bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relating protein conformational changes to packing efficiency and disorder
Authors: Bhardwaj Nitin , Gerstein Mark 
Published: April 2009

AbstractChanges in protein conformation play key roles in facilitating various biochemical processes, ranging from signaling and phosphorylation to transport and catalysis. While various factors that drive these motions such as environmental changes and binding of small molecules are well understood, specific causative effects on the structural features of the protein due to these conformational changes have not been studied on a large scale. Here, we study protein conformational changes in relation to two key structural metrics: packing efficiency and disorder. Packing has been shown to be crucial for protein stability and function by many protein design and engineering studies. We study changes in packing efficiency during conformational changes, thus extending the analysis from a static context to a dynamic perspective and report some interesting observations. First, we study various proteins that adopt alternate conformations and find that tendencies to show motion and change in packing efficiency are correlated: residues that change their packing efficiency show larger motions. Second, our results suggest that residues that show higher changes in packing during motion are located on the changing interfaces which are formed during these conformational changes. These changing interfaces are slightly different from shear or static interfaces that have been analyzed in previous studies. Third, analysis of packing efficiency changes in the context of secondary structure shows that, as expected, residues buried in helices show the least change in packing efficiency, whereas those embedded in bends are most likely to change packing. Finally, by relating protein disorder to motions, we show that marginally disordered residues which are ordered enough to be crystallized but have sequence patterns indicative of disorder show higher dislocation and a higher change in packing than ordered ones and are located mostly on the changing interfaces. Overall, our results demonstrate that between the two conformations, the cores of the proteins remain mostly intact, whereas the interfaces display the most elasticity, both in terms of disorder and change in packing efficiency. By doing a variety of tests, we also show that our observations are robust to the solvation state of the proteins.
On the occurrence of linear groups in proteins
Authors: Hollingsworth Scott A. , Berkholz Donald S. , Karplus P. Andrew 
Published: April 2009

AbstractLinear groups—polypeptide conformations based on a single repeating ϕ,ψ‐pair—are a foundational concept in protein structure, yet how they are presented in textbooks is based largely on theoretical studies from the early days of protein structure analysis. Now, ultra‐high resolution protein structures provide a resource for an accurate empirical and systematic assessment of the linear groups that truly exist in proteins. Here, a purely conformation‐based survey of linear groups shows that only three distinct ϕ,ψ‐regions occur: a diverse set of extended conformations mostly present as β‐strands, a broad population of polyproline‐II‐like spirals, and a tight cluster that includes the highly populated α‐helix and the conformationally‐similar but much less populated 310‐helix. Rare, short left‐handed α‐/310‐helical turns with repeating ϕ,ψ‐angles occur, but none are longer than three residues. Misperceptions dispelled by this study are the existence of 2.27‐ and π‐helices as linear groups, the existence of specific ideal ϕ,ψ‐angles for each linear group, and the existence of a substantive difference in the ϕ,ψ‐preferences for parallel versus antiparallel β‐strands. This study provides a concrete basis for updating and enhancing how we think about and teach the basics of protein structure.
Self‐association of streptococcus pyogenes collagen‐like constructs into higher order structures
Authors: Yoshizumi Ayumi , Yu Zhuoxin , Silva Teresita , Thiagarajan Geetha , Ramshaw John A. M. , Inouye Masayori , Brodsky Barbara 
Published: April 2009

AbstractA number of bacterial collagen‐like proteins with Gly as every third residue and a high Pro content have been observed to form stable triple‐helical structures despite the absence of hydroxyproline (Hyp). Here, the high yield cold‐shock expression system is used to obtain purified recombinant collagen‐like protein (V‐CL) from Streptococcus pyogenes containing an N‐terminal globular domain V followed by the collagen triple‐helix domain CL and the modified construct with two tandem collagen domains V‐CL‐CL. Both constructs and their isolated collagenous domains form stable triple‐helices characterized by very sharp thermal transitions at 35–37°C and by high values of calorimetric enthalpy. Procedures for the formation of collagen SLS crystallites lead to parallel arrays of in register V‐CL‐CL molecules, as well as centrosymmetric arrays of dimers joined at their globular domains. At neutral pH and high concentrations, the bacterial constructs all show a tendency towards aggregation. The isolated collagen domains, CL and CL‐CL, form units of diameter 4–5 nm which bundle together and twist to make larger fibrillar structures. Thus, although this S. pyogenes collagen‐like protein is a cell surface protein with no indication of participation in higher order structure, the triple‐helix domain has the potential of forming fibrillar structures even in the absence of hydroxyproline. The formation of fibrils suggests bacterial collagen proteins may be useful for biomaterials and tissue engineering applications.
Rate and extent of protein localization is controlled by peptide‐binding domain association kinetics and morphology
Authors: Mills Evan , Truong Kevin 
Published: April 2009

AbstractProtein localization is an important regulatory mechanism in many cell signaling pathways such as cytoskeletal organization and genetic regulation. The specific mechanism of protein localization determines the kinetics and morphological constraints of protein translocation, and thus affects the rate and extent of localization. To investigate the affect of localization kinetics and morphology on protein localization, we designed a protein localization system based on Ca2+‐calmodulin and Src homology 3 domain binding peptides that can translocate between specific localizations in response to a Ca2+signal. We used a stochastic biomolecular simulator to predict that such a protein localization system will exhibit slower and less complete translocations when the association kinetics of a binding domain and peptide are reduced. As well, we predicted that increasing the diffusion resistance by manipulating the morphology of the system would similarly impair translocation speed and completeness. We then constructed a network of synthetic fusion proteins and showed that these predictions could be qualitatively confirmedin vitro. This work provides a basis for explaining the different characteristics (rate and extent) of protein transport and localization in cells as a consequence of the kinetics and morphology of the transport mechanism.
Design, generation, and testing of mammalian expression modules that tag membrane proteins
Authors: Pang John , Zeng Xiaokun , Xiao Rui‐ping , Lakatta Edward G. , Lin Li 
Published: April 2009

AbstractThe expression of mammalian membrane proteins in laboratory cell lines allows their biological functions to be characterized and carefully dissected. However, it is often difficult to design and generate effective antibodies for membrane proteins in the desired studies. As a result, expressed membrane proteins cannot be detected or characterized via common biochemical approaches such as western blotting, immunoprecipitation, or immunohistochemical analysis, and their cellular behaviors cannot be sufficiently investigated. To circumvent such roadblocks, we designed and generated two sets of expression modules that consist of sequences encoding for three essential components: (1) a signal peptide from human receptor for advanced glycation end products that targets the intended protein to the endoplasmic reticulum for cell surface expression; (2) an antigenic epitope tag that elicits specific antibody recognition; and (3) a series of restriction sites that facilitate subcloning of the target membrane protein. The modules were designed with the flexibility to change the epitope tag to suit the specific tagging needs. The modules were subcloned into expression vectors, and were successfully tested with both Type I and Type III human membrane proteins: the receptor for advanced glycation end products, the Toll‐like receptor 4, and the angiotensin II receptor 1. These expressed membrane proteins are readily detected by western blotting, and are immunoprecipitated by antibodies to their relative epitope tags. Immunohistochemical and biochemical analyses also show that the expressed proteins are located at cell surface, and maintain their modifications and biological functions. Thus, the designed modules serve as an effective tool that facilitates biochemical studies of membrane proteins.
Insight into a strategy for attenuating AmpC‐mediated β‐lactam resistance: Structural basis for selective inhibition of the glycoside hydrolase NagZ
Authors: Balcewich Misty D. , Stubbs Keith A. , He Yuan , James Terrence W. , Davies Gideon J. , Vocadlo David J. , Mark Brian L. 
Published: April 2009

AbstractNagZ is an exo‐N‐acetyl‐β‐glucosaminidase, found within Gram‐negative bacteria, that acts in the peptidoglycan recycling pathway to cleave N‐acetylglucosamine residues off peptidoglycan fragments. This activity is required for resistance to cephalosporins mediated by inducible AmpC β‐lactamase. NagZ uses a catalytic mechanism involving a covalent glycosyl enzyme intermediate, unlike that of the human exo‐N‐acetyl‐β‐glucosaminidases: O‐GlcNAcase and the β‐hexosaminidase isoenzymes. These latter enzymes, which remove GlcNAc from glycoconjugates, use a neighboring‐group catalytic mechanism that proceeds through an oxazoline intermediate. Exploiting these mechanistic differences we previously developed 2‐N‐acyl derivatives of O‐(2‐acetamido‐2‐deoxy‐D‐glucopyranosylidene)amino‐N‐phenylcarbamate (PUGNAc), which selectively inhibits NagZ over the functionally related human enzymes and attenuate antibiotic resistance in Gram‐negatives that harbor inducible AmpC. To understand the structural basis for the selectivity of these inhibitors for NagZ, we have determined its crystallographic structure in complex with N‐valeryl‐PUGNAc, the most selective known inhibitor of NagZ over both the human β‐hexosaminidases and O‐GlcNAcase. The selectivity stems from the five‐carbon acyl chain of N‐valeryl‐PUGNAc, which we found ordered within the enzyme active site. In contrast, a structure determination of a human O‐GlcNAcase homologue bound to a related inhibitor N‐butyryl‐PUGNAc, which bears a four‐carbon chain and is selective for both NagZ and O‐GlcNAcase over the human β‐hexosamnidases, reveals that this inhibitor induces several conformational changes in the active site of this O‐GlcNAcase homologue. A comparison of these complexes, and with the human β‐hexosaminidases, reveals how selectivity for NagZ can be engineered by altering the 2‐N‐acyl substituent of PUGNAc to develop inhibitors that repress AmpC mediated β‐lactam resistance.
DNA sequence selectivity of human topoisomerase I‐mediated DNA cleavage induced by camptothecin
Authors: Punchihewa Chandanamali , Carver Megan , Yang Danzhou 
Published: April 2009

AbstractIn probing the mechanism of inhibition of hypoxia inducible factor (HIF‐1) by campothecins, we investigated the ability of human topoisomerase I to bind and cleave HIF‐1 response element (HRE), which contains the known camptothecin‐mediated topoisomerase I cleavage site 5′‐TG. We observed that the selection of 5′‐TG by human topoisomerase I and topotecan depends to a large extent on the specific flanking sequences, and that the presence of a G at the −2 position (where cleavage occurs between −1 and +1) prevents the HRE site from being a preferred site for such cleavage. Furthermore, the presence of −2 T/A can induce the cleavage at a less preferred TC or TA site. However, in the absence of a more preferred site, the HRE site is shown to be cleaved by human topoisomerase I in the presence of topotecan. Thus, it is implied that the −2 base has a significant influence on the selection of the camptothecin‐mediated Topo I cleavage site, which can overcome the preference for +1G. While the cleavage site recognition has been known to be based on the concerted effect of several bases spanning the cleavage site, such a determining effect of an individual base has not been previously recognized. A possible base‐specific interaction between DNA and topoisomerase I may be responsible for this sequence selectivity.
Delineating Anopheles gambiae coactivator associated arginine methyltransferase 1 automethylation using top–down high resolution tandem mass spectrometry
Authors: Kuhn Peter , Xu Qingge , Cline Erika , Zhang Di , Ge Ying , Xu Wei 
Published: April 2009

AbstractCoactivator‐associated arginine methyltransferase 1 (CARM1), originally defined as a coactivator for steroid receptors, is a member of the protein arginine methyltransferases. Here, we report the discovery and characterization of an automethylation event by AgCARM1, a CARM1 homologue in the mosquito Anopheles gambiae, using top–down high resolution tandem mass spectrometry, which allows fine mapping of modifications in the intact protein accurately and quantitatively without priori knowledge. Unexpectedly, we found that AgCARM1 has already been predominantly dimethylated during its expression in Escherichia coli. A single arginine methylation site, R485, was identified which is conserved among CARM1 in insects. No methylation was observed in the intact AgCARM1R485K mutant where R485 is mutated to lysine, which confirms that R485 is the only detectable methylation site. Using AgCARM1 methyltransferase defective mutants, we confirmed that this is an automethylation event and show the automethylation of AgCARM1 occurs intermolecularly. This study represents the first comprehensive characterization of an automethylation event by top–down mass spectrometry. The unexpected high percentage of automethylated recombinant AgCARM1 expressed in E. coli may shed light on other bacterially expressed post‐translational modifying enzymes, which could be modified but overlooked in biochemical and structural studies. Top–down high resolution tandem mass spectrometry thus provides unique opportunities for revealing unexpected protein modification, localizing specific modification to one amino acid, and delineating molecular mechanism of an enzyme.
Direct and indirect roles of His‐418 in metal binding and in the activity of β‐galactosidase (E. coli)
Authors: Juers Douglas H. , Rob Beatrice , Dugdale Megan L. , Rahimzadeh Nastaron , Giang Clarence , Lee Michelle , Matthews Brian W. , Huber Reuben E. 
Published: April 2009

AbstractThe active site of ß‐galactosidase (E. coli) contains a Mg2+ ion ligated by Glu‐416, His‐418 and Glu‐461 plus three water molecules. A Na+ ion binds nearby. To better understand the role of the active site Mg2+ and its ligands, His‐418 was substituted with Asn, Glu and Phe. The Asn‐418 and Glu‐418 variants could be crystallized and the structures were shown to be very similar to native enzyme. The Glu‐418 variant showed increased mobility of some residues in the active site, which explains why the substitutions at the Mg2+ site also reduce Na+ binding affinity. The Phe variant had reduced stability, bound Mg2+ weakly and could not be crystallized. All three variants have low catalytic activity due to large decreases in the degalactosylation rate. Large decreases in substrate binding affinity were also observed but transition state analogs bound as well or better than to native. The results indicate that His‐418, together with the Mg2+, modulate the central role of Glu‐461 in binding and as a general acid/base catalyst in the overall catalytic mechanism. Glucose binding as an acceptor was also dramatically decreased, indicating that His‐418 is very important for the formation of allolactose (the natural inducer of the lac operon).
Probing the conformation of the resting state of a bacterial multidrug ABC transporter, BmrA, by a site‐directed spin labeling approach
Authors: Do Cao Marie‐Ange , Crouzy Serge , Kim Miyeon , Becchi Michel , Cafiso David S. , Pietro Attilio Di , Jault Jean‐Michel 
Published: April 2009

AbstractPreviously published 3‐D structures of a prototypic ATP‐binding cassette (ABC) transporter, MsbA, have been recently corrected revealing large rigid‐body motions possibly linked to its catalytic cycle. Here, a closely related multidrug bacterial ABC transporter, BmrA, was studied using site‐directed spin labeling by focusing on a region connecting the transmembrane domain and the nucleotide‐binding domain (NBD). Electron paramagnetic resonance (EPR) spectra of single spin‐labeled cysteine mutants suggests that, in the resting state, this sub‐domain essentially adopts a partially extended conformation, which is consistent with the crystal structures of MsbA and Sav1866. Interestingly, one of the single point mutants (Q333C) yielded an immobilized EPR spectrum that could arise from a direct interaction with a vicinal tyrosine residue. Inspection of different BmrA models pointed to Y408, within the NBD, as the putative interacting partner, and its mutation to a Phe residue indeed dramatically modified the EPR spectra of the spin labeled Q333C. Moreover, unlike the Y408F mutation, the Y408A mutation abolished both ATPase activity and drug transport of BmrA, suggesting that a nonpolar bulky residue is required at this position. The spatial proximity of Q333 and Y408 was also confirmed by formation of a disulfide bond when both Q333 and T407 (or S409) were replaced jointly by a cysteine residue. Overall, these results indicate that the two regions surrounding Q333 and Y408 are close together in the 3‐D structure of BmrA and that residues within these two sub‐domains are essential for proper functioning of this transporter.
Motif‐directed flexible backbone design of functional interactions
Authors: Havranek James J. , Baker David 
Published: April 2009

AbstractComputational protein design relies on a number of approximations to efficiently search the huge sequence space available to proteins. The fixed backbone and rotamer approximations in particular are important for formulating protein design as a discrete combinatorial optimization problem. However, the resulting coarse‐grained sampling of possible side‐chain terminal positions is problematic for the design of protein function, which depends on precise positioning of side‐chain atoms. Although backbone flexibility can greatly increase the conformation freedom of side‐chain functional groups, it is not obvious which backbone movements will generate the critical constellation of atoms responsible for protein function. Here, we report an automated method for identifying protein backbone movements that can give rise to any specified set of desired side‐chain atomic placements and interactions, using protein–DNA interfaces as a model system. We use a library of previously observed protein–DNA interactions (motifs) and a rotamer‐based description of side‐chain conformation freedom to identify placements for the protein backbone that can give rise to a favorable side‐chain interaction with DNA. We describe a tree‐search algorithm for identifying those combinations of interactions from the library that can be realized with minimal perturbation of the protein backbone. We compare the efficiency of this method with the alternative approach of building and screening alternate backbone conformations.
Evolutionary constraints on structural similarity in orthologs and paralogs
Authors: Peterson Mark E. , Chen Feng , Saven Jeffery G. , Roos David S. , Babbitt Patricia C. , Sali Andrej 
Published: April 2009

AbstractAlthough a quantitative relationship between sequence similarity and structural similarity has long been established, little is known about the impact of orthology on the relationship between protein sequence and structure. Among homologs, orthologs (derived by speciation) more frequently have similar functions than paralogs (derived by duplication). Here, we hypothesize that an orthologous pair will tend to exhibit greater structural similarity than a paralogous pair at the same level of sequence similarity. To test this hypothesis, we used 284,459 pairwise structure‐based alignments of 12,634 unique domains from SCOP as well as orthology and paralogy assignments from OrthoMCL DB. We divided the comparisons by sequence identity and determined whether the sequence‐structure relationship differed between the orthologs and paralogs. We found that at levels of sequence identity between 30 and 70%, orthologous domain pairs indeed tend to be significantly more structurally similar than paralogous pairs at the same level of sequence identity. An even larger difference is found when comparing ligand binding residues instead of whole domains. These differences between orthologs and paralogs are expected to be useful for selecting template structures in comparative modeling and target proteins in structural genomics.
Real‐time response in AdS/CFT with application to spinors
Authors: Iqbal N. , Liu H. 
Published: April 2009

AbstractWe discuss a simple derivation of the real‐time AdS/CFT prescription as an analytic continuation of the corresponding problem in Euclidean signature. We then extend the formalism to spinor operators and apply it to the examples of real‐time fermionic correlators in CFTs dual to pure AdS and the BTZ black hole.
Is N = 8 supergravity a finite field theory?
Authors: Stelle K.S. 
Published: April 2009

AbstractAdvances in calculational technique permit the study of ultraviolet structure in maximal super Yang‐Mills and maximal supergravity theories at heretofore unattainable loop orders. Hints from string theory suggest that maximal supergravity might have a similar ultraviolet behavior in D = 4 spacetime dimensions as maximal super Yang‐Mills theory and so be ultraviolet convergent. Yet what is known of field theoretic nonrenormalization theorems suggests only that ${1 \over 2}$‐BPS counterterms are excluded. A key test of the relative finiteness properties of the two theories will be the ultraviolet divergences in D = 5 maximal supergravity at the four‐loop level.
A century of process safety—And more
Authors: Crowl Daniel A. 
Published: April 2009

AbstractIn November of 2008 the American Institute of Chemical Engineers convened in Philadelphia to celebrate their 100th anniversary. During that celebration a special session was offered entitled “A Century of Process Safety.” The session was co‐chaired by Dan Crowl of Michigan Tech University and Bruce Vaughen of Cabot Corporation. The session was sponsored by the AIChE Education Division, the AIChE Center for Chemical Process Safety, and the AIChE Safety and Health Division.This session brought together noted AIChE process safety professionals to review the history of process safety at AIChE and to highlight the technical and educational accomplishments achieved. This included a history of (a) safety in industry, (b) the U.S. Occupational Safety and Health Administration, (c) the Safety and Health Division, (d) the Center for Chemical Process Safety, and (e) the Safety and Chemical Engineering Education (SACHE) Program. Two chemical companies, Dupont and Air Products, presented historical perspectives on their safety programs and provided perspectives on recent industrial progress.This article provides an introduction to this unique series of papers and also presents additional historical detail. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2009