bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and functional relations among thioredoxins of different species
Authors: Eklund Hans , Gleason Florence K. , Holmgren Arne 
Published: May 2005

AbstractThree‐dimensional models have been constructed of homologous thioredoxins and protein disulfide isomerases based on the high resolution x‐ray crystallographic structure of the oxidized form of Escherichia coli thioredoxin. The thioredoxins, from archebacteria to humans, have 27–69% sequence identity to E. coli thioredoxin. The models indicate that all the proteins have similar three‐dimensional structures despite the large variation in amino acid sequences. As expected, residues in the active site region of thioredoxins are highly conserved. These include Asp‐26, Ala‐29, Trp‐31, Cys‐32, Gly‐33, Pro‐34, Cys‐35, Asp‐61, Pro‐76, and Gly‐92. Similar residues occur in most protein disulfide isomerase sequences. Most of these residues form the surface around the active site that appears to facilitate interactions with other enzymes.Other structurally important residues are also conserved. A proline at position 40 causes a kink in the alpha‐2 helix and thus provides the proper position of the active site residues at the amino end of this helix. Pro‐76 is important in maintaining the native structure of the molecule. In addition, residues forming the internal contact surfaces between the secondary structural elements are generally unchanged such as Phe‐12, Val‐25, and Phe‐27.
Detection of common three‐dimensional substructures in proteins
Authors: Vriend Gerrit , Sander Chris 
Published: May 2005

AbstractWe present a fully automatic algorithm for three‐dimensional alignment of protein structures and for the detection of common substructures and structural repeats. Given two proteins, the algorithm first identifies all pairs of structurally similar fragments and subsequently clusters into larger units pairs of fragments that are compatible in three dimensions. The detection of similar substructures is independent of insertion/deletion penalties and can be chosen to be independent of the topology of loop connections and to allow for reversal of chain direction. Using distance geometry filters and other approximations, the algorithm, implemented in the WHAT IF program, is so fast that structural comparison of a single protein with the entire database of known protein structures can be performed routinely on a workstation. The method reproduces known non‐trivial superpositions such as plastocyanin on azurin. In addition, we report surprising structural similarity between ubiquitin and a (2Fe‐2S) ferredoxin.
Sesam: A relational database for structure and sequence of macromolecules
Authors: Huysmans Martina , Richelle Jean , Wodak Shoshana J. 
Published: May 2005

AbstractA system is described that provides ways of integrating data on protein structure, sequence, and survey results, with molecular graphics and molecular mechanics software. Its major component is the relational database SESAM, presently implemented under the commercial package SYBASE. By desin, the database allows full integration—within the same data organization—of raw data on protein structure, sequence, ligands, and heterogroups, obtained from the Brookhaven Protein Databank, with pure sequence information available from other databanks such as SWISS‐PROT. It contains in addition higher level descriptions of structural and topological properties, as well as survey results, obtained by executing specialized computer programs. Aside from the very useful attribute of closely combining structural and nonstructural information, other important features distinguish it from analogous systems developed elsewhere. It includes a molecular dictionary with complete description of geometric properties and energy parameters used in modeling and conformational energy calculations. Using this dictionary, structural data are validated by checking for localized inconsistencies in atomic coordinates, atomic symbols, chirality definitions, and flagging errors and incomplete entries. Because of both the dictionary and the validation procedures, SESAM can be readily interfaced with conventional molecular graphics and mechanics software packages, or with other specialized application programs. With the aid of appropriate interfaces, data access is sufficiently fast for SESAM to be interrogated interactively. Prototypes of user interfaces, as well as an interface with the molecular graphics package BRUGEL, are described and the power of the system is illustrated in applications such as homology‐based protein modeling, computer‐aided protein design, protein structure predictions, analysis of local structure motifs, and of relationships between protein sequence and structure.
Expert system for predicting protein localization sites in gram‐negative bacteria
Authors: Nakai Kenta , Kanehisa Minoru 
Published: May 2005

AbstractWe have developed an expert system that makes use of various kinds of knowledge organized as “if‐then” rules for predicting protein localization sites in Gram‐negative bacteria, given the amino acid sequence information alone. We considered four localization sites: the cytoplasm, the inner (cytoplasmic) membrane, the periplasm, and the outer membrane. Most rules were derived from experimental observations. For example, the rule to recognize an inner membrane protein is the presence of either a hydrophobic stretch in the predicted mature protein or an uncleavable N‐terminal signal sequence. Lipoproteins are first recognized by a consensus pattern and then assumed present at either the inner or outer membrane. These two possibilities are further discriminated by examining an acidic residue in the mature N‐terminal portion. Furthermore, we found an empirical rule that periplasmic and outer membrane proteins were successfully discriminated by their different amino acid composition. Overall, our system could predict 83% of the localization sites of proteins in our database.
Effect of urey–bradley–shimanouchi force field on the harmonic dynamics of proteins
Authors: Derreumaux Philippe , Vergoten Géarard 
Published: May 2005

AbstractA normal mode analysis of bovine pancreatic trypsin inhibitor is carried out by using a Urey‐Bradley–Shimanouchi potential energy function. The density of vibrational states, the magnitudes, and time scales of the atomic fluctuations are compared with experimental and theoretical results obtained by the more commonly used potential energy functions. The atomic fluctuations of Lys‐15 are subject to extensive considerations as this residue is buried in the trypsin specificity pocket. It is found that Arg‐17 is likely to be of importance in order to understand the way BPTI binds on trypsin.
Asymmetric inclusion by de novo designed proteins: Fluorescence probe studies on amphiphilic α‐helix bundles
Authors: Morii Hisayuki , Ichimura Kunihiro , Uedaira Hatsuho 
Published: May 2005

AbstractThe inclusion feature and supersecondary structure of the de novo designed proteins which are constructed with several amphiphilic α‐helices and flexible linkage parts were investigated with fluorescence probes. Five types of small proteins (or peptides) have been designed, which are composed of 2, 3, 4, 4, and 6 helices, respectively, and are linked with only linear junctions except for one of 4‐helix proteins. All of these proteins have inclusion ability for hydrophobic fluorophores. Further, by the analysis of fluorescence polarization anisotropy, it was suggested that these proteins include guest molecules in compact helix bundles constructed with about 4 helices. Asymmetric inclusion of both monomer and stacked dimer of acridine orange derivatives was found by means of induced circular dichroism except for the 4‐helix protein with cross‐junction. The chirality of the included dimer proved to be in accordance with the chiral sense of α‐helical coiled‐coil. The 6‐helix protein has especially high efficiency in inclusion for any fluorophores examined in this study and brings about a significant blue‐shift of maximal emission for 8‐anilino‐1‐naphthalenesulfonate.
Crystallization and preliminary analysis of enzyme‐substrate complexes of pyruvate kinase from rabbit muscle
Authors: Schmidt‐Bäse Karen , Buchbinder Jenny L. , Reed George H. , Rayment Ivan 
Published: May 2005

AbstractPyruvate kinase from rabbit muscle has been crystallized in a form suitable for high resolution X‐ray analysis. Complexes of the enzyme with Mn2+ and either pyruvate or oxalate crystallize from solutions of polyethyleneglycol 8000 at pH 6.0. Crystals obtained from solutions of the complexes with pyruvate or oxalate appear isomorphous and belong to the triclinic space group P1. The crystals have unit cell dimensions a = 83.3(4) Å, b = 109.4(6) Å, c = 145.7(7) Å, α = 94.9°, β = 93.6°, γ = 112.2°. These crystals diffract to better than 2.4 Å resolution and are stable in the X‐ray beam for at least 20 hr. Electron paramagnetic resonance measurements on a single crystal show that Mn2+ is bound to the crystalline protein.
Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
Authors: Ichiye Toshiko , Karplus Martin 
Published: May 2005

AbstractA method is described for identifying collective motions in proteins from molecular dynamics trajectories or normal mode simulations. The method makes use of the covariances of atomic positional fluctuations. It is illustrated by an analysis of the bovine pancreatic trypsin inhibitor. Comparison of the covariance and cross‐correlation matrices shows that the relative motions have many similar features in the different simulations. Many regions of the protein, especially regions of secondary structure, move in a correlated manner. Anharmonic effects, which are included in the molecular dynamics simulations but not in the normal analysis, are of some importance in determining the larger scale collective motions, but not the more local fluctuations. Comparisons of molecular dynamics simulations in the present and absence of solvent indicate that the environment is of significance for the long‐range motions.
Crystal parameters and molecular replacement of an anticholera toxin peptide complex
Authors: Shoham Menachem , Proctor Peter , Hughes Diane , Baldwin Eric T. 
Published: May 2005

AbstractTE33 is an Fab fragment of a monoclonal antibody raised against a 15‐residue long peptide (CTP3), corresponding in sequence to residues 50–64 of the cholera toxin B subunit. Crystals of the complex between TE33 and CTP3 have been grown from 20% (w/v) polyethylene glycol‐8000 at pH 4.0. The crystals are orthorhombic, space group P21212, with unit cell dimensions a = 104.15, b = 110.61, and c = 40.68 Å. X‐Ray data have been collected to a resolution of 2.3 Å. The asymmetric unit contains one molecule of Fab and one molecule of CTP3. The presence of CTP3 has been demonstrated by fluorescence quenching of the dissolved crystal after X‐ray data collection. A molecular replacement solution was found based on the coordinates of DB3, an antiprogesterone Fab fragment.
Crystallization and preliminary X‐ray investigation of a recombinant form of rat catechol O‐methyltransferase
Authors: Vidgren Jukka , Tilgmann Carola , Lundström Kenneth , Liljas Anders 
Published: May 2005

AbstractRat catechol O‐methyltransferase cDNA was introduced into an E. coli expression vector pKEX14, which utilizes the inducible T7 promoter. Active and soluble recombinant catechol O‐methyltransferase was produced in bacteria and purified to electrophoretic homogeneity by chromatographic procedures. The purified enzyme has been crystallized by the method of vapor diffusion using polyethylene glycol as precipitant. The space group is P3121 or P3221 with a = b = 51.3 Å and c = 168.5 Å and one molecule in the asymmetric unit. The crystals diffract beyond 3.2 Å and are suitable for three‐dimensional X‐ray structure determination.
A single tryptic fragment of colicin E1 can form an ion channel: Stoichiometry confirms kinetics
Authors: Levinthal Françoise , Todd A. Paul , Hubbell Wayne L. , Levinthal Cyrus 
Published: May 2005

AbstractThe molecularity of the ion channel formed by peptide fragments of colicin has taken on particular significance since the length of the active peptide has been shown to be less than 90 amino acids and the lumen size at least 8 Å. Cell survival experiments show that killing by colicin obeys single‐hit statistics, and ion leakage rates from phospholipid vesicles are first order in colicin concentration. However, interpretation in molecular terms is generally complicated by the requirement of large numbers of colicin molecules per cell or vesicle.We have measured the discharge of potential across membranes of small phospholipid vesicles by following the changes in binding of potential sensitive spin labeled phosphonium ions as a function of the number of colicin fragments added. Because of the sensitivity of the method, it was possible to reliably investigate the effect of colicin in a range where there was no more than 0.2 colicins per vesicle. The quantitative results of these experiments yield a direct molecular stoichiometry and demonstrate that one C‐terminal fragment of the colicin molecule per one vesicle is sufficient to induce a rapid ion flux in these vesicles. In addition, the experiments confirm earlier findings that the colicin fragments do not migrate from one vesicle to another at pH 4.5. Similar results are obtained with large unilamellar vesicles.
Information‐theoretical entropy as a measure of sequence variability
Authors: Shenkin Peter S. , Erman Batu , Mastrandrea Lucy D. 
Published: May 2005

AbstractWe propose the use of the information‐theoretical entropy, S = −Σpi log2 Pi, as a measure of variability at a given position in a set of aligned sequences. pi stands for the fraction of times the i‐th type appears at a position. For protein sequences, the sum has up to 20 terms, for nucleotide sequences, up to 4 terms, and for codon sequences, up to 61 terms. We compare S and VS, a related measure, in detail with VK, the traditional measure of immunoglobulin sequence variability, both in the abstract and as applied to the immunoglobulins. We conclude that S has desirable mathematical properties that VK lacks and has intuitive and statistical meanings that accord well with the notion of variability. We find that VK and the S‐based measures are highly correlated for the immunoglobulins. We show by analysis of sequence data and by means of a mathematical model that this correlation is due to a strong tendency for the frequency of occurrence of amino acid types at a given position to be log‐linear. It is not known whether the immunoglobulins are typical or atypical of protein families in this regard, nor is the origin of the observed rank‐frequency distribution obvious, although we discuss several possible etiologies.
On the helix sense of gramicidin A single channels
Authors: Koeppe Roger E. , Providence Lyndon L. , Greathouse Denise V. , Heitz Frédéric , Trudelle Yves , Purdie Neil , Andersen Olaf S. 
Published: May 2005

AbstractIn order to resolve whether gramicidin A channels are formed by right‐ or left‐handed β‐helices, we synthesized an optically reversed (or mirror image) analogue of gramicidin A, called gramicidin A−, to test whether it forms channels that have the same handedness as channels formed by gramicidin M− (F. Heitz et al., Biophys. J. 40:87–89, 1982). In gramicidin M− the four tryptophan residues have been replaced with phenylalanine, and the circular dichroism (CD) spectrum therfore reflects almost exclusively contributions from the polypeptide backbone. The CD spectrum of gramicidin M− in dimyristoylphosphatidylcholine vesicles is consistent with a left‐handed helical backbone folding motif (F. Heitz et al., Biophys. Chem. 24:149–160, 1986), and the CD spectra of gramicidins A and A− are essentially mirror images of each other. Based on hybrid channel experiments, gramicidin A− and M− channels are structurally equivalent, while gramicidin A and A− channels are nonequivalent, being of opposite helix sense. Gramicidin A− channels are therefore left‐handed, and natural gramicidin A channels in phospholipid bilayers are right‐handed β6.3‐helical dimers.
Crystallization and preliminary X‐ray diffraction studies of the human major histocompatibility antigen HLA‐B27
Authors: Gorga Joan C. , Madden Dean R. , Prendergast John K. , Wiley Don C. , Strominger Jack L. 
Published: May 2005

AbstractThe class I major histocompatibility (MHC) antigen HLA‐B27 was purified by immunoaffinity chromatography from the homozygous human B lymphoblastoid cell line LG‐2. Detergent‐soluble HLA‐B27 was cleaved with the protease papain to remove the hydrophobic transmembrane region and the cytoplasmic tail. Crystals of the resulting water‐soluble extracellular fragments were obtained in hanging drops by the vapor‐diffusion method. The crystals are triclinic, space group P1, with unit cell dimensions a = 45.9 Å, b = 71.0 Å, c = 83.7 Å, α = 79.4°, β = 88.5°, γ = 89.9°, and diffract beyond 2.5 Å resolution.
Activity of crystalline turkey egg white lysozyme
Authors: Howell P. Lynne , Warren Charles , Amatayakul‐Chantler Supavadee , Petsko Gregory A. , Hajdu Janos 
Published: May 2005

AbstractHexagonal crystals of turkey egg white lysozyme have been examined for activity in order to evaluate their potential for use in time‐resolved X‐ray crystallographic experiments. Substrates used in this study were hexa‐N‐acetylglucosamine (hexa‐GlcNAc) and a modified analogue of hexa‐GlcNAc where the terminal sugar ring was opened by reduction with tritiated sodium borohydride. This gave a labeled β‐N‐acetylglucosaminitol unit at the sixth position of the sugar chain and allowed easy quantitation of enzymatic cleavage on TLC plates. Using these substrates, it has been shown that turkey egg white lysozyme is enzymatically active in the crystal. Enzyme dispersed in the buffer surrounding the crystal does not show detectable activity under conditions relevant to an X‐ray experiment. Unmodified hexa‐GlcNAc is hydrolyzed into di‐, tri‐, and tetrasaccharides in the crystal. This cleavage pattern is different from that obtained with hen egg white lysozyme in solution and likely causes of the differences are discussed. The reduced radiolabeled oligosaccharide has a unique cleavage pattern with trisaccharides as the products. The specific activity of the enzyme with the radiolabelled analogue was 9.8 (± 1.0) × 10−7 mmol/min/mg protein at 22°C in the crystal.
Folding of RNase T1 is decelerated by a specific tertiary contact in a folding intermediate
Authors: Kiefhaber Thomas , Grunert Hans‐Peter , Hahn Ulrich , Schmid Franz X. 
Published: May 2005

AbstractThe replacement of tryptophan 59 of ribonuclease T1 by a tyrosine residue does not change the stability of the protein. However, it leads to a strong acceleration of a major, proline‐limited reaction that is unusually slow in the refolding of the wild‐type protein. The distribution of fast‐ and slow‐folding species and the kinetic mechanism of slow folding are not changed by the mutation. Trp‐59 is in close contact to Pro‐39 in native RNase T1 and probably also in an intermediate that forms rapidly during folding. We suggest that this specific interaction interferes with the trans→cis reisomerization of the Tyr‐38–Pro‐39 bond at the stage of a native‐like folding intermediate. The steric hindrance is abolished either by changing Trp‐59 to a less bulky residue, such as tyrosine, or, by a destabilization of folding intermediates at increased concentrations of denaturant. Under such conditions folding of the wild‐type protein and of the W59Y variant no longer differ. These results provide strong support for the proposal that trans→cis isomerization of Pro‐39 is responsible for the major, very slow refolding reaction of RNase T1. They also indicate that specific tertiary interactions in folding intermediates do exist, but do not necessarily facilitate folding. They can have adverse effects and decelerate ratelimiting steps by trapping partially folded structures.
Substrate mobility in a deeply buried active site: Analysis of norcamphor bound to cytochrome P‐450cam as determined by a 201‐psec molecular dynamics simulation
Authors: Bass Michael B. , Paulsen Mark D. , Ornstein Rick L. 
Published: May 2005

AbstractWhile cytochrome P‐450cam, catalyzes the hydroxylation of camphor to 5‐exo‐hydroxycamphor with 100% stereospecificity, norcamphor is hydroxylated by this enzyme yielding 45% 5‐exo‐, 47% 6‐exo‐, and 8% 3‐exo‐hydroxynorcamphor (Atkins, W.M., Sligar, S.G., J. Am. Chem. Soc. 109:3754–3760, 1987). The present study describes a 201‐psec molecular dynamics (MD) simulation of norcamphorbound cytochrome P‐450cam to elucidate the relationship between substrate conformational mobility and formation of alternative products. First, these data suggest that the product specificity is, at least partially, due to the mobility of the substrate within the active site. Second, the high mobility of norcamphor in the active site leads to an average increase in separation between the home iron and the substrate of about 1.0 Å; this increase in separation may be the cause of the uncoupling of electron transfer when norcamphor is the substrate. Third, the active site water located in the norcamphor‐bound crystal structure possesses mobility that correlates well with the spin‐state equilibrium of this enzyme–substrate complex. © 1992 Wiley‐Liss, Inc.
Molecular modeling of an antigenic complex between a viral peptide and a class I major histocompatibility glycoprotein
Authors: Rognan Didier , Reddehase Matthias J. , Koszinowski Ulrich H. , Folkers Gerd 
Published: May 2005

AbstractComputer simulation of the conformations of short antigenic peptides (5–10 residues) either free or bound to their receptor, the major histocompatibility complex (MHC)‐encoded glycoprotein H‐2 Ld, was employed to explain experimentally determined differences in the antigenic activities within a set of related peptides. Starting for each sequence from the most probable conformations disclosed by a pattern‐recognition technique, several energy‐minimized structures were subjected to molecular dynamics simulations (MD) either in vacuo or solvated by water molecules. Notably, antigenic potencies were found to correlate to the peptides propensity to form and maintain an overall α‐helical conformation through regular i,i+4 hydrogen bonds. Accordingly, less active or inactive peptides showed a strong tendency to form i,i+3 hydrogen bonds at their N‐terminal end. Experimental data documented that the C‐terminal residue is critical for interaction of the peptide with H‐2 Ld. This finding could be satisfactorily explained by a 3‐D Q.S.A.R. analysis postulating interactions between ligand and receptor by hydrophobic forces. A 3‐D model is proposed for the complex between a high‐affinity nonapeptide and the H‐2 Ld receptor. First, the H‐2 Ld molecule was built from X‐ray coordinates of two homologous proteins: HLA‐A2 and HLA‐Aw68, energy‐minimized and studied by MD simulations. With HLA‐A2 as template, the only realistic simulation was achieved for a solvated model with minor deviations of the MD mean structure from the X‐ray conformation. Water simulation of the H‐2 Ld protein in complex with the antigenic nonapeptide was then achieved with the template‐derived optimal parameters. The bound peptide retains mainly its α‐helical conformation and binds to hydrophobic residues of H‐2 Ld that correspond to highly polymorphic positions of MHC proteins. The orientation of the nonapeptide in the binding cleft is in accordance with the experimentally determined distribution of its MHC receptor‐binding residues (agretope residues). Thus, computer simulation was successfully employed to explain functional data and predicts α‐helical conformation for the bound peptide. © 1992 Wiley‐Liss, Inc.