgesia in animal models of both inflammatory and neuropathic pain and with less severe adverse effects. Furthermore, such opioid peptides may allow to explore unprecedented modalities of ligand-receptor interactions, helping to characterize biased agonism at opioid receptors: exploiting functional selectivity at opioid receptor may lead to identify innovative analgesic with improved pharmacological responses and optimized side effects. Thus, innovative opioid peptides, as those outlined in this review, are promising candidates to develop more effective opioid analgesics to be employed as medications for chronic pain states, as inflammatory or neuropathic pain. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Assessment of the best N(3-) donors in preparation of [M(N)(PNP)]-based (M=(99m)Tc-; (188)Re) target-specific radiopharmaceuticals: Comparison among succinic dihydrazide (SDH), N-methyl-S-methyl dithiocarbazate (HDTCZ) and PEGylated N-methyl-S-methyl dithiocarbazate (HO2C-PEG600-DTCZ).

PubMed

Carta, Davide; Jentschel, Christian; Thieme, Stefan; Salvarese, Nicola; Morellato, Nicolò; Refosco, Fiorenzo; Ruzza, Paolo; Bergmann, Ralf; Pietzsch, Hans-Jurgen; Bolzati, Cristina

2014-08-01

Succinic dihydrazide (SDH), N-methyl-S-methyl dithiocarbazate (HDTCZ) and PEGylated N-methyl-S-methyl dithiocarbazate (HO2C-PEG600-DTCZ) are nitrido nitrogen atom donors employed for the preparation of nitride [M(N)]-complexes (M=(99m)Tc and (188)Re). This study aims to compare the capability and the efficiency of these three N(3-) group donors, in the preparation of [M(N)PNP]-based target-specific compounds (M=(99m)Tc, (188)Re; PNP=aminodiphosphine). For this purpose, three different kit formulations (SDH kit; HO2C-PEG600-DTCZ kit; HDTCZ kit) were assembled and used in the preparation of [M(N)(cys~)(PNP3)](0/+) complexes (cys~=cysteine derivate ligands). For each formulation, the radiochemical yield (RCY) of the [M(N)(~cys)(PNP3)] compounds, was determined by HPLC. The deviation of the percentage of RCY, due to changes in concentration of the N(3-) donors and of the exchanging ligand, was determined. For (99m)Tc, data clearly show that HDTCZ is the most efficient donor of N(3-); however, SDH is the most suitable nitrido nitrogen atom donor for the preparation of [(99m)Tc(N)(PNP)]-based target-specific agents with high specific activity. When HO2C-PEG600-DTCZ or HDTCZ are used in N(3-) donation, high amounts of the exchanging ligand (10(-4)M) were required for the formation of the final complex in acceptable yield. The possibility to use microgram amounts of HDTCZ also in [(188)Re(N)] preparation (0.050mg) reduces its ability to compete in ligand exchange reactions, minimizing the quantity of chelators required to obtain the final complex in high yield. This finding can be exploit for increasing the radiolabeling efficiency in [(188)Re(N)]-radiopharmaceutical preparations compared to the previously reported HDTCZ-based procedure, notwithstanding a purification process could be necessary to improve the specific activity of the complexes. Copyright © 2014 Elsevier Inc. All rights reserved.

Theory and experimental results of transfer-NOE experiments. 1. The influence of the off rate versus cross-relaxation rates

NASA Astrophysics Data System (ADS)

Lippens, R. M.; Cerf, C.; Hallenga, K.

The theory of the transferred nuclear Overhauser effect is presented in the framework of an extended relaxation matrix representation. This matrix representation allows a coherent description of all one- and two-dimensional experiments. We present analytical solutions for the buildup of magnetization in the 2D transfer-NOE experiment, for all ratios of the off rate k to the cross-relaxation rates R involved. We show that systematic deviations in distance determination occur when the off rate becomes comparable to or smaller than the relaxation rates. Experimental results on the peptide/protein system oxytocin/neurophysin confirming this analysis are presented. The importance of residual mobility in the bound ligand, as demonstrated by the experimental data, is also discussed.

Template CoMFA Generates Single 3D-QSAR Models that, for Twelve of Twelve Biological Targets, Predict All ChEMBL-Tabulated Affinities

PubMed Central

Cramer, Richard D.

2015-01-01

The possible applicability of the new template CoMFA methodology to the prediction of unknown biological affinities was explored. For twelve selected targets, all ChEMBL binding affinities were used as training and/or prediction sets, making these 3D-QSAR models the most structurally diverse and among the largest ever. For six of the targets, X-ray crystallographic structures provided the aligned templates required as input (BACE, cdk1, chk2, carbonic anhydrase-II, factor Xa, PTP1B). For all targets including the other six (hERG, cyp3A4 binding, endocrine receptor, COX2, D2, and GABAa), six modeling protocols applied to only three familiar ligands provided six alternate sets of aligned templates. The statistical qualities of the six or seven models thus resulting for each individual target were remarkably similar. Also, perhaps unexpectedly, the standard deviations of the errors of cross-validation predictions accompanying model derivations were indistinguishable from the standard deviations of the errors of truly prospective predictions. These standard deviations of prediction ranged from 0.70 to 1.14 log units and averaged 0.89 (8x in concentration units) over the twelve targets, representing an average reduction of almost 50% in uncertainty, compared to the null hypothesis of “predicting” an unknown affinity to be the average of known affinities. These errors of prediction are similar to those from Tanimoto coefficients of fragment occurrence frequencies, the predominant approach to side effect prediction, which template CoMFA can augment by identifying additional active structural classes, by improving Tanimoto-only predictions, by yielding quantitative predictions of potency, and by providing interpretable guidance for avoiding or enhancing any specific target response. PMID:26065424

Long-term variability in the date of monsoon onset over western India

NASA Astrophysics Data System (ADS)

Adamson, George C. D.; Nash, David J.

2013-06-01

The date of onset of the southwest monsoon in western India is critical for farmers as it influences the timing of crop plantation and the duration of the summer rainy season. Identifying long-term variability in the date of monsoon onset is difficult, however, as onset dates derived from the reanalysis of instrumental rainfall data are only available for the region from 1879. This study uses documentary evidence and newly uncovered instrumental data to reconstruct annual monsoon onset dates for western India for the period 1781-1878, extending the existing record by 97 years. The mean date of monsoon onset over the Mumbai (Bombay) area during the reconstruction period was 10 June with a standard deviation of 6.9 days. This is similar to the mean and standard deviation of the date of monsoon onset derived from instrumental data for the twentieth century. The earliest identified onset date was 23 May (in 1802 and 1839) and the latest 22 June (in 1825). The longer-term perspective provided by this study suggests that the climatic regime that governs monsoon advance over western India did not change substantially from 1781 to 1955. Monsoon onset over Mumbai has occurred at a generally later date since this time. Our results indicate that this change is unprecedented during the last 230 years. Following a discussion of the results, the nature of the relationship between the date of monsoon onset and the El Niño-Southern Oscillation is discussed. This relationship is shown to have been stable since 1781.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tracy, Patrick J.; Kasper, Justin C.; Zurbuchen, Thomas H.

Observations of velocity distribution functions from the Advanced Composition Explorer/Solar Wind Ion Composition Spectrometer heavy ion composition instrument are used to calculate ratios of kinetic temperature and Coulomb collisional interactions of an unprecedented 50 ion species in the solar wind. These ions cover a mass per charge range of 1–5.5 amu/e and were collected in the time range of 1998–2011. We report the first calculation of the Coulomb thermalization rate between each of the heavy ion (A > 4 amu) species present in the solar wind along with protons (H{sup +}) and alpha particles (He{sup 2+}). From these rates, wemore » find that protons are the dominant source of Coulomb collisional thermalization for heavy ions in the solar wind and use this fact to calculate a collisional age for those heavy ion populations. The heavy ion thermal properties are well organized by this collisional age, but we find that the temperature of all heavy ions does not simply approach that of protons as Coulomb collisions become more important. We show that He{sup 2+} and C{sup 6+} follow a monotonic decay toward equal temperatures with protons with increasing collisional age, but O{sup 6+} shows a noted deviation from this monotonic decay. Furthermore, we show that the deviation from monotonic decay for O{sup 6+} occurs in solar wind of all origins, as determined by its Fe/O ratio. The observed differences in heavy ion temperature behavior point toward a local heating mechanism that favors ions depending on their charge and mass.« less

Modification of gold nanoparticle loaded on activated carbon with bis(4-methoxysalicylaldehyde)-1,2-phenylenediamine as new sorbent for enrichment of some metal ions.

PubMed

Karimipour, Gholamreza; Ghaedi, Mehrorang; Sahraei, Reza; Daneshfar, Ali; Biyareh, Mehdi Nejati

2012-01-01

In this study, a new sorbent based on the gold nanoparticle loaded in activated carbon (Au-NP-AC) was synthesized and modified by bis(4-methoxy salicylaldehyde)-1,2-phenylenediamine (BMSAPD). This sorbent, which is abbreviated as Au-NP-AC-BMSAPD, has been applied for the enrichment and preconcentration of trace amounts of Co(2+), Cu(2+), Ni(2+), Fe(2+), Pb(2+), and Zn(2+) ions in real samples. All metal ions under study were retained on the Au-NP-AC-BMSAPD sorbent by complexation of the ions with the BMSAPD ligand, providing an efficient preconcentration fashion. The retained metal ions were then eluted from the sorbent by HNO(3) and detected by flame atomic absorption spectrometry. The analytical parameters including pH, amount of ligand, and the nature of the eluent and solid phase were evaluated to obtain the optimum condition for the preconcentration factor. Following the optimum conditions, a preconcentration factor of 200 was obtained for all the metal ions under study with detection limits of 1.4-2.6 ng mL(-1). The method has been successfully applied for the extraction and determination of the ion content in the same real samples with recoveries in the range of 95-99.6% and a relative standard deviation lower than 4.0%.

T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors.

PubMed

Magis, Cedrik; Stricher, François; van der Sloot, Almer M; Serrano, Luis; Notredame, Cedric

2010-07-16

This study addresses the relation between structural and functional similarity in proteins. We introduce a novel method named tree based on root mean square deviation (T-RMSD), which uses distance RMSD (dRMSD) variations to build fine-grained structure-based classifications of proteins. The main improvement of the T-RMSD over similar methods, such as Dali, is its capacity to produce the equivalent of a bootstrap value for each cluster node. We validated our approach on two domain families studied extensively for their role in many biological and pathological pathways: the small GTPase RAS superfamily and the cysteine-rich domains (CRDs) associated with the tumor necrosis factor receptors (TNFRs) family. Our analysis showed that T-RMSD is able to automatically recover and refine existing classifications. In the case of the small GTPase ARF subfamily, T-RMSD can distinguish GTP- from GDP-bound states, while in the case of CRDs it can identify two new subgroups associated with well defined functional features (ligand binding and formation of ligand pre-assembly complex). We show how hidden Markov models (HMMs) can be built on these new groups and propose a methodology to use these models simultaneously in order to do fine-grained functional genomic annotation without known 3D structures. T-RMSD, an open source freeware incorporated in the T-Coffee package, is available online. 2010 Elsevier Ltd. All rights reserved.

Transport and retention of zinc oxide nanoparticles in porous media: effects of natural organic matter versus natural organic ligands at circumneutral pH.

PubMed

Jones, Edward H; Su, Chunming

2014-06-30

The potential toxicity of nanoparticles (NPs) has received considerable attention, but there is little knowledge relating to the fate and transport of engineered ZnO NPs in the environment. Column experiments were performed at pH 7.3-7.6 to generate effluent concentrations and retention profiles for assessing the fate and transport of ZnO NPs (PZC=9.3, nominal size 20 nm) in saturated quartz sands (256 μm) in the presence of low natural organic matter (NOM) concentrations (1 mg/L humic and fulvic acids) and millimolar natural organic ligands (NOL) levels (formic, oxalic, and citric acids). At circumneutral pHs, ZnO NPs were positively charged and immobile in sand. The presence of NOM decreased the attachment efficiency facilitating ZnO transport through sand columns. Conversely, ZnO transport in the presence of formic and oxalic acids was only slightly improved when compared to ZnO in DI water; whereas, citric acid showed no improvement. The distinct difference between NOM and NOL may have important implications with regard to ZnO transport in the subsurface environment. Experimental results suggested the presence of both favorable and unfavorable nanoparticle interactions causes significant deviations from classical colloid filtration theory (CFT). Copyright © 2014 Elsevier B.V. All rights reserved.

Structure-Activity Relationships of Small Molecule Autotaxin Inhibitors with a Discrete Binding Mode.

PubMed

Miller, Lisa M; Keune, Willem-Jan; Castagna, Diana; Young, Louise C; Duffy, Emma L; Potjewyd, Frances; Salgado-Polo, Fernando; Engel García, Paloma; Semaan, Dima; Pritchard, John M; Perrakis, Anastassis; Macdonald, Simon J F; Jamieson, Craig; Watson, Allan J B

2017-01-26

Autotaxin (ATX) is a secreted enzyme responsible for the hydrolysis of lysophosphatidylcholine (LPC) to the bioactive lysophosphatidic acid (LPA) and choline. The ATX-LPA signaling pathway is implicated in cell survival, migration, and proliferation; thus, the inhibition of ATX is a recognized therapeutic target for a number of diseases including fibrotic diseases, cancer, and inflammation, among others. Many of the developed synthetic inhibitors for ATX have resembled the lipid chemotype of the native ligand; however, a small number of inhibitors have been described that deviate from this common scaffold. Herein, we report the structure-activity relationships (SAR) of a previously reported small molecule ATX inhibitor. We show through enzyme kinetics studies that analogues of this chemotype are noncompetitive inhibitors, and by using a crystal structure with ATX we confirm the discrete binding mode.

Characterization of Semiconductor Nanocrystal Assemblies as Components of Optoelectronic Devices

NASA Astrophysics Data System (ADS)

Malfavon-Ochoa, Mario

This dissertation presents new insight into the ability of small molecule passivated NCs to achieve intimate approach distances, despite being well passivated, while developing guiding principles in the area of ligand mediated microstructure control and the resulting macroscopic optical and electronic properties that close packing of high quality NCs enables. NC ligand coverage will be characterized quantitatively through thermogravimetric analysis (TGA), and qualitatively by photoluminescence and electroluminescence, in the case of functional devices; illustrating the importance of practitioner dependent control of ligand coverage through variations in the dispersion precipitation purification procedure. A unique examination of the relative contribution of energy and charge transfer in NC LEDs will demonstrate the ability to achieve charge transfer, at a level competitive with energy transfer, to well passivated NCs at various wt% loading in a polymer matrix. The observation of potential dependent recombination zones within an active layer further suggest novel, NC surface passivation mediated control of blend microstructure during solution processing towards the development of a bi-continuous network. Next, NC self-assembly and resulting microstructure dependent optical and electronic properties will be examined through electroluminescence and high-resolution transmission electron microscopy (TEM) micrographs of functional NC/polymer bulk heterojunction LEDs. The joint characterization of NC optical properties, and self-assembly microstructure provide a deeper understanding of the significant and inseparable effects of minimal changes in NC surface passivation on structure and function, and emphasize the potential to rely on strongly passivating ligands to control physical properties and processing parameters concurrently towards higher efficiency devices via low cost processing. Finally, micro-contact printing of blazed transmission gratings, using stable dispersions of core and core/shell NCs will be shown to produce close packed assemblies of NCs forming near-wavelength luminescent superstructures separated in space. We show the dominant contribution of a two-monolayer thick sharp interface CdS shell to the diffraction efficiency, and necessarily the refractive index, of the NCs, independent of core size. Utilization of these gratings as in-coupling elements at various positions within a device architecture are also examined. These new observations were achieved by unprecedented control of NC architecture during dispersion processing, while maintaining high luminescence, made possible by optimized NC surface passivation. These studies enable the formation of new LED architectures, and new optoelectronic devices based on angle resolved, monochromatic fluorescence from diffraction gratings prepared from simple solution processing approaches. Further, the novel observation of angle amplified interfering fluorescence from these features is argued to be a result of long range radiative coupling and superradiance enabled by the monodispersity and high-quality NC surface passivation described herein.

Heavy Metal Stress and Some Mechanisms of Plant Defense Response

PubMed Central

Emamverdian, Abolghassem; Ding, Yulong; Mokhberdoran, Farzad; Xie, Yinfeng

2015-01-01

Unprecedented bioaccumulation and biomagnification of heavy metals (HMs) in the environment have become a dilemma for all living organisms including plants. HMs at toxic levels have the capability to interact with several vital cellular biomolecules such as nuclear proteins and DNA, leading to excessive augmentation of reactive oxygen species (ROS). This would inflict serious morphological, metabolic, and physiological anomalies in plants ranging from chlorosis of shoot to lipid peroxidation and protein degradation. In response, plants are equipped with a repertoire of mechanisms to counteract heavy metal (HM) toxicity. The key elements of these are chelating metals by forming phytochelatins (PCs) or metallothioneins (MTs) metal complex at the intra- and intercellular level, which is followed by the removal of HM ions from sensitive sites or vacuolar sequestration of ligand-metal complex. Nonenzymatically synthesized compounds such as proline (Pro) are able to strengthen metal-detoxification capacity of intracellular antioxidant enzymes. Another important additive component of plant defense system is symbiotic association with arbuscular mycorrhizal (AM) fungi. AM can effectively immobilize HMs and reduce their uptake by host plants via binding metal ions to hyphal cell wall and excreting several extracellular biomolecules. Additionally, AM fungi can enhance activities of antioxidant defense machinery of plants. PMID:25688377

Entropy–enthalpy transduction caused by conformational shifts can obscure the forces driving protein–ligand binding

PubMed Central

Fenley, Andrew T.; Muddana, Hari S.; Gilson, Michael K.

2012-01-01

Molecular dynamics simulations of unprecedented duration now can provide new insights into biomolecular mechanisms. Analysis of a 1-ms molecular dynamics simulation of the small protein bovine pancreatic trypsin inhibitor reveals that its main conformations have different thermodynamic profiles and that perturbation of a single geometric variable, such as a torsion angle or interresidue distance, can select for occupancy of one or another conformational state. These results establish the basis for a mechanism that we term entropy–enthalpy transduction (EET), in which the thermodynamic character of a local perturbation, such as enthalpic binding of a small molecule, is camouflaged by the thermodynamics of a global conformational change induced by the perturbation, such as a switch into a high-entropy conformational state. It is noted that EET could occur in many systems, making measured entropies and enthalpies of folding and binding unreliable indicators of actual thermodynamic driving forces. The same mechanism might also account for the high experimental variance of measured enthalpies and entropies relative to free energies in some calorimetric studies. Finally, EET may be the physical mechanism underlying many cases of entropy–enthalpy compensation. PMID:23150595

Solvent-like ligand-coated ultrasmall cadmium selenide nanocrystals: strong electronic coupling in a self-organized assembly.

PubMed

Lawrence, Katie N; Johnson, Merrell A; Dolai, Sukanta; Kumbhar, Amar; Sardar, Rajesh

2015-07-21

Strong inter-nanocrystal electronic coupling is a prerequisite for delocalization of exciton wave functions and high conductivity. We report 170 meV electronic coupling energy of short chain poly(ethylene glycol) thiolate-coated ultrasmall (<2.5 nm in diameter) CdSe semiconductor nanocrystals (SNCs) in solution. Cryo-transmission electron microscopy analysis showed the formation of a pearl-necklace assembly of nanocrystals in solution with regular inter-nanocrystal spacing. The electronic coupling was studied as a function of CdSe nanocrystal size where the smallest nanocrystals exhibited the largest coupling energy. The electronic coupling in spin-cast thin-film (<200 nm in thickness) of poly(ethylene glycol) thiolate-coated CdSe SNCs was studied as a function of annealing temperature, where an unprecedentedly large, ∼400 meV coupling energy was observed for 1.6 nm diameter SNCs, which were coated with a thin layer of poly(ethylene glycol) thiolates. Small-angle X-ray scattering measurements showed that CdSe SNCs maintained an order array inside the films. The strong electronic coupling of SNCs in a self-organized film could facilitate the large-scale production of highly efficient electronic materials for advanced optoelectronic device application.

Cp[prime]M(NO)R[sub 2]: 16-electron piano-stool molecules of molybdenum and tungsten

DOE Office of Scientific and Technical Information (OSTI.GOV)

Legzdins, P.; Veltheer, J.E.

1993-02-01

A long-term goal of this research program is the development of organometallic nitrosyl complexes as specific reactants or selective catalysts for organic or organometallic transformations of practical significance. To attain this goal specifically with Cp[prime]M(NO)R[sub 2] system the authors developed new methods for their synthesis, established their characteristic physical and chemical properties, and are currently endeavoring to exploit those properties which are unique to the complexes. During our investigations, the authors have discovered that the Cp[prime]M(NO)R[sub 2] complexes react with a variety of small molecules, often in an unprecedented manner. The authors have also established several unique transformations that aremore » not exhibited by all members of this group of complexes. Indeed, the authors found that the chemical properties of these systems are often dependent on the metal, the nature of the R groups, and the type of Cp[prime] ligand. In this Account the authors summarize the synthesis, characterization, comparative reactivity, and distinctive chemical properties of the 16-electron Cp[prime]M(NO)R[sub 2] complexes known to date. 35 refs., 7 figs.« less

Direct Profiling the Post-Translational Modification Codes of a Single Protein Immobilized on a Surface Using Cu-free Click Chemistry.

PubMed

Kim, Kyung Lock; Park, Kyeng Min; Murray, James; Kim, Kimoon; Ryu, Sung Ho

2018-05-23

Combinatorial post-translational modifications (PTMs), which can serve as dynamic "molecular barcodes", have been proposed to regulate distinct protein functions. However, studies of combinatorial PTMs on single protein molecules have been hindered by a lack of suitable analytical methods. Here, we describe erasable single-molecule blotting (eSiMBlot) for combinatorial PTM profiling. This assay is performed in a highly multiplexed manner and leverages the benefits of covalent protein immobilization, cyclic probing with different antibodies, and single molecule fluorescence imaging. Especially, facile and efficient covalent immobilization on a surface using Cu-free click chemistry permits multiple rounds (>10) of antibody erasing/reprobing without loss of antigenicity. Moreover, cumulative detection of coregistered multiple data sets for immobilized single-epitope molecules, such as HA peptide, can be used to increase the antibody detection rate. Finally, eSiMBlot enables direct visualization and quantitative profiling of combinatorial PTM codes at the single-molecule level, as we demonstrate by revealing the novel phospho-codes of ligand-induced epidermal growth factor receptor. Thus, eSiMBlot provides an unprecedentedly simple, rapid, and versatile platform for analyzing the vast number of combinatorial PTMs in biological pathways.

Restoring Natural Killer Cell Immunity against Multiple Myeloma in the Era of New Drugs

PubMed Central

Pittari, Gianfranco; Vago, Luca; Festuccia, Moreno; Bonini, Chiara; Mudawi, Deena; Giaccone, Luisa; Bruno, Benedetto

2017-01-01

Transformed plasma cells in multiple myeloma (MM) are susceptible to natural killer (NK) cell-mediated killing via engagement of tumor ligands for NK activating receptors or “missing-self” recognition. Similar to other cancers, MM targets may elude NK cell immunosurveillance by reprogramming tumor microenvironment and editing cell surface antigen repertoire. Along disease continuum, these effects collectively result in a progressive decline of NK cell immunity, a phenomenon increasingly recognized as a critical determinant of MM progression. In recent years, unprecedented efforts in drug development and experimental research have brought about emergence of novel therapeutic interventions with the potential to override MM-induced NK cell immunosuppression. These NK-cell enhancing treatment strategies may be identified in two major groups: (1) immunomodulatory biologics and small molecules, namely, immune checkpoint inhibitors, therapeutic antibodies, lenalidomide, and indoleamine 2,3-dioxygenase inhibitors and (2) NK cell therapy, namely, adoptive transfer of unmanipulated and chimeric antigen receptor-engineered NK cells. Here, we summarize the mechanisms responsible for NK cell functional suppression in the context of cancer and, specifically, myeloma. Subsequently, contemporary strategies potentially able to reverse NK dysfunction in MM are discussed. PMID:29163516

Direct Profiling the Post-Translational Modification Codes of a Single Protein Immobilized on a Surface Using Cu-free Click Chemistry

PubMed Central

2018-01-01

Combinatorial post-translational modifications (PTMs), which can serve as dynamic “molecular barcodes”, have been proposed to regulate distinct protein functions. However, studies of combinatorial PTMs on single protein molecules have been hindered by a lack of suitable analytical methods. Here, we describe erasable single-molecule blotting (eSiMBlot) for combinatorial PTM profiling. This assay is performed in a highly multiplexed manner and leverages the benefits of covalent protein immobilization, cyclic probing with different antibodies, and single molecule fluorescence imaging. Especially, facile and efficient covalent immobilization on a surface using Cu-free click chemistry permits multiple rounds (>10) of antibody erasing/reprobing without loss of antigenicity. Moreover, cumulative detection of coregistered multiple data sets for immobilized single-epitope molecules, such as HA peptide, can be used to increase the antibody detection rate. Finally, eSiMBlot enables direct visualization and quantitative profiling of combinatorial PTM codes at the single-molecule level, as we demonstrate by revealing the novel phospho-codes of ligand-induced epidermal growth factor receptor. Thus, eSiMBlot provides an unprecedentedly simple, rapid, and versatile platform for analyzing the vast number of combinatorial PTMs in biological pathways.

Probing the structure of Leishmania donovani chagasi DHFR-TS: comparative protein modeling and protein-ligand interaction studies.

PubMed

Maganti, Lakshmi; Manoharan, Prabu; Ghoshal, Nanda

2010-09-01

Dihydrofolate reductase (DHFR) has been used successfully as a drug target in the area of anti-bacterial, anti-cancer and anti-malarial therapy. It also acts as a drug target for Leishmaniasis. Inhibition of DHFR leads to cell death through lack of thymine (nucleotide metabolism). Although the crystal structures of Leishmania major and Trypanosoma cruzi DHFR-thymidylate synthase (TS) have been resolved, to date there is no three-dimensional (3D)-structural information on DHFR-TS of Leishmania donovani chagasi, which causes visceral leishmaniasis. Our aim in this study was to model the 3D structure of L. donovani chagasi DHFR-TS, and to investigate the structural requirements for its inhibition. In this paper we describe a highly refined homology model of L. donovani chagasi DHFR-TS based on available crystallographic structures by using the Homology module of Insight II. Structural refinement and minimization of the generated L. donovani chagasi DHFR-TS model employed the Discover 3 module of Insight II and molecular dynamic simulations. The model was further validated through use of the PROCHECK, Verify_3D, PROSA, PSQS and ERRAT programs, which confirm that the model is reliable. Superimposition of the model structure with the templates L. major A chain, L. major B chain And T. cruzi A chain showed root mean square deviations of 0.69 A, 0.71 A and 1.11 A, respectively. Docking analysis of the L. donovani chagasi DHFR-TS model with methotrexate enabled us to identify specific residues, viz. Val156, Val30, Lys95, Lys75 and Arg97, within the L. donovani chagasi DHFR-TS binding pocket, that play an important role in ligand or substrate binding. Docking studies clearly indicated that these five residues are important determinants for binding as they have strong hydrogen bonding interactions with the ligand.

Mooring Measurements of the Abyssal Circulations in the Western Pacific Ocean

NASA Astrophysics Data System (ADS)

Wang, J.; Wang, F.

2016-12-01

A scientific observing network in the western tropical Pacific has initially been established by the Institute of Oceanology, Chinese Academy of Sciences (IOCAS). Using fifteen moorings that gives unprecedented measurements in the intermediate and abyssal layers, we present multi-timescale variations of the deep ocean circulations prior to and during 2015 El Niño event. The deep ocean velocities increase equatorward with high standard deviation and nearly zero mean. The deep ocean currents mainly flow in meridional direction in the central Philippine Basin, and are dominated by a series of alternating westward and eastward zonal jets in the Caroline Basin. The currents in the deep channel connecting the East and West Mariana Basins mainly flow southeastward. Seasonal variation is only present in the deep jets in the Caroline Basin, associating with vertical propagating annual Rossby wave. The high-frequency flow bands are dominated by diurnal, and semi-diurnal tidal currents, and near-inertial currents. The rough topography has a strong influence on the abyssal circulations, including the intensifications in velocity and internal tidal energy, and the formation of upwelling flow.

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids

PubMed Central

Sales, Mark; Plecs, Joseph J.; Holton, James M.; Alber, Tom

2007-01-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Å resolution using a designed metal binding site to coordinate a single Yb2+ ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Å. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures. PMID:17766380

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.

PubMed

Sales, Mark; Plecs, Joseph J; Holton, James M; Alber, Tom

2007-10-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Angstrom resolution using a designed metal binding site to coordinate a single Yb(2+) ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Angstrom. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures.

Possibility to realize spin-orbit-induced correlated physics in iridium fluorides

NASA Astrophysics Data System (ADS)

Rossi, M.; Retegan, M.; Giacobbe, C.; Fumagalli, R.; Efimenko, A.; Kulka, T.; Wohlfeld, K.; Gubanov, A. I.; Moretti Sala, M.

2017-06-01

Recent theoretical predictions of "unprecedented proximity" of the electronic ground state of iridium fluorides to the SU(2) symmetric jeff=1 /2 limit, relevant for superconductivity in iridates, motivated us to investigate their crystal and electronic structure. To this aim, we performed high-resolution x-ray powder diffraction, Ir L3-edge resonant inelastic x-ray scattering, and quantum chemical calculations on Rb2[IrF6] and other iridium fluorides. Our results are consistent with the Mott insulating scenario predicted by Birol and Haule [Phys. Rev. Lett. 114, 096403 (2015), 10.1103/PhysRevLett.114.096403], but we observe a sizable deviation of the jeff=1 /2 state from the SU(2) symmetric limit. Interactions beyond the first coordination shell of iridium are negligible, hence the iridium fluorides do not show any magnetic ordering down to at least 20 K. A larger spin-orbit coupling in iridium fluorides compared to oxides is ascribed to a reduction of the degree of covalency, with consequences on the possibility to realize spin-orbit-induced strongly correlated physics in iridium fluorides.

A deeper look at the GD1 stream: density variations and wiggles

NASA Astrophysics Data System (ADS)

de Boer, T. J. L.; Belokurov, V.; Koposov, S. E.; Ferrarese, L.; Erkal, D.; Côté, P.; Navarro, J. F.

2018-06-01

Using deep photometric data from Canada-France-Hawaii Telescope/Megacam, we study the morphology and density of the GD-1 stream, one of the longest and coldest stellar streams in the Milky Way. Our deep data recovers the lower main sequence of the stream with unprecedented quality, clearly separating it from Milky Way foreground and background stars. An analysis of the distance to different parts of the stream shows that GD-1 lies at a heliocentric distance between 8 and 10 kpc, with only a shallow gradient across 45° on the sky. Matched filter maps of the stream density show clear density variations, such as deviations from a single orbital track and tentative evidence for stream fanning. We also detect a clear underdensity in the middle of the stream track at φ1 = -45° surrounded by overdense stream segments on either side. This location is a promising candidate for the elusive missing progenitor of the GD-1 stream. We conclude that the GD-1 stream has clearly been disturbed by interactions with the Milky Way disc or other subhaloes.

Structural and spectroscopic studies of a rare non-oxido V(v) complex crystallized from aqueous solution† †Electronic supplementary information (ESI) available: Tables containing crystallographic data and structure refinements for Na[V(L)2]·2H2O(cr) (CCDC 1413557) (Table S1) and Na[VO2(HL)](cr) (CCDC 1418830) (Table S2), concentrations of the solution samples for NMR (Table S3), 13C NMR spectra of V(v)/glutaroimide-dioxime complexes in H2 17O (Fig. S1), ESI-MS spectra of V(v)/glutaroimide-dioxime complexes in 17O-enriched H2O diluted and sprayed in methanol (Fig. S2), and EPR spectra of Na[V(L)2]·2H2O(s) at 4 K and 300 K (Fig. S3). CCDC 1413557–1418830. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc03958d Click here for additional data file. Click here for additional data file.

PubMed Central

Leggett, C. J.; Parker, B. F.; Zhang, Z.; Dau, P. D.; Lukens, W. W.; Peterson, S. M.; Cardenas, A. J. P.; Warner, M. G.; Gibson, J. K.; Arnold, J.

2016-01-01

A non-oxido V(v) complex with glutaroimide-dioxime (H3L), a ligand for recovering uranium from seawater, was synthesized from aqueous solution as Na[V(L)2]·2H2O, and the structure determined by X-ray diffraction. It is the first non-oxido V(v) complex that has been directly synthesized in and crystallized from aqueous solution. The distorted octahedral structure contains two fully deprotonated ligands (L3–) coordinating to V5+, each in a tridentate mode via the imide N (R V–N = 1.96 Å) and oxime O atoms (R V–O = 1.87–1.90 Å). Using 17O-labelled vanadate as the starting material, concurrent 17O/51V/1H/13C NMR, in conjunction with ESI-MS, unprecedentedly demonstrated the stepwise displacement of the oxido V 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 O bonds by glutaroimide-dioxime and verified the existence of the “bare” V5+/glutaroimide-dioxime complex, [V(L)2]–, in aqueous solution. In addition, the crystal structure of an intermediate 1 : 1 V(v)/glutaroimide-dioxime complex, [VO2(HL)]–, in which the oxido bonds of vanadate are only partially displaced, corroborates the observations by NMR and ESI-MS. Results from this work provide important insights into the strong sorption of vanadium on poly(amidoxime) sorbents in the recovery of uranium from seawater. Also, because vanadium plays important roles in biological systems, the syntheses of the oxido and non-oxido V5+ complexes and the unprecedented demonstration of the displacement of the oxido VO bonds help with the on-going efforts to develop new vanadium compounds that could be of importance in biological applications. PMID:28660055

TLR9-based immunotherapy for the treatment of allergic diseases.

PubMed

Farrokhi, Shokrollah; Abbasirad, Narjes; Movahed, Ali; Khazaei, Hossein Ali; Pishjoo, Masoud; Rezaei, Nima

2017-03-01

Toll-like receptors (TLRs), a family of pattern recognition receptors expressed on many cell types of innate immunity, recognize the pathogen-associated molecular patterns of microbes. The hygiene hypothesis suggests that a reduced microbial exposure in early childhood increases the susceptibility to allergic diseases due to deviation in development of the immune system. TLRs are key roles in the right and healthy direction of adaptive immunity with the induction of T-helper 2 toward Th1 immune responses and regulatory T cells. TLR ligand CpG-ODN-based immunomodulation is independent of allergen and it mainly affects innate immune system. While, CpG-oligodeoxynucleotide-based vaccination is allergen specific and induces adaptive immune system. The use of agonists of TLR9 in two distinct strategies of immunotherapy, immunomodulation and vaccination, could be presented as the curative method for the treatment of allergic diseases.

A stable silicon(0) compound with a Si=Si double bond.

PubMed

Wang, Yuzhong; Xie, Yaoming; Wei, Pingrong; King, R Bruce; Schaefer, Henry F; von R Schleyer, Paul; Robinson, Gregory H

2008-08-22

Dative, or nonoxidative, ligand coordination is common in transition metal complexes; however, this bonding motif is rare in compounds of main group elements in the formal oxidation state of zero. Here, we report that the potassium graphite reduction of the neutral hypervalent silicon-carbene complex L:SiCl4 {where L: is:C[N(2,6-Pri2-C6H3)CH]2 and Pri is isopropyl} produces L:(Cl)Si-Si(Cl):L, a carbene-stabilized bis-silylene, and L:Si=Si:L, a carbene-stabilized diatomic silicon molecule with the Si atoms in the formal oxidation state of zero. The Si-Si bond distance of 2.2294 +/- 0.0011 (standard deviation) angstroms in L:Si=Si:L is consistent with a Si=Si double bond. Complementary computational studies confirm the nature of the bonding in L:(Cl)Si-Si(Cl):L and L:Si=Si:L.

Novel pyrrolopyridinone derivatives as anticancer inhibitors towards Cdc7: QSAR studies based on dockings by solvation score approach.

PubMed

Wu, Xiangxiang; Zeng, Huahui; Zhu, Xin; Ma, Qiujuan; Hou, Yimin; Wu, Xuefen

2013-11-20

A series of pyrrolopyridinone derivatives as specific inhibitors towards the cell division cycle 7 (Cdc7) was taken into account, and the efficacy of these compounds was analyzed by QSAR and docking approaches to gain deeper insights into the interaction mechanism and ligands selectivity for Cdc7. By regression analysis the prediction models based on Grid score and Zou-GB/SA score were found, respectively with good quality of fits (r(2)=0.748, 0.951; r(cv)(2)=0.712, 0.839). The accuracy of the models was validated by test set and the deviation of the predicted values in validation set using Zou-GB/SA score was smaller than that using Grid score, suggesting that the model based on Zou-GB/SA score provides a more effective method for predicting potencies of Cdc7 inhibitors. Copyright © 2013 Elsevier B.V. All rights reserved.

Prediction of heat capacities of solid inorganic salts from group contributions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mostafa, A.T.M.G.; Eakman, J.M.; Yarbro, S.L.

1997-01-01

A group contribution technique is proposed to predict the coefficients in the heat capacity correlation, C{sub p} = a + bT + c/T{sup 2} + dT{sup 2}, for solid inorganic salts. The results from this work are compared with fits to experimental data from the literature. It is shown to give good predictions for both simple and complex solid inorganic salts. Literature heat capacities for a large number (664) of solid inorganic salts covering a broad range of cations (129), anions (17) and ligands (2) have been used in regressions to obtain group contributions for the parameters in the heatmore » capacity temperature function. A mean error of 3.18% is found when predicted values are compared with literature values for heat capacity at 298{degrees} K. Estimates of the error standard deviation from the regression for each additivity constant are also determined.« less

Bis(O-n-butyl dithio­carbonato-κ2 S,S′)bis­(pyridine-κN)manganese(II)

PubMed Central

Alam, Naveed; Ehsan, Muhammad Ali; Zeller, Matthias; Mazhar, Muhammad; Arifin, Zainudin

2011-01-01

The structure of the title manganese complex, [Mn(C5H9OS2)2(C5H5N)2] or [Mn(S2CO-n-Bu)2(C5H5N)2], consists of discrete monomeric entities with Mn2+ ions located on centres of inversion. The metal atom is coordinated by a six-coordinate trans-N2S4 donor set with the pyridyl N atoms located in the apical positions. The observed slight deviations from octa­hedral geometry are caused by the bite angle of the bidentate κ2-S2CO-n-Bu ligands [69.48 (1)°]. The O(CH2)3(CH3) chains of the O-n-butyl dithio­carbonate units are disordered over two sets of sites with an occupancy ratio of 0.589 (2):0.411 (2). PMID:22090847

Bis(O-n-butyl dithio-carbonato-κS,S')bis-(pyridine-κN)manganese(II).

PubMed

Alam, Naveed; Ehsan, Muhammad Ali; Zeller, Matthias; Mazhar, Muhammad; Arifin, Zainudin

2011-08-01

The structure of the title manganese complex, [Mn(C(5)H(9)OS(2))(2)(C(5)H(5)N)(2)] or [Mn(S(2)CO-n-Bu)(2)(C(5)H(5)N)(2)], consists of discrete monomeric entities with Mn(2+) ions located on centres of inversion. The metal atom is coordinated by a six-coordinate trans-N(2)S(4) donor set with the pyridyl N atoms located in the apical positions. The observed slight deviations from octa-hedral geometry are caused by the bite angle of the bidentate κ(2)-S(2)CO-n-Bu ligands [69.48 (1)°]. The O(CH(2))(3)(CH(3)) chains of the O-n-butyl dithio-carbonate units are disordered over two sets of sites with an occupancy ratio of 0.589 (2):0.411 (2).

Positive Self-Perceptions of Aging and Lower Rate of Overnight Hospitalization in the US Population Over Age 50.

PubMed

Sun, Jennifer K; Kim, Eric S; Smith, Jacqui

2017-01-01

The aging of the baby boomer generation has led to an unprecedented rise in the number of US adults reaching old age, prompting an urgent call for innovative and cost-effective ways to address the increasing health care needs of the aging population. Studying the role of psychosocial factors on health care use could offer insight into how to minimize hospitalizations among older adults. We use prospective data from a subsample of 4735 participants (mean [standard deviation] age = 69 [8.79] years, 61% women) from the Health and Retirement Study, a nationally representative study of US adults over age 50, to examine the association between self-perceptions of aging (SPA) and self-reported overnight hospitalizations after adjusting for a comprehensive list of sociodemographic, health-related, and behavioral factors. Over the 4-year follow-up period, there were a total of 5196 overnight hospitalizations, and 44% of the sample reported being hospitalized overnight at least once. After adjusting for sociodemographic factors, each standard deviation increase in positive SPA was associated with a lower rate of overnight hospitalization (incidence rate ratio = 0.75; 95% confidence interval = 0.71-0.80, p < .001). After dividing respondents into quartiles of SPA, we observed a dose-response relationship with individuals in higher quartiles showing increasingly lower rates of overnight hospitalization. Positive self-perceptions of aging are associated with a lower rate of hospitalization among older adults over a 4-year period. Future research should examine the factors that contribute to older adults' SPA and explore the pathways through which attitudes toward aging influence the use of health care resources.

Characterizing the temporal variability of L-band backscatter using dense UAVSAR time-series in preparation for the NISAR mission

NASA Astrophysics Data System (ADS)

Lavalle, M.; Lee, A.; Shiroma, G. X. H.; Rosen, P. A.

2017-12-01

The NASA-ISRO SAR (NISAR) mission will deliver unprecedented global maps of L-band HH/HV backscatter every 12 days with resolution ranging from a few to tens of meters in support of ecosystem, solid Earth and cryosphere science and applications. Understanding and modeling the temporal variability of L-band backscatter over temporal scales of years, months and days is critical for developing retrieval algorithms that can robustly extract the biophysical variables of interest (e.g., forest biomass, soil moisture, etc.) from NISAR time series. In this talk, we will focus on the 5-year time series of 60 JPL/UAVSAR polarimetric images collected near the Sacramento Delta to characterize the inter-annual, seasonal and short-scale variability of the L-band polarimetric backscatter for a broad range of land cover types. Our preliminary analysis reveals that backscatter from man-made structures is very stable over time, whereas backscatter from bare soil and herbaceous vegetation fluctuates over time with standard deviation of 2.3 dB. Land-cover classes with larger biomass such as trees and tall vegetation show about 1.5 dB standard deviation in temporal backscatter variability. Closer examination of high-spatial resolution UAVSAR imagery reveal also that vegetation structure, speckle noise and horizontal forest heterogeneity in the Sacramento Delta area can significantly affect the point-wise backscatter value. In our talk, we will illustrate the long UAVSAR time series, describe our data analysis strategy, show the results of polarimetric variability for different land cover classes and number of looks, and discuss the implications for the development of NISAR L2/L3 retrieval algorithms of ecosystem science.

A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain.

PubMed

Panel, Nicolas; Sun, Young Joo; Fuentes, Ernesto J; Simonson, Thomas

2017-01-01

PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB) continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or "PB/LIE" free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α 2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo . The overall performance of the model should allow its use in the design of new PDZ ligands in the future.

A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain

PubMed Central

Panel, Nicolas; Sun, Young Joo; Fuentes, Ernesto J.; Simonson, Thomas

2017-01-01

PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB) continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or “PB/LIE” free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo. The overall performance of the model should allow its use in the design of new PDZ ligands in the future. PMID:29018806

In silico approaches and proportional odds model towards identifying selective ADAM17 inhibitors from anti-inflammatory natural molecules.

PubMed

Borah, Pallab Kumar; Chakraborty, Sourav; Jha, Anupam N; Rajkhowa, Sanchaita; Duary, Raj Kumar

2016-11-01

ADAM metallopeptidase domain 17 (ADAM17) is an attractive target for the development of new anti-inflammatory drugs. We aimed to identify selective inhibitors of ADAM17 against matrix metalloproteinase enzymes (MMP-1, MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-13, and MMP-16) which have substantial structural similarity. Target proteins were docked with 29 anti-inflammatory natural molecule ligands and a known selective inhibitor IK682. The ligands were screened based on Lipinski rules, interaction with the ADAM17 active site cavity, and then ranked using the proportional odds model multinomial logistic regression. Silymarin was the most selective inhibitor of ADAM17 exhibiting H-bonding with Glu 406, Gly 349, Glu 398, Asn 447, Tyr 433, and Lys 432. Molecular dynamics simulations were carried out for 10ns. The root mean square deviation (RMSD), root mean squared fluctuations (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and H-bonding indicated the induced metastability. A comparison of the principal component analysis revealed that the silymarin complex also explored lesser region compared to IK682 complex. A control study on ADAM17 protein (2OI0) is included. These observations present silymarin (widely present in plants such as milk thistle (Silybum maianum), wild artichokes (Cynara cardunculus), turmeric (Curcuma longa) roots, coriander (Coriandrum sativum) seeds, etc.) as a promising natural template for development of ADAM17 selective drugs. Copyright © 2016 Elsevier Inc. All rights reserved.

Identification of Novel Compounds against an R294K Substitution of Influenza A (H7N9) Virus Using Ensemble Based Drug Virtual Screening

PubMed Central

Tran, Nhut; Van, Thanh; Nguyen, Hieu; Le, Ly

2015-01-01

Influenza virus H7N9 foremost emerged in China in 2013 and killed hundreds of people in Asia since they possessed all mutations that enable them to resist to all existing influenza drugs, resulting in high mortality to human. In the effort to identify novel inhibitors combat resistant strains of influenza virus H7N9; we performed virtual screening targeting the Neuraminidase (NA) protein against natural compounds of traditional Chinese medicine database (TCM) and ZINC natural products. Compounds expressed high binding affinity to the target protein was then evaluated for molecular properties to determine drug-like molecules. 4 compounds showed their binding energy less than -11Kcal/mol were selected for molecular dynamics (MD) simulation to capture intermolecular interactions of ligand-protein complexes. The molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method was utilized to estimate binding free energy of the complex. In term of stability, NA-7181 (IUPAC namely {9-Hydroxy-10-[3-(trifluoromrthyl) cyclohexyl]-4.8-diazatricyclo [6.4.0.02,6]dodec-4-yl}(perhydro-1H-inden-5-yl)formaldehyde) achieved stable conformation after 20ns and 27ns for ligand and protein root mean square deviation, respectively. In term of binding free energy, 7181 gave the negative value of -30.031 (KJ/mol) indicating the compound obtained a favourable state in the active site of the protein. PMID:25589893

In Silico Molecular Modeling and Docking Studies on Novel Mutants (E229V, H225P and D230C) of the Nucleotide-Binding Domain of Homo sapiens Hsp70.

PubMed

Elengoe, Asita; Hamdan, Salehhuddin

2017-12-01

In this study, we explored the possibility of determining the synergistic interactions between nucleotide-binding domain (NBD) of Homo sapiens heat-shock 70 kDa protein (Hsp70) and E1A 32 kDa of adenovirus serotype 5 motif (PNLVP) in the efficiency of killing of tumor cells in cancer treatment. At present, the protein interaction between NBD and PNLVP motif is still unknown, but believed to enhance the rate of virus replication in tumor cells. Three mutant models (E229V, H225P and D230C) were built and simulated, and their interactions with PNLVP motif were studied. The PNLVP motif showed the binding energy and intermolecular energy values with the novel E229V mutant at -7.32 and -11.2 kcal/mol. The E229V mutant had the highest number of hydrogen bonds (7). Based on the root mean square deviation, root mean square fluctuation, hydrogen bonds, salt bridge, secondary structure, surface-accessible solvent area, potential energy and distance matrices analyses, it was proved that the E229V had the strongest and most stable interaction with the PNLVP motif among all the four protein-ligand complex structures. The knowledge of this protein-ligand complex model would help in designing Hsp70 structure-based drug for cancer therapy.

Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: protein-ligand interactions in the light of the alanine scanning and free energy decomposition methods.

PubMed

Saíz-Urra, Liane; Cabrera, Miguel Angel; Froeyen, Matheus

2011-02-01

Currently, bacterial diseases cause a death toll around 2 million people a year encouraging the search for new antimicrobial agents. DNA gyrase is a well-established antibacterial target consisting of two subunits, GyrA and GyrB, in a heterodimer A(2)B(2). GyrA is involved in DNA breakage and reunion and GyrB catalyzes the hydrolysis of ATP. The GyrB subunit from Escherichia coli has been investigated, namely the ATP binding pocket both considering the protein without ligands and bound with the inhibitors clorobiocin, novobiocin and 5'-adenylyl-β-γ-imidodiphosphate. The stability of the systems was studied by molecular dynamics simulation with the further analysis of the time dependent root-mean-square coordinate deviation (RMSD) from the initial structure, and temperature factors. Moreover, exploration of the conformational space of the systems during the MD simulation was carried out by a clustering data mining technique using the average-linkage algorithm. Recognizing the key residues in the binding site of the enzyme that are involved in the binding mode with the aforementioned inhibitors was investigated by using two techniques: free energy decomposition and computational alanine scanning. The results from these simulations highlight the important residues in the ATP binding site and can be useful in the design process of potential new inhibitors. Copyright © 2010 Elsevier Inc. All rights reserved.

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.

PubMed

Godschalk, Frithjof; Genheden, Samuel; Söderhjelm, Pär; Ryde, Ulf

2013-05-28

Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) is a popular method to calculate the free energy of the binding of ligands to proteins. It involves molecular dynamics (MD) simulations with an explicit solvent of the protein-ligand complex to give a set of snapshots for which energies are calculated with an implicit solvent. This change in the solvation method (explicit → implicit) would strictly require that the energies are reweighted with the implicit-solvent energies, which is normally not done. In this paper we calculate MM/GBSA energies with two generalised Born models for snapshots generated by the same methods or by explicit-solvent simulations for five synthetic N-acetyllactosamine derivatives binding to galectin-3. We show that the resulting energies are very different both in absolute and relative terms, showing that the change in the solvent model is far from innocent and that standard MM/GBSA is not a consistent method. The ensembles generated with the various solvent models are quite different with root-mean-square deviations of 1.2-1.4 Å. The ensembles can be converted to each other by performing short MD simulations with the new method, but the convergence is slow, showing mean absolute differences in the calculated energies of 6-7 kJ mol(-1) after 2 ps simulations. Minimisations show even slower convergence and there are strong indications that the energies obtained from minimised structures are different from those obtained by MD.

A Macrocyclic Chelator That Selectively Binds Ln 4+ over Ln 3+ by a Factor of 10 29

DOE PAGES

Pham, Tiffany A.; Altman, Alison B.; Stieber, S. Chantal E.; ...

2016-06-24

A tetravalent cerium macrocyclic complex (CeLK 4) was prepared with an octadentate terephthalamide ligand comprised of hard catecholate donors and characterized in the solution state by spectrophotometric titrations and electrochemistry and in the crystal by X-ray diffraction. The solution-state studies showed that L exhibits a remarkably high affinity toward Ce 4+, with log β 110 = 61(2) and ΔG = -348 kJ/mol, compared with log β 110 = 32.02(2) for the analogous Pr 3+ complex. In addition, L exhibits an unusual preference for forming CeL 4- relative to formation of the analogous actinide complex, ThL 4- , which has βmore » 110 = 53.7(5). The extreme stabilization of tetravalent cerium relative to its trivalent state is also evidenced by the shift of 1.91 V in the redox potential of the Ce 3+/Ce 4+ couple of the complex (measured at -0.454 V vs SHE). The unprecedented behavior prompted an electronic structure analysis using L 3 - and M 5,4-edge X-ray absorption near-edge structure (XANES) spectroscopies and configuration interaction calculations, which showed that 4f-orbital bonding in CeLK 4 has partial covalent character due to ligand-to-metal charge transfer (LMCT) in the ground state. The experimental results are presented in the context of earlier measurements on tetravalent cerium compounds, indicating that the amount of LMCT for CeLK 4 is similar to that observed for [Et 4N] 2[CeCl 6] and CeO 2 and significantly less than that for the organometallic sandwich compound cerocene, (C 8H 8) 2Ce. A simple model to rationalize changes in 4f orbital bonding for tri- and tetravalent lanthanide and actinide compounds is also provided.« less

Tuning different kinds of entangled metal-organic frameworks by modifying the spacer group of aliphatic dicarboxylate ligands and the reactant ratio.

PubMed

Yang, Jin-Xia; Zhai, Ji-Quan; Zhang, Xin; Qin, Ye-Yan; Yao, Yuan-Gen

2016-01-14

Taking advantage of the conformational flexibility of the bpp ligand and aliphatic dicarboxylic acids, six interesting entangled coordination polymers, {[Cd(fum)(bpp)(H2O)]·(H2O)}n (), {[Cd(fum)(bpp)2]·(H2O)5}n (), {[Cd2(suc)1.5(bpp)2(NO3)(H2O)2]·6H2O}n (), {[Cd(suc)(bpp)2]·(H2O)1.5}n (), {[Cd2(glu)2(bpp)3]·10H2O}n (), and {Cd(adp)(bpp)(H2O)}n () have been prepared and structurally characterized (bpp = 1,3-bi(4-pyridyl)propane, fum = fumaric, suc = succinate, glu = glutaric, adp = adipic). Compounds and are comprised of undulated 2D 4(4)-sql networks. In the structure of compound , two identical undulated layers are parallelly interpenetrated with each other to give a 2D → 2D interpenetrating framework. For , the dangling arms projected from 2D layers are intercalated into the neighboring sheets, producing a 2D → 3D polythreading framework. Compound shows a rare example of a 2D self-penetrating framework with a (3,4)-connected (4(2)·6(3)·8)(4(2)·6) topology. Compound presents an unusual 2D self-threading network with a novel 4-connected {4(2)·6(3)·8} topology. Compound displays a 3D self-penetrating system based on a 2D → 3D parallel polycatenation array. Compound exhibits an unprecedented 3D self-penetrating structure having both 1D + 1D → 1D polycatenation and 3D + 3D → 3D interpenetration characteristics. A comparison of these six compounds demonstrates that both the different spacer lengths of the aliphatic dicarboxylates and reactant ratios appear to play a significant role in the assembly of entangled frameworks. In addition, thermal stabilities and photoluminescence properties of have been examined in the solid state at room temperature.

A perspective on the future role of brain pet imaging in exercise science.

PubMed

Boecker, Henning; Drzezga, Alexander

2016-05-01

Positron Emission Tomography (PET) bears a unique potential for examining the effects of physical exercise (acute or chronic) within the central nervous system in vivo, including cerebral metabolism, neuroreceptor occupancy, and neurotransmission. However, application of Neuro-PET in human exercise science is as yet surprisingly sparse. To date the field has been dominated by non-invasive neuroelectrical techniques (EEG, MEG) and structural/functional magnetic resonance imaging (sMRI/fMRI). Despite PET having certain inherent disadvantages, in particular radiation exposure and high costs limiting applicability at large scale, certain research questions in human exercise science can exclusively be addressed with PET: The "metabolic trapping" properties of (18)F-FDG PET as the most commonly used PET-tracer allow examining the neuronal mechanisms underlying various forms of acute exercise in a rather unconstrained manner, i.e. under realistic training scenarios outside the scanner environment. Beyond acute effects, (18)F-FDG PET measurements under resting conditions have a strong prospective for unraveling the influence of regular physical activity on neuronal integrity and potentially neuroprotective mechanisms in vivo, which is of special interest for aging and dementia research. Quantification of cerebral glucose metabolism may allow determining the metabolic effects of exercise interventions in the entire human brain and relating the regional cerebral rate of glucose metabolism (rCMRglc) with behavioral, neuropsychological, and physiological measures. Apart from FDG-PET, particularly interesting applications comprise PET ligand studies that focus on dopaminergic and opioidergic neurotransmission, both key transmitter systems for exercise-related psychophysiological effects, including mood changes, reward processing, antinociception, and in its most extreme form 'exercise dependence'. PET ligand displacement approaches even allow quantifying specific endogenous neurotransmitter release under acute exercise interventions, to which modern PET/MR hybrid technology will be additionally fruitful. Experimental studies exploiting the unprecedented multimodal imaging capacities of PET/MR in human exercise sciences are as yet pending. Copyright © 2015 Elsevier Inc. All rights reserved.

Investigation of the interaction between the atypical agonist c[YpwFG] and MOR.

PubMed

Gentilucci, Luca; Squassabia, Federico; De Marco, Rossella; Artali, Roberto; Cardillo, Giuliana; Tolomelli, Alessandra; Spampinato, Santi; Bedini, Andrea

2008-05-01

Endogenous and exogenous opiates are currently considered the drugs of choice for treating different kinds of pain. However, their prolonged use produces several adverse symptoms, and in addition, many forms of pain are resistant to any kind of therapy. Therefore, the discovery of compounds active towards mu-opioid receptors (MORs) by alternative pharmacological mechanisms could be of value for developing novel classes of analgesics. There is evidence that some unusual molecules can bind opioid receptors, albeit lacking some of the typical opioid pharmacophoric features. In particular, the recent discovery of a few compounds that showed agonist behavior even in the absence of the primary pharmacophore, namely a protonable amine, led to a rediscussion of the importance of ionic interactions in stabilizing the ligand-receptor complex and in activating signal transduction. Very recently, we synthesized a library of cyclic analogs of the endogenous, MOR-selective agonist endomorphin-1 (YPWF-NH(2)), containing a Gly5 bridge between Tyr1 and Phe4. The cyclopeptide c[YpwFG] showed good affinity and agonist behavior. This atypical MOR agonist does not have the protonable Tyr amine. In order to gain more information about plausible mechanisms of interaction between c[YpwFG] and the opioid receptor, we synthesized a selected set of derivatives containing different bridges between Tyr1 and Phe4, and tested their affinities towards mu-opioid receptors. We performed conformational analysis of the cyclopeptides by NMR spectroscopy and molecular dynamics, and investigated plausible, unprecedented modes of interaction with the MOR by molecular docking. The successive quantum mechanics/molecular mechanics investigation of the complexes obtained by the molecular docking procedure furnished a more detailed description of the binding mode and the electronic properties of the ligands. The comparison with the binding mode of the potent agonist JOM-6 seems to indicate that the cyclic endomorphin-1 analogs interact with the receptor by way of an alternative mechanism, still maintaining the ability to activate the receptor.

Germylenes and stannylenes stabilized within N2PE rings (E = Ge or Sn): combined experimental and theoretical study.

PubMed

Vrána, Jan; Ketkov, Sergey; Jambor, Roman; Růžička, Aleš; Lyčka, Antonín; Dostál, Libor

2016-06-21

The deprotonation of aminophosphanes PhP(NHR)2 (R = t-Bu or Dip; Dip = 2,6-i-Pr2C6H3) and t-BuP(NHDip)2 using n-BuLi gave, depending on the stoichiometry, both the dilithium compounds {[PhP(Nt-Bu)2]Li2}2 (), [PhP(Nt-Bu)(NDip)]Li2·(Et2O) (), [t-BuP(NDip)2]Li2·(Et2O)2 () and [t-BuP(NDip)2]Li2·(tmeda)2 (), and the monolithium compounds [PhP(NHt-Bu)(NR)]Li·(tmeda) (R = t-Bu , Dip ) and [t-BuP(NHDip)(NDip)]Li·(tmeda) (). Treatment of , and with GeCl2·dioxane or SnCl2 in a 1 : 1 stoichiometric ratio gave the corresponding tetrylenes [PhP(Nt-Bu)2]E (E = Ge , Sn ), [PhP(Nt-Bu)(NDip)]Ge () and [t-BuP(NDip)2]E (E = Ge , Sn ). The heteroleptic germylene [Ph(H)P(Nt-Bu)2]GeCl () was obtained by the reaction of the monolithium compound [PhP(NHt-Bu)(Nt-Bu)]Li·(tmeda) () with GeCl2·dioxane in a 1 : 1 stoichiometric ratio, as a result of a spontaneous NH → PH tautomeric shift in the ligand backbone. In contrast, an analogous reaction with SnCl2 produced only stannylene along with the PhP(NHt-Bu)2 starting material, suggesting scrambling of the ligands rather than a NH → PH tautomeric shift. Finally, heating in solution led to P-C bond cleavage and formation of the bis(imino)phosphide [DipNPNDip]Li·(tmeda) (). The reaction of with GeCl2·dioxane, SnCl2 or PbCl2 in a 2 : 1 stoichiometric ratio yielded the unprecedented tetrylenes [DipNPNDip]2E (E = Ge , Sn and Pb ), in which the tetrylene center is incorporated within two N2PE rings. Treatment of the monolithium compound with n-BuLi and K (or KC8) gave [t-BuNPNt-Bu]Li·(tmeda) () and{[t-BuNPNt-Bu]K(tmeda)}2 (), respectively. In contrast to the reaction with , similar reactions of with GeCl2·dioxane and SnCl2 resulted in the known compounds cis-[P(μ-Nt-Bu)2P(t-BuN)2]E (E = Ge, Sn); evidently the t-Bu groups do not provide sufficient steric shielding to protect the bis(imino)phosphide backbone as in the case of . The bonding situation in a set of selected compounds (, ) has been subjected to a theoretical survey with particular emphasis on the nature of the bonding between the ligand and the central metal and the bonding within the NPN core of the ligand, showing significant differences among the studied complexes.

Comparison of the crystal structure and function to wild-type and His25Ala mutant human heme oxygenase-1.

PubMed

Zhou, Wen-Pu; Zhong, Wen-Wei; Zhang, Xue-Hong; Ding, Jian-Ping; Zhang, Zi-Li; Xia, Zhen-Wei

2009-03-01

Human heme oxygenase-1 (hHO-1) is a rate-limiting enzyme in heme metabolism. It regulates serum bilirubin level. Site-directed mutagenesis studies indicate that the proximal residue histidine 25 (His25) plays a key role in hHO-1 activity. A highly purified hHO-1 His25Ala mutant was generated and crystallized with a new expression system. The crystal structure of the mutant was determined by X-ray diffraction technology and molecular replacement at the resolution of 2.8 A, and the model of hHO-1 His25Ala mutant was refined. The final crystallographic and free R factors were 0.245 and 0.283, respectively. The standard bond length deviation was 0.007 A, and the standard bond angle deviation was 1.3 degrees . The mutation of His25 to Ala led to an empty pocket underneath the ferric ion in the heme, leading to loss of binding iron ligand. Although this did not cause an overall structural change, the enzymatic activity of the mutant hHO-1 was reduced by 90%. By supplementing imidazole, the HO-1 activity was restored approximately 90% to its normal level. These data suggest that Ala25 remains unchanged in the structure compared to His25, but the important catalytic function of hHO-1 is lost. Thus, it appears that His25 is a crucial residue for proper hHO-1 catalysis.

Heterobimetallic porphyrin complexes displaying triple dynamics: coupled metal motions controlled by constitutional evolution.

PubMed

Le Gac, Stéphane; Fusaro, Luca; Roisnel, Thierry; Boitrel, Bernard

2014-05-07

A bis-strap porphyrin ligand (1), with an overhanging carboxylic acid group on each side of the macrocycle, has been investigated toward the formation of dynamic libraries of bimetallic complexes with Hg(II), Cd(II), and Pb(II). Highly heteroselective metalation processes occurred in the presence of Pb(II), with Hg(II) or Cd(II) bound out-of-plane to the N-core and "PbOAc" bound to a carboxylate group of a strap on the opposite side. The resulting complexes, 1(Hg)·PbOAc and 1(Cd)·PbOAc, display three levels of dynamics. The first is strap-level (interactional dynamics), where the PbOAc moiety swings between the left and right side of the strap owing to a second sphere of coordination with lateral amide functions. The second is ligand-level (motional dynamics), where 1(Hg)·PbOAc and 1(Cd)·PbOAc exist as two degenerate states in equilibrium controlled by a chemical effector (AcO(-)). The process corresponds to a double translocation of the metal ions according to an intramolecular migration of Hg(II) or Cd(II) through the N-core, oscillating between the two equivalent overhanging carbonyl groups, coupled to an intermolecular pathway for PbOAc exchanging between the two equivalent overhanging carboxylate groups (N-core(up) ⇆ N-core(down) coupled to strap(down) ⇆ strap(up), i.e., coupled motion #1 in the abstract graphic). The third is library-level (constitutional dynamics), where a dynamic constitutional evolution of the system was achieved by the successive addition of two chemical effectors (DMAP and then AcO(-)). It allowed shifting equilibrium forward and backward between 1(Hg)·PbOAc and the corresponding homobimetallic complexes 1(Hg2)·DMAP and 1(Pb)·PbOAc. The latter displays a different ligand-level dynamics, in the form of an intraligand coupled migration of the Pb(II) ions (N-core(up) ⇆ strap(up) coupled to strap(down) ⇆ N-core(down), i.e., coupled motion #2 in the abstract graphic). In addition, the neutral "bridged" complexes 1HgPb and 1CdPb, with the metal ions on opposite sides both bound to the N-core and to a carboxylate of a strap, were structurally characterized. These results establish an unprecedented approach in supramolecular coordination chemistry, by considering the reversible interaction of a metal ion with the porphyrin N-core as a new source of self-organization processes. This work should provide new inspirations for the design of innovative adaptative materials and devices.

In situ formation of the first proteinogenically functionalized [TeW6O24O2(Glu)]7– structure reveals unprecedented chemical and geometrical features of the Anderson-type cluster† †Electronic supplementary information (ESI) available: Full experimental details and additional figures are provided. See DOI: 10.1039/c6cc07004c Click here for additional data file. Click here for additional data file. Click here for additional data file.

PubMed Central

Molitor, Christian; Bijelic, Aleksandar

2016-01-01

The chemistry of polyoxometalates (POMs) in a protein environment is an almost unexplored but highly relevant research field as important biological and pharmacological attributes of certain POMs are based on their interactions with proteins. We report on the A-type Anderson–Evans polyoxotungstate, [TeW6O24]6– (TEW), mediated crystallization of Coreopsis grandiflora aurone synthase (cgAUS1) using ∼0.24 mM protein and 1.0 mM TEW. The 1.78 Å crystal structure reveals the covalent binding of TEW to the protein under the formation of an unprecedented polyoxotungstate cluster, [TeW6O24O2(Glu)]7– (GluTEW). The polyoxotungstate–protein complex exhibits the first covalent bond between a protein and the A-type Anderson–Evans cluster, an archetype where up to now no hybrid structures exist. The polyoxotungstate is modified at two of its six addenda tungsten atoms, which covalently bind to the carboxylic oxygen atoms of glutamic acid (Glu157), leading to W–O distances of ∼2.35 Å. This ligand substitution reaction is accompanied by a reduction of the coordination number of two μ3 polyoxotungstate oxygen atoms. This is so far unique since all known hybridizations of the Anderson–Evans POM with organic units have been obtained via the functionalization of the B-type Anderson–Evans structure through its bridging oxygen atoms. The structure reported here proves the reactivity of this POM archetype's addenda atoms as it has been administered into the protein solution as a pre-assembled cluster. Moreover, the novel cluster [TeW6O24O2(Glu)]7– displays the great versatility of the Anderson–Evans POM class. PMID:27722437

Homogenous electrocatalytic oxygen reduction rates correlate with reaction overpotential in acidic organic solutions

DOE PAGES

Pegis, Michael L.; McKeown, Bradley A.; Kumar, Neeraj; ...

2016-10-28

Improvement of electrocatalysts for the oxygen reduction reaction (ORR) is critical for the advancement of fuel cell technologies. Herein, we report a series of eleven soluble iron porphyrin ORR electrocatalysts that possess turnover frequencies (TOFs) from 3 s -1 to an unprecedented 2.2 x 10 6 s -1. These TOFs correlate with the ORR overpotential, which can be changed by modulating the ancillary ligand, by varying the reaction conditions or by changing the catalyst’s protonation state. This is the first such correlation for homogeneous ORR electrocatalysis, and it demonstrates that the remarkably fast TOFs are a consequence of the highmore » overpotential. Computational studies indicate that the correlation is analogous to the volcano plot analysis developed for heterogeneous ORR materials. This unique parallel between homo- and heterogeneous ORR electrocatalysts allows a fundamental understanding of intrinsic barriers associated with the ORR, which can aid the design of new catalytic systems that operate at low overpotential. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. Additional data is given in the Electronic Supporting Information.« less

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

PubMed

Hölzer, Martin; Krähling, Verena; Amman, Fabian; Barth, Emanuel; Bernhart, Stephan H; Carmelo, Victor A O; Collatz, Maximilian; Doose, Gero; Eggenhofer, Florian; Ewald, Jan; Fallmann, Jörg; Feldhahn, Lasse M; Fricke, Markus; Gebauer, Juliane; Gruber, Andreas J; Hufsky, Franziska; Indrischek, Henrike; Kanton, Sabina; Linde, Jörg; Mostajo, Nelly; Ochsenreiter, Roman; Riege, Konstantin; Rivarola-Duarte, Lorena; Sahyoun, Abdullah H; Saunders, Sita J; Seemann, Stefan E; Tanzer, Andrea; Vogel, Bertram; Wehner, Stefanie; Wolfinger, Michael T; Backofen, Rolf; Gorodkin, Jan; Grosse, Ivo; Hofacker, Ivo; Hoffmann, Steve; Kaleta, Christoph; Stadler, Peter F; Becker, Stephan; Marz, Manja

2016-10-07

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.

From Medicinal Chemistry to Human Health: Current Approaches to Drug Discovery for Cancer and Neglected Tropical Diseases.

PubMed

Ferreira, Leonardo G; Oliva, Glaucius; Andricopulo, Adriano D

2018-01-01

Scientific and technological breakthroughs have compelled the current players in drug discovery to increasingly incorporate knowledge-based approaches. This evolving paradigm, which has its roots attached to the recent advances in medicinal chemistry, molecular and structural biology, has unprecedentedly demanded the development of up-to-date computational approaches, such as bio- and chemo-informatics. These tools have been pivotal to catalyzing the ever-increasing amount of data generated by the molecular sciences, and to converting the data into insightful guidelines for use in the research pipeline. As a result, ligand- and structure-based drug design have emerged as key pathways to address the pharmaceutical industry's striking demands for innovation. These approaches depend on a keen integration of experimental and molecular modeling methods to surmount the main challenges faced by drug candidates - in vivo efficacy, pharmacodynamics, metabolism, pharmacokinetics and safety. To that end, the Laboratório de Química Medicinal e Computacional (LQMC) of the Universidade de São Paulo has developed forefront research on highly prevalent and life-threatening neglected tropical diseases and cancer. By taking part in global initiatives for pharmaceutical innovation, the laboratory has contributed to the advance of these critical therapeutic areas through the use of cutting-edge strategies in medicinal chemistry.

Large-scale generation of human iPSC-derived neural stem cells/early neural progenitor cells and their neuronal differentiation.

PubMed

D'Aiuto, Leonardo; Zhi, Yun; Kumar Das, Dhanjit; Wilcox, Madeleine R; Johnson, Jon W; McClain, Lora; MacDonald, Matthew L; Di Maio, Roberto; Schurdak, Mark E; Piazza, Paolo; Viggiano, Luigi; Sweet, Robert; Kinchington, Paul R; Bhattacharjee, Ayantika G; Yolken, Robert; Nimgaonka, Vishwajit L; Nimgaonkar, Vishwajit L

2014-01-01

Induced pluripotent stem cell (iPSC)-based technologies offer an unprecedented opportunity to perform high-throughput screening of novel drugs for neurological and neurodegenerative diseases. Such screenings require a robust and scalable method for generating large numbers of mature, differentiated neuronal cells. Currently available methods based on differentiation of embryoid bodies (EBs) or directed differentiation of adherent culture systems are either expensive or are not scalable. We developed a protocol for large-scale generation of neuronal stem cells (NSCs)/early neural progenitor cells (eNPCs) and their differentiation into neurons. Our scalable protocol allows robust and cost-effective generation of NSCs/eNPCs from iPSCs. Following culture in neurobasal medium supplemented with B27 and BDNF, NSCs/eNPCs differentiate predominantly into vesicular glutamate transporter 1 (VGLUT1) positive neurons. Targeted mass spectrometry analysis demonstrates that iPSC-derived neurons express ligand-gated channels and other synaptic proteins and whole-cell patch-clamp experiments indicate that these channels are functional. The robust and cost-effective differentiation protocol described here for large-scale generation of NSCs/eNPCs and their differentiation into neurons paves the way for automated high-throughput screening of drugs for neurological and neurodegenerative diseases.

Simultaneous Binding of Two Peptidyl Ligands by a Src Homology 2 Domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yanyan; Zhang, Jinjin; Yuan, Chunhua

Src homology 2 (SH2) domains mediate protein-protein interactions by recognizing phosphotyrosine (pY)-containing sequences of target proteins. In all of the SH2 domain-pY peptide interactions described to date, the SH2 domain binds to a single pY peptide. Here, determination of the cocrystal structure of the N-terminal SH2 domain of phosphatase SHP-2 bound to a class IV peptide (VIpYFVP) revealed a noncanonical 1:2 (protein-peptide) complex. The first peptide binds in a canonical manner with its pY side chain inserted in the usual binding pocket, while the second pairs up with the first to form two antiparallel {beta}-strands that extend the central {beta}-sheetmore » of the SH2 domain. This unprecedented binding mode was confirmed in the solution phase by NMR experiments and shown to be adopted by pY peptides derived from cellular proteins. Site-directed mutagenesis and surface plasmon resonance studies revealed that the binding of the first peptide is pY-dependent, but phosphorylation is not required for the second peptide. Our findings suggest a potential new function for the SH2 domain as a molecular clamp to promote dimerization of signaling proteins.« less

Rhodium-catalysed syn-carboamination of alkenes via a transient directing group.

PubMed

Piou, Tiffany; Rovis, Tomislav

2015-11-05

Alkenes are the most ubiquitous prochiral functional groups--those that can be converted from achiral to chiral in a single step--that are accessible to synthetic chemists. For this reason, difunctionalization reactions of alkenes (whereby two functional groups are added to the same double bond) are particularly important, as they can be used to produce highly complex molecular architectures. Stereoselective oxidation reactions, including dihydroxylation, aminohydroxylation and halogenation, are well established methods for functionalizing alkenes. However, the intermolecular incorporation of both carbon- and nitrogen-based functionalities stereoselectively across an alkene has not been reported. Here we describe the rhodium-catalysed carboamination of alkenes at the same (syn) face of a double bond, initiated by a carbon-hydrogen activation event that uses enoxyphthalimides as the source of both the carbon and the nitrogen functionalities. The reaction methodology allows for the intermolecular, stereospecific formation of one carbon-carbon and one carbon-nitrogen bond across an alkene, which is, to our knowledge, unprecedented. The reaction design involves the in situ generation of a bidentate directing group and the use of a new cyclopentadienyl ligand to control the reactivity of rhodium. The results provide a new way of synthesizing functionalized alkenes, and should lead to the convergent and stereoselective assembly of amine-containing acyclic molecules.

Beyond the bolus: transgenic tools for investigating the neurophysiology of learning and memory.

PubMed

Lykken, Christine; Kentros, Clifford G

2014-10-01

Understanding the neural mechanisms underlying learning and memory in the entorhinal-hippocampal circuit is a central challenge of systems neuroscience. For more than 40 years, electrophysiological recordings in awake, behaving animals have been used to relate the receptive fields of neurons in this circuit to learning and memory. However, the vast majority of such studies are purely observational, as electrical, surgical, and pharmacological circuit manipulations are both challenging and relatively coarse, being unable to distinguish between specific classes of neurons. Recent advances in molecular genetic tools can overcome many of these limitations, enabling unprecedented control over neural activity in behaving animals. Expression of pharmaco- or optogenetic transgenes in cell-type-specific "driver" lines provides unparalleled anatomical and cell-type specificity, especially when delivered by viral complementation. Pharmacogenetic transgenes are specially designed neurotransmitter receptors exclusively activated by otherwise inactive synthetic ligands and have kinetics similar to traditional pharmacology. Optogenetic transgenes use light to control the membrane potential, and thereby operate at the millisecond timescale. Thus, activation of pharmacogenetic transgenes in specific neuronal cell types while recording from other parts of the circuit allows investigation of the role of those neurons in the steady state, whereas optogenetic transgenes allow one to determine the immediate network response. © 2014 Lykken and Kentros; Published by Cold Spring Harbor Laboratory Press.

Bioorthogonal chemistry: strategies and recent development

PubMed Central

Ramil, Carlo P.; Lin, Qing

2013-01-01

The use of covalent chemistry to track biomolecules in their native environment—a focus of bioorthogonal chemistry—has received considerable interests recently among chemical biologists and organic chemists alike. To facilitate wider adoption of bioorthogonal chemistry in biomedical research, a central effort in the last few years has been focused on the optimization of a few known bioorthogonal reactions, particularly with respective to reaction kinetics improvement, novel genetic encoding systems, and fluorogenic reactions for bioimaging. During these optimizations, three strategies have emerged, including the use of ring strain for substrate activation in the cycloaddition reactions, the discovery of new ligands and privileged substrates for accelerated metal-catalysed reactions, and the design of substrates with pre-fluorophore structures for rapid “turn-on” fluorescence after selective bioorthogonal reactions. In addition, new bioorthogonal reactions based on either modified or completely unprecedented reactant pairs have been reported. Finally, increasing attention has been directed toward the development of mutually exclusive bioorthogonal reactions and their applications in multiple labeling of a biomolecule in cell culture. In this feature article, we wish to present the recent progress in bioorthogonal reactions through the selected examples that highlight the above-mentioned strategies. Considering increasing sophistication in bioorthogonal chemistry development, we strive to project several exciting opportunities where bioorthogonal chemistry can make a unique contribution to biology in near future. PMID:24145483

Nanoprobe-Enhanced, Split Aptamer-Based Electrochemical Sandwich Assay for Ultrasensitive Detection of Small Molecules.

PubMed

Zhao, Tao; Liu, Ran; Ding, Xiaofan; Zhao, Juncai; Yu, Haixiang; Wang, Lei; Xu, Qing; Wang, Xuan; Lou, Xinhui; He, Miao; Xiao, Yi

2015-08-04

It is quite challenging to improve the binding affinity of antismall molecule aptamers. We report that the binding affinity of anticocaine split aptamer pairs improved by up to 66-fold by gold nanoparticles (AuNP)-attached aptamers due to the substantially increased local concentration of aptamers and multiple and simultaneous ligand interactions. The significantly improved binding affinity enables the detection of small molecule targets with unprecedented sensitivity, as demonstrated in nanoprobe-enhanced split aptamer-based electrochemical sandwich assays (NE-SAESA). NE-SAESA replaces the traditional molecular reporter probe with AuNPs conjugated to multiple reporter probes. The increased binding affinity allowed us to use 1,000-fold lower reporter probe concentrations relative to those employed in SAESA. We show that the near-elimination of background in NE-SAESA effectively improves assay sensitivity by ∼1,000-100,000-fold for ATP and cocaine detection, relative to equivalent SAESA. With the ongoing development of new strategies for the selection of aptamers, we anticipate that our sensor platform should offer a generalizable approach for the high-sensitivity detection of diverse targets. More importantly, we believe that NE-SAESA represents a novel strategy to improve the binding affinity between a small molecule and its aptamer and potentially can be extended to other detection platforms.

Fine-Tuning of the Carbon Dioxide Capture Capability of Diamine-Grafted Metal-Organic Framework Adsorbents Through Amine Functionalization.

PubMed

Jo, Hyuna; Lee, Woo Ram; Kim, Nam Woo; Jung, Hyun; Lim, Kwang Soo; Kim, Jeong Eun; Kang, Dong Won; Lee, Hanyeong; Hiremath, Vishwanath; Seo, Jeong Gil; Jin, Hailian; Moon, Dohyun; Han, Sang Soo; Hong, Chang Seop

2017-02-08

A combined sonication and microwave irradiation procedure provides the most effective functionalization of ethylenediamine (en) and branched primary diamines of 1-methylethylenediamine (men) and 1,1-dimethylethylenediamine (den) onto the open metal sites of Mg 2 (dobpdc) (1). The CO 2 capacities of the advanced adsorbents 1-en and 1-men under simulated flue gas conditions are 19 wt % and 17.4 wt %, respectively, which are the highest values reported among amine-functionalized metal-organic frameworks (MOFs) to date. Moreover, 1-den exhibits both a significant working capacity (12.2 wt %) and superb CO 2 uptake (11 wt %) at 3 % CO 2 . Additionally, this framework showcases the superior recyclability; ultrahigh stability after exposure to O 2 , moisture, and SO 2 ; and exceptional CO 2 adsorption capacity under humid conditions, which are unprecedented among MOFs. We also elucidate that the performance of CO 2 adsorption can be controlled by the structure of the diamine ligands grafted such as the number of amine end groups or the presence of side groups, which provides the first systematic and comprehensive demonstration of fine-tuning of CO 2 uptake capability using different amines. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatially restricted G protein-coupled receptor activity via divergent endocytic compartments.

PubMed

Jean-Alphonse, Frederic; Bowersox, Shanna; Chen, Stanford; Beard, Gemma; Puthenveedu, Manojkumar A; Hanyaloglu, Aylin C

2014-02-14

Postendocytic sorting of G protein-coupled receptors (GPCRs) is driven by their interactions between highly diverse receptor sequence motifs with their interacting proteins, such as postsynaptic density protein (PSD95), Drosophila disc large tumor suppressor (Dlg1), zonula occludens-1 protein (zo-1) (PDZ) domain proteins. However, whether these diverse interactions provide an underlying functional specificity, in addition to driving sorting, is unknown. Here we identify GPCRs that recycle via distinct PDZ ligand/PDZ protein pairs that exploit their recycling machinery primarily for targeted endosomal localization and signaling specificity. The luteinizing hormone receptor (LHR) and β2-adrenergic receptor (B2AR), two GPCRs sorted to the regulated recycling pathway, underwent divergent trafficking to distinct endosomal compartments. Unlike B2AR, which traffics to early endosomes (EE), LHR internalizes to distinct pre-early endosomes (pre-EEs) for its recycling. Pre-EE localization required interactions of the LHR C-terminal tail with the PDZ protein GAIP-interacting protein C terminus, inhibiting its traffic to EEs. Rerouting the LHR to EEs, or EE-localized GPCRs to pre-EEs, spatially reprograms MAPK signaling. Furthermore, LHR-mediated activation of MAPK signaling requires internalization and is maintained upon loss of the EE compartment. We propose that combinatorial specificity between GPCR sorting sequences and interacting proteins dictates an unprecedented spatiotemporal control in GPCR signal activity.

Rare‐Earth‐ and Uranium‐Mesoionic Carbenes: A New Class of f‐Block Carbene Complex Derived from an N‐Heterocyclic Olefin

PubMed Central

Seed, John A.; Gregson, Matthew; Tuna, Floriana; Chilton, Nicholas F.; Wooles, Ashley J.; McInnes, Eric J. L.

2017-01-01

Abstract Neutral mesoionic carbenes (MICs) have emerged as an important class of carbene, however they are found in the free form or ligated to only a few d‐block ions. Unprecedented f‐block MIC complexes [M(N′′)3{CN(Me)C(Me)N(Me)CH}] (M=U, Y, La, Nd; N′′=N(SiMe3)2) are reported. These complexes were prepared by a formal 1,4‐proton migration reaction when the metal triamides [M(N′′)3] were treated with the N‐heterocyclic olefin H2C=C(NMeCH)2, which constitutes a new, general way to prepare MIC complexes. Quantum chemical calculations on the 5f3 uranium(III) complex suggest the presence of a U=C donor‐acceptor bond, composed of a MIC→U σ‐component and a U(5f)→MIC(2p) π‐back‐bond, but for the d0f0 Y and La and 4f3 Nd congeners only MIC→M σ‐bonding is found. Considering the generally negligible π‐acidity of MICs, this is surprising and highlights that greater consideration should possibly be given to recognizing MICs as potential π‐acid ligands when coordinated to strongly reducing metals. PMID:28719735

Thermospheric density and wind retrieval from Swarm observations

NASA Astrophysics Data System (ADS)

Visser, Pieter; Doornbos, Eelco; van den IJssel, Jose; Teixeira da Encarnação, João

2013-11-01

The three-satellite ESA Swarm mission aims at mapping the Earth's global geomagnetic field at unprecedented spatial and temporal resolution and precision. Swarm also aims at observing thermospheric density and possibly horizontal winds. Precise orbit determination (POD) and Thermospheric Density and Wind (TDW) chains form part of the Swarm Constellation and Application Facility (SCARF), which will provide the so-called Level 2 products. The POD and TDW chains generate the orbit, accelerometer calibration, and thermospheric density and wind Level 2 products. The POD and TDW chains have been tested with data from the CHAMP and GRACE missions, indicating that a 3D orbit precision of about 10 cm can be reached. In addition, POD allows to determine daily accelerometer bias and scale factor values with a precision of around 10-15 nm/s2 and 0.01-0.02, respectively, for the flight direction. With these accelerometer calibration parameter values, derived thermospheric density is consistent at the 9-11% level (standard deviation) with values predicted by models (taking into account that model values are 20-30% higher). The retrieval of crosswinds forms part of the processing chain, but will be challenging. The Swarm observations will be used for further developing and improving density and wind retrieval algorithms.

Towards a framework for testing general relativity with extreme-mass-ratio-inspiral observations

NASA Astrophysics Data System (ADS)

Chua, A. J. K.; Hee, S.; Handley, W. J.; Higson, E.; Moore, C. J.; Gair, J. R.; Hobson, M. P.; Lasenby, A. N.

2018-07-01

Extreme-mass-ratio-inspiral observations from future space-based gravitational-wave detectors such as LISA will enable strong-field tests of general relativity with unprecedented precision, but at prohibitive computational cost if existing statistical techniques are used. In one such test that is currently employed for LIGO black hole binary mergers, generic deviations from relativity are represented by N deformation parameters in a generalized waveform model; the Bayesian evidence for each of its 2N combinatorial submodels is then combined into a posterior odds ratio for modified gravity over relativity in a null-hypothesis test. We adapt and apply this test to a generalized model for extreme-mass-ratio inspirals constructed on deformed black hole spacetimes, and focus our investigation on how computational efficiency can be increased through an evidence-free method of model selection. This method is akin to the algorithm known as product-space Markov chain Monte Carlo, but uses nested sampling and improved error estimates from a rethreading technique. We perform benchmarking and robustness checks for the method, and find order-of-magnitude computational gains over regular nested sampling in the case of synthetic data generated from the null model.

Results from the Wilkinson Microwave Anisotropy Probe

NASA Technical Reports Server (NTRS)

Komatsu, E.; Bennett, Charles L.; Komatsu, Eiichiro

2015-01-01

The Wilkinson Microwave Anisotropy Probe (WMAP) mapped the distribution of temperature and polarization over the entire sky in five microwave frequency bands. These full-sky maps were used to obtain measurements of temperature and polarization anisotropy of the cosmic microwave background with the unprecedented accuracy and precision. The analysis of two-point correlation functions of temperature and polarization data gives determinations of the fundamental cosmological parameters such as the age and composition of the universe, as well as the key parameters describing the physics of inflation, which is further constrained by three-point correlation functions. WMAP observations alone reduced the flat ? cold dark matter (Lambda Cold Dark Matter) cosmological model (six) parameter volume by a factor of > 68, 000 compared with pre-WMAP measurements. The WMAP observations (sometimes in combination with other astrophysical probes) convincingly show the existence of non-baryonic dark matter, the cosmic neutrino background, flatness of spatial geometry of the universe, a deviation from a scale-invariant spectrum of initial scalar fluctuations, and that the current universe is undergoing an accelerated expansion. The WMAP observations provide the strongest ever support for inflation; namely, the structures we see in the universe originate from quantum fluctuations generated during inflation.

The role of fluctuations and interactions in pedestrian dynamics

NASA Astrophysics Data System (ADS)

Corbetta, Alessandro; Meeusen, Jasper; Benzi, Roberto; Lee, Chung-Min; Toschi, Federico

Understanding quantitatively the statistical behaviour of pedestrians walking in crowds is a major scientific challenge of paramount societal relevance. Walking humans exhibit a rich (stochastic) dynamics whose small and large deviations are driven, among others, by own will as well as by environmental conditions. Via 24/7 automatic pedestrian tracking from multiple overhead Microsoft Kinect depth sensors, we collected large ensembles of pedestrian trajectories (in the order of tens of millions) in different real-life scenarios. These scenarios include both narrow corridors and large urban hallways, enabling us to cover and compare a wide spectrum of typical pedestrian dynamics. We investigate the pedestrian motion measuring the PDFs, e.g. those of position, velocity and acceleration, and at unprecedentedly high statistical resolution. We consider the dependence of PDFs on flow conditions, focusing on diluted dynamics and pair-wise interactions (''collisions'') for mutual avoidance. By means of Langevin-like models we provide models for the measured data, inclusive typical fluctuations and rare events. This work is part of the JSTP research programme ``Vision driven visitor behaviour analysis and crowd management'' with Project Number 341-10-001, which is financed by the Netherlands Organisation for Scientific Research (NWO).

Precise CCD positions of Himalia using Gaia DR1 in 2015-2016

NASA Astrophysics Data System (ADS)

Peng, H. W.; Peng, Q. Y.; Wang, N.

2017-05-01

In order to obtain high-precision CCD positions of Himalia, the sixth Jovian satellite, a total of 598 CCD observations have been obtained during the years 2015-2016. The observations were made by using the 2.4 and 1 m telescopes administered by Yunnan Observatories over 27 nights. Several factors that would influence the positional precision of Himalia were analysed, including the reference star catalogue used, the geometric distortion and the phase effect. By taking advantage of its unprecedented positional precision, the recently released catalogue Gaia Data Release 1 was chosen to match reference stars in the CCD frames of both Himalia and open clusters, which were observed for deriving the geometric distortion. The latest version of sofa library was used to calculate the positions of reference stars. The theoretical positions of Himalia were retrieved from the Jet Propulsion Laboratory Horizons System that includes the satellite ephemeris JUP300, while the positions of Jupiter were based on the planetary ephemeris DE431. Our results showed that the means of observed minus computed (O - C) residuals are 0.071 and -0.001 arcsec in right ascension and declination, respectively. Their standard deviations are estimated at about 0.03 arcsec in each direction.

Inference of the electron temperature in ICF implosions from the hard X-ray spectral continuum

NASA Astrophysics Data System (ADS)

Kagan, Grigory; Landen, O. L.; Svyatsky, D.; Sio, H.; Kabadi, N. V.; Simpson, R. A.; Gatu Johnson, M.; Frenje, J. A.; Petrasso, R. D.; Shah, R. C.; Joshi, T. R.; Hakel, P.; Weber, T. E.; Rinderknecht, H. G.; Thorn, D.; Schneider, M.; Bradley, D.; Kilkenny, J.

2017-10-01

The NIF Continuum Spectrometer, scheduled to be first deployed in Fall of 2017, will infer the imploded core electron temperature from the free-free continuum self-emission spectra of photons with energies of 20 to 30 keV. However, this hard X-ray radiation is emitted by the tail of the electron distribution, which likely deviates from Maxwellian and thus obscures interpretation of the data. We investigate resulting modifications to the X-ray spectra. The logarithmic slope of the spectrum from the more realistic, non-thermal tail of the electron distribution is found to decrease more rapidly at higher photon energies, as compared to the perfectly Maxwellian case. Interpreting the spectrum with assumption of Maxwellian electrons enforced is shown to give an electron temperature that is lower than the actual one. Conversely, due to its connection with the non-thermal features in the electron distribution, hard X-ray emission can provide unprecedented information about kinetic processes in the hot DT core. This work was performed under the auspices of the U.S. Dept. of Energy by the Los Alamos National Security, LLC, Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396.

The Correlation between Mixing Length and Metallicity on the Giant Branch: Implications for Ages in the Gaia Era

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tayar, Jamie; Somers, Garrett; Pinsonneault, Marc H.

2017-05-01

In the updated APOGEE- Kepler catalog, we have asteroseismic and spectroscopic data for over 3000 first ascent red giants. Given the size and accuracy of this sample, these data offer an unprecedented test of the accuracy of stellar models on the post-main-sequence. When we compare these data to theoretical predictions, we find a metallicity dependent temperature offset with a slope of around 100 K per dex in metallicity. We find that this effect is present in all model grids tested, and that theoretical uncertainties in the models, correlated spectroscopic errors, and shifts in the asteroseismic mass scale are insufficient tomore » explain this effect. Stellar models can be brought into agreement with the data if a metallicity-dependent convective mixing length is used, with Δ α {sub ML,YREC} ∼ 0.2 per dex in metallicity, a trend inconsistent with the predictions of three-dimensional stellar convection simulations. If this effect is not taken into account, isochrone ages for red giants from the Gaia data will be off by as much as a factor of two even at modest deviations from solar metallicity ([Fe/H] = −0.5).« less

Towards a framework for testing general relativity with extreme-mass-ratio-inspiral observations

NASA Astrophysics Data System (ADS)

Chua, A. J. K.; Hee, S.; Handley, W. J.; Higson, E.; Moore, C. J.; Gair, J. R.; Hobson, M. P.; Lasenby, A. N.

2018-04-01

Extreme-mass-ratio-inspiral observations from future space-based gravitational-wave detectors such as LISA will enable strong-field tests of general relativity with unprecedented precision, but at prohibitive computational cost if existing statistical techniques are used. In one such test that is currently employed for LIGO black-hole binary mergers, generic deviations from relativity are represented by N deformation parameters in a generalised waveform model; the Bayesian evidence for each of its 2N combinatorial submodels is then combined into a posterior odds ratio for modified gravity over relativity in a null-hypothesis test. We adapt and apply this test to a generalised model for extreme-mass-ratio inspirals constructed on deformed black-hole spacetimes, and focus our investigation on how computational efficiency can be increased through an evidence-free method of model selection. This method is akin to the algorithm known as product-space Markov chain Monte Carlo, but uses nested sampling and improved error estimates from a rethreading technique. We perform benchmarking and robustness checks for the method, and find order-of-magnitude computational gains over regular nested sampling in the case of synthetic data generated from the null model.

The simultaneous evolution of author and paper networks

PubMed Central

Börner, Katy; Maru, Jeegar T.; Goldstone, Robert L.

2004-01-01

There has been a long history of research into the structure and evolution of mankind's scientific endeavor. However, recent progress in applying the tools of science to understand science itself has been unprecedented because only recently has there been access to high-volume and high-quality data sets of scientific output (e.g., publications, patents, grants) and computers and algorithms capable of handling this enormous stream of data. This article reviews major work on models that aim to capture and recreate the structure and dynamics of scientific evolution. We then introduce a general process model that simultaneously grows coauthor and paper citation networks. The statistical and dynamic properties of the networks generated by this model are validated against a 20-year data set of articles published in PNAS. Systematic deviations from a power law distribution of citations to papers are well fit by a model that incorporates a partitioning of authors and papers into topics, a bias for authors to cite recent papers, and a tendency for authors to cite papers cited by papers that they have read. In this TARL model (for topics, aging, and recursive linking), the number of topics is linearly related to the clustering coefficient of the simulated paper citation network. PMID:14976254

A principal component analysis of the dynamics of subdomains and binding sites in human serum albumin.

PubMed

Paris, Guillaume; Ramseyer, Christophe; Enescu, Mironel

2014-05-01

The conformational dynamics of human serum albumin (HSA) was investigated by principal component analysis (PCA) applied to three molecular dynamics trajectories of 200 ns each. The overlap of the essential subspaces spanned by the first 10 principal components (PC) of different trajectories was about 0.3 showing that the PCA based on a trajectory length of 200 ns is not completely convergent for this protein. The contributions of the relative motion of subdomains and of the subdomains (internal) distortion to the first 10 PCs were found to be comparable. Based on the distribution of the first 3 PC, 10 protein conformers are identified showing relative root mean square deviations (RMSD) between 2.3 and 4.6 Å. The main PCs are found to be delocalized over the whole protein structure indicating that the motions of different protein subdomains are coupled. This coupling is considered as being related to the allosteric effects observed upon ligand binding to HSA. On the other hand, the first PC of one of the three trajectories describes a conformational transition of the protein domain I that is close to that experimentally observed upon myristate binding. This is a theoretical support for the older hypothesis stating that changes of the protein onformation favorable to binding can precede the ligand complexation. A detailed all atoms PCA performed on the primary Sites 1 and 2 confirms the multiconformational character of the HSA binding sites as well as the significant coupling of their motions. Copyright © 2013 Wiley Periodicals, Inc.

Mutations in the VLGR1 Gene Implicate G-Protein Signaling in the Pathogenesis of Usher Syndrome Type II

PubMed Central

Weston, Michael D.; Luijendijk, Mirjam W. J.; Humphrey, Kurt D.; Möller, Claes; Kimberling, William J.

2004-01-01

Usher syndrome type II (USH2) is a genetically heterogeneous autosomal recessive disorder with at least three genetic subtypes (USH2A, USH2B, and USH2C) and is classified phenotypically as congenital hearing loss and progressive retinitis pigmentosa. The VLGR1 (MASS1) gene in the 5q14.3-q21.1 USH2C locus was considered a likely candidate on the basis of its protein motif structure and expressed-sequence-tag representation from both cochlear and retinal subtracted libraries. Denaturing high-performance liquid chromatography and direct sequencing of polymerase-chain-reaction products amplified from 10 genetically independent patients with USH2C and 156 other patients with USH2 identified four isoform-specific VLGR1 mutations (Q2301X, I2906FS, M2931FS, and T6244X) from three families with USH2C, as well as two sporadic cases. All patients with VLGR1 mutations are female, a significant deviation from random expectations. The ligand(s) for the VLGR1 protein is unknown, but on the basis of its potential extracellular and intracellular protein-protein interaction domains and its wide mRNA expression profile, it is probable that VLGR1 serves diverse cellular and signaling processes. VLGR1 mutations have been previously identified in both humans and mice and are associated with a reflex-seizure phenotype in both species. The identification of additional VLGR1 mutations to test whether a phenotype/genotype correlation exists, akin to that shown for other Usher syndrome disease genes, is warranted. PMID:14740321

A flexible docking scheme to explore the binding selectivity of PDZ domains.

PubMed

Gerek, Z Nevin; Ozkan, S Banu

2010-05-01

Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using ROSETTALIGAND, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 A. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately.

DockoMatic: automated peptide analog creation for high throughput virtual screening.

PubMed

Jacob, Reed B; Bullock, Casey W; Andersen, Tim; McDougal, Owen M

2011-10-01

The purpose of this manuscript is threefold: (1) to describe an update to DockoMatic that allows the user to generate cyclic peptide analog structure files based on protein database (pdb) files, (2) to test the accuracy of the peptide analog structure generation utility, and (3) to evaluate the high throughput capacity of DockoMatic. The DockoMatic graphical user interface interfaces with the software program Treepack to create user defined peptide analogs. To validate this approach, DockoMatic produced cyclic peptide analogs were tested for three-dimensional structure consistency and binding affinity against four experimentally determined peptide structure files available in the Research Collaboratory for Structural Bioinformatics database. The peptides used to evaluate this new functionality were alpha-conotoxins ImI, PnIA, and their published analogs. Peptide analogs were generated by DockoMatic and tested for their ability to bind to X-ray crystal structure models of the acetylcholine binding protein originating from Aplysia californica. The results, consisting of more than 300 simulations, demonstrate that DockoMatic predicts the binding energy of peptide structures to within 3.5 kcal mol(-1), and the orientation of bound ligand compares to within 1.8 Å root mean square deviation for ligand structures as compared to experimental data. Evaluation of high throughput virtual screening capacity demonstrated that Dockomatic can collect, evaluate, and summarize the output of 10,000 AutoDock jobs in less than 2 hours of computational time, while 100,000 jobs requires approximately 15 hours and 1,000,000 jobs is estimated to take up to a week. Copyright © 2011 Wiley Periodicals, Inc.

Electronic properties of thiolate compounds of oxomolybdenum(V) and their tungsten and selenium analogues. Effects of /sup 17/O, /sup 98/Mo, and /sup 95/Mo isotope substitution upon ESR spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanson, G.R.; Brunette, A.A.; McDonell, A.C.

1981-04-22

The series of crystalline, mononuclear B/sup +/(MO(XR)/sub 4/)/sup -/ and triply bridged binuclear B/sup +/(M/sub 2/O/sub 2/(XR)/sub 6/(OMe))/sup -/(M = Mo, W; X = S, Se; R = aryl; B = quaternary cation) salts have been isolated and the anions (MoO(SR)/sub 4/)/sup -/ (R = Et, CH/sub 2/Ph) stabilized in solution at -60/sup 0/C. The mononuclear anions are intensely colored due to a ligand-to-metal charge-transfer transition which is absent in the binuclear species. The magnetic susceptibilities of (Et/sub 4/N)(MO(SPh)/sub 4/) show a Curie dependence in the range 300 to 4.2 K with minor deviations in the tungsten compound. The behaviormore » is essentially that of magnetically dilute 4d/sup 1/ and 5d/sup 1/ systems exhibiting a tetragonal ligand field and greatly reduced spin-orbit coupling on the metal. The presence of strong spin-spin coupling in the binuclear compounds leads to magnetic moments close to 0. ESR spectra (at X- and Q-band frequencies) of the mononuclear anions exhibit axial symmetry, and /sup 98/Mo and /sup 95/Mo isotope substitution and computer simulation permit accurate extraction of the g and hyperfine tensor anisotropies. Exceptionally arrow line widths permit observation of /sup 17/O-superhyperfine coupling in /sup 17/O-enriched (/sup 98/MoO(SPh)/sub 4/)/sup -/(a = 2.2 x 10/sup -4/cm/sup -1/).« less

Data quality in drug discovery: the role of analytical performance in ligand binding assays

NASA Astrophysics Data System (ADS)

Wätzig, Hermann; Oltmann-Norden, Imke; Steinicke, Franziska; Alhazmi, Hassan A.; Nachbar, Markus; El-Hady, Deia Abd; Albishri, Hassan M.; Baumann, Knut; Exner, Thomas; Böckler, Frank M.; El Deeb, Sami

2015-09-01

Despite its importance and all the considerable efforts made, the progress in drug discovery is limited. One main reason for this is the partly questionable data quality. Models relating biological activity and structures and in silico predictions rely on precisely and accurately measured binding data. However, these data vary so strongly, such that only variations by orders of magnitude are considered as unreliable. This can certainly be improved considering the high analytical performance in pharmaceutical quality control. Thus the principles, properties and performances of biochemical and cell-based assays are revisited and evaluated. In the part of biochemical assays immunoassays, fluorescence assays, surface plasmon resonance, isothermal calorimetry, nuclear magnetic resonance and affinity capillary electrophoresis are discussed in details, in addition radiation-based ligand binding assays, mass spectrometry, atomic force microscopy and microscale thermophoresis are briefly evaluated. In addition, general sources of error, such as solvent, dilution, sample pretreatment and the quality of reagents and reference materials are discussed. Biochemical assays can be optimized to provide good accuracy and precision (e.g. percental relative standard deviation <10 %). Cell-based assays are often considered superior related to the biological significance, however, typically they cannot still be considered as really quantitative, in particular when results are compared over longer periods of time or between laboratories. A very careful choice of assays is therefore recommended. Strategies to further optimize assays are outlined, considering the evaluation and the decrease of the relevant error sources. Analytical performance and data quality are still advancing and will further advance the progress in drug development.

Crystal structure of mer-tris-{2,6-di-fluoro-3-[5-(2-fluoro-phen-yl)pyridin-2-yl-κN]pyridin-4-yl-κC4}iridium(III) di-chloro-methane hemisolvate n-hexane hemisolvate.

PubMed

Kang, Youngjin; Park, Ki-Min; Kim, Jinho

2017-12-01

The asymmetric unit of the title compound, [Ir(C 17 H 11 F 2 N 2 ) 3 ]·0.5CH 3 (CH 2 ) 4 CH 3 ·0.5CH 2 Cl 2 , comprises one Ir III atom, three 2,6-di-fluoro-3-[5-(2-fluoro-phen-yl)pyridin-2-yl]pyridin-4-yl ligands and half each of an n -hexane and a di-chloro-methane solvent mol-ecule located about crystallographic inversion centres. The Ir III atom displays a distorted octa-hedral coordination geometry, having three C , N -chelating 2,6-di-fluoro-3-[5-(2-fluoro-phen-yl)pyridin-2-yl]pyridin-4-yl ligands arranged in a meridional manner. The Ir III ion lies almost in the equatorial plane [deviation = 0.0069 (15) Å]. The average distance [2.041 (3) Å] of Ir-C bonds is slightly shorter than that [2.076 (3) Å] of Ir-N bonds. A variety of intra- and inter-molecular C-H⋯F and C-H⋯π hydrogen bonds, as well as inter-molecular C-F⋯π inter-actions, contribute to the stabilization of the mol-ecular and crystal structures, and result in the formation of a two-dimensional network parallel to the ab plane. No inter-actions between n -hexane solvent mol-ecules and the other components in the title compound are observed.

Carboxylic acid derivatives display potential selectivity for human histone deacetylase 6: Structure-based virtual screening, molecular docking and dynamics simulation studies.

PubMed

Uba, Abdullahi Ibrahim; Yelekçi, Kemal

2018-08-01

Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of α-tubulin, making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available, providing avenues for structure-based drug design campaign. Here, in our continuous effort to identify potentially selective HDAC6 inhibitors, structure-based virtual screening of ∼72 461 compounds was carried out using Autodock Vina. The top 100 compounds with calculated ΔG < -10 kcal/mol were manually inspected for binding mode orientation. Furthermore, the top 20 compounds with reasonable binding modes were evaluated for selectivity by further docking against HDAC6 and HDAC7 using Autodock4. Four compounds with a carboxylic fragment, displayed potential selectivity for HDAC6 over HDAC7, and were found to have good druglike and ADMET properties. Their docking complexes were then submitted to 10 ns-molecular dynamics (MD) simulation using nanoscale MD (NAMD) software, to examine the stability of ligand binding modes. These predicted inhibitors remained bound to HDAC6 in the presence of water and ions, and the root-mean-square deviation (RMSD), radius of gyration (Rg) and nonbond distance (protein-ligand) profiles suggested that they might be stable over time of the simulation. This study may provide scaffolds for further lead optimization towards the design of HDAC6 inhibitors with improved selectivity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ligand structure and mechanical properties of single-nanoparticle-thick membranes.

PubMed

Salerno, K Michael; Bolintineanu, Dan S; Lane, J Matthew D; Grest, Gary S

2015-06-01

The high mechanical stiffness of single-nanoparticle-thick membranes is believed to result from the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with a nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH(3)) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Moreover, the particular end group (COOH or CH(3)) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.

PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures.

PubMed

Shin, Jae-Min; Cho, Doo-Ho

2005-01-01

PDB-Ligand (http://www.idrtech.com/PDB-Ligand/) is a three-dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). It is also a database tool that allows one to browse, classify, superimpose and visualize these structures. As of May 2004, there are about 4870 types of small molecular ligands, experimentally determined as a complex with protein or DNA in the PDB. The proteins that a given ligand binds are often homologous and present the same binding structure to the ligand. However, there are also many instances wherein a given ligand binds to two or more unrelated proteins, or to the same or homologous protein in different binding environments. PDB-Ligand serves as an interactive structural analysis and clustering tool for all the ligand-binding structures in the PDB. PDB-Ligand also provides an easier way to obtain a number of different structure alignments of many related ligand-binding structures based on a simple and flexible ligand clustering method. PDB-Ligand will be a good resource for both a better interpretation of ligand-binding structures and the development of better scoring functions to be used in many drug discovery applications.

Pharmacoinformatics exploration of polyphenol oxidases leading to novel inhibitors by virtual screening and molecular dynamic simulation study.

PubMed

Hassan, Mubashir; Abbas, Qamar; Ashraf, Zaman; Moustafa, Ahmed A; Seo, Sung-Yum

2017-06-01

Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis. The 3D structures of PPO1 and PPO2 were built through homology modeling, while the 3D crystal structures of PPO3 and PPO4 were retrieved from PDB. Pharmacophore modeling was performed using LigandScout 3.1 software and top five models were selected to screen the libraries (2601 of Aurora and 727, 842 of ZINC). Top 10 hit compounds (C1-10) were short-listed having strong binding affinities for PPO1-4. Drug and synthetic accessibility (SA) scores along with absorption, distribution, metabolism, excretion and toxicity (ADMET) assessment were employed to scrutinize the best lead hit. C4 (name) hit showed the best predicted SA score (5.75), ADMET properties and drug-likeness behavior among the short-listed compounds. Furthermore, docking simulations were performed to check the binding affinity of C1-C10 compounds against target proteins (PPOs). The binding affinity values of complex between C4 and PPOs were higher than those of other complexes (-11.70, -12.1, -9.90 and -11.20kcal/mol with PPO1, PPO2, PPO3, or PPO4, respectively). From comparative docking energy and binding analyses, PPO2 may be considered as better target for melanogenesis than others. The potential binding modes of C4, C8 and C10 against PPO2 were explored using molecular dynamics simulations. The root mean square deviation and fluctuation (RMSD/RMSF) graphs results depict the significance of C4 over the other compounds. Overall, bioactivity and ligand efficiency profiles suggested that the proposed hit may be more effective inhibitors for melanogenesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Composition of inner-source heavy pickup ions at 1 AU: SOHO/CELIAS/CTOF observations. Implications for the production mechanisms

NASA Astrophysics Data System (ADS)

Taut, A.; Berger, L.; Drews, C.; Wimmer-Schweingruber, R. F.

2015-04-01

Context. Pickup ions in the inner heliosphere mainly originate in two sources, one interstellar and one in the inner solar system. In contrast to the interstellar source that is comparatively well understood, the nature of the inner source has not been clearly identified. Former results obtained with the Solar Wind Ion Composition Spectrometer on-board the Ulysses spacecraft revealed that the composition of inner-source pickup ions is similar, but not equal, to the elemental solar-wind composition. These observations suffered from very low counting statistics of roughly one C+ count per day. Aims: Because the composition of inner-source pickup ions could lead to identifying their origin, we used data from the Charge-Time-Of-Flight sensor on-board the Solar and Heliospheric Observatory. It offers a large geometry factor that results in about 100 C+ counts per day combined with an excellent mass-per-charge resolution. These features enable a precise determination of the inner-source heavy pickup ion composition at 1 AU. To address the production mechanisms of inner-source pickup ions, we set up a toy model based on the production scenario involving the passage of solar-wind ions through thin dust grains to explain the observed deviations of the inner-source PUI and the elemental solar-wind composition. Methods: An in-flight calibration of the sensor allows identification of heavy pickup ions from pulse height analysis data by their mass-per-charge. A statistical analysis was performed to derive the inner-source heavy pickup ion relative abundances of N+, O+, Ne+, Mg+, Mg2+, and Si+ compared to C+. Results: Our results for the inner-source pickup ion composition are in good agreement with previous studies and confirm the deviations from the solar-wind composition. The large geometry factor of the Charge-Time-of-Flight sensor even allowed the abundance ratios of the two most prominent pickup ions, C+ and O+, to be investigated at varying solar-wind speeds. We found that the O+/C+ ratio increases systematically with higher solar-wind speeds. This observation is an unprecedented feature characterising the production of inner-source pickup ions. Comparing our observations to the toy model results, we find that both the deviation from the solar-wind composition and the solar-wind-speed dependent O+/C+ ratio can be explained.

Ligand structure and mechanical properties of single-nanoparticle thick membranes

DOE PAGES

Salerno, Kenneth Michael; Bolintineanu, Dan S.; Lane, J. Matthew D.; ...

2015-06-16

We believe that the high mechanical stiffness of single-nanoparticle-thick membranes is the result of the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with amore » nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH 3) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Additionally, the particular end group (COOH or CH 3) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salerno, Kenneth Michael; Bolintineanu, Dan S.; Lane, J. Matthew D.

We believe that the high mechanical stiffness of single-nanoparticle-thick membranes is the result of the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with amore » nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH 3) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Additionally, the particular end group (COOH or CH 3) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.« less

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.

PubMed

Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila

2016-10-01

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

Screening of matrix metalloproteinases available from the protein data bank: insights into biological functions, domain organization, and zinc binding groups.

PubMed

Nicolotti, Orazio; Miscioscia, Teresa Fabiola; Leonetti, Francesco; Muncipinto, Giovanni; Carotti, Angelo

2007-01-01

A total of 142 matrix metalloproteinase (MMP) X-ray crystallographic structures were retrieved from the Protein Data Bank (PDB) and analyzed by an automated and efficient routine, developed in-house, with a series of bioinformatic tools. Highly informative heat maps and hierarchical clusterograms provided a reliable and comprehensive representation of the relationships existing among MMPs, enlarging and complementing the current knowledge in the field. Multiple sequence and structural alignments permitted better location and display of key MMP motifs and quantification of the residue consensus at each amino acid position in the most critical binding subsites of MMPs. The MMP active site consensus sequences, the C-alpha root-mean-square deviation (RMSd) analysis of diverse enzymatic subsites, and the examination of the chemical nature, binding topologies, and zinc binding groups (ZBGs) of ligands extracted from crystallographic complexes provided useful insights on the structural arrangements of the most potent MMP inhibitors.

Ligand placement based on prior structures: the guided ligand-replacement method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klei, Herbert E.; Bristol-Myers Squibb, Princeton, NJ 08543-4000; Moriarty, Nigel W., E-mail: nwmoriarty@lbl.gov

2014-01-01

A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods formore » modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR leverages prior knowledge from earlier structures to facilitate ligand placement in the current structure.« less

Prediction of toxicity of zinc and nickel mixtures to Artemia sp. at various salinities: From additivity to antagonism.

PubMed

Damasceno, Évila Pinheiro; de Figuerêdo, Lívia Pitombeira; Pimentel, Marcionília Fernandes; Loureiro, Susana; Costa-Lotufo, Letícia Veras

2017-08-01

Few studies have examined the toxicity of metal mixtures to marine organisms exposed to different salinities. The aim of the present study was to investigate the acute toxicity of zinc and nickel exposures singly and in combination to Artemia sp. under salinities of 10, 17, and 35 psu. The mixture concentrations were determined according to individual toxic units (TUs) to follow a fixed ratio design. Zinc was more toxic than nickel, and both their individual toxicities were higher at lower salinities. These changes in toxicity can be attributed to the Biotic Ligand Model (BLM) rather than to metal speciation. To analyze the mixture effect, the observed data were compared with the expected mixture effects predicted by the concentration addition (CA) model and by deviations for synergistic/antagonistic interactions and dose-level and dose-ratio dependencies. For a salinity of 35 psu, the mixture had no deviations; therefore, the effects were additive. After decreasing the salinity to 17 psu, the toxicity pattern changed to antagonism at low concentrations and synergism at higher equivalent LC 50 levels. For the lowest salinity tested (10 psu), antagonism was observed. The speciations of both metals were similar when in a mixture and when isolated, and changes in toxicity patterns are more related to the organism's physiology than metal speciation. Therefore, besides considering chemical interactions in real-world scenarios, where several chemicals can be present, the influence of abiotic factors, such as salinity, should also be considered. Copyright © 2017 Elsevier Inc. All rights reserved.

Analysis of the structure and dynamics of human serum albumin.

PubMed

Guizado, T R Cuya

2014-10-01

Human serum albumin (HSA) is a biologically relevant protein that binds a variety of drugs and other small molecules. No less than 50 structures are deposited in the RCSB Protein Data Bank (PDB). Based on these structures, we first performed a clustering analysis. Despite the diversity of ligands, only two well defined conformations are detected, with a deviation of 0.46 nm between the average structures of the two clusters, while deviations within each cluster are smaller than 0.08 nm. Those two conformations are representative of the apoprotein and the HSA-myristate complex already identified in previous literature. Considering the structures within each cluster as a representative sample of the dynamical states of the corresponding conformation, we scrutinize the structural and dynamical differences between both conformations. Analysis of the fluctuations within each cluster set reveals that domain II is the most rigid one and better matches both structures. Then, taking this domain as reference, we show that the structural difference between both conformations can be expressed in terms of twist and hinge motions of domains I and III, respectively. We also characterize the dynamical difference between conformations by computing correlations and principal components for each set of dynamical states. The two conformations display different collective motions. The results are compared with those obtained from the trajectories of short molecular dynamics simulations, giving consistent outcomes. Let us remark that, beyond the relevance of the results for the structural and dynamical characterization of HAS conformations, the present methodology could be extended to other proteins in the PDB archive.

Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction.

PubMed

Pérot, Stéphanie; Regad, Leslie; Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A; Villoutreix, Bruno O; Camproux, Anne-Claude

2013-01-01

Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket properties for ligand binding.

Insights into an Original Pocket-Ligand Pair Classification: A Promising Tool for Ligand Profile Prediction

PubMed Central

Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A.; Villoutreix, Bruno O.; Camproux, Anne-Claude

2013-01-01

Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket properties for ligand binding. PMID:23840299

Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity

NASA Astrophysics Data System (ADS)

Kajita, Masashi K.; Aihara, Kazuyuki; Kobayashi, Tetsuya J.

2017-07-01

Specific interactions between receptors and their target ligands in the presence of nontarget ligands are crucial for biological processes such as T cell ligand discrimination. To discriminate between the target and nontarget ligands, cells have to increase specificity to the target ligands by amplifying the small differences in affinity among ligands. In addition, sensitivity to the ligand concentration and quick discrimination are also important to detect low amounts of target ligands and facilitate fast cellular decision making after ligand recognition. In this work we propose a mechanism for nonlinear specificity amplification (ultraspecificity) based on zero-order saturating reactions, which was originally proposed to explain nonlinear sensitivity amplification (ultrasensitivity) to the ligand concentration. In contrast to the previously proposed proofreading mechanisms that amplify the specificity by a multistep reaction, our model can produce an optimal balance of specificity, sensitivity, and quick discrimination. Furthermore, we show that a model for insensitivity to a large number of nontarget ligands can be naturally derived from a model with the zero-order ultraspecificity. The zero-order ultraspecificity, therefore, may provide an alternative way to understand ligand discrimination from the viewpoint of nonlinear properties in biochemical reactions.

Cationic Gold Clusters Ligated with Differently Substituted Phosphines: Effect of Substitution on Ligand Reactivity and Binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Grant E.; Olivares, Astrid M.; Hill, David E.

2015-01-01

We present a systematic study of the effect of the number of methyl (Me) and cyclohexyl (Cy) functional groups in monodentate phosphine ligands on the solution-phase synthesis of ligated sub-nanometer gold clusters and their gas-phase fragmentation pathways. Small mixed ligand cationic gold clusters were synthesized using ligand exchange reactions between pre-formed triphenylphosphine ligated (PPh3) gold clusters and monodentate Me- and Cy-substituted ligands in solution and characterized using electrospray ionization mass spectrometry (ESI-MS) and collision-induced dissociation (CID) experiments. Under the same experimental conditions, larger gold-PPh3 clusters undergo efficient exchange of unsubstituted PPh3 ligands for singly Me- and Cy-substituted PPh2Me and PPh2Cymore » ligands. The efficiency of ligand exchange decreases with an increasing number of Me or Cy groups in the substituted phosphine ligands. CID experiments performed for a series of ligand-exchanged gold clusters indicate that loss of a neutral Me-substituted ligand is preferred over loss of a neutral PPh¬3 ligand while the opposite trend is observed for Cy-substituted ligands. The branching ratio of the competing ligand loss channels is strongly correlated with the electron donating ability of the phosphorous lone pair as determined by the relative proton affinity of the ligand. The results indicate that the relative ligand binding energies increase in the order PMe3 < PPhMe2 < PPh2Me < PPh3< PPh2Cy < PPhCy2< PCy3. Furthermore, the difference in relative ligand binding energies increases with the number of substituted PPh3-mMem or PPh3-mCym ligands (L) exchanged onto each cluster. This study provides the first experimental determination of the relative binding energies of ligated gold clusters containing differently substituted monophosphine ligands, which are important to controlling their synthesis and reactivity in solution. The results also indicate that ligand substitution is an important parameter that must be considered in theoretical modeling of these complex systems« less

Risk and dynamics of unprecedented hot months in South East China

NASA Astrophysics Data System (ADS)

Thompson, Vikki; Dunstone, Nick J.; Scaife, Adam A.; Smith, Doug M.; Hardiman, Steven C.; Ren, Hong-Li; Lu, Bo; Belcher, Stephen E.

2018-06-01

The Yangtze region of South East China has experienced several extreme hot summer months in recent years. Such events can have devastating socio-economic impacts. We use a large ensemble of initialised climate simulations to assess the current chance of unprecedented hot summer months in the Yangtze River region. We find a 10% chance of an unprecedented hot summer month each year. Our simulations suggest that monthly mean temperatures up to 3 °C hotter than the current record are possible. The dynamics of these unprecedented extremes highlights the occurrence of a stationary atmospheric wave, the Silk Road Pattern, in a significant number of extreme hot events. We present evidence that this atmospheric wave is driven by variability in the Indian summer monsoon. Other extreme events are associated with a westward shift in the western North Pacific subtropical high. The most extreme simulated events exhibit combined characteristics of both the Silk Road Pattern and the shifted western North Pacific subtropical high.

Ligand solvation in molecular docking.

PubMed

Shoichet, B K; Leach, A R; Kuntz, I D

1999-01-01

Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.

Assessment of automatic ligand building in ARP/wARP.

PubMed

Evrard, Guillaume X; Langer, Gerrit G; Perrakis, Anastassis; Lamzin, Victor S

2007-01-01

The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.

Through-Space Charge Interaction Substituent Effects in Molecular Catalysis Leading to the Design of the Most Efficient Catalyst of CO2-to-CO Electrochemical Conversion.

PubMed

Azcarate, Iban; Costentin, Cyrille; Robert, Marc; Savéant, Jean-Michel

2016-12-28

The starting point of this study of through-space substituent effects on the catalysis of the electrochemical CO 2 -to-CO conversion by iron(0) tetraphenylporphyrins is the linear free energy correlation between through-structure electronic effects and the iron(I/0) standard potential that we established separately. The introduction of four positively charged trimethylanilinium groups at the para positions of the tetraphenylporphyrin (TPP) phenyls results in an important positive deviation from the correlation and a parallel improvement of the catalytic Tafel plot. The assignment of this catalysis boosting effect to the Coulombic interaction of these positive charges with the negative charge borne by the initial Fe 0 -CO 2 adduct is confirmed by the negative deviation observed when the four positive charges are replaced by four negative charges borne by sulfonate groups also installed in the para positions of the TPP phenyls. The climax of this strategy of catalysis boosting by means of Coulombic stabilization of the initial Fe 0 -CO 2 adduct is reached when four positively charged trimethylanilinium groups are introduced at the ortho positions of the TPP phenyls. The addition of a large concentration of a weak acid-phenol-helps by cleaving one of the C-O bonds of CO 2 . The efficiency of the resulting catalyst is unprecedented, as can be judged by the catalytic Tafel plot benchmarking with all presently available catalysts of the electrochemical CO 2 -to-CO conversion. The maximal turnover frequency (TOF) is as high as 10 6 s -1 and is reached at an overpotential of only 220 mV; the extrapolated TOF at zero overpotential is larger than 300 s -1 . This catalyst leads to a highly selective formation of CO (practically 100%) in spite of the presence of a high concentration of phenol, which could have favored H 2 evolution. It is also very stable, showing no significant alteration after more than 80 h of electrolysis.

Flying Under the LiDAR: Relating Forest Structure to Bat Community Diversity

NASA Astrophysics Data System (ADS)

Swanson, A. C.; Weishampel, J. F.

2015-12-01

Bats are important to many ecological processes such as pollination, insect (and by proxy, disease) control, and seed dispersal and can be used to monitor ecosystem health. However, they are facing unprecedented extinction risks from habitat degradation as well as pressures from pathogens (e.g., white-nose syndrome) and wind turbines. LiDAR allows ecologists to measure structural variables of forested landscapes with increased precision and accuracy at broader spatial scales than previously possible. This study used airborne LiDAR to classify forest habitat/canopy structure at the Ordway-Swisher Biological Station (OSBS) in north central Florida. LiDAR data were acquired by the NEON airborne observation platform in summer 2014. OSBS consists of open-canopy pine savannas, closed-canopy hardwood hammocks, and seasonally wet prairies. Multiple forest structural parameters (e.g., mean, maximum, and standard deviation of height returns) were derived from LiDAR point clouds using the USDA software program FUSION. K-means clustering was used to segregate each 5x5 m raster across the ~3765 ha OSBS area into six different clusters based on the derived canopy metrics. Cluster averages for maximum, mean, and standard deviation of return heights ranged from 0 to 19.4 m, 0 to 15.3 m, and 0 to 3.0 m, respectively. To determine the relationships among these landscape-canopy features and bat species diversity and abundances, AnaBat II bat detectors were deployed from May to September in 2015 stratified by these distinct clusters. Bat calls were recorded from sunset to sunrise during each sampling period. Species were identified using AnalookW. A statistical regression model selection approach was performed in order to evaluate how forest attributes such as understory clutter, open regions, open and closed canopy, etc. influence bat communities. This knowledge provides a deeper understanding of habitat-species interactions to better manage survival of these species.

Computational Methods in Drug Discovery

PubMed Central

Sliwoski, Gregory; Kothiwale, Sandeepkumar; Meiler, Jens

2014-01-01

Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature. PMID:24381236

Critical ligand binding reagent preparation/selection: when specificity depends on reagents.

PubMed

Rup, Bonita; O'Hara, Denise

2007-05-11

Throughout the life cycle of biopharmaceutical products, bioanalytical support is provided using ligand binding assays to measure the drug product for pharmacokinetic, pharmacodynamic, and immunogenicity studies. The specificity and selectivity of these ligand binding assays are highly dependent on the ligand binding reagents. Thus the selection, characterization, and management processes for ligand binding reagents are crucial to successful assay development and application. This report describes process considerations for selection and characterization of ligand binding reagents that are integral parts of the different phases of assay development. Changes in expression, purification, modification, and storage of the ligand binding reagents may have a profound effect on the ligand binding assay performance. Thus long-term management of the critical ligand binding assay reagents is addressed including suggested characterization criteria that allow ligand binding reagents to be used in as consistent a manner as possible. Examples of challenges related to the selection, modification, and characterization of ligand binding reagents are included.

Concerted Dynamic Motions of an FABP4 Model and Its Ligands Revealed by Microsecond Molecular Dynamics Simulations

PubMed Central

2015-01-01

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4–ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level. PMID:25231537

Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations.

PubMed

Li, Yan; Li, Xiang; Dong, Zigang

2014-10-14

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4-ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level.

Analysis of macromolecules, ligands and macromolecule-ligand complexes

DOEpatents

Von Dreele, Robert B [Los Alamos, NM

2008-12-23

A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

Photoluminescent lanthanide-organic bilayer networks with 2,3-pyrazinedicarboxylate and oxalate.

PubMed

Soares-Santos, Paula C R; Cunha-Silva, Luís; Paz, Filipe A Almeida; Ferreira, Rute A S; Rocha, João; Carlos, Luís D; Nogueira, Helena I S

2010-04-05

The hydrothermal reaction between lanthanide nitrates and 2,3-pyrazinedicarboxylic acid led to a new series of two-dimensional (2D) lanthanide-organic frameworks: [Ln(2)(2,3-pzdc)(2)(ox)(H(2)O)(2)](n) [where 2,3-pzdc(2-) = 2,3-pyrazinedicarboxylate, ox(2-) = oxalate, and Ln(III) = Ce, Nd, Sm, Eu, Gd, Tb, or Er]. The structural details of these materials were determined by single-crystal X-ray diffraction (for Ce(3+) and Nd(3+)) that revealed the formation of a layered structure. Cationic monolayers of {(infinity)(2)[Ln(2,3-pzdc)(H(2)O)](+)} are interconnected via the ox(2-) ligand leading to the formation of neutral (infinity)(2)[Ln(2)(2,3-pzdc)(2)(ox)(H(2)O)(2)] bilayer networks; structural cohesion of the crystalline packing is reinforced by the presence of highly directional O-H...O hydrogen bonds between adjacent bilayers. Under the employed hydrothermal conditions 2,3-pyrazinedicarboxylic acid can be decomposed into ox(2-) and 2-pyrazinecarboxylate (2-pzc(-)), as unequivocally proved by the isolation of the discrete complex [Tb(2)(2-pzc)(4)(ox)(H(2)O)(6)].10H(2)O. Single-crystal X-ray diffraction of this latter complex revealed its co-crystallization with an unprecedented (H(2)O)(16) water cluster. Photoluminescence measurements were performed for the Nd(3+), Sm(3+), Eu(3+), and Tb(3+) compounds which show, under UV excitation at room temperature, the Ln(3+) characteristic intra-4f(N) emission peaks. The energy level of the triplet states of 2,3-pyrazinedicarboxylic acid (18939 cm(-1)) and oxalic acid (24570 cm(-1)) was determined from the 12 K emission spectrum of the Gd(3+) compound. The (5)D(0) and (5)D(4) lifetime values (0.333 +/- 0.006 and 0.577 +/- 0.017 ms) and the absolute emission quantum yields (0.13 +/- 0.01 and 0.05 +/- 0.01) were determined for the Eu(3+) and Tb(3+) compounds, respectively. For the Eu(3+) compound the energy transfer efficiency arising from the ligands' excited states was estimated (0.93 +/- 0.01).

LigandRNA: computational predictor of RNA–ligand interactions

PubMed Central

Philips, Anna; Milanowska, Kaja; Łach, Grzegorz; Bujnicki, Janusz M.

2013-01-01

RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA–small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA–ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a “meta-predictor” leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl. PMID:24145824

Dynamic biochemical tissue analysis detects functional L-selectin ligands on colon cancer tissues

PubMed Central

Carlson, Grady E.; Martin, Eric W.; Shirure, Venktesh S.; Malgor, Ramiro; Resto, Vicente A.; Goetz, Douglas J.; Burdick, Monica M.

2017-01-01

A growing body of evidence suggests that L-selectin ligands presented on circulating tumor cells facilitate metastasis by binding L-selectin presented on leukocytes. Commonly used methods for detecting L-selectin ligands on tissues, e.g., immunostaining, are performed under static, no-flow conditions. However, such analysis does not assay for functional L-selectin ligands, specifically those ligands that promote adhesion under shear flow conditions. Recently our lab developed a method, termed dynamic biochemical tissue analysis (DBTA), to detect functional selectin ligands in situ by probing tissues with L-selectin-coated microspheres under hemodynamic flow conditions. In this investigation, DBTA was used to probe human colon tissues for L-selectin ligand activity. The detection of L-selectin ligands using DBTA was highly specific. Furthermore, DBTA reproducibly detected functional L-selectin ligands on diseased, e.g., cancerous or inflamed, tissues but not on noncancerous tissues. In addition, DBTA revealed a heterogeneous distribution of functional L-selectin ligands on colon cancer tissues. Most notably, detection of L-selectin ligands by immunostaining using HECA-452 antibody only partially correlated with functional L-selectin ligands detected by DBTA. In summation, the results of this study demonstrate that DBTA detects functional selectin ligands to provide a unique characterization of pathological tissue. PMID:28282455

Impairment of Fas-ligand-caveolin-1 interaction inhibits Fas-ligand translocation to rafts and Fas-ligand-induced cell death.

PubMed

Glukhova, Xenia A; Trizna, Julia A; Proussakova, Olga V; Gogvadze, Vladimir; Beletsky, Igor P

2018-01-22

Fas-ligand/CD178 belongs to the TNF family proteins and can induce apoptosis through death receptor Fas/CD95. The important requirement for Fas-ligand-dependent cell death induction is its localization to rafts, cholesterol- and sphingolipid-enriched micro-domains of membrane, involved in regulation of different signaling complexes. Here, we demonstrate that Fas-ligand physically associates with caveolin-1, the main protein component of rafts. Experiments with cells overexpressing Fas-ligand revealed a FasL N-terminal pre-prolin-rich region, which is essential for the association with caveolin-1. We found that the N-terminal domain of Fas-ligand bears two caveolin-binding sites. The first caveolin-binding site binds the N-terminal domain of caveolin-1, whereas the second one appears to interact with the C-terminal domain of caveolin-1. The deletion of both caveolin-binding sites in Fas-ligand impairs its distribution between cellular membranes, and attenuates a Fas-ligand-induced cytotoxicity. These results demonstrate that the interaction of Fas-ligand and caveolin-1 represents a molecular basis for Fas-ligand translocation to rafts, and the subsequent induction of Fas-ligand-dependent cell death. A possibility of a similar association between other TNF family members and caveolin-1 is discussed.

Functionalization of Cadmium Selenide Quantum Dots with Poly(ethylene glycol): Ligand Exchange, Surface Coverage, and Dispersion Stability.

PubMed

Wenger, Whitney Nowak; Bates, Frank S; Aydil, Eray S

2017-08-22

Semiconductor quantum dots synthesized using rapid mixing of precursors by injection into a hot solution of solvents and surfactants have surface ligands that sterically stabilize the dispersions in nonpolar solvents. Often, these ligands are exchanged to disperse the quantum dots in polar solvents, but quantitative studies of quantum dot surfaces before and after ligand exchange are scarce. We studied exchanging trioctylphosphine (TOP) and trioctylphosphine oxide (TOPO) ligands on as-synthesized CdSe quantum dots dispersed in hexane with a 2000 g/mol thiolated poly(ethylene glycol) (PEG) polymer. Using infrared spectroscopy we quantify the absolute surface concentration of TOP/TOPO and PEG ligands per unit area before and after ligand exchange. While 50-85% of the TOP/TOPO ligands are removed upon ligand exchange, only a few are replaced with PEG. Surprisingly, the remaining TOP/TOPO ligands outnumber the PEG ligands, but these few PEG ligands are sufficient to disperse the quantum dots in polar solvents such as chloroform, tetrahydrofuran, and water. Moreover, as-synthesized quantum dots once easily dispersed in hexane are no longer dispersible in nonpolar solvents after ligand exchange. A subtle coverage-dependent balance between attractive PEG-solvent interactions and repulsive TOP/TOPO-solvent interactions determines the dispersion stability.

Dynamic biochemical tissue analysis detects functional L-selectin ligands on colon cancer tissues.

PubMed

Carlson, Grady E; Martin, Eric W; Shirure, Venktesh S; Malgor, Ramiro; Resto, Vicente A; Goetz, Douglas J; Burdick, Monica M

2017-01-01

A growing body of evidence suggests that L-selectin ligands presented on circulating tumor cells facilitate metastasis by binding L-selectin presented on leukocytes. Commonly used methods for detecting L-selectin ligands on tissues, e.g., immunostaining, are performed under static, no-flow conditions. However, such analysis does not assay for functional L-selectin ligands, specifically those ligands that promote adhesion under shear flow conditions. Recently our lab developed a method, termed dynamic biochemical tissue analysis (DBTA), to detect functional selectin ligands in situ by probing tissues with L-selectin-coated microspheres under hemodynamic flow conditions. In this investigation, DBTA was used to probe human colon tissues for L-selectin ligand activity. The detection of L-selectin ligands using DBTA was highly specific. Furthermore, DBTA reproducibly detected functional L-selectin ligands on diseased, e.g., cancerous or inflamed, tissues but not on noncancerous tissues. In addition, DBTA revealed a heterogeneous distribution of functional L-selectin ligands on colon cancer tissues. Most notably, detection of L-selectin ligands by immunostaining using HECA-452 antibody only partially correlated with functional L-selectin ligands detected by DBTA. In summation, the results of this study demonstrate that DBTA detects functional selectin ligands to provide a unique characterization of pathological tissue.

Methods for Identifying Ligands that Target Nucleic Acid Molecules and Nucleic Acid Structural Motifs

NASA Technical Reports Server (NTRS)

Childs-Disney, Jessica L. (Inventor); Disney, Matthew D. (Inventor)

2017-01-01

Disclosed are methods for identifying a nucleic acid (e.g., RNA, DNA, etc.) motif which interacts with a ligand. The method includes providing a plurality of ligands immobilized on a support, wherein each particular ligand is immobilized at a discrete location on the support; contacting the plurality of immobilized ligands with a nucleic acid motif library under conditions effective for one or more members of the nucleic acid motif library to bind with the immobilized ligands; and identifying members of the nucleic acid motif library that are bound to a particular immobilized ligand. Also disclosed are methods for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a nucleic acid molecule comprising a particular nucleic acid motif, as well as methods for identifying a nucleic acid which interacts with a ligand.

A web server for analysis, comparison and prediction of protein ligand binding sites.

PubMed

Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S

2016-03-25

One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL http://crdd.osdd.net/raghava/lpicom .

Fluorescence resonance energy-transfer affects the determination of the affinity between ligand and proteins obtained by fluorescence quenching method

NASA Astrophysics Data System (ADS)

Xiao, Jianbo; Wei, Xinlin; Wang, Yuanfeng; Liu, Chunxi

2009-11-01

The interaction between esculin and serum albumins was investigated to illustrate that the fluorescence resonance energy-transfer (FRET) affects the determination of the binding constants obtained by fluorescence quenching method. The binding constants ( Ka) obtained by the double-logarithm curve for esculin-BSA and esculin-HSA were 1.02 × 10 7 and 2.07 × 10 4 L/mol, respectively. These results from synchronous fluorescence showed that the Tyr and Trp residues of HSA were affected more deeply than those in BSA. The excitation profile of esculin showed that in the presence of BSA and HSA, the S 0 → S 1 transition of esculin ( λexmax≈340 nm) appears, which is similar to the λemmax of BSA and HSA. The critical distance ( R0) between BSA and esculin is higher than that of HSA, which showed that the affinity of esculin and HSA should be higher than that of BSA. After centrifugation, the concentrations of esculin bound to albumins were determined by means of the fluorescence of esculin. It was found that much more esculin was bound to HSA than to BSA. However, the bound models for BSA and HSA are almost the same. The concentration of esculin bound to serum albumin at first decreased with the addition of esculin and then increased. From above results, it can be concluded that the affinity of esculin and HSA should be higher than that of esculin and BSA. This example showed that in the presence of FRET, the binding constants between ligands and proteins based on fluorescence quenching might be deviated.

Fluorescence resonance energy-transfer affects the determination of the affinity between ligand and proteins obtained by fluorescence quenching method.

PubMed

Xiao, Jianbo; Wei, Xinlin; Wang, Yuanfeng; Liu, Chunxi

2009-11-01

The interaction between esculin and serum albumins was investigated to illustrate that the fluorescence resonance energy-transfer (FRET) affects the determination of the binding constants obtained by fluorescence quenching method. The binding constants (K(a)) obtained by the double-logarithm curve for esculin-BSA and esculin-HSA were 1.02x10(7) and 2.07x10(4)L/mol, respectively. These results from synchronous fluorescence showed that the Tyr and Trp residues of HSA were affected more deeply than those in BSA. The excitation profile of esculin showed that in the presence of BSA and HSA, the S(0)-->S(1) transition of esculin (lambda(ex)(max) approximately 340nm) appears, which is similar to the lambda(em)(max) of BSA and HSA. The critical distance (R(0)) between BSA and esculin is higher than that of HSA, which showed that the affinity of esculin and HSA should be higher than that of BSA. After centrifugation, the concentrations of esculin bound to albumins were determined by means of the fluorescence of esculin. It was found that much more esculin was bound to HSA than to BSA. However, the bound models for BSA and HSA are almost the same. The concentration of esculin bound to serum albumin at first decreased with the addition of esculin and then increased. From above results, it can be concluded that the affinity of esculin and HSA should be higher than that of esculin and BSA. This example showed that in the presence of FRET, the binding constants between ligands and proteins based on fluorescence quenching might be deviated.

Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy.

PubMed

Walder, Robert; Van Patten, William J; Adhikari, Ayush; Perkins, Thomas T

2018-01-23

Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA's attachment point to a coverslip. Importantly, this algorithm was performed at low force (10-20 pN) and relatively fast (15-25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA's overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ∼40 min and versatility by aligning polyprotein- and PEG-based protein-ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.

Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: a combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay.

PubMed

Uba, Abdullahi Ibrahim; Yelekçi, Kemal

2017-10-23

Histone deacetylases (HDACs) have gained increased attention as targets for anticancer drug design and development. HDAC inhibitors have proven to be effective for reversing the malignant phenotype in HDAC-dependent cancer cases. However, lack of selectivity of the many HDAC inhibitors in clinical use and trials contributes to toxicities to healthy cells. It is believed that, the continued identification of isoform-selective inhibitors will eliminate these undesirable adverse effects - a task that remains a major challenge to HDAC inhibitor designs. Here, in an attempt to identify isoform-selective inhibitors, a large compound library containing 2,703,000 compounds retrieved from Otava database was screened against class I HDACs by exhaustive approach of structure-based virtual screening using rDOCK and Autodock Vina. A total of 41 compounds were found to show high-isoform selectivity and were further redocked into their respective targets using Autodock4. Thirty-six compounds showed remarkable isoform selectivity and passed drug-likeness and absorption, distribution, metabolism, elimination and toxicity prediction tests using ADMET Predictor™ and admetSAR. Furthermore, to study the stability of ligand binding modes, 10 ns-molecular dynamics (MD) simulations of the free HDAC isoforms and their complexes with respective best-ranked ligands were performed using nanoscale MD software. The inhibitors remained bound to their respective targets over time of the simulation and the overall potential energy, root-mean-square deviation, root-mean-square fluctuation profiles suggested that the detected compounds may be potential isoform-selective HDAC inhibitors or serve as promising scaffolds for further optimization towards the design of selective inhibitors for cancer therapy.

Ultrasensitivity and sharp threshold theorems for multisite systems

NASA Astrophysics Data System (ADS)

Dougoud, M.; Mazza, C.; Vinckenbosch, L.

2017-02-01

This work studies the ultrasensitivity of multisite binding processes where ligand molecules can bind to several binding sites. It considers more particularly recent models involving complex chemical reactions in allosteric phosphorylation processes and for transcription factors and nucleosomes competing for binding on DNA. New statistics-based formulas for the Hill coefficient and the effective Hill coefficient are provided and necessary conditions for a system to be ultrasensitive are exhibited. It is first shown that the ultrasensitivity of binding processes can be approached using sharp-threshold theorems which have been developed in applied probability theory and statistical mechanics for studying sharp threshold phenomena in reliability theory, random graph theory and percolation theory. Special classes of binding process are then introduced and are described as density dependent birth and death process. New precise large deviation results for the steady state distribution of the process are obtained, which permits to show that switch-like ultrasensitive responses are strongly related to the multi-modality of the steady state distribution. Ultrasensitivity occurs if and only if the entropy of the dynamical system has more than one global minimum for some critical ligand concentration. In this case, the Hill coefficient is proportional to the number of binding sites, and the system is highly ultrasensitive. The classical effective Hill coefficient I is extended to a new cooperativity index I q , for which we recommend the computation of a broad range of values of q instead of just the standard one I  =  I 0.9 corresponding to the 10%-90% variation in the dose-response. It is shown that this single choice can sometimes mislead the conclusion by not detecting ultrasensitivity. This new approach allows a better understanding of multisite ultrasensitive systems and provides new tools for the design of such systems.

Validation and extraction of molecular-geometry information from small-molecule databases.

PubMed

Long, Fei; Nicholls, Robert A; Emsley, Paul; Graǽulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Murshudov, Garib N

2017-02-01

A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 Å resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database.

Two-dimensional metal-organic frameworks with high thermoelectric efficiency through metal ion selection.

PubMed

He, Yuping; Spataru, Catalin D; Léonard, Francois; Jones, Reese E; Foster, Michael E; Allendorf, Mark D; Alec Talin, A

2017-07-26

Two-dimensional (2D) materials have attracted much attention due to their novel properties. An exciting new class of 2D materials based on metal-organic frameworks (MOFs) has recently emerged, displaying high electrical conductivity, a rarity among organic nanoporous materials. The emergence of these materials raises intriguing questions about their fundamental electronic, optical, and thermal properties, but few studies exist in this regard. Here we present an atomistic study of the thermoelectric properties of crystalline 2D MOFs X 3 (HITP) 2 with X = Ni, Pd or Pt, and HITP = 2,3,6,7,10,11-hexaiminotriphenylene, using both ab initio transport models and classical molecular dynamics simulations. We find that these materials have a high Seebeck coefficient and low thermal conductivity, making them promising for thermoelectric applications. Furthermore, we explore the dependence of thermoelectric transport properties on the atomic structure by comparing the calculated band structure, band alignment, and electronic density of states of the three 2D MOFs, and find that the thermoelectric transport properties strongly depend on both the interaction between the ligands and the metal ions, and the d orbital splitting of the metal ions induced by the ligands. This demonstrates that selection of the metal ion is a powerful approach to control and enhance the thermoelectric properties. Interestingly we reveal an unexpected effect where, unlike for electrons, the thermal and electrical current may not be equally carried by the holes, leading to a significant deviation from the Wiedemann-Franz law. The results of this work provide fundamental guidance to optimize the existing 2D MOFs, and to design and discover new families of MOF-like materials for thermoelectric applications.

A preliminary X-ray diffraction study of the laccase from Coriolus zonatus in the native state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyashenko, A. V.; Zhukhlistova, N. E.; Stepanova, E. V.

2006-03-15

The copper-containing enzyme laccase is involved, owing to its oxidase activity, in the biodegradation of lignins-one of the most important bioconversion processes. On the basis of the X-ray diffraction data for the laccase from Coriolus zonatus, the spatial structure of this enzyme is determined with a resolution of 3.2 A. R and R{sub free} are 0.2347 and 0.2976, respectively, and the rms deviations of the bond lengths and the bond angles are 0.009 and 1.547 A, respectively. The three-domain structure of the laccase from Coriolus zonatus is confirmed, where each domain is represented by a protein from the cupredoxin family.more » The spatial organization of the active center of the protein is established. The mononuclear center contains a copper ion Cu(1) with the atoms of S{sub C}ys453, ND1{sub H}is395, and ND1{sub H}is458 ligands. The trinuclear center is formed by copper ions Cu(2), Cu(3), and Cu(4), surrounded by ligands of eight nitrogen atoms of the histidines of the first and third domains of the protein His66, His109, His454, His111, His400, His452, His64, and His398. The Cu(1) ion is located at distances of 11.84 and 13.22 A from the Cu(2) and Cu(3) ions, respectively. The distance between the Cu(2) and Cu(3) ions is 5.14 A and the Cu(4)-Cu(2) and Cu(4)-Cu(3) distances are 4.75 and 4.41 A, respectively.« less

Analysis of zinc binding sites in protein crystal structures.

PubMed

Alberts, I L; Nadassy, K; Wodak, S J

1998-08-01

The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.

Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space.

PubMed

Stegemann, Björn; Klebe, Gerhard

2012-02-01

Small molecules are recognized in protein-binding pockets through surface-exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein-ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise to unexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein-cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein-binding pockets, and the local folding patterns next to the cofactor-binding site. State-of-the-art clustering techniques have been applied to group the different protein-cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process. Copyright © 2011 Wiley Periodicals, Inc.

Modification of the 5' terminus of oligodeoxyribonucleotides for conjugation with ligands.

PubMed

Asseline, U; Thuong, N T

2001-08-01

Ligands can be introduced at the 5' terminus of an oligonucleotide by adding a linker to the ligand and modifying the 5' terminus of the oligonucleotide. These are then reacted to give the ligand-oligonucleotide conjugate. This unit describes the addition of carboxylated and aminoalkylated linkers, and phosphorothioate, phosphate, and masked thiol groups to the 5' terminus of an oligonucleotide. The addition of linkers to ligands and the final reaction that produces the ligand-conjugated oligonucleotide are described elsewhere in the series. This approach is particularly useful when there is a limited amount of ligand available, when the ligand is sensitive to chemical conditions required for oligonucleotide deprotection, or when the ligand is weakly soluble in solvents required for phosphoramidite- or H-phosphonate-mediated oligonucleotide synthesis.

ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.

PubMed

Konc, Janez; Janežič, Dušanka

2014-07-01

The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki.si/ligands. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Access to unusual polycyclic spiro-enones from 2,2'-bis(allyloxy)-1,1'-binaphthyls using Grubbs' catalysts: an unprecedented one-pot RCM/Claisen sequence.

PubMed

Piedra, Estefanía; Francos, Javier; Nebra, Noel; Suárez, Francisco J; Díez, Josefina; Cadierno, Victorio

2011-07-21

Treatment of 2,2'-bis(allyloxy)-1,1'-binaphthyls with the first-generation Grubbs' carbene under MW-irradiation results in the formation of new polycyclic spiro-enones through an unprecedented RCM/Claisen sequence.

Autophagy-Related Protein ATG18 Regulates Apicoplast Biogenesis in Apicomplexan Parasites

PubMed Central

Bansal, Priyanka; Tripathi, Anuj; Thakur, Vandana; Mohmmed, Asif

2017-01-01

ABSTRACT Mechanisms by which 3′-phosphorylated phosphoinositides (3′-PIPs) regulate the development of apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii are poorly understood. The catabolic process of autophagy, which is dependent on autophagy-related proteins (ATGs), is one of the major targets of 3′-PIPs in yeast and mammals. In the present study, we identified autophagy-related protein ATG18 as an effector of 3′-PIPs in these parasites. P. falciparum ATG18 (PfATG18) and T. gondii ATG18 (TgATG18) interact with 3′-PIPs but exhibited differences in their specificity of interaction with the ligand PIP. The conditional knockdown of T. gondii or P. falciparum ATG18 (Tg/PfATG18) impaired replication of parasites and resulted in their delayed death. Intriguingly, ATG18 depletion resulted in the loss of the apicomplexan parasite-specific nonphotosynthetic plastid-like organelle apicoplast, which harbors the machinery for biosynthesis of key metabolites, and the interaction of ATG18 to phosphatidylinositol 3-phosphate (PI3P) was critical for apicoplast inheritance. Furthermore, ATG18 regulates membrane association and apicoplast localization of ATG8. These findings provide insights into a novel noncanonical role of ATG18 in apicoplast inheritance. This function of ATG18 in organelle biogenesis is unprecedented in any organism and may be conserved across most apicomplexan parasites. PMID:29089429

Topological ferrimagnetic behaviours of coordination polymers containing manganese(II) chains with mixed azide and carboxylate bridges and alternating F/AF/AF'/AF'/AF interactions.

PubMed

Wang, Yan-Qin; Liu, Hou-Ting; Qi, Yan; Gao, En-Qing

2014-08-21

Two Mn(ii) complexes with azide and a new zwitterionic tetracarboxylate ligand 1,2,4,5-tetrakis(4-carboxylatopyridinium-1-methylene)benzene (L(1)), {[Mn5(L(1))2(N3)8(OH)2]·12H2O}n () and {[Mn5(L(1))2(N3)8(H2O)2](ClO4)2·6H2O}n (), have been synthesized and characterized crystallographically and magnetically. and contain similar alternating chains constructed by azide and carboxylate bridges. The independent sets of bridges alternate in an ABCCB sequence between adjacent Mn(ii) ions: (EO-N3)2 double bridges (EO = end-on) (denoted as A), [(EO-N3)(OCO)2] triple bridges (denoted as B) and [(EO-N3)(OCO)] double bridges (denoted as C). The alternating chains are interlinked into 2D coordination networks by the tetrapyridinium spacers. Magnetic studies demonstrate that the magnetic coupling through the double EO azide bridges is ferromagnetic and that through mixed azide/carboxylate bridges is antiferromagnetic. The unprecedented F/AF/AF'/AF'/AF coupling sequence along the chain dictates an uncompensated ground spin state (S = 5/2 per Mn5 unit) and leads to one-dimensional topological ferrimagnetism, which features a minimum in the χT versus T plot.

Dual transcriptome sequencing reveals resistance of TLR4 ligand-activated bone marrow-derived macrophages to inflammation mediated by the BET inhibitor JQ1

PubMed Central

Das, Amitabh; Chai, Jin Choul; Yang, Chul-su; Lee, Young Seek; Das, Nando Dulal; Jung, Kyoung Hwa; Chai, Young Gyu

2015-01-01

Persistent macrophage activation is associated with the expression of various pro-inflammatory genes, cytokines and chemokines, which may initiate or amplify inflammatory disorders. A novel synthetic BET inhibitor, JQ1, was proven to exert immunosuppressive activities in macrophages. However, a genome-wide search for JQ1 molecular targets has not been undertaken. The present study aimed at evaluating the anti-inflammatory function and underlying genes that are targeted by JQ1 in LPS-stimulated primary bone marrow-derived macrophages (BMDMs) using global transcriptomic RNA sequencing and quantitative real-time PCR. Among the annotated genes, transcriptional sequencing of BMDMs that were treated with JQ1 revealed a selective effect on LPS-induced gene expression in which the induction of cytokines/chemokines, interferon-stimulated genes, and prominent (transcription factors) TFs was suppressed. Additionally, we found that JQ1 reduced the expression of previously unidentified genes that are important in inflammation. Importantly, these inflammatory genes were not affected by JQ1 treatment alone. Furthermore, we confirmed that JQ1 reduced cytokines/chemokines in the supernatants of LPS treated BMDMs. Moreover, the biological pathways and gene ontology of the differentially expressed genes were determined in the JQ1 treatment of BMDMs. These unprecedented results suggest that the BET inhibitor JQ1 is a candidate for the prevention or therapeutic treatment of inflammatory disorders. PMID:26582142

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach.

PubMed

Domenyuk, Valeriy; Zhong, Zhenyu; Stark, Adam; Xiao, Nianqing; O'Neill, Heather A; Wei, Xixi; Wang, Jie; Tinder, Teresa T; Tonapi, Sonal; Duncan, Janet; Hornung, Tassilo; Hunter, Andrew; Miglarese, Mark R; Schorr, Joachim; Halbert, David D; Quackenbush, John; Poste, George; Berry, Donald A; Mayer, Günter; Famulok, Michael; Spetzler, David

2017-02-20

Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~10 11 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 10 6 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients.

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach

PubMed Central

Domenyuk, Valeriy; Zhong, Zhenyu; Stark, Adam; Xiao, Nianqing; O’Neill, Heather A.; Wei, Xixi; Wang, Jie; Tinder, Teresa T.; Tonapi, Sonal; Duncan, Janet; Hornung, Tassilo; Hunter, Andrew; Miglarese, Mark R.; Schorr, Joachim; Halbert, David D.; Quackenbush, John; Poste, George; Berry, Donald A.; Mayer, Günter; Famulok, Michael; Spetzler, David

2017-01-01

Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~1011 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 106 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients. PMID:28218293

Direct synthesis of all-inorganic heterostructured CdSe/CdS QDs in aqueous solution for improved photocatalytic hydrogen generation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhi-Jun; Fan, Xiang-Bing; Li, Xu-Bing

2017-01-01

Here we present a facile aqueous approach to synthesize heterostructured CdSe/CdS QDs with all-inorganic chalcogenide S2- ligands under mild conditions. High-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and steady-state emission spectroscopy demonstrate that the heterostructured CdSe/CdS QDs with sulfur-rich surface composition are formed by heterogeneous nucleation of Cd2+ and S2- precursors on the CdSe QDs. After adsorption of small Ni(OH)(2) clusters over the surface in situ, the CdSe/CdS-Ni(OH)(2) photocatalyst enables H-2 production efficiently with an internal quantum yield of 52% under visible light irradiation at 455 nm, up to an 8-fold increase ofmore » activity to that of spherical CdSe QDs-Ni(OH)(2) under the same conditions. Femtosecond transient absorption spectroscopy, X-ray transient absorption (XTA) spectroscopy, steady-state and time-resolved emission spectroscopy show that the quasi-type-II band alignment in the CdSe/CdS heterostructure is responsible for the efficiency enhancement of light harvesting and surface/interfacial charge separation in solar energy conversion. The unprecedented results exemplify an easily accessible pattern of aqueous synthesis of all-inorganic heterostructured QDs for advanced photosynthetic H-2 evolution.« less

PDBToSDF: Create ligand structure files from PDB file.

PubMed

Muppalaneni, Naresh Babu; Rao, Allam Appa

2011-01-01

Protein Data Bank (PDB) file contains atomic data for protein and ligand in protein-ligand complexes. Structure data file (SDF) contains data for atoms, bonds, connectivity and coordinates of molecule for ligands. We describe PDBToSDF as a tool to separate the ligand data from pdb file for the calculation of ligand properties like molecular weight, number of hydrogen bond acceptors, hydrogen bond receptors easily.

Synthesis and studies of polypeptide materials: Enantioselective polymerization of gamma-benzyl glutamate-N-carboxyanhydride and synthesis of optically active poly(beta-peptides)

NASA Astrophysics Data System (ADS)

Cheng, Jianjun

A class of zero-valent transition metal complexes have been developed by Deming et al for the controlled polymerization of alpha-aminoacid-N-carboxyanhydrides (alpha-NCAs). This discovery provided a superior starting point for the development of enantioselective polymerizations of racemic alpha-NCAs. Bidentate chiral ligands were synthesized and tested for their abilities to induce enantioselective polymerization of gamma-benzyl-glutamate NCA (Glu NCA) when they were coordinated to zero-valent nickel complexes. When optically active 2-pyridinyl oxazoline ligands were mixed with bis(1,5-cyclooctadiene)nickel in THF, chiral nickel complexes were formed that selectively polymerized one enantiomer of Glu NCA over the other. The highest selectivity was observed with the nickel complex of (S)-4-tert-butyl-2-pyridinyl oxazoline, which gave a ratio of enantiomeric polymerization rate constants (kD/kL) of 5.2. It was found that subtle modification of this ligand by incorporation of additional substituents had a substantial impact on initiator enantioselectivities. In separate efforts, methodology was developed for the general synthesis of optically active beta-aminoacid-N-carboxyanhydrides (beta-NCAs) via cyclization of Nbeta-Boc- or Nbeta-Cbz-beta-amino acids using phosphorus tribromide. The beta-NCA molecules could be polymerized in good yields using strong bases or transition metal complexes to give optically active poly(beta-peptides) bearing proteinogenic side chains. The resulting poly(beta-peptides), which have moderate molecular weights, adopt stable helical conformations in solution. Poly(beta-homoglutamate and poly(beta-homolysine), the side-chain deprotected polymers, were found to display pH dependent helix-coil conformation transitions in aqueous solution, similar to their alpha-analogs. A novel method for poly(beta-aspartate) synthesis was developed via the polymerization of L-aspartate alkyl ester beta lactams using metal-amido complexes. Poly(beta-aspartates) bearing short ethylene glycol side chains were obtained with controlled molecular weights and narrow molecular weight distributions when Sc(N(TMS)2)3 was used as initiator for the beta-lactam polymerizations. Polymer chain lengths could be controlled by both stoichiometry and monomer conversion, characteristic of a living polymerization system. Di- and tri-block copoly(beta-peptides) with desired chain lengths were also synthesized using this method. It was found that these techniques were generally applicable for the synthesis of poly(beta-peptides), bearing other proteinogetic side chains. Synthesis and studies of polypeptide materials were extended to unexplored areas by incorporation of both alpha- and beta-amino acid residues into single polymer chains. Two sequence specific polypeptides bearing alternating beta-alpha, or beta-alpha-alpha amino acid residues were synthesized. Both polymers were found to adopt unprecedented stable conformations in solution.

Versatile reactivities of rare-earth metal dialkyl complexes supported by a neutral pyrrolyl-functionalized β-diketiminato ligand.

PubMed

Zhu, Xiancui; Li, Yang; Guo, Dianjun; Wang, Shaowu; Wei, Yun; Zhou, Shuangliu

2018-03-12

Herein, rare-earth metal dialkyl complexes supported by a neutral pyrrolyl-functionalized β-diketiminato ligand with the formula LRE(CH 2 SiMe 3 ) 2 (thf) (RE = Y (1a), Dy (1b), Er (1c), Yb (1d); L = MeC(NDipp)CHC(Me)NCH 2 CH 2 NC 4 H 2 -2,5-Me 2 , Dipp = 2,6- i Pr 2 C 6 H 3 ) were synthesized via the reactions of the β-diketimine HL with the rare-earth metal trialkyl complexes RE(CH 2 SiMe 3 ) 3 (thf) 2 in high yields. The reactivities of 1 with pyridine derivatives, unsaturated substrates, and elemental sulfur were investigated, and some interesting chemical transformations were observed. Ligand exchange and activation of sp 2 and sp 3 C-H bonds occurred during the reactions with pyridine derivatives to afford different types of mononuclear rare-earth metal pyridyl complexes, namely, LEr(CH 2 SiMe 3 ) 2 (η 1 -NC 5 H 4 ) (2c), LRE(η 3 -CH 2 -2-NC 5 H 2 -4,6-Me 2 ) 2 (RE = Y (3a), Er (3c)), and LRE(CH 2 SiMe 3 )(η 2 -(C,N)-2-(2-C 6 H 4 NC 5 H 4 )) (RE = Er (4c), Yb = (4d)). Similarly, activation of the sp C-H bond occurred during the reaction of phenylacetylene with 1c to produce the dinuclear erbium alkynyl complex [LEr(CH 2 SiMe 3 )(μ-C[triple bond, length as m-dash]CPh)] 2 (5c). The mixed amidinate-β-diketiminato ytterbium complex LYb[(Dipp)NC(CH 2 SiMe 3 )N(Dipp)](CH 2 SiMe 3 ) (6d) was obtained by the insertion of bis(2,6-diisopropylphenyl)carbodiimide into a Yb-alkyl bond, as well as via the direct alkane elimination of a CH 2 SiMe 3 moiety with bis(2,6-diisopropylphenyl)formamidine to afford the erbium complex LEr(DippNCHNDipp)(CH 2 SiMe 3 ) (7c). A rare sp 2 C-H bond oxidation of the β-diketiminato backbone with elemental sulfur insertion was detected to provide the unprecedented dinuclear rare-earth metal thiolate complexes (LRE) 2 (μ-SCH 2 SiMe 3 ) 2 (μ-SCC(Me)(NDipp)C(Me)NCH 2 CH 2 NC 4 H 2 Me 2 -2,5) (RE = Y (8a), Er (8c)) in the reactions of S 8 with 1a and 1c, respectively. The molecular structures of the complexes 1-8 were determined by single-crystal X-ray diffraction analyses.

Metal–organic complexation in the marine environment

PubMed Central

Luther, George W; Rozan, Timothy F; Witter, Amy; Lewis, Brent

2001-01-01

We discuss the voltammetric methods that are used to assess metal–organic complexation in seawater. These consist of titration methods using anodic stripping voltammetry (ASV) and cathodic stripping voltammetry competitive ligand experiments (CSV-CLE). These approaches and a kinetic approach using CSV-CLE give similar information on the amount of excess ligand to metal in a sample and the conditional metal ligand stability constant for the excess ligand bound to the metal. CSV-CLE data using different ligands to measure Fe(III) organic complexes are similar. All these methods give conditional stability constants for which the side reaction coefficient for the metal can be corrected but not that for the ligand. Another approach, pseudovoltammetry, provides information on the actual metal–ligand complex(es) in a sample by doing ASV experiments where the deposition potential is varied more negatively in order to destroy the metal–ligand complex. This latter approach gives concentration information on each actual ligand bound to the metal as well as the thermodynamic stability constant of each complex in solution when compared to known metal–ligand complexes. In this case the side reaction coefficients for the metal and ligand are corrected. Thus, this method may not give identical information to the titration methods because the excess ligand in the sample may not be identical to some of the actual ligands binding the metal in the sample. PMID:16759421

Electronic spectra and photophysics of platinum(II) complexes with alpha-diimine ligands - Solid-state effects. I - Monomers and ligand pi dimers

NASA Technical Reports Server (NTRS)

Miskowski, Vincent M.; Houlding, Virginia H.

1989-01-01

Two types of emission behavior for Pt(II) complexes containing alpha-diimine ligands have been observed in dilute solution. If the complex also has weak field ligands such as chloride, ligand field (d-d) excited states become the lowest energy excited states. If only strong field ligands are present, a diimine 3(pi-pi/asterisk/) state becomes the lowest. In none of the cases studied did metal-to-ligand charge transfer excited state lie lowest.

Single-molecule force spectroscopy study of interactions between angiotensin II type 1 receptor and different biased ligands in living cells.

PubMed

Li, Wenhui; Xu, Jiachao; Kou, Xiaolong; Zhao, Rong; Zhou, Wei; Fang, Xiaohong

2018-05-01

Angiotensin II type 1 receptor (AT1R), a typical G protein-coupled receptor, plays a key role in regulating many cardiovascular functions. Different ligands can bind with AT1R to selectively activate either G protein (Gq) or β-arrestin (β-arr) pathway, or both pathways, but the molecular mechanism is not clear yet. In this work, we used, for the first time, atomic force microscopy-based single molecule force spectroscopy (SMFS) to study the interactions of AT1R with three types of ligands, balanced ligand, Gq-biased ligand, and β-arr-biased ligand, in living cells. The results revealed their difference in binding force and binding stability. The complex of the Gq-biased ligand-AT1R overcame two energy barriers with an intermediate state during dissociation, whereas that of β-arr-biased ligand-AT1R complex overcame one energy barrier. This indicated that AT1R had different ligand-binding conformational substates and underwent different structural changes to activate downstream signaling pathways with variable agonist efficacies. Quantitative analysis of AT1R-ligand binding in living cells at the single-molecule level offers a new tool to study the molecular mechanism of AT1R biased activation. Graphical Abstract Single-molecule force measurement on the living cell expressing AT1R-eGFP with a ligand modified AFM tip (left), the dynamic force spectra of β-arrestin biased ligands-AT1R (middle), and Gq-biased ligands-AT1R (right). The complexes of β-arr-biased ligand-AT1R overcame one energy barrier, with one linear region in the spectra, whereas the Gq-biased ligand-AT1R complexes overcame two energy barriers with two linear regions.

Modeling and analysis of PET studies with norepinephrine transporter ligands: the search for a reference region.

PubMed

Logan, Jean; Ding, Yu-Shin; Lin, Kuo-Shyan; Pareto, Deborah; Fowler, Joanna; Biegon, Anat

2005-07-01

The development of positron emission tomography (PET) ligands for the norepinephrine transporter (NET) has been slow compared to the development of radiotracers for others systems, such as the dopamine (DAT) or the serotonin transporters (SERT). The main reason for this appears to be the high nonspecific (non-NET) binding exhibited by many of these tracers, which makes the identification of a reference region difficult. With other PET ligands the use of a reference region increases the reproducibility of the outcome measure in test/retest studies. The focus of this work is to identify a suitable reference region or means of normalizing data for the NET ligands investigated. We have analyzed the results of PET studies in the baboon brain with labeled reboxetine derivatives (S,S)-[(11)C]O-methyl reboxetine (SS-MRB), (S,S)-[(18)F]fluororeboxetine (SS-FRB) as well as O-[(11)C]nisoxetine and N-[(11)C]nisoxetine (NIS), and, for comparison, the less active (R,R) enantiomers (RR-MRB, RR-FRB) in terms of the distribution volume (DV) using measured arterial input functions. (1) For a given subject, a large variation in DV for successive baseline studies was observed in regions with both high and low NET density. (2) The occipital cortex and the basal ganglia were found to be the regions with the smallest change between baseline (SS-MRB) and pretreatment with cocaine, and were therefore used as a composite reference region for calculation of a distribution volume ratio (DVR). (3) The variability [as measured by the coefficient of variation (CV) = standard deviation/mean] in the distribution volume ratio (DVR) of thalamus (to reference region) was considerably reduced over that of the DV using this composite reference region. (4) Pretreatment with nisoxetine (1.0 mg/kg 10 min prior to tracer) in one study produced (in decreasing order) reductions in thalamus, cerebellum, cingulate and frontal cortex consistent with known NET densities. (5) [(11)C]Nisoxetine had a higher background non-NET binding (DV) than the other tracers reported here with basal ganglia (a non-NET region) higher than thalamus. The reboxetine derivatives show a lot of promise as tracers for human PET studies of the norepinephrine system. We have identified a strategy for normalizing DVs to a reference region with the understanding that the DVR for these tracers may not be related to the binding potential in the same way as, for example, for the dopamine tracers, since the non-NET binding may differ between the target and nontarget regions. From our baboon studies the average DVR for thalamus (n = 18) for SS-MRB is 1.8; however, the lower limit is most likely less than 1 due to this difference in non-NET binding.

Theoretical studies of molecular structure, electronic structure, spectroscopic properties and the ancillary ligand effect: a comparison of tris-chelate ML3-type and ML2X-type species for gallium(III) complexes with N,O-donor phenolic ligand, 2-(2-hydroxyphenyl)benzothiazole.

PubMed

Tong, Yi-Ping; Lin, Yan-Wen

2011-02-01

Two Ga(III) complexes with main ligand, 2-(2-hydroxyphenyl)benzothiazole (HL'), namely mixed-ligand ML2X-type [GaL'2X'] (1) (HX'=acetic acid, as ancillary ligand) and the meridianal tris-chelate [GaL'3] (2) have been investigated by the density functional theory (DFT/TDDFT) level calculations. Both 1 and 2 can be presented as a similar "mixed-ligand ML2X-type" species. The molecular geometries, electronic structures, metal-ligand bonding property of Ga-O (N) (main ligand), Ga-O (N) (ancillary ligand) interactions, and the ancillary ligand effect on their HOMO-LUMO gap, their absorption/emission property, and their absorption/emission wavelengths/colors for them have been discussed in detail based on the orbital interactions, the partial density of states (PDOS), and so on. The current investigation also indicates that it is quite probable that by introduction of different ancillary ligands, a series of new mixed-ligand ML2X-type complexes for group 13 metals can be designed with their absorption/emission property and the absorption/emission wavelengths and colors being tuned. Copyright © 2011 Elsevier B.V. All rights reserved.

Binding constant of cell adhesion receptors and substrate-immobilized ligands depends on the distribution of ligands

NASA Astrophysics Data System (ADS)

Li, Long; Hu, Jinglei; Xu, Guangkui; Song, Fan

2018-01-01

Cell-cell adhesion and the adhesion of cells to tissues and extracellular matrix, which are pivotal for immune response, tissue development, and cell locomotion, depend sensitively on the binding constant of receptor and ligand molecules anchored on the apposing surfaces. An important question remains of whether the immobilization of ligands affects the affinity of binding with cell adhesion receptors. We have investigated the adhesion of multicomponent membranes to a flat substrate coated with immobile ligands using Monte Carlo simulations of a statistical mesoscopic model with biologically relevant parameters. We find that the binding of the adhesion receptors to ligands immobilized on the substrate is strongly affected by the ligand distribution. In the case of ligand clusters, the receptor-ligand binding constant can be significantly enhanced due to the less translational entropy loss of lipid-raft domains in the model cell membranes upon the formation of additional complexes. For ligands randomly or uniformly immobilized on the substrate, the binding constant is rather decreased since the receptors localized in lipid-raft domains have to pay an energetic penalty in order to bind ligands. Our findings help to understand why cell-substrate adhesion experiments for measuring the impact of lipid rafts on the receptor-ligand interactions led to contradictory results.

Magnetization due to localized states on graphene grain boundary

PubMed Central

Dutta, Sudipta; Wakabayashi, Katsunori

2015-01-01

Magnetism in graphene has been found to originate from various defects, e.g., vacancy, edge formation, add-atoms etc. Here, we discuss about an alternate route of achieving magnetism in graphene via grain boundary. During chemical vapor deposition of graphene, several graphene nucleation centers grow independently and face themselves with unusual bonding environment, giving rise to the formation of grain boundaries. We investigate the origin of magnetism in such grain boundaries within first-principles calculations, by letting two nucleation centers interact with each other at their interface. We observe formation of unprecedented point defect, consisting of fused three-membered and larger carbon rings, which induces net magnetization to graphene quantum dots. In case of periodic lattices, the appearance of array of point defects leads to the formation of magnetic grain boundaries. The net magnetization on these defects arises due to the deviation from bipartite characteristics of pristine graphene. We observe magnetic grain boundary induced dispersion less flat bands near Fermi energy, showing higher localization of electrons. These flat bands can be accessed via small doping, leading to enhanced magnetism. Moreover, the grain boundaries can induce asymmetric spin conduction behavior along the cross boundary direction. These properties can be exploited for sensor and spin-filtering applications. PMID:26145161

How well are the climate indices related to the GRACE-observed total water storage changes in China?

NASA Astrophysics Data System (ADS)

Devaraju, B.; Vishwakarma, B.; Sneeuw, N. J.

2017-12-01

The fresh water availability over land masses is changing rapidly under the influence of climate change and human intervention. In order to manage our water resources and plan for a better future, we need to demarcate the role of climate change. The total water storage change in a region can be obtained from the GRACE satellite mission. On the other hand, many climate change indicators, for example ENSO, are derived from sea surface temperature. In this contribution we investigate the relationship between the total water storage change over China with the climate indices using statistical time-series decomposition techniques, such as Seasonal and Trend decomposition using Loess (STL), Principal Component Analysis (PCA) and Canonical Correlation Analysis (CCA). The anomalies in climate variables, such as sea surface temperature, are responsible for anomalous precipitation and thus an anomalous total water storage change over land. Therefore, it is imperative that we use a GRACE product that can capture anomalous water storage changes with unprecedented accuracy. Since filtering decreases the sensitivity of GRACE products substantially, we use the data-driven method of deviation for recovering the signal lost due to filtering. To this end, we are able to obtain the spatial fingerprint of individual climate index on total water storage change observed over China.

Minimizing Isolate Catalyst Motion in Metal-Assisted Chemical Etching for Deep Trenching of Silicon Nanohole Array.

PubMed

Kong, Lingyu; Zhao, Yunshan; Dasgupta, Binayak; Ren, Yi; Hippalgaonkar, Kedar; Li, Xiuling; Chim, Wai Kin; Chiam, Sing Yang

2017-06-21

The instability of isolate catalysts during metal-assisted chemical etching is a major hindrance to achieve high aspect ratio structures in the vertical and directional etching of silicon (Si). In this work, we discussed and showed how isolate catalyst motion can be influenced and controlled by the semiconductor doping type and the oxidant concentration ratio. We propose that the triggering event in deviating isolate catalyst motion is brought about by unequal etch rates across the isolate catalyst. This triggering event is indirectly affected by the oxidant concentration ratio through the etching rates. While the triggering events are stochastic, the doping concentration of silicon offers a good control in minimizing isolate catalyst motion. The doping concentration affects the porosity at the etching front, and this directly affects the van der Waals (vdWs) forces between the metal catalyst and Si during etching. A reduction in the vdWs forces resulted in a lower bending torque that can prevent the straying of the isolate catalyst from its directional etching, in the event of unequal etch rates. The key understandings in isolate catalyst motion derived from this work allowed us to demonstrate the fabrication of large area and uniformly ordered sub-500 nm nanoholes array with an unprecedented high aspect ratio of ∼12.

An alternate binding site for PPARγ ligands

PubMed Central

Hughes, Travis S.; Giri, Pankaj Kumar; de Vera, Ian Mitchelle S.; Marciano, David P.; Kuruvilla, Dana S.; Shin, Youseung; Blayo, Anne-Laure; Kamenecka, Theodore M.; Burris, Thomas P.; Griffin, Patrick R.; Kojetin, Douglas J.

2014-01-01

PPARγ is a target for insulin sensitizing drugs such as glitazones, which improve plasma glucose maintenance in patients with diabetes. Synthetic ligands have been designed to mimic endogenous ligand binding to a canonical ligand-binding pocket to hyperactivate PPARγ. Here we reveal that synthetic PPARγ ligands also bind to an alternate site, leading to unique receptor conformational changes that impact coregulator binding, transactivation and target gene expression. Using structure-function studies we show that alternate site binding occurs at pharmacologically relevant ligand concentrations, and is neither blocked by covalently bound synthetic antagonists nor by endogenous ligands indicating non-overlapping binding with the canonical pocket. Alternate site binding likely contributes to PPARγ hyperactivation in vivo, perhaps explaining why PPARγ full and partial or weak agonists display similar adverse effects. These findings expand our understanding of PPARγ activation by ligands and suggest that allosteric modulators could be designed to fine tune PPARγ activity without competing with endogenous ligands. PMID:24705063

Group Additivity in Ligand Binding Affinity: An Alternative Approach to Ligand Efficiency.

PubMed

Reynolds, Charles H; Reynolds, Ryan C

2017-12-26

Group additivity is a concept that has been successfully applied to a variety of thermochemical and kinetic properties. This includes drug discovery, where functional group additivity is often assumed in ligand binding. Ligand efficiency can be recast as a special case of group additivity where ΔG/HA is the group equivalent (HA is the number of non-hydrogen atoms in a ligand). Analysis of a large data set of protein-ligand binding affinities (K i ) for diverse targets shows that in general ligand binding is distinctly nonlinear. It is possible to create a group equivalent scheme for ligand binding, but only in the context of closely related proteins, at least with regard to size. This finding has broad implications for drug design from both experimental and computational points of view. It also offers a path forward for a more general scheme to assess the efficiency of ligand binding.

All-inorganic Germanium nanocrystal films by cationic ligand exchange

DOE PAGES

Wheeler, Lance M.; Nichols, Asa W.; Chernomordik, Boris D.; ...

2016-01-21

In this study, we introduce a new paradigm for group IV nanocrystal surface chemistry based on room temperature surface activation that enables ionic ligand exchange. Germanium nanocrystals synthesized in a gas-phase plasma reactor are functionalized with labile, cationic alkylammonium ligands rather than with traditional covalently bound groups. We employ Fourier transform infrared and 1H nuclear magnetic resonance spectroscopies to demonstrate the alkylammonium ligands are freely exchanged on the germanium nanocrystal surface with a variety of cationic ligands, including short inorganic ligands such as ammonium and alkali metal cations. This ionic ligand exchange chemistry is used to demonstrate enhanced transport inmore » germanium nanocrystal films following ligand exchange as well as the first photovoltaic device based on an all-inorganic germanium nanocrystal absorber layer cast from solution. This new ligand chemistry should accelerate progress in utilizing germanium and other group IV nanocrystals for optoelectronic applications.« less

Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

PubMed Central

DeLuca, Samuel; Khar, Karen; Meiler, Jens

2015-01-01

RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand) making it unfeasible for use in virtual High Throughput Screening (vHTS). To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial ‘low-resolution’ docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10–15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the ‘high-resolution’ full atom refinement step. PMID:26207742

Interactions of Multimodal Ligands with Proteins: Insights into Selectivity Using Molecular Dynamics Simulations.

PubMed

Parimal, Siddharth; Garde, Shekhar; Cramer, Steven M

2015-07-14

Fundamental understanding of protein-ligand interactions is important to the development of efficient bioseparations in multimodal chromatography. Here we employ molecular dynamics (MD) simulations to investigate the interactions of three different proteins--ubiquitin, cytochrome C, and α-chymotrypsinogen A, sampling a range of charge from +1e to +9e--with two multimodal chromatographic ligands containing similar chemical moieties--aromatic, carboxyl, and amide--in different structural arrangements. We use a spherical harmonic expansion to analyze ligand and individual moiety density profiles around the proteins. We find that the Capto MMC ligand, which contains an additional aliphatic group, displays stronger interactions than Nuvia CPrime ligand with all three proteins. Studying the ligand densities at the moiety level suggests that hydrophobic interactions play a major role in determining the locations of high ligand densities. Finally, the greater structural flexibility of the Capto MMC ligand compared to that of the Nuvia cPrime ligand allows for stronger structural complementarity and enables stronger hydrophobic interactions. These subtle and not-so-subtle differences in binding affinities and modalities for multimodal ligands can result in significantly different binding behavior towards proteins with important implications for bioprocessing.

Distinct Iron-binding Ligands in the Upper Water Column at Station ALOHA

NASA Astrophysics Data System (ADS)

Bundy, R.; Boiteau, R.; Repeta, D.

2016-02-01

The distribution and chemical properties of iron-binding organic ligands at station ALOHA were examined using a combination of solid phase extraction (SPE) followed by high pressure liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICPMS). HPLC-ICPMS ligand measurements were complemented by competitive ligand exchange adsorptive cathodic stripping voltammetry (CLE-ACSV) analysis using salicylaldoxime as the added ligand. By HPLC-ICPMS, we find enhanced concentrations of distinct naturally-occurring polar iron-binding ligands present at the surface and in the chlorophyll maximum. Lower concentrations were found in the subsurface, where a suite of non-polar ligands was detected. Siderophores were present at the deepest depths sampled at station ALOHA, down to 400m. Incubation studies provided evidence for the production of iron-binding ligands associated with nutrient amended phytoplankton growth in surface waters, and as a result of microbial particle remineralization in the subsurface water column. Ligands classes identified via SPE were then compared to CLE-ACSV ligand measurements, as well as the conditional stability constants measured from model polar and non-polar siderophores, yielding insight to the sources of iron-binding ligands throughout the water column at station ALOHA.

AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

PubMed Central

Ravindranath, Pradeep Anand; Sanner, Michel F.

2016-01-01

Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

PubMed Central

Seeliger, Daniel; de Groot, Bert L.

2010-01-01

Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures), however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo) structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 Å backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 Å backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available. PMID:20066034

Lineage-specific co-evolution of the Egf receptor/ligand signaling system.

PubMed

Laisney, Juliette A G C; Braasch, Ingo; Walter, Ronald B; Meierjohann, Svenja; Schartl, Manfred

2010-01-27

The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr ligands. This fish-specific occurrence of Egf receptor specialization offers unique opportunities to study the functions of different Egf receptor-ligand combinations and their biological outputs in vertebrates. Furthermore, our results strongly support the use of homologous ligands in future studies, as sufficient cross-specificity is very unlikely for this ligand/receptor system.

Lineage-specific co-evolution of the Egf receptor/ligand signaling system

PubMed Central

2010-01-01

Background The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. Results We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Conclusions Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr ligands. This fish-specific occurrence of Egf receptor specialization offers unique opportunities to study the functions of different Egf receptor-ligand combinations and their biological outputs in vertebrates. Furthermore, our results strongly support the use of homologous ligands in future studies, as sufficient cross-specificity is very unlikely for this ligand/receptor system. PMID:20105326

Education for Survival: An Historical Perspective

ERIC Educational Resources Information Center

Aldrich, Richard

2010-01-01

At the beginning of the twenty-first century it is essential to review the nature and aims of education, both formal and informal, in the light of the unprecedented situation in which the human race is placed, and to give priority to education for survival. This article begins by identifying that unprecedented situation. We live on an…

Nanosized (mu12-Pt)Pd164-xPtx(CO)72(PPh3)20 (x approximately 7) containing Pt-centered four-shell 165-atom Pd-Pt core with unprecedented intershell bridging carbonyl ligands: comparative analysis of icosahedral shell-growth patterns with geometrically related Pd145(CO)x(PEt3)30 (x approximately 60) containing capped three-shell Pd145 core.

PubMed

Mednikov, Evgueni G; Jewell, Matthew C; Dahl, Lawrence F

2007-09-19

Presented herein are the preparation and crystallographic/microanalytical/magnetic/spectroscopic characterization of the Pt-centered four-shell 165-atom Pd-Pt cluster, (mu(12)-Pt)Pd(164-x)Pt(x)(CO)(72)(PPh(3))(20) (x approximately 7), 1, that replaces the geometrically related capped three-shell icosahedral Pd(145) cluster, Pd(145)(CO)(x)(PEt(3))(30) (x approximately 60), 2, as the largest crystallographically determined discrete transition metal cluster with direct metal-metal bonding. A detailed comparison of their shell-growth patterns gives rise to important stereochemical implications concerning completely unexpected structural dissimilarities as well as similarities and provides new insight concerning possible synthetic approaches for generation of multi-shell metal clusters. 1 was reproducibly prepared in small yields (<10%) from the reaction of Pd(10)(CO)(12)(PPh(3))(6) with Pt(CO)(2)(PPh(3))(2). Its 165-atom metal-core geometry and 20 PPh(3) and 72 CO ligands were established from a low-temperature (100 K) CCD X-ray diffraction study. The well-determined crystal structure is attributed largely to 1 possessing cubic T(h) (2/m3) site symmetry, which is the highest crystallographic subgroup of the noncrystallographic pseudo-icosahedral I(h) (2/m35) symmetry. The "full" four-shell Pd-Pt anatomy of 1 consists of: (a) shell 1 with the centered (mu(12)-Pt) atom encapsulated by the 12-atom icosahedral Pt(x)Pd(12-x) cage, x = 1.2(3); (b) shell 2 with the 42-atom nu(2) icosahedral Pt(x)Pd(42-x) cage, x = 3.5(5); (c) shell 3 with the anti-Mackay 60-atom semi-regular rhombicosidodecahedral Pt(x)Pd(60-x) cage, x = 2.2(6); (d) shell 4 with the 50-atom nu(2) pentagonal dodecahedral Pd(50) cage. The total number of crystallographically estimated Pt atoms, 8 +/- 3, which was obtained from least-squares (Pt(x)/Pd(1-x))-occupancy analysis of the X-ray data that conclusively revealed the central atom to be pure Pt (occupancy factor, x = 1.00(3)), is fortuitously in agreement with that of 7.6(7) found from an X-ray Pt/Pd microanalysis (WDS spectrometer) on three crystals of 1. Our utilization of this site-occupancy (Pt(x)Pd(1-x))-analysis for shells 1-3 originated from the microanalytical results; otherwise, the presumed metal-core composition would have been (mu(12)-Pt)Pd(164). [Alternatively, the (mu(12)-Pt)M(164) core-geometry of 1 may be viewed as a pseudo-Ih Pt-centered six-shell successive nu(1) polyhedral system, each with radially equivalent vertex atoms: Pt@M(12)(icosahedron)@M(30)(icosidodecahedron)@M(12)(icosahedron)@M(60)(rhombicosidodecahedron)@M(30)(icosidodecahedron)@M(20)(pentagonal dodecahedron)]. Completely surprising structural dissimilarities between 1 and 2 are: (1) to date 1 is only reproducibly isolated as a heterometallic Pd-Pt cluster with a central Pt instead of Pd atom; (2) the 50 atoms comprising the outer fourth nu(2) pentagonal dodecahedral shell in 1 are less than the 60 atoms of the inner third shell in 1, in contradistinction to shell-by-shell growth processes in all other known shell-based structures; (3) the 10 fewer PR3 ligands in 1 necessitate larger bulky PPh(3) ligands to protect the Pd-Pt core-geometry; (4) the 72 CO ligands consist of six bridging COs within each of the 12 pentagons in shell 4 that are coordinated to intershell metal atoms. SQUID magnetometry measurements showed a single-crystal sample of 1 to be diamagnetic over the entire temperature range of 10-300 K.

Heterometallic mixed-valence copper(I,II) cyanides that were tuned by using the chelate effect: discovery of famous Cairo pentagonal tiling and unprecedented (3,4)-connected {8(3)}2{8(6)} topological 3D net.

PubMed

Qin, Ying-Lian; Yao, Ru-Xin; Wu, Guo-Xing; Liu, Min-Min; Zhang, Xian-Ming

2013-07-01

By using environmentally friendly [Ni(CN)4](2-) as a cyanide source, three new heterometallic cyano-bridged mixed-valence Cu(I)/Cu(II) coordination polymers with three different electronic configurations (d(8)-d(10)), that is, [Cu2Ni(CN)5(H2O)3] (1), [Cu2Ni(CN)5(pn)H2O] (2), and [Cu3Ni(CN)6(pn)2] (3, pn = 1,2-propane diamine) have been synthesized by gradually increasing the amount of pn. Compound 1, which was hydrothermally synthesized in the absence of pn ligand, exhibits the famous 2D Cairo pentagonal tiling, in which the Cu(I), Cu(II), and Ni(II) atoms act as trigonal, T-shaped, and square-planar nodes, respectively. Notably, there are three water molecules located at the meridianal positions of the octahedrally coordinated Cu(II) atom in compound 1. A similar reaction, except for the addition of a small amount of pn, generated a similar Cairo pentagonal tiling layer in which two of the water molecules that were located at the meridianal positions of the octahedrally coordinated Cu(II) atom were replaced by a chelating pn group. Another similar hydrothermal reaction, with the addition of a larger amount of pn, yielded compound 3, which showed a related two-fold-interpenetrated (3,4)-connected 3D framework with an unprecedented {8(3)}2{8(6)} topology in which the Cu(II) atom was chelated by two pn groups. These structural changes between compounds 1-3 can be explained by the chelating effect of the pn group. The replacement of two meridianally coordinated water molecules on the octahedral Cu(II) atom in compound 1 by a pn group gives compound 2, which shows similar Cairo tiling, and a further increase in the amount of pn results in the formation of the [Cu(NC)2(pn)2] unit and the two-fold-interpenetrated 3D framework of compound 3. The mixed-valence properties of compounds 1, 2, and 3 were confirmed by variable-temperature magnetic-susceptibility measurements. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lessons from isolable nickel(I) precursor complexes for small molecule activation.

PubMed

Yao, Shenglai; Driess, Matthias

2012-02-21

Small-molecule activation by transition metals is essential to numerous organic transformations, both biological and industrial. Creating useful metal-mediated activation systems often depends on stabilizing the metal with uncommon low oxidation states and low coordination numbers. This provides a redox-active metal center with vacant coordination sites well suited for interacting with small molecules. Monovalent nickel species, with their d(9) electronic configuration, are moderately strong one-electron reducing agents that are synthetically attractive if they can be isolated. They represent suitable reagents for closing the knowledge gap in nickel-mediated activation of small molecules. Recently, the first strikingly stable dinuclear β-diketiminate nickel(I) precursor complexes were synthesized, proving to be suitable promoters for small-molecule binding and activation. They have led to many unprecedented nickel complexes bearing activated small molecules in different reduction stages. In this Account, we describe selected achievements in the activation of nitrous oxide (N(2)O), O(2), the heavier chalcogens (S, Se, and Te), and white phosphorus (P(4)) through this β-diketiminatonickel(I) precursor species. We emphasize the reductive activation of O(2), owing to its promise in oxidation processes. The one-electron-reduced O(2) activation product, that is, the corresponding β-diketiminato-supported Ni-O(2) complex, is a genuine superoxonickel(II) complex, representing an important intermediate in the early stages of O(2) activation. It selectively acts as an oxygen-atom transfer agent, hydrogen-atom scavenger, or both towards exogenous organic substrates to yield oxidation products. The one-electron reduction of the superoxonickel(II) moiety was examined by using elemental potassium, β-diketiminatozinc(II) chloride, and β-diketiminatoiron(I) complexes, affording the first heterobimetallic complexes featuring a [NiO(2)M] subunit (M is K, Zn, or Fe). Through density functional theory (DFT) calculations, the geometric and electronic structures of these complexes were established and their distinctive reactivity, including the unprecedented monooxygenase-like activity of a bis(μ-oxo)nickel-iron complex, was studied. The studies have further led to other heterobimetallic complexes containing a [NiO(2)M] core, which are useful for understanding the influence of the heterometal on structure-reactivity relationships. The activation of N(2)O led directly to the hydrogen-atom abstraction product bis(μ-hydroxo)nickel(II) species and prevented isolation of any intermediate. In contrast, the activation of elemental S, Se, and Te with the same nickel(I) reagent furnished activation products with superchalcogenido E(2)(-) (E is S, Se, or Te) and dichalcogenido E(2)(2-) ligand in different activation stages. The isolable supersulfidonickel(II) subunit may serve as a versatile building block for the synthesis of heterobimetallic disulfidonickel(II) complexes with a [NiS(2)M] core. In the case of white phosphorus, the P(4) molecule has been coordinated to the nickel(I) center of dinuclear β-diketiminatonickel(I) precursor complexes; however, the whole P(4) subunit is a weaker electron acceptor than the dichalcogen ligands E(2), thus remaining unreduced. This P(4) binding mode is rare and could open new doors for subsequent functionalization of P(4). Our advances in understanding how these small molecules are bound to a nickel(I) center and are activated for further transformation offer promise for designing new catalysts. These nickel-containing complexes offer exceptional potential for nickel-mediated transformations of organic molecules and as model compounds for mimicking active sites of nickel-containing metalloenzymes.

Interfacial functionalization and engineering of nanoparticles

NASA Astrophysics Data System (ADS)

Song, Yang

The intense research interest in nanoscience and nanotechnology is largely fueled by the unique properties of nanoscale materials. In this dissertation, the research efforts are focused on surface functionalization and interfacial engineering of functional nanoparticles in the preparation of patchy nanoparticles (e.g., Janus nanoparticles and Neapolitan nanoparticles) such that the nanoparticle structures and properties may be manipulated to an unprecedented level of sophistication. Experimentally, Janus nanoparticles were prepared by an interfacial engineering method where one hemisphere of the originally hydrophobic nanoparticles was replaced with hydrophilic ligands at the air|liquid or solid|liquid interface. The amphiphilic surface characters of the Janus nanoparticles were verified by contact angle measurements, as compared to those of the bulk-exchange counterparts where the two types of ligands were distributed rather homogeneously on the nanoparticle surface. In a further study, a mercapto derivative of diacetylene was used as the hydrophilic ligands to prepare Janus nanoparticles by using hydrophobic hexanethiolate-protected gold nanoparticles as the starting materials. Exposure to UV irradiation led to effective covalent cross-linking between the diacetylene moieties of neighboring ligands and hence marked enhancement of the structural integrity of the Janus nanoparticles, which was attributable to the impeded surface diffusion of the thiol ligands on the nanoparticle surface, as manifested in fluorescence measurements of aged nanoparticles. More complicated bimetallic AgAu Janus nanoparticles were prepared by interfacial galvanic exchange reactions of a Langmuir-Blodgett monolayer of 1-hexanethiolate-passivated silver nanoparticles on a glass slide with gold(I)-mercaptopropanediol complex in a water/ethanol solution. The resulting nanoparticles exhibited an asymmetrical distribution not only of the organic capping ligands on the nanoparticle surface but also of the metal elements in the nanoparticle cores, in contrast to the bulk-exchange counterparts where these distributions were homogeneous within the nanoparticles, as manifested in contact angle, UV--vis, XPS, and TEM measurements. More interestingly, the electrocatalytic performance of the Janus nanoparticles was markedly better than the bulk-exchange ones, suggesting that the segregated distribution of the polar ligands from the apolar ones might further facilitate charge transfer from Ag to Au in the nanoparticle cores, leading to additional improvement of the adsorption and reduction of oxygen. This interfacial protocol was then adopted to prepare trimetallic Ag AuPt Neapolitan nanoparticles by two sequential galvanic exchange reactions of 1-hexanethiolate-capped silver nanoparticles with gold(I)-thiomalic acid and platinum(II)-hexanethiolate complexes. As both reactions were confined to an interface, the Au and Pt elements were situated on two opposite poles of the original Ag nanoparticles, which was clearly manifested in elemental mapping of the nanoparticles, and consistent with the damping and red-shift of the nanoparticle surface plasmon resonance. As nanoscale analogs to conventional amphiphilic molecules, the resulting Janus nanoparticles were found to form oil-in-water micelle-like or water-in-oil reverse micelle-like superparticulate structures depending on the solvent media. These unique characteristics were exploited for the effective transfer of diverse guest nanoparticles between organic and water phase. The transfer of hydrophobic nanoparticles from organic to water media or water-soluble nanoparticles to the organic phase was evidenced by TEM, DLS, UV-Vis, and PL measurements. In particular, line scans based on EDS analysis showed that the vesicle-like structures consisted of multiple layers of the Janus nanoparticles, which encapsulated the guest nanoparticles in the cores. The results highlight the unique effectiveness of using Janus nanoparticles in the formation of functional nanocomposites. Part of the dissertation research was also devoted to graphene quantum dots (GQDs)-supported platinum (Pt/G) nanoparticles and their electrocatalytic activity in oxygen reduction reaction. These Pt/G nanocomposites were prepared by a hydrothermal procedure at controlled temperatures. Spectroscopic measurements based on FTIR, Raman and XPS confirmed the formation of various oxygenated structural defects on GQDs and the variation of their concentrations with the hydrothermal conditions. Interestingly, electrocatalytic activity of GQD/Pt composites exhibited a volcano-shaped variation with the GQD structural defects, with the best identified as the samples prepared at 160 °C for 6 h where the mass activity was found to meet the DOE target for 2015. This remarkable performance was accounted for by the deliberate manipulation of the adsorption of oxygen and reaction intermediates on platinum by the GQD structural defects through partial charge transfer. The strategy presented herein may offer a new paradigm in the design and engineering of nanoparticle catalysts for fuel cell electrochemistry. In addition, studies were also carried out to study intervalence charge transfer between ferrocenyl moieties bonded on carbon nanoparticle surfaces by diazonium reaction. Electrochemical studies exhibited two pairs of voltammetric waves with a difference of their formal potentials at about 78 mV, suggesting nanoparticle-mediated intraparticle charge delocalization at mixed valence as a result of the strong core-ligand covalent bonds and the conductive sp 2 carbon matrix of the graphitic cores. Consistent behaviors were observed in near-infrared measurements, indicating that the particles behaved analogously to a Class I/II mixed-valence compound.

On the binding determinants of the glutamate agonist with the glutamate receptor ligand binding domain.

PubMed

Speranskiy, Kirill; Kurnikova, Maria

2005-08-30

Ionotropic glutamate receptors (GluRs) are ligand-gated membrane channel proteins found in the central neural system that mediate a fast excitatory response of neurons. In this paper, we report theoretical analysis of the ligand-protein interactions in the binding pocket of the S1S2 (ligand binding) domain of the GluR2 receptor in the closed conformation. By utilizing several theoretical methods ranging from continuum electrostatics to all-atom molecular dynamics simulations and quantum chemical calculations, we were able to characterize in detail glutamate agonist binding to the wild-type and E705D mutant proteins. A theoretical model of the protein-ligand interactions is validated via direct comparison of theoretical and Fourier transform infrared spectroscopy (FTIR) measured frequency shifts of the ligand's carboxylate group vibrations [Jayaraman et al. (2000) Biochemistry 39, 8693-8697; Cheng et al. (2002) Biochemistry 41, 1602-1608]. A detailed picture of the interactions in the binding site is inferred by analyzing contributions to vibrational frequencies produced by protein residues forming the ligand-binding pocket. The role of mobility and hydrogen-bonding network of water in the ligand-binding pocket and the contribution of protein residues exposed in the binding pocket to the binding and selectivity of the ligand are discussed. It is demonstrated that the molecular surface of the protein in the ligand-free state has mainly positive electrostatic potential attractive to the negatively charged ligand, and the potential produced by the protein in the ligand-binding pocket in the closed state is complementary to the distribution of the electrostatic potential produced by the ligand itself. Such charge complementarity ensures specificity to the unique charge distribution of the ligand.

Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening

NASA Astrophysics Data System (ADS)

Zavodszky, Maria I.; Sanschagrin, Paul C.; Kuhn, Leslie A.; Korde, Rajesh S.

2002-12-01

For the successful identification and docking of new ligands to a protein target by virtual screening, the essential features of the protein and ligand surfaces must be captured and distilled in an efficient representation. Since the running time for docking increases exponentially with the number of points representing the protein and each ligand candidate, it is important to place these points where the best interactions can be made between the protein and the ligand. This definition of favorable points of interaction can also guide protein structure-based ligand design, which typically focuses on which chemical groups provide the most energetically favorable contacts. In this paper, we present an alternative method of protein template and ligand interaction point design that identifies the most favorable points for making hydrophobic and hydrogen-bond interactions by using a knowledge base. The knowledge-based protein and ligand representations have been incorporated in version 2.0 of SLIDE and resulted in dockings closer to the crystal structure orientations when screening a set of 57 known thrombin and glutathione S-transferase (GST) ligands against the apo structures of these proteins. There was also improved scoring enrichment of the dockings, meaning better differentiation between the chemically diverse known ligands and a ˜15,000-molecule dataset of randomly-chosen small organic molecules. This approach for identifying the most important points of interaction between proteins and their ligands can equally well be used in other docking and design techniques. While much recent effort has focused on improving scoring functions for protein-ligand docking, our results indicate that improving the representation of the chemistry of proteins and their ligands is another avenue that can lead to significant improvements in the identification, docking, and scoring of ligands.

Radiochemical studies of 99mTc complexes of modified cysteine ligands and bifunctional chelating agents.

PubMed

Pillai, M R; Kothari, K; Banerjee, S; Samuel, G; Suresh, M; Sarma, H D; Jurisson, S

1999-07-01

The synthesis of four novel ligands using the amino-acid cysteine and its ethyl carboxylate derivative is described. The synthetic method involves a two-step procedure, wherein the intermediate Schiff base formed by the condensation of the amino group of the cysteine substrate and salicylaldehyde is reduced to give the target ligands. The intermediates and the final products were characterized by high resolution nuclear magnetic resonance spectroscopy. Complexation studies of the ligands with 99mTc were optimized using stannous tartrate as the reducing agent under varying reaction conditions. The complexes were characterized using standard quality control techniques such as thin layer chromatography, paper electrophoresis, and paper chromatography. Lipophilicities of the complexes were estimated by solvent extraction into chloroform. Substantial changes in net charge and lipophilicity of the 99mTc complexes were observed on substituting the carboxylic acid functionality in ligands I and II with the ethyl carboxylate groups (ligands II and IV). All the ligands formed 99mTc complexes in high yield. Whereas the complexes with ligands I and II were observed to be hydrophilic in nature and not extractable into CHCl3, ligands III and IV resulted in neutral and lipophilic 99mTc complexes. The 99mTc complex with ligand II was not stable and on storage formed a hydrophilic and nonextractable species. The biodistribution of the complexes of ligands I and II showed that they cleared predominantly through the kidneys, whereas the complexes with ligands III and IV were excreted primarily through the hepatobiliary system. No significant brain uptake was observed with the 99mTc complexes with ligands III and IV despite their favorable properties of neutrality, lipophilicity, and conversion into a hydrophilic species. These ligands offer potential for use as bifunctional chelating agents.

The Functions of Auxilin and Rab11 in Drosophila Suggest That the Fundamental Role of Ligand Endocytosis in Notch Signaling Cells Is Not Recycling

PubMed Central

Bilder, David; Fischer, Janice A.

2011-01-01

Notch signaling requires ligand internalization by the signal sending cells. Two endocytic proteins, epsin and auxilin, are essential for ligand internalization and signaling. Epsin promotes clathrin-coated vesicle formation, and auxilin uncoats clathrin from newly internalized vesicles. Two hypotheses have been advanced to explain the requirement for ligand endocytosis. One idea is that after ligand/receptor binding, ligand endocytosis leads to receptor activation by pulling on the receptor, which either exposes a cleavage site on the extracellular domain, or dissociates two receptor subunits. Alternatively, ligand internalization prior to receptor binding, followed by trafficking through an endosomal pathway and recycling to the plasma membrane may enable ligand activation. Activation could mean ligand modification or ligand transcytosis to a membrane environment conducive to signaling. A key piece of evidence supporting the recycling model is the requirement in signaling cells for Rab11, which encodes a GTPase critical for endosomal recycling. Here, we use Drosophila Rab11 and auxilin mutants to test the ligand recycling hypothesis. First, we find that Rab11 is dispensable for several Notch signaling events in the eye disc. Second, we find that Drosophila female germline cells, the one cell type known to signal without clathrin, also do not require auxilin to signal. Third, we find that much of the requirement for auxilin in Notch signaling was bypassed by overexpression of both clathrin heavy chain and epsin. Thus, the main role of auxilin in Notch signaling is not to produce uncoated ligand-containing vesicles, but to maintain the pool of free clathrin. Taken together, these results argue strongly that at least in some cell types, the primary function of Notch ligand endocytosis is not for ligand recycling. PMID:21448287

Ligand-dependent exciton dynamics and photovoltaic properties of PbS quantum dot heterojunction solar cells.

PubMed

Chang, Jin; Ogomi, Yuhei; Ding, Chao; Zhang, Yao Hong; Toyoda, Taro; Hayase, Shuzi; Katayama, Kenji; Shen, Qing

2017-03-01

The surface chemistry of colloidal quantum dots (QDs) plays an important role in determining the photoelectric properties of QD films and the corresponding quantum dot heterojunction solar cells (QDHSCs). To investigate the effects of the ligand structure on the photovoltaic performance and exciton dynamics of QDHSCs, PbS QDHSCs were fabricated by the solid state ligand exchange method with mercaptoalkanoic acid as the cross-linking ligand. Temperature-dependent photoluminescence and ultrafast transient absorption spectra show that the electronic coupling and charge transfer rate within QD ensembles were monotonically enhanced as the ligand length decreased. However, in practical QDHSCs, the second shortest ligand 3-mercaptopropionic acid (MPA) showed higher power conversion efficiency than the shortest ligand thioglycolic acid (TGA). This could be attributed to the difference in their surface trap states, supported by thermally stimulated current measurements. Moreover, compared with the non-conjugated ligand MPA, the conjugated ligand 4-mercaptobenzoic acid (MBA) introduces less trap states and has a similar charge transfer rate in QD ensembles, but has poor photovoltaic properties. This unexpected result could be contributed by the QD-ligand orbital mixing, leading to the charge transfer from QDs to ligands instead of charge transfer between adjacent QDs. This work highlights the significant effects of ligand structures on the photovoltaic properties and exciton dynamics of QDHSCs, which would shed light on the further development of QD-based photoelectric devices.

Structural and theoretical basis for ligand exchange on thiolate monolayer protected gold nanoclusters.

PubMed

Heinecke, Christine L; Ni, Thomas W; Malola, Sami; Mäkinen, Ville; Wong, O Andrea; Häkkinen, Hannu; Ackerson, Christopher J

2012-08-15

Ligand exchange reactions are widely used for imparting new functionality on or integrating nanoparticles into devices. Thiolate-for-thiolate ligand exchange in monolayer protected gold nanoclusters has been used for over a decade; however, a firm structural basis of this reaction has been lacking. Herein, we present the first single-crystal X-ray structure of a partially exchanged Au(102)(p-MBA)(40)(p-BBT)(4) (p-MBA = para-mercaptobenzoic acid, p-BBT = para-bromobenzene thiol) with p-BBT as the incoming ligand. The crystal structure shows that 2 of the 22 symmetry-unique p-MBA ligand sites are partially exchanged to p-BBT under the initial fast kinetics in a 5 min timescale exchange reaction. Each of these ligand-binding sites is bonded to a different solvent-exposed Au atom, suggesting an associative mechanism for the initial ligand exchange. Density functional theory calculations modeling both thiol and thiolate incoming ligands postulate a mechanistic pathway for thiol-based ligand exchange. The discrete modification of a small set of ligand binding sites suggests Au(102)(p-MBA)(44) as a powerful platform for surface chemical engineering.

Expression of human peroxisome proliferator-activated receptors ligand binding domain-maltose binding protein fusion protein in Escherichia coli: a convenient and reliable method for preparing receptor for screening ligands.

PubMed

Li, Changqing; Tian, Mi; Yuan, Ye; Zhou, Qinxin

2008-12-01

Human peroxisome proliferator-activated receptors (hPPARs) are ligand-activated transcription factors and are the target for the treatment of many diseases. Screening of their ligands is mainly based on assays of ligand binding to the ligand binding domain (LBD) of hPPARs.However, such assays are difficult because of the preparation of hPPARs LBD. In order to yield functional hPPARs LBD for screening ligands, hPPARs LBD was fused with maltose-binding protein(MBP) using the pMAL-p2x expression system through the gene engineering technique. The radioligand binding assay showed that MBP did not affect ligand binding with hPPARs LBD in the fusion proteins, which means that MBP-hPPARs LBD can be used instead of hPPARs LBD in ligand screening work. The results show that the new strategy using MBP as a fusion tag for preparing hPPARs LBD for screening ligands is a convenient and reliable method. It may be used to easily obtain the other nuclear receptors.

Unmasking of CD22 Co-receptor on Germinal Center B-cells Occurs by Alternative Mechanisms in Mouse and Man*

PubMed Central

Macauley, Matthew S.; Kawasaki, Norihito; Peng, Wenjie; Wang, Shui-Hua; He, Yuan; Arlian, Britni M.; McBride, Ryan; Kannagi, Reiji; Khoo, Kay-Hooi; Paulson, James C.

2015-01-01

CD22 is an inhibitory B-cell co-receptor whose function is modulated by sialic acid (Sia)-bearing glycan ligands. Glycan remodeling in the germinal center (GC) alters CD22 ligands, with as yet no ascribed biological consequence. Here, we show in both mice and humans that loss of high affinity ligands on GC B-cells unmasks the binding site of CD22 relative to naive and memory B-cells, promoting recognition of trans ligands. The conserved modulation of CD22 ligands on GC B-cells is striking because high affinity glycan ligands of CD22 are species-specific. In both species, the high affinity ligand is based on the sequence Siaα2–6Galβ1–4GlcNAc, which terminates N-glycans. The human ligand has N-acetylneuraminic acid (Neu5Ac) as the sialic acid, and the high affinity ligand on naive B-cells contains 6-O-sulfate on the GlcNAc. On human GC B-cells, this sulfate modification is lost, giving rise to lower affinity CD22 ligands. Ligands of CD22 on naive murine B-cells do not contain the 6-O-sulfate modification. Instead, the high affinity ligand for mouse CD22 has N-glycolylneuraminic acid (Neu5Gc) as the sialic acid, which is replaced on GC B-cells with Neu5Ac. Human naive and memory B-cells express sulfated glycans as high affinity CD22 ligands, which are lost on GC B-cells. In mice, Neu5Gc-containing glycans serve as high affinity CD22 ligands that are replaced by Neu5Ac-containing glycans on GC B-cells. Our results demonstrate that loss of high affinity CD22 ligands on GC B-cells occurs in both mice and humans through alternative mechanisms, unmasking CD22 relative to naive and memory B-cells. PMID:26507663

Unmasking of CD22 Co-receptor on Germinal Center B-cells Occurs by Alternative Mechanisms in Mouse and Man.

PubMed

Macauley, Matthew S; Kawasaki, Norihito; Peng, Wenjie; Wang, Shui-Hua; He, Yuan; Arlian, Britni M; McBride, Ryan; Kannagi, Reiji; Khoo, Kay-Hooi; Paulson, James C

2015-12-11

CD22 is an inhibitory B-cell co-receptor whose function is modulated by sialic acid (Sia)-bearing glycan ligands. Glycan remodeling in the germinal center (GC) alters CD22 ligands, with as yet no ascribed biological consequence. Here, we show in both mice and humans that loss of high affinity ligands on GC B-cells unmasks the binding site of CD22 relative to naive and memory B-cells, promoting recognition of trans ligands. The conserved modulation of CD22 ligands on GC B-cells is striking because high affinity glycan ligands of CD22 are species-specific. In both species, the high affinity ligand is based on the sequence Siaα2-6Galβ1-4GlcNAc, which terminates N-glycans. The human ligand has N-acetylneuraminic acid (Neu5Ac) as the sialic acid, and the high affinity ligand on naive B-cells contains 6-O-sulfate on the GlcNAc. On human GC B-cells, this sulfate modification is lost, giving rise to lower affinity CD22 ligands. Ligands of CD22 on naive murine B-cells do not contain the 6-O-sulfate modification. Instead, the high affinity ligand for mouse CD22 has N-glycolylneuraminic acid (Neu5Gc) as the sialic acid, which is replaced on GC B-cells with Neu5Ac. Human naive and memory B-cells express sulfated glycans as high affinity CD22 ligands, which are lost on GC B-cells. In mice, Neu5Gc-containing glycans serve as high affinity CD22 ligands that are replaced by Neu5Ac-containing glycans on GC B-cells. Our results demonstrate that loss of high affinity CD22 ligands on GC B-cells occurs in both mice and humans through alternative mechanisms, unmasking CD22 relative to naive and memory B-cells. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Ligand interaction scan: a general method for engineering ligand-sensitive protein alleles.

PubMed

Erster, Oran; Eisenstein, Miriam; Liscovitch, Mordechai

2007-05-01

The ligand interaction scan (LIScan) method is a general procedure for engineering small molecule ligand-regulated forms of a protein that is complementary to other 'reverse' genetic and chemical-genetic methods for drug-target validation. It involves insertional mutagenesis by a chemical-genetic 'switch', comprising a genetically encoded peptide module that binds with high affinity to a small-molecule ligand. We demonstrated the method with TEM-1 beta-lactamase, using a tetracysteine hexapeptide insert and a biarsenical fluorescein ligand (FlAsH).

Evidence of trem2 variant associated with triple risk of Alzheimer's disease.

PubMed

Abduljaleel, Zainularifeen; Al-Allaf, Faisal A; Khan, Wajahatullah; Athar, Mohammad; Shahzad, Naiyer; Taher, Mohiuddin M; Elrobh, Mohamed; Alanazi, Mohammed S; El-Huneidi, Waseem

2014-01-01

Alzheimer's disease is one of the main causes of dementia among elderly individuals and leads to the neurodegeneration of different areas of the brain, resulting in memory impairments and loss of cognitive functions. Recently, a rare variant that is associated with 3-fold higher risk of Alzheimer's disease onset has been found. The rare variant discovered is a missense mutation in the loop region of exon 2 of Trem2 (rs75932628-T, Arg47His). The aim of this study was to investigate the evidence for potential structural and functional significance of Trem2 gene variant (Arg47His) through molecular dynamics simulations. Our results showed the alteration caused due to the variant in TREM2 protein has significant effect on the ligand binding affinity as well as structural configuration. Based on molecular dynamics (MD) simulation under salvation, the results confirmed that native form of the variant (Arg47His) might be responsible for improved compactness, hence thereby improved protein folding. Protein simulation was carried out at different temperatures. At 300K, the deviation of the theoretical model of TREM2 protein increased from 2.0 Å at 10 ns. In contrast, the deviation of the Arg47His mutation was maintained at 1.2 Å until the end of the simulation (t = 10 ns), which indicated that Arg47His had reached its folded state. The mutant residue was a highly conserved region and was similar to "immunoglobulin V-set" and "immunoglobulin-like folds". Taken together, the result from this study provides a biophysical insight on how the studied variant could contribute to the genetic susceptibility to Alzheimer's disease.

A lanthanide complex with dual biosensing properties: CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts) with europium DOTA-tetraglycinate.

PubMed

Coman, Daniel; Kiefer, Garry E; Rothman, Douglas L; Sherry, A Dean; Hyder, Fahmeed

2011-12-01

Responsive contrast agents (RCAs) composed of lanthanide(III) ion (Ln3R) complexes with a variety of1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (DOTA4S) derivatives have shown great potential as molecular imaging agents for MR. A variety of LnDOTA–tetraamide complexes have been demonstrated as RCAs for molecular imaging using chemical exchange saturation transfer (CEST). The CEST method detects proton exchange between bulk water and any exchangeable sites on the ligand itself or an inner sphere of bound water that is shifted by a paramagnetic Ln3R ion bound in the core of the macrocycle. It has also been shown that molecular imaging is possible when the RCA itself is observed (i.e. not its effect on bulk water) using a method called biosensor imaging of redundant deviation in shifts (BIRDS). The BIRDS method utilizes redundant information stored in the nonexchangeable proton resonances emanating from the paramagnetic RCA for ambient factors such as temperature and/or pH.Thus, CEST and BIRDS rely on exchangeable and nonexchangeable protons, respectively, for biosensing. We posited that it would be feasible to combine these two biosensing features into the same RCA (i.e. dual CEST and BIRDS properties). A complex between europium(III) ion (Eu3R) and DOTA–tetraglycinate [DOTA–(gly)S4] was used to demonstrate that its CEST characteristics are preserved, while its BIRDS properties are also detectable. The in vitro temperature sensitivity of EuDOTA–(gly)S4 was used to show that qualitative MR contrast with CEST can be calibrated using quantitative MR mapping with BIRDS, thereby enabling quantitative molecular imaging at high spatial resolution.

Differential hydrogen/deuterium exchange mass spectrometry analysis of protein–ligand interactions

PubMed Central

Chalmers, Michael J; Busby, Scott A; Pascal, Bruce D; West, Graham M; Griffin, Patrick R

2011-01-01

Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule–receptor interactions, this technique has also been applied to study protein–protein complexes, such as mapping antibody–antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein–ligand interactions has had an impact on biology and drug discovery. PMID:21329427

Investing Wisely and Quickly: Use of ARRA Funds in America's Great City Schools

ERIC Educational Resources Information Center

Naik, Manish; Yorkman, Michell; Casserly, Michael

2010-01-01

President Obama signed the American Recovery and Reinvestment Act of 2009 (the Recovery Act or ARRA) into law on February 17, 2009. This federal stimulus package provided an unprecedented infusion of new education aid for the nation's schools--more than $100 billion. To determine how the unprecedented federal infusion of education funding was…

Stabilization of peroxisome proliferator-activated receptor alpha by the ligand.

PubMed

Hirotani, M; Tsukamoto, T; Bourdeaux, J; Sadano, H; Osumi, T

2001-10-19

Peroxisome proliferator-activated receptor (PPAR) constitutes a subfamily among a large group of ligand-activated transcription factors, the nuclear receptor superfamily. We studied the effects of ligand on the intracellular behaviors of PPARalpha. Although nuclear localization of PPARalpha was not affected by a selective ligand, Wy14643, we observed that exogenously expressed PPARalpha was rapidly degraded in HeLa cells, and the ligand significantly stabilized the protein. The stability of PPARalpha was also improved by coexpression of the heterodimer partner retinoid X receptor (RXR) alpha, and further stabilization was not observed with the ligand. These results indicate that PPARalpha is stabilized through heterodimerization with RXR, and the excess protein unpaired with RXR is rapidly turned over, if not bound by an appropriate ligand. These observations on PPARalpha are in sharp contrast to the ligand-stimulated degradation reported on PPARgamma. The ligand-dependent stabilization would have physiological significance when the synthesis of PPARalpha is elevated exceeding the available level of RXR. Copyright 2001 Academic Press.

A mixed valence zinc dithiolene system with spectator metal and reactor ligands.

PubMed

Ratvasky, Stephen C; Mogesa, Benjamin; van Stipdonk, Michael J; Basu, Partha

2016-08-16

Neutral complexes of zinc with N,N'-diisopropylpiperazine-2,3-dithione ( i Pr 2 Dt 0 ) and N,N'-dimethylpiperazine-2,3-dithione (Me 2 Dt 0 ) with chloride or maleonitriledithiolate (mnt 2- ) as coligands have been synthesized and characterized. The molecular structures of these zinc complexes have been determined using single crystal X-ray diffractometry. Complexes recrystallize in monoclinic P type systems with zinc adopting a distorted tetrahedral geometry. Two zinc complexes with mixed-valent dithiolene ligands exhibit ligand-to-ligand charge transfer bands. Optimized geometries, molecular vibrations and electronic structures of charge-transfer complexes were calculated using density functional theory (B3LYP/6-311G+(d,p) level). Redox orbitals are shown to be almost exclusively ligand in nature, with a HOMO based heavily on the electron-rich maleonitriledithiolate ligand, and a LUMO comprised mostly of the electron-deficient dithione ligand. Charge transfer is thus believed to proceed from dithiolate HOMO to dithione LUMO, showing ligand-to-ligand redox interplay across a d 10 metal.

Ligand Entry and Exit Pathways in the β2-adrenergic Receptor

PubMed Central

Wang, Ting; Duan, Yong

2009-01-01

The recently determined crystal structure of the human β2-adrenergic (β2AR) G-protein coupled receptor provides an excellent structural basis for exploring β2AR -ligand binding and dissociation process. Based on this crystal structure, we simulated ligand exit from the β2AR receptor by applying the random acceleration molecular dynamics (RAMD) simulation method. The simulation results showed that the extracellular opening on the receptor surface was the most frequently observed egress point (referred to as pathway A) and a few other pathways through inter-helical clefts were also observed with significantly lower frequencies. In the egress trajectories along pathway A, the D192-K305 salt bridge between the extracellular loop 2 (ECL2) and the apex of the transmembrane helix 7 (TM7) was exclusively broken. The spatial occupancy maps of the ligand computed from the 100 RAMD simulation trajectories indicated that the receptor-ligand interactions that restrained the ligand in the binding pocket were the major resistance encountered by the ligand during exit and no second barrier was notable. We next performed RAMD simulations by using a putative ligand-free conformation of the receptor as input structure. This conformation was obtained in a standard MD simulation in the absence of the ligand and it differed from the ligand-bound conformation in a hydrophobic patch bridging ECL2 and TM7 due to the rotation of F193 of ECL2. Results from the RAMD simulations with this putative ligand-free conformation suggest that the cleft formed by the hydrophobic bridge, TM2, TM3 and TM7 on the extracellular surface likely serves as a more specific ligand-entry site and the ECL2-TM7 hydrophobic junction can be partially interrupted upon the entry of ligand that pushes F193 to rotate, resulting in a conformation as observed in the ligand-bound crystal structure. These results may help design β2AR-targeting drugs with improved efficacy as well as understand the receptor subtype-selectivity of ligand binding in the β family of the adrenergic receptors that share almost identical ligand-binding pockets but show notable amino acid sequence divergence in the putative ligand-entry site, including ECL2 and the extracellular end of TM7. PMID:19665031

[Supercomputer investigation of the protein-ligand system low-energy minima].

PubMed

Oferkin, I V; Sulimov, A V; Katkova, E V; Kutov, D K; Grigoriev, F V; Kondakova, O A; Sulimov, V B

2015-01-01

The accuracy of the protein-ligand binding energy calculations and ligand positioning is strongly influenced by the choice of the docking target function. This work demonstrates the evaluation of the five different target functions used in docking: functions based on MMFF94 force field and functions based on PM7 quantum-chemical method accounting or without accounting the implicit solvent model (PCM, COSMO or SGB). For these purposes the ligand positions corresponding to the minima of the target function and the experimentally known ligand positions in the protein active site (crystal ligand positions) were compared. Each function was examined on the same test-set of 16 protein-ligand complexes. The new parallelized docking program FLM based on Monte Carlo search algorithm was developed to perform the comprehensive low-energy minima search and to calculate the protein-ligand binding energy. This study demonstrates that the docking target function based on the MMFF94 force field can be used to detect the crystal or near crystal positions of the ligand by the finding the low-energy local minima spectrum of the target function. The importance of solvent accounting in the docking process for the accurate ligand positioning is also shown. The accuracy of the ligand positioning as well as the correlation between the calculated and experimentally determined protein-ligand binding energies are improved when the MMFF94 force field is substituted by the new PM7 method with implicit solvent accounting.

Role of ligands in permanganate oxidation of organics.

PubMed

Jiang, Jin; Pang, Su-Yan; Ma, Jun

2010-06-01

We previously demonstrated that several ligands such as phosphate, pyrophosphate, EDTA, and humic acid could significantly enhance permanganate oxidation of triclosan (one phenolic biocide), which was explained by the contribution of ligand-stabilized reactive manganese intermediates in situ formed upon permanganate reduction. To further understand the underlying mechanism, we comparatively investigated the influence of ligands on permanganate oxidation of bisphenol A (BPA, one phenolic endocrine-disrupting chemical), carbamazepine (CBZ, a pharmaceutical containing the olefinic group), and methyl p-tolyl sulfoxide (TMSO, a typical oxygen-atom acceptor). Selected ligands exerted oxidation enhancement for BPA but had negligible influence for CBZ and TMSO. This was mainly attributed to the effects of identified Mn(III) complexes, which would otherwise disproportionate spontaneously in the absence of ligands. The one-electron oxidant Mn(III) species exhibited no reactivity toward CBZ and TMSO for which the two-electron oxygen donation may be the primary oxidation mechanism but readily oxidized BPA. The latter case was a function of pH, the complexing ligand, and the molar [Mn(III)]:[ligand] ratio, generally consistent with the patterns of ligand-affected permanganate oxidation. Moreover, the combination of the one-electron reduction of Mn(III) (Mn(III) + e(-) -->Mn(II)) and the Mn(VII)/Mn(II) reaction in excess ligands (Mn(VII) + 4Mn(II) ----> (ligands) 5Mn(III)) suggested a catalytic role of the Mn(III)/Mn(II) pair in permanganate oxidation of some phenolics in the presence of ligands.

PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions.

PubMed

Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G; Kihara, Daisuke

2014-08-27

Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets.

PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

PubMed Central

Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G.; Kihara, Daisuke

2014-01-01

Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets. PMID:25167137

Adsorption of hairy particles with mobile ligands: Molecular dynamics and density functional study

NASA Astrophysics Data System (ADS)

Borówko, M.; Sokołowski, S.; Staszewski, T.; Pizio, O.

2018-01-01

We study models of hairy nanoparticles in contact with a hard wall. Each particle is built of a spherical core with a number of ligands attached to it and each ligand is composed of several spherical, tangentially jointed segments. The number of segments is the same for all ligands. Particular models differ by the numbers of ligands and of segments per ligand, but the total number of segments is constant. Moreover, our model assumes that the ligands are tethered to the core in such a manner that they can "slide" over the core surface. Using molecular dynamics simulations we investigate the differences in the structure of a system close to the wall. In order to characterize the distribution of the ligands around the core, we have calculated the end-to-end distances of the ligands and the lengths and orientation of the mass dipoles. Additionally, we also employed a density functional approach to obtain the density profiles. We have found that if the number of ligands is not too high, the proposed version of the theory is capable to predict the structure of the system with a reasonable accuracy.

Articles including thin film monolayers and multilayers

DOEpatents

Li, DeQuan; Swanson, Basil I.

1995-01-01

Articles of manufacture including: (a) a base substrate having an oxide surface layer, and a multidentate ligand, capable of binding a metal ion, attached to the oxide surface layer of the base substrate, (b) a base substrate having an oxide surface layer, a multidentate ligand, capable of binding a metal ion, attached to the oxide surface layer of the base substrate, and a metal species attached to the multidentate ligand, (c) a base substrate having an oxide surface layer, a multidentate ligand, capable of binding a metal ion, attached to the oxide surface layer of the base substrate, a metal species attached to the multidentate ligand, and a multifunctional organic ligand attached to the metal species, and (d) a base substrate having an oxide surface layer, a multidentate ligand, capable of binding a metal ion, attached to the oxide surface layer of the base substrate, a metal species attached to the multidentate ligand, a multifunctional organic ligand attached to the metal species, and a second metal species attached to the multifunctional organic ligand, are provided, such articles useful in detecting the presence of a selected target species, as nonliear optical materials, or as scavengers for selected target species.

Developing Ligands for Palladium(II)-Catalyzed C–H Functionalization: Intimate Dialogue between Ligand and Substrate

PubMed Central

Engle, Keary M.; Yu, Jin-Quan

2013-01-01

Homogeneous transition metal–catalyzed reactions are indispensable to all facets of modern chemical synthesis. It is thus difficult to imagine that for much of the early 20th century, the reactivity and selectivity of all known homogeneous metal catalysts paled in comparison to their heterogeneous and biological counterparts. In the intervening decades, advances in ligand design bridged this divide, such that today some of the most demanding bond-forming events are mediated by ligand-supported homogeneous metal species. While ligand design has propelled many areas of homogeneous catalysis, in the field of Pd(II)-catalyzed C–H functionalization, suitable ligand scaffolds are lacking, which has hampered the development of broadly practical transformations based on C–H functionalization logic. In this review, we offer an account of our research employing three ligand scaffolds, mono-N-protected amino acids, 2,6-disubstituted pyridines, and 2,2′-bipyridines, to address challenges posed by several synthetically versatile substrate classes. Drawing on this work, we discuss principles of ligand design, such as the need to match a ligand to a particular substrate class, and how ligand traits such as tunability and modularity can be advantageous in reaction discovery. PMID:23565982

Ligand-Asymmetric Janus Quantum Dots for Efficient Blue-Quantum Dot Light-Emitting Diodes.

PubMed

Cho, Ikjun; Jung, Heeyoung; Jeong, Byeong Guk; Hahm, Donghyo; Chang, Jun Hyuk; Lee, Taesoo; Char, Kookheon; Lee, Doh C; Lim, Jaehoon; Lee, Changhee; Cho, Jinhan; Bae, Wan Ki

2018-06-19

We present ligand-asymmetric Janus quantum dots (QDs) to improve the device performance of quantum dot light-emitting diodes (QLEDs). Specifically, we devise blue QLEDs incorporating blue QDs with asymmetrically modified ligands, in which the bottom ligand of QDs in contact with ZnO electron-transport layer serves as a robust adhesive layer and an effective electron-blocking layer and the top ligand ensures uniform deposition of organic hole transport layers with enhanced hole injection properties. Suppressed electron overflow by the bottom ligand and stimulated hole injection enabled by the top ligand contribute synergistically to boost the balance of charge injection in blue QDs and therefore the device performance of blue QLEDs. As an ultimate achievement, the blue QLED adopting ligand-asymmetric QDs displays 2-fold enhancement in peak external quantum efficiency (EQE = 3.23%) compared to the case of QDs with native ligands (oleic acid) (peak EQE = 1.49%). The present study demonstrates an integrated strategy to control over the charge injection properties into QDs via ligand engineering that enables enhancement of the device performance of blue QLEDs and thus promises successful realization of white light-emitting devices using QDs.

The Synthesis and X-ray Structural Characterization of mer and fac isomers of the Technetium(I) Nitrosyl Complex [TcCl(2)(NO)(PNPpr)].

PubMed

Nicholson, T L; Mahmood, A; Refosco, F; Tisato, F; Müller, P; Jones, A G

2009-08-01

The nitrosyl complex H[TcNOCl(4)] reacts with the tridentate ligand bis[(2-diphenylphosphino)propyl]amine (PNPpr) to yield a mixture of the mer or fac isomers of [TcCl(2)(NO)(PNPpr)]. In acetonitrile, where the ligand is freely soluble, reaction occurs at room temperature to yield mostly the mer isomer with the linear nitrosyl ligand cis to the amine ligand; and the phosphine ligands arranged in a mutually trans orientation. The reaction in methanol requires reflux to dissolve the lipophilic ligand and generates the fac isomer of [TcCl2(NO)(PNPpr)] as the major product, with the tridentate ligand in a facial arrangement, leaving the chlorides and nitrosyl ligand in the remaining facial sites. The steric bulk of the tridentate ligand's diphenylphophino- moieties results in a significant distortion from octahedral geometry, with the P-Tc-P bond angle expanded to 99.48(4)°. The infrared spectra display absorptions from these nitrosyl ligands in the 1700 and 1800 cm(-1) regions for the fac and mer isomers respectively. The ESI(+) mass spectra each display the parent ion at 647 m/z.

Synthesis and binding properties of new selective ligands for the nucleobase opposite the AP site.

PubMed

Abe, Yukiko; Nakagawa, Osamu; Yamaguchi, Rie; Sasaki, Shigeki

2012-06-01

DNA is continuously damaged by endogenous and exogenous factors such as oxidative stress or DNA alkylating agents. These damaged nucleobases are removed by DNA N-glycosylase and form apurinic/apyrimidinic sites (AP sites) as intermediates in the base excision repair (BER) pathway. AP sites are also representative DNA damages formed by spontaneous hydrolysis. The AP sites block DNA polymerase and a mismatch nucleobase is inserted opposite the AP sites by polymerization to cause acute toxicities and mutations. Thus, AP site specific compounds have attracted much attention for therapeutic and diagnostic purposes. In this study, we have developed nucleobase-polyamine conjugates as the AP site binding ligand by expecting that the nucleobase part would play a role in the specific recognition of the nucleobase opposite the AP site by the Watson-Crick base pair formation and that the polyamine part should contribute to the access of the ligand to the AP site by a non-specific interaction to the DNA phosphate backbone. The nucleobase conjugated with 3,3'-diaminodipropylamine (A-ligand, G-ligand, C-ligand, T-ligand and U-ligand) showed a specific stabilization of the duplex containing the AP site depending on the complementary combination with the nucleobase opposite the AP site; that is A-ligand to T, G-ligand to C, C-ligand to G, T- and U-ligand to A. The thermodynamic binding parameters clearly indicated that the specific stabilization is due to specific binding of the ligands to the complementary AP site. These results have suggested that the complementary base pairs of the Watson-Crick type are formed at the AP site. Copyright © 2012 Elsevier Ltd. All rights reserved.

Proximity labeling of cis-ligands of CD22/Siglec-2 reveals stepwise α2,6 sialic acid-dependent and -independent interactions.

PubMed

Alborzian Deh Sheikh, Amin; Akatsu, Chizuru; Imamura, Akihiro; Abdu-Allah, Hajjaj H M; Takematsu, Hiromu; Ando, Hiromune; Ishida, Hideharu; Tsubata, Takeshi

2018-01-01

Lectins expressed on the cell surface are often bound and regulated by the membrane molecules containing the glycan ligands on the same cell (cis-ligands). However, molecular nature and function of cis-ligands are generally poorly understood partly because of weak interaction between lectins and glycan ligands. Cis-ligands are most extensively studied in CD22 (also known as Siglec-2), an inhibitory B lymphocyte receptor specifically recognizing α2,6 sialic acids. CD22, CD45 and IgM are suggested to be ligands of CD22. Here we labeled molecules in the proximity of CD22 in situ on B cell surface using biotin-tyramide. Molecules including CD22, CD45 and IgM were labeled in wild-type but not ST6GalI -/- B cells that lack α2,6 sialic acids, indicating that these molecules associate with CD22 by lectin-glycan interaction, and are therefore cis-ligands. In ST6GalI -/- B cells, these cis-ligands are located in a slightly more distance from CD22. Thus, the lectin-glycan interaction recruits cis-ligands already located in the relative proximity of CD22 through non-lectin-glycan interaction to the close proximity. Moreover, cis-ligands are labeled in Cmah -/- B cells that lack Neu5Gc preferred by mouse CD22 as efficiently as in wild-type B cells, indicating that very low affinity lectin-glycan interaction is sufficient for recruiting cis-ligands, and can be detected by proximity labeling. Thus, proximity labeling with tyramide appears to be a useful method to identify cis-ligands and to analyze their interaction with the lectins. Copyright © 2017 Elsevier Inc. All rights reserved.

Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins

NASA Astrophysics Data System (ADS)

Poornima, C. S.; Dean, P. M.

1995-12-01

Water molecules are known to play an important rôle in mediating protein-ligand interactions. If water molecules are conserved at the ligand-binding sites of homologous proteins, such a finding may suggest the structural importance of water molecules in ligand binding. Structurally conserved water molecules change the conventional definition of `binding sites' by changing the shape and complementarity of these sites. Such conserved water molecules can be important for site-directed ligand/drug design. Therefore, five different sets of homologous protein/protein-ligand complexes have been examined to identify the conserved water molecules at the ligand-binding sites. Our analysis reveals that there are as many as 16 conserved water molecules at the FAD binding site of glutathione reductase between the crystal structures obtained from human and E. coli. In the remaining four sets of high-resolution crystal structures, 2-4 water molecules have been found to be conserved at the ligand-binding sites. The majority of these conserved water molecules are either bound in deep grooves at the protein-ligand interface or completely buried in cavities between the protein and the ligand. All these water molecules, conserved between the protein/protein-ligand complexes from different species, have identical or similar apolar and polar interactions in a given set. The site residues interacting with the conserved water molecules at the ligand-binding sites have been found to be highly conserved among proteins from different species; they are more conserved compared to the other site residues interacting with the ligand. These water molecules, in general, make multiple polar contacts with protein-site residues.

Gas adsorption and gas mixture separations using mixed-ligand MOF material

DOEpatents

Hupp, Joseph T [Northfield, IL; Mulfort, Karen L [Chicago, IL; Snurr, Randall Q [Evanston, IL; Bae, Youn-Sang [Evanston, IL

2011-01-04

A method of separating a mixture of carbon dioxiode and hydrocarbon gas using a mixed-ligand, metal-organic framework (MOF) material having metal ions coordinated to carboxylate ligands and pyridyl ligands.

Role of Polymer-grafted Nanoparticle Interactions in Supercrystal Self-Assembly

NASA Astrophysics Data System (ADS)

Horst, Nathan; Waltmann, Curt; Travesset, Alex

Many successful strategies are available for the programmable self-assembly of nanoparticle superlattices. In this talk, we discuss the the case of nanoparticles with grafted polymer ligands. For very short polymers, the phase diagram is rationalized by borrowing results from hard-sphere packing models. Although a clear correlation exists between the maximum of the packing fraction of hard spheres and supercrystal equilibrium phases found experimentally, these systems are flexible, which leads to clear deviations from the sphere packing model. Using theoretical and computational models, we present an investigation of the interactions of polymer-grafted nanoparticles, focusing on the role of the rigidity of the chain, and how it affects the resulting two and three-dimensional superlattice structures. Comparison with an experimental system of gold nanoparticles grafted with polyethylene glycol is also presented. Supported by the U.S. Department of Energy (U.S. DOE), Office of Basic Energy Sciences, Division of Materials Sciences and Engineering. Ames Laboratory is operated for the U.S. DOE by Iowa State University under Contract No. DE-AC02-07CH11358.

Simulations of a Membrane-Anchored Peptide: Structure, Dynamics, and Influence on Bilayer Properties

PubMed Central

Jensen, Morten Ø.; Mouritsen, Ole G.; Peters, Günther H.

2004-01-01

A three-dimensional structure of a model decapeptide is obtained by performing molecular dynamics simulations of the peptide in explicit water. Interactions between an N-myristoylated form of the folded peptide anchored to dipalmitoylphosphatidylcholine fluid phase lipid membranes are studied at different applied surface tensions by molecular dynamics simulations. The lipid membrane environment influences the conformational space explored by the peptide. The overall secondary structure of the anchored peptide is found to deviate at times from its structure in aqueous solution through reversible conformational transitions. The peptide is, despite the anchor, highly mobile at the membrane surface with the peptide motion along the bilayer normal being integrated into the collective modes of the membrane. Peptide anchoring moderately alters the lateral compressibility of the bilayer by changing the equilibrium area of the membrane. Although membrane anchoring moderately affects the elastic properties of the bilayer, the model peptide studied here exhibits conformational flexibility and our results therefore suggest that peptide acylation is a feasible way to reinforce peptide-membrane interactions whereby, e.g., the lifetime of receptor-ligand interactions can be prolonged. PMID:15189854

Manifestations of Kitaev physics in thermodynamic properties of hexagonal iridates and α-RuCl3

NASA Astrophysics Data System (ADS)

Tsirlin, Alexander

Kitaev model is hard to achieve in real materials. Best candidates available so far are hexagonal iridates M2IrO3 (M = Li and Na) and the recently discovered α-RuCl3 featuring hexagonal layers coupled by weak van der Waals bonding. I will review recent progress in crystal growth of these materials and compare their thermodynamic properties. Both hexagonal iridates and α-RuCl3 feature highly anisotropic Curie-Weiss temperatures that not only differ in magnitude but also change sign depending on the direction of the applied magnetic field. Néel temperatures are largely suppressed compared to the energy scale of the Curie-Weiss temperatures. These experimental observations will be linked to features of the electronic structure and to structural peculiarities associated with deviations from the ideal hexagonal symmetry. I will also discuss how the different nature of ligand atoms affects electronic structure and magnetic superexchange. This work has been done in collaboration with M. Majumder, M. Schmidt, M. Baenitz, F. Freund, and P. Gegenwart.

Crystal structure of di-chlorido-{4-[(E)-(meth-oxy-imino-κN)meth-yl]-1,3-thia-zol-2-amine-κN (3)}palladium(II).

PubMed

Dyakonenko, Viktorita V; Zholob, Olga O; Orysyk, Svitlana I; Pekhnyo, Vasily I

2015-01-01

In the title compound, [PdCl2(C5H7N3OS)], the Pd(II) atom adopts a distorted square-planar coordination sphere defined by two N atoms of the bidentate ligand and two Cl atoms. The mean deviation from the coordination plane is 0.029 Å. The methyl group is not coplanar with the plane of the metallacycle [torsion angle C-O-N-C = 20.2 (4)°]. Steric repulsion between the methyl group and atoms of the metallacycle is manifested by shortened intra-molecular H⋯C contacts of 2.27, 2.38 and 2.64 Å, as compared with the sum of the van der Waals radii of 2.87 Å. The amino group participates via one H atom in the formation of an intra-molecular N-H⋯Cl hydrogen bond. In the crystal, the other H atom of the amino group links mol-ecules via bifurcated N-H⋯(Cl,O) hydrogen bonds into chains parallel to [001].

A global benchmark study using affinity-based biosensors

PubMed Central

Rich, Rebecca L.; Papalia, Giuseppe A.; Flynn, Peter J.; Furneisen, Jamie; Quinn, John; Klein, Joshua S.; Katsamba, Phini S.; Waddell, M. Brent; Scott, Michael; Thompson, Joshua; Berlier, Judie; Corry, Schuyler; Baltzinger, Mireille; Zeder-Lutz, Gabrielle; Schoenemann, Andreas; Clabbers, Anca; Wieckowski, Sebastien; Murphy, Mary M.; Page, Phillip; Ryan, Thomas E.; Duffner, Jay; Ganguly, Tanmoy; Corbin, John; Gautam, Satyen; Anderluh, Gregor; Bavdek, Andrej; Reichmann, Dana; Yadav, Satya P.; Hommema, Eric; Pol, Ewa; Drake, Andrew; Klakamp, Scott; Chapman, Trevor; Kernaghan, Dawn; Miller, Ken; Schuman, Jason; Lindquist, Kevin; Herlihy, Kara; Murphy, Michael B.; Bohnsack, Richard; Andrien, Bruce; Brandani, Pietro; Terwey, Danny; Millican, Rohn; Darling, Ryan J.; Wang, Liann; Carter, Quincy; Dotzlaf, Joe; Lopez-Sagaseta, Jacinto; Campbell, Islay; Torreri, Paola; Hoos, Sylviane; England, Patrick; Liu, Yang; Abdiche, Yasmina; Malashock, Daniel; Pinkerton, Alanna; Wong, Melanie; Lafer, Eileen; Hinck, Cynthia; Thompson, Kevin; Primo, Carmelo Di; Joyce, Alison; Brooks, Jonathan; Torta, Federico; Bagge Hagel, Anne Birgitte; Krarup, Janus; Pass, Jesper; Ferreira, Monica; Shikov, Sergei; Mikolajczyk, Malgorzata; Abe, Yuki; Barbato, Gaetano; Giannetti, Anthony M.; Krishnamoorthy, Ganeshram; Beusink, Bianca; Satpaev, Daulet; Tsang, Tiffany; Fang, Eric; Partridge, James; Brohawn, Stephen; Horn, James; Pritsch, Otto; Obal, Gonzalo; Nilapwar, Sanjay; Busby, Ben; Gutierrez-Sanchez, Gerardo; Gupta, Ruchira Das; Canepa, Sylvie; Witte, Krista; Nikolovska-Coleska, Zaneta; Cho, Yun Hee; D’Agata, Roberta; Schlick, Kristian; Calvert, Rosy; Munoz, Eva M.; Hernaiz, Maria Jose; Bravman, Tsafir; Dines, Monica; Yang, Min-Hsiang; Puskas, Agnes; Boni, Erica; Li, Jiejin; Wear, Martin; Grinberg, Asya; Baardsnes, Jason; Dolezal, Olan; Gainey, Melicia; Anderson, Henrik; Peng, Jinlin; Lewis, Mark; Spies, Peter; Trinh, Quyhn; Bibikov, Sergei; Raymond, Jill; Yousef, Mohammed; Chandrasekaran, Vidya; Feng, Yuguo; Emerick, Anne; Mundodo, Suparna; Guimaraes, Rejane; McGirr, Katy; Li, Yue-Ji; Hughes, Heather; Mantz, Hubert; Skrabana, Rostislav; Witmer, Mark; Ballard, Joshua; Martin, Loic; Skladal, Petr; Korza, George; Laird-Offringa, Ite; Lee, Charlene S.; Khadir, Abdelkrim; Podlaski, Frank; Neuner, Phillippe; Rothacker, Julie; Rafique, Ashique; Dankbar, Nico; Kainz, Peter; Gedig, Erk; Vuyisich, Momchilo; Boozer, Christina; Ly, Nguyen; Toews, Mark; Uren, Aykut; Kalyuzhniy, Oleksandr; Lewis, Kenneth; Chomey, Eugene; Pak, Brian J.; Myszka, David G.

2013-01-01

To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used. PMID:19133223

Virtual Screening and Molecular Dynamics Simulations from a Bank of Molecules of the Amazon Region Against Functional NS3-4A Protease-Helicase Enzyme of Hepatitis C Virus.

PubMed

Pinheiro, Alan Sena; Duarte, Jaqueline Bianca Carvalho; Alves, Cláudio Nahum; de Molfetta, Fábio Alberto

2015-07-01

Hepatitis C virus (HCV) infection is a disease that affects approximately 3% of the global population and requires new therapeutic agents without the inconvenience associated with current anti-HCV treatment. This paper reports on a study of a virtual screening and a molecular dynamics simulation of compounds derived from natural products from the Amazon region that are potentially effective against the NS3-4A enzyme of HCV, which plays an important role in the replication process of this virus. According to the results of the molecular docking calculations and subsequent consensual analysis, the best scored compounds showed interactions between hydrogen and residues of the catalytic triad as well as interactions with residues that guide ligands to the active site of the enzyme. They also showed stability in the molecular dynamics simulation, as the structures preserved important interactions at the active site of the enzyme. The root mean square deviation (RMSD) values were stabilized at the end of the simulation time. Such compounds are considered promising as novel therapies against HCV.

EGF receptor ligands: recent advances.

PubMed

Singh, Bhuminder; Carpenter, Graham; Coffey, Robert J

2016-01-01

Seven ligands bind to and activate the mammalian epidermal growth factor (EGF) receptor (EGFR/ERBB1/HER1): EGF, transforming growth factor-alpha (TGFA), heparin-binding EGF-like growth factor (HBEGF), betacellulin (BTC), amphiregulin (AREG), epiregulin (EREG), and epigen (EPGN). Of these, EGF, TGFA, HBEGF, and BTC are thought to be high-affinity ligands, whereas AREG, EREG, and EPGN constitute low-affinity ligands. This focused review is meant to highlight recent studies related to actions of the individual EGFR ligands, the interesting biology that has been uncovered, and relevant advances related to ligand interactions with the EGFR.

Shedding Light on Anesthetic Mechanisms: Application of Photoaffinity Ligands

PubMed Central

Woll, Kellie A.; Dailey, William P.; Brannigan, Grace; Eckenhoff, Roderic G.

2016-01-01

Anesthetic photoaffinity ligands have had an increasing presence within anesthesiology research. These ligands mimic parent general anesthetics, and allow investigators to study anesthetic interactions with receptors and enzymes; identify novel targets; and determine distribution within biological systems. To date nearly all general anesthetics used in medicine have a corresponding photoaffinity ligand represented in the literature. In this review we examine all aspects of the current methodologies, including ligand design, characterization and deployment. Finally we offer points of consideration and highlight the future outlook as more photoaffinity ligands emerge within the field. PMID:27464974

Shedding Light on Anesthetic Mechanisms: Application of Photoaffinity Ligands.

PubMed

Woll, Kellie A; Dailey, William P; Brannigan, Grace; Eckenhoff, Roderic G

2016-11-01

Anesthetic photoaffinity ligands have had an increasing presence within anesthesiology research. These ligands mimic parent general anesthetics and allow investigators to study anesthetic interactions with receptors and enzymes; identify novel targets; and determine distribution within biological systems. To date, nearly all general anesthetics used in medicine have a corresponding photoaffinity ligand represented in the literature. In this review, we examine all aspects of the current methodologies, including ligand design, characterization, and deployment. Finally we offer points of consideration and highlight the future outlook as more photoaffinity ligands emerge within the field.

Liquid phase low temperature method for production of methanol from synthesis gas and catalyst formulations therefor

DOEpatents

Mahajan, Devinder

2005-07-26

The invention provides a homogenous catalyst for the production of methanol from purified synthesis gas at low temperature and low pressure which includes a transition metal capable of forming transition metal complexes with coordinating ligands and an alkoxide, the catalyst dissolved in a methanol solvent system, provided the transition metal complex is not transition metal carbonyl. The coordinating ligands can be selected from the group consisting of N-donor ligands, P-donor ligands, O-donor ligands, C-donor ligands, halogens and mixtures thereof.

Scoring ligand similarity in structure-based virtual screening.

PubMed

Zavodszky, Maria I; Rohatgi, Anjali; Van Voorst, Jeffrey R; Yan, Honggao; Kuhn, Leslie A

2009-01-01

Scoring to identify high-affinity compounds remains a challenge in virtual screening. On one hand, protein-ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand-based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three-dimensional reference ligand. Our hypothesis is that a hybrid approach, using ligand-based scoring to rank dockings selected by protein-ligand scoring, can ensure that high-ranking molecules mimic the shape and chemistry of a known ligand while also complementing the binding site. Results from applying this approach to screen nearly 70 000 National Cancer Institute (NCI) compounds for thrombin inhibitors tend to support the hypothesis. EON ligand-based ranking of docked molecules yielded the majority (4/5) of newly discovered, low to mid-micromolar inhibitors from a panel of 27 assayed compounds, whereas ranking docked compounds by protein-ligand scoring alone resulted in one new inhibitor. Since the results depend on the choice of scoring function, an analysis of properties was performed on the top-scoring docked compounds according to five different protein-ligand scoring functions, plus EON scoring using three different reference compounds. The results indicate that the choice of scoring function, even among scoring functions measuring the same types of interactions, can have an unexpectedly large effect on which compounds are chosen from screening. Furthermore, there was almost no overlap between the top-scoring compounds from protein-ligand versus ligand-based scoring, indicating the two approaches provide complementary information. Matchprint analysis, a new addition to the SLIDE (Screening Ligands by Induced-fit Docking, Efficiently) screening toolset, facilitated comparison of docked molecules' interactions with those of known inhibitors. The majority of interactions conserved among top-scoring compounds for a given scoring function, and from the different scoring functions, proved to be conserved interactions in known inhibitors. This was particularly true in the S1 pocket, which was occupied by all the docked compounds. (c) 2009 John Wiley & Sons, Ltd.

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

PubMed

Kim, Seonghoon; Lee, Jumin; Jo, Sunhwan; Brooks, Charles L; Lee, Hui Sun; Im, Wonpil

2017-06-05

Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification. Based on the displayed structure, Ligand Reader & Modeler generates the ligand force field parameters and necessary structure files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can define chemical substitution sites and draw substituents in each site on the sketchpad to generate a set of combinatorial structure files and corresponding force field parameters for throughput or alchemical free energy simulations. Finally, the output from Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a functional module of CHARMM-GUI at http://www.charmm-gui.org/input/ligandrm. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiong, J.-P.; Stehle, T.; Zhang, R.

The structural basis for the divalent cation-dependent binding of heterodimeric alpha beta integrins to their ligands, which contain the prototypical Arg-Gly-Asp sequence, is unknown. Interaction with ligands triggers tertiary and quaternary structural rearrangements in integrins that are needed for cell signaling. Here we report the crystal structure of the extracellular segment of integrin alpha Vbeta 3 in complex with a cyclic peptide presenting the Arg-Gly-Asp sequence. The ligand binds at the major interface between the alpha V and beta 3 subunits and makes extensive contacts with both. Both tertiary and quaternary changes are observed in the presence of ligand. Themore » tertiary rearrangements take place in beta A, the ligand-binding domain of beta 3; in the complex, beta A acquires two cations, one of which contacts the ligand Asp directly and the other stabilizes the ligand-binding surface. Ligand binding induces small changes in the orientation of alpha V relative to beta 3.« less

Ligand and receptor dynamics contribute to the mechanism of graded PPARγ agonism

PubMed Central

Hughes, Travis S.; Chalmers, Michael J.; Novick, Scott; Kuruvilla, Dana S.; Chang, Mi Ra; Kamenecka, Theodore M.; Rance, Mark; Johnson, Bruce A.; Burris, Thomas P.; Griffin, Patrick R.; Kojetin, Douglas J.

2011-01-01

SUMMARY Ligand binding to proteins is not a static process, but rather involves a number of complex dynamic transitions. A flexible ligand can change conformation upon binding its target. The conformation and dynamics of a protein can change to facilitate ligand binding. The conformation of the ligand, however, is generally presumed to have one primary binding mode, shifting the protein conformational ensemble from one state to another. We report solution NMR studies that reveal peroxisome proliferator-activated receptor γ (PPARγ) modulators can sample multiple binding modes manifesting in multiple receptor conformations in slow conformational exchange. Our NMR, hydrogen/deuterium exchange and docking studies reveal that ligand-induced receptor stabilization and binding mode occupancy correlate with the graded agonist response of the ligand. Our results suggest that ligand and receptor dynamics affect the graded transcriptional output of PPARγ modulators. PMID:22244763

Organic iron (III) complexing ligands during an iron enrichment experiment in the western subarctic North Pacific

NASA Astrophysics Data System (ADS)

Kondo, Yoshiko; Takeda, Shigenobu; Nishioka, Jun; Obata, Hajime; Furuya, Ken; Johnson, William Keith; Wong, C. S.

2008-06-01

Complexation of iron (III) with natural organic ligands was investigated during a mesoscale iron enrichment experiment in the western subarctic North Pacific (SEEDS II). After the iron infusions, ligand concentrations increased rapidly with subsequent decreases. While the increases of ligands might have been partly influenced by amorphous iron colloids formation (12-29%), most in-situ increases were attributable to the <200 kDa fraction. Dilution of the fertilized patch may have contributed to the rapid decreases of the ligands. During the bloom decline, ligand concentration increased again, and the high concentrations persisted for 10 days. The conditional stability constant was not different between inside and outside of the fertilized patch. These results suggest that the chemical speciation of the released iron was strongly affected by formation of the ligands; the production of ligands observed during the bloom decline will strongly impact the iron cycle and bioavailability in the surface water.

Ligand Shaping in Induced Fit Docking of MraY Inhibitors. Polynomial Discriminant and Laplacian Operator as Biological Activity Descriptors.

PubMed

Lungu, Claudiu N; Diudea, Mircea V; Putz, Mihai V

2017-06-27

Docking-i.e., interaction of a small molecule (ligand) with a proteic structure (receptor)-represents the ground of drug action mechanism of the vast majority of bioactive chemicals. Ligand and receptor accommodate their geometry and energy, within this interaction, in the benefit of receptor-ligand complex. In an induced fit docking, the structure of ligand is most susceptible to changes in topology and energy, comparative to the receptor. These changes can be described by manifold hypersurfaces, in terms of polynomial discriminant and Laplacian operator. Such topological surfaces were represented for each MraY (phospho-MurNAc-pentapeptide translocase) inhibitor, studied before and after docking with MraY. Binding affinities of all ligands were calculated by this procedure. For each ligand, Laplacian and polynomial discriminant were correlated with the ligand minimum inhibitory concentration (MIC) retrieved from literature. It was observed that MIC is correlated with Laplacian and polynomial discriminant.

Interactions between alkaline earth cations and oxo ligands. DFT study of the affinity of the Mg²+ cation for phosphoryl ligands.

PubMed

da Costa, Leonardo Moreira; de Mesquita Carneiro, José Walkimar; Paes, Lilian Weitzel Coelho

2011-08-01

DFT (B3LYP/6-31+G(d)) calculations of Mg(2+) affinities for a set of phosphoryl ligands were performed. Two types of ligands were studied: a set of trivalent [O = P(R)] and a set of pentavalent phosphoryl ligands [O = P(R)(3)] (R = H, F, Cl, Br, OH, OCH(3), CH(3), CN, NH(2) and NO(2)), with R either bound directly to the phosphorus atom or to the para position of a phenyl ring. The affinity of the Mg(2+) cation for the ligands was quantified by means of the enthalpy for the substitution of one water molecule in the [Mg(H(2)O)(6)](2+) complex for a ligand. The enthalpy of substitution was correlated with electronic and geometric parameters. Electron-donor groups increase the interaction between the cation and the ligand, while electron-acceptor groups decrease the interaction enthalpy.

Structural Analysis of Chemokine Receptor–Ligand Interactions

PubMed Central

2017-01-01

This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

Optical Absorbance Enhancement in PbS QD/Cinnamate Ligand Complexes.

PubMed

Kroupa, Daniel M; Vörös, Márton; Brawand, Nicholas P; Bronstein, Noah; McNichols, Brett W; Castaneda, Chloe V; Nozik, Arthur J; Sellinger, Alan; Galli, Giulia; Beard, Matthew C

2018-06-08

We studied the optical absorption enhancement in colloidal suspensions of PbS quantum dots (QD) upon ligand exchange from oleate to a series of cinnamate ligands. By combining experiments and ab initio simulations, we elucidate physical parameters that govern the optical absorption enhancement. We find that, within the cinnamate/PbS QD system, the optical absorption enhancement scales linearly with the electronic gap of the ligand, indicating that the ligand/QD coupling occurs equally efficient between the QD and ligand HOMO and their respective LUMO levels. Disruption of the conjugation that connects the aromatic ring and its substituents to the QD core causes a reduction of the electronic coupling. Our results further support the notion that the ligand/QD complex should be considered as a distinct chemical system with emergent behavior rather than a QD core with ligands whose sole purpose is to passivate surface dangling bonds and prevent agglomeration.

Regulation of expression of the ligand for CD40 on T helper lymphocytes.

PubMed

Castle, B E; Kishimoto, K; Stearns, C; Brown, M L; Kehry, M R

1993-08-15

Activated Th cells deliver contact-dependent signals to resting B lymphocytes that initiate and drive B cell proliferation. Recently, a ligand for the B lymphocyte membrane protein, CD40, has been identified that delivers contact-dependent Th cell signals to B cells. A dimeric soluble form of CD40 was produced and used to further characterize the regulation of expression of the CD40 ligand. Expression of the CD40 ligand was rapidly induced after Th lymphocyte activation, and its stability depended upon whether Th cells were activated with soluble or plastic-bound stimuli. Th cells activated with soluble stimuli rapidly turned over cell-surface CD40 ligand whereas Th cells activated with plastic-bound stimuli exhibited more stable CD40 ligand expression for up to 48 h. Removal of activated Th cells from the plastic-bound stimulus resulted in a rapid turnover of CD40 ligand, suggesting that continuous stimulation could maintain CD40 ligand expression. Ligation by soluble CD40 could also stabilize expression of CD40 ligand on the Th cell surface. Both CD40 ligand and IL-2 were transiently synthesized from 1 to 12 h after Th cell activation and had similar kinetics of synthesis. In Con A-activated Th cells newly synthesized CD40 ligand exhibited an initial high turnover (1.5 h t1/2) and after 5 h of Th cell activation became more stable (10-h t1/2). In Th cells activated with plastic-bound anti-CD3, CD40 ligand exhibited a similar biphasic turnover except that the rapid turnover phase began significantly later. This delay could allow more time for newly synthesized CD40 ligand to assemble or associate with other molecules and thus become stabilized on the cell surface. Newly synthesized CD40 ligand in Con A-activated Th cells appeared to not be efficient in delivering Th cell-dependent contact signals to resting B cells, implying the need for assembly or accessory proteins. Regulation of CD40 ligand expression was consistent with all the characteristics of Th cell-delivered contact signals to B cells and may contribute to the high degree of specificity in B cell responses.

Architecture effects on multivalent interactions by polypeptide-based multivalent ligands

NASA Astrophysics Data System (ADS)

Liu, Shuang

Multivalent interactions are characterized by the simultaneous binding between multiple ligands and multiple binding sites, either in solutions or at interfaces. In biological systems, most multivalent interactions occur between protein receptors and carbohydrate ligands through hydrogen-bonding and hydrophobic interactions. Compared with weak affinity binding between one ligand and one binding site, i.e. monovalent interaction, multivalent interactioins provide greater avidity and specificity, and therefore play unique roles in a broad range of biological activities. Moreover, the studies of multivalent interactions are also essential for producing effective inhibitors and effectors of biological processes that could have important therapeutic applications. Synthetic multivalent ligands have been designed to mimic the biological functions of natural multivalent interactions, and various types of scaffolds have been used to display multiple ligands, including small molecules, linear polymers, dendrimers, nanoparticle surfaces, monolayer surfaces and liposomes. Studies have shown that multivalent interactions can be highly affected by various architectural parameters of these multivalent ligands, including ligand identities, valencies, spacing, ligand densities, nature of linker arms, scaffold length and scaffold conformation. Most of these multivalent ligands are chemically synthesized and have limitations of controlling over sequence and conformation, which is a barrier for mimicking ordered and controlled natural biological systems. Therefore, multivalent ligands with precisely controlled architecture are required for improved structure-function relationship studies. Protein engineering methods with subsequent chemical coupling of ligands provide significant advantages of controlling over backbone conformation and functional group placement, and therefore have been used to synthesize recombinant protein-based materials with desired properties similar to natural protein materials, including structural as well as functional proteins. Therefore, polypeptide-based multivalent scaffolds are used to display ligands to assess the contribution of different architectural parameters to the multivalent binding events. In this work, a family of alanine-rich alpha-helical glycopolypeptides was designed and synthesized by a combination of protein engineering and chemical coupling, to display two types of saccharide ligands for two different multivalent binding systems. The valencies, chain length and spacing between adjacent ligands of these multivalent ligands were designed in order to study architecture effects on multivalent interactions. The polypeptides and their glycoconjugates were characterized via various methods, including SDS-PAGE, NMR, HPLC, amino acid analysis (AAA), MALDI, circular dichroism (CD) and GPC. In the first multivalent binding system, cholera toxin B pentamer (CT B5) was chosen to be the protein receptor due to its well-characterized structure, lack of significant steric interference of binding to multiple binding sites, and requirement of only simple monosaccharide as ligands. Galactopyranoside was incorporated into polypeptide scaffolds through amine-carboxylic acid coupling to the side chains of glutamic acid residues. The inhibition and binding to CT B5 of these glycopolypeptide ligands were evaluated by direct enzyme-linked assay (DELA). As a complement method, weak affinity chromatography (WAC) was also used to evaluate glycopolypeptides binding to a CT B5 immobilized column. The architecture effects on CT B 5 inhibition are discussed. In the second system, cell surface receptor L-selectin was targeted by polypeptide-based multivalent ligands containing disulfated galactopyranoside ligands, due to its important roles in various immunological activities. The effects of glycopolypeptide architectural variables L-selectin shedding were evaluated via ELISA-based assays. These polypeptide-based multivalent ligands are suggested to be useful for elucidating architecture effects on multivalent interactions, manipulating multivalent interactions and the subsequent cellular responses in different systems. These materials have great potential applications in therapeutics and could also provide guidelines for design of multivalent ligands for other protein receptors.

Free-energy relationships in ion channels activated by voltage and ligand

PubMed Central

Chowdhury, Sandipan

2013-01-01

Many ion channels are modulated by multiple stimuli, which allow them to integrate a variety of cellular signals and precisely respond to physiological needs. Understanding how these different signaling pathways interact has been a challenge in part because of the complexity of underlying models. In this study, we analyzed the energetic relationships in polymodal ion channels using linkage principles. We first show that in proteins dually modulated by voltage and ligand, the net free-energy change can be obtained by measuring the charge-voltage (Q-V) relationship in zero ligand condition and the ligand binding curve at highly depolarizing membrane voltages. Next, we show that the voltage-dependent changes in ligand occupancy of the protein can be directly obtained by measuring the Q-V curves at multiple ligand concentrations. When a single reference ligand binding curve is available, this relationship allows us to reconstruct ligand binding curves at different voltages. More significantly, we establish that the shift of the Q-V curve between zero and saturating ligand concentration is a direct estimate of the interaction energy between the ligand- and voltage-dependent pathway. These free-energy relationships were tested by numerical simulations of a detailed gating model of the BK channel. Furthermore, as a proof of principle, we estimate the interaction energy between the ligand binding and voltage-dependent pathways for HCN2 channels whose ligand binding curves at various voltages are available. These emerging principles will be useful for high-throughput mutagenesis studies aimed at identifying interaction pathways between various regulatory domains in a polymodal ion channel. PMID:23250866

Dual-Ligand Modified Polymer-Lipid Hybrid Nanoparticles for Docetaxel Targeting Delivery to Her2/neu Overexpressed Human Breast Cancer Cells.

PubMed

Yang, Zhe; Tang, Wenxin; Luo, Xingen; Zhang, Xiaofang; Zhang, Chao; Li, Hao; Gao, Di; Luo, Huiyan; Jiang, Qing; Liu, Jie

2015-08-01

In this study, a dual-ligand polymer-lipid hybrid nanoparticle drug delivery vehicle comprised of an anti-HER2/neu peptide (AHNP) mimic with a modified HIV-1 Tat (mTAT) was established for the targeted treatment of Her2/neu-overexpressing cells. The resultant dual-ligand hybrid nanoparticles (NPs) consisted of a poly(lactide-co-glycolide) core, a near 90% surface coverage of the lipid monolayer, and a 5.7 nm hydrated polyethylene glycol shell. Ligand density optimization study revealed that cellular uptake efficiency of the hybrid NPs could be manipulated by controlling the surface-ligand densities. Furthermore, the cell uptake kinetics and mechanism studies showed that the dual-ligand modifications of hybrid NPs altered the cellular uptake pathway from caveolae-mediated endocytosis (CvME) to the multiple endocytic pathways, which would significantly enhance the NP internalization. Upon the systemic investigation of the cellular uptake behavior of dual-ligand hybrid NPs, docetaxel (DTX), a hydrophobic anticancer drug, was successfully encapsulated into dual-ligand hybrid NPs with high drug loading for Her2/neu-overexpressing SK-BR-3 breast cancer cell treatment. The DTX-loaded dual-ligand hybrid NPs showed a decreased burst release and a more gradual sustained drug release property. Because of the synergistic effect of dual-ligand modification, DTX-loaded dual-ligand hybrid NPs exerted substantially better therapeutic potency against SK-BR-3 cancer cells than other NP formulations and free DTX drugs. These results demonstrate that the dual-ligand hybrid NPs could be a promising vehicle for targeted drug delivery to treat breast cancer.

Conserving hidden diversity the unprecedented challenge of the survey and manage mandate

Treesearch

Sally Duncan

2004-01-01

When the Northwest Forest Plan became law via the record of decision in 1994, it contained an unprecedented provision for conducting regionwide surveys of poorly known and usually ignored taxa, such as fungi, mollusks, lichens, and mosses. The purpose was to enhance the very limited understanding of persistence issues for these taxa and, thereafter, to develop science-...

How Comedians Learn to Use Humor to Raise Awareness and Consciousness about Social and Political Issues

ERIC Educational Resources Information Center

Goldman, Nancy Ann

2011-01-01

During these unprecedented complicated times, there is an equally unprecedented need for an informed citizenry. Many of us watch democracy get played out on the 24-hour news networks. Still others bear witness to it in the social commentaries embedded in the entertainment provided by late night comedians like Jon Stewart. Humor provides a largely…

Ligand-receptor binding affinities from saturation transfer difference (STD) NMR spectroscopy: the binding isotherm of STD initial growth rates.

PubMed

Angulo, Jesús; Enríquez-Navas, Pedro M; Nieto, Pedro M

2010-07-12

The direct evaluation of dissociation constants (K(D)) from the variation of saturation transfer difference (STD) NMR spectroscopy values with the receptor-ligand ratio is not feasible due to the complex dependence of STD intensities on the spectral properties of the observed signals. Indirect evaluation, by competition experiments, allows the determination of K(D), as long as a ligand of known affinity is available for the protein under study. Herein, we present a novel protocol based on STD NMR spectroscopy for the direct measurements of receptor-ligand dissociation constants (K(D)) from single-ligand titration experiments. The influence of several experimental factors on STD values has been studied in detail, confirming the marked impact on standard determinations of protein-ligand affinities by STD NMR spectroscopy. These factors, namely, STD saturation time, ligand residence time in the complex, and the intensity of the signal, affect the accumulation of saturation in the free ligand by processes closely related to fast protein-ligand rebinding and longitudinal relaxation of the ligand signals. The proposed method avoids the dependence of the magnitudes of ligand STD signals at a given saturation time on spurious factors by constructing the binding isotherms using the initial growth rates of the STD amplification factors, in a similar way to the use of NOE growing rates to estimate cross relaxation rates for distance evaluations. Herein, it is demonstrated that the effects of these factors are cancelled out by analyzing the protein-ligand association curve using STD values at the limit of zero saturation time, when virtually no ligand rebinding or relaxation takes place. The approach is validated for two well-studied protein-ligand systems: the binding of the saccharides GlcNAc and GlcNAcbeta1,4GlcNAc (chitobiose) to the wheat germ agglutinin (WGA) lectin, and the interaction of the amino acid L-tryptophan to bovine serum albumin (BSA). In all cases, the experimental K(D) measured under different experimental conditions converged to the thermodynamic values. The proposed protocol allows accurate determinations of protein-ligand dissociation constants, extending the applicability of the STD NMR spectroscopy for affinity measurements, which is of particular relevance for those proteins for which a ligand of known affinity is not available.

Estimation of affinities of ligands in mixtures via magnetic recovery of target-ligand complexes and chromatographic analyses: chemometrics and an experimental model

PubMed Central

2011-01-01

Abstract Background The combinatorial library strategy of using multiple candidate ligands in mixtures as library members is ideal in terms of cost and efficiency, but needs special screening methods to estimate the affinities of candidate ligands in such mixtures. Herein, a new method to screen candidate ligands present in unknown molar quantities in mixtures was investigated. Results The proposed method involves preparing a processed-mixture-for-screening (PMFS) with each mixture sample and an exogenous reference ligand, initiating competitive binding among ligands from the PMFS to a target immobilized on magnetic particles, recovering target-ligand complexes in equilibrium by magnetic force, extracting and concentrating bound ligands, and analyzing ligands in the PMFS and the concentrated extract by chromatography. The relative affinity of each candidate ligand to its reference ligand is estimated via an approximation equation assuming (a) the candidate ligand and its reference ligand bind to the same site(s) on the target, (b) their chromatographic peak areas are over five times their intercepts of linear response but within their linear ranges, (c) their binding ratios are below 10%. These prerequisites are met by optimizing primarily the quantity of the target used and the PMFS composition ratio. The new method was tested using the competitive binding of biotin derivatives from mixtures to streptavidin immobilized on magnetic particles as a model. Each mixture sample containing a limited number of candidate biotin derivatives with moderate differences in their molar quantities were prepared via parallel-combinatorial-synthesis (PCS) without purification, or via the pooling of individual compounds. Some purified biotin derivatives were used as reference ligands. This method showed resistance to variations in chromatographic quantification sensitivity and concentration ratios; optimized conditions to validate the approximation equation could be applied to different mixture samples. Relative affinities of candidate biotin derivatives with unknown molar quantities in each mixture sample were consistent with those estimated by a homogenous method using their purified counterparts as samples. Conclusions This new method is robust and effective for each mixture possessing a limited number of candidate ligands whose molar quantities have moderate differences, and its integration with PCS has promise to routinely practice the mixture-based library strategy. PMID:21545719

A new analysis of charge transfer and polarization for ligand-metal bonding - Model studies of Al4CO and Al4NH3

NASA Technical Reports Server (NTRS)

Bagus, P. S.; Hermann, K.; Bauschlicher, C. W., Jr.

1984-01-01

The nature of the bonding of CO and NH3 ligands to Al is analyzed, and the intra-unit charge polarization and inter-unit donation for the interaction of ligands with metals are studied. The consequences of metal-to-ligand and ligand-to-metal charge transfer are separately considered by performing a constrained space orbital variation (CSOV) with the electrons of the metal member of the complex in the field of frozen ligand. The electrons of the metal atoms are then frozen in the relaxed distribution given by the CSOV SCF wave function and the ligand electrons are allowed to relax. Quantitative measures of the importance of inter-unit charge transfers and intra-unit polarization are obtained using results of SCF studies of Al4CO and Al4NH3 clusters chosen to simulate the adsorption of the ligands at an on-top side of the Al(111) surface. The electrostatic attraction of the effective dipole moments of the metal and ligand units makes an important contribution to the bond.

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

NASA Astrophysics Data System (ADS)

Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim

2018-01-01

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.

Water oxidation catalyzed by mononuclear ruthenium complexes with a 2,2'-bipyridine-6,6'-dicarboxylate (bda) ligand: how ligand environment influences the catalytic behavior.

PubMed

Staehle, Robert; Tong, Lianpeng; Wang, Lei; Duan, Lele; Fischer, Andreas; Ahlquist, Mårten S G; Sun, Licheng; Rau, Sven

2014-02-03

A new water oxidation catalyst [Ru(III)(bda)(mmi)(OH2)](CF3SO3) (2, H2bda = 2,2'-bipyridine-6,6'-dicarboxylic acid; mmi = 1,3-dimethylimidazolium-2-ylidene) containing an axial N-heterocyclic carbene ligand and one aqua ligand was synthesized and fully characterized. The kinetics of catalytic water oxidation by 2 were measured using stopped-flow technique, and key intermediates in the catalytic cycle were probed by density functional theory calculations. While analogous Ru-bda water oxidation catalysts [Ru(bda)L2] (L = pyridyl ligands) are supposed to catalyze water oxidation through a bimolecular coupling pathway, our study points out that 2, surprisingly, undergoes a single-site water nucleophilic attack (acid-base) pathway. The diversion of catalytic mechanisms is mainly ascribed to the different ligand environments, from nonaqua ligands to an aqua ligand. Findings in this work provide some critical proof for our previous hypothesis about how alternation of ancillary ligands of water oxidation catalysts influences their catalytic efficiency.

Characterization and validation of fluorescent receptor ligands: a case study of the ionotropic serotonin receptor.

PubMed

Hovius, Ruud

2013-01-01

The application of fluorescent receptor ligands has become widespread, incited by two important reasons. "Seeing is believing"-it is possible to visualize in real time in live cells ligand-receptor interactions, and to locate the receptors with subcellular precision allowing one to follow, e.g., internalization of the ligand-receptor complex. The high sensitivity of photon detection permits observation of on the one hand receptor-ligand interactions on cells with low, native receptor abundance, and on the other of individual fluorophores unveiling the stochastic properties of single ligand-receptor complexes.The major bottlenecks that impede extensive use of fluorescent ligands are due to possible dramatic changes of the pharmacological properties of a ligand upon chemical modification and fluorophore conjugation, aggravated by the observation that different fluorophores can provoke very dissimilar effects. This makes it virtually impossible to predict beforehand which labelling strategy to use to produce a fluorescent ligand with the desired qualities.Here, we focus on the design, synthesis, and evaluation of a high-affinity fluorescent antagonist for the ionotropic serotonin type-3 receptor.

Characterization of Colloidal Quantum Dot Ligand Exchange by X-ray Photoelectron Spectroscopy

NASA Astrophysics Data System (ADS)

Atewologun, Ayomide; Ge, Wangyao; Stiff-Roberts, Adrienne D.

2013-05-01

Colloidal quantum dots (CQDs) are chemically synthesized semiconductor nanoparticles with size-dependent wavelength tunability. Chemical synthesis of CQDs involves the attachment of long organic surface ligands to prevent aggregation; however, these ligands also impede charge transport. Therefore, it is beneficial to exchange longer surface ligands for shorter ones for optoelectronic devices. Typical characterization techniques used to analyze surface ligand exchange include Fourier-transform infrared spectroscopy, x-ray diffraction, transmission electron microscopy, and nuclear magnetic resonance spectroscopy, yet these techniques do not provide a simultaneously direct, quantitative, and sensitive method for evaluating surface ligands on CQDs. In contrast, x-ray photoelectron spectroscopy (XPS) can provide nanoscale sensitivity for quantitative analysis of CQD surface ligand exchange. A unique aspect of this work is that a fingerprint is identified for shorter surface ligands by resolving the regional XPS spectrum corresponding to different types of carbon bonds. In addition, a deposition technique known as resonant infrared matrix-assisted pulsed laser evaporation is used to improve the CQD film uniformity such that stronger XPS signals are obtained, enabling more accurate analysis of the ligand exchange process.

EGF receptor ligands: recent advances

PubMed Central

Singh, Bhuminder; Carpenter, Graham; Coffey, Robert J.

2016-01-01

Seven ligands bind to and activate the mammalian epidermal growth factor (EGF) receptor (EGFR/ERBB1/HER1): EGF, transforming growth factor-alpha (TGFA), heparin-binding EGF-like growth factor (HBEGF), betacellulin (BTC), amphiregulin (AREG), epiregulin (EREG), and epigen (EPGN). Of these, EGF, TGFA, HBEGF, and BTC are thought to be high-affinity ligands, whereas AREG, EREG, and EPGN constitute low-affinity ligands. This focused review is meant to highlight recent studies related to actions of the individual EGFR ligands, the interesting biology that has been uncovered, and relevant advances related to ligand interactions with the EGFR. PMID:27635238

Measurement of Nanomolar Dissociation Constants by Titration Calorimetry and Thermal Shift Assay – Radicicol Binding to Hsp90 and Ethoxzolamide Binding to CAII

PubMed Central

Zubrienė, Asta; Matulienė, Jurgita; Baranauskienė, Lina; Jachno, Jelena; Torresan, Jolanta; Michailovienė, Vilma; Cimmperman, Piotras; Matulis, Daumantas

2009-01-01

The analysis of tight protein-ligand binding reactions by isothermal titration calorimetry (ITC) and thermal shift assay (TSA) is presented. The binding of radicicol to the N-terminal domain of human heat shock protein 90 (Hsp90αN) and the binding of ethoxzolamide to human carbonic anhydrase (hCAII) were too strong to be measured accurately by direct ITC titration and therefore were measured by displacement ITC and by observing the temperature-denaturation transitions of ligand-free and ligand-bound protein. Stabilization of both proteins by their ligands was profound, increasing the melting temperature by more than 10 ºC, depending on ligand concentration. Analysis of the melting temperature dependence on the protein and ligand concentrations yielded dissociation constants equal to 1 nM and 2 nM for Hsp90αN-radicicol and hCAII-ethoxzolamide, respectively. The ligand-free and ligand-bound protein fractions melt separately, and two melting transitions are observed. This phenomenon is especially pronounced when the ligand concentration is equal to about half the protein concentration. The analysis compares ITC and TSA data, accounts for two transitions and yields the ligand binding constant and the parameters of protein stability, including the Gibbs free energy and the enthalpy of unfolding. PMID:19582223

Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

PubMed

Rydzewski, J; Nowak, W

2017-12-01

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter. Copyright © 2017 Elsevier B.V. All rights reserved.

Decoding the Role of Water Dynamics in Ligand-Protein Unbinding: CRF1R as a Test Case.

PubMed

Bortolato, Andrea; Deflorian, Francesca; Weiss, Dahlia R; Mason, Jonathan S

2015-09-28

The residence time of a ligand-protein complex is a crucial aspect in determining biological effect in vivo. Despite its importance, the prediction of ligand koff still remains challenging for modern computational chemistry. We have developed aMetaD, a fast and generally applicable computational protocol to predict ligand-protein unbinding events using a molecular dynamics (MD) method based on adiabatic-bias MD and metadynamics. This physics-based, fully flexible, and pose-dependent ligand scoring function evaluates the maximum energy (RTscore) required to move the ligand from the bound-state energy basin to the next. Unbinding trajectories are automatically analyzed and translated into atomic solvation factor (SF) values representing the water dynamics during the unbinding event. This novel computational protocol was initially tested on two M3 muscarinic receptor and two adenosine A2A receptor antagonists and then evaluated on a test set of 12 CRF1R ligands. The resulting RTscores were used successfully to classify ligands with different residence times. Additionally, the SF analysis was used to detect key differences in the degree of accessibility to water molecules during the predicted ligand unbinding events. The protocol provides actionable working hypotheses that are applicable in a drug discovery program for the rational optimization of ligand binding kinetics.

Structure-based Understanding of Binding Affinity and Mode ...

EPA Pesticide Factsheets

The flexible hydrophobic ligand binding pocket (LBP) of estrogen receptor α (ERα) allows the binding of a wide variety of endocrine disruptors. Upon ligand binding, the LBP reshapes around the contours of the ligand and stabilizes the complex by complementary hydrophobic interactions and specific hydrogen bonds with the ligand. Here we present a framework for quantitative analysis of the steric and electronic features of the human ERα-ligand complex using three dimensional (3D) protein-ligand interaction description combined with 3D-QSAR approach. An empirical hydrophobicity density field is applied to account for hydrophobic contacts of ligand within the LBP. The obtained 3D-QSAR model revealed that hydrophobic contacts primarily determine binding affinity and govern binding mode with hydrogen bonds. Several residues of the LBP appear to be quite flexible and adopt a spectrum of conformations in various ERα-ligand complexes, in particular His524. The 3D-QSAR was combined with molecular docking based on three receptor conformations to accommodate receptor flexibility. The model indicates that the dynamic character of the LBP allows accommodation and stable binding of structurally diverse ligands, and proper representation of the protein flexibility is critical for reasonable description of binding of the ligands. Our results provide a quantitative and mechanistic understanding of binding affinity and mode of ERα agonists and antagonists that may be applicab

Investigation of differences in the binding affinities of two analogous ligands for untagged and tagged p38 kinase using thermodynamic integration MD simulation.

PubMed

Sun, Ying-Chieh; Hsu, Wen-Chi; Hsu, Chia-Jen; Chang, Chia-Ming; Cheng, Kai-Hsiang

2015-11-01

Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influenced by the presence or absence of the peptide tag in p38 kinase. This possible effect of protein length on the binding affinity of a ligand-which is seldom addressed in the literature-is important because, even when two labs claim to have performed experiments with the same protein, they may actually have studied variants of the same protein with different lengths because they applied different protein expression conditions/procedures. Thus, if we wanted to compare ligand binding affinities measured in the two labs, it would be necessary to account for any variation in ligand binding affinity with protein length. The pair of ligand-p38 kinase complexes examined in this work (pdb codes: 3d7z and 3lhj, respectively) were ideal for investigating this effect. The experimentally determined binding energy for the ref ligand with the untagged p38 kinase was -10.9 kcal mol(-1), while that for the analog ligand with the tagged p38 kinase was -11.9 kcal mol(-1). The present TI-MD simulation of the mutation of the ref ligand into the analog ligand while the ligand is bound to the untagged p38 kinase predicted that the binding affinity of the analog ligand is 2.0 kcal mol(-1) greater than that of the ref ligand. A similar simulation also indicated that the same was true for ligand binding to the tagged protein, but in this case the binding affinity for the analog ligand is 2.5 kcal mol(-1) larger than that for the ref ligand. These results therefore suggest that the presence of the peptide tag on p38 kinase increased the difference in the binding energies of the ligands by a small amount of 0.5 kcal mol(-1). This result supports the assumption that the presence of a peptide tag has only a minor effect on ΔG values. The error bars in the computed ΔG values were then estimated via confidence interval analysis and a time autocorrelation function for the quantity dV/dλ. The estimated correlation time was ~0.5 ps and the error bar in the ΔG values estimated using nanosecond-scale simulations was ±0.3 kcal mol(-1) at a confidence level of 95%. These predicted results can be verified in future experiments and should prove useful in subsequent similar studies. Graphical Abstract Thermodynamic cycles for binding of two analogous ligands with untagged and tagged p38 kinases and associated Gibbs free energy.

The Structure of the Transcriptional Repressor KstR in Complex with CoA Thioester Cholesterol Metabolites Sheds Light on the Regulation of Cholesterol Catabolism in Mycobacterium tuberculosis*

PubMed Central

Ho, Ngoc Anh Thu; Dawes, Stephanie S.; Crowe, Adam M.; Casabon, Israël; Gao, Chen; Kendall, Sharon L.; Baker, Edward N.; Eltis, Lindsay D.; Lott, J. Shaun

2016-01-01

Cholesterol can be a major carbon source for Mycobacterium tuberculosis during infection, both at an early stage in the macrophage phagosome and later within the necrotic granuloma. KstR is a highly conserved TetR family transcriptional repressor that regulates a large set of genes responsible for cholesterol catabolism. Many genes in this regulon, including kstR, are either induced during infection or are essential for survival of M. tuberculosis in vivo. In this study, we identified two ligands for KstR, both of which are CoA thioester cholesterol metabolites with four intact steroid rings. A metabolite in which one of the rings was cleaved was not a ligand. We confirmed the ligand-protein interactions using intrinsic tryptophan fluorescence and showed that ligand binding strongly inhibited KstR-DNA binding using surface plasmon resonance (IC50 for ligand = 25 nm). Crystal structures of the ligand-free form of KstR show variability in the position of the DNA-binding domain. In contrast, structures of KstR·ligand complexes are highly similar to each other and demonstrate a position of the DNA-binding domain that is unfavorable for DNA binding. Comparison of ligand-bound and ligand-free structures identifies residues involved in ligand specificity and reveals a distinctive mechanism by which the ligand-induced conformational change mediates DNA release. PMID:26858250