bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circular dichroism of the parallel β helical proteins pectate lyase C and E
Authors: Sieber Volker , Jurnak Frances , Moe Gregory R. 
Published: May 2005

AbstractThe pectate lyases, PelC and PelE, have an unusual folding motif, known as a parallel β‐helix, in which the polypeptide chain is coiled into a larger helix composed of three parallel β‐sheets connected by loops having variable lengths and conformations. Since the regular secondary structure consists almost entirely of parallel β‐sheets these proteins provide a unique opportunity to study the effect of parallel β‐helical structure on circular dichroism (CD). We report here the CD spectra of PelC and PelE in the presence and absence of Ca2+, derive the parallel β‐helical components of the spectra, and compare these results with previous CD studies of parallel β‐sheet structure. The shape and intensity of the parallel β‐sheet spectrum is distinctive and may be useful in identifying other proteins that contain the parallel β‐helical folding motif. © 1995 Wiley‐Liss, Inc.
Local moves: An efficient algorithm for simulation of protein folding
Authors: Elofsson Arne , Le Grand Scott M. , Eisenberg David 
Published: May 2005

AbstractWe have enhanced genetic algorithms and Monte Carlo methods for simulation of protein folding by introducing “local moves” in dihedral space. A local move consists of changes in backbone dihedral angles in a sequential window while the positions of all atoms outside the window remain unchanged. We find three advantages of local moves: (1) For some energy functions, protein conformations of lower energy are found; (2) these low energy conformations are found in fewer steps; and (3) the simulations are less sensitive to the details of the annealing protocol. To distinguish the effectiveness of local move algorithm from the complexity of the energy function, we have used several different energy functions. These energy functions include the Profile score (Bowie et al., Science 253:164–170, 1991), the knowledge‐based energy function used by Bowie and Eisenberg 1994 (Proc. Natl. Acad. Sci. U.S.A. 91:4434–4440, 1994), two energy terms developed as suggested by Sippl and coworkers (Hendlich et al., J. Mol. Biol. 216:167180, 1990), and AMBER (Weiner and Kollman, J. Comp. Chem. 2:287‐303, 1981). Besides these energy functions we have used three energy functions that include knowledge of the native structures: the RMSD from the native structure, the distance matrix error, and an energy term based on the distance between different residue types called DBIN. In some of these simulations the main advantage of local moves is the reduced dependence on the details of the annealing schedule. In other simulations, local moves are superior to other algorithms as structures with lower energy are found. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray diffraction studies of complexes between an influenza hemagglutinin and fab fragments of two different monoclonal antibodies
Authors: Gigant Benoît , Fleury Damien , Bizebard Thierry , Skehel John J. , Knossow Marcel 
Published: May 2005

AbstractFab fragments from two different monoclonal antibodies (BH151 and HC45) which bind to the same antigenic region of the influenza hemagglutinin were crystallized as complexes with the hemagglutinin. The complexes crystallize in PEG 600, pH 6.0, and PEG 2000, pH 8.5, respectively. Both crystals belong to space group P321, with very similar unit cell dimensions. © 1995 Wiley‐Liss, Inc.
Why do protein architectures have boltzmann‐like statistics?
Authors: Finkelstein Alexei V. , Badretdinov Azat Ya. , Gutin Alexander M. 
Published: May 2005

AbstractA theoretical study has shown that the occurrence of various structural elements in stable folds of random copolymers is exponentially dependent on the own energy of the element. A similar occurrence‐on‐energy dependence is observed in globular proteins1 from the level of amino acid conformations to the level of overall architectures. Thus, the structural features stabilized by many random sequences are typical of globular proteins while the features rarely observed in proteins are those which are stabilized by only a minor part of the random sequences. © 1995 Wiley‐Liss, Inc.
Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis
Authors: Hayward Steven , Kitao Akio , Gō Nobuhiro 
Published: May 2005

AbstractA comparison of a normal mode analysis and principal component analysis of a 200‐ps molecular dynamics trajectory of bovine pancreatic trypsin inhibitor in vacuum has been made in order to further elucidate the harmonic and anharmonic aspects in the dynamics of proteins. An anharmonicity factor is defined which measures the degree of anharmonicity in the modes, be they principal modes or normal modes, and it is shown that the principal mode system naturally divides into anharmonic modes with peak frequencies below 80 cm−1, and harmonic modes with frequencies above this value. In general the larger the mean‐square fluctuation of a principal mode, the greater the degree of anharmonicity in its motion. The anharmonic modes represent only 12% of the total number of variables, but account for 98% of the total mean‐square fluctuation. The transitional nature of the anharmonic motion is demonstrated. The results strongly suggest that in a large subspace, the free energy surface, as probed by the simulation, is approximated by a multi‐dimensional parabola which is just a resealed version of the parabola corresponding to the harmonic approximation to the conformational energy surface at a single minimum. After 200 ps, the resealing factor, termed the “normal mode resealing factor,” has apparently converged to a value whereby the mean‐square fluctuation within the subspace is about twice that predicted by the normal mode analysis. © 1995 Wiley‐Liss, Inc.
Three‐dimensional model of the α‐subunit of bacterial luciferase
Authors: Sandalova Tatyana , Lindqvist Ylva 
Published: May 2005

AbstractThe predicted secondary structure of both subunits of bacterial luciferase is in accordance with a regular 8‐fold α/β‐barrel structure. The 3D profile1,2 confirmed that luciferase subunits are compatible with the α/β‐barrel despite the absence of sequence similarity with any α/β‐barrel protein. The three‐dimensional structure of 260 residues of the α‐chain of luciferase was modeled from coordinates of glycolate oxidase and then energy minimized. The model obtained satisfies the criteria for the structure of a globular protein and is in accordance with known experimental data. From the model it is possible to predict active site residues involved in binding and catalysis. These predictions, and thus also the model, can be tested by protein engineering experiments. © 1995 Wiley‐Liss, Inc.
A critical assessment of comparative molecular modeling of tertiary structures of proteins*
Authors: Mosimann Steven , Meleshko Ron , James Michael N. G. 
Published: May 2005

AbstractIn spite of the tremendous increase in the rate at which protein structures are being determined, there is still an enormous gap between the numbers of known DNA‐derived sequences and the numbers of three‐dimensional structures. In order to shed light on the biological functions of the molecules, researchers often resort to comparative molecular modeling. Earlier work has shown that when the sequence alignment is in error, then the comparative model is guaranteed to be wrong. In addition, loops, the sites of insertions and deletions in families of homologous proteins, are exceedingly difficult to model. Thus, many of the current problems in comparative molecular modeling are minor versions of the global protein folding problem. In order to assess objectively the current state of comparative molecular modeling, 13 groups submitted blind predictions of seven different proteins of undisclosed tertiary structure. This assessment shows that where sequence identity between the target and the template structure is high (> 70%), comparative molecular modeling is highly successful. On the other hand, automated modeling techniques and sophisticated energy minimization methods fail to improve upon the starting structures when the sequence identity is low (∼30%). Based on these results it appears that insertions and deletions are still major problems. Successfully deducing the correct sequence alignment when the local similarity is low is still difficult. We suggest some minimal testing of submitted coordinates that should be required of authors before papers on comparative molecular modeling are accepted for publication in journals. © 1995 Wiley‐Liss, Inc.
Evaluation of comparative protein modeling by MODELLER
Authors: Šali Andrej , Potterton Liz , Yuan Feng , van Vlijmen Herman , Karplus Martin 
Published: May 2005

AbstractWe evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for comparative protein modeling by satisfaction of spatial restraints. The models have good stereochemistry and are at least as similar to the crystallographic structures as the closest template structures. The largest errors occur in the regions that were not aligned correctly or where the template structures are not similar to the correct structure. These regions correspond predominantly to exposed loops, insertions of any length, and non‐conserved side chains. When a template structure with more than 40% sequence identity to the target protein is available, the model is likely to have about 90% of the mainchain atoms modeled with an rms deviation from the X‐ray structure of ≈ 1 Å, in large part because the templates are likely to be that similar to the X‐ray structure of the target. This rms deviation is comparable to the overall differences between refined NMR and X‐ray crystallography structures of the same protein. © 1995 Wiley‐Liss, Inc.
Threading a database of protein cores
Authors: Madej Thomas , Gibrat Jean‐François , Bryant Stephen H. 
Published: May 2005

AbstractWe present an analysis of 10 blind predictions prepared for a recent conference, “Critical Assessment of Techniques for Protein Structure Prediction.”1 The sequences of these proteins are not detectably similar to those of any protein in the structure database then available, but we attempted, by a threading method, to recognize similarity to known domain folds. Four of the 10 proteins, as we subsequently learned, do indeed show significant similarity to then‐known structures. For 2 of these proteins the predictions were accurate, in the sense that a similar structure was at or near the top of the list of threading scores, and the threading alignment agreed well with the corresponding structural alignment. For the best predicted model mean alignment error relative to the optimal structural alignment was 2.7 residues, arising entirely from small “register shifts” of strands or helices. In the analysis we attempt to identify factors responsible for these successes and failures. Since our threading method does not use gap penalties, we may readily distinguish between errors arising from our prior definition of the “cores” of known structures and errors arising from inherent limitations in the threading potential. It would appear from the results that successful substructure recognition depends most critically on accurate definition of the “fold” of a database protein. This definition must correctly delineate substructures that are, and are not, likely to be conserved during protein evolution. © 1995 Wiley‐Liss, Inc.
Progress in fold recognition
Authors: Flöckner Hannes , Braxenthaler Michael , Lackner Peter , Jaritz Markus , Ortner Maria , Sippl Manfred J. 
Published: May 2005

AbstractThe prediction experiment reveals that fold recognition has become a powerful tool in structural biology. We applied our fold recognition technique to 13 target sequences. In two cases, replication terminating protein and prosequence of subtilisin, the predicted structures are very similar to the experimentally determined folds. For the first time, in a public blind test, the unknown structures of proteins have been predicted ahead of experiment to an accuracy approaching molecular detail. In two other cases the approximate folds have been predicted correctly. According to the assessors there were 12 recognizable folds among the target proteins. In our postprediction analysis we find that in 7 cases our fold recognition technique is successful. In several of the remaining cases the predicted folds have interesting features in common with the experimental results. We present our procedure, discuss the results, and comment on several fundamental and technical problems encountered in fold recognition. © 1995 Wiley‐Liss, Inc.
Evaluation of current techniques for Ab initio protein structure prediction
Authors: Defay Tom , Cohen Fred E. 
Published: May 2005

AbstractThe results of a protein structure prediction contest are reviewed. Twelve different groups entered predictions on 14 proteins of known sequence whose structures had been determined but not yet disseminated to the scientific community. Thus, these represent true tests of the current state of structure prediction methodologies. From this work, it is clear that accurate tertiary structure prediction is not yet possible. However, protein fold and motif prediction are possible when the motif is recognizably similar to another known structure. Internal symmetry and the information inherent in an aligned family of homologous sequences facilitate predictive efforts. Novel folds remain a major challenge for prediction efforts. © 1995 Wiley‐Liss, Inc.
Toward understanding the structure and interactions of microtubules and motor proteins
Authors: Wade R. H. , Horowitz R. , Milligan R. A. 
Published: May 2005

AbstractTo obtain an overall three‐dimensional picture of the interaction between microtubules and the motor proteins of the kinesin family it will be necessary to take account of both atomic resolution structures obtained by X‐ray crystallography and medium resolution reconstructions obtained by electron cryomicroscopy. We examine the problems associated with obtaining the required structural information from electron micrographs of vitreous ice‐embedded microtubules decorated with motor domains. We find that the minus‐end directed motor, ncd, decorates microtubules with an 80 Å periodicity as for kinesin. Our theoretical analysis and experiments with ncd illustrate the difficulty in determining unambiguously the surface lattice organization by diffraction analysis of micrographs. 3D reconstructions of decorated microtubules are required to accurately locate the motor domains. Helical diffraction theory is not usually applicable because microtubules are cylindrical structures that rarely have complete helical symmetry. We propose using a back‐projection method based on the long pitch helices formed by individual protofilaments. Model reconstructions show that this approach is feasible. © 1995 Wiley‐Liss, Inc.
Binding geometry of α‐helices that recognize DNA
Authors: Suzuki Masashi , Gerstein Mark 
Published: May 2005

AbstractMany transcription factors have an α‐helix that binds to DNA bases in a specific fashion. The DNA‐binding geometry of these recognition helices varies substantially. We define a set of parameters to describe the binding geometry of recognition helices and analyze specific stereochemical elements that determine particular geometries. Because the convex surface of the helix must fit into the concave surface of the DNA major groove, the number of degrees of freedom of the recognition helix is reduced from a possible six to a single angle, which we call α. The chemically interacting DNA bases and amino acid residues must lie along a common line and have the same spacing along it. This pairing of base positions with residue positions seems to restrict the binding geometry further to a set of discrete values for α. © 1995 Wiley‐Liss, Inc.
Fermenter production of an artificial fab fragment, rationally designed for the antigen cystatin, and its optimized crystallization through constant domain shuffling
Authors: Schiweck Wolfram , Skerra Arne 
Published: May 2005

AbstractThe synthetic antibody model “M41” was rationally designed with a binding site complementary to chicken egg white cystatin as the prescribed antigen. In order to permit comparison between the computer model and an experimental three‐dimensional structure of the artificial protein, its X‐ray crystallographic analysis was pursued. For this purpose, M41 was expressed as a recombinant Fab fragment in E. coli by medium cell density fermentation employing the tightly regulated tetracycline promoter. The Fab fragment was efficiently purified via a His‐6 tail fused to its heavy chain and immobilized metal affinity chromatography. To raise the chances for the productive formation of crystal packing contacts, three versions of the Fab fragment were generated with differing constant domains. One of these, the variant with murine CK and CH1γ1 domains, was successfully crystallized by microseeding in a sitting drop. The orthorhombic crystals exhibited symmetry of the space group P212121 with unit cell dimensions a = 104.7 Å, b = 113.9 Å, c = 98.8 Å and diffracted X‐rays to a nominal resolution of 2.5 Å. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray crystallographic analysis of ImmE7 protein of colicin E7
Authors: Ku Wen‐Yen , Wang Ching‐Shao , Chen Chieh‐Yen , Chak Kin‐Fu , Safo Martin K. , Yuan Hanna S. 
Published: May 2005

AbstractThe ImmE7 protein, which can bind specifically to the DNase colicin E7 and neutralize its bactericidal activity, has been purified and crystallized in two different crystal forms by vapor diffusion method. The orthorhombic crystals belong to space group I222 or I212121 and have unit cell dimensions a = 75.1 Å, b = 50.5 Å, and c = 45.4 Å. The second form is monoclinic space group P21 with ceil dimensions a = 29.3 Å, b = 102.7 Å, c = 53.0 Å and β = 91.5°. The orthorhombic crystals diffract to 1.8 Å resolution, and are suitable for high‐resolution X‐ray analysis. © 1995 Wiley‐Liss, Inc.
Crystallization and X‐ray analysis of a single fab binding domain from protein L of Peptostreptococcus magnus
Authors: Sohi Maninder K. , Wan Tommy , Sutton Brian J. , Atkinson Tony , Atkinson Max A. , Murphy Jonathan P. , Bottomley Stephen P. , Gore Michael G. 
Published: May 2005

AbstractProtein L is a multi domain cell wall constituent of certain strains of Peptostreptococcus magnus which binds to the variable domain of immunoglobulin κ‐light chains. A single immunoglobulin‐binding domain of Mr = 9000 from this protein has been isolated and crystallized. The crystals are of space group P42212, with cell dimensions a = b = 66.9 Å, c = 68.3 Å, and diffract to at least 2.2 Å resolution. The asymmetric unit of the crystal contains two molecules of the protein L domain, related by a noncrystallographic 2‐fold axis, as revealed by a self‐rotation function calculated with native diffraction data. © 1995 Wiley‐Liss, Inc.
Microstructural modification of nc‐Si/SiOx films during plasma‐enhanced chemical vapor deposition
Authors: Zhang X. W. 
Published: May 2005

AbstractNanocrystalline‐silicon embedded silicon oxide films are prepared by plasma‐enhanced chemical vapor deposition (PECVD) at 300 °C without post‐heat treatment. Measurements of XPS, IR, XRD, and HREM are performed. Microstructural modifications are found occurring throughout the film deposition. The silica network with a high oxide state is suggested to be formed directly under the abduction of the former deposited layer, rather than processing repeatedly from the original low‐oxide state of silica. Nanocrystalline silicon particles with a size of 6–10 nm are embedded in the SiOx film matrix, indicating the potential application in Si‐based optoelectronic integrity. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A time‐of‐flight mass analyzer with high resolving power
Authors: Grix R. , Kutscher R. , Li G. , Grüner U. , Wollnik H. , Matsuda H. 
Published: May 2005

AbstractIt is shown that time‐of‐flight mass analyzers are capable of reaching high mass resolving powers as compared to sector field instruments. By combining a new electron‐impact ion source with an optimized grid‐free ion mirror, mass resolving powers m/Δm of about 20000 are reached.
Cytidylate cyclase activity: Identification of cytidine 3′,5′‐cyclic monophosphate and four novel cytidine cyclic phosphates as biosynthetic products from cytidine triphosphate
Authors: Newton R. P. , Hakeem N. A. , Salvage B. J. , Wassenaar G. , Kingston E. E. 
Published: May 2005

AbstractIdentification of cytidine 3′,5′‐cyclic monophosphate (cyclic CMP) as one of the products resulting from the incubation of dialysed cell‐free preparations from rat brain, liver and kidney with cytidine 5′‐triphosphate (CTP) is described. The non‐acidic precipitable products after incubation of the tissue preparations with unlabelled, with 14C‐single labelled, and with 14C‐ and 32P‐dual labelled CTP were examined by thin‐layer chromatography and high‐pressure liquid chromatography, isotopic ratio determination, UV absorbance spectrophotometry, selective hydrolysis with nucleotidase, phosphodiesterase and acid, and by fast atom bombardment mass spectrometry with mass‐analysed ion kinetic energy spectrum scanning. In addition to cyclic CMP and unchanged CTP, the products of the reaction were found to include cytidine monophosphate (CMP) and cytidine diphosphate (CDP) together with four novel cytidine compounds identified as cytidine 3′,5′‐cyclic pyrophosphate, cytidine 2′‐monosphosphate 3′,5′‐cyclic monophosphate, cytidine 2′‐O‐aspartyl‐3′,5′‐cyclic monophosphate and cytidine 2′‐O‐glutamyl‐3′,5′‐cyclic monosphate. The evidence presented constitutes conclusive proof of the natural occurrence of cytidylate cyclase activity; the four novel cytidine cyclic phosphates described provide a feasible explanation of the discrepancies in previous reports which have led to the controversy which exists concerning the existence of cytidylate cyclase activity.
Identification of C4H9O+ isomers by collisional activation mass spectrometry
Authors: Maquestiau André , Beugnies Didier , Flammang Robert , Houriet Raymond , Bouchoux Guy 
Published: May 2005

AbstractC4H9O+ ions have been produced in the high pressure ion source of a triple sector mass spectrometer either by protonation of C4H8O isomers using methane as the reagent gas, or by methylation of C3H6O isomers using iodomethane or chloromethane as reagent gas. The collisional activation spectra of these mass selected C4H9O+ ions (m/z 73) allow the identification of several stable isomers in the gas phase.
Differentiation of methyl substituted fluorenes, anthracenes and benz[a]anthracenes using surface‐catalyzed oxidation reactions and negative ion chemical ionization mass spectrometry
Authors: Stemmler Elizabeth A. , Buchanan Michelle V. , Marshall Alan G. 
Published: May 2005

AbstractMethyl‐substituted polycyclic aromatic hydrocarbons (PAH) are shown to undergo surface‐catalyzed reactions with oxygen. These reactions generate oxidized products, which include aldehydes, quinones, and anhydrides. The products dominate the O2/N2 negative ion chemical ionization (NICI) mass spectra of methyl‐PAH when the ion source temperature is elevated to 300°C. The NICI mass spectra of methyl‐PAH measured under these conditions show ions that can be used to distinguish the position of methyl groups substituted on fluorene, anthracene, and benz[a]anthracene isomers.