FOB-SH: Fragment orbital-based surface hopping for charge carrier transport in organic and biological molecules and materials

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

Spencer, J.; Gajdos, F.; Blumberger, J., E-mail: j.blumberger@ucl.ac.uk

2016-08-14

We introduce a fragment orbital-based fewest switches surface hopping method, FOB-SH, designed to efficiently simulate charge carrier transport in strongly fluctuating condensed phase systems such as organic semiconductors and biomolecules. The charge carrier wavefunction is expanded and the electronic Hamiltonian constructed in a set of singly occupied molecular orbitals of the molecular sites that mediate the charge transfer. Diagonal elements of the electronic Hamiltonian (site energies) are obtained from a force field, whereas the off-diagonal or electronic coupling matrix elements are obtained using our recently developed analytic overlap method. We derive a general expression for the exact forces on themore » adiabatic ground and excited electronic state surfaces from the nuclear gradients of the charge localized electronic states. Applications to electron hole transfer in a model ethylene dimer and through a chain of ten model ethylenes validate our implementation and demonstrate its computational efficiency. On the larger system, we calculate the qualitative behaviour of charge mobility with change in temperature T for different regimes of the intermolecular electronic coupling. For small couplings, FOB-SH predicts a crossover from a thermally activated regime at low temperatures to a band-like transport regime at higher temperatures. For higher electronic couplings, the thermally activated regime disappears and the mobility decreases according to a power law. This is interpreted by a gradual loss in probability for resonance between the sites as the temperature increases. The polaron hopping model solved for the same system gives a qualitatively different result and underestimates the mobility decay at higher temperatures. Taken together, the FOB-SH methodology introduced here shows promise for a realistic investigation of charge carrier transport in complex organic, aqueous, and biological systems.« less

FOB-SH: Fragment orbital-based surface hopping for charge carrier transport in organic and biological molecules and materials

NASA Astrophysics Data System (ADS)

Spencer, J.; Gajdos, F.; Blumberger, J.

2016-08-01

We introduce a fragment orbital-based fewest switches surface hopping method, FOB-SH, designed to efficiently simulate charge carrier transport in strongly fluctuating condensed phase systems such as organic semiconductors and biomolecules. The charge carrier wavefunction is expanded and the electronic Hamiltonian constructed in a set of singly occupied molecular orbitals of the molecular sites that mediate the charge transfer. Diagonal elements of the electronic Hamiltonian (site energies) are obtained from a force field, whereas the off-diagonal or electronic coupling matrix elements are obtained using our recently developed analytic overlap method. We derive a general expression for the exact forces on the adiabatic ground and excited electronic state surfaces from the nuclear gradients of the charge localized electronic states. Applications to electron hole transfer in a model ethylene dimer and through a chain of ten model ethylenes validate our implementation and demonstrate its computational efficiency. On the larger system, we calculate the qualitative behaviour of charge mobility with change in temperature T for different regimes of the intermolecular electronic coupling. For small couplings, FOB-SH predicts a crossover from a thermally activated regime at low temperatures to a band-like transport regime at higher temperatures. For higher electronic couplings, the thermally activated regime disappears and the mobility decreases according to a power law. This is interpreted by a gradual loss in probability for resonance between the sites as the temperature increases. The polaron hopping model solved for the same system gives a qualitatively different result and underestimates the mobility decay at higher temperatures. Taken together, the FOB-SH methodology introduced here shows promise for a realistic investigation of charge carrier transport in complex organic, aqueous, and biological systems.

Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces

NASA Astrophysics Data System (ADS)

Xie, Yun; Zhou, Jian; Jiang, Shaoyi

2010-02-01

In this work, the parallel tempering Monte Carlo (PTMC) algorithm is applied to accurately and efficiently identify the global-minimum-energy orientation of a protein adsorbed on a surface in a single simulation. When applying the PTMC method to simulate lysozyme orientation on charged surfaces, it is found that lysozyme could easily be adsorbed on negatively charged surfaces with "side-on" and "back-on" orientations. When driven by dominant electrostatic interactions, lysozyme tends to be adsorbed on negatively charged surfaces with the side-on orientation for which the active site of lysozyme faces sideways. The side-on orientation agrees well with the experimental results where the adsorbed orientation of lysozyme is determined by electrostatic interactions. As the contribution from van der Waals interactions gradually dominates, the back-on orientation becomes the preferred one. For this orientation, the active site of lysozyme faces outward, which conforms to the experimental results where the orientation of adsorbed lysozyme is co-determined by electrostatic interactions and van der Waals interactions. It is also found that despite of its net positive charge, lysozyme could be adsorbed on positively charged surfaces with both "end-on" and back-on orientations owing to the nonuniform charge distribution over lysozyme surface and the screening effect from ions in solution. The PTMC simulation method provides a way to determine the preferred orientation of proteins on surfaces for biosensor and biomaterial applications.

Active Site Desolvation and Thermostability Trade-Offs in the Evolution of Catalytically Diverse Triazine Hydrolases.

PubMed

Sugrue, Elena; Carr, Paul D; Scott, Colin; Jackson, Colin J

2016-11-15

The desolvation of ionizable residues in the active sites of enzymes and the subsequent effects on catalysis and thermostability have been studied in model systems, yet little about how enzymes can naturally evolve to include active sites with highly reactive and desolvated charges is known. Variants of triazine hydrolase (TrzN) with significant differences in their active sites have been isolated from different bacterial strains: TrzN from Nocardioides sp. strain MTD22 contains a catalytic glutamate residue (Glu241) that is surrounded by hydrophobic and aromatic second-shell residues (Pro214 and Tyr215), whereas TrzN from Nocardioides sp. strain AN3 has a noncatalytic glutamine residue (Gln241) at an equivalent position, surrounded by hydrophilic residues (Thr214 and His215). To understand how and why these variants have evolved, a series of TrzN mutants were generated and characterized. These results show that desolvation by second-shell residues increases the pK a of Glu241, allowing it to act as a general acid at neutral pH. However, significant thermostability trade-offs are required to incorporate the ionizable Glu241 in the active site and to then enclose it in a hydrophobic microenvironment. Analysis of high-resolution crystal structures shows that there are almost no structural changes to the overall configuration of the active site due to these mutations, suggesting that the changes in activity and thermostability are purely based on the altered electrostatics. The natural evolution of these enzyme isoforms provides a unique system in which to study the fundamental process of charged residue desolvation in enzyme catalysis and its relative contribution to the creation and evolution of an enzyme active site.

Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design

NASA Astrophysics Data System (ADS)

Sheng, Chunquan; Ji, Haitao; Miao, Zhenyuan; Che, Xiaoyin; Yao, Jianzhong; Wang, Wenya; Dong, Guoqiang; Guo, Wei; Lü, Jiaguo; Zhang, Wannian

2009-06-01

Myristoyl-CoA:protein N-myristoyltransferase (NMT) is a cytosolic monomeric enzyme that catalyzes the transfer of the myristoyl group from myristoyl-CoA to the N-terminal glycine of a number of eukaryotic cellular and viral proteins. Recent experimental data suggest NMT from parasites could be a promising new target for the design of novel antiparasitic agents with new mode of action. However, the active site topology and inhibitor specificity of these enzymes remain unclear. In this study, three-dimensional models of NMT from Plasmodium falciparum (PfNMT), Leishmania major (LmNMT) and Trypanosoma brucei (TbNMT) were constructed on the basis of the crystal structures of fungal NMTs using homology modeling method. The models were further refined by energy minimization and molecular dynamics simulations. The active sites of PfNMT, LmNMT and TbNMT were characterized by multiple copy simultaneous search (MCSS). MCSS functional maps reveal that PfNMT, LmNMT and TbNMT share a similar active site topology, which is defined by two hydrophobic pockets, a hydrogen-bonding (HB) pocket, a negatively-charged HB pocket and a positively-charged HB pocket. Flexible docking approaches were then employed to dock known inhibitors into the active site of PfNMT. The binding mode, structure-activity relationships and selectivity of inhibitors were investigated in detail. From the results of molecular modeling, the active site architecture and certain key residues responsible for inhibitor binding were identified, which provided insights for the design of novel inhibitors of parasitic NMTs.

Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination

PubMed Central

Rowley, Paul A.; Kachroo, Aashiq H.; Ma, Chien-Hui; Maciaszek, Anna D.; Guga, Piotr; Jayaram, Makkuni

2015-01-01

Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5′ to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions. PMID:25999343

Active site nanospace of aminoacyl tRNA synthetase: difference between the class I and class II synthetases.

PubMed

Dutta, Saheb; Choudhury, Kaberi; Banik, Sindrila Dutta; Nandi, Nilashis

2014-03-01

The present work is aimed at understanding the origin of the difference in the molecular organization of the active site nanospaces of the class I and class II aminoacyl tRNA synthetases (aaRSs) which are tunnel-like structures. The active site encloses the cognate amino acid (AA) and the adenosine triphosphate (ATP) to carry out aminoacylation reaction. Comparison of the structures of the active site of the class I and class II (aaRSs) shows that the nanodimensional tunnels are curved in opposite directions in the two classes. We investigated the origin of this difference using quantum mechanical computation of electrostatic potential (ESP) of substrates, surrounding residues and ions, using Atoms in Molecule (AIM) Theory and charge population analysis. We show that the difference is principally due to the variation in the spatial charge distribution of ATP in the two classes which correspond to extended and bent conformations of ATP. The present computation shows that the most feasible pathway for nucleophilic attack to alphaP is oppositely directed for class I and class II aaRSs. The available crystal structures show that the cognate AA is indeed located along the channel favorable for nucleophilic attack as predicted by the ESP analysis. It is also shown that the direction of the channel changes its orientation when the orientation of ATP is changed from extended to a bent like structure. We further used the AIM theory to confirm the direction of the approach of AA in each case and the results corroborate the results from the ESP analysis. The opposite curvatures of the active site nanospaces in class I and class II aaRSs are related with the influence of the charge distributions of the extended and bent conformations of ATP, respectively. The results of the computation of electrostatic potential by successive addition of active site residues show that their roles on the reaction are similar in both classes despite the difference in the organization of the active sites of class I and class II aaRSs. The difference in mechanism in two classes as pointed out in recent study (S. Dutta Banik and N. Nandi, J. Biomol. Struct. Dyn. 30, 701 (2012)) is related with the fact that the relative arrangement of the ATP with respect to the AA is opposite in class I and class II aaRSs as explained in the present work. The charge population difference between the reacting centers (which are the alphaP atom of ATP (q(p)) and the attacking oxygen atom of carboxylic acid group (q(o)), respectively) denoted by delta(q), is a measure of the propensity of nucleophilic attack. The population analysis of the substrate AA shows that a non-negligible difference exists between the attacking oxygens of AA in class I (syn) and in class II (anti) which is one reason for the lower value of delta(q) in class II relative to class I. The population analysis of the AA, ATP, Mg+2 ions and active site residues shows that the difference in delta(q) values of the two classes is substantially reduced. When ions and residues are considered. Thus, the bent state of ATP, Mg+2 ions and active site residues complements it cognate AA to carry out the nucleophilic reaction in class I as efficiently as occurs in class I (with the extended state of ATP, single Mg+2 ion and active site residues). This could be one reason for the two different conformations of ATP in the two classes. The mutual arrangements of AA and ATP in each aaRS are guided by the spatial charge distribution of ATP (extended and bent). The present work shows that the construction of nanospace complements the arrangement of the substrate (AA and ATP).

Chicken scFvs with an Artificial Cysteine for Site-Directed Conjugation

PubMed Central

Kim, Soohyun; Kim, Hyori; Chung, Junho

2016-01-01

For the site-directed conjugation of chemicals and radioisotopes to the chicken-derived single-chain variable fragment (scFv), we investigated amino acid residues replaceable with cysteine. By replacing each amino acid of the 157 chicken variable region framework residues (FR, 82 residues on VH and 75 on VL) with cysteine, 157 artificial cysteine mutants were generated and characterized. At least 27 residues on VL and 37 on VH could be replaced with cysteine while retaining the binding activity of the original scFv. We prepared three VL (L5, L6 and L7) and two VH (H13 and H16) mutants as scFv-Ckappa fusion proteins and showed that PEG-conjugation to the sulfhydryl group of the artificial cysteine was achievable in all five mutants. Because the charge around the cysteine residue affects the in vivo stability of thiol-maleimide conjugation, we prepared 16 charge-variant artificial cysteine mutants by replacing the flanking residues of H13 with charged amino acids and determined that the binding activity was not affected in any of the mutants except one. We prepared four charge-variant H13 artificial cysteine mutants (RCK, DCE, ECD and ECE) as scFv-Ckappa fusion proteins and confirmed that the reactivity of the sulfhydryl group on cysteine is active and their binding activity is retained after the conjugation process. PMID:26764487

Direct evidence of charge separation in a metal-organic framework: efficient and selective photocatalytic oxidative coupling of amines via charge and energy transfer.

PubMed

Xu, Caiyun; Liu, Hang; Li, Dandan; Su, Ji-Hu; Jiang, Hai-Long

2018-03-28

The selective aerobic oxidative coupling of amines under mild conditions is an important laboratory and commercial procedure yet a great challenge. In this work, a porphyrinic metal-organic framework, PCN-222, was employed to catalyze the reaction. Upon visible light irradiation, the semiconductor-like behavior of PCN-222 initiates charge separation, evidently generating oxygen-centered active sites in Zr-oxo clusters indicated by enhanced porphyrin π-cation radical signals. The photogenerated electrons and holes further activate oxygen and amines, respectively, to give the corresponding redox products, both of which have been detected for the first time. The porphyrin motifs generate singlet oxygen based on energy transfer to further promote the reaction. As a result, PCN-222 exhibits excellent photocatalytic activity, selectivity and recyclability, far superior to its organic counterpart, for the reaction under ambient conditions via combined energy and charge transfer.

Effect of electrical polarization of hydroxyapatite ceramics on new bone formation.

PubMed

Itoh, S; Nakamura, S; Kobayashi, T; Shinomiya, K; Yamashita, K; Itoh, S

2006-03-01

Large surface charges can be induced on hydroxyapatite (HAp) ceramics by proton transport polarization, but this does not affect beta-tricalcium phosphate (TCP) because of its low polarizability. We wished to examine differences in osteogenic cell activity and new bone growth between positively or negatively surface-charged HAp and HAp/TCP plates using a calvarial bone defect model. In the first group of rats, test pieces were placed with their positively charged surfaces face down on the dura mater. In the second group, test pieces were placed with their negatively charged surfaces face down on the dura mater. A third group received noncharged test pieces. Histological examination, including enzymatic staining for osteoblasts and osteoclasts, was carried out. While no bone formation was observed at the pericranium, direct bone formation on the cranial bone debris and new bone growth expanded from the margins of the sites of injury to bridge across both the positively and negatively charged surfaces of HAp and HAp/TCP plates occurred. Electrical polarization of implanted plates, including positive charge, led to enhanced osteoblast activity, though decreased osteoclast activity was seen on the positively charged plate surface. Thus, polarization of HAp ceramics may modulate new bone formation and resorption.

Effect of phosphorylation of myelin basic protein by MAPK on its interactions with actin and actin binding to a lipid membrane in vitro.

PubMed

Boggs, Joan M; Rangaraj, Godha; Gao, Wen; Heng, Yew-Meng

2006-01-17

Myelin basic protein (MBP) binds to negatively charged lipids on the cytosolic surface of oligodendrocyte membranes and is most likely responsible for adhesion of these surfaces in the multilayered myelin sheath. It can also polymerize actin, bundle F-actin filaments, and bind actin filaments to lipid bilayers through electrostatic interactions. MBP consists of a number of posttranslationally modified isomers of varying charge, some resulting from phosphorylation at several sites by different kinases, including mitogen-activated protein kinase (MAPK). Phosphorylation of MBP in oligodendrocytes occurs in response to various extracellular stimuli. Phosphorylation/dephosphorylation of MBP also occurs in the myelin sheath in response to electrical activity in the brain. Here we investigate the effect of phosphorylation of MBP on its interaction with actin in vitro by phosphorylating the most highly charged unmodified isomer, C1, at two sites with MAPK. Phosphorylation decreased the ability of MBP to polymerize actin and to bundle actin filaments but had no effect on the dissociation constant of the MBP-actin complex or on the ability of Ca2+-calmodulin to dissociate the complex. The most significant effect of phosphorylation on the MBP-actin complex was a dramatic reduction in its ability to bind to negatively charged lipid bilayers. The effect was much greater than that reported earlier for another charge isomer of MBP, C8, in which six arginines were deiminated to citrulline, resulting in a reduction of net positive charge of 6. These results indicate that although average electrostatic forces are the primary determinant of the interaction of MBP with actin, phosphorylation may have an additional effect due to a site-specific electrostatic effect or to a conformational change. Thus, phosphorylation of MBP, which occurs in response to various extracellular signals in both myelin and oligodendrocytes, attenuates the ability of MBP to polymerize and bundle actin and to bind it to a negatively charged membrane.

Elucidating the Charge Transfer Mechanism in Radical Polymer Thin Films

NASA Astrophysics Data System (ADS)

Mukherjee, Sanjoy; Boudouris, Bryan

The active role of polymers in organic electronics has attracted significant attention in recent decades. Beyond conventional conjugated polymers, recently radical polymers have received a great deal of consideration by the community. Radical polymers are redox-active macromolecules with non-conjugated backbones functionalized with persistent radical sites. Because of their nascent nature, many open questions regarding the physics of their solid-state charge transfer mechanism still exist. In order to address these questions, well-defined radical polymers were synthesized and blended in a manner such that there was tight control over the radical density within the conducting thin films. We demonstrate that the systematic manipulation of the radical-to-radical spacing in open-shell macromolecules leads to exponential changes in the macroscopic electrical conductivity, and temperature-independent charge transport behaviour. Thus, a clear picture emerges that charge transfer in radical polymers is dictated by a tunnelling mechanism between proximal sites. This behavior is consistent with a distinct mechanism similar to redox reactions in biological media, but is unique relative to transport in common conjugated polymers. These results constitute the first experimental insight into the mechanism of solid-state electrical conduction in radical polymers.

Visualizing excitations at buried heterojunctions in organic semiconductor blends.

PubMed

Jakowetz, Andreas C; Böhm, Marcus L; Sadhanala, Aditya; Huettner, Sven; Rao, Akshay; Friend, Richard H

2017-05-01

Interfaces play a crucial role in semiconductor devices, but in many device architectures they are nanostructured, disordered and buried away from the surface of the sample. Conventional optical, X-ray and photoelectron probes often fail to provide interface-specific information in such systems. Here we develop an all-optical time-resolved method to probe the local energetic landscape and electronic dynamics at such interfaces, based on the Stark effect caused by electron-hole pairs photo-generated across the interface. Using this method, we found that the electronically active sites at the polymer/fullerene interfaces in model bulk-heterojunction blends fall within the low-energy tail of the absorption spectrum. This suggests that these sites are highly ordered compared with the bulk of the polymer film, leading to large wavefunction delocalization and low site energies. We also detected a 100 fs migration of holes from higher- to lower-energy sites, consistent with these charges moving ballistically into more ordered polymer regions. This ultrafast charge motion may be key to separating electron-hole pairs into free charges against the Coulomb interaction.

Visualizing excitations at buried heterojunctions in organic semiconductor blends

NASA Astrophysics Data System (ADS)

Jakowetz, Andreas C.; Böhm, Marcus L.; Sadhanala, Aditya; Huettner, Sven; Rao, Akshay; Friend, Richard H.

2017-05-01

Interfaces play a crucial role in semiconductor devices, but in many device architectures they are nanostructured, disordered and buried away from the surface of the sample. Conventional optical, X-ray and photoelectron probes often fail to provide interface-specific information in such systems. Here we develop an all-optical time-resolved method to probe the local energetic landscape and electronic dynamics at such interfaces, based on the Stark effect caused by electron-hole pairs photo-generated across the interface. Using this method, we found that the electronically active sites at the polymer/fullerene interfaces in model bulk-heterojunction blends fall within the low-energy tail of the absorption spectrum. This suggests that these sites are highly ordered compared with the bulk of the polymer film, leading to large wavefunction delocalization and low site energies. We also detected a 100 fs migration of holes from higher- to lower-energy sites, consistent with these charges moving ballistically into more ordered polymer regions. This ultrafast charge motion may be key to separating electron-hole pairs into free charges against the Coulomb interaction.

Kinetic analysis of butyrylcholinesterase-catalyzed hydrolysis of acetanilides.

PubMed

Masson, Patrick; Froment, Marie-Thérèse; Gillon, Emilie; Nachon, Florian; Darvesh, Sultan; Schopfer, Lawrence M

2007-09-01

The aryl-acylamidase (AAA) activity of butyrylcholinesterase (BuChE) has been known for a long time. However, the kinetic mechanism of aryl-acylamide hydrolysis by BuChE has not been investigated. Therefore, the catalytic properties of human BuChE and its peripheral site mutant (D70G) toward neutral and charged aryl-acylamides were determined. Three neutral (o-nitroacetanilide, m-nitroacetanilide, o-nitrophenyltrifluoroacetamide) and one positively charged (3-(acetamido) N,N,N-trimethylanilinium, ATMA) acetanilides were studied. Hydrolysis of ATMA by wild-type and D70G enzymes showed a long transient phase preceding the steady state. The induction phase was characterized by a hysteretic "burst". This reflects the existence of two enzyme states in slow equilibrium with different catalytic properties. Steady-state parameters for hydrolysis of the three acetanilides were compared to catalytic parameters for hydrolysis of esters giving the same acetyl intermediate. Wild-type BuChE showed substrate activation while D70G displayed a Michaelian behavior with ATMA as with positively charged esters. Owing to the low affinity of BuChE for amide substrates, the hydrolysis kinetics of neutral amides was first order. Acylation was the rate-determining step for hydrolysis of aryl-acetylamide substrates. Slow acylation of the enzyme, relative to that by esters may, in part, be due suboptimal fit of the aryl-acylamides in the active center of BuChE. The hypothesis that AAA and esterase active sites of BuChE are non-identical was tested with mutant BuChE. It was found that mutations on the catalytic serine, S198C and S198D, led to complete loss of both activities. The silent variant (FS117) had neither esterase nor AAA activity. Mutation in the peripheral site (D70G) had the same effect on esterase and AAA activities. Echothiophate inhibited both activities identically. It was concluded that the active sites for esterase and AAA activities are identical, i.e. S198. This excludes any other residue present in the gorge for being the catalytic nucleophile pole.

Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes.

PubMed

Amrein, Beat A; Bauer, Paul; Duarte, Fernanda; Janfalk Carlsson, Åsa; Naworyta, Agata; Mowbray, Sherry L; Widersten, Mikael; Kamerlin, Shina C L

2015-10-02

Potato epoxide hydrolase 1 exhibits rich enantio- and regioselectivity in the hydrolysis of a broad range of substrates. The enzyme can be engineered to increase the yield of optically pure products as a result of changes in both enantio- and regioselectivity. It is thus highly attractive in biocatalysis, particularly for the generation of enantiopure fine chemicals and pharmaceuticals. The present work aims to establish the principles underlying the activity and selectivity of the enzyme through a combined computational, structural, and kinetic study using the substrate trans -stilbene oxide as a model system. Extensive empirical valence bond simulations have been performed on the wild-type enzyme together with several experimentally characterized mutants. We are able to computationally reproduce the differences between the activities of different stereoisomers of the substrate and the effects of mutations of several active-site residues. In addition, our results indicate the involvement of a previously neglected residue, H104, which is electrostatically linked to the general base H300. We find that this residue, which is highly conserved in epoxide hydrolases and related hydrolytic enzymes, needs to be in its protonated form in order to provide charge balance in an otherwise negatively charged active site. Our data show that unless the active-site charge balance is correctly treated in simulations, it is not possible to generate a physically meaningful model for the enzyme that can accurately reproduce activity and selectivity trends. We also expand our understanding of other catalytic residues, demonstrating in particular the role of a noncanonical residue, E35, as a "backup base" in the absence of H300. Our results provide a detailed view of the main factors driving catalysis and regioselectivity in this enzyme and identify targets for subsequent enzyme design efforts.

Microelectrophoretic study of calcium oxalate monohydrate in macromolecular solutions

NASA Technical Reports Server (NTRS)

Curreri, P. A.; Onoda, G. Y., Jr.; Finlayson, B.

1987-01-01

Electrophoretic mobilities were measured for calcium oxalate monohydrate (COM) in solutions containing macromolecules. Two mucopolysaccharides (sodium heparin and chondroitin sulfate) and two proteins (positively charged lysozyme and negatively charged bovine serum albumin) were studied as adsorbates. The effects of pH, calcium oxalate surface charge (varied by calcium or oxalate ion activity), and citrate concentration were investigated. All four macromolecules showed evidence for adsorption. The macromolecule concentrations needed for reversing the surface charge indicated that the mucopolysaccharides have greater affinity for the COM surface than the proteins. Citrate ions at high concentrations appear to compete effectively with the negative protein for surface sites but show no evidence for competing with the positively charged protein.

Light harvesting and charge management by Ni4S3 modified metal-organic frameworks and rGO in the process of photocatalysis.

PubMed

Liu, Duanduan; Jin, Zhiliang; Zhang, Yongke; Wang, Guorong; Ma, Bingzhen

2018-06-01

Harvesting and charge management is obtained by means of Ni 4 S 3 modified Metal-organic Frameworks (MOF) and rGO, namely, the Uio-66 (Zr)/rGO combined with Ni 4 S 3 photocatalyst was successfully prepared with the solvothermal method. The Ni 4 S 3 acted as the electron transfer agent greatly improve the electrons transmission from the excited state dye to the rGO/MOF surface for proton reduction reaction. The hydrogen production amount over EY-sensitized rGO/MOF/Ni 4 S 3 photocatalyst has reached 280 μmol for 5 h, which is about 14 times than that of the pure Ni 4 S 3 photocatalyst and 185 times than that of the pure rGO/MOF photocatalyst under visible light irradiation (λ ≥ 420 nm). In the composite, the rGO acts as electron-transfer mediator and Ni 4 S 3 serves as H 2 -evolution active site. A series of studies shown that the Ni 4 S 3 modified MOF and rGO provided more active sites and improved the efficiency of photo-generated charge separation by means of several characterizations such as SEM, XRD, XPS, Element Mapping, UV-vis DRS, BET, Photocurrent, Voltammetric Scanning, Fluorescence Spectra and FTIR. and the results of which were in good agreement with each other. The photoelectron migration rate and photogenerated charge separation efficiency of the composite can be obviously increased with graphene as a good electron acceptor and transfer medium and Ni 4 S 3 as hydrogen producing active site. Copyright © 2018 Elsevier Inc. All rights reserved.

Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors.

PubMed

Prior, Stephen H; Fulcher, Yan G; Koppisetti, Rama K; Jurkevich, Alexander; Van Doren, Steven R

2015-11-03

Matrix metalloproteinase-7 (MMP-7) sheds signaling proteins from cell surfaces to activate bacterial killing, wound healing, and tumorigenesis. The mechanism targeting soluble MMP-7 to membranes has been investigated. Nuclear magnetic resonance structures of the zymogen, free and bound to membrane mimics without and with anionic lipid, reveal peripheral binding to bilayers through paramagnetic relaxation enhancements. Addition of cholesterol sulfate partially embeds the protease in the bilayer, restricts its diffusion, and tips the active site away from the bilayer. Its insertion of hydrophobic residues organizes the lipids, pushing the head groups and sterol sulfate outward toward the enzyme's positive charge on the periphery of the enlarged interface. Fluorescence probing demonstrates a similar mode of binding to plasma membranes and internalized vesicles of colon cancer cells. Binding of bilayered micelles induces allosteric activation and conformational change in the auto-inhibitory peptide and the adjacent scissile site, illustrating a potential intermediate in the activation of the zymogen. Copyright © 2015 Elsevier Ltd. All rights reserved.

The doping effect on the catalytic activity of graphene for oxygen evolution reaction in a lithium-air battery: a first-principles study.

PubMed

Ren, Xiaodong; Wang, Beizhou; Zhu, Jinzhen; Liu, Jianjun; Zhang, Wenqing; Wen, Zhaoyin

2015-06-14

A lithium-air battery as an energy storage technology can be used in electric vehicles due to its large energy density. However, its poor rate capability, low power density and large overpotential problems limit its practical usage. In this paper, the first-principles thermodynamic calculations were performed to study the catalytic activity of X-doped graphene (X = B, N, Al, Si, and P) materials as potential cathodes to enhance charge reactions in a lithium-air battery. Among these materials, P-doped graphene exhibits the highest catalytic activity in reducing the charge voltage by 0.25 V, while B-doped graphene has the highest catalytic activity in decreasing the oxygen evolution barrier by 0.12 eV. By combining these two catalytic effects, B,P-codoped graphene was demonstrated to have an enhanced catalytic activity in reducing the O2 evolution barrier by 0.70 eV and the charge voltage by 0.13 V. B-doped graphene interacts with Li2O2 by Li-sited adsorption in which the electron-withdrawing center can enhance charge transfer from Li2O2 to the substrate, facilitating reduction of O2 evolution barrier. In contrast, X-doped graphene (X = N, Al, Si, and P) prefers O-sited adsorption toward Li2O2, forming a X-O2(2-)···Li(+) interface structure between X-O2(2-) and the rich Li(+) layer. The active structure of X-O2(2-) can weaken the surrounding Li-O2 bonds and significantly reduce Li(+) desorption energy at the interface. Our investigation is helpful in developing a novel catalyst to enhance oxygen evolution reaction (OER) in Li-air batteries.

Disentangling Transient Charge Density and Metal–Ligand Covalency in Photoexcited Ferricyanide with Femtosecond Resonant Inelastic Soft X-ray Scattering

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

Jay, Raphael M.; Norell, Jesper; Eckert, Sebastian

Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time-resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal–ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. π-Back-donation is found to be mainly determined by themore » metal site occupation, whereas the ligand hole instead influences σ-donation. Here, our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes.« less

Disentangling Transient Charge Density and Metal–Ligand Covalency in Photoexcited Ferricyanide with Femtosecond Resonant Inelastic Soft X-ray Scattering

DOE PAGES

Jay, Raphael M.; Norell, Jesper; Eckert, Sebastian; ...

2018-06-11

Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time-resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal–ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. π-Back-donation is found to be mainly determined by themore » metal site occupation, whereas the ligand hole instead influences σ-donation. Here, our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes.« less

Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics

PubMed Central

Shirke, Abhijit N.; Basore, Danielle; Holton, Samantha; Su, An; Baugh, Evan; Butterfoss, Glenn L.; Makhatadze, George

2016-01-01

Cutinases are esterases of industrial importance for applications in recycling and surface modification of polyesters. The cutinase from Thielavia terrestris (TtC) is distinct in terms of its ability to retain its stability and activity in acidic pH. Stability and activity in acidic pHs are desirable for esterases as the pH of the reaction tends to go down with the generation of acid. The pH stability and activity are governed by the charged state of the residues involved in catalysis or in substrate binding. In this study, we performed the detailed structural and biochemical characterization of TtC coupled with surface charge analysis to understand its acidic tolerance. The stability of TtC in acidic pH was rationalized by evaluating the contribution of charge interactions to the Gibbs free energy of unfolding at varying pHs. The activity of TtC was found to be limited by substrate binding affinity, which is a function of the surface charge. Additionally, the presence of glycosylation affects the biochemical characteristics of TtC owing to steric interactions with residues involved in substrate binding. PMID:26758295

Metastable Atom-Activated Dissociation Mass Spectrometry of Phosphorylated and Sulfonated Peptides in Negative Ion Mode

NASA Astrophysics Data System (ADS)

Cook, Shannon L.; Jackson, Glen P.

2011-06-01

The dissociation behavior of phosphorylated and sulfonated peptide anions was explored using metastable atom-activated dissociation mass spectrometry (MAD-MS) and collision-induced dissociation (CID). A beam of high kinetic energy helium (He) metastable atoms was exposed to isolated phosphorylated and sulfonated peptides in the 3- and 2- charge states. Unlike CID, where phosphate losses are dominant, the major dissociation channels observed using MAD were Cα - C peptide backbone cleavages and neutral losses of CO2, H2O, and [CO2 + H2O] from the charge reduced (oxidized) product ion, consistent with an electron detachment dissociation (EDD) mechanism such as Penning ionization. Regardless of charge state or modification, MAD provides ample backbone cleavages with little modification loss, which allows for unambiguous PTM site determination. The relative abundance of certain fragment ions in MAD is also demonstrated to be somewhat sensitive to the number and location of deprotonation sites, with backbone cleavage somewhat favored adjacent to deprotonated sites like aspartic acid residues. MAD provides a complementary dissociation technique to CID, ECD, ETD, and EDD for peptide sequencing and modification identification. MAD offers the unique ability to analyze highly acidic peptides that contain few to no basic amino acids in either negative or positive ion mode.

Semi-idealized modeling of lightning initiation related to vertical air motion and cloud microphysics

NASA Astrophysics Data System (ADS)

Wang, Fei; Zhang, Yijun; Zheng, Dong; Xu, Liangtao; Zhang, Wenjuan; Meng, Qing

2017-10-01

A three-dimensional charge-discharge numerical model is used, in a semi-idealized mode, to simulate a thunder-storm cell. Characteristics of the graupel microphysics and vertical air motion associated with the lightning initiation are revealed, which could be useful in retrieving charge strength during lightning when no charge-discharge model is available. The results show that the vertical air motion at the lightning initiation sites ( W ini) has a cubic polynomial correlation with the maximum updraft of the storm cell ( W cell-max), with the adjusted regression coefficient R 2 of approximately 0.97. Meanwhile, the graupel mixing ratio at the lightning initiation sites ( q g-ini) has a linear correlation with the maximum graupel mixing ratio of the storm cell ( q g-cell-max) and the initiation height ( z ini), with the coefficients being 0.86 and 0.85, respectively. These linear correlations are more significant during the middle and late stages of lightning activity. A zero-charge zone, namely, the area with very low net charge density between the main positive and negative charge layers, appears above the area of q g-cell-max and below the upper edge of the graupel region, and is found to be an important area for lightning initiation. Inside the zero-charge zone, large electric intensity forms, and the ratio of q ice (ice crystal mixing ratio) to q g (graupel mixing ratio) illustrates an exponential relationship to q g-ini. These relationships provide valuable clues to more accurately locating the high-risk area of lightning initiation in thunderstorms when only dual-polarization radar data or outputs from numerical models without charging/discharging schemes are available. The results can also help understand the environmental conditions at lightning initiation sites.

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

Jay, Raphael M.; Norell, Jesper; Eckert, Sebastian

Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time-resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal–ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. π-Back-donation is found to be mainly determined by themore » metal site occupation, whereas the ligand hole instead influences σ-donation. Here, our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes.« less

Passive colloids work together to become Active

NASA Astrophysics Data System (ADS)

Kandula, Hima Nagamanasa; Wang, Wei; Zhang, Jie; Wu, Huanxin; Han, Ming; Luijten, Erik; Granick, Steve

In recent years there is growing body of research to design self-propelled colloids to gain insights into non-equilibrium systems including living matter. While most active colloids developed hitherto entail prefabrication of Janus colloids and possess single fixed active site, we present one simple system where active colloids are formed in-situ naturally with multiple active sites and are reversible as well as reconfigurable. A binary mixture of Brownian colloids which have opposite polarizations when subjected to an AC electric field spontaneously assemble into clusters which are propelled by asymmetric induced charge electro osmosis. We find that tuning the relative sizes of the two species allows for the control over the number of active sites. More interestingly, the patches are dynamic enabling reconfiguration of the active cluster. Consequently, the clusters are active not only in motion but also in their structure.

Artificial phosphorylation sites modulate the activity of a voltage-gated potassium channel

NASA Astrophysics Data System (ADS)

Ariyaratne, Amila; Zocchi, Giovanni

2015-03-01

The KvAP potassium channel is representative of a family of voltage-gated ion channels where the membrane potential is sensed by a transmembrane helix containing several positively charged arginines. Previous work by Wang and Zocchi [A. Wang and G. Zocchi, PLoS ONE 6, e18598 (2011), 10.1371/journal.pone.0018598] showed how a negatively charged polyelectrolyte attached in proximity to the voltage sensing element can bias the opening probability of the channel. Here we introduce three phosphorylation sites at the same location and show that the response curve of the channel shifts by about 20 mV upon phosphorylation, while other characteristics such as the single-channel conductance are unaffected. In summary, we construct an artificial phosphorylation site which confers allosteric regulation to the channel.

Active synthetic soil

NASA Technical Reports Server (NTRS)

Ming, Douglas W. (Inventor); Henninger, Donald L. (Inventor); Allen, Earl R. (Inventor); Golden, Dadigamuwage C. (Inventor)

1995-01-01

A synthetic soil/fertilizer for horticultural application having all the agronutrients essential for plant growth is disclosed. The soil comprises a synthetic apatite fertilizer having sulfur, magnesium, and micronutrients dispersed in a calcium phosphate matrix, a zeolite cation exchange medium saturated with a charge of potassium and nitrogen cations, and an optional pH buffer. Moisture dissolves the apatite and mobilizes the nutrient elements from the apatite matrix and the zeolite charge sites.

Active synthetic soil

NASA Technical Reports Server (NTRS)

Ming, Douglas W. (Inventor); Henninger, Donald L. (Inventor); Golden, Dadigamuwage C. (Inventor); Allen, Earl R. (Inventor)

1995-01-01

A synthetic soil/fertilizer for horticultural application having all the agronutrients essential for plant growth is disclosed. The soil comprises a synthetic apatite fertilizer having sulfur, magnesium and micronutrients dispersed in a calcium phosphate matrix, a zeolite cation exchange medium saturated with a charge of potassium and nitrogen cations, and an optional pH buffer. Moisture dissolves the apatite and mobilizes the nutrient elements from the apatite matrix and the zeolite charge sites.

Cleavage-site specificity of prolyl endopeptidase FAP investigated with a full-length protein substrate.

PubMed

Huang, Chih-Hsiang; Suen, Ching-Shu; Lin, Ching-Ting; Chien, Chia-Hui; Lee, Hsin-Ying; Chung, Kuei-Min; Tsai, Ting-Yueh; Jiaang, Weir-Tong; Hwang, Ming-Jing; Chen, Xin

2011-06-01

Fibroblast activation protein (FAP) is a prolyl-cleaving endopeptidase proposed as an anti-cancer drug target. It is necessary to define its cleavage-site specificity to facilitate the identification of its in vivo substrates and to understand its biological functions. We found that the previously identified substrate of FAP, α(2)-anti-plasmin, is not a robust substrate in vitro. Instead, an intracellular protein, SPRY2, is cleavable by FAP and more suitable for investigation of its substrate specificity in the context of the full-length globular protein. FAP prefers uncharged residues, including small or bulky hydrophobic amino acids, but not charged amino acids, especially acidic residue at P1', P3 and P4 sites. Molecular modelling analysis shows that the substrate-binding site of FAP is surrounded by multiple tyrosine residues and some negatively charged residues, which may exert least preference for substrates with acidic residues. This provides an explanation why FAP cannot cleave interleukins, which have a glutamate at either P4 or P2', despite their P3-P2-P1 sites being identical to SPRY2 or α-AP. Our study provided new information on FAP cleavage-site specificity, which differs from the data obtained by profiling with a peptide library or with the denatured protein, gelatin, as the substrate. Furthermore, our study suggests that negatively charged residues should be avoided when designing FAP inhibitors.

Real-Time Visualization of Active Species in a Single-Site Metal–Organic Framework Photocatalyst

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

Yang, Sizhuo; Pattengale, Brian; Lee, Sungsik

In this work, we report a new single-site photocatalyst (Co-Ru-UIO- 67(bpy)) based on a metal-organic framework platform with incorporated molecular photosensitizer and catalyst. We show that this catalyst not only demonstrates exceptional activity for light-driven H2 production but also can be recycled without loss of activity. Using the combination of optical transient absorption spectroscopy and in situ X-ray absorption spectroscopy, we not only captured the key CoI intermediate species formed after ultrafast charge transfer from the incorporated photosensitizer but also identified the rate-limiting step in the catalytic cycle, providing insight into the catalysis mechanism of these single-site metal-organic framework photocatalysts.

Positive selection in octopus haemocyanin indicates functional links to temperature adaptation.

PubMed

Oellermann, Michael; Strugnell, Jan M; Lieb, Bernhard; Mark, Felix C

2015-07-05

Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.

Transition Metal Ions in Zeolites: Coordination and activation of O2

PubMed Central

Smeets, Pieter J.; Woertink, Julia S.; Sels, Bert F.; Solomon, Edward I.; Schoonheydt, Robert A.

2010-01-01

Zeolites containing transition metal ions (TMI) often show promising activity as heterogeneous catalysts in pollution abatement and selective oxidation reactions. In this paper, two aspects of research on the TMI Cu, Co and Fe in zeolites are discussed: (i) coordination to the lattice and (ii) activated oxygen species. At low loading, TMI preferably occupy exchange sites in six-membered oxygen rings (6MR) where the TMI preferentially coordinate with the oxygen atoms of Al tetrahedra. High TMI loadings result in a variety of TMI species formed at the zeolite surface. Removal of the extra-lattice oxygens during high temperature pretreatments can result in auto-reduction. Oxidation of reduced TMI sites often results in the formation of highly reactive oxygen species. In Cu-ZSM-5, calcination with O2 results in the formation of a species, which was found to be a crucial intermediate in both the direct decomposition of NO and N2O and the selective oxidation of methane into methanol. An activated oxygen species, called α-oxygen, is formed in Fe-ZSM5 and reported to be the active site in the partial oxidation of methane and benzene into methanol and phenol, respectively. However, this reactive α-oxygen can only be formed with N2O, not with O2. O2 activated Co intermediates in Faujasite (FAU) zeolites can selectively oxidize α-pinene and epoxidize styrene. In Co-FAU, CoIII superoxo and peroxo complexes are suggested to be the active cores, whereas in Cu and Fe-ZSM-5 various monomeric and dimeric sites have been proposed, but no consensus has been obtained. Very recently, the active site in Cu-ZSM-5 was identified as a bent [Cu-O-Cu]2+ core (Proc. Natl. Acad. Sci. USA 2009, 106, 18908-18913). Overall, O2 activation depends on the interplay of structural factors such as type of zeolite, size of the channels and cages and chemical factors such as Si/Al ratio and the nature, charge and distribution of the charge balancing cations. The presence of several different TMI sites hinders the direct study of the spectroscopic features of the active site. Spectroscopic techniques capable of selectively probing these sites, even if they only constitute a minor fraction of the total amount of TMI sites, are thus required. Fundamental knowledge of the geometric and electronic structure of the reactive active site can help in the design of novel selective oxidation catalysts. PMID:20380459

Structural charge site influence on the interlayer hydration of expandable three-sheet clay minerals

USGS Publications Warehouse

Kerns, Raymond L.; Mankin, Charles J.

1968-01-01

Previous investigations have demonstrated the influences of interlayer cation composition, relative humidity, temperature, and magnitude of interlayer surface charge on the interlayer hydration of montmorillonites and vermiculites. It has been suggested that the sites of layer charge deficiencies may also have an influence upon the amount of hydration that can take place in the interlayers of expandable clay minerals. If the interlayer cation-to-layer bonds are considered as ideally electrostatic, the magnitude of the forces resisting expansion may be expressed as a form of Coulomb's law. If this effect is significant, expandable structures in which the charge-deficiency sites are predominantly in the tetrahedral sheet should have less pronounced swelling properties than should structures possessing charge deficiencies located primarily in the octahedral sheet.Three samples that differed in location of layer charge sites were selected for study. An important selection criterion was a non-correlation between tetrahedral charge sites and high surface-charge density, and between octahedral charge sites and low surface-charge density.The effects of differences in interlayer cation composition were eliminated by saturating portions of each sample with the same cations. Equilibrium (001) d values at controlled constant humidities were used as a measure of the relative degree of interlayer hydration.Although no correlation could be made between the degree of interlayer hydration and total surface-charge density, the investigation does not eliminate total surface-charge density as being significant to the swelling properties of three-sheet clay-mineral structures. The results do indicate a correlation between more intense expandability and predominance of charge deficiencies in the octahedral sheet. Conversely, less intense swelling behavior is associated with predominantly tetrahedral charge deficiencies.

Principles and Practices of Water Quality Monitoring

Treesearch

J.L. Michael

2001-01-01

There are many activities in forest management that may affect water quality, i.e., timber harvestine, road building,mechanical and chemical site preparation, release operations, fuel reduction,wildlife opening maintenance, etc. How severely they affect water quality depends on how well the person in charge of the operation understands the activity itself, the...

Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces

PubMed Central

Haider, Kamran; Wickstrom, Lauren; Ramsey, Steven; Gilson, Michael K.; Kurtzman, Tom

2016-01-01

The principles underlying water reorganization around simple non-polar solutes are well understood and provide the framework for classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and with other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side-chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments. PMID:27169482

Polysaccharide/Surfactant complexes at the air-water interface - effect of the charge density on interfacial and foaming behaviors.

PubMed

Ropers, M H; Novales, B; Boué, F; Axelos, M A V

2008-11-18

The binding of a cationic surfactant (hexadecyltrimethylammonium bromide, CTAB) to a negatively charged natural polysaccharide (pectin) at air-solution interfaces was investigated on single interfaces and in foams, versus the linear charge densities of the polysaccharide. Besides classical methods to investigate polymer/surfactant systems, we applied, for the first time concerning these systems, the analogy between the small angle neutron scattering by foams and the neutron reflectivity of films to measure in situ film thicknesses of foams. CTAB/pectin foam films are much thicker than the pure surfactant foam film but similar for high- and low-charged pectin/CTAB systems despite the difference in structure of complexes at interfaces. The improvement of the foam properties of CTAB bound to pectin is shown to be directly related to the formation of pectin-CTAB complexes at the air-water interface. However, in opposition to surface activity, there is no specific behavior for the highly charged pectin: foam properties depend mainly upon the bulk charge concentration, while the interfacial behavior is mainly governed by the charge density of pectin. For the highly charged pectin, specific cooperative effects between neighboring charged sites along the chain are thought to be involved in the higher surface activity of pectin/CTAB complexes. A more general behavior can be obtained at lower charge density either by using a low-charged pectin or by neutralizing the highly charged pectin in decreasing pH.

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

Actions and Mechanisms of Polyunsaturated Fatty Acids on Voltage-Gated Ion Channels.

PubMed

Elinder, Fredrik; Liin, Sara I

2017-01-01

Polyunsaturated fatty acids (PUFAs) act on most ion channels, thereby having significant physiological and pharmacological effects. In this review we summarize data from numerous PUFAs on voltage-gated ion channels containing one or several voltage-sensor domains, such as voltage-gated sodium (Na V ), potassium (K V ), calcium (Ca V ), and proton (H V ) channels, as well as calcium-activated potassium (K Ca ), and transient receptor potential (TRP) channels. Some effects of fatty acids appear to be channel specific, whereas others seem to be more general. Common features for the fatty acids to act on the ion channels are at least two double bonds in cis geometry and a charged carboxyl group. In total we identify and label five different sites for the PUFAs. PUFA site 1 : The intracellular cavity. Binding of PUFA reduces the current, sometimes as a time-dependent block, inducing an apparent inactivation. PUFA site 2 : The extracellular entrance to the pore. Binding leads to a block of the channel. PUFA site 3 : The intracellular gate. Binding to this site can bend the gate open and increase the current. PUFA site 4 : The interface between the extracellular leaflet of the lipid bilayer and the voltage-sensor domain. Binding to this site leads to an opening of the channel via an electrostatic attraction between the negatively charged PUFA and the positively charged voltage sensor. PUFA site 5 : The interface between the extracellular leaflet of the lipid bilayer and the pore domain. Binding to this site affects slow inactivation. This mapping of functional PUFA sites can form the basis for physiological and pharmacological modifications of voltage-gated ion channels.

Actions and Mechanisms of Polyunsaturated Fatty Acids on Voltage-Gated Ion Channels

PubMed Central

Elinder, Fredrik; Liin, Sara I.

2017-01-01

Polyunsaturated fatty acids (PUFAs) act on most ion channels, thereby having significant physiological and pharmacological effects. In this review we summarize data from numerous PUFAs on voltage-gated ion channels containing one or several voltage-sensor domains, such as voltage-gated sodium (NaV), potassium (KV), calcium (CaV), and proton (HV) channels, as well as calcium-activated potassium (KCa), and transient receptor potential (TRP) channels. Some effects of fatty acids appear to be channel specific, whereas others seem to be more general. Common features for the fatty acids to act on the ion channels are at least two double bonds in cis geometry and a charged carboxyl group. In total we identify and label five different sites for the PUFAs. PUFA site 1: The intracellular cavity. Binding of PUFA reduces the current, sometimes as a time-dependent block, inducing an apparent inactivation. PUFA site 2: The extracellular entrance to the pore. Binding leads to a block of the channel. PUFA site 3: The intracellular gate. Binding to this site can bend the gate open and increase the current. PUFA site 4: The interface between the extracellular leaflet of the lipid bilayer and the voltage-sensor domain. Binding to this site leads to an opening of the channel via an electrostatic attraction between the negatively charged PUFA and the positively charged voltage sensor. PUFA site 5: The interface between the extracellular leaflet of the lipid bilayer and the pore domain. Binding to this site affects slow inactivation. This mapping of functional PUFA sites can form the basis for physiological and pharmacological modifications of voltage-gated ion channels. PMID:28220076

Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 1. Peptides to Proteins

NASA Astrophysics Data System (ADS)

Donohoe, Gregory C.; Khakinejad, Mahdiar; Valentine, Stephen J.

2015-04-01

Ion mobility spectrometry (IMS) coupled with hydrogen deuterium exchange (HDX)-mass spectrometry (MS) has been used to study the conformations of negatively-charged peptide and protein ions. Results are presented for ion conformers of angiotensin 1, a synthetic peptide (SP), bovine insulin, ubiquitin, and equine cytochrome c. In general, the SP ion conformers demonstrate a greater level of HDX efficiency as a greater proportion of the sites undergo HDX. Additionally, these ions exhibit the fastest rates of exchange. Comparatively, the angiotensin 1 ions exhibit a lower rate of exchange and HDX level presumably because of decreased accessibility of exchange sites by charge sites. The latter are likely confined to the peptide termini. Insulin ions show dramatically reduced HDX levels and exchange rates, which can be attributed to decreased conformational flexibility resulting from the disulfide bonds. For the larger ubiquitin and protein ions, increased HDX is observed for larger ions of higher charge state. For ubiquitin, a conformational transition from compact to more elongated species (from lower to higher charge states) is reflected by an increase in HDX levels. These results can be explained by a combination of interior site protection by compact conformers as well as decreased access by charge sites. The elongated cytochrome c ions provide the largest HDX levels where higher values correlate with charge state. These results are consistent with increased exchange site accessibility by additional charge sites. The data from these enhanced IMS-HDX experiments are described in terms of charge site location, conformer rigidity, and interior site protection.

Ionizable side chains at catalytic active sites of enzymes.

PubMed

Jimenez-Morales, David; Liang, Jie; Eisenberg, Bob

2012-05-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å(3). The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.

Ionizable Side Chains at Catalytic Active Sites of Enzymes

PubMed Central

Jimenez-Morales, David; Liang, Jie

2012-01-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

Electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations.

PubMed

Wade, R C; Gabdoulline, R R; Lüdemann, S K; Lounnas, V

1998-05-26

To bind at an enzyme's active site, a ligand must diffuse or be transported to the enzyme's surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it. Although the driving force for ligand binding is often ascribed to the hydrophobic effect, electrostatic interactions also influence the binding process of both charged and nonpolar ligands. First, electrostatic steering of charged substrates into enzyme active sites is discussed. This is of particular relevance for diffusion-influenced enzymes. By comparing the results of Brownian dynamics simulations and electrostatic potential similarity analysis for triose-phosphate isomerases, superoxide dismutases, and beta-lactamases from different species, we identify the conserved features responsible for the electrostatic substrate-steering fields. The conserved potentials are localized at the active sites and are the primary determinants of the bimolecular association rates. Then we focus on a more subtle effect, which we will refer to as "ionic tethering." We explore, by means of molecular and Brownian dynamics simulations and electrostatic continuum calculations, how salt links can act as tethers between structural elements of an enzyme that undergo conformational change upon substrate binding, and thereby regulate or modulate substrate binding. This is illustrated for the lipase and cytochrome P450 enzymes. Ionic tethering can provide a control mechanism for substrate binding that is sensitive to the electrostatic properties of the enzyme's surroundings even when the substrate is nonpolar.

The electrokinetic behavior of calcium oxalate monohydrate in macromolecular solutions

NASA Technical Reports Server (NTRS)

Curreri, P. A.; Onoda, G. Y., Jr.; Finlayson, B.

1988-01-01

Electrophoretic mobilities were measured for calcium oxalate monohydrate (COM) in solutions containing macromolecules. Two mucopolysaccharides (sodium heparin and chrondroitin sulfate) and two proteins (positively charged lysozyme and negatively charged bovine serum albumin) were studied as adsorbates. The effects of pH, calcium oxalate surface charge (varied by calcium or oxalate ion activity), and citrate concentration were investigated. All four macromolecules showed evidence for chemical adsorption. The macromolecule concentrations needed for reversing the surface charge indicated that the mucopopolysacchrides have greater affinity for the COM surface than the proteins. The amount of proteins that can chemically adsorb appears to be limited to approximately one monomolecular layer. When the surface charge is high, an insufficient number of proteins can chemically adsorb to neutralize or reverse the surface charge. The remaining surface charge is balanced by proteins held near the surface by longer range electrostatic forces only. Citrate ions at high concentrations appear to compete effectively with the negative protein for surface sites but show no evidence for competing with the positively charged protein.

A Measure of the Promiscuity of Proteins and Characteristics of Residues in the Vicinity of the Catalytic Site That Regulate Promiscuity

PubMed Central

Chakraborty, Sandeep; Rao, Basuthkar J.

2012-01-01

Promiscuity, the basis for the evolution of new functions through ‘tinkering’ of residues in the vicinity of the catalytic site, is yet to be quantitatively defined. We present a computational method Promiscuity Indices Estimator (PROMISE) - based on signatures derived from the spatial and electrostatic properties of the catalytic residues, to estimate the promiscuity (PromIndex) of proteins with known active site residues and 3D structure. PromIndex reflects the number of different active site signatures that have congruent matches in close proximity of its native catalytic site, the quality of the matches and difference in the enzymatic activity. Promiscuity in proteins is observed to follow a lognormal distribution (μ = 0.28, σ = 1.1 reduced chi-square = 3.0E-5). The PROMISE predicted promiscuous functions in any protein can serve as the starting point for directed evolution experiments. PROMISE ranks carboxypeptidase A and ribonuclease A amongst the more promiscuous proteins. We have also investigated the properties of the residues in the vicinity of the catalytic site that regulates its promiscuity. Linear regression establishes a weak correlation (R2∼0.1) between certain properties of the residues (charge, polar, etc) in the neighborhood of the catalytic residues and PromIndex. A stronger relationship states that most proteins with high promiscuity have high percentages of charged and polar residues within a radius of 3 Å of the catalytic site, which is validated using one-tailed hypothesis tests (P-values∼0.05). Since it is known that these characteristics are key factors in catalysis, their relationship with the promiscuity index cross validates the methodology of PROMISE. PMID:22359655

Site energies and charge transfer rates near pentacene grain boundaries from first-principles calculations

NASA Astrophysics Data System (ADS)

Kobayashi, Hajime; Tokita, Yuichi

2015-03-01

Charge transfer rates near pentacene grain boundaries are derived by calculating the site energies and transfer integrals of 37 pentacene molecules using first-principles calculations. The site energies decrease considerably near the grain boundaries, and electron traps of up to 300 meV and hole barriers of up to 400 meV are generated. The charge transfer rates across the grain boundaries are found to be reduced by three to five orders of magnitude with a grain boundary gap of 4 Å because of the reduction in the transfer integrals. The electron traps and hole barriers also reduce the electron and hole transfer rates by factors of up to 10 and 50, respectively. It is essential to take the site energies into consideration to determine charge transport near the grain boundaries. We show that the complex site energy distributions near the grain boundaries can be represented by an equivalent site energy difference, which is a constant for any charge transfer pass. When equivalent site energy differences are obtained for various grain boundary structures by first-principles calculations, the effects of the grain boundaries on the charge transfer rates are introduced exactly into charge transport simulations, such as the kinetic Monte Carlo method.

Atomistic simulation on charge mobility of amorphous tris(8-hydroxyquinoline) aluminum (Alq3): origin of Poole-Frenkel-type behavior.

PubMed

Nagata, Yuki; Lennartz, Christian

2008-07-21

The atomistic simulation of charge transfer process for an amorphous Alq(3) system is reported. By employing electrostatic potential charges, we calculate site energies and find that the standard deviation of site energy distribution is about twice as large as predicted in previous research. The charge mobility is calculated via the Miller-Abrahams formalism and the master equation approach. We find that the wide site energy distribution governs Poole-Frenkel-type behavior of charge mobility against electric field, while the spatially correlated site energy is not a dominant mechanism of Poole-Frenkel behavior in the range from 2x10(5) to 1.4x10(6) V/cm. Also we reveal that randomly meshed connectivities are, in principle, required to account for the Poole-Frenkel mechanism. Charge carriers find a zigzag pathway at low electric field, while they find a straight pathway along electric field when a high electric field is applied. In the space-charge-limited current scheme, the charge-carrier density increases with electric field strength so that the nonlinear behavior of charge mobility is enhanced through the strong charge-carrier density dependence of charge mobility.

Effect of Siloxane Ring Strain and Cation Charge Density on the Formation of Coordinately Unsaturated Metal Sites on Silica: Insights from Density Functional Theory (DFT) Studies

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

Das, Ujjal; Zhang, Guanghui; Hu, Bo

2015-10-28

Amorphous silica (SiO 2) is commonly used as a support in heterogeneous catalysis. However, due to the structural disorder and temperature induced change of surface morphology, the structures of silica supported metal catalysts are difficult to determine. Most studies are primarily focused on understanding the interactions of different types of surface hydroxyl groups with metal ions. In comparison, the effect of siloxane ring size on the structure of silica supported metal catalysts and how it affects catalytic activity is poorly understood. Here, we have used density functional theory calculations to understand the effect of siloxane ring strain on structure andmore » activity of different monomeric Lewis acid metal sites on silica. In particular, we have found that large siloxane rings favor strong dative bonding interaction between metal ion and surface hydroxyls, leading to the formation of high-coordinate metal sites. In comparison, metal-silanol interaction is weak in small siloxane rings, resulting in low-coordinate metal sites. The physical origin of this size dependence is associated with siloxane ring strain, and, a correlation between metal-silanol interaction energy and ring strain energy has been observed. In addition to ring strain, the strength of the metal-silanol interaction also depends on the positive charge density of the cations. In fact, a correlation also exists between metal-silanol interaction energy and charge density of several first-row transition and post-transition metals. The theoretical results are compared with the EXAFS data of monomeric Zn(II) and Ga(III) ions grafted on silica. In conclusion, the molecular level insights of how metal ion coordination on silica depends on siloxane ring strain and cation charge density will be useful in the synthesis of new catalysts.« less

Excited-State Charge Separation in the Photochemical Mechanism of the Light-Driven Enzyme Protochlorophyllide Oxidoreductase**

PubMed Central

Heyes, Derren J; Hardman, Samantha J O; Hedison, Tobias M; Hoeven, Robin; Greetham, Greg M; Towrie, Michael; Scrutton, Nigel S

2015-01-01

The unique light-driven enzyme protochlorophyllide oxidoreductase (POR) is an important model system for understanding how light energy can be harnessed to power enzyme reactions. The ultrafast photochemical processes, essential for capturing the excitation energy to drive the subsequent hydride- and proton-transfer chemistry, have so far proven difficult to detect. We have used a combination of time-resolved visible and IR spectroscopy, providing complete temporal resolution over the picosecond–microsecond time range, to propose a new mechanism for the photochemistry. Excited-state interactions between active site residues and a carboxyl group on the Pchlide molecule result in a polarized and highly reactive double bond. This so-called “reactive” intramolecular charge-transfer state creates an electron-deficient site across the double bond to trigger the subsequent nucleophilic attack of NADPH, by the negatively charged hydride from nicotinamide adenine dinucleotide phosphate. This work provides the crucial, missing link between excited-state processes and chemistry in POR. Moreover, it provides important insight into how light energy can be harnessed to drive enzyme catalysis with implications for the design of light-activated chemical and biological catalysts. PMID:25488797

The change in hydrogen bond strength accompanying charge rearrangement: Implications for enzymatic catalysis

PubMed Central

Shan, Shu-ou; Herschlag, Daniel

1996-01-01

The equilibrium for formation of the intramolecular hydrogen bond (KHB) in a series of substituted salicylate monoanions was investigated as a function of ΔpKa, the difference between the pKa values of the hydrogen bond donor and acceptor, in both water and dimethyl sulfoxide. The dependence of log KHB upon ΔpKa is linear in both solvents, but is steeper in dimethyl sulfoxide (slope = 0.73) than in water (slope = 0.05). Thus, hydrogen bond strength can undergo substantially larger increases in nonaqueous media than aqueous solutions as the charge density on the donor or acceptor atom increases. These results support a general mechanism for enzymatic catalysis, in which hydrogen bonding to a substrate is strengthened as charge rearranges in going from the ground state to the transition state; the strengthening of the hydrogen bond would be greater in a nonaqueous enzymatic active site than in water, thus providing a rate enhancement for an enzymatic reaction relative to the solution reaction. We suggest that binding energy of an enzyme is used to fix the substrate in the low-dielectric active site, where the strengthening of the hydrogen bond in the course of a reaction is increased. PMID:8962076

Excited-state charge separation in the photochemical mechanism of the light-driven enzyme protochlorophyllide oxidoreductase.

PubMed

Heyes, Derren J; Hardman, Samantha J O; Hedison, Tobias M; Hoeven, Robin; Greetham, Greg M; Towrie, Michael; Scrutton, Nigel S

2015-01-26

The unique light-driven enzyme protochlorophyllide oxidoreductase (POR) is an important model system for understanding how light energy can be harnessed to power enzyme reactions. The ultrafast photochemical processes, essential for capturing the excitation energy to drive the subsequent hydride- and proton-transfer chemistry, have so far proven difficult to detect. We have used a combination of time-resolved visible and IR spectroscopy, providing complete temporal resolution over the picosecond-microsecond time range, to propose a new mechanism for the photochemistry. Excited-state interactions between active site residues and a carboxyl group on the Pchlide molecule result in a polarized and highly reactive double bond. This so-called "reactive" intramolecular charge-transfer state creates an electron-deficient site across the double bond to trigger the subsequent nucleophilic attack of NADPH, by the negatively charged hydride from nicotinamide adenine dinucleotide phosphate. This work provides the crucial, missing link between excited-state processes and chemistry in POR. Moreover, it provides important insight into how light energy can be harnessed to drive enzyme catalysis with implications for the design of light-activated chemical and biological catalysts. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron transfer across a thermal gradient

PubMed Central

Craven, Galen T.

2016-01-01

Charge transfer is a fundamental process that underlies a multitude of phenomena in chemistry and biology. Recent advances in observing and manipulating charge and heat transport at the nanoscale, and recently developed techniques for monitoring temperature at high temporal and spatial resolution, imply the need for considering electron transfer across thermal gradients. Here, a theory is developed for the rate of electron transfer and the associated heat transport between donor–acceptor pairs located at sites of different temperatures. To this end, through application of a generalized multidimensional transition state theory, the traditional Arrhenius picture of activation energy as a single point on a free energy surface is replaced with a bithermal property that is derived from statistical weighting over all configurations where the reactant and product states are equienergetic. The flow of energy associated with the electron transfer process is also examined, leading to relations between the rate of heat exchange among the donor and acceptor sites as functions of the temperature difference and the electronic driving bias. In particular, we find that an open electron transfer channel contributes to enhanced heat transport between sites even when they are in electronic equilibrium. The presented results provide a unified theory for charge transport and the associated heat conduction between sites at different temperatures. PMID:27450086

S28 peptidases: lessons from a seemingly 'dysfunctional' family of two.

PubMed

Kozarich, John W

2010-06-28

A recent paper in BMC Structural Biology reports the crystal structure of human prolylcarboxypeptidase (PRCP), one of the two members of the S28 peptidase family. Comparison of the substrate-binding site of PRCP with that of its family partner, dipeptidyl dipeptidase 7 (DPP7), helps to explain the different enzymatic activities of these structurally similar proteins, and also reveals a novel apparent charge-relay system in PRCP involving the active-site catalytic histidine. See research article: http://www.biomedcentral.com/1472-6807/10/16/

Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase.

PubMed

Schwans, Jason P; Sunden, Fanny; Gonzalez, Ana; Tsai, Yingssu; Herschlag, Daniel

2013-11-05

Within the idiosyncratic enzyme active-site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near charged groups or within hydrophobic pockets, Tyr57 of a Pseudomonas putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semisynthesis, (13)C NMR spectroscopy, absorbance spectroscopy, and X-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from the introduction of nearby anionic groups, arises from accompanying active-site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen-bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen-bond donors, two Tyr side chains, and a water molecule positioned by other side chains and by a water-mediated hydrogen-bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can greatly facilitate our understanding of enzyme active-site energetics. The extensive data set provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects.

Uncovering the Determinants of a Highly Perturbed Tyrosine pKa in the Active Site of Ketosteroid Isomerase†

PubMed Central

Schwans, Jason P.; Sunden, Fanny; Gonzalez, Ana; Tsai, Yingssu; Herschlag, Daniel

2013-01-01

Within the idiosyncratic enzyme active site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near to charged groups or within hydrophobic pockets, Tyr57 of a P. putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semi-synthesis, 13C NMR spectroscopy, absorbance spectroscopy, and x-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from introduction of nearby anionic groups arise from accompanying active site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen bond donors, two Tyr side chains and a water molecule, positioned by other side chains and by a water-mediated hydrogen bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions, rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can greatly facilitate our understanding of enzyme active site energetics. The extensive dataset provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects. PMID:24151972

Transition State Charge Stabilization and Acid-Base Catalysis of mRNA Cleavage by the Endoribonuclease RelE

PubMed Central

Dunican, Brian F.; Hiller, David A.; Strobel, Scott A.

2015-01-01

The bacterial toxin RelE is a ribosome-dependent endoribonuclease. It is part of a type II toxin-antitoxin system that contributes to antibiotic resistance and biofilm formation. During amino acid starvation RelE cleaves mRNA in the ribosomal A-site, globally inhibiting protein translation. RelE is structurally similar to microbial RNases that employ general acid-base catalysis to facilitate RNA cleavage. The RelE active-site is atypical for acid-base catalysis, in that it is enriched for positively charged residues and lacks the prototypical histidine-glutamate catalytic pair, making the mechanism of mRNA cleavage unclear. In this study we use a single-turnover kinetic analysis to measure the effect of pH and phosphorothioate substitution on the rate constant for cleavage of mRNA by wild-type RelE and seven active-site mutants. Mutation and thio-effects indicate a major role for stabilization of increased negative change in the transition state by arginine 61. The wild-type RelE cleavage rate constant is pH-independent, but the reaction catalyzed by many of the mutants is strongly pH dependent, suggestive of general acid-base catalysis. pH-rate curves indicate that wild-type RelE operates with the pKa of at least one catalytic residue significantly downshifted by the local environment. Mutation of any single active-site residue is sufficient to disrupt this microenvironment and revert the shifted pKa back above neutrality. pH-rate curves are consistent with K54 functioning as a general base and R81 as a general acid. The capacity of RelE to effect a large pKa shift and facilitate a common catalytic mechanism by uncommon means furthers our understanding of other atypical enzymatic active sites. PMID:26535789

Micro-reaction chamber electrodes for neural stimulation and recording.

PubMed

Shanmugasundaram, Balaji; Gluckman, Bruce J

2011-01-01

Biocompatible electrodes with smaller geometric area are preferred to improve the selectivity of the neural recording and stimulation applications. We introduce the concept of a micro-reaction chamber (μRC) in which a volume within the electrode back plane is used to confine and sequester the electrochemical reactions used for charge passage. The URC electrode design helps decrease impedance and improves the charge storage capacity without altering the geometry of the active site. Here we demonstrate that μRC electrodes fabricated from 50 μm diameter microwire have significantly improved charge storage capacity and lowered impedance at physiologically relevant frequencies in phosphate buffered saline solution compared with other designs.

Monoubiquitination Inhibits the Actin Bundling Activity of Fascin*

PubMed Central

Lin, Shengchen; Lu, Shuang; Mulaj, Mentor; Fang, Bin; Keeley, Tyler; Wan, Lixin; Hao, Jihui; Muschol, Martin; Sun, Jianwei; Yang, Shengyu

2016-01-01

Fascin is an actin bundling protein that cross-links individual actin filaments into straight, compact, and stiff bundles, which are crucial for the formation of filopodia, stereocillia, and other finger-like membrane protrusions. The dysregulation of fascin has been implicated in cancer metastasis, hearing loss, and blindness. Here we identified monoubiquitination as a novel mechanism that regulates fascin bundling activity and dynamics. The monoubiquitination sites were identified to be Lys247 and Lys250, two residues located in a positive charge patch at the actin binding site 2 of fascin. Using a chemical ubiquitination method, we synthesized chemically monoubiquitinated fascin and determined the effects of monoubiquitination on fascin bundling activity and dynamics. Our data demonstrated that monoubiquitination decreased the fascin bundling EC50, delayed the initiation of bundle assembly, and accelerated the disassembly of existing bundles. By analyzing the electrostatic properties on the solvent-accessible surface of fascin, we proposed that monoubiquitination introduced steric hindrance to interfere with the interaction between actin filaments and the positively charged patch at actin binding site 2. We also identified Smurf1 as a E3 ligase regulating the monoubiquitination of fascin. Our findings revealed a previously unidentified regulatory mechanism for fascin, which will have important implications for the understanding of actin bundle regulation under physiological and pathological conditions. PMID:27879315

A docking study of enhanced intracellular survival protein from Mycobacterium tuberculosis with human DUSP16/MKP-7.

PubMed

Yoon, Hye Jin; Kim, Kyoung Hoon; Yang, Jin Kuk; Suh, Se Won; Kim, Hyunsik; Jang, Soonmin

2013-11-01

The intracellular pathogen Mycobacterium tuberculosis (Mtb) causes tuberculosis, and one of its secreted effector proteins, called enhanced intracellular survival (Eis) protein, enhances its survival in macrophages. Mtb Eis activates JNK-specific dual-specificity protein phosphatase 16 (DUSP16)/mitogen-activated protein kinase phosphatase-7 (MKP-7) through the acetylation on Lys55, thus inactivating JNK by dephosphorylation. Based on the recently reported crystal structure of Mtb Eis, a docking model for the binding of Mtb Eis to DUSP16/MKP-7 was generated. In the docking model, the substrate helix containing Lys55 of DUSP16/MKP-7 fits nicely into the active-site cleft of Mtb Eis; the twisted β-sheet of Eis domain II embraces the substrate helix from one side. Most importantly, the side-chain of Lys55 is inserted toward acetyl-CoA and the resulting distance is 4.6 Å between the NZ atom of Lys55 and the carbonyl carbon of the acetyl group in acetyl-CoA. The binding of Mtb Eis and DUSP16/MKP-7 is maintained by strong electrostatic interactions. The active-site cleft of Mtb Eis has a negatively charged surface formed by Asp25, Glu138, Asp286, Glu395 and the terminal carboxylic group of Phe396. In contrast, DUSP16/MKP-7 contains five basic residues, Lys52, Lys55, Arg56, Arg57 and Lys62, which point toward the negatively charged surface of the active-site pocket of Mtb Eis. Thus, the current docking model suggests that the binding of DUSP16/MKP-7 to Mtb Eis should be established by charge complementarity in addition to a very favorable geometric arrangement. The suggested mode of binding requires the dissociation of the hexameric Mtb Eis into dimers or monomers. This study may be useful for future studies aiming to develop inhibitors of Mtb Eis as a new anti-tuberculosis drug candidate.

Temperature Dependence of Magnetically Active Charge Excitations in Magnetite across the Verwey Transition

NASA Astrophysics Data System (ADS)

Taguchi, M.; Chainani, A.; Ueda, S.; Matsunami, M.; Ishida, Y.; Eguchi, R.; Tsuda, S.; Takata, Y.; Yabashi, M.; Tamasaku, K.; Nishino, Y.; Ishikawa, T.; Daimon, H.; Todo, S.; Tanaka, H.; Oura, M.; Senba, Y.; Ohashi, H.; Shin, S.

2015-12-01

We study the electronic structure of bulk single crystals and epitaxial films of Fe3 O4 . Fe 2 p core level spectra show clear differences between hard x-ray (HAX) and soft x-ray photoemission spectroscopy (PES). The bulk-sensitive spectra exhibit temperature (T ) dependence across the Verwey transition, which is missing in the surface-sensitive spectra. By using an extended impurity Anderson full-multiplet model—and in contrast to an earlier peak assignment—we show that the two distinct Fe species (A and B site) and the charge modulation at the B site are responsible for the newly found double peaks in the main peak above TV and its T -dependent evolution. The Fe 2 p HAXPES spectra show a clear magnetic circular dichroism (MCD) in the metallic phase of magnetized 100-nm-thick films. The model calculations also reproduce the MCD and identify the contributions from magnetically distinct A and B sites. Valence band HAXPES shows a finite density of states at EF for the polaronic half metal with a remnant order above TV and a clear gap formation below TV. The results indicate that the Verwey transition is driven by changes in the strongly correlated and magnetically active B -site electronic states, consistent with resistivity and optical spectra.

Determination of the Bridging Ligand in the Active Site of Tyrosinase.

PubMed

Zou, Congming; Huang, Wei; Zhao, Gaokun; Wan, Xiao; Hu, Xiaodong; Jin, Yan; Li, Junying; Liu, Junjun

2017-10-28

Tyrosinase is a type-3 copper enzyme that is widely distributed in plants, fungi, insects, and mammals. Developing high potent inhibitors against tyrosinase is of great interest in diverse fields including tobacco curing, food processing, bio-insecticides development, cosmetic development, and human healthcare-related research. In the crystal structure of Agaricus bisporus mushroom tyrosinase, there is an oxygen atom bridging the two copper ions in the active site. It is unclear whether the identity of this bridging oxygen is a water molecule or a hydroxide anion. In the present study, we theoretically determine the identity of this critical bridging oxygen by performing first-principles hybrid quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area (QM/MM-PBSA) calculations along with a thermodynamic cycle that aim to improve the accuracy. Our results show that the binding with water molecule is energy favored and the QM/MM-optimized structure is very close to the crystal structure, whereas the binding with hydroxide anions causes the increase of energy and significant structural changes of the active site, indicating that the identity of the bridging oxygen must be a water molecule rather than a hydroxide anion. The different binding behavior between water and hydroxide anions may explain why molecules with a carboxyl group or too many negative charges have lower inhibitory activity. In light of this, the design of high potent active inhibitors against tyrosinase should satisfy both the affinity to the copper ions and the charge neutrality of the entire molecule.

Re-engineering of CYP2C9 to probe acid-base substrate selectivity.

PubMed

Tai, Guoying; Dickmann, Leslie J; Matovic, Nicholas; DeVoss, James J; Gillam, Elizabeth M J; Rettie, Allan E

2008-10-01

A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites.

Re-engineering of CYP2C9 to Probe Acid-Base Substrate Selectivity

PubMed Central

Tai, Guoying; Dickmann, Leslie J.; Matovic, Nicholas; DeVoss, James J.; Gillam, Elizabeth M. J.; Rettie, Allan E.

2009-01-01

A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites. PMID:18606741

Electrostatically Embedded Many-Body Expansion for Neutral and Charged Metalloenzyme Model Systems.

PubMed

Kurbanov, Elbek K; Leverentz, Hannah R; Truhlar, Donald G; Amin, Elizabeth A

2012-01-10

The electrostatically embedded many-body (EE-MB) method has proven accurate for calculating cohesive and conformational energies in clusters, and it has recently been extended to obtain bond dissociation energies for metal-ligand bonds in positively charged inorganic coordination complexes. In the present paper, we present four key guidelines that maximize the accuracy and efficiency of EE-MB calculations for metal centers. Then, following these guidelines, we show that the EE-MB method can also perform well for bond dissociation energies in a variety of neutral and negatively charged inorganic coordination systems representing metalloenzyme active sites, including a model of the catalytic site of the zinc-bearing anthrax toxin lethal factor, a popular target for drug development. In particular, we find that the electrostatically embedded three-body (EE-3B) method is able to reproduce conventionally calculated bond-breaking energies in a series of pentacoordinate and hexacoordinate zinc-containing systems with an average absolute error (averaged over 25 cases) of only 0.98 kcal/mol.

Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations

PubMed Central

Wade, Rebecca C.; Gabdoulline, Razif R.; Lüdemann, Susanna K.; Lounnas, Valère

1998-01-01

To bind at an enzyme’s active site, a ligand must diffuse or be transported to the enzyme’s surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it. Although the driving force for ligand binding is often ascribed to the hydrophobic effect, electrostatic interactions also influence the binding process of both charged and nonpolar ligands. First, electrostatic steering of charged substrates into enzyme active sites is discussed. This is of particular relevance for diffusion-influenced enzymes. By comparing the results of Brownian dynamics simulations and electrostatic potential similarity analysis for triose-phosphate isomerases, superoxide dismutases, and β-lactamases from different species, we identify the conserved features responsible for the electrostatic substrate-steering fields. The conserved potentials are localized at the active sites and are the primary determinants of the bimolecular association rates. Then we focus on a more subtle effect, which we will refer to as “ionic tethering.” We explore, by means of molecular and Brownian dynamics simulations and electrostatic continuum calculations, how salt links can act as tethers between structural elements of an enzyme that undergo conformational change upon substrate binding, and thereby regulate or modulate substrate binding. This is illustrated for the lipase and cytochrome P450 enzymes. Ionic tethering can provide a control mechanism for substrate binding that is sensitive to the electrostatic properties of the enzyme’s surroundings even when the substrate is nonpolar. PMID:9600896

Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution.

PubMed

Buckle, A M; Schreiber, G; Fersht, A R

1994-08-02

We have solved, refined, and analyzed the 2.0-å resolution crystal structure of a 1:1 complex between the bacterial ribonuclease, barnase, and a Cys-->Ala(40,82) double mutant of its intracellular polypeptide inhibitor, barstar. Barstar inhibits barnase by sterically blocking the active site with a helix and adjacent loop segment. Almost half of the 14 hydrogen bonds between barnase and barstar involve two charged residues, and a third involve one charged partner. The electrostatic contribution to the overall binding energy is considerably greater than for other protein-protein interactions. Consequently, the very high rate constant for the barnase-barstar association (10(8) s-1 M-1) is most likely due to electrostatic steering effects. The barnase active-site residue His102 is located in a pocket on the surface of barstar, and its hydrogen bonds with Asp39 and Gly31 residues of barstar are directly responsible for the pH dependence of barnase-barstar binding. There is a high degree of complementarity both of the shape and of the charge of the interacting surfaces, but neither is perfect. The surface complementarity is slightly poorer than in protease-inhibitor complexes but a little better than in antibody-antigen interactions. However, since the burial of solvent in the barnase-barstar interface improves the fit significantly by filling in the majority of gaps, as well as stabilizing unfavorable electrostatic interactions, its role seems to be more important than in other protein-protein complexes. The electrostatic interactions between barnase and barstar are very similar to those between barnase and the tetranucleotide d(CGAC). In the barnase-barstar complex, the two phosphate-binding sites in the barnase active site are occupied by Asp39 and Gly43 of barstar. However, barstar has no equivalent for a guanine base of an RNA substrate, resulting in the occupation of the guanine recognition site in the barnase-barstar complex by nine ordered water molecules. Upon barnase-barstar binding, entropy losses resulting from the immobilization of segments of the protein chain and the energetic costs of conformational changes are minimized due to the essentially preformed active site of barnase. However, a certain degree of flexibility within the barnase active site is required to allow for the structural differences between barnase-barstar binding and barnase-RNA binding. A comparison between the bound and the free barstar structure shows that the overall structural response to barnase-binding is significant. This response can be best described as outwardly oriented, rigid-body movements of the four alpha-helices of barstar, resulting in the structure of bound barstar being somewhat expanded.

A negative charge in transmembrane segment 1 of domain II of the cockroach sodium channel is critical for channel gating and action of pyrethroid insecticides

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

Du Yuzhe; Song Weizhong; Groome, James R.

2010-08-15

Voltage-gated sodium channels are the primary target of pyrethroids, an important class of synthetic insecticides. Pyrethroids bind to a distinct receptor site on sodium channels and prolong the open state by inhibiting channel deactivation and inactivation. Recent studies have begun to reveal sodium channel residues important for pyrethroid binding. However, how pyrethroid binding leads to inhibition of sodium channel deactivation and inactivation remains elusive. In this study, we show that a negatively charged aspartic acid residue at position 802 (D802) located in the extracellular end of transmembrane segment 1 of domain II (IIS1) is critical for both the action ofmore » pyrethroids and the voltage dependence of channel activation. Charge-reversing or -neutralizing substitutions (K, G, or A) of D802 shifted the voltage dependence of activation in the depolarizing direction and reduced channel sensitivity to deltamethrin, a pyrethroid insecticide. The charge-reversing mutation D802K also accelerated open-state deactivation, which may have counteracted the inhibition of sodium channel deactivation by deltamethrin. In contrast, the D802G substitution slowed open-state deactivation, suggesting an additional mechanism for neutralizing the action of deltamethrin. Importantly, Schild analysis showed that D802 is not involved in pyrethroid binding. Thus, we have identified a sodium channel residue that is critical for regulating the action of pyrethroids on the sodium channel without affecting the receptor site of pyrethroids.« less

Dual Active Site in the Endolytic Transglycosylase gp144 of Bacteriophage phiKZ.

PubMed

Chertkov, O V; Armeev, G A; Uporov, I V; Legotsky, S A; Sykilinda, N N; Shaytan, A K; Klyachko, N L; Miroshnikov, K A

2017-01-01

Lytic transglycosylases are abundant peptidoglycan lysing enzymes that degrade the heteropolymers of bacterial cell walls in metabolic processes or in the course of a bacteriophage infection. The conventional catalytic mechanism of transglycosylases involves only the Glu or Asp residue. Endolysin gp144 of Pseudomonas aeruginosa bacteriophage phiKZ belongs to the family of Gram-negative transglycosylases with a modular composition and C -terminal location of the catalytic domain. Glu115 of gp144 performs the predicted role of a catalytic residue. However, replacement of this residue does not completely eliminate the activity of the mutant protein. Site-directed mutagenesis has revealed the participation of Tyr197 in the catalytic mechanism, as well as the presence of a second active site involving Glu178 and Tyr147. The existence of the dual active site was supported by computer modeling and monitoring of the molecular dynamics of the changes in the conformation and surface charge distribution as a consequence of point mutations.

Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site

PubMed Central

Stafford, Kate A.; Palmer III, Arthur G.

2014-01-01

Ribonuclease H1 (RNase H) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. Despite extensive study, especially of the E. coli homolog, the interaction of the highly negatively charged active site with catalytically required magnesium ions remains poorly understood. In this work, we describe molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states. Collectively, these results suggest that the active site is highly rigid in the apo state of all homologs studied and is conformationally preorganized to favor the binding of a magnesium ion. Notably, representatives of bacterial, eukaryotic, and retroviral RNases H all exhibit similar active-site rigidity, suggesting that this dynamic feature is only subtly modulated by amino acid sequence and is primarily imposed by the distinctive RNase H protein fold. PMID:25075292

Ni-Nanocluster Modified Black TiO2 with Dual Active Sites for Selective Photocatalytic CO2 Reduction.

PubMed

Billo, Tadesse; Fu, Fang-Yu; Raghunath, Putikam; Shown, Indrajit; Chen, Wei-Fu; Lien, Hsiang-Ting; Shen, Tzu-Hsien; Lee, Jyh-Fu; Chan, Ting-Shan; Huang, Kuo-You; Wu, Chih-I; Lin, M C; Hwang, Jih-Shang; Lee, Chih-Hao; Chen, Li-Chyong; Chen, Kuei-Hsien

2018-01-01

One of the key challenges in artificial photosynthesis is to design a photocatalyst that can bind and activate the CO 2 molecule with the smallest possible activation energy and produce selective hydrocarbon products. In this contribution, a combined experimental and computational study on Ni-nanocluster loaded black TiO 2 (Ni/TiO 2[Vo] ) with built-in dual active sites for selective photocatalytic CO 2 conversion is reported. The findings reveal that the synergistic effects of deliberately induced Ni nanoclusters and oxygen vacancies provide (1) energetically stable CO 2 binding sites with the lowest activation energy (0.08 eV), (2) highly reactive sites, (3) a fast electron transfer pathway, and (4) enhanced light harvesting by lowering the bandgap. The Ni/TiO 2[Vo] photocatalyst has demonstrated highly selective and enhanced photocatalytic activity of more than 18 times higher solar fuel production than the commercial TiO 2 (P-25). An insight into the mechanisms of interfacial charge transfer and product formation is explored. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Site-Specific Measurement of Water Dynamics in the Substrate Pocket of Ketosteroid Isomerase Using Time-Resolved Vibrational Spectroscopy

PubMed Central

Jha, Santosh Kumar; Ji, Minbiao; Gaffney, Kelly J.; Boxer, Steven G.

2012-01-01

Little is known about the reorganization capacity of water molecules at the active sites of enzymes and how this couples to the catalytic reaction. Here, we study the dynamics of water molecules at the active site of a highly proficient enzyme, Δ5-3-ketosteroid isomerase (KSI), during a light-activated mimic of its catalytic cycle. Photo-excitation of a nitrile containing photo-acid, coumarin183 (C183), mimics the change in charge density that occurs at the active site of KSI during the first step of the catalytic reaction. The nitrile of C183 is exposed to water when bound to the KSI active site, and we used time-resolved vibrational spectroscopy as a site-specific probe to study the solvation dynamics of water molecules in the vicinity of the nitrile. We observed that water molecules at the active site of KSI are highly rigid, during the light-activated catalytic cycle, compared to the solvation dynamics observed in bulk water. Based upon this result we hypothesize that rigid water dipoles at the active site might help in the maintenance of the pre-organized electrostatic environment required for efficient catalysis. The results also demonstrate the utility of nitrile probes in measuring the dynamics of local (H-bonded) water molecules in contrast to the commonly used fluorescence methods which measure the average behavior of primary and subsequent spheres of solvation. PMID:22931297

Combined density functional theory (DFT) and continuum calculations of pKa in carbonic anhydrase.

PubMed

Jiao, Dian; Rempe, Susan B

2012-07-31

Deprotonation of zinc-bound water in carbonic anhydrase II is the rate-limiting step in the catalysis of carbon dioxide between gas- and water-soluble forms. To understand the factors determining the extent of dissociation, or pK(a), of the zinc-bound water, we apply quantum chemistry calculations to the active site coupled with a continuum model of the surrounding environment. Experimentally determined changes in pK(a) associated with mutations of the active site are well reproduced by this approach. Analysis of the active site structure and charge/dipole values provides evidence that mutations cause changes in both conformation of the active site structure and local polarization, which accounts for the shifts in pK(a). More specifically, the shifts in pK(a) correlate with the dipole moments of the zinc-bound water upon deprotonation. The data further support the conclusion that the distinct pK(a) values found in mutations of the same type, but applied to different sites, result from asymmetric ligation and different electronic environments around the zinc ion.

43 CFR 3830.96 - What if I pay only part of the service charges and fees for oil shale claims or previously...

Code of Federal Regulations, 2013 CFR

2013-10-01

... charges and fees for oil shale claims or previously-recorded mining claims or sites? 3830.96 Section 3830... the service charges and fees for oil shale claims or previously-recorded mining claims or sites? (a... maintenance fees, or oil shale fees, for previously-recorded mining claims or sites, or any combination of...

43 CFR 3830.96 - What if I pay only part of the service charges and fees for oil shale claims or previously...

Code of Federal Regulations, 2014 CFR

2014-10-01

... charges and fees for oil shale claims or previously-recorded mining claims or sites? 3830.96 Section 3830... the service charges and fees for oil shale claims or previously-recorded mining claims or sites? (a... maintenance fees, or oil shale fees, for previously-recorded mining claims or sites, or any combination of...

43 CFR 3830.96 - What if I pay only part of the service charges and fees for oil shale claims or previously...

Code of Federal Regulations, 2011 CFR

2011-10-01

... charges and fees for oil shale claims or previously-recorded mining claims or sites? 3830.96 Section 3830... the service charges and fees for oil shale claims or previously-recorded mining claims or sites? (a... maintenance fees, or oil shale fees, for previously-recorded mining claims or sites, or any combination of...

43 CFR 3830.96 - What if I pay only part of the service charges and fees for oil shale claims or previously...

Code of Federal Regulations, 2012 CFR

2012-10-01

... charges and fees for oil shale claims or previously-recorded mining claims or sites? 3830.96 Section 3830... the service charges and fees for oil shale claims or previously-recorded mining claims or sites? (a... maintenance fees, or oil shale fees, for previously-recorded mining claims or sites, or any combination of...

Micro-Reaction Chamber Electrodes for Neural Stimulation and Recording

PubMed Central

Shanmugasundaram, Balaji; Gluckman, Bruce J.

2012-01-01

Biocompatible electrodes with smaller geometric area are preferred to improve the selectivity of the neural recording and stimulation applications. We introduce the concept of a micro-reaction chamber (µRC) in which a volume within the electrode back plane is used to confine and sequester the electrochemical reactions used for charge passage. The µRC electrode design helps decrease impedance and improves the charge storage capacity without altering the geometry of the active site. Here we demonstrate that µRC electrodes fabricated from 50 µm diameter microwire have significantly improved charge storage capacity and lowered impedance at physiologically relevant frequencies in phosphate buffered saline solution compared with other designs. PMID:22254394

Redox-dependent open and closed forms of the active site of the bacterial respiratory nitric-oxide reductase revealed by cyanide binding studies.

PubMed

Grönberg, Karin L C; Watmough, Nicholas J; Thomson, Andrew J; Richardson, David J; Field, Sarah J

2004-04-23

The bacterial respiratory nitric-oxide reductase (NOR) catalyzes the respiratory detoxification of nitric oxide in bacteria and Archaea. It is a member of the well known super-family of heme-copper oxidases but has a [heme Fe-non-heme Fe] active site rather than the [heme Fe-Cu(B)] active site normally associated with oxygen reduction. Paracoccus denitrificans NOR is spectrally characterized by a ligand-to-metal charge transfer absorption band at 595 nm, which arises from the high spin ferric heme iron of a micro-oxo-bridged [heme Fe(III)-O-Fe(III)] active site. On reduction of the nonheme iron, the micro-oxo bridge is broken, and the ferric heme iron is hydroxylated or hydrated, depending on the pH. At present, the catalytic cycle of NOR is a matter of much debate, and it is not known to which redox state(s) of the enzyme nitric oxide can bind. This study has used cyanide to probe the nature of the active site in a number of different redox states. Our observations suggest that the micro-oxo-bridged [heme Fe(III)-O-Fe(III)] active site represents a closed or resting state of NOR that can be opened by reduction of the non-heme iron.

Charge-regulation phase transition on surface lattices of titratable sites adjacent to electrolyte solutions: An analog of the Ising antiferromagnet in a magnetic field

PubMed Central

Shore, Joel D.; Thurston, George M.

2018-01-01

We report a charge-patterning phase transition on two-dimensional square lattices of titratable sites, here regarded as protonation sites, placed in a low-dielectric medium just below the planar interface between this medium and a salt solution. We calculate the work-of-charging matrix of the lattice with use of a linear Debye-Hückel model, as input to a grand-canonical partition function for the distribution of occupancy patterns. For a large range of parameter values, this model exhibits an approximate inverse cubic power-law decrease of the voltage produced by an individual charge, as a function of its in-lattice separation from neighboring titratable sites. Thus, the charge coupling voltage biases the local probabilities of proton binding as a function of the occupancy of sites for many neighbors beyond the nearest ones. We find that even in the presence of these longer-range interactions, the site couplings give rise to a phase transition in which the site occupancies exhibit an alternating, checkerboard pattern that is an analog of antiferromagnetic ordering. The overall strength W of this canonical charge coupling voltage, per unit charge, is a function of the Debye length, the charge depth, the Bjerrum length, and the dielectric coefficients of the medium and the solvent. The alternating occupancy transition occurs above a curve of thermodynamic critical points in the (pH-pK,W) plane, the curve representing a charge-regulation analog of variation of the Néel temperature of an Ising antiferromagnet as a function of an applied, uniform magnetic field. The analog of a uniform magnetic field in the antiferromagnet problem is a combination of pH-pK and W, and 1/W is the analog of the temperature in the antiferromagnet problem. We use Monte Carlo simulations to study the occupancy patterns of the titratable sites, including interactions out to the 37th nearest-neighbor category (a distance of 74 lattice constants), first validating simulations through comparison with exact and approximate results for the nearest-neighbor case. We then use the simulations to map the charge-patterning phase boundary in the (pH-pK,W) plane. The physical parameters that determine W provide a framework for identifying and designing real surfaces that could exhibit charge-patterning phase transitions. PMID:26764648

Charge-regulation phase transition on surface lattices of titratable sites adjacent to electrolyte solutions: An analog of the Ising antiferromagnet in a magnetic field.

PubMed

Shore, Joel D; Thurston, George M

2015-12-01

We report a charge-patterning phase transition on two-dimensional square lattices of titratable sites, here regarded as protonation sites, placed in a low-dielectric medium just below the planar interface between this medium and a salt solution. We calculate the work-of-charging matrix of the lattice with use of a linear Debye-Hückel model, as input to a grand-canonical partition function for the distribution of occupancy patterns. For a large range of parameter values, this model exhibits an approximate inverse cubic power-law decrease of the voltage produced by an individual charge, as a function of its in-lattice separation from neighboring titratable sites. Thus, the charge coupling voltage biases the local probabilities of proton binding as a function of the occupancy of sites for many neighbors beyond the nearest ones. We find that even in the presence of these longer-range interactions, the site couplings give rise to a phase transition in which the site occupancies exhibit an alternating, checkerboard pattern that is an analog of antiferromagnetic ordering. The overall strength W of this canonical charge coupling voltage, per unit charge, is a function of the Debye length, the charge depth, the Bjerrum length, and the dielectric coefficients of the medium and the solvent. The alternating occupancy transition occurs above a curve of thermodynamic critical points in the (pH-pK,W) plane, the curve representing a charge-regulation analog of variation of the Néel temperature of an Ising antiferromagnet as a function of an applied, uniform magnetic field. The analog of a uniform magnetic field in the antiferromagnet problem is a combination of pH-pK and W, and 1/W is the analog of the temperature in the antiferromagnet problem. We use Monte Carlo simulations to study the occupancy patterns of the titratable sites, including interactions out to the 37th nearest-neighbor category (a distance of √74 lattice constants), first validating simulations through comparison with exact and approximate results for the nearest-neighbor case. We then use the simulations to map the charge-patterning phase boundary in the (pH-pK,W) plane. The physical parameters that determine W provide a framework for identifying and designing real surfaces that could exhibit charge-patterning phase transitions.

Charge-regulation phase transition on surface lattices of titratable sites adjacent to electrolyte solutions: An analog of the Ising antiferromagnet in a magnetic field

NASA Astrophysics Data System (ADS)

Shore, Joel D.; Thurston, George M.

2015-12-01

We report a charge-patterning phase transition on two-dimensional square lattices of titratable sites, here regarded as protonation sites, placed in a low-dielectric medium just below the planar interface between this medium and a salt solution. We calculate the work-of-charging matrix of the lattice with use of a linear Debye-Hückel model, as input to a grand-canonical partition function for the distribution of occupancy patterns. For a large range of parameter values, this model exhibits an approximate inverse cubic power-law decrease of the voltage produced by an individual charge, as a function of its in-lattice separation from neighboring titratable sites. Thus, the charge coupling voltage biases the local probabilities of proton binding as a function of the occupancy of sites for many neighbors beyond the nearest ones. We find that even in the presence of these longer-range interactions, the site couplings give rise to a phase transition in which the site occupancies exhibit an alternating, checkerboard pattern that is an analog of antiferromagnetic ordering. The overall strength W of this canonical charge coupling voltage, per unit charge, is a function of the Debye length, the charge depth, the Bjerrum length, and the dielectric coefficients of the medium and the solvent. The alternating occupancy transition occurs above a curve of thermodynamic critical points in the (p H-p K ,W ) plane, the curve representing a charge-regulation analog of variation of the Néel temperature of an Ising antiferromagnet as a function of an applied, uniform magnetic field. The analog of a uniform magnetic field in the antiferromagnet problem is a combination of p H-p K and W , and 1 /W is the analog of the temperature in the antiferromagnet problem. We use Monte Carlo simulations to study the occupancy patterns of the titratable sites, including interactions out to the 37th nearest-neighbor category (a distance of √{74 } lattice constants), first validating simulations through comparison with exact and approximate results for the nearest-neighbor case. We then use the simulations to map the charge-patterning phase boundary in the (p H-p K ,W ) plane. The physical parameters that determine W provide a framework for identifying and designing real surfaces that could exhibit charge-patterning phase transitions.

Insights into intermolecular interactions, electrostatic properties and the stability of C646 in the binding pocket of p300 histone acetyltransferase enzyme: a combined molecular dynamics and charge density study.

PubMed

Sivanandam, Magudeeswaran; Saravanan, Kandasamy; Kumaradhas, Poomani

2017-10-30

Histone acetyltransferases (HATs) and histone deacetylases (HDACs) are enzymes that exhibit an important transcription activity. Dysfunction of these enzymes may lead to different diseases including cancer, cardiovascular, and other diseases. Therefore, these enzymes are the potential target for the generation of new therapeutics. C646 is a synthetic p300 HAT inhibitor; its structural and the electrostatic properties are the paradigm to understand its activity in the active site of p300 HAT enzyme. The docked C646 molecule in the active site forms expected key intermolecular interactions with the amino acid residues Trp1436, Tyr1467, and one water molecule (W1861); and these interactions are important for acetylation reaction. When compare the active site structure of C646 with the gas-phase structure, it is confirmed that the electron density distribution of polar bonds are highly altered, when the molecule present in the active site. In the gas-phase structure of C646, a large negative regions of electrostatic potential is found at the vicinity of O(4), O(5), and O(6) atoms; whereas, the negative region of these atoms are reduced in the active site. The molecular dynamics (MD) simulation also performed, it reveals the conformational stability and the intermolecular interactions of C646 molecule in the active site of p300.

Self-optimizing, highly surface-active layered metal dichalcogenide catalysts for hydrogen evolution

NASA Astrophysics Data System (ADS)

Liu, Yuanyue; Wu, Jingjie; Hackenberg, Ken P.; Zhang, Jing; Wang, Y. Morris; Yang, Yingchao; Keyshar, Kunttal; Gu, Jing; Ogitsu, Tadashi; Vajtai, Robert; Lou, Jun; Ajayan, Pulickel M.; Wood, Brandon C.; Yakobson, Boris I.

2017-09-01

Low-cost, layered transition-metal dichalcogenides (MX2) based on molybdenum and tungsten have attracted substantial interest as alternative catalysts for the hydrogen evolution reaction (HER). These materials have high intrinsic per-site HER activity; however, a significant challenge is the limited density of active sites, which are concentrated at the layer edges. Here we unravel electronic factors underlying catalytic activity on MX2 surfaces, and leverage the understanding to report group-5 MX2 (H-TaS2 and H-NbS2) electrocatalysts whose performance instead mainly derives from highly active basal-plane sites, as suggested by our first-principles calculations and performance comparisons with edge-active counterparts. Beyond high catalytic activity, they are found to exhibit an unusual ability to optimize their morphology for enhanced charge transfer and accessibility of active sites as the HER proceeds, offering a practical advantage for scalable processing. The catalysts reach 10 mA cm-2 current density at an overpotential of ˜50-60 mV with a loading of 10-55 μg cm-2, surpassing other reported MX2 candidates without any performance-enhancing additives.

Speciation dynamics of metals in dispersion of nanoparticles with discrete distribution of charged binding sites.

PubMed

Polyakov, Pavel D; Duval, Jérôme F L

2014-02-07

We report a comprehensive theory to evaluate the kinetics of complex formation between metal ions and charged spherical nanoparticles. The latter consist of an ion-impermeable core surrounded by a soft shell layer characterized by a discrete axisymmetric 2D distribution of charged sites that bind metal ions. The theory explicitly integrates the conductive diffusion of metal ions from bulk solution toward the respective locations of the reactive sites within the particle shell volume. The kinetic constant k for outer-sphere nanoparticle-metal association is obtained from the sum of the contributions stemming from all reactive sites, each evaluated from the corresponding incoming flux of metal ions derived from steady-state Poisson-Nernst-Planck equations. Illustrations are provided to capture the basic intertwined impacts of particle size, overall particle charge, spatial heterogeneity in site distribution, type of particle (hard, core-shell or porous) and concentration of the background electrolyte on k. As a limit, k converges with predictions from previously reported analytical expressions derived for porous particles with low and high charge density, cases that correspond to coulombic and mean-field (smeared-out) electrostatic treatments, respectively. The conditions underlying the applicability of these latter approaches are rigorously identified in terms of (i) the extent of overlap between electric double layers around charged neighbouring sites, and (ii) the magnitude of the intraparticulate metal concentration gradient. For the first time, the proposed theory integrates the differentiated impact of the local potential around the charged binding sites amidst the overall particle field, together with that of the so-far discarded intraparticulate flux of metal ions.

Monoubiquitination Inhibits the Actin Bundling Activity of Fascin.

PubMed

Lin, Shengchen; Lu, Shuang; Mulaj, Mentor; Fang, Bin; Keeley, Tyler; Wan, Lixin; Hao, Jihui; Muschol, Martin; Sun, Jianwei; Yang, Shengyu

2016-12-30

Fascin is an actin bundling protein that cross-links individual actin filaments into straight, compact, and stiff bundles, which are crucial for the formation of filopodia, stereocillia, and other finger-like membrane protrusions. The dysregulation of fascin has been implicated in cancer metastasis, hearing loss, and blindness. Here we identified monoubiquitination as a novel mechanism that regulates fascin bundling activity and dynamics. The monoubiquitination sites were identified to be Lys 247 and Lys 250 , two residues located in a positive charge patch at the actin binding site 2 of fascin. Using a chemical ubiquitination method, we synthesized chemically monoubiquitinated fascin and determined the effects of monoubiquitination on fascin bundling activity and dynamics. Our data demonstrated that monoubiquitination decreased the fascin bundling EC 50 , delayed the initiation of bundle assembly, and accelerated the disassembly of existing bundles. By analyzing the electrostatic properties on the solvent-accessible surface of fascin, we proposed that monoubiquitination introduced steric hindrance to interfere with the interaction between actin filaments and the positively charged patch at actin binding site 2. We also identified Smurf1 as a E3 ligase regulating the monoubiquitination of fascin. Our findings revealed a previously unidentified regulatory mechanism for fascin, which will have important implications for the understanding of actin bundle regulation under physiological and pathological conditions. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

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

Wang, Xianwei; State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062; Zhang, John Z. H.

2015-11-14

Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. Inmore » this study, quantum mechanical calculation of protein’s internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.« less

Active site electrostatics protect genome integrity by blocking abortive hydrolysis during DNA recombination

PubMed Central

Ma, Chien-Hui; Rowley, Paul A; Macieszak, Anna; Guga, Piotr; Jayaram, Makkuni

2009-01-01

Water, acting as a rogue nucleophile, can disrupt transesterification steps of important phosphoryl transfer reactions in DNA and RNA. We have unveiled this risk, and identified safeguards instituted against it, during strand cleavage and joining by the tyrosine site-specific recombinase Flp. Strand joining is threatened by a latent Flp endonuclease activity (type I) towards the 3′-phosphotyrosyl intermediate resulting from strand cleavage. This risk is not alleviated by phosphate electrostatics; neutralizing the negative charge on the scissile phosphate through methylphosphonate (MeP) substitution does not stimulate type I endonuclease. Rather, protection derives from the architecture of the recombination synapse and conformational dynamics within it. Strand cleavage is protected against water by active site electrostatics. Replacement of the catalytic Arg-308 of Flp by alanine, along with MeP substitution, elicits a second Flp endonuclease activity (type II) that directly targets the scissile phosphodiester bond in DNA. MeP substitution, combined with appropriate active site mutations, will be useful in revealing anti-hydrolytic mechanisms engendered by systems that mediate DNA relaxation, DNA transposition, site-specific recombination, telomere resolution, RNA splicing and retrohoming of mobile introns. PMID:19440204

Local anesthetics QX 572 and benzocaine act at separate sites on the batrachotoxin-activated sodium channel

PubMed Central

1981-01-01

We have studied the effect of local anesthetics QX 572, which is permanently charged, and benzocaine, which is neutral, on batrachotoxin- activated sodium channels in mouse neuroblastoma N18 cells. The dose- response curves for each drug suggest that QX 752 and benzocaine each act on a single class of binding sites. The dissociation constants are 3.15 X 10(-5) M for QX 572 and 2.65 X 10(-4) M for benzocaine. Equilibrium and kinetic experiments indicate that both drugs are competitive inhibitors of batrachotoxin. When benzocaine and QX 572 are present with batrachotoxin, they are much more effective at inhibiting Na+ flux than would be predicted by a one-site model. Our results indicate that QX 572 and benzocaine bind to separate sites, each of which interacts competitively with batrachotoxin. PMID:6267160

Localization and characterization of an alpha-thrombin-binding site on platelet glycoprotein Ib alpha.

PubMed

De Marco, L; Mazzucato, M; Masotti, A; Ruggeri, Z M

1994-03-04

Glycoprotein (GP) Ib alpha is required for expression of the highest affinity alpha-thrombin-binding site on platelets, possibly contributing to platelet activation through a pathway involving cleavage of a specific receptor. This function may be important for the initiation of hemostasis and may also play a role in the development of pathological vascular occlusion. We have now identified a discrete sequence in the extracytoplasmic domain of GP Ib alpha, including residues 271-284 of the mature protein, which appears to be part of the high affinity alpha-thrombin-binding site. Synthetic peptidyl mimetics of this sequence inhibit alpha-thrombin binding to GP Ib as well as platelet activation and aggregation induced by subnanomolar concentrations of the agonist; they also inhibit alpha-thrombin binding to purified glycocalicin, the isolated extracytoplasmic portion of GP Ib alpha. The inhibitory peptides interfere with the clotting of fibrinogen by alpha-thrombin but not with the amidolytic activity of the enzyme on a small synthetic substrate, a finding compatible with the concept that the identified GP Ib alpha sequence interacts with the anion-binding exosite of alpha-thrombin but not with its active proteolytic site. The crucial structural elements of this sequence necessary for thrombin binding appear to be a cluster of negatively charged residues as well as three tyrosine residues that, in the native protein, may be sulfated. GP Ib alpha has no significant overall sequence homology with the thrombin inhibitor, hirudin, nor with the specific thrombin receptor on platelets; all three molecules, however, possess a distinct region rich in negatively charged residues that appear to be involved in thrombin binding. This may represent a case of convergent evolution of unrelated proteins for high affinity interaction with the same ligand.

On the different roles of anions and cations in the solvation of enzymes in ionic liquids.

PubMed

Klähn, Marco; Lim, Geraldine S; Seduraman, Abirami; Wu, Ping

2011-01-28

The solvation of the enzyme Candida antarctica lipase B (CAL-B) was studied in eight different ionic liquids (ILs). The influence of enzyme-ion interactions on the solvation of CAL-B and the structure of the enzyme-IL interface are analyzed. CAL-B and ILs are described with molecular dynamics (MD) simulations in combination with an atomistic empirical force field. The considered cations are based on imidazolium or guanidinium that are paired with nitrate, tetrafluoroborate or hexafluorophosphate anions. The interactions of CAL-B with ILs are dominated by Coulomb interactions with anions, while the second largest contribution stems from van der Waals interactions with cations. The enzyme-ion interaction strength is determined by the ion size and the magnitude of the ion surface charge. The solvation of CAL-B in ILs is unfavorable compared to water because of large formation energies for the CAL-B solute cages in ILs. The internal energy in the IL and of CAL-B increases linearly with the enzyme-ion interaction strength. The average electrostatic potential on the surface of CAL-B is larger in ILs than in water, due to a weaker screening of charged enzyme residues. Ion densities increased moderately in the vicinity of charged residues and decreased close to non-polar residues. An aggregation of long alkyl chains close to non-polar regions and the active site entrance of CAL-B are observed in one IL that involved long non-polar decyl groups. In ILs that contain 1-butyl-3-methylimidazolium cations, the diffusion of one or two cations into the active site of CAL-B occurs during MD simulations. This suggests a possible obstruction of the active site in these ILs. Overall, the results indicate that small ions lead to a stronger electrostatic screening within the solvent and stronger interactions with the enzyme. Also a large ion surface charge, when more hydrophilic ions are used, increases enzyme-IL interactions. An increase of these interactions destabilizes the enzyme and impedes enzyme solvation due to an increase in solute cage formation energies.

The role of electronic coupling between substrate and 2D MoS2 nanosheets in electrocatalytic production of hydrogen.

PubMed

Voiry, Damien; Fullon, Raymond; Yang, Jieun; de Carvalho Castro E Silva, Cecilia; Kappera, Rajesh; Bozkurt, Ibrahim; Kaplan, Daniel; Lagos, Maureen J; Batson, Philip E; Gupta, Gautam; Mohite, Aditya D; Dong, Liang; Er, Dequan; Shenoy, Vivek B; Asefa, Tewodros; Chhowalla, Manish

2016-09-01

The excellent catalytic activity of metallic MoS2 edges for the hydrogen evolution reaction (HER) has led to substantial efforts towards increasing the edge concentration. The 2H basal plane is less active for the HER because it is less conducting and therefore possesses less efficient charge transfer kinetics. Here we show that the activity of the 2H basal planes of monolayer MoS2 nanosheets can be made comparable to state-of-the-art catalytic properties of metallic edges and the 1T phase by improving the electrical coupling between the substrate and the catalyst so that electron injection from the electrode and transport to the catalyst active site is facilitated. Phase-engineered low-resistance contacts on monolayer 2H-phase MoS2 basal plane lead to higher efficiency of charge injection in the nanosheets so that its intrinsic activity towards the HER can be measured. We demonstrate that onset potentials and Tafel slopes of ∼-0.1 V and ∼50 mV per decade can be achieved from 2H-phase catalysts where only the basal plane is exposed. We show that efficient charge injection and the presence of naturally occurring sulfur vacancies are responsible for the observed increase in catalytic activity of the 2H basal plane. Our results provide new insights into the role of contact resistance and charge transport on the performance of two-dimensional MoS2 nanosheet catalysts for the HER.

Highly efficient supercapacitor electrode with two-dimensional tungsten disulfide and reduced graphene oxide hybrid nanosheets

NASA Astrophysics Data System (ADS)

Tu, Chao-Chi; Lin, Lu-Yin; Xiao, Bing-Chang; Chen, Yu-Shiang

2016-07-01

Two-dimensional (2D) nanostructures with their high surface area and large in-plane conductivity have been regarded as promising materials for supercapacitors (SCs). Tungsten disulfide (WS2) is highly suitable for charge accumulation with its abundant active sites in the interspacing between the 2D structures and the intraspacing of each atomic layer, as well as on the tungsten centers with the charges generated by the Faradaic reactions. This study proposes the preparation of well-constructed WS2/reduced graphene oxide (RGO) nanosheets using a simple molten salt process as the electroactive material for SCs, which presents a high specific capacitance (CF) of 2508.07 F g-1 at the scan rate of 1 mV s-1, because of the synergic effect of WS2 with its large charge-accumulating sites on the 2D planes and RGO with its highly enhanced conductivity and improved connections in the WS2 networks. The excellent cycling stability of 98.6% retention after 5000 cycles charge/discharge process and the Coulombic efficiency close to 100% for the entire measurement are also achieved for the WS2/RGO-based SC electrode. The results suggest the potential for the combination of the 2D metal sulfide and carbon materials as the charge storage material to solve the energy problems and attain a sustainable society.

Spectroscopy of Photovoltaic Materials: Charge-Transfer Complexes and Titanium Dioxide

NASA Astrophysics Data System (ADS)

Dillon, Robert John

The successful function of photovoltaic (PV) and photocatalytic (PC) systems centers primarily on the creation and photophysics of charge separated electron-hole pairs. The pathway leading to separate carriers varies by material; organic materials typically require multiple events to charge separate, whereas inorganic semiconductors can directly produce free carriers. In this study, time-resolved spectroscopy is used to provide insight into two such systems: 1) organic charge-transfer (CT) complexes, where electrons and holes are tightly bound to each other, and 2) Au-TiO2 core-shell nanostructures, where free carriers are directly generated. 1) CT complexes are structurally well defined systems consisting of donor molecules, characterized by having low ionization potentials, and acceptor molecules, characterized by having high electron affinities. Charge-transfer is the excitation of an electron from the HOMO of a donor material directly into the LUMO of the acceptor material, leading to an electron and hole separated across the donor:acceptor interface. The energy of the CT transition is often less than that of the bandgaps of donor and acceptor materials individually, sparking much interest if PV systems can utilize the CT band to generate free carriers from low energy photons. In this work we examine the complexes formed between acceptors tetracyanobenzene (TCNB) and tetracyanoquinodimethane (TCNQ) with several aromatic donors. We find excitation of the charge-transfer band of these systems leads to strongly bound electron-hole pairs that exclusively undergo recombination to the ground state. In the case of the TCNB complexes, our initial studies were flummoxed by the samples' generally low threshold for photo and mechanical damage. As our results conflicted with previous literature, a significant portion of this study was spent quantifying the photodegradation process. 2) Unlike the previous system, free carriers are directly photogenerated in TiO2, and the prime consideration is avoiding loss due to recombination of the electron and hole. In this study, four samples of core-shell Au-TiO 2 nanostructures are analyzed for their photocatalytic activity and spectroscopic properties. The samples were made with increasingly crystalline TiO2 shells. The more crystalline samples had higher photocatalytic activities, attributed to longer carrier lifetimes. The observed photophysics of these samples vary with excitation wavelength and detection method used. We find the time-resolved photoluminescence correlates with the samples' photocatalytic activities only when high energy, excitation wavelength less than or equal to 300 nm is used, while transient absorption experiments show no correlation regardless of excitation source. The results imply that photoexcitation with high energy photons can generate both reactive surface sites and photoluminescent surface sites in parallel. Both types of sites then undergo similar electron-hole recombination processes that depend on the crystallinity of the TiO2 shell. Surface sites created by low energy photons, as well as bulk TiO2 carrier dynamics that are probed by transient absorption, do not appear to be sensitive to the same dynamics that determine chemical reactivity.

Single-Site Active Iron-Based Bifunctional Oxygen Catalyst for a Compressible and Rechargeable Zinc-Air Battery.

PubMed

Ma, Longtao; Chen, Shengmei; Pei, Zengxia; Huang, Yan; Liang, Guojin; Mo, Funian; Yang, Qi; Su, Jun; Gao, Yihua; Zapien, Juan Antonio; Zhi, Chunyi

2018-02-27

The exploitation of a high-efficient, low-cost, and stable non-noble-metal-based catalyst with oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) simultaneously, as air electrode material for a rechargeable zinc-air battery is significantly crucial. Meanwhile, the compressible flexibility of a battery is the prerequisite of wearable or/and portable electronics. Herein, we present a strategy via single-site dispersion of an Fe-N x species on a two-dimensional (2D) highly graphitic porous nitrogen-doped carbon layer to implement superior catalytic activity toward ORR/OER (with a half-wave potential of 0.86 V for ORR and an overpotential of 390 mV at 10 mA·cm -2 for OER) in an alkaline medium. Furthermore, an elastic polyacrylamide hydrogel based electrolyte with the capability to retain great elasticity even under a highly corrosive alkaline environment is utilized to develop a solid-state compressible and rechargeable zinc-air battery. The creatively developed battery has a low charge-discharge voltage gap (0.78 V at 5 mA·cm -2 ) and large power density (118 mW·cm -2 ). It could be compressed up to 54% strain and bent up to 90° without charge/discharge performance and output power degradation. Our results reveal that single-site dispersion of catalytic active sites on a porous support for a bifunctional oxygen catalyst as cathode integrating a specially designed elastic electrolyte is a feasible strategy for fabricating efficient compressible and rechargeable zinc-air batteries, which could enlighten the design and development of other functional electronic devices.

Influence of a Confined Methanol Solvent on the Reactivity of Active Sites in UiO-66.

PubMed

Caratelli, Chiara; Hajek, Julianna; Rogge, Sven M J; Vandenbrande, Steven; Meijer, Evert Jan; Waroquier, Michel; Van Speybroeck, Veronique

2018-02-19

UiO-66, composed of Zr-oxide bricks and terephthalate linkers, is currently one of the most studied metal-organic frameworks due to its exceptional stability. Defects can be introduced in the structure, creating undercoordinated Zr atoms which are Lewis acid sites. Here, additional Brønsted sites can be generated by coordinated protic species from the solvent. In this Article, a multilevel modeling approach was applied to unravel the effect of a confined methanol solvent on the active sites in UiO-66. First, active sites were explored with static periodic density functional theory calculations to investigate adsorption of water and methanol. Solvent was then introduced in the pores with grand canonical Monte Carlo simulations, followed by a series of molecular dynamics simulations at operating conditions. A hydrogen-bonded network of methanol molecules is formed, allowing the protons to shuttle between solvent methanol, adsorbed water, and the inorganic brick. Upon deprotonation of an active site, the methanol solvent aids the transfer of protons and stabilizes charged configurations via hydrogen bonding, which could be crucial in stabilizing reactive intermediates. The multilevel modeling approach adopted here sheds light on the important role of a confined solvent on the active sites in the UiO-66 material, introducing dynamic acidity in the system at finite temperatures by which protons may be easily shuttled from various positions at the active sites. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Electrode Reaction Pathway in Oxide Anode for Solid Oxide Fuel Cells

NASA Astrophysics Data System (ADS)

Li, Wenyuan

Oxide anodes for solid oxide fuel cells (SOFC) with the advantage of fuel flexibility, resistance to coarsening, small chemical expansion and etc. have been attracting increasing interest. Good performance has been reported with a few of perovskite structure anodes, such as (LaSr)(CrMn)O3. However, more improvements need to be made before meeting the application requirement. Understanding the oxidation mechanism is crucial for a directed optimization, but it is still on the early stage of investigation. In this study, reaction mechanism of oxide anodes is investigated on doped YCrO 3 with H2 fuel, in terms of the origin of electrochemical activity, rate-determining steps (RDS), extension of reactive zone, and the impact from overpotential under service condition to those properties. H2 oxidation on the YCs anodes is found to be limited by charge transfer and H surface diffusion. A model is presented to describe the elementary steps in H2 oxidation. From the reaction order results, it is suggested that any models without taking H into the charge transfer step are invalid. The nature of B site element determines the H2 oxidation kinetics primarily. Ni displays better adsorption ability than Co. However, H adsorption ability of such oxide anode is inferior to that of Ni metal anode. In addition, the charge transfer step is directly associated with the activity of electrons in the anode; therefore it can be significantly promoted by enhancement of the electron activity. It is found that A site Ca doping improves the polarization resistance about 10 times, by increasing the activity of electrons to promote the charge transfer process. For the active area in the oxide anode, besides the traditional three-phase boundary (3PB), the internal anode surface as two-phase boundary (2PB) is proven to be capable of catalytically oxidizing the H2 fuel also when the bulk lattice is activated depending on the B site elements. The contribution from each part is estimated by switching the electrolyte to change 3PB kinetics. Compared to Ni, Co doping activates the bulk oxygen more significantly, promoting the reaction at 2PB. The active surface reaction zone is found to be enlarged by the electrolyte with high oxygen activity (SSZ vs. YSZ) when charge transfer is one of the RDS. Due to the larger exchange current for charge transfer in 3PB with SSZ electrolyte, the adsorption gradient zone is broadened, leading to enhanced surface reaction kinetics. The potential application of such finding is demonstrated on SSZ/YSZ/SSZ sandwich, showing largely improved electrode performance, opening a wide door for the utilization of electrolytes that are too expensive, fragile or instable to be used before. The bulk path way in 2PB reaction can be affected by overpotential in terms of local vacancy concentration, built-in electrical field and stability. It is proven that an uneven distribution of lattice oxygen is established under operation conditions with overpotential by both qualitative analysis and analytic solution. An electrostatic field force is present besides the concentration gradient in the anode lattice to control the motion of oxygen ions. Compared to the usual estimation based on chemical diffusion mechanism, the real deviation of ionic defects concentration under polarization from the equilibrium state near electrode/electrolyte interface is smaller with the built-in electrical field. The overpotential is demonstrated to be able to open up or shut down the bulk pathway depending on the ionic defects of electrodes. The analysis on the bulk pathway in terms of local charged species and various potentials provides new insight in anion diffusion and electrode stability.

Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer.

PubMed

Donnini, Serena; Ullmann, R Thomas; Groenhof, Gerrit; Grubmüller, Helmut

2016-03-08

In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approach to maintain neutrality of the simulation box in constant pH molecular dynamics simulations, while maintaining an accurate description of all protonation fluctuations. Specifically, we introduce a proton buffer that, like a buffer in experiment, can exchange protons with the biomolecule enabling its charge to fluctuate. To keep the total charge of the system constant, the uptake and release of protons by the buffer are coupled to the titration of the biomolecule with a constraint. We find that, because the fluctuation of the total charge (number of protons) of a typical biomolecule is much smaller than the number of titratable sites of the biomolecule, the number of buffer sites required to maintain overall charge neutrality without compromising the charge fluctuations of the biomolecule, is typically much smaller than the number of titratable sites, implying markedly enhanced simulation and sampling efficiency.

Variation effect on the insecticide activity of DDT analogues. A chemometric approach

NASA Astrophysics Data System (ADS)

Itoh, S.; Nagashima, U.

2002-08-01

We investigated a variation effect on the insecticide activity of DDT analogues by using the first principles electronic structure calculations and the neural network analysis. It has been found that the charge distribution at the specific atomic sites in the DDT molecule is related to their toxicity. This approach can contribute to designing a new insecticide and a new harmlessness process of the DDT analogues.

Structural and Biochemical Studies of TIGAR (TP53-induced Glycolysis and Apoptosis Regulator)

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

Li, H.; Jogl, G

2009-01-01

Activation of the p53 tumor suppressor by cellular stress leads to variable responses ranging from growth inhibition to apoptosis. TIGAR is a novel p53-inducible gene that inhibits glycolysis by reducing cellular levels of fructose-2,6-bisphosphate, an activator of glycolysis and inhibitor of gluconeogenesis. Here we describe structural and biochemical studies of TIGAR from Danio rerio. The overall structure forms a histidine phosphatase fold with a phosphate molecule coordinated to the catalytic histidine residue and a second phosphate molecule in a position not observed in other phosphatases. The recombinant human and zebra fish enzymes hydrolyze fructose-2,6-bisphosphate as well as fructose-1,6-bisphosphate but notmore » fructose 6-phosphate in vitro. The TIGAR active site is open and positively charged, consistent with its enzymatic function as bisphosphatase. The closest related structures are the bacterial broad specificity phosphatase PhoE and the fructose-2,6-bisphosphatase domain of the bifunctional 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase. The structural comparison shows that TIGAR combines an accessible active site as observed in PhoE with a charged substrate-binding pocket as seen in the fructose-2,6-bisphosphatase domain of the bifunctional enzyme.« less

Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.

PubMed

Jacques, Benoit; Coinçon, Mathieu; Sygusch, Jurgen

2018-03-28

Crystal structures of two bacterial metal (Zn) dependent D-fructose 1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 Å resolution. The ligand complexes cryotrapped in native or mutant H. pylori aldolase crystals enabled a novel mechanistic description of FBP C 3 -C 4 bond cleavage. The reaction mechanism uses active site remodelling during the catalytic cycle implicating relocation of the Zn cofactor that is mediated by conformational changes of active site loops. Substrate binding initiates conformational changes, triggered upon P 1 -phosphate binding, which liberates the Zn chelating His180, allowing it to act as a general base for the proton abstraction at the FBP C 4 -hydroxyl group. A second zinc chelating His83 hydrogen bonds the substrate C 4 - hydroxyl group and assists cleavage by stabilizing the developing negative charge during proton abstraction. Cleavage is concerted with relocation of the metal cofactor from an interior to a surface exposed site, thereby stabilizing the nascent enediolate form. Conserved residue Glu142 is essential for protonation of the enediolate form, prior to product release. A D-tagatose 1,6-bisphosphate enzymatic complex reveals how His180 mediated proton abstraction controls stereospecificity of the cleavage reaction. Recognition and discrimination of the reaction products, dihydroxyacetone-P and D-glyceraldehyde-3-P, occurs via charged hydrogen bonds between hydroxyl groups of the triose-Ps and conserved residues, Asp82 and Asp255, respectively, and are crucial aspects of the enzyme's role in gluconeogenesis. Conformational changes in mobile loops β5-α7 and β6-α8 (containing catalytic residues Glu142 and His180, respectively) drive active site remodelling enabling the relocation of the metal cofactor. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Electric and hybrid vehicle program; Site Operator Program

NASA Astrophysics Data System (ADS)

Warren, J. F.

1992-05-01

Activities during the second quarter included the second meeting of the Site Operators in Phoenix, AZ in late April. The meeting was held in conjunction with the Solar and Electric 500 Race activities. Delivery of vehicles ordered previously has begun, although two of the operators are experiencing some delays in receiving their vehicles. Public demonstration activities continue, with an apparent increasing level of awareness and interest being displayed by the public. Initial problems with the Site Operator Database have been corrected and revised copies of the program have been supplied to the program participants. Operating and Maintenance data is being supplied and submitted to INEL on a monthly basis. Interest in the Site Operator Program is being reflected in requests for information from several organizations from across the country, representing a wide diversity of interests. These organizations have been referred to existing Site Operators with the explanation that the program will not be adding new participants, but that most of the existing organizations are willing to work with other groups. The exception to this was the addition of Potomac Electric Power Company (PEPCO) to the program. PEPCO has been awarded a subcontract to operate and maintain the DOE owned G-Van and Escort located in Washington, DC. They will provide data on these vehicles, as well as a Solectria Force which PEPCO has purchased. The Task Force intends to be actively involved in the infrastructure development in a wide range of areas. These include, among others, personnel development, safety, charging, and servicing. Work continues in these areas. York Technical College (YORK) has completed the draft outline for the EV Technician course. This is being circulated to organizations around the country for comments. Kansas State University (KSU) is working with a private sector company to develop a energy dispensing meter for opportunity charging in public areas.

E2 superfamily of ubiquitin-conjugating enzymes: constitutively active or activated through phosphorylation in the catalytic cleft.

PubMed

Valimberti, Ilaria; Tiberti, Matteo; Lambrughi, Matteo; Sarcevic, Boris; Papaleo, Elena

2015-10-14

Protein phosphorylation is a modification that offers a dynamic and reversible mechanism to regulate the majority of cellular processes. Numerous diseases are associated with aberrant regulation of phosphorylation-induced switches. Phosphorylation is emerging as a mechanism to modulate ubiquitination by regulating key enzymes in this pathway. The molecular mechanisms underpinning how phosphorylation regulates ubiquitinating enzymes, however, are elusive. Here, we show the high conservation of a functional site in E2 ubiquitin-conjugating enzymes. In catalytically active E2s, this site contains aspartate or a phosphorylatable serine and we refer to it as the conserved E2 serine/aspartate (CES/D) site. Molecular simulations of substrate-bound and -unbound forms of wild type, mutant and phosphorylated E2s, provide atomistic insight into the role of the CES/D residue for optimal E2 activity. Both the size and charge of the side group at the site play a central role in aligning the substrate lysine toward E2 catalytic cysteine to control ubiquitination efficiency. The CES/D site contributes to the fingerprint of the E2 superfamily. We propose that E2 enzymes can be divided into constitutively active or regulated families. E2s characterized by an aspartate at the CES/D site signify constitutively active E2s, whereas those containing a serine can be regulated by phosphorylation.

ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism.

PubMed

Parke, Courtney L; Wojcik, Edward J; Kim, Sunyoung; Worthylake, David K

2010-02-19

Motor proteins couple steps in ATP binding and hydrolysis to conformational switching both in and remote from the active site. In our kinesin.AMPPPNP crystal structure, closure of the active site results in structural transformations appropriate for microtubule binding and organizes an orthosteric two-water cluster. We conclude that a proton is shared between the lytic water, positioned for gamma-phosphate attack, and a second water that serves as a general base. To our knowledge, this is the first experimental detection of the catalytic base for any ATPase. Deprotonation of the second water by switch residues likely triggers subsequent large scale structural rearrangements. Therefore, the catalytic base is responsible for initiating nucleophilic attack of ATP and for relaying the positive charge over long distances to initiate mechanotransduction. Coordination of switch movements via sequential proton transfer along paired water clusters may be universal for nucleotide triphosphatases with conserved active sites, such as myosins and G-proteins.

Inhibition of m3 muscarinic acetylcholine receptors by local anaesthetics

PubMed Central

Hollmann, Markus W; Ritter, Carsten H; Henle, Philipp; de Klaver, Manuela; Kamatchi, Ganesan L; Durieux, Marcel E

2001-01-01

Muscarinic m1 receptors are inhibited by local anaesthetics (LA) at nM concentrations. To elucidate in more detail the site(s) of LA interaction, we compared these findings with LA effects on m3 muscarinic receptors. We expressed receptors in Xenopus oocytes. Using two-electrode voltage clamp, we measured the effects of lidocaine, QX314 (permanently charged) and benzocaine (permanently uncharged) on Ca2+-activated Cl−-currents (ICl(Ca)), elicited by acetyl-β-methylcholine bromide (MCh). We also characterized the interaction of lidocaine with [3H]-quinuclydinyl benzylate ([3H]-QNB) binding to m3 receptors. Antisense-injection was used to determine the role of specific G-protein α subunits in mediating the inhibitory effects of LA. Using chimeric receptor constructs we investigated which domains of the muscarinic receptors contribute to the binding site for LA. Lidocaine inhibited m3-signalling in a concentration-dependent, reversible, non-competitive manner with an IC50 of 370 nM, approximately 21 fold higher than the IC50 (18 nM) reported for m1 receptors. Intracellular inhibition of both signalling pathways by LA was similar, and dependent on the Gq- protein α subunit. In contrast to results reported for the m1 receptor, the m3 receptor lacks the major extracellular binding site for charged LA. The N-terminus and third extracellular loop of the m1 muscarinic receptor molecule were identified as requirements to obtain extracellular inhibition by charged LA. PMID:11325812

Active sites of ligand-protected Au{sub 25} nanoparticle catalysts for CO{sub 2} electroreduction to CO

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

Alfonso, Dominic R., E-mail: alfonso@netl.doe.gov; Kauffman, Douglas; Matranga, Christopher

2016-05-14

Recent experimental studies have reported the electrochemical reduction of carbon dioxide (CO{sub 2}) into CO at atomically precise negatively charged Au{sub 25}{sup −} nanoclusters. The studies showed CO{sub 2} conversion at remarkably low overpotentials, but the exact mechanisms and nature of the active sites remain unclear. We used first-principles density functional theory and continuum solvation models to examine the role of the cluster during electrochemical CO{sub 2} reduction and analyze the free energies of proposed intermediate species. Contrary to previous assumptions, our results show that the fully ligand protected cluster is not an active CO{sub 2} reduction catalyst because formationmore » of the crucial carboxyl intermediate required very high electrochemical potentials. Instead, our calculations suggest that the reduction process likely occurs on a dethiolated gold site, and adsorbed carboxyl intermediate formation was significantly stabilized at dethiolated gold sites. These findings point to the crucial role of exposed metal sites during electrochemical CO{sub 2} reduction at gold nanocluster catalysts.« less

High-Field Asymmetric-Waveform Ion Mobility Spectrometry and Electron Detachment Dissociation of Isobaric Mixtures of Glycosaminoglycans

NASA Astrophysics Data System (ADS)

Kailemia, Muchena J.; Park, Melvin; Kaplan, Desmond A.; Venot, Andre; Boons, Geert-Jan; Li, Lingyun; Linhardt, Robert J.; Amster, I. Jonathan

2014-02-01

High-field asymmetric waveform ion mobility spectrometry (FAIMS) is shown to be capable of resolving isomeric and isobaric glycosaminoglycan negative ions and to have great utility for the analysis of this class of molecules when combined with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and tandem mass spectrometry. Electron detachment dissociation (EDD) and other ion activation methods for tandem mass spectrometry can be used to determine the sites of labile sulfate modifications and for assigning the stereochemistry of hexuronic acid residues of glycosaminoglycans (GAGs). However, mixtures with overlapping mass-to-charge values present a challenge, as their precursor species cannot be resolved by a mass analyzer prior to ion activation. FAIMS is shown to resolve two types of mass-to-charge overlaps. A mixture of chondroitin sulfate A (CSA) oligomers with 4-10 saccharides units produces ions of a single mass-to-charge by electrospray ionization, as the charge state increases in direct proportion to the degree of polymerization for these sulfated carbohydrates. FAIMS is shown to resolve the overlapping charge. A more challenging type of mass-to-charge overlap occurs for mixtures of diastereomers. FAIMS is shown to separate two sets of epimeric GAG tetramers. For the epimer pairs, the complexity of the separation is reduced when the reducing end is alkylated, suggesting that anomers are also resolved by FAIMS. The resolved components were activated by EDD and the fragment ions were analyzed by FTICR-MS. The resulting tandem mass spectra were able to distinguish the two epimers from each other.

A theoretical model to determine the capacity performance of shape-specific electrodes

NASA Astrophysics Data System (ADS)

Yue, Yuan; Liang, Hong

2018-06-01

A theory is proposed to explain and predict the electrochemical process during reaction between lithium ions and electrode materials. In the model, the process of reaction is proceeded into two steps, surface adsorption and diffusion of lithium ions. The surface adsorption is an instantaneous process for lithium ions to adsorb onto the surface sites of active materials. The diffusion of lithium ions into particles is determined by the charge-discharge condition. A formula to determine the maximum specific capacity of active materials at different charging rates (C-rates) is derived. The maximum specific capacity is correlated to characteristic parameters of materials and cycling - such as size, aspect ratio, surface area, and C-rate. Analysis indicates that larger particle size or greater aspect ratio of active materials and faster C-rates can reduce maximum specific capacity. This suggests that reducing particle size of active materials and slowing the charge-discharge speed can provide enhanced electrochemical performance of a battery cell. Furthermore, the model is validated by published experimental results. This model brings new understanding in quantification of electrochemical kinetics and capacity performance. It enables development of design strategies for novel electrodes and future generation of energy storage devices.

Water molecules in the nucleotide binding cleft of actin: effects on subunit conformation and implications for ATP hydrolysis.

PubMed

Saunders, Marissa G; Voth, Gregory A

2011-10-14

In the monomeric actin crystal structure, the positions of a highly organized network of waters are clearly visible within the active site. However, the recently proposed models of filamentous actin (F-actin) did not extend to including these waters. Since the water network is important for ATP hydrolysis, information about water position is critical to understanding the increased rate of catalysis upon filament formation. Here, we show that waters in the active site are essential for intersubdomain rotational flexibility and that they organize the active-site structure. Including the crystal structure waters during simulation setup allows us to observe distinct changes in the active-site structure upon the flattening of the actin subunit, as proposed in the Oda model for F-actin. We identify changes in both protein position and water position relative to the phosphate tail that suggest a mechanism for accelerating the rate of nucleotide hydrolysis in F-actin by stabilizing charge on the β-phosphate and by facilitating deprotonation of catalytic water. Copyright © 2011 Elsevier Ltd. All rights reserved.

Tests and refinements of a general structure-activity model for avian repellents.

PubMed

Clark, L; Shah, P

1994-02-01

We tested the robustness of a structure-activity model for avian trigeminal chemoirritants. Fourteen benzoates and acetophenones were tested using European starlingsSturnus vulgaris as a bioassay. In general, the previously proposed model was a reasonable predictor of repellency (i.e., irritant potency). We found that the presence of a phenyl ring was critical to repellency. Basicity of the molecule is the next most critical feature influencing repellency. The presence of an acidic function within the electron-withdrawing functionality seriously detracts from repellency. The presence or absence of an electron-withdrawing or -donating group may potentiate repellent effects, but its presence is not critical, so long as the phenyl ring is electron rich. Our data suggest that there is ano-aminoacetophenone/methyl anthranilate trigeminal chemoreceptor in birds analogous to the mammalian capsaicin receptor. Both receptors contain a benzene site. However, birds seem to lack the associated thiol/hydrogen-bonding site present in mammals which is needed to activate the benzene site. Rather, birds may possess an associated exposed charged site that in turn may interact with the stimulus to activate the benzene site. These differences may explain the differential sensitivity of birds and mammals to aromatic irritants.

Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion

NASA Astrophysics Data System (ADS)

Singh, R.; Yadav, R. A.

2014-09-01

Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU-) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5sbnd C6 bond length increases and loses its double bond character while the C4sbnd C5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled Nsbnd H stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled.

Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion.

PubMed

Singh, R; Yadav, R A

2014-09-15

Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU-) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5C6 bond length increases and loses its double bond character while the C4C5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled NH stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled. Copyright © 2014 Elsevier B.V. All rights reserved.

On-line LC-MS approach combining collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced species for the trace-level characterization of proteins with post-translational modifications.

PubMed

Wu, Shiaw-Lin; Hühmer, Andreas F R; Hao, Zhiqi; Karger, Barry L

2007-11-01

We have expanded our recent on-line LC-MS platform for large peptide analysis to combine collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced (CRCID) species derived from ETD to determine sites of phosphorylation and glycosylation modifications, as well as the sequence of large peptide fragments (i.e., 2000-10,000 Da) from complex proteins, such as beta-casein, epidermal growth factor receptor (EGFR), and tissue plasminogen activator (t-PA) at the low femtomol level. The incorporation of an additional CID activation step for a charge-reduced species, isolated from ETD fragment ions, improved ETD fragmentation when precursor ions with high m/z (approximately >1000) were automatically selected for fragmentation. Specifically, the identification of the exact phosphorylation sites was strengthened by the extensive coverage of the peptide sequence with a near-continuous product ion series. The identification of N-linked glycosylation sites in EGFR and an O-linked glycosylation site in t-PA were also improved through the enhanced identification of the peptide backbone sequence of the glycosylated precursors. The new strategy is a good starting survey scan to characterize enzymatic peptide mixtures over a broad range of masses using LC-MS with data-dependent acquisition, as the three activation steps can provide complementary information to each other. In general, large peptides can be extensively characterized by the ETD and CRCID steps, including sites of modification from the generated, near-continuous product ion series, supplemented by the CID-MS2 step. At the same time, small peptides (e.g.,

Directed divergent evolution of a thermostable D-tagatose epimerase towards improved activity for two hexose substrates.

PubMed

Bosshart, Andreas; Hee, Chee Seng; Bechtold, Matthias; Schirmer, Tilman; Panke, Sven

2015-03-02

Functional promiscuity of enzymes can often be harnessed as the starting point for the directed evolution of novel biocatalysts. Here we describe the divergent morphing of an engineered thermostable variant (Var8) of a promiscuous D-tagatose epimerase (DTE) into two efficient catalysts for the C3 epimerization of D-fructose to D-psicose and of L-sorbose to L-tagatose. Iterative single-site randomization and screening of 48 residues in the first and second shells around the substrate-binding site of Var8 yielded the eight-site mutant IDF8 (ninefold improved kcat for the epimerization of D-fructose) and the six-site mutant ILS6 (14-fold improved epimerization of L-sorbose), compared to Var8. Structure analysis of IDF8 revealed a charged patch at the entrance of its active site; this presumably facilitates entry of the polar substrate. The improvement in catalytic activity of variant ILS6 is thought to relate to subtle changes in the hydration of the bound substrate. The structures can now be used to select additional sites for further directed evolution of the ketohexose epimerase. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase

PubMed Central

Patra, Niladri; Ioannidis, Efthymios I.

2016-01-01

Catechol O-methyltransferase (COMT) is a SAM- and Mg2+-dependent methyltransferase that regulates neurotransmitters through methylation. Simulations and experiments have identified divergent catecholamine substrate orientations in the COMT active site: molecular dynamics simulations have favored a monodentate coordination of catecholate substrates to the active site Mg2+, and crystal structures instead preserve bidentate coordination along with short (2.65 Å) methyl donor-acceptor distances. We carry out longer dynamics (up to 350 ns) to quantify interconversion between bidentate and monodentate binding poses. We provide a systematic determination of the relative free energy of the monodentate and bidentate structures in order to identify whether structural differences alter the nature of the methyl transfer mechanism and source of enzymatic rate enhancement. We demonstrate that the bidentate and monodentate binding modes are close in energy but separated by a 7 kcal/mol free energy barrier. Analysis of interactions in the two binding modes reveals that the driving force for monodentate catecholate orientations in classical molecular dynamics simulations is derived from stronger electrostatic stabilization afforded by alternate Mg2+ coordination with strongly charged active site carboxylates. Mixed semi-empirical-classical (SQM/MM) substrate C-O distances (2.7 Å) for the bidentate case are in excellent agreement with COMT X-ray crystal structures, as long as charge transfer between the substrates, Mg2+, and surrounding ligands is permitted. SQM/MM free energy barriers for methyl transfer from bidentate and monodentate catecholate configurations are comparable at around 21–22 kcal/mol, in good agreement with experiment (18–19 kcal/mol). Overall, the work suggests that both binding poses are viable for methyl transfer, and accurate descriptions of charge transfer and electrostatics are needed to provide balanced relative barriers when multiple binding poses are accessible, for example in other transferases. PMID:27564542

ptchg: A FORTRAN program for point-charge calculations of electric field gradients (EFGs)

NASA Astrophysics Data System (ADS)

Spearing, Dane R.

1994-05-01

ptchg, a FORTRAN program, has been developed to calculate electric field gradients (EFG) around an atomic site in crystalline solids using the point-charge direct-lattice summation method. It uses output from the crystal structure generation program Atoms as its input. As an application of ptchg, a point-charge calculation of the EFG quadrupolar parameters around the oxygen site in SiO 2 cristobalite is demonstrated. Although point-charge calculations of electric field gradients generally are limited to ionic compounds, the computed quadrupolar parameters around the oxygen site in SiO 2 cristobalite, a highly covalent material, are in good agreement with the experimentally determined values from nuclear magnetic resonance (NMR) spectroscopy.

R1 in the Shaker S4 occupies the gating charge transfer center in the resting state

PubMed Central

Lin, Meng-chin A.; Hsieh, Jui-Yi; Mock, Allan F.

2011-01-01

During voltage-dependent activation in Shaker channels, four arginine residues in the S4 segment (R1–R4) cross the transmembrane electric field. It has been proposed that R1–R4 movement is facilitated by a “gating charge transfer center” comprising a phenylalanine (F290) in S2 plus two acidic residues, one each in S2 and S3. According to this proposal, R1 occupies the charge transfer center in the resting state, defined as the conformation in which S4 is maximally retracted toward the cytoplasm. However, other evidence suggests that R1 is located extracellular to the charge transfer center, near I287 in S2, in the resting state. To investigate the resting position of R1, we mutated I287 to histidine (I287H), paired it with histidine mutations of key voltage sensor residues, and determined the effect of extracellular Zn2+ on channel activity. In I287H+R1H, Zn2+ generated a slow component of activation with a maximum amplitude (Aslow,max) of ∼56%, indicating that only a fraction of voltage sensors can bind Zn2+ at a holding potential of −80 mV. Aslow,max decreased after applying either depolarizing or hyperpolarizing prepulses from −80 mV. The decline of Aslow,max after negative prepulses indicates that R1 moves inward to abolish ion binding, going beyond the point where reorientation of the I287H and R1H side chains would reestablish a binding site. These data support the proposal that R1 occupies the charge transfer center upon hyperpolarization. Consistent with this, pairing I287H with A359H in the S3–S4 loop generated a Zn2+-binding site. At saturating concentrations, Aslow,max reached 100%, indicating that Zn2+ traps the I287H+A359H voltage sensor in an absorbing conformation. Transferring I287H+A359H into a mutant background that stabilizes the resting state significantly enhanced Zn2+ binding at −80 mV. Our results strongly support the conclusion that R1 occupies the gating charge transfer center in the resting conformation. PMID:21788609

DNA mimic proteins: functions, structures, and bioinformatic analysis.

PubMed

Wang, Hao-Ching; Ho, Chun-Han; Hsu, Kai-Cheng; Yang, Jinn-Moon; Wang, Andrew H-J

2014-05-13

DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.

Coarse-Grained Model for Water Involving a Virtual Site.

PubMed

Deng, Mingsen; Shen, Hujun

2016-02-04

In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones.

Spectroscopic investigation (FT-IR, FT-Raman), HOMO-LUMO, NBO, and molecular docking analysis of N-ethyl-N-nitrosourea, a potential anticancer agent

NASA Astrophysics Data System (ADS)

Singh, Priyanka; Islam, S. S.; Ahmad, Hilal; Prabaharan, A.

2018-02-01

Nitrosourea plays an important role in the treatment of cancer. N-ethyl-N-nitrosourea, also known as ENU, (chemical formula C3H7N3O2), is a highly potent mutagen. The chemical is an alkylating agent and acts by transferring the ethyl group of ENU to nucleobases (usually thymine) in nucleic acids. The molecular structure of N-ethyl-N-nitrosourea has been elucidated using experimental (FT-IR and FT-Raman) and theoretical (DFT) techniques. APT charges, Mulliken atomic charges, Natural bond orbital, Electrostatic potential, HOMO-LUMO and AIM analysis were performed to identify the reactive sites and charge transfer interactions. Furthermore, to evaluate the anticancer activity of ENU molecular docking studies were carried out against 2JIU protein.

The Polar and Electrical Nature of Dye Binding Sites on Human Red Blood Cell Membranes.

DTIC Science & Technology

positive charges at the binding sites. By increasing the concentration of the anionic BPB (or by the addition of the anionic detergent sodium lauryl ... sulfate ) these positive charges appear to be successively titrated, rendering the membrane binding sites electrically neutral at this pH. The average

Roles of s3 site residues of nattokinase on its activity and substrate specificity.

PubMed

Wu, Shuming; Feng, Chi; Zhong, Jin; Huan, Liandong

2007-09-01

Nattokinase (Subtilisin NAT, NK) is a bacterial serine protease with high fibrinolytic activity. To probe their roles on protease activity and substrate specificity, three residues of S3 site (Gly(100), Ser(101) and Leu(126)) were mutated by site-directed mutagenesis. Kinetics parameters of 20 mutants were measured using tetrapeptides as substrates, and their fibrinolytic activities were determined by fibrin plate method. Results of mutation analysis showed that Gly(100) and Ser(101) had reverse steric and electrostatic effects. Residues with bulky or positively charged side chains at position 100 decreased the substrate binding and catalytic activity drastically, while residues with the same characters at position 101 could obviously enhance protease and fibrinolytic activity of NK. Mutation of Leu(126) might impair the structure of the active cleft and drastically decreased the activity of NK. Kinetics studies of the mutants showed that S3 residues were crucial to keep protease activity while they moderately affected substrate specificity of NK. The present study provided some original insight into the P3-S3 interaction in NK and other subtilisins, as well as showed successful protein engineering cases to improve NK as a potential therapeutic agent.

Building better water models using the shape of the charge distribution of a water molecule

NASA Astrophysics Data System (ADS)

Dharmawardhana, Chamila Chathuranga; Ichiye, Toshiko

2017-11-01

The unique properties of liquid water apparently arise from more than just the tetrahedral bond angle between the nuclei of a water molecule since simple three-site models of water are poor at mimicking these properties in computer simulations. Four- and five-site models add partial charges on dummy sites and are better at modeling these properties, which suggests that the shape of charge distribution is important. Since a multipole expansion of the electrostatic potential describes a charge distribution in an orthogonal basis set that is exact in the limit of infinite order, multipoles may be an even better way to model the charge distribution. In particular, molecular multipoles up to the octupole centered on the oxygen appear to describe the electrostatic potential from electronic structure calculations better than four- and five-site models, and molecular multipole models give better agreement with the temperature and pressure dependence of many liquid state properties of water while retaining the computational efficiency of three-site models. Here, the influence of the shape of the molecular charge distribution on liquid state properties is examined by correlating multipoles of non-polarizable water models with their liquid state properties in computer simulations. This will aid in the development of accurate water models for classical simulations as well as in determining the accuracy needed in quantum mechanical/molecular mechanical studies and ab initio molecular dynamics simulations of water. More fundamentally, this will lead to a greater understanding of how the charge distribution of a water molecule leads to the unique properties of liquid water. In particular, these studies indicate that p-orbital charge out of the molecular plane is important.

Electron transport in ethanol & methanol absorbed defected graphene

NASA Astrophysics Data System (ADS)

Dandeliya, Sushmita; Srivastava, Anurag

2018-05-01

In the present paper, the sensitivity of ethanol and methanol molecules on surface of single vacancy defected graphene has been investigated using density functional theory (DFT). The changes in structural and electronic properties before and after adsorption of ethanol and methanol were analyzed and the obtained results show high adsorption energy and charge transfer. High adsorption happens at the active site with monovacancy defect on graphene surface. Present work confirms that the defected graphene increases the surface reactivity towards ethanol and methanol molecules. The presence of molecules near the active site affects the electronic and transport properties of defected graphene which makes it a promising choice for designing methanol and ethanol sensor.

Contributions of residues of pancreatic phospholipase A2 to interfacial binding, catalysis, and activation.

PubMed

Yu, B Z; Rogers, J; Tsai, M D; Pidgeon, C; Jain, M K

1999-04-13

Primary rate and equilibrium parameters for 60 site-directed mutants of bovine pancreatic phospholipase A2 (PLA2) are analyzed so incremental contributions of the substitution of specific residues can be evaluated. The magnitude of the change is evaluated so a functional role in the context of the N- and C-domains of PLA2 can be assigned, and their relationship to the catalytic residues and to the i-face that makes contact with the interface. The effect of substitutions and interfacial charge is characterized by the equilibrium dissociation constant for dissociation of the bound enzyme from the interface (Kd), the dissociation constant for dissociation of a substrate mimic from the active site of the bound enzyme (KL), and the interfacial Michaelis constants, KM and kcat. Activity is lost (>99.9%) on the substitution of H48 and D49, the catalytic residues. A more than 95% decrease in kcat is seen with the substitution of F5, I9, D99, A102, or F106, which form the substrate binding pocket. Certain residues, which are not part of the catalytic site or the substrate binding pocket, also modulate kcat. Interfacial anionic charge lowers Kd, and induces kcat activation through K56, K53, K119, or K120. Significant changes in KL are seen by the substitution of N6, I9, F22, Y52, K53, N71, Y73, A102, or A103. Changes in KM [=(k2+k-1)/k1] are attributed to kcat (=k2) and KL (=k-1/k1). Some substitutions change more than one parameter, implying an allosteric effect of the binding to the interface on KS, and the effect of the interfacial anionic charge on kcat. Interpreted in the context of the overall structure, results provide insights into the role of segments and domains in the microscopic events of catalytic turnover and processivity, and their allosteric regulation. We suggest that the interfacial recognition region (i-face) of PLA2, due to the plasticity of certain segments and domains, exercises an allosteric control on the substrate binding and chemical step.

The energy landscape of adenylate kinase during catalysis

PubMed Central

Kerns, S. Jordan; Agafonov, Roman V.; Cho, Young-Jin; Pontiggia, Francesco; Otten, Renee; Pachov, Dimitar V.; Kutter, Steffen; Phung, Lien A.; Murphy, Padraig N.; Thai, Vu; Alber, Tom; Hagan, Michael F.; Kern, Dorothee

2014-01-01

Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, MD simulations, and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events, phosphoryl transfer (>105-fold) and lid-opening (103-fold). In contrast, mutation of an essential active-site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid-opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a pre-organized active site. PMID:25580578

Theoretical characterization on the size-dependent electron and hole trapping activity of chloride-passivated CdSe nanoclusters

NASA Astrophysics Data System (ADS)

Cui, Yingqi; Cui, Xianhui; Zhang, Li; Xie, Yujuan; Yang, Mingli

2018-04-01

Ligand passivation is often used to suppress the surface trap states of semiconductor quantum dots (QDs) for their continuous photoluminescence output. The suppression process is related to the electrophilic/nucleophilic activity of surface atoms that varies with the structure and size of QD and the electron donating/accepting nature of ligand. Based on first-principles-based descriptors and cluster models, the electrophilic/nucleophilic activities of bare and chloride-coated CdSe clusters were studied to reveal the suppression mechanism of Cl-passivated QDs and compared to experimental observations. The surface atoms of bare clusters have higher activity than inner atoms and their activity decreases with cluster size. In the ligand-coated clusters, the Cd atom remains as the electrophilic site, while the nucleophilic site of Se atoms is replaced by Cl atoms. The activities of Cd and Cl atoms in the coated clusters are, however, remarkably weaker than those in bare clusters. Cluster size, dangling atoms, ligand coverage, electronegativity of ligand atoms, and solvent (water) were found to have considerable influence on the activity of surface atoms. The suppression of surface trap states in Cl-passivated QDs was attributed to the reduction of electrophilic/nucleophilic activity of Cd/Se/Cl atoms. Both saturation to under-coordinated surface atoms and proper selection for the electron donating/accepting strength of ligands are crucial for eliminating the charge carrier traps. Our calculations predicted a similar suppressing effect of chloride ligands with experiments and provided a simple but effective approach to assess the charge carrier trapping behaviors of semiconductor QDs.

Matriptase shedding is closely coupled with matriptase zymogen activation and requires de novo proteolytic cleavage likely involving its own activity

PubMed Central

Barndt, Robert; Gu, Yayun; Chen, Chien-Yu; Tseng, I-Chu; Su, Sheng-Fang; Wang, Jehng-Kang; Johnson, Michael D.

2017-01-01

The type 2 transmembrane serine protease matriptase is involved in many pathophysiological processes probably via its enzymatic activity, which depends on the dynamic relationship between zymogen activation and protease inhibition. Matriptase shedding can prolong the life of enzymatically active matriptase and increase accessibility to substrates. We show here that matriptase shedding occurs via a de novo proteolytic cleavage at sites located between the SEA domain and the CUB domain. Point or combined mutations at the four positively charged amino acid residues in the region following the SEA domain allowed Arg-186 to be identified as the primary cleavage site responsible for matriptase shedding. Kinetic studies further demonstrate that matriptase shedding is temporally coupled with matriptase zymogen activation. The onset of matriptase shedding lags one minute behind matriptase zymogen activation. Studies with active site triad Ser-805 point mutated matriptase, which no longer undergoes zymogen activation or shedding, further suggests that matriptase shedding depends on matriptase zymogen activation, and that matriptase proteolytic activity may be involved in its own shedding. Our studies uncover an autonomous mechanism coupling matriptase zymogen activation, proteolytic activity, and shedding such that a proportion of newly generated active matriptase escapes HAI-1-mediated rapid inhibition by shedding into the extracellular milieu. PMID:28829816

Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis

PubMed Central

Lee, Tai-Sung; Wong, Kin-Yiu; Giambasu, George M.; York, Darrin M.

2016-01-01

Herein we summarize our progress toward the understanding of hammerhead ribozyme (HHR) catalysis through a multiscale simulation strategy. Simulation results collectively paint a picture of HHR catalysis: HHR first folds to form an electronegative active site pocket to recruit a threshold occupation of cationic charges, either a Mg2+ ion or multiple monovalent cations. Catalytically active conformations that have good in-line fitness are supported by specific metal ion coordination patterns that involve either a bridging Mg2+ ion or multiple Na+ ions, one of which is also in a bridging coordination pattern. In the case of a single Mg2+ ion bound in the active site, the Mg2+ ion undergoes a migration that is coupled with deprotonation of the nucleophile (C17:O2′). As the reaction proceeds, the Mg2+ ion stabilizes the accumulating charge of the leaving group and significantly increases the general acid ability of G8:O2′. Further computational mutagenesis simulations suggest that the disruptions due to mutations may severely impact HHR catalysis at different stages of the reaction. Catalytic mechanisms supported by the simulation results are consistent with available structural and biochemical experiments, and together they advance our understanding of HHR catalysis. PMID:24156941

The Generation of Dehydroalanine Residues in Protonated Polypeptides: Ion/Ion Reactions for Introducing Selective Cleavages

NASA Astrophysics Data System (ADS)

Peng, Zhou; Bu, Jiexun; McLuckey, Scott A.

2017-09-01

We examine a gas-phase approach for converting a subset of amino acid residues in polypeptide cations to dehydroalanine (Dha). Subsequent activation of the modified polypeptide ions gives rise to specific cleavage N-terminal to the Dha residue. This process allows for the incorporation of selective cleavages in the structural characterization of polypeptide ions. An ion/ion reaction within the mass spectrometer between a multiply protonated polypeptide and the sulfate radical anion introduces a radical site into the multiply protonated polypeptide reactant. Subsequent collisional activation of the polypeptide radical cation gives rise to radical side chain loss from one of several particular amino acid side chains (e.g., leucine, asparagine, lysine, glutamine, and glutamic acid) to yield a Dha residue. The Dha residues facilitate preferential backbone cleavages to produce signature c- and z-ions, demonstrated with cations derived from melittin, mechano growth factor (MGF), and ubiquitin. The efficiencies for radical side chain loss and for subsequent generation of specific c- and z-ions have been examined as functions of precursor ion charge state and activation conditions using cations of ubiquitin as a model for a small protein. It is noted that these efficiencies are not strongly dependent on ion trap collisional activation conditions but are sensitive to precursor ion charge state. Moderate to low charge states show the greatest overall yields for the specific Dha cleavages, whereas small molecule losses (e.g., water/ammonia) dominate at the lowest charge states and proton catalyzed amide bond cleavages that give rise to b- and y-ions tend to dominate at high charge states. [Figure not available: see fulltext.

Cost consideration as a factor affecting recreation site decisions

Treesearch

Allan Marsinko; John Dwyer; Herb Schroeder

2001-01-01

Because they are charged with providing opportunities for all potential site users, it is important that managers at public sites understand the characteristics and behaviors of different user groups. Recreationists who are sensitive to cost may be more sensitive to certain changes in policies, such as fees and other charges, than those who are not sensitive to costs....

Surface potential-governed cellular osteogenic differentiation on ferroelectric polyvinylidene fluoride trifluoroethylene films.

PubMed

Tang, Bolin; Zhang, Bo; Zhuang, Junjun; Wang, Qi; Dong, Lingqing; Cheng, Kui; Weng, Wenjian

2018-07-01

Surface potential of biomaterials can dramatically influence cellular osteogenic differentiation. In this work, a wide range of surface potential on ferroelectric polyvinylidene fluoride trifluoroethylene (P(VDF-TrFE)) films was designed to get insight into the interfacial interaction of cell-charged surface. The P(VDF-TrFE) films poled by contact electric poling at various electric fields obtained well stabilized surface potential, with wide range from -3 to 915 mV. The osteogenic differentiation level of cells cultured on the films was strongly dependent on surface potential and reached the optimum at 391 mV in this system. Binding specificity assay indicated that surface potential could effectively govern the binding state of the adsorbed fibronectin (FN) with integrin. Molecular dynamic (MD) simulation further revealed that surface potential brought a significant difference in the relative distance between RGD and synergy PHSRN sites of adsorbed FN, resulting in a distinct integrin-FN binding state. These results suggest that the full binding of integrin α5β1 with both RGD and PHSRN sites of FN possesses a strong ability to activate osteogenic signaling pathway. This work sheds light on the underlying mechanism of osteogenic differentiation behavior on charged material surfaces, and also provides a guidance for designing a reasonable charged surface to enhance osteogenic differentiation. The ferroelectric P(VDF-TrFE) films with steady and a wide range of surface potential were designed to understand underlying mechanism of cell-charged surface interaction. The results showed that the charged surface well favored upregulation of osteogenic differentiation of MC3T3-E1 cells, and more importantly, a highest level occurred on the film with a moderate surface potential. Experiments and molecular dynamics simulation demonstrated that the surface potential could govern fibronectin conformation and then the integrin-fibronectin binding. We propose that a full binding state of integrin α5β1 with fibronectin induces effective activation of integrin-mediated FAK/ERK signaling pathway to upregulate cellular osteogenic differentiation. This work provides a guidance for designing a reasonable charged surface to enhance osteogenic differentiation. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Doping Li-rich cathode material Li2MnO3 : Interplay between lattice site preference, electronic structure, and delithiation mechanism

NASA Astrophysics Data System (ADS)

Hoang, Khang

2017-12-01

We report a detailed first-principles study of doping in Li2MnO3 , in both the dilute doping limit and heavy doping, using hybrid density-functional calculations. We find that Al, Fe, Mo, and Ru impurities are energetically most favorable when incorporated into Li2MnO3 at the Mn site, whereas Mg is most favorable when doped at the Li sites. Nickel, on the other hand, can be incorporated at the Li site and/or the Mn site, and the distribution of Ni over the lattice sites can be tuned by tuning the material preparation conditions. There is a strong interplay among the lattice site preference and charge and spin states of the dopant, the electronic structure of the doped material, and the delithiation mechanism. The calculated electronic structure and voltage profile indicate that in Ni-, Mo-, or Ru-doped Li2MnO3 , oxidation occurs on the electrochemically active transition-metal ion(s) before it does on oxygen during the delithiation process. The role of the dopants is to provide charge compensation and bulk electronic conduction mechanisms in the initial stages of delithiation, hence enabling the oxidation of the lattice oxygen in the later stages. This work thus illustrates how the oxygen-oxidation mechanism can be used in combination with the conventional mechanism involving transition-metal cations in design of high-capacity battery cathode materials.

Theoretical analysis of the electronic properties of the sex pheromone and its analogue derivatives in the female processionary moth Thaumetopoea pytiocampa.

PubMed

Chamorro, Ester R; Sequeira, Alfredo F; Zalazar, M Fernanda; Peruchena, Nélida M

2008-09-15

In the present work, the distribution of the electronic charge density of the natural sex pheromone, the (Z)-13-hexadecen-11-ynyl acetate, in the female processionary moth, Thaumetopoea pytiocampa, and its nine analogue derivatives was studied within the framework of the Density Functional Theory and the Atoms in Molecules (AIM) Theory at B3LYP/6-31G *//B3LYP/6-31++G * * level. Additionally, molecular electrostatic potential (MEP) maps of the previously mentioned compounds were computed and compared. Furthermore, the substitution of hydrogen atoms from the methyl group in the acetate group by electron withdrawing substituents (i.e., halogen atoms) as well as the replacement effect of hydrogen by electron donor substituents (+I effect) as methyl group, were explored. The key feature of the topological distribution of the charge density in analogue compounds, such as the variations of the topological properties encountered in the region formed by neighbouring atoms from the substitution site were presented and discussed. Using topological parameters, such as electronic charge density, Laplacian, kinetic energy density, and potential energy density evaluated at bond critical points (BCP), we provide here a detailed analysis of the nature of the chemical bonding of these molecules. In addition, the atomic properties (population, charge, energy, volume, and dipole moment) were determined on selected atoms. These properties were analyzed at the substitution site (with respect to the natural sex pheromone) and related to the biological activity and to the possible binding site with the pheromone binding protein, (PBP). Moreover, the Laplacian function of the electronic density was used to locate electrophilic regions susceptible to be attacked (by deficient electron atoms or donor hydrogen). Our results indicate that the change in the atomic properties, such as electronic population and atomic volume, are sensitive indicators of the loss of the biological activity in the analogues studied here. The crucial interaction between the acetate group of the natural sex pheromone and the PBP is most likely to be a hydrogen bonding and the substitution of hydrogen atoms by electronegative atoms in the pheromone molecule reduces the hydrogen acceptor capacity. This situation is mirrored by the diminish of the electronic population on carbon and oxygen atoms at the carbonylic group in the halo-acetate group. Additionally, the modified acetate group (with electronegative atoms) shows new charge concentration critical points or regions of concentration of charge density in which an electrophilic attack can also occur. Finally, the use of the topological analysis based in the charge density distribution and its Laplacian function, in conjunction with MEP maps provides valuable information about the steric volume and electronic requirement of the sex pheromone for binding to the PBP.

Electric field changes on Au nanoparticles on semiconductor supports--the molecular voltmeter and other methods to observe adsorbate-induced charge-transfer effects in Au/TiO2 nanocatalysts.

PubMed

McEntee, Monica; Stevanovic, Ana; Tang, Wenjie; Neurock, Matthew; Yates, John T

2015-02-11

Infrared (IR) studies of Au/TiO2 catalyst particles indicate that charge transfer from van der Waals-bound donor or acceptor molecules on TiO2 to or from Au occurs via transport of charge carriers in the semiconductor TiO2 support. The ΔνCO on Au is shown to be proportional to the polarizability of the TiO2 support fully covered with donor or acceptor molecules, producing a proportional frequency shift in νCO. Charge transfer through TiO2 is associated with the population of electron trap sites in the bandgap of TiO2 and can be independently followed by changes in photoluminescence intensity and by shifts in the broad IR absorbance region for electron trap sites, which is also proportional to the polarizability of donors by IR excitation. Density functional theory calculations show that electron transfer from the donor molecules to TiO2 and to supported Au particles produces a negative charge on the Au, whereas the transfer from the Au particles to the TiO2 support into acceptor molecules results in a positive charge on the Au. These changes along with the magnitudes of the shifts are consistent with the Stark effect. A number of experiments show that the ∼3 nm Au particles act as "molecular voltmeters" in influencing ΔνCO. Insulator particles, such as SiO2, do not display electron-transfer effects to Au particles on their surface. These studies are preliminary to doping studies of semiconductor-oxide particles by metal ions which modify Lewis acid/base oxide properties and possibly strongly modify the electron-transfer and catalytic activity of supported metal catalyst particles.

Surfactant protein B: lipid interactions of synthetic peptides representing the amino-terminal amphipathic domain.

PubMed Central

Bruni, R; Taeusch, H W; Waring, A J

1991-01-01

The mechanisms by which pulmonary surfactant protein B (SP-B) affects the surface activity of surfactant lipids are unclear. We have studied the peptide/lipid interactions of the amino-terminal amphipathic domain of SP-B by comparing the secondary conformations and surface activities of a family of synthetic peptides based on the native human SP-B sequence, modified by site-specific amino acid substitutions. Circular dichroism measurements show an alpha-helical structure correlating with the ability of the peptides to interact with lipids and with the surface activity of peptide/lipid dispersions. Amino acid substitutions altering either the charge or the hydrophobicity of the residues lowered the helical content and reduced the association of the aminoterminal segment with lipid dispersions. Surface activity of peptide/lipid mixtures was maximally altered by reversal of charge in synthetic peptides. These observations indicate that electrostatic interactions and hydrophobicity are important factors in determining optimal structure and function of surfactant peptides in lipid dispersions. Images PMID:1871144

Driving Protein Conformational Changes with Light: Photoinduced Structural Rearrangement in a Heterobimetallic Oxidase.

PubMed

Maugeri, Pearson T; Griese, Julia J; Branca, Rui M; Miller, Effie K; Smith, Zachary R; Eirich, Jürgen; Högbom, Martin; Shafaat, Hannah S

2018-01-31

The heterobimetallic R2lox protein binds both manganese and iron ions in a site-selective fashion and activates oxygen, ultimately performing C-H bond oxidation to generate a tyrosine-valine cross-link near the active site. In this work, we demonstrate that, following assembly, R2lox undergoes photoinduced changes to the active site geometry and metal coordination motif. Through spectroscopic, structural, and mass spectrometric characterization, the photoconverted species is found to consist of a tyrosinate-bound iron center following light-induced decarboxylation of a coordinating glutamate residue and cleavage of the tyrosine-valine cross-link. This process occurs with high quantum efficiencies (Φ = 3%) using violet and near-ultraviolet light, suggesting that the photodecarboxylation is initiated via ligand-to-metal charge transfer excitation. Site-directed mutagenesis and structural analysis suggest that the cross-linked tyrosine-162 is the coordinating residue. One primary product is observed following irradiation, indicating potential use of this class of proteins, which contains a putative substrate channel, for controlled photoinduced decarboxylation processes, with relevance for in vivo functionality of R2lox as well as application in environmental remediation.

Probes of the catalytic site of cysteine dioxygenase.

PubMed

Chai, Sergio C; Bruyere, John R; Maroney, Michael J

2006-06-09

The first major step of cysteine catabolism, the oxidation of cysteine to cysteine sulfinic acid, is catalyzed by cysteine dioxygenase (CDO). In the present work, we utilize recombinant rat liver CDO and cysteine derivatives to elucidate structural parameters involved in substrate recognition and x-ray absorption spectroscopy to probe the interaction of the active site iron center with cysteine. Kinetic studies using cysteine structural analogs show that most are inhibitors and that a terminal functional group bearing a negative charge (e.g. a carboxylate) is required for binding. The substrate-binding site has no stringent restrictions with respect to the size of the amino acid. Lack of the amino or carboxyl groups at the alpha-carbon does not prevent the molecules from interacting with the active site. In fact, cysteamine is shown to be a potent activator of the enzyme without being a substrate. CDO was also rendered inactive upon complexation with the metal-binding inhibitors azide and cyanide. Unlike many non-heme iron dioxygenases that employ alpha-keto acids as cofactors, CDO was shown to be the only dioxygenase known to be inhibited by alpha-ketoglutarate.

Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site.

PubMed Central

Liaw, S. H.; Kuo, I.; Eisenberg, D.

1995-01-01

Glutamine synthetase (GS) catalyzes the ATP-dependent condensation of ammonia and glutamate to yield glutamine, ADP, and inorganic phosphate in the presence of divalent cations. Bacterial GS is an enzyme of 12 identical subunits, arranged in two rings of 6, with the active site between each pair of subunits in a ring. In earlier work, we have reported the locations within the funnel-shaped active site of the substrates glutamate and ATP and of the two divalent cations, but the site for ammonia (or ammonium) has remained elusive. Here we report the discovery by X-ray crystallography of a binding site on GS for monovalent cations, Tl+ and Cs+, which is probably the binding site for the substrate ammonium ion. Fourier difference maps show the following. (1) Tl+ and Cs+ bind at essentially the same site, with ligands being Glu 212, Tyr 179, Asp 50', Ser 53' of the adjacent subunit, and the substrate glutamate. From its position adjacent to the substrate glutamate and the cofactor ADP, we propose that this monovalent cation site is the substrate ammonium ion binding site. This proposal is supported by enzyme kinetics. Our kinetic measurements show that Tl+, Cs+, and NH4+ are competitive inhibitors to NH2OH in the gamma-glutamyl transfer reaction. (2) GS is a trimetallic enzyme containing two divalent cation sites (n1, n2) and one monovalent cation site per subunit. These three closely spaced ions are all at the active site: the distance between n1 and n2 is 6 A, between n1 and Tl+ is 4 A, and between n2 and Tl+ is 7 A. Glu 212 and the substrate glutamate are bridging ligands for the n1 ion and Tl+. (3) The presence of a monovalent cation in this site may enhance the structural stability of GS, because of its effect of balancing the negative charges of the substrate glutamate and its ligands and because of strengthening the "side-to-side" intersubunit interaction through the cation-protein bonding. (4) The presence of the cofactor ADP increases the Tl+ binding to GS because ADP binding induces movement of Asp 50' toward this monovalent cation site, essentially forming the site. This observation supports a two-step mechanism with ordered substrate binding: ATP first binds to GS, then Glu binds and attacks ATP to form gamma-glutamyl phosphate and ADP, which complete the ammonium binding site. The third substrate, an ammonium ion, then binds to GS, and then loses a proton to form the more active species ammonia, which attacks the gamma-glutamyl phosphate to yield Gln. (5) Because the products (Glu or Gln) of the reactions catalyzed by GS are determined by the molecule (water or ammonium) attacking the intermediate gamma-glutamyl phosphate, this negatively charged ammonium binding pocket has been designed naturally for high affinity of ammonium to GS, permitting glutamine synthesis to proceed in aqueous solution. PMID:8563633

Tungsten-doped TiO2/reduced Graphene Oxide nano-composite photocatalyst for degradation of phenol: A system to reduce surface and bulk electron-hole recombination.

PubMed

Yadav, Manisha; Yadav, Asha; Fernandes, Rohan; Popat, Yaksh; Orlandi, Michele; Dashora, Alpa; Kothari, D C; Miotello, Antonio; Ahuja, B L; Patel, Nainesh

2017-12-01

Recombination of photogenerated charges is the main factor affecting the photocatalytic activity of TiO 2 . Here, we report a combined strategy of suppressing both the bulk as well as the surface recombination processes by doping TiO 2 with tungsten and forming a nanocomposite with reduced graphene oxide (rGO), respectively. Sol-gel method was used to dope and optimize the concentration of W in TiO 2 powder. UV-Vis, XPS, PL and time resolved PL spectra along with DFT calculations indicate that W 6+ in TiO 2 lattice creates an impurity level just below the conduction band of TiO 2 to act as a trapping site of electrons, which causes to improve the lifetime of the photo-generated charges. Maximum reduction in the PL intensity and the improvement in charge carrier lifetime was observed for TiO 2 doped with 1 at.% W (1W-TiO 2 ), which also displayed the highest photo-activity for the degradation of p-nitro phenol pollutant in water. Tuning of rGO/TiO 2 ratio (weight) disclosed that the highest activity can be achieved with the composite formed by taking equal amounts of TiO 2 and rGO (1:1), in which the strong interaction between TiO 2 and rGO causes an effective charge transfer via bonds formed near the interface as indicated by XPS. Both these optimized concentrations were utilized to form the composite rGO/1W-TiO 2 , which showed the highest activity in photo-degradation of p-nitro phenol (87%) as compared to rGO/TiO 2 (42%), 1W-TiO 2 (62%) and pure TiO 2 (29%) in 180 min. XPS and PL results revealed that in the present nanocomposite, tungsten species traps the excited electron to reduce the interband recombination in the bulk, while the interaction between TiO 2 and rGO creates a channel for fast transfer of excited electrons towards the latter before being recombined on the surface defect sites. Copyright © 2017 Elsevier Ltd. All rights reserved.

NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity.

PubMed

Caulkins, Bethany G; Young, Robert P; Kudla, Ryan A; Yang, Chen; Bittbauer, Thomas J; Bastin, Baback; Hilario, Eduardo; Fan, Li; Marsella, Michael J; Dunn, Michael F; Mueller, Leonard J

2016-11-23

Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography-the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry-to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate C α and positive charge at C4' of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites.

NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity

PubMed Central

2016-01-01

Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5′-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography—the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry—to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4′ of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites. PMID:27779384

Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania

NASA Astrophysics Data System (ADS)

Zuccotto, Fabio; Martin, Andrew C. R.; Laskowski, Roman A.; Thornton, Janet M.; Gilbert, Ian H.

1998-05-01

Dihydrofolate reductase has successfully been used as a drug target in the area of anti-cancer, anti-bacterial and anti-malarial chemotherapy. Little has been done to evaluate it as a drug target for treatment of the trypanosomiases and leishmaniasis. A crystal structure of Leishmania major dihydrofolate reductase has been published. In this paper, we describe the modelling of Trypanosoma cruzi and Trypanosoma brucei dihydrofolate reductases based on this crystal structure. These structures and models have been used in the comparison of protozoan, bacterial and human enzymes in order to highlight the different features that can be used in the design of selective anti-protozoan agents. Comparison has been made between residues present in the active site, the accessibility of these residues, charge distribution in the active site, and the shape and size of the active sites. Whilst there is a high degree of similarity between protozoan, human and bacterial dihydrofolate reductase active sites, there are differences that provide potential for selective drug design. In particular, we have identified a set of residues which may be important for selective drug design and identified a larger binding pocket in the protozoan than the human and bacterial enzymes.

The X-ray Crystal Structures of Human {alpha}-Phosphomannomutase 1 Reveal the Structural Basis of Congenital Disorder of Glycosylation Type 1a

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

Silvaggi,N.; Zhang, C.; Lu, Z.

2006-01-01

Carbohydrate-deficient glycoprotein syndrome type 1a (CDG-1a) is a congenital disease characterized by severe defects in nervous system development. It is caused by mutations in alpha -phosphomannomutase (of which there are two isozymes, {alpha}-PMM1 and {alpha}-PPM2). Here we report the X-ray crystal structures of human {alpha}-PMM1 in the open conformation, with and without the bound substrate, {alpha}-D-mannose 1-phosphate. {alpha}-PMM1, like most Haloalkanoic Acid Dehalogenase Superfamily (HADSF) members, consists of two domains, the cap and core, which open to bind substrate and then close to provide a solvent exclusive environment for catalysis. The substrate phosphate group is observed at a positively chargedmore » site of the cap domain, rather than at the core domain phosphoryl-transfer site defined by the D19 nucleophile and Mg{sup 2+} cofactor. This suggests that substrate binds first to the cap and then is swept into the active site upon cap closure. The orientation of the acid/base residue D21 suggests that {alpha}-PMM uses a different method of protecting the aspartylphosphate from hydrolysis than the HADSF member {beta}-phosphoglucomutase. It is hypothesized that the electrostatic repulsion of positive charges at the interface of the cap and core domains stabilizes {alpha}-PMM1 in the open conformation, and that the negatively charged substrate binds to the cap, thereby facilitating its closure over the core domain. The two isozymes {alpha}-PMM1 and {alpha}-PMM2 are shown to have a conserved active-site structure and to display similar kinetic properties. Analysis of the known mutation sites in the context of the structures reveals the genotype-phenotype relationship underlying CDG-1a.« less

Conformational changes in the M2 muscarinic receptor induced by membrane voltage and agonist binding

PubMed Central

Navarro-Polanco, Ricardo A; Galindo, Eloy G Moreno; Ferrer-Villada, Tania; Arias, Marcelo; Rigby, J Ryan; Sánchez-Chapula, José A; Tristani-Firouzi, Martin

2011-01-01

Abstract The ability to sense transmembrane voltage is a central feature of many membrane proteins, most notably voltage-gated ion channels. Gating current measurements provide valuable information on protein conformational changes induced by voltage. The recent observation that muscarinic G-protein-coupled receptors (GPCRs) generate gating currents confirms their intrinsic capacity to sense the membrane electrical field. Here, we studied the effect of voltage on agonist activation of M2 muscarinic receptors (M2R) in atrial myocytes and how agonist binding alters M2R gating currents. Membrane depolarization decreased the potency of acetylcholine (ACh), but increased the potency and efficacy of pilocarpine (Pilo), as measured by ACh-activated K+ current, IKACh. Voltage-induced conformational changes in M2R were modified in a ligand-selective manner: ACh reduced gating charge displacement while Pilo increased the amount of charge displaced. Thus, these ligands manifest opposite voltage-dependent IKACh modulation and exert opposite effects on M2R gating charge displacement. Finally, mutations in the putative ligand binding site perturbed the movement of the M2R voltage sensor. Our data suggest that changes in voltage induce conformational changes in the ligand binding site that alter the agonist–receptor interaction in a ligand-dependent manner. Voltage-dependent GPCR modulation has important implications for cellular signalling in excitable tissues. Gating current measurement allows for the tracking of subtle conformational changes in the receptor that accompany agonist binding and changes in membrane voltage. PMID:21282291

Enhanced charge carrier transport properties in colloidal quantum dot solar cells via organic and inorganic hybrid surface passivation† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6ta06835a Click here for additional data file.

PubMed Central

Hong, John; Hou, Bo; Lim, Jongchul; Pak, Sangyeon; Kim, Byung-Sung; Cho, Yuljae; Lee, Juwon; Lee, Young-Woo; Giraud, Paul; Lee, Sanghyo; Park, Jong Bae; Morris, Stephen M.; Snaith, Henry J.; Kim, Jong Min

2016-01-01

Colloidal quantum dots (CQDs) are extremely promising as photovoltaic materials. In particular, the tunability of their electronic band gap and cost effective synthetic procedures allow for the versatile fabrication of solar energy harvesting cells, resulting in optimal device performance. However, one of the main challenges in developing high performance quantum dot solar cells (QDSCs) is the improvement of the photo-generated charge transport and collection, which is mainly hindered by imperfect surface functionalization, such as the presence of surface electronic trap sites and the initial bulky surface ligands. Therefore, for these reasons, finding effective methods to efficiently decorate the surface of the as-prepared CQDs with new short molecular length chemical structures so as to enhance the performance of QDSCs is highly desirable. Here, we suggest employing hybrid halide ions along with the shortest heterocyclic molecule as a robust passivation structure to eliminate surface trap sites while decreasing the charge trapping dynamics and increasing the charge extraction efficiency in CQD active layers. This hybrid ligand treatment shows a better coordination with Pb atoms within the crystal, resulting in low trap sites and a near perfect removal of the pristine initial bulky ligands, thereby achieving better conductivity and film structure. Compared to halide ion-only treated cells, solar cells fabricated through this hybrid passivation method show an increase in the power conversion efficiency from 5.3% for the halide ion-treated cells to 6.8% for the hybrid-treated solar cells. PMID:29308200

Omega-oxidation impairs oxidizability of polyenoic fatty acids by 15-lipoxygenases: consequences for substrate orientation at the active site.

PubMed Central

Ivanov, I; Schwarz, K; Holzhütter, H G; Myagkova, G; Kühn, H

1998-01-01

During oxygenation by 15-lipoxygenases, polyenoic fatty acids are bound at the active site in such a way that the omega-terminus of the fatty acids penetrates into the substrate binding pocket. In contrast, for arachidonic acid 5-lipoxygenation, an inverse head to tail orientation has been suggested. However, an inverse orientation may be hindered by the large energy barrier associated with burying the charged carboxylate group in the hydrophobic environment of the substrate binding cleft. We studied the oxygenation kinetics of omega-modified fatty acids by 15-lipoxygenases and found that omega-hydroxylation strongly impaired substrate affinity (higher Km), but only moderately altered Vmax. In contrast, omega-carboxylation completely prevented the lipoxygenase reaction; however, methylation of the additional carboxylate group restored the activity. Arg403 of the human 15-lipoxygenase has been implicated in fatty acid binding by forming a salt bridge with the carboxylate group, and thus mutation of this amino acid to an uncharged residue was supposed to favour an inverse substrate orientation. The prepared Arg403-->Leu mutant of the rabbit 15-lipoxygenase was found to be a less effective catalyst of linoleic acid oxygenation. However, the oxygenation rate of omega-hydroxyarachidonic acid was similar when the wild-type and mutant enzyme were compared, and the patterns of oxygenation products were identical for both enzyme species. These data suggest that introduction of a polar, or even charged residue, at the omega-terminus of substrate fatty acids in connection with mutation of Arg403 may not alter substrate alignment at the active site of 15-lipoxygenases. PMID:9820810

Identification of a Novel EF-Loop in the N-terminus of TRPM2 Channel Involved in Calcium Sensitivity

PubMed Central

Luo, Yuhuan; Yu, Xiafei; Ma, Cheng; Luo, Jianhong; Yang, Wei

2018-01-01

As an oxidative stress sensor, transient receptor potential melastatin 2 (TRPM2) channel is involved in many physiological and pathological processes including warmth sensing, ischemia injury, inflammatory diseases and diabetes. Intracellular calcium is critical for TRPM2 channel activation and the IQ-like motif in the N-terminus has been shown to be important by mediating calmodulin binding. Sequence analysis predicted two potential EF-loops in the N-terminus of TRPM2. Site-directed mutagenesis combining with functional assay showed that substitution with alanine of several residues, most of which are conserved in the typical EF-loop, including D267, D278, D288, and E298 dramatically reduced TRPM2 channel currents. By further changing the charges or side chain length of these conserved residues, our results indicate that the negative charge of D267 and the side chain length of D278 are critical for calcium-induced TRPM2 channel activation. G272I mutation also dramatically reduced the channel currents, suggesting that this site is critical for calcium-induced TRPM2 channel activation. Furthermore, D267A mutant dramatically reduced the currents induced by calcium alone compared with that by ADPR, indicating that D267 residue in D267–D278 motif is the most important site for calcium sensitivity of TRPM2. In addition, inside-out recordings showed that mutations at D267, G272, D278, and E298 had no effect on single-channel conductance. Taken together, our data indicate that D267–D278 motif in the N-terminus as a novel EF-loop is critical for calcium-induced TRPM2 channel activation.

"Hot spots" growth on single nanowire controlled by electric charge.

PubMed

Xi, Shaobo; Liu, Xuehua; He, Ting; Tian, Lei; Wang, Wenhui; Sun, Rui; He, Weina; Zhang, Xuetong; Zhang, Jinping; Ni, Weihai; Zhou, Xiaochun

2016-06-09

"Hot spots" - a kind of highly active site, which are usually composed of some unique units, such as defects, interfaces, catalyst particles or special structures - can determine the performance of nanomaterials. In this paper, we study a model system, i.e. "hot spots" on a single Ag nanowire in the galvanic replacement reaction (GRR), by dark-field microscopy. The research reveals that electric charge can be released by the formation reaction of AgCl, and consequently the electrochemical potential on Ag nanowire drops. The electric charge could induce the reduction of Ag(+) to form the "hot spots" on the nanowire during the GRR. The appearance probability of "hot spots" is almost even along the Ag nanowire, while it is slightly lower near the two ends. The spatial distance between adjacent "hot spots" is also controlled by the charge, and obeys a model based on Boltzmann distribution. In addition, the distance distribution here has an advantage in electron transfer and energy saving. Therefore, it's necessary to consider the functions of electric charge during the synthesis or application of nanomaterials.

Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor

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

Brosey, Chris A.; Ho, Chris; Long, Winnie Z.

Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex (CTC) formation. In this paper, we define molecular pathways linking AIF's active site to allosteric switching regions by characterizing dimer-permissive mutants using small-angle X-ray scattering (SAXS) and crystallography and by probing AIF-CTC communication networks using molecular dynamics simulations. Collective results identify two pathways propagating allostery from the CTC active site: (1) active-site H454 links to S480 of AIF's central β-strand to modulate a hydrophobic border at the dimerization interface, and (2)more » an interaction network links AIF's FAD cofactor, central β-strand, and Cβ-clasp whereby R529 reorientation initiates C-loop release during CTC formation. Finally, this knowledge of AIF allostery and its flavoswitch mechanism provides a foundation for biologically understanding and biomedically controlling its participation in mitochondrial homeostasis and cell death.« less

Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor

DOE PAGES

Brosey, Chris A.; Ho, Chris; Long, Winnie Z.; ...

2016-11-03

Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex (CTC) formation. In this paper, we define molecular pathways linking AIF's active site to allosteric switching regions by characterizing dimer-permissive mutants using small-angle X-ray scattering (SAXS) and crystallography and by probing AIF-CTC communication networks using molecular dynamics simulations. Collective results identify two pathways propagating allostery from the CTC active site: (1) active-site H454 links to S480 of AIF's central β-strand to modulate a hydrophobic border at the dimerization interface, and (2)more » an interaction network links AIF's FAD cofactor, central β-strand, and Cβ-clasp whereby R529 reorientation initiates C-loop release during CTC formation. Finally, this knowledge of AIF allostery and its flavoswitch mechanism provides a foundation for biologically understanding and biomedically controlling its participation in mitochondrial homeostasis and cell death.« less

How to harvest solar energy with the photosynthetic reaction center

NASA Astrophysics Data System (ADS)

Balaeff, Alexander; Reyes, Justin

Photosynthetic reaction center (PRC) is a protein complex that performs a key step in photosynthesis: the electron-hole separation driven by photon absorbtion. The PRC has a great promise for applications in solar energy harvesting and photosensing. Such applications, however, are hampered by the difficulty in extracting the photogenerated electric charge from the PRC. To that end, it was proposed to attach the PRC to a molecular wire through which the charge could be collected. In order to find the attachment point for the wire that would maximize the rate of charge outflow from the PRC, we performed a computational study of the PRC from the R. virdis bacterium. An ensemble of PRC structures generated by a molecular dynamics simulation was used to calculate the rate of charge transport from the site of initial charge separation to several trial sites on the protein surface. The Pathways model was used to calculate the charge transfer rate in each step of the network of heme co-factors through which the charge transport was presumed to proceed. A simple kinetic model was then used to determine the overall rate of the multistep charge transport. The calculations revealed several candidate sites for the molecular wire attachment, recommended for experimental verification.

Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism

PubMed Central

Zhao, Haiyan; Lin, Zihan; Lynn, Anna Y.; Varnado, Brittany; Beutler, John A.; Murelli, Ryan P.; Le Grice, Stuart F. J.; Tang, Liang

2015-01-01

Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 Å. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg2+ from Ca2+. Using a metal ion chelator β-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution. PMID:26450964

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

Sanders, L.K.; Xian, W.; Guaqueta, C.

The aim for deterministic control of the interactions between macroions in aqueous media has motivated widespread experimental and theoretical work. Although it has been well established that like-charged macromolecules can aggregate under the influence of oppositely charged condensing agents, the specific conditions for the stability of such aggregates can only be determined empirically. We examine these conditions, which involve an interplay of electrostatic and osmotic effects, by using a well defined model system composed of F-actin, an anionic rod-like polyelectrolyte, and lysozyme, a cationic globular protein with a charge that can be genetically modified. The structure and stability of actin-lysozymemore » complexes for different lysozyme charge mutants and salt concentrations are examined by using synchrotron x-ray scattering and molecular dynamics simulations. We provide evidence that supports a structural transition from columnar arrangements of F-actin held together by arrays of lysozyme at the threefold interstitial sites of the actin sublattice to marginally stable complexes in which lysozyme resides at twofold bridging sites between actin. The reduced stability arises from strongly reduced partitioning of salt between the complex and the surrounding solution. Changes in the stability of actin-lysozyme complexes are of biomedical interest because their formation has been reported to contribute to the persistence of airway infections in cystic fibrosis by sequestering antimicrobials such as lysozyme. We present x-ray microscopy results that argue for the existence of actin-lysozyme complexes in cystic fibrosis sputum and demonstrate that, for a wide range of salt conditions, charge-reduced lysozyme is not sequestered in ordered complexes while retaining its bacterial killing activity.« less

Validation of ISS Floating Potential Measurement Unit Electron Densities and Temperatures

NASA Technical Reports Server (NTRS)

Coffey, Victoria N.; Minow, Joseph I.; Parker, Linda N.; Bui, Them; Wright, Kenneth, Jr.; Koontz, Steven L.; Schneider, T.; Vaughn, J.; Craven, P.

2007-01-01

Validation of the Floating Potential Measurement Unit (FPMU) electron density and temperature measurements is an important step in the process of evaluating International Space Station spacecraft charging issues .including vehicle arcing and hazards to crew during extravehicular activities. The highest potentials observed on Space Station are due to the combined VxB effects on a large spacecraft and the collection of ionospheric electron and ion currents by the 160 V US solar array modules. Ionospheric electron environments are needed for input to the ISS spacecraft charging models used to predict the severity and frequency of occurrence of ISS charging hazards. Validation of these charging models requires comparing their predictions with measured FPMU values. Of course, the FPMU measurements themselves must also be validated independently for use in manned flight safety work. This presentation compares electron density and temperatures derived from the FPMU Langmuir probes and Plasma Impedance Probe against the independent density and temperature measurements from ultraviolet imagers, ground based incoherent scatter radar, and ionosonde sites.

Charge Transfer in Multiple Site Chemical Systems.

DTIC Science & Technology

1985-05-30

oxidation either chemically (using excess Ce+(IV)) or electrochemically (using a reticulated vitreous carbon electrode potentiostated at +1.20 V vs.. SCE...The resulting polymers form fairly stable, electrochemically active films on the cxidizing electrode, which can be Pt, SnO2 or vitreous carbon ...surface, including platinum and glassy carbon electrodes. The redox couples incorporated include polypyrydyl omplexes of iron, ruthenium and osmium

Metal cation controls phosphate release in the myosin ATPase.

PubMed

Ge, Jinghua; Huang, Furong; Nesmelov, Yuri E

2017-11-01

Myosin is an enzyme that utilizes ATP to produce a conformational change generating a force. The kinetics of the myosin reverse recovery stroke depends on the metal cation complexed with ATP. The reverse recovery stroke is slow for MgATP and fast for MnATP. The metal ion coordinates the γ phosphate of ATP in the myosin active site. It is accepted that the reverse recovery stroke is correlated with the phosphate release; therefore, magnesium "holds" phosphate tighter than manganese. Magnesium and manganese are similar ions in terms of their chemical properties and the shell complexation; hence, we propose to use these ions to study the mechanism of the phosphate release. Analysis of octahedral complexes of magnesium and manganese show that the partial charge of magnesium is higher than that of manganese and the slightly larger size of manganese ion makes its ionic potential smaller. We hypothesize that electrostatics play a role in keeping and releasing the abstracted γ phosphate in the active site, and the stronger electric charge of magnesium ion holds γ phosphate tighter. We used stable myosin-nucleotide analog complex and Raman spectroscopy to examine the effect of the metal cation on the relative position of γ phosphate analog in the active site. We found that in the manganese complex, the γ phosphate analog is 0.01 nm further away from ADP than in the magnesium complex. We conclude that the ionic potential of the metal cation plays a role in the retention of the abstracted phosphate. © 2017 The Protein Society.

Electrochemical oxidation of nitrogen-heterocyclic compounds at boron-doped diamond electrode.

PubMed

Xing, Xuan; Zhu, Xiuping; Li, Hongna; Jiang, Yi; Ni, Jinren

2012-01-01

Nitrogen-heterocyclic compounds (NHCs) are toxic and bio-refractory contaminants widely spread in environment. This study investigated electrochemical degradation of NHCs at boron-doped diamond (BDD) anode with particular attention to the effect of different number and position of nitrogen atoms in molecular structure. Five classical NHCs with similar structures including indole (ID), quinoline (QL), isoquinoline (IQL), benzotriazole (BT) and benzimidazole (BM) were selected as the target compounds. Results of bulk electrolysis showed that degradation of all NHCs was fit to a pseudo first-order equation. The five compounds were degraded with the following sequence: ID>QL>IQL>BT>BM in terms of their rates of oxidation. Quantum chemical calculation was combined with experimental results to describe the degradation character of NHCs at BDD anode. A linear relationship between degradation rate and delocalization energy was observed, which demonstrated that electronic charge was redistributed through the conjugation system and accumulated at the active sites under the attack of hydroxyl radicals produced at BDD anode. Moreover, atom charge was calculated by semi empirical PM3 method and active sites of NHCs were identified respectively. Analysis of intermediates by GC-MS showed agreement with calculation results. Copyright © 2011 Elsevier Ltd. All rights reserved.

Charge neutralization in the active site of the catalytic trimer of aspartate transcarbamoylase promotes diverse structural changes.

PubMed

Endrizzi, James A; Beernink, Peter T

2017-11-01

A classical model for allosteric regulation of enzyme activity posits an equilibrium between inactive and active conformations. An alternative view is that allosteric activation is achieved by increasing the potential for conformational changes that are essential for catalysis. In the present study, substitution of a basic residue in the active site of the catalytic (C) trimer of aspartate transcarbamoylase with a non-polar residue results in large interdomain hinge changes in the three chains of the trimer. One conformation is more open than the chains in both the wild-type C trimer and the catalytic chains in the holoenzyme, the second is closed similar to the bisubstrate-analog bound conformation and the third hinge angle is intermediate to the other two. The active-site 240s loop conformation is very different between the most open and closed chains, and is disordered in the third chain, as in the holoenzyme. We hypothesize that binding of anionic substrates may promote similar structural changes. Further, the ability of the three catalytic chains in the trimer to access the open and closed active-site conformations simultaneously suggests a cyclic catalytic mechanism, in which at least one of the chains is in an open conformation suitable for substrate binding whereas another chain is closed for catalytic turnover. Based on the many conformations observed for the chains in the isolated catalytic trimer to date, we propose that allosteric activation of the holoenzyme occurs by release of quaternary constraint into an ensemble of active-site conformations. © 2017 The Protein Society.

Engineering Nucleotide Specificity of Succinyl-CoA Synthetase in Blastocystis: The Emerging Role of Gatekeeper Residues.

PubMed

Vashisht, Kapil; Verma, Sonia; Gupta, Sunita; Lynn, Andrew M; Dixit, Rajnikant; Mishra, Neelima; Valecha, Neena; Hamblin, Karleigh A; Maytum, Robin; Pandey, Kailash C; van der Giezen, Mark

2017-01-24

Charged, solvent-exposed residues at the entrance to the substrate binding site (gatekeeper residues) produce electrostatic dipole interactions with approaching substrates, and control their access by a novel mechanism called "electrostatic gatekeeper effect". This proof-of-concept study demonstrates that the nucleotide specificity can be engineered by altering the electrostatic properties of the gatekeeper residues outside the binding site. Using Blastocystis succinyl-CoA synthetase (SCS, EC 6.2.1.5), we demonstrated that the gatekeeper mutant (ED) resulted in ATP-specific SCS to show high GTP specificity. Moreover, nucleotide binding site mutant (LF) had no effect on GTP specificity and remained ATP-specific. However, via combination of the gatekeeper mutant with the nucleotide binding site mutant (ED+LF), a complete reversal of nucleotide specificity was obtained with GTP, but no detectable activity was obtained with ATP. This striking result of the combined mutant (ED+LF) was due to two changes; negatively charged gatekeeper residues (ED) favored GTP access, and nucleotide binding site residues (LF) altered ATP binding, which was consistent with the hypothesis of the "electrostatic gatekeeper effect". These results were further supported by molecular modeling and simulation studies. Hence, it is imperative to extend the strategy of the gatekeeper effect in a different range of crucial enzymes (synthetases, kinases, and transferases) to engineer substrate specificity for various industrial applications and substrate-based drug design.

Crystal structures of two tropinone reductases: Different reaction stereospecificities in the same protein fold

PubMed Central

Nakajima, Keiji; Yamashita, Atsuko; Akama, Hiroyuki; Nakatsu, Toru; Kato, Hiroaki; Hashimoto, Takashi; Oda, Jun’ichi; Yamada, Yasuyuki

1998-01-01

A pair of tropinone reductases (TRs) share 64% of the same amino acid residues and belong to the short-chain dehydrogenase/reductase family. In the synthesis of tropane alkaloids in several medicinal plants, the TRs reduce a carbonyl group of an alkaloid intermediate, tropinone, to hydroxy groups with different diastereomeric configurations. To clarify the structural basis for their different reaction stereospecificities, we determined the crystal structures of the two enzymes at 2.4- and 2.3-Å resolutions. The overall folding of the two enzymes was almost identical. The conservation was not confined within the core domains that are conserved within the protein family but extended outside the core domain where each family member has its characteristic structure. The binding sites for the cofactor and the positions of the active site residues were well conserved between the two TRs. The substrate binding site was composed mostly of hydrophobic amino acids in both TRs, but the presence of different charged residues conferred different electrostatic environments on the two enzymes. A modeling study indicated that these charged residues play a major role in controlling the binding orientation of tropinone within the substrate binding site, thereby determining the stereospecificity of the reaction product. The results obtained herein raise the possibility that in certain cases different stereospecificities can be acquired in enzymes by changing a few amino acid residues within substrate binding sites. PMID:9560196

Tunable Mobility in Double-Gated MoTe2 Field-Effect Transistor: Effect of Coulomb Screening and Trap Sites.

PubMed

Ji, Hyunjin; Joo, Min-Kyu; Yi, Hojoon; Choi, Homin; Gul, Hamza Zad; Ghimire, Mohan Kumar; Lim, Seong Chu

2017-08-30

There is a general consensus that the carrier mobility in a field-effect transistor (FET) made of semiconducting transition-metal dichalcogenides (s-TMDs) is severely degraded by the trapping/detrapping and Coulomb scattering of carriers by ionic charges in the gate oxides. Using a double-gated (DG) MoTe 2 FET, we modulated and enhanced the carrier mobility by adjusting the top- and bottom-gate biases. The relevant mechanism for mobility tuning in this device was explored using static DC and low-frequency (LF) noise characterizations. In the investigations, LF-noise analysis revealed that for a strong back-gate bias the Coulomb scattering of carriers by ionized traps in the gate dielectrics is strongly screened by accumulation charges. This significantly reduces the electrostatic scattering of channel carriers by the interface trap sites, resulting in increased mobility. The reduction of the number of effective trap sites also depends on the gate bias, implying that owing to the gate bias, the carriers are shifted inside the channel. Thus, the number of active trap sites decreases as the carriers are repelled from the interface by the gate bias. The gate-controlled Coulomb-scattering parameter and the trap-site density provide new handles for improving the carrier mobility in TMDs, in a fundamentally different way from dielectric screening observed in previous studies.

Recombination properties of dislocations in GaN

NASA Astrophysics Data System (ADS)

Yakimov, Eugene B.; Polyakov, Alexander Y.; Lee, In-Hwan; Pearton, Stephen J.

2018-04-01

The recombination activity of threading dislocations in n-GaN with different dislocation densities and different doping levels was studied using electron beam induced current (EBIC). The recombination velocity on a dislocation, also known as the dislocation recombination strength, was calculated. The results suggest that dislocations in n-GaN giving contrast in EBIC are charged and surrounded by a space charge region, as evidenced by the observed dependence of dislocation recombination strength on dopant concentration. For moderate (below ˜108 cm-2) dislocation densities, these defects do not primarily determine the average diffusion length of nonequilibrium charge carriers, although locally, dislocations are efficient recombination sites. In general, it is observed that the effect of the growth method [standard metalorganic chemical vapor deposition (MOCVD), epitaxial lateral overgrowth versions of MOCVD, and hydride vapor phase epitaxy] on the recombination activity of dislocations is not very pronounced, although the average diffusion lengths can widely differ for various samples. The glide of basal plane dislocations at room temperature promoted by low energy electron irradiation does not significantly change the recombination properties of dislocations.

Columnar mesophases of hexabenzocoronene derivatives. II. Charge carrier mobility

NASA Astrophysics Data System (ADS)

Kirkpatrick, James; Marcon, Valentina; Kremer, Kurt; Nelson, Jenny; Andrienko, Denis

2008-09-01

Combining atomistic molecular dynamic simulations, Marcus-Hush theory description of charge transport rates, and master equation description of charge dynamics, we correlate the temperature-driven change of the mesophase structure with the change of charge carrier mobilities in columnar phases of hexabenzocoronene derivatives. The time dependence of fluctuations in transfer integrals shows that static disorder is predominant in determining charge transport characteristics. Both site energies and transfer integrals are distributed because of disorder in the molecular arrangement. It is shown that the contributions to the site energies from polarization and electrostatic effects are of opposite sign for positive charges. We look at three mesophases of hexabenzocoronene: herringbone, discotic, and columnar disordered. All results are compared to time resolved microwave conductivity data and show excellent agreement with no fitting parameters.

Columnar mesophases of hexabenzocoronene derivatives. II. Charge carrier mobility.

PubMed

Kirkpatrick, James; Marcon, Valentina; Kremer, Kurt; Nelson, Jenny; Andrienko, Denis

2008-09-07

Combining atomistic molecular dynamic simulations, Marcus-Hush theory description of charge transport rates, and master equation description of charge dynamics, we correlate the temperature-driven change of the mesophase structure with the change of charge carrier mobilities in columnar phases of hexabenzocoronene derivatives. The time dependence of fluctuations in transfer integrals shows that static disorder is predominant in determining charge transport characteristics. Both site energies and transfer integrals are distributed because of disorder in the molecular arrangement. It is shown that the contributions to the site energies from polarization and electrostatic effects are of opposite sign for positive charges. We look at three mesophases of hexabenzocoronene: herringbone, discotic, and columnar disordered. All results are compared to time resolved microwave conductivity data and show excellent agreement with no fitting parameters.

Evaluation of newly synthesized and commercially available charged cyclomaltooligosaccharides (cyclodextrins) for capillary electrokinetic chromatography.

PubMed

Culha, Mustafa; Schell, Fred M; Fox, Shannon; Green, Thomas; Betts, Thomas; Sepaniak, Michael J

2004-01-22

A highly new charged cyclodextrin (CD) derivatives, (6-O-carboxymethyl-2,3-di-O-methyl)cyclomaltoheptaoses (CDM-beta-CDs), was synthesized and characterized as anionic reagents for capillary electrophoresis (CE) in an electrokinetic chromatography mode of separation. Substitution with dimethyl groups at the secondary hydroxyl sites of the CD is aimed at influencing the magnitude and selectivity of analyte-CD interactions, while substitution by carboxymethyl groups at the primary hydroxyl sites provides for high charge and electrophoretic mobility. Full regioselective methylation at the secondary hydroxyl sites was achieved in this work, while substitution at the primary hydroxyl sites generated a mixture of multiply charged products. The separation performance of CDM-beta-CD was evaluated using a variety of analyte mixtures. The results obtained from commercially available negatively charged cyclodextrins, heptakis(2,3-di-O-methyl-6-O-sulfo)cyclomaltoheptaose (HDMS-beta-CD) and O-(carboxymethyl)cyclomaltoheptaose (CM-beta-CD) with an average degree of substitution one (DS 1), were compared to CDM-beta-CD using a sample composed of eight positional isomers of dihydroxynaphthalene. Four hydroxylated polychlorobiphenyl derivatives, a group of chiral and isomeric catchecins, and chiral binaphthyl compounds were also separated with CDM-beta-CD. The effect of adding neutral beta-cyclodextrin (beta-CD) into the running buffer containing charged cyclodextrins was investigated and provided evidence of significant inter-CD interactions. Under certain running buffer conditions, the charged cyclodextrins also appear to adsorb to the capillary walls to various degrees.

Heterogeneous Single-Atom Catalyst for Visible-Light-Driven High-Turnover CO2 Reduction: The Role of Electron Transfer.

PubMed

Gao, Chao; Chen, Shuangming; Wang, Ying; Wang, Jiawen; Zheng, Xusheng; Zhu, Junfa; Song, Li; Zhang, Wenkai; Xiong, Yujie

2018-03-01

Visible-light-driven conversion of CO 2 into chemical fuels is an intriguing approach to address the energy and environmental challenges. In principle, light harvesting and catalytic reactions can be both optimized by combining the merits of homogeneous and heterogeneous photocatalysts; however, the efficiency of charge transfer between light absorbers and catalytic sites is often too low to limit the overall photocatalytic performance. In this communication, it is reported that the single-atom Co sites coordinated on the partially oxidized graphene nanosheets can serve as a highly active and durable heterogeneous catalyst for CO 2 conversion, wherein the graphene bridges homogeneous light absorbers with single-atom catalytic sites for the efficient transfer of photoexcited electrons. As a result, the turnover number for CO production reaches a high value of 678 with an unprecedented turnover frequency of 3.77 min -1 , superior to those obtained with the state-of-the-art heterogeneous photocatalysts. This work provides fresh insights into the design of catalytic sites toward photocatalytic CO 2 conversion from the angle of single-atom catalysis and highlights the role of charge kinetics in bridging the gap between heterogeneous and homogeneous photocatalysts. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluating the Substrate Selectivity of Alkyladenine DNA Glycosylase: The Synergistic Interplay of Active Site Flexibility and Water Reorganization.

PubMed

Lenz, Stefan A P; Wetmore, Stacey D

2016-02-09

Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair (BER) pathway by cleaving the N-glycosidic bond that connects nucleobases to the sugar-phosphate backbone in DNA. AAG targets a range of structurally diverse purine lesions using nonspecific DNA-protein π-π interactions. Nevertheless, the enzyme discriminates against the natural purines and is inhibited by pyrimidine lesions. This study uses molecular dynamics simulations and seven different neutral or charged substrates, inhibitors, or canonical purines to probe how the bound nucleotide affects the conformation of the AAG active site, and the role of active site residues in dictating substrate selectivity. The neutral substrates form a common DNA-protein hydrogen bond, which results in a consistent active site conformation that maximizes π-π interactions between the aromatic residues and the nucleobase required for catalysis. Nevertheless, subtle differences in DNA-enzyme contacts for different neutral substrates explain observed differential catalytic efficiencies. In contrast, the exocyclic amino groups of the natural purines clash with active site residues, which leads to catalytically incompetent DNA-enzyme complexes due to significant reorganization of active site water. Specifically, water resides between the A nucleobase and the active site aromatic amino acids required for catalysis, while a shift in the position of the general base (E125) repositions (potentially nucleophilic) water away from G. Despite sharing common amino groups, the methyl substituents in cationic purine lesions (3MeA and 7MeG) exhibit repulsion with active site residues, which repositions the damaged bases in the active site in a manner that promotes their excision. Overall, we provide a structural explanation for the diverse yet discriminatory substrate selectivity of AAG and rationalize key kinetic data available for the enzyme. Specifically, our results highlight the complex interplay of many different DNA-protein interactions used by AAG to facilitate BER, as well as the crucial role of the general base and water (nucleophile) positioning. The insights gained from our work will aid the understanding of the function of other enzymes that use flexible active sites to exhibit diverse substrate specificity.

Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

PubMed Central

Sigala, Paul A.; Kraut, Daniel A.; Caaveiro, Jose M. M.; Pybus, Brandon; Ruben, Eliza A.; Ringe, Dagmar; Petsko, Gregory A.; Herschlag, Daniel

2009-01-01

Enzymes are classically proposed to accelerate reactions by binding substrates within active site environments that are structurally preorganized to optimize binding interactions with reaction transition states rather than ground states. This is a remarkably formidable task considering the limited 0.1 – 1 Å scale of most substrate rearrangements. The flexibility of active site functional groups along the coordinate of substrate rearrangement, the distance scale on which enzymes can distinguish structural rearrangement, and the energetic significance of discrimination on that scale remain open questions that are fundamental to a basic physical understanding of enzyme active sites and catalysis. We bring together high resolution X-ray crystallography, 1H and 19F NMR spectroscopy, quantum mechanical calculations, and transition state analog binding measurements to test the distance scale on which non-covalent forces can constrain side chain and ligand relaxation or translation along a specific coordinate and the energetic consequences of such geometric constraints within the active site of bacterial ketosteroid isomerase (KSI). Our results strongly suggest that packing and binding interactions within the KSI active site can constrain local side chain reorientation and prevent hydrogen bond shortening by 0.1 Å or less. Further, this constraint has substantial energetic effects on ligand binding and stabilization of negative charge within the oxyanion hole. These results provide evidence that subtle geometric effects, indistinguishable in most X-ray crystallographic structures, can have significant energetic consequences and highlight the importance of using synergistic experimental approaches to dissect enzyme function. PMID:18808119

Active-site monovalent cations revealed in a 1.55-Å-resolution hammerhead ribozyme structure.

PubMed

Anderson, Michael; Schultz, Eric P; Martick, Monika; Scott, William G

2013-10-23

We have obtained a 1.55-Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni under conditions that permit detailed observations of Na(+) ion binding in the ribozyme's active site. At least two such Na(+) ions are observed. The first Na(+) ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical with that previously observed for divalent cations. A second Na(+) ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with that of previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na(+), but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na(+) directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active-site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest-resolution ribozyme structure in the Protein Data Bank. Copyright © 2013 Elsevier Ltd. All rights reserved.

Model for screened, charge-regulated electrostatics of an eye lens protein: Bovine gammaB-crystallin

PubMed Central

Wahle, Christopher W.; Martini, K. Michael; Hollenbeck, Dawn M.; Langner, Andreas; Ross, David S.; Hamilton, John F.; Thurston, George M.

2018-01-01

We model screened, site-specific charge regulation of the eye lens protein bovine gammaB-crystallin (γ B) and study the probability distributions of its proton occupancy patterns. Using a simplified dielectric model, we solve the linearized Poisson-Boltzmann equation to calculate a 54 × 54 work-of-charging matrix, each entry being the modeled voltage at a given titratable site, due to an elementary charge at another site. The matrix quantifies interactions within patches of sites, including γB charge pairs. We model intrinsic pK values that would occur hypothetically in the absence of other charges, with use of experimental data on the dependence of pK values on aqueous solution conditions, the dielectric model, and literature values. We use Monte Carlo simulations to calculate a model grand-canonical partition function that incorporates both the work-of-charging and the intrinsic pK values for isolated γB molecules and we calculate the probabilities of leading proton occupancy configurations, for 4 < pH < 8 and Debye screening lengths from 6 to 20 Å. We select the interior dielectric value to model γB titration data. At pH 7.1 and Debye length 6.0 Å, on a given γB molecule the predicted top occupancy pattern is present nearly 20% of the time, and 90% of the time one or another of the first 100 patterns will be present. Many of these occupancy patterns differ in net charge sign as well as in surface voltage profile. We illustrate how charge pattern probabilities deviate from the multinomial distribution that would result from use of effective pK values alone and estimate the extents to which γB charge pattern distributions broaden at lower pH and narrow as ionic strength is lowered. These results suggest that for accurate modeling of orientation-dependent γB-γB interactions, consideration of numerous pairs of proton occupancy patterns will be needed. PMID:29346981

Model for screened, charge-regulated electrostatics of an eye lens protein: Bovine gammaB-crystallin.

PubMed

Wahle, Christopher W; Martini, K Michael; Hollenbeck, Dawn M; Langner, Andreas; Ross, David S; Hamilton, John F; Thurston, George M

2017-09-01

We model screened, site-specific charge regulation of the eye lens protein bovine gammaB-crystallin (γB) and study the probability distributions of its proton occupancy patterns. Using a simplified dielectric model, we solve the linearized Poisson-Boltzmann equation to calculate a 54×54 work-of-charging matrix, each entry being the modeled voltage at a given titratable site, due to an elementary charge at another site. The matrix quantifies interactions within patches of sites, including γB charge pairs. We model intrinsic pK values that would occur hypothetically in the absence of other charges, with use of experimental data on the dependence of pK values on aqueous solution conditions, the dielectric model, and literature values. We use Monte Carlo simulations to calculate a model grand-canonical partition function that incorporates both the work-of-charging and the intrinsic pK values for isolated γB molecules and we calculate the probabilities of leading proton occupancy configurations, for 4

Model for screened, charge-regulated electrostatics of an eye lens protein: Bovine gammaB-crystallin

NASA Astrophysics Data System (ADS)

Wahle, Christopher W.; Martini, K. Michael; Hollenbeck, Dawn M.; Langner, Andreas; Ross, David S.; Hamilton, John F.; Thurston, George M.

2017-09-01

We model screened, site-specific charge regulation of the eye lens protein bovine gammaB-crystallin (γ B ) and study the probability distributions of its proton occupancy patterns. Using a simplified dielectric model, we solve the linearized Poisson-Boltzmann equation to calculate a 54 ×54 work-of-charging matrix, each entry being the modeled voltage at a given titratable site, due to an elementary charge at another site. The matrix quantifies interactions within patches of sites, including γ B charge pairs. We model intrinsic p K values that would occur hypothetically in the absence of other charges, with use of experimental data on the dependence of p K values on aqueous solution conditions, the dielectric model, and literature values. We use Monte Carlo simulations to calculate a model grand-canonical partition function that incorporates both the work-of-charging and the intrinsic p K values for isolated γ B molecules and we calculate the probabilities of leading proton occupancy configurations, for 4

Relative transmembrane segment rearrangements during BK channel activation resolved by structurally assigned fluorophore–quencher pairing

PubMed Central

Pantazis, Antonios

2012-01-01

Voltage-activated proteins can sense, and respond to, changes in the electric field pervading the cell membrane by virtue of a transmembrane helix bundle, the voltage-sensing domain (VSD). Canonical VSDs consist of four transmembrane helices (S1–S4) of which S4 is considered a principal component because it possesses charged residues immersed in the electric field. Membrane depolarization compels the charges, and by extension S4, to rearrange with respect to the field. The VSD of large-conductance voltage- and Ca-activated K+ (BK) channels exhibits two salient inconsistencies from the canonical VSD model: (1) the BK channel VSD possesses an additional nonconserved transmembrane helix (S0); and (2) it exhibits a “decentralized” distribution of voltage-sensing charges, in helices S2 and S3, in addition to S4. Considering these unique features, the voltage-dependent rearrangements of the BK VSD could differ significantly from the standard model of VSD operation. To understand the mode of operation of this unique VSD, we have optically tracked the relative motions of the BK VSD transmembrane helices during activation, by manipulating the quenching environment of site-directed fluorescent labels with native and introduced Trp residues. Having previously reported that S0 and S4 diverge during activation, in this work we demonstrate that S4 also diverges from S1 and S2, whereas S2, compelled by its voltage-sensing charged residues, moves closer to S1. This information contributes spatial constraints for understanding the BK channel voltage-sensing process, revealing the structural rearrangements in a non-canonical VSD. PMID:22802360

Anaerobic Dehalogenation of Chloroanilines by Dehalococcoides mccartyi Strain CBDB1 and Dehalobacter Strain 14DCB1 via Different Pathways as Related to Molecular Electronic Structure.

PubMed

Zhang, Shangwei; Wondrousch, Dominik; Cooper, Myriel; Zinder, Stephen H; Schüürmann, Gerrit; Adrian, Lorenz

2017-04-04

Dehalococcoides mccartyi strain CBDB1 and Dehalobacter strain 14DCB1 are organohalide-respiring microbes of the phyla Chloroflexi and Firmicutes, respectively. Here, we report the transformation of chloroanilines by these two bacterial strains via dissimilar dehalogenation pathways and discuss the underlying mechanism with quantum chemically calculated net atomic charges of the substrate Cl, H, and C atoms. Strain CBDB1 preferentially removed Cl doubly flanked by two Cl or by one Cl and NH 2 , whereas strain 14DCB1 preferentially dechlorinated Cl that has an ortho H. For the CBDB1-mediated dechlorination, comparative analysis with Hirshfeld charges shows that the least-negative Cl discriminates active from nonactive substrates in 14 out of 15 cases and may represent the preferred site of primary attack through cob(I)alamin. For the latter trend, three of seven active substrates provide strong evidence, with partial support from three of the remaining four substrates. Regarding strain 14DCB1, the most positive carbon-attached H atom discriminates active from nonactive chloroanilines in again 14 out of 15 cases. Here, regioselectivity is governed for 10 of the 11 active substrates by the most positive H attached to the highest-charge (most positive or least negative) aromatic C carrying the Cl to be removed. These findings suggest the aromatic ring H as primary site of attack through the supernucleophile Co(I), converting an initial H bond to a full electron transfer as start of the reductive dehalogenation. For both mechanisms, one- and two-electron transfer to Cl (strain CBDB1) or H (strain 14DCB1) are compatible with the presently available data. Computational chemistry research into reaction intermediates and pathways may further aid in understanding the bacterial reductive dehalogenation at the molecular level.

Effect of the size-selective silver clusters on lithium peroxide morphology in lithium–oxygen batteries

DOE PAGES

Lu, Jun; Cheng, Lei; Lau, Kah Chun; ...

2014-09-12

Lithium–oxygen batteries have the potential needed for long-range electric vehicles, but the charge and discharge chemistries are complex and not well understood. The active sites on cathode surfaces and their role in electrochemical reactions in aprotic lithium–oxygen cells are difficult to ascertain because the exact nature of the sites is unknown. In this paper, we report the deposition of subnanometre silver clusters of exact size and number of atoms on passivated carbon to study the discharge process in lithium–oxygen cells. The results reveal dramatically different morphologies of the electrochemically grown lithium peroxide dependent on the size of the clusters. Thismore » dependence is found to be due to the influence of the cluster size on the formation mechanism, which also affects the charge process. Finally, the results of this study suggest that precise control of subnanometre surface structure on cathodes can be used as a means to improve the performance of lithium–oxygen cells.« less

Cooperative communication within and between single nanocatalysts

NASA Astrophysics Data System (ADS)

Zou, Ningmu; Zhou, Xiaochun; Chen, Guanqun; Andoy, Nesha May; Jung, Won; Liu, Guokun; Chen, Peng

2018-06-01

Enzymes often show catalytic allostery in which reactions occurring at different sites communicate cooperatively over distances of up to a few nanometres. Whether such effects can occur with non-biological nanocatalysts remains unclear, even though these nanocatalysts can undergo restructuring and molecules can diffuse over catalyst surfaces. Here we report that phenomenologically similar, but mechanistically distinct, cooperative effects indeed exist for nanocatalysts. Using spatiotemporally resolved single-molecule catalysis imaging, we find that catalytic reactions on a single Pd or Au nanocatalyst can communicate with each other, probably via hopping of positively charged holes on the catalyst surface, over 102 nanometres and with a temporal memory of 101 to 102 seconds, giving rise to positive cooperativity among its surface active sites. Similar communication is also observed between individual nanocatalysts, however it operates via a molecular diffusion mechanism involving negatively charged product molecules, and its communication distance is many micrometres. Generalization of these long-range intra- and interparticle catalytic communication mechanisms may introduce a novel conceptual framework for understanding nanoscale catalysis.

[Molecular Dynamics of N- and C-terminal Interactions during Autoinhibition and Activation of Formin mDial].

PubMed

Orshanskiy, I A; Popinako, A V; Volokh, O I; Shaitan, K V; Sokolova, O S

2015-01-01

With the method of molecular dynamics, pairs of amino acid residues have been identified on the surface of the interacting formin mDial domains: DID-DAD, which are responsible for the autoinhibition of formin, and the GTPase Rho-DID domain, and control activation. It was found that the most stable interactions are ionic interactions between Glu178 residue and Arg248 residue, as well as hydrophobic interactions between Thr175 and Phe247. The strongest interactions proved to be between the DID domain with Rho-GTPase. These interactions are mediated by specific triple ionic interactions between positively charged amino acid in Rho, and a triplet of amino acids in DID, consisting of two negatively charged amino acids, separated by one uncharged. Binding sites for Rho-GTPase and DAD partially overlap, but various amino acids on the DID participate in interactions with different domains. We discuss the possible conformational changes in formin domains during activation and inactivation.

Interaction of the BKCa channel gating ring with dendrotoxins

PubMed Central

Takacs, Zoltan; Imredy, John P; Bingham, Jon-Paul; Zhorov, Boris S; Moczydlowski, Edward G

2014-01-01

Two classes of small homologous basic proteins, mamba snake dendrotoxins (DTX) and bovine pancreatic trypsin inhibitor (BPTI), block the large conductance Ca2+-activated K+ channel (BKCa, KCa1.1) by production of discrete subconductance events when added to the intracellular side of the membrane. This toxin-channel interaction is unlikely to be pharmacologically relevant to the action of mamba venom, but as a fortuitous ligand-protein interaction, it has certain biophysical implications for the mechanism of BKCa channel gating. In this work we examined the subconductance behavior of 9 natural dendrotoxin homologs and 6 charge neutralization mutants of δ-dendrotoxin in the context of current structural information on the intracellular gating ring domain of the BKCa channel. Calculation of an electrostatic surface map of the BKCa gating ring based on the Poisson-Boltzmann equation reveals a predominantly electronegative surface due to an abundance of solvent-accessible side chains of negatively charged amino acids. Available structure-activity information suggests that cationic DTX/BPTI molecules bind by electrostatic attraction to site(s) on the gating ring located in or near the cytoplasmic side portals where the inactivation ball peptide of the β2 subunit enters to block the channel. Such an interaction may decrease the apparent unitary conductance by altering the dynamic balance of open versus closed states of BKCa channel activation gating. PMID:25483585

Formation, Migration, and Reactivity of Au CO Complexes on Gold Surfaces

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

Wang, Jun; McEntee, Monica; Tang, Wenjie

2016-01-12

Here, we report experimental as well as theoretical evidence that suggests Au CO complex formation upon the exposure of CO to active sites (step edges and threading dislocations) on a Au(111) surface. Room-temperature scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy, transmission infrared spectroscopy, and density functional theory calculations point to Au CO complex formation and migration. Room-temperature STM of the Au(111) surface at CO pressures in the range from 10^ 8 to 10^ 4 Torr (dosage up to 10^6 langmuir) indicates Au atom extraction from dislocation sites of the herringbone reconstruction, mobile Au CO complex formation and diffusion, and Aumore » adatom cluster formation on both elbows and step edges on the Au surface. The formation and mobility of the Au CO complex result from the reduced Au Au bonding at elbows and step edges leading to stronger Au CO bonding and to the formation of a more positively charged CO (CO +) on Au. These studies indicate that the mobile Au CO complex is involved in the Au nanoparticle formation and reactivity, and that the positive charge on CO increases due to the stronger adsorption of CO at Au sites with lower coordination numbers.« less

Pyrovanadolysis: a Pyrophosphorolysis-like Reaction Mediated by Pyrovanadate MN2plus and DNA Polymerase of Bacteriophage T7

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

B Akabayov; A Kulczyk; S Akabayov

2011-12-31

DNA polymerases catalyze the 3'-5'-pyrophosphorolysis of a DNA primer annealed to a DNA template in the presence of pyrophosphate (PP{sub i}). In this reversal of the polymerization reaction, deoxynucleotides in DNA are converted to deoxynucleoside 5'-triphosphates. Based on the charge, size, and geometry of the oxygen connecting the two phosphorus atoms of PP{sub i}, a variety of compounds was examined for their ability to carry out a reaction similar to pyrophosphorolysis. We describe a manganese-mediated pyrophosphorolysis-like activity using pyrovanadate (VV) catalyzed by the DNA polymerase of bacteriophage T7. We designate this reaction pyrovanadolysis. X-ray absorption spectroscopy reveals a shorter Mn-Vmore » distance of the polymerase-VV complex than the Mn-P distance of the polymerase-PP{sub i} complex. This structural arrangement at the active site accounts for the enzymatic activation by Mn-VV. We propose that the Mn{sup 2+}, larger than Mg{sup 2+}, fits the polymerase active site to mediate binding of VV into the active site of the polymerase. Our results may be the first documentation that vanadium can substitute for phosphorus in biological processes.« less

Adsorption of transgenic insecticidal Cry1Ab protein to silica particles. Effects on transport and bioactivity.

PubMed

Madliger, Michael; Gasser, Christoph A; Schwarzenbach, René P; Sander, Michael

2011-05-15

Bt crops are genetically modified to be resistant against insect pests by expressing insecticidal Cry proteins. The processes governing the fate and bioavailability of the expressed transgenic Cry proteins in soils are poorly understood. We studied adsorption of Cry1Ab to negatively charged silica (SiO(2)) particles, a major soil constituent and a model for negatively charged mineral surfaces, at pH 5 to 10 and ionic strengths I = 10 mM to 250 mM, both in solution depletion and saturated column transport experiments. Cry1Ab-SiO(2) interactions were dominated by patch-controlled electrostatic attraction (PCEA), as evident from increasing Cry1Ab attraction to SiO(2) with decreasing I at pH at which both Cry1Ab and SiO(2) were net negatively charged. Experimental and modeling evidence is provided that the surface heterogeneity of SiO(2) particles modulated PCEA, leading to a fraction of adsorption sites with slow Cry1Ab desorption kinetics. Desorption rates from these sites increased upon increasing the solution pH. In toxicity bioassays, we demonstrated that Cry1Ab retained insecticidal activity when adsorbed to SiO(2), suggesting high protein conformational stability during adsorption-desorption cycles. Models predicting Cry1A protein adsorption in soils therefore need to account for combined effects of the nonuniform protein surface charge distribution and of sorbent surface heterogeneity.

Improvement of calcium mineral separation contrast using anionic reagents: electrokinetics properties and flotation

NASA Astrophysics Data System (ADS)

Lafhaj, Z.; Filippov, L. O.; Filippova, I. V.

2017-07-01

The flotation separation of salt type calcium minerals is problematic, due to the similarities in their same active Ca2+ related site for interaction with anionic collectors and similar physicochemical characteristics such as solubility, zero-point charge, surface speciation and Ca-site density. The work was performed to achieve effective and selective separation of the calcium-minerals using pure minerals samples: orange calcite with Mg impurities, optic calcite with impurities level and an apatite. The pure samples surface was examined using techniques sensitive near-surface like infrared spectroscopy (FTIR) and chemical composition was obtained by ICPMS. The isoelectric point (IEP) and point of zero charge (PZC) in electrolyte were recorded using electrophoresis method at different ionic strengths of the solution. Mechanisms of charge development at the mineral-water interface are discussed. The time of contact as important parameter for the charge equilibrium was deduced from kinetics study and fixed to 30 minutes. The difference in the values obtained between IEP and PZSE can be explained by the presence of a specific adsorption of cations and anions on the surface. The effect of pure anionic collectors such as oleic and linoleic acid were studied. At low pH, both collectors lead to a good recovery for the calcites. The flotation recovery of optic calcite at pH 9 with sodium oleate is higher than with sodium linoleate. At alkaline pH, apatite showed a better recovery with sodium linoleate.

DNA-binding and oxidative properties of cationic phthalocyanines and their dimeric complexes with anionic phthalocyanines covalently linked to oligonucleotides.

PubMed

Kuznetsova, A A; Lukyanets, E A; Solovyeva, L I; Knorre, D G; Fedorova, O S

2008-12-01

Design of chemically modified oligonucleotides for regulation of gene expression has attracted considerable attention over the past decades. One actively pursued approach involves antisense or antigene oligonucleotide constructs carrying reactive groups, many of these based on transition metal complexes. The complexes of Fe(II) and Co(II) with phthalocyanines are extremely good catalysts of oxidation of organic compounds with molecular oxygen and hydrogen peroxide. The binding of positively charged Fe(II) and Co(II) phthalocyanines with single- and double-stranded DNA was investigated. It was shown that these phthalocyanines interact with nucleic acids through an outside binding mode. The site-directed modification of single-stranded DNA by O2 and H2O2 in the presence of dimeric complexes of negatively and positively charged Fe(II) and Co(II) phthalocyanines was investigated. These complexes were formed directly on single-stranded DNA through interaction between negatively charged phthalocyanine in conjugate and positively charged phthalocyanine in solution. The resulting oppositely charged phthalocyanine complexes showed significant increase of catalytic activity compared with monomeric forms of phthalocyanines Fe(II) and Co(II). These complexes catalyzed the DNA oxidation with high efficacy and led to direct DNA strand cleavage. It was determined that oxidation of DNA by molecular oxygen catalyzed by complex of Fe(II)-phthalocyanines proceeds with higher rate than in the case of Co(II)-phthalocyanines but the latter led to a greater extent of target DNA modification.

Two-dimensional porous architecture of protonated GCN and reduced graphene oxide via electrostatic self-assembly strategy for high photocatalytic hydrogen evolution under visible light

NASA Astrophysics Data System (ADS)

Pu, Chenchen; Wan, Jun; Liu, Enzhou; Yin, Yunchao; Li, Juan; Ma, Yongning; Fan, Jun; Hu, Xiaoyun

2017-03-01

Herein, porous protonated graphitic carbon nitride (pGCN) is prepared from bulk g-C3N4 (GCN) directly by acidic cutting and hydrothermal process. The holey structure not only provides a lot of bounds on the accelerated and photo induced charge transfer and thus reduce the aggregation, but also endows the GCN with more exposure to the active site. The pGCN is obtained with an increased band gap of 2.91 eV together with a higher specific surface area of 82.76 m2g-1. Meanwhile, the positively charged GCN resulted from the protonation pretreatment is beneficial for improving the interaction with negatively charged GO sheets. Compared with GCN, pGCN-rGO displays a significant decrease of PL intensities and an apparently enhancement of visible-light absorption, resulting a lower charge recombination rate and a better light absorption. Besides, the enhanced charge separation is demonstrated by photoluminescence emission spectroscopy and the transient photocurrent measurement. The photocatalytic performance studies for the degradation of MB indicate that pGCN-rGO exhibits the highest adsorption ability towards dye molecules. In addition, the pGCN-5 wt% rGO composite shows the optimal photocatalytic activity, the photodegradation rate of MB is 99.4% after 80 min of irradiation and the H2 evolution performance up to 557 μmol g-1h-1 under visible light, which is much higher than the other control samples.

The energy landscape of adenylate kinase during catalysis

DOE PAGES

Kerns, S. Jordan; Agafonov, Roman V.; Cho, Young-Jin; ...

2015-01-12

Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. In this paper, we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg 2+ cofactor activates two distinct molecular events: phosphoryl transfer (>10 5-fold) and lid opening (10 3-fold). In contrast, mutation of an essential active site arginine decelerates phosphorylmore » transfer 10 3-fold without substantially affecting lid opening. Finally, our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.« less

Location of alkali metal binding sites in endothelin A selective receptor antagonists, cyclo(D-Trp-D-Asp-Pro-D-Val-Leu) and cyclo(D-Trp-D-Asp-Pro-D-Ile-Leu), from multistep collisionally activated decompositions.

PubMed

Ngoka, L C; Gross, M L

2000-02-01

We previously showed by using mass spectrometry that endothelin A selective receptor antagonists BQ123 and JKC301 form novel coordination compounds with sodium ions. This property may underlie the ability of an ET(A) antagonist to induce net tubular sodium reabsorption in the proximal tubule cells and reverse acute renal failure induced by severe ischemia. We have now defined the metal binding sites on BQ123 and JKC301 by subjecting the metal-containing peptides to multiple stages of collisionally activated decomposition (CAD) in an ion trap mass spectrometer. When submitted to low-energy CAD, the ring opens at the Asp-Pro amide bond. The metal ion, which bonds, inter alia, to the carbonyl oxygen of the proline residue, acts as a fixed charge site, and directs a charge-remote, sequence-specific fragmentation of the ring-opened peptide. Amino acid residues are sequentially cleaved from the C-terminal end, and the terminal aziridinone structure moves one step toward the N-terminus with each C-terminal amino acid residue removed. These observations are the basis of a new method to sequence cyclic peptides. Amino acid residues are observed as sets of three ions, a*(n)PD, b*(n)PD and c*(n)PD where n is the number of amino acid residues in the peptide. Copyright 2000 John Wiley & Sons, Ltd.

Comparison of designed and randomly generated catalysts for simple chemical reactions.

PubMed

Kipnis, Yakov; Baker, David

2012-09-01

There has been recent success in designing enzymes for simple chemical reactions using a two-step protocol. In the first step, a geometric matching algorithm is used to identify naturally occurring protein scaffolds at which predefined idealized active sites can be realized. In the second step, the residues surrounding the transition state model are optimized to increase transition state binding affinity and to bolster the primary catalytic side chains. To improve the design methodology, we investigated how the set of solutions identified by the design calculations relate to the overall set of solutions for two different chemical reactions. Using a TIM barrel scaffold in which catalytically active Kemp eliminase and retroaldolase designs were obtained previously, we carried out activity screens of random libraries made to be compositionally similar to active designs. A small number of active catalysts were found in screens of 10³ variants for each of the two reactions, which differ from the computational designs in that they reuse charged residues already present in the native scaffold. The results suggest that computational design considerably increases the frequency of catalyst generation for active sites involving newly introduced catalytic residues, highlighting the importance of interaction cooperativity in enzyme active sites. Copyright © 2012 The Protein Society.

Activation of CO2 by supported Cu clusters.

PubMed

Iyemperumal, Satish Kumar; Deskins, N Aaron

2017-11-01

Catalytic reduction of carbon dioxide to useful chemicals is a potent way to mitigate this greenhouse gas, but the challenge lies in finding active reduction catalysts. Using density functional theory we studied CO 2 activation over TiO 2 -supported Cu clusters of size 1-4 atoms. The linear to bent transformation of CO 2 is necessary for activation, and we found that all the clusters stabilized bent CO 2 , along with a significant gain of electrons on the CO 2 (indicative of activation). On all the TiO 2 supported Cu clusters, the interfacial sites were found to stabilize the bent CO 2 adsorption, where the active site of adsorption on Cu dimer, trimer and tetramer was on the Cu atom farthest away from the TiO 2 surface. Particularly, the Cu dimer stabilized bent CO 2 very strongly, although this species was found to be unstable on the surface. A synthesis technique that could stabilize the Cu dimer could therefore lead to a very active catalyst. Furthermore we found (using vibrational and charge analysis) that the active sites for the CO 2 activation predominantly had 0 and +1 oxidation states; the oxidation state of Cu is known to directly affect CO 2 reduction activity. Our study shows TiO 2 -supported small Cu clusters can be active catalysts for CO 2 reduction and also provides further motivation for theoretical and experimental studies of metal clusters.

Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis.

PubMed

Liu, Shijia; Shao, Shangjin; Li, Linlin; Cheng, Zhi; Tian, Li; Gao, Peiji; Wang, Lushan

2015-12-11

Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Remedial action suitability for the Cornhusker Army Ammunition Plant site

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

Nonavinakere, S.; Rappa, P. III

1995-12-31

Numerous Department of Defense (DOD) sites across the nation are contaminated with explosive wastes due to munitions production during World War II, Korean Conflict and Vietnam Conflict. Production activities included explosives manufacturing, loading, packing, assembling, machining, casting and curing. Contaminants often present at these sites include TNT, RDX, HMX, Tetryl 2,4-DNT, 2,6-DNT, 1,3-DNB, 1,3,5-TNB and nitrobenzene. The Cornhusker Army Ammunition Plant (CAAP) is one such DOD site that has been determined to be contaminated with explosives. The CAAP is located approximately 2 miles west of the City of Grand Island in Hall County, Nebraska. The plant produced artillery, bombs, boosters,more » supplementary charges and various other experimental explosives. The purpose of this paper is to provide an overview of the site background, review of the remedial alternatives evaluation process and rationale behind the selection of present remedial action.« less

Effect of replacing the aspartic acid/glutamic acid residues of bullfrog sialic acid binding lectin with asparagine/glutamine and arginine on the inhibition of cell proliferation in murine leukemia P388 cells.

PubMed

Ogawa, Yuko; Iwama, Masanori; Ohgi, Kazuko; Tsuji, Tsutomu; Irie, Masachika; Itagaki, Tadashi; Kobayashi, Hiroko; Inokuchi, Norio

2002-06-01

The sialic acid binding lectin from bullfrog oocytes (cSBL) is known to have anti-tumor activity. In a previous report, to elucidate the relationship between the net charge and anti-tumor activity of cSBL, we examined the effect of chemical modifications of cSBL with a water-soluble carbodiimide in the presence of various nucleophiles. The results suggested that the anti-tumor activity and internalization into tumor cells increased with an increase in the net charge of cSBL. However, in the chemically modified cSBL, a modification site was observed on average in two of the carboxyl groups of cSBL. To confirm these previous results and to determine which modified carboxyl group contributes to the increase in anti-tumor activity, we prepared mutants with substitutions of Asn/Gln and Arg at three acidic amino acid residues of cSBL and studied their anti-tumor activity and internalization efficiency. The results showed the enhancing effect of charge on anti-tumor activity and internalization, and suggested that the replacement of D24 and E88 of cSBL with arginine is more effective than that of E97. The double mutant D24RE88R showed comparable anti-tumor activity to the ethylenediamine-modified cSBL reported previously. The mutant was well-characterized as a pure cSBL derivative suitable for studying the mechanism of the anti-tumor action of cSBL.

Tunable electrical conductivity in metal-organic framework thin film devices

DOEpatents

Talin, Albert Alec; Allendorf, Mark D.; Stavila, Vitalie; Leonard, Francois

2016-08-30

A composition including a porous metal organic framework (MOF) including an open metal site and a guest species capable of charge transfer that can coordinate with the open metal site, wherein the composition is electrically conductive. A method including infiltrating a porous metal organic framework (MOF) including an open metal site with a guest species that is capable of charge transfer; and coordinating the guest species to the open metal site to form a composition including an electrical conductivity greater than an electrical conductivity of the MOF.

Tunable electrical conductivity in metal-organic framework thin film devices

DOEpatents

Talin, Albert Alec; Allendorf, Mark D.; Stavila, Vitalie; Leonard, Francois

2016-05-24

A composition including a porous metal organic framework (MOF) including an open metal site and a guest species capable of charge transfer that can coordinate with the open metal site, wherein the composition is electrically conductive. A method including infiltrating a porous metal organic framework (MOF) including an open metal site with a guest species that is capable of charge transfer; and coordinating the guest species to the open metal site to form a composition including an electrical conductivity greater than an electrical conductivity of the MOF.

Crystal Structures of Active Fully Assembled Substrate- and Product-Bound Complexes of UDP-N-Acetylmuramic Acid:l-Alanine Ligase (MurC) from Haemophilus influenzae

PubMed Central

Mol, Clifford D.; Brooun, Alexei; Dougan, Douglas R.; Hilgers, Mark T.; Tari, Leslie W.; Wijnands, Robert A.; Knuth, Mark W.; McRee, Duncan E.; Swanson, Ronald V.

2003-01-01

UDP-N-acetylmuramic acid:l-alanine ligase (MurC) catalyzes the addition of the first amino acid to the cytoplasmic precursor of the bacterial cell wall peptidoglycan. The crystal structures of Haemophilus influenzae MurC in complex with its substrate UDP-N-acetylmuramic acid (UNAM) and Mg2+ and of a fully assembled MurC complex with its product UDP-N-acetylmuramoyl-l-alanine (UMA), the nonhydrolyzable ATP analogue AMPPNP, and Mn2+ have been determined to 1.85- and 1.7-Å resolution, respectively. These structures reveal a conserved, three-domain architecture with the binding sites for UNAM and ATP formed at the domain interfaces: the N-terminal domain binds the UDP portion of UNAM, and the central and C-terminal domains form the ATP-binding site, while the C-terminal domain also positions the alanine. An active enzyme structure is thus assembled at the common domain interfaces when all three substrates are bound. The MurC active site clearly shows that the γ-phosphate of AMPPNP is positioned between two bound metal ions, one of which also binds the reactive UNAM carboxylate, and that the alanine is oriented by interactions with the positively charged side chains of two MurC arginine residues and the negatively charged alanine carboxyl group. These results indicate that significant diversity exists in binding of the UDP moiety of the substrate by MurC and the subsequent ligases in the bacterial cell wall biosynthesis pathway and that alterations in the domain packing and tertiary structure allow the Mur ligases to bind sequentially larger UNAM peptide substrates. PMID:12837790

Crystal structures of active fully assembled substrate- and product-bound complexes of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) from Haemophilus influenzae.

PubMed

Mol, Clifford D; Brooun, Alexei; Dougan, Douglas R; Hilgers, Mark T; Tari, Leslie W; Wijnands, Robert A; Knuth, Mark W; McRee, Duncan E; Swanson, Ronald V

2003-07-01

UDP-N-acetylmuramic acid:L-alanine ligase (MurC) catalyzes the addition of the first amino acid to the cytoplasmic precursor of the bacterial cell wall peptidoglycan. The crystal structures of Haemophilus influenzae MurC in complex with its substrate UDP-N-acetylmuramic acid (UNAM) and Mg(2+) and of a fully assembled MurC complex with its product UDP-N-acetylmuramoyl-L-alanine (UMA), the nonhydrolyzable ATP analogue AMPPNP, and Mn(2+) have been determined to 1.85- and 1.7-A resolution, respectively. These structures reveal a conserved, three-domain architecture with the binding sites for UNAM and ATP formed at the domain interfaces: the N-terminal domain binds the UDP portion of UNAM, and the central and C-terminal domains form the ATP-binding site, while the C-terminal domain also positions the alanine. An active enzyme structure is thus assembled at the common domain interfaces when all three substrates are bound. The MurC active site clearly shows that the gamma-phosphate of AMPPNP is positioned between two bound metal ions, one of which also binds the reactive UNAM carboxylate, and that the alanine is oriented by interactions with the positively charged side chains of two MurC arginine residues and the negatively charged alanine carboxyl group. These results indicate that significant diversity exists in binding of the UDP moiety of the substrate by MurC and the subsequent ligases in the bacterial cell wall biosynthesis pathway and that alterations in the domain packing and tertiary structure allow the Mur ligases to bind sequentially larger UNAM peptide substrates.

Tales of Dihydrofolate Binding to R67 Dihydrofolate Reductase

PubMed Central

2015-01-01

Homotetrameric R67 dihydrofolate reductase possesses 222 symmetry and a single active site pore. This situation results in a promiscuous binding site that accommodates either the substrate, dihydrofolate (DHF), or the cofactor, NADPH. NADPH interacts more directly with the protein as it is larger than the substrate. In contrast, the p-aminobenzoyl-glutamate tail of DHF, as monitored by nuclear magnetic resonance and crystallography, is disordered when bound. To explore whether smaller active site volumes (which should decrease the level of tail disorder by confinement effects) alter steady state rates, asymmetric mutations that decreased the half-pore volume by ∼35% were constructed. Only minor effects on kcat were observed. To continue exploring the role of tail disorder in catalysis, 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide-mediated cross-linking between R67 DHFR and folate was performed. A two-folate, one-tetramer complex results in the loss of enzyme activity where two symmetry-related K32 residues in the protein are cross-linked to the carboxylates of two bound folates. The tethered folate could be reduced, although with a ≤30-fold decreased rate, suggesting decreased dynamics and/or suboptimal positioning of the cross-linked folate for catalysis. Computer simulations that restrain the dihydrofolate tail near K32 indicate that cross-linking still allows movement of the p-aminobenzoyl ring, which allows the reaction to occur. Finally, a bis-ethylene-diamine-α,γ-amide folate adduct was synthesized; both negatively charged carboxylates in the glutamate tail were replaced with positively charged amines. The Ki for this adduct was ∼9-fold higher than for folate. These various results indicate a balance between folate tail disorder, which helps the enzyme bind substrate while dynamics facilitates catalysis. PMID:26637016

Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin.

PubMed

Pozzi, Nicola; Zerbetto, Mirco; Acquasaliente, Laura; Tescari, Simone; Frezzato, Diego; Polimeno, Antonino; Gohara, David W; Di Cera, Enrico; De Filippis, Vincenzo

2016-07-19

Thrombin exists as an ensemble of active (E) and inactive (E*) conformations that differ in their accessibility to the active site. Here we show that redistribution of the E*-E equilibrium can be achieved by perturbing the electrostatic properties of the enzyme. Removal of the negative charge of the catalytic Asp102 or Asp189 in the primary specificity site destabilizes the E form and causes a shift in the 215-217 segment that compromises substrate entrance. Solution studies and existing structures of D102N document stabilization of the E* form. A new high-resolution structure of D189A also reveals the mutant in the collapsed E* form. These findings establish a new paradigm for the control of the E*-E equilibrium in the trypsin fold.

B 36N 36 fullerene-like nanocages: A novel material for drug delivery

NASA Astrophysics Data System (ADS)

Ganji, M. D.; Yazdani, H.; Mirnejad, A.

2010-07-01

We study interaction between B 36N 36 fullerene-like nanocage and glycine amino acid from the first- principles. Binding energy is calculated and glycine binding to the pure C 60 fullerene is compared. We also analyze the electronic structure and charge Mulliken population for the energetically most favorable complexes. Our results indicate that glycine can form stable bindings with B 36N 36 nanocage via their carbonyl oxygen (O) active site while, the C 60 fullerene might be unable to form stable bindings to glycine amino acid via their active sites, which is consistence with recent experimental and theoretical investigations. Thus, we arrive at the prediction that the B 36N 36 nanocage can be implemented as a novel material for drug delivery applications.

Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise.

PubMed

Liu, Chaoren; Beratan, David N; Zhang, Peng

2016-04-21

System-environment interactions are essential in determining charge-transfer (CT) rates and mechanisms. We developed a computationally accessible method, suitable to simulate CT in flexible molecules (i.e., DNA) with hundreds of sites, where the system-environment interactions are explicitly treated with numerical noise modeling of time-dependent site energies and couplings. The properties of the noise are tunable, providing us a flexible tool to investigate the detailed effects of correlated thermal fluctuations on CT mechanisms. The noise is parametrizable by molecular simulation and quantum calculation results of specific molecular systems, giving us better molecular resolution in simulating the system-environment interactions than sampling fluctuations from generic spectral density functions. The spatially correlated thermal fluctuations among different sites are naturally built-in in our method but are not readily incorporated using approximate spectral densities. Our method has quantitative accuracy in systems with small redox potential differences (

Charge states and lattice sites of dilute implanted Sn in ZnO

NASA Astrophysics Data System (ADS)

Mølholt, T. E.; Gunnlaugsson, H. P.; Johnston, K.; Mantovan, R.; Röder, J.; Adoons, V.; Mokhles Gerami, A.; Masenda, H.; Matveyev, Y. A.; Ncube, M.; Unzueta, I.; Bharuth-Ram, K.; Gislason, H. P.; Krastev, P.; Langouche, G.; Naidoo, D.; Ólafsson, S.; Zenkevich, A.; ISOLDE Collaboration

2017-04-01

The common charge states of Sn are 2+  and 4+. While charge neutrality considerations favour 2+  to be the natural charge state of Sn in ZnO, there are several reports suggesting the 4+  state instead. In order to investigate the charge states, lattice sites, and the effect of the ion implantation process of dilute Sn atoms in ZnO, we have performed 119Sn emission Mössbauer spectroscopy on ZnO single crystal samples following ion implantation of radioactive 119In (T ½  =  2.4 min) at temperatures between 96 K and 762 K. Complementary perturbed angular correlation measurements on 111mCd implanted ZnO were also conducted. Our results show that the 2+  state is the natural charge state for Sn in defect free ZnO and that the 4+  charge state is stabilized by acceptor defects created in the implantation process.

The role of the anionic and cationic pt sites in the adsorption site preference of water and ethanol on defected Pt4/Pt(111) substrates: A density functional theory investigation within the D3 van der waals corrections

NASA Astrophysics Data System (ADS)

Seminovski, Yohanna; Amaral, Rafael C.; Tereshchuk, Polina; Da Silva, Juarez L. F.

2018-01-01

Platinum (Pt) atoms in the bulk face-centered cubic structure have neutral charge because they are equivalent by symmetry, however, in clean Pt surfaces, the effective charge on Pt atoms can turn slightly negative (anionic) or positive (cationic) while increasing substantially in magnitude for defected (low-coordinated) Pt sites. The effective charge affect the adsorption properties of molecular species on Pt surfaces and it can compete in importance with the coupling of the substrate-molecule electronic states. Although several studies have been reported due to the importance of Pt for catalysis, our understanding of the role played by low-coordinated sites is still limited. Here, we employ density functional theory within the Perdew-Burke-Ernzerhof exchange-correlation functional and the D3 van der Waals (vdW) correction to investigate the role of the cationic and anionic Pt sites on the adsorption properties of ethanol and water on defected Pt4/Pt(111) substrates. Four substrates were carefully selected, namely, two two-dimensional (2D) Pt4 configurations (2D-strand and 2D-island) and two tri-dimensional (3D) Pt4 (3D-fcc and 3D-hcp), to understand the role of coordination, effective charge, and coupling of the electronic states in the adsorption properties. From the Bader charge analysis, we identified the cationic and anionic sites among the Pt atoms exposed to the vacuum region in the Pt4/Pt(111) substrates. We found that ethanol and water bind via the anionic O atoms to the low-coordinated defected Pt sites of the substrates, where the angle PtOH is nearly 100° for most configurations. In the 3D-fcc or 3D-hcp defected configurations, the lowest-coordinated Pt atoms are anionic, hence, those Pt sites are not preferable for the adsorption of O atoms. The charge transfer from water and ethanol to the Pt substrates has similar magnitude for all cases, which implies similar Coulomb contribution to the adsorption energy. Moreover, we found a correlation of the adsorption energy with the shift of the center of gravity of the occupied d-states of Pt sites.

Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP).

PubMed

Vanommeslaeghe, Kenno; Van Alsenoy, Christian; De Proft, Frank; Martins, José C; Tourwé, Dirk; Geerlings, Paul

2003-08-21

Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.

Report of the Task Force on SSC Magnet System Test Site

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

NONE

1984-10-01

The Task Force on SSC Magnet Systems test Site was appointed by Maury Tigner, Director of the SSC, Phase 1 in August 1984. In brief, the charge asked the Task Force to make a critical evaluation of potential test sites for a major SSC magnet System Test Facility (STF) with regard to: (1) availability of the needed space, utilities, staff and other requirements on the desired time scale; and (2) the cost of preparing the sites for the tests and for operating the facilities during the test period. The charge further suggests that, by virtue of existing facilities and availabilitymore » of experienced staff, BNL and FNAL are the two best candidate sites and that is therefore appears appropriate to restrict the considerations of the Task Force to these sites. During the subsequent deliberations of the Task Force, no new facts were revealed that altered the assumptions of the charge in this regard. The charge does not ask for a specific site recommendation for the STF. Indeed, an agreement on such a recommendation would be difficult to achieve considering the composition of the Task Force, wherein a large fraction of the membership is drawn from the two contending laboratories. Instead, we have attempted to describe the purpose of the facility, outline a productive test program, list the major facilities required, carefully review the laboratories` responses to the facility requirements, and make objective comparisons of the specific features and capabilities offered.« less

Surface and interlayer base-characters in lepidocrocite titanate: The adsorption and intercalation of fatty acid

NASA Astrophysics Data System (ADS)

Maluangnont, Tosapol; Arsa, Pornanan; Limsakul, Kanokporn; Juntarachairot, Songsit; Sangsan, Saithong; Gotoh, Kazuma; Sooknoi, Tawan

2016-06-01

While layered double hydroxides (LDHs) with positively-charged sheets are well known as basic materials, layered metal oxides having negatively-charged sheets are not generally recognized so. In this article, the surface and interlayer base-characters of O2- sites in layered metal oxides have been demonstrated, taking lepidocrocite titanate K0.8Zn0.4Ti1.6O4 as an example. The low basicity (0.04 mmol CO2/g) and low desorption temperature (50-300 °C) shown by CO2- TPD suggests that O2- sites at the external surfaces is weakly basic, while those at the interlayer space are mostly inaccessible to CO2. The liquid-phase adsorption study, however, revealed the uptake as much as 37% by mass of the bulky palmitic acid (C16 acid). The accompanying expansion of the interlayer space by ~0.1 nm was detected by PXRD and TEM. In an opposite manner to the external surfaces, the interlayer O2- sites can deprotonate palmitic acid, forming the salt (i.e., potassium palmitate) occluded between the sheets. Two types of basic sites are proposed based on ultrafast 1H MAS NMR and FTIR results. The interlayer basic sites in lepidocrocite titanate leads to an application of this material as a selective and stable two-dimensional (2D) basic catalyst, as demonstrated by the ketonization of palmitic acid into palmitone (C31 ketone). Tuning of the catalytic activity by varying the type of metal (Zn, Mg, and Li) substituting at TiIV sites was also illustrated.

User Data Package for Compressed Natural Gas (CNG) Vehicles for Navy Applications

DTIC Science & Technology

1991-04-01

already available). GENERAL CONSIDERATIONS The advantages and disadvantages for implementing a CNG-fueled vehicle fleet at a specific site vary. However...at the user’s site , if a guaranteed minimum quantity of CNG will be purchased annually by the fleet operator. Utilities are also establishing special...at low pressure and compressed on- site , several additional charges must be added to the cost charged by the natural gas supplier (see Table 1). The

Quantifying reactivity for electrophilic aromatic substitution reactions with Hirshfeld charge.

PubMed

Liu, Shubin

2015-03-26

An electrophilic aromatic substitution is a process where one atom or group on an aromatic ring is replaced by an incoming electrophile. The reactivity and regioselectivity of this category of reactions is significantly impacted by the group that is already attached to the aromatic ring. Groups promoting substitution at the ortho/para and meta position are called ortho/para and meta directing groups, respectively. Earlier, we have shown that regioselectivity of the electrophilic aromatic substitution is dictated by the nucleophilicity of the substituted aromatic ring, which is proportional to the Hirshfeld charge on the regioselective site. Ortho/para directing groups have the largest negative charge values at the ortho/para positions, whereas meta directing groups often have the largest negative charge value at the meta position. The electron donation or acceptance feature of a substitution group is irrelevant to the regioselectivity. In this contribution, we extend our previous study by quantifying the reactivity for this kind of reactions. To that end, we examine the transition-state structure and activation energy of an identity reaction for a series of monosubstituted-benzene molecules reacting with hydrogen fluoride using BF3 as the catalyst in the gas phase. A total of 18 substitution groups will be considered, nine of which are ortho/para directing and the other nine groups meta directing. From this study, we found that the barrier height of these reactions strongly correlates with the Hirshfeld charge on the regioselective site for both ortho/para and meta directing groups, with the correlation coefficient R(2) both better than 0.96. We also discovered a less accurate correlation between the barrier height and HOMO energy. These results reconfirm the validity and effectiveness of employing the Hirshfeld charge as a reliable descriptor of both reactivity and regioselectivity for this vastly important category of chemical transformations.

Role of the Muon in Semiconductor Research

NASA Astrophysics Data System (ADS)

Mengyan, Rick (P. W.)

Muons are used in semiconductor research as an experimentally accessible analog to the isolated Hydrogen (H) impurity - a complex that is very difficult (or impossible) to study by other means. Hydrogen impurities of any concentration can modify the electrical, optical or magnetic properties of the host. For instance, H can be incorporated to remove electrically active levels from the energy gap (i.e. passivation) while some can form isolated centers that tend to be responsible for the trap and release of charge carriers and participate in site and charge-state dynamics which certainly affect the electrical properties of the host. Therefore, it can be quite useful to characterize these impurities in semiconducting materials that are of interest for use in devices. A muon has the same charge and spin as a proton but a mass that is nine times lighter. When implanted in a target material, a positively charged muon can behave as a light proton or bind with an electron to form a complex known as Muonium (Mu) with properties that are very similar to that of ionic or neutral H, respectively. A result of these similarities and direct non-destructive implantation is that Mu provides a direct measure of local electronic structure, thermal stability and charge-state transitions of these impurity centers. Since any material can be subjected to muon implantation and it is the muons themselves that mimic the H impurity centers, these measurements do not depend (at all) on the host's solubility of hydrogen nor do they require some minimum concentration; unlike many other techniques, such as EPR, ENDOR, NMR, or IR vibrational spectroscopy. Here we summarize major contributions muons have made to the field of semiconductor research followed by a few case studies to demonstrate the technique and detailed knowledge of the physical and electronic structures as well as dynamics (e.g.: charge-state and site transitions; local motion; long-range diffusion) of Mu/H that can be obtained.

A Power-Efficient Wireless System With Adaptive Supply Control for Deep Brain Stimulation.

PubMed

Lee, Hyung-Min; Park, Hangue; Ghovanloo, Maysam

2013-09-01

A power-efficient wireless stimulating system for a head-mounted deep brain stimulator (DBS) is presented. A new adaptive rectifier generates a variable DC supply voltage from a constant AC power carrier utilizing phase control feedback, while achieving high AC-DC power conversion efficiency (PCE) through active synchronous switching. A current-controlled stimulator adopts closed-loop supply control to automatically adjust the stimulation compliance voltage by detecting stimulation site potentials through a voltage readout channel, and improve the stimulation efficiency. The stimulator also utilizes closed-loop active charge balancing to maintain the residual charge at each site within a safe limit, while receiving the stimulation parameters wirelessly from the amplitude-shift-keyed power carrier. A 4-ch wireless stimulating system prototype was fabricated in a 0.5-μm 3M2P standard CMOS process, occupying 2.25 mm². With 5 V peak AC input at 2 MHz, the adaptive rectifier provides an adjustable DC output between 2.5 V and 4.6 V at 2.8 mA loading, resulting in measured PCE of 72 ~ 87%. The adaptive supply control increases the stimulation efficiency up to 30% higher than a fixed supply voltage to 58 ~ 68%. The prototype wireless stimulating system was verified in vitro .

A Power-Efficient Wireless System With Adaptive Supply Control for Deep Brain Stimulation

PubMed Central

Lee, Hyung-Min; Park, Hangue; Ghovanloo, Maysam

2014-01-01

A power-efficient wireless stimulating system for a head-mounted deep brain stimulator (DBS) is presented. A new adaptive rectifier generates a variable DC supply voltage from a constant AC power carrier utilizing phase control feedback, while achieving high AC-DC power conversion efficiency (PCE) through active synchronous switching. A current-controlled stimulator adopts closed-loop supply control to automatically adjust the stimulation compliance voltage by detecting stimulation site potentials through a voltage readout channel, and improve the stimulation efficiency. The stimulator also utilizes closed-loop active charge balancing to maintain the residual charge at each site within a safe limit, while receiving the stimulation parameters wirelessly from the amplitude-shift-keyed power carrier. A 4-ch wireless stimulating system prototype was fabricated in a 0.5-μm 3M2P standard CMOS process, occupying 2.25 mm². With 5 V peak AC input at 2 MHz, the adaptive rectifier provides an adjustable DC output between 2.5 V and 4.6 V at 2.8 mA loading, resulting in measured PCE of 72 ~ 87%. The adaptive supply control increases the stimulation efficiency up to 30% higher than a fixed supply voltage to 58 ~ 68%. The prototype wireless stimulating system was verified in vitro. PMID:24678126

Charge transport kinetics in a robust radical-substituted polymer/nanocarbon composite electrode

NASA Astrophysics Data System (ADS)

Sato, Kan; Oyaizu, Kenichi; Nishide, Hiroyuki

We have reported a series of organic radical-substituted polymers as new-type charge storage and transport materials which could be used for energy related devices such as batteries and solar cells. Redox-active radical moieties introduced to the non-conjugated polymer backbones enable the rapid electron transfer among the adjacent radical sites, and thus large diffusive flux of electrical charge at a bulk scale. Here we present the elucidated charge transport kinetics in a radical polymer/single-walled carbon nanotube (SWNT) composite electrode. The synergetic effect of electrical conduction by a three-dimensional SWNT network and electron self-exchange reaction by radical polymers contributed to the 105-fold (per 1 g of added SWNT) boosting of electrochemical reactions and exceptionally large current density (greater than 1 A/cm2) as a rechargeable electrode. A totally organic-based secondary battery with a submicron thickness was fabricated to demonstrate the splendid electrochemical performances. Grants-in-Aid for Scientific Research (No. 24225003, 15J00888) and the Leading Graduate Program in Science and Engineering, from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT).

Studies on ocular and parenteral application potentials of azithromycin- loaded anionic, cationic and neutral-charged emulsions.

PubMed

Tamilvanan, Shunmugaperumal; Khanum, Ramona; Senthilkumar, Sudalimuthu Ramachandran; Muthuraman, Marimuthu; Rajasekharan, Thenrajan

2013-10-01

Ocular and parenteral application potentials of azithromycin-containing, non-phospholipid-based cationic nanosized emulsion in comparison to the phospholipid-based anionic and neutral-charged nanosized emulsions were investigated. Various physical, chemical, nonclinical toxicity and antimicrobial activity studies (mean droplet diameter, surface charge, creaming index, entrapment efficiency, accelerated, long-term and freeze-thaw cycling stabilities, TLC study, modified hen's egg chorioallantoic membrane (HET-CAM) test, in vitro hemolysis test, in vitro and in vivo myotoxicity, and in vitro antimicrobial activity) were conducted for assessing the potentials of these three types of emulsions. Following autoclave sterilization, all of these emulsions exhibited a nanometer range mean particle diameter (200 ± 29 to 434 ± 13 nm). While the anionic and cationic emulsions did show high negative (-34.2 ± 1.23 mV) and positive zeta potential (42.6 ± 1.45 mV) values, the neutral-charged emulsion did not. Even with 5 freeze-thaw cycles, the cationic emulsion remained stable whereas other two emulsions underwent phase-separation. The hen's egg chorioallantoic membrane test revealed an irritation score value that was higher for the anionic emulsion than for cationic or neutral-charged emulsion. A significantly higher % hemolysis value was also noticed for the anionic emulsion when compared to the % hemolysis value of cationic emulsion (ANOVA, P ‹ 0.05). However, all of the emulsions showed a lesser intracellular creatine kinase (CK) release/plasma CK level in comparison to the positive control (phenytoin) indicating their lesser myotoxicity at the injection site . When compared to anionic and neutral-charged emulsions, the possible controlled drug release from cationic emulsion delayed the in vitro antimicrobial action against H.influenzae and S.pneumoniae.

Trapped charge densities in Al{sub 2}O{sub 3}-based silicon surface passivation layers

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

Jordan, Paul M., E-mail: Paul.Jordan@namlab.com; Simon, Daniel K.; Dirnstorfer, Ingo

2016-06-07

In Al{sub 2}O{sub 3}-based passivation layers, the formation of fixed charges and trap sites can be strongly influenced by small modifications in the stack layout. Fixed and trapped charge densities are characterized with capacitance voltage profiling and trap spectroscopy by charge injection and sensing, respectively. Al{sub 2}O{sub 3} layers are grown by atomic layer deposition with very thin (∼1 nm) SiO{sub 2} or HfO{sub 2} interlayers or interface layers. In SiO{sub 2}/Al{sub 2}O{sub 3} and HfO{sub 2}/Al{sub 2}O{sub 3} stacks, both fixed charges and trap sites are reduced by at least a factor of 5 compared with the value measured inmore » pure Al{sub 2}O{sub 3}. In Al{sub 2}O{sub 3}/SiO{sub 2}/Al{sub 2}O{sub 3} or Al{sub 2}O{sub 3}/HfO{sub 2}/Al{sub 2}O{sub 3} stacks, very high total charge densities of up to 9 × 10{sup 12} cm{sup −2} are achieved. These charge densities are described as functions of electrical stress voltage, time, and the Al{sub 2}O{sub 3} layer thickness between silicon and the HfO{sub 2} or the SiO{sub 2} interlayer. Despite the strong variation of trap sites, all stacks reach very good effective carrier lifetimes of up to 8 and 20 ms on p- and n-type silicon substrates, respectively. Controlling the trap sites in Al{sub 2}O{sub 3} layers opens the possibility to engineer the field-effect passivation in the solar cells.« less

Resonance energy transfer between sites in rat liver glutathione S-transferase, 1-1, selectively modified at cysteine-17 and cysteine-111.

PubMed

Hu, L; Colman, R F

1997-02-18

Monobromobimane (mBBr) can label both Cys111 and Cys17 of rat liver glutathione S-transferase, 1-1 (GST 1-1). However, selective modification of Cys111 was achieved by the maleimide-based sulfhydryl reagents N-ethylmaleimide (NEM) and fluorescein 5-maleimide (NFM). Incubation of GST 1-1 with 5 mM NEM for 30 min at pH 7.5 and 25 degrees C leads to the formation of modified enzyme with 92% residual activity toward 1-chloro-2,4-dinitrobenzene and completely blocks Cys111 from subsequent reaction with either NFM or mBBr. Reaction of GST 1-1 with 0.2 mM NFM under the same conditions affords a modified enzyme with only 14% residual activity even though NFM and NEM target the same Cys111. The results indicate that when the bulky fluorescein is covalently bound to Cys111, the ligand projects into both the xenobiotic binding site and the glutathione site. After NEM or NFM modification of GST 1-1, the enzyme was further modified by monobromobimane at Cys17 with loss of activity. Together with the only tryptophan (Trp20), fluorescein linked to Cys111 and bimane to Cys17 provide three fluorescent probes to study the solution structure of GST 1-1. Fluorescence spectral analysis suggests that Trp20 and bimane linked to Cys17 are located in a relatively hydrophobic environment, while fluorescein linked to Cys111 is located in a charged environment. These fluorescent probes constitute three sets of donor-acceptor pairs for the measurement of fluorescence energy transfer, and distances calculated from such measurements are 20 A between Trp20 and bimane at Cys17, 19 A between Trp20 and fluorescein at Cys111, and < 22 A between bimane at Cys17 and fluorescein at Cys111. Molecular modeling studies indicate that fluorescein lies between the two subunits, is surrounded by charged residues, and is extended into the xenobiotic binding site. They also suggest that mBBr must approach from the dimer interface in order to reach the reaction site at Cys17.

Introduction of unnatural amino acids into chalcone isomerase.

PubMed

Bednar, R A; McCaffrey, C; Shan, K

1991-01-01

The active site cysteine residue of chalcone isomerase was rapidly and selectively modified under denaturing conditions with a variety of electrophilic reagents. These denatured and modified enzyme were renatured to produce enzyme derivatives containing a series of unnatural amino acids in the active site. Addition of methyl, ethyl, butyl, heptyl, and benzyl groups to the cysteine sulfur does not abolish catalytic activity, although the activity decreases as the steric bulk of the amino acid side-chain increases. Modification of the cysteine to introduce a charged homoglutamate or a neutral homoglutamine analogue results in retention of 22% of the catalytic activity. Addition of a methylthio group (SMe) to the cysteine residue of native chalcone isomerase preserves 85% of the catalytic activity measured with 2',4',4-trihydroxychalcone, 2',4',6',4-tetrahydroxychalcone, or 2'-hydroxy-4-methoxychalcone as substrates. The competitive inhibition constant for 4',4-dihydroxychalcone, the substrate inhibition constant for 2',4',4-trihydroxychalcone, and other steady-state kinetic parameters for the methanethiolated enzyme are very similar to those of the native enzyme. The strong binding of 4',4-dihydroxychalcone to the methanethiolated enzyme shows that there is no steric repulsion between this modified amino acid residue and the substrate analogue. This structure-activity study clearly demonstrates that the active site cysteine residue does not function as an acid-base or nucleophilic group in producing the catalysis or substrate inhibition observed with chalcone isomerase. The method presented in this paper allows for the rapid introduction of a series of unnatural amino acids into the active site as a means of probing the structure-function relationship.

Interactions of p-Nitrobenzene Diazonium Fluoroborate and Analogs with the Active Sites of Acetylcholine-Receptor and -Esterase*

PubMed Central

Mautner, Henry G.; Bartels, Eva

1970-01-01

p-Nitrobenzene diazonium fluoroborate (NDF) is a potent inhibitor of the carbamylcholine-induced depolarization of the electroplax and of acetylcholinesterase. It probably forms covalent bonds with the acetylcholine-receptor and -esterase at the active site of the proteins. Its inhibitory strength is at least the same as that of trimethylammonium diazonium fluoroborate (TDF). The p-acetoxy analog, with its weaker electron-withdrawing group, is about ten times weaker as an inhibitor than the trimethylammonium or p-nitro analogs, both of which have strong electron-withdrawing groups. After treatment of the electroplax preparation with dithiothreitol, NDF remains an irreversible receptor-inhibitor, while TDF becomes a potent reversible receptor-activator. TDF is self-inhibitory: applied before reduction, it no longer depolarizes. Although the first observations on TDF suggested that the compound labels both proteins by virtue of the steric complementary of its trimethylammonium group to a negative subsite in the proteins, the present study indicates that it is the positively charged diazonium group that reacts with the active sites of the proteins to form a covalent bond with an appropriate amino-acid residue. PMID:5272331

Description and control of dissociation channels in gas-phase protein complexes

NASA Astrophysics Data System (ADS)

Thachuk, Mark; Fegan, Sarah K.; Raheem, Nigare

2016-08-01

Using molecular dynamics simulations of a coarse-grained model of the charged apo-hemoglobin protein complex, this work expands upon our initial report [S. K. Fegan and M. Thachuk, J. Am. Soc. Mass Spectrom. 25, 722-728 (2014)] about control of dissociation channels in the gas phase using specially designed charge tags. Employing a charge hopping algorithm and a range of temperatures, a variety of dissociation channels are found for activated gas-phase protein complexes. At low temperatures, a single monomer unfolds and becomes charge enriched. At higher temperatures, two additional channels open: (i) two monomers unfold and charge enrich and (ii) two monomers compete for unfolding with one eventually dominating and the other reattaching to the complex. At even higher temperatures, other more complex dissociation channels open with three or more monomers competing for unfolding. A model charge tag with five sites is specially designed to either attract or exclude charges. By attaching this tag to the N-terminus of specific monomers, the unfolding of those monomers can be decidedly enhanced or suppressed. In other words, using charge tags to direct the motion of charges in a protein complex provides a mechanism for controlling dissociation. This technique could be used in mass spectrometry experiments to direct forces at specific attachment points in a protein complex, and hence increase the diversity of product channels available for quantitative analysis. In turn, this could provide insight into the function of the protein complex in its native biological environment. From a dynamics perspective, this system provides an interesting example of cooperative behaviour involving motions with differing time scales.

Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases.

PubMed

Hardianto, Ari; Yusuf, Muhammad; Liu, Fei; Ranganathan, Shoba

2017-12-28

(-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is a tumour promoter, PKC isozymes act as tumour promoters or suppressors, depending on the cancer type. In particular, PKCε is frequently implicated in cancer promotion, making it a potential target for anticancer drugs. To improve isozyme selectivity of balanol, exhaustive structural and activity relationship (SAR) studies have been performed in the last two decades, but with limited success. More recently, fluorination on balanol has shown improved selectivity for PKCε, although the fluorine effect is not yet clearly understood. Understanding the origin to this fluorine-based selectivity will be valuable for designing better balanol-based ATP mimicking inhibitors. Computational approaches such as molecular dynamics (MD) simulations can decipher the fluorine effect, provided that correct charges have been assigned to a ligand. Balanol analogues have multiple ionisable functional groups and the effect of fluorine substitutions on the exact charge state of each analogue bound to PKA and to PKCε needs to be thoroughly investigated in order to design highly selective inhibitors for therapeutic applications. We explored the charge states of novel fluorinated balanol analogues using MD simulations. For different potential charge states of these analogues, Molecular Mechanics Generalized Born Surface Area (MMGBSA) binding energy values were computed. This study suggests that balanol and the most potent fluorinated analogue (5S fluorine substitution on the azepane ring), have charges on the azepane ring (N1), and the phenolic (C6''OH) and the carboxylate (C15''O 2 H) groups on the benzophenone moiety, when bound to PKCε as well as PKA. To the best our knowledge, this is the first study showing that the phenolate group is charged in balanol and its analogues binding to the ATP site of PKCε. Correct charge assignments of ligands are important to obtain predicted binding energy values from MD simulations that reflect experimental values. Both fluorination and the local enzymatic environment of the ATP site can influence the exact charge states of balanol analogues. Overall, this study is highly valuable for further rational design of potent balanol analogues selective to PKCε.

Structure of a Berberine Bridge Enzyme-Like Enzyme with an Active Site Specific to the Plant Family Brassicaceae.

PubMed

Daniel, Bastian; Wallner, Silvia; Steiner, Barbara; Oberdorfer, Gustav; Kumar, Prashant; van der Graaff, Eric; Roitsch, Thomas; Sensen, Christoph W; Gruber, Karl; Macheroux, Peter

2016-01-01

Berberine bridge enzyme-like (BBE-like) proteins form a multigene family (pfam 08031), which is present in plants, fungi and bacteria. They adopt the vanillyl alcohol-oxidase fold and predominantly show bi-covalent tethering of the FAD cofactor to a cysteine and histidine residue, respectively. The Arabidopsis thaliana genome was recently shown to contain genes coding for 28 BBE-like proteins, while featuring four distinct active site compositions. We determined the structure of a member of the AtBBE-like protein family (termed AtBBE-like 28), which has an active site composition that has not been structurally and biochemically characterized thus far. The most salient and distinguishing features of the active site found in AtBBE-like 28 are a mono-covalent linkage of a histidine to the 8α-position of the flavin-isoalloxazine ring and the lack of a second covalent linkage to the 6-position, owing to the replacement of a cysteine with a histidine. In addition, the structure reveals the interaction of a glutamic acid (Glu426) with an aspartic acid (Asp369) at the active site, which appear to share a proton. This arrangement leads to the delocalization of a negative charge at the active site that may be exploited for catalysis. The structure also indicates a shift of the position of the isoalloxazine ring in comparison to other members of the BBE-like family. The dioxygen surrogate chloride was found near the C(4a) position of the isoalloxazine ring in the oxygen pocket, pointing to a rapid reoxidation of reduced enzyme by dioxygen. A T-DNA insertional mutant line for AtBBE-like 28 results in a phenotype, that is characterized by reduced biomass and lower salt stress tolerance. Multiple sequence analysis showed that the active site composition found in AtBBE-like 28 is only present in the Brassicaceae, suggesting that it plays a specific role in the metabolism of this plant family.

Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.

PubMed

Jung, Young-Sang; Cai, Mengli; Clore, G Marius

2010-02-05

The solution structure of the IIA-IIB complex of the N,N'-diacetylchitobiose (Chb) transporter of the Escherichia coli phosphotransferase system has been solved by NMR. The active site His-89 of IIA(Chb) was mutated to Glu to mimic the phosphorylated state and the active site Cys-10 of IIB(Chb) was substituted by serine to prevent intermolecular disulfide bond formation. Binding is weak with a K(D) of approximately 1.3 mm. The two complementary interaction surfaces are largely hydrophobic, with the protruding active site loop (residues 9-16) of IIB(Chb) buried deep within the active site cleft formed at the interface of two adjacent subunits of the IIA(Chb) trimer. The central hydrophobic portion of the interface is surrounded by a ring of polar and charged residues that provide a relatively small number of electrostatic intermolecular interactions that serve to correctly align the two proteins. The conformation of the active site loop in unphosphorylated IIB(Chb) is inconsistent with the formation of a phosphoryl transition state intermediate because of steric hindrance, especially from the methyl group of Ala-12 of IIB(Chb). Phosphorylation of IIB(Chb) is accompanied by a conformational change within the active site loop such that its path from residues 11-13 follows a mirror-like image relative to that in the unphosphorylated state. This involves a transition of the phi/psi angles of Gly-13 from the right to left alpha-helical region, as well as smaller changes in the backbone torsion angles of Ala-12 and Met-14. The resulting active site conformation is fully compatible with the formation of the His-89-P-Cys-10 phosphoryl transition state without necessitating any change in relative translation or orientation of the two proteins within the complex.

Point mutations abolishing the mannose-binding capability of boar spermadhesin AQN-1.

PubMed

Ekhlasi-Hundrieser, Mahnaz; Calvete, Juan J; Von Rad, Bettina; Hettel, Christiane; Nimtz, Manfred; Töpfer-Petersen, Edda

2008-05-01

The mannose-binding capability of recombinant wild-type boar spermadhesin AQN-1 and of its site-directed mutants in the highly-conserved region around of the single glycosylation site (asparagine 50) of some spermadhesins, where the carbohydrate binding site has been proposed to be located, was checked using a solid-phase assay and a biotinylated mannose ligand. Substitution of glycine 54 by amino acids bearing an unipolar side chain did not cause significant decrease in the mannose-binding activity. However, amino acids with uncharged polar side chains or having a charged polar side chain abolished the binding of biotinylated mannose to the corresponding AQN-1 mutants. The results suggest that the higher surface accessibility of amino acids possessing polar side chains compared to those bearing nonpolar groups may sterically interfere with monosaccharide binding. The location of the mannose-binding site in AQN-1 appears to be topologically conserved in other heparin-binding boar spermadhesins, i.e., AQN-3 and AWN, but departs from the location of the mannose-6-phosphate-recognition site of PSP-II. This indicates that different spermadhesin molecules have evolved non-equivalent carbohydrate-binding capabilities, which may underlie their distinct patterns of biological activities.

On the advancement of quantum dot solar cell performance through enhanced charge carrier dynamics

NASA Astrophysics Data System (ADS)

Baker, David R.

The quantum dot solar cell is one of the few solar technologies which promises to compete with fossil fuels, but work is still needed to increase its performance. Electron transfer kinetics at interfaces and limitations of the redox couple within the cell, are responsible for lowering power conversion efficiency. Several techniques which are able to increase electron transfer within the working electrode and at the counter electrode/electrolyte interface are discussed in this dissertation. Trap sites on the surface of CdSe quantum dots are created when mercaptopropionic acid (MPA) is added to the suspension. The trap sites are emissive creating a loss pathway for photogenerated charges which will manifest as reduced photocurrent. MPA displaces amines on the surface of CdSe creating Se vacancies. Emission properties are controlled by the concentration of MPA. Because trap sites are generated, a more successful method to sensitize TiO2 films is the SILAR technique which directly grows quantum dots on the desired surface. Anodically etched TiO2 nanotubes yield photocurrents 20% greater than TiO2 nanoparticles because of longer electron diffusion lengths. Peak incident photon to charge carrier efficiencies of TiO2 nanotube samples show a doubling of photocurrent in the visible region compared to nanoparticles. The TiO2 substrates are sensitized with CdS by the SILAR process which is found to utilize both the inside and outside surfaces of the TiO2 nanotubes. Etched TiO2 nanotubes are removed from the underlying titanium foil in order to use spectroscopic techniques. Ultrafast transient absorption shows the extremely fast nature of charge injection from SILAR CdS into TiO 2 nanotubes. Surface area analysis of TiO2 nanotube powder gives an area of 77m2/g, a value 1.5 times larger than traditional TiO2 nanoparticles. By isolating the counter electrode with a salt bridge the effect of the polysulfide electrolyte is found to act as an electron scavenger on the working electrode. Though activity at the platinum counter electrode increases with the presence of polysulfides, the activity is too low to counteract scavenging at the working electrode. Cu2S, CoS and PbS electrochemically show promise as alternatives to platinum. Cu2S and CoS produce higher photocurrents and fill factors, greatly improving cell performance.

Deconvoluting AMP-activated protein kinase (AMPK) adenine nucleotide binding and sensing

PubMed Central

Gu, Xin; Yan, Yan; Novick, Scott J.; Kovach, Amanda; Goswami, Devrishi; Ke, Jiyuan; Tan, M. H. Eileen; Wang, Lili; Li, Xiaodan; de Waal, Parker W.; Webb, Martin R.; Griffin, Patrick R.; Xu, H. Eric

2017-01-01

AMP-activated protein kinase (AMPK) is a central cellular energy sensor that adapts metabolism and growth to the energy state of the cell. AMPK senses the ratio of adenine nucleotides (adenylate energy charge) by competitive binding of AMP, ADP, and ATP to three sites (CBS1, CBS3, and CBS4) in its γ-subunit. Because these three binding sites are functionally interconnected, it remains unclear how nucleotides bind to individual sites, which nucleotides occupy each site under physiological conditions, and how binding to one site affects binding to the other sites. Here, we comprehensively analyze nucleotide binding to wild-type and mutant AMPK protein complexes by quantitative competition assays and by hydrogen-deuterium exchange MS. We also demonstrate that NADPH, in addition to the known AMPK ligand NADH, directly and competitively binds AMPK at the AMP-sensing CBS3 site. Our findings reveal how AMP binding to one site affects the conformation and adenine nucleotide binding at the other two sites and establish CBS3, and not CBS1, as the high affinity exchangeable AMP/ADP/ATP-binding site. We further show that AMP binding at CBS4 increases AMP binding at CBS3 by 2 orders of magnitude and reverses the AMP/ATP preference of CBS3. Together, these results illustrate how the three CBS sites collaborate to enable highly sensitive detection of cellular energy states to maintain the tight ATP homeostastis required for cellular metabolism. PMID:28615457

Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment

PubMed Central

Hughes, Samantha J; Tanner, Julian A; Hindley, Alison D; Miller, Andrew D; Gould, Ian R

2003-01-01

Background Charging of transfer-RNA with cognate amino acid is accomplished by the aminoacyl-tRNA synthetases, and proceeds through an aminoacyl adenylate intermediate. The lysyl-tRNA synthetase has evolved an active site that specifically binds lysine and ATP. Previous molecular dynamics simulations of the heat-inducible Escherichia coli lysyl-tRNA synthetase, LysU, have revealed differences in the binding of ATP and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme. The possibility that this asymmetry results in different binding affinities for the ligands is addressed here by a parallel computational and biochemical study. Results Biochemical experiments employing isothermal calorimetry, steady-state fluorescence and circular dichroism are used to determine the order and stoichiometries of the lysine and nucleotide binding events, and the associated thermodynamic parameters. An ordered mechanism of substrate addition is found, with lysine having to bind prior to the nucleotide in a magnesium dependent process. Two lysines are found to bind per dimer, and trigger a large conformational change. Subsequent nucleotide binding causes little structural rearrangement and crucially only occurs at a single catalytic site, in accord with the simulations. Molecular dynamics based free energy calculations of the ATP binding process are used to determine the binding affinities of each site. Significant differences in ATP binding affinities are observed, with only one active site capable of realizing the experimental binding free energy. Half-of-the-sites models in which the nucleotide is only present at one active site achieve their full binding potential irrespective of the subunit choice. This strongly suggests the involvement of an anti-cooperative mechanism. Pathways for relaying information between the two active sites are proposed. Conclusions The asymmetry uncovered here appears to be a common feature of oligomeric aminoacyl-tRNA synthetases, and may play an important functional role. We suggest a manner in which catalytic efficiency could be improved by LysU operating in an alternating sites mechanism. PMID:12787471

Potential Electrostatic Interactions in Multiple Regions Affect Human Metapneumovirus F-Mediated Membrane Fusion

PubMed Central

Chang, Andres; Hackett, Brent A.; Winter, Christine C.; Buchholz, Ursula J.

2012-01-01

The recently identified human metapneumovirus (HMPV) is a worldwide respiratory virus affecting all age groups and causing pneumonia and bronchiolitis in severe cases. Despite its clinical significance, no specific antiviral agents have been approved for treatment of HMPV infection. Unlike the case for most paramyxoviruses, the fusion proteins (F) of a number of strains, including the clinical isolate CAN97-83, can be triggered by low pH. We recently reported that residue H435 in the HRB linker domain acts as a pH sensor for HMPV CAN97-83 F, likely through electrostatic repulsion forces between a protonated H435 and its surrounding basic residues, K295, R396, and K438, at low pH. Through site-directed mutagenesis, we demonstrated that a positive charge at position 435 is required but not sufficient for F-mediated membrane fusion. Arginine or lysine substitution at position 435 resulted in a hyperfusogenic F protein, while replacement with aspartate or glutamate abolished fusion activity. Studies with recombinant viruses carrying mutations in this region confirmed its importance. Furthermore, a second region within the F2 domain identified as being rich in charged residues was found to modulate fusion activity of HMPV F. Loss of charge at residues E51, D54, and E56 altered local folding and overall stability of the F protein, with dramatic consequences for fusion activity. As a whole, these studies implicate charged residues and potential electrostatic interactions in function, pH sensing, and overall stability of HMPV F. PMID:22761366

Proton transfer and protein quake in photoreceptor activation

NASA Astrophysics Data System (ADS)

Xie, Aihua

2002-03-01

Proteins are able to perform an enormous variety of functions, while using only a limited number of underlying processes. One of these is proton transfer, found in a range of receptors and enzymes. It is conceivable that proton transfer is essential in biological energy transduction, but it is less evident how proton transfer is employed in receptor activation during biological signal transduction. An important question regarding receptor activation is how a localized event of detecting a stimulus at the active site drives global conformational changes involving protein surface for signal relay. We will present structural, kinetic and energetic studies on the activation mechanism of a prototype PAS domain photoreceptor, photoactive yellow protein (PYP). Our data reveal that the putative signaling state of PYP upon absorption of a blue photon is formed during a large-amplitude protein quake triggered by the formation of a new buried charge in a hydrophobic pocket at the active site of PYP via intramolecular proton transfer. This mechanism for protein quakes driven by proton transfer and electrostatic interactions may play roles during the functioning of other receptor proteins and non-receptor proteins that require large conformational changes.

Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.

PubMed

Speranzini, Valentina; Rotili, Dante; Ciossani, Giuseppe; Pilotto, Simona; Marrocco, Biagina; Forgione, Mariantonietta; Lucidi, Alessia; Forneris, Federico; Mehdipour, Parinaz; Velankar, Sameer; Mai, Antonello; Mattevi, Andrea

2016-09-01

Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors.

Structural studies of viperin, an antiviral radical SAM enzyme.

PubMed

Fenwick, Michael K; Li, Yue; Cresswell, Peter; Modis, Yorgo; Ealick, Steven E

2017-06-27

Viperin is an IFN-inducible radical S -adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45-362) complexed with S -adenosylhomocysteine (SAH) or 5'-deoxyadenosine (5'-dAdo) and l-methionine (l-Met). Viperin contains a partial (βα) 6 -barrel fold with a disordered N-terminal extension (residues 45-74) and a partially ordered C-terminal extension (residues 285-362) that bridges the partial barrel to form an overall closed barrel structure. Cys84, Cys88, and Cys91 located after the first β-strand bind a [4Fe-4S] cluster. The active site architecture of viperin with bound SAH (a SAM analog) or 5'-dAdo and l-Met (SAM cleavage products) is consistent with the canonical mechanism of 5'-deoxyadenosyl radical generation. The viperin structure, together with sequence alignments, suggests that vertebrate viperins are highly conserved and that fungi contain a viperin-like ortholog. Many bacteria and archaebacteria also express viperin-like enzymes with conserved active site residues. Structural alignments show that viperin is similar to several other radical SAM enzymes, including the molybdenum cofactor biosynthetic enzyme MoaA and the RNA methyltransferase RlmN, which methylates specific nucleotides in rRNA and tRNA. The viperin putative active site contains several conserved positively charged residues, and a portion of the active site shows structural similarity to the GTP-binding site of MoaA, suggesting that the viperin substrate may be a nucleoside triphosphate of some type.

Universal Disorder in Organic Semiconductors Due to Fluctuations in Space Charge

NASA Astrophysics Data System (ADS)

Wu, Tzu-Cheng

This thesis concerns the study of charge transport in organic semiconductors. These materials are widely used as thin-film photoconductors in copiers and laser printers, and for their electroluminescent properties in organic light-emitting diodes. Much contemporary research is directed towards improving the efficiency of organic photovoltaic devices, which is limited to a large extent by the spatial and energetic disorder that hinders the charge mobility. One contribution to energetic disorder arises from the strong Coulomb interactions between injected charges with one another, but to date this has been largely ignored. We present a mean-field model for the effect of mutual interactions between injected charges hopping from site to site in an organic semiconductor. Our starting point is a modified Fröhlich Hamiltonian in which the charge is linearly coupled to the amplitudes of a wide band of dispersionless plasma modes having a Lorentzian distribution of frequencies. We show that in most applications of interest the hopping rates are fast enough while the plasma frequencies are low enough that random thermal fluctuations in the plasma density give rise to an energetically disordered landscape that is effectively stationary for many thousands of hops. Moreover, the distribution of site energies is Gaussian, and the energy-energy correlation function decays inversely with distance; as such, it can be argued that this disorder contributes to the Poole-Frenkel field dependence seen in a wide variety of experiments. Remarkably, the energetic disorder is universal; although it is caused by the fluctuations in the charge density, it is independent of the charge concentration.

CoMoS2/rGO/C3N4 ternary heterojunctions catalysts with high photocatalytic activity and stability for hydrogen evolution under visible light irradiation

NASA Astrophysics Data System (ADS)

Xu, Xuejun; Si, Zhichun; Liu, Liping; Wang, Zehao; Chen, Ze; Ran, Rui; He, Yonghong; Weng, Duan

2018-03-01

Noble metal free MoS2/g-C3N4 catalyst has attracted intense attentions for visible light photocatalytic hydrogen evolution as a result of its earth abundance, low cost and unique heterojunctions stacked with two dimensional sheets. However, the low charge separation efficiency resulted from the poor conductivity of g-C3N4 and MoS2, and lack of abundant active sites from coordinative unsaturated atoms in MoS2, restricts the photocatalytic hydrogen evolution activity and stability enhancement of MoS2/C3N4 composite catalysts. Herein, CoMoS2/rGO/g-C3N4 catalysts with ternary heterojunctions are prepared by facile solvothermal method, which exhibit high visible light photocatalytic activity and stability for hydrogen evolution. The optimal hydrogen evolution rate of CoMoS2/rGO/g-C3N4 catalysts is 684 μmol g-1 h-1 when the content of CoMoS2 is 2% and the content of rGO is 0.5%. The stability of CoMoS2/rGO/C3N4 catalysts just decrease about 3% after 4 cycling runs for 16 h. The good catalytic performances of catalysts are attributed to the synergistic effect among the g-C3N4 nanosheets, rGO nanosheets and CoMoS2 nanosheets. The high conductivity of rGO nanosheets enhances the electron-hole separation and charge transfer, and Co doping increases the active sites for hydrogen evolution due to the increase of unsaturated atoms in CoMoS2 nanosheets.

Structure of UreG/UreF/UreH Complex Reveals How Urease Accessory Proteins Facilitate Maturation of Helicobacter pylori Urease

PubMed Central

Fong, Yu Hang; Wong, Ho Chun; Yuen, Man Hon; Lau, Pak Ho; Chen, Yu Wai; Wong, Kam-Bo

2013-01-01

Urease is a metalloenzyme essential for the survival of Helicobacter pylori in acidic gastric environment. Maturation of urease involves carbamylation of Lys219 and insertion of two nickel ions at its active site. This process requires GTP hydrolysis and the formation of a preactivation complex consisting of apo-urease and urease accessory proteins UreF, UreH, and UreG. UreF and UreH form a complex to recruit UreG, which is a SIMIBI class GTPase, to the preactivation complex. We report here the crystal structure of the UreG/UreF/UreH complex, which illustrates how UreF and UreH facilitate dimerization of UreG, and assembles its metal binding site by juxtaposing two invariant Cys66-Pro67-His68 metal binding motif at the interface to form the (UreG/UreF/UreH)2 complex. Interaction studies revealed that addition of nickel and GTP to the UreG/UreF/UreH complex releases a UreG dimer that binds a nickel ion at the dimeric interface. Substitution of Cys66 and His68 with alanine abolishes the formation of the nickel-charged UreG dimer. This nickel-charged UreG dimer can activate urease in vitro in the presence of the UreF/UreH complex. Static light scattering and atomic absorption spectroscopy measurements demonstrated that the nickel-charged UreG dimer, upon GTP hydrolysis, reverts to its monomeric form and releases nickel to urease. Based on our results, we propose a mechanism on how urease accessory proteins facilitate maturation of urease. PMID:24115911

Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study.

PubMed

Tahan, A; Monajjemi, M

2011-12-01

Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.

Heparin-induced conformational changes of fibronectin within the extracellular matrix promote hMSC osteogenic differentiation.

PubMed

Li, Bojun; Lin, Zhe; Mitsi, Maria; Zhang, Yang; Vogel, Viola

2015-01-01

An increasing body of evidence suggests important roles of extracellular matrix (ECM) in regulating stem cell fate. This knowledge can be exploited in tissue engineering applications for the design of ECM scaffolds appropriate to direct stem cell differentiation. By probing the conformation of fibronectin (Fn) using fluorescence resonance energy transfer (FRET), we show here that heparin treatment of the fibroblast-derived ECM scaffolds resulted in more extended conformations of fibrillar Fn in ECM. Since heparin is a highly negatively charged molecule while fibronectin contains segments of positively charged modules, including FnIII13, electrostatic interactions between Fn and heparin might interfere with residual quaternary structure in relaxed fibronectin fibers thereby opening up buried sites. The conformation of modules FnIII12-14 in particular, which contain one of the heparin binding sites as well as binding sites for many growth factors, may be activated by heparin, resulting in alterations in growth factor binding to Fn. Indeed, upregulated osteogenic differentiation was observed when hMSCs were seeded on ECM scaffolds that had been treated with heparin and were subsequently chemically fixed. In contrast, either rigidifying relaxed fibers by fixation alone, or heparin treatment without fixation had no effect. We hypothesize that fibronectin's conformations within the ECM are activated by heparin such as to coordinate with other factors to upregulate hMSC osteogenic differentiation. Thus, the conformational changes of fibronectin within the ECM could serve as a 'converter' to tune hMSC differentiation in extracellular matrices. This knowledge could also be exploited to promote osteogenic stem cell differentiation on biomedical surfaces.

Molecular Dynamics Simulation Study of Solvent and State of Charge Effects on Solid-Phase Structure and Counterion Binding in a Nitroxide Radical Containing Polymer Energy Storage Material

DOE PAGES

Kemper, Travis W.; Gennett, Thomas; Larsen, Ross E.

2016-10-19

Here we performed molecular dynamics simulations to understand the effects of solvent swelling and state of charge (SOC) on the redox active, organic radical cathode material poly(2,2,6,6-tetramethylpiperidinyloxy methacrylate) (PTMA). We show that the polar solvent acetonitrile primarily solvates the nitroxide radical without disrupting the packing of the (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) pendant groups of PTMA. We also simulated bulk PTMA in different SOC, 25%, 50%, 75%, and 100%, by converting the appropriate number of TEMPO groups to the cation charge state and adding BF 4 - counterions to the simulation. At each SOC the packing of PTMA, the solvent, and the counterionsmore » were examined. The binding of the anion to the nitroxide cation site was examined using the potential of mean force and found to be on the order of tens of meV, with a binding energy that decreased with increasing SOC. Additionally, we found that the cation state is stabilized by the presence of a nearby anion by more than 1 eV, and the implications of this stabilization on charge transport are discussed. Finally, we describe the implications of our results for how the SOC of an organic electrode affects electron and anion charge transport during the charging and discharging processes.« less

NREL Charges Forward to Reduce Time at EV Stations | News | NREL

Science.gov Websites

station siting, travel patterns, grid resources, and business cases. At the same time, it is clear that Charges Forward to Reduce Time at EV Stations NREL Charges Forward to Reduce Time at EV Stations charging stations in Europe that will begin to approach the refueling time of gasoline vehicles. Photo

41 CFR 102-173.45 - Is there a registration charge for domain names?

Code of Federal Regulations, 2011 CFR

2011-01-01

...-INTERNET GOV DOMAIN Registration § 102-173.45 Is there a registration charge for domain names? The General... operations. For current registration charges, please visit the GSA Web site at http://www.nic.gov. GSA does... that may be provided by GSA, and a recurring annual charge that will not exceed $500 for all dot-gov...

41 CFR 102-173.45 - Is there a registration charge for domain names?

Code of Federal Regulations, 2013 CFR

2013-07-01

...-INTERNET GOV DOMAIN Registration § 102-173.45 Is there a registration charge for domain names? The General... operations. For current registration charges, please visit the GSA Web site at http://www.nic.gov. GSA does... that may be provided by GSA, and a recurring annual charge that will not exceed $500 for all dot-gov...

41 CFR 102-173.45 - Is there a registration charge for domain names?

Code of Federal Regulations, 2010 CFR

2010-07-01

...-INTERNET GOV DOMAIN Registration § 102-173.45 Is there a registration charge for domain names? The General... operations. For current registration charges, please visit the GSA Web site at http://www.nic.gov. GSA does... that may be provided by GSA, and a recurring annual charge that will not exceed $500 for all dot-gov...

41 CFR 102-173.45 - Is there a registration charge for domain names?

Code of Federal Regulations, 2014 CFR

2014-01-01

...-INTERNET GOV DOMAIN Registration § 102-173.45 Is there a registration charge for domain names? The General... operations. For current registration charges, please visit the GSA Web site at http://www.nic.gov. GSA does... that may be provided by GSA, and a recurring annual charge that will not exceed $500 for all dot-gov...

41 CFR 102-173.45 - Is there a registration charge for domain names?

Code of Federal Regulations, 2012 CFR

2012-01-01

...-INTERNET GOV DOMAIN Registration § 102-173.45 Is there a registration charge for domain names? The General... operations. For current registration charges, please visit the GSA Web site at http://www.nic.gov. GSA does... that may be provided by GSA, and a recurring annual charge that will not exceed $500 for all dot-gov...

Partial Ionic Character beyond the Pauling Paradigm: Metal Nanoparticles

DOE PAGES

Duanmu, Kaining; Truhlar, Donald G.

2014-11-12

A canonical perspective on the chemical bond is the Pauling paradigm: a bond in a molecule containing only identical atoms has no ionic character. However, we show that homonuclear silver clusters have very uneven charge distributions (for example, the C 2v structure of Ag 4 has a larger dipole moment than formaldehyde or acetone), and we show how to predict the charge distribution from coordination numbers and Hirshfeld charges. The new charge model is validated against Kohn–Sham calculations of dipole moments with four approximations for the exchange–correlation functional. We report Kohn–Sham studies of the binding energies of CO on silvermore » monomer and silver clusters containing 2–18 atoms. We also find that an accurate charge model is essential for understanding the site dependence of binding. In particular we find that atoms with more positive charges tend to have higher binding energies, which can be used for guidance in catalyst modeling and design. Furthermore, the nonuniform charge distribution of silver clusters predisposes the site preference of binding of carbon monoxide, and we conclude that nonuniform charge distributions are an important property for understanding binding of metal nanoparticles in general.« less

Cytochemical analysis of alkaline phosphatase and esterase activities and of lectin-binding and anionic sites in rat and mouse Peyer's patch M cells.

PubMed

Owen, R L; Bhalla, D K

1983-10-01

M cells in Peyer's patch follicle epithelium endocytose and transport luminal materials to intraepithelial lymphocytes. We examined (1) enzymatic characteristics of the epithelium covering mouse and rat Peyer's patches by using cytochemical techniques, (2) distribution of lectin-binding sites by peroxidase-labeled lectins, and (3) anionic site distribution by using cationized ferritin to develop a profile of M cell surface properties. Alkaline phosphatase activity resulted in deposits of dense reaction product over follicle surfaces but was markedly reduced over M cells, unlike esterase which formed equivalent or greater product over M cells. Concanavalin A, ricinus communis agglutinin, wheat germ agglutinin and peanut agglutinin reacted equally with M cells and with surrounding enterocytes over follicle surfaces. Cationized ferritin distributed in a random fashion along microvillus membranes of both M cells and enterocytes, indicating equivalent anionic site distribution. Staining for alkaline phosphatase activity provides a new approach for distinguishing M cells from enterocytes at the light microscopic level. Identical binding of lectins indicates that M cells and enterocytes share common glycoconjugates even though molecular groupings may differ. Lectin binding and anionic charge similarities of M cells and enterocytes may facilitate antigen sampling by M cells of particles and compounds that adhere to intestinal surfaces in non-Peyer's patch areas.

Spectroscopic (FTIR, FT-Raman), molecular electrostatic potential, NBO and HOMO-LUMO analysis of P-bromobenzene sulfonyl chloride based on DFT calculations

NASA Astrophysics Data System (ADS)

Jeyavijayan, S.

2015-02-01

The FTIR and FT-Raman spectra of P-bromobenzene sulfonyl chloride (P-BBSC) have been recorded in the regions 4000-400 cm-1 and 3500-50 cm-1, respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method. A good agreement between experimental and calculated normal modes of vibrations has been observed. A detailed interpretation of the infrared and Raman spectra of P-BBSC is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms. The UV-vis spectral analysis of P-BBSC has also been done which confirms the charge transfer of the molecule.

Improvement thermostability of Pseudoalteromonas carrageenovora arylsulfatase by rational design.

PubMed

Zhu, Yanbing; Qiao, Chaochao; Li, Hebin; Li, Lijun; Xiao, Anfeng; Ni, Hui; Jiang, Zedong

2018-03-01

This study aimed to improve the thermostability of arylsulfatase from Pseudoalteromonas carrageenovora. A total of 10 single-site mutants were chosen using the PoPMuSiC program, and two mutants of K253N and P314T showed enhanced thermal stability. By saturation mutagenesis and thermostability analysis, K253H and P314T were the best mutants at the two sites. Combinational mutations of K253H, P314T and H260L were subsequently introduced, and the best mutant of K253H/H260L was selected. Thermal inactivation analysis showed the half-life (t 1/2 ) value at 55°C for K253H/H260L was 7.7-fold that of the wild-type enzyme (WT), meanwhile this mutant maintained the specific enzyme activity. Structure modeling demonstrated that the additional hydrogen bonds, optimization of surface charge-charge interactions, and increasing of hydrophobic interaction could account for the improved thermostability imparted by K253H/H260L. Copyright © 2017. Published by Elsevier B.V.

A comprehensive search for calcium binding sites critical for TMEM16A calcium-activated chloride channel activity

PubMed Central

Tien, Jason; Peters, Christian J; Wong, Xiu Ming; Cheng, Tong; Jan, Yuh Nung; Jan, Lily Yeh; Yang, Huanghe

2014-01-01

TMEM16A forms calcium-activated chloride channels (CaCCs) that regulate physiological processes such as the secretions of airway epithelia and exocrine glands, the contraction of smooth muscles, and the excitability of neurons. Notwithstanding intense interest in the mechanism behind TMEM16A-CaCC calcium-dependent gating, comprehensive surveys to identify and characterize potential calcium sensors of this channel are still lacking. By aligning distantly related calcium-activated ion channels in the TMEM16 family and conducting systematic mutagenesis of all conserved acidic residues thought to be exposed to the cytoplasm, we identify four acidic amino acids as putative calcium-binding residues. Alterations of the charge, polarity, and size of amino acid side chains at these sites alter the ability of different divalent cations to activate the channel. Furthermore, TMEM16A mutant channels containing double cysteine substitutions at these residues are sensitive to the redox potential of the internal solution, providing evidence for their physical proximity and solvent accessibility. DOI: http://dx.doi.org/10.7554/eLife.02772.001 PMID:24980701

Arginine residues on the opposite side of the active site stimulate the catalysis of ribosome depurination by ricin A chain by interacting with the P-protein stalk.

PubMed

Li, Xiao-Ping; Kahn, Peter C; Kahn, Jennifer Nielsen; Grela, Przemyslaw; Tumer, Nilgun E

2013-10-18

Ricin inhibits protein synthesis by depurinating the α-sarcin/ricin loop (SRL). Ricin holotoxin does not inhibit translation unless the disulfide bond between the A (RTA) and B (RTB) subunits is reduced. Ricin holotoxin did not bind ribosomes or depurinate them but could depurinate free RNA. When RTA is separated from RTB, arginine residues located at the interface are exposed to the solvent. Because this positively charged region, but not the active site, is blocked by RTB, we mutated arginine residues at or near the interface of RTB to determine if they are critical for ribosome binding. These variants were structurally similar to wild type RTA but could not bind ribosomes. Their K(m) values and catalytic rates (k(cat)) for an SRL mimic RNA were similar to those of wild type, indicating that their activity was not altered. However, they showed an up to 5-fold increase in K(m) and up to 38-fold decrease in kcat toward ribosomes. These results suggest that the stalk binding stimulates the catalysis of ribosome depurination by RTA. The mutated arginines have side chains behind the active site cleft, indicating that the ribosome binding surface of RTA is on the opposite side of the surface that interacts with the SRL. We propose that stalk binding stimulates the catalysis of ribosome depurination by orienting the active site of RTA toward the SRL and thereby allows docking of the target adenine into the active site. This model may apply to the translation factors that interact with the stalk.

Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-ray photoreduction.

PubMed

Gudmundsson, Mikael; Kim, Seonah; Wu, Miao; Ishida, Takuya; Momeni, Majid Hadadd; Vaaje-Kolstad, Gustav; Lundberg, Daniel; Royant, Antoine; Ståhlberg, Jerry; Eijsink, Vincent G H; Beckham, Gregg T; Sandgren, Mats

2014-07-04

Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of enzymes that employ a copper-mediated, oxidative mechanism to cleave glycosidic bonds. The LPMO catalytic mechanism likely requires that molecular oxygen first binds to Cu(I), but the oxidation state in many reported LPMO structures is ambiguous, and the changes in the LPMO active site required to accommodate both oxidation states of copper have not been fully elucidated. Here, a diffraction data collection strategy minimizing the deposited x-ray dose was used to solve the crystal structure of a chitin-specific LPMO from Enterococcus faecalis (EfaCBM33A) in the Cu(II)-bound form. Subsequently, the crystalline protein was photoreduced in the x-ray beam, which revealed structural changes associated with the conversion from the initial Cu(II)-oxidized form with two coordinated water molecules, which adopts a trigonal bipyramidal geometry, to a reduced Cu(I) form in a T-shaped geometry with no coordinated water molecules. A comprehensive survey of Cu(II) and Cu(I) structures in the Cambridge Structural Database unambiguously shows that the geometries observed in the least and most reduced structures reflect binding of Cu(II) and Cu(I), respectively. Quantum mechanical calculations of the oxidized and reduced active sites reveal little change in the electronic structure of the active site measured by the active site partial charges. Together with a previous theoretical investigation of a fungal LPMO, this suggests significant functional plasticity in LPMO active sites. Overall, this study provides molecular snapshots along the reduction process to activate the LPMO catalytic machinery and provides a general method for solving LPMO structures in both copper oxidation states. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

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

Smith, Dayle MA; Xiong, Yijia; Straatsma, TP

2012-05-09

Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexiblemore » in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.« less

Photoinduced High-Frequency Charge Oscillations in Dimerized Systems

NASA Astrophysics Data System (ADS)

Yonemitsu, Kenji

2018-04-01

Photoinduced charge dynamics in dimerized systems is studied on the basis of the exact diagonalization method and the time-dependent Schrödinger equation for a one-dimensional spinless-fermion model at half filling and a two-dimensional model for κ-(bis[ethylenedithio]tetrathiafulvalene)2X [κ-(BEDT-TTF)2X] at three-quarter filling. After the application of a one-cycle pulse of a specifically polarized electric field, the charge densities at half of the sites of the system oscillate in the same phase and those at the other half oscillate in the opposite phase. For weak fields, the Fourier transform of the time profile of the charge density at any site after photoexcitation has peaks for finite-sized systems that correspond to those of the steady-state optical conductivity spectrum. For strong fields, these peaks are suppressed and a new peak appears on the high-energy side, that is, the charge densities mainly oscillate with a single frequency, although the oscillation is eventually damped. In the two-dimensional case without intersite repulsion and in the one-dimensional case, this frequency corresponds to charge-transfer processes by which all the bonds connecting the two classes of sites are exploited. Thus, this oscillation behaves as an electronic breathing mode. The relevance of the new peak to a recently found reflectivity peak in κ-(BEDT-TTF)2X after photoexcitation is discussed.

Optical backbone-sidechain charge transfer transitions in proteins sensitive to secondary structure and modifications.

PubMed

Mandal, I; Paul, S; Venkatramani, R

2018-04-17

The absorption of light by proteins can induce charge transfer (CT) transitions in the UV-visible range of the electromagnetic spectrum. Metal-ligand complexes or active site prosthetic groups which absorb in the visible region exhibit prominent CT transitions. Furthermore, the protein backbone also exhibits CT transitions in the far UV range. In this manuscript, we present a detailed computational study of new near UV-visible CT transitions that involve amino acids with charged side chains. Specifically, using time dependent density functional theory calculations, we examine the absorption spectra of naturally charged amino acids (Lys, Glu, Arg, Asp and His), extracted from solution phase protein structures generated by classical molecular dynamics simulations, and phosphorylated amino acids (Tyr, Thr and Ser) from experimentally determined protein structures. We show that amino acids with charged sidechains present a directed electronic donor-bridge-acceptor paradigm, with the lowest energy optical excitations demonstrating peptide backbone-sidechain charge separations. The UV-visible spectral range of the backbone-sidechain CT transitions is determined by the chemical nature of the donor, bridge and acceptor groups within each amino acid, amino acid conformation and the protein secondary structure where the amino acids are located. Photoinduced CT occurs in opposite directions for the anionic and cationic amino acids along the ground state dipole moment vector for the chromophores. We find that photoinduced charge separation is more facile for the anionic amino acids (Asp, Glu, pSer, pThr and pTyr) relative to that for the cationic amino acids (Lys, Arg and Hsp). Our results provide a foundation for the development of spectroscopic markers based on the recently proposed Protein Charge Transfer Spectra (ProCharTS) which are relevant for the study of DNA-binding or intrinsically disordered proteins that are rich in charged amino acids.

Highly stable CuO incorporated TiO(2) catalyst for photo-catalytic hydrogen production from H(2)O.

PubMed

Bandara, J; Udawatta, C P K; Rajapakse, C S K

2005-11-01

A CuO incorporated TiO(2) catalyst was found to be an active photo-catalyst for the reduction of H(2)O under sacrificial conditions. The catalytic activity originates from the photogeneration of excited electrons in the conduction bands of both TiO(2) and CuO resulting in a build-up of excess electrons in the conduction band of CuO. Consequently, the accumulation of excess electrons in CuO causes a negative shift in the Fermi level of CuO. The efficient inter-particle charge transfer leads to a higher catalytic activity and the formation of highly reduced states of TiO(2)/CuO, which are stable even under oxygen saturated condition. Negative shift in the Fermi level of CuO of the catalyst TiO(2)/CuO gains the required over-voltage necessary for efficient water reduction reaction. The function of CuO is to help the charge separation and to act as a water reduction site. The amount of CuO and crystalline structure were found to be crucial for the catalytic activity and the optimum CuO loading was ca. approximately 5-10%(w/w).

Defect Engineering and Phase Junction Architecture of Wide-Bandgap ZnS for Conflicting Visible Light Activity in Photocatalytic H₂ Evolution.

PubMed

Fang, Zhibin; Weng, Sunxian; Ye, Xinxin; Feng, Wenhui; Zheng, Zuyang; Lu, Meiliang; Lin, Sen; Fu, Xianzhi; Liu, Ping

2015-07-01

ZnS is among the superior photocatalysts for H2 evolution, whereas the wide bandgap restricts its performance to only UV region. Herein, defect engineering and phase junction architecture from a controllable phase transformation enable ZnS to achieve the conflicting visible-light-driven activities for H2 evolution. On the basis of first-principle density functional theory calculations, electron spin resonance and photoluminescence results, etc., it is initially proposed that the regulated sulfur vacancies in wurtzite phase of ZnS play the key role of photosensitization units for charge generation in visible light and active sites for effective electron utilization. The symbiotic sphalerite-wurtzite phase junctions that dominate the charge-transfer kinetics for photoexciton separation are the indispensable configuration in the present systems. Neither ZnS samples without phase junction nor those without enough sulfur vacancies conduct visible-light photocatalytic H2 evolution, while the one with optimized phase junctions and maximum sulfur vacancies shows considerable photocatalytic activity. This work will not only contribute to the realization of visible light photocatalysis for wide-bandgap semiconductors but also broaden the vision on the design of highly efficient transition metal sulfide photocatalysts.

38 CFR 36.4232 - Allowable fees and charges; manufactured home unit.

Code of Federal Regulations, 2013 CFR

2013-07-01

... charges; manufactured home unit. 36.4232 Section 36.4232 Pensions, Bonuses, and Veterans' Relief... Manufactured Homes and Lots, Including Site Preparation Financing Manufactured Home Units § 36.4232 Allowable fees and charges; manufactured home unit. (a) Incident to the origination of a guaranteed loan for the...

38 CFR 36.4232 - Allowable fees and charges; manufactured home unit.

Code of Federal Regulations, 2010 CFR

2010-07-01

... charges; manufactured home unit. 36.4232 Section 36.4232 Pensions, Bonuses, and Veterans' Relief... Manufactured Homes and Lots, Including Site Preparation Financing Manufactured Home Units § 36.4232 Allowable fees and charges; manufactured home unit. (a) Incident to the origination of a guaranteed loan for the...

38 CFR 36.4232 - Allowable fees and charges; manufactured home unit.

Code of Federal Regulations, 2012 CFR

2012-07-01

... charges; manufactured home unit. 36.4232 Section 36.4232 Pensions, Bonuses, and Veterans' Relief... Manufactured Homes and Lots, Including Site Preparation Financing Manufactured Home Units § 36.4232 Allowable fees and charges; manufactured home unit. (a) Incident to the origination of a guaranteed loan for the...

38 CFR 36.4232 - Allowable fees and charges; manufactured home unit.

Code of Federal Regulations, 2011 CFR

2011-07-01

... charges; manufactured home unit. 36.4232 Section 36.4232 Pensions, Bonuses, and Veterans' Relief... Manufactured Homes and Lots, Including Site Preparation Financing Manufactured Home Units § 36.4232 Allowable fees and charges; manufactured home unit. (a) Incident to the origination of a guaranteed loan for the...

38 CFR 36.4232 - Allowable fees and charges; manufactured home unit.

Code of Federal Regulations, 2014 CFR

2014-07-01

... charges; manufactured home unit. 36.4232 Section 36.4232 Pensions, Bonuses, and Veterans' Relief... Manufactured Homes and Lots, Including Site Preparation Financing Manufactured Home Units § 36.4232 Allowable fees and charges; manufactured home unit. (a) Incident to the origination of a guaranteed loan for the...

Workplace Charging Behavior of Nissan Leafs in The EV Project at Six Work Sites

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

Rohrbaugh, David; Smart, John

2014-11-01

This paper documents findings from analysis of data collected from Nissan Leafs enrolled in The EV Project who parked and charged at six workplaces with EV charging equipment. It will be published as a white paper on INL's website, accessible by the general public.

Perchlorate adsorption and desorption on activated carbon and anion exchange resin.

PubMed

Yoon, In-Ho; Meng, Xiaoguang; Wang, Chao; Kim, Kyoung-Woong; Bang, Sunbaek; Choe, Eunyoung; Lippincott, Lee

2009-05-15

The mechanisms of perchlorate adsorption on activated carbon (AC) and anion exchange resin (SR-7 resin) were investigated using Raman, FTIR, and zeta potential analyses. Batch adsorption and desorption results demonstrated that the adsorption of perchlorate by AC and SR-7 resin was reversible. The reversibility of perchlorate adsorption by the resin was also proved by column regeneration test. Solution pH significantly affected perchlorate adsorption and the zeta potential of AC, while it did not influence perchlorate adsorption and the zeta potential of resin. Zeta potential measurements showed that perchlorate was adsorbed on the negatively charged AC surface. Raman spectra indicated the adsorption resulted in an obvious position shift of the perchlorate peak, suggesting that perchlorate was associated with functional groups on AC at neutral pH through interactions stronger than electrostatic interaction. The adsorbed perchlorate on the resin exhibited a Raman peak at similar position as the aqueous perchlorate, indicating that perchlorate was adsorbed on the resin through electrostatic attraction between the anion and positively charged surface sites.

Structure and function in rhodopsin: Rhodopsin mutants with a neutral amino acid at E134 have a partially activated conformation in the dark state*

PubMed Central

Kim, Jong-Myoung; Altenbach, Christian; Thurmond, Robin L.; Khorana, H. Gobind; Hubbell, Wayne L.

1997-01-01

The Glu-134–Arg-135 residues in rhodopsin, located near the cytoplasmic end of the C helix, are involved in G protein binding, or activation, or both. Furthermore, the charge-neutralizing mutation Glu-134 to Gln-134 produces hyperactivity in the activated state and produces constitutive activity in opsin. The Glu/Asp-Arg charge pair is highly conserved in equivalent positions in other G protein-coupled receptors. To investigate the structural consequences of charge-neutralizing mutations at Glu-134 and Arg-135 in rhodopsin, single spin-labeled side chains were introduced at sites in the cytoplasmic domains of helices C (140), E (227), F (250), or G (316) to serve as “molecular sensors” of the local helix bundle conformation. In each of the spin-labeled rhodopsins, a Gln substitution was introduced at either Glu-134 or Arg-135, and the electron paramagnetic resonance spectrum of the spin label was used to monitor the structural response of the helix bundle. The results indicate that a Gln substitution at Glu-134 induces a photoactivated conformation around helices C and G even in the dark state, an observation of potential relevance to the hyperactivity and constitutive activity of the mutant. In contrast, little change is induced in helix F, which has been shown to undergo a dominant motion upon photoactivation. This result implies that the multiple helix motions accompanying photoactivation are not strongly coupled and can be induced to take place independently. Gln substitution at Arg-135 produces only minor structural changes in the dark- or light-activated conformation, suggesting that this residue is not a determinant of structure in the regions investigated, although it may be functionally important. PMID:9405602

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains.

PubMed

Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A

2011-05-19

A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society

Photoelectron Spectroscopy of the Doubly-Charged Anions [MIVO(mnt)2]2- (M=Mo, W; mnt=S2C2(CN)22-): Access to the Ground and Excited States of the [MvO(mnt)2]-Anion

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

Waters, Tom; Wang, Xue B.; Yang, Xin

2004-04-21

Photodetachment photoelectron spectroscopy was used to investigate the electronic structure of the doubly charged complexes [MIVO(mnt)2]2- (M=Mo, W;mnt=1,2 dicyanoethenedithiolato). These dianions are stable in the gas phase and are minimal models for the active sites of the dimethyl sulfoxide reductase family of molybdenum enzymes and of related tungsten enzymes. Adiabatic and vertical electron binding energies for both species were measured, providing detailed information about molecular orbital energy levels of the parent dianions as well as the ground and excited states of the product anions [MvO(mnt)2]. Density functional theory calculations were used to assist assignment of the detachment features.

SSA AND VA DISABILITY PROGRAMS: Re-Examination of Disability Criteria Needed to Help Ensure Program Integrity

DTIC Science & Technology

2002-08-01

Insurance DOT Dictionary of Occupational Titles O*NET Occupational Information Network SGA substantial gainful activity SSA Social Security Administration...Examining Disability Criteria broader social changes that focus on building and supporting the work capacities of people with disabilities. To this...available at no charge on the GAO Web site at http://www.gao.gov. If you have any Page 35 GAO-02-597 Re-Examining Disability Criteria questions about

Isotope-labeled aspartate sidechain as a non-perturbing infrared probe: Application to investigate the dynamics of a carboxylate buried inside a protein

NASA Astrophysics Data System (ADS)

Abaskharon, Rachel M.; Brown, Stephen P.; Zhang, Wenkai; Chen, Jianxin; Smith, Amos B.; Gai, Feng

2017-09-01

Because of their negatively charged carboxylates, aspartate and glutamate are frequently found at the active or binding site of proteins. However, studying a specific carboxylate in proteins that contain multiple aspartates and/or glutamates via infrared spectroscopy is difficult due to spectral overlap. We show, herein, that isotopic-labeling of the aspartate sidechain can overcome this limitation as the resultant 13COO- asymmetric stretching vibration resides in a transparent region of the protein IR spectrum. Applicability of this site-specific vibrational probe is demonstrated by using it to assess the dynamics of an aspartate ion buried inside a small protein via two-dimensional infrared spectroscopy.

Platinum-Coated Hollow Graphene Nanocages as Cathode Used in Lithium-Oxygen Batteries

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

Wu, Feng; Xing, Yi; Zeng, Xiaoqiao

2016-08-31

One of the formidable challenges facing aprotic lithium-oxygen (Li-O-2) batteries is the high charge overpotential, which induces the formation of byproducts, loss in efficiency, and poor cycling performance. Herein, the synthesis of the ultrasmall Pt-coated hollow graphene nano cages as cathode in Li-O-2 batteries is reported. The charge voltage plateau can reduce to 3.2 V at the current density of 100 mA g(-1), even maintain below 3.5 V when the current density increased to 500 mA g(-1). The unique hollow graphene nanocages matrix can not only provide numerous nanoscale tri-phase regions as active sites for efficient oxygen reduction, but alsomore » offer sufficient amount of mesoscale pores for rapid oxygen diffusion. Furthermore, with strong atomic-level oxygen absorption into its subsurface, ultrasmall Pt catalytically serves as the nucleation site for Li2O2 growth. The Li2O2 is subsequently induced into a favorable form with small size and amorphous state, decomposed more easily during recharge. Meanwhile, the conductive hollow graphene substrate can enhance the catalytic activity of noble metal Pt catalysts due to the graphene-metal interfacial interaction. Benefiting from the above synergistic effects between the hollow graphene nanocages and the nanosized Pt catalysts, the ultrasmall Pt-decorated graphene nanocage cathode exhibits enhanced electrochemical performances.« less

Tuning near-gap electronic structure, interface charge transfer and visible light response of hybrid doped graphene and Ag3PO4 composite: Dopant effects

PubMed Central

He, Chao-Ni; Huang, Wei-Qing; Xu, Liang; Yang, Yin-Cai; Zhou, Bing-Xin; Huang, Gui-Fang; Peng, P.; Liu, Wu-Ming

2016-01-01

The enhanced photocatalytic performance of doped graphene (GR)/semiconductor nanocomposites have recently been widely observed, but an understanding of the underlying mechanisms behind it is still out of reach. As a model system to study the dopant effects, we investigate the electronic structures and optical properties of doped GR/Ag3PO4 nanocomposites using the first-principles calculations, demonstrating that the band gap, near-gap electronic structure and interface charge transfer of the doped GR/Ag3PO4(100) composite can be tuned by the dopants. Interestingly, the doping atom and C atoms bonded to dopant become active sites for photocatalysis because they are positively or negatively charged due to the charge redistribution caused by interaction. The dopants can enhance the visible light absorption and photoinduced electron transfer. We propose that the N atom may be one of the most appropriate dopants for the GR/Ag3PO4 photocatalyst. This work can rationalize the available experimental results about N-doped GR-semiconductor composites, and enriches our understanding on the dopant effects in the doped GR-based composites for developing high-performance photocatalysts. PMID:26923338

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

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

Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggestmore » that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCEPost-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.« less

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

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

Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggestmore » that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCE Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.« less

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

DOE PAGES

Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.; ...

2017-11-28

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggestmore » that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCE Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.« less

New Role of Flavin as a General Acid-Base Catalyst with No Redox Function in Type 2 Isopentenyl-diphosphate Isomerase*S⃞

PubMed Central

Unno, Hideaki; Yamashita, Satoshi; Ikeda, Yosuke; Sekiguchi, Shin-ya; Yoshida, Norie; Yoshimura, Tohru; Kusunoki, Masami; Nakayama, Toru; Nishino, Tokuzo; Hemmi, Hisashi

2009-01-01

Using FMN and a reducing agent such as NAD(P)H, type 2 isopentenyl-diphosphate isomerase catalyzes isomerization between isopentenyl diphosphate and dimethylallyl diphosphate, both of which are elemental units for the biosynthesis of highly diverse isoprenoid compounds. Although the flavin cofactor is expected to be integrally involved in catalysis, its exact role remains controversial. Here we report the crystal structures of the substrate-free and complex forms of type 2 isopentenyl-diphosphate isomerase from the thermoacidophilic archaeon Sulfolobus shibatae, not only in the oxidized state but also in the reduced state. Based on the active-site structures of the reduced FMN-substrate-enzyme ternary complexes, which are in the active state, and on the data from site-directed mutagenesis at highly conserved charged or polar amino acid residues around the active site, we demonstrate that only reduced FMN, not amino acid residues, can catalyze proton addition/elimination required for the isomerase reaction. This discovery is the first evidence for this long suspected, but previously unobserved, role of flavins just as a general acid-base catalyst without playing any redox roles, and thereby expands the known functions of these versatile coenzymes. PMID:19158086

New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.

PubMed

Unno, Hideaki; Yamashita, Satoshi; Ikeda, Yosuke; Sekiguchi, Shin-Ya; Yoshida, Norie; Yoshimura, Tohru; Kusunoki, Masami; Nakayama, Toru; Nishino, Tokuzo; Hemmi, Hisashi

2009-04-03

Using FMN and a reducing agent such as NAD(P)H, type 2 isopentenyl-diphosphate isomerase catalyzes isomerization between isopentenyl diphosphate and dimethylallyl diphosphate, both of which are elemental units for the biosynthesis of highly diverse isoprenoid compounds. Although the flavin cofactor is expected to be integrally involved in catalysis, its exact role remains controversial. Here we report the crystal structures of the substrate-free and complex forms of type 2 isopentenyl-diphosphate isomerase from the thermoacidophilic archaeon Sulfolobus shibatae, not only in the oxidized state but also in the reduced state. Based on the active-site structures of the reduced FMN-substrate-enzyme ternary complexes, which are in the active state, and on the data from site-directed mutagenesis at highly conserved charged or polar amino acid residues around the active site, we demonstrate that only reduced FMN, not amino acid residues, can catalyze proton addition/elimination required for the isomerase reaction. This discovery is the first evidence for this long suspected, but previously unobserved, role of flavins just as a general acid-base catalyst without playing any redox roles, and thereby expands the known functions of these versatile coenzymes.

Environmental controls on the activity of aquifer microbial communities in the 300 area of the Hanford site.

PubMed

Konopka, Allan; Plymale, Andrew E; Carvajal, Denny A; Lin, Xueju; McKinley, James P

2013-11-01

Aquifer microbes in the 300 Area of the Hanford Site in southeastern Washington State, USA, are located in an oligotrophic environment and are periodically exposed to U(VI) concentrations that can range up to 10 μM in small sediment fractures. Assays of (3)H-leucine incorporation indicated that both sediment-associated and planktonic microbes were metabolically active, and that organic C was growth-limiting in the sediments. Although bacteria suspended in native groundwater retained high activity when exposed to 100 μM U(VI), they were inhibited by U(VI) <1 μM in synthetic groundwater that lacked added bicarbonate. Chemical speciation modeling suggested that positively charged species and particularly (UO2)3(OH)5 (+) rose in concentration as more U(VI) was added to synthetic groundwater, but that carbonate complexes dominated U(VI) speciation in natural groundwater. U toxicity was relieved when increasing amounts of bicarbonate were added to synthetic groundwater containing 4.5 μM U(VI). Pertechnetate, an oxyanion that is another contaminant of concern at the Hanford Site, was not toxic to groundwater microbes at concentrations up to 125 μM.

The role of surface/interfacial Cu{sup 2+} sites in the photocatalytic activity of coupled CuO-TiO{sub 2} nanocomposites.

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

Li, G.; Dimitrijevic, N. M.; Chen, L.

Coupled CuO-TiO{sub 2} nanocomposite photocatalysts were prepared by a deposition precipitation method and were characterized with a variety of techniques. Electron paramagnetic resonance (EPR) spectroscopy was employed to study the local structures of surface/interfacial Cu{sup 2+}+ sites using Cu{sup 2+} as a sensitive paramagnetic probe. The addition of bulk CuO to TiO{sub 2} led to decreased photocatalytic efficiency in the degradation of methylene blue. However, doping with a very small amount of CuO (0.1 wt % copper loading) significantly enhanced the photocatalytic activity of TiO{sub 2}. EPR study of the TiO{sub 2} surface revealed the presence of both highly dispersedmore » CuO clusters and substitutional Cu{sup 2+} sites (Ti-O-Cu linkages) at 0.1 wt % copper loading. The data suggest that the Ti-O-Cu linkages contributed to the improved photooxidative activity of the 0.1% CuO-TiO{sub 2} nanocomposite. In contrast, at higher loadings the bulk form of CuO created charge recombination centers lowering the photoactivity of the composites.« less

Physico-chemical studies of the experimental and theoretical properties of organic nonlinear optical material 4-chloro-4'methoxy benzylideneaniline

NASA Astrophysics Data System (ADS)

George, Merin; John, Nimmy L.; Saravana Kumar, M.; Subashini, A.; Sajan, D.

2017-01-01

The FT-IR, FT-Raman and UV-visible spectral analysis of 4-chloro 4'-methoxy benzylidene aniline were done experimentally and interpreted with the aid of normal coordinate analysis based on density functional theory (DFT) at the B3LYP/6-311++G (d, p) level of theory. Natural Bond orbital analysis was performed to understand the charge transfer interactions and reactive sites within the system. HOMO-LUMO analysis and first static and dynamic hyperpolarizability calculations were carried out in order to confirm the NLO activity of CMOBA. Photophysical characterization was done to understand the fluorescence emission and lifetime of CMOBA leading to application in blue OLEDs. The Molecular Electrostatic Potential Map was simulated to identify the active sites for electrophilic and nucleophilic attack or the active sites of the molecule which can bind to proteins. Molecular docking analysis revealed its potential as an inhibitor for different proteins which are responsible for cancer and many inflammatory diseases such as rheumatoid arthritis, inflammatory bowel disease, Crohn's disease and psoriasis. Experimental studies of invitro antiproliferative effect by MTT assay verified the anticancer properties of CMOBA.

Oxygen reduction reaction activity and structural stability of Pt-Au nanoparticles prepared by arc-plasma deposition.

PubMed

Takahashi, Shuntaro; Chiba, Hiroshi; Kato, Takashi; Endo, Shota; Hayashi, Takehiro; Todoroki, Naoto; Wadayama, Toshimasa

2015-07-28

The oxygen reduction reaction (ORR) activity and durability of various Au(x)/Pt100 nanoparticles (where x is the atomic ratio of Au against Pt) are evaluated herein. The samples were fabricated on a highly-oriented pyrolytic graphite substrate at 773 K through sequential arc-plasma depositions of Pt and Au. The electrochemical hydrogen adsorption charges (electrochemical surface area), particularly the characteristic currents caused by the corner and edge sites of the Pt nanoparticles, decrease with increasing Au atomic ratio (x). In contrast, the specific ORR activities of the Au(x)/Pt100 samples were dependent on the atomic ratios of Pt and Au: the Au28/Pt100 sample showed the highest specific activity among all the investigated samples (x = 0-42). As for ORR durability evaluated by applying potential cycles between 0.6 and 1.0 V in oxygen-saturated 0.1 M HClO4, Au28/Pt100 was the most durable sample against the electrochemical potential cycles. The results clearly showed that the Au atoms located at coordinatively-unsaturated sites, e.g. at the corners or edges of the Pt nanoparticles, can improve the ORR durability by suppressing unsaturated-site-induced degradation of the Pt nanoparticles.

Highly efficient nonprecious metal catalyst prepared with metal–organic framework in a continuous carbon nanofibrous network

PubMed Central

Shui, Jianglan; Chen, Chen; Grabstanowicz, Lauren; Zhao, Dan; Liu, Di-Jia

2015-01-01

Fuel cell vehicles, the only all-electric technology with a demonstrated >300 miles per fill travel range, use Pt as the electrode catalyst. The high price of Pt creates a major cost barrier for large-scale implementation of polymer electrolyte membrane fuel cells. Nonprecious metal catalysts (NPMCs) represent attractive low-cost alternatives. However, a significantly lower turnover frequency at the individual catalytic site renders the traditional carbon-supported NPMCs inadequate in reaching the desired performance afforded by Pt. Unconventional catalyst design aiming at maximizing the active site density at much improved mass and charge transports is essential for the next-generation NPMC. We report here a method of preparing highly efficient, nanofibrous NPMC for cathodic oxygen reduction reaction by electrospinning a polymer solution containing ferrous organometallics and zeolitic imidazolate framework followed by thermal activation. The catalyst offers a carbon nanonetwork architecture made of microporous nanofibers decorated by uniformly distributed high-density active sites. In a single-cell test, the membrane electrode containing such a catalyst delivered unprecedented volumetric activities of 3.3 A⋅cm−3 at 0.9 V or 450 A⋅cm−3 extrapolated at 0.8 V, representing the highest reported value in the literature. Improved fuel cell durability was also observed. PMID:26261338

Highly efficient nonprecious metal catalyst prepared with metal–organic framework in a continuous carbon nanofibrous network

DOE PAGES

Shui, Jianglan; Chen, Chen; Grabstanowicz, Lauren; ...

2015-08-25

Fuel cell vehicles, the only all-electric technology with a demonstrated >300 miles per fill travel range, use Pt as the electrode catalyst. The high price of Pt creates a major cost barrier for large-scale implementation of polymer electrolyte membrane fuel cells. Nonprecious metal catalysts (NPMCs) represent attractive low-cost alternatives. However, a significantly lower turnover frequency at the individual catalytic site renders the traditional carbon-supported NPMCs inadequate in reaching the desired performance afforded by Pt. Unconventional catalyst design aiming at maximizing the active site density at much improved mass and charge transports is essential for the next-generation NPMC. We report heremore » a method of preparing highly efficient, nanofibrous NPMC for cathodic oxygen reduction reaction by electrospinning a polymer solution containing ferrous organometallics and zeolitic imidazolate framework followed by thermal activation. The catalyst offers a carbon nanonetwork architecture made of microporous nanofibers decorated by uniformly distributed high-density active sites. In a single-cell test, the membrane electrode containing such a catalyst delivered unprecedented volumetric activities of 3.3 A∙cm -3 at 0.9 V or 450 A∙cm -3 extrapolated at 0.8 V, representing the highest reported value in the literature. Improved fuel cell durability was also observed.« less

Highly efficient nonprecious metal catalyst prepared with metal-organic framework in a continuous carbon nanofibrous network.

PubMed

Shui, Jianglan; Chen, Chen; Grabstanowicz, Lauren; Zhao, Dan; Liu, Di-Jia

2015-08-25

Fuel cell vehicles, the only all-electric technology with a demonstrated >300 miles per fill travel range, use Pt as the electrode catalyst. The high price of Pt creates a major cost barrier for large-scale implementation of polymer electrolyte membrane fuel cells. Nonprecious metal catalysts (NPMCs) represent attractive low-cost alternatives. However, a significantly lower turnover frequency at the individual catalytic site renders the traditional carbon-supported NPMCs inadequate in reaching the desired performance afforded by Pt. Unconventional catalyst design aiming at maximizing the active site density at much improved mass and charge transports is essential for the next-generation NPMC. We report here a method of preparing highly efficient, nanofibrous NPMC for cathodic oxygen reduction reaction by electrospinning a polymer solution containing ferrous organometallics and zeolitic imidazolate framework followed by thermal activation. The catalyst offers a carbon nanonetwork architecture made of microporous nanofibers decorated by uniformly distributed high-density active sites. In a single-cell test, the membrane electrode containing such a catalyst delivered unprecedented volumetric activities of 3.3 A ⋅ cm(-3) at 0.9 V or 450 A ⋅ cm(-3) extrapolated at 0.8 V, representing the highest reported value in the literature. Improved fuel cell durability was also observed.

Long-range electrostatic complementarity governs substrate recognition by human chymotrypsin C, a key regulator of digestive enzyme activation.

PubMed

Batra, Jyotica; Szabó, András; Caulfield, Thomas R; Soares, Alexei S; Sahin-Tóth, Miklós; Radisky, Evette S

2013-04-05

Human chymotrypsin C (CTRC) is a pancreatic serine protease that regulates activation and degradation of trypsinogens and procarboxypeptidases by targeting specific cleavage sites within their zymogen precursors. In cleaving these regulatory sites, which are characterized by multiple flanking acidic residues, CTRC shows substrate specificity that is distinct from that of other isoforms of chymotrypsin and elastase. Here, we report the first crystal structure of active CTRC, determined at 1.9-Å resolution, revealing the structural basis for binding specificity. The structure shows human CTRC bound to the small protein protease inhibitor eglin c, which binds in a substrate-like manner filling the S6-S5' subsites of the substrate binding cleft. Significant binding affinity derives from burial of preferred hydrophobic residues at the P1, P4, and P2' positions of CTRC, although acidic P2' residues can also be accommodated by formation of an interfacial salt bridge. Acidic residues may also be specifically accommodated in the P6 position. The most unique structural feature of CTRC is a ring of intense positive electrostatic surface potential surrounding the primarily hydrophobic substrate binding site. Our results indicate that long-range electrostatic attraction toward substrates of concentrated negative charge governs substrate discrimination, which explains CTRC selectivity in regulating active digestive enzyme levels.

Activation barriers for methylation of DNA bases by dimethyl sulfate

NASA Astrophysics Data System (ADS)

Eichler, Daniel R.; Papadantonakis, George A.

2017-12-01

The SN2 transition states of the methylation reaction of DNA bases with dimethyl sulfate were examined employing DFT/ M06-2X/6-31+G∗ and DFT/B3LYP-D3/6-311+G (2df, 2p) levels of theory. Solvation effects were examined using the conductor-like polarizable continuum model (CPCM). Calculation results and feedback from electrostatic potential maps show that in water, charge separation lowers the activation barriers relative to the gas phase for the reactions at N7 of guanine, N3 of adenine and cytosine. Also, the reaction at the O6 site of guanine is governed by steric interference and exhibits a higher activation barrier in water.

Electrochemical studies on nanometal oxide-activated carbon composite electrodes for aqueous supercapacitors

NASA Astrophysics Data System (ADS)

Ho, Mui Yen; Khiew, Poi Sim; Isa, Dino; Chiu, Wee Siong

2014-11-01

In present study, the electrochemical performance of eco-friendly and cost-effective titanium oxide (TiO2)-based and zinc oxide-based nanocomposite electrodes were studied in neutral aqueous Na2SO3 electrolyte, respectively. The electrochemical properties of these composite electrodes were studied using cyclic voltammetry (CV), galvanostatic charge-discharge (CD) and electrochemical impedance spectroscopy (EIS). The experimental results reveal that these two nanocomposite electrodes achieve the highest specific capacitance at fairly low oxide loading onto activated carbon (AC) electrodes, respectively. Considerable enhancement of the electrochemical properties of TiO2/AC and ZnO/AC nanocomposite electrodes is achieved via synergistic effects contributed from the nanostructured metal oxides and the high surface area mesoporous AC. Cations and anions from metal oxides and aqueous electrolyte such as Ti4+, Zn2+, Na+ and SO32- can occupy some pores within the high-surface-area AC electrodes, forming the electric double layer at the electrode-electrolyte interface. Additionally, both TiO2 and ZnO nanoparticles can provide favourable surface adsorption sites for SO32- anions which subsequently facilitate the faradaic processes for pseudocapacitive effect. These two systems provide the low cost material electrodes and the low environmental impact electrolyte which offer the increased charge storage without compromising charge storage kinetics.

Hydrogenated MoS2 QD-TiO2 heterojunction mediated efficient solar hydrogen production.

PubMed

Saha, Arka; Sinhamahapatra, Apurba; Kang, Tong-Hyun; Ghosh, Subhash C; Yu, Jong-Sung; Panda, Asit B

2017-11-09

Herein, we report the development of a hydrogenated MoS 2 QD-TiO 2 (HMT) heterojunction as an efficient photocatalytic system via a one-pot hydrothermal reaction followed by hydrogenation. This synthetic strategy facilitates the formation of MoS 2 QDs with an enhanced band gap and a proper heterojunction between them and TiO 2 , which accelerates charge transfer process. Hydrogenation leads to oxygen vacancies in TiO 2 , enhancing the visible light absorption capacity through narrowing its band gap, and sulfur vacancies in MoS 2 , which enhance the active sites for hydrogen adsorption. Due to the band gap reduction of hydrogenated TiO 2 and the band gap enhancement of the MoS 2 QDs, the energy states are rearranged to create a reverse movement of electrons and holes facilitated the charge transfer process which enhance life-time of photo-generated charges. The photocatalyst showed stable, efficient and exceptionally high noble metal free sunlight-induced hydrogen production with a maximum rate of 3.1 mmol g -1 h -1 . The developed synthetic strategy also provides flexibility towards the shape of the MoS 2 , e.g. QDs/single or few layers, on TiO 2 and offers the opportunity to design novel visible light active photocatalysts for different applications.

Hierarchical FeTiO3-TiO2 hollow spheres for efficient simulated sunlight-driven water oxidation.

PubMed

Han, Taoran; Chen, Yajie; Tian, Guohui; Wang, Jian-Qiang; Ren, Zhiyu; Zhou, Wei; Fu, Honggang

2015-10-14

Oxygen generation is the key step for the photocatalytic overall water splitting and considered to be kinetically more challenging than hydrogen generation. Here, an effective water oxidation catalyst of hierarchical FeTiO3-TiO2 hollow spheres are prepared via a two-step sequential solvothermal processes and followed by thermal treatment. The existence of an effective heterointerface and built-in electric field in the surface space charge region in FeTiO3-TiO2 hollow spheres plays a positive role in promoting the separation of photoinduced electron-hole pairs. Surface photovoltage, transient-state photovoltage, fluorescence and electrochemical characterization are used to investigate the transfer process of photoinduced charge carriers. The photogenerated charge carriers in the hierarchical FeTiO3-TiO2 hollow spheres with a proper molar ratio display much higher separation efficiency and longer lifetime than those in the FeTiO3 alone. Moreover, it is suggested that the hierarchical porous hollow structure can contribute to the enhancement of light utilization, surface active sites and material transportation through the framework walls. This specific synergy significantly contributes to the remarkable improvement of the photocatalytic water oxidation activity of the hierarchical FeTiO3-TiO2 hollow spheres under simulated sunlight (AM1.5).

Ion/Ion Reactions with "Onium" Reagents: An Approach for the Gas-phase Transfer of Organic Cations to Multiply-Charged Anions

NASA Astrophysics Data System (ADS)

Gilbert, Joshua D.; Prentice, Boone M.; McLuckey, Scott A.

2015-05-01

The use of ion/ion reactions to effect gas-phase alkylation is demonstrated. Commonly used fixed-charge "onium" cations are well-suited for ion/ion reactions with multiply deprotonated analytes because of their tendency to form long-lived electrostatic complexes. Activation of these complexes results in an SN2 reaction that yields an alkylated anion with the loss of a neutral remnant of the reagent. This alkylation process forms the basis of a general method for alkylation of deprotonated analytes generated via electrospray, and is demonstrated on a variety of anionic sites. SN2 reactions of this nature are demonstrated empirically and characterized using density functional theory (DFT). This method for modification in the gas phase is extended to the transfer of larger and more complex R groups that can be used in later gas-phase synthesis steps. For example, N-cyclohexyl- N'-(2-morpholinoethyl)carbodiimide (CMC) is used to transfer a carbodiimide functionality to a peptide anion containing a carboxylic acid. Subsequent activation yields a selective reaction between the transferred carbodiimide group and a carboxylic acid, suggesting the carbodiimide functionality is retained through the transfer process. Many different R groups are transferable using this method, allowing for new possibilities for charge manipulation and derivatization in the gas phase.

Controlling the Local Electronic Properties of Si(553)-Au through Hydrogen Doping

NASA Astrophysics Data System (ADS)

Hogan, C.; Speiser, E.; Chandola, S.; Suchkova, S.; Aulbach, J.; Schäfer, J.; Meyer, S.; Claessen, R.; Esser, N.

2018-04-01

We propose a quantitative and reversible method for tuning the charge localization of Au-stabilized stepped Si surfaces by site-specific hydrogenation. This is demonstrated for Si(553)-Au as a model system by combining density functional theory simulations and reflectance anisotropy spectroscopy experiments. We find that controlled H passivation is a two-step process: step-edge adsorption drives excess charge into the conducting metal chain "reservoir" and renders it insulating, while surplus H recovers metallic behavior. Our approach illustrates a route towards microscopic manipulation of the local surface charge distribution and establishes a reversible switch of site-specific chemical reactivity and magnetic properties on vicinal surfaces.

Testing a structural model for viral DNA packaging motor function by optical tweezers measurements, site directed mutagenesis, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Keller, Nicholas A.; Migliori, Amy D.; Arya, Gaurav; Rao, Venigalla B.; Smith, Douglas E.

2013-09-01

Many double-stranded DNA viruses employ a molecular motor to package DNA into preformed capsid shells. Based on structures of phage T4 motor proteins determined by X-ray crystallography and cryo-electron microscopy, Rao, Rossmann and coworkers recently proposed a structural model for motor function. They proposed that DNA is ratcheted by a large conformational change driven by electrostatic interactions between charged residues at an interface between two globular domains of the motor protein. We have conducted experiments to test this model by studying the effect on packaging under applied load of site-directed changes altering these residues. We observe significant impairment of packaging activity including reductions in packaging rate, percent time packaging, and time active under high load. We show that these measured impairments correlate well with alterations in free energies associated with the conformational change predicted by molecular dynamics simulations.

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase.

PubMed

Sevastik, Robin; Himo, Fahmi

2007-12-01

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.

Quantum mechanical/molecular mechanical and docking study of the novel analogues based on hybridization of common pharmacophores as potential anti-breast cancer agents

PubMed Central

Asadi, Parvin; Khodarahmi, Ghadamali; Farrokhpour, Hossein; Hassanzadeh, Farshid; Saghaei, Lotfollah

2017-01-01

In an attempt to identify some new potential leads as anti-breast cancer agents, novel hybrid compounds were designed by molecular hybridization approach. These derivatives were structurally derived from hybrid benzofuran–imidazole and quinazolinone derivatives, which had shown good cytotoxicity against the breast cancer cell line (MCF-7). Since aromatase enzyme (CYP19) is highly expressed in the MCF-7 cell line, the binding of these novel hybrid compounds to aromatase was investigated using the docking method. In this study, due to the positive charge on the imidazole ring of the designed ligands and also, the presence of heme iron in the active site of the enzyme, it was decided to optimize the ligand inside the protein to obtain more realistic atomic charges for it. Quantum mechanical/molecular mechanical (QM/MM) method was used to obtain more accurate atomic charges of ligand for docking calculations by considering the polarization effects of CYP19 on ligands. It was observed that the refitted charge improved the binding energy of the docked compounds. Also, the results showed that these novel hybrid compounds were adopted properly within the aromatase binding site, thereby suggesting that they could be potential inhibitors of aromatase. The main binding modes in these complexes were through hydrophobic and H bond interactions showing agreement with the basic physicochemical features of known anti aromatase compounds. Finally, the complex structures obtained from the docking study were used for single point QM/MM calculations to obtain more accurate electronic interaction energy, considering the electronic polarization of the ligand by its protein environment. PMID:28626481

Charged particle detectors with active detector surface for partial energy deposition of the charged particles and related methods

DOEpatents

Gerts, David W; Bean, Robert S; Metcalf, Richard R

2013-02-19

A radiation detector is disclosed. The radiation detector comprises an active detector surface configured to generate charge carriers in response to charged particles associated with incident radiation. The active detector surface is further configured with a sufficient thickness for a partial energy deposition of the charged particles to occur and permit the charged particles to pass through the active detector surface. The radiation detector further comprises a plurality of voltage leads coupled to the active detector surface. The plurality of voltage leads is configured to couple to a voltage source to generate a voltage drop across the active detector surface and to separate the charge carriers into a plurality of electrons and holes for detection. The active detector surface may comprise one or more graphene layers. Timing data between active detector surfaces may be used to determine energy of the incident radiation. Other apparatuses and methods are disclosed herein.

Directed Evolution of a Thermostable Quorum-quenching Lactonase from the Amidohydrolase Superfamily*

PubMed Central

Chow, Jeng Yeong; Xue, Bo; Lee, Kang Hao; Tung, Alvin; Wu, Long; Robinson, Robert C.; Yew, Wen Shan

2010-01-01

A thermostable quorum-quenching lactonase from Geobacillus kaustophilus HTA426 (GI: 56420041) was used as an initial template for in vitro directed evolution experiments. This enzyme belongs to the phosphotriesterase-like lactonase (PLL) group of enzymes within the amidohydrolase superfamily that hydrolyze N-acylhomoserine lactones (AHLs) that are involved in virulence pathways of quorum-sensing pathogenic bacteria. Here we have determined the N-butyryl-l-homoserine lactone-liganded structure of the catalytically inactive D266N mutant of this enzyme to a resolution of 1.6 Å. Using a tunable, bioluminescence-based quorum-quenching molecular circuit, the catalytic efficiency was enhanced, and the AHL substrate range increased through two point mutations on the loops at the C-terminal ends of the third and seventh β-strands. This E101N/R230I mutant had an increased value of kcat/Km of 72-fold toward 3-oxo-N-dodecanoyl-l-homoserine lactone. The evolved mutant also exhibited lactonase activity toward N-butyryl-l-homoserine lactone, an AHL that was previously not hydrolyzed by the wild-type enzyme. Both the purified wild-type and mutant enzymes contain a mixture of zinc and iron and are colored purple and brown, respectively, at high concentrations. The origin of this coloration is suggested to be because of a charge transfer complex involving the β-cation and Tyr-99 within the enzyme active site. Modulation of the charge transfer complex alters the lactonase activity of the mutant enzymes and is reflected in enzyme coloration changes. We attribute the observed enhancement in catalytic reactivity of the evolved enzyme to favorable modulations of the active site architecture toward productive geometries required for chemical catalysis. PMID:20980257

Charge stabilization and entropy reduction of central lysine residues in fructose-bisphosphate aldolase.

PubMed

St-Jean, Miguel; Blonski, Casimir; Sygusch, Jurgen

2009-06-02

Fructose-1,6-bisphosphate muscle aldolase is an essential glycolytic enzyme that catalyzes reversible carbon-carbon bond formation by cleaving fructose 1,6-bisphosphate to yield dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde phosphate. To elucidate the mechanistic role of conserved amino acid Asp-33, Asn-33 and Ser-33 mutants were examined by kinetic and structural analyses. The mutations significantly compromised enzymatic activity and carbanion oxidation in presence of DHAP. Detailed structural analysis demonstrated that, like native crystals, Asp-33 mutant crystals, soaked in DHAP solutions, trapped Schiff base-derived intermediates covalently attached to Lys-229. The mutant structures, however, exhibited an abridged conformational change with the helical region (34-65) flanking the active site as well as pK(a) reductions and increased side chain disorder by central lysine residues, Lys-107 and Lys-146. These changes directly affect their interaction with the C-terminal Tyr-363, consistent with the absence of active site binding by the C-terminal region in the presence of phosphate. Lys-146 pK(a) reduction and side chain disorder would further compromise charge stabilization during C-C bond cleavage and proton transfer during enamine formation. These mechanistic impediments explain diminished catalytic activity and a reduced level of carbanion oxidation and are consistent with rate-determining proton transfer observed in the Asn-33 mutant. Asp-33 reduces the entropic cost and augments the enthalpic gain during catalysis by rigidifying Lys-107 and Lys-146, stabilizing their protonated forms, and promoting a conformational change triggered by substrate or obligate product binding, which lower kinetic barriers in C-C bond cleavage and Schiff base-enamine interconversion.

Directed evolution of a thermostable quorum-quenching lactonase from the amidohydrolase superfamily.

PubMed

Chow, Jeng Yeong; Xue, Bo; Lee, Kang Hao; Tung, Alvin; Wu, Long; Robinson, Robert C; Yew, Wen Shan

2010-12-24

A thermostable quorum-quenching lactonase from Geobacillus kaustophilus HTA426 (GI: 56420041) was used as an initial template for in vitro directed evolution experiments. This enzyme belongs to the phosphotriesterase-like lactonase (PLL) group of enzymes within the amidohydrolase superfamily that hydrolyze N-acylhomoserine lactones (AHLs) that are involved in virulence pathways of quorum-sensing pathogenic bacteria. Here we have determined the N-butyryl-L-homoserine lactone-liganded structure of the catalytically inactive D266N mutant of this enzyme to a resolution of 1.6 Å. Using a tunable, bioluminescence-based quorum-quenching molecular circuit, the catalytic efficiency was enhanced, and the AHL substrate range increased through two point mutations on the loops at the C-terminal ends of the third and seventh β-strands. This E101N/R230I mutant had an increased value of k(cat)/K(m) of 72-fold toward 3-oxo-N-dodecanoyl-L-homoserine lactone. The evolved mutant also exhibited lactonase activity toward N-butyryl-L-homoserine lactone, an AHL that was previously not hydrolyzed by the wild-type enzyme. Both the purified wild-type and mutant enzymes contain a mixture of zinc and iron and are colored purple and brown, respectively, at high concentrations. The origin of this coloration is suggested to be because of a charge transfer complex involving the β-cation and Tyr-99 within the enzyme active site. Modulation of the charge transfer complex alters the lactonase activity of the mutant enzymes and is reflected in enzyme coloration changes. We attribute the observed enhancement in catalytic reactivity of the evolved enzyme to favorable modulations of the active site architecture toward productive geometries required for chemical catalysis.

Reply to ``Comment on `Spin- and charge-ordering in oxygen-vacancy-ordered mixed-valence Sr4Fe4O11 ' ''

NASA Astrophysics Data System (ADS)

Ravindran, P.; Vidya, R.; Fjellvåg, H.; Kjekshus, A.

2008-04-01

Recently, using density-functional theoretical calculations, we have reported [Phys. Rev. B 74, 054422 (2006)] that formal Fe3+ ions reside at the square-pyramidal site and Fe4+ ions in the octahedral site in Sr4Fe4O11 . Based on the interpretation of experimental structural and Mössbauer data from the literature, Adler concludes that our previous first-principles results disagree with experiments on the assignment of oxidation states to Fe in the square-pyramidal and octahedral environments in Sr4Fe4O11 . From a critical examination of the structure data for Sr4Fe4O11 and related oxides with Fe in different oxidation states and theoretically simulated Mössbauer parameters (hyperfine field, isomer shift, and quadrupole splitting), here we show that information on charges residing on the different constituents cannot be directly derived either from experimental structure or Mössbauer data. From additional analyses of the chemical bonding on the basis of charge density, charge transfer, electron localization function, crystal orbital Hamilton population, Born effective charge, and partial density of states, we substantiate our previous assignment of formal Fe3+ and Fe4+ to the square-pyramidal and octahedral sites, respectively, in Sr4Fe4O11 .

Ionic charge distributions of energetic particles from solar flares

NASA Technical Reports Server (NTRS)

Mullan, D. J.; Waldron, W. L.

1986-01-01

The effects which solar flare X-rays have on the charge states of solar cosmic rays is determined quantitatively. Rather than to characterize the charge distribution by temperature alone, it is proposed that the X-ray flux at the acceleration site also is used. The effects of flare X-rays are modeled mathematically.

Tuning charge transfer in the LaTiO3/RO/LaNiO3 (R = rare-earth) superlattices by the rare-earth oxides interfaces from a first-principles calculation

NASA Astrophysics Data System (ADS)

Yao, Fen; Zhang, Lifang; Meng, Junling; Liu, Xiaojuan; Zhang, Xiong; Zhang, Wenwen; Meng, Jian; Zhang, Hongjie

2018-03-01

We investigate the internal charge transfer at the isopolar interfaces in LaTiO3/RO/LaNiO3 (R = La, Ce, Pr, Nd, Sm, Gd, Tb, Dy, Ho, Er, Tm, and Lu) superlattices by means of density functional theory calculations. The charge transfer from Ti sites to Ni sites in all superlattices is induced by the electronegativity difference between the elements Ti and Ni, and the lanthanide oxides interfaces can modulate the amount of charge transfer. Comparison of the perovskite heterostructures with the different rare-earth interfaces shows that increasing the deviations of bond angles from 180.0° and the oxygen motions near the interfaces enhance charge transfer. The 4f electrons themselves of rare-earth elements have faint influences on charge transfer. In addition, the reasons why our calculated 4f states of Sm and Tm elements disagree with the experimental systems have been provided. It is hoped that all the calculated results could be used to design new functional nanoelectronic devices in perovskite oxides.

Convective transport of electric charge within the planetary boundary layer

NASA Astrophysics Data System (ADS)

Nicoll, Keri; Harrison, Giles; Silva, Hugo; Silgado, Rui; Melgao, Marta

2017-04-01

Turbulent and convective processes within the planetary boundary layer are responsible for the transport of moisture, momentum and particulate matter, but are also of major importance in determining the electrical charge structure of the lower atmosphere. This paper presents rare experimental measurements of vertical profiles of charge measured during fair weather conditions by specially instrumented radiosonde balloons over Alqueva, Portugal during the summer of 2014. Space charge was measured directly using a sensitive electrometer, rather than the conventional method of deriving it from electric field measurements. The high frequency of balloon flights enabled the diurnal variation in the vertical profile of charge within the boundary layer to be examined in detail, with much smaller levels of charge (up to 20pC m-3) observed during stable night time periods than during the day. Following sunrise, the evolution of the charge profile was much more complex, showing a dependence on lofting of surface aerosol due to daytime convection. This produced charge up to 92pC m-3 up to 500m above the surface. The diurnal variation in the integrated column of charge above the measurement site was also found to track closely with the diurnal variation in near surface charge as measured by an electric field mill at the same site, confirming the importance of the link between surface charge generation processes and aloft. Co-located lidar backscatter measurements were also made during the measurement campaign and will be discussed here in the context of the effect of aerosol on the vertical charge profile.

Investigation of the Origin of Catalytic Activity in Oxide-Supported Nanoparticle Gold

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

Harrison, Ian

Since Haruta’s discovery in 1987 of the surprising catalytic activity of supported Au nanoparticles, we have seen a very large number of experimental and theoretical efforts to explain this activity and to fully understand the nature of the behavior of the responsible active sites. In 2011, we discovered that a dual catalytic site at the perimeter of ~3nm diameter Au particles supported on TiO 2 is responsible for oxidative catalytic activity. O 2 molecules bind with Au atoms and Ti4+ ions in the TiO 2 support and the weakened O-O bond dissociates at low temperatures, proceeding to produce O atomsmore » which act as oxidizing agents for the test molecule, CO. The papers supported by DOE have built on this finding and have been concerned with two aspects of the behavior of Au/TiO 2 catalysts: (1). Mechanistic behavior of dual catalytic sites in the oxidation of organic molecules such as ethylene and acetic acid; (2). Studies of the electronic properties of the TiO 2 (110) single crystal in relation to its participation in charge transfer at the occupied dual catalytic site. A total of 20 papers have been produced through DOE support of this work. The papers combine IR spectroscopic investigations of Au/TiO 2 catalysts with surface science on the TiO 2(110) and TiO 2 nanoparticle surfaces with modern density functional modeling. The primary goals of the work were to investigate the behavior of the dual Au/Ti 4+ site for the partial oxidation of alcohols to acids, the hydrogenation of aldehydes and ketones to alcohols, and the condensation of oxygenate intermediates- all processes related to the utilization of biomass in the production of useful chemical energy sources.« less

Energetics of halogen impurities in thorium dioxide

NASA Astrophysics Data System (ADS)

Kuganathan, Navaratnarajah; Ghosh, Partha S.; Arya, Ashok K.; Dey, Gautam K.; Grimes, Robin W.

2017-11-01

Defect energies for halogen impurity atoms (Cl, Br and I) in thoria are calculated using the generalized gradient approximation and projector augmented plane wave potentials under the framework of density functional theory. The energy to place a halogen atom at a pre-existing lattice site is the incorporation energy. Seven sites are considered: octahedral interstitial, O vacancy, Th vacancy, Th-O di-vacancy cluster (DV) and the three O-Th-O tri-vacancy cluster (NTV) configurations. For point defects and vacancy clusters, neutral and all possible defect charge states up to full formal charge are considered. The most favourable incorporation site for Cl is the singly charged positive oxygen vacancy while for Br and I it is the NTV1 cluster. By considering the energy to form the defect sites, solution energies are generated. These show that in both ThO2-x and ThO2 the most favourable solution equilibrium site for halides is the single positively charged oxygen vacancy (although in ThO2, I demonstrates the same solubility in the NTV1 and DV clusters). Solution energies are much lower in ThO2-x than in ThO2 indicating that stoichiometry is a significant factor in determining solubility. In ThO2, all three halogens are highly insoluble and in ThO2-x Br and I remain insoluble. Although ½Cl2 is soluble in ThO2-x alternative phases such as ZrCl4 exist which are of lower energy.

Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling

NASA Astrophysics Data System (ADS)

Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Donohoe, Gregory C.; Valentine, Stephen J.

2016-03-01

Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M - 2H]2- ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites, whereas for the more diffuse [M - 3H]3- ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M - 2H]2- ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M - 3H]3- ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.

Cadmium mobility in sediments and soils from a coal mining area on Tibagi River watershed: environmental risk assessment.

PubMed

Galunin, Evgeny; Ferreti, Jeferson; Zapelini, Iago; Vieira, Isadora; Ricardo Teixeira Tarley, César; Abrão, Taufik; Santos, Maria Josefa

2014-01-30

The risk of cadmium contamination in the Tibagi River watershed (Parana State, Brazil) affected by past coal mining activities was assessed through sorption-desorption modeling for sediment and soil samples. The acidic character of the samples resulted in more competition between the cadmium ions and protons, thereby influencing the cadmium sorption-desorption. The sorption isotherms were fitted to the Langmuir and Freundlich single models and to the dual-site Langmuir-Freundlich (or Sips) model. The single-site models indicated a low-energy character of sorption sites on the sample sorption sites, whereas the dual-site model explained the availability of higher-affinity and lower-affinity non-specific sites. The correlation of the sorption and desorption constants with the physicochemical and mineralogical characteristics of the samples showed that the cadmium sorption behavior was significantly affected by the pH, point of zero charge, and also by the magnesium, aluminum, calcium and manganese amounts. Besides, the desorption rate and hysteresis index suggested a high risk of cadmium mobilization along the Tibagi River basin. Copyright © 2013 Elsevier B.V. All rights reserved.

The Pseudomonas aeruginosa Catabolite Repression Control Protein Crc Is Devoid of RNA Binding Activity

PubMed Central

Djinovic-Carugo, Kristina; Bläsi, Udo

2013-01-01

The Crc protein has been shown to mediate catabolite repression control in Pseudomonas, leading to a preferential assimilation of carbon sources. It has been suggested that Crc acts as a translational repressor of mRNAs, encoding functions involved in uptake and breakdown of different carbon sources. Moreover, the regulatory RNA CrcZ, the level of which is increased in the presence of less preferred carbon sources, was suggested to bind to and sequester Crc, resulting in a relief of catabolite repression. Here, we determined the crystal structure of Pseudomonas aeruginosa Crc, a member of apurinic/apyrimidinic (AP) endonuclease family, at 1.8 Å. Although Crc displays high sequence similarity with its orthologs, there are amino acid alterations in the area corresponding to the active site in AP proteins. Unlike typical AP endonuclease family proteins, Crc has a reduced overall positive charge and the conserved positively charged amino-acid residues of the DNA-binding surface of AP proteins are partially substituted by negatively charged, polar and hydrophobic residues. Crc protein purified to homogeneity from P. aeruginosa did neither display DNase activity, nor did it bind to previously identified RNA substrates. Rather, the RNA chaperone Hfq was identified as a contaminant in His-tagged Crc preparations purified by one step Ni-affinity chromatography from Escherichia coli, and was shown to account for the RNA binding activity observed with the His-Crc preparations. Taken together, these data challenge a role of Crc as a direct translational repressor in carbon catabolite repression in P. aeruginosa. PMID:23717639

The Pseudomonas aeruginosa catabolite repression control protein Crc is devoid of RNA binding activity.

PubMed

Milojevic, Tetyana; Grishkovskaya, Irina; Sonnleitner, Elisabeth; Djinovic-Carugo, Kristina; Bläsi, Udo

2013-01-01

The Crc protein has been shown to mediate catabolite repression control in Pseudomonas, leading to a preferential assimilation of carbon sources. It has been suggested that Crc acts as a translational repressor of mRNAs, encoding functions involved in uptake and breakdown of different carbon sources. Moreover, the regulatory RNA CrcZ, the level of which is increased in the presence of less preferred carbon sources, was suggested to bind to and sequester Crc, resulting in a relief of catabolite repression. Here, we determined the crystal structure of Pseudomonas aeruginosa Crc, a member of apurinic/apyrimidinic (AP) endonuclease family, at 1.8 Å. Although Crc displays high sequence similarity with its orthologs, there are amino acid alterations in the area corresponding to the active site in AP proteins. Unlike typical AP endonuclease family proteins, Crc has a reduced overall positive charge and the conserved positively charged amino-acid residues of the DNA-binding surface of AP proteins are partially substituted by negatively charged, polar and hydrophobic residues. Crc protein purified to homogeneity from P. aeruginosa did neither display DNase activity, nor did it bind to previously identified RNA substrates. Rather, the RNA chaperone Hfq was identified as a contaminant in His-tagged Crc preparations purified by one step Ni-affinity chromatography from Escherichia coli, and was shown to account for the RNA binding activity observed with the His-Crc preparations. Taken together, these data challenge a role of Crc as a direct translational repressor in carbon catabolite repression in P. aeruginosa.

Saharan dust plume charging observed over the UK

NASA Astrophysics Data System (ADS)

Harrison, R. Giles; Nicoll, Keri A.; Marlton, Graeme J.; Ryder, Claire L.; Bennett, Alec J.

2018-05-01

A plume of Saharan dust and Iberian smoke was carried across the southern UK on 16th October 2017, entrained into an Atlantic cyclone which had originated as Hurricane Ophelia. The dust plume aloft was widely noticed as it was sufficiently dense to redden the visual appearance of the sun. Time series of backscatter from ceilometers at Reading and Chilbolton show two plumes: one carried upwards to 2.5 km, and another below 800 m into the boundary layer, with a clear slot between. Steady descent of particles at about 50 cm s‑1 continued throughout the morning, and coarse mode particles reached the surface. Plumes containing dust are frequently observed to be strongly charged, often through frictional effects. This plume passed over atmospheric electric field sensors at Bristol, Chilbolton and Reading. Consistent measurements at these three sites indicated negative plume charge. The lower edge plume charge density was (‑8.0 ± 3.3) nC m‑2, which is several times greater than that typical for stratiform water clouds, implying an active in situ charge generation mechanism such as turbulent triboelectrification. A meteorological radiosonde measuring temperature and humidity was launched into the plume at 1412 UTC, specially instrumented with charge and turbulence sensors. This detected charge in the boundary layer and in the upper plume region, and strong turbulent mixing was observed throughout the atmosphere’s lowest 4 km. The clear slot region, through which particles sedimented, was anomalously dry compared with modelled values, with water clouds forming intermittently in the air beneath. Electrical aspects of dust should be included in numerical models, particularly the charge-related effects on cloud microphysical properties, to accurately represent particle behaviour and transport.

40 CFR 221.5 - Processing fees.

Code of Federal Regulations, 2010 CFR

2010-07-01

... be charged in connection with each application for a permit for dumping in an existing dump site... with each application for a permit for dumping in a dump site other than a dump site designated in this...

40 CFR 221.5 - Processing fees.

Code of Federal Regulations, 2011 CFR

2011-07-01

... be charged in connection with each application for a permit for dumping in an existing dump site... with each application for a permit for dumping in a dump site other than a dump site designated in this...

Topological phase transition and the effect of Hubbard interactions on the one-dimensional topological Kondo insulator

NASA Astrophysics Data System (ADS)

Pillay, Jason C.; McCulloch, Ian P.

2018-05-01

The effect of a local Kondo coupling and Hubbard interaction on the topological phase of the one-dimensional topological Kondo insulator (TKI) is numerically investigated using the infinite matrix-product state density-matrix renormalization group algorithm. The ground state of the TKI is a symmetry-protected topological (SPT) phase protected by inversion symmetry. It is found that on its own, the Hubbard interaction that tends to force fermions into a one-charge per site order is insufficient to destroy the SPT phase. However, when the local Kondo Hamiltonian term that favors a topologically trivial ground state with a one-charge per site order is introduced, the Hubbard interaction assists in the destruction of the SPT phase. This topological phase transition occurs in the charge sector where the correlation length of the charge excitation diverges while the correlation length of the spin excitation remains finite. The critical exponents, central charge, and the phase diagram separating the SPT phase from the topologically trivial phase are presented.

Rationally Designed Sensing Selectivity and Sensitivity of an Aerolysin Nanopore via Site-Directed Mutagenesis.

PubMed

Wang, Ya-Qian; Cao, Chan; Ying, Yi-Lun; Li, Shuang; Wang, Ming-Bo; Huang, Jin; Long, Yi-Tao

2018-04-27

Selectivity and sensitivity are two key parameters utilized to describe the performance of a sensor. In order to investigate selectivity and sensitivity of the aerolysin nanosensor, we manipulated its surface charge at different locations via single site-directed mutagenesis. To study the selectivity, we replaced the positively charged R220 at the entrance of the pore with negatively charged glutamic acid, resulting in barely no current blockages for sensing negatively charged oligonucleotides. For the sensitivity, we substituted the positively charged lumen-exposed amino acid K238 located at trans-ward third of the β-barrel stem with glutamic acid. This leads to a surprisingly longer duration time at +140 mV, which is about 20 times slower in translocation speed for Poly(dA) 4 compared to that of wild-type aerolysin, indicating the stronger pore-analyte interactions and enhanced sensitivity. Therefore, it is both feasible and understandable to rationally design confined biological nanosensors for single molecule detection with high selectivity and sensitivity.

Mapping of Residues Forming the Voltage Sensor of the Voltage-Dependent Anion-Selective Channel

NASA Astrophysics Data System (ADS)

Thomas, Lorie; Blachly-Dyson, Elizabeth; Colombini, Marco; Forte, Michael

1993-06-01

Voltage-gated ion-channel proteins contain "voltage-sensing" domains that drive the conformational transitions between open and closed states in response to changes in transmembrane voltage. We have used site-directed mutagenesis to identify residues affecting the voltage sensitivity of a mitochondrial channel, the voltage-dependent anion-selective channel (VDAC). Although charge changes at many sites had no effect, at other sites substitutions that increased positive charge also increased the steepness of voltage dependance and substitutions that decreased positive charge decreased voltage dependance by an appropriate amount. In contrast to the plasma membrane K^+ and Na^+ channels, these residues are distributed over large parts of the VDAC protein. These results have been used to define the conformational transitions that accompany voltage gating of an ion channel. This gating mechanism requires the movement of large portions of the VDAC protein through the membrane.

IRIS Toxicological Review of Libby Amphibole Asbestos ...

EPA Pesticide Factsheets

On August 25, 2011, the draft Toxicological Review of Libby Amphibole Asbestos and the charge to external peer reviewers were released for external peer review and public comment. The Toxicological Review and charge were reviewed internally by EPA and by other federal agencies and White House Offices before public release. In the new IRIS process (May 2009), introduced by the EPA Administrator, all written comments on IRIS assessments submitted by other federal agencies and White House Offices will be made publicly available. Accordingly, interagency comments and the interagency science consultation draft of the IRIS Toxicological Review of Libby Amphibole Asbestos and the charge to external peer reviewers are posted on this site. The project supports OSWER and Region 8 site clean-up and related risk management initiatives at this Superfund site. As with all IRIS assessments, the draft document will undergo agency review, OMB/interagency review and independent external peer review before being included on the IRIS data base.

The binding of quinone to the photosynthetic reaction centers: kinetics and thermodynamics of reactions occurring at the QB-site in zwitterionic and anionic liposomes.

PubMed

Mavelli, Fabio; Trotta, Massimo; Ciriaco, Fulvio; Agostiano, Angela; Giotta, Livia; Italiano, Francesca; Milano, Francesco

2014-07-01

Liposomes represent a versatile biomimetic environment for studying the interaction between integral membrane proteins and hydrophobic ligands. In this paper, the quinone binding to the QB-site of the photosynthetic reaction centers (RC) from Rhodobacter sphaeroides has been investigated in liposomes prepared with either the zwitterionic phosphatidylcholine (PC) or the negatively charged phosphatidylglycerol (PG) to highlight the role of the different phospholipid polar heads. Quinone binding (K Q) and interquinone electron transfer (L AB) equilibrium constants in the two type of liposomes were obtained by charge recombination reaction of QB-depleted RC in the presence of increasing amounts of ubiquinone-10 over the temperature interval 6-35 °C. The kinetic of the charge recombination reactions has been fitted by numerically solving the ordinary differential equations set associated with a detailed kinetic scheme involving electron transfer reactions coupled with quinone release and uptake. The entire set of traces at each temperature was accurately fitted using the sole quinone release constants (both in a neutral and a charge separated state) as adjustable parameters. The temperature dependence of the quinone exchange rate at the QB-site was, hence, obtained. It was found that the quinone exchange regime was always fast for PC while it switched from slow to fast in PG as the temperature rose above 20 °C. A new method was introduced in this paper for the evaluation of constant K Q using the area underneath the charge recombination traces as the indicator of the amount of quinone bound to the QB-site.

MD-2 residues tyrosine 42, arginine 69, aspartic acid 122, and leucine 125 provide species specificity for lipid IVA.

PubMed

Meng, Jianmin; Drolet, Joshua R; Monks, Brian G; Golenbock, Douglas T

2010-09-03

Lipopolysaccharide (LPS) activates the innate immune response through the Toll-like receptor 4 (TLR4).MD-2 complex. A synthetic lipid A precursor, lipid IV(A), induces an innate immune response in mice but not in humans. Both TLR4 and MD-2 are required for the agonist activity of lipid IV(A) in mice, with TLR4 interacting through specific surface charges at the dimerization interface. In this study, we used site-directed mutagenesis to identify the MD-2 residues that determine lipid IV(A) species specificity. A single mutation of murine MD-2 at the hydrophobic pocket entrance, E122K, substantially reduced the response to lipid IV(A). Combining the murine MD-2 E122K with the murine TLR4 K367E/S386K/R434Q mutations completely abolished the response to lipid IV(A), effectively converting the murine cellular response to a human-like response. In human cells, however, simultaneous mutations of K122E, K125L, Y41F, and R69G on human MD-2 were required to promote a response to lipid IV(A). Combining the human MD-2 quadruple mutations with the human TLR4 E369K/Q436R mutations completely converted the human MD-2/human TLR4 receptor to a murine-like receptor. Because MD-2 residues 122 and 125 reside at the dimerization interface near the pocket entrance, surface charge differences here directly affect receptor dimerization. In comparison, residues 42 and 69 reside at the MD-2/TLR4 interaction surface opposite the dimerization interface. Surface charge differences there likely affect the binding angle and/or rigidity between MD-2 and TLR4, exerting an indirect influence on receptor dimerization and activation. Thus, surface charge differences at the two MD-2/TLR4 interfaces determine the species-specific activation of lipid IV(A).

Molecular Recognition of Endocytic Codes in Receptor Tyrosine Kinases

DTIC Science & Technology

1999-06-01

and B), substitution of Glu for Thr at residue 508 failed to induce actin aggregation in COS-7 cells (Fig. 9, panels C and D), comparable to lack...of effects of the kinase inactive Kd3-D460N mutant (Fig. 9, panels G and H). In contrast, substitution of 2 Glu residues whose charge may more...studies of Mekl where substitution of an Asp or Glu residue for 1 serine phosphoryl- ation site partially activated the enzyme and substitution of 2

Mineral induced phosphorylation of glycolate ion--a metaphor in chemical evolution

NASA Technical Reports Server (NTRS)

Kolb, V.; Zhang, S.; Xu, Y.; Arrhenius, G.

1997-01-01

Bilateral surface-active minerals with excess positive charge concentrate glycolate and trimetaphosphate ion from l0(-3) m aqueous solution to half-saturation of the internal surface sites, and induce phosphorylation of glycolate ion in the mineral with trimetaphosphate, sorbed from l0(-2) m solution. By utilizing reactants from dilute solution at near-neutral pH, and eliminating the need for participating organic nitrogen compounds, the reaction comprises several elements considered necessary for geochemical realism in models for molecular evolution.

Structural and Functional Analysis of HIV-1 Coreceptors: Roles of Charged Residues and Posttranslational Modifications on Coreceptor Activity

DTIC Science & Technology

2000-01-01

to sites of inflammation. They may have additional functions. For example analysis of CXCR4 knockout mice show that CXCR4, which is chemotactic for... mice had similar phenotypes (195). Homozygous knockout of CXCR4 or SDF-1 results in embyonic lethality. Though CCR5 appears to be dispensable, other...chemokine receptors have vital functions. CXCR5 knockout mice have B-cell homing defects (118), and CXCR2 knockout mice overproduce B-cells and

Structural and Functional Analysis of HIV-1 Coreceptors: Roles of Charged Residues and Posttranslational Modifications on Coreceptor Activity

DTIC Science & Technology

2000-01-01

various organs and to sites of inflammation. They may have additional functions. For example analysis of CXCR4 knockout mice show that CXCR4, which...SDF-1 knockout mice had similar phenotypes (195). Homozygous knockout of CXCR4 or SDF-1 results in embyonic lethality. Though CCR5 appears to be...dispensable, other chemokine receptors have vital functions. CXCR5 knockout mice have B-cell homing defects (118), and CXCR2 knockout mice

Macroscopic and spectroscopic investigations of the adsorption of nitroaromatic compounds on graphene oxide, reduced graphene oxide, and graphene nanosheets.

PubMed

Chen, Xiaoxiao; Chen, Baoliang

2015-05-19

The surface properties and adsorption mechanisms of graphene materials are important for potential environmental applications. The adsorption of m-dinitrobenzene, nitrobenzene, and p-nitrotoluene onto graphene oxide (GO), reduced graphene oxide (RGO), and graphene (G) nanosheets was investigated using IR spectroscopy to probe the molecular interactions of graphene materials with nitroaromatic compounds (NACs). The hydrophilic GO displayed the weakest adsorption capability. The adsorption of RGO and G was significantly increased due to the recovery of hydrophobic π-conjugation carbon atoms as active sites. RGO nanosheets, which had more defect sites than did GO or G nanosheets, resulted in the highest adsorption of NACs which was 10-50 times greater than the reported adsorption of carbon nanotubes. Superior adsorption was dominated by various interaction modes including π-π electron donor-acceptor interactions between the π-electron-deficient phenyls of the NACs and the π-electron-rich matrix of the graphene nanosheets, and the charge electrostatic and polar interactions between the defect sites of graphene nanosheets and the -NO2 of the NAC. The charge transfer was initially proved by FTIR that a blue shift of asymmetric -NO2 stretching was observed with a concomitant red shift of symmetric -NO2 stretching after m-dinitrobenzene was adsorbed. The multiple interaction mechanisms of the adsorption of NAC molecule onto flat graphene nanosheets favor the adsorption, detection, and transformation of explosives.

Identification of the heparin binding site on adeno-associated virus serotype 3B (AAV-3B)

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

Lerch, Thomas F.; Chapman, Michael S., E-mail: chapmami@ohsu.edu

2012-02-05

Adeno-associated virus is a promising vector for gene therapy. In the current study, the binding site on AAV serotype 3B for the heparan sulfate proteoglycan (HSPG) receptor has been characterized. X-ray diffraction identified a disaccharide binding site at the most positively charged region on the virus surface. The contributions of basic amino acids at this and other sites were characterized using site-directed mutagenesis. Both heparin and cell binding are correlated to positive charge at the disaccharide binding site, and transduction is significantly decreased in AAV-3B vectors mutated at this site to reduce heparin binding. While the receptor attachment sites ofmore » AAV-3B and AAV-2 are both in the general vicinity of the viral spikes, the exact amino acids that participate in electrostatic interactions are distinct. Diversity in the mechanisms of cell attachment by AAV serotypes will be an important consideration for the rational design of improved gene therapy vectors.« less

Identification of the heparin binding site on adeno-associated virus serotype 3B (AAV-3B)

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

Lerch, Thomas F.; Chapman, Michael S.

2012-05-24

Adeno-associated virus is a promising vector for gene therapy. In the current study, the binding site on AAV serotype 3B for the heparan sulfate proteoglycan (HSPG) receptor has been characterized. X-ray diffraction identified a disaccharide binding site at the most positively charged region on the virus surface. The contributions of basic amino acids at this and other sites were characterized using site-directed mutagenesis. Both heparin and cell binding are correlated to positive charge at the disaccharide binding site, and transduction is significantly decreased in AAV-3B vectors mutated at this site to reduce heparin binding. While the receptor attachment sites ofmore » AAV-3B and AAV-2 are both in the general vicinity of the viral spikes, the exact amino acids that participate in electrostatic interactions are distinct. Diversity in the mechanisms of cell attachment by AAV serotypes will be an important consideration for the rational design of improved gene therapy vectors.« less

A Theoretical Secure Enterprise Architecture for Multi Revenue Generating Smart Grid Sub Electric Infrastructure

ERIC Educational Resources Information Center

Chaudhry, Hina

2013-01-01

This study is a part of the smart grid initiative providing electric vehicle charging infrastructure. It is a refueling structure, an energy generating photovoltaic system and charge point electric vehicle charging station. The system will utilize advanced design and technology allowing electricity to flow from the site's normal electric service…

Progressive Design of Plasmonic Metal-Semiconductor Ensemble toward Regulated Charge Flow and Improved Vis-NIR-Driven Solar-to-Chemical Conversion.

PubMed

Han, Chuang; Quan, Quan; Chen, Hao Ming; Sun, Yugang; Xu, Yi-Jun

2017-04-01

Surface plasmon resonance (SPR)-mediated photocatalysis without the bandgap limitations of traditional semiconductor has aroused significant attention in solar-to-chemical energy conversion. However, the photocatalytic efficiency barely initiated by the SPR effects is still challenged by the low concentration and ineffective extraction of energetic hot electrons, slow charge migration rates, random charge diffusion directions, and the lack of highly active sites for redox reactions. Here, the tunable, progressive harvesting of visible-to-near infrared light (vis-NIR, λ > 570 nm) by designing plasmonic Au nanorods and metal (Au, Ag, or Pt) nanoparticle codecorated 1D CdS nanowire (1D CdS NW) ensemble is reported. The intimate integration of these metal nanostructures with 1D CdS NWs promotes the extraction and manipulated directional separation and migration of hot charge carriers in a more effective manner. Such cooperative synergy with tunable control of interfacial interaction, morphology optimization, and cocatalyst strategy results in the distinctly boosted performance for vis-NIR-driven plasmonic photocatalysis. This work highlights the significance of rationally progressive design of plasmonic metal-semiconductor-based composite system for boosting the regulated directional flow of hot charge carrier and thus the more efficient use of broad-spectrum solar energy conversion. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Excess lithium storage and charge compensation in nanoscale Li4+xTi5O12

NASA Astrophysics Data System (ADS)

Wang, Feng; Wu, Lijun; Ma, Chao; Su, Dong; Zhu, Yimei; Graetz, Jason

2013-10-01

Lithium titanate spinel (Li4Ti5O12; LTO) is a promising candidate for anodes in lithium-ion batteries due to its excellent cyclability and safety performance, and has been known as a ‘zero-strain’ material that allows reversible lithium insertion-deinsertion with little change in the lattice parameters. For a better understanding of lithium reaction mechanisms in this material, it has been of great interest to identify where lithium is inserted and how it migrates during charge and discharge, which is often difficult with x-ray and electron scattering techniques due to the low scattering power of lithium. In this study, we employed atomic-resolution annular bright-field imaging to directly image the lithium on interstitial sites in nanoscale LTO, and electron energy-loss spectroscopy to measure local lithium occupancy and electronic structure at different states of charge. During lithiation, charge compensation occurs primarily at O sites, rather than at Ti sites, and no significant change was found in the projected density of states (Ti 3d) until the voltage was lowered to ˜50 mV or below. The Li K-edge spectra were simulated via ab initio calculations, providing a direct correlation between the near-edge fine structure and the local lithium coordination. During the initial states of discharge, lithium ions on 8a sites migrate to 16c sites (above 740 mV). Further lithiation causes the partial re-occupation of 8a sites, initially in the near-surface region at ˜600 mV, and then in the bulk at lower voltages (˜50 mV). We attribute the enhanced capacity in nanostructured LTO to extra storage of lithium in the near-surface region, primarily at {111} facets.

An alkaline active xylanase: insights into mechanisms of high pH catalytic adaptation.

PubMed

Mamo, Gashaw; Thunnissen, Marjolein; Hatti-Kaul, Rajni; Mattiasson, Bo

2009-09-01

The alkaliphilic bacterium, Bacillus halodurans S7, produces an alkaline active xylanase (EC 3.2.1.8), which differs from many other xylanases in being operationally stable under alkaline conditions as well as at elevated temperature. Compared to non-alkaline active xylanases, this enzyme has a high percent composition of acidic amino acids which results in high ratio of negatively to positively charged residues. A positive correlation was observed between the charge ratio and the pH optima of xylanases. The recombinant xylanase was crystallized using a hanging drop diffusion method. The crystals belong to the space group P2(1)2(1)2(1) and the structure was determined at a resolution of 2.1 A. The enzyme has the common eight-fold TIM-barrel structure of family 10 xylanases; however, unlike non-alkaline active xylanases, it has a highly negatively charged surface and a deeper active site cleft. Mutational analysis of non-conserved amino acids which are close to the acid/base residue has shown that Val169, Ile170 and Asp171 are important to hydrolyze xylan at high pH. Unlike the wild type xylanase which has optimum pH at 9-9.5, the triple mutant xylanase (V169A, I170F and D171N), which was constructed using sequence information of alkaline sensitive xylanses was optimally active around pH 7. Compared to non-alkaline active xylanases, the alkaline active xylanases have highly acidic surfaces and fewer solvent exposed alkali labile residues. Based on these results obtained from sequence, structural and mutational analysis, the possible mechanisms of high pH stability and catalysis are discussed. This will provide useful information to understand the mechanism of high pH adaptation and engineering of enzymes that can be operationally stable at high pH.

Photoelectric charging of partially sunlit dielectric surfaces in space

NASA Technical Reports Server (NTRS)

De, B. R.; Criswell, D. R.

1977-01-01

Sunlight-shadow effects may substantially alter the charging situation for a dielectric surface. The sunlight-shadow boundary tends to be the site of intense multipole electric fields. Charges on a sunlit dielectric surface have a finite effective mobility. The charge distribution tends to resemble that on a conducting surface. A boundary between a conducting and a dielectric surface may not represent a conductivity discontinuity when this boundary is sunlit; charges may migrate at a nontrivial rate across the boundary. A contracting or expanding sunlit area may experience a supercharging.

Solar-Assisted Electric Vehicle Charging Station Interim Report

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

Lapsa, Melissa Voss; Durfee, Norman; Maxey, L Curt

2011-09-01

Oak Ridge National Laboratory (ORNL) has been awarded $6.8 million in the Department of Energy (DOE) American Recovery and Reinvestment Act (ARRA) funds as part of an overall $114.8 million ECOtality grant with matching funds from regional partners to install 125 solar-assisted Electric Vehicle (EV) charging stations across Knoxville, Nashville, Chattanooga, and Memphis. Significant progress has been made toward completing the scope with the installation of 25 solar-assisted charging stations at ORNL; six stations at Electric Power Research Institute (EPRI); and 27 stations at Nissan's Smyrna and Franklin sites, with three more stations under construction at Nissan's new lithium-ion batterymore » plant. Additionally, the procurement process for contracting the installation of 34 stations at Knoxville, the University of Tennessee Knoxville (UTK), and Nashville sites is underway with completion of installation scheduled for early 2012. Progress is also being made on finalizing sites and beginning installations of 30 stations in Nashville, Chattanooga, and Memphis by EPRI and Tennessee Valley Authority (TVA). The solar-assisted EV charging station project has made great strides in fiscal year 2011. A total of 58 solar-assisted EV parking spaces have been commissioned in East and Middle Tennessee, and progress on installing the remaining 67 spaces is well underway. The contract for the 34 stations planned for Knoxville, UTK, and Nashville should be underway in October with completion scheduled for the end of March 2012; the remaining three Nissan stations are under construction and scheduled to be complete in November; and the EPRI/TVA stations for Chattanooga, Vanderbilt, and Memphis are underway and should be complete by the end of March 2012. As additional Nissan LEAFs are being delivered, usage of the charging stations has increased substantially. The project is on course to complete all 125 solar-assisted EV charging stations in time to collect meaningful data by the end of government fiscal year 2012. Lessons learned from the sites completed thus far are being incorporated and are proving to be invaluable in completion of the remaining sites.« less

Tracking Hole Transport in DNA Hairpins Using a Phenylethynylguanine Nucleobase.

PubMed

Brown, Kristen E; Singh, Arunoday P N; Wu, Yi-Lin; Mishra, Ashutosh Kumar; Zhou, Jiawang; Lewis, Frederick D; Young, Ryan M; Wasielewski, Michael R

2017-08-30

The hole transport dynamics of DNA hairpins possessing a stilbene electron acceptor and donor along with a modified guanine (G) nucleobase, specifically 8-(4'-phenylethynyl)deoxyguanosine, or EG, have been investigated. The nearly indistinguishable oxidation potentials of EG and G and unique spectroscopic characteristics of EG +• make it well-suited for directly observing transient hole occupation during charge transport between a stilbene electron donor and acceptor. In contrast to the cation radical G +• , EG +• possesses a strong absorption near 460 nm and has a distinct Raman-active ethynyl stretch. Both spectroscopic characteristics are easily distinguished from those of the stilbene donor/acceptor radical ion chromophores. Employing EG, we observe its role as a shallow hole trap, or as an intermediate hole transport site when a deeper trap state is present. Using a combination of ultrafast absorption and stimulated Raman spectroscopies, the hole-transport dynamics are observed to be similar in systems having EG vs G bases, with small perturbations to the charge transport rates and yields. These results show EG can be deployed at specified locations throughout the sequence to report on hole occupancy, thereby enabling detailed monitoring of the hole transport dynamics with base-site specificity.

How Native and Alien Metal Cations Bind ATP: Implications for Lithium as a Therapeutic Agent

NASA Astrophysics Data System (ADS)

Dudev, Todor; Grauffel, Cédric; Lim, Carmay

2017-02-01

Adenosine triphosphate (ATP), the major energy currency of the cell, exists in solution mostly as ATP-Mg. Recent experiments suggest that Mg2+ interacts with the highly charged ATP triphosphate group and Li+ can co-bind with the native Mg2+ to form ATP-Mg-Li and modulate the neuronal purine receptor response. However, it is unclear how the negatively charged ATP triphosphate group binds Mg2+ and Li+ (i.e. which phosphate group(s) bind Mg2+/Li+) and how the ATP solution conformation depends on the type of metal cation and the metal-binding mode. Here, we reveal the preferred ATP-binding mode of Mg2+/Li+ alone and combined: Mg2+ prefers to bind ATP tridentately to each of the three phosphate groups, but Li+ prefers to bind bidentately to the terminal two phosphates. We show that the solution ATP conformation depends on the cation and its binding site/mode, but it does not change significantly when Li+ binds to Mg2+-loaded ATP. Hence, ATP-Mg-Li, like Mg2+-ATP, can fit in the ATP-binding site of the host enzyme/receptor, activating specific signaling pathways.

Proton transfer in organic scaffolds

NASA Astrophysics Data System (ADS)

Basak, Dipankar

This dissertation focuses on the fundamental understanding of the proton transfer process and translating the knowledge into design/development of new organic materials for efficient non-aqueous proton transport. For example, what controls the shuttling of a proton between two basic sites? a) Distance between two groups? or b) the basicity? c) What is the impact of protonation on molecular conformation when the basic sites are attached to rigid scaffolds? For this purpose, we developed several tunable proton sponges and studied proton transfer in these scaffolds theoretically as well as experimentally. Next we moved our attention to understand long-range proton conduction or proton transport. We introduced liquid crystalline (LC) proton conductor based on triphenylene molecule and established that activation energy barrier for proton transport is lower in the LC phase compared to the crystalline phase. Furthermore, we investigated the impact of several critical factors: the choice of the proton transferring groups, mobility of the charge carriers, intrinsic vs. extrinsic charge carrier concentrations and the molecular architectures on long-range proton transport. The outcome of this research will lead to a deeper understanding of non-aqueous proton transfer process and aid the design of next generation proton exchange membrane (PEM) for fuel cell.

Synthesis of hierarchically meso-macroporous TiO2/CdS heterojunction photocatalysts with excellent visible-light photocatalytic activity.

PubMed

Zhao, Haixin; Cui, Shu; Yang, Lan; Li, Guodong; Li, Nan; Li, Xiaotian

2018-02-15

Photocatalysts with a hierarchically porous structure have attracted considerable attention owing to their wide pore size distribution and high surface area, which enhance the efficiency of transporting species to active sites. In this study, hierarchically meso-macroporous TiO 2 photocatalysts decorated with highly dispersed CdS nanoparticles were synthesized via hydrolysis, followed by a hydrothermal treatment. The textural mesopores and interconnected pore framework provided more accessible active sites and efficient mass transport for the photocatalytic process. The light collection efficiency was enhanced because of multiple scattering of incident light in the macropores. Moreover, the formation of a heterojunction between the CdS and TiO 2 nanoparticles extended the photoresponse of TiO 2 to the visible-light range and enhanced the charge separation efficiency. Therefore, the hierarchically meso-macroporous TiO 2 /CdS photocatalysts exhibited excellent photocatalytic activity for the degradation of rhodaming B under visible-light irradiation. Trapping experiments demonstrated that superoxide radicals (O 2 - ) and hydroxyl radicals (OH) were the main active species in photocatalysis. A reasonable photocatalytic mechanism of TiO 2 /CdS heterojunction photocatalysts was also presented. Copyright © 2017 Elsevier Inc. All rights reserved.

Study of lithium cation in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-05-12

We present a potential model for Li(+)-water clusters based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM) that is to take ABEEM charges of the cation and all atoms, bonds, and lone pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The model allows point charges on cationic site and seven sites of an ABEEM-7P water molecule to fluctuate responding to the cluster geometry. The water molecules in the first sphere of Li(+) are strongly structured and there is obvious charge transfer between the cation and the water molecules; therefore, the charge constraint on the ionic cluster includes the charged constraint on the Li(+) and the first-shell water molecules and the charge neutrality constraint on each water molecule in the external hydration shells. The newly constructed potential model based on ABEEM/MM is first applied to ionic clusters and reproduces gas-phase state properties of Li(+)(H(2)O)(n) (n = 1-6 and 8) including optimized geometries, ABEEM charges, binding energies, frequencies, and so on, which are in fair agreement with those measured by available experiments and calculated by ab initio methods. Prospects and benefits introduced by this potential model are pointed out.

Simulation of the charge migration in DNA under irradiation with heavy ions.

PubMed

Belov, Oleg V; Boyda, Denis L; Plante, Ianik; Shirmovsky, Sergey Eh

2015-01-01

A computer model to simulate the processes of charge injection and migration through DNA after irradiation by a heavy charged particle was developed. The most probable sites of charge injection were obtained by merging spatial models of short DNA sequence and a single 1 GeV/u iron particle track simulated by the code RITRACKS (Relativistic Ion Tracks). Charge migration was simulated by using a quantum-classical nonlinear model of the DNA-charge system. It was found that charge migration depends on the environmental conditions. The oxidative damage in DNA occurring during hole migration was simulated concurrently, which allowed the determination of probable locations of radiation-induced DNA lesions.

Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data.

PubMed

Tripathi, Arti; Gupta, Kritika; Khare, Shruti; Jain, Pankaj C; Patel, Siddharth; Kumar, Prasanth; Pulianmackal, Ajai J; Aghera, Nilesh; Varadarajan, Raghavan

2016-11-01

Understanding how mutations affect protein activity and organismal fitness is a major challenge. We used saturation mutagenesis combined with deep sequencing to determine mutational sensitivity scores for 1,664 single-site mutants of the 101 residue Escherichia coli cytotoxin, CcdB at seven different expression levels. Active-site residues could be distinguished from buried ones, based on their differential tolerance to aliphatic and charged amino acid substitutions. At nonactive-site positions, the average mutational tolerance correlated better with depth from the protein surface than with accessibility. Remarkably, similar results were observed for two other small proteins, PDZ domain (PSD95 pdz3 ) and IgG-binding domain of protein G (GB1). Mutational sensitivity data obtained with CcdB were used to derive a procedure for predicting functional effects of mutations. Results compared favorably with those of two widely used computational predictors. In vitro characterization of 80 single, nonactive-site mutants of CcdB showed that activity in vivo correlates moderately with thermal stability and solubility. The inability to refold reversibly, as well as a decreased folding rate in vitro, is associated with decreased activity in vivo. Upon probing the effect of modulating expression of various proteases and chaperones on mutant phenotypes, most deleterious mutants showed an increased in vivo activity and solubility only upon over-expression of either Trigger factor or SecB ATP-independent chaperones. Collectively, these data suggest that folding kinetics rather than protein stability is the primary determinant of activity in vivo This study enhances our understanding of how mutations affect phenotype, as well as the ability to predict fitness effects of point mutations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evaluation of reduced point charge models of proteins through Molecular Dynamics simulations: application to the Vps27 UIM-1-Ubiquitin complex.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2014-02-01

Reduced point charge models of amino acids are designed, (i) from local extrema positions in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions, and (ii) from local maxima positions in promolecular electron density distribution functions. Corresponding charge values are fitted versus all-atom Amber99 MEPs. To easily generate reduced point charge models for protein structures, libraries of amino acid templates are built. The program GROMACS is used to generate stable Molecular Dynamics trajectories of an Ubiquitin-ligand complex (PDB: 1Q0W), under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a nul mass and radius. The results illustrate how the intra- and inter-molecular H-bond interactions are affected by the degree of reduction of the point charge models and give directions for their implementation; a special attention to the atoms selected to locate the virtual sites and to the Coulomb-14 interactions is needed. Results obtained at various temperatures suggest that the use of reduced point charge models allows to probe local potential hyper-surface minima that are similar to the all-atom ones, but are characterized by lower energy barriers. It enables to generate various conformations of the protein complex more rapidly than the all-atom point charge representation. Copyright © 2013 Elsevier Inc. All rights reserved.

A gain-of-function mutation in the M-domain of cardiac myosin-binding protein-C increases binding to actin.

PubMed

Bezold, Kristina L; Shaffer, Justin F; Khosa, Jaskiran K; Hoye, Elaine R; Harris, Samantha P

2013-07-26

The M-domain is the major regulatory subunit of cardiac myosin-binding protein-C (cMyBP-C) that modulates actin and myosin interactions to influence muscle contraction. However, the precise mechanism(s) and the specific residues involved in mediating the functional effects of the M-domain are not fully understood. Positively charged residues adjacent to phosphorylation sites in the M-domain are thought to be critical for effects of cMyBP-C on cross-bridge interactions by mediating electrostatic binding with myosin S2 and/or actin. However, recent structural studies revealed that highly conserved sequences downstream of the phosphorylation sites form a compact tri-helix bundle. Here we used site-directed mutagenesis to probe the functional significance of charged residues adjacent to the phosphorylation sites and conserved residues within the tri-helix bundle. Results confirm that charged residues adjacent to phosphorylation sites and residues within the tri-helix bundle are important for mediating effects of the M-domain on contraction. In addition, four missense variants within the tri-helix bundle that are associated with human hypertrophic cardiomyopathy caused either loss-of-function or gain-of-function effects on force. Importantly, the effects of the gain-of-function variant, L348P, increased the affinity of the M-domain for actin. Together, results demonstrate that functional effects of the M-domain are not due solely to interactions with charged residues near phosphorylatable serines and provide the first demonstration that the tri-helix bundle contributes to the functional effects of the M-domain, most likely by binding to actin.

The decoration of Nb-doped TiO2 microspheres by reduced graphene oxide for enhanced CO gas sensing

NASA Astrophysics Data System (ADS)

Liang, Feng; Chen, Shimin; Xie, Wei; Zou, Changwei

2018-03-01

Reduced graphene oxide (rGO) was used to improve the CO sensing properties of Nb-doped TiO2 (TiO2:Nb) microspheres by an improved ultrasonic spray pyrolysis deposition method. The responses of the sensor dramatically increased as the CO gas concentration increased from 100 to 1000 ppm, which indicated that rGO/TiO2:Nb-based sensor had a wide detection range for CO gas. Moreover, the conductivity of sensor based on the rGO/TiO2:Nb would be greatly improved than that of sensors without decoration by rGO. The enhanced gas sensing performance of the rGO/TiO2:Nb can be attributed to two reasons. Firstly, rGO could facilitate charge transport from TiO2 to graphene which provided a preferential pathway for the charge currents. Secondly, the decorated TiO2 by rGO could provide more active sites such as oxygen vacancy (VO) which could capture electrons from the conductance band and form a space-charge region.

Spectroscopic evidence for an engineered, catalytically active Trp radical that creates the unique reactivity of lignin peroxidase.

PubMed

Smith, Andrew T; Doyle, Wendy A; Dorlet, Pierre; Ivancich, Anabella

2009-09-22

The surface oxidation site (Trp-171) in lignin peroxidase (LiP) required for the reaction with veratryl alcohol a high-redox-potential (1.4 V) substrate, was engineered into Coprinus cinereus peroxidase (CiP) by introducing a Trp residue into a heme peroxidase that has similar protein fold but lacks this activity. To create the catalytic activity toward veratryl alcohol in CiP, it was necessary to reproduce the Trp site and its negatively charged microenvironment by means of a triple mutation. The resulting D179W+R258E+R272D variant was characterized by multifrequency EPR spectroscopy. The spectra unequivocally showed that a new Trp radical [g values of g(x) = 2.0035(5), g(y) = 2.0027(5), and g(z) = 2.0022(1)] was formed after the [Fe(IV)=O Por(*+)] intermediate, as a result of intramolecular electron transfer between Trp-179 and the porphyrin. Also, the EPR characterization crucially showed that [Fe(IV)=O Trp-179(*)] was the reactive intermediate with veratryl alcohol. Accordingly, our work shows that it is necessary to take into account the physicochemical properties of the radical, fine-tuned by the microenvironment, as well as those of the preceding [Fe(IV)=O Por(*+)] intermediate to engineer a catalytically competent Trp site for a given substrate. Manipulation of the microenvironment of the Trp-171 site in LiP allowed the detection by EPR spectroscopy of the Trp-171(*), for which direct evidence has been missing so far. Our work also highlights the role of Trp residues as tunable redox-active cofactors for enzyme catalysis in the context of peroxidases with a unique reactivity toward recalcitrant substrates that require oxidation potentials not realized at the heme site.

High-affinity cannabinoid binding site in brain: A possible marijuana receptor

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

Nye, J.S.

The mechanism by which delta{sup 9} tetrahydrocannabinol (delta{sup 9}THC), the major psychoactive component of marijuana or hashish, produces its potent psychological and physiological effects is unknown. To find receptor binding sites for THC, we designed a water-soluble analog for use as a radioligand. 5{prime}-Trimethylammonium-delta{sup 8}THC (TMA) is a positively charged analog of delta-{sup 8}THC modified on the 5{prime} carbon, a portion of the molecule not important for its psychoactivity. We have studied the binding of ({sup 3}H)-5{prime}-trimethylammonium-delta-{sup 8}THC (({sup 3}H)TMA) to rat neuronal membranes. ({sup 3}H)TMA binds saturably and reversibly to brain membranes with high affinity to apparently one classmore » of sites. Highest binding site density occurs in brain, but several peripheral organs also display specific binding. Detergent solubilizes the sites without affecting their pharmacologial properties. Molecular sieve chromatography reveals a bimodal peak of ({sup 3}H)TMA binding activity of approximately 60,000 daltons apparent molecular weight.« less

21 CFR 1304.45 - Internet Web site disclosure requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

..., professional degree, and States of licensure of the pharmacist-in-charge, and a telephone number at which the pharmacist-in-charge can be contacted. (4) A list of the States in which the pharmacy is licensed to dispense...

21 CFR 1304.45 - Internet Web site disclosure requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., professional degree, and States of licensure of the pharmacist-in-charge, and a telephone number at which the pharmacist-in-charge can be contacted. (4) A list of the States in which the pharmacy is licensed to dispense...

21 CFR 1304.45 - Internet Web site disclosure requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., professional degree, and States of licensure of the pharmacist-in-charge, and a telephone number at which the pharmacist-in-charge can be contacted. (4) A list of the States in which the pharmacy is licensed to dispense...

21 CFR 1304.45 - Internet Web site disclosure requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

..., professional degree, and States of licensure of the pharmacist-in-charge, and a telephone number at which the pharmacist-in-charge can be contacted. (4) A list of the States in which the pharmacy is licensed to dispense...

21 CFR 1304.45 - Internet Web site disclosure requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

..., professional degree, and States of licensure of the pharmacist-in-charge, and a telephone number at which the pharmacist-in-charge can be contacted. (4) A list of the States in which the pharmacy is licensed to dispense...

Sulfonium Ion Derivatization, Isobaric Stable Isotope Labeling and Data Dependent CID- and ETD-MS/MS for Enhanced Phosphopeptide Quantitation, Identification and Phosphorylation Site Characterization

PubMed Central

Lu, Yali; Zhou, Xiao; Stemmer, Paul M.; Reid, Gavin E.

2014-01-01

An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded ‘fixed charge’ sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS3, and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S,S′-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of ‘light’ (S(CH3)2) and ‘heavy’ (S(CD3)2) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS3 or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency. PMID:21952753

Cost-effective electric vehicle charging infrastructure siting for Delhi

DOE PAGES

Sheppard, Colin J. R.; Gopal, Anand R.; Harris, Andrew; ...

2016-06-10

Plug-in electric vehicles (PEVs) represent a substantial opportunity for governments to reduce emissions of both air pollutants and greenhouse gases. The Government of India has set a goal of deploying 6-7 million hybrid and PEVs on Indian roads by the year 2020. The uptake of PEVs will depend on, among other factors like high cost, how effectively range anxiety is mitigated through the deployment of adequate electric vehicle charging stations (EVCS) throughout a region. The Indian Government therefore views EVCS deployment as a central part of their electric mobility mission. The plug-in electric vehicle infrastructure (PEVI) model - an agent-basedmore » simulation modeling platform - was used to explore the cost-effective siting of EVCS throughout the National Capital Territory (NCT) of Delhi, India. At 1% penetration in the passenger car fleet, or ~10 000 battery electric vehicles (BEVs), charging services can be provided to drivers for an investment of $4.4 M (or $ 440/BEV) by siting 2764 chargers throughout the NCT of Delhi with an emphasis on the more densely populated and frequented regions of the city. The majority of chargers sited by this analysis were low power, Level 1 chargers, which have the added benefit of being simpler to deploy than higher power alternatives. The amount of public infrastructure needed depends on the access that drivers have to EVCS at home, with 83% more charging capacity required to provide the same level of service to a population of drivers without home chargers compared to a scenario with home chargers. Results also depend on the battery capacity of the BEVs adopted, with approximately 60% more charging capacity needed to achieve the same level of service when vehicles are assumed to have 57 km versus 96 km of range.« less

Cost-effective electric vehicle charging infrastructure siting for Delhi

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

Sheppard, Colin J. R.; Gopal, Anand R.; Harris, Andrew

Plug-in electric vehicles (PEVs) represent a substantial opportunity for governments to reduce emissions of both air pollutants and greenhouse gases. The Government of India has set a goal of deploying 6-7 million hybrid and PEVs on Indian roads by the year 2020. The uptake of PEVs will depend on, among other factors like high cost, how effectively range anxiety is mitigated through the deployment of adequate electric vehicle charging stations (EVCS) throughout a region. The Indian Government therefore views EVCS deployment as a central part of their electric mobility mission. The plug-in electric vehicle infrastructure (PEVI) model - an agent-basedmore » simulation modeling platform - was used to explore the cost-effective siting of EVCS throughout the National Capital Territory (NCT) of Delhi, India. At 1% penetration in the passenger car fleet, or ~10 000 battery electric vehicles (BEVs), charging services can be provided to drivers for an investment of $4.4 M (or $ 440/BEV) by siting 2764 chargers throughout the NCT of Delhi with an emphasis on the more densely populated and frequented regions of the city. The majority of chargers sited by this analysis were low power, Level 1 chargers, which have the added benefit of being simpler to deploy than higher power alternatives. The amount of public infrastructure needed depends on the access that drivers have to EVCS at home, with 83% more charging capacity required to provide the same level of service to a population of drivers without home chargers compared to a scenario with home chargers. Results also depend on the battery capacity of the BEVs adopted, with approximately 60% more charging capacity needed to achieve the same level of service when vehicles are assumed to have 57 km versus 96 km of range.« less

Cost-effective electric vehicle charging infrastructure siting for Delhi

NASA Astrophysics Data System (ADS)

Sheppard, Colin J. R.; Gopal, Anand R.; Harris, Andrew; Jacobson, Arne

2016-06-01

Plug-in electric vehicles (PEVs) represent a substantial opportunity for governments to reduce emissions of both air pollutants and greenhouse gases. The Government of India has set a goal of deploying 6-7 million hybrid and PEVs on Indian roads by the year 2020. The uptake of PEVs will depend on, among other factors like high cost, how effectively range anxiety is mitigated through the deployment of adequate electric vehicle charging stations (EVCS) throughout a region. The Indian Government therefore views EVCS deployment as a central part of their electric mobility mission. The plug-in electric vehicle infrastructure (PEVI) model—an agent-based simulation modeling platform—was used to explore the cost-effective siting of EVCS throughout the National Capital Territory (NCT) of Delhi, India. At 1% penetration in the passenger car fleet, or ˜10 000 battery electric vehicles (BEVs), charging services can be provided to drivers for an investment of 4.4 M (or 440/BEV) by siting 2764 chargers throughout the NCT of Delhi with an emphasis on the more densely populated and frequented regions of the city. The majority of chargers sited by this analysis were low power, Level 1 chargers, which have the added benefit of being simpler to deploy than higher power alternatives. The amount of public infrastructure needed depends on the access that drivers have to EVCS at home, with 83% more charging capacity required to provide the same level of service to a population of drivers without home chargers compared to a scenario with home chargers. Results also depend on the battery capacity of the BEVs adopted, with approximately 60% more charging capacity needed to achieve the same level of service when vehicles are assumed to have 57 km versus 96 km of range.

An Analytical Planning Model to Estimate the Optimal Density of Charging Stations for Electric Vehicles.

PubMed

Ahn, Yongjun; Yeo, Hwasoo

2015-01-01

The charging infrastructure location problem is becoming more significant due to the extensive adoption of electric vehicles. Efficient charging station planning can solve deeply rooted problems, such as driving-range anxiety and the stagnation of new electric vehicle consumers. In the initial stage of introducing electric vehicles, the allocation of charging stations is difficult to determine due to the uncertainty of candidate sites and unidentified charging demands, which are determined by diverse variables. This paper introduces the Estimating the Required Density of EV Charging (ERDEC) stations model, which is an analytical approach to estimating the optimal density of charging stations for certain urban areas, which are subsequently aggregated to city level planning. The optimal charging station's density is derived to minimize the total cost. A numerical study is conducted to obtain the correlations among the various parameters in the proposed model, such as regional parameters, technological parameters and coefficient factors. To investigate the effect of technological advances, the corresponding changes in the optimal density and total cost are also examined by various combinations of technological parameters. Daejeon city in South Korea is selected for the case study to examine the applicability of the model to real-world problems. With real taxi trajectory data, the optimal density map of charging stations is generated. These results can provide the optimal number of chargers for driving without driving-range anxiety. In the initial planning phase of installing charging infrastructure, the proposed model can be applied to a relatively extensive area to encourage the usage of electric vehicles, especially areas that lack information, such as exact candidate sites for charging stations and other data related with electric vehicles. The methods and results of this paper can serve as a planning guideline to facilitate the extensive adoption of electric vehicles.

Long-range Electrostatic Complementarity Governs Substrate Recognition by Human Chymotrypsin C, a Key Regulator of Digestive Enzyme Activation*

PubMed Central

Batra, Jyotica; Szabó, András; Caulfield, Thomas R.; Soares, Alexei S.; Sahin-Tóth, Miklós; Radisky, Evette S.

2013-01-01

Human chymotrypsin C (CTRC) is a pancreatic serine protease that regulates activation and degradation of trypsinogens and procarboxypeptidases by targeting specific cleavage sites within their zymogen precursors. In cleaving these regulatory sites, which are characterized by multiple flanking acidic residues, CTRC shows substrate specificity that is distinct from that of other isoforms of chymotrypsin and elastase. Here, we report the first crystal structure of active CTRC, determined at 1.9-Å resolution, revealing the structural basis for binding specificity. The structure shows human CTRC bound to the small protein protease inhibitor eglin c, which binds in a substrate-like manner filling the S6-S5′ subsites of the substrate binding cleft. Significant binding affinity derives from burial of preferred hydrophobic residues at the P1, P4, and P2′ positions of CTRC, although acidic P2′ residues can also be accommodated by formation of an interfacial salt bridge. Acidic residues may also be specifically accommodated in the P6 position. The most unique structural feature of CTRC is a ring of intense positive electrostatic surface potential surrounding the primarily hydrophobic substrate binding site. Our results indicate that long-range electrostatic attraction toward substrates of concentrated negative charge governs substrate discrimination, which explains CTRC selectivity in regulating active digestive enzyme levels. PMID:23430245

Luminescence properties of the dinuclear copper complex in the active site of hemocyanins.

PubMed

Beltramini, M; di Muro, P; Rocco, G P; Salvato, B

1994-09-01

The deoxygenated form of hemocyanin, containing a dinuclear Cu(I) active site, emits luminescence in the red with maximum around 1.54 microns-1 (650 nm). The luminescence of deoxyhemocyanin (deoxy-Hc) from arthropod species is detectable at room temperature, the quantum yield being 2.4-2.7 x 10(-3); in contrast, the emission from molluscan proteins can be detected only at liquid nitrogen temperature. The luminescence emission is an inherent property of the bis[Cu(I)-(histidine)3] complex of the deoxygenated form of the protein to which both Cu(I) ions contribute equally to the overall emission. Luminescence is not observed with the oxygenated and the oxidized forms of hemocyanin, in which the metal is in the Cu(II) state, and in the metal-depleted or apo-Hc form. Based on steady-state and time-resolved measurements and references to Cu(I) model compounds, the luminescence emission is attributed to a triplet excited state of a Cu(I)-to-N (histidine) charge transfer transition 3d-pi*. Acrylamide quenching experiments indicate that the metal active site is very shielded from the solvent. This property of deoxy-Hc enables us to directly follow reactions that modify either the copper oxidation number or the metal-to-protein stoichiometry.

Butyrylcholinesterase for protection from organophosphorus poisons; catalytic complexities and hysteretic behavior

PubMed Central

Masson, Patrick; Lockridge, Oksana

2009-01-01

Butyrylcholinesterase is a promiscuous enzyme that displays complex kinetic behavior. It is toxicologically important because it detoxifies organophosphorus poisons (OP) by making a covalent bond with the OP. The OP and the butyrylcholinesterase are both inactivated in the process. Inactivation of butyrylcholinesterase has no adverse effects. However inactivation of acetylcholinesterase in nerve synapses can be lethal. OP-inhibited butyrylcholinesterase and acetylcholinesterase can be reactivated with oximes provided the OP has not aged. Strategies for preventing the toxicity of OP include a) treatment with an OP scavenger, b) reaction of nonaged enzyme with oximes, c) reactivation of aged enzyme, d) slowing down aging with peripheral site ligands, and e) design of mutants that rapidly hydrolyze OP. Option (a) has progressed through phase I clinical trials with human butyrylcholinesterase. Option (b) is in routine clinical use. The others are at the basic research level. Butyrylcholinesterase displays complex kinetic behavior including activation by positively charged esters, ability to hydrolyze amides, and a lag time (hysteresis) preceding hydrolysis of benzoylcholine and N-methyl indoxyl acetate. Mass spectrometry has identified new OP binding motifs on tyrosine and lysine in proteins that have no active site serine. It is proposed, but not yet proven, that low dose exposure involves OP modification of proteins that have no active site serine. PMID:20004171

Site preference for luminescent activator ions in doped fluoroperovskite RbZnF3.

PubMed

Saroj, Sanjay Kumar; Nagarajan, Rajamani

2018-08-05

With the dual objective of investigating the site preferences of larger sized activator ions and to append luminescence property to the perovskite structured RbZnF 3 , doping of manganese(II), cerium(III), europium(III) and terbium(III) ions (5 mol%) was carried out. Although cubic symmetry of RbZnF 3 was preserved for all the doped samples, site preference of rare-earth ions for the A-site Rb + leading to an inverse perovskite arrangement has been noticed from careful analysis of lattice parameters from refinement of powder X-ray diffraction data. Undoped RbZnF 3 exhibited rod-like morphology in the transmission electron microscopic image. In addition to an intense band around 230 nm assignable to the charge transfer from ZnF 3 - to Rb + , typical transitions of respective dopant ions were observed in their UV-visible spectra. The doped samples showed luminescence in blue, green and red regions and time decay experiments suggested uniform dispersion of them without any clustering effect. The lower phonon energy of RbZnF 3 matrix by virtue of the presence of heavier rubidium at the A-site together with its doping with rare-earth ions resulting in an inverse perovskite like arrangement could favour their utility in various practical applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Utilization of charge-transfer complexation for the detection of carcinogenic substances in foods: Spectroscopic characterization of ethyl carbamate with some traditional π-acceptors

NASA Astrophysics Data System (ADS)

Adam, Abdel Majid A.; Refat, Moamen S.; Saad, Hosam A.

2013-04-01

The study of toxic and carcinogenic substances in foods represents one of the most demanding areas in food safety, due to their repercussions for public health. One potentially toxic compound for humans is ethyl carbamate (EC). EC is a multi-site genotoxic carcinogen of widespread occurrence in fermented foods and alcoholic beverages. Structural and thermal stability of charge-transfer complexes formed between EC as a donor with quinol (QL), picric acid (PA), chloranilic acid (CLA), p-chloranil (p-CHL) and 1,3-dinitrobenzene (DNB) as acceptors were reported. Elemental analysis (CHN), electronic absorption spectra, photometric titration, IR, and 1H NMR spectra show that the interaction between EC and acceptors was stabilized by hydrogen bonding, via a 1:1 stoichiometry. Thermogravimetric (TG) analysis indicates that the formation of molecular CT complexes was stable, exothermic and spontaneous. Finally, the CT complexes were screened for their antibacterial and antifungal activities. The results indicated that the [(EC)(QL)] complex exhibited strong antimicrobial activities against various bacterial and fungal strains compared with standard drugs.

Electronically shielded solid state charged particle detector

DOEpatents

Balmer, D.K.; Haverty, T.W.; Nordin, C.W.; Tyree, W.H.

1996-08-20

An electronically shielded solid state charged particle detector system having enhanced radio frequency interference immunity includes a detector housing with a detector entrance opening for receiving the charged particles. A charged particle detector having an active surface is disposed within the housing. The active surface faces toward the detector entrance opening for providing electrical signals representative of the received charged particles when the received charged particles are applied to the active surface. A conductive layer is disposed upon the active surface. In a preferred embodiment, a nonconductive layer is disposed between the conductive layer and the active surface. The conductive layer is electrically coupled to the detector housing to provide a substantially continuous conductive electrical shield surrounding the active surface. The inner surface of the detector housing is supplemented with a radio frequency absorbing material such as ferrite. 1 fig.

Electronically shielded solid state charged particle detector

DOEpatents

Balmer, David K.; Haverty, Thomas W.; Nordin, Carl W.; Tyree, William H.

1996-08-20

An electronically shielded solid state charged particle detector system having enhanced radio frequency interference immunity includes a detector housing with a detector entrance opening for receiving the charged particles. A charged particle detector having an active surface is disposed within the housing. The active surface faces toward the detector entrance opening for providing electrical signals representative of the received charged particles when the received charged particles are applied to the active surface. A conductive layer is disposed upon the active surface. In a preferred embodiment, a nonconductive layer is disposed between the conductive layer and the active surface. The conductive layer is electrically coupled to the detector housing to provide a substantially continuous conductive electrical shield surrounding the active surface. The inner surface of the detector housing is supplemented with a radio frequency absorbing material such as ferrite.

Importance of the Active Site "Canopy" Residues in an O2-Tolerant [NiFe]-Hydrogenase.

PubMed

Brooke, Emily J; Evans, Rhiannon M; Islam, Shams T A; Roberts, Gerri M; Wehlin, Sara A M; Carr, Stephen B; Phillips, Simon E V; Armstrong, Fraser A

2017-01-10

The active site of Hyd-1, an oxygen-tolerant membrane-bound [NiFe]-hydrogenase from Escherichia coli, contains four highly conserved residues that form a "canopy" above the bimetallic center, closest to the site at which exogenous agents CO and O 2 interact, substrate H 2 binds, and a hydrido intermediate is stabilized. Genetic modification of the Hyd-1 canopy has allowed the first systematic and detailed kinetic and structural investigation of the influence of the immediate outer coordination shell on H 2 activation. The central canopy residue, arginine 509, suspends a guanidine/guanidinium side chain at close range above the open coordination site lying between the Ni and Fe atoms (N-metal distance of 4.4 Å): its replacement with lysine lowers the H 2 oxidation rate by nearly 2 orders of magnitude and markedly decreases the H 2 /D 2 kinetic isotope effect. Importantly, this collapse in rate constant can now be ascribed to a very unfavorable activation entropy (easily overriding the more favorable activation enthalpy of the R509K variant). The second most important canopy residue for H 2 oxidation is aspartate 118, which forms a salt bridge to the arginine 509 headgroup: its mutation to alanine greatly decreases the H 2 oxidation efficiency, observed as a 10-fold increase in the potential-dependent Michaelis constant. Mutations of aspartate 574 (also salt-bridged to R509) to asparagine and proline 508 to alanine have much smaller effects on kinetic properties. None of the mutations significantly increase sensitivity to CO, but neutralizing the expected negative charges from D118 and D574 decreases O 2 tolerance by stabilizing the oxidized resting Ni III -OH state ("Ni-B"). An extensive model of the catalytic importance of residues close to the active site now emerges, whereby a conserved gas channel culminates in the arginine headgroup suspended above the Ni and Fe.

The role of collagen charge clusters in the modulation of matrix metalloproteinase activity.

PubMed

Lauer, Janelle L; Bhowmick, Manishabrata; Tokmina-Roszyk, Dorota; Lin, Yan; Van Doren, Steven R; Fields, Gregg B

2014-01-24

Members of the matrix metalloproteinase (MMP) family selectively cleave collagens in vivo. Several substrate structural features that direct MMP collagenolysis have been identified. The present study evaluated the role of charged residue clusters in the regulation of MMP collagenolysis. A series of 10 triple-helical peptide (THP) substrates were constructed in which either Lys-Gly-Asp or Gly-Asp-Lys motifs replaced Gly-Pro-Hyp (where Hyp is 4-hydroxy-L-proline) repeats. The stabilities of THPs containing the two different motifs were analyzed, and kinetic parameters for substrate hydrolysis by six MMPs were determined. A general trend for virtually all enzymes was that, as Gly-Asp-Lys motifs were moved from the extreme N and C termini to the interior next to the cleavage site sequence, kcat/Km values increased. Additionally, all Gly-Asp-Lys THPs were as good or better substrates than the parent THP in which Gly-Asp-Lys was not present. In turn, the Lys-Gly-Asp THPs were also always better substrates than the parent THP, but the magnitude of the difference was considerably less compared with the Gly-Asp-Lys series. Of the MMPs tested, MMP-2 and MMP-9 most greatly favored the presence of charged residues with preference for the Gly-Asp-Lys series. Lys-Gly-(Asp/Glu) motifs are more commonly found near potential MMP cleavage sites than Gly-(Asp/Glu)-Lys motifs. As Lys-Gly-Asp is not as favored by MMPs as Gly-Asp-Lys, the Lys-Gly-Asp motif appears advantageous over the Gly-Asp-Lys motif by preventing unwanted MMP hydrolysis. More specifically, the lack of Gly-Asp-Lys clusters may diminish potential MMP-2 and MMP-9 collagenolytic activity. The present study indicates that MMPs have interactions spanning the P23-P23' subsites of collagenous substrates.

The influence of charge and the distribution of charge in the polar region of phospholipids on the activity of UDP-glucuronosyltransferase.

PubMed

Zakim, D; Eibl, H

1992-07-05

Studies of the mechanism of lipid-induced regulation of the microsomal enzyme UDP-glucuronosyltransferase have been extended by examining the influence of charge within the polar region on the ability of lipids to activate delipidated pure enzyme. The effects of net negative charge, of charge separation in phosphocholine, and of the distribution of charge in the polar region of lipids were studied using the GT2p isoform isolated from pig liver. Prior experiments have shown that lipids with net negative charge inhibit the enzyme (Zakim, D., Cantor, M., and Eibl, H. (1988) J. Biol. Chem. 263, 5164-5169). The current experiments show that the extent of inhibition on a molar basis increases as the net negative charge increases from -1 to -2. The inhibitory effect of negatively charged lipids is on the functional state of the enzyme and is not due to electrostatic repulsion of negatively charged substrates of the enzyme. Although the inhibitory effect of net negative charge is removed when negative charge is balanced by a positive charge due to a quaternary nitrogen, neutrality of the polar region is not a sufficient condition for activation of the enzyme. In addition to a balance of charge between Pi and the quaternary nitrogen, the distance between the negative and positive charges and the orientation of the dipole created by them are critical for activation of GT2p. The negative and positive charges must be separated by the equivalent of three -CH2- groups for optimal activation by a lipid. Shortening this distance by one -CH2- unit leads to a lipid that is ineffective in activating the enzyme. Reversal of the orientation of the dipole in which the negative charge is on the polymethylene side of the lipid-water interface and the positive charge extends into water also produces a lipid that is not effective for activating GT2p. On the other hand, lipids with phosphoserine as the polar region, which has the "normal" P-N distance but carries a net negative charge, do not inhibit GT2p. This result again illustrates the importance of the dipole of phosphocholine for modulating the functional state of GT2p.

Construction of Polarized Carbon-Nickel Catalytic Surfaces for Potent, Durable, and Economic Hydrogen Evolution Reactions.

PubMed

Zhou, Min; Weng, Qunhong; Popov, Zakhar I; Yang, Yijun; Antipina, Liubov Yu; Sorokin, Pavel B; Wang, Xi; Bando, Yoshio; Golberg, Dmitri

2018-05-22

Electrocatalytic hydrogen evolution reaction (HER) in alkaline solution is hindered by its sluggish kinetics toward water dissociation. Nickel-based catalysts, as low-cost and effective candidates, show great potentials to replace platinum (Pt)-based materials in the alkaline media. The main challenge regarding this type of catalysts is their relatively poor durability. In this work, we conceive and construct a charge-polarized carbon layer derived from carbon quantum dots (CQDs) on Ni 3 N nanostructure (Ni 3 N@CQDs) surfaces, which simultaneously exhibit durable and enhanced catalytic activity. The Ni 3 N@CQDs shows an overpotential of 69 mV at a current density of 10 mA cm -2 in a 1 M KOH aqueous solution, lower than that of Pt electrode (116 mV) at the same conditions. Density functional theory (DFT) simulations reveal that Ni 3 N and interfacial oxygen polarize charge distributions between originally equal C-C bonds in CQDs. The partially negatively charged C sites become effective catalytic centers for the key water dissociation step via the formation of new C-H bond (Volmer step) and thus boost the HER activity. Furthermore, the coated carbon is also found to protect interior Ni 3 N from oxidization/hydroxylation and therefore guarantees its durability. This work provides a practical design of robust and durable HER electrocatalysts based on nonprecious metals.

Vibrational spectroscopic and DFT calculation studies of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile

NASA Astrophysics Data System (ADS)

Premkumar, S.; Jawahar, A.; Mathavan, T.; Kumara Dhas, M.; Milton Franklin Benial, A.

2015-03-01

The vibrational spectra of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile were recorded using fourier transform-infrared and fourier transform-Raman spectrometer. The optimized structural parameters, vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals, thermodynamic properties, temperature dependence of thermodynamic parameters, first order hyperpolarizability and natural bond orbital calculations of the molecule were performed using the Gaussian 09 program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using the VEDA 4.0 program. The calculated first order hyperpolarizability of ABOBPC molecule was obtained as 6.908 × 10-30 issue, which was 10.5 times greater than urea. The nonlinear optical activity of the molecule was also confirmed by the frontier molecular orbitals and natural bond orbital analysis. The frontier molecular orbitals analysis shows that the lower energy gap of the molecule, which leads to the higher value of first order hyperpolarizability. The natural bond orbital analysis indicates that the nonlinear optical activity of the molecule arises due to the π → π∗ transitions. The Mulliken atomic charge distribution confirms the presence of intramolecular charge transfer within the molecule. The reactive site of the molecule was predicted from the molecular electrostatic potential contour map. The values of thermo dynamic parameters were increasing with increasing temperature.

Hydrogen-impurity complexes in III V semiconductors

NASA Astrophysics Data System (ADS)

Ulrici, W.

2004-12-01

This review summarizes the presently available knowledge concerning hydrogen-impurity complexes in III-V compounds. The impurities form shallow acceptors on group III sites (Be, Zn, Cd) and on group V sites (C, Si, Ge) as well as shallow donors on group V sites (S, Se, Te) and on group III sites (Si, Sn). These complexes are mainly revealed by their hydrogen stretching modes. Therefore, nearly all information about their structure and dynamic properties is derived from vibrational spectroscopy. The complexes of shallow impurities with hydrogen have been most extensively investigated in GaAs, GaP and InP. This holds also for Mg-H in GaN. The complexes exhibit a different microscopic structure, which is discussed in detail. The isoelectronic impurity nitrogen, complexed with one hydrogen atom, is investigated in detail in GaAs and GaP. Those complexes can exist in different charge states. The experimental results such as vibrational frequencies, the microscopic structure and the activation energy for reorientation for many of these complexes are in very good agreement with results of ab initio calculations. Different types of oxygen-hydrogen complexes in GaAs and GaP are described, with one hydrogen atom or two hydrogen atoms bonded to oxygen. Three of these complexes in GaAs were found to be electrically active.

Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin.

PubMed

van de Locht, A; Lamba, D; Bauer, M; Huber, R; Friedrich, T; Kröger, B; Höffken, W; Bode, W

1995-11-01

Rhodniin is a highly specific inhibitor of thrombin isolated from the assassin bug Rhodnius prolixus. The 2.6 Angstrum crystal structure of the non-covalent complex between recombinant rhodniin and bovine alpha-thrombin reveals that the two Kazal-type domains of rhodniin bind to different sites of thrombin. The amino-terminal domain binds in a substrate-like manner to the narrow active-site cleft of thrombin; the imidazole group of the P1 His residue extends into the S1 pocket to form favourable hydrogen/ionic bonds with Asp189 at its bottom, and additionally with Glu192 at its entrance. The carboxy-terminal domain, whose distorted reactive-site loop cannot adopt the canonical conformation, docks to the fibrinogen recognition exosite via extensive electrostatic interactions. The rather acidic polypeptide linking the two domains is displaced from the thrombin surface, with none of its residues involved in direct salt bridges with thrombin. The tight (Ki = 2 x 10(-13) M) binding of rhodniin to thrombin is the result of the sum of steric and charge complementarity of the amino-terminal domain towards the active-site cleft, and of the electrostatic interactions between the carboxy-terminal domain and the exosite.

In silico identification of a therapeutic target for photo-activated disinfection with indocyanine green: Modeling and virtual screening analysis of Arg-gingipain from Porphyromonas gingivalis.

PubMed

Pourhajibagher, Maryam; Bahador, Abbas

2017-06-01

Porphyromonas gingivalis is a momentous bacterial etiological agent associated with periodontitis, peri-implantitis as well as endodontic infections. The potential advantage of Photo-activated disinfection (PAD) as a promising novel approach is the choice of a suitable target site, specific photosensitizer, and wavelength of light for delivery of the light from source to target. Since Arg-gingipain is a cysteine proteinase that is involved in the virulence of P. gingivalis, it was evaluated as a target site for PAD with indocyanine green (ICG) as a photosensitizer. In this study, we used a range of in silico strategies, bioinformatics tools, biological databases, and computer simulation molecular modeling to evaluate the capacity of Arg-gingipain. The predicted structure of Arg-gingipain indicated that it is located outside the cell and has nine domains and 17 ligands, including two calcium ions and three sodium ions with positive charges which can be a site of interaction for anionic ICG. Based on the results of this study, anionic ICG desires to bind and interact with residues of Arg-gingipain during PAD as a main site to enhance the yield of treatment of endo-periodontal lesions. Copyright © 2017 Elsevier B.V. All rights reserved.

Charge and Spin Dynamics of the Hubbard Chains

NASA Technical Reports Server (NTRS)

Park, Youngho; Liang, Shoudan

1999-01-01

We calculate the local correlation functions of charge and spin for the one-chain and two-chain Hubbard model using density matrix renormalization group method and the recursion technique. Keeping only finite number of states we get good accuracy for the low energy excitations. We study the charge and spin gaps, bandwidths and weights of the spectra for various values of the on-site Coulomb interaction U and the electron filling. In the low energy part, the local correlation functions are different for the charge and spin. The bandwidths are proportional to t for the charge and J for the spin respectively.

Stress Induced Charge-Ordering Process in LiMn 2O 4

DOE PAGES

Chen, Yan; Yu, Dunji; An, Ke

2016-07-25

In this letter we report the stress-induced Mn charge-ordering process in the LiMn 2O 4 spinel, evidenced by the lattice strain evolutions due to the Jahn–Teller effects. In situ neutron diffraction reveals the initial stage of this process at low stress, indicating the eg electron localization at the preferential Mn sites during the early phase transition as an underlying charge-ordering mechanism in the charge-frustrated LiMn 2O 4. The initial stage of this transition exhibits as a progressive lattice and charge evolution, without showing a first-order behavior.

Harvesting visible light with MoO3 nanorods modified by Fe(iii) nanoclusters for effective photocatalytic degradation of organic pollutants.

PubMed

Alam, U; Kumar, S; Bahnemann, D; Koch, J; Tegenkamp, C; Muneer, M

2018-02-07

The photocatalytic performance of MoO 3 is limited due to its weak visible light absorption ability and quick recombination of charge carriers. In the present work, we report the facile synthesis of Fe(iii)-grafted MoO 3 nanorods using a hydrothermal method followed by an impregnation technique with the aim of enhancing the light harvesting ability and photocatalytic efficiency of MoO 3 . The prepared samples were characterized through the standard analytical techniques of XRD, SEM-EDS, TEM, XPS, UV-Vis-DRS, FT-IR, TG-DTA and PL spectrophotometry. XPS and TEM analyses reveal that Fe(iii) ions are successfully grafted onto the surface of the MoO 3 nanorod with intimate interfacial contact. The photocatalytic performances of the prepared samples were investigated by studying the degradation of methylene blue (MB), rhodamine B (RhB) and 4-nitrophenol (4-NP) under visible light irradiation. The surface-modified MoO 3 with Fe(iii) ions showed excellent photocatalytic activity towards the degradation of the above-mentioned pollutants, where Fe(iii) ions act as effective cocatalytic sites to produce hydroxyl radicals through multi-electron reduction of oxygen molecules. The improved photocatalytic activity could be ascribed to the effective separation of charge carriers and efficient production of hydroxyl radicals via the rapid capture of electrons by Fe(iii) through a well-known photoinduced interfacial charge transfer mechanism. Based on scavenger analysis study, a mechanism for the enhanced photocatalytic activity has been discussed and proposed. The concept of surface grafting onto large bandgap semiconductors with ubiquitous elements opens up a new avenue for the development of visible-light-responsive photocatalysts with excellent photocatalytic activity.

Dual structure in the charge excitation spectrum of electron-doped cuprates

NASA Astrophysics Data System (ADS)

Bejas, Matías; Yamase, Hiroyuki; Greco, Andrés

2017-12-01

Motivated by the recent resonant x-ray scattering (RXS) and resonant inelastic x-ray scattering (RIXS) experiments for electron-doped cuprates, we study the charge excitation spectrum in a layered t -J model with the long-range Coulomb interaction. We show that the spectrum is not dominated by a specific type of charge excitations, but by different kinds of charge fluctuations, and is characterized by a dual structure in the energy space. Low-energy charge excitations correspond to various types of bond-charge fluctuations driven by the exchange term (J term), whereas high-energy charge excitations are due to usual on-site charge fluctuations and correspond to plasmon excitations above the particle-hole continuum. The interlayer coupling, which is frequently neglected in many theoretical studies, is particularly important to the high-energy charge excitations.

A Density Functional Study of Atomic Hydrogen and Oxygen Chemisorptions on the (0001) Surface of Double Hexagonal Close Packed Americium

NASA Astrophysics Data System (ADS)

Dholabhai, Pratik; Atta-Fynn, Raymond; Ray, Asok

2008-03-01

Ab initio total energy calculations within the framework of density functional theory have been performed for atomic hydrogen and oxygen chemisorptions on the (0001) surface of double hexagonal packed americium using a full-potential all-electron linearized augmented plane wave plus local orbitals (FLAPW+lo) method. The three-fold hollow hcp site was found to be the most stable site for H adsorption, while the two-fold bridge adsorption site was found to be the most stable site for O adsorption. Chemisorption energies and adsorption geometries for different adsorption sites will be discussed. The change in work functions, magnetic moments, partial charges inside muffin-tins, difference charge density distributions and density of states for the bare Am slab and the Am slab after adsorption of the adatom will be discussed. The implications of chemisorption on Am 5f electron localization-delocalization will also be discussed.

33 CFR 72.01-5 - Local Notice to Mariners.

Code of Federal Regulations, 2011 CFR

2011-07-01

...” is mailed to the public free of charge. Note to § 72.01-5: You may also access Local Notice to Mariners free of charge on the Internet from the Coast Guard Navigation Center's Web site (http://www...

33 CFR 72.01-5 - Local Notice to Mariners.

Code of Federal Regulations, 2010 CFR

2010-07-01

...” is mailed to the public free of charge. Note to § 72.01-5: You may also access Local Notice to Mariners free of charge on the Internet from the Coast Guard Navigation Center's Web site (http://www...

33 CFR 72.01-5 - Local Notice to Mariners.

Code of Federal Regulations, 2012 CFR

2012-07-01

...” is mailed to the public free of charge. Note to § 72.01-5: You may also access Local Notice to Mariners free of charge on the Internet from the Coast Guard Navigation Center's Web site (http://www...

Characterization of monoclonal antibodies that strongly inhibit Electrophorus electricus acetylcholinesterase.

PubMed

Remy, M H; Frobert, Y; Grassi, J

1995-08-01

In this study, we describe three different monoclonal antibodies (mAbs Elec-403, Elec-408, and Elec-410) directed against Electrophorus electricus acetylcholinesterase (AChE) which were selected as inhibitors for this enzyme. Two of these antibodies (Elec-403 and Elec-410), recognized overlapping but different epitopes, competed with snake venom toxin fasciculin for binding to the enzyme, and thus apparently recognized the peripheral site of AChE. In addition, the binding of Elec-403 was antagonized by 1,5-bis(4-allyldimethylammoniumphenyl)pentan-3-one dibromide (BW284C51) and propidium, indicating that the corresponding epitope encompassed the anionic site involved in the binding of these low-molecular-mass inhibitors. The third mAb (Elec-408), was clearly bound to another site on the AChE molecule, and its inhibitory effect was cumulative with those of Elec-403, Elec-410, and fasciculin. All mAbs bound AChE with high affinity and were as strong inhibitors with an apparent Ki values less than 0.1 nM. Elec-403 was particularly efficient with an inhibitory activity similar to that of fasciculin. Inhibition was observed with both charged (acetylthiocholine) and neutral substrates (o-nitrophenyl acetate) and had the characteristics of a non-competitive process. Elec-403 and Elec-410 probably exert their effect by triggering allosteric transitions from the peripheral site to the active site. The epitope recognized by mAb Elec-408 has not been localized, but it may correspond to a new regulatory site on AChE.

Inhibition of cyclin-dependent kinase CDK1 by oxindolimine ligands and corresponding copper and zinc complexes.

PubMed

Miguel, Rodrigo Bernardi; Petersen, Philippe Alexandre Divina; Gonzales-Zubiate, Fernando A; Oliveira, Carla Columbano; Kumar, Naresh; do Nascimento, Rafael Rodrigues; Petrilli, Helena Maria; da Costa Ferreira, Ana Maria

2015-10-01

Oxindolimine-copper(II) and zinc(II) complexes that previously have shown to induce apoptosis, with DNA and mitochondria as main targets, exhibit here significant inhibition of kinase CDK1/cyclin B protein. Copper species are more active than the corresponding zinc, and the free ligand shows to be less active, indicating a major influence of coordination in the process, and a further modulation by the coordinated ligand. Molecular docking and classical molecular dynamics provide a better understanding of the effectiveness and kinase inhibition mechanism by these compounds, showing that the metal complex provides a stronger interaction than the free ligand with the ATP-binding site. The metal ion introduces charge in the oxindole species, giving it a more rigid conformation that then becomes more effective in its interactions with the protein active site. Analogous experiments resulted in no significant effect regarding phosphatase inhibition. These results can explain the cytotoxicity of these metal complexes towards different tumor cells, in addition to its capability of binding to DNA, and decreasing membrane potential of mitochondria.

Hollow Fluffy Co3O4 Cages as Efficient Electroactive Materials for Supercapacitors and Oxygen Evolution Reaction.

PubMed

Zhou, Xuemei; Shen, Xuetao; Xia, Zhaoming; Zhang, Zhiyun; Li, Jing; Ma, Yuanyuan; Qu, Yongquan

2015-09-16

Nano-/micrometer multiscale hierarchical structures not only provide large surface areas for surface redox reactions but also ensure efficient charge conductivity, which is of benefit for utilization in areas of electrochemical energy conversion and storage. Herein, hollow fluffy cages (HFC) of Co3O4, constructed of ultrathin nanosheets, were synthesized by the formation of Co(OH)2 hollow cages and subsequent calcination at 250 °C. The large surface area (245.5 m2 g(-1)) of HFC Co3O4 annealed at 250 °C ensures the efficient interaction between electrolytes and electroactive components and provides more active sites for the surface redox reactions. The hierarchical structures minimize amount of the grain boundaries and facilitate the charge transfer process. Thin thickness of nanosheets (2-3 nm) ensures the highly active sites for the surface redox reactions. As a consequence, HFC Co3O4 as the supercapacitor electrode exhibits a superior rate capability, shows an excellent cycliability of 10,000 cycles at 10 A g(-1), and delivers large specific capacitances of 948.9 and 536.8 F g(-1) at 1 and 40 A g(-1), respectively. Catalytic studies of HFC Co3O4 for oxygen evolution reaction display a much higher turnover frequency of 1.67×10(-2) s(-1) in pH 14.0 KOH electrolyte at 400 mV overpotential and a lower Tafel slope of 70 mV dec(-1). HFC Co3O4 with the efficient electrochemical activity and good stability can remain a promising candidate for the electrochemical energy conversion and storage.

The Effectiveness of Commercial Internet Web Sites: A User's Perspective.

ERIC Educational Resources Information Center

Bell, Hudson; Tang, Nelson K. H.

1998-01-01

A user survey of 60 company Web sites (electronic commerce, entertainment and leisure, financial and banking services, information services, retailing and travel, and tourism) determined that 30% had facilities for conducting online transactions and only 7% charged for site access. Overall, Web sites were rated high in ease of access, content, and…

Near UV-Visible electronic absorption originating from charged amino acids in a monomeric protein† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00880e

PubMed Central

Prasad, Saumya; Mandal, Imon; Singh, Shubham; Paul, Ashim; Mandal, Bhubaneswar

2017-01-01

Electronic absorption spectra of proteins are primarily characterized over the ultraviolet region (185–320 nm) of the electromagnetic spectrum. While recent studies on peptide aggregates have revealed absorption beyond 350 nm, monomeric proteins lacking aromatic amino acids, disulphide bonds, and active site prosthetic groups are expected to remain optically silent beyond 250 nm. Here, in a joint theoretical and experimental investigation, we report the distinctive UV-Vis absorption spectrum between 250 nm [ε = 7338 M–1 cm–1] and 800 nm [ε = 501 M–1 cm–1] in a synthetic 67 residue protein (α3C), in monomeric form, devoid of aromatic amino acids. Systematic control studies with high concentration non-aromatic amino acid solutions revealed significant absorption beyond 250 nm for charged amino acids which constitute over 50% of the sequence composition in α3C. Classical atomistic molecular dynamics (MD) simulations of α3C reveal dynamic interactions between multiple charged sidechains of Lys and Glu residues present in α3C. Time-dependent density functional theory calculations on charged amino acid residues sampled from the MD trajectories of α3C reveal that the distinctive absorption features of α3C may arise from two different types of charge transfer (CT) transitions involving spatially proximal Lys/Glu amino acids. Specifically, we show that the charged amino (NH3+)/carboxylate (COO–) groups of Lys/Glu sidechains act as electronic charge acceptors/donors for photoinduced electron transfer either from/to the polypeptide backbone or to each other. Further, the sensitivity of the CT spectra to close/far/intermediate range of encounters between sidechains of Lys/Glu owing to the three dimensional protein fold can create the long tail in the α3C absorption profile between 300 and 800 nm. Finally, we experimentally demonstrate the sensitivity of α3C absorption spectrum to temperature and pH-induced changes in protein structure. Taken together, our investigation significantly expands the pool of spectroscopically active biomolecular chromophores and adds an optical 250–800 nm spectral window, which we term ProCharTS (Protein Charge Transfer Spectra), for label free probes of biomolecular structure and dynamics. PMID:28970921

Functional role of R462 in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae.

PubMed

Li, Fengxue; Xu, Dingguo

2015-08-01

Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding mode, we in this work further investigate the functional role of active site arginine residue, R462, in the degradation of hyaluronan. The site directed mutagenesis simulation of R462A and R462Q were modeled using a combined quantum mechanical and molecular mechanical method. The overall substrate binding features upon mutations do not have significant changes. The energetic profiles for the reaction processes are essentially the same as that in wild type enzyme, but significant activation barrier height changes can be observed. Both mutants were shown to accelerate the overall enzymatic activity, e.g., R462A can reduce the barrier height by about 2.8 kcal mol(-1), while R462Q reduces the activation energy by about 2.9 kcal mol(-1). Consistent with the active site model calculated using density functional theory, our results can support that the positive charge on R462 guanidino side chain group plays a negative role in the catalysis. Finally, the functional role of R462 was proposed to facilitate the formation of initial enzyme-substrate complex, but not in the subsequent catalytic degradation reaction. Graphical Abstract Degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae.

Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogues

PubMed Central

Lietzan, Adam D.; St. Maurice, Martin

2014-01-01

Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP- and bicarbonate-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. It has been hypothesized that the reactive enolpyruvate intermediate is stabilized through a bidentate interaction with the metal ion in the CT domain active site. Whereas bidentate ligands are commonly observed in enzymes catalyzing reactions proceeding through an enolpyruvate intermediate, no bidentate interaction has yet been observed in the CT domain of PC. Here, we report three X-ray crystal structures of the Rhizobium etli PC CT domain with the bound inhibitors oxalate, 3-hydroxypyruvate, and 3-bromopyruvate. Oxalate, a stereoelectronic mimic of the enolpyruvate intermediate, does not interact directly with the metal ion. Instead, oxalate is buried in a pocket formed by several positively charged amino acid residues and the metal ion. Furthermore, both 3-hydroxypyruvate and 3-bromopyruvate, analogs of the reaction product oxaloacetate, bind in an identical manner to oxalate suggesting that the substrate maintains its orientation in the active site throughout catalysis. Together, these structures indicate that the substrates, products and intermediates in the PC-catalyzed reaction are not oriented in the active site as previously assumed. The absence of a bidentate interaction with the active site metal appears to be a unique mechanistic feature among the small group of biotin-dependent enzymes that act on α-keto acid substrates. PMID:24157795

The active site of hydroxynitrile lyase from Prunus amygdalus: Modeling studies provide new insights into the mechanism of cyanogenesis

PubMed Central

Dreveny, Ingrid; Kratky, Christoph; Gruber, Karl

2002-01-01

The FAD-dependent hydroxynitrile lyase from almond (Prunus amygdalus, PaHNL) catalyzes the cleavage of R-mandelonitrile into benzaldehyde and hydrocyanic acid. Catalysis of the reverse reaction—the enantiospecific formation of α-hydroxynitriles—is now widely utilized in organic syntheses as one of the few industrially relevant examples of enzyme-mediated C–C bond formation. Starting from the recently determined X-ray crystal structure, systematic docking calculations with the natural substrate were used to locate the active site of the enzyme and to identify amino acid residues involved in substrate binding and catalysis. Analysis of the modeled substrate complexes supports an enzymatic mechanism that includes the flavin cofactor as a mere "spectator" of the reaction and relies on general acid/base catalysis by the conserved His-497. Stabilization of the negative charge of the cyanide ion is accomplished by a pronounced positive electrostatic potential at the binding site. PaHNL activity requires the FAD cofactor to be bound in its oxidized form, and calculations of the pKa of enzyme-bound HCN showed that the observed inactivation upon cofactor reduction is largely caused by the reversal of the electrostatic potential within the active site. The suggested mechanism closely resembles the one proposed for the FAD-independent, and structurally unrelated HNL from Hevea brasiliensis. Although the actual amino acid residues involved in the catalytic cycle are completely different in the two enzymes, a common motif for the mechanism of cyanogenesis (general acid/base catalysis plus electrostatic stabilization of the cyanide ion) becomes evident. PMID:11790839

Allosteric modulation of Ras positions Q61 for a direct role in catalysis

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

Buhrman, Greg; Holzapfel, Genevieve; Fetics, Susan

2010-11-03

Ras and its effector Raf are key mediators of the Ras/Raf/MEK/ERK signal transduction pathway. Mutants of residue Q61 impair the GTPase activity of Ras and are found prominently in human cancers. Yet the mechanism through which Q61 contributes to catalysis has been elusive. It is thought to position the catalytic water molecule for nucleophilic attack on the {gamma}-phosphate of GTP. However, we previously solved the structure of Ras from crystals with symmetry of the space group R32 in which switch II is disordered and found that the catalytic water molecule is present. Here we present a structure of wild-type Rasmore » with calcium acetate from the crystallization mother liquor bound at a site remote from the active site and likely near the membrane. This results in a shift in helix 3/loop 7 and a network of H-bonding interactions that propagates across the molecule, culminating in the ordering of switch II and placement of Q61 in the active site in a previously unobserved conformation. This structure suggests a direct catalytic role for Q61 where it interacts with a water molecule that bridges one of the {gamma}-phosphate oxygen atoms to the hydroxyl group of Y32 to stabilize the transition state of the hydrolysis reaction. We propose that Raf together with the binding of Ca{sup 2+} and a negatively charged group mimicked in our structure by the acetate molecule induces the ordering of switch I and switch II to complete the active site of Ras.« less

The Structural Basis of Substrate Recognition in an exo-b-d-glucosaminidase Involved in Chitosan Hydrolysis

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

Van Bueren, A.; Ghinet, M; Gregg, K

2009-01-01

Family 2 of the glycoside hydrolase classification is one of the largest families. Structurally characterized members of this family include enzymes with ?-galactosidase activity (Escherichia coli LacZ), ?-glucuronidase activity (Homo sapiens GusB), and ?-mannosidase activity (Bacteroides thetaiotaomicron BtMan2A). Here, we describe the structure of a family 2 glycoside hydrolase, CsxA, from Amycolatopsis orientalis that has exo-?-d-glucosaminidase (exo-chitosanase) activity. Analysis of a product complex (1.85 A resolution) reveals a unique negatively charged pocket that specifically accommodates the nitrogen of nonreducing end glucosamine residues, allowing this enzyme to discriminate between glucose and glucosamine. This also provides structural evidence for the role ofmore » E541 as the catalytic nucleophile and D469 as the catalytic acid/base. The structures of an E541A mutant in complex with a natural ?-1,4-d-glucosamine tetrasaccharide substrate and both E541A and D469A mutants in complex with a pNP-?-d-glucosaminide synthetic substrate provide insight into interactions in the + 1 subsite of this enzyme. Overall, a comparison with the active sites of other GH2 enzymes highlights the unique architecture of the CsxA active site, which imparts specificity for its cationic substrate.« less

The Structural Basis of Substrate Recognition in an exo-beta-d-Glucosaminidase Involved in Chitosan Hydrolysis

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

Lammerts van Bueren, A.; Ghinet, M; Gregg, K

2009-01-01

Family 2 of the glycoside hydrolase classification is one of the largest families. Structurally characterized members of this family include enzymes with beta-galactosidase activity (Escherichia coli LacZ), beta-glucuronidase activity (Homo sapiens GusB), and beta-mannosidase activity (Bacteroides thetaiotaomicron BtMan2A). Here, we describe the structure of a family 2 glycoside hydrolase, CsxA, from Amycolatopsis orientalis that has exo-beta-D-glucosaminidase (exo-chitosanase) activity. Analysis of a product complex (1.85 A resolution) reveals a unique negatively charged pocket that specifically accommodates the nitrogen of nonreducing end glucosamine residues, allowing this enzyme to discriminate between glucose and glucosamine. This also provides structural evidence for the role ofmore » E541 as the catalytic nucleophile and D469 as the catalytic acid/base. The structures of an E541A mutant in complex with a natural beta-1,4-D-glucosamine tetrasaccharide substrate and both E541A and D469A mutants in complex with a pNP-beta-D-glucosaminide synthetic substrate provide insight into interactions in the +1 subsite of this enzyme. Overall, a comparison with the active sites of other GH2 enzymes highlights the unique architecture of the CsxA active site, which imparts specificity for its cationic substrate.« less

Zwitterionic versus canonical amino acids over the various defects in zeolites: A two-layer ONIOM calculation

PubMed Central

Yang, Gang; Zhou, Lijun

2014-01-01

Defects are often considered as the active sites for chemical reactions. Here a variety of defects in zeolites are used to stabilize zwitterionic glycine that is not self-stable in gas phase; in addition, effects of acidic strengths and zeolite channels on zwitterionic stabilization are demonstrated. Glycine zwitterions can be stabilized by all these defects and energetically prefer to canonical structures over Al and Ga Lewis acidic sites rather than Ti Lewis acidic site, silanol and titanol hydroxyls. For titanol (Ti-OH), glycine interacts with framework Ti and hydroxyl sites competitively, and the former with Lewis acidity predominates. The transformations from canonical to zwitterionic glycine are obviously more facile over Al and Ga Lewis acidic sites than over Ti Lewis acidic site, titanol and silanol hydroxyls. Charge transfers that generally increase with adsorption energies are found to largely decide the zwitterionic stabilization effects. Zeolite channels play a significant role during the stabilization process. In absence of zeolite channels, canonical structures predominate for all defects; glycine zwitterions remain stable over Al and Ga Lewis acidic sites and only with synergy of H-bonding interactions can exist over Ti Lewis acidic site, while automatically transform to canonical structures over silanol and titanol hydroxyls. PMID:25307449

Photocatalytic removal of 2,4-dichlorophenoxyacetic acid herbicide on copper oxide/titanium dioxide prepared by co-precipitation method

NASA Astrophysics Data System (ADS)

Lee, Shu Chin; Hasan, Norhasnita; Lintang, Hendrik O.; Shamsuddin, Mustaffa; Yuliati, Leny

2016-02-01

In this work, suppression of the charge recombination on the titanium dioxide (TiO2) was reported by the addition of copper oxide (CuO), which led to a higher activity of TiO2 for removal of 2,4-dichlorophenoxyacetic acid (2,4-D) herbicide. A series of CuO/TiO2 with CuO loadings of 0.1-1 wt% was prepared through a co-precipitation method. X-ray diffraction patterns revealed that the presence of CuO could not be detected as the low loading amount of CuO might have good dispersion on the surface of TiO2. Diffuse reflectance UV-visible spectra suggested that low loading amount of CuO did not influence the optical property of TiO2. Fluorescence spectroscopy revealed that TiO2 possessed a dominant emission peak of 407 nm at an excitation wavelength of 218 nm. The increasing loading amount of CuO decreased the emission intensity of TiO2, suggesting the successful reduction of charge recombination. After irradiation under UV light for 1 h, CuO(0.1 wt%)/TiO2 gave the highest percentage removal of the herbicide among the samples. The optimum loading amount of CuOmight improve the charge separation and reduce the electron-hole recombination on TiO2 without blocking the active sites, thus leading to the improved photocatalytic activity. This work showed that CuO/TiO2 is a potential photocatalyst for environmental remediation.

Unified superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange adsorptive separations

PubMed Central

Kisley, Lydia; Chen, Jixin; Mansur, Andrea P.; Shuang, Bo; Kourentzi, Katerina; Poongavanam, Mohan-Vivekanandan; Chen, Wen-Hsiang; Dhamane, Sagar; Willson, Richard C.; Landes, Christy F.

2014-01-01

Chromatographic protein separations, immunoassays, and biosensing all typically involve the adsorption of proteins to surfaces decorated with charged, hydrophobic, or affinity ligands. Despite increasingly widespread use throughout the pharmaceutical industry, mechanistic detail about the interactions of proteins with individual chromatographic adsorbent sites is available only via inference from ensemble measurements such as binding isotherms, calorimetry, and chromatography. In this work, we present the direct superresolution mapping and kinetic characterization of functional sites on ion-exchange ligands based on agarose, a support matrix routinely used in protein chromatography. By quantifying the interactions of single proteins with individual charged ligands, we demonstrate that clusters of charges are necessary to create detectable adsorption sites and that even chemically identical ligands create adsorption sites of varying kinetic properties that depend on steric availability at the interface. Additionally, we relate experimental results to the stochastic theory of chromatography. Simulated elution profiles calculated from the molecular-scale data suggest that, if it were possible to engineer uniform optimal interactions into ion-exchange systems, separation efficiencies could be improved by as much as a factor of five by deliberately exploiting clustered interactions that currently dominate the ion-exchange process only accidentally. PMID:24459184

Unified superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange adsorptive separations.

PubMed

Kisley, Lydia; Chen, Jixin; Mansur, Andrea P; Shuang, Bo; Kourentzi, Katerina; Poongavanam, Mohan-Vivekanandan; Chen, Wen-Hsiang; Dhamane, Sagar; Willson, Richard C; Landes, Christy F

2014-02-11

Chromatographic protein separations, immunoassays, and biosensing all typically involve the adsorption of proteins to surfaces decorated with charged, hydrophobic, or affinity ligands. Despite increasingly widespread use throughout the pharmaceutical industry, mechanistic detail about the interactions of proteins with individual chromatographic adsorbent sites is available only via inference from ensemble measurements such as binding isotherms, calorimetry, and chromatography. In this work, we present the direct superresolution mapping and kinetic characterization of functional sites on ion-exchange ligands based on agarose, a support matrix routinely used in protein chromatography. By quantifying the interactions of single proteins with individual charged ligands, we demonstrate that clusters of charges are necessary to create detectable adsorption sites and that even chemically identical ligands create adsorption sites of varying kinetic properties that depend on steric availability at the interface. Additionally, we relate experimental results to the stochastic theory of chromatography. Simulated elution profiles calculated from the molecular-scale data suggest that, if it were possible to engineer uniform optimal interactions into ion-exchange systems, separation efficiencies could be improved by as much as a factor of five by deliberately exploiting clustered interactions that currently dominate the ion-exchange process only accidentally.

Adsorption and Conformation Change of Helical Peptides on Colloidal Silica

NASA Astrophysics Data System (ADS)

Read, Michael; Zhang, Shuguang; Mayes, Anne; Burkett, Sandra

2001-03-01

Helical conformations of short peptides in solution are partly stabilized by the pattern of electrostatic charge formed by the amino acid sequence. We have studied the role of electrostatics in the adsorption and helix-coil transition of peptides on oxide surfaces. Adsorption isotherms, along with a combination of spectroscopic techniques, show that this is a reversible equilibrium process. Strong electrostatic forces between ionic side chains and charged surface sites increase the adsorbed amount, and promote a loss of helicity in the adsorbed state qualitatively different from that observed upon thermal or chemical perturbation. The electrical dipole of the peptide, arising from the amino acid side chains, serves to orient the molecules on the surface. Effects of adsorption, orientation, and conformation change on the activity of peptides in model biological reactions, as well as the relevance of this simplified system to protein adsorption, are considered.

Systems, methods and computer readable media for estimating capacity loss in rechargeable electrochemical cells

DOEpatents

Gering, Kevin L.

2013-06-18

A system includes an electrochemical cell, monitoring hardware, and a computing system. The monitoring hardware periodically samples charge characteristics of the electrochemical cell. The computing system periodically determines cell information from the charge characteristics of the electrochemical cell. The computing system also periodically adds a first degradation characteristic from the cell information to a first sigmoid expression, periodically adds a second degradation characteristic from the cell information to a second sigmoid expression and combines the first sigmoid expression and the second sigmoid expression to develop or augment a multiple sigmoid model (MSM) of the electrochemical cell. The MSM may be used to estimate a capacity loss of the electrochemical cell at a desired point in time and analyze other characteristics of the electrochemical cell. The first and second degradation characteristics may be loss of active host sites and loss of free lithium for Li-ion cells.

Monodisperse, polymeric microspheres produced by irradiation of slowly thawing frozen drops

NASA Technical Reports Server (NTRS)

Rhim, Won-Kyu (Inventor); Hyson, Michael T. (Inventor); Chung, Sang-Kun (Inventor); Colvin, Michael S. (Inventor); Chang, Manchium (Inventor)

1991-01-01

Monodisperse, polymeric microspheres are formed by injecting uniformly shaped droplets of radiation polymerizable monomers, preferably a biocompatible monomer, having covalent binding sites such as hydroxyethylmethacrylate, into a zone, impressing a like charge on the droplet so that they mutually repel each other, spheroidizing the droplets within the zone and collecting the droplets in a pool of cryogenic liquid. As the droplets enter the liquid, they freeze into solid, glassy microspheres, which vaporizes a portion of the cryogenic liquid to form a layer. The like-charged microspheres, suspended within the layer, move to the edge of the vessel holding the pool, are discharged, fall and are collected. The collected microspheres are irradiated while frozen in the cryogenic liquid to form latent free radicals. The frozen microspheres are then slowly thawed to activate the free radicals which polymerize the monomer to form evenly-sized, evenly-shaped, monodisperse polymeric microspheres.

Apollo 17 Lunar Surface Experiments package

NASA Image and Video Library

1972-05-10

S72-37260 (November 1972) --- The remote antenna for the Lunar Seismic Profiling Experiment, Numbered S-203, a component of the Apollo Lunar Surface Experiments Package which will be carried on the Apollo 17 lunar landing mission. LSPE components are four geophones similar to those used in earlier active seismic experiments an electronics package in the ALSEP central station, and eight explosive packages which will be deployed during the geology traverse. The four geophones will be placed one in the center and at each corner of a 90-meter equilateral triangle. Explosive charges placed on the surface will generate seismic waves of varying strengths to provide data on the structural profile of the landing site. After the charges have been fired by ground command, the experiment will settle down into a passive listening mode, detecting moonquakes, meteorite impacts and the thump caused by the Lunar Module ascent stage impact. The antenna is of the telescoping type.

Apollo 17 Lunar Surface Experiment equipment

NASA Image and Video Library

1972-11-30

S72-37259 (November 1972) --- The Geophone Module and Cable Reels of the Lunar Seismic Profiling Experiment (S-203), a component of the Apollo Lunar Surface Experiments Package which will be carried on the Apollo 17 lunar landing mission. LSPE components are four geophones similar to those used in an earlier active seismic experiment, an electronics package in the ALSEP central station, and eight explosive packages which will be deployed during the geology traverse. The four geophones will be placed one in the center and one at each corner of a 90-meter equilateral triangle. Explosive charges placed on the surface will generate seismic waves of varying strengths to provide data on the structural profile of the landing site. After the charges have been fired by ground command, the experiment will settle down into a passive listening mode, detecting moonquakes, meteorite impacts and the thump caused by the Lunar Module ascent stage impact.

Kinetic and calorimetric study of the adsorption of dyes on mesoporous activated carbon prepared from coconut coir dust.

PubMed

Macedo, Jeremias de Souza; da Costa Júnior, Nivan Bezerra; Almeida, Luis Eduardo; Vieira, Eunice Fragoso da Silva; Cestari, Antonio Reinaldo; Gimenez, Iara de Fátima; Villarreal Carreño, Neftali Lênin; Barreto, Ledjane Silva

2006-06-15

Mesoporous activated carbon has been prepared from coconut coir dust as support for adsorption of some model dye molecules from aqueous solutions. The methylene blue (MB) and remazol yellow (RY) molecules were chosen for study of the adsorption capacity of cationic and anionic dyes onto prepared activated carbon. The adsorption kinetics was studied with the Lagergren first- and pseudo-second-order kinetic models as well as the intraparticle diffusion model. The results for both dyes suggested a multimechanism sorption process. The adsorption mechanisms in the systems dyes/AC follow pseudo-second-order kinetics with a significant contribution of intraparticle diffusion. The samples simultaneously present acidic and basic sites able to act as anchoring sites for basic and acidic dyes, respectively. Calorimetric studies reveal that dyes/AC interaction forces are correlated with the pH of the solution, which can be related to the charge distribution on the AC surface. These AC samples also exhibited very short equilibrium times for the adsorption of both dyes, which is an economically favorable requisite for the activated carbon described in this work, in addition to the local abundance of the raw material.

Alternative Fuels Data Center: Workplace Charging Success: lynda.com

Science.gov Websites

installed its first on-site PEV charger - a "Juice Bar" with two Level 2 and two Level 1 outlets Francisco, which is housed in a LEED certified building that offers two charging stations. As lynda.com adds

Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model.

PubMed

Das, Debananda; Koh, Yasuhiro; Tojo, Yasushi; Ghosh, Arun K; Mitsuya, Hiroaki

2009-12-01

Reliable and robust prediction of the binding affinity for drug molecules continues to be a daunting challenge. We simulated the binding interactions and free energy of binding of nine protease inhibitors (PIs) with wild-type and various mutant proteases by performing GBSA simulations in which each PI's partial charge was determined by quantum mechanics (QM) and the partial charge accounts for the polarization induced by the protease environment. We employed a hybrid solvation model that retains selected explicit water molecules in the protein with surface-generalized Born (SGB) implicit solvent. We examined the correlation of the free energy with the antiviral potency of PIs with regard to amino acid substitutions in protease. The GBSA free energy thus simulated showed strong correlations (r > 0.75) with antiviral IC(50) values of PIs when amino acid substitutions were present in the protease active site. We also simulated the binding free energy of PIs with P2-bis-tetrahydrofuranylurethane (bis-THF) or related cores, utilizing a bis-THF-containing protease crystal structure as a template. The free energy showed a strong correlation (r = 0.93) with experimentally determined anti-HIV-1 potency. The present data suggest that the presence of selected explicit water in protein and protein polarization-induced quantum charges for the inhibitor, compared to lack of explicit water and a static force-field-based charge model, can serve as an improved lead optimization tool and warrants further exploration.

Stabilization of enzymes in ionic liquids via modification of enzyme charge.

PubMed

Nordwald, Erik M; Kaar, Joel L

2013-09-01

Due to the propensity of ionic liquids (ILs) to inactivate enzymes, the development of strategies to improve enzyme utility in these solvents is critical to fully exploit ILs for biocatalysis. We have developed a strategy to broadly improve enzyme utility in ILs based on elucidating the effect of charge modifications on the function of enzymes in IL environments. Results of stability studies in aqueous-IL mixtures indicated a clear connection between the ratio of enzyme-containing positive-to-negative sites and enzyme stability in ILs. Stability studies of the effect of [BMIM][Cl] and [EMIM][EtSO4 ] on chymotrypsin specifically found an optimum ratio of positively-charged amine-to-negatively-charged acid groups (0.39). At this ratio, the half-life of chymotrypsin was increased 1.6- and 4.3-fold relative to wild-type chymotrypsin in [BMIM][Cl] and [EMIM][EtSO4 ], respectively. The half-lives of lipase and papain were similarly increased as much as 4.0 and 2.4-fold, respectively, in [BMIM][Cl] by modifying the ratio of positive-to-negative sites of each enzyme. More generally, the results of stability studies found that modifications that reduce the ratio of enzyme-containing positive-to-negative sites improve enzyme stability in ILs. Understanding the impact of charge modification on enzyme stability in ILs may ultimately be exploited to rationally engineer enzymes for improved function in IL environments. Copyright © 2013 Wiley Periodicals, Inc.

Enhanced charge ordering transition in doped CaFeO3 through steric templating

NASA Astrophysics Data System (ADS)

Jiang, Lai; Saldana-Greco, Diomedes; Schick, Joseph T.; Rappe, Andrew M.

2014-06-01

We report a density functional theory investigation of B-site doped CaFeO3, a prototypical charge ordered perovskite. At 290 K, CaFeO3 undergoes a metal-insulator transition and a charge disproportionation reaction 2Fe4+→Fe5++Fe3+. We observe that when Zr dopants occupy a (001) layer, the band gap of the resulting solid solution increases to 0.93 eV due to a two-dimensional Jahn-Teller-type distortion, where FeO6 cages on the xy plane elongate along x and y alternatively between neighboring Fe sites. Furthermore, we show that the rock-salt ordering of the Fe5+ and Fe3+ cations can be enhanced when the B-site dopants are arranged in a (111) plane due to a collective steric effect that facilitates the size discrepancy between the Fe5+O6 and Fe3+O6 octahedra and therefore gives rise to a larger band gap. The enhanced charge disproportionation in these solid solutions is verified by rigorously calculating the oxidation states of the Fe cations with different octahedral cage sizes. We therefore predict that the corresponding transition temperature will increase due to the enhanced charge ordering and larger band gap. The compositional, structural, and electrical relationships exploited in this paper can be extended to a variety of perovskites and nonperovskite oxides, providing guidance in the structural manipulation of electrical properties of functional materials.

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

PubMed Central

Sigala, Paul A.; Fafarman, Aaron T.; Schwans, Jason P.; Fried, Stephen D.; Fenn, Timothy D.; Caaveiro, Jose M. M.; Pybus, Brandon; Ringe, Dagmar; Petsko, Gregory A.; Boxer, Steven G.; Herschlag, Daniel

2013-01-01

Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol–Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations. PMID:23798390

Porous mesocarbon microbeads with graphitic shells: constructing a high-rate, high-capacity cathode for hybrid supercapacitor

PubMed Central

Lei, Yu; Huang, Zheng-Hong; Yang, Ying; Shen, Wanci; Zheng, Yongping; Sun, Hongyu; Kang, Feiyu

2013-01-01

Li4Ti5O12/activated carbon hybrid supercapacitor can combine the advantages of both lithium-ion battery and supercapacitor, which may meet the requirements for developing high-performance hybrid electric vehicles. Here we proposed a novel “core-shell” porous graphitic carbon (PGC) to replace conventional activated carbon for achieving excellent cell performance. In this PGC structure made from mesocarbon microbead (MCMB), the inner core is composed of porous amorphous carbon, while the outer shell is graphitic carbon. The abundant porosity and the high surface area not only offer sufficient reaction sites to store electrical charge physically, but also can accelerate the liquid electrolyte to penetrate the electrode and the ions to reach the reacting sites. Meanwhile, the outer graphitic shells of the porous carbon microbeads contribute to a conductive network which will remarkably facilitate the electron transportation, and thus can be used to construct a high-rate, high-capacity cathode for hybrid supercapacitor, especially at high current densities. PMID:23963328

ZnO nanoparticles modulate the ionic transport and voltage regulation of lysenin nanochannels.

PubMed

Bryant, Sheenah L; Eixenberger, Josh E; Rossland, Steven; Apsley, Holly; Hoffmann, Connor; Shrestha, Nisha; McHugh, Michael; Punnoose, Alex; Fologea, Daniel

2017-12-16

The insufficient understanding of unintended biological impacts from nanomaterials (NMs) represents a serious impediment to their use for scientific, technological, and medical applications. While previous studies have focused on understanding nanotoxicity effects mostly resulting from cellular internalization, recent work indicates that NMs may interfere with transmembrane transport mechanisms, hence enabling contributions to nanotoxicity by affecting key biological activities dependent on transmembrane transport. In this line of inquiry, we investigated the effects of charged nanoparticles (NPs) on the transport properties of lysenin, a pore-forming toxin that shares fundamental features with ion channels such as regulation and high transport rate. The macroscopic conductance of lysenin channels greatly diminished in the presence of cationic ZnO NPs. The inhibitory effects were asymmetrical relative to the direction of the electric field and addition site, suggesting electrostatic interactions between ZnO NPs and a binding site. Similar changes in the macroscopic conductance were observed when lysenin channels were reconstituted in neutral lipid membranes, implicating protein-NP interactions as the major contributor to the reduced transport capabilities. In contrast, no inhibitory effects were observed in the presence of anionic SnO 2 NPs. Additionally, we demonstrate that inhibition of ion transport is not due to the dissolution of ZnO NPs and subsequent interactions of zinc ions with lysenin channels. We conclude that electrostatic interactions between positively charged ZnO NPs and negative charges within the lysenin channels are responsible for the inhibitory effects on the transport of ions. These interactions point to a potential mechanism of cytotoxicity, which may not require NP internalization.

Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library*

PubMed Central

Kiefer, Jonathan D.; Srinivas, Raja R.; Lobner, Elisabeth; Tisdale, Alison W.; Mehta, Naveen K.; Yang, Nicole J.; Tidor, Bruce; Wittrup, K. Dane

2016-01-01

The Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus is an attractive binding scaffold because of its small size (7 kDa), high thermal stability (Tm of 98 °C), and absence of cysteines and glycosylation sites. However, as a DNA-binding protein, Sso7d is highly positively charged, introducing a strong specificity constraint for binding epitopes and leading to nonspecific interaction with mammalian cell membranes. In the present study, we report charge-neutralized variants of Sso7d that maintain high thermal stability. Yeast-displayed libraries that were based on this reduced charge Sso7d (rcSso7d) scaffold yielded binders with low nanomolar affinities against mouse serum albumin and several epitopes on human epidermal growth factor receptor. Importantly, starting from a charge-neutralized scaffold facilitated evolutionary adaptation of binders to differentially charged epitopes on mouse serum albumin and human epidermal growth factor receptor, respectively. Interestingly, the distribution of amino acids in the small and rigid binding surface of enriched rcSso7d-based binders is very different from that generally found in more flexible antibody complementarity-determining region loops but resembles the composition of antibody-binding energetic hot spots. Particularly striking was a strong enrichment of the aromatic residues Trp, Tyr, and Phe in rcSso7d-based binders. This suggests that the rigidity and small size of this scaffold determines the unusual amino acid composition of its binding sites, mimicking the energetic core of antibody paratopes. Despite the high frequency of aromatic residues, these rcSso7d-based binders are highly expressed, thermostable, and monomeric, suggesting that the hyperstability of the starting scaffold and the rigidness of the binding surface confer a high tolerance to mutation. PMID:27582495

Cation Exchange in the Presence of Oil in Porous Media

PubMed Central

2017-01-01

Cation exchange is an interfacial process during which cations on a clay surface are replaced by other cations. This study investigates the effect of oil type and composition on cation exchange on rock surfaces, relevant for a variety of oil-recovery processes. We perform experiments in which brine with a different composition than that of the in situ brine is injected into cores with and without remaining oil saturation. The cation-exchange capacity (CEC) of the rocks was calculated using PHREEQC software (coupled to a multipurpose transport simulator) with the ionic composition of the effluent histories as input parameters. We observe that in the presence of crude oil, ion exchange is a kinetically controlled process and its rate depends on residence time of the oil in the pore, the temperature, and kinetic rate of adsorption of the polar groups on the rock surface. The cation-exchange process occurs in two stages during two phase flow in porous media. Initially, the charged sites of the internal surface of the clays establish a new equilibrium by exchanging cations with the aqueous phase. At later stages, the components of the aqueous and oleic phases compete for the charged sites on the external surface or edges of the clays. When there is sufficient time for crude oil to interact with the rock (i.e., when the core is aged with crude oil), a fraction of the charged sites are neutralized by the charged components stemming from crude oil. Moreover, the positively charged calcite and dolomite surfaces (at the prevailing pH environment of our experiments) are covered with the negatively charged components of the crude oil and therefore less mineral dissolution takes place when oil is present in porous media. PMID:28580442

24 CFR 954.303 - Eligible project costs.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., improvements necessary to permit the use by handicapped persons, and the abatement of lead-based paint hazards... the site improvements may be charged against the HOME grant. Site improvements include roads, streets...

Modification by protons of frog skeletal muscle KATP channels: effects on ion conduction and nucleotide inhibition.

PubMed Central

Vivaudou, M; Forestier, C

1995-01-01

1. The molecular mechanisms underlying pH regulation of skeletal muscle ATP-sensitive K+ (KATP) channels were studied using the patch clamp technique in the inside-out configuration. Two effects of intracellular protons were studied in detail: the decrease in magnitude of single-channel currents and the increase in open probability (Po) of nucleotide-inhibited channels. 2. The pH dependence of inward unit currents under different ionic conditions was in poor agreement with either a direct block of the pore by protons or an indirect proton-induced conformational change, but was compatible with the protonation of surface charges located near the cytoplasmic entrance of the pore. This latter electrostatic mechanism was modelled using Gouy-Chapman-Stern theory, which predicted the data accurately with a surface charge density of about 0.1 negative elementary charges per square nanometre and a pK (pH value for 50% effect) value for protonation of these charges of 6.25. The same mechanism, i.e. neutralization of negative surface charges by cation binding, could also account for the previously reported reduction of inward unit currents by Mg2+. 3. Intracellular alkalization did not affect Po of the KATP channels. Acidification increased Po. In the presence of 0.1 mM ATP (no Mg2+), the channel activation vs. pH relationship could be fitted with a sigmoid curve with a Hill coefficient slightly above 2 and a pK value of 6. This latter value was dependent on the ATP concentration, decreasing from 6.3 in 30 microM ATP to 5.3 in 1 microM ATP. 4. Conversely, the channel inhibition vs. ATP concentration curve was shifted to the right when the pH was lowered. At pH 7.1, the ATP concentration causing half-maximal inhibition was about 10 microM. At pH 5.4, it was about 400 microM. The Hill coefficient values remained slightly below 2. Similar effects were observed when ADP was used as the inhibitory nucleotide. 5. These results confirm that a reciprocal competitive link exists between proton and nucleotide binding sites. Quantitatively, they are in full agreement with a steady-state model of a KATP channel possessing four identical protonation sites (microscopic pK, 6) allosterically connected to the channel open state and two identical nucleotide sites (microscopic ATP dissociation constant, approximately 30 microM) connected to the closed state. Images Figure 13 PMID:7473225

Amine-Modulated/Engineered Interfaces of NiMo Electrocatalysts for Improved Hydrogen Evolution Reaction in Alkaline Solutions.

PubMed

Gao, Wei; Gou, Wangyan; Zhou, Xuemei; Ho, Johnny C; Ma, Yuanyuan; Qu, Yongquan

2018-01-17

The interface between electrolytes and electrocatalysts would largely determine their corresponding activity and stability. Herein, modulating the surface characteristics of NiMo nanoparticles by various adsorbed amines gives the tunability on their interfacial properties and subsequently improves their catalytic performance for hydrogen evolution reaction (HER) in alkaline solutions. Diamines can significantly improve their HER activity by decreasing the charge-transfer resistance and modulating the electronic structures of interfacial active sites. Importantly, among various amines, ethylenediamine facilitates the HER activity of NiMo with a remarkable decrease of 268 mV in the overpotential to reach 10 mA cm -2 as compared with that of the unmodified NiMo in 1.0 M KOH. This method provides a novel strategy of regulating the interfacial properties to strengthen the catalytic performance of electrocatalysts.

Photoinduced ultrafast charge-order melting: Charge-order inversion and nonthermal effects

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

van Veenendaal, Michel

2016-09-01

The effect of photoexcitation is studied for a system with checkerboard charge order induced by displacements of ligands around a metal site. The motion of the ligands is treated classically and the electronic charges are simplified to two-level molecular bond charges. The calculations are done for a checkerboard charge-ordered system with about 100 000 ligand oscillators coupled to a fixed-temperature bath. The initial photoexcitation is followed by a rapid decrease in the charge-order parameter within 50–100 femtoseconds while leaving the correlation length almost unchanged. Depending on the fluence, a complete melting of the charge order occurs in less than amore » picosecond. While for low fluences, the system returns to its original state, for full melting, it recovers to its broken-symmetry state leading to an inversion of the charge order. For small long-range interactions, recovery can be slow due to domain formation.« less

Photoinduced ultrafast charge-order melting: Charge-order inversion and nonthermal effects

DOE PAGES

van Veenendaal, Michel

2016-09-01

The effect of photoexcitation is studied for a system with checkerboard charge order induced by displacements of ligands around a metal site. The motion of the ligands is treated classically and the electronic charges are simplified to two-level molecular bond charges. The calculations are done for a checkerboard charge-ordered system with about 100 000 ligand oscillators coupled to a fixed-temperature bath. The initial photoexcitation is followed by a rapid decrease in the charge-order parameter within 50–100 femtoseconds while leaving the correlation length almost unchanged. Depending on the fluence, a complete melting of the charge order occurs in less than amore » picosecond. While for low fluences, the system returns to its original state, for full melting, it recovers to its broken-symmetry state leading to an inversion of the charge order. Finally, for small long-range interactions, recovery can be slow due to domain formation.« less

Electronic behaviour of Au-Pt alloys and the 4f binding energy shift anomaly in Au bimetallics- X-ray spectroscopy studies

NASA Astrophysics Data System (ADS)

Wang, Dongniu; Cui, Xiaoyu; Xiao, Qunfeng; Hu, Yongfeng; Wang, Zhiqiang; Yiu, Y. M.; Sham, T. K.

2018-06-01

The electronic structure and charge redistribution of 6s conduction charge and 5d charge in Au and Pt alloys, Au9Pt and AuPt9 have been investigated using a charge compensation model. It is found that, both the Au and Pt 4f binding energy (BE) exhibits a negative shift in the alloys relatively to the pure metal in apparent disagreement with electroneutrality considerations (Au is the most electronegative metallic element); more interestingly, the negative Au 4f BE shift in Au-Pt alloy is in contrast to previous observations for a large number of Au bimetallic systems with more electropositive hosts in which the more electropositive the host„ the more positive the Au 4f BE shift. This anomaly is counter intuitive to electronegativity considerations. This dilemma was resolved by the charge compensation model in which both electronegativity and charge neutrality can be satisfied and the overall charge flow δ, onto Au is small and positive and δ arises from charge flow of 6s conduction charge, Δnc onto Au site, which is partially compensated by the depletion of 6d charge Δnd at the Au site (δ = Δnc+ Δnd ˜0.1 >0). The much larger Coulomb interaction between 4f and 5d than that between 4f and 6s results in positive 4f BE shifts. The Au 4f BE shift in Au-Pt alloys together with 193Au Mössbauer data were used in the charge compensation model analysis which shows that the model is still valid in that the Au 4f shift in Au-Pt alloy arises from mainly conduction charge gain with little depletion of d charge at the Au site. The model also works for Pt. The Au and Pt 5d character in the alloys have been examined with valence band spectra which show both maintain their d characteristic in dilute alloys with Pt d piling up at the Fermi level, and the top of the Au valence band being pushed toward the Fermi level; this is confirmed with DFT densities of state calculations. When Pt is diluted in Au, it gains d charge as evident from the reduction in whiteline intensity at the Pt L3-edge XANES. What emerges from this work is a picture in which the s-d charge compensation in Au bimetallic alloys is triggered by electronegativity difference between Au and the host. For Au-Pt and Au-Pd systems, the difference in electronegativity is very small, conduction charge transfer dominates, and the Au 4f shift is negative whereas in most Au bimetallics, the larger the electronegativity difference, the larger the compensation and the larger the Au 4f shifts.

FIRST-PRINCIPLES CALCULATIONS OF CHARGE STATES AND FORMATION ENERGIES OF Mg, Al, and Be TRANSMUTANTS IN 3C-SiC

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

Hu, Shenyang Y.; Setyawan, Wahyu; Jiang, Weilin

2014-08-28

The Vienna Ab-initio Simulation Package (VASP) is employed to calculate charge states and the formation energies of Mg, Al and Be transmutants at different lattice sites in 3C-SiC. The results provide important information on the dependence of the most stable charge state and formation energy of Mg, Al, Be and vacancies on electron potentials.

What is the Impact of Utility Demand Charges on a DCFC host

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

Francfort, James Edward

The PEV Electric Vehicle Supply Equipment (EVSE) delivered by The EV Project included both AC Level 2 and DCFC units. Over 100 of these dual-port Blink DC fast chargers were deployed by The EV Project. These DCFCs were installed in workplaces and in publicly accessible locations near traffic hubs, retail centers, parking lots, restaurants, and similar locations. The Blink DCFC is capable of charging at power up to 60 kW. Its dual-port design sequences the charge from one port to the other, delivering power to only one of two vehicles connected at a time. The actual power delivered through amore » port is determined by the PEV’s on-board battery management system (BMS). Both the power and the total energy used to recharge a PEV can represent a significant cost for the charging site host. Many electric utilities impose fees for power demand as part of their commercial rate structure. The demand charge incurred by a customer is related to the peak power used during a monthly billing cycle. This is in contrast to the cumulative total energy usage that is the more familiar utility charge seen for most residential services. A demand charge is typically assessed for the highest average power over any 15 minute interval during the monthly billing cycle. One objective of The EV Project was to identify and elucidate the motivations and barriers to potential DCFC site hosts. The application of electric utility demand charges is one such potential barrier. This subject was introduced in the paper: DC Fast Charge - Demand Charge Reduction1. It discussed demand charge impact in general terms in order to focus on potential mitigation actions. This paper identifies specific cases in order to quantify the impact of demand charges on EV Project DCFC hosts.« less

Non-contact, non-destructive, quantitative probing of interfacial trap sites for charge carrier transport at semiconductor-insulator boundary

NASA Astrophysics Data System (ADS)

Choi, Wookjin; Miyakai, Tomoyo; Sakurai, Tsuneaki; Saeki, Akinori; Yokoyama, Masaaki; Seki, Shu

2014-07-01

The density of traps at semiconductor-insulator interfaces was successfully estimated using microwave dielectric loss spectroscopy with model thin-film organic field-effect transistors. The non-contact, non-destructive analysis technique is referred to as field-induced time-resolved microwave conductivity (FI-TRMC) at interfaces. Kinetic traces of FI-TRMC transients clearly distinguished the mobile charge carriers at the interfaces from the immobile charges trapped at defects, allowing both the mobility of charge carriers and the number density of trap sites to be determined at the semiconductor-insulator interfaces. The number density of defects at the interface between evaporated pentacene on a poly(methylmethacrylate) insulating layer was determined to be 1012 cm-2, and the hole mobility was up to 6.5 cm2 V-1 s-1 after filling the defects with trapped carriers. The FI-TRMC at interfaces technique has the potential to provide rapid screening for the assessment of interfacial electronic states in a variety of semiconductor devices.

Total Charge Movement per Channel

PubMed Central

Sigg, Daniel; Bezanilla, Francisco

1997-01-01

One measure of the voltage dependence of ion channel conductance is the amount of gating charge that moves during activation and vice versa. The limiting slope method, introduced by Almers (Almers, W. 1978. Rev. Physiol. Biochem. Pharmacol. 82:96–190), exploits the relationship of charge movement and voltage sensitivity, yielding a lower limit to the range of single channel gating charge displacement. In practice, the technique is plagued by low experimental resolution due to the requirement that the logarithmic voltage sensitivity of activation be measured at very low probabilities of opening. In addition, the linear sequential models to which the original theory was restricted needed to be expanded to accommodate the complexity of mechanisms available for the activation of channels. In this communication, we refine the theory by developing a relationship between the mean activation charge displacement (a measure of the voltage sensitivity of activation) and the gating charge displacement (the integral of gating current). We demonstrate that recording the equilibrium gating charge displacement as an adjunct to the limiting slope technique greatly improves accuracy under conditions where the plots of mean activation charge displacement and gross gating charge displacement versus voltage can be superimposed. We explore this relationship for a wide variety of channel models, which include those having a continuous density of states, nonsequential activation pathways, and subconductance states. We introduce new criteria for the appropriate use of the limiting slope procedure and provide a practical example of the theory applied to low resolution simulation data. PMID:8997663

Charge-patterning phase transition on a surface lattice of titratable sites adjacent to an electrolyte solution

NASA Astrophysics Data System (ADS)

Shore, Joel; Thurston, George

We discuss a model for a charge-patterning phase transition on a two-dimensional square lattice of titratable sites, here regarded as protonation sites, placed on a square lattice in a dielectric medium just below the planar interface between this medium and an aqueous salt solution. Within Debye-Huckel theory, the analytical form of the electrostatic repulsion between protonated sites exhibits an approximate inverse cubic power-law decrease beyond short distances. The problem can thus be mapped onto the two-dimensional antiferromagnetic Ising model with this longer-range interaction, which we study with Monte Carlo simulations. As we increase pH, the occupation probability of a site decreases from 1 at low pH to 0 at high pH. For sufficiently-strong interaction strengths, a phase transition occurs as the occupation probability of 1/2 is approached: the charges arrange themselves into a checkerboard pattern. This ordered phase persists over a range of pH until a transition occurs back to a disordered state. This state is the analogue of the Neel state in the antiferromagnetic Ising spin model. More complicated ordered phases are expected for sufficiently strong interactions (with occupation probabilities of 1/4 and 3/4) and if the lattice is triangular rather than square. This work was supported by NIH EY018249 (GMT).

Failures and anomalies attributed to spacecraft charging

NASA Technical Reports Server (NTRS)

Leach, R. D.; Alexander, M. B. (Editor)

1995-01-01

The effects of spacecraft charging can be very detrimental to electronic systems utilized in space missions. Assuring that subsystems and systems are protected against charging is an important engineering function necessary to assure mission success. Spacecraft charging is expected to have a significant role in future space activities and programs. Objectives of this reference publication are to present a brief overview of spacecraft charging, to acquaint the reader with charging history, including illustrative cases of charging anomalies, and to introduce current spacecraft charging prevention activities of the Electromagnetics and Environments Branch, Marshall Space Flight Center (MSFC), National Aeronautics and Space Administration (NASA).

Effect of the surface charge discretization on electric double layers: a Monte Carlo simulation study.

PubMed

Madurga, Sergio; Martín-Molina, Alberto; Vilaseca, Eudald; Mas, Francesc; Quesada-Pérez, Manuel

2007-06-21

The structure of the electric double layer in contact with discrete and continuously charged planar surfaces is studied within the framework of the primitive model through Monte Carlo simulations. Three different discretization models are considered together with the case of uniform distribution. The effect of discreteness is analyzed in terms of charge density profiles. For point surface groups, a complete equivalence with the situation of uniformly distributed charge is found if profiles are exclusively analyzed as a function of the distance to the charged surface. However, some differences are observed moving parallel to the surface. Significant discrepancies with approaches that do not account for discreteness are reported if charge sites of finite size placed on the surface are considered.

Synthesis of nanoporous CuO/TiO2/Pd-NiO composite catalysts by chemical dealloying and their performance for methanol and ethanol electro-oxidation

NASA Astrophysics Data System (ADS)

Niu, Mengying; Xu, Wence; Zhu, Shengli; Liang, Yanqin; Cui, Zhenduo; Yang, Xianjin; Inoue, Akihisa

2017-09-01

Nanoporous CuO/TiO2/Pd-NiO-x (x = 0, 1, 3, 5, 7 at%) catalysts have been synthesized by dealloying Cu-Ti-Pd-Ni alloy ribbons in acid solution. The nanoporous structure and chemical composition of the catalysts distribute uniformly. Based on the electrochemical active area (EASA), electrocatalytic activity and stability, the np-CuO/TiO2/Pd-NiO-3 catalyst possesses the best performance for methanol and ethanol electro-oxidation. For methanol and ethanol electro-oxidation, the anodic current densities in forward scan of the np-CuO/TiO2/Pd-NiO-3 catalyst are about 5.6 times and 2.1 times larger than that of the np-CuO/TiO2/Pd catalyst, respectively. The introduction of NiO provides more electrochemical active sites due to the improved geometrical and bifunctional mechanism. NiO promotes the adsorption of oxygen-containing species (OHads) on the catalyst surface, and electron effect between Pd and Ni is favorable for charge transfer. This accelerates the removal of intermediate products during the oxidation process. The electrocatalytic processes of methanol and ethanol oxidation in alkaline solution are controlled by both charge transfer and diffusion.

40 CFR 60.37e - Compliance, performance testing, and monitoring guidelines.

Code of Federal Regulations, 2010 CFR

2010-07-01

... requirements: (1) Establish maximum charge rate and minimum secondary chamber temperature as site-specific... above the maximum charge rate or below the minimum secondary chamber temperature measured as 3-hour... below the minimum secondary chamber temperature shall constitute a violation of the established...

Faster Electron Injection and More Active Sites for Efficient Photocatalytic H2 Evolution in g-C3 N4 /MoS2 Hybrid.

PubMed

Shi, Xiaowei; Fujitsuka, Mamoru; Kim, Sooyeon; Majima, Tetsuro

2018-03-01

Herein, the structural effect of MoS 2 as a cocatalyst of photocatalytic H 2 generation activity of g-C 3 N 4 under visible light irradiation is studied. By using single-particle photoluminescence (PL) and femtosecond time-resolved transient absorption spectroscopies, charge transfer kinetics between g-C 3 N 4 and two kinds of nanostructured MoS 2 (nanodot and monolayer) are systematically investigated. Single-particle PL results show the emission of g-C 3 N 4 is quenched by MoS 2 nanodots more effectively than MoS 2 monolayers. Electron injection rate and efficiency of g-C 3 N 4 /MoS 2 -nanodot hybrid are calculated to be 5.96 × 10 9 s -1 and 73.3%, respectively, from transient absorption spectral measurement, which are 4.8 times faster and 2.0 times higher than those of g-C 3 N 4 /MoS 2 -monolayer hybrid. Stronger intimate junction between MoS 2 nanodots and g-C 3 N 4 is suggested to be responsible for faster and more efficient electron injection. In addition, more unsaturated terminal sulfur atoms can serve as the active site in MoS 2 nanodot compared with MoS 2 monolayer. Therefore, g-C 3 N 4 /MoS 2 nanodot exhibits a 7.9 times higher photocatalytic activity for H 2 evolution (660 µmol g- 1 h -1 ) than g-C 3 N 4 /MoS 2 monolayer (83.8 µmol g -1 h -1 ). This work provides deep insight into charge transfer between g-C 3 N 4 and nanostructured MoS 2 cocatalysts, which can open a new avenue for more rationally designing MoS 2 -based catalysts for H 2 evolution. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrokinetic remediation of plutonium-contaminated nuclear site wastes: results from a pilot-scale on-site trial.

PubMed

Agnew, Kieran; Cundy, Andrew B; Hopkinson, Laurence; Croudace, Ian W; Warwick, Phillip E; Purdie, Philip

2011-02-28

This paper examines the field-scale application of a novel low-energy electrokinetic technique for the remediation of plutonium-contaminated nuclear site soils, using soil wastes from the Atomic Weapons Establishment (AWE) Aldermaston site, Berkshire, UK as a test medium. Soils and sediments with varying composition, contaminated with Pu through historical site operations, were electrokinetically treated at laboratory-scale with and without various soil pre-conditioning agents. Results from these bench-scale trials were used to inform a larger on-site remediation trial, using an adapted containment pack with battery power supply. 2.4 m(3) (ca. 4t onnes) of Pu-contaminated soil was treated for 60 days at a power consumption of 33 kWh/m(3), and then destructively sampled. Radiochemical data indicate mobilisation of Pu in the treated soil, and migration (probably as a negatively charged Pu-citrate complex) towards the anodic compartment of the treatment cell. Soil in the cathodic zone of the treatment unit was remediated to a level below free-release disposal thresholds (1.7 Bq/g, or <0.4 Bq/g above background activities). The data show the potential of this method as a low-cost, on-site tool for remediation of radioactively contaminated soils and wastes which can be operated remotely on working sites, with minimal disruption to site infrastructure or operations. Copyright © 2010 Elsevier B.V. All rights reserved.

Characterization of Membrane Patch-Ion Channel Probes for Scanning Ion Conductance Microscopy.

PubMed

Shi, Wenqing; Zeng, Yuhan; Zhu, Cheng; Xiao, Yucheng; Cummins, Theodore R; Hou, Jianghui; Baker, Lane A

2018-05-01

Integration of dual-barrel membrane patch-ion channel probes (MP-ICPs) to scanning ion conductance microscopy (SICM) holds promise of providing a revolutionized approach of spatially resolved chemical sensing. A series of experiments are performed to further the understanding of the system and to answer some fundamental questions, in preparation for future developments of this approach. First, MP-ICPs are constructed that contain different types of ion channels including transient receptor potential vanilloid 1 and large conductance Ca2 + -activated K + channels to establish the generalizability of the methods. Next, the capability of the MP-ICP platforms in single ion channel activity measurements is proved. In addition, the interplay between the SICM barrel and the ICP barrel is studied. For ion channels gated by uncharged ligands, channel activity at the ICP barrel is unaffected by the SICM barrel potential; whereas for ion channels that are gated by charged ligands, enhanced channel activity can be obtained by biasing the SICM barrel at potentials with opposite polarity to the charge of the ligand molecules. Finally, a proof-of-principle experiment is performed and site-specific molecular/ionic flux sensing is demonstrated at single-ion-channel level, which show that the MP-ICP platform can be used to quantify local molecular/ionic concentrations. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Magnetic Photocatalyst BiVO₄/Mn-Zn ferrite/Reduced Graphene Oxide: Synthesis Strategy and Its Highly Photocatalytic Activity.

PubMed

Xie, Taiping; Li, Hui; Liu, Chenglun; Yang, Jun; Xiao, Tiancun; Xu, Longjun

2018-05-29

Magnetic photocatalyst BiVO₄/Mn-Zn ferrite (Mn 1- x Zn x Fe₂O₄)/reduced graphene oxide (RGO) was synthesized by a simple calcination and reduction method. The magnetic photocatalyst held high visible light-absorption ability with low band gap energy and wide absorption wavelength range. Electrochemical impedance spectroscopies illustrated good electrical conductivity which indicated low charge-transfer resistance due to incorporation of Mn 1- x Zn x Fe₂O₄ and RGO. The test of photocatalytic activity showed that the degradation ratio of rhodamine B (RhB) reached 96.0% under visible light irradiation after only 1.5 h reaction. The photocatalytic mechanism for the prepared photocatalyst was explained in detail. Here, the incorporation of RGO enhanced the specific surface area compared with BiVO4/Mn 1- x Zn x Fe₂O₄.The larger specific surface area provided more active surface sites, more free space to improve the mobility of photo-induced electrons, and further facilitated the effective migration of charge carriers, leading to the remarkable improvement of photocatalytic performance. Meanwhile, RGO was the effective acceptor as well as transporter of photo-generated electron hole pairs. •O₂ - was the most active species in the photocatalytic reaction. BiVO₄/Mn 1- x Zn x Fe₂O₄/RGO had quite a wide application in organic contaminants removal or environmental pollution control.

Polyelectrolyte coating on superparamagnetic iron oxide nanoparticles as interface between magnetic core and biorelevant media

PubMed Central

Farkas, Katalin; Földesi, Imre; Szekeres, Márta; Illés, Erzsébet; Tóth, Ildikó Y.; Nesztor, Daniel; Szabó, Tamás

2016-01-01

Nanoparticles do not exist in thermodynamical equilibrium because of high surface free energy, thus they have only kinetic stability. Spontaneous changes can be delayed by designed surface coating. In biomedical applications, superparamagnetic iron oxide nanoparticles (SPIONs) require an optimized coating in order to fulfil the expectation of medicine regulatory agencies and ultimately that of biocompatibility. In this work, we show the high surface reactivity of naked SPIONs due to ≡Fe–OH sites, which can react with H+/OH− to form pH- and ionic strength-dependent charges. We explain the post-coating of naked SPIONs with organic polyacids via multi-site complex bonds formed spontaneously. The excess polyacids can be removed from the medium. The free COOH groups in coating are prone to react with active biomolecules like proteins. Charging and pH- and salt-dependent behaviour of carboxylated SPIONs were characterized quantitatively. The interrelation between the coating quality and colloidal stability measured under biorelevant conditions is discussed. Our coagulation kinetics results allow us to predict colloidal stability both on storage and in use; however, a simpler method would be required to test SPION preparations. Haemocompatibility tests (smears) support our qualification for good and bad SPION manufacturing; the latter ‘promises’ fatal outcome in vivo. PMID:27920900

Redox-linked Conformational Dynamics in Apoptosis Inducing Factor

PubMed Central

Sevrioukova, Irina F.

2009-01-01

Apoptosis inducing factor (AIF) is a bifunctional mitochondrial flavoprotein critical for energy metabolism and induction of caspase-independent apoptosis, whose exact role in normal mitochondria remains unknown. Upon reduction with NADH, AIF undergoes dimerization and forms tight, long-lived FADH2-NAD charge-transfer complexes (CTC) proposed to be functionally important. To get a deeper insight into structure/function relations and redox mechanism of this vitally important protein, we determined the x-ray structures of oxidized and NADH-reduced forms of naturally folded recombinant murine AIF. Our structures reveal that CTC with the pyridine nucleotide is stabilized by (i) π-stacking interactions between coplanar nicotinamide, isoalloxazine and Phe309 rings, (ii) rearrangement of multiple aromatic residues in the C-terminal domain, likely serving as an electron delocalization site, and (iii) an extensive hydrogen-bonding network involving His453, a key residue undergoing a conformational switch to directly interact and orient the nicotinamide in position optimal for charge transfer. Via the His453-containing peptide, redox changes in the active site are transmitted to the surface, promoting AIF dimerization and restricting access to a primary nuclear localization signal through which the apoptogenic form is transported to the nucleus. Structural findings agree with the biochemical data and support the hypothesis that both normal and apoptogenic functions of AIF are controlled by NADH. PMID:19447115

Absence of ballistic charge transport in the half-filled 1D Hubbard model

NASA Astrophysics Data System (ADS)

Carmelo, J. M. P.; Nemati, S.; Prosen, T.

2018-05-01

Whether in the thermodynamic limit of lattice length L → ∞, hole concentration mηz = - 2 Sηz/L = 1 -ne → 0, nonzero temperature T > 0, and U / t > 0 the charge stiffness of the 1D Hubbard model with first neighbor transfer integral t and on-site repulsion U is finite or vanishes and thus whether there is or there is no ballistic charge transport, respectively, remains an unsolved and controversial issue, as different approaches yield contradictory results. (Here Sηz = - (L -Ne) / 2 is the η-spin projection and ne =Ne / L the electronic density.) In this paper we provide an upper bound on the charge stiffness and show that (similarly as at zero temperature), for T > 0 and U / t > 0 it vanishes for mηz → 0 within the canonical ensemble in the thermodynamic limit L → ∞. Moreover, we show that at high temperature T → ∞ the charge stiffness vanishes as well within the grand-canonical ensemble for L → ∞ and chemical potential μ →μu where (μ -μu) ≥ 0 and 2μu is the Mott-Hubbard gap. The lack of charge ballistic transport indicates that charge transport at finite temperatures is dominated by a diffusive contribution. Our scheme uses a suitable exact representation of the electrons in terms of rotated electrons for which the numbers of singly occupied and doubly occupied lattice sites are good quantum numbers for U / t > 0. In contrast to often less controllable numerical studies, the use of such a representation reveals the carriers that couple to the charge probes and provides useful physical information on the microscopic processes behind the exotic charge transport properties of the 1D electronic correlated system under study.

Trypsin treatment of reaction centers from Rhodobacter sphaeroides in the dark and under illumination: protein structural changes follow charge separation.

PubMed

Brzezinski, P; Andréasson, L E

1995-06-06

Reaction centers from Rhodobacter sphaeroides R-26 were treated with trypsin in the dark and during illumination (in the charge-separated state). Trypsination resulted in a time-dependent modification of the reaction centers, reflected in changes in the charge recombination rate, in the inhibition of QA- to QB electron transfer, and eventually to inhibition of charge separation. Comparisons of centers with ubiquinone or anthraquinone in the QA site, in which the charge recombination pathways are different, indicate that trypsination affects charges close to the QA(-)-binding site. Studies of light-induced voltage changes from moving charges in reaction centers incorporated in lipid layers on a Teflon film, a technique which allows the discrimination of effects on donor and acceptor sides, indicate that the acceptor side is preferentially degraded by trypsin in the dark. Tryptic digestion during illumination generally resulted in a marked strengthening and acceleration of the effects seen already during dark treatment, but new effects were also detected in gel electrophoretic peptide patterns, in optical spectra, and in the kinetic measurements. Optical kinetic measurements revealed that the donor side of the reaction centers became susceptible to modification by trypsin during illumination as seen in the value of the binding constant for soluble cytochrome c2 which increased by a factor of 2, whereas it was much less affected after trypsination of reaction centers in the dark. The influence of illumination on the rate and mode by which trypsin acts on reaction centers indicates that changes in the protein conformation follow charge separation.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparison of Wearable Activity Tracker with Actigraphy for Sleep Evaluation and Circadian Rest-Activity Rhythm Measurement in Healthy Young Adults.

PubMed

Lee, Hyun-Ah; Lee, Heon-Jeong; Moon, Joung-Ho; Lee, Taek; Kim, Min-Gwan; In, Hoh; Cho, Chul-Hyun; Kim, Leen

2017-03-01

The purpose of this study was to evaluate the applicability of data obtained from a wearable activity tracker (Fitbit Charge HR) to medical research. This was performed by comparing the wearable activity tracker (Fitbit Charge HR) with actigraphy (Actiwatch 2) for sleep evaluation and circadian rest-activity rhythm measurement. Sixteen healthy young adults (female participants, 62.5%; mean age, 22.8 years) wore the Fitbit Charge HR and the Actiwatch 2 on the same wrist; a sleep log was recorded over a 14-day period. We compared the sleep variables and circadian rest-activity rhythm measures with Wilcoxon signed-rank tests and Spearman's correlations. The periods and acrophases of the circadian rest-activity rhythms and the sleep start times did not differ and correlated significantly between the Fitbit Charge HR and the Actiwatch 2. The Fitbit Charge HR tended to overestimate the sleep durations compared with the Actiwatch 2. However, the sleep durations showed high correlation between the two devices for all days. We found that the Fitbit Charge HR showed high accuracy in sleep evaluation and circadian rest-activity rhythm measurement when compared with actigraphy for healthy young adults. The results suggest that the Fitbit Charge HR could be applicable on medical research as an alternative tool to actigraphy for sleep evaluation and measurement of the circadian rest-activity rhythm.

An Analytical Planning Model to Estimate the Optimal Density of Charging Stations for Electric Vehicles

PubMed Central

Ahn, Yongjun; Yeo, Hwasoo

2015-01-01

The charging infrastructure location problem is becoming more significant due to the extensive adoption of electric vehicles. Efficient charging station planning can solve deeply rooted problems, such as driving-range anxiety and the stagnation of new electric vehicle consumers. In the initial stage of introducing electric vehicles, the allocation of charging stations is difficult to determine due to the uncertainty of candidate sites and unidentified charging demands, which are determined by diverse variables. This paper introduces the Estimating the Required Density of EV Charging (ERDEC) stations model, which is an analytical approach to estimating the optimal density of charging stations for certain urban areas, which are subsequently aggregated to city level planning. The optimal charging station’s density is derived to minimize the total cost. A numerical study is conducted to obtain the correlations among the various parameters in the proposed model, such as regional parameters, technological parameters and coefficient factors. To investigate the effect of technological advances, the corresponding changes in the optimal density and total cost are also examined by various combinations of technological parameters. Daejeon city in South Korea is selected for the case study to examine the applicability of the model to real-world problems. With real taxi trajectory data, the optimal density map of charging stations is generated. These results can provide the optimal number of chargers for driving without driving-range anxiety. In the initial planning phase of installing charging infrastructure, the proposed model can be applied to a relatively extensive area to encourage the usage of electric vehicles, especially areas that lack information, such as exact candidate sites for charging stations and other data related with electric vehicles. The methods and results of this paper can serve as a planning guideline to facilitate the extensive adoption of electric vehicles. PMID:26575845

Human Health and Ecological Risk Assessment for the Operation of the Explosives Waste Treatment Facility at Site 300 of the Lawrence Livermore National Laboratory Volume 1: Report of Results

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

Gallegos, G; Daniels, J; Wegrecki, A

2006-04-24

This document contains the human health and ecological risk assessment for the Resource Recovery and Conservation Act (RCRA) permit renewal for the Explosives Waste Treatment Facility (EWTF). Volume 1 is the text of the risk assessment, and Volume 2 (provided on a compact disc) is the supporting modeling data. The EWTF is operated by the Lawrence Livermore National Laboratory (LLNL) at Site 300, which is located in the foothills between the cities of Livermore and Tracy, approximately 17 miles east of Livermore and 8 miles southwest of Tracy. Figure 1 is a map of the San Francisco Bay Area, showingmore » the location of Site 300 and other points of reference. One of the principal activities of Site 300 is to test what are known as ''high explosives'' for nuclear weapons. These are the highly energetic materials that provide the force to drive fissionable material to criticality. LLNL scientists develop and test the explosives and the integrated non-nuclear components in support of the United States nuclear stockpile stewardship program as well as in support of conventional weapons and the aircraft, mining, oil exploration, and construction industries. Many Site 300 facilities are used in support of high explosives research. Some facilities are used in the chemical formulation of explosives; others are locations where explosive charges are mechanically pressed; others are locations where the materials are inspected radiographically for such defects as cracks and voids. Finally, some facilities are locations where the machined charges are assembled before they are sent to the on-site test firing facilities, and additional facilities are locations where materials are stored. Wastes generated from high-explosives research are treated by open burning (OB) and open detonation (OD). OB and OD treatments are necessary because they are the safest methods for treating explosives wastes generated at these facilities, and they eliminate the requirement for further handling and transportation that would be required if the wastes were treated off site.« less

Optical and thermal charge-transfer processes occurring in a series of three-centered, cyanide-bridged intervalent charge-transfer complexes

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

Pfennig, B.W.; Bocarsly, A.B.

1992-01-09

The mixed-valent compound (Pt(NH{sub 3}){sub 4}){sub 2}((NC){sub 5}Fe-CN-Pt(NH{sub 3}){sub 4}-NC-Fe(CN){sub 5} was used as the starting point for the synthesis and characterization of two series of trinuclear {open_quotes}M-Pt-M{close_quotes} compounds. The first group of complexes have the general formula Na{sub 2}(L(NC){sub 4}Fe-CN-Pt(NH{sub 3}){sub 4}-NC-Fe(CN){sub 4}L) (where the sixth coordination site on the terminal iron units has been varied using six different substituted pyridine or pyrazine ligands, L), and the secondary group of compounds have the general formula (Pt(NH){sub 3}){sub 4}){sub 2}((NC){sub 5}M-CN-Pt(NH{sub 3}){sub 4}-NC-M(CN){sub 5}) (where M = Fe, Ru, and Os). All of the compounds yielded an absorption spectrum containingmore » an intervalent charge-transfer (IT) band in the visible. Both series of complexes were modeled using Marcus-Hush theory to estimate the reorganization energies for the optical electron-transfer processes, electron-transfer rate constants, thermal-activation barriers, and the degrees of delocalization of these species. In addition, the kinetics of formation, photochemical decomposition, and a novel solvent-gated charge-transfer process are discussed. 26 refs., 10 figs., 4 tabs.« less

High-energy Collision-induced Dissociation by MALDI TOF/TOF Causes Charge-Remote Fragmentation of Steroid Sulfates

PubMed Central

Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B.; Holy, Timothy E.; Gross, Michael L.

2014-01-01

A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote-fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers. PMID:24781458

High-energy collision-induced dissociation by MALDI TOF/TOF causes charge-remote fragmentation of steroid sulfates.

PubMed

Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B; Holy, Timothy E; Gross, Michael L

2014-08-01

A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids, including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers.

Extracellular determinants of anion discrimination of the Cl-/H+ antiporter protein CLC-5.

PubMed

De Stefano, Silvia; Pusch, Michael; Zifarelli, Giovanni

2011-12-23

Mammalian CLC proteins comprise both Cl- channels and Cl-/H+ antiporters that carry out fundamental physiological tasks by transporting Cl- across plasma membrane and intracellular compartments. The NO3- over Cl- preference of a plant CLC transporter has been pinpointed to a conserved serine residue located at Scen and it is generally assumed that the other two binding sites of CLCs, Sext and Sin, do not substantially contribute to anion selectivity. Here we show for the Cl-/H+ antiporter CLC-5 that the conserved and extracellularly exposed Lys210 residue is critical to determine the anion specificity for transport activity. In particular, mutations that neutralize or invert the charge at this position reverse the NO3- over Cl- preference of WT CLC-5 at a concentration of 100 mm, but do not modify the coupling stoichiometry with H+. The importance of the electrical charge is shown by chemical modification of K210C with positively charged cysteine-reactive compounds that reintroduce the WT preference for Cl-. At saturating extracellular anion concentrations, neutralization of Lys210 is of little impact on the anion preference, suggesting an important role of Lys210 on the association rate of extracellular anions to Sext.

C@SiNW/TiO2 Core-Shell Nanoarrays with Sandwiched Carbon Passivation Layer as High Efficiency Photoelectrode for Water Splitting

PubMed Central

Devarapalli, Rami Reddy; Debgupta, Joyashish; Pillai, Vijayamohanan K.; Shelke, Manjusha V.

2014-01-01

One-dimensional heterostructure nanoarrays are efficiently promising as high performance electrodes for photo electrochemical (PEC) water splitting applications, wherein it is highly desirable for the electrode to have a broad light absorption, efficient charge separation and redox properties as well as defect free surface with high area suitable for fast interfacial charge transfer. We present highly active and unique photoelectrode for solar H2 production, consisting of silicon nanowires (SiNWs)/TiO2 core-shell structures. SiNWs are passivated to reduce defect sites and protected against oxidation in air or water by forming very thin carbon layer sandwiched between SiNW and TiO2 surfaces. This carbon layer decreases recombination rates and also enhances the interfacial charge transfer between the silicon and TiO2. A systematic investigation of the role of SiNW length and TiO2 thickness on photocurrent reveals enhanced photocurrent density up to 5.97 mA/cm2 at 1.0 V vs.NHE by using C@SiNW/TiO2 nanoarrays with photo electrochemical efficiency of 1.17%. PMID:24810865

Enhanced Charge Collection in MOF‐525–PEDOT Nanotube Composites Enable Highly Sensitive Biosensing

PubMed Central

Huang, Tzu‐Yen; Kung, Chung‐Wei; Liao, Yu‐Te; Kao, Sheng‐Yuan; Cheng, Mingshan; Chang, Ting‐Hsiang; Henzie, Joel; Alamri, Hatem R.; Alothman, Zeid A.

2017-01-01

Abstract With the aim of a reliable biosensing exhibiting enhanced sensitivity and selectivity, this study demonstrates a dopamine (DA) sensor composed of conductive poly(3,4‐ethylenedioxythiophene) nanotubes (PEDOT NTs) conformally coated with porphyrin‐based metal–organic framework nanocrystals (MOF‐525). The MOF‐525 serves as an electrocatalytic surface, while the PEDOT NTs act as a charge collector to rapidly transport the electron from MOF nanocrystals. Bundles of these particles form a conductive interpenetrating network film that together: (i) improves charge transport pathways between the MOF‐525 regions and (ii) increases the electrochemical active sites of the film. The electrocatalytic response is measured by cyclic voltammetry and differential pulse voltammetry techniques, where the linear concentration range of DA detection is estimated to be 2 × 10−6–270 × 10−6 m and the detection limit is estimated to be 0.04 × 10−6 m with high selectivity toward DA. Additionally, a real‐time determination of DA released from living rat pheochromocytoma cells is realized. The combination of MOF5‐25 and PEDOT NTs creates a new generation of porous electrodes for highly efficient electrochemical biosensing. PMID:29201623

Multilayer Black Phosphorus Exfoliated with the Aid of Sodium Hydroxide: An Improvement in Electrochemical Energy Storage

NASA Astrophysics Data System (ADS)

Liu, Wanying; Zhu, Yabo; Chen, Zhiyan; Lei, Jia; Feng, Peizhong

2018-05-01

We generated multilayer black phosphorus (MBP) as a precipitate in centrifugation under 3000 rpm for 25 min, preceded by liquid exfoliation, in which saturated sodium hydroxide (NaOH(s)) was added as an exfoliation auxiliary. The MBP exfoliated with NaOH(s) was characterized by scanning electron microscope, energy dispersive x-ray detector, x-ray diffraction, x-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy. Its electrochemical performance was investigated by cyclic voltammetry, charge/discharge and electrochemical impedance spectroscopy. It was found that the appropriate amount of NaOH(s) can make MBP present a ladder-shaped structure or plackets on the layer edge, which may provide more active sites and channels for charge storage to improve its electrochemical performance. The specific capacitance of MBP samples exfoliated with appropriate amounts of NaOH(s) can quickly enter a relatively stable range of 110-90 F/g after the 75th cycle, and finally stabilize at about 90 F/g after thousands of cycles under the current density of 2 A/g, which demonstrates their good stability in the range of long charge/discharge cycles. MBP exhibits double-layer capacitance properties.

Investigation of the charge-orbital ordering mechanism in single-layered Pr0.5Ca1.5MnO4

NASA Astrophysics Data System (ADS)

Rangkuti, C. N.; Majidi, M. A.

2018-04-01

Motivated by the experimental study of half-doped single-layered Pr0.5Ca1.5MnO4 showing charge, orbital, and spin orderings [1], we propose a model to theoretically study the system to explain such ordering phenomena. The ground state electron configuration reveals that the charges form a checkerboard pattern with alternating Mn3+/Mn4+ sites, while the orbitals are aligned in zigzag chains [1, 2]. We calculate the ground state energy of this system to find the most preferable configuration by comparing three types of configurations (charge-unordered, charge-ordered, and charge-orbital-ordered states). The calculations are based on a tight-binding model representing effective electron hoppings among Mn ions in MnO2-plane. We take into account the horizontally- and vertically-oriented orbital and spin degrees of freedom at Mn sites. We assume that the hopping integral values depend on the relative orientation between the corresponding orbitals of adjacent Mn ions. The interaction terms we incorporate into our effective Hamiltonian include inter-orbital, intra-orbital Hubbard repulsions, and Jahn-Teller distortion [2]. We absorb the exchange interaction between spins into local self-energy that we calculate within dynamical mean field algorithm [2]. Within our model we show a circumstance in which the charge-orbital ordered configuration has the lowest energy, consistent with the ground state ordering revealed by the experimental data.

Site-directed mutagenesis of serine 158 demonstrates its role in spinach leaf sucrose-phosphate synthase modulation

NASA Technical Reports Server (NTRS)

Toroser, D.; McMichael, R. Jr; Krause, K. P.; Kurreck, J.; Sonnewald, U.; Stitt, M.; Huber, S. C.; Davies, E. (Principal Investigator)

1999-01-01

Site-directed mutagenesis of spinach sucrose-phosphate synthase (SPS) was performed to investigate the role of Ser158 in the modulation of spinach leaf SPS. Tobacco plants expressing the spinach wild-type (WT), S158A, S158T and S157F/S158E SPS transgenes were produced. Expression of transgenes appeared not to reduce expression of the tobacco host SPS. SPS activity in the WT and the S158T SPS transgenics showed light/dark modulation, whereas the S158A and S157F/S158E mutants were not similarly light/dark modulated: the S158A mutant enzyme was not inactivated in the dark, and the S157F/S158E was not activated in the light. The inability to modulate the activity of the S158A mutant enzyme by protein phosphorylation was demonstrated in vitro. The WT spinach enzyme immunopurified from dark transgenic tobacco leaves had a low initial activation state, and could be activated by PP2A and subsequently inactivated by SPS-kinase plus ATP. Rapid purification of the S158A mutant enzyme from dark leaves of transgenic plants using spinach-specific monoclonal antibodies yielded enzyme that had a high initial activation state, and pre-incubation with leaf PP2A or ATP plus SPS-kinase (the PKIII enzyme) caused little modulation of activity. The results demonstrate the regulatory significance of Ser158 as the major site responsible for dark inactivation of spinach SPS in vivo, and indicate that the significance of phosphorylation is the introduction of a negative charge at the Ser158 position.

Active pixel sensor array with electronic shuttering

NASA Technical Reports Server (NTRS)

Fossum, Eric R. (Inventor)

2002-01-01

An active pixel cell includes electronic shuttering capability. The cell can be shuttered to prevent additional charge accumulation. One mode transfers the current charge to a storage node that is blocked against accumulation of optical radiation. The charge is sampled from a floating node. Since the charge is stored, the node can be sampled at the beginning and the end of every cycle. Another aspect allows charge to spill out of the well whenever the charge amount gets higher than some amount, thereby providing anti blooming.

76 FR 75522 - Notice of a Public Meeting of the Wyoming Advisory Committee to the U.S. Commission on Civil Rights

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-02

... wireless lines, and the Commission will not refund any incurred charges. Callers will incur no charge for... work of the Committee are directed to the Commission's Web site, http://www.usccr.gov , or may contact...

Glomerular anionic site distribution in nonproteinuric rats. A computer-assisted morphometric analysis.

PubMed

Pilia, P A; Swain, R P; Williams, A V; Loadholt, C B; Ainsworth, S K

1985-12-01

The cationic ultrastructural tracer polyethyleneimine (PEI: pI approximately equal to 11.0), binds electrophysically to uniformly spaced discrete electron-dense anionic sites present in the laminae rarae of the rat glomerular basement membrane (GBM), mesangial reflections of the GBM, Bowman's capsule, and tubular basement membranes when administered intravenously. Computer-assisted morphometric analysis of glomerular anionic sites reveals that the maximum concentration of stainable lamina rara externa (lre) sites (21/10,000 A GBM) occurs 60 minutes after PEI injection with a site-site interspacing of 460 A. Lamina rara interna (lri) sites similarly demonstrate a maximum concentration (20/10,000 A GBM) at 60 minutes with a periodicity of 497 A. The concentration and distribution of anionic sites within the lri was irregular in pattern and markedly decreased in number, while the lre possesses an electrical field that is highly regular at all time intervals analyzed (15, 30, 60, 120, 180, 240, and 300 minutes). Immersion and perfusion of renal tissue with PEI reveals additional heavy staining of the epithelial and endothelial cell sialoprotein coatings. PEI appears to bind to glomerular anionic sites reversibly: ie, between 60 and 180 minutes the concentration of stained sites decreases. At 300 minutes, the interspacing once again approaches the 60-minute concentration. This suggests a dynamic turnover or dissociation followed by a reassociation of glomerular negatively charged PEI binding sites. In contrast, morphometric analysis of anionic sites stained with lysozyme and protamine sulfate reveals interspacings of 642 A and 585 A, respectively; in addition, these tracers produce major glomerular ultrastructural alterations and induce transient proteinuria. PEI does not induce proteinuria in rats, nor does it produce glomerular morphologic alterations when ten times the tracer dosage is administered intravenously. These findings indicate that the choice of ultrastructural charge tracer, the method of administering the tracer, and the time selected for analysis of tissue after administration of tracer significantly influences results. Morphometric analysis of the distribution of glomerular anionic sites in nonproteinuric rats provides a method of evaluating quantitative alterations of the glomerular charge barrier in renal disease models.

Organic and inorganic molecules as probes of mineral surfaces (Invited)

NASA Astrophysics Data System (ADS)

Sverjensky, D. A.

2010-12-01

Although the multi-site nature of mineral surfaces is to be expected based on the underlying crystal structure, definitive evidence of the need to use more than one site in modelling proton surface charge or adsorption of a single adsorbate at the mineral-water interface is lacking. Instead, a single-site approach affords a practical way of averaging over all possible crystal planes and sites in a powdered mineral sample. Extensive analysis of published proton surface charge and adsorption of metals on oxide mineral surfaces can be undertaken with a single site density for each mineral based on tritium exchange or estimation from averages of the site densities of likely exposed surfaces. Even in systems with competing metals (e.g. Cu and Pb on hematite), the same site density as used for proton surface charge can be employed depending on the reaction stoichiometry. All of this indicates that protons and metals can bind to a great variety of sites with the same overall site density. However, simple oxyanions such as carbonate, sulfate, selenate, arsenate and arsenite require a much lower site density for a given mineral. For example, on goethite these oxyanions utilize a site density that correlates with the BET surface area of the goethite. In this way, the oxyanions can be thought of as selectively probing the available sites on the mineral. The correlation probably arises because goethites with different BET surface areas have different proportions of singly and multiply-bonded oxygens, and only the singly-bonded oxygens are useful for inner-sphere surface complexation by the ligand exchange mechanism. Small organic molecules behave in a remarkably similar way. For example, adsorption of oxalate on goethite, and aspartate, glutamate, dihydroxyphenylalanine, lysine and arginine on rutile are all consistent with a much smaller site density than those required for metals such as calcium or neodymium. Overall, these results suggest that both inorganic oxyanions and organic molecules containing carboxylate functional groups serve as much more sensitive probes of the surface structures of minerals than do protons or metals.

Do surfaces of positive electrostatic potential on different halogen derivatives in molecules attract? like attracting like!

PubMed

Varadwaj, Arpita; Varadwaj, Pradeep R; Yamashita, Koichi

2018-03-15

Coulomb's law states that like charges repel, and unlike charges attract. However, it has recently been theoretically revealed that two similarly charged conducting spheres will almost always attract each other when both are in close proximity. Using multiscale first principles calculations, we illustrate practical examples of several intermolecular complexes that are formed by the consequences of attraction between positive atomic sites of similar or dissimilar electrostatic surface potential on interacting molecules. The results of the quantum theory of atoms in molecules and symmetry adapted perturbation theory support the attraction between the positive sites, characterizing the F•••X (X = F, Cl, Br) intermolecular interactions in a series of 20 binary complexes as closed-shell type, although the molecular electrostatic surface potential approach does not (a failure!). Dispersion that has an r -6 dependence, where r is the equilibrium distance of separation, is found to be the sole driving force pushing the two positive sites to attract. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

pH Dependence of a Mammalian Polyamine Oxidase: Insights into Substrate Specificity and the Role of Lysine 315†

PubMed Central

Pozzi, Michelle Henderson; Gawandi, Vijay; Fitzpatrick, Paul F.

2009-01-01

Mammalian polyamine oxidases (PAO) catalyze the oxidation of N1-acetylspermine and N1-acetylspermidine to produce N-acetyl-3-aminopropanaldehyde and spermidine or putrescine. Structurally, PAO is a member of the monoamine oxidase family of flavoproteins. The effects of pH on kinetic parameters of mouse PAO have been determined to provide insight into the protonation state of the polyamine required for catalysis and the roles of ionizable residues in the active site in amine oxidation. For N1-acetylspermine, N1-acetylspermidine, and spermine, the kcat/Kamine-pH profiles are bell-shaped. In each case the profile agrees with that expected if the productive form of the substrate has a single positively charged nitrogen. The pKi-pH profiles for a series of polyamine analogs are most consistent with the nitrogen at the site of oxidation being neutral and one other nitrogen being positively charged in the reactive form of the substrate. With N1-acetylspermine as substrate, the value of kred, the limiting rate constant for flavin reduction, is pH dependent, decreasing below a pKa value of 7.3, again consistent with the requirement for an uncharged nitrogen for substrate oxidation. Lys315 in PAO corresponds to a conserved active site residue found throughout the monoamine oxidase family. Mutation of Lys315 to methionine has no effect on the kcat/Kamine profile for spermine, the kred value with N1-acetylspermine is only 1.8-fold lower in the mutant protein, and the pKa in the kred-pH profile with N1-acetylspermine shifts to 7.8. These results rule out Lys315 as a source of a pKa in the kcat/Kamine or kcat/kred profiles. They also establish that this residue does not play a critical role in amine oxidation by PAO. PMID:19199575

Proton transport facilitating water-oxidation: the role of second sphere ligands surrounding the catalytic metal cluster.

PubMed

Bao, Han; Dilbeck, Preston L; Burnap, Robert L

2013-10-01

The ability of PSII to extract electrons from water, with molecular oxygen as a by-product, is a remarkable biochemical and evolutionary innovation. From an evolutionary perspective, the invention of PSII approximately 2.7 Ga led to the accelerated accumulation of biomass in the biosphere and the accumulation of oxygen in the atmosphere, a combination that allowed for the evolution of a much more complex and extensive biosphere than would otherwise have been possible. From the biochemical and enzymatic perspective, PSII is remarkable because of the thermodynamic and kinetic obstacles that needed to have been overcome to oxidize water as the ultimate photosynthetic electron donor. This article focuses on how proton release is an integral part of how these kinetic and thermodynamic obstacles have been overcome: the sequential removal of protons from the active site of H2O-oxidation facilitates the multistep oxidation of the substrate water at the Mn4CaOx, the catalytic heart of the H2O-oxidation reaction. As noted previously, the facilitated deprotonation of the Mn4CaOx cluster exerts a redox-leveling function preventing the accumulation of excess positive charge on the cluster, which might otherwise hinder the already energetically difficult oxidation of water. Using recent results, including the characteristics of site-directed mutants, the role of the second sphere of amino acid ligands and the associated network of water molecules surrounding the Mn4CaOx is discussed in relation to proton transport in other systems. In addition to the redox-leveling function, a trapping function is assigned to the proton release step occurring immediately prior to the dioxygen chemistry. This trapping appears to involve a yet-to-be clarified gating mechanism that facilitates to coordinated release of a proton from the neighborhood of the active site thereby insuring that the backward charge-recombination reaction does not out-compete the forward reaction of dioxygen chemistry during this final step of H2O-oxidation.

Vibrational spectroscopic and DFT calculation studies of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile.

PubMed

Premkumar, S; Jawahar, A; Mathavan, T; Kumara Dhas, M; Milton Franklin Benial, A

2015-03-05

The vibrational spectra of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile were recorded using fourier transform-infrared and fourier transform-Raman spectrometer. The optimized structural parameters, vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals, thermodynamic properties, temperature dependence of thermodynamic parameters, first order hyperpolarizability and natural bond orbital calculations of the molecule were performed using the Gaussian 09 program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using the VEDA 4.0 program. The calculated first order hyperpolarizability of ABOBPC molecule was obtained as 6.908×10(-30) issue, which was 10.5 times greater than urea. The nonlinear optical activity of the molecule was also confirmed by the frontier molecular orbitals and natural bond orbital analysis. The frontier molecular orbitals analysis shows that the lower energy gap of the molecule, which leads to the higher value of first order hyperpolarizability. The natural bond orbital analysis indicates that the nonlinear optical activity of the molecule arises due to the π→π(∗) transitions. The Mulliken atomic charge distribution confirms the presence of intramolecular charge transfer within the molecule. The reactive site of the molecule was predicted from the molecular electrostatic potential contour map. The values of thermo dynamic parameters were increasing with increasing temperature. Copyright © 2014 Elsevier B.V. All rights reserved.

Mechanism of Flavoprotein l-6-Hydroxynicotine Oxidase: pH and Solvent Isotope Effects and Identification of Key Active Site Residues.

PubMed

Fitzpatrick, Paul F; Chadegani, Fatemeh; Zhang, Shengnan; Dougherty, Vi

2017-02-14

The flavoenzyme l-6-hydroxynicotine oxidase is a member of the monoamine oxidase family that catalyzes the oxidation of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine during microbial catabolism of nicotine. While the enzyme has long been understood to catalyze oxidation of the carbon-carbon bond, it has recently been shown to catalyze oxidation of a carbon-nitrogen bond [Fitzpatrick, P. F., et al. (2016) Biochemistry 55, 697-703]. The effects of pH and mutagenesis of active site residues have now been utilized to study the mechanism and roles of active site residues. Asn166 and Tyr311 bind the substrate, while Lys287 forms a water-mediated hydrogen bond with flavin N5. The N166A and Y311F mutations result in ∼30- and ∼4-fold decreases in k cat /K m and k red for (S)-6-hydroxynicotine, respectively, with larger effects on the k cat /K m value for (S)-6-hydroxynornicotine. The K287M mutation results in ∼10-fold decreases in these parameters and a 6000-fold decrease in the k cat /K m value for oxygen. The shapes of the pH profiles are not altered by the N166A and Y311F mutations. There is no solvent isotope effect on the k cat /K m value for amines. The results are consistent with a model in which both the charged and neutral forms of the amine can bind, with the former rapidly losing a proton to a hydrogen bond network of water and amino acids in the active site prior to the transfer of hydride to the flavin.

Screening and identification of potential PTP1B allosteric inhibitors using in silico and in vitro approaches.

PubMed

Shinde, Ranajit Nivrutti; Kumar, G Siva; Eqbal, Shahbaz; Sobhia, M Elizabeth

2018-01-01

Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for Type 2 diabetes due to its specific role as a negative regulator of insulin signaling pathways. Discovery of active site directed PTP1B inhibitors is very challenging due to highly conserved nature of the active site and multiple charge requirements of the ligands, which makes them non-selective and non-permeable. Identification of the PTP1B allosteric site has opened up new avenues for discovering potent and selective ligands for therapeutic intervention. Interactions made by potent allosteric inhibitor in the presence of PTP1B were studied using Molecular Dynamics (MD). Computationally optimized models were used to build separate pharmacophore models of PTP1B and TCPTP, respectively. Based on the nature of interactions the target residues offered, a receptor based pharmacophore was developed. The pharmacophore considering conformational flexibility of the residues was used for the development of pharmacophore hypothesis to identify potentially active inhibitors by screening large compound databases. Two pharmacophore were successively used in the virtual screening protocol to identify potential selective and permeable inhibitors of PTP1B. Allosteric inhibition mechanism of these molecules was established using molecular docking and MD methods. The geometrical criteria values confirmed their ability to stabilize PTP1B in an open conformation. 23 molecules that were identified as potential inhibitors were screened for PTP1B inhibitory activity. After screening, 10 molecules which have good permeability values were identified as potential inhibitors of PTP1B. This study confirms that selective and permeable inhibitors can be identified by targeting allosteric site of PTP1B.

Unusual conformation of the SxN motif in the crystal structure of penicillin-binding protein A from Mycobacterium tuberculosis.

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

Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher

PBPA from Mycobacterium tuberculosis is a class B-like penicillin-binding protein (PBP) that is not essential for cell growth in M. tuberculosis, but is important for proper cell division in Mycobacterium smegmatis. We have determined the crystal structure of PBPA at 2.05 {angstrom} resolution, the first published structure of a PBP from this important pathogen. Compared to other PBPs, PBPA has a relatively small N-terminal domain, and conservation of a cluster of charged residues within this domain suggests that PBPA is more related to class B PBPs than previously inferred from sequence analysis. The C-terminal domain is a typical transpeptidase foldmore » and contains the three conserved active-site motifs characterisitic of penicillin-interacting enzymes. While the arrangement of the SxxK and KTG motifs is similar to that observed in other PBPs, the SxN motif is markedly displaced away from the active site, such that its serine (Ser281) is not involved in hydrogen bonding with residues of the other two motifs. A disulfide bridge between Cys282 (the 'x' of the SxN motif) and Cys266, which resides on an adjacent loop, may be responsible for this unusual conformation. Another interesting feature of the structure is a relatively long connection between {beta}5 and {alpha}11, which restricts the space available in the active site of PBPA and suggests that conformational changes would be required to accommodate peptide substrate or {beta}-lactam antibiotics during acylation. Finally, the structure shows that one of the two threonines postulated to be targets for phosphorylation is inaccessible (Thr362), whereas the other (Thr437) is well placed on a surface loop near the active site.« less

Environment sensitive fluorescent analogue of biologically active oxazoles differentially recognizes human serum albumin and bovine serum albumin: Photophysical and molecular modeling studies

NASA Astrophysics Data System (ADS)

Maiti, Jyotirmay; Biswas, Suman; Chaudhuri, Ankur; Chakraborty, Sandipan; Chakraborty, Sibani; Das, Ranjan

2017-03-01

An environment sensitive fluorophore, 4-(5-(4-(dimethylamino)phenyl)oxazol-2-yl)benzoic acid (DMOBA), that closely mimics biologically active 2,5-disubstituited oxazoles has been designed to probe two homologous serum proteins, human serum albumin (HSA) and bovine serum albumin (BSA) by means of photophysical and molecular modeling studies. This fluorescent analogue exhibits solvent polarity sensitive fluorescence due to an intramolecular charge transfer in the excited state. In comparison to water, the steady state emission spectra of DMOBA in BSA is characterized by a greater blue shift ( 10 nm) and smaller Stokes' shift ( 5980 cm- 1) in BSA than HSA (Stokes'shift 6600 cm- 1), indicating less polar and more hydrophobic environment of the dye in the former than the latter. The dye-protein binding interactions are remarkably stronger for BSA than HSA which is evident from higher value of the association constant for the DMOBA-BSA complex (Ka 5.2 × 106 M- 1) than the DMOBA-HSA complex (Ka 1.0 × 106 M- 1). Fӧrster resonance energy transfer studies revealed remarkably less efficient energy transfer (8%) between the donor tryptophans in BSA and the acceptor DMOBA dye than that (30%) between the single tryptophan moiety in HSA and the dye, which is consistent with a much larger distance between the donor (tryptophan)-acceptor (dye) pair in BSA (34.5 Å) than HSA (25.4 Å). Site specific competitive binding assays have confirmed on the location of the dye in Sudlow's site II of BSA and in Sudlow's site I of HSA, respectively. Molecular modeling studies have shown that the fluorescent analogue is tightly packed in the binding site of BSA due to strong steric complementarity, where, binding of DMOBA to BSA is primarily dictated by the van der Waals and hydrogen bonding interactions. In contrast, in HSA the steric complementarity is less significant and binding is primarily guided by polar interactions and van der Waals interactions appear to be less significant in the formation of the HSA-DMOBA complex. Electrostatic interactions contribute significantly in the binding of DMOBA to HSA (- 2.09 kcal/mol) compared to BSA (- 0.47 kcal/mol). Electrostatic surface potential calculation reveals that the DMOBA binding site within HSA is highly charged compared to BSA.

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

On Born's Conjecture about Optimal Distribution of Charges for an Infinite Ionic Crystal

NASA Astrophysics Data System (ADS)

Bétermin, Laurent; Knüpfer, Hans

2018-04-01

We study the problem for the optimal charge distribution on the sites of a fixed Bravais lattice. In particular, we prove Born's conjecture about the optimality of the rock salt alternate distribution of charges on a cubic lattice (and more generally on a d-dimensional orthorhombic lattice). Furthermore, we study this problem on the two-dimensional triangular lattice and we prove the optimality of a two-component honeycomb distribution of charges. The results hold for a class of completely monotone interaction potentials which includes Coulomb-type interactions for d≥3 . In a more general setting, we derive a connection between the optimal charge problem and a minimization problem for the translated lattice theta function.

Dimeric Fe (II, III) complex of quinoneoxime as functional model of PAP enzyme: Mössbauer, magneto-structural and DNA cleavage studies

NASA Astrophysics Data System (ADS)

Salunke-Gawali, Sunita; Ahmed, Khursheed; Varret, François; Linares, Jorge; Zaware, Santosh; Date, Sadgopal; Rane, Sandhya

2008-07-01

Purple acid phosphatase, ( PAP), is known to contain dinuclear Fe2 + 2, + 3 site with characteristic Fe + 3 ← Tyr ligand to metal charge transfer in coordination. Phthiocoloxime (3-methyl-2-hydroxy-1,4-naphthoquinone-1-oxime) ligand L, mimics (His/Tyr) ligation with controlled and unique charge transfers resulting in valence tautomeric coordination with mixed valent diiron site in model compound Fe-1: [μ-OH-Fe2 + 2, + 3 ( o-NQCH3ox) ( o-NSQCH3ox)2 (CAT) H2O]. Fe-2: [Fe + 3( o-NQCH3ox) ( p-NQCH3ox)2]2 a molecularly associated dimer of phthiocoloxime synthesized for comparison of charge transfer. 57Fe Mössbauer studies was used to quantitize unusual valences due to ligand in dimeric Fe-1 and Fe-2 complexes which are supported by EPR and SQUID studies. 57Fe Mössbauer spectra for Fe-1 at 300 K indicates the presence of two quadrupole split asymmetric doublets due to the differences in local coordination geometries of [Fe + 3]A and [Fe + 2]B sites. The hyperfine interaction parameters are δ A = 0.152, (Δ E Q)A = 0.598 mm/s with overlapping doublet at δ B = 0.410 and (Δ E Q)B = 0.468 mm/s. Due to molecular association tendency of ligand, dimer Fe-2 possesses 100% Fe + 3(h.s.) hexacoordinated configuration with isomer shift δ = 0.408 mm/s. Slightly distorted octahedral symmetry created by NQCH3ox ligand surrounding Fe + 3(h.s.) state generates small field gradient indicated by quadrupole split Δ E Q = 0.213 mm/s. Decrease of isomer shifts together with variation of quadrupole splits with temperature in Fe-1 dimer compared to Fe-2 is result of charge transfers in [Fe2 + 2, + 3 SQ] complexes. EPR spectrum of Fe-1 shows two strong signals at g 1 = 4.17 and g 2 = 2.01 indicative of S = 3/2 spin state with an intermediate spin of Fe + 3(h.s.) configuration. SQUID data of χ _m^{corr} .T were best fitted by using HDVV spin pair model S = 2, 3/2 resulting in antiferromagnetic exchange ( J = -13.5 cm - 1 with an agreement factor of R = 1.89 × 10 - 5). The lower J value of antiferromagnetic exchange leads to Fe+3μ-(OH) Fe + 2 bridging in Fe-1 dimer instead of μ-oxo bridge. The intermolecular association through H-bonds may lead to weakly coupled antiferromagnetic interaction between two Fe-2 molecules having Fe + 3(h.s.) centers. Using S = 5/2, 5/2 spin pair model we obtained best-fitted parameters such as J = -12.4 cm - 1, g = 2.3 with R = 3.58 × 10 - 5. Synthetic strategy results in non-equivalent iron sites in Fe-1 dimer analogues to PAP enzyme hence its reconstitution results in pUC-19 DNA cleavage activity, as physiological functionality of APase. It is compared with nuclease activity of Fe-2 RAPase.

75 FR 2850 - Notice of Proposed New Fee Sites; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-19

... planning to charge fees at eight recreation sites. All sites have recently been reconstructed or amenities... Springs Guard Station will be available for overnight rental. A financial analysis is being completed to... improve deteriorating resource conditions and recreation experiences. A financial analysis is being...

Structure-electrochemical evolution of a Mn-rich P2 Na 2/3Fe 0.2Mn 0.8O 2 Na-ion battery cathode

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

Dose, Wesley M.; Sharma, Neeraj; Pramudita, James C.

The structural evolution of electrode materials directly influences the performance of sodium-ion batteries. In this work, in situ synchrotron X-ray diffraction is used to investigate the evolution of the crystal structure of a Mn-rich P2-phase Na 2/3Fe 0.2Mn 0.8O 2 cathode. A single-phase reaction takes place for the majority of the discharge–charge cycle at ~C/10, with only a short, subtle hexagonal P2 to hexagonal P2 two-phase region early in the first charge. Thus, a higher fraction of Mn compared to previous studies is demonstrated to stabilize the P2 structure at high and low potentials, with neither “Z”/OP4 phases in themore » charged state nor significant quantities of the P'2 phase in the discharged state between 1.5 and 4.2 V. Notably, sodium ions inserted during discharge are located on both available crystallographic sites, albeit with a preference for the site sharing edges with the MO 6 octahedral unit. The composition Na ~0.70Fe 0.2Mn 0.8O 2 prompts a reversible single-phase sodium redistribution between the two sites. Sodium ions vacate the site sharing faces (Naf), favoring the site sharing edges (Nae) to give a Nae/Naf site occupation of 4:1 in the discharged state. This site preference could be an intermediate state prior to the formation of the P'2 phase. Furthermore, this work shows how the Mn-rich Na 2/3Fe 0.2Mn 0.8O 2 composition and its sodium-ion distribution can minimize phase transitions during battery function, especially in the discharged state.« less

Structure-electrochemical evolution of a Mn-rich P2 Na 2/3Fe 0.2Mn 0.8O 2 Na-ion battery cathode

DOE PAGES

Dose, Wesley M.; Sharma, Neeraj; Pramudita, James C.; ...

2017-08-04

The structural evolution of electrode materials directly influences the performance of sodium-ion batteries. In this work, in situ synchrotron X-ray diffraction is used to investigate the evolution of the crystal structure of a Mn-rich P2-phase Na 2/3Fe 0.2Mn 0.8O 2 cathode. A single-phase reaction takes place for the majority of the discharge–charge cycle at ~C/10, with only a short, subtle hexagonal P2 to hexagonal P2 two-phase region early in the first charge. Thus, a higher fraction of Mn compared to previous studies is demonstrated to stabilize the P2 structure at high and low potentials, with neither “Z”/OP4 phases in themore » charged state nor significant quantities of the P'2 phase in the discharged state between 1.5 and 4.2 V. Notably, sodium ions inserted during discharge are located on both available crystallographic sites, albeit with a preference for the site sharing edges with the MO 6 octahedral unit. The composition Na ~0.70Fe 0.2Mn 0.8O 2 prompts a reversible single-phase sodium redistribution between the two sites. Sodium ions vacate the site sharing faces (Naf), favoring the site sharing edges (Nae) to give a Nae/Naf site occupation of 4:1 in the discharged state. This site preference could be an intermediate state prior to the formation of the P'2 phase. Furthermore, this work shows how the Mn-rich Na 2/3Fe 0.2Mn 0.8O 2 composition and its sodium-ion distribution can minimize phase transitions during battery function, especially in the discharged state.« less

High-resolution non-contact measurement of the electrical activity of plants in situ using optical recording

PubMed Central

Zhao, Dong-Jie; Chen, Yang; Wang, Zi-Yang; Xue, Lin; Mao, Tong-Lin; Liu, Yi-Min; Wang, Zhong-Yi; Huang, Lan

2015-01-01

The limitations of conventional extracellular recording and intracellular recording make high-resolution multisite recording of plant bioelectrical activity in situ challenging. By combining a cooled charge-coupled device camera with a voltage-sensitive dye, we recorded the action potentials in the stem of Helianthus annuus and variation potentials at multiple sites simultaneously with high spatial resolution. The method of signal processing using coherence analysis was used to determine the synchronization of the selected signals. Our results provide direct visualization of the phloem, which is the distribution region of the electrical activities in the stem and leaf of H. annuus, and verify that the phloem is the main action potential transmission route in the stems of higher plants. Finally, the method of optical recording offers a unique opportunity to map the dynamic bioelectrical activity and provides an insight into the mechanisms of long-distance electrical signal transmission in higher plants. PMID:26333536

On the Applicability of DLVO Theory to the Prediction of Clay Colloids Stability.

PubMed

Missana; Adell

2000-10-01

The stability behavior of Na-montmorillonite colloids has been studied by combining the analysis of their surface charge properties and time-resolved dynamic light scattering experiments. The chemical surface model for several types of clays, including montmorillonite, has to take into account the double surface charge contribution due to their permanent structural charge and to their pH-dependent charge, which is developed at the edge sites, therefore, these stability studies were carried out as a function of both ionic strength and pH. DLVO theory is largely applied for the prediction of the stability of many colloidal systems, including the natural ones. This work shows that the stability behavior of Na-montmorillonite colloids cannot be satisfactorily reproduced by DLVO theory, using the surface parameters experimentally obtained. Particularly, this theory is unable to explain their pH-dependent stability behavior caused by the small charge at the edge sites. Based on these results, a literature review of DLVO stability prediction of clay colloids was performed. It confirmed that this theory is not capable of taking into account the double contribution to the total surface charge and, at the same time, pointed out the main uncertainties related to the appropriate use of the input parameters for the calculation as, for example, the Hamaker constant or the surface potential. Copyright 2000 Academic Press.

Vibrationally induced center reconfiguration in co-doped GaN:Eu, Mg epitaxial layers: Local hydrogen migration vs. activation of non-radiative channels

NASA Astrophysics Data System (ADS)

Mitchell, B.; Lee, D.; Lee, D.; Fujiwara, Y.; Dierolf, V.

2013-12-01

Europium doped gallium nitride (GaN:Eu) is a promising candidate as a material for red light emitting diodes. When Mg was co-doped into GaN:Eu, additional incorporation environments were discovered that show high excitation efficiency at room temperature and have been attributed to the coupling of Mg-H complexes to the majority Eu site. Electron beam irradiation, indirect and resonant (direct) laser excitation were found to modify these complexes, indicating that vibrational energy alone can trigger the migration of the H while the presence of additional charges and excess energy controls the type of reconfiguration and the activation of non-radiative decay channels.

Molecular dynamics simulations of apo, holo, and inactivator bound GABA-at reveal the role of active site residues in PLP dependent enzymes.

PubMed

Gökcan, Hatice; Monard, Gerald; Sungur Konuklar, F Aylin

2016-07-01

The pyridoxal 5-phosphate (PLP) cofactor is a significant organic molecule in medicinal chemistry. It is often found covalently bound to lysine residues in proteins to form PLP dependent enzymes. An example of this family of PLP dependent enzymes is γ-aminobutyric acid aminotransferase (GABA-AT) which is responsible for the degradation of the neurotransmitter GABA. Its inhibition or inactivation can be used to prevent the reduction of GABA concentration in brain which is the source of several neurological disorders. As a test case for PLP dependent enzymes, we have performed molecular dynamics simulations of GABA-AT to reveal the roles of the protein residues and its cofactor. Three different states have been considered: the apoenzyme, the holoenzyme, and the inactive state obtained after the suicide inhibition by vigabatrin. Different protonation states have also been considered for PLP and two key active site residues: Asp298 and His190. Together, 24 independent molecular dynamics trajectories have been simulated for a cumulative total of 2.88 µs. Our results indicate that, unlike in aqueous solution, the PLP pyridine moiety is protonated in GABA-AT. This is a consequence of a pKa shift triggered by a strong charge-charge interaction with an ionic "diad" formed by Asp298 and His190 that would help the activation of the first half-reaction of the catalytic mechanism in GABA-AT: the conversion of PLP to free pyridoxamine phosphate (PMP). In addition, our MD simulations exhibit additional strong hydrogen bond networks between the protein and PLP: the phosphate group is held in place by the donation of at least three hydrogen bonds while the carbonyl oxygen of the pyridine ring interacts with Gln301; Phe181 forms a π-π stacking interaction with the pyridine ring and works as a gate keeper with the assistance of Val300. All these interactions are hypothesized to help maintain free PMP in place inside the protein active site to facilitate the second half-reaction in GABA-AT: the regeneration of PLP-bound GABA-AT (i.e., the holoenzyme). Proteins 2016; 84:875-891. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Influence of silver nanoparticles on titanium oxide and nitrogen doped titanium oxide thin films for sun light photocatalysis

NASA Astrophysics Data System (ADS)

Madhavi, V.; Kondaiah, P.; Mohan Rao, G.

2018-04-01

Decreasing recombination of photogenerated charge carriers in photocatalysts is a critical issue for enhancing the efficiency of dye degradation. It is one of the greatest challenges to reduce the recombination of photo generated charge carriers in semiconductor. In this paper, we report that there is an enhancement of photocatalytic activity in presence of Sun light, by introducing Plasmon (silver nanoparticles (Ag)) onto the titanium oxide (TiO2) and nitrogen incorporated titanium oxide (N-TiO2) films. These silver nanoparticles facilitate the charge transport and separation of charge carriers. In this paper we find that the phase transformation accurse from rutile to anatase with increase of nitrogen flow rates. The FE-SEM analysis showed the micro structure changes to dense columnar growth with increase of nitrogen flow rates. XPS studies of the N-TiO2 thin films revealed that the substitution of N atoms within the O sites plays a crucial role in narrowing the band gap of the TiO2. This enables the absorption of visible light radiation and leads to operation of the film as a highly reactive and effective photocatalysis. The synergetic effect of silver nanoparticles on TiO2 and N-TiO2 films tailored the photocatalytic acitivity, charge transfer mechanism, and photocurrent studies. The silver nanoparticle loaded N-TiO2 films showed highest degradation of 95% compare to the N-TiO2 films. The photo degradation rate constant of Ag/N-TiO2 film was larger than the N-TiO2 films.

Charge transport mechanism in p-type copper ion containing triazine thiolate metallopolymer thin film devices

NASA Astrophysics Data System (ADS)

K, Deepak; Roy, Amit; Anjaneyulu, P.; Kandaiah, Sakthivel; Pinjare, Sampatrao L.

2017-10-01

The charge transport mechanism in copper ions containing 1,3,5-Triazine-2,4,6-trithiolate (CuTCA) based polymer device in sandwich (Ag/CuTCA/Cu) geometry is studied. The current-voltage (I-V) characteristics of the metallopolymer CuTCA device have shown a transition in the charge transport mechanism from Ohmic to Space-charge limited conduction when temperature and voltage are varied. The carriers in CuTCA devices exhibit hopping transport, in which carriers hop from one site to the other. The hole mobility in this polymer device is found to be dependent on electric field E ( μpα√{E } ) and temperature, which suggests that the polymer has inherent disorder. The electric-field coefficient γ and zero-field mobility μ0 are temperature dependent. The values of mobility and activation energies are estimated from temperature (90-140 K) dependent charge transport studies and found to be in the range of 1 × 10-11-8 × 10-12 m2/(V s) and 16.5 meV, respectively. Temperature dependent electric-field coefficient γ is in the order of 17.8 × 10-4 (m/V)1/2, and the value of zero-field mobility μ0 is in the order of 1.2 × 10-11 m2/(V s) at 140 K. A constant phase element (Q) is used to model the device parameters, which are extracted using the Impedance spectroscopy technique. The bandgap of the polymer is estimated to be 2.6 eV from UV-Vis reflectance spectra.

Quantum Phase Transition and Local Entanglement in Extended Hubbard Model on Anisotropic Triangular Lattices

NASA Astrophysics Data System (ADS)

Gao, Ji-Ming; Tang, Rong-An; Zhang, Zheng-Mei; Xue, Ju-Kui

2016-11-01

Using a mean-field theory based upon Hartree—Fock approximation, we theoretically investigate the competition between the metallic conductivity, spin order and charge order phases in a two-dimensional half-filled extended Hubbard model on anisotropic triangular lattice. Bond order, double occupancy, spin and charge structure factor are calculated, and the phase diagram of the extended Hubbard model is presented. It is found that the interplay of strong interaction and geometric frustration leads to exotic phases, the charge fluctuation is enhanced and three kinds of charge orders appear with the introduction of the nearest-neighbor interaction. Moreover, for different frustrations, it is also found that the antiferromagnetic insulating phase and nonmagnetic insulating phase are rapidly suppressed, and eventually disappeared as the ratio between the nearest-neighbor interaction and on-site interaction increases. This indicates that spin order is also sensitive to the nearest-neighbor interaction. Finally, the single-site entanglement is calculated and it is found that a clear discontinuous of the single-site entanglement appears at the critical points of the phase transition. Supported by National Natural Science Foundation of China under Grant Nos.11274255, 11475027 and 11305132, Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20136203110001, and Technology of Northwest Normal University, China under Grants No. NWNU-LKQN-11-26

Influence of Coherent Tunneling and Incoherent Hopping on the Charge Transfer Mechanism in Linear Donor-Bridge-Acceptor Systems.

PubMed

Li, Guangqi; Govind, Niranjan; Ratner, Mark A; Cramer, Christopher J; Gagliardi, Laura

2015-12-17

The mechanism of charge transfer has been observed to change from tunneling to hopping with increasing numbers of DNA base pairs in polynucleotides and with the length of molecular wires. The aim of this paper is to investigate this transition by examining the population dynamics using a tight-binding Hamiltonian with model parameters to describe a linear donor-bridge-acceptor (D-B-A) system. The model includes a primary vibration and an electron-vibration coupling at each site. A further coupling of the primary vibration with a secondary phonon bath allows the system to dissipate energy to the environment and reach a steady state. We apply the quantum master equation (QME) approach, based on second-order perturbation theory in a quantum dissipative system, to examine the dynamical processes involved in charge-transfer and follow the population transfer rate at the acceptor, ka, to shed light on the transition from tunneling to hopping. With a small tunneling parameter, V, the on-site population tends to localize and form polarons, and the hopping mechanism dominates the transfer process. With increasing V, the population tends to be delocalized and the tunneling mechanism dominates. The competition between incoherent hopping and coherent tunneling governs the mechanism of charge transfer. By varying V and the total number of sites, we also examine the onset of the transition from tunneling to hopping with increasing length.

Reactivity of 12-tungstophosphoric acid and its inhibitor potency toward Na+/K+-ATPase: A combined 31P NMR study, ab initio calculations and crystallographic analysis.

PubMed

Bošnjaković-Pavlović, Nada; Bajuk-Bogdanović, Danica; Zakrzewska, Joanna; Yan, Zeyin; Holclajtner-Antunović, Ivanka; Gillet, Jean-Michel; Spasojević-de Biré, Anne

2017-11-01

Influence of 12-tungstophosphoric acid (WPA) on conversion of adenosine triphosphate (ATP) to adenosine diphosphate (ADP) in the presence of Na + /K + -ATPase was monitored by 31 P NMR spectroscopy. It was shown that WPA exhibits inhibitory effect on Na + /K + -ATPase activity. In order to study WPA reactivity and intermolecular interactions between WPA oxygen atoms and different proton donor types (D=O, N, C), we have considered data for WPA based compounds from the Cambridge Structural Database (CSD), the Crystallographic Open Database (COD) and the Inorganic Crystal Structure Database (ICSD). Binding properties of Keggin's anion in biological systems are illustrated using Protein Data Bank (PDB). This work constitutes the first determination of theoretical Bader charges on polyoxotungstate compound via the Atom In Molecule theory. An analysis of electrostatic potential maps at the molecular surface and charge of WPA, resulting from DFT calculations, suggests that the preferred protonation site corresponds to WPA bridging oxygen. These results enlightened WPA chemical reactivity and its potential biological applications such as the inhibition of the ATPase activity. Copyright © 2017 Elsevier Inc. All rights reserved.

Electro-oxidation of methanol on gold in alkaline media: Adsorption characteristics of reaction intermediates studied using time resolved electro-chemical impedance and surface plasmon resonance techniques

NASA Astrophysics Data System (ADS)

Assiongbon, K. A.; Roy, D.

2005-12-01

Electro-catalytic oxidation of methanol is the anode reaction in direct methanol fuel cells. We have studied the adsorption characteristics of the intermediate reactants of this multistep reaction on a gold film electrode in alkaline solutions by combining surface plasmon resonance (SPR) measurements with Fourier transform electro-chemical impedance spectroscopy (FT-EIS). Methanol oxidation in this system shows no significant effects of "site poisoning" by chemisorbed CO. Our results suggest that OH - chemisorbed onto Au acts as a stabilizing agent for the surface species of electro-active methanol. Double layer charging/discharging and adsorption/desorption of OH - show more pronounced effects than adsorption/oxidation of methanol in controlling the surface charge density of the Au substrate. These effects are manifested in both the EIS and the SPR data, and serve as key indicators of the surface reaction kinetics. The data presented here describe the important role of adsorbed OH - in electro-catalysis of methanol on Au, and demonstrate how SPR and FT-EIS can be combined for quantitative probing of catalytically active metal-solution interfaces.

Identification of catalytic sites for oxygen reduction and oxygen evolution in N-doped graphene materials: Development of highly efficient metal-free bifunctional electrocatalyst

PubMed Central

Yang, Hong Bin; Miao, Jianwei; Hung, Sung-Fu; Chen, Jiazang; Tao, Hua Bing; Wang, Xizu; Zhang, Liping; Chen, Rong; Gao, Jiajian; Chen, Hao Ming; Dai, Liming; Liu, Bin

2016-01-01

Oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are critical to renewable energy conversion and storage technologies. Heteroatom-doped carbon nanomaterials have been reported to be efficient metal-free electrocatalysts for ORR in fuel cells for energy conversion, as well as ORR and OER in metal-air batteries for energy storage. We reported that metal-free three-dimensional (3D) graphene nanoribbon networks (N-GRW) doped with nitrogen exhibited superb bifunctional electrocatalytic activities for both ORR and OER, with an excellent stability in alkaline electrolytes (for example, KOH). For the first time, it was experimentally demonstrated that the electron-donating quaternary N sites were responsible for ORR, whereas the electron-withdrawing pyridinic N moieties in N-GRW served as active sites for OER. The unique 3D nanoarchitecture provided a high density of the ORR and OER active sites and facilitated the electrolyte and electron transports. As a result, the as-prepared N-GRW holds great potential as a low-cost, highly efficient air cathode in rechargeable metal-air batteries. Rechargeable zinc-air batteries with the N-GRW air electrode in a two-electrode configuration exhibited an open-circuit voltage of 1.46 V, a specific capacity of 873 mAh g−1, and a peak power density of 65 mW cm−2, which could be continuously charged and discharged with an excellent cycling stability. Our work should open up new avenues for the development of various carbon-based metal-free bifunctional electrocatalysts of practical significance. PMID:27152333

The K+/site and H+/site stoichiometry of mitochondrial electron transport.

PubMed

Reynafarje, B; Lehninger, A L

1978-09-25

Electrode measurements of the average number of H+ ejected and K+ taken up (in the presence of valinomycin) per pair of electrons passing the energy-conserving sites of the respiratory chain of rat liver and rat heart mitochondria have given identical values of the H+/site and 5+/site ratios very close to 4 in the presence of N-ethylmaleimide, an inhibitor of interfering respiration-coupled uptake of H+ + H2PO4-. The K+/site uptake ratio of 4 not only shows that inward movement of K+ provides quantitative charge-compensation for the 4 H+ ejected, but also confirms that 4 charges are separated per pair of electrons per site. When N-ethylmaleimide is omitted, the H+/site ejection ratio is depressed, because of the interfering secondary uptake of H/+ with H2PO4- on the phosphate carrier, but the K+/site uptake ratio remains at 4.0. Addition of phosphate or acetate, which can carry H+ into respiring mitochondria, further depresses the H+/site ratio, but does not affect the K+/site ratio, which remains at 4.0. These and other considerations thus confirm our earlier stoichiometric measurements that the average H+/site ratio is 4.0 and also show that the K+/site uptake ratio can be used as a measure of the intrinsic H+/site ratio, regardless of the presence of phosphate in the medium and without the necessity of adding N-ethylmaleimide or other inhibitors of H+ + H2PO4- transport.

Temperature and frequency dependent conductivity of bismuth zinc vanadate semiconducting glassy system

NASA Astrophysics Data System (ADS)

Punia, R.; Kundu, R. S.; Dult, Meenakshi; Murugavel, S.; Kishore, N.

2012-10-01

The ac conductivity of bismuth zinc vanadate glasses with compositions 50V2O5. xBi2O3. (50-x) ZnO has been studied in the frequency range 10-1 Hz to 2 MHz and in temperature range 333.16 K to 533.16 K. The temperature and frequency dependent conductivity is found to obey Jonscher's universal power law for all the compositions of bismuth zinc vanadate glass system. The dc conductivity (σdc), crossover frequency (ωH), and frequency exponent (s) have been estimated from the fitting of experimental data of ac conductivity with Jonscher's universal power law. Enthalpy to dissociate the cation from its original site next to a charge compensating center (Hf) and enthalpy of migration (Hm) have also been estimated. It has been observed that mobility of charge carriers and ac conductivity in case of zinc vanadate glass system increases with increase in Bi2O3 content. In order to determine the conduction mechanism, the ac conductivity and its frequency exponent have been analyzed in the frame work of various theoretical models based on classical hopping over barriers and quantum mechanical tunneling. The ac conduction takes place via tunneling of overlapping large polarons in all the compositions of presently studied vanadate glasses. The fitting of experimental data of ac conductivity with overlapping large polarons tunneling model has also been done. The parameters; density of states at Fermi level (N(EF)), activation energy associated with charge transfer between the overlapping sites (WHO), inverse localization length (α) and polaron radius (rp) obtained from fitting of this model with experimental data are reasonable.

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation

PubMed Central

Gu, Hong; Zhang, Shuming; Wong, Kin-Yiu; Radak, Brian K.; Dissanayake, Thakshila; Kellerman, Daniel L.; Dai, Qing; Miyagi, Masaru; Anderson, Vernon E.; York, Darrin M.; Piccirilli, Joseph A.; Harris, Michael E.

2013-01-01

Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can provide insight into biological catalysis. Catalysis of RNA 2′-O-transphosphorylation by ribonuclease A is proposed to involve electrostatic stabilization and acid/base catalysis, although the structure of the rate-limiting transition state is uncertain. Here, we describe coordinated kinetic isotope effect (KIE) analyses, molecular dynamics simulations, and quantum mechanical calculations to model the transition state and mechanism of RNase A. Comparison of the 18O KIEs on the 2′O nucleophile, 5′O leaving group, and nonbridging phosphoryl oxygens for RNase A to values observed for hydronium- or hydroxide-catalyzed reactions indicate a late anionic transition state. Molecular dynamics simulations using an anionic phosphorane transition state mimic suggest that H-bonding by protonated His12 and Lys41 stabilizes the transition state by neutralizing the negative charge on the nonbridging phosphoryl oxygens. Quantum mechanical calculations consistent with the experimental KIEs indicate that expulsion of the 5′O remains an integral feature of the rate-limiting step both on and off the enzyme. Electrostatic interactions with positively charged amino acid site chains (His12/Lys41), together with proton transfer from His119, render departure of the 5′O less advanced compared with the solution reaction and stabilize charge buildup in the transition state. The ability to obtain a chemically detailed description of 2′-O-transphosphorylation transition states provides an opportunity to advance our understanding of biological catalysis significantly by determining how the catalytic modes and active site environments of phosphoryl transferases influence transition state structure. PMID:23878223

FTIR Studies of Internal Water Molecules of Bacteriorhodopsin: Structural Analysis of Halide-bound D85S and D212N Mutants in the Schiff Base Region

NASA Astrophysics Data System (ADS)

Shibata, Mikihiro; Kandori, Hideki

2007-12-01

Bacteriorhodopsin (BR), a membrane protein found in Halobacterium salinarum, functions as a light-driven proton pump. The Schiff base region has a quadropolar structure with positive charges located at the protonated Schiff base and Arg82, and counterbalancing negative charges located at Asp85 and Asp212 (Figure 1A). It is known that BR lacks a proton-pumping activity if Asp85 or Asp212 is neutralized by mutation. On the other hand, binding of C1- brings different effects for pumping functions in mutants at D85 and D212 position. While C1--bound D85T and D85S pump C1-, photovoltage measurements suggested that C1--bound D212N pumps protons at low pH. In this study, we measured low-temperature FTIR spectra of D85S and D212N containing various halides to compare the halide binding site of both proteins. In the case of D85S, the N-D stretching vibrations of the Schiff base were halide-dependent. This result suggests that the halide is a hydrogen-bond acceptor of the Schiff base, being consistent with the X-ray crystal structure. On the other hand, no halide dependence was observed for vibrational bands of the retinal skeleton and the Schiff base in the D212N mutant. This result suggests that the halide does not form a hydrogen bond with the Schiff base directly, unlike the mutation at D85 position. Halide-dependent water bands in the Schiff base region also differ between D85S and D212N. From these results, halide binding site of both proteins and role of two negative charges in BR will be discussed.

Two-track virtual screening approach to identify both competitive and allosteric inhibitors of human small C-terminal domain phosphatase 1

NASA Astrophysics Data System (ADS)

Park, Hwangseo; Lee, Hye Seon; Ku, Bonsu; Lee, Sang-Rae; Kim, Seung Jun

2017-08-01

Despite a wealth of persuasive evidence for the involvement of human small C-terminal domain phosphatase 1 (Scp1) in the impairment of neuronal differentiation and in Huntington's disease, small-molecule inhibitors of Scp1 have been rarely reported so far. This study aims to the discovery of both competitive and allosteric Scp1 inhibitors through the two-track virtual screening procedure. By virtue of the improvement of the scoring function by implementing a new molecular solvation energy term and by reoptimizing the atomic charges for the active-site Mg2+ ion cluster, we have been able to identify three allosteric and five competitive Scp1 inhibitors with low-micromolar inhibitory activity. Consistent with the results of kinetic studies on the inhibitory mechanisms, the allosteric inhibitors appear to be accommodated in the peripheral binding pocket through the hydrophobic interactions with the nonpolar residues whereas the competitive ones bind tightly in the active site with a direct coordination to the central Mg2+ ion. Some structural modifications to improve the biochemical potency of the newly identified inhibitors are proposed based on the binding modes estimated with docking simulations.

Defect engineering of mesoporous nickel ferrite and its application for highly enhanced water oxidation catalysis

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

Yue, Qiudi; Liu, Cunming; Wan, Yangyang

Spinel nickel ferrite (NiFe2O4) emerges as a promising low-cost catalyst for water splitting but it usually shows low catalytic activity because of its limited number of active sites and poor conductivity. For the first time, herein we have successfully overcome its weaknesses using defect engineering approach by creating oxygen vacancies in NiFe2O4. The existence of oxygen vacancy not only shifts up the d-band center, strengthens the adsorption of H2O, and thus provides more active catalytic sites, but also tunes the electron configuration and creates massive number of defective donor states in the band gap to facilitate charge transfer processes. Themore » optimal defective catalyst showed significantly enhanced catalytic OER performance with an OER overpotential as low as 0.35 V at 10 mA cm-2 and a Tafel slope of only ~40 mV dec-1. Moreover, the impressive specific mass and area current density of 17.5 A g-1 and 0.106 A m-2 at 1.58 V vs. RHE have been achieved, which are ~23 and ~36 times higher than that of defect-free counterpart, respectively.« less

Radiotherapy and risk of implantable cardioverter-defibrillator malfunctions: experimental data from direct exposure at increasing doses.

PubMed

Zecchin, Massimo; Artico, Jessica; Morea, Gaetano; Severgnini, Mara; Bianco, Elisabetta; De Luca, Antonio; Fantasia, Anna Zorzin; Salvatore, Luca; Milan, Vittorino; Lucarelli, Matteo; Dissegna, Roberta; Cannatà, Antonio; Sinagra, Gianfranco

2018-04-01

During radiotherapy, in patients with implantable cardioverter-defibrillators (ICDs) malfunctions are considered more likely if doses more than 2 Gy reach the ICD site; however, most malfunctions occur with high-energy (>10 MV) radiations, and the risk is less defined using 6-MV linear accelerators. The purpose of the study is to experimentally evaluate the occurrence of malfunctions in ICDs radiated with a 6-MV linear accelerator at increasing photon doses. Thirty-two ICDs from all manufacturers (31 explanted and one demo) were evaluated; all devices with a sufficient battery charge underwent multiple radiations with a 6-MV photon beam reaching a cumulative dose at ICD site of 0.5, 1, 2, 3, 5 and 10 Gy and interrogated after every session. All antitachycardia therapies were left enabled; two ICDs were connected to a rhythm simulator (one simulating a complete atrioventricular block without ventricular activity) and visually monitored by external ECG and the ICD programmer during radiation. Thirteen ICDs were excluded before radiation because of battery depletion; after radiation up to the cumulative dose at the cardiac implantable electronic device site of 10 Gy, in the remaining 19 devices, programmation and battery charge remained unchanged and no switch to safety mode was observed; oversensing, pacing inhibition or inappropriate antitachycardia therapy were neither recorded nor visually observed during radiation. With a low-energy accelerator, neither malfunctions nor electromagnetic interferences were detected radiating the ICDs at doses usually reaching the ICD pocket during radiotherapy sessions. In this context, magnet application to avoid oversensing and inappropriate therapy seems, therefore, useless.

Soil Carbon and Nitrogen Pools and Assessment of Soil Mitigation of N Removal for Biomass for Energy in the coastal Douglas-fir zone of Oregon, Washington and British Columbia.

NASA Astrophysics Data System (ADS)

Harrison, Robert; James, Jason; Dietzen, Christiana; Littke, Kimberly

2017-04-01

Biomass, carbon and nitrogen pools in soil (1 m depth) and tree components in 68 intensively-managed Douglas-fir plantations in western Oregon and Washington USA, and British Columbia Canada. The potential removal of N with bole-only and total aboveground harvesting was compared to total ecosystem pools of N to determine the relative removals compared to the total ecosystem N pools to assign a risk rating to each potential harvest site for N removal, with <=10% of total removed being a threshhold at which there would be little potential for N removal concerns over a 55-year rotation, and 30% or greater a cause for significan concern or the potential amelioration of losses with N fertilization. Additional research on 22 of the sites for deep rooting and soil C and N pools up to 4 m depth showed that there were unanticipated and formerly unrecognized large pools of C and N below 1 m depth, and as deep as we were capable of sampling (4 m). Analysis of organic matter in the soil profiles indicate significant differences in binding of organic matter to mineral components of soil at depth, dependent on pH-dependent charge sources primarily associated with volcanic activity in the region. Characterization of PZNC and pH dependent charge at one site showed substantial anion exchange capacity and the ability to bind organic acids and DOC leaching through the soil profile.

Characterization of the binding of 2-mercaptobenzimidazole to bovine serum albumin.

PubMed

Teng, Yue; Zou, Luyi; Huang, Ming; Zong, Wansong

2015-04-01

2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment is potentially harmful to human health. In this article, the interaction of MBI with bovine serum albumin (BSA) was explored using spectroscopic and molecular docking methods under physiological conditions. The positively charged MBI can spontaneously bind with the negatively charged BSA through electrostatic forces with one binding site. The site marker competition experiments and the molecular docking study revealed that MBI bound into site II (subdomain IIIA) of BSA, which further led to some secondary structure and microenvironmental changes of BSA. This work provides useful information on understanding the toxicological actions of MBI at the molecular level. Copyright © 2015 John Wiley & Sons, Ltd.

Advanced batteries for load-leveling - The utility perspective on system integration

NASA Astrophysics Data System (ADS)

Delmonaco, J. L.; Lewis, P. A.; Roman, H. T.; Zemkoski, J.

1982-09-01

Rechargeable battery systems for applications as utility load-leveling units, particularly in urban areas, are discussed. Particular attention is given to advanced lead-acid, zinc-halogen, sodium-sulfer, and lithium-iron sulfide battery systems, noting that battery charging can proceed at light load hours and requires no fuel on-site. Each battery site will have a master site controller and related subsystems necessary for ensuring grid-quality power output from the batteries and charging when feasible. The actual interconnection with the grid is envisioned as similar to transmission, subtransmission, or distribution systems similar to cogeneration or wind-derived energy interconnections. Analyses are presented of factors influencing the planning economics, impacts on existing grids through solid-state converters, and operational and maintenance considerations. Finally, research directions towards large scale battery implementation are outlined.

(abstract) Satellite Physical Oceanography Data Available From an EOSDIS Archive

NASA Technical Reports Server (NTRS)

Digby, Susan A.; Collins, Donald J.

1996-01-01

The Physical Oceanography Distributed Active Archive Center (PO.DAAC) at the Jet Propulsion Laboratory archives and distributes data as part of the Earth Observing System Data and Information System (EOSDIS). Products available from JPL are largely satellite derived and include sea-surface height, surface-wind speed and vectors, integrated water vapor, atmospheric liquid water, sea-surface temperature, heat flux, and in-situ data as it pertains to satellite data. Much of the data is global and spans fourteen years.There is email access, a WWW site, product catalogs, and FTP capabilities. Data is free of charge.

Systems Based Study of the Therapeutic Potential of Small Charged Molecules for the Inhibition of IL-1 Mediated Cartilage Degradation

PubMed Central

Kar, Saptarshi; Smith, David W.; Gardiner, Bruce S.; Grodzinsky, Alan J.

2016-01-01

Inflammatory cytokines are key drivers of cartilage degradation in post-traumatic osteoarthritis. Cartilage degradation mediated by these inflammatory cytokines has been extensively investigated using in vitro experimental systems. Based on one such study, we have developed a computational model to quantitatively assess the impact of charged small molecules intended to inhibit IL-1 mediated cartilage degradation. We primarily focus on the simplest possible computational model of small molecular interaction with the IL-1 system—direct binding of the small molecule to the active site on the IL-1 molecule itself. We first use the model to explore the uptake and release kinetics of the small molecule inhibitor by cartilage tissue. Our results show that negatively charged small molecules are excluded from the negatively charged cartilage tissue and have uptake kinetics in the order of hours. In contrast, the positively charged small molecules are drawn into the cartilage with uptake and release timescales ranging from hours to days. Using our calibrated computational model, we subsequently explore the effect of small molecule charge and binding constant on the rate of cartilage degradation. The results from this analysis indicate that the small molecules are most effective in inhibiting cartilage degradation if they are either positively charged and/or bind strongly to IL-1α, or both. Furthermore, our results showed that the cartilage structural homeostasis can be restored by the small molecule if administered within six days following initial tissue exposure to IL-1α. We finally extended the scope of the computational model by simulating the competitive inhibition of cartilage degradation by the small molecule. Results from this model show that small molecules are more efficient in inhibiting cartilage degradation by binding directly to IL-1α rather than binding to IL-1α receptors. The results from this study can be used as a template for the design and development of more pharmacologically effective osteoarthritis drugs, and to investigate possible therapeutic options. PMID:27977731

44 CFR 353.6 - Schedule of services.

Code of Federal Regulations, 2010 CFR

2010-10-01

... shall be charged the full cost of site-specific services based upon the appropriate professional hourly... will be charged to the licensee by FEMA, at the rate and cost incurred. (a) When a State seeks formal.... This provision does not apply where an operating license has been granted or the application denied or...

38 CFR 36.4254 - Fees and charges.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 38 Pensions, Bonuses, and Veterans' Relief 2 2011-07-01 2011-07-01 false Fees and charges. 36.4254 Section 36.4254 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) LOAN GUARANTY Guaranty of Loans to Veterans to Purchase Manufactured Homes and Lots, Including Site Preparation Combination and Manufactured Home Lot...

Structure investigation of codeine drug using mass spectrometry, thermal analyses and semi-emperical molecular orbital (MO) calculations

NASA Astrophysics Data System (ADS)

Zayed, M. A.; Hawash, M. F.; Fahmey, M. A.

2006-05-01

Codeine is an analgesic with uses similar to morphine, but it has a mild sedative effect. It is preferable used as phosphate form and it is often administrated by mouth with aspirin or paracetamol. Therefore, it is important to investigate its structure to know the active groups and weak bonds responsible for its medical activity. Consequently in the present work, codeine was investigated by mass spectrometry and thermal analyses (TG, DTG and DTA) and confirming by semi-empirical MO-calculation (PM3 method) in the neutral and positively charged forms of the drug. Some results of studying the d-block element complexes of codeine were used to declare the relationship between drug structure and its chemical reactivity in vitro system. The mass spectra and thermal analyses fragmentation pathways were proposed and compared to each other to select the most suitable scheme representing the correct fragmentation of this drug. From EI mass spectra, the main primary cleavage site of the charged drug molecule is that due to β-cleavage to nitrogen atom in its skeleton. It occurs in two parallel mechanisms with the same possibility, i.e. no difference in appearance activation energy between them. In the neutral drug form the primary site cleavage is that occurs in the ether ring. Thermal analyses of the neutral form of the drug revealed the high response of the drug to the temperature variation with very fast rate. It decomposed in several sequential steps in the temperature range 200-600 °C. The initial thermal fragments are very similar to that obtained by mass spectrometric fragmentation. Therefore, comparison between mass and thermal helps in selection of the proper pathway representing the fragmentation of this drug. This comparison successfully confirmed by MOC. These calculations give the bond order, charge distribution, heat of formation and possible hybridization of some atoms in different position of the drug skeleton. This helps the successful choice of the weakest bond at which both mass and thermal fragmentation occurs. Therefore, the best fragmentation pathway of this drug is correctly selected. The effect of such fragmentation on the drug behavior in the human body can be expected as a result of comparing these data with that obtained on studying codeine metal complexes using mass and thermal fragmentation techniques.

Suppression of space charge in crosslinked polyethylene filled with poly(stearyl methacrylate)-grafted SiO2 nanoparticles

NASA Astrophysics Data System (ADS)

Zhang, Ling; Khani, Mohammad M.; Krentz, Timothy M.; Huang, Yanhui; Zhou, Yuanxiang; Benicewicz, Brian C.; Nelson, J. Keith; Schadler, Linda S.

2017-03-01

Incorporating inorganic nanoparticles (NPs) into polymer matrices provides a promising solution for suppressing space charge effects that can lead to premature failure of electrical insulation used in high voltage direct current engineering. However, realizing homogeneous NP dispersion is a great challenge especially in high-molecular-weight polymers. Here, we address this issue in crosslinked polyethylene by grafting matrix-compatible polymer brushes onto spherical colloidal SiO2 NPs (10-15 nm diameter) to obtain a uniform NP dispersion, thus achieving enhanced space charge suppression, improved DC breakdown strength, and restricted internal field distortion (≤10.6%) over a wide range of external DC fields from -30 kV/mm to -100 kV/mm at room temperature. The NP dispersion state is the key to ensuring an optimized distribution of deep trapping sites. A well-dispersed system provides sufficient charge trapping sites and shows better performance compared to ones with large aggregates. This surface ligand strategy is attractive for future nano-modification of many engineering insulating polymers.