Cryo-EM of dynamic protein complexes in eukaryotic DNA replication.

PubMed

Sun, Jingchuan; Yuan, Zuanning; Bai, Lin; Li, Huilin

2017-01-01

DNA replication in Eukaryotes is a highly dynamic process that involves several dozens of proteins. Some of these proteins form stable complexes that are amenable to high-resolution structure determination by cryo-EM, thanks to the recent advent of the direct electron detector and powerful image analysis algorithm. But many of these proteins associate only transiently and flexibly, precluding traditional biochemical purification. We found that direct mixing of the component proteins followed by 2D and 3D image sorting can capture some very weakly interacting complexes. Even at 2D average level and at low resolution, EM images of these flexible complexes can provide important biological insights. It is often necessary to positively identify the feature-of-interest in a low resolution EM structure. We found that systematically fusing or inserting maltose binding protein (MBP) to selected proteins is highly effective in these situations. In this chapter, we describe the EM studies of several protein complexes involved in the eukaryotic DNA replication over the past decade or so. We suggest that some of the approaches used in these studies may be applicable to structural analysis of other biological systems. © 2016 The Protein Society.

On the Structural Plasticity of the Human Genome: Chromosomal Inversions Revisited

PubMed Central

Alves, Joao M; Lopes, Alexandra M; Chikhi, Lounès; Amorim, António

2012-01-01

With the aid of novel and powerful molecular biology techniques, recent years have witnessed a dramatic increase in the number of studies reporting the involvement of complex structural variants in several genomic disorders. In fact, with the discovery of Copy Number Variants (CNVs) and other forms of unbalanced structural variation, much attention has been directed to the detection and characterization of such rearrangements, as well as the identification of the mechanisms involved in their formation. However, it has long been appreciated that chromosomes can undergo other forms of structural changes - balanced rearrangements - that do not involve quantitative variation of genetic material. Indeed, a particular subtype of balanced rearrangement – inversions – was recently found to be far more common than had been predicted from traditional cytogenetics. Chromosomal inversions alter the orientation of a specific genomic sequence and, unless involving breaks in coding or regulatory regions (and, disregarding complex trans effects, in their close vicinity), appear to be phenotypically silent. Such a surprising finding, which is difficult to reconcile with the classical interpretation of inversions as a mechanism causing subfertility (and ultimately reproductive isolation), motivated a new series of theoretical and empirical studies dedicated to understand their role in human genome evolution and to explore their possible association to complex genetic disorders. With this review, we attempt to describe the latest methodological improvements to inversions detection at a genome wide level, while exploring some of the possible implications of inversion rearrangements on the evolution of the human genome. PMID:23730202

Structural study of complexes formed by acidic and neutral organophosphorus reagents

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

Braatz, Alexander D.; Antonio, Mark R.; Nilsson, Mikael

The coordination of the trivalent 4f ions, Ln = La 3+, Dy 3+, and Lu 3+, with neutral and acidic organophosphorus reagents, both individually and combined, was studied by use of X-ray absorption spectroscopy. These studies provide metrical information about the interatomic interactions between these cations and the ligands tri- n-butyl phosphate (TBP) and di- n-butyl phosphoric acid (HDBP), whose behavior are of practical importance to chemical separation processes that are currently used on an industrial scale. Previous studies have suggested the existence of complexes involving a mixture of ligands, accounting for extraction synergy. Through systematic variation of the aqueousmore » phase acidity and extractant concentration and combination, we have found that complexes with Ln and TBP : HDBP at any mixture and HDBP alone involve direct Ln–O interactions involving 6 oxygen atoms and distant Ln–P interactions involving on average 3–5 phosphorus atoms per Ln ion. It was also found that Ln complexes formed by TBP alone seem to favor eight oxygen coordination, though we were unable to obtain metrical results regarding the distant Ln–P interactions due to the low signal attributed to a lower concentration of Ln ions in the organic phases. Our study does not support the existence of mixed Ln–TBP–HDBP complexes but, rather, indicates that the lanthanides are extracted as either Ln–HDBP complexes or Ln–TBP complexes and that these complexes exist in different ratios depending on the conditions of the extraction system. Furthermore, this fundamental structural information offers insight into the solvent extraction processes that are taking place and are of particular importance to issues arising from the separation and disposal of radioactive materials from used nuclear fuel.« less

Structural study of complexes formed by acidic and neutral organophosphorus reagents

DOE PAGES

Braatz, Alexander D.; Antonio, Mark R.; Nilsson, Mikael

2016-12-23

The coordination of the trivalent 4f ions, Ln = La 3+, Dy 3+, and Lu 3+, with neutral and acidic organophosphorus reagents, both individually and combined, was studied by use of X-ray absorption spectroscopy. These studies provide metrical information about the interatomic interactions between these cations and the ligands tri- n-butyl phosphate (TBP) and di- n-butyl phosphoric acid (HDBP), whose behavior are of practical importance to chemical separation processes that are currently used on an industrial scale. Previous studies have suggested the existence of complexes involving a mixture of ligands, accounting for extraction synergy. Through systematic variation of the aqueousmore » phase acidity and extractant concentration and combination, we have found that complexes with Ln and TBP : HDBP at any mixture and HDBP alone involve direct Ln–O interactions involving 6 oxygen atoms and distant Ln–P interactions involving on average 3–5 phosphorus atoms per Ln ion. It was also found that Ln complexes formed by TBP alone seem to favor eight oxygen coordination, though we were unable to obtain metrical results regarding the distant Ln–P interactions due to the low signal attributed to a lower concentration of Ln ions in the organic phases. Our study does not support the existence of mixed Ln–TBP–HDBP complexes but, rather, indicates that the lanthanides are extracted as either Ln–HDBP complexes or Ln–TBP complexes and that these complexes exist in different ratios depending on the conditions of the extraction system. Furthermore, this fundamental structural information offers insight into the solvent extraction processes that are taking place and are of particular importance to issues arising from the separation and disposal of radioactive materials from used nuclear fuel.« less

Low-spin manganese(II) and high-spin manganese(III) complexes derived from disalicylaldehyde oxaloyldihydrazone: Synthesis, spectral characterization and electrochemical studies

NASA Astrophysics Data System (ADS)

Syiemlieh, Ibanphylla; Kumar, Arvind; Kurbah, Sunshine D.; De, Arjune K.; Lal, Ram A.

2018-01-01

Low-spin manganese(II) complexes [MnII(H2slox)].H2O (1), [MnII(H2slox)(SL)] (where SL (secondary ligand) = pyridine (py, 2), 2-picoline (2-pic, 3), 3-picoline (3-pic, 4), and 4-picoline (4-pic, 5) and high-spin manganese(III) complex Na(H2O)4[MnIII(slox)(H2O)2].2.5H2O have been synthesized from disalicyaldehyde oxaloyldihydrazone in methanolic - water medium. The composition of complexes has been established by elemental analyses and thermoanalytical data. The structures of the complexes have been discussed on the basis of data obtained from molar conductance, UV visible, 1H NMR, infrared spectra, magnetic moment and electron paramagnetic resonance spectroscopic studies. Conductivity measurements in DMF suggest that the complexes (1-5) are non-electrolyte while the complex (6) is 1:1 electrolyte. The electronic spectral studies and magnetic moment data suggest five - coordinate square pyramidal structure for the complexes (2-5) and square planar geometry for manganese(II) in complex (1). In complex (6), both sodium and manganese(III) have six coordinate octahedral geometry. IR spectral studies reveal that the dihydrazone coordinates to the manganese centre in keto form in complexes (1-5) and in enol form in complex (6). In all complexes, the ligand is present in anti-cis configuration. Magnetic moment and EPR studies indicate manganese in +2 oxidation state in complexes (1-5), with low-spin square planar complex (1) and square pyramidal stereochemistries complexes (2-5) while in +3 oxidation state in high-spin distorted octahedral stereochemistry in complex (6). The complex (1) involves significant metal - metal interaction in the solid state. All of the complexes show only one metal centred electron transfer reaction in DMF solution in cyclic voltammetric studies. The complexes (1-5) involve MnII→MnI redox reaction while the complex (6) involves MnIII→MnII redox reaction, respectively.

THE CRYSTALLOGRAPHIC INVESTIGATION OF AuCl /center dot/ PCl$sub 3$ AND IBOGAINE /center dot/ HBr

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

Arai-wessel, G.J.

1960-01-01

The structure of the two compounds is completely dlfferent, one being an inorganic complex and the other being an organic alkaloid complex. The difference in crystal constitution caused a difference in behavior with regard to radiation, requiring the use of specific crysthllographic methods for each. Interferences involved in determining their crystal structure are compared and discussed. (N.W.R.)

3D RNA and functional interactions from evolutionary couplings

PubMed Central

Weinreb, Caleb; Riesselman, Adam; Ingraham, John B.; Gross, Torsten; Sander, Chris; Marks, Debora S.

2016-01-01

Summary Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability models of sequence co-variation to infer evolutionarily constrained nucleotide-nucleotide interactions within RNA molecules, and nucleotide-amino acid interactions in RNA-protein complexes. The predicted contacts allow all-atom blinded 3D structure prediction at good accuracy for several known RNA structures and RNA-protein complexes. For unknown structures, we predict contacts in 160 non-coding RNA families. Beyond 3D structure prediction, evolutionary couplings help identify important functional interactions, e.g., at switch points in riboswitches and at a complex nucleation site in HIV. Aided by accelerating sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA. PMID:27087444

Structure of a preternary complex involving a prokaryotic NHEJ DNA polymerase.

PubMed

Brissett, Nigel C; Martin, Maria J; Pitcher, Robert S; Bianchi, Julie; Juarez, Raquel; Green, Andrew J; Fox, Gavin C; Blanco, Luis; Doherty, Aidan J

2011-01-21

In many prokaryotes, a specific DNA primase/polymerase (PolDom) is required for nonhomologous end joining (NHEJ) repair of DNA double-strand breaks (DSBs). Here, we report the crystal structure of a catalytically active conformation of Mycobacterium tuberculosis PolDom, consisting of a polymerase bound to a DNA end with a 3' overhang, two metal ions, and an incoming nucleotide but, significantly, lacking a primer strand. This structure represents a polymerase:DNA complex in a preternary intermediate state. This polymerase complex occurs in solution, stabilizing the enzyme on DNA ends and promoting nucleotide extension of short incoming termini. We also demonstrate that the invariant Arg(220), contained in a conserved loop (loop 2), plays an essential role in catalysis by regulating binding of a second metal ion in the active site. We propose that this NHEJ intermediate facilitates extension reactions involving critically short or noncomplementary DNA ends, thus promoting break repair and minimizing sequence loss during DSB repair. Copyright © 2011 Elsevier Inc. All rights reserved.

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

PubMed Central

Seeliger, Daniel; de Groot, Bert L.

2010-01-01

Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures), however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo) structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 Å backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 Å backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available. PMID:20066034

An unexpected N-terminal loop in PD-1 dominates binding by nivolumab

PubMed Central

Tan, Shuguang; Zhang, Hao; Chai, Yan; Song, Hao; Tong, Zhou; Wang, Qihui; Qi, Jianxun; Wong, Gary; Zhu, Xiaodong; Liu, William J.; Gao, Shan; Wang, Zhongfu; Shi, Yi; Yang, Fuquan; Gao, George F.; Yan, Jinghua

2017-01-01

Cancer immunotherapy by targeting of immune checkpoint molecules has been a research ‘hot-spot' in recent years. Nivolumab, a human monoclonal antibody targeting PD-1, has been widely used clinically since 2014. However, the binding mechanism of nivolumab to PD-1 has not yet been shown, despite a recent report describing the complex structure of pembrolizumab/PD-1. It has previously been speculated that PD-1 glycosylation is involved in nivolumab recognition. Here we report the complex structure of nivolumab with PD-1 and evaluate the effects of PD-1 N-glycosylation on the interactions with nivolumab. Structural and functional analyses unexpectedly reveal an N-terminal loop outside the IgV domain of PD-1. This loop is not involved in recognition of PD-L1 but dominates binding to nivolumab, whereas N-glycosylation is not involved in binding at all. Nivolumab binds to a completely different area than pembrolizumab. These results provide the basis for the design of future inhibitory molecules targeting PD-1. PMID:28165004

The disasters of war in Darfur, 1950-2004.

PubMed

Reyna, Stephen P

2010-01-01

This article investigates the conflict that had been developing since the 1950s in Darfur and which in 2003 and 2004 burst into intense warfare. A 'complex-structuring of violence' standpoint explains the warfare. The argument is organised in two parts. The first section formulates the position by introducing Darfur, next evaluating the prevailing barbarisation perspective's attempts to explicate Darfur warring and, finally, formally presenting the complex structuring standpoint. The second section offers evidence bearing upon this standpoint. This involves information showing that four interrelated structural realms form a causal complex producing the violence. The article ends with discussion of the US government's role in Darfurian disasters of war.

Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

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

Makino, Debora Lika, E-mail: dmakino@biochem.mpg.de; Conti, Elena

The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryoticmore » exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented.« less

Crystallization of Mitochondrial Respiratory Complex II from Chicken Heart: a Membrane Protein Complex Diffracting to 2.0 Å.

PubMed Central

Huang, Li-shar; Borders, Toni M.; Shen, John T.; Wang, Chung-Jen; Berry, Edward

2006-01-01

Synopsis A multi-subunit mitochondrial membrane protein complex involved in the Krebs Cycle and respiratory chain has been crystallized in a form suitable for near-atomic resolution structure determination. A procedure is presented for preparation of diffraction-quality crystals of a vertebrate mitochondrial respiratory Complex II. The crystals have the potential to diffract to at least 2.0 Å with optimization of post-crystal-growth treatment and cryoprotection. This should allow determination of the structure of this important and medically relevant membrane protein complex at near-atomic resolution and provide great detail of the mode of binding of substrates and inhibitors at the two substrate-binding sites. PMID:15805592

Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family.

PubMed

Contessa, Gian Marco; Orsale, Maria; Melino, Sonia; Torre, Vincent; Paci, Maurizio; Desideri, Alessandro; Cicero, Daniel O

2005-03-01

The NMR high-resolution structure of calmodulin complexed with a fragment of the olfactory cyclic-nucleotide gated channel is described. This structure shows features that are unique for this complex, including an active role of the linker connecting the N- and C-lobes of calmodulin upon binding of the peptide. Such linker is not only involved in the formation of an hydrophobic pocket to accommodate a bulky peptide residue, but it also provides a positively charged region complementary to a negative charge of the target. This complex of calmodulin with a target not belonging to the kinase family was used to test the residual dipolar coupling (RDC) approach for the determination of calmodulin binding modes to peptides. Although the complex here characterized belongs to the (1--14) family, high Q values were obtained with all the 1:1 complexes for which crystalline structures are available. Reduction of the RDC data set used for the correlation analysis to structured regions of the complex allowed a clear identification of the binding mode. Excluded regions comprise calcium binding loops and loops connecting the EF-hand motifs.

Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2015-01-01

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid-ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.

Structural changes of homodimers in the PDB.

PubMed

Koike, Ryotaro; Amemiya, Takayuki; Horii, Tatsuya; Ota, Motonori

2018-04-01

Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods. An application, SCPC, compares two structures of protein complexes and decides the match of binding mode. Another application, Motion Tree, identifies rigid-body motions in various sizes and magnitude from the two structural complexes with the same binding mode. This approach was applied to all available homodimers in the Protein Data Bank (PDB). We defined two complex-specific motions: interface motion and subunit-spanning motion. In the former, each subunit of a complex constitutes a rigid body, and the relative movement between subunits occurs at the interface. In the latter, structural parts from distinct subunits constitute a rigid body, providing the relative movement spanning subunits. All structural changes were classified and examined. It was revealed that the complex-specific motions were common in the homodimers, detected in around 40% of families. The dimeric interfaces were likely to be small and flat for interface motion, while large and rugged for subunit-spanning motion. Interface motion was accompanied by a drastic change in contacts at the interface, while the change in the subunit-spanning motion was moderate. These results indicate that the interface properties of homodimers correlated with the type of complex-specific motion. The study demonstrates that the pipeline of SCPC and Motion Tree is useful for the massive analysis of structural change of protein complexes. Copyright © 2017 Elsevier Inc. All rights reserved.

Using the self-select paradigm to delineate the nature of speech motor programming.

PubMed

Wright, David L; Robin, Don A; Rhee, Jooyhun; Vaculin, Amber; Jacks, Adam; Guenther, Frank H; Fox, Peter T

2009-06-01

The authors examined the involvement of 2 speech motor programming processes identified by S. T. Klapp (1995, 2003) during the articulation of utterances differing in syllable and sequence complexity. According to S. T. Klapp, 1 process, INT, resolves the demands of the programmed unit, whereas a second process, SEQ, oversees the serial order demands of longer sequences. A modified reaction time paradigm was used to assess INT and SEQ demands. Specifically, syllable complexity was dependent on syllable structure, whereas sequence complexity involved either repeated or unique syllabi within an utterance. INT execution was slowed when articulating single syllables in the form CCCV compared to simpler CV syllables. Planning unique syllables within a multisyllabic utterance rather than repetitions of the same syllable slowed INT but not SEQ. The INT speech motor programming process, important for mental syllabary access, is sensitive to changes in both syllable structure and the number of unique syllables in an utterance.

Evidence from in vivo manipulations of lipid composition in mutants that the delta 3-trans-hexadecenoic acid-containing phosphatidylglycerol is involved in the biogenesis of the light-harvesting chlorophyll a/b-protein complex of Chlamydomonas reinhardtii.

PubMed

Dubertret, G; Mirshahi, A; Mirshahi, M; Gerard-Hirne, C; Tremolieres, A

1994-12-01

The phosphatidylglycerol containing the unusual delta 3-trans hexadecenoic fatty acid is specifically found in photosynthetic membranes of eukaryotic organisms. Its involvement in the biogenesis and the structure of the light-harvesting chlorophyll a/b-protein complex has been evidenced by in vivo targeting this lipid to photosynthetic membranes of Chlamydomonas reinhardtii mutants lacking this lipid. In the mf1 and mf2 mutants, this deficiency results in (a) the absence of the oligomeric light-harvesting complex of photosystem 2; (b) an extensive destacking of thylakoid membranes; (c) a very low 77-K fluorescence emission in the photosystem-2 region. We show in this paper that these deficiencies result from modifications in the pigment and polypeptide compositions of the photosystem-2 light-harvesting complex; it contains less chlorophyll b and some of its constitutive polypeptides are absent or reduced in amount, while immunologically related polypeptides of lower molecular mass accumulate. The direct involvement of the lack of trans-C16: 1-phosphatidylglycerol in these deficiencies is evidenced by the partial restoration of normal characteristics of the light-harvesting complex (pigment and polypeptide composition, oligomerization) after liposome-mediated, in vivo incorporation of this lipid into the photosynthetic membranes of the mf2 mutant. Trans-C16:1-phosphatidylglycerol, therefore, is involved in the biogenesis of the photosystem-2 light-harvesting chlorophyll a/b-protein complex through a mechanism that may prevent degradation processes. Its contribution to the structural conformation of neosynthesized monomers and to their organization into stable oligomeric form is discussed.

Structure and dynamics of thylakoids in land plants.

PubMed

Pribil, Mathias; Labs, Mathias; Leister, Dario

2014-05-01

Thylakoids of land plants have a bipartite structure, consisting of cylindrical grana stacks, made of membranous discs piled one on top of the other, and stroma lamellae which are helically wound around the cylinders. Protein complexes predominantly located in the stroma lamellae and grana end membranes are either bulky [photosystem I (PSI) and the chloroplast ATP synthase (cpATPase)] or are involved in cyclic electron flow [the NAD(P)H dehydrogenase (NDH) and PGRL1-PGR5 heterodimers], whereas photosystem II (PSII) and its light-harvesting complex (LHCII) are found in the appressed membranes of the granum. Stacking of grana is thought to be due to adhesion between Lhcb proteins (LHCII or CP26) located in opposed thylakoid membranes. The grana margins contain oligomers of CURT1 proteins, which appear to control the size and number of grana discs in a dosage- and phosphorylation-dependent manner. Depending on light conditions, thylakoid membranes undergo dynamic structural changes that involve alterations in granum diameter and height, vertical unstacking of grana, and swelling of the thylakoid lumen. This plasticity is realized predominantly by reorganization of the supramolecular structure of protein complexes within grana stacks and by changes in multiprotein complex composition between appressed and non-appressed membrane domains. Reversible phosphorylation of LHC proteins (LHCPs) and PSII components appears to initiate most of the underlying regulatory mechanisms. An update on the roles of lipids, proteins, and protein complexes, as well as possible trafficking mechanisms, during thylakoid biogenesis and the de-etiolation process complements this review.

Synthesis, structure, biochemical, and docking studies of a new dinitrosyl iron complex [Fe2(μ-SC4H3SCH2)2(NO)4

NASA Astrophysics Data System (ADS)

Davidovich, P. B.; Fischer, A. I.; Korchagin, D. V.; Panchuk, V. V.; Shchukarev, A. V.; Garabadzhiu, A. V.; Belyaev, A. N.

2015-07-01

A new dinitrosyl iron complex of binuclear structure [Fe2(μ-S-2-methylthiophene)2(NO)4] was first synthesized and structurally characterized by XRD and theoretical methods. Using caspase-3 as an example it was shown that [Fe2(μ-S-2-methylthiophene)2(NO)4] and its analog [Fe2(μ-S-2-methylfurane)2(NO)4] can inhibit the action of active site cysteine proteins; the difference in inhibitory activity was explained by molecular docking studies. Biochemical and in silico studies give grounds that the biological activity of dinitrosyl iron complexes is a μ-SR bridging ligand structure function. Thus the rational design strategy of [Fe2(μ-SR)2(NO)4] complexes can be applied to make NO prodrugs with high affinity to therapeutically significant targets involved in cancer and inflammation.

Structural and Functional Analyses of the Proteins Involved in the Iron-Sulfur Cluster Biosynthesis

NASA Astrophysics Data System (ADS)

Wada, Kei

The iron-sulfur (Fe-S) clusters are ubiquitous prosthetic groups that are required to maintain such fundamental life processes as respiratory chain, photosynthesis and the regulation of gene expression. Assembly of intracellular Fe-S cluster requires the sophisticated biosynthetic systems called ISC and SUF machineries. To shed light on the molecular mechanism of Fe-S cluster assembly mediated by SUF machinery, several structures of the SUF components and their sub-complex were determined. The structural findings together with biochemical characterization of the core-complex (SufB-SufC-SufD complex) have led me to propose a working model for the cluster biosynthesis in the SUF machinery.

Exosites in the substrate specificity of blood coagulation reactions.

PubMed

Bock, P E; Panizzi, P; Verhamme, I M A

2007-07-01

The specificity of blood coagulation proteinases for substrate, inhibitor, and effector recognition is mediated by exosites on the surfaces of the catalytic domains, physically separated from the catalytic site. Some thrombin ligands bind specifically to either exosite I or II, while others engage both exosites. The involvement of different, overlapping constellations of exosite residues enables binding of structurally diverse ligands. The flexibility of the thrombin structure is central to the mechanism of complex formation and the specificity of exosite interactions. Encounter complex formation is driven by electrostatic ligand-exosite interactions, followed by conformational rearrangement to a stable complex. Exosites on some zymogens are in low affinity proexosite states and are expressed concomitant with catalytic site activation. The requirement for exosite expression controls the specificity of assembly of catalytic complexes on the coagulation pathway, such as the membrane-bound factor Xa*factor Va (prothrombinase) complex, and prevents premature assembly. Substrate recognition by prothrombinase involves a two-step mechanism with initial docking of prothrombin to exosites, followed by a conformational change to engage the FXa catalytic site. Prothrombin and its activation intermediates bind prothrombinase in two alternative conformations determined by the zymogen to proteinase transition that are hypothesized to involve prothrombin (pro)exosite I interactions with FVa, which underpin the sequential activation pathway. The role of exosites as the major source of substrate specificity has stimulated development of exosite-targeted anticoagulants for treatment of thrombosis.

Force-Manipulation Single-Molecule Spectroscopy Studies of Enzymatic Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter; He, Yufan; Lu, Maolin; Cao, Jin; Guo, Qing

2014-03-01

Subtle conformational changes play a crucial role in protein functions, especially in enzymatic reactions involving complex substrate-enzyme interactions and chemical reactions. We applied AFM-enhanced and magnetic tweezers-correlated single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing. Our results support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.

The Development of Logical Structures for E-Learning Evaluation

ERIC Educational Resources Information Center

Tudevdagva, Uranchimeg; Hardt, Wolfram; Dolgor, Jargalmaa

2013-01-01

This paper deals with development of logical structures for e-learning evaluation. Evaluation is a complex task into which many different groups of people are involved. As a rule these groups have different understanding and varying expectations on e-learning evaluation. Using logical structures for e-learning evaluation we can join the different…

Crystal structure of Clostridium botulinum whole hemagglutinin reveals a huge triskelion-shaped molecular complex.

PubMed

Amatsu, Sho; Sugawara, Yo; Matsumura, Takuhiro; Kitadokoro, Kengo; Fujinaga, Yukako

2013-12-06

Clostridium botulinum HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. At least two properties of HA contribute to these roles: the sugar-binding activity and the barrier-disrupting activity that depends on E-cadherin binding of HA. HA consists of three different proteins, HA1, HA2, and HA3, whose structures have been partially solved and are made up mainly of β-strands. Here, we demonstrate structural and functional reconstitution of whole HA and present the complete structure of HA of serotype B determined by x-ray crystallography at 3.5 Å resolution. This structure reveals whole HA to be a huge triskelion-shaped molecule. Our results suggest that whole HA is functionally and structurally separable into two parts: HA1, involved in recognition of cell-surface carbohydrates, and HA2-HA3, involved in paracellular barrier disruption by E-cadherin binding.

Spectroscopic characterization of charge-transfer complexes of morpholine with chloranilic and picric acids in organic media: crystal structure of bis(morpholinium 2,4,6-trinitrocyclohexanolate).

PubMed

Refat, Moamen S; El-Zayat, Lamia A; Yeşilel, Okan Zafer

2010-02-01

Electron donor-acceptor interaction of morpholine (morp) with chloranilic acid (cla) and picric acid (pa) as pi-acceptors was investigated spectrophotometrically and found to form stable charge-transfer (CT) complexes (n-pi*) of [(Hmorp)(2)(cla)] and [(Hmorp)(pa)](2). The donor site involved in CT interaction is morpholine nitrogen. These complexes are easily synthesized from the reaction of morp with cla and pa within MeOH and CHCl(3) solvents, respectively. (1)HNMR, IR, elemental analyses, and UV-vis techniques characterize the two morpholinium charge-transfer complexes. Benesi-Hildebrand and its modification methods were applied to the determination of association constant (K), molar extinction coefficient (epsilon). The X-ray crystal structure was carried out for the interpretation the predict structure of the [(Hmorp)(pa)](2) complex. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Spectroscopic characterization of charge-transfer complexes of morpholine with chloranilic and picric acids in organic media: Crystal structure of bis(morpholinium 2,4,6-trinitrocyclohexanolate)

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; El-Zayat, Lamia A.; Yeşilel, Okan Zafer

2010-02-01

Electron donor-acceptor interaction of morpholine (morp) with chloranilic acid (cla) and picric acid (pa) as π-acceptors was investigated spectrophotometrically and found to form stable charge-transfer (CT) complexes (n-π*) of [(Hmorp) 2(cla)] and [(Hmorp)(pa)] 2. The donor site involved in CT interaction is morpholine nitrogen. These complexes are easily synthesized from the reaction of morp with cla and pa within MeOH and CHCl 3 solvents, respectively. 1HNMR, IR, elemental analyses, and UV-vis techniques characterize the two morpholinium charge-transfer complexes. Benesi-Hildebrand and its modification methods were applied to the determination of association constant ( K), molar extinction coefficient ( ɛ). The X-ray crystal structure was carried out for the interpretation the predict structure of the [(Hmorp)(pa)] 2 complex.

Building a Culture of Collaboration in Schools

ERIC Educational Resources Information Center

Sutton, Paul S.; Shouse, Andrew W.

2016-01-01

Teaching is complex; teachers and school leaders crave more meaningful collaborative experiences to make sense of that complexity. However, the structural, cultural, and historical factors involved with schooling impede the extent to which teachers can collaborate. Teachers spend five to six periods of the day teaching classes, largely working in…

Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase

PubMed Central

Mittag, Tanja; Marsh, Joseph; Grishaev, Alexander; Orlicky, Stephen; Lin, Hong; Sicheri, Frank; Tyers, Mike; Forman-Kay, Julie D.

2010-01-01

Summary Intrinsically disordered proteins can form highly dynamic complexes with partner proteins. One such dynamic complex involves the intrinsically disordered Sic1 with its partner Cdc4 in regulation of yeast cell cycle progression. Phosphorylation of six N-terminal Sic1 sites leads to equilibrium engagement of each phosphorylation site with the primary binding pocket in Cdc4, the substrate recognition subunit of a ubiquitin ligase. ENSEMBLE calculations utilizing experimental NMR and small-angle x-ray scattering data reveal significant transient structure in both phosphorylation states of the isolated ensembles (Sic1 and pSic1) that modulates their electrostatic potential, suggesting a structural basis for the proposed strong contribution of electrostatics to binding. A structural model of the dynamic pSic1-Cdc4 complex demonstrates the spatial arrangements in the ubiquitin ligase complex. These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. PMID:20399186

Structural Basis for the Interaction of the Golgi-Associated Retrograde Protein (GARP) Complex with the t-SNARE Syntaxin 6

PubMed Central

Abascal-Palacios, Guillermo; Schindler, Christina; Rojas, Adriana L; Bonifacino, Juan S.; Hierro, Aitor

2016-01-01

Summary The Golgi-Associated Retrograde Protein (GARP) is a tethering complex involved in the fusion of endosome-derived transport vesicles to the trans-Golgi network through interaction with components of the Syntaxin 6/Syntaxin 16/Vti1a/VAMP4 SNARE complex. The mechanisms by which GARP and other tethering factors engage the SNARE fusion machinery are poorly understood. Herein we report the structural basis for the interaction of the human Ang2 subunit of GARP with Syntaxin 6 and the closely related Syntaxin 10. The crystal structure of Syntaxin 6 Habc domain in complex with a peptide from the N terminus of Ang2 shows a novel binding mode in which a di-tyrosine motif of Ang2 interacts with a highly conserved groove in Syntaxin 6. Structure-based mutational analyses validate the crystal structure and support the phylogenetic conservation of this interaction. The same binding determinants are found in other tethering proteins and syntaxins, suggesting a general interaction mechanism. PMID:23932592

Regimes of Flow over Complex Structures of Endothelial Glycocalyx: A Molecular Dynamics Simulation Study.

PubMed

Jiang, Xi Zhuo; Feng, Muye; Ventikos, Yiannis; Luo, Kai H

2018-04-10

Flow patterns on surfaces grafted with complex structures play a pivotal role in many engineering and biomedical applications. In this research, large-scale molecular dynamics (MD) simulations are conducted to study the flow over complex surface structures of an endothelial glycocalyx layer. A detailed structure of glycocalyx has been adopted and the flow/glycocalyx system comprises about 5,800,000 atoms. Four cases involving varying external forces and modified glycocalyx configurations are constructed to reveal intricate fluid behaviour. Flow profiles including temporal evolutions and spatial distributions of velocity are illustrated. Moreover, streamline length and vorticity distributions under the four scenarios are compared and discussed to elucidate the effects of external forces and glycocalyx configurations on flow patterns. Results show that sugar chain configurations affect streamline length distributions but their impact on vorticity distributions is statistically insignificant, whilst the influence of the external forces on both streamline length and vorticity distributions are trivial. Finally, a regime diagram for flow over complex surface structures is proposed to categorise flow patterns.

Solution structure of the core SMN–Gemin2 complex

PubMed Central

Sarachan, Kathryn L.; Valentine, Kathleen G.; Gupta, Kushol; Moorman, Veronica R.; Gledhill, John M.; Bernens, Matthew; Tommos, Cecilia; Wand, A. Joshua; Van Duyne, Gregory D.

2012-01-01

In humans, assembly of spliceosomal snRNPs (small nuclear ribonucleoproteins) begins in the cytoplasm where the multi-protein SMN (survival of motor neuron) complex mediates the formation of a seven-membered ring of Sm proteins on to a conserved site of the snRNA (small nuclear RNA). The SMN complex contains the SMN protein Gemin2 and several additional Gemins that participate in snRNP biosynthesis. SMN was first identified as the product of a gene found to be deleted or mutated in patients with the neurodegenerative disease SMA (spinal muscular atrophy), the leading genetic cause of infant mortality. In the present study, we report the solution structure of Gemin2 bound to the Gemin2-binding domain of SMN determined by NMR spectroscopy. This complex reveals the structure of Gemin2, how Gemin2 binds to SMN and the roles of conserved SMN residues near the binding interface. Surprisingly, several conserved SMN residues, including the sites of two SMA patient mutations, are not required for binding to Gemin2. Instead, they form a conserved SMN/Gemin2 surface that may be functionally important for snRNP assembly. The SMN–Gemin2 structure explains how Gemin2 is stabilized by SMN and establishes a framework for structure–function studies to investigate snRNP biogenesis as well as biological processes involving Gemin2 that do not involve snRNP assembly. PMID:22607171

Bcs1p can rescue a large and productive cytochrome bc(1) complex assembly intermediate in the inner membrane of yeast mitochondria.

PubMed

Conte, Laura; Trumpower, Bernard L; Zara, Vincenzo

2011-01-01

The yeast cytochrome bc(1) complex, a component of the mitochondrial respiratory chain, is composed of ten distinct protein subunits. In the assembly of the bc(1) complex, some ancillary proteins, such as the chaperone Bcs1p, are actively involved. The deletion of the nuclear gene encoding this chaperone caused the arrest of the bc(1) assembly and the formation of a functionally inactive bc(1) core structure of about 500-kDa. This immature bc(1) core structure could represent, on the one hand, a true assembly intermediate or, on the other hand, a degradation product and/or an incorrect product of assembly. The experiments here reported show that the gradual expression of Bcs1p in the yeast strain lacking this protein was progressively able to rescue the bc(1) core structure leading to the formation of the functional homodimeric bc(1) complex. Following Bcs1p expression, the mature bc(1) complex was also progressively converted into two supercomplexes with the cytochrome c oxidase complex. The capability of restoring the bc(1) complex and the supercomplexes was also possessed by the mutated yeast R81C Bcsp1. Notably, in the human ortholog BCS1L, the corresponding point mutation (R45C) was instead the cause of a severe bc(1) complex deficiency. Differently from the yeast R81C Bcs1p, two other mutated Bcs1p's (K192P and F401I) were unable to recover the bc(1) core structure in yeast. This study identifies for the first time a productive assembly intermediate of the yeast bc(1) complex and gives new insights into the molecular mechanisms involved in the last steps of bc(1) assembly. Copyright © 2010 Elsevier B.V. All rights reserved.

Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO).

PubMed

Alborghetti, Marcos Rodrigo; Furlan, Ariane da Silva; da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

2013-01-01

Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.

Structural Analysis of Intermolecular Interactions in the Kinesin Adaptor Complex Fasciculation and Elongation Protein Zeta 1/ Short Coiled-Coil Protein (FEZ1/SCOCO)

PubMed Central

da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L.; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

2013-01-01

Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth. PMID:24116125

Application of linker technique to trap transiently interacting protein complexes for structural studies

PubMed Central

Reddy Chichili, Vishnu Priyanka; Kumar, Veerendra; Sivaraman, J.

2016-01-01

Protein-protein interactions are key events controlling several biological processes. We have developed and employed a method to trap transiently interacting protein complexes for structural studies using glycine-rich linkers to fuse interacting partners, one of which is unstructured. Initial steps involve isothermal titration calorimetry to identify the minimum binding region of the unstructured protein in its interaction with its stable binding partner. This is followed by computational analysis to identify the approximate site of the interaction and to design an appropriate linker length. Subsequently, fused constructs are generated and characterized using size exclusion chromatography and dynamic light scattering experiments. The structure of the chimeric protein is then solved by crystallization, and validated both in vitro and in vivo by substituting key interacting residues of the full length, unlinked proteins with alanine. This protocol offers the opportunity to study crucial and currently unattainable transient protein interactions involved in various biological processes. PMID:26985443

The Eighteen-Electron Rule

ERIC Educational Resources Information Center

Mitchell, P. R.; Parish, R. V.

1969-01-01

Discusses the stability of the structures of transition metal complexes (primarily carbonyls and organometallic compounds) having 18 electrons or less in their valence shell. Presents molecular orbital diagrams for various structures involving alpha and pi bonding and describes the conditions under which the 18 electron rule applies. (RR)

Portrait of an Enzyme, a Complete Structural Analysis of a Multimodular beta-N-Acetylglucosaminidase from Clostridium perfringens

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

Ficko-Blean, E.; Gregg, K; Adams, J

2009-01-01

Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging. Clostridium perfringens is a prevalent human pathogen that harbors a wide array of large, extracellular carbohydrate-active enzymes and is an excellent and relevant model system to approach this problem. Here we describe the complete structure of C. perfringens GH84C (NagJ), a 1001-amino acid multimodular homolog of the C. perfringens ?-toxin, which was determined using a combination of smallmore » angle x-ray scattering and x-ray crystallography. The resulting structure reveals unprecedented insight into how catalysis, carbohydrate-specific adherence, and the formation of molecular complexes with other enzymes via an ultra-tight protein-protein interaction are spatially coordinated in an enzyme involved in a host-pathogen interaction.« less

Structural insights into the p97-Ufd1-Npl4 complex

PubMed Central

Pye, Valerie E.; Beuron, Fabienne; Keetch, Catherine A.; McKeown, Ciaran; Robinson, Carol V.; Meyer, Hemmo H.; Zhang, Xiaodong; Freemont, Paul S.

2007-01-01

p97/VCP (Cdc48 in yeast) is an essential and abundant member of the AAA+ family of ATPases and is involved in a number of diverse cellular pathways through interactions with different adaptor proteins. The two most characterized adaptors for p97 are p47 and the Ufd1 (ubiquitin fusion degradation 1)-Npl4 (nuclear protein localization 4) complex. p47 directs p97 to membrane fusion events and has been shown to be involved in protein degradation. The Ufd1-Npl4 complex directs p97 to an essential role in endoplasmic reticulum-associated degradation and an important role in mitotic spindle disassembly postmitosis. Here we describe the structural features of the Ufd1-Npl4 complex and its interaction with p97 with the aid of EM and other biophysical techniques. The Ufd1-Npl4 heterodimer has an elongated bilobed structure that is ≈80 × 30 Å in dimension. One Ufd1-Npl4 heterodimer is shown to interact with one p97 hexamer to form the p97-Ufd1-Npl4 complex. The Ufd1-Npl4 heterodimer emanates from one region on the periphery of the N-D1 plane of the p97 hexamer. Intriguingly, the p97-p47 and the p97-Ufd1-Npl4 complexes are significantly different in stoichiometry, symmetry, and quaternary arrangement, reflecting their specific actions and their ability to interact with additional cofactors that cooperate with p97 in diverse cellular pathways. PMID:17202270

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens.

PubMed

Pan, Joshua; Meyers, Robin M; Michel, Brittany C; Mashtalir, Nazar; Sizemore, Ann E; Wells, Jonathan N; Cassel, Seth H; Vazquez, Francisca; Weir, Barbara A; Hahn, William C; Marsh, Joseph A; Tsherniak, Aviad; Kadoch, Cigall

2018-05-23

Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex. Finally, by integrating functional networks with large protein-protein interaction networks, we discovered novel protein complexes involving recently evolved genes of unknown function. Taken together, these findings demonstrate the utility of genetic perturbation screens alone, and in combination with large-scale biophysical data, to enhance our understanding of mammalian protein complexes in normal and disease states. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Spectroscopic and structural studies of the first complex formed between salinomycin and organic amine

NASA Astrophysics Data System (ADS)

Antoszczak, Michał; Janczak, Jan; Brzezinski, Bogumił; Huczyński, Adam

2017-02-01

For the first time, the crystalline complex of salinomycin with benzylamine was obtained and its molecular structure was studied using single crystal X-ray diffraction, FT-IR, 1H NMR, 13C NMR, 2D NMR and ESI MS methods. These studies provided evidence that the proton from the carboxylic group of salinomycin (SAL) is transferred to the amine group of benzylamine (BnA) forming the host-guest complex (SAL-BnA). It was shown that the SAL-BnA complex both in solid state and in chloroform solution is stabilized by the intramolecular O-H⋯O hydrogen bonds and also by the intermolecular hydrogen bonding interactions of the carboxylate, ketone and/or hydroxyl groups of SAL with water molecules present in the investigated system. The solvated acetonitrile molecules are additionally located in the voids between the SAL-BnA complex molecules in the crystal structure, while water molecules involved in the dihydrated crystalline SAL-BnA complex partially move into the solvent upon dissolution in chloroform.

Structural and functional analysis of the human POT1-TPP1 telomeric complex

DOE PAGES

Rice, Cory; Shastrula, Prashanth Krishna; Kossenkov, Andrew V.; ...

2017-04-10

POT1 and TPP1 are part of the shelterin complex and are essential for telomere length regulation and maintenance. Naturally occurring mutations of the telomeric POT1–TPP1 complex are implicated in familial glioma, melanoma and chronic lymphocytic leukaemia. Here we report the atomic structure of the interacting portion of the human telomeric POT1–TPP1 complex and suggest how several of these mutations contribute to malignant cancer. The POT1 C-terminus (POT1C) forms a bilobal structure consisting of an OB-fold and a holiday junction resolvase domain. TPP1 consists of several loops and helices involved in extensive interactions with POT1C. Biochemical data shows that several ofmore » the cancer-associated mutations, partially disrupt the POT1–TPP1 complex, which affects its ability to bind telomeric DNA efficiently. A defective POT1–TPP1 complex leads to longer and fragile telomeres, which in turn promotes genomic instability and cancer.« less

Structural and functional analysis of the human POT1-TPP1 telomeric complex

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

Rice, Cory; Shastrula, Prashanth Krishna; Kossenkov, Andrew V.

POT1 and TPP1 are part of the shelterin complex and are essential for telomere length regulation and maintenance. Naturally occurring mutations of the telomeric POT1–TPP1 complex are implicated in familial glioma, melanoma and chronic lymphocytic leukaemia. Here we report the atomic structure of the interacting portion of the human telomeric POT1–TPP1 complex and suggest how several of these mutations contribute to malignant cancer. The POT1 C-terminus (POT1C) forms a bilobal structure consisting of an OB-fold and a holiday junction resolvase domain. TPP1 consists of several loops and helices involved in extensive interactions with POT1C. Biochemical data shows that several ofmore » the cancer-associated mutations, partially disrupt the POT1–TPP1 complex, which affects its ability to bind telomeric DNA efficiently. A defective POT1–TPP1 complex leads to longer and fragile telomeres, which in turn promotes genomic instability and cancer.« less

Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.

PubMed

Peng, Yingjie; Zhong, Chen; Huang, Wei; Ding, Jianping

2008-09-01

Isocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into alpha-ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca(2+), which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP-IDHs reveal that eukaryotic NADP-IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118-124 and residues 284-287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi-closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca(2+) in the pseudo-Michaelis complex or with NADPH, AKG, and Ca(2+) in the product state. The conformational changes of eukaryotic NADP-IDHs are quite different from those of Escherichia coli NADP-IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP-IDHs is more complex than that of EcIDH, and involves more fine-tuned conformational changes.

Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction

PubMed Central

Peng, Yingjie; Zhong, Chen; Huang, Wei; Ding, Jianping

2008-01-01

Isocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into α-ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca2+, which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP-IDHs reveal that eukaryotic NADP-IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118–124 and residues 284–287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi-closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca2+ in the pseudo-Michaelis complex or with NADPH, AKG, and Ca2+ in the product state. The conformational changes of eukaryotic NADP-IDHs are quite different from those of Escherichia coli NADP-IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP-IDHs is more complex than that of EcIDH, and involves more fine-tuned conformational changes. PMID:18552125

Complex structure of a bacterial class 2 histone deacetylase homologue with a trifluoromethylketone inhibitor

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

Nielsen, Tine Kragh; Hildmann, Christian; Riester, Daniel

2007-04-01

The crystal structure of HDAH FB188 in complex with a trifluoromethylketone at 2.2 Å resolution is reported and compared to a previously determined inhibitor complex. Histone deacetylases (HDACs) have emerged as attractive targets in anticancer drug development. To date, a number of HDAC inhibitors have been developed and most of them are hydroxamic acid derivatives, typified by suberoylanilide hydroxamic acid (SAHA). Not surprisingly, structural information that can greatly enhance the design of novel HDAC inhibitors is so far only available for hydroxamic acids in complex with HDAC or HDAC-like enzymes. Here, the first structure of an enzyme complex with amore » nonhydroxamate HDAC inhibitor is presented. The structure of the trifluoromethyl ketone inhibitor 9,9,9-trifluoro-8-oxo-N-phenylnonanamide in complex with bacterial FB188 HDAH (histone deacetylase-like amidohydrolase from Bordetella/Alcaligenes strain FB188) has been determined. HDAH reveals high sequential and functional homology to human class 2 HDACs and a high structural homology to human class 1 HDACs. Comparison with the structure of HDAH in complex with SAHA reveals that the two inhibitors superimpose well. However, significant differences in binding to the active site of HDAH were observed. In the presented structure the O atom of the trifluoromethyl ketone moiety is within binding distance of the Zn atom of the enzyme and the F atoms participate in interactions with the enzyme, thereby involving more amino acids in enzyme–inhibitor binding.« less

Structural Reorganization and the Cooperative Binding of Single-stranded Telomere DNA in Sterkiella nova*

PubMed Central

Buczek, Pawel; Horvath, Martin P.

2009-01-01

In Sterkiella nova, α and β telomere proteins bind cooperatively with single-stranded DNA to form a ternary α·β·DNA complex. Association of telomere protein subunits is DNA-dependent, and α-β association enhances DNA affinity. To further understand the molecular basis for binding cooperativity, we characterized several possible stepwise assembly pathways using isothermal titration calorimetry. In one path, α and DNA first form a stable α·DNA complex followed by addition of β in a second step. Binding energy accumulates with nearly equal free energy of association for each of these steps. Heat capacity is nonetheless dramatically different with ΔCp = −305 ± 3 cal mol−1 K−1 for α binding with DNA and ΔCp = −2010 ± 20 cal mol−1 K−1 for addition of β to complete the α·β·DNA complex. By examining alternate routes including titration of single-stranded DNA with a preformed α·β complex, a significant portion of binding energy and heat capacity could be assigned to structural reorganization involving protein-protein interactions and repositioning of the DNA. Structural reorganization probably affords a mechanism to regulate high affinity binding of telomere single-stranded DNA with important implications for telomere biology. Regulation of telomere complex dissociation is thought to involve post-translational modifications in the lysine-rich C-terminal portion of β. We observed no difference in binding energetics or crystal structure when comparing complexes prepared with full-length β or a C-terminally truncated form, supporting interesting parallels between the intrinsically disordered regions of histones and this portion of β. PMID:17082188

Mi2, an auto-antigen for dermatomyositis, is an ATP-dependent nucleosome remodeling factor.

PubMed

Wang, H B; Zhang, Y

2001-06-15

Dynamic changes in chromatin structure play an important role in transcription regulation. Recent studies have revealed two mechanisms that alter chromatin structure. One involves ATP-dependent chromatin remodeling, and the other involves acetylation of the core histone tails. We have previously purified and characterized a multi-subunit protein complex, NuRD, which possesses both nucleosome remodeling and histone deacetylase activities. Despite extensive biochemical characterization of the complex, little is known about the functions of its individual components. In this study, we focused on Mi2, a component of the NuRD complex. We found that, similar to the native NuRD complex, recombinant Mi2 is a DNA-dependent, nucleosome-stimulated ATPase. Kinetic analysis of the ATP hydrolysis reaction indicated that the differential stimulation of the Mi2 ATPase by DNA and nucleosomes were primarily due to their differential effects on the turnover number of the reaction. Furthermore, we demonstrated that recombinant Mi2 is an efficient nucleosome remodeling factor when compared to that of the native NuRD complex. Our results define the biochemical function of Mi2 and set the stage for understanding the mechanism of nucleosome remodeling in a defined reconstituted system.

Mi2, an auto-antigen for dermatomyositis, is an ATP-dependent nucleosome remodeling factor

PubMed Central

Wang, Heng-Bin; Zhang, Yi

2001-01-01

Dynamic changes in chromatin structure play an important role in transcription regulation. Recent studies have revealed two mechanisms that alter chromatin structure. One involves ATP-dependent chromatin remodeling, and the other involves acetylation of the core histone tails. We have previously purified and characterized a multi-subunit protein complex, NuRD, which possesses both nucleosome remodeling and histone deacetylase activities. Despite extensive biochemical characterization of the complex, little is known about the functions of its individual components. In this study, we focused on Mi2, a component of the NuRD complex. We found that, similar to the native NuRD complex, recombinant Mi2 is a DNA-dependent, nucleosome-stimulated ATPase. Kinetic analysis of the ATP hydrolysis reaction indicated that the differential stimulation of the Mi2 ATPase by DNA and nucleosomes were primarily due to their differential effects on the turnover number of the reaction. Furthermore, we demonstrated that recombinant Mi2 is an efficient nucleosome remodeling factor when compared to that of the native NuRD complex. Our results define the biochemical function of Mi2 and set the stage for understanding the mechanism of nucleosome remodeling in a defined reconstituted system. PMID:11410659

Structural design/margin assessment

NASA Technical Reports Server (NTRS)

Ryan, R. S.

1993-01-01

Determining structural design inputs and the structural margins following design completion is one of the major activities in space exploration. The end result is a statement of these margins as stability, safety factors on ultimate and yield stresses, fracture limits (fracture control), fatigue lifetime, reuse criteria, operational criteria and procedures, stability factors, deflections, clearance, handling criteria, etc. The process is normally called a load cycle and is time consuming, very complex, and involves much more than structures. The key to successful structural design is the proper implementation of the process. It depends on many factors: leadership and management of the process, adequate analysis and testing tools, data basing, communications, people skills, and training. This process and the various factors involved are discussed.

Using DCOM to support interoperability in forest ecosystem management decision support systems

Treesearch

W.D. Potter; S. Liu; X. Deng; H.M. Rauscher

2000-01-01

Forest ecosystems exhibit complex dynamics over time and space. Management of forest ecosystems involves the need to forecast future states of complex systems that are often undergoing structural changes. This in turn requires integration of quantitative science and engineering components with sociopolitical, regulatory, and economic considerations. The amount of data...

Using Simple Manipulatives to Improve Student Comprehension of a Complex Biological Process: Protein Synthesis

ERIC Educational Resources Information Center

Guzman, Karen; Bartlett, John

2012-01-01

Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article…

The evaluative imaging of mental models - Visual representations of complexity

NASA Technical Reports Server (NTRS)

Dede, Christopher

1989-01-01

The paper deals with some design issues involved in building a system that could visually represent the semantic structures of training materials and their underlying mental models. In particular, hypermedia-based semantic networks that instantiate classification problem solving strategies are thought to be a useful formalism for such representations; the complexity of these web structures can be best managed through visual depictions. It is also noted that a useful approach to implement in these hypermedia models would be some metrics of conceptual distance.

Mononuclear Cu/O2 Complexes

PubMed Central

Cramer, Christopher J.; Tolman, William B.

2008-01-01

Using interwoven experimental and theoretical methods, detailed studies of several structurally defined 1:1 Cu/O2 complexes have provided important fundamental chemical information useful for understanding the nature of intermediates involved in aerobic oxidations in synthetic and enzymatic copper-mediated catalysis. In particular, these studies have shed new light onto the factors that influence the mode of O2 coordination (end-on vs. side-on) and the electronic structure, which can vary between Cu(II)-superoxo and Cu(III)-peroxo extremes. PMID:17458929

Antiplasmodial activities of gold(I) complexes involving functionalized N-heterocyclic carbenes.

PubMed

Hemmert, Catherine; Ramadani, Arba Pramundita; Boselli, Luca; Fernández Álvarez, Álvaro; Paloque, Lucie; Augereau, Jean-Michel; Gornitzka, Heinz; Benoit-Vical, Françoise

2016-07-01

A series of twenty five molecules, including imidazolium salts functionalized by N-, O- or S-containing groups and their corresponding cationic, neutral or anionic gold(I) complexes were evaluated on Plasmodium falciparum in vitro and then on Vero cells to determine their selectivity. Among them, eight new compounds were synthesized and fully characterized by spectroscopic methods. The X-ray structures of three gold(I) complexes are presented. Except one complex (18), all the cationic gold(I) complexes show potent antiplasmodial activity with IC50 in the micro- and submicromolar range, correlated with their lipophilicity. Structure-activity relationships enable to evidence a lead-complex (21) displaying a good activity (IC50=210nM) close to the value obtained with chloroquine (IC50=514nM) and a weak cytotoxicity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Learning from Transitioning to New Technology That Supports Online and Blended Learning: A Case Study

ERIC Educational Resources Information Center

Lock, Jennifer; Johnson, Carol

2017-01-01

Transitioning from one technology to another within educational institutions is complex and multi-faceted, and requires time. Such a transition involves more than making the new technology available for use. It requires knowing the people involved, designing differentiated support structures, and integrating various resources to meet their…

Effects of surfactants on lipase structure, activity, and inhibition.

PubMed

Delorme, Vincent; Dhouib, Rabeb; Canaan, Stéphane; Fotiadu, Frédéric; Carrière, Frédéric; Cavalier, Jean-François

2011-08-01

Lipase inhibitors are the main anti-obesity drugs prescribed these days, but the complexity of their mechanism of action is making it difficult to develop new molecules for this purpose. The efficacy of these drugs is known to depend closely on the physico-chemistry of the lipid-water interfaces involved and on the unconventional behavior of the lipases which are their target enzymes. The lipolysis reaction which occurs at an oil-water interface involves complex equilibria between adsorption-desorption processes, conformational changes and catalytic mechanisms. In this context, surfactants can induce significant changes in the partitioning of the enzyme and the inhibitor between the water phase and lipid-water interfaces. Surfactants can be found at the oil-water interface where they compete with lipases for adsorption, but also in solution in the form of micellar aggregates and monomers that may interact with hydrophobic parts of lipases in solution. These various interactions, combined with the emulsification and dispersion of insoluble substrates and inhibitors, can either promote or decrease the activity and the inhibition of lipases. Here, we review some examples of the various effects of surfactants on lipase structure, activity and inhibition, which show how complex the various equilibria involved in the lipolysis reaction tend to be.

Biomechanics of metastatic disease in the vertebral column.

PubMed

Whyne, Cari M

2014-06-01

Metastatic disease in the vertebral column compromises the structural stability of the spine leading to increased risk of fracture. The complex patterns of osteolytic and osteoblastic disease within the bony spine have motivated a multimodal approach to better characterize the biomechanics of tumor-involved bone. This review presents our current understanding of the biomechanical behavior of metastatically involved vertebrae, and experimental and computational image-based approaches that have been employed to quantify structural integrity in preclinical models with translation to clinical data sets.

Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.

PubMed

Lin, C H; Patel, D J

1997-11-01

Structural studies by nuclear magnetic resonance (NMR) of RNA and DNA aptamer complexes identified through in vitro selection and amplification have provided a wealth of information on RNA and DNA tertiary structure and molecular recognition in solution. The RNA and DNA aptamers that target ATP (and AMP) with micromolar affinity exhibit distinct binding site sequences and secondary structures. We report below on the tertiary structure of the AMP-DNA aptamer complex in solution and compare it with the previously reported tertiary structure of the AMP-RNA aptamer complex in solution. The solution structure of the AMP-DNA aptamer complex shows, surprisingly, that two AMP molecules are intercalated at adjacent sites within a rectangular widened minor groove. Complex formation involves adaptive binding where the asymmetric internal bubble of the free DNA aptamer zippers up through formation of a continuous six-base mismatch segment which includes a pair of adjacent three-base platforms. The AMP molecules pair through their Watson-Crick edges with the minor groove edges of guanine residues. These recognition G.A mismatches are flanked by sheared G.A and reversed Hoogsteen G.G mismatch pairs. The AMP-DNA aptamer and AMP-RNA aptamer complexes have distinct tertiary structures and binding stoichiometries. Nevertheless, both complexes have similar structural features and recognition alignments in their binding pockets. Specifically, AMP targets both DNA and RNA aptamers by intercalating between purine bases and through identical G.A mismatch formation. The recognition G.A mismatch stacks with a reversed Hoogsteen G.G mismatch in one direction and with an adenine base in the other direction in both complexes. It is striking that DNA and RNA aptamers selected independently from libraries of 10(14) molecules in each case utilize identical mismatch alignments for molecular recognition with micromolar affinity within binding-site pockets containing common structural elements.

COMPUTER SIMULATIONS OF LUNG AIRWAY STRUCTURES USING DATA-DRIVEN SURFACE MODELING TECHNIQUES

EPA Science Inventory

ABSTRACT

Knowledge of human lung morphology is a subject critical to many areas of medicine. The visualization of lung structures naturally lends itself to computer graphics modeling due to the large number of airways involved and the complexities of the branching systems...

The Structure of Visuospatial Memory in Adulthood

ERIC Educational Resources Information Center

Mammarella, Irene C.; Borella, Erika; Pastore, Massimiliano; Pazzaglia, Francesca

2013-01-01

The present study aimed to investigate the structure of visuospatial memory in adulthood. Adults 40-89 years of age (n = 160) performed simple storage and complex visuospatial span tasks. Simple storage tasks were distinguished into three presentation formats: (i) visual, which involved maintaining shapes and textures; (ii) spatial-sequential,…

Disentangling polydispersity in the PCNA−p15PAF complex, a disordered, transient and multivalent macromolecular assembly

PubMed Central

Cordeiro, Tiago N.; Chen, Po-chia; De Biasio, Alfredo; Sibille, Nathalie; Blanco, Francisco J.; Hub, Jochen S.; Crehuet, Ramon

2017-01-01

Abstract The intrinsically disordered p15PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15PAF and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling. By using explicit ensemble descriptions for the individual species, built using integrative approaches and molecular dynamics (MD) simulations, we collectively interpreted multiple SAXS profiles as population-weighted thermodynamic mixtures. The analysis demonstrates that the N-terminus of p15PAF penetrates the PCNA ring and emerges on the back face. This observation substantiates the role of p15PAF as a drag regulating PCNA processivity during DNA repair. Our study reveals the power of ensemble-based approaches to decode structural, dynamic, and thermodynamic information from SAXS data. This strategy paves the way for deciphering the structural bases of flexible, transient and multivalent macromolecular assemblies involved in pivotal biological processes. PMID:28180305

Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson-Crick' interactions.

PubMed

Chandrasekhar, Sosale; Naik, Tangali R Ravikumar; Nayak, Susanta K; Row, Tayur N Guru

2010-06-15

The titled complex, obtained by co-crystallization (EtOH/25 degrees C), is apparently the only known complex of the free bases. Its crystal structure, as determined by X-ray diffraction at both 90 K and 313 K, showed that one A-T pair involves a Hoogsteen interaction, and the other a Watson-Crick interaction but only with respect to the adenine unit. The absence of a clear-cut Watson-Crick base pair raises intriguing questions about the basis of the DNA double helix. Copyright 2010 Elsevier Ltd. All rights reserved.

Social network extraction based on Web: 1. Related superficial methods

NASA Astrophysics Data System (ADS)

Khairuddin Matyuso Nasution, Mahyuddin

2018-01-01

Often the nature of something affects methods to resolve the related issues about it. Likewise, methods to extract social networks from the Web, but involve the structured data types differently. This paper reveals several methods of social network extraction from the same sources that is Web: the basic superficial method, the underlying superficial method, the description superficial method, and the related superficial methods. In complexity we derive the inequalities between methods and so are their computations. In this case, we find that different results from the same tools make the difference from the more complex to the simpler: Extraction of social network by involving co-occurrence is more complex than using occurrences.

Structural insights into the histone H1-nucleosome complex

PubMed Central

Zhou, Bing-Rui; Feng, Hanqiao; Kato, Hidenori; Dai, Liang; Yang, Yuedong; Zhou, Yaoqi; Bai, Yawen

2013-01-01

Linker H1 histones facilitate formation of higher-order chromatin structures and play important roles in various cell functions. Despite several decades of effort, the structural basis of how H1 interacts with the nucleosome remains elusive. Here, we investigated Drosophila H1 in complex with the nucleosome, using solution nuclear magnetic resonance spectroscopy and other biophysical methods. We found that the globular domain of H1 bridges the nucleosome core and one 10-base pair linker DNA asymmetrically, with its α3 helix facing the nucleosomal DNA near the dyad axis. Two short regions in the C-terminal tail of H1 and the C-terminal tail of one of the two H2A histones are also involved in the formation of the H1–nucleosome complex. Our results lead to a residue-specific structural model for the globular domain of the Drosophila H1 in complex with the nucleosome, which is different from all previous experiment-based models and has implications for chromatin dynamics in vivo. PMID:24218562

Singlet-triplet fission of carotenoid excitation in light-harvesting LH2 complexes of purple phototrophic bacteria.

PubMed

Klenina, I B; Makhneva, Z K; Moskalenko, A A; Gudkov, N D; Bolshakov, M A; Pavlova, E A; Proskuryakov, I I

2014-03-01

The current generally accepted structure of light-harvesting LH2 complexes from purple phototrophic bacteria conflicts with the observation of singlet-triplet carotenoid excitation fission in these complexes. In LH2 complexes from the purple bacterium Allochromatium minutissimum, a drop in the efficiency of carotenoid triplet generation is demonstrated, which correlates with the extent of selective photooxidation of bacteriochlorophylls absorbing at ~850 nm. We conclude that singlet-triplet fission of carotenoid excitation proceeds with participation of these excitonically coupled bacteriochlorophylls. In the framework of the proposed mechanism, the contradiction between LH2 structure and photophysical properties of carotenoids is eliminated. The possibility of singlet-triplet excitation fission involving a third mediator molecule was not considered earlier.

Using the Self-Select Paradigm to Delineate the Nature of Speech Motor Programming

PubMed Central

Wright, David L.; Robin, Don A.; Rhee, Jooyhun; Vaculin, Amber; Jacks, Adam; Guenther, Frank H.; Fox, Peter T.

2015-01-01

Purpose The authors examined the involvement of 2 speech motor programming processes identified by S. T. Klapp (1995, 2003) during the articulation of utterances differing in syllable and sequence complexity. According to S. T. Klapp, 1 process, INT, resolves the demands of the programmed unit, whereas a second process, SEQ, oversees the serial order demands of longer sequences. Method A modified reaction time paradigm was used to assess INT and SEQ demands. Specifically, syllable complexity was dependent on syllable structure, whereas sequence complexity involved either repeated or unique syllabi within an utterance. Results INT execution was slowed when articulating single syllables in the form CCCV compared to simpler CV syllables. Planning unique syllables within a multisyllabic utterance rather than repetitions of the same syllable slowed INT but not SEQ. Conclusions The INT speech motor programming process, important for mental syllabary access, is sensitive to changes in both syllable structure and the number of unique syllables in an utterance. PMID:19474396

Neuropsychiatry of complex visual hallucinations.

PubMed

Mocellin, Ramon; Walterfang, Mark; Velakoulis, Dennis

2006-09-01

To describe the phenomenology and pathophysiology of complex visual hallucinations (CVH) in various organic states, in particular Charles Bonnet syndrome and peduncular hallucinosis. Three cases of CVH in the setting of pontine infarction, thalamic infarction and temporoparietal epileptiform activity are presented and the available psychiatric, neurological and biological literature on the structures of the central nervous system involved in producing hallucinatory states is reviewed. Complex visual hallucinations can arise from a variety of processes involving the retinogeniculocalcarine tract, or ascending brainstem modulatory structures. The cortical activity responsible for hallucinations results from altered or reduced input into these regions, or a loss of ascending inhibition of their afferent pathways. A significant degree of overlaps exists between the concepts of Charles Bonnet syndrome and peduncular hallucinosis. The fluidity of these eponymous syndromes reduces their validity and meaning, and may result in an inappropriate attribution of the underlying pathology. An understanding of how differing pathologies may produce CVH allows for the appropriate tailoring of treatment, depending on the site and nature of the lesion and content of perceptual disturbance.

Synthesis and characterization of bright green terbium coordination complex derived from 1,4-bis(carbonylmethyl)terephthalate: Structure and luminescence properties

NASA Astrophysics Data System (ADS)

Ma, Mengjiao; Li, Congcong; Shu, Dengkun; Wang, Chaohua; Xi, Peng

2018-02-01

A photoluminescent terbium (Tb) complex involving a novel benzoic-acid compound with a unique coordinated structure, namely 1,4-bis(carbonylmethyl)terephthalate (BCMT), has been designed and synthesized. The new coordinate structure and energy-transfer mechanism between the ligand and Tb(III) ions were investigated in detail. The results demonstrated that the BCMT-Tb(III) complex shows strong fluorescence intensity (4 × 106 a.u.) and long fluorescence lifetime (1.302 ms), owing to the favorable degree of energy matching between the triplet excited level of the ligand and the resonant level of Tb(III) ions. Based on the analysis of three-dimensional luminescence spectra, the as-prepared Tb(III) complex can be effectively excited in the range of 250-310 nm, and it shows high color purity, with a bright green appearance.

Three-dimensional structure of E. Coli purine nucleoside phosphorylase at 0.99 Å resolution

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

Timofeev, V. I., E-mail: tostars@mail.ru; Abramchik, Yu. A., E-mail: ugama@yandex.ru; Zhukhlistova, N. E., E-mail: inna@ns.crys.ras.ru

2016-03-15

Purine nucleoside phosphorylases (PNPs) catalyze the reversible phosphorolysis of nucleosides and are key enzymes involved in nucleotide metabolism. They are essential for normal cell function and can catalyze the transglycosylation. Crystals of E. coli PNP were grown in microgravity by the capillary counterdiffusion method through a gel layer. The three-dimensional structure of the enzyme was determined by the molecular-replacement method at 0.99 Å resolution. The structural features are considered, and the structure of E. coli PNP is compared with the structures of the free enzyme and its complexes with purine base derivatives established earlier. A comparison of the environment ofmore » the purine base in the complex of PNP with formycin A and of the pyrimidine base in the complex of uridine phosphorylase with thymidine revealed the main structural features of the base-binding sites. Coordinates of the atomic model determined with high accuracy were deposited in the Protein Data Bank (PDB-ID: 4RJ2).« less

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

NASA Astrophysics Data System (ADS)

D'Urzo, Annalisa; Konijnenberg, Albert; Rossetti, Giulia; Habchi, Johnny; Li, Jinyu; Carloni, Paolo; Sobott, Frank; Longhi, Sonia; Grandori, Rita

2015-03-01

Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered NTAIL domain and the phosphoprotein X domain (PXD) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire NTAIL domain bound to PXD at atomic resolution.

Age-related patterns of forest complexity and carbon storage in pine and aspen-birch ecosystems of northern Minnesota, USA

Treesearch

John B. Bradford; Douglas N. Kastendick

2010-01-01

Forest managers are seeking strategies to create stands that can adapt to new climatic conditions and simultaneously help mitigate increases in atmospheric CO2. Adaptation strategies often focus on enhancing resilience by maximizing forest complexity in terms of species composition and size structure, while mitigation involves sustaining carbon...

"Structure and dynamics in complex chemical systems: Gaining new insights through recent advances in time-resolved spectroscopies.” ACS Division of Physical Chemistry Symposium presented at the Fall National ACS Meeting in Boston, MA, August 2015

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

Crawford, Daniel

8-Session Symposium on STRUCTURE AND DYNAMICS IN COMPLEX CHEMICAL SYSTEMS: GAINING NEW INSIGHTS THROUGH RECENT ADVANCES IN TIME-RESOLVED SPECTROSCOPIES. The intricacy of most chemical, biochemical, and material processes and their applications are underscored by the complex nature of the environments in which they occur. Substantial challenges for building a global understanding of a heterogeneous system include (1) identifying unique signatures associated with specific structural motifs within the heterogeneous distribution, and (2) resolving the significance of each of multiple time scales involved in both small- and large-scale nuclear reorganization. This symposium focuses on the progress in our understanding of dynamics inmore » complex systems driven by recent innovations in time-resolved spectroscopies and theoretical developments. Such advancement is critical for driving discovery at the molecular level facilitating new applications. Broad areas of interest include: Structural relaxation and the impact of structure on dynamics in liquids, interfaces, biochemical systems, materials, and other heterogeneous environments.« less

Fault diagnosis of sensor networked structures with multiple faults using a virtual beam based approach

NASA Astrophysics Data System (ADS)

Wang, H.; Jing, X. J.

2017-07-01

This paper presents a virtual beam based approach suitable for conducting diagnosis of multiple faults in complex structures with limited prior knowledge of the faults involved. The "virtual beam", a recently-proposed concept for fault detection in complex structures, is applied, which consists of a chain of sensors representing a vibration energy transmission path embedded in the complex structure. Statistical tests and adaptive threshold are particularly adopted for fault detection due to limited prior knowledge of normal operational conditions and fault conditions. To isolate the multiple faults within a specific structure or substructure of a more complex one, a 'biased running' strategy is developed and embedded within the bacterial-based optimization method to construct effective virtual beams and thus to improve the accuracy of localization. The proposed method is easy and efficient to implement for multiple fault localization with limited prior knowledge of normal conditions and faults. With extensive experimental results, it is validated that the proposed method can localize both single fault and multiple faults more effectively than the classical trust index subtract on negative add on positive (TI-SNAP) method.

Structural insights into the rhabdovirus transcription/replication complex.

PubMed

Ivanov, Ivan; Yabukarski, Filip; Ruigrok, Rob W H; Jamin, Marc

2011-12-01

The rhabdoviruses have a non-segmented single stranded negative-sense RNA genome. Their multiplication in a host cell requires three viral proteins in addition to the viral RNA genome. The nucleoprotein (N) tightly encapsidates the viral RNA, and the N-RNA complex serves as the template for both transcription and replication. The viral RNA-dependent RNA polymerase is a two subunit complex that consists of a large subunit, L, and a non-catalytic cofactor, the phosphoprotein, P. P also acts as a chaperone of nascent RNA-free N by forming a N(0)-P complex that prevents N from binding to cellular RNAs and from polymerizing in the absence of RNA. Here, we discuss the recent molecular and structural studies of individual components and multi-molecular complexes that are involved in the transcription/replication complex of these viruses with regard to their implication in viral transcription and replication. Copyright © 2011 Elsevier B.V. All rights reserved.

Synthesis, crystal structures, and characterization of double complex salts [Au(en)2][Rh(NO2)6]·2H2O and [Au(en)2][Rh(NO2)6

NASA Astrophysics Data System (ADS)

Plyusnin, Pavel E.; Makotchenko, Evgenia V.; Shubin, Yury V.; Baidina, Iraida A.; Korolkov, Ilya V.; Sheludyakova, Liliya A.; Korenev, Sergey V.

2015-11-01

Double complex salts of rhodium(III) and gold(III) of the composition [Au(en)2][Rh(NO2)6]·2H2O (1) and [Au(en)2][Rh(NO2)6] (2) have been prepared. Crystal structures of the compounds have been determined by single crystal X-ray diffraction. The compounds have been characterized by PXRD, IR, far-IR, CHN and DTA. The complexes have a layered structures. The presence of water in 1 makes the structure of the hydrated DCS less dense as compared to the anhydrous one. The environment of the cation and the anion in the two structures is the same, oxygen atoms of the nitro groups are involved in hydrogen bonds N-H⋯O, N⋯O distances being approximately the same. The structures of 1 and 2 are notable in having shortened contacts between the gold atoms and the oxygen atoms of the nitro groups of the neighboring complex anions. The thermal behavior of the complexes in a hydrogen atmosphere was investigated. The final product of thermolysis prepared at the temperature 600°C is a two-phase mixture of pure metallic gold and the solid solution Rh0.93Au0.07.

Preparation and Structural Properties of InIII–H Complexes

PubMed Central

Sickerman, Nathaniel S.; Henry, Renée M.; Ziller, Joseph W.

2013-01-01

The use of the tripodal ligands tris[(N'-tert-butylureaylato)-N-ethyl]aminato ([H3buea]3−) and the sulfonamide-based N,N',N"-[2,2',2"-nitrilotris(ethane-2,1-diyl)]tris(2,4,6-trimethylbenzene-sulfonamidato) ([MST]3−) has led to the synthesis of two structurally distinct In(III)–OH complexes. The first example of a five-coordinate indium(III) complex with a terminal hydroxide ligand, K[InIIIH3buea(OH)], was prepared by addition of In(OAc)3 and water to a deprotonated solution of H6buea. X-ray diffraction analysis, as well as FTIR and 1H NMR spectroscopic methods, provided evidence for the formation of a monomeric In(III)–OH complex. The complex contains an intramolecular hydrogen bonding (H-bonding) network involving the In(III)–OH unit and [H3buea]3− ligand, which aided in isolation of the complex. Isotope labeling studies verified the source of the hydroxo ligand as water. Treatment of the [InIIIMST] complex with a mixture of 15-crown-5 ether and NaOH led to isolation of the complex [15-crown-5⊃NaI-(μ-OH)-InIIIMST], whose solid-state structure was confirmed using X-ray diffraction methods. Nuclear magnetic resonance studies on this complex suggest it retains its heterobimetallic structure in solution. PMID:25309019

Discrepancy between experimental and theoretical excitation transfer rates in LH2 bacteriochlorophyll-protein complexes of purple bacteria.

PubMed

Borisov, A Y

2008-02-01

Discrepancy is revealed between the values of excitation transfer times measured experimentally, and those calculated, for the atomic structures of B800 --> B850 bacteriochlorophylls within the LH2 light-harvesting pigment-protein complex of the purple bacterium Rhodopseudomonas acidophila. The value 2.9-3.2 ps for the B800 --> B850 excitation transfer, calculated on the basis of atomic structure of LH2, is about 4-times longer than that measured for this bacterium (0.7 ps). This discrepancy appears common in at least two purple bacteria. Possible sources responsible for this discrepancy are discussed. It may either signify some drawback/s/ in our notions about the precise in vivo structure of LH2 complexes, for example, possible changes of LH2 structure during crystallization, or it may reflect our ignorance of some mechanisms involved in excitation migration.

A role for the membrane Golgi protein Ema in autophagy.

PubMed

Kim, Sungsu; DiAntonio, Aaron

2012-08-01

Autophagy is a cellular homeostatic response that involves degradation of self-components by the double-membraned autophagosome. The biogenesis of autophagosomes has been well described, but the ensuing processes after autophagosome formation are not clear. In our recent study, we proposed a model in which the Golgi complex contributes to the growth of autophagic structures, and that the Drosophila melanogaster membrane protein Ema promotes this process. In fat body cells of the D. melanogaster ema mutant, the recruitment of the Golgi complex protein Lava lamp (Lva) to autophagic structures is impaired and autophagic structures are very small. In addition, in the ema mutant autophagic turnover of SQSTM1/p62 and mitophagy are impaired. Our study not only identifies a role for Ema in autophagy, but also supports the hypothesis that the Golgi complex may be a potential membrane source for the biogenesis and development of autophagic structures.

Modelling and simulating a crisis management system: an organisational perspective

NASA Astrophysics Data System (ADS)

Chaawa, Mohamed; Thabet, Inès; Hanachi, Chihab; Ben Said, Lamjed

2017-04-01

Crises are complex situations due to the dynamism of the environment, its unpredictability and the complexity of the interactions among several different and autonomous involved organisations. In such a context, establishing an organisational view as well as structuring organisations' communications and their functioning is a crucial requirement. In this article, we propose a multi-agent organisational model (OM) to abstract, simulate and analyse a crisis management system (CMS). The objective is to evaluate the CMS from an organisational view, to assess its strength as well as its weakness and to provide deciders with some recommendations for a more flexible and reactive CMS. The proposed OM is illustrated through a real case study: a snowstorm in a Tunisian region. More precisely, we made the following contribution: firstly, we provide an environmental model that identifies the concepts involved in the crisis. Then, we define a role model that copes with the involved actors. In addition, we specify the organisational structure and the interaction model that rule communications and structure actors' functioning. Those models, built following the GAIA methodology, abstract the CMS from an organisational perspective. Finally, we implemented a customisable multi-agent simulator based on the Janus platform to analyse, through several performed simulations, the organisational model.

Unraveling secrets of telomeres: one molecule at a time

PubMed Central

Lin, Jiangguo; Kaur, Parminder; Countryman, Preston; Opresko, Patricia L.; Wang, Hong

2016-01-01

Telomeres play important roles in maintaining the stability of linear chromosomes. Telomere maintenance involves dynamic actions of multiple proteins interacting with long repetitive sequences and complex dynamic DNA structures, such as G-quadruplexes, T-loops and t-circles. Given the heterogeneity and complexity of telomeres, single-molecule approaches are essential to fully understand the structure-function relationships that govern telomere maintenance. In this review, we present a brief overview of the principles of single-molecule imaging and manipulation techniques. We then highlight results obtained from applying these single-molecule techniques for studying structure, dynamics and functions of G-quadruplexes, telomerase, and shelterin proteins. PMID:24569170

Characterizing complex structural variation in germline and somatic genomes

PubMed Central

Quinlan, Aaron R.; Hall, Ira M.

2011-01-01

Genome structural variation (SV) is a major source of genetic diversity in mammals and a hallmark of cancer. While SV is typically defined by its canonical forms – duplication, deletion, insertion, inversion and translocation – recent breakpoint mapping studies have revealed a surprising number of “complex” variants that evade simple classification. Complex SVs are defined by clustered breakpoints that arose through a single mutation but cannot be explained by one simple end-joining or recombination event. Some complex variants exhibit profoundly complicated rearrangements between distinct loci from multiple chromosomes, while others involve more subtle alterations at a single locus. These diverse and unpredictable features present a challenge for SV mapping experiments. Here, we review current knowledge of complex SV in mammals, and outline techniques for identifying and characterizing complex variants using next-generation DNA sequencing. PMID:22094265

Impact of zeolite-Y framework on the geometry and reactivity of Ru (III) benzimidazole complexes - A DFT study

NASA Astrophysics Data System (ADS)

Selvaraj, Tamilmani; Rajalingam, Renganathan; Balasubramanian, Viswanathan

2018-03-01

A detailed comparative Density Functional Theory (DFT) study is made to understand the structural changes of the guest complex due to steric and electronic interactions with the host framework. In this study, Ru(III) benzimidazole and 2- ethyl Ru(III) benzimidazole complexes encapsulated in a supercage of zeolite Y. The zeolitic framework integrity is not disturbed by the intrusion of the large guest complex. A blue shift in the d-d transition observed in the UV-Visible spectroscopic studies of the zeolite encapsulated complexes and they shows a higher catalytic efficiency. Encapsulation of zeolite matrix makes the metal center more viable to nucleophilic attack and favors the phenol oxidation reaction. Based on the theoretical calculations, transition states and structures of reaction intermediates involved in the catalytic cycles are derived.

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Kawaguchi, Kazutomo; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

Crystal structure of hexagonal MnAl(4).

PubMed

Pauling, L

1987-06-01

A structure is proposed for the hexagonal form of MnAl(4), with a(H) = 28.4 A and c(H) = 12.43 A, on the basis of a high-resolution electron micrograph and comparison with crystals of known structures. The proposed structure involves seven 104-atom complexes of 20 Friauf polyhedra, sharing some atoms with one another. It is closely related to the 23.36-A cubic structure of MnAl(4) and to the 14.19-A cubic structure of Mg(32)(Al,Zn)(49).

ULg Spectra: An Interactive Software Tool to Improve Undergraduate Students' Structural Analysis Skills

ERIC Educational Resources Information Center

Agnello, Armelinda; Carre, Cyril; Billen, Roland; Leyh, Bernard; De Pauw, Edwin; Damblon, Christian

2018-01-01

The analysis of spectroscopic data to solve chemical structures requires practical skills and drills. In this context, we have developed ULg Spectra, a computer-based tool designed to improve the ability of learners to perform complex reasoning. The identification of organic chemical compounds involves gathering and interpreting complementary…

Disulfide Trapping for Modeling and Structure Determination of Receptor: Chemokine Complexes.

PubMed

Kufareva, Irina; Gustavsson, Martin; Holden, Lauren G; Qin, Ling; Zheng, Yi; Handel, Tracy M

2016-01-01

Despite the recent breakthrough advances in GPCR crystallography, structure determination of protein-protein complexes involving chemokine receptors and their endogenous chemokine ligands remains challenging. Here, we describe disulfide trapping, a methodology for generating irreversible covalent binary protein complexes from unbound protein partners by introducing two cysteine residues, one per interaction partner, at selected positions within their interaction interface. Disulfide trapping can serve at least two distinct purposes: (i) stabilization of the complex to assist structural studies and/or (ii) determination of pairwise residue proximities to guide molecular modeling. Methods for characterization of disulfide-trapped complexes are described and evaluated in terms of throughput, sensitivity, and specificity toward the most energetically favorable crosslinks. Due to abundance of native disulfide bonds at receptor:chemokine interfaces, disulfide trapping of their complexes can be associated with intramolecular disulfide shuffling and result in misfolding of the component proteins; because of this, evidence from several experiments is typically needed to firmly establish a positive disulfide crosslink. An optimal pipeline that maximizes throughput and minimizes time and costs by early triage of unsuccessful candidate constructs is proposed. © 2016 Elsevier Inc. All rights reserved.

Crystallization of bi-functional ligand protein complexes.

PubMed

Antoni, Claudia; Vera, Laura; Devel, Laurent; Catalani, Maria Pia; Czarny, Bertrand; Cassar-Lajeunesse, Evelyn; Nuti, Elisa; Rossello, Armando; Dive, Vincent; Stura, Enrico Adriano

2013-06-01

Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects. Copyright © 2013 Elsevier Inc. All rights reserved.

Multicriteria decision analysis: Overview and implications for environmental decision making

USGS Publications Warehouse

Hermans, Caroline M.; Erickson, Jon D.; Erickson, Jon D.; Messner, Frank; Ring, Irene

2007-01-01

Environmental decision making involving multiple stakeholders can benefit from the use of a formal process to structure stakeholder interactions, leading to more successful outcomes than traditional discursive decision processes. There are many tools available to handle complex decision making. Here we illustrate the use of a multicriteria decision analysis (MCDA) outranking tool (PROMETHEE) to facilitate decision making at the watershed scale, involving multiple stakeholders, multiple criteria, and multiple objectives. We compare various MCDA methods and their theoretical underpinnings, examining methods that most realistically model complex decision problems in ways that are understandable and transparent to stakeholders.

Reaction of an Iron(IV) Nitrido Complex with Cyclohexadienes: Cycloaddition and Hydrogen-Atom Abstraction

PubMed Central

2015-01-01

The iron(IV) nitrido complex PhB(MesIm)3Fe≡N reacts with 1,3-cyclohexadiene to yield the iron(II) pyrrolide complex PhB(MesIm)3Fe(η5-C4H4N) in high yield. The mechanism of product formation is proposed to involve sequential [4 + 1] cycloaddition and retro Diels–Alder reactions. Surprisingly, reaction with 1,4-cyclohexadiene yields the same iron-containing product, albeit in substantially lower yield. The proposed reaction mechanism, supported by electronic structure calculations, involves hydrogen-atom abstraction from 1,4-cyclohexadiene to provide the cyclohexadienyl radical. This radical is an intermediate in substrate isomerization to 1,3-cyclohexadiene, leading to formation of the pyrrolide product. PMID:25068927

EARP, a multisubunit tethering complex involved in endocytic recycling

PubMed Central

Schindler, Christina; Chen, Yu; Pu, Jing; Guo, Xiaoli; Bonifacino, Juan S.

2015-01-01

Recycling of endocytic receptors to the cell surface involves passage through a series of membrane-bound compartments by mechanisms that are poorly understood. In particular, it is unknown if endocytic recycling requires the function of multisubunit tethering complexes, as is the case for other intracellular trafficking pathways. Herein we describe a tethering complex named Endosome-Associated Recycling Protein (EARP) that is structurally related to the previously described Golgi-Associated Retrograde Protein (GARP) complex. Both complexes share the Ang2, Vps52 and Vps53 subunits, but EARP comprises an uncharacterized protein, Syndetin, in place of the Vps54 subunit of GARP. This change determines differential localization of EARP to recycling endosomes and GARP to the Golgi complex. EARP interacts with the target-SNARE Syntaxin 6 and various cognate SNAREs. Depletion of Syndetin or Syntaxin 6 delays recycling of internalized transferrin to the cell surface. These findings implicate EARP in canonical membrane-fusion events in the process of endocytic recycling. PMID:25799061

Numerical simulation of colloidal self-assembly of super-hydrophobic arachnid cerotegument structures.

PubMed

Filippov, Alexander É; Wolff, Jonas O; Seiter, Michael; Gorb, Stanislav N

2017-10-07

Certain arachnids exhibit complex coatings of their exoskeleton, consisting of globular structures with complex surface features. This, so-called, cerotegument is formed by a multi-component colloidal secretion that self-assembles and cures on the body surface, and leads to high water repellency. Previous ultrastructural studies revealed the involvement of different glandular cells that contribute different components to the secretion mixture, but the overall process of self-assembly into the complex regular structures observed remained highly unclear. Here we study this process from a theoretical point of view, starting from the so-called Tammes-problem. We show that slight changes of simple parameters lead to a variety of morphologies that are highly similar to the ones observed in the species specific cerotegument structures of whip-spiders. These results are not only important for our understanding of the formation of globular hierarchical structures in nature, but also for the fabrication of novel surface coatings by colloidal lithography. Copyright © 2017 Elsevier Ltd. All rights reserved.

Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography.

PubMed

Johnstone, Timothy C; Nolan, Elizabeth M

2017-10-25

Enterobactin is a secondary metabolite produced by Enterobacteriaceae for acquiring iron, an essential metal nutrient. The biosynthesis and utilization of enterobactin permits many Gram-negative bacteria to thrive in environments where low soluble iron concentrations would otherwise preclude survival. Despite extensive work carried out on this celebrated molecule since its discovery over 40 years ago, the ferric enterobactin complex has eluded crystallographic structural characterization. We report the successful growth of single crystals containing ferric enterobactin using racemic crystallization, a method that involves cocrystallization of a chiral molecule with its mirror image. The structures of ferric enterobactin and ferric enantioenterobactin obtained in this work provide a definitive assignment of the stereochemistry at the metal center and reveal secondary coordination sphere interactions. The structures were employed in computational investigations of the interactions of these complexes with two enterobactin-binding proteins, which illuminate the influence of metal-centered chirality on these interactions. This work highlights the utility of small-molecule racemic crystallography for obtaining elusive structures of coordination complexes.

Structure of MyTH4-FERM domains in myosin VIIa tail bound to cargo.

PubMed

Wu, Lin; Pan, Lifeng; Wei, Zhiyi; Zhang, Mingjie

2011-02-11

The unconventional myosin VIIa (MYO7A) is one of the five proteins that form a network of complexes involved in formation of stereocilia. Defects in these proteins cause syndromic deaf-blindness in humans [Usher syndrome I (USH1)]. Many disease-causing mutations occur in myosin tail homology 4-protein 4.1, ezrin, radixin, moesin (MyTH4-FERM) domains in the myosin tail that binds to another USH1 protein, Sans. We report the crystal structure of MYO7A MyTH4-FERM domains in complex with the central domain (CEN) of Sans at 2.8 angstrom resolution. The MyTH4 and FERM domains form an integral structural and functional supramodule binding to two highly conserved segments (CEN1 and 2) of Sans. The MyTH4-FERM/CEN complex structure provides mechanistic explanations for known deafness-causing mutations in MYO7A MyTH4-FERM. The structure will also facilitate mechanistic and functional studies of MyTH4-FERM domains in other myosins.

Catalytic Oxygen Evolution by a Bioinorganic Model of the Photosystem II Oxygen-Evolving Complex

ERIC Educational Resources Information Center

Howard, Derrick L.; Tinoco, Arthur D.; Brudvig, Gary W.; Vrettos, John S.; Allen, Bertha Connie

2005-01-01

Bioinorganic models of the manganese Mn4 cluster are important not only as aids in understanding the structure and function of the oxygen-evolving complex (OEC), but also in developing artificial water-oxidation catalysts. The mechanism of water oxidation by photosystem II (PSII) is thought to involve the formation of a high-valent terminal Mn-oxo…

Photomagnetic Switching of the Complex [Nd(dmf)[subscript 4](H[subscript 2]O)[subscript 3]([mu]-CN)Fe(CN)[subscript 5

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

Svendsen, Helle; Overgaard, Jacob; Chevallier, Marie

2009-10-21

Single-crystal XRD experiments (see picture) reveal the excited-state structure of the photomagnetic heterobimetallic title complex. The system shows a decrease in all the iron-ligand bond lengths, suggesting that photoexcitation involves a ligand-to-metal charge transfer or a change in the superexchange coupling between the metal centers.

Solid-state acid-base interactions in complexes of heterocyclic bases with dicarboxylic acids: crystallography, hydrogen bond analysis, and 15N NMR spectroscopy.

PubMed

Li, Z Jane; Abramov, Yuriy; Bordner, Jon; Leonard, Jason; Medek, Ales; Trask, Andrew V

2006-06-28

A cancer candidate, compound 1, is a weak base with two heterocyclic basic nitrogens and five hydrogen-bonding functional groups, and is sparingly soluble in water rendering it unsuitable for pharmaceutical development. The crystalline acid-base pairs of 1, collectively termed solid acid-base complexes, provide significant increases in the solubility and bioavailability compared to the free base, 1. Three dicarboxylic acid-base complexes, sesquisuccinate 2, dimalonate 3, and dimaleate 4, show the most favorable physicochemical profiles and are studied in greater detail. The structural analyses of the three complexes using crystal structure and solid-state NMR reveal that the proton-transfer behavior in these organic acid-base complexes vary successively correlating with Delta pKa. As a result, 2 is a neutral complex, 3 is a mixed ionic and zwitterionic complex and 4 is an ionic salt. The addition of the acidic components leads to maximized hydrogen bond interactions forming extended three-dimensional networks. Although structurally similar, the packing arrangements of the three complexes are considerably different due to the presence of multiple functional groups and the flexible backbone of 1. The findings in this study provide insight into the structural characteristics of complexes involving heterocyclic bases and carboxylic acids, and demonstrate that X-ray crystallography and 15N solid-state NMR are truly complementary in elucidating hydrogen bonding interactions and the degree of proton transfer of these complexes.

High Molecular Weight Forms of Mammalian Respiratory Chain Complex II

PubMed Central

Nůsková, Hana; Holzerová, Eliška; Vrbacký, Marek; Pecina, Petr; Hejzlarová, Kateřina; Kľučková, Katarína; Rohlena, Jakub; Neuzil, Jiri; Houštěk, Josef

2013-01-01

Mitochondrial respiratory chain is organised into supramolecular structures that can be preserved in mild detergent solubilisates and resolved by native electrophoretic systems. Supercomplexes of respiratory complexes I, III and IV as well as multimeric forms of ATP synthase are well established. However, the involvement of complex II, linking respiratory chain with tricarboxylic acid cycle, in mitochondrial supercomplexes is questionable. Here we show that digitonin-solubilised complex II quantitatively forms high molecular weight structures (CIIhmw) that can be resolved by clear native electrophoresis. CIIhmw structures are enzymatically active and differ in electrophoretic mobility between tissues (500 – over 1000 kDa) and cultured cells (400–670 kDa). While their formation is unaffected by isolated defects in other respiratory chain complexes, they are destabilised in mtDNA-depleted, rho0 cells. Molecular interactions responsible for the assembly of CIIhmw are rather weak with the complexes being more stable in tissues than in cultured cells. While electrophoretic studies and immunoprecipitation experiments of CIIhmw do not indicate specific interactions with the respiratory chain complexes I, III or IV or enzymes of the tricarboxylic acid cycle, they point out to a specific interaction between CII and ATP synthase. PMID:23967256

Study of Nanocomposites of Amino Acids and Organic Polyethers by Means of Mass Spectrometry and Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Zobnina, V. G.; Kosevich, M. V.; Chagovets, V. V.; Boryak, O. A.

A problem of elucidation of structure of nanomaterials based on combination of proteins and polyether polymers is addressed on the monomeric level of single amino acids and oligomers of PEG-400 and OEG-5 polyethers. Efficiency of application of combined approach involving experimental electrospray mass spectrometry and computer modeling by molecular dynamics simulation is demonstrated. It is shown that oligomers of polyethers form stable complexes with amino acids valine, proline, histidine, glutamic, and aspartic acids. Molecular dynamics simulation has shown that stabilization of amino acid-polyether complexes is achieved due to winding of the polymeric chain around charged groups of amino acids. Structural motives revealed for complexes of single amino acids with polyethers can be realized in structures of protein-polyether nanoparticles currently designed for drug delivery.

Scaffolding Students' Skill Development by First Introducing Advanced Techniques through the Synthesis and [superscript 15]N NMR Analysis of Cinnamamides

ERIC Educational Resources Information Center

Shuldburg, Sara; Carroll, Jennifer

2017-01-01

An advanced undergraduate experiment involving the synthesis and characterization of a series of six unique cinnamamides is described. This experiment allows for a progressive mastery of skills students need to tackle more complex NMR structure elucidation problems. Characterization of the products involves IR spectroscopy, GCMS, and proton,…

Crystal Structure of the Heme d1 Biosynthesis Enzyme NirE in Complex with Its Substrate Reveals New Insights into the Catalytic Mechanism of S-Adenosyl-l-methionine-dependent Uroporphyrinogen III Methyltransferases*

PubMed Central

Storbeck, Sonja; Saha, Sayantan; Krausze, Joern; Klink, Björn U.; Heinz, Dirk W.; Layer, Gunhild

2011-01-01

During the biosynthesis of heme d1, the essential cofactor of cytochrome cd1 nitrite reductase, the NirE protein catalyzes the methylation of uroporphyrinogen III to precorrin-2 using S-adenosyl-l-methionine (SAM) as the methyl group donor. The crystal structure of Pseudomonas aeruginosa NirE in complex with its substrate uroporphyrinogen III and the reaction by-product S-adenosyl-l-homocysteine (SAH) was solved to 2.0 Å resolution. This represents the first enzyme-substrate complex structure for a SAM-dependent uroporphyrinogen III methyltransferase. The large substrate binds on top of the SAH in a “puckered” conformation in which the two pyrrole rings facing each other point into the same direction either upward or downward. Three arginine residues, a histidine, and a methionine are involved in the coordination of uroporphyrinogen III. Through site-directed mutagenesis of the nirE gene and biochemical characterization of the corresponding NirE variants the amino acid residues Arg-111, Glu-114, and Arg-149 were identified to be involved in NirE catalysis. Based on our structural and biochemical findings, we propose a potential catalytic mechanism for NirE in which the methyl transfer reaction is initiated by an arginine catalyzed proton abstraction from the C-20 position of the substrate. PMID:21632530

High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1

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

Jacobsen, Julian O. B.; Allen, Mark D.; Freund, Stefan M. V.

2016-05-23

In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and the C-terminal RNA-binding domain of S. cerevisiae Tho1 have been determined. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014 ▸), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1,more » which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined.« less

Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends.

PubMed

Chuzhanova, Nadia; Abeysinghe, Shaun S; Krawczak, Michael; Cooper, David N

2003-09-01

Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions. Copyright 2003 Wiley-Liss, Inc.

Structural characterization of POM6 Fab and mouse prion protein complex identifies key regions for prions conformational conversion.

PubMed

Baral, Pravas Kumar; Swayampakula, Mridula; Aguzzi, Adriano; James, Michael N G

2018-05-01

Conversion of the cellular prion protein PrP C into its pathogenic isoform PrP S c is the hallmark of prion diseases, fatal neurodegenerative diseases affecting many mammalian species including humans. Anti-prion monoclonal antibodies can arrest the progression of prion diseases by stabilizing the cellular form of the prion protein. Here, we present the crystal structure of the POM6 Fab fragment, in complex with the mouse prion protein (moPrP). The prion epitope of POM6 is in close proximity to the epitope recognized by the purportedly toxic antibody fragment, POM1 Fab also complexed with moPrP. The POM6 Fab recognizes a larger binding interface indicating a likely stronger binding compared to POM1. POM6 and POM1 exhibit distinct biological responses. Structural comparisons of the bound mouse prion proteins from the POM6 Fab:moPrP and POM1 Fab:moPrP complexes reveal several key regions of the prion protein that might be involved in initiating mis-folding events. The structural data of moPrP:POM6 Fab complex are available in the PDB under the accession number www.rcsb.org/pdb/search/structidSearch.do?structureId=6AQ7. © 2018 Federation of European Biochemical Societies.

Where to attach dye molecules to a protein: lessons from the computer program WHAT IF

NASA Astrophysics Data System (ADS)

Altenberg-Greulich, B.; Vriend, G.

2001-10-01

Genomic and proteomic projects are producing a flood of data that all require interpretation which often is best performed based on a three dimensional structure of the molecule(s) involved. These structures can be determined experimentally, or modelled by homology. Because of the complexity of the questions and the heterogeneity of the data, the software used for modelling proteins must become even more versatile. We describe several case studies in which the questions asked, the data, and the requirements on the software all are very different. It is shown how structural knowledge about a protein helps to determine the best place to bind a fluorescent dye. Such dyes are needed to determine protein-protein, protein-DNA interactions or intrinsic fluorescence microscopy. Further, using dyes you can trace molecules in the cell and thus get a handle on subcellular localisation. The first example (OCT-1) involves the search for free amino groups in a protein-DNA complex. The second example (BPTI) is a case, in which the amino acid distribution shows that amino groups are spread all over the structure, so that the natural structure has to be modified to get an answer. The third example (HFE) involves a model built by homology. In this case the amino group distribution can also be predicted. All these studies were performed using the WHAT IF software package. This package is available including source code, documentation, etc. See http://www.cmbi.kun.nl/whatif/

Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

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

Xiao, Xiao; Yang, Hanjing; Arutiunian, Vagan

The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species aftermore » RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.« less

Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization

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

Guan, Jian; Bywaters, Stephanie M.; Brendle, Sarah A.

2015-09-15

Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope.more » Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays. - Highlights: • We present HPV16-Fab complexes from neutralizing mAbs: H16.1A, H16.14J, and H263.A2. • The structure-function analysis revealed predominantly monovalent binding of each mAb. • Capsid–Fab interactions involved multiple loops from symmetry related L1 proteins. • Besides the known FG and HI loops, epitope mapping also identified DE, EF, and BC loops. • Neutralizing assays complement the structures to show multiple neutralization mechanisms.« less

Crystal structure of glucose isomerase in complex with xylitol inhibitor in one metal binding mode.

PubMed

Bae, Ji-Eun; Kim, In Jung; Nam, Ki Hyun

2017-11-04

Glucose isomerase (GI) is an intramolecular oxidoreductase that interconverts aldoses and ketoses. These characteristics are widely used in the food, detergent, and pharmaceutical industries. In order to obtain an efficient GI, identification of novel GI genes and substrate binding/inhibition have been studied. Xylitol is a well-known inhibitor of GI. In Streptomyces rubiginosus, two crystal structures have been reported for GI in complex with xylitol inhibitor. However, a structural comparison showed that xylitol can have variable conformation at the substrate binding site, e.g., a nonspecific binding mode. In this study, we report the crystal structure of S. rubiginosus GI in a complex with xylitol and glycerol. Our crystal structure showed one metal binding mode in GI, which we presumed to represent the inactive form of the GI. The metal ion was found only at the M1 site, which was involved in substrate binding, and was not present at the M2 site, which was involved in catalytic function. The O 2 and O 4 atoms of xylitol molecules contributed to the stable octahedral coordination of the metal in M1. Although there was no metal at the M2 site, no large conformational change was observed for the conserved residues coordinating M2. Our structural analysis showed that the metal at the M2 site was not important when a xylitol inhibitor was bound to the M1 site in GI. Thus, these findings provided important information for elucidation or engineering of GI functions. Copyright © 2017 Elsevier Inc. All rights reserved.

The Representation of Anatomical Structures through Computer Animation for Scientific, Educational and Artistic Applications.

ERIC Educational Resources Information Center

Stredney, Donald Larry

An overview of computer animation and the techniques involved in its creation is provided in the introduction to this masters thesis, which focuses on the problems encountered by students in learning the forms and functions of complex anatomical structures and ways in which computer animation can address these problems. The objectives for,…

Corporate Structure Events Involving Regulated Utilities: The Need for a Multidisciplinary, Multijurisdictional Approach

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

Hempling, Scott

2006-08-15

The repeal of PUHCA has occasioned important questions on the appropriate role for regulation in the area of utility corporate structure, including complex process and jurisdictional issues. There is a disproportionality between the importance of these questions and the lack of attention that has been given them by our regulatory and political communities. (author)

Cognitive Structure and the Affective Domain: On Knowing and Feeling in Biology.

ERIC Educational Resources Information Center

Thompson, Tressa L.; Mintzes, Joel J.

2002-01-01

Explores the structural complexity and propositional validity of knowledge about and attitudes toward sharks and the relationships among knowledge and attitudes. Uses concept mapping and a Likert-type attitude inventory for assessment and involves (n=238) participants from 5th, 8th, and 11th grades and college-level and senior citizens. Reports…

The development of episodic memory: items, contexts, and relations.

PubMed

Yim, Hyungwook; Dennis, Simon J; Sloutsky, Vladimir M

2013-11-01

Episodic memory involves the formation of relational structures that bind information about the stimuli people experience to the contexts in which they experience them. The ability to form and retain such structures may be at the core of the development of episodic memory. In the first experiment reported here, 4- and 7-year-olds were presented with paired-associate learning tasks requiring memory structures of different complexity. A multinomial-processing tree model was applied to estimate the use of different structures in the two age groups. The use of two-way list-context-to-target structures and three-way structures was found to increase between the ages of 4 and 7. Experiment 2 demonstrated that the ability to form increasingly complex relational memory structures develops between the ages of 4 and 7 years and that this development extends well into adulthood. These results have important implications for theories of memory development.

Structure and Electronic Spectra of Purine-Methyl Viologen Charge Transfer Complexes

PubMed Central

Jalilov, Almaz S.; Patwardhan, Sameer; Singh, Arunoday; Simeon, Tomekia; Sarjeant, Amy A.; Schatz, George C.; Lewis, Frederick D.

2014-01-01

The structure and properties of the electron donor-acceptor complexes formed between methyl viologen (MV) and purine nucleosides and nucleotides in water and the solid state have been investigated using a combination of experimental and theoretical methods. Solution studies were performed using UV-vis and 1H NMR spectroscopy. Theoretical calculations were performed within the framework of density functional theory (DFT). Energy decomposition analysis indicates that dispersion and induction (charge-transfer) interactions dominate the total binding energy, whereas electrostatic interactions are largely repulsive. The appearance of charge transfer bands in the absorption spectra of the complexes are well described by time-dependent (TD) DFT and are further explained in terms of the redox properties of purine monomers and solvation effects. Crystal structures are reported for complexes of methyl viologen with the purines 2′-deoxyguanosine 3′-monophosphate GMP (DAD′DAD′ type) and 7-deazaguanosine zG (DAD′ADAD′ type). Comparison of the structures determined in the solid state and by theoretical methods in solution provides valuable insights into the nature of charge-transfer interactions involving purine bases as electron donors. PMID:24294996

The neuronal porosome complex in health and disease

PubMed Central

Naik, Akshata R; Lewis, Kenneth T

2015-01-01

Cup-shaped secretory portals at the cell plasma membrane called porosomes mediate the precision release of intravesicular material from cells. Membrane-bound secretory vesicles transiently dock and fuse at the base of porosomes facing the cytosol to expel pressurized intravesicular contents from the cell during secretion. The structure, isolation, composition, and functional reconstitution of the neuronal porosome complex have greatly progressed, providing a molecular understanding of its function in health and disease. Neuronal porosomes are 15 nm cup-shaped lipoprotein structures composed of nearly 40 proteins, compared to the 120 nm nuclear pore complex composed of >500 protein molecules. Membrane proteins compose the porosome complex, making it practically impossible to solve its atomic structure. However, atomic force microscopy and small-angle X-ray solution scattering studies have provided three-dimensional structural details of the native neuronal porosome at sub-nanometer resolution, providing insights into the molecular mechanism of its function. The participation of several porosome proteins previously implicated in neurotransmission and neurological disorders, further attest to the crosstalk between porosome proteins and their coordinated involvement in release of neurotransmitter at the synapse. PMID:26264442

Syntheses and characterizations of two new energetic copper–amine-DNANT complexes and their effects on thermal decomposition of RDX

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

Qiu, Qianqian; Xu, Kangzhen, E-mail: xukz@nwu.edu.cn; Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon

Two novel copper complexes of dinitroacetonitrile (DNANT), Cu(NH{sub 3}){sub 4}(DNANT){sub 2} (1) and Cu(en){sub 2}(DNATN){sub 2} (2), have been synthesized for the first time through an unique reaction, and structurally characterized. The single-crystal X-ray structural analysis shows that the Cu{sup 2+} cations in the two complexes share a similar four-coordinated structure, which however does not directly involve the main energetic DNANT{sup −} anion. The differential scanning calorimetry (DSC) study reveals that the two complexes have higher thermal stability and lower sensitivity than the analogous FOX-7 complexes, and exhibit good catalytic action to the decomposition of RDX. - Graphical abstract: Cu(NH{submore » 3}){sub 4}(DNANT){sub 2} (1) and Cu(en){sub 2}(DNATN){sub 2} (2) have been first synthesized through an unique reaction. Cu{sup 2+} ion shares a similar four-coordinated structure in the two complexes. Display Omitted - Highlights: • A new reaction is unexpectedly found, and reaction process was discussed in this work. • Cu(NH{sub 3}){sub 4} (DNANT){sub 2}and Cu(en){sub 2}(DNATN){sub 2} were first synthesized through an unique reaction. • The structures and properties of the two complexes were discussed in detail, and they all present good application performances. • The adjacent amino-hydrazino group in AHDNE exhibits high reactivity. The work is another typical example for the reactivity.« less

Short-Chain 3-Hydroxyacyl-Coenzyme A Dehydrogenase Associates with a Protein Super-Complex Integrating Multiple Metabolic Pathways

PubMed Central

Narayan, Srinivas B.; Master, Stephen R.; Sireci, Anthony N.; Bierl, Charlene; Stanley, Paige E.; Li, Changhong; Stanley, Charles A.; Bennett, Michael J.

2012-01-01

Proteins involved in mitochondrial metabolic pathways engage in functionally relevant multi-enzyme complexes. We previously described an interaction between short-chain 3-hydroxyacyl-coenzyme A dehydrogenase (SCHAD) and glutamate dehydrogenase (GDH) explaining the clinical phenotype of hyperinsulinism in SCHAD-deficient patients and adding SCHAD to the list of mitochondrial proteins capable of forming functional, multi-pathway complexes. In this work, we provide evidence of SCHAD's involvement in additional interactions forming tissue-specific metabolic super complexes involving both membrane-associated and matrix-dwelling enzymes and spanning multiple metabolic pathways. As an example, in murine liver, we find SCHAD interaction with aspartate transaminase (AST) and GDH from amino acid metabolic pathways, carbamoyl phosphate synthase I (CPS-1) from ureagenesis, other fatty acid oxidation and ketogenesis enzymes and fructose-bisphosphate aldolase, an extra-mitochondrial enzyme of the glycolytic pathway. Most of the interactions appear to be independent of SCHAD's role in the penultimate step of fatty acid oxidation suggesting an organizational, structural or non-enzymatic role for the SCHAD protein. PMID:22496890

Speech as a breakthrough signaling resource in the cognitive evolution of biological complex adaptive systems.

PubMed

Mattei, Tobias A

2014-12-01

In self-adapting dynamical systems, a significant improvement in the signaling flow among agents constitutes one of the most powerful triggering events for the emergence of new complex behaviors. Ackermann and colleagues' comprehensive phylogenetic analysis of the brain structures involved in acoustic communication provides further evidence of the essential role which speech, as a breakthrough signaling resource, has played in the evolutionary development of human cognition viewed from the standpoint of complex adaptive system analysis.

Neuroarchitecture and neuroanatomy of the Drosophila central complex: A GAL4-based dissection of protocerebral bridge neurons and circuits.

PubMed

Wolff, Tanya; Iyer, Nirmala A; Rubin, Gerald M

2015-05-01

Insects exhibit an elaborate repertoire of behaviors in response to environmental stimuli. The central complex plays a key role in combining various modalities of sensory information with an insect's internal state and past experience to select appropriate responses. Progress has been made in understanding the broad spectrum of outputs from the central complex neuropils and circuits involved in numerous behaviors. Many resident neurons have also been identified. However, the specific roles of these intricate structures and the functional connections between them remain largely obscure. Significant gains rely on obtaining a comprehensive catalog of the neurons and associated GAL4 lines that arborize within these brain regions, and on mapping neuronal pathways connecting these structures. To this end, small populations of neurons in the Drosophila melanogaster central complex were stochastically labeled using the multicolor flip-out technique and a catalog was created of the neurons, their morphologies, trajectories, relative arrangements, and corresponding GAL4 lines. This report focuses on one structure of the central complex, the protocerebral bridge, and identifies just 17 morphologically distinct cell types that arborize in this structure. This work also provides new insights into the anatomical structure of the four components of the central complex and its accessory neuropils. Most strikingly, we found that the protocerebral bridge contains 18 glomeruli, not 16, as previously believed. Revised wiring diagrams that take into account this updated architectural design are presented. This updated map of the Drosophila central complex will facilitate a deeper behavioral and physiological dissection of this sophisticated set of structures. © 2014 Wiley Periodicals, Inc.

Evidence that the assembly of the yeast cytochrome bc1 complex involves the formation of a large core structure in the inner mitochondrial membrane.

PubMed

Zara, Vincenzo; Conte, Laura; Trumpower, Bernard L

2009-04-01

The assembly status of the cytochrome bc(1) complex has been analyzed in distinct yeast deletion strains in which genes for one or more of the bc(1) subunits were deleted. In all the yeast strains tested, a bc(1) sub-complex of approximately 500 kDa was found when the mitochondrial membranes were analyzed by blue native electrophoresis. The subsequent molecular characterization of this sub-complex, carried out in the second dimension by SDS/PAGE and immunodecoration, revealed the presence of the two catalytic subunits, cytochrome b and cytochrome c(1), associated with the noncatalytic subunits core protein 1, core protein 2, Qcr7p and Qcr8p. Together, these bc(1) subunits build up the core structure of the cytochrome bc(1) complex, which is then able to sequentially bind the remaining subunits, such as Qcr6p, Qcr9p, the Rieske iron-sulfur protein and Qcr10p. This bc(1) core structure may represent a true assembly intermediate during the maturation of the bc(1) complex; first, because of its wide distribution in distinct yeast deletion strains and, second, for its characteristics of stability, which resemble those of the intact homodimeric bc(1) complex. By contrast, the bc(1) core structure is unable to interact with the cytochrome c oxidase complex to form respiratory supercomplexes. The characterization of this novel core structure of the bc(1) complex provides a number of new elements clarifying the molecular events leading to the maturation of the yeast cytochrome bc(1) complex in the inner mitochondrial membrane.

Evidence that assembly of the yeast cytochrome bc1 complex involves formation of a large core structure in the inner mitochondrial membrane

PubMed Central

Zara, Vincenzo; Conte, Laura; Trumpower, Bernard L.

2009-01-01

The assembly status of the cytochrome bc1 complex has been analyzed in distinct yeast deletion strains in which genes for one or more of the bc1 subunits had been deleted. In all the yeast strains tested a bc1 sub-complex of about 500 kDa was found when the mitochondrial membranes were analyzed by blue native electrophoresis. The subsequent molecular characterization of this sub-complex, carried out in the second dimension by SDS-PAGE and immunodecoration, revealed the presence of the two catalytic subunits cytochrome b and cytochrome c1, associated with the non catalytic subunits core protein 1, core protein 2, Qcr7p and Qcr8p. Altogether these bc1 subunits build up the core structure of the cytochrome bc1 complex which is then able to sequentially bind the remaining subunits, such as Qcr6p, Qcr9p, the Rieske iron-sulfur protein and Qcr10p. This bc1 core structure may represent a true assembly intermediate during the maturation of the bc1 complex, first because of its wide distribution in distinct yeast deletion strains and second for its characteristics of stability which resemble those of the intact homodimeric bc1 complex. Differently from this latter, however, the bc1 core structure is not able to interact with the cytochrome c oxidase complex to form respiratory supercomplexes. The characterization of this novel core structure of the bc1 complex provides a number of new elements for clarification of the molecular events leading to the maturation of the yeast cytochrome bc1 complex in the inner mitochondrial membrane. PMID:19236481

Three-dimensional structure of thymidine phosphorylase from E. coli in complex with 3'-azido-2'-fluoro-2',3'-dideoxyuridine

NASA Astrophysics Data System (ADS)

Timofeev, V. I.; Abramchik, Yu. A.; Fateev, I. V.; Zhukhlistova, N. E.; Murav'eva, T. I.; Kuranova, I. P.; Esipov, R. S.

2013-11-01

The three-dimensional structures of thymidine phosphorylase from E. coli containing the bound sulfate ion in the phosphate-binding site and of the complex of thymidine phosphorylase with sulfate in the phosphate-binding site and the inhibitor 3'-azido-2'-fluoro-2',3'-dideoxyuridine (N3F-ddU) in the nucleoside-binding site were determined at 1.55 and 1.50 Å resolution, respectively. The amino-acid residues involved in the ligand binding and the hydrogen-bond network in the active site occupied by a large number of bound water molecules are described. A comparison of the structure of thymidine phosphorylase in complex with N3F-ddU with the structure of pyrimidine nucleoside phosphorylase from St. Aureus in complex with the natural substrate thymidine (PDB_ID: 3H5Q) shows that the substrate and the inhibitor in the nucleoside-binding pocket have different orientations. It is suggested that the position of N3F-ddU can be influenced by the presence of the azido group, which prefers a hydrophobic environment. In both structures, the active sites of the subunits are in the open conformation.

A novel amido-pyrophosphate Mn(II) chelate complex with the synthetic ligand O{P(O)[NHC(CH3)3]2}2 (L): [Mn(L)2{OC(H)N(CH3)2}2]Cl2·2H2O.

PubMed

Tarahhomi, Atekeh; Pourayoubi, Mehrdad; Fejfarová, Karla; Dušek, Michal

2013-03-01

The title complex, trans-bis(dimethylformamide-κO)bis{N,N'-N'',N'''-tetra-tert-butyl[oxybis(phosphonic diamide-κO)]}manganese(II) dichloride dihydrate, [Mn(C16H40N4O3P2)2(C3H7NO)2]Cl2·2H2O, is the first example of a bis-chelate amido-pyrophosphate (pyrophosphoramide) complex containing an O[P(O)(NH)2]2 fragment. Its asymmetric unit contains half of the complex dication, one chloride anion and one water molecule. The Mn(II) atom, located on an inversion centre, is octahedrally coordinated, with a slight elongation towards the monodentate dimethylformamide ligand. Structural features of the title complex, such as the P=O bond lengths and the planarity of the chelate ring, are compared with those of previously reported complexes with six-membered chelates involving the fragments C(O)NHP(O), (X)NP(O) [X = C(O), C(S), S(O)2 and P(O)] and O[P(O)(N)2]2. This analysis shows that the six-membered chelate rings are less puckered in pyrophosphoramide complexes containing a P(O)OP(O) skeleton, such as the title compound. The extended structure of the title complex involves a linear aggregate mediated by N-H...O and N-H...Cl hydrogen bonds, in which the chloride anion is an acceptor in two additional O-H...Cl hydrogen bonds.

Respiratory complex I: 'steam engine' of the cell?

PubMed

Efremov, Rouslan G; Sazanov, Leonid A

2011-08-01

Complex I is the first enzyme of the respiratory chain and plays a central role in cellular energy production. It has been implicated in many human neurodegenerative diseases, as well as in ageing. One of the biggest membrane protein complexes, it is an L-shaped assembly consisting of hydrophilic and membrane domains. Previously, we have determined structures of the hydrophilic domain in several redox states. Last year was marked by fascinating breakthroughs in the understanding of the complete structure. We described the architecture of the membrane domain and of the entire bacterial complex I. X-ray analysis of the larger mitochondrial enzyme has also been published. The core subunits of the bacterial and mitochondrial enzymes have remarkably similar structures. The proposed mechanism of coupling between electron transfer and proton translocation involves long-range conformational changes, coordinated in part by a long α-helix, akin to the coupling rod of a steam engine. Copyright © 2011 Elsevier Ltd. All rights reserved.

Defense Against Pathogens: Structural Insights into the Mechanism of Chitin Induced Activation of Innate Immunity.

PubMed

Squeglia, Flavia; Berisio, Rita; Shibuya, Naoto; Kaku, Hanae

2017-11-24

Pattern recognition receptors on the plant cell surface mediate the recognition of microbe-associated molecular patterns, in a process which activates downstream immune signaling. These receptors are plasma membrane-localized kinases which need to be autophosphorylated to activate downstream responses. Perception of attacks from fungi occurs through recognition of chitin, a polymer of an N-acetylglucosamine which is a characteristic component of the cell walls of fungi. This process is regulated in Arabidopsis by chitin elicitor receptor kinase CERK1. A more complex process characterizes rice, in which regulation of chitin perception is operated by a complex composed of OsCERK1, a homolog of CERK1, and the chitin elicitor binding protein OsCEBiP. Recent literature has provided a mechanistic description of the complex regulation of activation of innate immunity in rice and an advance in the structural description of molecular players involved in this process. This review describes the current status of the understanding of molecular events involved in innate immunity activation in rice. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate

DOE PAGES

Cao, Hongnan; Tan, Kemin; Wang, Fengbin; ...

2016-04-29

CalE6 from Micromonospora echinospora is a (pyridoxal 50 phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. Here, we report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis andmore » holoenzyme maturation.« less

Stabilization of non-productive conformations underpins rapid electron transfer to electron-transferring flavoprotein.

PubMed

Toogood, Helen S; van Thiel, Adam; Scrutton, Nigel S; Leys, David

2005-08-26

Crystal structures of protein complexes with electron-transferring flavoprotein (ETF) have revealed a dual protein-protein interface with one region serving as anchor while the ETF FAD domain samples available space within the complex. We show that mutation of the conserved Glu-165beta in human ETF leads to drastically modulated rates of interprotein electron transfer with both medium chain acyl-CoA dehydrogenase and dimethylglycine dehydrogenase. The crystal structure of free E165betaA ETF is essentially identical to that of wild-type ETF, but the crystal structure of the E165betaA ETF.medium chain acyl-CoA dehydrogenase complex reveals clear electron density for the FAD domain in a position optimal for fast interprotein electron transfer. Based on our observations, we present a dynamic multistate model for conformational sampling that for the wild-type ETF. medium chain acyl-CoA dehydrogenase complex involves random motion between three distinct positions for the ETF FAD domain. ETF Glu-165beta plays a key role in stabilizing positions incompatible with fast interprotein electron transfer, thus ensuring high rates of complex dissociation.

The fuzzy cube and causal efficacy: representation of concomitant mechanisms in stroke.

PubMed

Jobe, Thomas H.; Helgason, Cathy M.

1998-04-01

Twentieth century medical science has embraced nineteenth century Boolean probability theory based upon two-valued Aristotelian logic. With the later addition of bit-based, von Neumann structured computational architectures, an epistemology based on randomness has led to a bivalent epidemiological methodology that dominates medical decision making. In contrast, fuzzy logic, based on twentieth century multi-valued logic, and computational structures that are content addressed and adaptively modified, has advanced a new scientific paradigm for the twenty-first century. Diseases such as stroke involve multiple concomitant causal factors that are difficult to represent using conventional statistical methods. We tested which paradigm best represented this complex multi-causal clinical phenomenon-stroke. We show that the fuzzy logic paradigm better represented clinical complexity in cerebrovascular disease than current probability theory based methodology. We believe this finding is generalizable to all of clinical science since multiple concomitant causal factors are involved in nearly all known pathological processes.

Mechanism and Substrate Recognition of Human Holo ACP Synthase

PubMed Central

Bunkoczi, Gabor; Pasta, Saloni; Joshi, Anil; Wu, Xiaoqiu; Kavanagh, Kathryn L.; Smith, Stuart; Oppermann, Udo

2007-01-01

Summary Mammals utilize a single phosphopantetheinyl transferase for the posttranslational modification of at least three different apoproteins: the carrier protein components of cytosolic and mitochondrial fatty acid synthases and the aminoadipate semialdehyde reductase involved in lysine degradation. We determined the crystal structure of the human phosphopantetheinyl transferase, a eukaryotic phosphopantetheinyl transferase characterized, complexed with CoA and Mg2+, and in ternary complex with CoA and ACP. The involvement of key residues in ligand binding and catalysis was confirmed by mutagenesis and kinetic analysis. Human phosphopantetheinyl transferase exhibits an α/β fold and 2-fold pseudosymmetry similar to the Sfp phosphopantetheinyl transferase from Bacillus subtilis. Although the bound ACP exhibits a typical four-helix structure, its binding is unusual in that it is facilitated predominantly by hydrophobic interactions. A detailed mechanism is proposed describing the substrate binding and catalytic process. PMID:18022563

Crystal structure of hexagonal MnAl4

PubMed Central

Pauling, Linus

1987-01-01

A structure is proposed for the hexagonal form of MnAl4, with aH = 28.4 Å and cH = 12.43 Å, on the basis of a high-resolution electron micrograph and comparison with crystals of known structures. The proposed structure involves seven 104-atom complexes of 20 Friauf polyhedra, sharing some atoms with one another. It is closely related to the 23.36-Å cubic structure of MnAl4 and to the 14.19-Å cubic structure of Mg32(Al,Zn)49. Images PMID:16593837

Formation of wood secondary cell wall may involve two type cellulose synthase complexes in Populus.

PubMed

Xi, Wang; Song, Dongliang; Sun, Jiayan; Shen, Junhui; Li, Laigeng

2017-03-01

Cellulose biosynthesis is mediated by cellulose synthases (CesAs), which constitute into rosette-like cellulose synthase complexe (CSC) on the plasma membrane. Two types of CSCs in Arabidopsis are believed to be involved in cellulose synthesis in the primary cell wall and secondary cell walls, respectively. In this work, we found that the two type CSCs participated cellulose biosynthesis in differentiating xylem cells undergoing secondary cell wall thickening in Populus. During the cell wall thickening process, expression of one type CSC genes increased while expression of the other type CSC genes decreased. Suppression of different type CSC genes both affected the wall-thickening and disrupted the multilaminar structure of the secondary cell walls. When CesA7A was suppressed, crystalline cellulose content was reduced, which, however, showed an increase when CesA3D was suppressed. The CesA suppression also affected cellulose digestibility of the wood cell walls. The results suggest that two type CSCs are involved in coordinating the cellulose biosynthesis in formation of the multilaminar structure in Populus wood secondary cell walls.

Minireview: DNA Replication in Plant Mitochondria

PubMed Central

Cupp, John D.; Nielsen, Brent L.

2014-01-01

Higher plant mitochondrial genomes exhibit much greater structural complexity as compared to most other organisms. Unlike well-characterized metazoan mitochondrial DNA (mtDNA) replication, an understanding of the mechanism(s) and proteins involved in plant mtDNA replication remains unclear. Several plant mtDNA replication proteins, including DNA polymerases, DNA primase/helicase, and accessory proteins have been identified. Mitochondrial dynamics, genome structure, and the complexity of dual-targeted and dual-function proteins that provide at least partial redundancy suggest that plants have a unique model for maintaining and replicating mtDNA when compared to the replication mechanism utilized by most metazoan organisms. PMID:24681310

A rationale on the role of intermediate Au(III)-vitamin C complexation in the production of gold nanoparticles

NASA Astrophysics Data System (ADS)

Zümreoglu-Karan, B.

2009-07-01

Preparation of gold nanoparticles, particularly gold nanorods, by wet chemistry processes involves gold seeds, an Au(III) salt, structure directing surfactants, and metal ion additives in the growth solution into which a weak reducing agent is added. The most commonly employed weak reducing agent is l-ascorbic acid (vitamin C) which is known to reduce many metal ions in the solution phase and form complexes with relatively low stability constants. A purple-gray gold-ascorbate compound, obtained from the reaction of sodium tetrachloroaurate(III) with sodium ascorbate, is now reported. The compound possesses the expected structural features of vitamin C-metal complexes as verified by its 13C CP-MAS NMR spectrum. A discussion is also presented on the possibility of gold-ascorbate complexation operating in gold nanoparticle formation.

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution.

PubMed

Venkataraman, Sangita; Prasad, Burra V L S; Selvarajan, Ramasamy

2018-02-10

RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription. The core structural features of RdRps are conserved, despite the divergence in their sequences. The structure of RdRp resembles that of a cupped right hand and consists of fingers, palm and thumb subdomains. The catalysis involves the participation of conserved aspartates and divalent metal ions. Complexes of RdRps with substrates, inhibitors and metal ions provide a comprehensive view of their functional mechanism and offer valuable insights regarding the development of antivirals. In this article, we provide an overview of the structural aspects of RdRps and their complexes from the Group III, IV and V viruses and their structure-based phylogeny.

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution

PubMed Central

Venkataraman, Sangita; Prasad, Burra V L S; Selvarajan, Ramasamy

2018-01-01

RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription. The core structural features of RdRps are conserved, despite the divergence in their sequences. The structure of RdRp resembles that of a cupped right hand and consists of fingers, palm and thumb subdomains. The catalysis involves the participation of conserved aspartates and divalent metal ions. Complexes of RdRps with substrates, inhibitors and metal ions provide a comprehensive view of their functional mechanism and offer valuable insights regarding the development of antivirals. In this article, we provide an overview of the structural aspects of RdRps and their complexes from the Group III, IV and V viruses and their structure-based phylogeny. PMID:29439438

Structured analysis and modeling of complex systems

NASA Technical Reports Server (NTRS)

Strome, David R.; Dalrymple, Mathieu A.

1992-01-01

The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm.

Challenges in the management of massive intraorbital and hemifacial arteriovenous malformation as causing life-threatening epistaxis.

PubMed

Manuel, Anura Michelle; Kalimuthu, Santhi; Pathmanathan, Sitra Siri; Narayanan, Prepageran; Zainal Abidin, Zurina; Azmi, Khairul; Khalil, Alizan

2017-04-01

Arteriovenous malformations are congenital lesions that may evolve with time and manifest in a plethora of presentations. They can occur as torrential epistaxis when it extensively involves the facial region. Multi-imaging modalities are available to assist in characterizing the structure of the lesion as well as its location and extent. This complex disease requires a multidisciplinary team approach with preoperative embolization and surgery. We present a rare cause of life-threatening epistaxis in a gentleman with a longstanding orbital and hemifacial arteriovenous malformation and discuss the complexities involved in its management. Copyright © 2017. Published by Elsevier Taiwan.

Atomic description of the immune complex involved in heparin-induced thrombocytopenia

DOE PAGES

Cai, Zheng; Yarovoi, Serge V.; Zhu, Zhiqiang; ...

2015-09-22

Heparin-induced thrombocytopenia (HIT) is an autoimmune thrombotic disorder caused by immune complexes containing platelet factor 4 (PF4), antibodies to PF4 and heparin or cellular glycosaminoglycans (GAGs). Here we solve the crystal structures of the: (1) PF4 tetramer/fondaparinux complex, (2) PF4 tetramer/KKO-Fab complex (a murine monoclonal HIT-like antibody) and (3) PF4 monomer/RTO-Fab complex (a non-HIT anti-PF4 monoclonal antibody). Fondaparinux binds to the ‘closed’ end of the PF4 tetramer and stabilizes its conformation. This interaction in turn stabilizes the epitope for KKO on the ‘open’ end of the tetramer. Fondaparinux and KKO thereby collaborate to ‘stabilize’ the ternary pathogenic immune complex. Bindingmore » of RTO to PF4 monomers prevents PF4 tetramerization and inhibits KKO and human HIT IgG-induced platelet activation and platelet aggregation in vitro, and thrombus progression in vivo. Lastly, the atomic structures provide a basis to develop new diagnostics and non-anticoagulant therapeutics for HIT.« less

Harnessing glycomics technologies: integrating structure with function for glycan characterization

PubMed Central

Robinson, Luke N.; Artpradit, Charlermchai; Raman, Rahul; Shriver, Zachary H.; Ruchirawat, Mathuros; Sasisekharan, Ram

2013-01-01

Glycans, or complex carbohydrates, are a ubiquitous class of biological molecules which impinge on a variety of physiological processes ranging from signal transduction to tissue development and microbial pathogenesis. In comparison to DNA and proteins, glycans present unique challenges to the study of their structure and function owing to their complex and heterogeneous structures and the dominant role played by multivalency in their sequence-specific biological interactions. Arising from these challenges, there is a need to integrate information from multiple complementary methods to decode structure-function relationships. Focusing on acidic glycans, we describe here key glycomics technologies for characterizing their structural attributes, including linkage, modifications, and topology, as well as for elucidating their role in biological processes. Two cases studies, one involving sialylated branched glycans and the other sulfated glycosaminoglycans, are used to highlight how integration of orthogonal information from diverse datasets enables rapid convergence of glycan characterization for development of robust structure-function relationships. PMID:22522536

Neural substrates of decision-making.

PubMed

Broche-Pérez, Y; Herrera Jiménez, L F; Omar-Martínez, E

2016-06-01

Decision-making is the process of selecting a course of action from among 2 or more alternatives by considering the potential outcomes of selecting each option and estimating its consequences in the short, medium and long term. The prefrontal cortex (PFC) has traditionally been considered the key neural structure in decision-making process. However, new studies support the hypothesis that describes a complex neural network including both cortical and subcortical structures. The aim of this review is to summarise evidence on the anatomical structures underlying the decision-making process, considering new findings that support the existence of a complex neural network that gives rise to this complex neuropsychological process. Current evidence shows that the cortical structures involved in decision-making include the orbitofrontal cortex (OFC), anterior cingulate cortex (ACC), and dorsolateral prefrontal cortex (DLPFC). This process is assisted by subcortical structures including the amygdala, thalamus, and cerebellum. Findings to date show that both cortical and subcortical brain regions contribute to the decision-making process. The neural basis of decision-making is a complex neural network of cortico-cortical and cortico-subcortical connections which includes subareas of the PFC, limbic structures, and the cerebellum. Copyright © 2014 Sociedad Española de Neurología. Published by Elsevier España, S.L.U. All rights reserved.

Structure of the membrane domain of respiratory complex I.

PubMed

Efremov, Rouslan G; Sazanov, Leonid A

2011-08-07

Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Å resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.

Structural and functional properties of the HIV-1 RNA-tRNA(Lys)3 primer complex annealed by the nucleocapsid protein: comparison with the heat-annealed complex.

PubMed Central

Brulé, Fabienne; Marquet, Roland; Rong, Liwei; Wainberg, Mark A; Roques, Bernard P; Le Grice, Stuart F J; Ehresmann, Bernard; Ehresmann, Chantal

2002-01-01

The conversion of the single-stranded RNA genome into double-stranded DNA by virus-coded reverse transcriptase (RT) is an essential step of the retrovirus life cycle. In human immunodeficiency virus type 1 (HIV-1), RT uses the cellular tRNA(Lys)3 to initiate the (-) strand DNA synthesis. Placement of the primer tRNA(Lys)3 involves binding of its 3'-terminal 18 nt to a complementary region of genomic RNA termed PBS. However, the PBS sequence is not the unique determinant of primer usage and additional contacts are important. This placement is believed to be achieved in vivo by the nucleocapsid domain of Gag or by the mature protein NCp. Up to now, structural information essentially arose from heat-annealed primer-template complexes (Isel et al., J Mol Biol, 1995, 247:236-250; Isel et al., EMBO J, 1999, 18:1038-1048). Here, we investigated the formation of the primer-template complex mediated by NCp and compared structural and functional properties of heat- and NCp-annealed complexes. We showed that both heat- and NCp-mediated procedures allow comparable high yields of annealing. Then, we investigated structural features of both kinds of complexes by enzymatic probing, and we compared their relative efficiency in (-) strong stop DNA synthesis. We did not find any significant differences between these complexes, suggesting that information derived from the heat-annealed complex can be transposed to the NCp-mediated complex and most likely to complexes formed in vivo. PMID:11873759

A long-lived mesoscale convective complex. II - Evolution and structure of the mature complex

NASA Technical Reports Server (NTRS)

Wetzel, P. J.; Cotton, W. R.; Mcanelly, R. L.

1983-01-01

The present investigation is concerned with an eight-day episode, during which a series of mesoscale convective complexes (MCC) developed and moved across the country, producing heavy rain and some flooding over an extensive region. An overview of the considered period from August 3 to August 10, 1977 is presented, and the evolution of the August 4 storm is examined. The structure of the mature MCC is discussed, taking into account the August 4-5 storm, a comparative case involving the August 3-4 storm, and an evaluation of the observed phenomena. It is concluded that MCCs are basically tropical in nature and that their dynamics are dominated by buoyant accelerations. It was found that the MCCs developed a warm-core, divergent anticyclonic flow pattern in the upper troposphere which was not present prior to the development of convection. A similar structure is observed in tropical cloud clusters.

The structure of the nucleoprotein binding domain of lyssavirus phosphoprotein reveals a structural relationship between the N-RNA binding domains of Rhabdoviridae and Paramyxoviridae.

PubMed

Delmas, Olivier; Assenberg, Rene; Grimes, Jonathan M; Bourhy, Hervé

2010-01-01

The phosphoprotein P of non-segmented negative-sense RNA viruses is an essential component of the replication and transcription complex and acts as a co-factor for the viral RNA-dependent RNA polymerase. P recruits the viral polymerase to the nucleoprotein-bound viral RNA (N-RNA) via an interaction between its C-terminal domain and the N-RNA complex. We have obtained the structure of the C-terminal domain of P of Mokola virus (MOKV), a lyssavirus that belongs to the Rhabdoviridae family and mapped at the amino acid level the crucial positions involved in interaction with N and in the formation of the viral replication complex. Comparison of the N-RNA binding domains of P solved to date suggests that the N-RNA binding domains are structurally conserved among paramyxoviruses and rhabdoviruses in spite of low sequence conservation. We also review the numerous other functions of this domain and more generally of the phosphoprotein.

Automated dynamic analytical model improvement for damped structures

NASA Technical Reports Server (NTRS)

Fuh, J. S.; Berman, A.

1985-01-01

A method is described to improve a linear nonproportionally damped analytical model of a structure. The procedure finds the smallest changes in the analytical model such that the improved model matches the measured modal parameters. Features of the method are: (1) ability to properly treat complex valued modal parameters of a damped system; (2) applicability to realistically large structural models; and (3) computationally efficiency without involving eigensolutions and inversion of a large matrix.

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

Zhang, Jiang; Malmirchegini, G. Reza; Clubb, Robert T.

Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and non-covalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down mass spectrometry using electrospray ionization (ESI) and a 15-Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Native MS preserves the non-covalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of themore » Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore low fragmentation efficiency. Precursor ion activation allows steady increase of N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and 4 z ions on the α chain; 36 c ions and 2 z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer show similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. Finally, it may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.« less

Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms.

PubMed

Kloosterman, Wigard P; Tavakoli-Yaraki, Masoumeh; van Roosmalen, Markus J; van Binsbergen, Ellen; Renkens, Ivo; Duran, Karen; Ballarati, Lucia; Vergult, Sarah; Giardino, Daniela; Hansson, Kerstin; Ruivenkamp, Claudia A L; Jager, Myrthe; van Haeringen, Arie; Ippel, Elly F; Haaf, Thomas; Passarge, Eberhard; Hochstenbach, Ron; Menten, Björn; Larizza, Lidia; Guryev, Victor; Poot, Martin; Cuppen, Edwin

2012-06-28

Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyze the genomes of ten patients with congenital disease who were preselected to carry complex chromosomal rearrangements with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. In addition, nucleotide resolution analysis of 98 breakpoint junctions indicates that break repair involves nonhomologous or microhomology-mediated end joining. We observed that these eight rearrangements are balanced or contain sporadic deletions ranging in size between a few hundred base pairs and several megabases. The two remaining complex rearrangements did not display signs of DSBs and contain duplications, indicative of rearrangement processes involving template switching. Our work provides detailed insight into the characteristics of chromothripsis and supports a role for clustered DSBs driving some constitutional chromothripsis rearrangements. Copyright © 2012 The Authors. Published by Elsevier Inc. All rights reserved.

Perspectives for the use of structural information and chemical genetics to develop inhibitors of Janus kinases

PubMed Central

Haan, Claude; Behrmann, Iris; Haan, Serge

2010-01-01

Abstract Gain-of-function mutations in the genes encoding Janus kinases have been discovered in various haematologic diseases. Jaks are composed of a FERM domain, an SH2 domain, a pseudokinase domain and a kinase domain, and a complex interplay of the Jak domains is involved in regulation of catalytic activity and association to cytokine receptors. Most activating mutations are found in the pseudokinase domain. Here we present recently discovered mutations in the context of our structural models of the respective domains. We describe two structural hotspots in the pseudokinase domain of Jak2 that seem to be associated either to myeloproliferation or to lymphoblastic leukaemia, pointing at the involvement of distinct signalling complexes in these disease settings. The different domains of Jaks are discussed as potential drug targets. We present currently available inhibitors targeting Jaks and indicate structural differences in the kinase domains of the different Jaks that may be exploited in the development of specific inhibitors. Moreover, we discuss recent chemical genetic approaches which can be applied to Jaks to better understand the role of these kinases in their biological settings and as drug targets. PMID:20132407

Analysis of the interactions between GMF and Arp2/3 complex in two binding sites by molecular dynamics simulation.

PubMed

Popinako, A; Antonov, M; Dibrova, D; Chemeris, A; Sokolova, O S

2018-02-05

The Arp2/3 complex plays a key role in nucleating actin filaments branching. The glia maturation factor (GMF) competes with activators for interacting with the Arp2/3 complex and initiates the debranching of actin filaments. In this study, we performed a comparative analysis of interactions between GMF and the Arp2/3 complex and identified new amino acid residues involved in GMF binding to the Arp2/3 complex at two separate sites, revealed by X-ray and single particle EM techniques. Using molecular dynamics simulations we demonstrated the quantitative and qualitative changes in hydrogen bonds upon binding with GMF. We identified the specific amino acid residues in GMF and Arp2/3 complex that stabilize the interactions and estimated the mean force profile for the GMF using umbrella sampling. Phylogenetic and structural analyses of the recently defined GMF binding site on the Arp3 subunit indicate a new mechanism for Arp2/3 complex inactivation that involves interactions between the Arp2/3 complex and GMF at two binding sites. Copyright © 2018 Elsevier Inc. All rights reserved.

Identification of continuous interaction sites in PLA(2)-based protein complexes by peptide arrays.

PubMed

Fortes-Dias, Consuelo Latorre; Santos, Roberta Márcia Marques dos; Magro, Angelo José; Fontes, Marcos Roberto de Mattos; Chávez-Olórtegui, Carlos; Granier, Claude

2009-01-01

Crotoxin (CA.CB) is a beta-neurotoxin from Crotalus durissus terrificus snake venom that is responsible for main envenomation effects upon biting by this snake. It is a heterodimer of an acidic protein (CA) devoid of any biological activity per se and a basic, enzymatically active, PLA(2) counterpart (CB). Both lethal and enzymatic activities of crotoxin have been shown to be inhibited by CNF, a protein from the blood of C. d. terrificus snakes. CNF replaces CA in the CA.CB complex, forming a stable, non-toxic complex CNF.CB. The molecular sites involved in the tight interfacial protein-protein interactions in these PLA(2)-based complexes have not been clearly determined. To help address this question, we used the peptide arrays approach to map possible interfacial interaction sites in CA.CB and CNF.CB. Amino acid stretches putatively involved in these interactions were firstly identified in the primary structure of CB. Further analysis of the interfacial availability of these stretches in the presumed biologically active structure of CB, suggested two interaction main sites, located at the amino-terminus and beta-wing regions. Peptide segments at the carboxyl-terminus of CB were also suggested to play a secondary role in the binding of both CA and CNF.

Catecholase activity of dicopper(II)-bispidine complexes: stabilities and structures of intermediates, kinetics and reaction mechanism.

PubMed

Born, Karin; Comba, Peter; Daubinet, André; Fuchs, Alexander; Wadepohl, Hubert

2007-01-01

A mechanism for the oxidation of 3,5-di-tert-butylcatechol (dtbc) with dioxygen to the corresponding quinone (dtbq), catalyzed by bispidine-dicopper complexes (bispidines are various mono- and dinucleating derivatives of 3,7-diazabicyclo[3.3.1]nonane with bis-tertiary-amine-bispyridyl or bis-tertiary-amine-trispyridyl donor sets), is proposed on the basis of (1) the stoichiometry of the reaction as well as the stabilities and structures [X-ray, density functional theory (B3LYP, TZV)] of the bispidine-dicopper(II)-3,4,5,6-tetrachlorcatechol intermediates, (2) formation kinetics and structures (molecular mechanics, MOMEC) of the end-on peroxo-dicopper(II) complexes and (3) kinetics of the stoichiometric (anaerobic) and catalytic (aerobic) copper-complex-assisted oxidation of dtbc. This involves (1) the oxidation of the dicopper(I) complexes with dioxygen to the corresponding end-on peroxo-dicopper(II) complexes, (2) coordination of dtbc as a bridging ligand upon liberation of H(2)O(2) and (3) intramolecular electron transfer to produce dtbq, which is liberated, and the dicopper(I) catalyst. Although the bispidine complexes have reactivities comparable to those of recently published catalysts with macrocyclic ligands, which seem to reproduce the enzyme-catalyzed process in various reaction sequences, a strikingly different oxidation mechanism is derived from the bispidine-dicopper-catalyzed reaction.

A new supramolecular chromium(III) complex: Synthesis, structural determination, optical study, magnetic and antibacterial activity

NASA Astrophysics Data System (ADS)

Dridi, Rihab; Dhieb, Cyrine; Cherni, Saoussen Namouchi; Boudjada, Nassira Chniba; Sadfi Zouaoui, Najla; Zid, Mohamed Faouzi

2018-01-01

A new chromium (III) complex 1,5-Naphthyridine Trans-diaquadioxalatochromate (III) dihydrate, had been synthesized by self-assembly of chromium (III) nitrate with oxalic acid and 1,5-Naphthyridine. The complex was characterized by X-ray diffraction, Fourier Transform Infrared spectroscopy, thermogravimetric analysis and UV-Visible spectroscopy. The crystal morphology was carried out using Bravais-Friedel-Donnay-Harker (BFDH) model. Single crystal X-Ray structure determination revealed that the complex posses two crystallographically independent Cr(III) centers. Each Cr(III) has a distorted octahedron geometry involving two axial O atoms from two water molecules and four equatorial O atoms from two oxalate dianions forming trans-[Cr(C2O4)2(H2O)2]- complex anions. The charge compensation is accomplished by the incorporation of 1,5-Naphthyridine cations. Connection between these entities is ensured by means of strong hydrogen bonds giving rise to 3D supramolecular architecture. Hirshfeld surface analysis and the related 2D fingerprint plots were used for decoding plausible intermolecular interactions in the crystal packing. The magnetic properties of the complex had been investigated and discussed in the context of its structure. The antimicrobial activity was evaluated by disc diffusion method highlighting an antagonistic effect of the synthesized complex against Gram-positive and Gram-negative species.

Molecular envelope and atomic model of an anti-terminated glyQS T-box regulator in complex with tRNAGly

PubMed Central

Chetnani, Bhaskar

2017-01-01

Abstract A T-box regulator or riboswitch actively monitors the levels of charged/uncharged tRNA and participates in amino acid homeostasis by regulating genes involved in their utilization or biosynthesis. It has an aptamer domain for cognate tRNA recognition and an expression platform to sense the charge state and modulate gene expression. These two conserved domains are connected by a variable linker that harbors additional secondary structural elements, such as Stem III. The structural basis for specific tRNA binding is known, but the structural basis for charge sensing and the role of other elements remains elusive. To gain new structural insights on the T-box mechanism, a molecular envelope was calculated from small angle X-ray scattering data for the Bacillus subtilis glyQS T-box riboswitch in complex with an uncharged tRNAGly. A structural model of an anti-terminated glyQS T-box in complex with its cognate tRNAGly was derived based on the molecular envelope. It shows the location and relative orientation of various secondary structural elements. The model was validated by comparing the envelopes of the wild-type complex and two variants. The structural model suggests that in addition to a possible regulatory role, Stem III could aid in preferential stabilization of the T-box anti-terminated state allowing read-through of regulated genes. PMID:28531275

Structural model of the hUbA1-UbcH10 quaternary complex: in silico and experimental analysis of the protein-protein interactions between E1, E2 and ubiquitin.

PubMed

Correale, Stefania; de Paola, Ivan; Morgillo, Carmine Marco; Federico, Antonella; Zaccaro, Laura; Pallante, Pierlorenzo; Galeone, Aldo; Fusco, Alfredo; Pedone, Emilia; Luque, F Javier; Catalanotti, Bruno

2014-01-01

UbcH10 is a component of the Ubiquitin Conjugation Enzymes (Ubc; E2) involved in the ubiquitination cascade controlling the cell cycle progression, whereby ubiquitin, activated by E1, is transferred through E2 to the target protein with the involvement of E3 enzymes. In this work we propose the first three dimensional model of the tetrameric complex formed by the human UbA1 (E1), two ubiquitin molecules and UbcH10 (E2), leading to the transthiolation reaction. The 3D model was built up by using an experimentally guided incremental docking strategy that combined homology modeling, protein-protein docking and refinement by means of molecular dynamics simulations. The structural features of the in silico model allowed us to identify the regions that mediate the recognition between the interacting proteins, revealing the active role of the ubiquitin crosslinked to E1 in the complex formation. Finally, the role of these regions involved in the E1-E2 binding was validated by designing short peptides that specifically interfere with the binding of UbcH10, thus supporting the reliability of the proposed model and representing valuable scaffolds for the design of peptidomimetic compounds that can bind selectively to Ubcs and inhibit the ubiquitylation process in pathological disorders.

The structure and protein binding of amyloid-specific dye reagents.

PubMed

Stopa, Barbara; Piekarska, Barbara; Konieczny, Leszek; Rybarska, Janina; Spólnik, Paweł; Zemanek, Grzegorz; Roterman, Irena; Król, Marcin

2003-01-01

The self-assembling tendency and protein complexation capability of dyes related to Congo red and also some dyes of different structure were compared to explain the mechanism of Congo red binding and the reason for its specific affinity for beta-structure. Complexation with proteins was measured directly and expressed as the number of dye molecules bound to heat-aggregated IgG and to two light chains with different structural stability. Binding of dyes to rabbit antibodies was measured indirectly as the enhancement effect of the dye on immune complex formation. Self-assembling was tested using dynamic light scattering to measure the size of the supramolecular assemblies. In general the results show that the supramolecular form of a dye is the main factor determining its complexation capability. Dyes that in their compact supramolecular organization are ribbon-shaped may adhere to polypeptides of beta-conformation due to the architectural compatibility in this unique structural form. The optimal fit in complexation seems to depend on two contradictory factors involving, on the one hand, the compactness of the non-covalently stabilized supramolecular ligand, and the dynamic character producing its plasticity on the other. As a result, the highest protein binding capability is shown by dyes with a moderate self-assembling tendency, while those arranging into either very rigid or very unstable supramolecular entities are less able to bind.

Neuroarchitecture and neuroanatomy of the Drosophila central complex: A GAL4-based dissection of protocerebral bridge neurons and circuits

PubMed Central

Wolff, Tanya; Iyer, Nirmala A; Rubin, Gerald M

2015-01-01

Insects exhibit an elaborate repertoire of behaviors in response to environmental stimuli. The central complex plays a key role in combining various modalities of sensory information with an insect's internal state and past experience to select appropriate responses. Progress has been made in understanding the broad spectrum of outputs from the central complex neuropils and circuits involved in numerous behaviors. Many resident neurons have also been identified. However, the specific roles of these intricate structures and the functional connections between them remain largely obscure. Significant gains rely on obtaining a comprehensive catalog of the neurons and associated GAL4 lines that arborize within these brain regions, and on mapping neuronal pathways connecting these structures. To this end, small populations of neurons in the Drosophila melanogaster central complex were stochastically labeled using the multicolor flip-out technique and a catalog was created of the neurons, their morphologies, trajectories, relative arrangements, and corresponding GAL4 lines. This report focuses on one structure of the central complex, the protocerebral bridge, and identifies just 17 morphologically distinct cell types that arborize in this structure. This work also provides new insights into the anatomical structure of the four components of the central complex and its accessory neuropils. Most strikingly, we found that the protocerebral bridge contains 18 glomeruli, not 16, as previously believed. Revised wiring diagrams that take into account this updated architectural design are presented. This updated map of the Drosophila central complex will facilitate a deeper behavioral and physiological dissection of this sophisticated set of structures. J. Comp. Neurol. 523:997–1037, 2015. © 2014 Wiley Periodicals, Inc. PMID:25380328

Improving design phase evaluations for high pile rebound sites [summary].

DOT National Transportation Integrated Search

2016-05-01

In Florida, many structures are built on driven piles. Though it seems straightforward, pile : driving involves complex interactions between the pile, the hammer, the soil, and driving : procedures. Soils can even rebound, or push back, after each ha...

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

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

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in

2015-07-28

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging themore » ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.« less

Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study.

PubMed

Corbett, Michael S P; Mark, Alan E; Poger, David

2017-02-28

Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Gi- and Gs-coupled GPCRs show different modes of G-protein binding.

PubMed

Van Eps, Ned; Altenbach, Christian; Caro, Lydia N; Latorraca, Naomi R; Hollingsworth, Scott A; Dror, Ron O; Ernst, Oliver P; Hubbell, Wayne L

2018-03-06

More than two decades ago, the activation mechanism for the membrane-bound photoreceptor and prototypical G protein-coupled receptor (GPCR) rhodopsin was uncovered. Upon light-induced changes in ligand-receptor interaction, movement of specific transmembrane helices within the receptor opens a crevice at the cytoplasmic surface, allowing for coupling of heterotrimeric guanine nucleotide-binding proteins (G proteins). The general features of this activation mechanism are conserved across the GPCR superfamily. Nevertheless, GPCRs have selectivity for distinct G-protein family members, but the mechanism of selectivity remains elusive. Structures of GPCRs in complex with the stimulatory G protein, G s , and an accessory nanobody to stabilize the complex have been reported, providing information on the intermolecular interactions. However, to reveal the structural selectivity filters, it will be necessary to determine GPCR-G protein structures involving other G-protein subtypes. In addition, it is important to obtain structures in the absence of a nanobody that may influence the structure. Here, we present a model for a rhodopsin-G protein complex derived from intermolecular distance constraints between the activated receptor and the inhibitory G protein, G i , using electron paramagnetic resonance spectroscopy and spin-labeling methodologies. Molecular dynamics simulations demonstrated the overall stability of the modeled complex. In the rhodopsin-G i complex, G i engages rhodopsin in a manner distinct from previous GPCR-G s structures, providing insight into specificity determinants. Copyright © 2018 the Author(s). Published by PNAS.

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

PubMed Central

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

2008-01-01

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

MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation.

PubMed

Falconi, M; Oteri, F; Eliseo, T; Cicero, D O; Desideri, A

2008-08-01

The structural dynamics of the DNA binding domains of the human papillomavirus strain 16 and the bovine papillomavirus strain 1, complexed with their DNA targets, has been investigated by modeling, molecular dynamics simulations, and nuclear magnetic resonance analysis. The simulations underline different dynamical features of the protein scaffolds and a different mechanical interaction of the two proteins with DNA. The two protein structures, although very similar, show differences in the relative mobility of secondary structure elements. Protein structural analyses, principal component analysis, and geometrical and energetic DNA analyses indicate that the two transcription factors utilize a different strategy in DNA recognition and deformation. Results show that the protein indirect DNA readout is not only addressable to the DNA molecule flexibility but it is finely tuned by the mechanical and dynamical properties of the protein scaffold involved in the interaction.

Structure of the parainfluenza virus 5 F protein in its metastable, prefusion conformation.

PubMed

Yin, Hsien-Sheng; Wen, Xiaolin; Paterson, Reay G; Lamb, Robert A; Jardetzky, Theodore S

2006-01-05

Enveloped viruses have evolved complex glycoprotein machinery that drives the fusion of viral and cellular membranes, permitting entry of the viral genome into the cell. For the paramyxoviruses, the fusion (F) protein catalyses this membrane merger and entry step, and it has been postulated that the F protein undergoes complex refolding during this process. Here we report the crystal structure of the parainfluenza virus 5 F protein in its prefusion conformation, stabilized by the addition of a carboxy-terminal trimerization domain. The structure of the F protein shows that there are profound conformational differences between the pre- and postfusion states, involving transformations in secondary and tertiary structure. The positions and structural transitions of key parts of the fusion machinery, including the hydrophobic fusion peptide and two helical heptad repeat regions, clarify the mechanism of membrane fusion mediated by the F protein.

Community detection in complex networks using proximate support vector clustering

NASA Astrophysics Data System (ADS)

Wang, Feifan; Zhang, Baihai; Chai, Senchun; Xia, Yuanqing

2018-03-01

Community structure, one of the most attention attracting properties in complex networks, has been a cornerstone in advances of various scientific branches. A number of tools have been involved in recent studies concentrating on the community detection algorithms. In this paper, we propose a support vector clustering method based on a proximity graph, owing to which the introduced algorithm surpasses the traditional support vector approach both in accuracy and complexity. Results of extensive experiments undertaken on computer generated networks and real world data sets illustrate competent performances in comparison with the other counterparts.

A framework for evaluating complex networks measurements

NASA Astrophysics Data System (ADS)

Comin, Cesar H.; Silva, Filipi N.; Costa, Luciano da F.

2015-06-01

A good deal of current research in complex networks involves the characterization and/or classification of the topological properties of given structures, which has motivated several respective measurements. This letter proposes a framework for evaluating the quality of complex-network measurements in terms of their effective resolution, degree of degeneracy and discriminability. The potential of the suggested approach is illustrated with respect to comparing the characterization of several model and real-world networks by using concentric and symmetry measurements. The results indicate a markedly superior performance for the latter type of mapping.

An evolutionary link between capsular biogenesis and surface motility in bacteria.

PubMed

Agrebi, Rym; Wartel, Morgane; Brochier-Armanet, Céline; Mignot, Tâm

2015-05-01

Studying the evolution of macromolecular assemblies is important to improve our understanding of how complex cellular structures evolved, and to identify the functional building blocks that are involved. Recent studies suggest that the macromolecular complexes that are involved in two distinct processes in Myxococcus xanthus - surface motility and sporulation - are derived from an ancestral polysaccharide capsule assembly system. In this Opinion article, we argue that the available data suggest that the motility machinery evolved from this capsule assembly system following a gene duplication event, a change in carbohydrate polymer specificity and the acquisition of additional proteins by the motility complex, all of which are key features that distinguish the motility and sporulation systems. Furthermore, the presence of intermediates of these systems in bacterial genomes suggests a testable evolutionary model for their emergence and spread.

[The cinema as a device for teaching complexity in mental health].

PubMed

Delego, Adriana; Carroll, Hugo

2013-01-01

This article proposes the use of Cinema as an instrument for a complex approach to Teaching in the field of Clinical Psychiatry and Psychopathology in Mental Health. With this aim, intends a different look that pretends the approach not only to the conceptual structures on Psychopathology, but also to the complexity involved, choosing Cinema as a powerful way of "empathic recreation". Based on previous work by several authors, the theoretical framework that supports this modality is presented in the philosophical, cognitive, pedagogical-didactic aspects and their consequences into teaching within Mental Health. This task also implies addressing the historical evolution of the representation of subjectivity in fiction. In this way, a new perspective to those working in the field of mental health, as subjects involved in continuous learning processes, is presented. This perspective emphasizes the interactions underlying psychic problematical.

Novel Binding Motif and New Flexibility Revealed by Structural Analyses of a Pyruvate Dehydrogenase-Dihydrolipoyl Acetyltransferase Subcomplex from the Escherichia coli Pyruvate Dehydrogenase Multienzyme Complex*

PubMed Central

Arjunan, Palaniappa; Wang, Junjie; Nemeria, Natalia S.; Reynolds, Shelley; Brown, Ian; Chandrasekhar, Krishnamoorthy; Calero, Guillermo; Jordan, Frank; Furey, William

2014-01-01

The Escherichia coli pyruvate dehydrogenase multienzyme complex contains multiple copies of three enzymatic components, E1p, E2p, and E3, that sequentially carry out distinct steps in the overall reaction converting pyruvate to acetyl-CoA. Efficient functioning requires the enzymatic components to assemble into a large complex, the integrity of which is maintained by tethering of the displaced, peripheral E1p and E3 components to the E2p core through non-covalent binding. We here report the crystal structure of a subcomplex between E1p and an E2p didomain containing a hybrid lipoyl domain along with the peripheral subunit-binding domain responsible for tethering to the core. In the structure, a region at the N terminus of each subunit in the E1p homodimer previously unseen due to crystallographic disorder was observed, revealing a new folding motif involved in E1p-E2p didomain interactions, and an additional, unexpected, flexibility was discovered in the E1p-E2p didomain subcomplex, both of which probably have consequences in the overall multienzyme complex assembly. This represents the first structure of an E1p-E2p didomain subcomplex involving a homodimeric E1p, and the results may be applicable to a large range of complexes with homodimeric E1 components. Results of HD exchange mass spectrometric experiments using the intact, wild type 3-lipoyl E2p and E1p are consistent with the crystallographic data obtained from the E1p-E2p didomain subcomplex as well as with other biochemical and NMR data reported from our groups, confirming that our findings are applicable to the entire E1p-E2p assembly. PMID:25210042

Novel binding motif and new flexibility revealed by structural analyses of a pyruvate dehydrogenase-dihydrolipoyl acetyltransferase subcomplex from the Escherichia coli pyruvate dehydrogenase multienzyme complex.

PubMed

Arjunan, Palaniappa; Wang, Junjie; Nemeria, Natalia S; Reynolds, Shelley; Brown, Ian; Chandrasekhar, Krishnamoorthy; Calero, Guillermo; Jordan, Frank; Furey, William

2014-10-24

The Escherichia coli pyruvate dehydrogenase multienzyme complex contains multiple copies of three enzymatic components, E1p, E2p, and E3, that sequentially carry out distinct steps in the overall reaction converting pyruvate to acetyl-CoA. Efficient functioning requires the enzymatic components to assemble into a large complex, the integrity of which is maintained by tethering of the displaced, peripheral E1p and E3 components to the E2p core through non-covalent binding. We here report the crystal structure of a subcomplex between E1p and an E2p didomain containing a hybrid lipoyl domain along with the peripheral subunit-binding domain responsible for tethering to the core. In the structure, a region at the N terminus of each subunit in the E1p homodimer previously unseen due to crystallographic disorder was observed, revealing a new folding motif involved in E1p-E2p didomain interactions, and an additional, unexpected, flexibility was discovered in the E1p-E2p didomain subcomplex, both of which probably have consequences in the overall multienzyme complex assembly. This represents the first structure of an E1p-E2p didomain subcomplex involving a homodimeric E1p, and the results may be applicable to a large range of complexes with homodimeric E1 components. Results of HD exchange mass spectrometric experiments using the intact, wild type 3-lipoyl E2p and E1p are consistent with the crystallographic data obtained from the E1p-E2p didomain subcomplex as well as with other biochemical and NMR data reported from our groups, confirming that our findings are applicable to the entire E1p-E2p assembly. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Exploitation of molecular mobilities for advanced organic optoelectronic and photonic nano-materials

NASA Astrophysics Data System (ADS)

Gray, Tomoko O.

Electro-optically active organic materials have shown great potential in advanced technologies such as ultrafast electro-optical switches for broadband communication, light-emitting diodes, and photovoltaic cells. Currently, the maturity of chemical synthesis enables a sophisticated integration of the active elements into complex macromolecules. Also, the structure-property relationships of the isolated single electrically/optically active elements are well established. Unfortunately, such correlations involving single molecule are not applicable to complex unstructured condensed systems, in which unique mesoscale properties and complex dynamics of super-/supra-molecular structures are present. Our current challenge arises, in particular, from a deficiency of appropriate characterization tools that close the gap between phenomenological measurements and theoretical models. This work addresses submolecular mobilities relevant for opto-electronic functionalities of photoluminescent polymers and non-linear optical (NLO) materials. Thereby, I will introduce novel nanoscale thermomechanical characterization tools that are based on scanning force microscopy. From nanoscale thermomechanical measurements sub-/super-molecular mobilities of novel optoelectronic materials can be inferred and to some degree controlled. For instance, we have explored interfacial constraints as a engineering tool to control molecular mobility. This will be illustrated with electroluminescent polymers, which are prone to undesired pi-pi aggregation due to the rod-like structure---intrinsic to all conjugated polymers. The nanoscale confinement is used to reduced chain mobility, and thus, hinders undesired aggregation, and consequently, yields superior spectral stability. From the nanomaterial design perspective, I will also address mobility control with targeted molecular designs. This involves two classes of novel NLO materials, side-chain dendronized polymers and self-assembling molecular glasses. The side-chain dendronized polymers are, due to the structural complexity, self-constrained systems. Our thermomechanical investigations identified that a local relaxation mode associated to the NLO side-chain is the critical design parameter in yielding high mobility to the active element. Relaxation processes of the self-assembling molecular glasses are discussed from a thermodynamic perspective involving both enthalpic and entropic contributions, considering the very special nature of interactions for the NLO molecular glasses, i.e., the formation and dissociation of phenyl/perfluorophenyl quadrupol pairs.

Calabi-Yau structures on categories of matrix factorizations

NASA Astrophysics Data System (ADS)

Shklyarov, Dmytro

2017-09-01

Using tools of complex geometry, we construct explicit proper Calabi-Yau structures, that is, non-degenerate cyclic cocycles on differential graded categories of matrix factorizations of regular functions with isolated critical points. The formulas involve the Kapustin-Li trace and its higher corrections. From the physics perspective, our result yields explicit 'off-shell' models for categories of topological D-branes in B-twisted Landau-Ginzburg models.

Native top-down mass spectrometry for the structural characterization of human hemoglobin

DOE PAGES

Zhang, Jiang; Malmirchegini, G. Reza; Clubb, Robert T.; ...

2015-06-09

Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and non-covalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down mass spectrometry using electrospray ionization (ESI) and a 15-Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Native MS preserves the non-covalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of themore » Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore low fragmentation efficiency. Precursor ion activation allows steady increase of N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and 4 z ions on the α chain; 36 c ions and 2 z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer show similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. Finally, it may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.« less

Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions

PubMed Central

Almeida, Daniela; Maldonado, Emanuel; Vasconcelos, Vitor; Antunes, Agostinho

2015-01-01

Mitochondrial protein-coding genes (mt genes) encode subunits forming complexes of crucial cellular pathways, including those involved in the vital process of oxidative phosphorylation (OXPHOS). Despite the vital role of the mitochondrial genome (mt genome) in the survival of organisms, little is known with respect to its adaptive implications within marine invertebrates. The molluscan Class Cephalopoda is represented by a marine group of species known to occupy contrasting environments ranging from the intertidal to the deep sea, having distinct metabolic requirements, varied body shapes and highly advanced visual and nervous systems that make them highly competitive and successful worldwide predators. Thus, cephalopods are valuable models for testing natural selection acting on their mitochondrial subunits (mt subunits). Here, we used concatenated mt genes from 17 fully sequenced mt genomes of diverse cephalopod species to generate a robust mitochondrial phylogeny for the Class Cephalopoda. We followed an integrative approach considering several branches of interest–covering cephalopods with distinct morphologies, metabolic rates and habitats–to identify sites under positive selection and localize them in the respective protein alignment and/or tridimensional structure of the mt subunits. Our results revealed significant adaptive variation in several mt subunits involved in the energy production pathway of cephalopods: ND5 and ND6 from Complex I, CYTB from Complex III, COX2 and COX3 from Complex IV, and in ATP8 from Complex V. Furthermore, we identified relevant sites involved in protein-interactions, lining proton translocation channels, as well as disease/deficiencies related sites in the aforementioned complexes. A particular case, revealed by this study, is the involvement of some positively selected sites, found in Octopoda lineage in lining proton translocation channels (site 74 from ND5) and in interactions between subunits (site 507 from ND5) of Complex I. PMID:26285039

Protein crystallization studies

NASA Technical Reports Server (NTRS)

Lyne, James Evans

1996-01-01

The Structural Biology laboratory at NASA Marshall Spaceflight Center uses x-ray crystallographic techniques to conduct research into the three-dimensional structure of a wide variety of proteins. A major effort in the laboratory involves an ongoing study of human serum albumin (the principal protein in human plasma) and its interaction with various endogenous substances and pharmaceutical agents. Another focus is on antigenic and functional proteins from several pathogenic organisms including the human immunodeficiency virus (HIV) and the widespread parasitic genus, Schistosoma. My efforts this summer have been twofold: first, to identify clinically significant drug interactions involving albumin binding displacement and to initiate studies of the three-dimensional structure of albumin complexed with these agents, and secondly, to establish collaborative efforts to extend the lab's work on human pathogens.

Crystal structure of norcoclaurine-6-O-methyltransferase, a key rate-limiting step in the synthesis of benzylisoquinoline alkaloids.

PubMed

Robin, Adeline Y; Giustini, Cécile; Graindorge, Matthieu; Matringe, Michel; Dumas, Renaud

2016-09-01

Growing pharmaceutical interest in benzylisoquinoline alkaloids (BIA) coupled with their chemical complexity make metabolic engineering of microbes to create alternative platforms of production an increasingly attractive proposition. However, precise knowledge of rate-limiting enzymes and negative feedback inhibition by end-products of BIA metabolism is of paramount importance for this emerging field of synthetic biology. In this work we report the structural characterization of (S)-norcoclaurine-6-O-methyltransferase (6OMT), a key rate-limiting step enzyme involved in the synthesis of reticuline, the final intermediate to be shared between the different end-products of BIA metabolism, such as morphine, papaverine, berberine and sanguinarine. Four different crystal structures of the enzyme from Thalictrum flavum (Tf 6OMT) were solved: the apoenzyme, the complex with S-adenosyl-l-homocysteine (SAH), the complexe with SAH and the substrate and the complex with SAH and a feedback inhibitor, sanguinarine. The Tf 6OMT structural study provides a molecular understanding of its substrate specificity, active site structure and reaction mechanism. This study also clarifies the inhibition of Tf 6OMT by previously suggested feedback inhibitors. It reveals its high and time-dependent sensitivity toward sanguinarine. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

A chromatin remodelling complex that loads cohesin onto human chromosomes

NASA Astrophysics Data System (ADS)

Hakimi, Mohamed-Ali; Bochar, Daniel A.; Schmiesing, John A.; Dong, Yuanshu; Barak, Orr G.; Speicher, David W.; Yokomori, Kyoko; Shiekhattar, Ramin

2002-08-01

Nucleosomal DNA is arranged in a higher-order structure that presents a barrier to most cellular processes involving protein DNA interactions. The cellular machinery involved in sister chromatid cohesion, the cohesin complex, also requires access to the nucleosomal DNA to perform its function in chromosome segregation. The machineries that provide this accessibility are termed chromatin remodelling factors. Here, we report the isolation of a human ISWI (SNF2h)-containing chromatin remodelling complex that encompasses components of the cohesin and NuRD complexes. We show that the hRAD21 subunit of the cohesin complex directly interacts with the ATPase subunit SNF2h. Mapping of hRAD21, SNF2h and Mi2 binding sites by chromatin immunoprecipitation experiments reveals the specific association of these three proteins with human DNA elements containing Alu sequences. We find a correlation between modification of histone tails and association of the SNF2h/cohesin complex with chromatin. Moreover, we show that the association of the cohesin complex with chromatin can be regulated by the state of DNA methylation. Finally, we present evidence pointing to a role for the ATPase activity of SNF2h in the loading of hRAD21 on chromatin.

Dystrophic Cardiomyopathy: Complex Pathobiological Processes to Generate Clinical Phenotype

PubMed Central

Tsuda, Takeshi; Fitzgerald, Kristi K.

2017-01-01

Duchenne muscular dystrophy (DMD), Becker muscular dystrophy (BMD), and X-linked dilated cardiomyopathy (XL-DCM) consist of a unique clinical entity, the dystrophinopathies, which are due to variable mutations in the dystrophin gene. Dilated cardiomyopathy (DCM) is a common complication of dystrophinopathies, but the onset, progression, and severity of heart disease differ among these subgroups. Extensive molecular genetic studies have been conducted to assess genotype-phenotype correlation in DMD, BMD, and XL-DCM to understand the underlying mechanisms of these diseases, but the results are not always conclusive, suggesting the involvement of complex multi-layers of pathological processes that generate the final clinical phenotype. Dystrophin protein is a part of dystrophin-glycoprotein complex (DGC) that is localized in skeletal muscles, myocardium, smooth muscles, and neuronal tissues. Diversity of cardiac phenotype in dystrophinopathies suggests multiple layers of pathogenetic mechanisms in forming dystrophic cardiomyopathy. In this review article, we review the complex molecular interactions involving the pathogenesis of dystrophic cardiomyopathy, including primary gene mutations and loss of structural integrity, secondary cellular responses, and certain epigenetic and other factors that modulate gene expressions. Involvement of epigenetic gene regulation appears to lead to specific cardiac phenotypes in dystrophic hearts. PMID:29367543

Crystal structure of the Mus81-Eme1 complex.

PubMed

Chang, Jeong Ho; Kim, Jeong Joo; Choi, Jung Min; Lee, Jung Hoon; Cho, Yunje

2008-04-15

The Mus81-Eme1 complex is a structure-specific endonuclease that plays an important role in rescuing stalled replication forks and resolving the meiotic recombination intermediates in eukaryotes. We have determined the crystal structure of the Mus81-Eme1 complex. Both Mus81 and Eme1 consist of a central nuclease domain, two repeats of the helix-hairpin-helix (HhH) motif at their C-terminal region, and a linker helix. While each domain structure resembles archaeal XPF homologs, the overall structure is significantly different from those due to the structure of a linker helix. We show that a flexible intradomain linker that formed with 36 residues in the nuclease domain of Eme1 is essential for the recognition of DNA. We identified several basic residues lining the outer surface of the active site cleft of Mus81 that are involved in the interaction with a flexible arm of a nicked Holliday junction (HJ). These interactions might contribute to the optimal positioning of the opposite junction across the nick into the catalytic site, which provided the basis for the "nick and counternick" mechanism of Mus81-Eme1 and for the nicked HJ to be the favored in vitro substrate of this enzyme.

Transition Metal Intercalators as Anticancer Agents—Recent Advances

PubMed Central

Deo, Krishant M.; Pages, Benjamin J.; Ang, Dale L.; Gordon, Christopher P.; Aldrich-Wright, Janice R.

2016-01-01

The diverse anticancer utility of cisplatin has stimulated significant interest in the development of additional platinum-based therapies, resulting in several analogues receiving clinical approval worldwide. However, due to structural and mechanistic similarities, the effectiveness of platinum-based therapies is countered by severe side-effects, narrow spectrum of activity and the development of resistance. Nonetheless, metal complexes offer unique characteristics and exceptional versatility, with the ability to alter their pharmacology through facile modifications of geometry and coordination number. This has prompted the search for metal-based complexes with distinctly different structural motifs and non-covalent modes of binding with a primary aim of circumventing current clinical limitations. This review discusses recent advances in platinum and other transition metal-based complexes with mechanisms of action involving intercalation. This mode of DNA binding is distinct from cisplatin and its derivatives. The metals focused on in this review include Pt, Ru and Cu along with examples of Au, Ni, Zn and Fe complexes; these complexes are capable of DNA intercalation and are highly biologically active. PMID:27809241

Nucleotide Excision Repair and Transcriptional Regulation: TFIIH and Beyond.

PubMed

Compe, Emmanuel; Egly, Jean-Marc

2016-06-02

Transcription factor IIH (TFIIH) is a multiprotein complex involved in both transcription and DNA repair, revealing a striking functional link between these two processes. Some of its subunits also belong to complexes involved in other cellular processes, such as chromosome segregation and cell cycle regulation, emphasizing the multitasking capabilities of this factor. This review aims to depict the structure of TFIIH and to dissect the roles of its subunits in different cellular mechanisms. Our understanding of the biochemistry of TFIIH has greatly benefited from studies focused on diseases related to TFIIH mutations. We address the etiology of these disorders and underline the fact that TFIIH can be considered a promising target for therapeutic strategies.

The Interview as a Technique for Assessing Oral Ability: Some Guidelines for Its Use.

ERIC Educational Resources Information Center

Nambiar, Mohana

1990-01-01

Some guidelines are offered that detail the complexities involved in interviewing for language testing purposes. They cover strategies for structuring interviews (informal conversational, interview guide, standardized open-ended), questions, interviewing skills, and physical setting. (five references) (LB)

Functional Magnetic Resonance Imaging

ERIC Educational Resources Information Center

Voos, Avery; Pelphrey, Kevin

2013-01-01

Functional magnetic resonance imaging (fMRI), with its excellent spatial resolution and ability to visualize networks of neuroanatomical structures involved in complex information processing, has become the dominant technique for the study of brain function and its development. The accessibility of in-vivo pediatric brain-imaging techniques…

Self-equilibrated Tapered Three-stage Tensegrity Mast

NASA Astrophysics Data System (ADS)

Oh, C. L.; Choong, K. K.; Nishimura, T.; Lee, S. W.

2018-04-01

Investigation of tensegrity structures for the space application is ongoing owing to the characteristics of being lightweight and flexible. Tensegrity structures consist of struts and cables are self-stressed and stable under gravitational loading. Form-finding is an important process to obtain the configuration of tensegrity structures that are in self-equilibrated state. Form-finding of tensegrity structures involves a complex computational strategy in solving the geometrical and forces of the structures. This paper aims to form-finding for a tapered three-stage tensegrity mast. The form-finding strategy involves the assemblage of the tensegrity mast, establishment of equilibrium equations and determination of one possible set of coefficient beta. Several cases of configurations with various twist angles with range of 20°-40° are investigated. A configuration with 9 struts and 42 cables satisfying the material elastic conditions was successfully found. The scalable self-equilibrated tensegrity mast is recommended for space applications.

Structural properties of matrix metalloproteinases.

PubMed

Bode, W; Fernandez-Catalan, C; Tschesche, H; Grams, F; Nagase, H; Maskos, K

1999-04-01

Matrix metalloproteinases (MMPs) are involved in extracellular matrix degradation. Their proteolytic activity must be precisely regulated by their endogenous protein inhibitors, the tissue inhibitors of metalloproteinases (TIMPs). Disruption of this balance results in serious diseases such as arthritis, tumour growth and metastasis. Knowledge of the tertiary structures of the proteins involved is crucial for understanding their functional properties and interference with associated dysfunctions. Within the last few years, several three-dimensional MMP and MMP-TIMP structures became available, showing the domain organization, polypeptide fold and main specificity determinants. Complexes of the catalytic MMP domains with various synthetic inhibitors enabled the structure-based design and improvement of high-affinity ligands, which might be elaborated into drugs. A multitude of reviews surveying work done on all aspects of MMPs have appeared in recent years, but none of them has focused on the three-dimensional structures. This review was written to close the gap.

Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

NASA Astrophysics Data System (ADS)

Prasanna, M. D.; Row, T. N. Guru

2001-05-01

The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C-H⋯F and C-H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C-H⋯F and C-H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O-H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

DNA-lipid complexes: stability of honeycomb-like and spaghetti-like structures.

PubMed Central

May, S; Ben-Shaul, A

1997-01-01

A molecular level theory is presented for the thermodynamic stability of two (similar) types of structural complexes formed by (either single strand or supercoiled) DNA and cationic liposomes, both involving a monolayer-coated DNA as the central structural unit. In the "spaghetti" complex the central unit is surrounded by another, oppositely curved, monolayer, thus forming a bilayer mantle. The "honeycomb" complex is a bundle of hexagonally packed DNA-monolayer units. The formation free energy of these complexes, starting from a planar cationic/neutral lipid bilayer and bare DNA, is expressed as a sum of electrostatic, bending, mixing, and (for the honeycomb) chain frustration contributions. The electrostatic free energy is calculated using the Poisson-Boltzmann equation. The bending energy of the mixed lipid layers is treated in the quadratic curvature approximation with composition-dependent bending rigidity and spontaneous curvature. Ideal lipid mixing is assumed within each lipid monolayer. We found that the most stable monolayer-coated DNA units are formed when the charged/neutral lipid composition corresponds (nearly) to charge neutralization; the optimal monolayer radius corresponds to close DNA-monolayer contact. These conclusions are also valid for the honeycomb complex, as the chain frustration energy is found to be negligible. Typically, the stabilization energies for these structures are on the order of 1 k(B)T/A of DNA length, reflecting mainly the balance between the electrostatic and bending energies. The spaghetti complexes are less stable due to the additional bending energy of the external monolayer. A thermodynamic analysis is presented for calculating the equilibrium lipid compositions when the complexes coexist with excess bilayer. PMID:9370436

The solvation structure of alprazolam.

PubMed

Sridhar, Akshay; Johnston, Andrew J; Varathan, Luxmmi; McLain, Sylvia E; Biggin, Philip C

2016-08-10

Alprazolam is a benzodiazepine that is commonly prescribed for the treatment of anxiety and other related disorders. Like other benzodiazepines, it is thought to exert its effect through interaction with GABAA receptors. However, it has also been described as a potent and selective protein interaction inhibitor of bromodomain and extra-terminal (BET) proteins. Indeed, the only crystal structure of alprazolam bound to a protein is a complex between alprazolam and the BRD4 bromodomain. The structure shows that the complex also involves many water interactions that mediate contacts between the drug and the protein, a scenario that exists in many drug-protein complexes. How such waters relate to solvation patterns of small molecules may improve our understanding of what dictates their appearance or absence in bridging positions within complexes and thus will be important in terms of future rational drug-design. Here, we use neutron diffraction in conjunction with molecular dynamics simulations to provide a detailed analysis of how water molecules interact with alprazolam in methanol/water mixtures. The agreement between the neutron diffraction and the molecular dynamics is extremely good. We discuss the results in the context of drug design.

Expert-guided evolutionary algorithm for layout design of complex space stations

NASA Astrophysics Data System (ADS)

Qian, Zhiqin; Bi, Zhuming; Cao, Qun; Ju, Weiguo; Teng, Hongfei; Zheng, Yang; Zheng, Siyu

2017-08-01

The layout of a space station should be designed in such a way that different equipment and instruments are placed for the station as a whole to achieve the best overall performance. The station layout design is a typical nondeterministic polynomial problem. In particular, how to manage the design complexity to achieve an acceptable solution within a reasonable timeframe poses a great challenge. In this article, a new evolutionary algorithm has been proposed to meet such a challenge. It is called as the expert-guided evolutionary algorithm with a tree-like structure decomposition (EGEA-TSD). Two innovations in EGEA-TSD are (i) to deal with the design complexity, the entire design space is divided into subspaces with a tree-like structure; it reduces the computation and facilitates experts' involvement in the solving process. (ii) A human-intervention interface is developed to allow experts' involvement in avoiding local optimums and accelerating convergence. To validate the proposed algorithm, the layout design of one-space station is formulated as a multi-disciplinary design problem, the developed algorithm is programmed and executed, and the result is compared with those from other two algorithms; it has illustrated the superior performance of the proposed EGEA-TSD.

Matrix management in hospitals: testing theories of matrix structure and development.

PubMed

Burns, L R

1989-09-01

A study of 315 hospitals with matrix management programs was used to test several hypotheses concerning matrix management advanced by earlier theorists. The study verifies that matrix management involves several distinctive elements that can be scaled to form increasingly complex types of lateral coordinative devices. The scalability of these elements is evident only cross-sectionally. The results show that matrix complexity is not an outcome of program age, nor does matrix complexity at the time of implementation appear to influence program survival. Matrix complexity, finally, is not determined by the organization's task diversity and uncertainty. The results suggest several modifications in prevailing theories of matrix organization.

AN INTEGRATED PERSPECTIVE ON THE ASSESSMENT OF TECHNOLOGIES: INTEGRATE-HTA.

PubMed

Wahlster, Philip; Brereton, Louise; Burns, Jacob; Hofmann, Björn; Mozygemba, Kati; Oortwijn, Wija; Pfadenhauer, Lisa; Polus, Stephanie; Rehfuess, Eva; Schilling, Imke; van der Wilt, Gert Jan; Gerhardus, Ansgar

2017-01-01

Current health technology assessment (HTA) is not well equipped to assess complex technologies as insufficient attention is being paid to the diversity in patient characteristics and preferences, context, and implementation. Strategies to integrate these and several other aspects, such as ethical considerations, in a comprehensive assessment are missing. The aim of the European research project INTEGRATE-HTA was to develop a model for an integrated HTA of complex technologies. A multi-method, four-stage approach guided the development of the INTEGRATE-HTA Model: (i) definition of the different dimensions of information to be integrated, (ii) literature review of existing methods for integration, (iii) adjustment of concepts and methods for assessing distinct aspects of complex technologies in the frame of an integrated process, and (iv) application of the model in a case study and subsequent revisions. The INTEGRATE-HTA Model consists of five steps, each involving stakeholders: (i) definition of the technology and the objective of the HTA; (ii) development of a logic model to provide a structured overview of the technology and the system in which it is embedded; (iii) evidence assessment on effectiveness, economic, ethical, legal, and socio-cultural aspects, taking variability of participants, context, implementation issues, and their interactions into account; (iv) populating the logic model with the data generated in step 3; (v) structured process of decision-making. The INTEGRATE-HTA Model provides a structured process for integrated HTAs of complex technologies. Stakeholder involvement in all steps is essential as a means of ensuring relevance and meaningful interpretation of the evidence.

Mechanism of T7 RNAP pausing and termination at the T7 concatemer junction: a local change in transcription bubble structure drives a large change in transcription complex architecture.

PubMed

Nayak, Dhananjaya; Siller, Sylvester; Guo, Qing; Sousa, Rui

2008-02-15

The T7RNA polymerase (RNAP) elongation complex (EC) pauses and is destabilized at a unique 8 nucleotide (nt) sequence found at the junction of the head-to-tail concatemers of T7 genomic DNA generated during T7 DNA replication. The paused EC may recruit the T7 DNA processing machinery, which cleaves the concatemerized DNA within this 8 nt concatemer junction (CJ). Pausing of the EC at the CJ involves structural changes in both the RNAP and transcription bubble. However, these structural changes have not been fully defined, nor is it understood how the CJ sequence itself causes the EC to change its structure, to pause, and to become less stable. Here we use solution and RNAP-tethered chemical nucleases to probe the CJ transcript and changes in the EC structure as the polymerase pauses and terminates at the CJ. Together with extensive mutational scanning of regions of the polymerase that are likely to be involved in recognition of the CJ, we are able to develop a description of the events that occur as the EC transcribes through the CJ and subsequently pauses. In this process, a local change in the structure of the transcription bubble drives a large change in the architecture of the EC. This altered EC structure may then serve as the signal that recruits the processing machinery to the CJ.

Crystal structures of η''-Cu3+xSi and η'''-Cu3+xSi.

PubMed

Corrêa, Cinthia Antunes; Perez, Olivier; Kopeček, Jaromír; Brázda, Petr; Klementová, Mariana; Palatinus, Lukáš

2017-08-01

The binary phase diagram of Cu-Si is unexpectedly complex in the vicinity of Cu 3+x Si. The low-temperature region contains three closely related incommensurately modulated phases denoted, in order of increasing temperature of stability, η''', η'' and η'. The structure analysis of η' has been reported previously [Palatinus et al. (2011). Inorg. Chem. 50, 3743]. Here the structure model for the phases η'' and η''' is reported. The structures could be solved in superspace, but no superspace structure model could be constructed due to the complexity of the modulation functions. Therefore, the structures were described in a supercell approximation, which involved a 4 × 4 × 3 supercell for the η'' phase and a 14 × 14 × 3 supercell for the η''' phase. Both structures are very similar and differ only by a subtle symmetry lowering from η'' to η'''. A comparison of the structure models of η'' and η''' with the reported structure of η' suggests that the reported structure model of η' contains an incorrect assignment of atomic types.

Functional Anatomy of the Outflow Facilities.

PubMed

Pizzirani, Stefano; Gong, Haiyan

2015-11-01

In order to understand the pathophysiology, select optimal therapeutic options for patients and provide clients with honest expectations for cases of canine glaucoma, clinicians should be familiar with a rational understanding of the functional anatomy of the ocular structures involved in this group of diseases. The topographical extension and the structural and humoral complexity of the regions involved with the production and the outflow of aqueous humor undergo numerous changes with aging and disease. Therefore, the anatomy relative to the fluid dynamics of aqueous has become a pivotal yet flexible concept to interpret the different phenotypes of glaucoma. Copyright © 2015 Elsevier Inc. All rights reserved.

Over-expression and purification strategies for recombinant multi-protein oligomers: a case study of Mycobacterium tuberculosis σ/anti-σ factor protein complexes.

PubMed

Thakur, Krishan Gopal; Jaiswal, Ravi Kumar; Shukla, Jinal K; Praveena, T; Gopal, B

2010-12-01

The function of a protein in a cell often involves coordinated interactions with one or several regulatory partners. It is thus imperative to characterize a protein both in isolation as well as in the context of its complex with an interacting partner. High resolution structural information determined by X-ray crystallography and Nuclear Magnetic Resonance offer the best route to characterize protein complexes. These techniques, however, require highly purified and homogenous protein samples at high concentration. This requirement often presents a major hurdle for structural studies. Here we present a strategy based on co-expression and co-purification to obtain recombinant multi-protein complexes in the quantity and concentration range that can enable hitherto intractable structural projects. The feasibility of this strategy was examined using the σ factor/anti-σ factor protein complexes from Mycobacterium tuberculosis. The approach was successful across a wide range of σ factors and their cognate interacting partners. It thus appears likely that the analysis of these complexes based on variations in expression constructs and procedures for the purification and characterization of these recombinant protein samples would be widely applicable for other multi-protein systems. Copyright © 2010 Elsevier Inc. All rights reserved.

Molecular mechanism of peroxisome proliferator-activated receptor α activation by WY14643: a new mode of ligand recognition and receptor stabilization.

PubMed

Bernardes, Amanda; Souza, Paulo C T; Muniz, João R C; Ricci, Clarisse G; Ayers, Stephen D; Parekh, Nili M; Godoy, André S; Trivella, Daniela B B; Reinach, Peter; Webb, Paul; Skaf, Munir S; Polikarpov, Igor

2013-08-23

Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear transcription factors. They are involved in mediating numerous physiological effects in humans, including glucose and lipid metabolism. PPARα ligands effectively treat dyslipidemia and have significant antiinflammatory and anti-atherosclerotic activities. These effects and their ligand-dependent activity make nuclear receptors obvious targets for drug design. Here, we present the structure of the human PPARα in complex with WY14643, a member of fibrate class of drug, and a widely used PPAR activator. The crystal structure of this complex suggests that WY14643 induces activation of PPARα in an unusual bipartite mechanism involving conventional direct helix 12 stabilization and an alternative mode that involves a second ligand in the pocket. We present structural observations, molecular dynamics and activity assays that support the importance of the second site in WY14643 action. The unique binding mode of WY14643 reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering clues for improving the binding affinity and selectivity of ligand. We show that binding of WY14643 to PPARα was associated with antiinflammatory disease in a human corneal cell model, suggesting possible applications for PPARα ligands. Copyright © 2013 Elsevier Ltd. All rights reserved.

A combined experimental and DFT study of active structures and self-cycle mechanisms of mononuclear tungsten peroxo complexes in oxidation reactions

NASA Astrophysics Data System (ADS)

Jin, Peng; Wei, Donghui; Wen, Yiqiang; Luo, Mengfei; Wang, Xiangyu; Tang, Mingsheng

2011-04-01

Tungsten peroxo complexes have been widely used in olefin epoxidation, alcohol oxidation, Baeyer-Villiger oxidation and other oxidation reactions, however, there is still not a unanimous viewpoint for the active structure of mononuclear tungsten peroxo complex by now. In this paper, the catalysis of mononuclear tungsten peroxo complexes 0- 5 with or without acidic ligands for the green oxidation of cyclohexene to adipic acid in the absence of organic solvent and phase-transfer catalyst has been researched in experiment. Then we have suggested two possible kinds of active structures of mononuclear tungsten peroxo complexes including peroxo ring ( nA, n = 0-1) and hydroperoxo ( nB, n = 0-1) structures, which have been investigated using density functional theory (DFT). Moreover, the calculations on self-cycle mechanisms involving the two types of active structures of tungsten peroxo complexes with and without oxalic acid ligand have also been carried out at the B3LYP/[LANL2DZ/6-31G(d, p)] level. The highest energy barrier are 26.17 kcal/mol ( 0A, peroxo ring structure without oxalic acid ligand), 23.91 kcal/mol ( 1A, peroxo ring structure with oxalic acid ligand), 18.19 kcal/mol ( 0B, hydroperoxo structure without oxalic acid ligand) and 13.10 kcal/mol ( 1B, hydroperoxo structure with oxalic acid ligand) in the four potential energy profiles, respectively. The results indicate that both the energy barriers of active structure self-cycle processes with oxalic acid ligands are lower than those without oxalic acid ligands, so the active structures with oxalic acid ligands should be easier to recycle, which is in good agreement with our experimental results. However, due to the higher energy of product than that of the reactant, the energy profile of the self-cycle process of 1B shows that the recycle of 1B could not occur at all in theory. Moreover, the crystal data of peroxo ring structure with oxalic acid ligand could be found in some experimental references. Thus, the viewpoint that the peroxo ring active structure should be the real active structure has been proved in this paper.

A surprising role for conformational entropy in protein function

PubMed Central

Wand, A. Joshua; Moorman, Veronica R.; Harpole, Kyle W.

2014-01-01

Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a grand challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to experimentally access is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned and what the future may hold for this emerging view of protein function. PMID:23478875

A Phosphorylated Cytoplasmic Autoantigen, GW182, Associates with a Unique Population of Human mRNAs within Novel Cytoplasmic Speckles

PubMed Central

Eystathioy, Theophany; Chan, Edward K. L.; Tenenbaum, Scott A.; Keene, Jack D.; Griffith, Kevin; Fritzler, Marvin J.

2002-01-01

A novel human cellular structure has been identified that contains a unique autoimmune antigen and multiple messenger RNAs. This complex was discovered using an autoimmune serum from a patient with motor and sensory neuropathy and contains a protein of 182 kDa. The gene and cDNA encoding the protein indicated an open reading frame with glycine-tryptophan (GW) repeats and a single RNA recognition motif. Both the patient's serum and a rabbit serum raised against the recombinant GW protein costained discrete cytoplasmic speckles designated as GW bodies (GWBs) that do not overlap with the Golgi complex, endosomes, lysosomes, or peroxisomes. The mRNAs associated with GW182 represent a clustered set of transcripts that are presumed to reside within the GW complexes. We propose that the GW ribonucleoprotein complex is involved in the posttranscriptional regulation of gene expression by sequestering a specific subset of gene transcripts involved in cell growth and homeostasis. PMID:11950943

Multiple Hydrogen Bond Tethers for Grazing Formic Acid in Its Complexes with Phenylacetylene.

PubMed

Karir, Ginny; Kumar, Gaurav; Kar, Bishnu Prasad; Viswanathan, K S

2018-03-01

Complexes of phenylacetylene (PhAc) and formic acid (FA) present an interesting picture, where the two submolecules are tethered, sometimes multiply, by hydrogen bonds. The multiple tentacles adopted by PhAc-FA complexes stem from the fact that both submolecules can, in the same complex, serve as proton acceptors and/or proton donors. The acetylenic and phenyl π systems of PhAc can serve as proton acceptors, while the ≡C-H or -C-H of the phenyl ring can act as a proton donor. Likewise, FA also is amphiprotic. Hence, more than 10 hydrogen-bonded structures, involving O-H···π, C-H···π, and C-H···O contacts, were indicated by our computations, some with multiple tentacles. Interestingly, despite the multiple contacts in the complexes, the barrier between some of the structures is small, and hence, FA grazes around PhAc, even while being tethered to it, with hydrogen bonds. We used matrix isolation infrared spectroscopy to experimentally study the PhAc-FA complexes, with which we located global and a few local minima, involving primarily an O-H···π interaction. Experiments were corroborated by ab initio computations, which were performed using MP2 and M06-2X methods, with 6-311++G (d,p) and aug-cc-pVDZ basis sets. Single-point energy calculations were also done at MP2/CBS and CCSD(T)/CBS levels. The nature, strength, and origin of these noncovalent interactions were studied using AIM, NBO, and LMO-EDA analysis.

Human substantia nigra and ventral tegmental area involvement in computing social error signals during the ultimatum game

PubMed Central

Hétu, Sébastien; Luo, Yi; D’Ardenne, Kimberlee; Lohrenz, Terry

2017-01-01

Abstract As models of shared expectations, social norms play an essential role in our societies. Since our social environment is changing constantly, our internal models of it also need to change. In humans, there is mounting evidence that neural structures such as the insula and the ventral striatum are involved in detecting norm violation and updating internal models. However, because of methodological challenges, little is known about the possible involvement of midbrain structures in detecting norm violation and updating internal models of our norms. Here, we used high-resolution cardiac-gated functional magnetic resonance imaging and a norm adaptation paradigm in healthy adults to investigate the role of the substantia nigra/ventral tegmental area (SN/VTA) complex in tracking signals related to norm violation that can be used to update internal norms. We show that the SN/VTA codes for the norm’s variance prediction error (PE) and norm PE with spatially distinct regions coding for negative and positive norm PE. These results point to a common role played by the SN/VTA complex in supporting both simple reward-based and social decision making. PMID:28981876

Sample preparation for SFM imaging of DNA, proteins, and DNA-protein complexes.

PubMed

Ristic, Dejan; Sanchez, Humberto; Wyman, Claire

2011-01-01

Direct imaging is invaluable for understanding the mechanism of complex genome transactions where proteins work together to organize, transcribe, replicate, and repair DNA. Scanning (or atomic) force microscopy is an ideal tool for this, providing 3D information on molecular structure at nanometer resolution from defined components. This is a convenient and practical addition to in vitro studies as readily obtainable amounts of purified proteins and DNA are required. The images reveal structural details on the size and location of DNA-bound proteins as well as protein-induced arrangement of the DNA, which are directly correlated in the same complexes. In addition, even from static images, the different forms observed and their relative distributions can be used to deduce the variety and stability of different complexes that are necessarily involved in dynamic processes. Recently available instruments that combine fluorescence with topographic imaging allow the identification of specific molecular components in complex assemblies, which broadens the applications and increases the information obtained from direct imaging of molecular complexes. We describe here basic methods for preparing samples of proteins, DNA, and complexes of the two for topographic imaging and quantitative analysis. We also describe special considerations for combined fluorescence and topographic imaging of molecular complexes.

Design of specific peptide inhibitors of phospholipase A2: structure of a complex formed between Russell's viper phospholipase A2 and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS).

PubMed

Chandra, Vikas; Jasti, Jayasankar; Kaur, Punit; Dey, Sharmistha; Srinivasan, A; Betzel, Ch; Singh, T P

2002-10-01

Phospholipase A(2) (EC 3.1.1.4) is a key enzyme of the cascade mechanism involved in the production of proinflammatory compounds known as eicosanoids. The binding of phospholipase A(2) to membrane surfaces and the hydrolysis of phospholipids are thought to involve the formation of a hydrophobic channel into which a single substrate molecule diffuses before cleavage. In order to regulate the production of proinflammatory compounds, a specific peptide inhibitor of PLA(2), Leu-Ala-Ile-Tyr-Ser, has been designed. Phospholipase A(2) from Daboia russelli pulchella (DPLA(2)) and peptide Leu-Ala-Ile-Tyr-Ser (LAIYS) have been co-crystallized. The structure of the complex has been determined and refined to 2.0 A resolution. The structure contains two crystallographically independent molecules of DPLA(2), with one molecule of peptide specifically bound to one of them. The overall conformations of the two molecules are essentially similar except in three regions; namely, the calcium-binding loop including Trp31 (residues 25-34), the beta-wing consisting of two antiparallel beta-strands (residues 74-85) and the C-terminal region (residues 119-133). Of these, the most striking difference pertains to the orientation of Trp31 in the two molecules. The conformation of Trp31 in molecule A was suitable to allow the binding of peptide LAIYS, while that in molecule B prevented the entry of the ligand into the hydrophobic channel. The structure of the complex clearly showed that the OH group of Tyr of the inhibitor formed hydrogen bonds with both His48 N(delta1) and Asp49 O(delta1), while O(gamma)H of Ser was involved in a hydrogen bond with Trp31. Other peptide backbone atoms interact with protein through water molecules, while Leu, Ala and Ile form strong hydrophobic interactions with the residues of the hydrophobic channel.

Interaction and formation mechanism of binary complex between zein and propylene glycol alginate.

PubMed

Sun, Cuixia; Dai, Lei; Gao, Yanxiang

2017-02-10

The anti-solvent co-precipitation method was used to fabricate the zein-propylene glycol alginate (PGA) binary complex with different mass ratios of zein to PGA (20:1, 10:1, 5:1, 2:1 and 1:1) at pH 4.0. Results showed that attractive electrostatic interaction between zein and PGA occurred and negatively charged binary complex with large size and high turbidity was formed due to the charge neutralization. Hydrogen bonding and hydrophobic effects were involved in the interactions between zein and PGA, leading to the changed secondary structure and improved thermal stability of zein. Aggregates in the irregular shape with large size were obviously observed in the AFM images. PGA alone exhibited a fine filamentous network structure, while zein-PGA binary complex showed a rough branch-like pattern and the surface of "branch" was closely adsorbed by lots of spherical zein particles. Q in zein-PGA binary complex dispersions presented the improved photochemical and thermal stability. The potential mechanism of a two-step process was proposed to explain the formation of zein-PGA binary complexes. Copyright © 2016 Elsevier Ltd. All rights reserved.

An experimental study of phase transitions in a complex plasma

NASA Astrophysics Data System (ADS)

Smith, Bernard Albert Thomas, II

In semiconductor manufacturing, contamination due to particulates significantly decreases the yield and quality of device fabrication, therefore increasing the cost of production. Dust particle clouds can be found in almost all plasma processing environments including both plasma etching devices and in plasma deposition processes. Dust particles suspended within such plasmas will acquire an electric charge from collisions with free electrons in the plasma. If the ratio of inter-particle potential energy to the average kinetic energy is sufficient, the particles will form either a "liquid" structure with short range ordering or a crystalline structure with long range ordering. Otherwise, the dust particle system will remain in a gaseous state. Many experiments have been conducted over the past decade on such complex plasmas to discover the character of the systems formed, but more work is needed to fully understand these structures. This paper describes the processes involved in setting up the CASPER GEC RF Reference Cell and the modifications necessary to examine complex plasmas. Research conducted to characterize the system is outlined to demonstrate that the CASPER Cell behaves as other GEC Cells. In addition, further research performed shows the behavior of the complex plasma system in the CASPER Cell is similar to complex plasmas studied by other groups in this field. Along the way analysis routines developed specifically for this system are described. New research involving polydisperse dust distributions is carried out in the system once the initial characterization is finished. Next, a system to externally vary the DC bias in the CASPER Cell is developed and characterized. Finally, new research conducted to specifically examine how the complex plasma system reacts to a variable DC bias is reported. Specifically, the response of the interparticle spacing to various system parameters (including the external DC bias) is examined. Also, a previously unreported phenomenon, namely layer splitting, is examined.

Designed Single-Step Synthesis, Structure, and Derivative Textural Properties of Well-Ordered Layered Penta-Coordinate Silicon Alcoholate Complexes

PubMed Central

Li, Xiansen; Michaelis, Vladimir K.; Ong, Ta-Chung; Smith, Stacey J.; Griffin, Robert G.; Wang, Evelyn N.

2014-01-01

The controllable synthesis of well-ordered layered materials with specific nanoarchitecture poses a grand challenge in materials chemistry. We report the solvothermal synthesis of two structurally analogous 5-coordinate organosilicate complexes via a novel transesterification mechanism. Since the polycrystalline nature of the intrinsic hypervalent Si complex thwarts the endeavor in determining its structure, a novel strategy concerning the elegant addition of a small fraction of B species as an effective crystal growth mediator and a sacrificial agent is proposed to directly prepare diffraction-quality single crystals without disrupting the intrinsic elemental type. In the determined crystal structure, two monomeric primary building units (PBUs) self-assemble into a dimeric asymmetric secondary BU via strong Na+-O2− ionic bonds. The designed one-pot synthesis is straightforward, robust, and efficient, leading to a well-ordered (10ī)-parallel layered Si complex with its principal interlayers intercalated with extensive van der Waals gaps in spite of the presence of substantial Na+ counterions as a result of unique atomic arrangement in its structure. On the other hand, upon fast pyrolysis, followed by acid leaching, both complexes are converted into two SiO2 composites bearing BET surface areas of 163.3 and 254.7 m2 g−1 for the pyrolyzed intrinsic and B-assisted Si complexes, respectively. The transesterification methodology merely involving alcoholysis but without any hydrolysis side reaction is designed to have generalized applicability for use in synthesizing new layered metal-organic compounds with tailored PBUs and corresponding metal oxide particles with hierarchical porosity. PMID:24737615

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

Hartwig, J.F.

The products and mechanisms of the thermal reactions of several complexes of the general structure (PMe{sub 3}){sub 4}Ru(X)(Y) and (DMPM){sub 2}Ru(X)(Y) where X and Y are hydride, aryl, and benzyl groups, have been investigated. The mechanism of decomposition depends critically on the structure of the complex and the medium in which the thermolysis is carried out. The alkyl hydride complexes are do not react with alkane solvent, but undergo C-H activation processes with aromatic solvents by several different mechanisms. Thermolysis of (PMe{sub 3}){sub 4}Ru(Ph)(Me) or (PMe{sub 3}){sub 4}Ru(Ph){sub 2} leads to the ruthenium benzyne complex (PMe{sub 3}){sub 4}Ru({eta}{sup 2}-C{sub 6}H{submore » 4}) (1) by a mechanism which involves reversible dissociation of phosphine. In many ways its chemistry is analogous to that of early rather than late organo transition metal complexes. The synthesis, structure, variable temperature NMR spectroscopy and reactivity of ruthenium complexes containing aryloxide or arylamide ligands are reported. These complexes undergo cleavage of a P-C bond in coordinated trimethylphosphine, insertion of CO and CO{sub 2} and hydrogenolysis. Mechanistic studies on these reactions are described. The generation of a series of reactive ruthenium complexes of the general formula (PMe{sub 3}){sub 4}Ru(R)(enolate) is reported. Most of these enolates have been shown to bind to the ruthenium center through the oxygen atom. Two of the enolate complexes 8 and 9 exist in equilibrium between the O- and C-bound forms. The reactions of these compounds are reported, including reactions to form oxygen-containing metallacycles. The structure and reactivity of these ruthenium metallacycles is reported, including their thermal chemistry and reactivity toward protic acids, electrophiles, carbon monoxide, hydrogen and trimethylsilane. 243 refs., 10 tabs.« less

The intrinsically disordered C-terminal domain of the measles virus nucleoprotein interacts with the C-terminal domain of the phosphoprotein via two distinct sites and remains predominantly unfolded

PubMed Central

Bourhis, Jean-Marie; Receveur-Bréchot, Véronique; Oglesbee, Michael; Zhang, Xinsheng; Buccellato, Matthew; Darbon, Hervé; Canard, Bruno; Finet, Stéphanie; Longhi, Sonia

2005-01-01

Measles virus is a negative-sense, single-stranded RNA virus within theMononegavirales order,which includes several human pathogens, including rabies, Ebola, Nipah, and Hendra viruses. Themeasles virus nucleoprotein consists of a structured N-terminal domain, and of an intrinsically disordered C-terminal domain, NTAIL (aa 401–525), which undergoes induced folding in the presence of the C-terminal domain (XD, aa 459–507) of the viral phosphoprotein. With in NTAIL, an α-helical molecular recognition element (α-MoRE, aa 488–499) involved in binding to P and in induced folding was identified and then observed in the crystal structure of XD. Using small-angle X-ray scattering, we have derived a low-resolution structural model of the complex between XD and NTAIL, which shows that most of NTAIL remains disordered in the complex despite P-induced folding within the α-MoRE. The model consists of an extended shape accommodating the multiple conformations adopted by the disordered N-terminal region of NTAIL, and of a bulky globular region, corresponding to XD and to the C terminus of NTAIL (aa 486–525). Using surface plasmon resonance, circular dichroism, fluorescence spectroscopy, and heteronuclear magnetic resonance, we show that NTAIL has an additional site (aa 517–525) involved in binding to XD but not in the unstructured-to-structured transition. This work provides evidence that intrinsically disordered domains can establish complex interactions with their partners, and can contact them through multiple sites that do not all necessarily gain regular secondary structure. PMID:16046624

PalC, One of Two Bro1 Domain Proteins in the Fungal pH Signalling Pathway, Localizes to Cortical Structures and Binds Vps32

PubMed Central

Galindo, Antonio; Hervás-Aguilar, América; Rodríguez-Galán, Olga; Vincent, Olivier; Arst, Herbert N; Tilburn, Joan; Peñalva, Miguel A

2007-01-01

PalC, distantly related to Saccharomyces cerevisiaeperipheral endosomal sorting complexes required for transport III (ESCRT-III) component Bro1p and one of six Aspergillus nidulanspH signalling proteins, contains a Bro1 domain. Green fluorescent protein (GFP)-tagged PalC is recruited to plasma membrane-associated punctate structures upon alkalinization, when pH signalling is active. PalC recruitment to these structures is dependent on the seven transmembrane domain (7-TMD) receptor and likely pH sensor PalH. PalC is a two-hybrid interactor of the ESCRT-III Vps20/Vps32 subcomplex and binds Vps32 directly. This binding is largely impaired by Pro439Phe, Arg442Ala and Arg442His substitutions in a conserved region mediating interaction of Bro1p with Vps32p, but these substitutions do not prevent cortical punctate localization, indicating Vps32 independence. In contrast, Arg442Δ impairs Vps32 binding and prevents PalC-GFP recruitment to cortical structures. pH signalling involves a plasma membrane complex including the 7-TMD receptor PalH and the arrestin-like PalF and an endosomal membrane complex involving the PalB protease, the transcription factor PacC and the Vps32 binding, Bro1-domain-containing protein PalA. PalC, which localizes to cortical structures and can additionally bind a component of ESCRT-III, has the features required to bridge these two entities. A likely S. cerevisiaeorthologue of PalC has been identified, providing the basis for a unifying hypothesis of gene regulation by ambient pH in ascomycetes. PMID:17696968

Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex.

PubMed

Fukumura, Takuma; Makino, Fumiaki; Dietsche, Tobias; Kinoshita, Miki; Kato, Takayuki; Wagner, Samuel; Namba, Keiichi; Imada, Katsumi; Minamino, Tohru

2017-08-01

The bacterial flagellar type III export apparatus, which is required for flagellar assembly beyond the cell membranes, consists of a transmembrane export gate complex and a cytoplasmic ATPase complex. FlhA, FlhB, FliP, FliQ, and FliR form the gate complex inside the basal body MS ring, although FliO is required for efficient export gate formation in Salmonella enterica. However, it remains unknown how they form the gate complex. Here we report that FliP forms a homohexameric ring with a diameter of 10 nm. Alanine substitutions of conserved Phe-137, Phe-150, and Glu-178 residues in the periplasmic domain of FliP (FliPP) inhibited FliP6 ring formation, suppressing flagellar protein export. FliO formed a 5-nm ring structure with 3 clamp-like structures that bind to the FliP6 ring. The crystal structure of FliPP derived from Thermotoga maritia, and structure-based photo-crosslinking experiments revealed that Phe-150 and Ser-156 of FliPP are involved in the FliP-FliP interactions and that Phe-150, Arg-152, Ser-156, and Pro-158 are responsible for the FliP-FliO interactions. Overexpression of FliP restored motility of a ∆fliO mutant to the wild-type level, suggesting that the FliP6 ring is a functional unit in the export gate complex and that FliO is not part of the final gate structure. Copurification assays revealed that FlhA, FlhB, FliQ, and FliR are associated with the FliO/FliP complex. We propose that the assembly of the export gate complex begins with FliP6 ring formation with the help of the FliO scaffold, followed by FliQ, FliR, and FlhB and finally FlhA during MS ring formation.

Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex

PubMed Central

Fukumura, Takuma; Makino, Fumiaki; Dietsche, Tobias; Kinoshita, Miki; Kato, Takayuki; Wagner, Samuel; Namba, Keiichi; Imada, Katsumi

2017-01-01

The bacterial flagellar type III export apparatus, which is required for flagellar assembly beyond the cell membranes, consists of a transmembrane export gate complex and a cytoplasmic ATPase complex. FlhA, FlhB, FliP, FliQ, and FliR form the gate complex inside the basal body MS ring, although FliO is required for efficient export gate formation in Salmonella enterica. However, it remains unknown how they form the gate complex. Here we report that FliP forms a homohexameric ring with a diameter of 10 nm. Alanine substitutions of conserved Phe-137, Phe-150, and Glu-178 residues in the periplasmic domain of FliP (FliPP) inhibited FliP6 ring formation, suppressing flagellar protein export. FliO formed a 5-nm ring structure with 3 clamp-like structures that bind to the FliP6 ring. The crystal structure of FliPP derived from Thermotoga maritia, and structure-based photo-crosslinking experiments revealed that Phe-150 and Ser-156 of FliPP are involved in the FliP–FliP interactions and that Phe-150, Arg-152, Ser-156, and Pro-158 are responsible for the FliP–FliO interactions. Overexpression of FliP restored motility of a ∆fliO mutant to the wild-type level, suggesting that the FliP6 ring is a functional unit in the export gate complex and that FliO is not part of the final gate structure. Copurification assays revealed that FlhA, FlhB, FliQ, and FliR are associated with the FliO/FliP complex. We propose that the assembly of the export gate complex begins with FliP6 ring formation with the help of the FliO scaffold, followed by FliQ, FliR, and FlhB and finally FlhA during MS ring formation. PMID:28771466

Modeling of the structure-specific kinetics of abiotic, dark reduction of Hg(II) complexed by O/N and S functional groups in humic acids while accounting for time-dependent structural rearrangement

USDA-ARS?s Scientific Manuscript database

Redox transformations involving electron transfer from natural organic matter (NOM) are important for the mercury (Hg) biogeochemical cycle. In the water column light drives the reduction of Hg(II) to Hg(0), whereas in soils and sediments dark reduction of Hg(II) is of greater importance. The object...

Discovery of a Kelch-like ECH-associated protein 1-inhibitory tetrapeptide and its structural characterization

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

Sogabe, Satoshi; Sakamoto, Kotaro; Kamada, Yusuke

Keap1 constitutively binds to the transcription factor Nrf2 to promote its degradation, resulting in negative modulation of genes involved in cellular protection against oxidative stress. Keap1 is increasingly recognized as an attractive target for treating diseases involving oxidative stress, including cancer, atherosclerosis, diabetes, arthritis, and neurodegeneration. We used phage-display peptide screening to identify a tetrapeptide showing moderate binding affinity, which inhibits the interaction between Nrf2 and Keap1. The tetrapeptide does not include an ETGE motif, which is a commonly found consensus sequence in known peptidic inhibitors. In addition to affinity parameters, IC{sub 50}, K{sub D}, and thermodynamic parameters, the crystalmore » structure of the complex was determined to elucidate the binding conformation. The binding interactions resemble those of known small-molecule inhibitors as opposed to those of substrates and peptidic inhibitors. Although the tetrapeptide's affinity is not very high, our results may help facilitate the designing of small-molecule inhibitors during lead generation in drug discovery. - Highlights: • Keap1 inhibitory tetrapeptide with moderate affinity was discovered. • Crystal structure of the complex showed the unique binding mode. • Structural information gives a valuable insight for design of therapeutic compounds.« less

Probing the electronic structures of [Cu2(mu-XR2)]n+ diamond cores as a function of the bridging X atom (X = N or P) and charge (n = 0, 1, 2).

PubMed

Harkins, Seth B; Mankad, Neal P; Miller, Alexander J M; Szilagyi, Robert K; Peters, Jonas C

2008-03-19

A series of dicopper diamond core complexes that can be isolated in three different oxidation states ([Cu2(mu-XR2)]n+, where n = 0, 1, 2 and X = N or P) is described. Of particular interest is the relative degree of oxidation of the respective copper centers and the bridging XR2 units, upon successive oxidations. These dicopper complexes feature terminal phosphine and either bridging amido or phosphido donors, and as such their metal-ligand bonds are highly covalent. Cu K-edge, Cu L-edge, and P K-edge spectroscopies, in combination with solid-state X-ray structures and DFT calculations, provides a complementary electronic structure picture for the entire set of complexes that tracks the involvement of a majority of ligand-based redox chemistry. The electronic structure picture that emerges for these inorganic dicopper diamond cores shares similarities with the Cu2(mu-SR)2 CuA sites of cytochrome c oxidases and nitrous oxide reductases.

Synthesis, crystal structure, theoretical calculations and antimicrobial properties of [Pt(tetramethylthiourea)4] [Pt(CN)4]·4H2O

NASA Astrophysics Data System (ADS)

Sadaf, Haseeba; Isab, Anvarhusein A.; Ahmad, Saeed; Espinosa, Arturo; Mas-Montoya, Míriam; Khan, Islam Ullah; Ejaz; Rehman, Seerat-ur; Ali, Muhammad Akhtar Javed; Saleem, Muhammad; Ruiz, José; Janiak, Christoph

2015-04-01

A new platinum(II) complex, [Pt(Tmtu)4][Pt(CN)4]·4H2O (1) was synthesized by reaction of K2[PtCl4], KCN and tetramethylthiourea (Tmtu). Its structure was determined by X-ray crystallography. The [Pt(CN)4]2- anion shows regular square planar geometry at platinum, while in the [Pt(Tmtu)4]2+ cation the geometry at platinum is somewhat distorted. Hydrogen bonding between water molecules and the cyanide nitrogen of [Pt(CN)4]2- ions stabilizes the structure and leads to a supramolecular 2D network. DFT calculations support the experimentally found dinuclear (homocoordinated) ion-pair structure 1 as the most stable in comparison to noncovalent dimer [Pt(CN)2(Tmtu)2]222 that could, in turn, be involved in the formation sequence of 1. Antimicrobial activities of the complex were evaluated by minimum inhibitory concentration and the results showed that the complex exhibited moderate activities against gram-negative bacteria (Escherichiacoli, Pseudomonas aeruginosa) and molds (Aspergillus niger,Penicilliumcitrinum).

Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.

PubMed

Wu, Baixing; Zhang, Mengmeng; Su, Shichen; Liu, Hehua; Gan, Jianhua; Ma, Jinbiao

2018-06-22

Vernalization is a pivotal stage for some plants involving many epigenetic changes during cold exposure. In Arabidopsis, an essential step in vernalization for further flowering is successful silence the potent floral repressor Flowering Locus C (FLC) by repressing histone mark. AtVal1 is a multi-function protein containing five domains that participate into many recognition processes and is validated to recruit the repress histone modifier PHD-PRC2 complex and interact with components of the ASAP complex target to the FLC nucleation region through recognizing a cis element known as CME (cold memory element) by its plant-specific B3 domain. Here, we determine the crystal structure of the B3 domain in complex with Sph/RY motif in CME. Our structural analysis reveals the specific DNA recognition by B3 domain, combined with our in vitro experiments, we provide the structural insight into the important implication of AtVAL1-B3 domain in flowering process. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular envelope and atomic model of an anti-terminated glyQS T-box regulator in complex with tRNAGly.

PubMed

Chetnani, Bhaskar; Mondragón, Alfonso

2017-07-27

A T-box regulator or riboswitch actively monitors the levels of charged/uncharged tRNA and participates in amino acid homeostasis by regulating genes involved in their utilization or biosynthesis. It has an aptamer domain for cognate tRNA recognition and an expression platform to sense the charge state and modulate gene expression. These two conserved domains are connected by a variable linker that harbors additional secondary structural elements, such as Stem III. The structural basis for specific tRNA binding is known, but the structural basis for charge sensing and the role of other elements remains elusive. To gain new structural insights on the T-box mechanism, a molecular envelope was calculated from small angle X-ray scattering data for the Bacillus subtilis glyQS T-box riboswitch in complex with an uncharged tRNAGly. A structural model of an anti-terminated glyQS T-box in complex with its cognate tRNAGly was derived based on the molecular envelope. It shows the location and relative orientation of various secondary structural elements. The model was validated by comparing the envelopes of the wild-type complex and two variants. The structural model suggests that in addition to a possible regulatory role, Stem III could aid in preferential stabilization of the T-box anti-terminated state allowing read-through of regulated genes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms

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

Simonetti, Angelita; Marzi, Stefano; Fabbretti, Attilio

2013-06-01

The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region. Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2more » is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2–GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.« less

Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog

PubMed Central

Zhao, Xiaodong; Copeland, Daniel M.; Soares, Alexei S.; West, Ann H.

2008-01-01

Summary The crystal structure of the yeast SLN1 response regulator domain bound to both a phosphoryl analog (BeF3−) and Mg2+ ion in complex with its downstream phosphorelay signaling partner YPD1 has been determined at a resolution of 1.70 Å. Comparisons between the beryllium fluoride-activated complex and the unliganded (or apo) complex determined previously reveal modest but important differences. The SLN1-R1•Mg2+•BeF3− structure from the complex provides evidence for the first time that the mechanism of phosphorylation-induced activation is highly conserved between bacterial response regulator domains and this example from a eukaryotic organism. Residues in and around the active site undergo slight rearrangements in order to form bonds to the essential divalent cation and fluorine atoms of BeF3−. Two conserved switch-like residues (Thr 1173 and Phe 1192) occupy distinctly different positions in the apo- versus BeF3−-bound structures consistent with the “Y-T” coupling mechanism proposed for activation of CheY and other bacterial response regulators. Several loop regions and the α4-β5-α5 surface of the SLN1-R1 domain undergo subtle conformational changes (∼1-3 Å displacements relative to the apo-structure) that lead to significant changes in terms of contacts that are formed with YPD1. Detailed structural comparisons of protein-protein interactions in the apo- and BeF3−-bound complexes suggest at least a two-state equilibrium model for formation of a transient encounter complex, in which phosphorylation of the response regulator promotes the formation of a phosphotransfer-competent complex. In the BeF3−-activated complex, the position of His 64 from YPD1 is within ideal distance and near linear geometry with Asp 1144 from the SLN1-R1 domain for phosphotransfer to occur. The ground state structure presented here suggests that phosphoryl transfer will likely proceed through an associative mechanism involving formation of a pentacoordinate phosphorus intermediate. PMID:18076904

Cationic liposome/DNA complexes: from structure to interactions with cellular membranes.

PubMed

Caracciolo, Giulio; Amenitsch, Heinz

2012-10-01

Gene-based therapeutic approaches are based upon the concept that, if a disease is caused by a mutation in a gene, then adding back the wild-type gene should restore regular function and attenuate the disease phenotype. To deliver the gene of interest, both viral and nonviral vectors are used. Viruses are efficient, but their application is impeded by detrimental side-effects. Among nonviral vectors, cationic liposomes are the most promising candidates for gene delivery. They form stable complexes with polyanionic DNA (lipoplexes). Despite several advantages over viral vectors, the transfection efficiency (TE) of lipoplexes is too low compared with those of engineered viral vectors. This is due to lack of knowledge about the interactions between complexes and cellular components. Rational design of efficient lipoplexes therefore requires deeper comprehension of the interactions between the vector and the DNA as well as the cellular pathways and mechanisms involved. The importance of the lipoplex structure in biological function is revealed in the application of synchrotron small-angle X-ray scattering in combination with functional TE measurements. According to current understanding, the structure of lipoplexes can change upon interaction with cellular membranes and such changes affect the delivery efficiency. Recently, a correlation between the mechanism of gene release from complexes, the structure, and the physical and chemical parameters of the complexes has been established. Studies aimed at correlating structure and activity of lipoplexes are reviewed herein. This is a fundamental step towards rational design of highly efficient lipid gene vectors.

Structural equation modeling for observational studies

USGS Publications Warehouse

Grace, J.B.

2008-01-01

Structural equation modeling (SEM) represents a framework for developing and evaluating complex hypotheses about systems. This method of data analysis differs from conventional univariate and multivariate approaches familiar to most biologists in several ways. First, SEMs are multiequational and capable of representing a wide array of complex hypotheses about how system components interrelate. Second, models are typically developed based on theoretical knowledge and designed to represent competing hypotheses about the processes responsible for data structure. Third, SEM is conceptually based on the analysis of covariance relations. Most commonly, solutions are obtained using maximum-likelihood solution procedures, although a variety of solution procedures are used, including Bayesian estimation. Numerous extensions give SEM a very high degree of flexibility in dealing with nonnormal data, categorical responses, latent variables, hierarchical structure, multigroup comparisons, nonlinearities, and other complicating factors. Structural equation modeling allows researchers to address a variety of questions about systems, such as how different processes work in concert, how the influences of perturbations cascade through systems, and about the relative importance of different influences. I present 2 example applications of SEM, one involving interactions among lynx (Lynx pardinus), mongooses (Herpestes ichneumon), and rabbits (Oryctolagus cuniculus), and the second involving anuran species richness. Many wildlife ecologists may find SEM useful for understanding how populations function within their environments. Along with the capability of the methodology comes a need for care in the proper application of SEM.

Epigenetic regulation of vascular smooth muscle cell function in atherosclerosis.

PubMed

Findeisen, Hannes M; Kahles, Florian K; Bruemmer, Dennis

2013-04-01

Epigenetics involve heritable and acquired changes in gene transcription that occur independently of the DNA sequence. Epigenetic mechanisms constitute a hierarchic upper-level of transcriptional control through complex modifications of chromosomal components and nuclear structures. These modifications include, for example, DNA methylation or post-translational modifications of core histones; they are mediated by various chromatin-modifying enzymes; and ultimately they define the accessibility of a transcriptional complex to its target DNA. Integrating epigenetic mechanisms into the pathophysiologic concept of complex and multifactorial diseases such as atherosclerosis may significantly enhance our understanding of related mechanisms and provide promising therapeutic approaches. Although still in its infancy, intriguing scientific progress has begun to elucidate the role of epigenetic mechanisms in vascular biology, particularly in the control of smooth muscle cell phenotypes. In this review, we will summarize epigenetic pathways in smooth muscle cells, focusing on mechanisms involved in the regulation of vascular remodeling.

Epigenetic regulation of vascular smooth muscle cell function in atherosclerosis.

PubMed

Findeisen, Hannes M; Kahles, Florian K; Bruemmer, Dennis

2013-05-01

Epigenetics involve heritable and acquired changes in gene transcription that occur independently of the DNA sequence. Epigenetic mechanisms constitute a hierarchic upper-level of transcriptional control through complex modifications of chromosomal components and nuclear structures. These modifications include, for example, DNA methylation or post-translational modifications of core histones; they are mediated by various chromatin-modifying enzymes; and ultimately they define the accessibility of a transcriptional complex to its target DNA. Integrating epigenetic mechanisms into the pathophysiologic concept of complex and multifactorial diseases such as atherosclerosis may significantly enhance our understanding of related mechanisms and provide promising therapeutic approaches. Although still in its infancy, intriguing scientific progress has begun to elucidate the role of epigenetic mechanisms in vascular biology, particularly in the control of smooth muscle cell phenotypes. In this review, we will summarize epigenetic pathways in smooth muscle cells, focusing on mechanisms involved in the regulation of vascular remodeling.

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

Bae, Brian; Nayak, Dhananjaya; Ray, Ananya

RNA polymerase inhibitors like the CBR class that target the enzyme’s complex catalytic center are attractive leads for new antimicrobials. The catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound NTP and two Mg 2+ ions from a preinsertion state to a reactive configuration. CBR inhibitors target a crevice between the N-terminal portion of the bridge helix and a surrounding cap region within which the bridge helix is thought to rearrange during the nucleotide addition cycle. Here, we report crystal structures of CBR inhibitor/Escherichia coli RNA polymerasemore » complexes as well as biochemical tests that establish two distinct effects of the inhibitors on the RNA polymerase catalytic site. One effect involves inhibition of trigger-loop folding via the F loop in the cap, which affects both nucleotide addition and hydrolysis of 3'-terminal dinucleotides in certain backtracked complexes. The second effect is trigger-loop independent, affects only nucleotide addition and pyrophosphorolysis, and may involve inhibition of bridge-helix movements that facilitate reactive triphosphate alignment.« less

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA–protein interactions

PubMed Central

Khanova, Elena; Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S.

2012-01-01

Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA–protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes. PMID:22332141

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA-protein interactions.

PubMed

Khanova, Elena; Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

2012-04-01

Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA-protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes.

Neutron diffraction study of the in situ oxidation of UO(2).

PubMed

Desgranges, Lionel; Baldinozzi, Gianguido; Rousseau, Gurvan; Nièpce, Jean-Claude; Calvarin, Gilbert

2009-08-17

This paper discusses uranium oxide crystal structure modifications that are observed during the low-temperature oxidation which transforms UO(2) into U(3)O(8). The symmetries and the structural parameters of UO(2), beta-U(4)O(9), beta-U(3)O(7), and U(3)O(8) were determined by refining neutron diffraction patterns on pure single-phase samples. Neutron diffraction patterns were also collected during the in situ oxidation of powder samples at 483 K. The lattice parameters and relative ratios of the four pure phases were measured during the progression of the isothermal oxidation. The transformation of UO(2) into U(3)O(8) involves a complex modification of the oxygen sublattice and the onset of complex superstructures for U(4)O(9) and U(3)O(7), associated with regular stacks of complex defects known as cuboctahedra, which consist of 13 oxygen atoms. The kinetics of the oxidation process are discussed on the basis of the results of the structural analysis.

Solution NMR Structures of Productive and Non-productive Complexes between the A and B Domains of the Cytoplasmic Subunit of the Mannose Transporter of the Escherichia coli Phosphotransferase System*

PubMed Central

Hu, Jun; Hu, Kaifeng; Williams, David C.; Komlosh, Michal E.; Cai, Mengli; Clore, G. Marius

2008-01-01

Solution structures of complexes between the isolated A (IIAMan) and B (IIBMan) domains of the cytoplasmic component of the mannose transporter of Escherichia coli have been solved by NMR. The complex of wild-type IIAMan and IIBMan is a mixture of two species comprising a productive, phosphoryl transfer competent complex and a non-productive complex with the two active site histidines, His-10 of IIAMan and His-175 of IIBMan, separated by ∼25Å. Mutation of the active site histidine, His-10, of IIAMan to a glutamate, to mimic phosphorylation, results in the formation of a single productive complex. The apparent equilibrium dissociation constants for the binding of both wild-type and H10E IIAMan to IIBMan are approximately the same (KD ∼ 0.5 mm). The productive complex can readily accommodate a transition state involving a pentacoordinate phosphoryl group with trigonal bipyramidal geometry bonded to the Nε2 atom of His-10 of IIAMan and the Nδ1 atom of His-175 of IIBMan with negligible (<0.2Å) local backbone conformational changes in the immediate vicinity of the active site. The non-productive complex is related to the productive one by a ∼90° rotation and ∼37Å translation of IIBMan relative to IIAMan, leaving the active site His-175 of IIBMan fully exposed to solvent in the non-productive complex. The interaction surface on IIAMan for the non-productive complex comprises a subset of residues used in the productive complex and in both cases involves both subunits of IIAMan. The selection of the productive complex by IIAMan(H10E) can be attributed to neutralization of the positively charged Arg-172 of IIBMan at the center of the interface. The non-productive IIAMan-IIBMan complex may possibly be relevant to subsequent phosphoryl transfer from His-175 of IIBMan to the incoming sugar located on the transmembrane IICMan-IIDMan complex. PMID:18270202

Ruthenium(II) Complexes Containing Lutidine-Derived Pincer CNC Ligands: Synthesis, Structure, and Catalytic Hydrogenation of C-N bonds.

PubMed

Hernández-Juárez, Martín; López-Serrano, Joaquín; Lara, Patricia; Morales-Cerón, Judith P; Vaquero, Mónica; Álvarez, Eleuterio; Salazar, Verónica; Suárez, Andrés

2015-05-11

A series of Ru complexes containing lutidine-derived pincer CNC ligands have been prepared by transmetalation with the corresponding silver-carbene derivatives. Characterization of these derivatives shows both mer and fac coordination of the CNC ligands depending on the wingtips of the N-heterocyclic carbene fragments. In the presence of tBuOK, the Ru-CNC complexes are active in the hydrogenation of a series of imines. In addition, these complexes catalyze the reversible hydrogenation of phenantridine. Detailed NMR spectroscopic studies have shown the capability of the CNC ligand to be deprotonated and get involved in ligand-assisted activation of dihydrogen. More interestingly, upon deprotonation, the Ru-CNC complex 5 e(BF4 ) is able to add aldimines to the metal-ligand framework to yield an amido complex. Finally, investigation of the mechanism of the hydrogenation of imines has been carried out by means of DFT calculations. The calculated mechanism involves outer-sphere stepwise hydrogen transfer to the C-N bond assisted either by the pincer ligand or a second coordinated H2 molecule. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tridentate N2S ligand from 2,2′-dithiodibenzaldehyde and N,N-dimethylethylenediamine: Synthesis, structure, and characterization of a Ni(II) complex with relevance to Ni Superoxide Dismutase

PubMed Central

Zimmerman, Joshua R.; Smucker, Bradley W.; Dain, Ryan P.; VanStipdonk, Michael J.

2011-01-01

Nickel Superoxide Dismutase (NiSOD) and the A-cluster of Carbon Monoxide Dehydrogenase/Acetyl Coenzyme A Synthase (CODH/ACS) both feature active sites with Ni coordinated by thiolate and amide donors. It is likely that the particular set of donors is important in tuning the redox potential of the Ni center(s). We report herein an expansion of our efforts involving the use of 2,2′-dithiodibenzaldehyde (DTDB) as a synthon for metal-thiolate complexes to reactions with Ni complexes of N,N-dimethylethylenediamine (dmen). In the presence of coordinating counterions, these reactions result in monomeric square-planar complexes of the tridentate N2S donor ligand derived from the Schiff-base condensation of dmen and DTDB. In the absence of a coordinating counterion, we have isolated a Ni(II) complex with an asymmetric N2S2 donor set involving one amine and one imine N donor in addition to two thiolate donors. This latter complex is discussed with respect to its relevance to the active site of NiSOD. PMID:21666847

Crystal structure of a complete ternary complex of T-cell receptor, peptide-MHC, and CD4

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

Yin, Yiyuan; Wang, Xin Xiang; Mariuzza, Roy A

2012-07-11

Adaptive immunity depends on specific recognition by a T-cell receptor (TCR) of an antigenic peptide bound to a major histocompatibility complex (pMHC) molecule on an antigen-presenting cell (APC). In addition, T-cell activation generally requires binding of this same pMHC to a CD4 or CD8 coreceptor. Here, we report the structure of a complete TCR-pMHC-CD4 ternary complex involving a human autoimmune TCR, a myelin-derived self-peptide bound to HLA-DR4, and CD4. The complex resembles a pointed arch in which TCR and CD4 are each tilted ~65° relative to the T-cell membrane. By precluding direct contacts between TCR and CD4, the structure explainsmore » how TCR and CD4 on the T cell can simultaneously, yet independently, engage the same pMHC on the APC. The structure, in conjunction with previous mutagenesis data, places TCR-associated CD3εγ and CD3εδ subunits, which transmit activation signals to the T cell, inside the TCR-pMHC-CD4 arch, facing CD4. By establishing anchor points for TCR and CD4 on the T-cell membrane, the complex provides a basis for understanding how the CD4 coreceptor focuses TCR on MHC to guide TCR docking on pMHC during thymic T-cell selection.« less

Chitin-Like Molecules Associate with Cryptococcus neoformans Glucuronoxylomannan To Form a Glycan Complex with Previously Unknown Properties

PubMed Central

Ramos, Caroline L.; Fonseca, Fernanda L.; Rodrigues, Jessica; Guimarães, Allan J.; Cinelli, Leonardo P.; Miranda, Kildare; Nimrichter, Leonardo; Casadevall, Arturo; Travassos, Luiz R.

2012-01-01

In prior studies, we demonstrated that glucuronoxylomannan (GXM), the major capsular polysaccharide of the fungal pathogen Cryptococcus neoformans, interacts with chitin oligomers at the cell wall-capsule interface. The structural determinants regulating these carbohydrate-carbohydrate interactions, as well as the functions of these structures, have remained unknown. In this study, we demonstrate that glycan complexes composed of chitooligomers and GXM are formed during fungal growth and macrophage infection by C. neoformans. To investigate the required determinants for the assembly of chitin-GXM complexes, we developed a quantitative scanning electron microscopy-based method using different polysaccharide samples as inhibitors of the interaction of chitin with GXM. This assay revealed that chitin-GXM association involves noncovalent bonds and large GXM fibers and depends on the N-acetyl amino group of chitin. Carboxyl and O-acetyl groups of GXM are not required for polysaccharide-polysaccharide interactions. Glycan complex structures composed of cryptococcal GXM and chitin-derived oligomers were tested for their ability to induce pulmonary cytokines in mice. They were significantly more efficient than either GXM or chitin oligomers alone in inducing the production of lung interleukin 10 (IL-10), IL-17, and tumor necrosis factor alpha (TNF-α). These results indicate that association of chitin-derived structures with GXM through their N-acetyl amino groups generates glycan complexes with previously unknown properties. PMID:22562469

Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs

PubMed Central

Krepl, Miroslav; Cléry, Antoine; Blatter, Markus; Allain, Frederic H.T.; Sponer, Jiri

2016-01-01

RNA recognition motif (RRM) proteins represent an abundant class of proteins playing key roles in RNA biology. We present a joint atomistic molecular dynamics (MD) and experimental study of two RRM-containing proteins bound with their single-stranded target RNAs, namely the Fox-1 and SRSF1 complexes. The simulations are used in conjunction with NMR spectroscopy to interpret and expand the available structural data. We accumulate more than 50 μs of simulations and show that the MD method is robust enough to reliably describe the structural dynamics of the RRM–RNA complexes. The simulations predict unanticipated specific participation of Arg142 at the protein–RNA interface of the SRFS1 complex, which is subsequently confirmed by NMR and ITC measurements. Several segments of the protein–RNA interface may involve competition between dynamical local substates rather than firmly formed interactions, which is indirectly consistent with the primary NMR data. We demonstrate that the simulations can be used to interpret the NMR atomistic models and can provide qualified predictions. Finally, we propose a protocol for ‘MD-adapted structure ensemble’ as a way to integrate the simulation predictions and expand upon the deposited NMR structures. Unbiased μs-scale atomistic MD could become a technique routinely complementing the NMR measurements of protein–RNA complexes. PMID:27193998

The geometric structures, vibrational frequencies and redox properties of the actinyl coordination complexes ([AnO2(L)n](m); An = U, Pu, Np; L = H2O, Cl-, CO3(2-), CH3CO2(-), OH-) in aqueous solution, studied by density functional theory methods.

PubMed

Austin, Jonathan P; Sundararajan, Mahesh; Vincent, Mark A; Hillier, Ian H

2009-08-14

The geometric and electronic structures of the aqua, chloro, acetato, hydroxo and carbonato complexes of U, Np and Pu in both their (VI) and (V) oxidation states, and in an aqueous environment, have been studied using density functional theory methods. We have obtained micro-solvated structures derived from molecular dynamics simulations and included the bulk solvent using a continuum model. We find that two different hydrogen bonding patterns involving the axial actinyl oxygen atoms are sometimes possible, and may give rise to different An-O bond lengths and vibrational frequencies. These alternative structures are reflected in the experimental An-O bond lengths of the aqua and carbonato complexes. The variation of the redox potential of the uranyl complexes with the different ligands has been studied using both BP86 and B3LYP functionals. The relative values for the four uranium complexes having anionic ligands are in surprisingly good agreement with experiment, although the absolute values are in error by approximately 1 eV. The absolute error for the aqua species is much less, leading to an incorrect order of the redox potentials of the aqua and chloro species.

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

Janjusic, Tommy; Kartsaklis, Christos

Application analysis is facilitated through a number of program profiling tools. The tools vary in their complexity, ease of deployment, design, and profiling detail. Specifically, understand- ing, analyzing, and optimizing is of particular importance for scientific applications where minor changes in code paths and data-structure layout can have profound effects. Understanding how intricate data-structures are accessed and how a given memory system responds is a complex task. In this paper we describe a trace profiling tool, Glprof, specifically aimed to lessen the burden of the programmer to pin-point heavily involved data-structures during an application's run-time, and understand data-structure run-time usage.more » Moreover, we showcase the tool's modularity using additional cache simulation components. We elaborate on the tool's design, and features. Finally we demonstrate the application of our tool in the context of Spec bench- marks using the Glprof profiler and two concurrently running cache simulators, PPC440 and AMD Interlagos.« less

Structure Elucidation of Coxsackievirus A16 in Complex with GPP3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses.

PubMed

De Colibus, Luigi; Wang, Xiangxi; Tijsma, Aloys; Neyts, Johan; Spyrou, John A B; Ren, Jingshan; Grimes, Jonathan M; Puerstinger, Gerhard; Leyssen, Pieter; Fry, Elizabeth E; Rao, Zihe; Stuart, David I

2015-10-01

The replication of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), which are the major cause of hand, foot and mouth disease (HFMD) in children, can be inhibited by the capsid binder GPP3. Here, we present the crystal structure of CVA16 in complex with GPP3, which clarifies the role of the key residues involved in interactions with the inhibitor. Based on this model, in silico docking was performed to investigate the interactions with the two next-generation capsid binders NLD and ALD, which we show to be potent inhibitors of a panel of enteroviruses with potentially interesting pharmacological properties. A meta-analysis was performed using the available structural information to obtain a deeper insight into those structural features required for capsid binders to interact effectively and also those that confer broad-spectrum anti-enterovirus activity.

Similar Neural Correlates for Language and Sequential Learning: Evidence from Event-Related Brain Potentials

PubMed Central

Christiansen, Morten H.; Conway, Christopher M.; Onnis, Luca

2011-01-01

We used event-related potentials (ERPs) to investigate the time course and distribution of brain activity while adults performed (a) a sequential learning task involving complex structured sequences, and (b) a language processing task. The same positive ERP deflection, the P600 effect, typically linked to difficult or ungrammatical syntactic processing, was found for structural incongruencies in both sequential learning as well as natural language, and with similar topographical distributions. Additionally, a left anterior negativity (LAN) was observed for language but not for sequential learning. These results are interpreted as an indication that the P600 provides an index of violations and the cost of integration of expectations for upcoming material when processing complex sequential structure. We conclude that the same neural mechanisms may be recruited for both syntactic processing of linguistic stimuli and sequential learning of structured sequence patterns more generally. PMID:23678205

Genome-Wide Protein Interaction Screens Reveal Functional Networks Involving Sm-Like Proteins

PubMed Central

Fromont-Racine, Micheline; Mayes, Andrew E.; Brunet-Simon, Adeline; Rain, Jean-Christophe; Colley, Alan; Dix, Ian; Decourty, Laurence; Joly, Nicolas; Ricard, Florence; Beggs, Jean D.

2000-01-01

A set of seven structurally related Sm proteins forms the core of the snRNP particles containing the spliceosomal U1, U2, U4 and U5 snRNAs. A search of the genomic sequence of Saccharomyces cerevisiae has identified a number of open reading frames that potentially encode structurally similar proteins termed Lsm (Like Sm) proteins. With the aim of analysing all possible interactions between the Lsm proteins and any protein encoded in the yeast genome, we performed exhaustive and iterative genomic two-hybrid screens, starting with the Lsm proteins as baits. Indeed, extensive interactions amongst eight Lsm proteins were found that suggest the existence of a Lsm complex or complexes. These Lsm interactions apparently involve the conserved Sm domain that also mediates interactions between the Sm proteins. The screens also reveal functionally significant interactions with splicing factors, in particular with Prp4 and Prp24, compatible with genetic studies and with the reported association of Lsm proteins with spliceosomal U6 and U4/U6 particles. In addition, interactions with proteins involved in mRNA turnover, such as Mrt1, Dcp1, Dcp2 and Xrn1, point to roles for Lsm complexes in distinct RNA metabolic processes, that are confirmed in independent functional studies. These results provide compelling evidence that two-hybrid screens yield functionally meaningful information about protein–protein interactions and can suggest functions for uncharacterized proteins, especially when they are performed on a genome-wide scale. PMID:10900456

Actin Out: Regulation of the Synaptic Cytoskeleton

PubMed Central

Spence, Erin F.; Soderling, Scott H.

2015-01-01

The small size of dendritic spines belies the elaborate role they play in excitatory synaptic transmission and ultimately complex behaviors. The cytoskeletal architecture of the spine is predominately composed of actin filaments. These filaments, which at first glance might appear simple, are also surprisingly complex. They dynamically assemble into different structures and serve as a platform for orchestrating the elaborate responses of the spine during spinogenesis and experience-dependent plasticity. Multiple mutations associated with human neurodevelopmental and psychiatric disorders involve genes that encode regulators of the synaptic cytoskeleton. A major, unresolved question is how the disruption of specific actin filament structures leads to the onset and progression of complex synaptic and behavioral phenotypes. This review will cover established and emerging mechanisms of actin cytoskeletal remodeling and how this influences specific aspects of spine biology that are implicated in disease. PMID:26453304

Protein-Protein Interface and Disease: Perspective from Biomolecular Networks.

PubMed

Hu, Guang; Xiao, Fei; Li, Yuqian; Li, Yuan; Vongsangnak, Wanwipa

Protein-protein interactions are involved in many important biological processes and molecular mechanisms of disease association. Structural studies of interfacial residues in protein complexes provide information on protein-protein interactions. Characterizing protein-protein interfaces, including binding sites and allosteric changes, thus pose an imminent challenge. With special focus on protein complexes, approaches based on network theory are proposed to meet this challenge. In this review we pay attention to protein-protein interfaces from the perspective of biomolecular networks and their roles in disease. We first describe the different roles of protein complexes in disease through several structural aspects of interfaces. We then discuss some recent advances in predicting hot spots and communication pathway analysis in terms of amino acid networks. Finally, we highlight possible future aspects of this area with respect to both methodology development and applications for disease treatment.

The TubR-centromere complex adopts a double-ring segrosome structure in Type III partition systems.

PubMed

Martín-García, Bárbara; Martín-González, Alejandro; Carrasco, Carolina; Hernández-Arriaga, Ana M; Ruíz-Quero, Rubén; Díaz-Orejas, Ramón; Aicart-Ramos, Clara; Moreno-Herrero, Fernando; Oliva, María A

2018-05-14

In prokaryotes, the centromere is a specialized segment of DNA that promotes the assembly of the segrosome upon binding of the Centromere Binding Protein (CBP). The segrosome structure exposes a specific surface for the interaction of the CBP with the motor protein that mediates DNA movement during cell division. Additionally, the CBP usually controls the transcriptional regulation of the segregation system as a cell cycle checkpoint. Correct segrosome functioning is therefore indispensable for accurate DNA segregation. Here, we combine biochemical reconstruction and structural and biophysical analysis to bring light to the architecture of the segrosome complex in Type III partition systems. We present the particular features of the centromere site, tubC, of the model system encoded in Clostridium botulinum prophage c-st. We find that the split centromere site contains two different iterons involved in the binding and spreading of the CBP, TubR. The resulting nucleoprotein complex consists of a novel double-ring structure that covers part of the predicted promoter. Single molecule data provides a mechanism for the formation of the segrosome structure based on DNA bending and unwinding upon TubR binding.

User's guide for ENSAERO: A multidisciplinary program for fluid/structural/control interaction studies of aircraft (release 1)

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.

1994-01-01

Strong interactions can occur between the flow about an aerospace vehicle and its structural components resulting in several important aeroelastic phenomena. These aeroelastic phenomena can significantly influence the performance of the vehicle. At present, closed-form solutions are available for aeroelastic computations when flows are in either the linear subsonic or supersonic range. However, for aeroelasticity involving complex nonlinear flows with shock waves, vortices, flow separations, and aerodynamic heating, computational methods are still under development. These complex aeroelastic interactions can be dangerous and limit the performance of aircraft. Examples of these detrimental effects are aircraft with highly swept wings experiencing vortex-induced aeroelastic oscillations, transonic regime at which the flutter speed is low, aerothermoelastic loads that play a critical role in the design of high-speed vehicles, and flow separations that often lead to buffeting with undesirable structural oscillations. The simulation of these complex aeroelastic phenomena requires an integrated analysis of fluids and structures. This report presents a summary of the development, applications, and procedures to use the multidisciplinary computer code ENSAERO. This code is based on the Euler/Navier-Stokes flow equations and modal/finite-element structural equations.

Meaningful questions: The acquisition of auxiliary inversion in a connectionist model of sentence production.

PubMed

Fitz, Hartmut; Chang, Franklin

2017-09-01

Nativist theories have argued that language involves syntactic principles which are unlearnable from the input children receive. A paradigm case of these innate principles is the structure dependence of auxiliary inversion in complex polar questions (Chomsky, 1968, 1975, 1980). Computational approaches have focused on the properties of the input in explaining how children acquire these questions. In contrast, we argue that messages are structured in a way that supports structure dependence in syntax. We demonstrate this approach within a connectionist model of sentence production (Chang, 2009) which learned to generate a range of complex polar questions from a structured message without positive exemplars in the input. The model also generated different types of error in development that were similar in magnitude to those in children (e.g., auxiliary doubling, Ambridge, Rowland, & Pine, 2008; Crain & Nakayama, 1987). Through model comparisons we trace how meaning constraints and linguistic experience interact during the acquisition of auxiliary inversion. Our results suggest that auxiliary inversion rules in English can be acquired without innate syntactic principles, as long as it is assumed that speakers who ask complex questions express messages that are structured into multiple propositions. Copyright © 2017 Elsevier B.V. All rights reserved.

Simultaneous Speciation, Structure, and Equilibrium Constant Determination in the Ni2+-EDTA-CN- Ternary System via High-Resolution Laboratory X-ray Absorption Fine Structure Spectroscopy and Theoretical Calculations.

PubMed

Bajnóczi, Éva G; Németh, Zoltán; Vankó, György

2017-11-20

Even quite simple chemical systems can involve many components and chemical states, and sometimes it can be very difficult to differentiate them by their hardly separable physical-chemical properties. The Ni II -EDTA-CN - (EDTA = ethylenediaminetetraacetic acid) ternary system is a good example for this problem where, in spite of its fairly simple components and numerous investigations, several molecular combinations can exist, all of them not having been identified unambiguously yet. In order to achieve a detailed understanding of the reaction steps and chemical equilibria, methods are required in which the structural transitions in the different reaction steps can be followed via element-selective complex spectral feature sets. With the help of our recently developed von Hámos type high-resolution laboratory X-ray absorption spectrometer, both the structural variations and stability constants of the forming complexes were determined from the same measurement series, proving that X-ray absorption spectroscopy can be considered as a multifaced, table-top tool in coordination chemistry. Furthermore, with the help of theoretical calculations, independent structural evidence was also given for the formation of the [NiEDTA(CN)] 3- mixed complex.

State of the APC/C: Organization, function, and structure

PubMed Central

McLean, Janel R.; Chaix, Denis; Ohi, Melanie D.; Gould, Kathleen L.

2016-01-01

The ubiquitin-proteasome protein degradation system is involved in many essential cellular processes including cell cycle regulation, cell differentiation, and the unfolded protein response.The anaphase-promoting complex/cyclosome (APC/C), an evolutionary conserved E3 ubiquitin ligase, was discovered 15 years ago because of its pivotal role in cyclin degradation and mitotic progression. Since then, we have learned that the APC/C is a very large, complex E3 ligase composed of 13 subunits, yielding a molecular machine of approximately 1 MDa. The intricate regulation of the APC/C is mediated by the Cdc20 family of activators, pseudosubstrate inhibitors, protein kinases and phosphatases and the spindle assembly checkpoint. The large size, complexity, and dynamic nature of the APC/C represent significant obstacles toward high-resolution structural techniques; however, over the last decade, there have been a number of lower resolution APC/C structures determined using single particle electron microscopy. These structures, when combined with data generated from numerous genetic and biochemical studies, have begun to shed light on how APC/C activity is regulated. Here, we discuss the most recent developments in the APC/C field concerning structure, substrate recognition, and catalysis. PMID:21261459

Structural complexes in the squid giant axon membrane sensitive to ionic concentrations and cardiac glycosides

PubMed Central

Villegas, GM; Villegas, J

1976-01-01

Giant nerve fibers of squid Sepioteuthis sepiodea were incubated for 10 min in artificial sea water (ASW) under control conditions, in the absence of various ions, and in the presence of cardiac glycosides. The nerve fibers were fixed in OsO(4) and embedded in Epon, and structural complexes along the axolemma were studied. These complexes consist of a portion of axolemma exhibiting a three-layered substructure, an undercoating of a dense material (approximately 0.1μm in length and approximately 70-170 A in thickness), and a narrowing to disappearance of the axon-Schwann cell interspace. In the controls, the incidence of complexes per 1,000μm of axon perimeter was about 137. This number decreased to 10-25 percent when magnesium was not present in the incubating media, whatever the calcium concentration (88, 44, or 0 mM). In the presence of magnesium, the number and structural features of the complexes were preserved, though the number decreased to 65 percent when high calcium was simultaneously present. The complexes were also modified and decreased to 26-32 percent by incubating the nerves in solutions having low concentrations of sodium and potassium. The adding of 10(-5) M ouabain or strophanthoside to normal ASW incubating solution decreased them to 20-40 percent. Due to their sensitivity to changes in external ionic concentrations and to the presence of cardiac glycosides, the complexes are proposed to represent the structural correlate of specialized sites for active ion transport, although other factors may be involved. PMID:1254642

Multinational Business Gaming: Is Gender Important?

ERIC Educational Resources Information Center

Johnson, Scott D.; And Others

1997-01-01

A study investigated influence of gender on undergraduate students (n=119) involved in international business games. Females tended to view the simulation as less complex, have less cohesive group structures, and show less self-confidence than males. However, game performance measures showed no significant gender differences. Implications for…

Motivating Tomorrow's Biologists

ERIC Educational Resources Information Center

Musante, Susan

2012-01-01

The story of biology is far more complex and fascinating than straightforward facts or neatly labeled diagrams of structures and systems. Although exams can motivate students, the key to using these extrinsic motivators to increase student understanding lies in the way the assessments are designed and what they measure. Those involved in…

Sequential structures provide insights into the fidelity of RNA replication.

PubMed

Ferrer-Orta, Cristina; Arias, Armando; Pérez-Luque, Rosa; Escarmís, Cristina; Domingo, Esteban; Verdaguer, Nuria

2007-05-29

RNA virus replication is an error-prone event caused by the low fidelity of viral RNA-dependent RNA polymerases. Replication fidelity can be decreased further by the use of mutagenic ribonucleoside analogs to a point where viral genetic information can no longer be maintained. For foot-and-mouth disease virus, the antiviral analogs ribavirin and 5-fluorouracil have been shown to be mutagenic, contributing to virus extinction through lethal mutagenesis. Here, we report the x-ray structure of four elongation complexes of foot-and-mouth disease virus polymerase 3D obtained in presence of natural substrates, ATP and UTP, or mutagenic nucleotides, ribavirin triphosphate and 5-fluorouridine triphosphate with different RNAs as template-primer molecules. The ability of these complexes to synthesize RNA in crystals allowed us to capture different successive replication events and to define the critical amino acids involved in (i) the recognition and positioning of the incoming nucleotide or analog; (ii) the positioning of the acceptor base of the template strand; and (iii) the positioning of the 3'-OH group of the primer nucleotide during RNA replication. The structures identify key interactions involved in viral RNA replication and provide insights into the molecular basis of the low fidelity of viral RNA polymerases.

Structure and kinematics of a major tectonic contact, Michipicoten greenstone belt, Ontario

NASA Technical Reports Server (NTRS)

Mcgill, George E.

1992-01-01

The Michipicoten greenstone belt, Ontario, experienced a complex history of folding, faulting, and fabric development. Near Wawa, a major east-west contact, here named the Steep Hill Falls (SHF) contact, extends entirely across the belt. The SHF contact is both an angular unconformity and a fault and is interpreted to be a regionally significant tectonic contact separating distinct northern and southern terranes, both of which include volcanic rocks of probable island-arc origin. The amount of horizontal transport involved in bringing the two terranes together along the SHF contact is not known. Mapping and structural analysis suggest that regionally significant horizontal displacements took place, with movement vectors that changed with time. Early faults, folds, and fabrics imply north-south to northeast-southwest (with respect to present directions) convergence, with a vergence reversal occurring during this complex event. The most likely models infer early south vergence and later north vergence. Transecting the earliest structures are younger (but still Archean) northeast-striking steep cleavages with associated upright folds that may relate to northwest-southeast assembly of the Superior Province craton. The craton assembly event thus involved a transport direction at a high angle to that inferred for the earlier assembly of the Michipicoten greenstone belt.

Polyphenols in foods are more complex than often thought.

PubMed

Cheynier, Véronique

2005-01-01

Dietary polyphenols show a great diversity of structures, ranging from rather simple molecules (monomers and oligomers) to polymers. Higher-molecular-weight structures (with molecular weights of > 500) are usually designated as tannins, which refers to their ability to interact with proteins. Among them, condensed tannins (proanthocyanidins) are particularly important because of their wide distribution in plants and their contributions to major food qualities. All phenolic compounds are highly unstable and rapidly transformed into various reaction products when the plant cells are damaged (for instance, during food processing), thus adding to the complexity of dietary polyphenol composition. The polyphenol composition of plant-derived foods and beverages depends on that of the raw material used but also on the extraction process and subsequent biochemical and chemical reactions of plant polyphenols. The occurrence of specific tannin-like compounds (ie, thearubigins and theaflavins) arising from enzymatic oxidation is well documented in black tea. Various chemical reactions involving anthocyanins and/or flavanols have been demonstrated to occur during red wine aging. Current knowledge regarding the reaction mechanisms involved in some of these processes and the structures of the resulting products is reviewed. Their effects on organoleptic and nutritional quality are also discussed.

Structural Characterization of the Trimerization of TRAF6 Protein Through Molecular Dynamics Simulations.

PubMed

Biswas, Ria; Bagchi, Angshuman

2017-09-11

The tumour necrosis factor (TNF) receptor-associated factor (TRAF) family of proteins having E3 ligase activity are the key molecules involved in cellular immune response pathways. TRAF6 is a unique member of the TRAF superfamily differing from other members of the family, owing to its specific interactions with molecules outside the TNF receptor superfamily. The C-terminal domain of TRAF proteins contains the catalytic residues and are known to be involved in self-oligomerization forming a mushroom-shaped trimeric structure, which is the functional form of the protein. However, the monomeric crystal structure of TRAF6 C-terminal domain has been already determined, but the trimeric structure of the same is still not available. We here applied computational structural modelling and molecular dynamics simulations studies to get insights into the molecular interactions involved in determining the trimeric structure of the TRAF6 C-terminal domain. The non-availability of the trimeric structure of the TRAF6 C-terminal domain prevented the elucidation of the molecular mechanism of many different biological processes. Our results suggest that the trimer complex is transient in nature. The amino acid residues Lys340 and Glu345 in the coiled coil domain in the C-terminus of TRAF6 play a critical role in trimer structure formation. This structural modelling study may therefore be utilized to obtain the experimentally validated trimeric structure of this important protein.

Multimeric complexes among ankyrin-repeat and SOCS-box protein 9 (ASB9), ElonginBC, and Cullin 5: insights into the structure and assembly of ECS-type Cullin-RING E3 ubiquitin ligases.

PubMed

Thomas, Jemima C; Matak-Vinkovic, Dijana; Van Molle, Inge; Ciulli, Alessio

2013-08-06

Proteins of the ankyrin-repeat and SOCS-box (ASB) family act as the substrate-recognition subunits of ECS-type (ElonginBC-Cullin-SOCS-box) Cullin RING E3 ubiquitin ligase (CRL) complexes that catalyze the specific polyubiquitination of cellular proteins to target them for degradation by the proteasome. Therefore, ASB multimeric complexes are involved in numerous cell processes and pathways; however, their interactions, assembly, and biological roles remain poorly understood. To enhance our understanding of ASB CRL systems, we investigated the structure, affinity, and assembly of the quaternary multisubunit complex formed by ASB9, Elongin B, Elongin C (EloBC), and Cullin 5. Here, we describe the application of several biophysical techniques including differential scanning fluorimetry, isothermal titration calorimetry (ITC), nanoelectrospray ionization, and ion-mobility mass spectrometry (IM-MS) to provide structural and thermodynamic information for a quaternary ASB CRL complex. We find that ASB9 is unstable alone but forms a stable ternary complex with EloBC that binds with high affinity to the Cullin 5 N-terminal domain (Cul5NTD) but not to Cul2NTD. The structure of the monomeric ASB9-EloBC-Cul5NTD quaternary complex is revealed by molecular modeling and is consistent with IM-MS and temperature-dependent ITC data. This is the first experimental study to validate structural information for the assembly of the quaternary N-terminal region of an ASB CRL complex. The results suggest that ASB E3 ligase complexes function and assemble in an analogous manner to that of other CRL systems and provide a platform for further molecular investigation of this important protein family. The data reported here will also be of use for the future development of chemical probes to examine the biological function and modulation of other ECS-type CRL systems.

Multimeric Complexes among Ankyrin-Repeat and SOCS-box Protein 9 (ASB9), ElonginBC, and Cullin 5: Insights into the Structure and Assembly of ECS-type Cullin-RING E3 Ubiquitin Ligases

PubMed Central

2013-01-01

Proteins of the ankyrin-repeat and SOCS-box (ASB) family act as the substrate-recognition subunits of ECS-type (ElonginBC–Cullin–SOCS-box) Cullin RING E3 ubiquitin ligase (CRL) complexes that catalyze the specific polyubiquitination of cellular proteins to target them for degradation by the proteasome. Therefore, ASB multimeric complexes are involved in numerous cell processes and pathways; however, their interactions, assembly, and biological roles remain poorly understood. To enhance our understanding of ASB CRL systems, we investigated the structure, affinity, and assembly of the quaternary multisubunit complex formed by ASB9, Elongin B, Elongin C (EloBC), and Cullin 5. Here, we describe the application of several biophysical techniques including differential scanning fluorimetry, isothermal titration calorimetry (ITC), nanoelectrospray ionization, and ion-mobility mass spectrometry (IM–MS) to provide structural and thermodynamic information for a quaternary ASB CRL complex. We find that ASB9 is unstable alone but forms a stable ternary complex with EloBC that binds with high affinity to the Cullin 5 N-terminal domain (Cul5NTD) but not to Cul2NTD. The structure of the monomeric ASB9–EloBC–Cul5NTD quaternary complex is revealed by molecular modeling and is consistent with IM–MS and temperature-dependent ITC data. This is the first experimental study to validate structural information for the assembly of the quaternary N-terminal region of an ASB CRL complex. The results suggest that ASB E3 ligase complexes function and assemble in an analogous manner to that of other CRL systems and provide a platform for further molecular investigation of this important protein family. The data reported here will also be of use for the future development of chemical probes to examine the biological function and modulation of other ECS-type CRL systems. PMID:23837592

Structure, Dynamics, and Interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 Examined by Molecular Modeling, Simulation, and Electrostatic Studies

PubMed Central

Bhutani, Isha; Loharch, Saurabh; Gupta, Pawan; Madathil, Rethi; Parkesh, Raman

2015-01-01

The enzymes decaprenylphosphoryl-β-D-ribose oxidase (DprE1) and decaprenylphosphoryl-β-D-ribose-2-epimerase (DprE2) catalyze epimerization of decaprenylphosporyl ribose (DPR) todecaprenylphosporyl arabinose (DPA) and are critical for the survival of Mtb. Crystal structures of DprE1 so far reported display significant disordered regions and no structural information is known for DprE2. We used homology modeling, protein threading, molecular docking and dynamics studies to investigate the structural and dynamic features of Mtb DprE1 and DprE2 and DprE1-DprE2 complex. A three-dimensional model for DprE2 was generated using the threading approach coupled with ab initio modeling. A 50 ns simulation of DprE1 and DprE2 revealed the overall stability of the structures. Principal Component Analysis (PCA) demonstrated the convergence of sampling in both DprE1 and DprE2. In DprE1, residues in the 269–330 area showed considerable fluctuation in agreement with the regions of disorder observed in the reported crystal structures. In DprE2, large fluctuations were detected in residues 95–113, 146–157, and 197–226. The study combined docking and MD simulation studies to map and characterize the key residues involved in DprE1-DprE2 interaction. A 60 ns MD simulation for DprE1-DprE2 complex was also performed. Analysis of data revealed that the docked complex is stabilized by H-bonding, hydrophobic and ionic interactions. The key residues of DprE1 involved in DprE1-DprE2 interactions belong to the disordered region. We also examined the docked complex of DprE1-BTZ043 to investigate the binding pocket of DprE1 and its interactions with the inhibitor BTZ043. In summary, we hypothesize that DprE1-DprE2 interaction is crucial for the synthesis of DPA and DprE1-DprE2 complex may be a new therapeutic target amenable to pharmacological validation. The findings have important implications in tuberculosis (TB) drug discovery and will facilitate drug development efforts against TB. PMID:25789990

Structure, dynamics, and interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 examined by molecular modeling, simulation, and electrostatic studies.

PubMed

Bhutani, Isha; Loharch, Saurabh; Gupta, Pawan; Madathil, Rethi; Parkesh, Raman

2015-01-01

The enzymes decaprenylphosphoryl-β-D-ribose oxidase (DprE1) and decaprenylphosphoryl-β-D-ribose-2-epimerase (DprE2) catalyze epimerization of decaprenylphosporyl ribose (DPR) todecaprenylphosporyl arabinose (DPA) and are critical for the survival of Mtb. Crystal structures of DprE1 so far reported display significant disordered regions and no structural information is known for DprE2. We used homology modeling, protein threading, molecular docking and dynamics studies to investigate the structural and dynamic features of Mtb DprE1 and DprE2 and DprE1-DprE2 complex. A three-dimensional model for DprE2 was generated using the threading approach coupled with ab initio modeling. A 50 ns simulation of DprE1 and DprE2 revealed the overall stability of the structures. Principal Component Analysis (PCA) demonstrated the convergence of sampling in both DprE1 and DprE2. In DprE1, residues in the 269-330 area showed considerable fluctuation in agreement with the regions of disorder observed in the reported crystal structures. In DprE2, large fluctuations were detected in residues 95-113, 146-157, and 197-226. The study combined docking and MD simulation studies to map and characterize the key residues involved in DprE1-DprE2 interaction. A 60 ns MD simulation for DprE1-DprE2 complex was also performed. Analysis of data revealed that the docked complex is stabilized by H-bonding, hydrophobic and ionic interactions. The key residues of DprE1 involved in DprE1-DprE2 interactions belong to the disordered region. We also examined the docked complex of DprE1-BTZ043 to investigate the binding pocket of DprE1 and its interactions with the inhibitor BTZ043. In summary, we hypothesize that DprE1-DprE2 interaction is crucial for the synthesis of DPA and DprE1-DprE2 complex may be a new therapeutic target amenable to pharmacological validation. The findings have important implications in tuberculosis (TB) drug discovery and will facilitate drug development efforts against TB.

Protein docking by the interface structure similarity: how much structure is needed?

PubMed

Sinha, Rohita; Kundrotas, Petras J; Vakser, Ilya A

2012-01-01

The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.

Mechanism Underlying IκB Kinase Activation Mediated by the Linear Ubiquitin Chain Assembly Complex

PubMed Central

Fujita, Hiroaki; Akita, Mariko; Kato, Ryuichi; Sasaki, Yoshiteru; Wakatsuki, Soichi

2014-01-01

The linear ubiquitin chain assembly complex (LUBAC) ligase, consisting of HOIL-1L, HOIP, and SHARPIN, specifically generates linear polyubiquitin chains. LUBAC-mediated linear polyubiquitination has been implicated in NF-κB activation. NEMO, a component of the IκB kinase (IKK) complex, is a substrate of LUBAC, but the precise molecular mechanism underlying linear chain-mediated NF-κB activation has not been fully elucidated. Here, we demonstrate that linearly polyubiquitinated NEMO activates IKK more potently than unanchored linear chains. In mutational analyses based on the crystal structure of the complex between the HOIP NZF1 and NEMO CC2-LZ domains, which are involved in the HOIP-NEMO interaction, NEMO mutations that impaired linear ubiquitin recognition activity and prevented recognition by LUBAC synergistically suppressed signal-induced NF-κB activation. HOIP NZF1 bound to NEMO and ubiquitin simultaneously, and HOIP NZF1 mutants defective in interaction with either NEMO or ubiquitin could not restore signal-induced NF-κB activation. Furthermore, linear chain-mediated activation of IKK2 involved homotypic interaction of the IKK2 kinase domain. Collectively, these results demonstrate that linear polyubiquitination of NEMO plays crucial roles in IKK activation and that this modification involves the HOIP NZF1 domain and recognition of NEMO-conjugated linear ubiquitin chains by NEMO on another IKK complex. PMID:24469399

Imaging of DNA and Protein by SFM and Combined SFM-TIRF Microscopy.

PubMed

Grosbart, Małgorzata; Ristić, Dejan; Sánchez, Humberto; Wyman, Claire

2018-01-01

Direct imaging is invaluable for understanding the mechanism of complex genome transactions where proteins work together to organize, transcribe, replicate and repair DNA. Scanning (or atomic) force microscopy is an ideal tool for this, providing 3D information on molecular structure at nm resolution from defined components. This is a convenient and practical addition to in vitro studies as readily obtainable amounts of purified proteins and DNA are required. The images reveal structural details on the size and location of DNA bound proteins as well as protein-induced arrangement of the DNA, which are directly correlated in the same complexes. In addition, even from static images, the different forms observed and their relative distributions can be used to deduce the variety and stability of different complexes that are necessarily involved in dynamic processes. Recently available instruments that combine fluorescence with topographic imaging allow the identification of specific molecular components in complex assemblies, which broadens the applications and increases the information obtained from direct imaging of molecular complexes. We describe here basic methods for preparing samples of proteins, DNA and complexes of the two for topographic imaging and quantitative analysis. We also describe special considerations for combined fluorescence and topographic imaging of molecular complexes.

Crystal structure of plant light-harvesting complex shows the active, energy-transmitting state

PubMed Central

Barros, Tiago; Royant, Antoine; Standfuss, Jörg; Dreuw, Andreas; Kühlbrandt, Werner

2009-01-01

Plants dissipate excess excitation energy as heat by non-photochemical quenching (NPQ). NPQ has been thought to resemble in vitro aggregation quenching of the major antenna complex, light harvesting complex of photosystem II (LHC-II). Both processes are widely believed to involve a conformational change that creates a quenching centre of two neighbouring pigments within the complex. Using recombinant LHC-II lacking the pigments implicated in quenching, we show that they have no particular role. Single crystals of LHC-II emit strong, orientation-dependent fluorescence with an emission maximum at 680 nm. The average lifetime of the main 680 nm crystal emission at 100 K is 1.31 ns, but only 0.39 ns for LHC-II aggregates under identical conditions. The strong emission and comparatively long fluorescence lifetimes of single LHC-II crystals indicate that the complex is unquenched, and that therefore the crystal structure shows the active, energy-transmitting state of LHC-II. We conclude that quenching of excitation energy in the light-harvesting antenna is due to the molecular interaction with external pigments in vitro or other pigment–protein complexes such as PsbS in vivo, and does not require a conformational change within the complex. PMID:19131972

Structure of the Protease Domain of Memapsin 2 (β-Secretase) Complexed with Inhibitor

NASA Astrophysics Data System (ADS)

Hong, Lin; Koelsch, Gerald; Lin, Xinli; Wu, Shili; Terzyan, Simon; Ghosh, Arun K.; Zhang, Xuenjun C.; Tang, Jordan

2000-10-01

Memapsin 2 (β-secretase) is a membrane-associated aspartic protease involved in the production of β-amyloid peptide in Alzheimer's disease and is a major target for drug design. We determined the crystal structure of the protease domain of human memapsin 2 complexed to an eight-residue inhibitor at 1.9 angstrom resolution. The active site of memapsin 2 is more open and less hydrophobic than that of other human aspartic proteases. The subsite locations from S4 to S2' are well defined. A kink of the inhibitor chain at P2' and the change of chain direction of P3' and P4' may be mimicked to provide inhibitor selectivity.

Numerical Leak Detection in a Pipeline Network of Complex Structure with Unsteady Flow

NASA Astrophysics Data System (ADS)

Aida-zade, K. R.; Ashrafova, E. R.

2017-12-01

An inverse problem for a pipeline network of complex loopback structure is solved numerically. The problem is to determine the locations and amounts of leaks from unsteady flow characteristics measured at some pipeline points. The features of the problem include impulse functions involved in a system of hyperbolic differential equations, the absence of classical initial conditions, and boundary conditions specified as nonseparated relations between the states at the endpoints of adjacent pipeline segments. The problem is reduced to a parametric optimal control problem without initial conditions, but with nonseparated boundary conditions. The latter problem is solved by applying first-order optimization methods. Results of numerical experiments are presented.

Terrestrial laser scanning to quantify above-ground biomass of structurally complex coastal wetland vegetation

NASA Astrophysics Data System (ADS)

Owers, Christopher J.; Rogers, Kerrylee; Woodroffe, Colin D.

2018-05-01

Above-ground biomass represents a small yet significant contributor to carbon storage in coastal wetlands. Despite this, above-ground biomass is often poorly quantified, particularly in areas where vegetation structure is complex. Traditional methods for providing accurate estimates involve harvesting vegetation to develop mangrove allometric equations and quantify saltmarsh biomass in quadrats. However broad scale application of these methods may not capture structural variability in vegetation resulting in a loss of detail and estimates with considerable uncertainty. Terrestrial laser scanning (TLS) collects high resolution three-dimensional point clouds capable of providing detailed structural morphology of vegetation. This study demonstrates that TLS is a suitable non-destructive method for estimating biomass of structurally complex coastal wetland vegetation. We compare volumetric models, 3-D surface reconstruction and rasterised volume, and point cloud elevation histogram modelling techniques to estimate biomass. Our results show that current volumetric modelling approaches for estimating TLS-derived biomass are comparable to traditional mangrove allometrics and saltmarsh harvesting. However, volumetric modelling approaches oversimplify vegetation structure by under-utilising the large amount of structural information provided by the point cloud. The point cloud elevation histogram model presented in this study, as an alternative to volumetric modelling, utilises all of the information within the point cloud, as opposed to sub-sampling based on specific criteria. This method is simple but highly effective for both mangrove (r2 = 0.95) and saltmarsh (r2 > 0.92) vegetation. Our results provide evidence that application of TLS in coastal wetlands is an effective non-destructive method to accurately quantify biomass for structurally complex vegetation.

trans-Methylpyridine cyclen versus cross-bridged trans-methylpyridine cyclen. Synthesis, acid-base and metal complexation studies (metal = Co2+, Cu2+, and Zn2+).

PubMed

Bernier, Nicolas; Costa, Judite; Delgado, Rita; Félix, Vítor; Royal, Guy; Tripier, Raphaël

2011-05-07

The synthesis of the cross-bridged cyclen CRpy(2) {4,10-bis((pyridin-2-yl)methyl)-1,4,7,10-tetraazabicyclo[5.5.2]tetradecane}, a constrained analogue of the previously described trans-methylpyridine cyclen Cpy(2) is reported. The additional ethylene bridge confers to CRpy(2) proton-sponge type behaviour which was explored by NMR and potentiometric studies. Transition metal complexes have been synthesized (by complexation of both ligands with Co(2+), Cu(2+) and Zn(2+)) and characterized in solution and in the solid state. The single crystal X-ray structures of [CoCpy(2)](2+), [CuCpy(2)](2+) and [ZnCpy(2)](2+) complexes were determined. Stability constants of the complexes, including those of the cross-bridged derivative, were determined using potentiometric titration data and the kinetic inertness of the [CuCRpy(2)](2+) complex in an acidic medium (half-life values) was evaluated by spectrophotometry. The pre-organized structure of the cross-bridged ligand imposes an additional strain for the complexation leading to complexes with smaller thermodynamic stability in comparison with the related non-bridged ligand. The electrochemical study involving cyclic voltammetry underlines the importance of the ethylene cross-bridge on the redox properties of the transition metal complexes.

Stress Recovery and Error Estimation for Shell Structures

NASA Technical Reports Server (NTRS)

Yazdani, A. A.; Riggs, H. R.; Tessler, A.

2000-01-01

The Penalized Discrete Least-Squares (PDLS) stress recovery (smoothing) technique developed for two dimensional linear elliptic problems is adapted here to three-dimensional shell structures. The surfaces are restricted to those which have a 2-D parametric representation, or which can be built-up of such surfaces. The proposed strategy involves mapping the finite element results to the 2-D parametric space which describes the geometry, and smoothing is carried out in the parametric space using the PDLS-based Smoothing Element Analysis (SEA). Numerical results for two well-known shell problems are presented to illustrate the performance of SEA/PDLS for these problems. The recovered stresses are used in the Zienkiewicz-Zhu a posteriori error estimator. The estimated errors are used to demonstrate the performance of SEA-recovered stresses in automated adaptive mesh refinement of shell structures. The numerical results are encouraging. Further testing involving more complex, practical structures is necessary.

The plastid ndh genes code for an NADH-specific dehydrogenase: Isolation of a complex I analogue from pea thylakoid membranes

PubMed Central

Sazanov, Leonid A.; Burrows, Paul A.; Nixon, Peter J.

1998-01-01

The plastid genomes of several plants contain ndh genes—homologues of genes encoding subunits of the proton-pumping NADH:ubiquinone oxidoreductase, or complex I, involved in respiration in mitochondria and eubacteria. From sequence similarities with these genes, the ndh gene products have been suggested to form a large protein complex (Ndh complex); however, the structure and function of this complex remains to be established. Herein we report the isolation of the Ndh complex from the chloroplasts of the higher plant Pisum sativum. The purification procedure involved selective solubilization of the thylakoid membrane with dodecyl maltoside, followed by two anion-exchange chromatography steps and one size-exclusion chromatography step. The isolated Ndh complex has an apparent total molecular mass of approximately 550 kDa and according to SDS/PAGE consists of at least 16 subunits including NdhA, NdhI, NdhJ, NdhK, and NdhH, which were identified by N-terminal sequencing and immunoblotting. The Ndh complex showed an NADH- and deamino-NADH-specific dehydrogenase activity, characteristic of complex I, when either ferricyanide or the quinones menadione and duroquinone were used as electron acceptors. This study describes the isolation of the chloroplast analogue of the respiratory complex I and provides direct evidence for the function of the plastid Ndh complex as an NADH:plastoquinone oxidoreductase. Our results are compatible with a dual role for the Ndh complex in the chlororespiratory and cyclic photophosphorylation pathways. PMID:9448329

The Employment of Structures and Work Patterns in Organizations Involved in Modern, Complex, Multi-National Operations

DTIC Science & Technology

2011-06-01

This has a particular impact on Command Management, through which the Commander establishes and maintains his headquarters structures, collaborations...tend to be organized in a ‘planning-centric’ fashion. Analysis tends to focus upon the interpretation of environmental phenomena (e.g. events...These will be used in the next stage to organize scenario development. for the future of the conflict region including the impact of the military

A Method for the Calculation of Lattice Energies of Complex Crystals with Application to the Oxides of Molybdenum

NASA Technical Reports Server (NTRS)

Chaney, William S.

1961-01-01

A theoretical study has been made of molybdenum dioxide and molybdenum trioxide in order to extend the knowledge of factors Involved in the oxidation of molybdenum. New methods were developed for calculating the lattice energies based on electrostatic valence theory, and the coulombic, polarization, Van der Waals, and repulsion energie's were calculated. The crystal structure was examined and structure details were correlated with lattice energy.

Structural basis for spectrin recognition by ankyrin.

PubMed

Ipsaro, Jonathan J; Mondragón, Alfonso

2010-05-20

Maintenance of membrane integrity and organization in the metazoan cell is accomplished through intracellular tethering of membrane proteins to an extensive, flexible protein network. Spectrin, the principal component of this network, is anchored to membrane proteins through the adaptor protein ankyrin. To elucidate the atomic basis for this interaction, we determined a crystal structure of human betaI-spectrin repeats 13 to 15 in complex with the ZU5-ANK domain of human ankyrin R. The structure reveals the role of repeats 14 to 15 in binding, the electrostatic and hydrophobic contributions along the interface, and the necessity for a particular orientation of the spectrin repeats. Using structural and biochemical data as a guide, we characterized the individual proteins and their interactions by binding and thermal stability analyses. In addition to validating the structural model, these data provide insight into the nature of some mutations associated with cell morphology defects, including those found in human diseases such as hereditary spherocytosis and elliptocytosis. Finally, analysis of the ZU5 domain suggests it is a versatile protein-protein interaction module with distinct interaction surfaces. The structure represents not only the first of a spectrin fragment in complex with its binding partner, but also that of an intermolecular complex involving a ZU5 domain.

Structure of choline oxidase in complex with the reaction product glycine betaine.

PubMed

Salvi, Francesca; Wang, Yuan-Fang; Weber, Irene T; Gadda, Giovanni

2014-02-01

Choline oxidase from Arthrobacter globiformis, which is involved in the biosynthesis of glycine betaine from choline, has been extensively characterized in its mechanistic and structural properties. Despite the knowledge gained on the enzyme, the details of substrate access to the active site are not fully understood. The `loop-and-lid' mechanism described for the glucose-methanol-choline enzyme superfamily has not been confirmed for choline oxidase. Instead, a hydrophobic cluster on the solvent-accessible surface of the enzyme has been proposed by molecular dynamics to control substrate access to the active site. Here, the crystal structure of the enzyme was solved in complex with glycine betaine at pH 6.0 at 1.95 Å resolution, allowing a structural description of the ligand-enzyme interactions in the active site. This structure is the first of choline oxidase in complex with a physiologically relevant ligand. The protein structures with and without ligand are virtually identical, with the exception of a loop at the dimer interface, which assumes two distinct conformations. The different conformations of loop 250-255 define different accessibilities of the proposed active-site entrance delimited by the hydrophobic cluster on the other subunit of the dimer, suggesting a role in regulating substrate access to the active site.

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

PubMed

Patel, Trushar R; Chojnowski, Grzegorz; Astha; Koul, Amit; McKenna, Sean A; Bujnicki, Janusz M

2017-04-15

The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex

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

Ipsaro, Jonathan J.; Harper, Sandra L.; Messick, Troy E.

2010-09-07

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

Crystal Structure and Functional Interpretation of the Erythrocyte spectrin Tetramerization Domain Complex

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

J Ipsaro; S Harper; T Messick

2011-12-31

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

Learning to See the (W)holes

ERIC Educational Resources Information Center

Burns, Barbara A.; Jordan, Thomas M.

2006-01-01

Business managers are faced with complex decisions involving a wide range of issues--technical, social, environmental, and financial--and their interaction. Our education system focuses heavily on presenting structured problems and teaching students to apply a set of tools or methods to solve these problems. Yet the most difficult thing to teach…

An Application of Latent Variable Structural Equation Modeling for Experimental Research in Educational Technology

ERIC Educational Resources Information Center

Lee, Hyeon Woo

2011-01-01

As the technology-enriched learning environments and theoretical constructs involved in instructional design become more sophisticated and complex, a need arises for equally sophisticated analytic methods to research these environments, theories, and models. Thus, this paper illustrates a comprehensive approach for analyzing data arising from…

Individual and Situational Factors Associated with Social Barriers for Persons with Mobility Impairment

ERIC Educational Resources Information Center

McCaughey, Tiffany

2009-01-01

Decades of research have examined factors involved in complex, and sometimes stressful, interpersonal interactions between individuals with and without disabilities. The present study applies structural equation modeling to test an integrative model of individual and situational factors affecting encounters between able-bodied college students and…

Design and Implementation of the Game-Design and Learning Program

ERIC Educational Resources Information Center

Akcaoglu, Mete

2016-01-01

Design involves solving complex, ill-structured problems. Design tasks are consequently, appropriate contexts for children to exercise higher-order thinking and problem-solving skills. Although creating engaging and authentic design contexts for young children is difficult within the confines of traditional schooling, recently, game-design has…

Brain Mechanisms of Attentional Control.

ERIC Educational Resources Information Center

Wilke, Thomas

Lack of attentional control--inability to concentrate--has often made the difference between successful and unsuccessful performance on the part of athletes. Attention is controlled neurologically by a very complex interaction of a large portion of the cerebrum and is not localized to any one structure. The mechanism involves a memory retrieval…

Adaptation of neuronal signaling and cell stress response pathways in a multigenic response of Drosophila melanogaster to DDT selection

USDA-ARS?s Scientific Manuscript database

The adaptation of insect populations to insecticidal control is a continual threat human health and sustainable agriculture practices, but many complex genomic mechanisms involved remain poorly understood. A systems approach was applied to investigate the interconnections between structural and func...

Women and Men in the Class Structure.

ERIC Educational Resources Information Center

Collins, Randall

1988-01-01

Describes the stratification position of women as generally more complex than that of men, because of class distinction of organizational power. Asserts that many women, in presenting the front-stage image of an organization, in performing considerable surplus domestic labor, and in employment and leisure activities, are involved primarily in…

Defying Definition: Rethinking Education Aid Relationships in Solomon Islands

ERIC Educational Resources Information Center

Spratt, Rebecca

2016-01-01

The discourse of aid--its language, structures and practice--powerfully ascribes roles and attributes to those involved in aid relationships such as developed/developing, partner, recipient/donor etcetera. This discourse is driven by a complex system of diverse and often competing ideas, values, actors and relationships, within which individuals…

Protein adhesives

Treesearch

Charles R. Frihart; Linda F. Lorenz

2018-01-01

Nature uses a wide variety of chemicals for providing adhesion internally (e.g., cell to cell) and externally (e.g., mussels to ships and piers). This adhesive bonding is chemically and mechanically complex, involving a variety of proteins, carbohydrates, and other compounds.Consequently,the effect of protein structures on adhesive properties is only partially...

Concept Mapping for Critical Thinking: Efficacy, Timing, & Type

ERIC Educational Resources Information Center

Harris, Charles M.; Zha, Shenghua

2017-01-01

Many college students are not progressing in the development of their critical thinking skills. Concept mapping is a technique for facilitating validation of one's critical thinking by graphically depicting the structure of complex concepts. Each of our three studies of concept mapping involved approximately 240 students enrolled in four sections…

Structural investigation of the C-O complex in GaAs

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

Alt, H. Ch.; Kersch, A.; Wagner, H. E.

A carbon-oxygen complex occurring in gallium arsenide crystals after annealing at around 700 °C is studied. Fourier transform infrared absorption measurements on the associated vibrational band at 2060 cm-1 under uniaxial stress reveal that the center has tetragonal symmetry. From the intensity of the {sup 18}O-related satellite band it is concluded that four oxygen atoms are involved. Ab initio local density calculations show that a tetragonal CO{sub 4} molecule forms a stable entity in the gallium arsenide lattice.

Supramolecular complexes of Co(II), Ni(II) and Zn(II) p-hydroxybenzoates with caffeine: Synthesis, spectral characterization and crystal structure

NASA Astrophysics Data System (ADS)

Taşdemir, Erdal; Özbek, Füreya Elif; Sertçelik, Mustafa; Hökelek, Tuncer; Çelik, Raziye Çatak; Necefoğlu, Hacali

2016-09-01

Three novel complexes Co(II), Ni(II) and Zn(II) containing p-hydroxybenzoates and caffeine ligands were synthesized and characterized by elemental analysis, FT-IR and UV-vis Spectroscopy, molar conductivity and single crystal X-ray diffraction methods. The thermal properties of the synthesized complexes were investigated by TGA/DTA. The general formula of the complexes is [M(HOC6H4COO)2(H2O)4]·2(C8H10N4O2)·8H2O (where: M: Co, Ni and Zn). The IR studies showed that carboxylate groups of p-hydroxybenzoate ligands have monodentate coordination mode. The M2+ ions are octahedrally coordinated by two p-hydroxybenzoate ligands, four water molecules leading to an overall MO6 coordination environment. The medium-strength hydrogen bondings involving the uncoordinated caffeine ligands and water molecules, coordinated and uncoordinated water molecules and p-hydroxybenzoate ligands lead to three-dimensional supramolecular networks in the crystal structures.

Towards the Rational Design of MRI Contrast Agents: Electron Spin Relaxation Is Largely Unaffected by the Coordination Geometry of Gadolinium(III)–DOTA-Type Complexes

PubMed Central

Bean, Jonathan F.; Clarkson, Robert B.; Helm, Lothar; Moriggi, Loïck; Sherry, A. Dean

2009-01-01

Electron-spin relaxation is one of the determining factors in the efficacy of MRI contrast agents. Of all the parameters involved in determining relaxivity it remains the least well understood, particularly as it relates to the structure of the complex. One of the reasons for the poor understanding of electron-spin relaxation is that it is closely related to the ligand-field parameters of the Gd3+ ion that forms the basis of MRI contrast agents and these complexes generally exhibit a structural isomerism that inherently complicates the study of electron spin relaxation. We have recently shown that two DOTA-type ligands could be synthesised that, when coordinated to Gd3+, would adopt well defined coordination geometries and are not subject to the problems of intramolecular motion of other complexes. The EPR properties of these two chelates were studied and the results examined with theory to probe their electron-spin relaxation properties. PMID:18283704

The Origin of Hierarchical Structure Formation in Highly Grafted Symmetric Supramolecular Double-Comb Diblock Copolymers.

PubMed

Hofman, Anton H; Reza, Mehedi; Ruokolainen, Janne; Ten Brinke, Gerrit; Loos, Katja

2017-09-01

Involving supramolecular chemistry in self-assembling block copolymer systems enables design of complex macromolecular architectures that, in turn, could lead to complex phase behavior. It is an elegant route, as complicated and sensitive synthesis techniques can be avoided. Highly grafted double-comb diblock copolymers based on symmetric double hydrogen bond accepting poly(4-vinylpyridine)-block-poly(N-acryloylpiperidine) diblock copolymers and donating 3-nonadecylphenol amphiphiles are realized and studied systematically by changing the molecular weight of the copolymer. Double perpendicular lamellae-in-lamellae are formed in all complexes, independent of the copolymer molecular weight. Temperature-resolved measurements demonstrate that the supramolecular nature and ability to crystallize are responsible for the formation of such multiblock-like structures. Because of these driving forces and severe plasticization of the complexes in the liquid crystalline state, this supramolecular approach can be useful for steering self-assembly of both low- and high-molecular-weight block copolymer systems. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Defect states of complexes involving a vacancy on the boron site in boronitrene

NASA Astrophysics Data System (ADS)

Ngwenya, T. B.; Ukpong, A. M.; Chetty, N.

2011-12-01

First principles calculations have been performed to investigate the ground state properties of freestanding monolayer hexagonal boronitrene (h-BN). We have considered monolayers that contain native point defects and their complexes, which form when the point defects bind with the boron vacancy on the nearest-neighbor position. The changes in the electronic structure are analyzed to show the extent of localization of the defect-induced midgap states. The variations in formation energies suggest that defective h-BN monolayers that contain carbon substitutional impurities are the most stable structures, irrespective of the changes in growth conditions. The high energies of formation of the boron vacancy complexes suggest that they are less stable, and their creation by ion bombardment would require high-energy ions compared to point defects. Using the relative positions of the derived midgap levels for the double vacancy complex, it is shown that the quasi-donor-acceptor pair interpretation of optical transitions is consistent with stimulated transitions between electron and hole states in boronitrene.

Unravelling the nanostructure of strawberry fruit pectins by endo-polygalacturonase digestion and atomic force microscopy.

PubMed

Paniagua, Candelas; Kirby, Andrew R; Gunning, A Patrick; Morris, Victor J; Matas, Antonio J; Quesada, Miguel A; Mercado, José A

2017-06-01

Pectins analysed by AFM are visualized as individual chains, branched or unbranched, and aggregates. To investigate the nature of these structures, sodium carbonate soluble pectins from strawberry fruits were digested with endo-polygalacturonase M2 from Aspergillus aculeatus and visualized by AFM. A gradual decrease in the length of chains was observed as result of the treatment, reaching a minimum L N value of 22nm. The branches were not visible after 2h of enzymatic incubation. The size of complexes also diminished significantly with the enzymatic digestion. A treatment to hydrolyse rhamnogalacturonan II borate diester bonds neither affected chains length or branching nor complex size but reduced the density of aggregates. These results suggest that chains are formed by a mixture of homogalacturonan and more complex molecules composed by a homogalacturonan unit linked to an endo-PG resistant unit. Homogalacturonan is a structural component of the complexes and rhamnogalacturonan II could be involved in their formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Virtual Levels and Role Models: N-Level Structural Equations Model of Reciprocal Ratings Data.

PubMed

Mehta, Paras D

2018-01-01

A general latent variable modeling framework called n-Level Structural Equations Modeling (NL-SEM) for dependent data-structures is introduced. NL-SEM is applicable to a wide range of complex multilevel data-structures (e.g., cross-classified, switching membership, etc.). Reciprocal dyadic ratings obtained in round-robin design involve complex set of dependencies that cannot be modeled within Multilevel Modeling (MLM) or Structural Equations Modeling (SEM) frameworks. The Social Relations Model (SRM) for round robin data is used as an example to illustrate key aspects of the NL-SEM framework. NL-SEM introduces novel constructs such as 'virtual levels' that allows a natural specification of latent variable SRMs. An empirical application of an explanatory SRM for personality using xxM, a software package implementing NL-SEM is presented. Results show that person perceptions are an integral aspect of personality. Methodological implications of NL-SEM for the analyses of an emerging class of contextual- and relational-SEMs are discussed.

Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase.

PubMed

Coelho, Catarina; Foti, Alessandro; Hartmann, Tobias; Santos-Silva, Teresa; Leimkühler, Silke; Romão, Maria João

2015-10-01

Aldehyde oxidase (AOX) is a xanthine oxidase (XO)-related enzyme with emerging importance due to its role in the metabolism of drugs and xenobiotics. We report the first crystal structures of human AOX1, substrate free (2.6-Å resolution) and in complex with the substrate phthalazine and the inhibitor thioridazine (2.7-Å resolution). Analysis of the protein active site combined with steady-state kinetic studies highlight the unique features, including binding and substrate orientation at the active site, that characterize human AOX1 as an important drug-metabolizing enzyme. Structural analysis of the complex with the noncompetitive inhibitor thioridazine revealed a new, unexpected and fully occupied inhibitor-binding site that is structurally conserved among mammalian AOXs and XO. The new structural insights into the catalytic and inhibition mechanisms of human AOX that we now report will be of great value for the rational analysis of clinical drug interactions involving inhibition of AOX1 and for the prediction and design of AOX-stable putative drugs.

Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending

PubMed Central

Bebel, Aleksandra; Karaca, Ezgi; Kumar, Banushree; Stark, W Marshall; Barabas, Orsolya

2016-01-01

Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA difH, representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway. The structures reveal that activation of DNA strand cleavage and rejoining involves large conformational changes and DNA bending, suggesting how interaction with the cell division protein FtsK may license recombination at the septum. Together with biochemical and in vivo analysis, our structures also reveal how a small sequence asymmetry in difH defines protein conformation in the synaptic complex and orchestrates the order of DNA strand exchanges. Our results provide insights into the catalytic mechanism of Xer recombination and a model for regulation of recombination activity during cell division. DOI: http://dx.doi.org/10.7554/eLife.19706.001 PMID:28009253

Thermal modeling and analysis of structurally complex spacecraft using the IDEAS system

NASA Technical Reports Server (NTRS)

Garrett, L. B.

1983-01-01

Large antenna satellites of unprecedented sizes are needed for a number of applications. Antenna diameters on the order of 50 meters and upward are required. Such antennas involve the use of large expanses of lattice structures with hundreds or thousands of individual connecting members. In connection with the design of such structures, the consideration of thermal effects represents a crucial factor. Software capabilities have emerged which are coded to include major first order thermal effects and to purposely ignore, in the interest of computational efficiency, the secondary effects. The Interactive Design and Evaluation of Advanced Spacecraft (IDEAS) is one such system. It has been developed for an employment in connection with thermal-structural interaction analyses related to the design of large structurally complex classes of future spacecraft. An IDEAS overview is presented. Attention is given to a typical antenna analysis using IDEAS, the thermal and loading analyses of a tetrahedral truss spacecraft, and ecliptic and polar orbit analyses.

Structure of a Clostridium botulinum C143S thiaminase I/thiamin complex reveals active site architecture .

PubMed

Sikowitz, Megan D; Shome, Brateen; Zhang, Yang; Begley, Tadhg P; Ealick, Steven E

2013-11-05

Thiaminases are responsible for the degradation of thiamin and its metabolites. Two classes of thiaminases have been identified based on their three-dimensional structures and their requirements for a nucleophilic second substrate. Although the reactions of several thiaminases have been characterized, the physiological role of thiamin degradation is not fully understood. We have determined the three-dimensional X-ray structure of an inactive C143S mutant of Clostridium botulinum (Cb) thiaminase I with bound thiamin at 2.2 Å resolution. The C143S/thiamin complex provides atomic level details of the orientation of thiamin upon binding to Cb-thiaminase I and the identity of active site residues involved in substrate binding and catalysis. The specific roles of active site residues were probed by using site directed mutagenesis and kinetic analyses, leading to a detailed mechanism for Cb-thiaminase I. The structure of Cb-thiaminase I is also compared to the functionally similar but structurally distinct thiaminase II.

Dissection of the complex genetic basis of craniofacial anomalies using haploid genetics and interspecies hybrids in Nasonia wasps

PubMed Central

Werren, John H.; Cohen, Lorna B.; Gadau, Juergen; Ponce, Rita; Baudry, Emmanuelle; Lynch, Jeremy A.

2016-01-01

The animal head is a complex structure where numerous sensory, structural and alimentary structures are concentrated and integrated, and its ontogeny requires precise and delicate interactions among genes, cells, and tissues. Thus, it is perhaps unsurprising that craniofacial abnormalities are among the most common birth defects in people, or that these defects have a complex genetic basis involving interactions among multiple loci. Developmental processes that depend on such epistatic interactions become exponentially more difficult to study in diploid organisms as the number of genes involved increases. Here, we present hybrid haploid males of the wasp species pair Nasonia vitripennis and Nasonia giraulti, which have distinct male head morphologies, as a genetic model of craniofacial development that possesses the genetic advantages of haploidy, along with many powerful genomic tools. Viable, fertile hybrids can be made between the species, and quantitative trail loci related to shape differences have been identified. In addition, a subset of hybrid males show head abnormalities, including clefting at the midline and asymmetries. Crucially, epistatic interactions among multiple loci underlie several developmental differences and defects observed in the F2 hybrid males. Furthermore, we demonstrate an introgression of a chromosomal region from N. giraulti into N. vitripennis that shows an abnormality in relative eye size, which maps to a region containing a major QTL for this trait. Therefore, the genetic sources of head morphology can, in principle, be identified by positional cloning. Thus, Nasonia is well positioned to be a uniquely powerful model invertebrate system with which to probe both development and complex genetics of craniofacial patterning and defects. PMID:26721604

Coordination Polymer of M(II)-Pyrazinamide (M = Co, Cd) with Double End-to-End Thiocyanate Bridge

NASA Astrophysics Data System (ADS)

Ponco Prananto, Yuniar

2018-01-01

Pyrazinamide (pza, C4N2H3-CONH2) is a good ligand for coordination polymer. Their transition metal complexes are known to have antibacterial activities, magnetic properties, etc. Coordination polymers of M(II)-pyrazinamide with thiocyanate (M = Co (a), Cd (b)), prepared using bench-top layering technique with M(II):pza:SCN ratio of 1:2:2, is successfully crystallised at room temperature. Single crystal XRD was used to determine the crystal structure. Infrared and melting point determination were also performed. Crystal structure of both complexes, solved in Triclinic P-1, show that each octahedral metal centre is connected to two adjacent metal centres by double end-to-end thiocyanate bridge forming a 1D polymeric structure with M···M distances of 5.524 Å (in a) and 5.887 Å (in b). Two monodentate pyrazinamide ligands occupy the rest of the coordination sites on the metal centre in a trans relationship. Only in complex a, one lattice pyrazinamide molecule is involved in the asymmetric unit. Crystal packing of both a and b are also displaying non-covalent networks as a result of hydrogen-bonding involving the pyrazine ring, amide and carbonyl groups between adjacent chains and π···π interactions (only occurred in a). In addition, the observed melting points of both a and b are relatively close to each other (around 180°C), and ATR-IR spectra support the presence of the bridging thiocyanate and terminal pyrazinamide.

The Peptidoglycan-Binding Protein SjcF1 Influences Septal Junction Function and Channel Formation in the Filamentous Cyanobacterium Anabaena.

PubMed

Rudolf, Mareike; Tetik, Nalan; Ramos-León, Félix; Flinner, Nadine; Ngo, Giang; Stevanovic, Mara; Burnat, Mireia; Pernil, Rafael; Flores, Enrique; Schleiff, Enrico

2015-06-30

Filamentous, heterocyst-forming cyanobacteria exchange nutrients and regulators between cells for diazotrophic growth. Two alternative modes of exchange have been discussed involving transport either through the periplasm or through septal junctions linking adjacent cells. Septal junctions and channels in the septal peptidoglycan are likely filled with septal junction complexes. While possible proteinaceous factors involved in septal junction formation, SepJ (FraG), FraC, and FraD, have been identified, little is known about peptidoglycan channel formation and septal junction complex anchoring to the peptidoglycan. We describe a factor, SjcF1, involved in regulation of septal junction channel formation in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. SjcF1 interacts with the peptidoglycan layer through two peptidoglycan-binding domains and is localized throughout the cell periphery but at higher levels in the intercellular septa. A strain with an insertion in sjcF1 was not affected in peptidoglycan synthesis but showed an altered morphology of the septal peptidoglycan channels, which were significantly wider in the mutant than in the wild type. The mutant was impaired in intercellular exchange of a fluorescent probe to a similar extent as a sepJ deletion mutant. SjcF1 additionally bears an SH3 domain for protein-protein interactions. SH3 binding domains were identified in SepJ and FraC, and evidence for interaction of SjcF1 with both SepJ and FraC was obtained. SjcF1 represents a novel protein involved in structuring the peptidoglycan layer, which links peptidoglycan channel formation to septal junction complex function in multicellular cyanobacteria. Nonetheless, based on its subcellular distribution, this might not be the only function of SjcF1. Cell-cell communication is central not only for eukaryotic but also for multicellular prokaryotic systems. Principles of intercellular communication are well established for eukaryotes, but the mechanisms and components involved in bacteria are just emerging. Filamentous heterocyst-forming cyanobacteria behave as multicellular organisms and represent an excellent model to study prokaryotic cell-cell communication. A path for intercellular metabolite exchange appears to involve transfer through molecular structures termed septal junctions. They are reminiscent of metazoan gap junctions that directly link adjacent cells. In cyanobacteria, such structures need to traverse the peptidoglycan layers in the intercellular septa of the filament. Here we describe a factor involved in the formation of channels across the septal peptidoglycan layers, thus contributing to the multicellular behavior of these organisms. Copyright © 2015 Rudolf et al.

Combining density functional theory (DFT) and pair distribution function (PDF) analysis to solve the structure of metastable materials: the case of metakaolin.

PubMed

White, Claire E; Provis, John L; Proffen, Thomas; Riley, Daniel P; van Deventer, Jannie S J

2010-04-07

Understanding the atomic structure of complex metastable (including glassy) materials is of great importance in research and industry, however, such materials resist solution by most standard techniques. Here, a novel technique combining thermodynamics and local structure is presented to solve the structure of the metastable aluminosilicate material metakaolin (calcined kaolinite) without the use of chemical constraints. The structure is elucidated by iterating between least-squares real-space refinement using neutron pair distribution function data, and geometry optimisation using density functional modelling. The resulting structural representation is both energetically feasible and in excellent agreement with experimental data. This accurate structural representation of metakaolin provides new insight into the local environment of the aluminium atoms, with evidence of the existence of tri-coordinated aluminium. By the availability of this detailed chemically feasible atomic description, without the need to artificially impose constraints during the refinement process, there exists the opportunity to tailor chemical and mechanical processes involving metakaolin and other complex metastable materials at the atomic level to obtain optimal performance at the macro-scale.

Structural analysis of the human fibroblast growth factor receptor 4 kinase.

PubMed

Lesca, E; Lammens, A; Huber, R; Augustin, M

2014-11-11

The family of fibroblast growth factor receptors (FGFRs) plays an important and well-characterized role in a variety of pathological disorders. FGFR4 is involved in myogenesis and muscle regeneration. Mutations affecting the kinase domain of FGFR4 may cause cancer, for example, breast cancer or rhabdomyosarcoma. Whereas FGFR1-FGFR3 have been structurally characterized, the structure of the FGFR4 kinase domain has not yet been reported. In this study, we present four structures of the kinase domain of FGFR4, in its apo-form and in complex with different types of small-molecule inhibitors. The two apo-FGFR4 kinase domain structures show an activation segment similar in conformation to an autoinhibitory segment observed in the hepatocyte growth factor receptor kinase but different from the known structures of other FGFR kinases. The structures of FGFR4 in complex with the type I inhibitor Dovitinib and the type II inhibitor Ponatinib reveal the molecular interactions with different types of kinase inhibitors and may assist in the design and development of FGFR4 inhibitors. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structural and spectroscopic characterization of DMF complexes with nitrogen, carbon dioxide, ammonia and water. Infrared matrix isolation and theoretical studies

NASA Astrophysics Data System (ADS)

Sałdyka, Magdalena; Mielke, Zofia; Haupa, Karolina

2018-02-01

An infrared spectroscopic and MP2/6-311++G(2d,2p) study of the complexes between N,N-dimethylformamide (DMF) and nitrogen, carbon dioxide, water, ammonia trapped in solid argon matrices is reported. The 1:1 molecular complexes have been identified in the DMF/B/Ar matrices (B = N2, CO, H2O, NH3); their structures were determined by comparison of the spectra with the results of calculations. The analysis of the experimental and theoretical data indicate that the DMF-N2, CO complexes present in the matrices are stabilized by (C=)O⋯N and (C=)O⋯C van der Waals interactions. In turn, in the DMF-H2O, NH3 complexes the (C=)O⋯H(OH) and (C=)O⋯H(NH2) hydrogen bonding is present in which the carbonyl group of DMF acts as a proton acceptor. In all systems studied the C-H⋯X (X = N, C, O) bonding is a second intermolecular force stabilizing the planar complexes. Some spectral features indicate that for DMF-H2O, DMF-NH3 systems the nonplanar structures with the C=O⋯H interaction are also present. The study demonstrated the strong sensitivity of the CH stretching wavenumber to an involvement of the C-H and/or C=O groups of DMF in an intermolecular interaction.

Studying Nuclear Receptor Complexes in the Cellular Environment.

PubMed

Schaufele, Fred

2016-01-01

The ligand-regulated structure and biochemistry of nuclear receptor complexes are commonly determined by in vitro studies of isolated receptors, cofactors, and their fragments. However, in the living cell, the complexes that form are governed not just by the relative affinities of isolated cofactors for the receptor but also by the cell-specific sequestration or concentration of subsets of competing or cooperating cofactors, receptors, and other effectors into distinct subcellular domains and/or their temporary diversion into other cellular activities. Most methods developed to understand nuclear receptor function in the cellular environment involve the direct tagging of the nuclear receptor or its cofactors with fluorescent proteins (FPs) and the tracking of those FP-tagged factors by fluorescence microscopy. One of those approaches, Förster resonance energy transfer (FRET) microscopy, quantifies the transfer of energy from a higher energy "donor" FP to a lower energy "acceptor" FP attached to a single protein or to interacting proteins. The amount of FRET is influenced by the ligand-induced changes in the proximities and orientations of the FPs within the tagged nuclear receptor complexes, which is an indicator of the structure of the complexes, and by the kinetics of the interaction between FP-tagged factors. Here, we provide a guide for parsing information about the structure and biochemistry of nuclear receptor complexes from FRET measurements in living cells.

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

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR)more » domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90){sub 2}–Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes.« less

Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues

DOE PAGES

Nikolaienko, Roman M.; Hammel, Michal; Dubreuil, Véronique; ...

2016-08-18

Protein-tyrosine phosphatase receptor type G (RPTPγ/PTPRG) interacts in vitro with contactin-3-6 (CNTN3-6), a group of glycophosphatidylinositol-anchored cell adhesion molecules involved in the wiring of the nervous system. In addition to PTPRG, CNTNs associate with multiple transmembrane proteins and signal inside the cell via cis-binding partners to alleviate the absence of an intracellular region. Here, we use comprehensive biochemical and structural analyses to demonstrate that PTPRG·CNTN3-6 complexes share similar binding affinities and a conserved arrangement. Furthermore, as a first step to identifying PTPRG·CNTN complexes in vivo, we found that PTPRG and CNTN3 associate in the outer segments of mouse rod photoreceptormore » cells. In particular, PTPRG and CNTN3 form cis-complexes at the surface of photoreceptors yet interact in trans when expressed on the surfaces of apposing cells. Further structural analyses suggest that all CNTN ectodomains adopt a bent conformation and might lie parallel to the cell surface to accommodate these cis and trans binding modes. Taken together, these studies identify a PTPRG·CNTN complex in vivo and provide novel insights into PTPRG- and CNTN-mediated signaling.« less

Structural determinants for membrane association and dynamic organization of the hepatitis C virus NS3-4A complex

PubMed Central

Brass, Volker; Berke, Jan Martin; Montserret, Roland; Blum, Hubert E.; Penin, François; Moradpour, Darius

2008-01-01

Hepatitis C virus (HCV) NS3-4A is a membrane-associated multifunctional protein harboring serine protease and RNA helicase activities. It is an essential component of the HCV replication complex and a prime target for antiviral intervention. Here, we show that membrane association and structural organization of HCV NS3-4A are ensured in a cooperative manner by two membrane-binding determinants. We demonstrate that the N-terminal 21 amino acids of NS4A form a transmembrane α-helix that may be involved in intramembrane protein–protein interactions important for the assembly of a functional replication complex. In addition, we demonstrate that amphipathic helix α0, formed by NS3 residues 12–23, serves as a second essential determinant for membrane association of NS3-4A, allowing proper positioning of the serine protease active site on the membrane. These results allowed us to propose a dynamic model for the membrane association, processing, and structural organization of NS3-4A on the membrane. This model has implications for the functional architecture of the HCV replication complex, proteolytic targeting of host factors, and drug design. PMID:18799730

Fracture Testing of Integral Stiffened Structure

NASA Technical Reports Server (NTRS)

Newman, John A.; Smith, Stephen W.; Piascik, Robert S.; Dawicke, David S.; Johnston, William M.; Willard, Scott A.

2008-01-01

Laboratory testing was conducted to evaluate safety concerns for integrally-stiffened tanks that were found to have developed cracks during pressurization testing. Cracks occurred at fastener holes where additional stiffeners were attached to the integrally-stiffened tank structure. Tests were conducted to obtain material properties and to reproduce the crack morphologies that were observed in service to help determine if the tanks are safe for operation. Reproducing the cracking modes observed during pressurization testing required a complex loading state involving both a tensile load in the integrally-stiffened structure and a pin-load at a fastener hole.

Reproduction numbers for epidemic models with households and other social structures. I. Definition and calculation of R0

PubMed Central

Pellis, Lorenzo; Ball, Frank; Trapman, Pieter

2012-01-01

The basic reproduction number R0 is one of the most important quantities in epidemiology. However, for epidemic models with explicit social structure involving small mixing units such as households, its definition is not straightforward and a wealth of other threshold parameters has appeared in the literature. In this paper, we use branching processes to define R0, we apply this definition to models with households or other more complex social structures and we provide methods for calculating it. PMID:22085761

Mononuclear zinc(II) complexes of 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols: Synthesis, structural characterization, DNA binding and cheminuclease activities

NASA Astrophysics Data System (ADS)

Ravichandran, J.; Gurumoorthy, P.; Karthick, C.; Kalilur Rahiman, A.

2014-03-01

Four new zinc(II) complexes [Zn(HL1-4)Cl2] (1-4), where HL1-4 = 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols, have been isolated and fully characterized using various spectro-analytical techniques. The X-ray crystal structure of complex 4 shows the distorted trigonal-bipyramidal coordination geometry around zinc(II) ion. The crystal packing is stabilized by intermolecular NH⋯O hydrogen bonding interaction. The complexes display no d-d electronic band in the visible region due to d10 electronic configuration of zinc(II) ion. The electrochemical properties of the synthesized ligands and their complexes exhibit similar voltammogram at reduction potential due to electrochemically innocent Zn(II) ion, which evidenced that the electron transfer is due to the nature of the ligand. Binding interaction of complexes with calf thymus DNA was studied by UV-Vis absorption titration, viscometric titration and cyclic voltammetry. All complexes bind with CT DNA by intercalation, giving the binding affinity in the order of 2 > 1 ≫ 3 > 4. The prominent cheminuclease activity of complexes on plasmid DNA (pBR322 DNA) was observed in the absence and presence of H2O2. Oxidative pathway reveals that the underlying mechanism involves hydroxyl radical.

Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking.

PubMed Central

Harris, M E; Kazantsev, A V; Chen, J L; Pace, N R

1997-01-01

Bacterial ribonuclease P (RNase P), an endonuclease involved in tRNA maturation, is a ribonucleoprotein containing a catalytic RNA. The secondary structure of this ribozyme is well-established, and a low-resolution model of the three-dimensional structure of the ribozyme-substrate complex has been proposed based on site-specific crosslinking and phylogenetic comparative data [Harris ME et al., 1994 EMBO J 13:3953-3963]. However, several substructures of that model were poorly constrained by the available data. In the present analysis, additional constraints between elements within the Escherichia coli RNase P RNA-pre-tRNA complex were determined by intra- and intermolecular crosslinking experiments. Circularly permuted RNase P RNAs were used to position an azidophenacyl photoactive crosslinking agent specifically at strategic sites within the ribozyme-substrate complex. Crosslink sites were mapped by primer extension and confirmed by analysis of the mobility of the crosslinked RNA lariats on denaturing acrylamide gels relative to circular and linear RNA standards. Crosslinked species generally retained significant catalytic activity, indicating that the results reflect the native ribozyme structure. The crosslinking results support the general configuration of the structure model and predicate new positions and orientations for helices that were previously poorly constrained by the data set. The expanded library of crosslinking constraints was used, together with secondary and tertiary structure identified by phylogenetic sequence comparisons, to refine significantly the model of RNase P RNA with bound substrate pre-tRNA. The crosslinking results and data from chemical-modification and mutational studies are discussed in the context of the current structural perspective on this ribozyme. PMID:9174092

Exotic differentiable structures and general relativity

NASA Astrophysics Data System (ADS)

Brans, Carl H.; Randall, Duane

1993-02-01

We review recent developments in differential topology with special concern for their possible significance to physical theories, especially general relativity. In particular we are concerned here with the discovery of the existence of non-standard (“fake” or “exotic”) differentiable structures on topologically simple manifolds such asS 7, ℝ4 andS 3 X ℝ1. Because of the technical difficulties involved in the smooth case, we begin with an easily understood toy example looking at the role which the choice of complex structures plays in the formulation of two-dimensional vacuum electrostatics. We then briefly review the mathematical formalisms involved with differentiable structures on topological manifolds, diffeomorphisms and their significance for physics. We summarize the important work of Milnor, Freedman, Donaldson, and others in developing exotic differentiable structures on well known topological manifolds. Finally, we discuss some of the geometric implications of these results and propose some conjectures on possible physical implications of these new manifolds which have never before been considered as physical models.

Parasites Affect Food Web Structure Primarily through Increased Diversity and Complexity

PubMed Central

Dunne, Jennifer A.; Lafferty, Kevin D.; Dobson, Andrew P.; Hechinger, Ryan F.; Kuris, Armand M.; Martinez, Neo D.; McLaughlin, John P.; Mouritsen, Kim N.; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B.; Thieltges, David W.; Williams, Richard J.; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites “dominate” food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models. PMID:23776404

Parasites affect food web structure primarily through increased diversity and complexity

USGS Publications Warehouse

Dunne, Jennifer A.; Lafferty, Kevin D.; Dobson, Andrew P.; Hechinger, Ryan F.; Kuris, Armand M.; Martinez, Neo D.; McLaughlin, John P.; Mouritsen, Kim N.; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B.; Thieltges, David W.; Williams, Richard J.; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites ‘‘dominate’’ food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites’ roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites’ feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models.

Parasites affect food web structure primarily through increased diversity and complexity.

PubMed

Dunne, Jennifer A; Lafferty, Kevin D; Dobson, Andrew P; Hechinger, Ryan F; Kuris, Armand M; Martinez, Neo D; McLaughlin, John P; Mouritsen, Kim N; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B; Thieltges, David W; Williams, Richard J; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites "dominate" food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models.

Mantle dynamics and seismic tomography

PubMed Central

Tanimoto, Toshiro; Lay, Thorne

2000-01-01

Three-dimensional imaging of the Earth's interior, called seismic tomography, has achieved breakthrough advances in the last two decades, revealing fundamental geodynamical processes throughout the Earth's mantle and core. Convective circulation of the entire mantle is taking place, with subducted oceanic lithosphere sinking into the lower mantle, overcoming the resistance to penetration provided by the phase boundary near 650-km depth that separates the upper and lower mantle. The boundary layer at the base of the mantle has been revealed to have complex structure, involving local stratification, extensive structural anisotropy, and massive regions of partial melt. The Earth's high Rayleigh number convective regime now is recognized to be much more interesting and complex than suggested by textbook cartoons, and continued advances in seismic tomography, geodynamical modeling, and high-pressure–high-temperature mineral physics will be needed to fully quantify the complex dynamics of our planet's interior. PMID:11035784

Crystal and molecular structure of eight organic acid-base adducts from 2-methylquinoline and different acids

NASA Astrophysics Data System (ADS)

Zhang, Jing; Jin, Shouwen; Tao, Lin; Liu, Bin; Wang, Daqi

2014-08-01

Eight supramolecular complexes with 2-methylquinoline and acidic components as 4-aminobenzoic acid, 2-aminobenzoic acid, salicylic acid, 5-chlorosalicylic acid, 3,5-dinitrosalicylic acid, malic acid, sebacic acid, and 1,5-naphthalenedisulfonic acid were synthesized and characterized by X-ray crystallography, IR, mp, and elemental analysis. All of the complexes are organic salts except compound 2. All supramolecular architectures of 1-8 involve extensive classical hydrogen bonds as well as other noncovalent interactions. The results presented herein indicate that the strength and directionality of the classical hydrogen bonds (ionic or neutral) between acidic components and 2-methylquinoline are sufficient to bring about the formation of binary organic acid-base adducts. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, the complexes 1-8 displayed 2D-3D framework structure.

Speeding Up Sigmatropic Shifts-To Halve or to Hold.

PubMed

Tantillo, Dean J

2016-04-19

Catalysis is common. Rational catalyst design, however, is at the frontier of chemical science. Although the histories of physical organic and synthetic organic chemistry boast key chapters involving [3s,3s] sigmatropic shifts, catalysis of these reactions is much less common than catalysis of ostensibly more complex processes. The comparative dearth of catalysts for sigmatropic shifts is perhaps a result of the perception that transition state structures for these reactions, like their reactants, are nonpolar and therefore not amenable to selective stabilization and its associated barrier lowering. However, as demonstrated in this Account, transition state structures for [3s,3s] sigmatropic shifts can in fact have charge distributions that differ significantly from those of reactants, even for hydrocarbon substrates, allowing for barriers to be decreased and rates increased. In some cases, differences in charge distribution result from the inclusion of heteroatoms at specific positions in reactants, but in other cases differences are actually induced by catalysts. Perhaps surprisingly, strategies for complexation of transition state structures that remain nonpolar are also possible. In general, the strategies for catalysis employed can be characterized as involving either mechanistic intervention, where a catalyst induces a change from the concerted mechanism expected for a [3s,3s] sigmatropic shift to a multistep process (cutting the transformation into halves or smaller pieces) whose overall barrier is decreased relative to the concerted process, or transition state complexation, where a catalyst simply binds (holds) more tightly to the transition state structure for a [3s,3s] sigmatropic shift than to the reactant, leading to a lower barrier in the presence of the catalyst. Both of these strategies can be considered to be biomimetic in that enzymes frequently induce multistep processes and utilize selective transition state stabilization for the steps involved. In addition, transition state complexation was the principle around which catalytic antibodies were originally designed. The field of catalysis of sigmatropic shifts is now ready for rational design. The studies described here all provide evidence for the origins of rate acceleration, derived in large part from the results of quantum chemical calculations, that can now be applied to the design of new catalysts for [3s,3s] and other sigmatropic shifts.

Structure and reactivity of oxalate surface complexes on lepidocrocite derived from infrared spectroscopy, DFT-calculations, adsorption, dissolution and photochemical experiments

NASA Astrophysics Data System (ADS)

Borowski, Susan C.; Biswakarma, Jagannath; Kang, Kyounglim; Schenkeveld, Walter D. C.; Hering, Janet G.; Kubicki, James D.; Kraemer, Stephan M.; Hug, Stephan J.

2018-04-01

Oxalate, together with other ligands, plays an important role in the dissolution of iron(hdyr)oxides and the bio-availability of iron. The formation and properties of oxalate surface complexes on lepidocrocite were studied with a combination of infrared spectroscopy (IR), density functional theory (DFT) calculations, dissolution, and photochemical experiments. IR spectra measured as a function of time, concentration, and pH (50-200 μM oxalate, pH 3-7) showed that several surface complexes are formed at different rates and in different proportions. Measured spectra could be separated into three contributions described by Gaussian line shapes, with frequencies that agreed well with the theoretical frequencies of three different surface complexes: an outer-sphere complex (OS), an inner-sphere monodentate mononuclear complex (MM), and a bidentate mononuclear complex (BM) involving one O atom from each carboxylate group. At pH 6, OS was formed at the highest rate. The contribution of BM increased with decreasing pH. In dissolution experiments, lepidocrocite was dissolved at rates proportional to the surface concentration of BM, rather than to the total adsorbed concentration. Under UV-light (365 nm), BM was photolyzed at a higher rate than MM and OS. Although the comparison of measured spectra with calculated frequencies cannot exclude additional possible structures, the combined results allowed the assignment of three main structures with different reactivities consistent with experiments. The results illustrate the importance of the surface speciation of adsorbed ligands in dissolution and photochemical reactions.

Differential Dynamic Engagement within 24 SH3 Domain: Peptide Complexes Revealed by Co-Linear Chemical Shift Perturbation Analysis

PubMed Central

Stollar, Elliott J.; Lin, Hong; Davidson, Alan R.; Forman-Kay, Julie D.

2012-01-01

There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP) behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences. PMID:23251481

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery.

PubMed

Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y; Ahlgren, Eva-Christina; Al-Karadaghi, Salam; Thompson, James R; Isaya, Grazia

2016-09-30

Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN 42-210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN 42-210 ] 24 ·[NFS1] 24 ·[ISD11] 24 ·[ISCU] 24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN 42-210 ] 24 ·[ISCU] 24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN 42-210 trimer at each of its eight vertices. Binding of 12 [NFS1] 2 ·[ISD11] 2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN 42-210 to ISCU. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery*

PubMed Central

Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y.; Ahlgren, Eva-Christina; Al-Karadaghi, Salam; Thompson, James R.; Isaya, Grazia

2016-01-01

Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN42–210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN42–210]24·[NFS1]24·[ISD11]24·[ISCU]24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN42–210]24·[ISCU]24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN42–210 trimer at each of its eight vertices. Binding of 12 [NFS1]2·[ISD11]2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN42–210 to ISCU. PMID:27519411

Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps

PubMed Central

Rakesh, Ramachandran; Joseph, Agnel Praveen; Bhaskara, Ramachandra M.; Srinivasan, Narayanaswamy

2016-01-01

ABSTRACT Pre-mRNA splicing in eukaryotes is performed by the spliceosome, a highly complex macromolecular machine. SF3b is a multi-protein complex which recognizes the branch point adenosine of pre-mRNA as part of a larger U2 snRNP or U11/U12 di-snRNP in the dynamic spliceosome machinery. Although a cryo-EM map is available for human SF3b complex, the structure and relative spatial arrangement of all components in the complex are not yet known. We have recognized folds of domains in various proteins in the assembly and generated comparative models. Using an integrative approach involving structural and other experimental data, guided by the available cryo-EM density map, we deciphered a pseudo-atomic model of the closed form of SF3b which is found to be a “fuzzy complex” with highly flexible components and multiplicity of folds. Further, the model provides structural information for 5 proteins (SF3b10, SF3b155, SF3b145, SF3b130 and SF3b14b) and localization information for 4 proteins (SF3b10, SF3b145, SF3b130 and SF3b14b) in the assembly for the first time. Integration of this model with the available U11/U12 di-snRNP cryo-EM map enabled elucidation of an open form. This now provides new insights on the mechanistic features involved in the transition between closed and open forms pivoted by a hinge region in the SF3b155 protein that also harbors cancer causing mutations. Moreover, the open form guided model of the 5′ end of U12 snRNA, which includes the branch point duplex, shows that the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation with potential implications for branch point adenosine recognition fidelity. PMID:27618338

The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.

PubMed

Lee, Donghan; Walsh, Joseph D; Yu, Ping; Markus, Michelle A; Choli-Papadopoulou, Theodora; Schwieters, Charles D; Krueger, Susan; Draper, David E; Wang, Yun-Xing

2007-04-06

The L11 binding site is one of the most important functional sites in the ribosome. The N-terminal domain of L11 has been implicated as a "reversible switch" in facilitating the coordinated movements associated with EF-G-driven GTP hydrolysis. The reversible switch mechanism has been hypothesized to require conformational flexibility involving re-orientation and re-positioning of the two L11 domains, and warrants a close examination of the structure and dynamics of L11. Here we report the solution structure of free L11, and relaxation studies of free L11, L11 complexed to its 58 nt RNA recognition site, and L11 in a ternary complex with the RNA and thiostrepton antibiotic. The binding site of thiostrepton on L11 was also defined by analysis of structural and dynamics data and chemical shift mapping. The conclusions of this work are as follows: first, the binding of L11 to RNA leads to sizable conformation changes in the regions flanking the linker and in the hinge area that links a beta-sheet and a 3(10)-helix-turn-helix element in the N terminus. Concurrently, the change in the relative orientation may lead to re-positioning of the N terminus, as implied by a decrease of radius of gyration from 18.5 A to 16.2 A. Second, the regions, which undergo large conformation changes, exhibit motions on milliseconds-microseconds or nanoseconds-picoseconds time scales. Third, binding of thiostrepton results in more rigid conformations near the linker (Thr71) and near its putative binding site (Leu12). Lastly, conformational changes in the putative thiostrepton binding site are implicated by the re-emergence of cross-correlation peaks in the spectrum of the ternary complex, which were missing in that of the binary complex. Our combined analysis of both the chemical shift perturbation and dynamics data clearly indicates that thiostrepton binds to a pocket involving residues in the 3(10)-helix in L11.

The Structure of Free L11 and Functional Dynamics of L11 in Free, L11-rRNA(58nt) Binary and L11-rRNA(58nt)-thiostrepton Ternary Complexes

PubMed Central

Lee, Donghan; Walsh, Joseph D.; Yu, Ping; Markus, Michelle A.; Choli-Papadopoulou, Theodora; Schwieters, Charles D.; Krueger, Susan; Draper, David E.; Wang, Yun-Xing

2007-01-01

Summary The L11 binding site is one of the most important functional sites in the ribosome. The N-terminal domain of L11 has been implicated as a “reversible switch” in facilitating the coordinated movements associated with EF-G–driven GTP hydrolysis. The “reversible switch” mechanism has been hypothesized to require conformational flexibility involving re-orientation and re-positioning of the two L11 domains, and warrants a close examination of the structure and dynamics of L11. Here we report the solution structure of free L11, and relaxation studies of free L11, L11complexed to its 58 nt RNA recognition site, and L11 in a ternary complex with the RNA and thiostrepton antibiotic. The binding site of thiostrepton on L11 was also defined by analysis of structural and dynamics data and chemical shift mapping. The conclusions of this work are as follows: First, the binding of L11 to RNA leads to sizable conformation changes in the regions flanking the linker and in the hinge area that links a β-sheets and a 310-helix-turn-helix element in the N-terminus. Concurrently, the change in the relative orientation may lead to re-positioning of the N-terminus, as implied by a decrease of radius of gyration from 18.5 Å to 16.2 Å. Second, the regions, which undergo large conformation changes, exhibit motions on ms-μs or ns-ps time scales. Third, binding of thiostrepton results in more rigid conformations near the linker (Thr71) and near its putative binding site (Leu12). Lastly, conformational changes in the putative thiostrepton binding site are implicated by the re-emergence of cross-correlation peaks in the spectrum of the ternary complex, which were missing in that of the binary complex. Our combined analysis of both the chemical shift perturbation and dynamics data clearly indicates that thiostrepton binds to a pocket involving residues in the 310-helix in L11. PMID:17292917

Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria.

PubMed

Lery, Letícia M S; Bitar, Mainá; Costa, Mauricio G S; Rössle, Shaila C S; Bisch, Paulo M

2010-12-22

G. diazotrophicus and A. vinelandii are aerobic nitrogen-fixing bacteria. Although oxygen is essential for the survival of these organisms, it irreversibly inhibits nitrogenase, the complex responsible for nitrogen fixation. Both microorganisms deal with this paradox through compensatory mechanisms. In A. vinelandii a conformational protection mechanism occurs through the interaction between the nitrogenase complex and the FeSII protein. Previous studies suggested the existence of a similar system in G. diazotrophicus, but the putative protein involved was not yet described. This study intends to identify the protein coding gene in the recently sequenced genome of G. diazotrophicus and also provide detailed structural information of nitrogenase conformational protection in both organisms. Genomic analysis of G. diazotrophicus sequences revealed a protein coding ORF (Gdia0615) enclosing a conserved "fer2" domain, typical of the ferredoxin family and found in A. vinelandii FeSII. Comparative models of both FeSII and Gdia0615 disclosed a conserved beta-grasp fold. Cysteine residues that coordinate the 2[Fe-S] cluster are in conserved positions towards the metallocluster. Analysis of solvent accessible residues and electrostatic surfaces unveiled an hydrophobic dimerization interface. Dimers assembled by molecular docking presented a stable behaviour and a proper accommodation of regions possibly involved in binding of FeSII to nitrogenase throughout molecular dynamics simulations in aqueous solution. Molecular modeling of the nitrogenase complex of G. diazotrophicus was performed and models were compared to the crystal structure of A. vinelandii nitrogenase. Docking experiments of FeSII and Gdia0615 with its corresponding nitrogenase complex pointed out in both systems a putative binding site presenting shape and charge complementarities at the Fe-protein/MoFe-protein complex interface. The identification of the putative FeSII coding gene in G. diazotrophicus genome represents a large step towards the understanding of the conformational protection mechanism of nitrogenase against oxygen. In addition, this is the first study regarding the structural complementarities of FeSII-nitrogenase interactions in diazotrophic bacteria. The combination of bioinformatic tools for genome analysis, comparative protein modeling, docking calculations and molecular dynamics provided a powerful strategy for the elucidation of molecular mechanisms and structural features of FeSII-nitrogenase interaction.

Crystal Structure of Mistletoe Lectin I (ML-I) from Viscum album in Complex with 4-N-Furfurylcytosine at 2.85 Å Resolution.

PubMed

Ahmad, Malik Shoaib; Rasheed, Saima; Falke, Sven; Khaliq, Binish; Perbandt, Markus; Choudhary, M Iqbal; Markiewicz, Wojciech T; Barciszewski, Jan; Betzel, Christian

2018-05-23

Viscum album (the European mistletoe) is a semi-parasitic plant, which is of high medical interest. It is widely found in Europe, Asia and North America. It contains at least three distinct lectins (i.e. ML-I, II, and III), varying in molecular mass and specificity. Among them ML-I is in focus of medical research for various activities, including anti-cancer activities. To understand the molecular basis for such medical applications a few studies have already addressed the structural and functional analysis of ML-I in complex with ligands. In continuation of these efforts, we are reporting the crystal structure of ML from Viscum album in complex with the nucleic acid oxidation product 4-N-furfurylcytosine (FC) refined to 2.85 Å resolution. FC is known to be involved in different metabolic pathways related to oxidative stress and DNA modification. X-ray suitable hexagonal crystals of the ML-I/FC complex were grown within four days at 294 K using the hanging drop vapor diffusion method. Diffraction data were collected up to a resolution of 2.85 Å. The ligand affinity was verified via in-silico docking. The high-resolution structure was refined subsequently to analyze particularly the active site conformation and binding epitope of 4-N-furfurylcytosine. A distinct 2Fo-Fc electron density at the active site was interpreted as a single FC molecule. The specific binding of FC is achieved also through hydrophobic interactions involving Tyr76A, Tyr115A, Glu165A, and Leu157A of the ML-I A-chain. The binding energy of FC to the active site of ML-I was calculated as well to be -6.03 kcal mol-1. In comparison to other reported ML-I complexes we observed distinct differences in the vicinity of the nucleic acid base binding site upon interaction with FC. Therefore, data obtained will provide new insights in understanding the specificity, inhibition and cytotoxicity of the ML-I A-chain and related RIPs. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Crystal Structure of the Human Pol α B Subunit in Complex with the C-terminal Domain of the Catalytic Subunit*

PubMed Central

Suwa, Yoshiaki; Gu, Jianyou; Baranovskiy, Andrey G.; Babayeva, Nigar D.; Pavlov, Youri I.; Tahirov, Tahir H.

2015-01-01

In eukaryotic DNA replication, short RNA-DNA hybrid primers synthesized by primase-DNA polymerase α (Prim-Pol α) are needed to start DNA replication by the replicative DNA polymerases, Pol δ and Pol ϵ. The C terminus of the Pol α catalytic subunit (p180C) in complex with the B subunit (p70) regulates the RNA priming and DNA polymerizing activities of Prim-Pol α. It tethers Pol α and primase, facilitating RNA primer handover from primase to Pol α. To understand these regulatory mechanisms and to reveal the details of human Pol α organization, we determined the crystal structure of p70 in complex with p180C. The structured portion of p70 includes a phosphodiesterase (PDE) domain and an oligonucleotide/oligosaccharide binding (OB) domain. The N-terminal domain and the linker connecting it to the PDE domain are disordered in the reported crystal structure. The p180C adopts an elongated asymmetric saddle shape, with a three-helix bundle in the middle and zinc-binding modules (Zn1 and Zn2) on each side. The extensive p180C-p70 interactions involve 20 hydrogen bonds and a number of hydrophobic interactions resulting in an extended buried surface of 4080 Å2. Importantly, in the structure of the p180C-p70 complex with full-length p70, the residues from the N-terminal to the OB domain contribute to interactions with p180C. The comparative structural analysis revealed both the conserved features and the differences between the human and yeast Pol α complexes. PMID:25847248

Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding

NASA Astrophysics Data System (ADS)

Samanta, Sudipta; Mukherjee, Sanchita

2017-10-01

The p53 protein activation protects the organism from propagation of cells with damaged DNA having oncogenic mutations. In normal cells, activity of p53 is controlled by interaction with MDM2. The well understood p53-MDM2 interaction facilitates design of ligands that could potentially disrupt or prevent the complexation owing to its emergence as an important objective for cancer therapy. However, thermodynamic quantification of the p53-peptide induced structural changes of the MDM2-protein remains an area to be explored. This study attempts to understand the conformational free energy and entropy costs due to this complex formation from the histograms of dihedral angles generated from molecular dynamics simulations. Residue-specific quantification illustrates that, hydrophobic residues of the protein contribute maximum to the conformational thermodynamic changes. Thermodynamic quantification of structural changes of the protein unfold the fact that, p53 binding provides a source of inter-element cooperativity among the protein secondary structural elements, where the highest affected structural elements (α2 and α4) found at the binding site of the protein affects faraway structural elements (β1 and Loop1) of the protein. The communication perhaps involves water mediated hydrogen bonded network formation. Further, we infer that in inhibitory F19A mutation of P53, though Phe19 is important in the recognition process, it has less prominent contribution in the stability of the complex. Collectively, this study provides vivid microscopic understanding of the interaction within the protein complex along with exploring mutation sites, which will contribute further to engineer the protein function and binding affinity.

Searching for life in the Universe: unconventional methods for an unconventional problem.

PubMed

Nealson, K H; Tsapin, A; Storrie-Lombardi, M

2002-12-01

The search for life, on and off our planet, can be done by conventional methods with which we are all familiar. These methods are sensitive and specific, and are often capable of detecting even single cells. However, if the search broadens to include life that may be different (even subtly different) in composition, the methods and even the approach must be altered. Here we discuss the development of what we call non-earthcentric life detection--detecting life with methods that could detect life no matter what its form or composition. To develop these methods, we simply ask, can we define life in terms of its general properties and particularly those that can be measured and quantified? Taking such an approach we can search for life using physics and chemistry to ask questions about structure, chemical composition, thermodynamics, and kinetics. Structural complexity can be searched for using computer algorithms that recognize complex structures. Once identified, these structures can be examined for a variety of chemical traits, including elemental composition, chirality, and complex chemistry. A second approach involves defining our environment in terms of energy sources (i.e., reductants), and oxidants (e.g. what is available to eat and breathe), and then looking for areas in which such phenomena are inexplicably out of chemical equilibrium. These disequilibria, when found, can then be examined in detail for the presence of the structural and chemical complexity that presumably characterizes any living systems. By this approach, we move the search for life to one that should facilitate the detection of any earthly life it encountered, as well as any non-conventional life forms that have structure, complex chemistry, and live via some form of redox chemistry.

Spectroscopic, computational and electrochemical studies on the formation of the copper complex of 1-amino-4-hydroxy-9,10-anthraquinone and effect of it on superoxide formation by NADH dehydrogenase.

PubMed

Roy, Sanjay; Mondal, Palash; Sengupta, Partha Sarathi; Dhak, Debasis; Santra, Ramesh Chandra; Das, Saurabh; Guin, Partha Sarathi

2015-03-28

A 1 : 2 copper(II) complex of 1-amino-4-hydroxy-9,10-anthraquinone (QH) having the molecular formula CuQ2 was prepared and characterized by elemental analysis, NMR, FTIR, UV-vis and mass spectroscopy. The powder diffraction of the solid complex, magnetic susceptibility and ESR spectra were also recorded. The presence of the planar anthraquinone moiety in the complex makes it extremely difficult to obtain a single crystal suitable for X-ray diffraction studies. To overcome this problem, density functional theory (DFT) was used to evaluate an optimized structure of CuQ2. In the optimized structure, it was found that there is a tilt of the two planar aromatic anthraquinone rings of the complex with respect to each other in the two planes containing the O-Cu(II)-O plane. The present study is an important addition to the understanding of the structural aspects of metal-anthracyclines because there are only a few reports on the actual structures of metal-anthracyclines. The theoretical vibrational spectrum of the complex was assigned with the help of vibrational energy distribution analysis (VEDA) using potential energy distribution (PED) and compared with experimental results. Being important in producing the biochemical action of this class of molecules, the electrochemical behavior of the complex was studied in aqueous and non-aqueous solvents to find certain electrochemical parameters. In aqueous media, reduction involves a kinetic effect during electron transfer at an electrode surface, which was characterized very carefully using cyclic voltammetry. Electrochemical studies showed a significant modification in the electrochemical properties of 1-amino-4-hydroxy-9,10-anthraquinone (QH) when bound to Cu(II) in the complex compared to those observed for free QH. This suggests that the copper complex might be a good choice as a biologically active molecule, which was reflected in the lack of stimulated superoxide generation by the complex.

Fungal prion HET-s as a model for structural complexity and self-propagation in prions.

PubMed

Wan, William; Stubbs, Gerald

2014-04-08

The highly ordered and reproducible structure of the fungal prion HET-s makes it an excellent model system for studying the inherent properties of prions, self-propagating infectious proteins that have been implicated in a number of fatal diseases. In particular, the HET-s prion-forming domain readily folds into a relatively complex two-rung β-solenoid amyloid. The faithful self-propagation of this fold involves a diverse array of inter- and intramolecular structural features. These features include a long flexible loop connecting the two rungs, buried polar residues, salt bridges, and asparagine ladders. We have used site-directed mutagenesis and X-ray fiber diffraction to probe the relative importance of these features for the formation of β-solenoid structure, as well as the cumulative effects of multiple mutations. Using fibrillization kinetics and chemical stability assays, we have determined the biophysical effects of our mutations on the assembly and stability of the prion-forming domain. We have found that a diversity of structural features provides a level of redundancy that allows robust folding and stability even in the face of significant sequence alterations and suboptimal environmental conditions. Our findings provide fundamental insights into the structural interactions necessary for self-propagation. Propagation of prion structure seems to require an obligatory level of complexity that may not be reproducible in short peptide models.

Structural insights into the catalytic mechanism of a family 18 exo-chitinase

PubMed Central

van Aalten, D. M. F.; Komander, D.; Synstad, B.; Gåseidnes, S.; Peter, M. G.; Eijsink, V. G. H.

2001-01-01

Chitinase B (ChiB) from Serratia marcescens is a family 18 exo-chitinase whose catalytic domain has a TIM-barrel fold with a tunnel-shaped active site. We have solved structures of three ChiB complexes that reveal details of substrate binding, substrate-assisted catalysis, and product displacement. The structure of an inactive ChiB mutant (E144Q) complexed with a pentameric substrate (binding in subsites −2 to +3) shows closure of the “roof” of the active site tunnel. It also shows that the sugar in the −1 position is distorted to a boat conformation, thus providing structural evidence in support of a previously proposed catalytic mechanism. The structures of the active enzyme complexed to allosamidin (an analogue of a proposed reaction intermediate) and of the active enzyme soaked with pentameric substrate show events after cleavage of the glycosidic bond. The latter structure shows reopening of the roof of the active site tunnel and enzyme-assisted product displacement in the +1 and +2 sites, allowing a water molecule to approach the reaction center. Catalysis is accompanied by correlated structural changes in the core of the TIM barrel that involve conserved polar residues whose functions were hitherto unknown. These changes simultaneously contribute to stabilization of the reaction intermediate and alternation of the pKa of the catalytic acid during the catalytic cycle. PMID:11481469

E-type cyclins modulate telomere integrity in mammalian male meiosis.

PubMed

Manterola, Marcia; Sicinski, Piotr; Wolgemuth, Debra J

2016-06-01

We have shown that E-type cyclins are key regulators of mammalian male meiosis. Depletion of cyclin E2 reduced fertility in male mice due to meiotic defects, involving abnormal pairing and synapsis, unrepaired DNA, and loss of telomere structure. These defects were exacerbated by additional loss of cyclin E1, and complete absence of both E-type cyclins produces a meiotic catastrophe. Here, we investigated the involvement of E-type cyclins in maintaining telomere integrity in male meiosis. Spermatocytes lacking cyclin E2 and one E1 allele (E1+/-E2-/-) displayed a high rate of telomere abnormalities but can progress to pachytene and diplotene stages. We show that their telomeres exhibited an aberrant DNA damage repair response during pachynema and that the shelterin complex proteins TRF2 and RAP2 were significantly decreased in the proximal telomeres. Moreover, the insufficient level of these proteins correlated with an increase of γ-H2AX foci in the affected telomeres and resulted in telomere associations involving TRF1 and telomere detachment in later prophase-I stages. These results suggest that E-type cyclins are key modulators of telomere integrity during meiosis by, at least in part, maintaining the balance of shelterin complex proteins, and uncover a novel role of E-type cyclins in regulating chromosome structure during male meiosis.

Complex Hollow Nanostructures: Synthesis and Energy-Related Applications.

PubMed

Yu, Le; Hu, Han; Wu, Hao Bin; Lou, Xiong Wen David

2017-04-01

Hollow nanostructures offer promising potential for advanced energy storage and conversion applications. In the past decade, considerable research efforts have been devoted to the design and synthesis of hollow nanostructures with high complexity by manipulating their geometric morphology, chemical composition, and building block and interior architecture to boost their electrochemical performance, fulfilling the increasing global demand for renewable and sustainable energy sources. In this Review, we present a comprehensive overview of the synthesis and energy-related applications of complex hollow nanostructures. After a brief classification, the design and synthesis of complex hollow nanostructures are described in detail, which include hierarchical hollow spheres, hierarchical tubular structures, hollow polyhedra, and multi-shelled hollow structures, as well as their hybrids with nanocarbon materials. Thereafter, we discuss their niche applications as electrode materials for lithium-ion batteries and hybrid supercapacitors, sulfur hosts for lithium-sulfur batteries, and electrocatalysts for oxygen- and hydrogen-involving energy conversion reactions. The potential superiorities of complex hollow nanostructures for these applications are particularly highlighted. Finally, we conclude this Review with urgent challenges and further research directions of complex hollow nanostructures for energy-related applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Complexation of the calcium cation with antamanide: an experimental and theoretical study

NASA Astrophysics Data System (ADS)

Makrlík, Emanuel; Böhm, Stanislav; Vaňura, Petr; Ruzza, Paolo

2015-06-01

By using extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium Ca2+(aq) + 1 .Sr2+(nb) ? 1 .Ca2+(nb) + Sr2+(aq) occurring in the two-phase water-nitrobenzene system (1 = antamanide; aq = aqueous phase, nb = nitrobenzene phase) was determined as log Kex (Ca2+, 1 .Sr2+) = 1.6 ± 0.1. Further, the stability constant of the 1 .Ca2+ complex in nitrobenzene saturated with water was calculated for a temperature of 25 °C: log βnb (1 .Ca2+) = 10.9 ± 0.2. Finally, applying quantum mechanical density functional level of theory calculations, the most probable structure of the cationic complex species 1 .Ca2+ was derived. In the resulting complex, the 'central' cation Ca2+ is bound by six strong bonding interactions to the corresponding six carbonyl oxygen atoms of the parent ligand 1. Besides, the whole 1 .Ca2+ complex structure is stabilised by two intramolecular hydrogen bonds. The interaction energy of the considered 1 .Ca2+ complex, involving the Boys-Bernardi counterpoise corrections of the basis set superposition error, was found to be -1219.3 kJ/mol, confirming the formation of this cationic species.

Icosahedral quasicrystals of intermetallic compounds are icosahedral twins of cubic crystals of three kinds, consisting of large (about 5000 atoms) icosahedral complexes in either a cubic body-centered or a cubic face-centered arrangement or smaller (about 1350 atoms) icosahedral complexes in the β-tungsten arrangement

PubMed Central

Pauling, Linus

1989-01-01

The twofold-axis electron-diffraction photographs of icosahedral quasicrystals are of three kinds, reflecting three different structures of the cubic crystals that by icosahedral twinning form the quasicrystals. The first kind, represented by Al13Cu4Fe3, contains two very large icosahedral complexes, each of about 4680 atoms, in the body-centered arrangement, with six smaller icosahedral complexes (104 atoms each) in the principal interstices. The second kind, represented by Al5Mn, contains four of the very large complexes in the face-centered arrangement (cubic close packing), with four of the smaller clusters in the interstices. The third kind, represented by Al6CuLi3, contains eight icosahedral complexes, each of about 1350 atoms, in the β-W arrangement. The supporting evidence for these cubic structures is discussed as well as other evidence showing that the simple quasicrystal theory, which states that quasicrystals do not involve any translational identity operations, has to be modified. Images PMID:16594078

Ternary iron(II) complex with an emissive imidazopyridine arm from Schiff base cyclizations and its oxidative DNA cleavage activity.

PubMed

Mukherjee, Arindam; Dhar, Shanta; Nethaji, Munirathinam; Chakravarty, Akhil R

2005-01-21

The ternary iron(II) complex [Fe(L')(L")](PF6)3(1) as a synthetic model for the bleomycins, where L' and L" are formed from metal-mediated cyclizations of N,N'-(2-hydroxypropane-1,3-diyl)bis(pyridine-2-aldimine)(L), is synthesized and structurally characterized by X-ray crystallography. In the six-coordinate iron(ii) complex, ligands L' and L" show tetradentate and bidentate chelating modes of bonding. Ligand L' is formed from an intramolecular attack of the alcoholic OH group of L to one imine moiety leading to the formation of a stereochemically constrained five-membered ring. Ligand L" which is formed from an intermolecular reaction involving one imine moiety of L and pyridine-2-carbaldehyde has an emissive cationic imidazopyridine pendant arm. The complex binds to double-stranded DNA in the minor groove giving a Kapp value of 4.1 x 10(5) M(-1) and displays oxidative cleavage of supercoiled DNA in the presence of H2O2 following a hydroxyl radical pathway. The complex also shows photo-induced DNA cleavage activity on UV light exposure involving formation of singlet oxygen as the reactive species.

Exploring interaction of TNF and orthopoxviral CrmB protein by surface plasmon resonance and free energy calculation.

PubMed

Ivanisenko, Nikita V; Tregubchak, Tatiana V; Saik, Olga V; Ivanisenko, Vladimir A; Shchelkunov, Sergei N

2014-01-01

Inhibition of the activity of the tumor necrosis factor (TNF) has become the main strategy for treating inflammatory diseases. The orthopoxvirus TNF-binding proteins can bind and efficiently neutralize TNF. To analyze the mechanisms of the interaction between human (hTNF) or mouse (mTNF) TNF and the cowpox virus N-terminal binding domain (TNFBD-CPXV), also the variola virus N-terminal binding domain (TNFBD-VARV) and to define the amino acids most importantly involved in the formation of complexes, computer models, derived from the X-ray structure of a homologous hTNF/TNFRII complex, were used together with experiments. The hTNF/TNFBD-CPXV, hTNF/TNFBD-VARV, mTNF/TNFBD-CPXV, and mTNF/TNFBD-VARV complexes were used in the molecular dynamics (MD) simulations and MM/GBSA free energy calculations. The complexes were ordered as hTNF/TNFBD-CPXV, hTNF/TNFBD-VARV, mTNF/TNFBD-CPXV and mTNF/TNFBD-VARV according to increase in the binding affinity. The calculations were in agreement with surface plasmon resonance (SPR) measurements of the binding constants. Key residues involved in complex formation were identified.

The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities.

PubMed

Zhang, Y; LeRoy, G; Seelig, H P; Lane, W S; Reinberg, D

1998-10-16

Histone acetylation and deacetylation were found to be catalyzed by structurally distinct, multisubunit complexes that mediate, respectively, activation and repression of transcription. ATP-dependent nucleosome remodeling, mediated by different multisubunit complexes, was thought to be involved only in transcription activation. Here we report the isolation of a protein complex that contains both histone deacetylation and ATP-dependent nucleosome remodeling activities. The complex contains the histone deacetylases HDAC1/2, histone-binding proteins, the dermatomyositis-specific autoantigen Mi2beta, a polypeptide related to the metastasis-associated protein 1, and a novel polypeptide of 32 kDa. Patients with dermatomyositis have a high rate of malignancy. The finding that Mi2beta exists in a complex containing histone deacetylase and nucleosome remodeling activities suggests a role for chromatin reorganization in cancer metastasis.

Protein folding simulations: from coarse-grained model to all-atom model.

PubMed

Zhang, Jian; Li, Wenfei; Wang, Jun; Qin, Meng; Wu, Lei; Yan, Zhiqiang; Xu, Weixin; Zuo, Guanghong; Wang, Wei

2009-06-01

Protein folding is an important and challenging problem in molecular biology. During the last two decades, molecular dynamics (MD) simulation has proved to be a paramount tool and was widely used to study protein structures, folding kinetics and thermodynamics, and structure-stability-function relationship. It was also used to help engineering and designing new proteins, and to answer even more general questions such as the minimal number of amino acid or the evolution principle of protein families. Nowadays, the MD simulation is still undergoing rapid developments. The first trend is to toward developing new coarse-grained models and studying larger and more complex molecular systems such as protein-protein complex and their assembling process, amyloid related aggregations, and structure and motion of chaperons, motors, channels and virus capsides; the second trend is toward building high resolution models and explore more detailed and accurate pictures of protein folding and the associated processes, such as the coordination bond or disulfide bond involved folding, the polarization, charge transfer and protonate/deprotonate process involved in metal coupled folding, and the ion permeation and its coupling with the kinetics of channels. On these new territories, MD simulations have given many promising results and will continue to offer exciting views. Here, we review several new subjects investigated by using MD simulations as well as the corresponding developments of appropriate protein models. These include but are not limited to the attempt to go beyond the topology based Gō-like model and characterize the energetic factors in protein structures and dynamics, the study of the thermodynamics and kinetics of disulfide bond involved protein folding, the modeling of the interactions between chaperonin and the encapsulated protein and the protein folding under this circumstance, the effort to clarify the important yet still elusive folding mechanism of protein BBL, the development of discrete MD and its application in studying the alpha-beta conformational conversion and oligomer assembling process, and the modeling of metal ion involved protein folding. (c) 2009 IUBMB.

Cardiovirus Leader proteins bind exportins: Implications for virus replication and nucleocytoplasmic trafficking inhibition

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

Ciomperlik, Jessica J.; Basta, Holly A.; Palmenberg, Ann C., E-mail: acpalmen@wisc.edu

2016-01-15

Cardiovirus Leader proteins (L{sub X}) inhibit cellular nucleocytoplasmic trafficking by directing host kinases to phosphorylate Phe/Gly-containing nuclear pore proteins (Nups). Resolution of the Mengovirus L{sub M} structure bound to Ran GTPase, suggested this complex would further recruit specific exportins (karyopherins), which in turn mediate kinase selection. Pull-down experiments and recombinant complex reconstitution now confirm that Crm1 and CAS exportins form stable dimeric complexes with encephalomyocarditis virus L{sub E}, and also larger complexes with L{sub E}:Ran. shRNA knockdown studies support this idea. Similar activities could be demonstrated for recombinant L{sub S} and L{sub T} from Theiloviruses. When mutations were introduced tomore » alter the L{sub E} zinc finger domain, acidic domain, or dual phosphorylation sites, there was reduced exportin selection. These regions are not involved in Ran interactions, so the Ran and Crm1 binding sites on L{sub E} must be non-overlapping. The involvement of exportins in this mechanism is important to viral replication and the observation of trafficking inhibition by L{sub E}.« less

Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t

PubMed Central

Gupta, Asmita; Kailasam, Senthilkumar; Bansal, Manju

2016-01-01

Exportin-t (Xpot) transports mature 5′- and 3′-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes. PMID:27028637

Ynamides in Ring Forming Transformations

PubMed Central

WANG, XIAO-NA; YEOM, HYUN-SUK; FANG, LI-CHAO; HE, SHUZHONG; MA, ZHI-XIONG; KEDROWSKI, BRANT L.; HSUNG, RICHARD P.

2013-01-01

Conspectus The ynamide functional group activates carbon-carbon triple bonds through an attached nitrogen atom that bears an electron-withdrawing group. As a result, the alkyne has both electrophilic and nucleophilic properties. Through the selection of the electron-withdrawing group attached to nitrogen chemists can modulate the electronic properties and reactivity of ynamides, making these groups versatile synthetic building blocks. The reactions of ynamides also lead directly to nitrogen-containing products, which provides access to important structural motifs found in natural products and molecules of medicinal interest. Therefore, researchers have invested increasing time and research in the chemistry of ynamides in recent years. This Account surveys and assesses new organic transformations involving ynamides developed in our laboratory and in others around the world. We showcase the synthetic power of ynamides for rapid assembly of complex molecular structures. Among the recent reports of ynamide transformations, ring-forming reactions provide a powerful tool for generating molecular complexity quickly. In addition to their synthetic utility, such reactions are mechanistically interesting. Therefore, we focus primarily on the cyclization chemistry of ynamides. This Account highlights ynamide reactions that are useful in the rapid synthesis of cyclic and polycyclic structural manifolds. We discuss the mechanisms active in the ring formations and describe representative examples that demonstrate the scope of these reactions and provide mechanistic insights. In this discussion we feature examples of ynamide reactions involving radical cyclizations, ring-closing metathesis, transition metal and non-transition metal mediated cyclizations, cycloaddition reactions, and rearrangements. The transformations presented rapidly introduce structural complexity and include nitrogen within, or in close proximity to, a newly formed ring (or rings). Thus, ynamides have emerged as powerful synthons for nitrogen-containing heterocycles and nitrogen-substituted rings, and we hope this Account will promote continued interest in the chemistry of ynamides. PMID:24164363

Structural Basis of Rap Phosphatase Inhibition by Phr Peptides

PubMed Central

Gallego del Sol, Francisca; Marina, Alberto

2013-01-01

Two-component systems, composed of a sensor histidine kinase and an effector response regulator (RR), are the main signal transduction devices in bacteria. In Bacillus, the Rap protein family modulates complex signaling processes mediated by two-component systems, such as competence, sporulation, or biofilm formation, by inhibiting the RR components involved in these pathways. Despite the high degree of sequence homology, Rap proteins exert their activity by two completely different mechanisms of action: inducing RR dephosphorylation or blocking RR binding to its target promoter. However the regulatory mechanism involving Rap proteins is even more complex since Rap activity is antagonized by specific signaling peptides (Phr) through a mechanism that remains unknown at the molecular level. Using X-ray analyses, we determined the structure of RapF, the anti-activator of competence RR ComA, alone and in complex with its regulatory peptide PhrF. The structural and functional data presented herein reveal that peptide PhrF blocks the RapF-ComA interaction through an allosteric mechanism. PhrF accommodates in the C-terminal tetratricopeptide repeat domain of RapF by inducing its constriction, a conformational change propagated by a pronounced rotation to the N-terminal ComA-binding domain. This movement partially disrupts the ComA binding site by triggering the ComA disassociation, whose interaction with RapF is also sterically impaired in the PhrF-induced conformation of RapF. Sequence analyses of the Rap proteins, guided by the RapF-PhrF structure, unveil the molecular basis of Phr recognition and discrimination, allowing us to relax the Phr specificity of RapF by a single residue change. PMID:23526880

Probing binding hot spots at protein-RNA recognition sites.

PubMed

Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad

2016-01-29

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The structural bioinformatics library: modeling in biomolecular science and beyond.

PubMed

Cazals, Frédéric; Dreyfus, Tom

2017-04-01

Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

The neural correlates of obsessive-compulsive disorder: a multimodal perspective.

PubMed

Moreira, P S; Marques, P; Soriano-Mas, C; Magalhães, R; Sousa, N; Soares, J M; Morgado, P

2017-08-29

Obsessive-compulsive disorder (OCD) is one of the most debilitating psychiatric conditions. An extensive body of the literature has described some of the neurobiological mechanisms underlying the core manifestations of the disorder. Nevertheless, most reports have focused on individual modalities of structural/functional brain alterations, mainly through targeted approaches, thus possibly precluding the power of unbiased exploratory approaches. Eighty subjects (40 OCD and 40 healthy controls) participated in a multimodal magnetic resonance imaging (MRI) investigation, integrating structural and functional data. Voxel-based morphometry analysis was conducted to compare between-group volumetric differences. The whole-brain functional connectome, derived from resting-state functional connectivity (FC), was analyzed with the network-based statistic methodology. Results from structural and functional analysis were integrated in mediation models. OCD patients revealed volumetric reductions in the right superior temporal sulcus. Patients had significantly decreased FC in two distinct subnetworks: the first, involving the orbitofrontal cortex, temporal poles and the subgenual anterior cingulate cortex; the second, comprising the lingual and postcentral gyri. On the opposite, a network formed by connections between thalamic and occipital regions had significantly increased FC in patients. Integrative models revealed direct and indirect associations between volumetric alterations and FC networks. This study suggests that OCD patients display alterations in brain structure and FC, involving complex networks of brain regions. Furthermore, we provided evidence for direct and indirect associations between structural and functional alterations representing complex patterns of interactions between separate brain regions, which may be of upmost relevance for explaining the pathophysiology of the disorder.

Atypical behavior in the electron capture induced dissociation of biologically relevant transition metal ion complexes of the peptide hormone oxytocin

NASA Astrophysics Data System (ADS)

Kleinnijenhuis, Anne J.; Mihalca, Romulus; Heeren, Ron M. A.; Heck, Albert J. R.

2006-07-01

Doubly protonated ions of the disulfide bond containing nonapeptide hormone oxytocin and oxytocin complexes with different transition metal ions, that have biological relevance under physiological conditions, were subjected to electron capture dissociation (ECD) to probe their structural features in the gas phase. Although, all the ECD spectra were strikingly different, typical ECD behavior was observed for complexes of the nonapeptide hormone oxytocin with Ni2+, Co2+ and Zn2+, i.e., abundant c/z' and a'/y backbone cleavages and ECD characteristic S-S and S-C bond cleavages were observed. We propose that, although in the oxytocin-transition metal ion complexes the metal ions serve as the main initial capture site, the captured electron is transferred to other sites in the complex to form a hydrogen radical, which drives the subsequent typical ECD fragmentations. The complex of oxytocin with Cu2+ displayed noticeably different ECD behavior. The fragment ions were similar to fragment ions typically observed with low-energy collision induced dissociation (CID). We propose that the electrons captured by the oxytocin-Cu2+ complex might be favorably involved in reducing the Cu2+ metal ion to Cu+. Subsequent energy redistribution would explain the observed low-energy CID-type fragmentations. Electron capture resulted also in quite different specific cleavage sites for the complexes of oxytocin with Ni2+, Co2+ and Zn2+. This is an indication for structural differences in these complexes possibly linked to their significantly different biological effects on oxytocin-receptor binding, and suggests that ECD may be used to study subtle structural differences in transition metal ion-peptide complexes.

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

Li, XS; Michaelis, VK; Ong, TC

The controllable synthesis of well-ordered layered materials with specific nanoarchitecture poses a grand challenge in materials chemistry. Here the solvothermal synthesis of two structurally analogous 5-coordinate organosilicate complexes through a novel transesterification mechanism is reported. Since the polycrystalline nature of the intrinsic hypervalent Si complex thwarts the endeavor in determining its structure, a novel strategy concerning the elegant addition of a small fraction of B species as an effective crystal growth mediator and a sacrificial agent is proposed to directly prepare diffraction-quality single crystals without disrupting the intrinsic elemental type. In the determined crystal structure, two monomeric primary building unitsmore » (PBUs) self-assemble into a dimeric asymmetric secondary BU via strong Na+O2- ionic bonds. The designed one-pot synthesis is straightforward, robust, and efficient, leading to a well-ordered (10)-parallel layered Si complex with its principal interlayers intercalated with extensive van der Waals gaps in spite of the presence of substantial Na+ counter-ions as a result of unique atomic arrangement in its structure. However, upon fast pyrolysis, followed by acid leaching, both complexes are converted into two SiO2 composites bearing BET surface areas of 163.3 and 254.7m(2)g(-1) for the pyrolyzed intrinsic and B-assisted Si complexes, respectively. The transesterification methodology merely involving alcoholysis but without any hydrolysis side reaction is designed to have generalized applicability for use in synthesizing new layered metal-organic compounds with tailored PBUs and corresponding metal oxide particles with hierarchical porosity.« less

DockTrina: docking triangular protein trimers.

PubMed

Popov, Petr; Ritchie, David W; Grudinin, Sergei

2014-01-01

In spite of the abundance of oligomeric proteins within a cell, the structural characterization of protein-protein interactions is still a challenging task. In particular, many of these interactions involve heteromeric complexes, which are relatively difficult to determine experimentally. Hence there is growing interest in using computational techniques to model such complexes. However, assembling large heteromeric complexes computationally is a highly combinatorial problem. Nonetheless the problem can be simplified greatly by considering interactions between protein trimers. After dimers and monomers, triangular trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) are the most frequently observed quaternary structural motifs according to the three-dimensional (3D) complex database. This article presents DockTrina, a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation test. Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer. The method is tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures. DockTrina will be made available at http://nano-d.inrialpes.fr/software/docktrina. Copyright © 2013 Wiley Periodicals, Inc.

Developing a framework for qualitative engineering: Research in design and analysis of complex structural systems

NASA Technical Reports Server (NTRS)

Franck, Bruno M.

1990-01-01

The research is focused on automating the evaluation of complex structural systems, whether for the design of a new system or the analysis of an existing one, by developing new structural analysis techniques based on qualitative reasoning. The problem is to identify and better understand: (1) the requirements for the automation of design, and (2) the qualitative reasoning associated with the conceptual development of a complex system. The long-term objective is to develop an integrated design-risk assessment environment for the evaluation of complex structural systems. The scope of this short presentation is to describe the design and cognition components of the research. Design has received special attention in cognitive science because it is now identified as a problem solving activity that is different from other information processing tasks (1). Before an attempt can be made to automate design, a thorough understanding of the underlying design theory and methodology is needed, since the design process is, in many cases, multi-disciplinary, complex in size and motivation, and uses various reasoning processes involving different kinds of knowledge in ways which vary from one context to another. The objective is to unify all the various types of knowledge under one framework of cognition. This presentation focuses on the cognitive science framework that we are using to represent the knowledge aspects associated with the human mind's abstraction abilities and how we apply it to the engineering knowledge and engineering reasoning in design.

Sensitivity based coupling strengths in complex engineering systems

NASA Technical Reports Server (NTRS)

Bloebaum, C. L.; Sobieszczanski-Sobieski, J.

1993-01-01

The iterative design scheme necessary for complex engineering systems is generally time consuming and difficult to implement. Although a decomposition approach results in a more tractable problem, the inherent couplings make establishing the interdependencies of the various subsystems difficult. Another difficulty lies in identifying the most efficient order of execution for the subsystem analyses. The paper describes an approach for determining the dependencies that could be suspended during the system analysis with minimal accuracy losses, thereby reducing the system complexity. A new multidisciplinary testbed is presented, involving the interaction of structures, aerodynamics, and performance disciplines. Results are presented to demonstrate the effectiveness of the system reduction scheme.

Atpenins, potent and specific inhibitors of mitochondrial complex II (succinate-ubiquinone oxidoreductase)

PubMed Central

Miyadera, Hiroko; Shiomi, Kazuro; Ui, Hideaki; Yamaguchi, Yuichi; Masuma, Rokuro; Tomoda, Hiroshi; Miyoshi, Hideto; Osanai, Arihiro; Kita, Kiyoshi; Ōmura, Satoshi

2003-01-01

Enzymes in the mitochondrial respiratory chain are involved in various physiological events in addition to their essential role in the production of ATP by oxidative phosphorylation. The use of specific and potent inhibitors of complex I (NADH-ubiquinone reductase) and complex III (ubiquinol-cytochrome c reductase), such as rotenone and antimycin, respectively, has allowed determination of the role of these enzymes in physiological processes. However, unlike complexes I, III, and IV (cytochrome c oxidase), there are few potent and specific inhibitors of complex II (succinate-ubiquinone reductase) that have been described. In this article, we report that atpenins potently and specifically inhibit the succinate-ubiquinone reductase activity of mitochondrial complex II. Therefore, atpenins may be useful tools for clarifying the biochemical and structural properties of complex II, as well as for determining its physiological roles in mammalian tissues. PMID:12515859

Crystal Structure of Mycobacterium tuberculosis H37Rv AldR (Rv2779c), a Regulator of the ald Gene

PubMed Central

Dey, Abhishek; Shree, Sonal; Pandey, Sarvesh Kumar; Tripathi, Rama Pati; Ramachandran, Ravishankar

2016-01-01

Here we report the crystal structure of M. tuberculosis AldR (Rv2779c) showing that the N-terminal DNA-binding domains are swapped, forming a dimer, and four dimers are assembled into an octamer through crystal symmetry. The C-terminal domain is involved in oligomeric interactions that stabilize the oligomer, and it contains the effector-binding sites. The latter sites are 30–60% larger compared with homologs like MtbFFRP (Rv3291c) and can consequently accommodate larger molecules. MtbAldR binds to the region upstream to the ald gene that is highly up-regulated in nutrient-starved tuberculosis models and codes for l-alanine dehydrogenase (MtbAld; Rv2780). Further, the MtbAldR-DNA complex is inhibited upon binding of Ala, Tyr, Trp and Asp to the protein. Studies involving a ligand-binding site G131T mutant show that the mutant forms a DNA complex that cannot be inhibited by adding the amino acids. Comparative studies suggest that binding of the amino acids changes the relative spatial disposition of the DNA-binding domains and thereby disrupt the protein-DNA complex. Finally, we identified small molecules, including a tetrahydroquinoline carbonitrile derivative (S010-0261), that inhibit the MtbAldR-DNA complex. The latter molecules represent the very first inhibitors of a feast/famine regulatory protein from any source and set the stage for exploring MtbAldR as a potential anti-tuberculosis target. PMID:27006398

UBF complexes with phosphatidylinositol 4,5-bisphosphate in nucleolar organizer regions regardless of ongoing RNA polymerase I activity

PubMed Central

Sobol, Margarita; Yildirim, Sukriye; Philimonenko, Vlada V; Marášek, Pavel; Castaño, Enrique; Hozák, Pavel

2013-01-01

To maintain growth and division, cells require a large-scale production of rRNAs which occurs in the nucleolus. Recently, we have shown the interaction of nucleolar phosphatidylinositol 4,5-bisphosphate (PIP2) with proteins involved in rRNA transcription and processing, namely RNA polymerase I (Pol I), UBF, and fibrillarin. Here we extend the study by investigating transcription-related localization of PIP2 in regards to transcription and processing complexes of Pol I. To achieve this, we used either physiological inhibition of transcription during mitosis or inhibition by treatment the cells with actinomycin D (AMD) or 5,6-dichloro-1β-d-ribofuranosyl-benzimidazole (DRB). We show that PIP2 is associated with Pol I subunits and UBF in a transcription-independent manner. On the other hand, PIP2/fibrillarin colocalization is dependent on the production of rRNA. These results indicate that PIP2 is required not only during rRNA production and biogenesis, as we have shown before, but also plays a structural role as an anchor for the Pol I pre-initiation complex during the cell cycle. We suggest that throughout mitosis, PIP2 together with UBF is involved in forming and maintaining the core platform of the rDNA helix structure. Thus we introduce PIP2 as a novel component of the NOR complex, which is further engaged in the renewed rRNA synthesis upon exit from mitosis. PMID:24513678

Dependency visualization for complex system understanding

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

Smart, J. Allison Cory

1994-09-01

With the volume of software in production use dramatically increasing, the importance of software maintenance has become strikingly apparent. Techniques now sought and developed for reverse engineering and design extraction and recovery. At present, numerous commercial products and research tools exist which are capable of visualizing a variety of programming languages and software constructs. The list of new tools and services continues to grow rapidly. Although the scope of the existing commercial and academic product set is quite broad, these tools still share a common underlying problem. The ability of each tool to visually organize object representations is increasingly impairedmore » as the number of components and component dependencies within systems increases. Regardless of how objects are defined, complex ``spaghetti`` networks result in nearly all large system cases. While this problem is immediately apparent in modem systems analysis involving large software implementations, it is not new. As will be discussed in Chapter 2, related problems involving the theory of graphs were identified long ago. This important theoretical foundation provides a useful vehicle for representing and analyzing complex system structures. While the utility of directed graph based concepts in software tool design has been demonstrated in literature, these tools still lack the capabilities necessary for large system comprehension. This foundation must therefore be expanded with new organizational and visualization constructs necessary to meet this challenge. This dissertation addresses this need by constructing a conceptual model and a set of methods for interactively exploring, organizing, and understanding the structure of complex software systems.« less

Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly.

PubMed

Shalaeva, Daria N; Dibrova, Daria V; Galperin, Michael Y; Mulkidjanian, Armen Y

2015-05-27

Binding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearrangement in Apaf-1, which leads to oligomerization of Apaf-1/cytochrome c complexes into an apoptosome. Despite the availability of crystal structures of cytochrome c and Apaf-1 and cryo-electron microscopy models of the entire apoptosome, the binding mode of cytochrome c to Apaf-1, as well as the nature of the amino acid residues of Apaf-1 involved remain obscure. We investigated the interaction between cytochrome c and Apaf-1 by combining several modeling approaches. We have applied protein-protein docking and energy minimization, evaluated the resulting models of the Apaf-1/cytochrome c complex, and carried out a further analysis by means of molecular dynamics simulations. We ended up with a single model structure where all the lysine residues of cytochrome c that are known as functionally-relevant were involved in forming salt bridges with acidic residues of Apaf-1. This model has revealed three distinctive bifurcated salt bridges, each involving a single lysine residue of cytochrome c and two neighboring acidic resides of Apaf-1. Salt bridge-forming amino acids of Apaf-1 showed a clear evolutionary pattern within Metazoa, with pairs of acidic residues of Apaf-1, involved in bifurcated salt bridges, reaching their highest numbers in the sequences of vertebrates, in which the cytochrome c-mediated mechanism of apoptosome formation seems to be typical. The reported model of an Apaf-1/cytochrome c complex provides insights in the nature of protein-protein interactions which are hard to observe in crystallographic or electron microscopy studies. Bifurcated salt bridges can be expected to be stronger than simple salt bridges, and their formation might promote the conformational change of Apaf-1, leading to the formation of an apoptosome. Combination of structural and sequence analyses provides hints on the evolution of the cytochrome c-mediated apoptosis.

CryoEM and image sorting for flexible protein/DNA complexes.

PubMed

Villarreal, Seth A; Stewart, Phoebe L

2014-07-01

Intrinsically disordered regions of proteins and conformational flexibility within complexes can be critical for biological function. However, disorder, flexibility, and heterogeneity often hinder structural analyses. CryoEM and single particle image processing techniques offer the possibility of imaging samples with significant flexibility. Division of particle images into more homogenous subsets after data acquisition can help compensate for heterogeneity within the sample. We present the utility of an eigenimage sorting analysis for examining two protein/DNA complexes with significant conformational flexibility and heterogeneity. These complexes are integral to the non-homologous end joining pathway, and are involved in the repair of double strand breaks of DNA. Both complexes include the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and biotinylated DNA with bound streptavidin, with one complex containing the Ku heterodimer. Initial 3D reconstructions of the two DNA-PKcs complexes resembled a cryoEM structure of uncomplexed DNA-PKcs without additional density clearly attributable to the remaining components. Application of eigenimage sorting allowed division of the DNA-PKcs complex datasets into more homogeneous subsets. This led to visualization of density near the base of the DNA-PKcs that can be attributed to DNA, streptavidin, and Ku. However, comparison of projections of the subset structures with 2D class averages indicated that a significant level of heterogeneity remained within each subset. In summary, image sorting methods allowed visualization of extra density near the base of DNA-PKcs, suggesting that DNA binds in the vicinity of the base of the molecule and potentially to a flexible region of DNA-PKcs. Copyright © 2013 Elsevier Inc. All rights reserved.

Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII-TCR complex.

PubMed

Bello, Martiniano; Correa-Basurto, José

2016-04-01

Although crystallographic data have provided important molecular insight into the interactions in the pMHC-TCR complex, the inherent features of this structural approach cause it to only provide a static picture of the interactions. While unbiased molecular dynamics simulations (UMDSs) have provided important information about the dynamic structural behavior of the pMHC-TCR complex, most of them have modeled the pMHC-TCR complex as soluble, when in physiological conditions, this complex is membrane bound; therefore, following this latter UMDS protocol might hamper important dynamic results. In this contribution, we performed three independent 300 ns-long UMDSs of the pMHCII-TCR complex anchored in two opposing membranes to explore the structural and energetic properties of the recognition of pMHCII by the TCR. The conformational ensemble generated through UMDSs was subjected to clustering and Cartesian principal component analyses (cPCA) to explore the dynamical behavior of the pMHCII-TCR association. Furthermore, based on the conformational population sampled through UMDSs, the effective binding free energy, per-residue free energy decomposition, and alanine scanning mutations were explored for the native pMHCII-TCR complex, as well as for 12 mutations (p1-p12MHCII-TCR) introduced in the native peptide. Clustering analyses and cPCA provide insight into the rocking motion of the TCR onto pMHCII, together with the presence of new electrostatic interactions not observed through crystallographic methods. Energetic results provide evidence of the main contributors to the pMHC-TCR complex formation as well as the key residues involved in this molecular recognition process.

A high performance, ad-hoc, fuzzy query processing system for relational databases

NASA Technical Reports Server (NTRS)

Mansfield, William H., Jr.; Fleischman, Robert M.

1992-01-01

Database queries involving imprecise or fuzzy predicates are currently an evolving area of academic and industrial research. Such queries place severe stress on the indexing and I/O subsystems of conventional database environments since they involve the search of large numbers of records. The Datacycle architecture and research prototype is a database environment that uses filtering technology to perform an efficient, exhaustive search of an entire database. It has recently been modified to include fuzzy predicates in its query processing. The approach obviates the need for complex index structures, provides unlimited query throughput, permits the use of ad-hoc fuzzy membership functions, and provides a deterministic response time largely independent of query complexity and load. This paper describes the Datacycle prototype implementation of fuzzy queries and some recent performance results.

Explicit solution techniques for impact with contact constraints

NASA Technical Reports Server (NTRS)

Mccarty, Robert E.

1993-01-01

Modern military aircraft transparency systems, windshields and canopies, are complex systems which must meet a large and rapidly growing number of requirements. Many of these transparency system requirements are conflicting, presenting difficult balances which must be achieved. One example of a challenging requirements balance or trade is shaping for stealth versus aircrew vision. The large number of requirements involved may be grouped in a variety of areas including man-machine interface; structural integration with the airframe; combat hazards; environmental exposures; and supportability. Some individual requirements by themselves pose very difficult, severely nonlinear analysis problems. One such complex problem is that associated with the dynamic structural response resulting from high energy bird impact. An improved analytical capability for soft-body impact simulation was developed.

Explicit solution techniques for impact with contact constraints

NASA Astrophysics Data System (ADS)

McCarty, Robert E.

1993-08-01

Modern military aircraft transparency systems, windshields and canopies, are complex systems which must meet a large and rapidly growing number of requirements. Many of these transparency system requirements are conflicting, presenting difficult balances which must be achieved. One example of a challenging requirements balance or trade is shaping for stealth versus aircrew vision. The large number of requirements involved may be grouped in a variety of areas including man-machine interface; structural integration with the airframe; combat hazards; environmental exposures; and supportability. Some individual requirements by themselves pose very difficult, severely nonlinear analysis problems. One such complex problem is that associated with the dynamic structural response resulting from high energy bird impact. An improved analytical capability for soft-body impact simulation was developed.

Structure of the Mtb CarD/RNAP β-lobes complex reveals the molecular basis of interaction and presents a distinct DNA-binding domain for Mtb CarD.

PubMed

Gulten, Gulcin; Sacchettini, James C

2013-10-08

CarD from Mycobacterium tuberculosis (Mtb) is an essential protein shown to be involved in stringent response through downregulation of rRNA and ribosomal protein genes. CarD interacts with the β-subunit of RNAP and this interaction is vital for Mtb's survival during the persistent infection state. We have determined the crystal structure of CarD in complex with the RNAP β-subunit β1 and β2 domains at 2.1 Å resolution. The structure reveals the molecular basis of CarD/RNAP interaction, providing a basis to further our understanding of RNAP regulation by CarD. The structural fold of the CarD N-terminal domain is conserved in RNAP interacting proteins such as TRCF-RID and CdnL, and displays similar interactions to the predicted homology model based on the TRCF/RNAP β1 structure. Interestingly, the structure of the C-terminal domain, which is required for complete CarD function in vivo, represents a distinct DNA-binding fold. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dynamin Forms a Src Kinase–sensitive Complex with Cbl and Regulates Podosomes and Osteoclast Activity

PubMed Central

Bruzzaniti, Angela; Neff, Lynn; Sanjay, Archana; Horne, William C.; De Camilli, Pietro; Baron, Roland

2005-01-01

Podosomes are highly dynamic actin-containing adhesion structures found in osteoclasts, macrophages, and Rous sarcoma virus (RSV)-transformed fibroblasts. After integrin engagement, Pyk2 recruits Src and the adaptor protein Cbl, forming a molecular signaling complex that is critical for cell migration, and deletion of any molecule in this complex disrupts podosome ring formation and/or decreases osteoclast migration. Dynamin, a GTPase essential for endocytosis, is also involved in actin cytoskeleton remodeling and is localized to podosomes where it has a role in actin turnover. We found that dynamin colocalizes with Cbl in the actin-rich podosome belt of osteoclasts and that dynamin forms a complex with Cbl in osteoclasts and when overexpressed in 293VnR or SYF cells. The association of dynamin with Cbl in osteoclasts was decreased by Src tyrosine kinase activity and we found that destabilization of the dynamin-Cbl complex involves the recruitment of Src through the proline-rich domain of Cbl. Overexpression of dynamin increased osteoclast bone resorbing activity and migration, whereas overexpression of dynK44A decreased osteoclast resorption and migration. These studies suggest that dynamin, Cbl, and Src coordinately participate in signaling complexes that are important in the assembly and remodeling of the actin cytoskeleton, leading to changes in osteoclast adhesion, migration, and resorption. PMID:15872089

Strategic Decision Making Paradigms: A Primer for Senior Leaders

DTIC Science & Technology

2009-07-01

decision making . STRATEGIC DECISION MAKING Strategic Change: There are several strategic...influenced by stakeholders outside of the organization. The Ontology of Strategic Decision Making . Strategic decisions are non-routine and involve...Coates USAWC, July 2009 5 The Complexity of Strategic Decision Making Strategic decisions entail “ill-structured,”6 “messy” or

HDAC Inhibition Modulates Hippocampus-Dependent Long-Term Memory for Object Location in a CBP-Dependent Manner

ERIC Educational Resources Information Center

Haettig, Jakob; Stefanko, Daniel P.; Multani, Monica L.; Figueroa, Dario X.; McQuown, Susan C.; Wood, Marcelo A.

2011-01-01

Transcription of genes required for long-term memory not only involves transcription factors, but also enzymatic protein complexes that modify chromatin structure. Chromatin-modifying enzymes, such as the histone acetyltransferase (HAT) CREB (cyclic-AMP response element binding) binding protein (CBP), are pivotal for the transcriptional regulation…

Challenges to interdisciplinary discourse

Treesearch

David N. Wear

1999-01-01

Many of the world's critical problems involve hu­man interactions with nature and their long-term implications for environmental quality and the sustainability of resource/ecological systems. These problems are complex defined by the collective behaviors of people as well as by the structure and function of ecosystems suggesting that both the social and the...

Will concern for biodiversity spell doom to tropical forest management?

Treesearch

A.E. Lugo

1999-01-01

Arguments against active tropical management are analyzed in light of available data and new research that shows tropical forests to be more resilient after disturbances than previously thought. Tropical forest management involves a diverse array of human activity embedded in a complex social and natural environment. Within this milieu, forest structure and composition...

Sentence Repetition in Adolescents with Specific Language Impairments and Autism: An Investigation of Complex Syntax

ERIC Educational Resources Information Center

Riches, N. G.; Loucas, T.; Baird, G.; Charman, T.; Simonoff, E.

2010-01-01

Background: Recent studies have indicated that many children with autism spectrum disorders present with language difficulties that are similar to those of children with specific language impairments, leading some to argue for similar structural deficits in these two disorders. Aims: Repetition of sentences involving long-distance dependencies was…

Identifying Systems of Interaction in Mathematical Engagement

ERIC Educational Resources Information Center

Brown, Bruce J. L.

2014-01-01

Mathematical engagement is a complex process of interaction between the person and the world. This interaction is strongly influenced by the concepts and structure of the mathematical field, by the practical and symbolic tools of mathematics and by the focus of investigation in the world. This paper reports on research that involves a detailed…

Pathways to Adulthood: Educational Opportunities, Motivation and Attainment in Times of Social Change

ERIC Educational Resources Information Center

Schoon, Ingrid, Ed.; Silbereisen, Rainer K., Ed.

2017-01-01

Among the many life transitions that individuals must master throughout their lives, the transition to adulthood ranks very high in terms of importance, complexity and uniqueness. It involves the completion of education, and the assumption of new social roles and responsibilities, at a time when previous institutional structures that guided…

Exploring Essential Conditions: A Commentary on Bull et al. (2008)

ERIC Educational Resources Information Center

Borthwick, Arlene; Hansen, Randall; Gray, Lucy; Ziemann, Irina

2008-01-01

The editorial by Bull et al. (2008) on connections between informal and formal learning made explicit one element of solving what Koehler and Mishra (2008) termed a "wicked problem." This wicked (complex, ill-structured) problem involves working with teachers for effective integration of technology in support of student learning. The…

Receptor kinase signalling in plants and animals: distinct molecular systems with mechanistic similarities.

PubMed

Cock, J Mark; Vanoosthuyse, Vincent; Gaude, Thierry

2002-04-01

Plant genomes encode large numbers of receptor kinases that are structurally related to the tyrosine and serine/threonine families of receptor kinase found in animals. Here, we describe recent advances in the characterisation of several of these plant receptor kinases at the molecular level, including the identification of receptor complexes, small polypeptide ligands and cytosolic proteins involved in signal transduction and receptor downregulation. Phylogenetic analysis indicates that plant receptor kinases have evolved independently of the receptor kinase families found in animals. This hypothesis is supported by functional studies that have revealed differences between receptor kinase signalling in plants and animals, particularly concerning their interactions with cytosolic proteins. Despite these dissimilarities, however, plant and animal receptor kinases share many common features, such as their single membrane-pass structure, their inclusion in membrane-associated complexes, the involvement of dimerisation and trans autophosphorylation in receptor activation, and the existence of inhibitors and phosphatases that downregulate receptor activity. These points of convergence may represent features that are essential for a functional receptor-kinase signalling system.

Exploring Anti-Prion Glyco-Based and Aromatic Scaffolds: A Chemical Strategy for the Quality of Life.

PubMed

Blázquez-Sánchez, María Teresa; de Matos, Ana M; Rauter, Amélia P

2017-05-24

Prion diseases are fatal neurodegenerative disorders caused by protein misfolding and aggregation, affecting the brain progressively and consequently the quality of life. Alzheimer's is also a protein misfolding disease, causing dementia in over 40 million people worldwide. There are no therapeutics able to cure these diseases. Cellular prion protein is a high-affinity binding partner of amyloid β (Aβ) oligomers, the most toxic species in Alzheimer's pathology. These findings motivate the development of new chemicals for a better understanding of the events involved. Disease control is far from being reached by the presently known therapeutics. In this review we describe the synthesis and mode of action of molecular entities with intervention in prion diseases' biological processes and, if known, their role in Alzheimer's. A diversity of structures is covered, based on glycans, steroids and terpenes, heterocycles, polyphenols, most of them embodying aromatics and a structural complexity. These molecules may be regarded as chemical tools to foster the understanding of the complex mechanisms involved, and to encourage the scientific community towards further developments for the cure of these devastating diseases.

Resection and reconstruction of pelvic and extremity soft tissue sarcomas with major vascular involvement: Current concepts

PubMed Central

McGoldrick, Niall P; Butler, Joseph S; Lavelle, Maire; Sheehan, Stephen; Dudeney, Sean; O'Toole, Gary C

2016-01-01

Soft tissue sarcoma accounts for approximately 1% of all cancers diagnosed annually in the United States. When these rare malignant mesodermal tumours arise in the pelvis and extremities, they may potentially encase or invade large calibre vascular structures. This presents a major challenge in terms of safe excision while also leaving acceptable surgical margins. In recent times, the trend has been towards limb salvage with vascular reconstruction in preference to amputation. Newer orthopaedic and vascular reconstructive techniques including both synthetic and autogenous graft reconstruction have made complex limb-salvage surgery feasible. Despite this, limb-salvage surgery with concomitant vascular reconstruction remains associated with higher rates of post-operative complications including infection and amputation. In this review we describe the initial presentation and investigation of patients presenting with soft tissue sarcomas in the pelvis and extremities, which involve vascular structures. We further discuss the key surgical reconstructive principles and techniques available for the management of these complex tumours, drawn from our institution’s experience as a national tertiary referral sarcoma service. PMID:27190757

Resection and reconstruction of pelvic and extremity soft tissue sarcomas with major vascular involvement: Current concepts.

PubMed

McGoldrick, Niall P; Butler, Joseph S; Lavelle, Maire; Sheehan, Stephen; Dudeney, Sean; O'Toole, Gary C

2016-05-18

Soft tissue sarcoma accounts for approximately 1% of all cancers diagnosed annually in the United States. When these rare malignant mesodermal tumours arise in the pelvis and extremities, they may potentially encase or invade large calibre vascular structures. This presents a major challenge in terms of safe excision while also leaving acceptable surgical margins. In recent times, the trend has been towards limb salvage with vascular reconstruction in preference to amputation. Newer orthopaedic and vascular reconstructive techniques including both synthetic and autogenous graft reconstruction have made complex limb-salvage surgery feasible. Despite this, limb-salvage surgery with concomitant vascular reconstruction remains associated with higher rates of post-operative complications including infection and amputation. In this review we describe the initial presentation and investigation of patients presenting with soft tissue sarcomas in the pelvis and extremities, which involve vascular structures. We further discuss the key surgical reconstructive principles and techniques available for the management of these complex tumours, drawn from our institution's experience as a national tertiary referral sarcoma service.

'We didn't know anything, it was a mess!' Emergent structures and the effectiveness of a rescue operation multi-team system.

PubMed

Fleştea, Alina Maria; Fodor, Oana Cătălina; Curşeu, Petru Lucian; Miclea, Mircea

2017-01-01

Multi-team systems (MTS) are used to tackle unpredictable events and to respond effectively to fast-changing environmental contingencies. Their effectiveness is influenced by within as well as between team processes (i.e. communication, coordination) and emergent phenomena (i.e. situational awareness). The present case study explores the way in which the emergent structures and the involvement of bystanders intertwine with the dynamics of processes and emergent states both within and between the component teams. Our findings show that inefficient transition process and the ambiguous leadership generated poor coordination and hindered the development of emergent phenomena within the whole system. Emergent structures and bystanders substituted leadership functions and provided a pool of critical resources for the MTS. Their involvement fostered the emergence of situational awareness and facilitated contingency planning processes. However, bystander involvement impaired the emergence of cross-understandings and interfered with coordination processes between the component teams. Practitioner Summary: Based on a real emergency situation, the present research provides important theoretical and practical insights about the role of bystander involvement in the dynamics of multi-team systems composed to tackle complex tasks and respond to fast changing and unpredictable environmental contingencies.

Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition

PubMed Central

Kumar, Prashant; Reithofer, Viktoria; Reisinger, Manuel; Wallner, Silvia; Pavkov-Keller, Tea; Macheroux, Peter; Gruber, Karl

2016-01-01

Human dipeptidyl-peptidase III (hDPP III) is a zinc-dependent hydrolase cleaving dipeptides off the N-termini of various bioactive peptides. Thus, the enzyme is likely involved in a number of physiological processes such as nociception and is also implicated in several forms of cancer. We present high-resolution crystal structures of hDPP III in complex with opioid peptides (Met-and Leu-enkephalin, endomorphin-2) as well as with angiotensin-II and the peptide inhibitor IVYPW. These structures confirm the previously reported large conformational change of the enzyme upon ligand binding and show that the structure of the closed conformation is independent of the nature of the bound peptide. The overall peptide-binding mode is also conserved ensuring the correct positioning of the scissile peptide bond with respect to the catalytic zinc ion. The structure of the angiotensin-II complex shows, how longer peptides are accommodated in the binding cleft of hDPP III. Differences in the binding modes allow a distinction between real substrates and inhibitory peptides or “slow” substrates. The latter displace a zinc bound water molecule necessitating the energetically much less favoured anhydride mechanism as opposed to the favoured promoted-water mechanism. The structural data also form the necessary framework for the design of specific hDPP III inhibitors. PMID:27025154

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

Learning and memory: Steroids and epigenetics.

PubMed

Colciago, Alessandra; Casati, Lavinia; Negri-Cesi, Paola; Celotti, Fabio

2015-06-01

Memory formation and utilization is a complex process involving several brain structures in conjunction as the hippocampus, the amygdala and the adjacent cortical areas, usually defined as medial temporal lobe structures (MTL). The memory processes depend on the formation and modulation of synaptic connectivity affecting synaptic strength, synaptic plasticity and synaptic consolidation. The basic neurocognitive mechanisms of learning and memory are shortly recalled in the initial section of this paper. The effect of sex hormones (estrogens, androgens and progesterone) and of adrenocortical steroids on several aspects of memory processes are then analyzed on the basis of animal and human studies. A specific attention has been devoted to the different types of steroid receptors (membrane or nuclear) involved and on local metabolic transformations when required. The review is concluded by a short excursus on the steroid activated epigenetic mechanisms involved in memory formation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Atomic resolution model of the antibody Fc interaction with the complement C1q component.

PubMed

Schneider, Sebastian; Zacharias, Martin

2012-05-01

The globular C1q heterotrimer is a subunit of the C1 complement factor. Binding of the C1q subunit to the constant (Fc) part of antibody molecules is a first step and key event of complement activation. Although three-dimensional structures of C1q and antibody Fc subunits have been determined experimentally no atomic resolution structure of the C1q-Fc complex is known so far. Based on systematic protein-protein docking searches and Molecular Dynamics simulations a structural model of the C1q-IgG1-Fc-binding geometry has been obtained. The structural model is compatible with available experimental data on the interaction between the two partner proteins. It predicts a binding geometry that involves mainly the B-subunit of the C1q-trimer and both subunits of the IgG1-Fc-dimer with small conformational adjustments with respect to the unbound partners to achieve high surface complementarity. In addition to several charge-charge and polar contacts in the rim region of the interface it also involves nonpolar contacts between the two proteins and is compatible with the carbohydrate moiety of the Fc subunit. The model for the complex structure provides a working model for rationalizing available biochemical data on this important interaction and can form the basis for the design of Fc variants with a greater capacity to activate the complement system for example on binding to cancer cells or other target structures. Copyright © 2012 Elsevier Ltd. All rights reserved.

Hydrolysis mechanisms of BNPP mediated by facial copper(II) complexes bearing single alkyl guanidine pendants: cooperation between the metal centers and the guanidine pendants.

PubMed

Zhang, Xuepeng; Liu, Xueping; Phillips, David Lee; Zhao, Cunyuan

2016-01-28

The hydrolysis mechanisms of DNA dinucleotide analogue BNPP(-) (bis(p-nitrophenyl) phosphate) catalyzed by mononuclear/dinuclear facial copper(ii) complexes bearing single alkyl guanidine pendants were investigated using density functional theory (DFT) calculations. Active catalyst forms have been investigated and four different reaction modes are proposed accordingly. The [Cu2(L(1))2(μ-OH)](3+) (L(1) is 1-(2-guanidinoethyl)-1,4,7-triazacyclononane) complex features a strong μ-hydroxo mediated antiferromagnetic coupling between the bimetallic centers and the corresponding more stable open-shell singlet state. Three different reaction modes involving two catalysts and a substrate were proposed for L(1) entries and the mode 1 in which an inter-complex nucleophilic attack by a metal bound hydroxide was found to be more favorable. In the L(3)-involved reactions (L(3) is 1-(4-guanidinobutyl)-1,4,7-triazacyclononane), the reaction mode in which an in-plane intracomplex scissoring-like nucleophilic attack by a Cu(ii)-bound hydroxide was found to be more competitive. The protonated guanidine pendants in each proposed mechanism were found to play crucial roles in stabilizing the reaction structures via hydrogen bonds and in facilitating the departure of the leaving group via electrostatic attraction. The calculated results are consistent with the experimental observations that the Cu(ii)-L(3) complexes are hydrolytically more favorable than their L(1)-involved counterparts.

A Sponge-like Structure Involved in the Association and Transport of Maternal Products during Drosophila Oogenesis

PubMed Central

Wilsch-Bräuninger, Michaela; Schwarz, Heinz; Nüsslein-Volhard, Christiane

1997-01-01

Localization of maternally provided RNAs during oogenesis is required for formation of the antero–posterior axis of the Drosophila embryo. Here we describe a subcellular structure in nurse cells and oocytes which may function as an intracellular compartment for assembly and transport of maternal products involved in RNA localization. This structure, which we have termed “sponge body,” consists of ER-like cisternae, embedded in an amorphous electron-dense mass. It lacks a surrounding membrane and is frequently associated with mitochondria. The sponge bodies are not identical to the Golgi complexes. We suggest that the sponge bodies are homologous to the mitochondrial cloud in Xenopus oocytes, a granulo-fibrillar structure that contains RNAs involved in patterning of the embryo. Exuperantia protein, the earliest factor known to be required for the localization of bicoid mRNA to the anterior pole of the Drosophila oocyte, is highly enriched in the sponge bodies but not an essential structural component of these. RNA staining indicates that sponge bodies contain RNA. However, neither the intensity of this staining nor the accumulation of Exuperantia in the sponge bodies is dependent on the amount of bicoid mRNA present in the ovaries. Sponge bodies surround nuage, a possible polar granule precursor. Microtubules and microfilaments are not present in sponge bodies, although transport of the sponge bodies through the cells is implied by their presence in cytoplasmic bridges. We propose that the sponge bodies are structures that, by assembly and transport of included molecules or associated structures, are involved in localization of mRNAs in Drosophila oocytes. PMID:9348297

Gas-phase nitrosation of ethylene and related events in the C2H4NO+ landscape.

PubMed

Gerbaux, Pascal; Dechamps, Noemie; Flammang, Robert; Nam, Pham Cam; Nguyen, Minh Tho; Djazi, Fayçal; Berruyer, Florence; Bouchoux, Guy

2008-06-19

The C2H4NO(+) system has been examined by means of quantum chemical calculations using the G2 and G3B3 approaches and tandem mass spectrometry experiments. Theoretical investigation of the C2H4NO(+) potential-energy surface includes 19 stable C2H4NO(+) structures and a large set of their possible interconnections. These computations provide insights for the understanding of the (i) addition of the nitrosonium cation NO(+) to the ethylene molecule, (ii) skeletal rearrangements evidenced in previous experimental studies on comparable systems, and (iii) experimental identification of new C2H4NO(+) structures. It is predicted from computation that gas-phase nitrosation of ethylene may produce C2H4(*)NO(+) adducts, the most stable structure of which is a pi-complex, 1, stabilized by ca. 65 kJ/mol with respect to its separated components. This complex was produced in the gas phase by a transnitrosation process involving as reactant a complex between water and NO(+) (H2O.NO(+)) and the ethylene molecule and fully characterized by collisional experiments. Among the other C 2H 4NO (+) structures predicted by theory to be protected against dissociation or isomerization by significant energy barriers, five were also experimentally identified. These finding include structures CH3CHNO(+) (5), CH 3CNOH (+) ( 8), CH3NHCO(+) (18), CH3NCOH(+) (19), and an ion/neutral complex CH2O...HCNH(+) (12).

Bound vector solitons and soliton complexes for the coupled nonlinear Schrödinger equations.

PubMed

Sun, Zhi-Yuan; Gao, Yi-Tian; Yu, Xin; Liu, Wen-Jun; Liu, Ying

2009-12-01

Dynamic features describing the collisions of the bound vector solitons and soliton complexes are investigated for the coupled nonlinear Schrödinger (CNLS) equations, which model the propagation of the multimode soliton pulses under some physical situations in nonlinear fiber optics. Equations of such type have also been seen in water waves and plasmas. By the appropriate choices of the arbitrary parameters for the multisoliton solutions derived through the Hirota bilinear method, the periodic structures along the propagation are classified according to the relative relations of the real wave numbers. Furthermore, parameters are shown to control the intensity distributions and interaction patterns for the bound vector solitons and soliton complexes. Transformations of the soliton types (shape changing with intensity redistribution) during the collisions of those stationary structures with the regular one soliton are discussed, in which a class of inelastic properties is involved. Discussions could be expected to be helpful in interpreting such structures in the multimode nonlinear fiber optics and equally applied to other systems governed by the CNLS equations, e.g., the plasma physics and Bose-Einstein condensates.

Self-Assembly and Responsiveness of Polypeptide-Based Star and Triblock Copolymers

NASA Astrophysics Data System (ADS)

Savin, Daniel

This study involves the bottom-up design and tunability of responsive, peptide-based block polymers. The self-assembly of amphiphilic block polymers is dictated primarily by the balance between the hydrophobic core volume and the hydrophilic corona. In these studies, amphiphilic triblock and star copolymers containing poly(lysine) (PK), poly(leucine) (PL) and poly(glutamic acid) (PE) were synthesized and their solution properties studied using dynamic light scattering, circular dichroism spectroscopy and transmission electron microscopy. The peptide block in these structures can serve to introduce pH responsiveness (in the case of PK and PE), or can facilitate the formation of elongated or kinetically-trapped structures (in the case of PL.) This talk will present some recent studies in solution morphology transitions that occur in these materials under varying solution conditions. As the topological complexity of the polymers increases from diblock to linear triblock or star polymers, the solution morphology and response becomes much more complex. We present a systematic series of structures, with increasing complexity, that have applications as passive and active delivery vehicles, hydrogels, and responsive viscosity modifiers. NSF CHE-1539347.

Structural basis for midbody targeting of spastin by the ESCRT-III protein CHMP1B

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

Yang, Dong; Rimanchi, Neggy; Renvoise, Benoit

2009-01-15

The endosomal sorting complex required for transport (ESCRT) machinery, including ESCRT-III, localizes to the midbody and participates in the membrane-abscission step of cytokinesis. The ESCRT-III protein charged multivesicular body protein 1B (CHMP1B) is required for recruitment of the MIT domain-containing protein spastin, a microtubule-severing enzyme, to the midbody. The 2.5-{angstrom} structure of the C-terminal tail of CHMP1B with the MIT domain of spastin reveals a specific, high-affinity complex involving a noncanonical binding site between the first and third helices of the MIT domain. The structural interface is twice as large as that of the MIT domain of the VPS4-CHMP complex,more » consistent with the high affinity of the interaction. A series of unique hydrogen-bonding interactions and close packing of small side chains discriminate against the other ten human ESCRT-III subunits. Point mutants in the CHMP1B binding site of spastin block recruitment of spastin to the midbody and impair cytokinesis.« less

Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications

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

Hou, Gao-Lei; Valiev, Marat; Wang, Xue-Bin

Dicarboxylic acids represent an important class of water-soluble organic compounds found in the atmosphere. In this work we are studying properties of dicarboxylic acid homodimer complexes (HO 2(CH 2) nCO 2 -[HO 2(CH 2) nCO 2H], n = 0-12), as potentially important intermediates in aerosol formation processes. Our approach is based on experimental data from negative ion photoelectron spectra of the dimer complexes combined with updated measurements of the corresponding monomer species. These results are analyzed with quantum-mechanical calculations, which provide further information about equilibrium structures, thermochemical parameters associated with the complex formation, and evaporation rates. We find that uponmore » formation of the dimer complexes the electron binding energies increase by 1.3–1.7 eV (30.0–39.2 kcal/mol), indicating increased stability of the dimerized complexes. Calculations indicate that these dimer complexes are characterized by the presence of strong intermolecular hydrogen bonds with high binding energies and are thermodynamically favorable to form with low evaporation rates. Comparison with previously studied HSO 4 -[HO 2(CH 2) 2CO 2H] complex (J. Phys. Chem. Lett. 2013, 4, 779-785) shows that HO 2(CH 2) 2CO 2 -[HO 2(CH 2) 2CO 2H] has very similar thermochemical properties. These results imply that dicarboxylic acids not only can contribute to the heterogeneous complexes formation involving sulfuric acid and dicarboxylic acids, but also can promote the formation of homogenous complexes by involving dicarboxylic acids themselves.« less

Dynamics of nanoparticle-protein corona complex formation: analytical results from population balance equations.

PubMed

Darabi Sahneh, Faryad; Scoglio, Caterina; Riviere, Jim

2013-01-01

Nanoparticle-protein corona complex formation involves absorption of protein molecules onto nanoparticle surfaces in a physiological environment. Understanding the corona formation process is crucial in predicting nanoparticle behavior in biological systems, including applications of nanotoxicology and development of nano drug delivery platforms. This paper extends the modeling work in to derive a mathematical model describing the dynamics of nanoparticle corona complex formation from population balance equations. We apply nonlinear dynamics techniques to derive analytical results for the composition of nanoparticle-protein corona complex, and validate our results through numerical simulations. The model presented in this paper exhibits two phases of corona complex dynamics. In the first phase, proteins rapidly bind to the free surface of nanoparticles, leading to a metastable composition. During the second phase, continuous association and dissociation of protein molecules with nanoparticles slowly changes the composition of the corona complex. Given sufficient time, composition of the corona complex reaches an equilibrium state of stable composition. We find analytical approximate formulae for metastable and stable compositions of corona complex. Our formulae are very well-structured to clearly identify important parameters determining corona composition. The dynamics of biocorona formation constitute vital aspect of interactions between nanoparticles and living organisms. Our results further understanding of these dynamics through quantitation of experimental conditions, modeling results for in vitro systems to better predict behavior for in vivo systems. One potential application would involve a single cell culture medium related to a complex protein medium, such as blood or tissue fluid.

Triangle network motifs predict complexes by complementing high-error interactomes with structural information.

PubMed

Andreopoulos, Bill; Winter, Christof; Labudde, Dirk; Schroeder, Michael

2009-06-27

A lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles. We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS). PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes. Given high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that relatively little structural information would be sufficient for finding complexes involving most of the proteins and interactions in a typical PPIN.

Triangle network motifs predict complexes by complementing high-error interactomes with structural information

PubMed Central

Andreopoulos, Bill; Winter, Christof; Labudde, Dirk; Schroeder, Michael

2009-01-01

Background A lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles. Results We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS). PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes. Conclusion Given high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that relatively little structural information would be sufficient for finding complexes involving most of the proteins and interactions in a typical PPIN. PMID:19558694

Structure elucidation and absolute stereochemistry of isomeric monoterpene chromane esters.

PubMed

Batista, João M; Batista, Andrea N L; Mota, Jonas S; Cass, Quezia B; Kato, Massuo J; Bolzani, Vanderlan S; Freedman, Teresa B; López, Silvia N; Furlan, Maysa; Nafie, Laurence A

2011-04-15

Six novel monoterpene chromane esters were isolated from the aerial parts of Peperomia obtusifolia (Piperaceae) using chiral chromatography. This is the first time that chiral chromane esters of this kind, ones with a tethered chiral terpene, have been isolated in nature. Due to their structural features, it is not currently possible to assess directly their absolute stereochemistry using any of the standard classical approaches, such as X-ray crystallography, NMR, optical rotation, or electronic circular dichroism (ECD). Herein we report the absolute configuration of these molecules, involving four chiral centers, using vibrational circular dichroism (VCD) and density functional theory (DFT) (B3LYP/6-31G*) calculations. This work further reinforces the capability of VCD to determine unambiguously the absolute configuration of structurally complex molecules in solution, without crystallization or derivatization, and demonstrates the sensitivity of VCD to specify the absolute configuration for just one among a number of chiral centers. We also demonstrate the sufficiency of using the so-called inexpensive basis set 6-31G* compared to the triple-ζ basis set TZVP for absolute configuration analysis of larger molecules using VCD. Overall, this work extends our knowledge of secondary metabolites in plants and provides a straightforward way to determine the absolute configuration of complex natural products involving a chiral parent moiety combined with a chiral terpene adduct.

Plethystic vertex operators and boson-fermion correspondences

NASA Astrophysics Data System (ADS)

Fauser, Bertfried; Jarvis, Peter D.; King, Ronald C.

2016-10-01

We study the algebraic properties of plethystic vertex operators, introduced in (2010 J. Phys. A: Math. Theor. 43 405202), underlying the structure of symmetric functions associated with certain generalized universal character rings of subgroups of the general linear group, defined to stabilize tensors of Young symmetry type characterized by a partition of arbitrary shape π. Here we establish an extension of the well-known boson-fermion correspondence involving Schur functions and their associated (Bernstein) vertex operators: for each π, the modes generated by the plethystic vertex operators and their suitably constructed duals, satisfy the anticommutation relations of a complex Clifford algebra. The combinatorial manipulations underlying the results involve exchange identities exploiting the Hopf-algebraic structure of certain symmetric function series and their plethysms.

Structural characterization of the mitomycin 7-O-methyltransferase

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

Singh, Shanteri; Chang, Aram; Goff, Randal D.

2014-10-02

Mitomycins are quinone-containing antibiotics, widely used as antitumor drugs in chemotherapy. Mitomycin-7-O-methyltransferase (MmcR), a key tailoring enzyme involved in the biosynthesis of mitomycin in Streptomyces lavendulae, catalyzes the 7-O-methylation of both C9{beta}- and C9{alpha}-configured 7-hydroxymitomycins. We have determined the crystal structures of the MmcR-S-adenosylhomocysteine (SAH) binary complex and MmcR-SAH-mitomycin A (MMA) ternary complex at resolutions of 1.9 and 2.3 {angstrom}, respectively. The study revealed MmcR to adopt a common S-adenosyl-L-methionine-dependent O-methyltransferase fold and the presence of a structurally conserved active site general acid-base pair is consistent with a proton-assisted methyltransfer common to most methyltransferases. Given the importance of C7 alkylationmore » to modulate mitomycin redox potential, this study may also present a template toward the future engineering of catalysts to generate uniquely bioactive mitomycins.« less

SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

PubMed

Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio

2015-02-10

Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.

Dissecting the telomere-inner nuclear membrane interface formed in meiosis.

PubMed

Pendlebury, Devon F; Fujiwara, Yasuhiro; Tesmer, Valerie M; Smith, Eric M; Shibuya, Hiroki; Watanabe, Yoshinori; Nandakumar, Jayakrishnan

2017-12-01

Tethering telomeres to the inner nuclear membrane (INM) allows homologous chromosome pairing during meiosis. The meiosis-specific protein TERB1 binds the telomeric protein TRF1 to establish telomere-INM connectivity and is essential for mouse fertility. Here we solve the structure of the human TRF1-TERB1 interface to reveal the structural basis for telomere-INM linkage. Disruption of this interface abrogates binding and compromises telomere-INM attachment in mice. An embedded CDK-phosphorylation site within the TRF1-binding region of TERB1 provides a mechanism for cap exchange, a late-pachytene phenomenon involving the dissociation of the TRF1-TERB1 complex. Indeed, further strengthening this interaction interferes with cap exchange. Finally, our biochemical analysis implicates distinct complexes for telomere-INM tethering and chromosome-end protection during meiosis. Our studies unravel the structure, stoichiometry, and physiological implications underlying telomere-INM tethering, thereby providing unprecedented insights into the unique function of telomeres in meiosis.

The structure of control and data transfer management system for the GAMMA-400 scientific complex

NASA Astrophysics Data System (ADS)

Arkhangelskiy, A. I.; Bobkov, S. G.; Serdin, O. V.; Gorbunov, M. S.; Topchiev, N. P.

2016-02-01

A description of the control and data transfer management system for scientific instrumentation involved in the GAMMA-400 space project is given. The technical capabilities of all specialized equipment to provide the functioning of the scientific instrumentation and satellite support systems are unified in a single structure. Control of the scientific instruments is maintained using one-time pulse radio commands, as well as program commands in the form of 16-bit code words, which are transmitted via onboard control system and scientific data acquisition system. Up to 100 GByte of data per day can be transferred to the ground segment of the project. The correctness of the proposed and implemented structure, engineering solutions and electronic elemental base selection has been verified by the experimental working-off of the prototype of the GAMMA-400 scientific complex in laboratory conditions.

Paenilamicin: structure and biosynthesis of a hybrid nonribosomal peptide/polyketide antibiotic from the bee pathogen Paenibacillus larvae.

PubMed

Müller, Sebastian; Garcia-Gonzalez, Eva; Mainz, Andi; Hertlein, Gillian; Heid, Nina C; Mösker, Eva; van den Elst, Hans; Overkleeft, Herman S; Genersch, Elke; Süssmuth, Roderich D

2014-09-26

The spore-forming bacterium Paenibacillus larvae is the causative agent of American Foulbrood (AFB), a fatal disease of honey bees that occurs worldwide. Previously, we identified a complex hybrid nonribosomal peptide/polyketide synthesis (NRPS/PKS) gene cluster in the genome of P. larvae. Herein, we present the isolation and structure elucidation of the antibacterial and antifungal products of this gene cluster, termed paenilamicins. The unique structures of the paenilamicins give deep insight into the underlying complex hybrid NRPS/PKS biosynthetic machinery. Bee larval co-infection assays reveal that the paenilamicins are employed by P. larvae in fighting ecological niche competitors and are not directly involved in killing the bee larvae. Their antibacterial and antifungal activities qualify the paenilamicins as attractive candidates for drug development. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Graph Based Backtracking Algorithm for Solving General CSPs

NASA Technical Reports Server (NTRS)

Pang, Wanlin; Goodwin, Scott D.

2003-01-01

Many AI tasks can be formalized as constraint satisfaction problems (CSPs), which involve finding values for variables subject to constraints. While solving a CSP is an NP-complete task in general, tractable classes of CSPs have been identified based on the structure of the underlying constraint graphs. Much effort has been spent on exploiting structural properties of the constraint graph to improve the efficiency of finding a solution. These efforts contributed to development of a class of CSP solving algorithms called decomposition algorithms. The strength of CSP decomposition is that its worst-case complexity depends on the structural properties of the constraint graph and is usually better than the worst-case complexity of search methods. Its practical application is limited, however, since it cannot be applied if the CSP is not decomposable. In this paper, we propose a graph based backtracking algorithm called omega-CDBT, which shares merits and overcomes the weaknesses of both decomposition and search approaches.

Pupillary dynamics reveal computational cost in sentence planning.

PubMed

Sevilla, Yamila; Maldonado, Mora; Shalóm, Diego E

2014-01-01

This study investigated the computational cost associated with grammatical planning in sentence production. We measured people's pupillary responses as they produced spoken descriptions of depicted events. We manipulated the syntactic structure of the target by training subjects to use different types of sentences following a colour cue. The results showed higher increase in pupil size for the production of passive and object dislocated sentences than for active canonical subject-verb-object sentences, indicating that more cognitive effort is associated with more complex noncanonical thematic order. We also manipulated the time at which the cue that triggered structure-building processes was presented. Differential increase in pupil diameter for more complex sentences was shown to rise earlier as the colour cue was presented earlier, suggesting that the observed pupillary changes are due to differential demands in relatively independent structure-building processes during grammatical planning. Task-evoked pupillary responses provide a reliable measure to study the cognitive processes involved in sentence production.

Solution structures of chloroquine-ferriheme complexes modeled using MD simulation and investigated by EXAFS spectroscopy.

PubMed

Kuter, David; Streltsov, Victor; Davydova, Natalia; Venter, Gerhard A; Naidoo, Kevin J; Egan, Timothy J

2016-01-01

The interaction of chloroquine (CQ) and the μ-oxo dimer of iron(III) protoporphyrin IX (ferriheme) in aqueous solution was modeled using molecular dynamics (MD) simulations. Two models of the CQ-(μ-oxo ferriheme) complex were investigated, one involving CQ π-stacked with an unligated porphyrin face of μ-oxo ferriheme and the other in which CQ was docked between the two porphyrin rings. The feasibility of both models was tested by fitting computed structures to the experimental extended X-ray absorption fine structure (EXAFS) spectrum of the CQ-(μ-oxo ferriheme) complex in frozen aqueous solution. The docked model produced better agreement with experimental data, suggesting that this is the more likely structure in aqueous solution. The EXAFS fit indicated a longer than expected Fe-O bond of 1.87Å, accounting for the higher than expected magnetic moment of the complex. As a consequence, the asymmetric Fe-O-Fe stretch shifts much lower in frequency and was identified in the precipitated solid at 744cm(-1) with the aid of the O(18) isomer shift. Three important CQ-ferriheme interactions were identified in the docked structure. These were a hydrogen bond between the oxide bridge of μ-oxo ferriheme and the protonated quinolinium nitrogen atom of CQ; π-stacking between the quinoline ring of CQ and the porphyrin rings; and a close contact between the 7-chloro substituent of CQ and the porphyrin methyl hydrogen atoms. These interactions can be used to rationalize previously observed structure-activity relationships for quinoline-ferriheme association. Copyright © 2015 Elsevier Inc. All rights reserved.

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00980a Click here for additional data file.

PubMed Central

Aguayo-Ortiz, Rodrigo; Chávez-García, Cecilia; Straub, John E.

2017-01-01

γ-Secretase is an intramembrane-cleaving aspartyl protease that plays an essential role in the processing of a variety of integral membrane proteins. Its role in the ultimate cleavage step in the processing of amyloid precursor protein to form amyloid-β (Aβ) peptide makes it an important therapeutic target in Alzheimer's disease research. Significant recent advances have been made in structural studies of this critical membrane protein complex. However, details of the mechanism of activation of the enzyme complex remain unclear. Using a multiscale computational modeling approach, combining multiple coarse-grained microsecond dynamic trajectories with all-atom models, the structure and two conformational states of the γ-secretase complex were evaluated. The transition between enzymatic state 1 and state 2 is shown to critically depend on the protonation states of the key catalytic residues Asp257 and Asp385 in the active site domain. The active site formation, related to our γ-secretase state 2, is observed to involve a concerted movement of four transmembrane helices from the catalytic subunit, resulting in the required localization of the catalytic residues. Global analysis of the structural ensemble of the enzyme complex was used to identify collective fluctuations important to the mechanism of substrate recognition and demonstrate that the corresponding fluctuations observed were uncorrelated with structural changes associated with enzyme activation. Overall, this computational study provides essential insight into the role of structure and dynamics in the activation and function of γ-secretase. PMID:28970936

Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

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

Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert

Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This alsomore » represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.« less

Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

DOE PAGES

Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; ...

2015-06-02

Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This alsomore » represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.« less

Solubilization conditions for bovine heart mitochondrial membranes allow selective purification of large quantities of respiratory complexes I, III, and V.

PubMed

Shimada, Satoru; Maeda, Shintaro; Hikita, Masahide; Mieda-Higa, Kaoru; Uene, Shigefumi; Nariai, Yukiko; Shinzawa-Itoh, Kyoko

2018-04-24

Ascertaining the structure and functions of mitochondrial respiratory chain complexes is essential to understanding the biological mechanisms of energy conversion; therefore, numerous studies have examined these complexes. A fundamental part of that research involves devising a method for purifying samples with good reproducibility; the samples obtained need to be stable and their constituents need to retain the same structure and functions they possess when in mitochondrial membranes. Submitochondrial bovine heart particles were isolated using differential centrifugation to adjust to a membrane concentration of 46.0% (w/v) or 31.5% (w/v) based on weight. After 0.7% (w/v) deoxycholic acid, 0.4% (w/v) decyl maltoside, and 7.2% (w/v) potassium chloride were added to the mitochondrial membranes, those membranes were solubilized. At a membrane concentration of 46%, complex V was selectively solubilized, whereas at a concentration of 31.5% (w/v), complexes I and III were solubilized. Two steps-sucrose density gradient centrifugation and anion-exchange chromatography on a POROS HQ 20 μm column-enabled selective purification of samples that retained their structure and functions. These two steps enabled complexes I, III, and V to be purified in two days with a high yield. Complexes I, III, and V were stabilized with n-decyl-β-D-maltoside. A total of 200 mg-300 mg of those complexes from one bovine heart (1.1 kg muscle) was purified with good reproducibility, and the complexes retained the same functions they possessed while in mitochondrial membranes. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Structure and atomic correlations in molecular systems probed by XAS reverse Monte Carlo refinement

NASA Astrophysics Data System (ADS)

Di Cicco, Andrea; Iesari, Fabio; Trapananti, Angela; D'Angelo, Paola; Filipponi, Adriano

2018-03-01

The Reverse Monte Carlo (RMC) algorithm for structure refinement has been applied to x-ray absorption spectroscopy (XAS) multiple-edge data sets for six gas phase molecular systems (SnI2, CdI2, BBr3, GaI3, GeBr4, GeI4). Sets of thousands of molecular replicas were involved in the refinement process, driven by the XAS data and constrained by available electron diffraction results. The equilibrated configurations were analysed to determine the average tridimensional structure and obtain reliable bond and bond-angle distributions. Detectable deviations from Gaussian models were found in some cases. This work shows that a RMC refinement of XAS data is able to provide geometrical models for molecular structures compatible with present experimental evidence. The validation of this approach on simple molecular systems is particularly important in view of its possible simple extension to more complex and extended systems including metal-organic complexes, biomolecules, or nanocrystalline systems.

Functional liposomes and supported lipid bilayers: towards the complexity of biological archetypes.

PubMed

Berti, Debora; Caminati, Gabriella; Baglioni, Piero

2011-05-21

This perspective paper provides some illustrative examples on the interplay between information gathered on planar supported lipid bilayers (SLB) and unilamellar lipid vesicles (ULV) to get an integrated description of phenomena occurring at the nanoscale that involve locally bilayered structures. Similarities and differences are underlined and critically compared in terms of biomimetic fidelity and instrumental accessibility to structural and dynamical parameters, focusing on some recent reports that either explicitly address this comparison or introducing some studies that separately investigate the same process in SLB and lipid vesicles. Despite the structural similarity on the nanoscale, the different topology implies radically different characterization techniques that have evolved in sectorial and separated approaches. The quest for increasing levels of compositional complexity for bilayered systems should not result in a loss of structural and dynamical control: this is the central challenge of future research in this area, where the integrated approach highlighted in this contribution would enable improved levels of understanding. © The Owner Societies 2011

Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

PubMed

Montinaro, Francesco; Busby, George B J; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L; Capelli, Cristian

2017-01-01

The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries. Copyright © 2017 Montinaro et al.

The crystal structure of a partial mouse Notch-1 ankyrin domain: Repeats 4 through 7 preserve an ankyrin fold

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

Lubman, Olga Y.; Kopan, Raphael; Waksman, Gabriel

Folding and stability of proteins containing ankyrin repeats (ARs) is of great interest because they mediate numerous protein-protein interactions involved in a wide range of regulatory cellular processes. Notch, an ankyrin domain containing protein, signals by converting a transcriptional repression complex into an activation complex. The Notch ANK domain is essential for Notch function and contains seven ARs. Here, we present the 2.2 {angstrom} crystal structure of ARs 4-7 from mouse Notch 1 (m1ANK). These C-terminal repeats were resistant to degradation during crystallization, and their secondary and tertiary structures are maintained in the absence of repeats 1-3. The crystallized fragmentmore » adopts a typical ankyrin fold including the poorly conserved seventh AR, as seen in the Drosophila Notch ANK domain (dANK). The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation.« less

Structure of a Type-1 Secretion System ABC Transporter.

PubMed

Morgan, Jacob L W; Acheson, Justin F; Zimmer, Jochen

2017-03-07

Type-1 secretion systems (T1SSs) represent a widespread mode of protein secretion across the cell envelope in Gram-negative bacteria. The T1SS is composed of an inner-membrane ABC transporter, a periplasmic membrane-fusion protein, and an outer-membrane porin. These three components assemble into a complex spanning both membranes and providing a conduit for the translocation of unfolded polypeptides. We show that ATP hydrolysis and assembly of the entire T1SS complex is necessary for protein secretion. Furthermore, we present a 3.15-Å crystal structure of AaPrtD, the ABC transporter found in the Aquifex aeolicus T1SS. The structure suggests a substrate entry window just above the transporter's nucleotide binding domains. In addition, highly kinked transmembrane helices, which frame a narrow channel not observed in canonical peptide transporters, are likely involved in substrate translocation. Overall, the AaPrtD structure supports a polypeptide transport mechanism distinct from alternating access. Copyright © 2017 Elsevier Ltd. All rights reserved.

Insights into MHC class I peptide loading from the structure of the tapasin/ERp57 heterodimer

PubMed Central

Dong, Gang; Wearsch, Pamela A.; Peaper, David R.; Cresswell, Peter; Reinisch, Karin M.

2009-01-01

SUMMARY Tapasin is a glycoprotein critical for loading Major Histocompatibility Complex (MHC) class I molecules with high affinity peptides. It functions within the multimeric peptide-loading complex (PLC) as a disulfide-linked, stable heterodimer with the thiol oxidoreductase ERp57, and this covalent interaction is required to support optimal PLC activity. Here we present the 2.6 Å resolution structure of the tapasin/ERp57 core of the PLC. The structure reveals the basis for the stable dimerization of tapasin and ERp57 and provides the first example of a protein disulfide isomerase family member interacting with a substrate. Mutational analysis identified a conserved surface on tapasin that interacts with MHC class I molecules and is critical for the peptide loading and editing function of the tapasin-ERp57 heterodimer. By combining the tapasin/ERp57 structure with those of other defined PLC components we present a molecular model that illuminates the processes involved in MHC class I peptide loading. PMID:19119025

Crystal Structure and Functional Analysis of Homocitrate Synthase, an Essential Enzyme in Lysine Biosynthesis

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

Bulfer, Stacie L.; Scott, Erin M.; Couture, Jean-François

2010-01-12

Homocitrate synthase (HCS) catalyzes the first and committed step in lysine biosynthesis in many fungi and certain Archaea and is a potential target for antifungal drugs. Here we report the crystal structure of the HCS apoenzyme from Schizosaccharomyces pombe and two distinct structures of the enzyme in complex with the substrate 2-oxoglutarate (2-OG). The structures reveal that HCS forms an intertwined homodimer stabilized by domain-swapping between the N- and C-terminal domains of each monomer. The N-terminal catalytic domain is composed of a TIM barrel fold in which 2-OG binds via hydrogen bonds and coordination to the active site divalent metalmore » ion, whereas the C-terminal domain is composed of mixed {alpha}/{beta} topology. In the structures of the HCS apoenzyme and one of the 2-OG binary complexes, a lid motif from the C-terminal domain occludes the entrance to the active site of the neighboring monomer, whereas in the second 2-OG complex the lid is disordered, suggesting that it regulates substrate access to the active site through its apparent flexibility. Mutations of the active site residues involved in 2-OG binding or implicated in acid-base catalysis impair or abolish activity in vitro and in vivo. Together, these results yield new insights into the structure and catalytic mechanism of HCSs and furnish a platform for developing HCS-selective inhibitors.« less

Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit.

PubMed

Rudolph, Michael J; Vance, David J; Cassidy, Michael S; Rong, Yinghui; Shoemaker, Charles B; Mantis, Nicholas J

2016-08-01

In this report, we describe the X-ray crystal structures of two single domain camelid antibodies (VH H), F5 and F8, each in complex with ricin toxin's enzymatic subunit (RTA). F5 has potent toxin-neutralizing activity, while F8 has weak neutralizing activity. F5 buried a total of 1760 Å(2) in complex with RTA and made contact with three prominent secondary structural elements: α-helix B (Residues 98-106), β-strand h (Residues 113-117), and the C-terminus of α-helix D (Residues 154-156). F8 buried 1103 Å(2) in complex with RTA that was centered primarily on β-strand h. As such, the structural epitope of F8 is essentially nested within that of F5. All three of the F5 complementarity determining regions CDRs were involved in RTA contact, whereas F8 interactions were almost entirely mediated by CDR3, which essentially formed a seventh β-strand within RTA's centrally located β-sheet. A comparison of the two structures reported here to several previously reported (RTA-VH H) structures identifies putative contact sites on RTA, particularly α-helix B, associated with potent toxin-neutralizing activity. This information has implications for rational design of RTA-based subunit vaccines for biodefense. Proteins 2016; 84:1162-1172. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The Insula: A ‘Hub of Activity’ in Migraine

PubMed Central

Borsook, David; Veggeberg, Rosanna; Erpelding, Nathalie; Borra, Ronald; Linnman, Clas; Burstein, Rami; Becerra, Lino

2017-01-01

The insula, a ‘cortical hub’ buried within the lateral sulcus, is involved in a number of processes including goal-directed cognition, conscious awareness, autonomic regulation, interoception and somatosensation. While some of these processes are well known in the clinical presentation of migraine (i.e., autonomic and somatosensory alterations), other more complex behaviors in migraine, such as conscious awareness and error detection, are less well described. Since the insula processes and relays afferent inputs from brain areas involved in these functions to areas involved in higher cortical function such as frontal, temporal and parietal regions, it may be implicated as a brain region that translates the signals of altered internal milieu in migraine, along with other chronic pain conditions, through the insula into complex behaviors. Here we review how the insula function and structure is altered in migraine. As a brain region of a number of brain functions, it may serve as a model to study new potential clinical perspectives for migraine treatment. PMID:26290446

Anhidrotic ectodermal dysplasia presenting as atrophic rhinitis.

PubMed

Barman, Debasis; Mandal, Satadal; Nandi, Santanu; Banerjee, Pranabashish; Rashid, M A

2011-11-01

Ectodermal dysplasia is a complex group of familial disorders with numerous clinical characteristics, with an incidence of 7 in 10000 born alive children. Ectodermal dysplasia affects structures of ectodermal origin like the skin and its appendages as well as other non-ectodermal structures. The most common sites of involvement are the defects in the skin, hair, teeth, nails and sweat glands,which are of ectodermal origin. Though the dermatologists and paediatricians often manage such cases, we report one case of ectodermal dysplasia presenting with atrophic rhinitis.

Contamination source review for Building E3162, Edgewood Area, Aberdeen Proving Ground, Maryland

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

Miller, G.A.; Draugelis, A.K.; Rueda, J.

1995-09-01

This report was prepared by Argonne National Laboratory (ANL) to document the results of a contamination source review for Building E3162 at the Aberdeen Proving Ground (APG) in Maryland. The report may be used to assist the US Army in planning for the future use or disposition of this building. The review included a historical records search, physical inspection, photographic documentation, geophysical investigation, and collection of air samples. The field investigations were performed by ANL during 1994 and 1995. Building E3162 (APG designation) is part of the Medical Research Laboratories Building E3160 Complex. This research laboratory complex is located westmore » of Kings Creek, east of the airfield and Ricketts Point Road, and south of Kings Creek Road in the Edgewood Area of APG. The original structures in the E3160 Complex were constructed during World War 2. The complex was originally used as a medical research laboratory. Much of the research involved wound assessment involving chemical warfare agents. Building E3162 was used as a holding and study area for animals involved in non-agent burns. The building was constructed in 1952, placed on inactive status in 1983, and remains unoccupied. Analytical results from these air samples revealed no distinguishable difference in hydrocarbon and chlorinated solvent levels between the two background samples and the sample taken inside Building E3162.« less

Ischemic Ventricular Tachycardia Presenting as a Narrow Complex Tachycardia

PubMed Central

Page, Stephen P; Watts, Troy; Yeo, Wee Tiong; Mehul, Dhinoja

2014-01-01

This report describes a patient presenting with a narrow complex tachycardia in the context of prior myocardial infarction and impaired ventricular function. Electrophysiological studies confirmed ventricular tachycardia and activation and entrainment mapping demonstrated a critical isthmus within an area of scar involving the His-Purkinje system accounting for the narrow QRS morphology. This very rare case shares some similarities with upper septal ventricular tachycardia seen in patients with structurally normal hearts, but to our knowledge has not been seen previously in patients with ischemic heart disease. PMID:25057222

Structure and Reactivity of a Thermostable Prokaryotic Nitric-oxide Synthase That Forms a Long-lived Oxy-Heme Complex

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

Sudhamsu,J.; Crane, B.

2006-01-01

In an effort to generate more stable reaction intermediates involved in substrate oxidation by nitric-oxide synthases (NOSs), we have cloned, expressed, and characterized a thermostable NOS homolog from the thermophilic bacterium Geobacillus stearothermophilus (gsNOS). As expected, gsNOS forms nitric oxide (NO) from L-arginine via the stable intermediate N-hydroxy L-arginine (NOHA). The addition of oxygen to ferrous gsNOS results in long-lived heme-oxy complexes in the presence (Soret peak 427 nm) and absence (Soret peak 413 nm) of substrates L-arginine and NOHA. The substrate-induced red shift correlates with hydrogen bonding between substrate and heme-bound oxygen resulting in conversion to a ferric heme-superoxymore » species. In single turnover experiments with NOHA, NO forms only in the presence of H4B. The crystal structure of gsNOS at 3.2 A Angstroms of resolution reveals great similarity to other known bacterial NOS structures, with the exception of differences in the distal heme pocket, close to the oxygen binding site. In particular, a Lys-356 (Bacillus subtilis NOS) to Arg-365 (gsNOS) substitution alters the conformation of a conserved Asp carboxylate, resulting in movement of an Ile residue toward the heme. Thus, a more constrained heme pocket may slow ligand dissociation and increase the lifetime of heme-bound oxygen to seconds at 4 degC. Similarly, the ferric-heme NO complex is also stabilized in gsNOS. The slow kinetics of gsNOS offer promise for studying downstream intermediates involved in substrate oxidation.« less

A shift to randomness of brain oscillations in people with autism.

PubMed

Lai, Meng-Chuan; Lombardo, Michael V; Chakrabarti, Bhismadev; Sadek, Susan A; Pasco, Greg; Wheelwright, Sally J; Bullmore, Edward T; Baron-Cohen, Simon; Suckling, John

2010-12-15

Resting-state functional magnetic resonance imaging (fMRI) enables investigation of the intrinsic functional organization of the brain. Fractal parameters such as the Hurst exponent, H, describe the complexity of endogenous low-frequency fMRI time series on a continuum from random (H = .5) to ordered (H = 1). Shifts in fractal scaling of physiological time series have been associated with neurological and cardiac conditions. Resting-state fMRI time series were recorded in 30 male adults with an autism spectrum condition (ASC) and 33 age- and IQ-matched male volunteers. The Hurst exponent was estimated in the wavelet domain and between-group differences were investigated at global and voxel level and in regions known to be involved in autism. Complex fractal scaling of fMRI time series was found in both groups but globally there was a significant shift to randomness in the ASC (mean H = .758, SD = .045) compared with neurotypical volunteers (mean H = .788, SD = .047). Between-group differences in H, which was always reduced in the ASC group, were seen in most regions previously reported to be involved in autism, including cortical midline structures, medial temporal structures, lateral temporal and parietal structures, insula, amygdala, basal ganglia, thalamus, and inferior frontal gyrus. Severity of autistic symptoms was negatively correlated with H in retrosplenial and right anterior insular cortex. Autism is associated with a small but significant shift to randomness of endogenous brain oscillations. Complexity measures may provide physiological indicators for autism as they have done for other medical conditions. Copyright © 2010 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Structural basis for inhibition of TLR2 by staphylococcal superantigen-like protein 3 (SSL3)

PubMed Central

Koymans, Kirsten J.; Feitsma, Louris J.; Brondijk, T. Harma C.; Aerts, Piet C.; Lukkien, Eddie; Lössl, Philip; van Kessel, Kok P. M.; de Haas, Carla J. C.; van Strijp, Jos A. G.; Huizinga, Eric G.

2015-01-01

Toll-like receptors (TLRs) are crucial in innate recognition of invading micro-organisms and their subsequent clearance. Bacteria are not passive bystanders and have evolved complex evasion mechanisms. Staphylococcus aureus secretes a potent TLR2 antagonist, staphylococcal superantigen-like protein 3 (SSL3), which prevents receptor stimulation by pathogen-associated lipopeptides. Here, we present crystal structures of SSL3 and its complex with TLR2. The structure reveals that formation of the specific inhibitory complex is predominantly mediated by hydrophobic contacts between SSL3 and TLR2 and does not involve interaction of TLR2–glycans with the conserved LewisX binding site of SSL3. In the complex, SSL3 partially covers the entrance to the lipopeptide binding pocket in TLR2, reducing its size by ∼50%. We show that this is sufficient to inhibit binding of agonist Pam2CSK4 effectively, yet allows SSL3 to bind to an already formed TLR2–Pam2CSK4 complex. The binding site of SSL3 overlaps those of TLR2 dimerization partners TLR1 and TLR6 extensively. Combined, our data reveal a robust dual mechanism in which SSL3 interferes with TLR2 activation at two stages: by binding to TLR2, it blocks ligand binding and thus inhibits activation. Second, by interacting with an already formed TLR2–lipopeptide complex, it prevents TLR heterodimerization and downstream signaling. PMID:26283364

Oligomerization of G protein-coupled receptors: computational methods.

PubMed

Selent, J; Kaczor, A A

2011-01-01

Recent research has unveiled the complexity of mechanisms involved in G protein-coupled receptor (GPCR) functioning in which receptor dimerization/oligomerization may play an important role. Although the first high-resolution X-ray structure for a likely functional chemokine receptor dimer has been deposited in the Protein Data Bank, the interactions and mechanisms of dimer formation are not yet fully understood. In this respect, computational methods play a key role for predicting accurate GPCR complexes. This review outlines computational approaches focusing on sequence- and structure-based methodologies as well as discusses their advantages and limitations. Sequence-based approaches that search for possible protein-protein interfaces in GPCR complexes have been applied with success in several studies, but did not yield always consistent results. Structure-based methodologies are a potent complement to sequence-based approaches. For instance, protein-protein docking is a valuable method especially when guided by experimental constraints. Some disadvantages like limited receptor flexibility and non-consideration of the membrane environment have to be taken into account. Molecular dynamics simulation can overcome these drawbacks giving a detailed description of conformational changes in a native-like membrane. Successful prediction of GPCR complexes using computational approaches combined with experimental efforts may help to understand the role of dimeric/oligomeric GPCR complexes for fine-tuning receptor signaling. Moreover, since such GPCR complexes have attracted interest as potential drug target for diverse diseases, unveiling molecular determinants of dimerization/oligomerization can provide important implications for drug discovery.

Neptunium carbonato complexes in aqueous solution: an electrochemical, spectroscopic, and quantum chemical study.

PubMed

Ikeda-Ohno, Atsushi; Tsushima, Satoru; Takao, Koichiro; Rossberg, André; Funke, Harald; Scheinost, Andreas C; Bernhard, Gert; Yaita, Tsuyoshi; Hennig, Christoph

2009-12-21

The electrochemical behavior and complex structure of Np carbonato complexes, which are of major concern for the geological disposal of radioactive wastes, have been investigated in aqueous Na(2)CO(3) and Na(2)CO(3)/NaOH solutions at different oxidation states by using cyclic voltammetry, X-ray absorption spectroscopy, and density functional theory calculations. The end-member complexes of penta- and hexavalent Np in 1.5 M Na(2)CO(3) with pH = 11.7 have been determined as a transdioxo neptunyl tricarbonato complex, [NpO(2)(CO(3))(3)](n-) (n = 5 for Np(V), and 4 for Np(VI)). Hence, the electrochemical reaction of the Np(V/VI) redox couple merely results in the shortening/lengthening of bond distances mainly because of the change of the cationic charge of Np, without any structural rearrangement. This explains the observed reversible-like feature on their cyclic voltammograms. In contrast, the electrochemical oxidation of Np(V) in a highly basic carbonate solution of 2.0 M Na(2)CO(3)/1.0 M NaOH (pH > 13) yielded a stable heptavalent Np complex of [Np(VII)O(4)(OH)(2)](3-), indicating that the oxidation reaction from Np(V) to Np(VII) in the carbonate solution involves a drastic structural rearrangement from the transdioxo configuration to a square-planar-tetraoxo configuration, as well as exchanging the coordinating anions from carbonate ions (CO(3)(2-)) to hydroxide ions (OH(-)).

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.

Structural Basis for Methyl Transfer by a Radical SAM Enzyme

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

Boal, Amie K.; Grove, Tyler L.; McLaughlin, Monica I.

2014-10-02

The radical S-adenosyl-l-methionine (SAM) enzymes RlmN and Cfr methylate 23S ribosomal RNA, modifying the C2 or C8 position of adenosine 2503. The methyl groups are installed by a two-step sequence involving initial methylation of a conserved Cys residue (RlmN Cys{sup 355}) by SAM. Methyl transfer to the substrate requires reductive cleavage of a second equivalent of SAM. Crystal structures of RlmN and RlmN with SAM show that a single molecule of SAM coordinates the [4Fe-4S] cluster. Residue Cys{sup 355} is S-methylated and located proximal to the SAM methyl group, suggesting the SAM that is involved in the initial methyl transfermore » binds at the same site. Thus, RlmN accomplishes its complex reaction with structural economy, harnessing the two most important reactivities of SAM within a single site.« less

Ardnamurchan 3D cone-sheet architecture explained by a single elongate magma chamber

PubMed Central

Burchardt, Steffi; Troll, Valentin R.; Mathieu, Lucie; Emeleus, Henry C.; Donaldson, Colin H.

2013-01-01

The Palaeogene Ardnamurchan central igneous complex, NW Scotland, was a defining place for the development of the classic concepts of cone-sheet and ring-dyke emplacement and has thus fundamentally influenced our thinking on subvolcanic structures. We have used the available structural information on Ardnamurchan to project the underlying three-dimensional (3D) cone-sheet structure. Here we show that a single elongate magma chamber likely acted as the source of the cone-sheet swarm(s) instead of the traditionally accepted model of three successive centres. This proposal is supported by the ridge-like morphology of the Ardnamurchan volcano and is consistent with the depth and elongation of the gravity anomaly underlying the peninsula. Our model challenges the traditional model of cone-sheet emplacement at Ardnamurchan that involves successive but independent centres in favour of a more dynamical one that involves a single, but elongate and progressively evolving magma chamber system. PMID:24100542

Ardnamurchan 3D cone-sheet architecture explained by a single elongate magma chamber.

PubMed

Burchardt, Steffi; Troll, Valentin R; Mathieu, Lucie; Emeleus, Henry C; Donaldson, Colin H

2013-10-08

The Palaeogene Ardnamurchan central igneous complex, NW Scotland, was a defining place for the development of the classic concepts of cone-sheet and ring-dyke emplacement and has thus fundamentally influenced our thinking on subvolcanic structures. We have used the available structural information on Ardnamurchan to project the underlying three-dimensional (3D) cone-sheet structure. Here we show that a single elongate magma chamber likely acted as the source of the cone-sheet swarm(s) instead of the traditionally accepted model of three successive centres. This proposal is supported by the ridge-like morphology of the Ardnamurchan volcano and is consistent with the depth and elongation of the gravity anomaly underlying the peninsula. Our model challenges the traditional model of cone-sheet emplacement at Ardnamurchan that involves successive but independent centres in favour of a more dynamical one that involves a single, but elongate and progressively evolving magma chamber system.

The Assembly Pathway of Mitochondrial Respiratory Chain Complex I.

PubMed

Guerrero-Castillo, Sergio; Baertling, Fabian; Kownatzki, Daniel; Wessels, Hans J; Arnold, Susanne; Brandt, Ulrich; Nijtmans, Leo

2017-01-10

Mitochondrial complex I is the largest integral membrane enzyme of the respiratory chain and consists of 44 different subunits encoded in the mitochondrial and nuclear genome. Its biosynthesis is a highly complicated and multifaceted process involving at least 14 additional assembly factors. How these subunits assemble into a functional complex I and where the assembly factors come into play is largely unknown. Here, we applied a dynamic complexome profiling approach to elucidate the assembly of human mitochondrial complex I and its further incorporation into respiratory chain supercomplexes. We delineate the stepwise incorporation of all but one subunit into a series of distinct assembly intermediates and their association with known and putative assembly factors, which had not been implicated in this process before. The resulting detailed and comprehensive model of complex I assembly is fully consistent with recent structural data and the remarkable modular architecture of this multiprotein complex. Copyright © 2017 Elsevier Inc. All rights reserved.

True and masked three-coordinate T-shaped platinum(II) intermediates.

PubMed

Ortuño, Manuel A; Conejero, Salvador; Lledós, Agustí

2013-01-01

Although four-coordinate square-planar geometries, with a formally 16-electron counting, are absolutely dominant in isolated Pt(II) complexes, three-coordinate, 14-electron Pt(II) complexes are believed to be key intermediates in a number of platinum-mediated organometallic transformations. Although very few authenticated three-coordinate Pt(II) complexes have been characterized, a much larger number of complexes can be described as operationally three-coordinate in a kinetic sense. In these compounds, which we have called masked T-shaped complexes, the fourth position is occupied by a very weak ligand (agostic bond, solvent molecule or counteranion), which can be easily displaced. This review summarizes the structural features of the true and masked T-shaped Pt(II) complexes reported so far and describes synthetic strategies employed for their formation. Moreover, recent experimental and theoretical reports are analyzed, which suggest the involvement of such intermediates in reaction mechanisms, particularly C-H bond-activation processes.

Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNAArg: Pivotal Role of the D-loop.

PubMed

Stephen, Preyesh; Ye, Sheng; Zhou, Ming; Song, Jian; Zhang, Rongguang; Wang, En-Duo; Giegé, Richard; Lin, Sheng-Xiang

2018-05-25

Aminoacyl-tRNA synthetases are essential components in protein biosynthesis. Arginyl-tRNA synthetase (ArgRS) belongs to the small group of aminoacyl-tRNA synthetases requiring cognate tRNA for amino acid activation. The crystal structure of Escherichia coli (Eco) ArgRS has been solved in complex with tRNA Arg at 3.0-Å resolution. With this first bacterial tRNA complex, we are attempting to bridge the gap existing in structure-function understanding in prokaryotic tRNA Arg recognition. The structure shows a tight binding of tRNA on the synthetase through the identity determinant A20 from the D-loop, a tRNA recognition snapshot never elucidated structurally. This interaction of A20 involves 5 amino acids from the synthetase. Additional contacts via U20a and U16 from the D-loop reinforce the interaction. The importance of D-loop recognition in EcoArgRS functioning is supported by a mutagenesis analysis of critical amino acids that anchor tRNA Arg on the synthetase; in particular, mutations at amino acids interacting with A20 affect binding affinity to the tRNA and specificity of arginylation. Altogether the structural and functional data indicate that the unprecedented ArgRS crystal structure represents a snapshot during functioning and suggest that the recognition of the D-loop by ArgRS is an important trigger that anchors tRNA Arg on the synthetase. In this process, A20 plays a major role, together with prominent conformational changes in several ArgRS domains that may eventually lead to the mature ArgRS:tRNA complex and the arginine activation. Functional implications that could be idiosyncratic to the arginine identity of bacterial ArgRSs are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Uranyl extraction by N,N-dialkylamide ligands studied using static and dynamic DFT simulations.

PubMed

Sieffert, Nicolas; Wipff, Georges

2015-02-14

We report DFT static and dynamic studies on uranyl complexes [UO(2)(NO(3))x(H(2)O)(y)L(z)](2-x) involved in the uranyl extraction from water to an "oil" phase (hexane) by an amide ligand L (N,N-dimethylacetamide). Static DFT results "in solution" (continuum SMD models for water and hexane) predict that the stepwise formation of [UO(2)(NO(3))(2)L(2)] from the UO(2)(H(2)O)(5)(2+) species is energetically favourable, and allow us to compare cis/trans isomers of penta- and hexa-coordinated complexes and key intermediates in the two solvents. DFT-MD simulations of [UO(2)(NO(3))(2)L(2)], [UO(2)(NO(3))(2)(H(2)O)L(2)], and [UO(2)(NO(3))(H(2)O)L(2)](+) species in explicit solvent environments (water, hexane, or the water/hexane interface) represented at the MM or full-DFT level reveal a versatile solvent dependent binding mode of nitrates, also evidenced by metadynamics simulations. In water and at the interface, the latter exchange from bi- to monodentate, via in plane rotational motions in some cases. Remarkably, structures of complexes at the interface are more "water-like" than gas phase- or hexane-like. Thus, the order of U-O(NO(3))/U-O(L) bond distances observed in the gas phase (U-O(nit) < U-OL) is inverted at the interface and in water. Overall, the results are consistent with the experimental observation of uranyl extraction from nitric acid solutions by amide analogues (bearing "fatty" substituents), and allow us to propose possible extraction mechanisms, involving complexation of L "right at the interface". They also point to the importance of the solvent environment and the dynamics on the structure and stability of the complexes.

Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation

PubMed Central

Xu, Jiancong; Crowley, Michael F; Smith, Jeremy C

2009-01-01

The organization and assembly of the cellulosome, an extracellular multienzyme complex produced by anaerobic bacteria, is mediated by the high-affinity interaction of cohesin domains from scaffolding proteins with dockerins of cellulosomal enzymes. We have performed molecular dynamics simulations and free energy calculations on both the wild type (WT) and D39N mutant of the C. thermocellum Type I cohesin-dockerin complex in aqueous solution. The D39N mutation has been experimentally demonstrated to disrupt cohesin-dockerin binding. The present MD simulations indicate that the substitution triggers significant protein flexibility and causes a major change of the hydrogen-bonding network in the recognition strips—the conserved loop regions previously proposed to be involved in binding—through electrostatic and salt-bridge interactions between β-strands 3 and 5 of the cohesin and α-helix 3 of the dockerin. The mutation-induced subtle disturbance in the local hydrogen-bond network is accompanied by conformational rearrangements of the protein side chains and bound water molecules. Additional free energy perturbation calculations of the D39N mutation provide differences in the cohesin-dockerin binding energy, thus offering a direct, quantitative comparison with experiments. The underlying molecular mechanism of cohesin-dockerin complexation is further investigated through the free energy profile, that is, potential of mean force (PMF) calculations of WT cohesin-dockerin complex. The PMF shows a high-free energy barrier against the dissociation and reveals a stepwise pattern involving both the central β-sheet interface and its adjacent solvent-exposed loop/turn regions clustered at both ends of the β-barrel structure. PMID:19384997

Conformational Transitions in Molecular Systems

NASA Astrophysics Data System (ADS)

Bachmann, M.; Janke, W.

2008-11-01

Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

Epoxide hydrolase-lasalocid a structure provides mechanistic insight into polyether natural product biosynthesis.

PubMed

Wong, Fong T; Hotta, Kinya; Chen, Xi; Fang, Minyi; Watanabe, Kenji; Kim, Chu-Young

2015-01-14

Biosynthesis of some polyether natural products involves a kinetically disfavored epoxide-opening cyclic ether formation, a reaction termed anti-Baldwin cyclization. One such example is the biosynthesis of lasalocid A, an ionophore antibiotic polyether. During lasalocid A biosynthesis, an epoxide hydrolase, Lsd19, converts the bisepoxy polyketide intermediate into the tetrahydrofuranyl-tetrahydropyran product. We report the crystal structure of Lsd19 in complex with lasalocid A. The structure unambiguously shows that the C-terminal domain of Lsd19 catalyzes the intriguing anti-Baldwin cyclization. We propose a general mechanism for epoxide selection by ionophore polyether epoxide hydrolases.

Characterizing the Structure and Oligomerization of Major Royal Jelly Protein 1 (MRJP1) by Mass Spectrometry and Complementary Biophysical Tools.

PubMed

Mandacaru, Samuel C; do Vale, Luis H F; Vahidi, Siavash; Xiao, Yiming; Skinner, Owen S; Ricart, Carlos A O; Kelleher, Neil L; de Sousa, Marcelo Valle; Konermann, Lars

2017-03-21

Royal jelly (RJ) triggers the development of female honeybee larvae into queens. This effect has been attributed to the presence of major royal jelly protein 1 (MRJP1) in RJ. MRJP1 isolated from royal jelly is tightly associated with apisimin, a 54-residue α-helical peptide that promotes the noncovalent assembly of MRJP1 into multimers. No high-resolution structural data are available for these complexes, and their binding stoichiometry remains uncertain. We examined MRJP1/apisimin using a range of biophysical techniques. We also investigated the behavior of deglycosylated samples, as well as samples with reduced apisimin content. Our mass spectrometry (MS) data demonstrate that the native complexes predominantly exist in a (MRJP1 4 apisimin 4 ) stoichiometry. Hydrogen/deuterium exchange MS reveals that MRJP1 within these complexes is extensively disordered in the range of residues 20-265. Marginally stable secondary structure (likely antiparallel β-sheet) exists around residues 266-432. These weakly structured regions interchange with conformers that are extensively unfolded, giving rise to bimodal (EX1) isotope distributions. We propose that the native complexes have a "dimer of dimers" quaternary structure in which MRJP1 chains are bridged by apisimin. Specifically, our data suggest that apisimin acts as a linker that forms hydrophobic contacts involving the MRJP1 segment 316 VLFFGLV 322 . Deglycosylation produces large soluble aggregates, highlighting the role of glycans as aggregation inhibitors. Samples with reduced apisimin content form dimeric complexes with a (MRJP1 2 apisimin 1 ) stoichiometry. The information uncovered in this work will help pave the way toward a better understanding of the unique physiological role played by MRJP1 during queen differentiation.

Synthesis and structural characterization of lithium, sodium and potassium complexes supported by a tridentate amino-bisphenolate ligand

NASA Astrophysics Data System (ADS)

Durango-García, Clara J.; Rufino-Felipe, Ernesto; López-Cardoso, Marcela; Muñoz-Hernández, Miguel-Ángel; Montiel-Palma, Virginia

2018-07-01

Reactions of methylamino-N,N-bis(2-methylene-4,6-di-tert-butylphenol) (1) with one or two equivalents of bulk Li, Na or K metals in THF or DMSO render mono or dialkali metal complexes depending on the stoichiometric ratio of the reactants. The metal-methylamino-N-(2-methylene-4,6-tert-butylphenol)sbnd N-(2-methylene-4,6-tert-butylphenolate) complexes, 2Li, 2Na and 2K, are generated upon the substitution of a single phenol hydrogen of 1. In the solid state, complex 2Na is a dimer due to the establishment of two symmetric hydrogen bonds between two adjacent molecules. The Na center also engages into the formation of a ten-membered metallacycle ring with a butterfly-like structure. Due to dimerization, an intermolecular six-membered core is formed involving two sodium and four oxygen atoms. The weakly coordinated nitrogen atom from the ligand is nearly perpendicular to the hexagonal core. The dimetal-methylamino-N,N‧-bis(2-methylene-4,6-di-tert-butylphenolate) complexes, 3Li, 3Na and 3K result from metal substitution of the two phenol hydrogens from ligand 1. The SC-XRD structures of 3Li and 3Na are discreet, each incorporating two metal atoms in different coordination environments. Ten-membered rings with boat-boat conformations are also observed as are rhombic central M2O2 cores. The molecular structure of 3K in DMSO shows a higher degree of aggregation. It effectively comprises four K atoms, two ligand backbones and seven solvent molecules forming a central four-membered K2O2 ring perpendicular to an eight-membered structure formed also by K and O atoms spanning over the two ligand moieties.

Cationic copper (I) complexes with bulky 1,4-diaza-1,3-butadiene ligands - Synthesis, solid state structure and catalysis

NASA Astrophysics Data System (ADS)

Anga, Srinivas; Kottalanka, Ravi K.; Pal, Tigmansu; Panda, Tarun K.

2013-05-01

We report the full characterization of two glyoxal-based ligands N,N bis(diphenylmethyl)-1,4-diaza-1,3-butadiene ligand (DADPh2, 1) and more bulky N,N bis(triphenylmethyl)-1,4-diaza-1,3-butadiene ligand (DADPh3, 2) by the condensation reaction of glyoxal and diphenylmethanamine and triphenyl-methanamine respectively. The copper (I) complex of composition [Cu(DADPh2)2]PF6 (3) having two neutral bidentate N,N bis(diphenyl-methyl)-1,4-diaza-1,3-butadiene ligand was prepared by the reaction of [Cu(CH3CN)4]PF6 and 1 in 1:2 ratio in dichloromethane. In a similar reaction with N,N bis(triphenylmethyl)-1,4-diaza-1,3-butadiene ligand (2) and [Cu(CH3CN)4]PF6 in dichloromethane yielded corresponding heteroleptic copper (I) complex [Cu(DADPh3)(CH3CN)2]PF6 (4). Another copper (I) complex [Cu(DADPh2)(PPh3)]PF6 (5) can also be obtained by the one pot reaction involving ligand 1, [Cu(CH3CN)4]PF6 and triphenylphosphine. Solid state structures of all the five compounds were established by single crystal X-ray diffraction analysis. The solid state structures of the copper complexes 3-5 reveal a distorted tetrahedral geometry around the copper (I) centers. The copper complexes 3-5 were tested as catalysts for the coupling reaction of o-iodophenol and phenyl acetylene and it was observed that complex 4 exhibits the highest catalytic activity.

Structural characterization of molecular complexes formed by trimethoprim and cimitidine with 2,3,5,6-tetrachloro-1,4-benzoquinone

NASA Astrophysics Data System (ADS)

Balraj, C.; Ganesh, K.; Elango, K. P.

2011-07-01

Spectroscopic and spectrofluorimetric techniques have been employed to investigate the structure of the charge transfer (CT) complexes of Trimethoprim (TMP) and Cimitidine (CTD) drugs with 2,3,5,6-tetrachloro-1,4-benzoquinone ( p-chloranil, p-CHL). The stoichiometry of the complexes was found to be 1:2 for TMP- p-CHL system and 1:1 for CTD- p-CHL system. The thermodynamic results indicated that the formation of molecular complex between the donors and the acceptor is spontaneous and endothermic. The results of electronic spectral studies indicated that the formation constant for CTD- p-CHL system is found to be higher than that for TMP- p-CHL system. The observation is well supported by the results of fluorescence quenching studies and the association constants calculated for CTD- p-CHL system is 36.2 × 10 3 mol L -1 and that for TMP- p-CHL system is 2.6 × 10 3 mol L -1. The kinetic results, in both the cases, indicated that the interaction is first order each with respect to the concentration of the donor and the acceptor. The physico-chemical parameters viz. oscillator strength, dipole moment, ionization potential and dissociation energy of the complexes were also determined and discussed. Structural characterization of the complexes were done using FT-IR and 1H NMR spectral techniques and the results indicated that, in TMP, the free NH 2 group while in CTD the pyrazole N sbnd H moiety involves in complexation with the acceptor, p-CHL.

RNA polymerase II conserved protein domains as platforms for protein-protein interactions

PubMed Central

García-López, M Carmen

2011-01-01

RNA polymerase II establishes many protein-protein interactions with transcriptional regulators to coordinate gene expression, but little is known about protein domains involved in the contact with them. We use a new approach to look for conserved regions of the RNA pol II of S. cerevisiae located at the surface of the structure of the complex, hypothesizing that they might be involved in the interaction with transcriptional regulators. We defined five different conserved domains and demonstrate that all of them make contact with transcriptional regulators. PMID:21922063

Anomalous Putamen Volume in Children with Complex Motor Stereotypies

PubMed Central

Mahone, E. Mark; Crocetti, Deana; Tochen, Laura; Kline, Tina; Mostofsky, Stewart H.; Singer, Harvey S.

2016-01-01

Introduction Complex motor stereotypies in children are repetitive, rhythmic movements that have a predictable pattern and location, seem purposeful, but serve no obvious function, tend to be prolonged, and stop with distraction, e.g., arm/hand flapping, waving. They occur in both “primary” (otherwise typically developing) and secondary conditions. These movements are best defined as habitual behaviors and therefore pathophysiologically hypothesized to reside in premotor to posterior putamen circuits. This study sought to clarify the underlying neurobiological abnormality in children with primary complex motor stereotypies using structural neuroimaging, emphasizing brain regions hypothesized to underlie these atypical behaviors. Methods High-resolution anatomical MRI images, acquired at 3.0T, were analyzed in children ages 8–12 years (20 with primary complex motor stereotypies, 20 typically developing). Frontal lobe sub-regions and striatal structures were delineated for analysis. Results Significant reductions (p=0.045) in the stereotypies group were identified in total putamen volume, but not caudate, nucleus accumbens or frontal sub-regions. There were no group differences in total cerebral volume. Conclusion Findings of a smaller putamen provide preliminary evidence suggesting the potential involvement of the habitual pathway as the underlying anatomical site in primary complex motor stereotypies. PMID:27751663

DNA-Directed Assembly of Capture Tools for Constitutional Studies of Large Protein Complexes.

PubMed

Meyer, Rebecca; Faesen, Alex; Vogel, Katrin; Jeganathan, Sadasivam; Musacchio, Andrea; Niemeyer, Christof M

2015-06-10

Large supramolecular protein complexes, such as the molecular machinery involved in gene regulation, cell signaling, or cell division, are key in all fundamental processes of life. Detailed elucidation of structure and dynamics of such complexes can be achieved by reverse-engineering parts of the complexes in order to probe their interactions with distinctive binding partners in vitro. The exploitation of DNA nanostructures to mimic partially assembled supramolecular protein complexes in which the presence and state of two or more proteins are decisive for binding of additional building blocks is reported here. To this end, four-way DNA Holliday junction motifs bearing a fluorescein and a biotin tag, for tracking and affinity capture, respectively, are site-specifically functionalized with centromeric protein (CENP) C and CENP-T. The latter serves as baits for binding of the so-called KMN component, thereby mimicking early stages of the assembly of kinetochores, structures that mediate and control the attachment of microtubules to chromosomes in the spindle apparatus. Results from pull-down experiments are consistent with the hypothesis that CENP-C and CENP-T may bind cooperatively to the KMN network. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure-Function Relationship of the Bik1-Bim1 Complex.

PubMed

Stangier, Marcel M; Kumar, Anil; Chen, Xiuzhen; Farcas, Ana-Maria; Barral, Yves; Steinmetz, Michel O

2018-04-03

In budding yeast, the microtubule plus-end tracking proteins Bik1 (CLIP-170) and Bim1 (EB1) form a complex that interacts with partners involved in spindle positioning, including Stu2 and Kar9. Here, we show that the CAP-Gly and coiled-coil domains of Bik1 interact with the C-terminal ETF peptide of Bim1 and the C-terminal tail region of Stu2, respectively. The crystal structures of the CAP-Gly domain of Bik1 (Bik1CG) alone and in complex with an ETF peptide revealed unique, functionally relevant CAP-Gly elements, establishing Bik1CG as a specific C-terminal phenylalanine recognition domain. Unlike the mammalian CLIP-170-EB1 complex, Bik1-Bim1 forms ternary complexes with the EB1-binding motifs SxIP and LxxPTPh, which are present in diverse proteins, including Kar9. Perturbation of the Bik1-Bim1 interaction in vivo affected Bik1 localization and astral microtubule length. Our results provide insight into the role of the Bik1-Bim1 interaction for cell division, and demonstrate that the CLIP-170-EB1 module is evolutionarily flexible. Copyright © 2018 Elsevier Ltd. All rights reserved.

Damping Enhancement of Composite Panels by Inclusion of Shunted Piezoelectric Patches: A Wave-Based Modelling Approach.

PubMed

Chronopoulos, Dimitrios; Collet, Manuel; Ichchou, Mohamed

2015-02-17

The waves propagating within complex smart structures are hereby computed by employing a wave and finite element method. The structures can be of arbitrary layering and of complex geometric characteristics as long as they exhibit two-dimensional periodicity. The piezoelectric coupling phenomena are considered within the finite element formulation. The mass, stiffness and piezoelectric stiffness matrices of the modelled segment can be extracted using a conventional finite element code. The post-processing of these matrices involves the formulation of an eigenproblem whose solutions provide the phase velocities for each wave propagating within the structure and for any chosen direction of propagation. The model is then modified in order to account for a shunted piezoelectric patch connected to the composite structure. The impact of the energy dissipation induced by the shunted circuit on the total damping loss factor of the composite panel is then computed. The influence of the additional mass and stiffness provided by the attached piezoelectric devices on the wave propagation characteristics of the structure is also investigated.

Capturing a flavivirus pre-fusion intermediate.

PubMed

Kaufmann, Bärbel; Chipman, Paul R; Holdaway, Heather A; Johnson, Syd; Fremont, Daved H; Kuhn, Richard J; Diamond, Michael S; Rossmann, Michael G

2009-11-01

During cell entry of flaviviruses, low endosomal pH triggers the rearrangement of the viral surface glycoproteins to a fusion-active state that allows the release of the infectious RNA into the cytoplasm. In this work, West Nile virus was complexed with Fab fragments of the neutralizing mAb E16 and was subsequently exposed to low pH, trapping the virions in a pre-fusion intermediate state. The structure of the complex was studied by cryo-electron microscopy and provides the first structural glimpse of a flavivirus fusion intermediate near physiological conditions. A radial expansion of the outer protein layer of the virion was observed compared to the structure at pH 8. The resulting approximately 60 A-wide shell of low density between lipid bilayer and outer protein layer is likely traversed by the stem region of the E glycoprotein. By using antibody fragments, we have captured a structural intermediate of a virus that likely occurs during cell entry. The trapping of structural transition states by antibody fragments will be applicable for other processes in the flavivirus life cycle and delineating other cellular events that involve conformational rearrangements.

The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex

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

Wang, Ruiying; Zheng, Han; Preamplume, Gan

The repeat-associated mysterious proteins (RAMPs) comprise the most abundant family of proteins involved in prokaryotic immunity against invading genetic elements conferred by the clustered regularly interspaced short palindromic repeat (CRISPR) system. Cas6 is one of the first characterized RAMP proteins and is a key enzyme required for CRISPR RNA maturation. Despite a strong structural homology with other RAMP proteins that bind hairpin RNA, Cas6 distinctly recognizes single-stranded RNA. Previous structural and biochemical studies show that Cas6 captures the 5' end while cleaving the 3' end of the CRISPR RNA. Here, we describe three structures and complementary biochemical analysis of amore » noncatalytic Cas6 homolog from Pyrococcus horikoshii bound to CRISPR repeat RNA of different sequences. Our study confirms the specificity of the Cas6 protein for single-stranded RNA and further reveals the importance of the bases at Positions 5-7 in Cas6-RNA interactions. Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state.« less

Damping Enhancement of Composite Panels by Inclusion of Shunted Piezoelectric Patches: A Wave-Based Modelling Approach

PubMed Central

Chronopoulos, Dimitrios; Collet, Manuel; Ichchou, Mohamed; Shah, Tahir

2015-01-01

The waves propagating within complex smart structures are hereby computed by employing a wave and finite element method. The structures can be of arbitrary layering and of complex geometric characteristics as long as they exhibit two-dimensional periodicity. The piezoelectric coupling phenomena are considered within the finite element formulation. The mass, stiffness and piezoelectric stiffness matrices of the modelled segment can be extracted using a conventional finite element code. The post-processing of these matrices involves the formulation of an eigenproblem whose solutions provide the phase velocities for each wave propagating within the structure and for any chosen direction of propagation. The model is then modified in order to account for a shunted piezoelectric patch connected to the composite structure. The impact of the energy dissipation induced by the shunted circuit on the total damping loss factor of the composite panel is then computed. The influence of the additional mass and stiffness provided by the attached piezoelectric devices on the wave propagation characteristics of the structure is also investigated. PMID:28787972

Observing Consistency in Online Communication Patterns for User Re-Identification.

PubMed

Adeyemi, Ikuesan Richard; Razak, Shukor Abd; Salleh, Mazleena; Venter, Hein S

2016-01-01

Comprehension of the statistical and structural mechanisms governing human dynamics in online interaction plays a pivotal role in online user identification, online profile development, and recommender systems. However, building a characteristic model of human dynamics on the Internet involves a complete analysis of the variations in human activity patterns, which is a complex process. This complexity is inherent in human dynamics and has not been extensively studied to reveal the structural composition of human behavior. A typical method of anatomizing such a complex system is viewing all independent interconnectivity that constitutes the complexity. An examination of the various dimensions of human communication pattern in online interactions is presented in this paper. The study employed reliable server-side web data from 31 known users to explore characteristics of human-driven communications. Various machine-learning techniques were explored. The results revealed that each individual exhibited a relatively consistent, unique behavioral signature and that the logistic regression model and model tree can be used to accurately distinguish online users. These results are applicable to one-to-one online user identification processes, insider misuse investigation processes, and online profiling in various areas.

Structural Characterisation of Fenchone and its Complexes with Ethanol by Broadband Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Loru, Donatella; Sanz, M. Eugenia

2016-06-01

Although significant advances in understanding the human olfactory system have taken place over the last two decades, detailed information on how the interactions between odorants and olfactory receptors occur at the molecular level is still lacking. To achieve a better understanding on the molecular mechanisms involved in olfaction, we are investigating several odorants and their interactions with mimics of amino acid residues in olfactory receptors. We present here the structural characterisation of fenchone (C10H16O) and its complexes with ethanol (to mimic the side chain of serine) using a 2-8 GHz chirped-pulse Fourier transform microwave spectrometer built at King's College London. The rotational spectrum of the parent species and all the 13C and 18O isotopologues of fenchone was observed, and from the experimental rotational constants the substitution (r0) and effective (rs) structures of fenchone were determined. The rotational spectrum of fenchone-ethanol was observed by adding ethanol to the carrier gas and passing the mixture through a receptacle with fenchone. Several 1:1 complexes of fenchone-ethanol have been identified in the rotational spectrum. In all the complexes the ethanol molecule binds to the carbonyl group through an O-H· · · O hydrogen bond.

Pwp2 mediates UTP-B assembly via two structurally independent domains.

PubMed

Boissier, Fanny; Schmidt, Christina Maria; Linnemann, Jan; Fribourg, Sébastien; Perez-Fernandez, Jorge

2017-06-09

The SSU processome constitutes a large ribonucleoprotein complex involved in the early steps of ribosome biogenesis. UTP-B is one of the first multi-subunit protein complexes that associates with the pre-ribosomal RNA to form the SSU processome. To understand the molecular basis of the hierarchical assembly of the SSU-processome, we have undergone a structural and functional analysis of the UTP-B subunit Pwp2p. We show that Pwp2p is required for the proper assembly of UTP-B and for a productive association of UTP-B with pre-rRNA. These two functions are mediated by two distinct structural domains. The N-terminal domain of Pwp2p folds into a tandem WD-repeat (tWD) that associates with Utp21p, Utp18p, and Utp6p to form a core complex. The CTDs of Pwp2p and Utp21p mediate the assembly of the heterodimer Utp12p:Utp13p that is required for the stable incorporation of the UTP-B complex in the SSU processome. Finally, we provide evidence suggesting a role of UTP-B as a platform for the binding of assembly factors during the maturation of 20S rRNA precursors.

Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

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

Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

2015-12-15

All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H 2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H 2ase shows that these fusion complexes approach stable equilibrium conformations during the MDmore » simulations. Investigating protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H 2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.« less

A computational study of the chemokine receptor CXCR1 bound with interleukin-8

NASA Astrophysics Data System (ADS)

Wang, Yang; Severin Lupala, Cecylia; Wang, Ting; Li, Xuanxuan; Yun, Ji-Hye; Park, Jae-hyun; Jin, Zeyu; Lee, Weontae; Tan, Leihan; Liu, Haiguang

2018-03-01

CXCR1 is a G-protein coupled receptor, transducing signals from chemokines, in particular the interleukin-8 (IL8) molecules. This study combines homology modeling and molecular dynamics simulation methods to study the structure of CXCR1-IL8 complex. By using CXCR4-vMIP-II crystallography structure as the homologous template, CXCR1-IL8 complex structure was constructed, and then refined using all-atom molecular dynamics simulations. Through extensive simulations, CXCR1-IL8 binding poses were investigated in detail. Furthermore, the role of the N-terminal of CXCR1 receptor was studied by comparing four complex models differing in the N-terminal sequences. The results indicate that the receptor N-terminal affects the binding of IL8 significantly. With a shorter N-terminal domain, the binding of IL8 to CXCR1 becomes unstable. The homology modeling and simulations also reveal the key receptor-ligand residues involved in the electrostatic interactions known to be vital for complex formation. Project supported by the National Natural Science Foundation of China (Grant Nos. 11575021, U1530401, and U1430237) and the National Research Foundation of Korea (Grant Nos. NRF-2017R1A2B2008483 and NRF-2016R1A6A3A04010213).

Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues.

PubMed

Nikolaienko, Roman M; Hammel, Michal; Dubreuil, Véronique; Zalmai, Rana; Hall, David R; Mehzabeen, Nurjahan; Karuppan, Sebastian J; Harroch, Sheila; Stella, Salvatore L; Bouyain, Samuel

2016-10-07

Protein-tyrosine phosphatase receptor type G (RPTPγ/PTPRG) interacts in vitro with contactin-3-6 (CNTN3-6), a group of glycophosphatidylinositol-anchored cell adhesion molecules involved in the wiring of the nervous system. In addition to PTPRG, CNTNs associate with multiple transmembrane proteins and signal inside the cell via cis-binding partners to alleviate the absence of an intracellular region. Here, we use comprehensive biochemical and structural analyses to demonstrate that PTPRG·CNTN3-6 complexes share similar binding affinities and a conserved arrangement. Furthermore, as a first step to identifying PTPRG·CNTN complexes in vivo, we found that PTPRG and CNTN3 associate in the outer segments of mouse rod photoreceptor cells. In particular, PTPRG and CNTN3 form cis-complexes at the surface of photoreceptors yet interact in trans when expressed on the surfaces of apposing cells. Further structural analyses suggest that all CNTN ectodomains adopt a bent conformation and might lie parallel to the cell surface to accommodate these cis and trans binding modes. Taken together, these studies identify a PTPRG·CNTN complex in vivo and provide novel insights into PTPRG- and CNTN-mediated signaling. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

The Structure of Working Memory Abilities across the Adult Life Span

PubMed Central

Hale, Sandra; Rose, Nathan S.; Myerson, Joel; Strube, Michael J; Sommers, Mitchell; Tye-Murray, Nancy; Spehar, Brent

2010-01-01

The present study addresses three questions regarding age differences in working memory: (1) whether performance on complex span tasks decreases as a function of age at a faster rate than performance on simple span tasks; (2) whether spatial working memory decreases at a faster rate than verbal working memory; and (3) whether the structure of working memory abilities is different for different age groups. Adults, ages 20–89 (n=388), performed three simple and three complex verbal span tasks and three simple and three complex spatial memory tasks. Performance on the spatial tasks decreased at faster rates as a function of age than performance on the verbal tasks, but within each domain, performance on complex and simple span tasks decreased at the same rates. Confirmatory factor analyses revealed that domain-differentiated models yielded better fits than models involving domain-general constructs, providing further evidence of the need to distinguish verbal and spatial working memory abilities. Regardless of which domain-differentiated model was examined, and despite the faster rates of decrease in the spatial domain, age group comparisons revealed that the factor structure of working memory abilities was highly similar in younger and older adults and showed no evidence of age-related dedifferentiation. PMID:21299306

Emirati Women's Higher Educational Leadership Formation under Globalisation: Culture, Religion, Politics, and the Dialectics of Modernisation

ERIC Educational Resources Information Center

Samier, Eugenie

2015-01-01

The United Arab Emirates (UAE) is a small state transitioning from traditional communities into a modern society. This is a complex process: it involves instilling a national identity over tribal structures; modernising and technologising while retaining Islam; ensuring a high level of security while allowing for a liberal and relatively free…

In Touch with Molecules: Improving Student Learning with Innovative Molecular Models

ERIC Educational Resources Information Center

Davenport, Jodi; Silberglitt, Matt; Olson, Arthur

2013-01-01

How do viruses self-assemble? Why do DNA bases pair the way they do? What factors determine whether strands of proteins fold into sheets or helices? Why does handedness matter? A deep understanding of core issues in biology requires students to understand both complex spatial structures of molecules and the interactions involved in dynamic…

Structure Prediction of Protein Complexes

NASA Astrophysics Data System (ADS)

Pierce, Brian; Weng, Zhiping

Protein-protein interactions are critical for biological function. They directly and indirectly influence the biological systems of which they are a part. Antibodies bind with antigens to detect and stop viruses and other infectious agents. Cell signaling is performed in many cases through the interactions between proteins. Many diseases involve protein-protein interactions on some level, including cancer and prion diseases.

IRE/F Structure Analysis in Student Expositions during Nursing Practices with SDIS-GSEQ

ERIC Educational Resources Information Center

Ruiz Carrillo, Edgardo; Bravo Sánchez, Luisa; Meraz Martínez, Samuel; Cruz González, José Luiz

2017-01-01

Introduction: In clinical nursing practices where a student presents a class topic, the way in which discourse takes place has a complex formation that places him in an active subject position, but always under the coordination of the teacher. Presentations and activities carried out by the presenter in practice involve discourse-guided…

Similar Neural Correlates for Language and Sequential Learning: Evidence from Event-Related Brain Potentials

ERIC Educational Resources Information Center

Christiansen, Morten H.; Conway, Christopher M.; Onnis, Luca

2012-01-01

We used event-related potentials (ERPs) to investigate the time course and distribution of brain activity while adults performed (1) a sequential learning task involving complex structured sequences and (2) a language processing task. The same positive ERP deflection, the P600 effect, typically linked to difficult or ungrammatical syntactic…

Molecular characterization of HIV-1 Nef and ACOT8 interaction: insights from in silico structural predictions and in vitro functional assays

NASA Astrophysics Data System (ADS)

Serena, Michela; Giorgetti, Alejandro; Busato, Mirko; Gasparini, Francesca; Diani, Erica; Romanelli, Maria Grazia; Zipeto, Donato

2016-03-01

HIV-1 Nef interacts with several cellular proteins, among which the human peroxisomal thioesterase 8 (ACOT8). This interaction may be involved in the endocytosis regulation of membrane proteins and might modulate lipid composition in membrane rafts. Nef regions involved in the interaction have been experimentally characterized, whereas structural details of the ACOT8 protein are unknown. The lack of structural information hampers the comprehension of the functional consequences of the complex formation during HIV-1 infection. We modelled, through in silico predictions, the ACOT8 structure and we observed a high charge complementarity between Nef and ACOT8 surfaces, which allowed the identification of the ACOT8 putative contact points involved in the interaction. The predictions were validated by in vitro assays through the development of ACOT8 deletion mutants. Coimmunoprecipitation and immunofluorescence analyses showed that ACOT8 Arg45-Phe55 and Arg86-Pro93 regions are involved in Nef association. In addition, K91S mutation abrogated the interaction with Nef, indicating that Lys91 plays a key role in the interaction. Finally, when associated with ACOT8, Nef may be preserved from degradation. These findings improve the comprehension of the association between HIV-1 Nef and ACOT8, helping elucidating the biological effect of their interaction.

Perceptual learning modules in mathematics: enhancing students' pattern recognition, structure extraction, and fluency.

PubMed

Kellman, Philip J; Massey, Christine M; Son, Ji Y

2010-04-01

Learning in educational settings emphasizes declarative and procedural knowledge. Studies of expertise, however, point to other crucial components of learning, especially improvements produced by experience in the extraction of information: perceptual learning (PL). We suggest that such improvements characterize both simple sensory and complex cognitive, even symbolic, tasks through common processes of discovery and selection. We apply these ideas in the form of perceptual learning modules (PLMs) to mathematics learning. We tested three PLMs, each emphasizing different aspects of complex task performance, in middle and high school mathematics. In the MultiRep PLM, practice in matching function information across multiple representations improved students' abilities to generate correct graphs and equations from word problems. In the Algebraic Transformations PLM, practice in seeing equation structure across transformations (but not solving equations) led to dramatic improvements in the speed of equation solving. In the Linear Measurement PLM, interactive trials involving extraction of information about units and lengths produced successful transfer to novel measurement problems and fraction problem solving. Taken together, these results suggest (a) that PL techniques have the potential to address crucial, neglected dimensions of learning, including discovery and fluent processing of relations; (b) PL effects apply even to complex tasks that involve symbolic processing; and (c) appropriately designed PL technology can produce rapid and enduring advances in learning. Copyright © 2009 Cognitive Science Society, Inc.

The hippocampus and visual perception

PubMed Central

Lee, Andy C. H.; Yeung, Lok-Kin; Barense, Morgan D.

2012-01-01

In this review, we will discuss the idea that the hippocampus may be involved in both memory and perception, contrary to theories that posit functional and neuroanatomical segregation of these processes. This suggestion is based on a number of recent neuropsychological and functional neuroimaging studies that have demonstrated that the hippocampus is involved in the visual discrimination of complex spatial scene stimuli. We argue that these findings cannot be explained by long-term memory or working memory processing or, in the case of patient findings, dysfunction beyond the medial temporal lobe (MTL). Instead, these studies point toward a role for the hippocampus in higher-order spatial perception. We suggest that the hippocampus processes complex conjunctions of spatial features, and that it may be more appropriate to consider the representations for which this structure is critical, rather than the cognitive processes that it mediates. PMID:22529794

Network-based Arbitrated Quantum Signature Scheme with Graph State

NASA Astrophysics Data System (ADS)

Ma, Hongling; Li, Fei; Mao, Ningyi; Wang, Yijun; Guo, Ying

2017-08-01

Implementing an arbitrated quantum signature(QAS) through complex networks is an interesting cryptography technology in the literature. In this paper, we propose an arbitrated quantum signature for the multi-user-involved networks, whose topological structures are established by the encoded graph state. The determinative transmission of the shared keys, is enabled by the appropriate stabilizers performed on the graph state. The implementation of this scheme depends on the deterministic distribution of the multi-user-shared graph state on which the encoded message can be processed in signing and verifying phases. There are four parties involved, the signatory Alice, the verifier Bob, the arbitrator Trent and Dealer who assists the legal participants in the signature generation and verification. The security is guaranteed by the entanglement of the encoded graph state which is cooperatively prepared by legal participants in complex quantum networks.

Auditory psychophysics and perception.

PubMed

Hirsh, I J; Watson, C S

1996-01-01

In this review of auditory psychophysics and perception, we cite some important books, research monographs, and research summaries from the past decade. Within auditory psychophysics, we have singled out some topics of current importance: Cross-Spectral Processing, Timbre and Pitch, and Methodological Developments. Complex sounds and complex listening tasks have been the subject of new studies in auditory perception. We review especially work that concerns auditory pattern perception, with emphasis on temporal aspects of the patterns and on patterns that do not depend on the cognitive structures often involved in the perception of speech and music. Finally, we comment on some aspects of individual difference that are sufficiently important to question the goal of characterizing auditory properties of the typical, average, adult listener. Among the important factors that give rise to these individual differences are those involved in selective processing and attention.

Ligand placement based on prior structures: the guided ligand-replacement method

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

Klei, Herbert E.; Bristol-Myers Squibb, Princeton, NJ 08543-4000; Moriarty, Nigel W., E-mail: nwmoriarty@lbl.gov

2014-01-01

A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods formore » modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR leverages prior knowledge from earlier structures to facilitate ligand placement in the current structure.« less

Investigating the Structural Impacts of I64T and P311S Mutations in APE1-DNA Complex: A Molecular Dynamics Approach

PubMed Central

Doss, C. George Priya; NagaSundaram, N.

2012-01-01

Background Elucidating the molecular dynamic behavior of Protein-DNA complex upon mutation is crucial in current genomics. Molecular dynamics approach reveals the changes on incorporation of variants that dictate the structure and function of Protein-DNA complexes. Deleterious mutations in APE1 protein modify the physicochemical property of amino acids that affect the protein stability and dynamic behavior. Further, these mutations disrupt the binding sites and prohibit the protein to form complexes with its interacting DNA. Principal Findings In this study, we developed a rapid and cost-effective method to analyze variants in APE1 gene that are associated with disease susceptibility and evaluated their impacts on APE1-DNA complex dynamic behavior. Initially, two different in silico approaches were used to identify deleterious variants in APE1 gene. Deleterious scores that overlap in these approaches were taken in concern and based on it, two nsSNPs with IDs rs61730854 (I64T) and rs1803120 (P311S) were taken further for structural analysis. Significance Different parameters such as RMSD, RMSF, salt bridge, H-bonds and SASA applied in Molecular dynamic study reveals that predicted deleterious variants I64T and P311S alters the structure as well as affect the stability of APE1-DNA interacting functions. This study addresses such new methods for validating functional polymorphisms of human APE1 which is critically involved in causing deficit in repair capacity, which in turn leads to genetic instability and carcinogenesis. PMID:22384055

Chemical mapping of cytosines enzymatically flipped out of the DNA helix

PubMed Central

Liutkevičiūtė, Zita; Tamulaitis, Gintautas; Klimašauskas, Saulius

2008-01-01

Haloacetaldehydes can be employed for probing unpaired DNA structures involving cytosine and adenine residues. Using an enzyme that was structurally proven to flip its target cytosine out of the DNA helix, the HhaI DNA methyltransferase (M.HhaI), we demonstrate the suitability of the chloroacetaldehyde modification for mapping extrahelical (flipped-out) cytosine bases in protein–DNA complexes. The generality of this method was verified with two other DNA cytosine-5 methyltransferases, M.AluI and M.SssI, as well as with two restriction endonucleases, R.Ecl18kI and R.PspGI, which represent a novel class of base-flipping enzymes. Our results thus offer a simple and convenient laboratory tool for detection and mapping of flipped-out cytosines in protein–DNA complexes. PMID:18450817

Complex Patterns of Local Adaptation in Teosinte

PubMed Central

Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

2013-01-01

Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

Multiple crack detection in 3D using a stable XFEM and global optimization

NASA Astrophysics Data System (ADS)

Agathos, Konstantinos; Chatzi, Eleni; Bordas, Stéphane P. A.

2018-02-01

A numerical scheme is proposed for the detection of multiple cracks in three dimensional (3D) structures. The scheme is based on a variant of the extended finite element method (XFEM) and a hybrid optimizer solution. The proposed XFEM variant is particularly well-suited for the simulation of 3D fracture problems, and as such serves as an efficient solution to the so-called forward problem. A set of heuristic optimization algorithms are recombined into a multiscale optimization scheme. The introduced approach proves effective in tackling the complex inverse problem involved, where identification of multiple flaws is sought on the basis of sparse measurements collected near the structural boundary. The potential of the scheme is demonstrated through a set of numerical case studies of varying complexity.

Pathophysiology of Degenerative Mitral Regurgitation: New 3-Dimensional Imaging Insights.

PubMed

Antoine, Clemence; Mantovani, Francesca; Benfari, Giovanni; Mankad, Sunil V; Maalouf, Joseph F; Michelena, Hector I; Enriquez-Sarano, Maurice

2018-01-01

Despite its high prevalence, little is known about mechanisms of mitral regurgitation in degenerative mitral valve disease apart from the leaflet prolapse itself. Mitral valve is a complex structure, including mitral annulus, mitral leaflets, papillary muscles, chords, and left ventricular walls. All these structures are involved in physiological and pathological functioning of this valvuloventricular complex but up to now were difficult to analyze because of inherent limitations of 2-dimensional imaging. The advent of 3-dimensional echocardiography, computed tomography, and cardiac magnetic resonance imaging overcoming these limitations provides new insights into mechanistic analysis of degenerative mitral regurgitation. This review will detail the contribution of quantitative and qualitative dynamic analysis of mitral annulus and mitral leaflets by new imaging methods in the understanding of degenerative mitral regurgitation pathophysiology. © 2018 American Heart Association, Inc.

Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

NASA Astrophysics Data System (ADS)

Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

2013-12-01

Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors.

PubMed

Giastas, Petros; Andreou, Athena; Papakyriakou, Athanasios; Koutsioulis, Dimitris; Balomenou, Stavroula; Tzartos, Socrates J; Bouriotis, Vassilis; Eliopoulos, Elias E

2018-02-06

The cell wall peptidoglycan is recognized as a primary target of the innate immune system, and usually its disintegration results in bacterial lysis. Bacillus cereus, a close relative of the highly virulent Bacillus anthracis, contains 10 polysaccharide deacetylases. Among these, the peptidoglycan N-acetylglucosamine deacetylase Bc1974 is the highest homologue to the Bacillus anthracis Ba1977 that is required for full virulence and is involved in resistance to the host's lysozyme. These metalloenzymes belong to the carbohydrate esterase family 4 (CE4) and are attractive targets for the development of new anti-infective agents. Herein we report the first X-ray crystal structures of the NodB domain of Bc1974, the conserved catalytic core of CE4s, in the unliganded form and in complex with four known metalloenzyme inhibitors and two amino acid hydroxamates that target the active site metal. These structures revealed the presence of two conformational states of a catalytic loop known as motif-4 (MT4), which were not observed previously for peptidoglycan deacetylases, but were recently shown in the structure of a Vibrio clolerae chitin deacetylase. By employing molecular docking of a substrate model, we describe a catalytic mechanism that probably involves initial binding of the substrate in a receptive, more open state of MT4 and optimal catalytic activity in the closed state of MT4, consistent with the previous observations. The ligand-bound structures presented here, in addition to the five Bc1974 inhibitors identified, provide a valuable basis for the design of antibacterial agents that target the peptidoglycan deacetylase Ba1977.

Additional hydrogen bonds and base-pair kinetics in the symmetrical AMP-DNA aptamer complex.

PubMed Central

Nonin-Lecomte, S; Lin, C H; Patel, D J

2001-01-01

The solution structure of an adenosine monophosphate (AMP)-DNA aptamer complex has been determined previously [Lin, C. H., and Patel, D. J. (1997) Chem. Biol. 4:817-832]. On a symmetrical aptamer complex containing the same binding loop, but with better resolved spectra, we have identified two additional hydrogen bond-mediated associations in the binding loop. One of these involves a rapidly exchanging G imino proton. The phosphate group of the AMP ligand was identified as the acceptor by comparison with other aptamer complexes. Imino proton exchange measurements also yielded the dissociation constants of the stem and binding loop base pairs. This study shows that nuclear magnetic resonance-based imino proton exchange is a good probe for detection of weak hydrogen-bond associations. PMID:11721004

Synthesis and coordination chemistry of TpC*MI complexes where M=Mg, Ca, Sr, Ba and Zn and TpC*=tris[3-(2-methoxy-1,1-dimethyl)pyrazolyl]hydroborate.

PubMed

Chisholm, Malcolm H; Gallucci, Judith C; Yaman, Gulsah

2009-01-14

Reactions involving MI2 where M=Mg, Ca, Sr, Ba or Zn and M'TpC* where M'=Na or Tl and TpC*=tris[3-methoxy-1,1-dimethyl)pyrazolyl]hydroborate in tetrahydrofuran are described leading to the isolation and characterization of the complexes TpC*MgI, , TpC*CaI, , TpC*SrI, , TpC*SrI(THF), , TpC*BaI, , TpC*BaI(pz*H), , where pz*H=3-(2-methoxyl-1,1-dimethyl)pyrazole, TpC*BaI.1/2toluene, and TpC*ZnI, . The compounds , , , , and have been characterized by single-crystal X-ray crystallography. Compounds and are isostructural and are salt-like containing kappa6-TpM+ cations and I- anions. In all other structures, the iodide is bound to the metal and TpC* is kappa6 bonded to the group 2 M(2+) ions. Reactions involving TpC*CaI, , and sodium or lithium alkoxides or amides failed to yield the amide or alkoxide calcium TpC* derivative, though related reactions involving TpC*ZnI, , and KOSiMe3 proceeded quantitatively to yield kappa3TpC*ZnOSiMe3, , which was also structurally characterized and shown to have the kappa3-TpC* bound ligand.

The structure of the Mycobacterium smegmatis trehalose synthase reveals an unusual active site configuration and acarbose-binding mode†

PubMed Central

Caner, Sami; Nguyen, Nham; Aguda, Adeleke; Zhang, Ran; Pan, Yuan T; Withers, Stephen G; Brayer, Gary D

2013-01-01

Trehalose synthase (TreS) catalyzes the reversible conversion of maltose into trehalose in mycobacteria as one of three biosynthetic pathways to this nonreducing disaccharide. Given the importance of trehalose to survival of mycobacteria, there has been considerable interest in understanding the enzymes involved in its production; indeed the structures of the key enzymes in the other two pathways have already been determined. Herein, we present the first structure of TreS from Mycobacterium smegmatis, thereby providing insights into the catalytic machinery involved in this intriguing intramolecular reaction. This structure, which is of interest both mechanistically and as a potential pharmaceutical target, reveals a narrow and enclosed active site pocket within which intramolecular substrate rearrangements can occur. We also present the structure of a complex of TreS with acarbose, revealing a hitherto unsuspected oligosaccharide-binding site within the C-terminal domain. This may well provide an anchor point for the association of TreS with glycogen, thereby enhancing its role in glycogen biosynthesis and degradation. PMID:23735230

Structure and agency: reflections from an exploratory study of Vancouver indoor sex workers.

PubMed

Bungay, Vicky; Halpin, Michael; Atchison, Chris; Johnston, Caitlin

2011-01-01

Sex work research continues to be characterised by debates around decriminalization. Central to these debates are claims about the agency of those involved in the sex trade. Some researchers argue that individuals involved in the sex trade are victims of structural and interpersonal constraint, whilst others depict them as workers exercising choice. Drawing on structure-agency theory, a review of legal and media accounts of the sex trade and qualitative interviews with 21 indoor sex workers in Vancouver, Canada, we argue that both of these perspectives are insufficient. Rather than reducing the sex trade to part of a binary, we suggest that it is necessary to analyse sex work through the complex interplay of both structure and agency. Specifically, structural analyses undercover the numerous ways that sex workers are controlled, observed and influenced whilst agency perspectives elicit the means that sex workers continue to exercise control in spite of disadvantage. While we do not finalise decriminalisation debates, we do critique current Canadian laws for the lack of responsiveness to the lives of sex workers and their exploitative and contradictory stance on sex work.

Crystal Structure of Mycobacterium tuberculosis H37Rv AldR (Rv2779c), a Regulator of the ald Gene: DNA BINDING AND IDENTIFICATION OF SMALL MOLECULE INHIBITORS.

PubMed

Dey, Abhishek; Shree, Sonal; Pandey, Sarvesh Kumar; Tripathi, Rama Pati; Ramachandran, Ravishankar

2016-06-03

Here we report the crystal structure of M. tuberculosis AldR (Rv2779c) showing that the N-terminal DNA-binding domains are swapped, forming a dimer, and four dimers are assembled into an octamer through crystal symmetry. The C-terminal domain is involved in oligomeric interactions that stabilize the oligomer, and it contains the effector-binding sites. The latter sites are 30-60% larger compared with homologs like MtbFFRP (Rv3291c) and can consequently accommodate larger molecules. MtbAldR binds to the region upstream to the ald gene that is highly up-regulated in nutrient-starved tuberculosis models and codes for l-alanine dehydrogenase (MtbAld; Rv2780). Further, the MtbAldR-DNA complex is inhibited upon binding of Ala, Tyr, Trp and Asp to the protein. Studies involving a ligand-binding site G131T mutant show that the mutant forms a DNA complex that cannot be inhibited by adding the amino acids. Comparative studies suggest that binding of the amino acids changes the relative spatial disposition of the DNA-binding domains and thereby disrupt the protein-DNA complex. Finally, we identified small molecules, including a tetrahydroquinoline carbonitrile derivative (S010-0261), that inhibit the MtbAldR-DNA complex. The latter molecules represent the very first inhibitors of a feast/famine regulatory protein from any source and set the stage for exploring MtbAldR as a potential anti-tuberculosis target. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural basis for substrate recognition by the human N-terminal methyltransferase 1

DOE PAGES

Dong, Cheng; Mao, Yunfei; Tempel, Wolfram; ...

2015-11-05

α-N-terminal methylation represents a highly conserved and prevalent post-translational modification, yet its biological function has remained largely speculative. The recent discovery of α-N-terminal methyltransferase 1 (NTMT1) and its physiological substrates propels the elucidation of a general role of α-N-terminal methylation in mediating DNA-binding ability of the modified proteins. The phenotypes, observed from both NTMT1 knockdown in breast cancer cell lines and knockout mouse models, suggest the potential involvement of α-N-terminal methylation in DNA damage response and cancer development. In this study, we report the first crystal structures of human NTMT1 in complex with cofactor S-adenosyl-L-homocysteine (SAH) and six substrate peptides,more » respectively, and reveal that NTMT1 contains two characteristic structural elements (a β hairpin and an N-terminal extension) that contribute to its substrate specificity. Our complex structures, coupled with mutagenesis, binding, and enzymatic studies, also present the key elements involved in locking the consensus substrate motif XPK (X indicates any residue type other than D/E) into the catalytic pocket for α-N-terminal methylation and explain why NTMT1 prefers an XPK sequence motif. We propose a catalytic mechanism for α-N-terminal methylation. Overall, this study gives us the first glimpse of the molecular mechanism of α-N-terminal methylation and potentially contributes to the advent of therapeutic agents for human diseases associated with deregulated α-N-terminal methylation.« less

Structure of a SUMO-binding-motif mimic bound to Smt3p–Ubc9p: conservation of a noncovalent Ubiquitin-like protein–E2 complex as a platform for selective interactions within a SUMO pathway

PubMed Central

Duda, David M.; van Waardenburg, Robert C. A. M.; Borg, Laura A.; McGarity, Sierra; Nourse, Amanda; Waddell, M. Brett; Bjornsti, Mary-Ann; Schulman, Brenda A.

2007-01-01

Summary The SUMO ubiquitin-like proteins play regulatory roles in cell division, transcription, DNA repair, and protein subcellular localization. Paralleling other ubiquitin-like proteins, SUMO proteins are proteolytically processed to maturity, conjugated to targets by E1-E2-E3 cascades, and subsequently recognized by specific downstream effectors containing a SUMO-binding motif (SBM). SUMO and its E2 from the budding yeast S. cerevisiae, Smt3p and Ubc9p, are encoded by essential genes. Here we describe the 1.9 Å resolution crystal structure of a noncovalent Smt3p–Ubc9p complex. Unexpectedly, a heterologous portion of the crystallized complex derived from the expression construct mimics an SBM, and binds Smt3p in a manner resembling SBM binding to human SUMO family members. In the complex, Smt3p binds a surface distal from Ubc9's catalytic cysteine. The structure implies that a single molecule of Smt3p cannot bind concurrently to both the noncovalent binding site and the catalytic cysteine of a single Ubc9p molecule. However, formation of higher-order complexes can occur, where a single Smt3p covalently linked to one Ubc9p's catalytic cysteine also binds noncovalently to another molecule of Ubc9p. Comparison with other structures from the SUMO pathway suggests that formation of the noncovalent Smt3p–Ubc9p complex occurs mutually exclusively with many other Smt3p and Ubc9p interactions in the conjugation cascade. By contrast, high-resolution insights into how Smt3p–Ubc9p can also interact with downstream recognition machineries come from contacts with the SBM mimic. Interestingly, the overall architecture of the Smt3p–Ubc9p complex is strikingly similar to recent structures from the ubiquitin pathway. The results imply that noncovalent ubiquitin-like protein–E2 complexes are conserved platforms, which function as parts of larger assemblies involved many protein post-translational regulatory pathways. PMID:17475278

Probing the Energetics of Dynactin Filament Assembly and the Binding of Cargo Adaptor Proteins Using Molecular Dynamics Simulation and Electrostatics-Based Structural Modeling.

PubMed

Zheng, Wenjun

2017-01-10

Dynactin, a large multiprotein complex, binds with the cytoplasmic dynein-1 motor and various adaptor proteins to allow recruitment and transportation of cellular cargoes toward the minus end of microtubules. The structure of the dynactin complex is built around an actin-like minifilament with a defined length, which has been visualized in a high-resolution structure of the dynactin filament determined by cryo-electron microscopy (cryo-EM). To understand the energetic basis of dynactin filament assembly, we used molecular dynamics simulation to probe the intersubunit interactions among the actin-like proteins, various capping proteins, and four extended regions of the dynactin shoulder. Our simulations revealed stronger intersubunit interactions at the barbed and pointed ends of the filament and involving the extended regions (compared with the interactions within the filament), which may energetically drive filament termination by the capping proteins and recruitment of the actin-like proteins by the extended regions, two key features of the dynactin filament assembly process. Next, we modeled the unknown binding configuration among dynactin, dynein tails, and a number of coiled-coil adaptor proteins (including several Bicaudal-D and related proteins and three HOOK proteins), and predicted a key set of charged residues involved in their electrostatic interactions. Our modeling is consistent with previous findings of conserved regions, functional sites, and disease mutations in the adaptor proteins and will provide a structural framework for future functional and mutational studies of these adaptor proteins. In sum, this study yielded rich structural and energetic information about dynactin and associated adaptor proteins that cannot be directly obtained from the cryo-EM structures with limited resolutions.

Molecular determinants of orexin receptor-arrestin-ubiquitin complex formation.

PubMed

Jaeger, Werner C; Seeber, Ruth M; Eidne, Karin A; Pfleger, Kevin D G

2014-01-01

The orexin system regulates a multitude of key physiological processes, particularly involving maintenance of metabolic homeostasis. Consequently, there is considerable potential for pharmaceutical development for the treatment of disorders from narcolepsy to metabolic syndrome. It acts through the hormonal activity of two endogenous peptides, orexin A binding to orexin receptors 1 and 2 (OX₁ and OX₂) with similar affinity, and orexin B binding to OX₂ with higher affinity than OX₁ receptors. We have previously revealed data differentiating orexin receptor subtypes with respect to their relative stability in forming orexin receptor-arrestin-ubiquitin complexes measured by BRET. Recycling and cellular signalling distinctions were also observed. Here, we have investigated, using BRET, the molecular determinants involved in providing OX₂ receptors with greater β-arrestin-ubiquitin complex stability. The contribution of the C-terminal tail of the OX receptors was investigated by bulk substitution and site-specific mutagenesis using BRET and inositol phosphate assays. Replacement of the OX₁ receptor C-terminus with that of the OX₂ receptor did not result in the expected gain of function, indicating a role for intracellular domain configuration in addition to primary structure. Furthermore, two out of the three putative serine/threonine clusters in the C-terminus were found to be involved in OX₂ receptor-β-arrestin-ubiquitin complex formation. This study provides fundamental insights into the molecular elements that influence receptor-arrestin-ubiquitin complex formation. Understanding how and why the orexin receptors can be functionally differentiated brings us closer to exploiting these receptors as drug targets. © 2013 The Authors. British Journal of Pharmacology published by John Wiley &. Sons Ltd on behalf of The British Pharmacological Society.

Evidence for a Posttranscriptional Role of a TFIIICα-like Protein in Chironomus tentans

PubMed Central

Sabri, Nafiseh; Farrants, Ann-Kristin Östlund; Hellman, Ulf; Visa, Neus

2002-01-01

We have cloned and sequenced a cDNA that encodes for a nuclear protein of 238 kDa in the dipteran Chironomus tentans. This protein, that we call p2D10, is structurally similar to the α subunit of the general transcription factor TFIIIC. Using immunoelectron microscopy we have shown that a fraction of p2D10 is located at sites of transcription, which is consistent with a possible role of this protein in transcription initiation. We have also found that a large fraction of p2D10 is located in the nucleoplasm and in the nuclear pore complexes. Using gel filtration chromatography and coimmunoprecipitation methods, we have identified and characterized two p2D10-containing complexes that differ in molecular mass and composition. The heavy p2D10-containing complex contains at least one other component of the TFIIIC complex, TFIIIC-ε. Based on its molecular mass and composition, the heavy p2D10-containing complex may be the Pol III holoenzyme. The light p2D10-containing complex contains RNA together with at least two proteins that are thought to be involved in mRNA trafficking, RAE1 and hrp65. The observations reported here suggest that this new TFIIIC-α-like protein is involved in posttranscriptional steps of premRNA metabolism in Chironomus tentans. PMID:12006668

Nuclear factor 90 uses an ADAR2-like binding mode to recognize specific bases in dsRNA.

PubMed

Jayachandran, Uma; Grey, Heather; Cook, Atlanta G

2016-02-29

Nuclear factors 90 and 45 (NF90 and NF45) form a protein complex involved in the post-transcriptional control of many genes in vertebrates. NF90 is a member of the dsRNA binding domain (dsRBD) family of proteins. RNA binding partners identified so far include elements in 3' untranslated regions of specific mRNAs and several non-coding RNAs. In NF90, a tandem pair of dsRBDs separated by a natively unstructured segment confers dsRNA binding activity. We determined a crystal structure of the tandem dsRBDs of NF90 in complex with a synthetic dsRNA. This complex shows surprising similarity to the tandem dsRBDs from an adenosine-to-inosine editing enzyme, ADAR2 in complex with a substrate RNA. Residues involved in unusual base-specific recognition in the minor groove of dsRNA are conserved between NF90 and ADAR2. These data suggest that, like ADAR2, underlying sequences in dsRNA may influence how NF90 recognizes its target RNAs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comparison of energy interaction parameters for the complexation of Pr(III) with glutathione reduced (GSH) in absence and presence of Zn(II) in aqueous and aquated organic solvents using 4f?4f transition spectra as PROBE

NASA Astrophysics Data System (ADS)

Singh, Th. David; Sumitra, Ch.; Yaiphaba, N.; Devi, H. Debecca; Devi, M. Indira; Singh, N. Rajmuhon

2005-04-01

The coordination chemistry of glutathione reduced (GSH) is of great importance as it acts as excellent model system for the binding of metal ions. The GSH complexation with metal ions is involved in the toxicology of different metal ions. Its coordination behaviour for soft metal ions and hard metal ions is found different because of the structure of GSH and its different potential binding sites. In our work we have studied two chemically dissimilar metal ions viz. Pr(III), which prefer hard donor site like carboxylic groups and Zn(II) the soft metal ion which prefer peptide-NH and sulphydryl groups. The absorption difference and comparative absorption spectroscopy involving 4f-4f transitions of the heterobimetallic Complexation of GSH with Pr(III) and Zn(II) has been explored in aqueous and aquated organic solvents. The variation in the energy parameters like Slater-Condon ( F K), Racah ( E K) and Lande ( ξ4f), Nephelauxetic parameter ( β) and bonding parameter ( b1/2) are computed to explain the nature of complexation.