bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solvent polarity‐dependent structural refolding: A CD and NMR study of a 15 residue peptide
Authors: v. Stosch Andreas Graf , Jiménez M. Angeles , Kinzel Volker , Reed Jennifer 
Published: May 2005

AbstractA close association between the HIV surface protein gp120 and the CD4 T cell receptor initiates the viral multiplication cycle. A 15 amino acid peptide (LAV) within the CD4 binding domain of gp 120 has been shown to retain receptor binding ability. The structural behavior of the LAV peptide has been studied by CD and NMR methods in aqueous solution and upon addition of trifluoroethanol (TFE) to emulate the relatively apolar conditions at the membrane bound receptor. Previous work has shown that the LAV peptide folds into a β‐pleated structure in more polar buffer/TFE mixtures, while a concerted structural change can be observed at a concentration of 60% TFE (v/v). This abrupt, cooperative refolding from a regular β‐sheet to a helical secondary structure is known as “switch” behavior. Former CD experiments with LAV sequence variants have supported the assumption that four amino acids at the N‐terminus (LPCR) are indispensable for the “switch.” The tetrad has a strong β‐turn forming potential. The suggestion has been formulated that the tetrad can act as a nucleation site governing the refolding. The present NMR study of the LAV peptide in TFE gives evidence for a 310‐helix suggesting that the tetrad adopts a type III β‐turn and promotes the formation of a similar bend in the next overlapping tetrad until the sequence is restructured into a 310‐helix at a critical polarity favoring intrachain hydrogen bonds. © 1995 Wiley‐Liss, Inc.
Parametric sensitivity analysis of avian pancreatic polypeptide (APP)
Authors: Zhang Hong , Wong Chung F. , Thacher Tom , Rabitz Herschel 
Published: May 2005

AbstractComputer simulations utilizing a classical force field have been widely used to study biomolecular properties. It is important to identify the key force field parameters or structural groups controlling the molecular properties. In the present paper the sensitivity analysis method is applied to study how various partial charges and solvation parameters affect the equilibrium structure and free energy of avian pancreatic polypeptide (APP). The general shape of APP is characterized by its three principal moments of inertia. A molecular dynamics simulation of APP was carried out with the OPLS/Amber force field and a continuum model of solvation energy. The analysis pinpoints the parameters which have the largest (or smallest) impact on the protein equilibrium structure (i.e., the moments of inertia) or free energy. A display of the protein with its atoms colored according to their sensitivities illustrates the patterns of the interactions responsible for the protein stability. The results suggest that the electrostatic interactions play a more dominant role in protein stability than the part of the solvation effect modeled by the atomic solvation parameters. © 1995 Wiley‐Liss, Inc.
Metal search: A computer program that helps design tetrahedral metal‐binding sites
Authors: Clarke Neil D. , Yuan Shao‐Min 
Published: May 2005

AbstractWe describe a computer program (Metal Search) that helps design tetrahedrally coordinated metal binding sites in proteins of known structure. The program takes as input the backbone coordinates of a protein and outputs lists of four residues that might form tetrahedral sites if wild‐type amino acids were replaced by cysteine or histidine. The program also outputs the side chain dihedral angles of the amino acids and the coordinates of the predicted metal ion. The only function evaluated by Metal Search is the ability of side chains to meet simple geometric criteria for formation of a tetrahedral site, but these criteria are sufficient to produce a manageably small list that can then be evaluated by other means. The program has been used in the introduction of zinc binding sites in the designed four‐helix bundle protein α 4 and in the B1 domain of streptococcal protein G, and in both cases the tetrahedral coordination of a bound metal ion has been confirmed1 (Klemba, M., Gardner, K. H., Marino, S., Clarke, N. D., and Regan, L., Nature: Structural Biology 2:368–373, 1995). © 1995 Wiley‐Liss, Inc.
A strategy for theoretical binding constant, Ki, calculations for neuraminidase aromatic inhibitors designed on the basis of the active site structure of influenza virus neuraminidase
Authors: Jedrzejas Marek J. , Singh Sangeeta , Brouillette Wayne J. , Air Gillian M. , Luo Ming 
Published: May 2005

AbstractNeuraminidase (NA) is one of the two major surface antigens of influenza virus. It plays an indispensable role in the release and spread of progeny virus particles during infection. NA inhibitors reduce virus infection in animals. To improve the clinical efficacy of NA inhibitors, we have begun the design of non‐carbohydrate inhibitors based on the active site structure of NA. The approach is an iterative process of ligand modeling and electrostatic calculations followed by chemical synthesis of compounds, biological testing, and NA‐inhibitor complex structure determination by X‐ray crystallography. A strategy has been developed to calculate Ki for newly designed inhibitors. The calculations using the DelPhi program were performed for carbohydrate inhibitors and three preliminary benzoic acid inhibitors of neuraminidase (BANA) that have been synthesized and shown to bind to the active site of NA in the crystal structure. The calculated Kis of these inhibitors have an enlightening agreement with their in vitro biological activities. This demonstrates that the calculations produce informative results on the affinity of modeled inhibitors. GRID maps were also calculated and several pockets were identified for accepting possible new ligands. The calculated Kis for newly designed ligands suggest that these potential compounds will have high inhibitory activities. © 1995 Wiley‐Liss, Inc.
Purification, crystallization, and preliminary X‐ray analysis of PepX, an X‐prolyl dipeptidyl aminopeptidase from Lactococcus lactis
Authors: Chich Jean‐François , Rigolet Pascal , Nardi Michèle , Gripon Jean‐Claude , Ribadeau‐Dumas Bruno , Brunie Simone 
Published: May 2005

AbstractThe X‐prolyl dipeptidyl aminopeptidase PepX, a serine peptidase isolated originally from Lactococcus lactis subsp lactis NCDO 763, was cloned and overproduced in Escherichia coli. The enzyme was isolated in its active form in two purification steps. Crystals of PepX were grown by the hanging drop vapor diffusion method using polyethyleneglycol 4000 as precipitant at pH 5.0. The crystals are orthorhombic with cell dimensions a = 92.8 Å, b = 102.6 Å, and c = 101.6 Å, space group P21212, and probably contain one monomer of 87.5 kDa in the asymmetric unit. The crystals, very stable under X‐rays, diffract to at least 2.2 Å and are suitable for high‐resolution structural analysis. © 1995 Wiley‐Liss, Inc.
Crystallization of intact monoclonal antibodies
Authors: Harris Lisa J. , Skaletsky Eileen , McPherson Alexander 
Published: May 2005

AbstractAttempts were made to crystallize four monoclonal antibodies, one IgG2ak and three IgG1k. Using a PEG 3350 screen combined with detergents, and developed from our experiments with an IgG2ak antibody specific for canine lymphoma cells,1,2 crystals have now been obtained of two of these four immunoglobulins, an antiphenytoin and an antiphenobarbital antibody. A complex between the antiphenobarbital antibody and its drug antigen crystallized as well. The antibody for phenytoin has, to this point, produced only clustered microcrystals, marginally suitable for X‐ray analysis. Single crystals of the IgG1k antibody against phenobarbital, however, were characterized by X‐ray diffraction to be primitive monoclinic, with unit cell dimensions a = 67 Å, b = 193 Å, c = 74 Å, and β = 110°. These crystals have an entire IgG1k molecule as the asymmetric unit and they diffract to at least 3.2 Å resolution. © 1995 Wiley‐Liss, Inc.
Homology modeling by the ICM method
Authors: Cardozo Timothy , Totrov Maxim , Abagyan Ruben 
Published: May 2005

AbstractFive models have been built by the ICM method for the Comparative Modeling section of the Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. The targets have homologous proteins with known three‐dimensional structure with sequence identity ranging from 25 to 77%. After alignment of the target sequence with the related three‐dimensional structure, the modeling procedure consists of two subproblems: side‐chain prediction and loop prediction. The ICM method approaches these problems with the following steps: (1) a starting model is created based on the homologous structure with the conserved portion fixed and the noncon‐served portion having standard covalent geometry and free torsion angles; (2) the Biased Probability Monte Carlo (BPMC) procedure is applied to search the subspaces of either all the nonconservative side‐chain torsion angles or torsion angles in a loop backbone and surrounding side chains. A special algorithm was designed to generate low‐energy loop deformations. The BPMC procedure globally optimizes the energy function consisting of ECEPP/3 and solvation energy terms. Comparison of the predictions with the NMR or crystallographic solutions reveals a high proportion of correctly predicted side chains. The loops were not correctly predicted because imprinted distortions of the backbone increased the energy of the near‐native conformation and thus made the solution unrecognizable. Interestingly, the energy terms were found to be reliable and the sampling of conformational space sufficient. The implications of this finding for the strategies of future comparative modeling are discussed. © 1995 Wiley‐Liss, Inc.
The use of position‐specific rotamers in model building by homology
Authors: Chinea G. , Padron G. , Hooft R. W. W. , Sander C. , Vriend G. 
Published: May 2005

AbstractIn this study we concentrate on replacing side chains as a subtask of model building by homology. Two problems arise. How to determine potential low energy rotamers? And how to avoid the combinatorial explosion that results from the combination of many residues for which multiple good rotamers are predicted? We attempt to solve these problems by choosing position‐specific rather than generalized rotamers and by sorting the residues that have to be modelled as a function of their freedom in rotamer space. The practical advantages of our method are the quality of the models for cases of high backbone similarity, the small amount of human intervention needed, and the fact that the method automatically estimates the reliability with which each residue has been modeled. Other methods described in this issue are probably more suitable if large backbone rearrangements or loop insertions and deletions need to be modeled. © 1995 Wiley‐Liss, Inc.
Analysis of six protein structures predicted by comparative modeling techniques
Authors: Harrison Robert W. , Chatterjee Devjani , Weber Irene T. 
Published: May 2005

AbstractThe protein structures of six comparative modeling targets were predicted in a procedure that relied on improved energy minimization, without empirical rules, to position all new atoms. The structures of human nucleoside diphosphate kinase NM23‐H2, HPr from Mycoplasma capricolum, 2Fe‐2S ferredoxin from Haloarcula marismortui, eosinophil‐derived neurotoxin (EDN), mouse cellular retinoic acid protein I (CRABP1), and P450eryf were predicted with root mean square deviations on Cα atoms of 0.69, 0.73, 1.11, 1.48, 1.69, and 1.73 Å, respectively, compared to the target crystal structures. These differences increased as the sequence similarity between the target and parent proteins decreased from about 60 to 20% identity. More residues were predicted than form the common region shared by the two crystal structures. In most cases insertions or deletions between the target and the related protein of known structure were not correctly positioned. One two residue insertion in CRABP1 was predicted in the correct conformation, while a nine residue insertion in EDN was predicted in the correct spatial region, although not in the correct conformation. The positions of common cofactors and their binding sites were predicted correctly, even when overall sequence similarity was low. © 1995 Wiley‐Liss, Inc.
Docking of a human rhinovirus neutralizing antibody onto the viral capsid
Authors: Tormo José , Centeno Nuria B. , Fontana Emilia , Bubendorfer Thomas , Fita Ignacio , Blaas Dieter 
Published: May 2005

AbstractThe structure of the complex between the Fab fragment of a human rhinovirus serotype 2 (HRV2) neutralizing antibody (8F5) and a cross‐reactive synthetic peptide derived from the viral capsid protein VP2 has been recently determined by crystallographic methods.1 The conformation adopted by the peptide was very similar to and could be superimposed onto the corresponding region of the viral protein VP2 of human rhinovirus 1A (HRV1A) whose three‐dimensional structure is known.2 The structure of the Fab fragment determined in the complex was docked onto the viral capsid using the superimposition transformation found for the peptide. In the resulting model the Fab protrudes almost radially to about 60 Å from the surface of the virion without any major steric problem. The Fab fragment was then placed on each one of the 60 equivalent epitopes using the T = 1 icosahedral symmetry of the virus. The closest pairs of Fab fragments are related by viral 2‐fold axes and run almost parallel to each other without clashing. These axes of symmetry from the viral particle could thus be coincident with the dyad axes of the antibodies. Furthermore, comparison of the three‐dimensional structure of the Fab/peptide complex with the structure of the Fab fragment alone3 indicates that the flexibility of the antibody's elbow would facilitate bivalent attachment to the same viral particle. In accordance with the docking results, experimental determination of the stoichiometry of binding yielded a ratio of 30 IgG molecules per virion also suggesting bivalent attachment of antibody 8F5 onto the viral particle. The neutralization of viral infectivity, being neither aggregation (this paper) nor inhibition of receptor binding,4 might be mainly achieved by reducing viral spread from cell to cell and/or inhibition of uncoating. © 1995 Wiley‐Liss, Inc.
Crystallographic structure of metal‐free concanavalin A at 2.5 Å resolution
Authors: Bouckaert Julie , Loris Remy , Poortmans Freddy , Wyns Lode 
Published: May 2005

AbstractThe three‐dimensional structure of demetallized concanavalin A has been determined at 2.5 Å resolution and refined to a crystallographic R‐factor of 18%. The lectin activity of concanavalin A requires the binding of both a transition metal ion, generally Mn2+, and a Ca2+ ion in two neighboring sites in close proximity to the carbohydrate binding site. Large structural differences between the native and the metal‐free lectin are observed in the metal‐binding region and consequently for the residues involved in the specific binding of saccharides. The demetallization invokes a series of conformational changes in the protein backbone, apparently initiated mainly by the loss of the calcium ion. Most of the Mn2+ ligands retain their position, but the Ca2+ binding site is destroyed. The Ala207‐Asp208 peptide bond, in the β‐strand neighboring the metal‐binding sites, undergoes a cis to trans isomerization. The cis conformation for this bond is a highly conserved feature among the leguminous lectins and is critically maintained by the Ca2+ ion in metal‐bound concanavalin A. A further and major change adjacent to the isomerized bond is an expansion of the loop containing the monosaccharide ligand residues Leu99 and Tyr100. The dispersion of the ligand residues for the monosaccharide binding site (Asn14, Agr228, Asp208, Leu99, and Tyr100) in metalfree concanavalin A abolishes the lectin's ability to bind saccharides. Since the quaternary structure of legume lectins is essential to their biological role, the tetramer formation was analyzed. In the crystal (pH 5), the metal‐free concanavalin A dimers associate into a tetramer that is similar to the native one, but with a drastically reduced number of inter‐dimer interactions. This explains the tetramer dissociation into dimers below pH values of 6.5. © 1995 Wiley‐Liss, Inc.
Protein–protein interaction at crystal contacts
Authors: Janin Joel , Rodier Francis 
Published: May 2005

AbstractPacking contacts are crystal artifacts, yet they make use of the same forces that govern specific recognition in protein‐protein complexes and oligomeric proteins. They provide examples of a nonspecific protein‐protein interaction which can be compared to biologically relevant ones. We evaluate the number and size of pairwise interfaces in 152 crystal forms where the asymmetric unit contains a monomeric protein. In those crystal forms that have no element of 2‐fold symmetry, we find that molecules form 8 to 10 pairwise interfaces. The total area of the surface buried on each molecule is large, up to 4400 Å2. Pairwise interfaces bury 200–1200 Å2, like interfaces generated at random in a computer simulation, and less than interfaces in protease‐inhibitor or antigen‐antibody complexes, which bury 1500 Å2 or more. Thus, specific contacts occurring in such complexes extend over a larger surface than nonspecific ones. In crystal forms with 2‐fold symmetry, pairwise interfaces are fewer and larger on average than in the absence of 2‐fold symmetry. Some bury 1500–2500 Å2, like interfaces in oligomeric proteins, and create “crystal oligomers” which may have formed in the solution before crystallizing. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary crystallographic analysis of an amylopullulanase from the hyperthermophilic archaeon Pyrococcus woesei
Authors: Knapp Stefan , Rüdiger Andrea , Antranikian Garabed , Jorgensen Per L. , Ladenstein Rudolf 
Published: May 2005

AbstractThe thermostable amylopullulanase from Pyrococcus woesei was crystallized. Crystals, suitable for a crystallographic analysis up to a size of 0.6 mm in their longest dimension, have been obtained by the vapor diffusion method in a solution containing polyethyleneglycol 4000 (PEG 4000), isopropanol, and Tris/Cl− buffer pH 7.5. Crystals grown under these conditions form hexagonal rods and diffract to a maximum resolution of 3 Å. The crystals belong to the trigonal lattice type with the spacegroup P3121 or P3221, respectively, have the cell dimensions a = b = 96.8 Å, c = 196.2 Å, α = β = 90°,γ = 120°. The crystals have a theoretical packing density of 2.7 Å3/Da, assuming one molecule with a molecular weight of 88.8 kDa in the asymmetric unit. Furthermore the self‐rotation analysis of the dataset revealed only crystallographic symmetries. The merged native data of two crystals resulted in a 88% complete dataset. © 1995 Wiley‐Liss, Inc.
Stereochemistry and the mass spectra of some 1,3‐ and 3,1‐perhydrobenzoxazines
Authors: Pihlaja Kalevi , Vainiotalo Pirjo , Fülöp Ference , Bernáth Gábor 
Published: May 2005

Abstractcis‐Anellated 3‐methyl‐ (1) and cis (2)‐ and trans (3)‐anellated 2,3‐dimethyl‐1,3‐perhydrobenzoxazines and the corresponding 3,1‐perhydrobenzoxazines (4, 5a, 5b, and 6, respectively) have been prepared and their configurations assigned with 1H NMR spectroscopy. The electron‐impact induced fragmentations differentiate clearly the two sets of isomers since only the [MH]+ and [MMe]+ ions from 1–3 exhibit an appreciable retro Diels‐Alder reaction giving rise to the ions m/z 72 and/or m/z 86. Besides the main reaction, elimination of methyl radical, isomers 5a, 5b and 6 also eliminate C3H and C2H3O− forming the ions [C7H12NO]+ and [C8H16N]+, at m/z 126. The formation of the former is most favourable for 5a, 5b both for reasons of chemical composition and stereochemistry. The ion C6H10NO+ at m/z 112 represents the base peak of compound 4, i.e., a methyl group at the 2‐position is a better leaving group than a hydrogen atom and the ring nitrogen assists the α ‐cleavage of the cyclohexane ring in this case. Even the mass spectra of the isomeric cis‐ and trans‐annellated forms (2 vs 3 and 5a, 5b vs 6) can be distinguished from each other on the basis of some intensity differences caused by stereochemical effects. However, the two epimeric cis forms 5a and 5b gave indistinguishable spectra. The characteristic decompositions have been verified by low resolution, high resolution, metastable and collision‐induced dissociation techniques. The compounds studied could not be differentiated based on their ammonia or isobutane chemical‐ionization spectra.
Application of continuous‐flow liquid chromatography/fast‐atom bombardment mass spectrometry to the analysis of diagnostic acylcarnitines in human urine
Authors: Norwood Daniel L. , Kodo Naoki , Millington David S. , Gaskell S. J. 
Published: May 2005

AbstractAcylcarnitine profiles of diagnostic value were generated from the equivalent of 0.1 μL of raw urine using the continuous‐flow liquid chromatography/fast‐atom bombardment mass spectrometry (LC/FAB‐MS) interface for sample introduction. Further analysis was accomplished by gradient LC/MS using a commercially available packed fused‐silica microbore column.
Combined supercritical‐fluid chromatography/mass spectrometry in the analysis of diuron in plasma using on‐line phase‐system switching
Authors: Niessen W. M. A. , de Kraa M. A. G. , Verheij E. R. , Bergers P. J. M. , La Vos G. F. , Tjaden U. R. , van der Greef J. 
Published: May 2005

AbstractOn‐line sample pretreatment by means of the phase‐system switching approach is an interesting technique for the analysis of aqueous samples, e.g., plasma, by means of supercritical‐fluid chromatography. In order to analyse plasma samples the following analytical procedure is used. The plasma sample is injected on to a short precolumn, which is washed with water and subsequently dried with nitrogen. Next, the solutes are desorbed with the supercritical mobile phase, analysed with packed‐column supercritical‐fluid chromatography and detected with either a UV detector or a mass spectrometer, equipped with a moving‐belt interface. The herbicide diuron is selected as a test compound to study the feasibility of this approach. Using a selective detector the procedure is sufficiently sensitive to detect diuron in plasma, but not appropriate to detect the diuron metabolites in a post‐mortem plasma sample. These have been identified with liquid chromatography/mass spectrometry. The detection limit of diuron in plasma using the procedure described is about 30 ng/mL.
Mass spectrometry of sulphur‐containing compounds. 3. The behaviour of some diastereomeric β‐hydroxy‐γ‐fluoro alkyl aryl sulphoxides
Authors: Traldi P. , Bravo P. , Resnati G. , Bortolini O. 
Published: May 2005

AbstractThe electron ionization and chemical ionization mass spectrometry of some diastereomeric β‐hydroxy‐γ‐fluoro alkyl aryl sulphoxides is described and the mechanisms of the common fragmentation patterns are discussed with the aid of linked scans at constant B/E and at constant B2/E, mass‐analysed ion kinetic energy spectra and labelling experiments.