bluuebunny/crossref_metadata_2025 huggingface dataset:
Rigid‐body docking with mutant constraints of influenza hemagglutinin with antibody HC19
Authors: Cherfils Jacqueline , Bizebard Thierry , Knossow Marcel , Janin Joël
Published: May 2005

An automatic docking algorithm has been applied to the modeling of the complex between hemagglutinin from influenza virus and the Fab fragment of a monoclonal antibody raised against this antigen. We have introduced here the use of biochemical information provided by mutants of hemagglutinin. The docking procedure finds a small number of candidate solutions where three sites of escape mutations are buried and form hydrogen bonds in the interface. The localization of the epitope is improved by additional biochemical data about mutants that do not affect antibody binding. Five candidate solutions with low energy, reasonably well‐packed interfaces, and six to ten hydrogen bonds are compatible with mutant information. One of the five stands out as generally better than the others from these points of views. © 1994 John Wiley & Sons, Inc.
An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme
Authors: Arnold Gregory E. , Ornstein Rick L.
Published: May 2005

In this report we examine several solvent models for use in molecular dynamics simulations of protein molecules with the Discover program from Biosym Technologies. Our goal was to find a solvent system which strikes a reasonable balance among theoretical rigor, computational efficiency, and experimental reality. We chose phage T4 lysozyme as our model protein and analyzed 14 simulations using different solvent models. We tested both implicit and explicit solvent models using either a linear distance‐dependent dielectric or a constant dielectric. Use of a linear distance‐dependent dielectric with implicit solvent significantly diminished atomic fluctuations in the protein and kept the protein close to the starting crystal structure. In systems using a constant dielectric and explicit solvent, atomic fluctuations were much greater and the protein was able to sample a larger portion of conformational space. A series of nonbonded cutoff distances (9.0, 11.5, 15.0, 20.0 Å) using both abrupt and smooth truncation of the nonbonded cutoff distances were tested. The method of dual cutoffs was also tested. We found that a minimum nonbonded cutoff distance of 15.0 Å was needed in order to properly couple solvent and solute. Distances shorter than 15.0 Å resulted in a significant temperature gradient between the solvent and solute. In all trajectories using the proprietary Discover switching function, we found significant denaturation in the protein backbone; we were able to run successful trajectories only in those simulations that used no switching function. We were able to significantly reduce the computational burden by using dual cutoffs and still calculate a quality trajectory. In this method, we found that an outer cutoff distance of 15.0 Å and an inner cutoff distance of 11.5 worked well. While a 10 Å shell of explicit water yielded the best results, a 6 A shell of water yielded satisfactory results with nearly a 40% reduction in computational cost. © 1994 John Wiley & Sons, Inc.
Collective motions in proteins investigated by X‐ray diffuse scattering
Authors: Mizuguchi Kenji , Kidera Akinori , Gō Nobuhiro
Published: May 2005

We have developed theoretical models for analysis of X‐ray diffuse scattering from protein crystals. A series of models are proposed to be used for experimental data with different degrees of precision. First, we propose the normal mode model, where conformational dynamics of a protein is assumed to occur mostly in a limited conformational subspace spanned by a small number of low‐frequency normal modes in the protein. When high precision data are available, variances and covariances of the normal mode variables can be determined from experimental data using this model. For experimental data with lower degrees of precision, we introduce a series of simpler models. These models express the covariance matrix using relatively simple empirical correlation functions by assuming the correlation between a pair of atoms to be isotropic. As an application of these simpler models, we calculate diffuse‐scattering patterns from a human lysozyme crystal to examine how each adjustable parameter in the models affects general features of the resulting patterns. The results of the calculation are summarized as follows. (1) The higher order scattering makes a significant contribution at high resolutions. (2) The resulting simulated patterns are sensitive to changes in correlation lengths of about 1 Å, as well as to changes of the functional form of the correlation function. (3) But only the “average” value of the intra‐ and intermolecular correlation lengths seems to determine the gross features of the pattern. (4) The effect of the atom‐dependent amplitude of fluctuations is difficult to observe. © 1994 John Wiley & Sons, Inc.
A molecular dynamics approach for the generation of complete protein structures from limited coordinate data
Authors: van Gelder Celia W. G. , Leusen Frank J. J. , Leunissen Jack A. M. , Noordik Jan H.
Published: May 2005

Generation of full protein coordinates from limited information, e.g., the Cα coordinates, is an important step in protein homology modeling and structure determination, and molecular dynamics (MD) simulations may prove to be important in this task. We describe a new method, in which the protein backbone is built quickly in a rather crude way and then refined by minimization techniques. Subsequently, the side chains are positioned using extensive MD calculations. The method is tested on two proteins, and results compared to proteins constructed using two other MD‐based methods. In the first method, we supplemented an existing backbone building method with a new procedure to add side chains. The second one largely consists of available methodology. The constructed proteins are compared to the corresponding X‐ray structures, which became available during this study, and they are in good agreement (backbone RMS values of 0.5–0.7 Å, and all‐atom RMS values of 1.5–1.9 Å). This comparative study indicates that extensive MD simulations are able, to some extent, to generate details of the native protein structure, and may contribute to the development of a standardized methodology to predict reliably (parts of) protein structures when only partial coordinate data are available. © 1994 John Wiley & Sons, Inc.
Molecular dynamics studies on mutants of Cu, Zn superoxide dismutase: The functional role of charged residues in the electrostatic loop VII
Authors: Banci Lucia , Carloni Paolo , Orioli Pier Luigi
Published: May 2005

Molecular dynamics (MD) calculations have been performed on mutants of superoxide dismutase (SOD) on some residues present in the electrostatic loop. These calculations have provided the solution structures for the mutants Thr‐137 → IIe and Arg; Lys‐136 → Ala; Glu‐132 → Gln; Glu‐133 → Gln; Glu‐132, Glu‐133 → Gln‐132, Gln‐133 and → Gln‐132, Lys‐133. The structural and dynamic properties of these mutants have been correlated with the catalytic properties and available spectroscopic data. The water molecule present in the active site close to the copper ion in wild type (WT) SOD is missing in the MD average structure of the Thr‐137 → IIe mutant, while this molecule is present in the MD average structures of all the other mutants and of WT SOD. This agrees with the experimental data. This is an important result that shows the validity of our calculations and their ability to reproduce even subtle structural features. Addition of one or more positive charges on the 132 and/or 133 positions does not sizably perturb the structure of the active site channel, while the introduction of a positively charged residue (Arg) on position 137 has a large effect on the structure of the electrostatic loop. Analysis of the MD average structures of these mutants has pointed out that the simple electrostatic effects of charged residues in the channel are not the only factor relevant for enzymatic behavior but that the structure of the electrostatic loop and the location of the charged residues also contribute to the catalytic properties of SOD. © 1994 John Wiley & Sons, Inc.
An improved pair potential to recognize native protein folds
Authors: Bauer Aron , Beyer Anton
Published: May 2005

We present a novel method to improve a simple pair potential of mean force, derived from experimentally determined protein structures, in such a way that it recognizes native protein folds with high reliability. This improvement is based on the use of mutation data matrices to overcome difficulties arising from the poor statistics of small sample sizes. A set of 167 protein chains taken from the Brookhaven Protein Structure Data Base, selected from high‐resolution structures and avoiding homologous proteins, is used for generation of the potential set. The potential describes interresidue pair energies depending on distance and sequential separation, and is calculated using the Boltzmann equation. Its performance is evaluated by jackknife tests that try to identify the native fold for a given sequence among a large number of possible threadings on all structures in the set without allowing for gaps. Up to 94% of the protein chains are correctly assigned to their native folds, so that all proper single‐chain domains are recognized. © 1994 John Wiley & Sons, Inc.
Design of interchain disulfide bonds in the framework region of the Fv fragment of the monoclonal antibody B3
Authors: Jung Sun‐Hee , Pastan Ira , Lee B.
Published: May 2005

The Fv fragments are the smallest units of antibodies that retain the specific antigen binding characteristics of the whole molecule and are being used for the diagnosis and therapy of human diseases. These are noncovalently associated heterodimers of the heavy (V H) and the light (VL) chain variable domains, which, without modification, tend to dissociate, unfold, and/or nonspecific ally aggregate. The fragment is usually stabilized by producing it as a single chain recombinant molecule in which the two chains are linked by means of a short polypeptide linker. An alternative strategy is to connect the two chains by means of an interchain disulfide bond. We used molecular graphics and other modeling tools to identify two possible interchain disulfide bond sites in the framework region of the Fv fragment of the monoclonal mouse antibody (mAb) B3. The mAb B3 binds to many human cancer cells and is being used in the development of a new anticancer agent. The two sites identified are VH44–VL105 and VH111–VL48. (VH44–VL100 and VH105–VL43 in the numbering scheme of Kabat et al., “Sequence of Proteins of Immunological Interest,” U.S. DHHS, NIH publication No. 91–3242, 1991.) This design was recently tested using the chimeric protein composed of a truncated form of Pseudomonas exotoxin and the Fv fragment of mAb B3 with the engineered disulfide bond at VH44–VL105 (Brinkmann et al., Proc. Natl. Acad. Sci. U.S.A. 90:7538, 1993). The chimeric toxin was found to be just as active as the corresponding single chain counterpart and considerably more stable. Because these disulfide bond sites are in the framework region, they can be located from sequence alignment alone. We expect that the disulfide bond at these sites will stabilize the Fv fragment of most antibodies and the antigen‐specific portion of the T‐cell receptors, which are homologous. © 1994 Wiley‐Liss, Inc.
Combining evolutionary information and neural networks to predict protein secondary structure
Authors: Rost Burkhard , Sander Chris
Published: May 2005

Using evolutionary information contained in multiple sequence alignments as input to neural networks, secondary structure can be predicted at significantly increased accuracy. Here, we extend our previous three‐level system of neural networks by using additional input information derived from multiple alignments. Using a position‐specific conservation weight as part of the input increases performance. Using the number of insertions and deletions reduces the tendency for overprediction and increases overall accuracy. Addition of the global amino acid content yields a further improvement, mainly in predicting structural class. The final network system has a sustained overall accuracy of 71.6% in a multiple cross‐validation test on 126 unique protein chains. A test on a new set of 124 recently solved protein structures that have no significant sequence similarity to the learning set confirms the high level of accuracy. The average cross‐validated accuracy for all 250 sequence‐unique chains is above 72%. Using various data sets, the method is compared to alternative prediction methods, some of which also use multiple alignments: the performance advantage of the network system is at least 6 percentage points in three‐state accuracy. In addition, the network estimates secondary structure content from multiple sequence alignments about as well as circular dichroism spectroscopy on a single protein and classifies 75% of the 250 proteins correctly into one of four protein structural classes. Of particular practical importance is the definition of a position‐specific reliability index. For 40% of all residues the method has a sustained three‐state accuracy of 88%, as high as the overall average for homology modelling. A further strength of the method is greatly increased accuracy in predicting the placement of secondary structure segments. © 1994 Wiley‐Liss, Inc.
1.56 Å structure of mature truncated human fibroblast collagenase
Authors: Spurlino John C. , Smallwood Angela M. , Carlton Dennis D. , Banks Tracey M. , Vavra Karen J. , Johnson Jeffrey S. , Cook Ewell R. , Falvo Joseph , Wahl Robert C. , Pulvino Tricia A. , Wendoloski John J. , Smith Douglas L.
Published: May 2005

The X‐ray crystal structure of a 19 kDa active fragment of human fibroblast collagenase has been determined by the multiple isomorphous replacement method and refined at 1.56 Å resolution to an R‐factor of 17.4%. The current structure includes a bound hydroxamate inhibitor, 88 waters and three metal atoms (two zincs and a calcium). The overall topology of the enzyme, comprised of a five stranded β‐sheet and three α‐helices, is similar to the thermolysin‐like metalloproteinases. There are some important differences between the collagenase and thermolysin families of enzymes. The active site zinc ligands are all histidines (His‐218, His‐222, and His‐228). The presence of a second zinc ion in a structural role is a unique feature of the matrix metalloproteinases. The binding properties of the active site cleft are more dependent on the main chain conformation of the enzyme (and substrate) compared with thermolysin. A mechanism of action for peptide cleavage similar to that of thermolysin is proposed for fibroblast collagenase. © 1994 Wiley‐Liss, Inc.
Free energy simulations: The meaning of the individual contributions from a component analysis
Authors: Boresch Stefan , Archontis Georgios , Karplus Martin
Published: May 2005

A theoretical analysis is made of the decomposition into contributions from individual interactions of the free energy calculated by thermodynamic integration. It is demonstrated that such a decomposition, often referred to as “component analysis,” is meaningful, even though it is a function of the integration path. Moreover, it is shown that the path dependence can be used to determine the relation of the contribution of a given interaction to the state of the system.

To illustrate these conclusions, a simple transformation(Cl− to Br− in aqueous solution) is analyzed by use of the Reference Interaction Site Model‐Hypernetted Chain Closure integral equation approach; it avoids the calculational difficulties of macromolecular simulation while retaining their conceptual complexity. The difference in the solvation free energy between chloride and bromide is calculated, and the contributions of the Lennard‐Jones and electrostatic terms in the potential function are analyzed by the use of suitably chosen integration paths. The model is also used to examine the path dependence of individual contributions to the double free energy differences (ΔΔG or ΔΔA) that are often employed in free energy simulations of biological systems. The alchemical path, as contrasted with the experimental path, is shown to be appropriate for interpreting the effects of mutations on ligand binding and protein stability. The formulation is used to obtain a better understanding of the success of the Poisson‐Boltzmann continuum approach for determining the solvation properties of polar and ionic systems. © 1994 Wiley‐Liss, Inc.
Microtube batch protein crystallization: Applications to human immunodeficiency virus type 2 (HIV‐2) protease and human renin
Authors: Pav Susan , Lubbe Klaus , Dô Florence , Lamarre Daniel , Pargellis Christopher , Tong Liang
Published: May 2005

For therapeutically relevant targets, the evaluation of enzymes in complex with their inhibitors by cocrystallization and high resolution structural analysis has become a vital component of structure‐driven drug design and development. Two approaches, hanging drop vapor diffusion and a novel microtube batch method, were utilized in parallel to grow crystals of recombinant HIV ‐2 protease and recombinant human renin in complex with inhibitors. In the case of HIV ‐2 protease in complex with a reduced amide inhibitor, crystallization was achieved only by the microbatch method. In the case of human renin, the addition of precipitant was required for crystal growth. The microbatch method described here is a useful supplementary or alternative approach for screening parameters and generating crystals suitable for high resolution structural analysis. © 1994 Wiley‐Liss, Inc.
Homology modeling of the Abl‐SH3 domain
Authors: Pisabarro M. T. , Ortiz A. R. , Serrano L. , Wade R. C.
Published: May 2005

A tertiary structure model of the Abl‐SH3 domain is predicted by using homology modeling techniques coupled to molecular dynamics simulations. Two template proteins were used, Fyn‐SH3 and Spc‐SH3. The refined model was extensively checked for errors using criteria based on stereochemistry, packing, solvation free‐energy, accessible surface areas, and contact analyses. The different checking methods do not totally agree, as each one evaluates a different characteristic of protein structures. Several zones of the protein are more susceptible to incorporating errors. These include residues 13, 15, 35, 39, 45, 46, 50, and 60. An interesting finding is that the measurement of the Cα chirality correlated well with the rest of the criteria, suggesting that this parameter might be a good indicator of correct local conformation. Deviations of more than 4 degrees may be indicative of poor local structure. © 1994 Wiley‐Liss, Inc.
Conservation and prediction of solvent accessibility in protein families
Authors: Rost Burkhard , Sander Chris
Published: May 2005

Currently, the prediction of three‐dimensional (3D) protein structure from sequence alone is an exceedingly difficult task. As an intermediate step, a much simpler task has been pursued extensively: predicting 1D strings of secondary structure. Here, we present an analysis of another 1D projection from 3D structure: the relative solvent accessibility of each residue. We show that solvent accessibility is less conserved in 3D homologues than is secondary structure, and hence is predicted less accurately from automatic homology modeling; the correlation coefficient of relative solvent accessibility between 3D homologues is only 0.77, and the average accuracy of predictions based on sequence alignments is only 0.68. The latter number provides an effective upper limit on the accuracy of predicting accessibility from sequence when homology modeling is not possible. We introduce a neural network system that predicts relative solvent accessibility (projected onto ten discrete states) using evolutionary profiles of amino acid substitutions derived from multiple sequence alignments. Evaluated in a cross‐validation test on 238 unique proteins, the correlation between predicted and observed relative accessibility is 0.54. Interpreted in terms of a three‐state (buried, intermediate, exposed) description of relative accessibility, the fraction of correctly predicted residue states is about 58%. In absolute terms this accuracy appears poor, but given the relatively low conservation of accessibility in 3D families, the network system is not far from its likely optimal performance. The most reliably predicted fraction of the residues (50%) is predicted as accurately as by automatic homology modeling. Prediction is best for buried residues, e.g., 86% of the completely buried sites are correctly predicted as having 0% relative accessibility. © 1994 Wiley‐Liss, Inc.
Five‐stranded β‐sheet sandwiched with two α‐helices: A structural link between restriction endonucleases EcoRI and EcoRV
Authors: Venclovas Česlovas , Timinskas Albertas , Siksnys Virginijus
Published: May 2005

Examination of crystal structures of restriction endonucleases EcoRI and EcoRV complexes with their cognate DNA revealed a common structural element, which forms the core of both proteins. This element consists of a five‐stranded β‐sheet and two α‐helices packed against it and could be described as α–β sandwich in which helices and β‐strands lie in two stacked layers. While the spatial structure of this α–β sandwich is conserved in both enzymes, there are no detectable similarities between amino acid sequences except of a few residues involved in active site formation. Probably, other restriction endonucleases which have similar organization of the active site might possess similar structural element regardless of DNA sequence recognized and recognition elements in the enzyme used. © 1994 Wiley‐Liss, Inc.
Secondary structural predictions for the clostridial neurotoxins
Authors: Lebeda Frank J. , Olson Mark A.
Published: May 2005

The primary structures of a family of ten clostridial. Neurotoxins have recently been deduced yet little information is presently available concerning their secondary or tertiary structures. Because the overall similarity percentage of multiply aligned sequences is high, the secondary structures of these metalloendopeptidases are also expected to be conserved. The neural net program, PHD (Rost and Sander, Proc. Natl. Acad. Sci. USA 90:7558–7562, 1993), predicted that the secondary structures of the neurotoxins were indeed conserved in both single and multiple sequence modes of analysis. Predictions for the amounts of helical, extended, and loop states from the single sequence analyses were consistent with previously published data from circular dichroism studies on some of these neurotoxins. In the single analysis mode, only the aligned regions were predicted to show conservation of the three‐state structure. In contrast, the multiple sequence analysis predicted that a conserved state (variable loops) also exists in non‐aligned regions. Alignments with the primary structure of the prototypic metalloendopeptidase thermolysin showed that about 25% of the residues within this enzyme are similar to those in the neurotoxins. A comparison of thermolysin's known secondary structure with the predictions from this study showed that about 80% of thermolysin's residues could be structurally aligned with those in the neurotoxins. These predictions provide the necessary. Framework to build a homologous low‐resolution tertiary structure of the neurotoxin active site that will be essential in the development of synthetic inhibitors. © 1994 Wiley‐Liss, Inc.
Elusive affinities
Authors: Janin Joël
Published: May 2005

The affinity of two molecules for each other and its temperature dependence are determined by the change in enthalpy, free enthalpy, entropy, and heat capacity upon dissociation. As we know the forces that stabilize‐protein–protein or protein–DNA association and the three‐dimensional structures of the complex, we can in principle derive values for each one of these parameters. The calculation is done first in gas phase by molecular mechanics, then in solution with the help of hydration parameters calibrated on small molecules. However, estimates of enthalpy and entropy changes in gas phase have excessively large error bars even under the approximation that the components of the complex associate as rigid bodies. No reliable result can be expected at the end. The fit to experimental values derived from binding and calorimetric measurements is poor, except for the dissociation heat capacity. This parameter can be attributed mostly to the hydration step and it correlates with the size of the interface. Many protein–protein complexes have interface areas in the range 1200–2000 Å2 and only small conformation changes, so the rigid body approximation applies. It is less generally valid in protein–DNA complexes, which have interfaces covering 2200–3100 Å2, large dissociation heat capacities, and affect both the conformation and the dynamics of their components. © 1995 Wiley‐Liss, Inc.
Molecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion
Authors: Ryde Ulf
Published: May 2005

A detailed parameterization is presented of a zinc ion with one histidine and two cysteinate ligands, together with one or two water, hydroxide, aldehyde, alcohol, or alkoxide ligands. The parameterization is tailored for the active site of alcohol dehydrogenase and is obtained entirely from quantum chemical computations. The force‐field reproduces excellently the geometry of quantum chemically optimized zinc complexes as well as the crystallographic geometry of the active site of alcohol dehydrogenase and small organic structures. The parameterization is used in molecular dynamics simulations and molecular mechanical energy minimizations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion. The active‐site zinc ion seems to prefer four‐coordination over five‐coordination by at least 36 kJ/mol. The only stable binding site of a fifth ligand at the active‐site zinc ion is opposite to the normal substrate site, in a narrow cavity behind the zinc ion. Only molecules of the size of water or smaller may occupy this site. There are large fluctuations in the geometry of the zinc coordination sphere. A four‐coordinate water molecule alternates frequently (every 7 ps) between the substrate site and the fifth binding site and even two five coordinate water molecules may interchange ligation sites without prior dissociation. Ligand exchange at the zinc ion probably proceeds by a dissociative mechanism. The results show that it is essential to allow for bond stretching degrees of freedom in molecular dynamics simulations to get a correct description of the dynamics of the metal coordination sphere; bond length constraints may restrict the accessible part of the phase space and therefore lead to qualitatively erroneous results. © 1995 Wiley‐Liss, Inc.
Modulation of DNA‐binding specificity within the nuclear receptor family by substitutions at a single amino acid position
Authors: Zilliacus Johanna , Wright Anthony P. H. , Carlstedt‐Duke Jan , Nilsson Lennart , Gustafsson Jan‐Åke
Published: May 2005

Regulation of gene expression involves a large number of transcription factors with unique DNA‐binding properties. Many transcription factors belong to families of related proteins that bind to similar but distinct sequences. In this study we have analyzed how amino acid substitutions at a single position in the DNA‐binding domain modulate the DNA binding specificity within the nuclear receptor family of transcription factors. All possible amino acids were introduced at the first position in the DNA recognition helix, and the specificities of the mutants were analyzed using response elements containing all combinations of bases at two variable base pair positions. All mutant proteins were functional in DNA binding, and could be divided into classes of mutants with different response element specificities. By combining functional data with analysis of the structural effects of the mutations by molecular modeling, we could identify both prohibitive steric interactions as well as positive interactions, such as hydrogen bonds, that function as important determinants for specificity. Only the residues found naturally in the glucocorticoid and estrogen receptors, glycine and glutamate, produce unique binding specificities. The specificities of the other mutants overlap with each other somewhat but the substitutions clearly have potential to contribute to diversity within the nuclear receptor family. © 1995 Wiley‐Liss, Inc.
Three‐dimensional structure prediction of the NAD binding site of proton‐pumping transhydrogenase from Escherichia coli
Authors: Fjellström Ola , Olausson Torbjörn , Hu Xiang , Källebring Bruno , Rydström Jan , Ahmad Suhail , Bragg Philip D.
Published: May 2005

A three‐dimensional structure of the NAD site of Escerichia coli transhydrogenase has been predicted. The model is based on analysis of conserved residues among the transhydrogenases from five different sources, homologies with enzymes using NAD as cofactors or substrates, hydrophilicity profiles, and secondary structure predictions. The present model supports the hypothesis that there is one binding site, located relatively close to the N‐terminus of the α‐subunit. The proposed structure spans residues α145 to α287, and it includes five β‐strands and five α‐helices oriented in a typical open twisted α/β conformation. The amino acid sequence following the GXGXXG dinucleotide binding consensus sequence (residues α172 to α177) correlates exactly to a typical fingerprint region for ADP binding βαβ folds in dinucleotide binding enzymes. In the model, aspartic acid α195 forms hydrogen bonds to one or both hydroxyl groups on the adenosine ribose sugar moiety. Threonine α196 and alanine α256, located at the end of βB and βD, respectively, create a hydrophobic sandwich with the adenine part of NAD buried inside. The nicotinamide part is located in a hydrophobic cleft between αA and βE. Mutagenesis work has been carried out in order to test the predicted model and to determine whether residues within this domain are important for proton pumping directly. All data support the predicted structure, and no residue crucial for proton pumping Was detected. Since no three‐dimensional structure of transhydrogenase has been solved, a well based tertiary structure prediction is of great value for further experimental design in trying to elucidate the mechanism of the energy‐linked proton pump. © 1995 Wiley‐Liss, Inc.
A new protein folding recognition potential function
Authors: Wang Yanli , Lai Luhua , Han Yuzhen , Xu Xiaojie , Tang Youqi
Published: May 2005

On the study of protein inverse folding problem, one goal is to find simple and efficient potential to evaluate the compatibility between structure and a given sequence. We present here a novo empirical mean force potential to address the importance of electrostatic interactions in protein inverse folding study. It is based on protein main chain polar fraction and constructed in a way similar with Sippl's from a database of 64 known independent three‐dimensional protein structures. This potential was applied to recognize the protein native conformations among a conformation pool. Calculated results show that this potential is powerful in picking out native conformations, in addition it can also find structure similarity between proteins with low sequence similarity. The success of this new potential clearly shows the importance of electrostatic factors in protein inverse folding studies. © 1995 Wiley‐Liss, Inc.
Accurate general method for lattice approximation of three‐dimensional structure of a chain molecule
Authors: Rykunov Dmitry S. , Reva Boris A. , Finkelstein Alexey V.
Published: May 2005

An algorithm based on dynamic programming gives the lattice models having the minimal RMS deviations from the actual folds of protein (RNA, etc.) chains for a given lattice and a given orientation of the macromolecule relative to the lattice. The algorithm is applicable for 3‐D lattices of any kind. The accuracy of the lattice approximation increases when the distance between neighbor chain links is not rigidly fixed. Special repulsive potentials facilitate generation of self‐avoiding lattice chains. The results of model building show the efficiency and precisionof this proposed general method when compared with others. © 1995 Wiley‐Liss, Inc.
Exploring the binding preferences/specificity in the active site of human cathepsin E
Authors: Rao‐Naik Chetana , Guruprasad Kunchur , Batley Brian , Rapundalo Stephen , Hill Jeffrey , Blundell Tom , Kay John , Dunn Ben M.
Published: May 2005

Aspartic proteinases are produced in the human body by a variety of cells. Some of these proteins, examples of which are pepsin, gastricsin, and renin, are secreted and exert their effects in the extracellular spaces. Cathepsin D and cathepsin E on the other hand are intracellular enzymes. The least characterized of the human aspartic proteinases is cathepsin E. Presented here are results of studies designed to characterize the binding specificities in the active site of human cathepsin E with comparison to othermechanistically similar enzymes. A peptide series based on Lys‐Pro‐Ala‐Lys‐Phe*Nph‐Arg‐Leu was generatedto elucidate the specificity in the individual binding pockets with systematic substitutions in the P5− P2 and P2′‐P3′ based on charge, hydrophobicity, and hydrogen bonding. Also, to explore the S2 binding preferences, asecond series of peptides based on Lys‐Pro‐Ile‐Glu‐Phe*Nph‐Arg‐Leu was generated with systematic replacements in the P2 position. Kinetic parameters were determined forboth sets of peptides. The results were correlated to a rule‐based structural model of human cathepsin E, constructed on the known three‐dimensional structures of several highly homologous aspartic proteinases; porcine pepsin, bovine chymosin, yeast proteinase A, human cathepsin D, andmouse and human renin. Important specificity‐determining interactions were found in the S3 (Glu13) and S2 (Thr‐222, Gln‐287, Leu‐289, Ile‐300)subsites. © 1995 Wiley‐Liss, Inc.
Comparison of the effects of hydrophobicity, amphiphilicity, and α‐helicity on the activities of antimicrobial peptides
Authors: Pathak Naveen , Salas‐Auvert Rodolfo , Ruche Gaël , Janna Marie‐hélène , McCarthy David , Harrison Roger G.
Published: May 2005

Multiple linear regression was used to quantify the dependence of the antimicrobial activity of 13 peptides upon three calculated or experimentally determined parameters: mean hydrophobicity, mean hydrophobic moment, and α‐helix content. Mean hydrophobic moment is a measure of the amphiphilicity of peptides in an α‐helical conformation. Antimicrobial activity was quantified as the reciprocal of the measured minimal inhibitory concentration (MIC) against Escherichia coli. One of the peptides was magainin 2, and the remainder were novel peptides designed for this study. The multiple linear regression results revealed that the amphiphilicity of the peptides was the most important factor governing anti‐microbial activity compared to mean hydrophobicity orα‐helix content. A better regression cf the data was obtained using In(1/MIC + constant) as the dependent variable than with either 1/MIC or In(1/MIC). These results should be useful in designing peptides with higher antimicrobial activity. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray investigation of recombinant human interleukin 10
Authors: Cook William J. , Windsor William T. , Murgolo Nicholas J. , Tindall Stephen H. , Nagabhushan Tattanahalli L. , Walter Mark R.
Published: May 2005

Crystals of recombinant human interleukin 10 have been grown from solutions of ammonium sulfate. The crystals are tetragonal, space group P41212 or P43212; the unit cell axes are a = 36.5 Å and c = 221.9 Å. There is the equivalent of one polypeptide chain in the asymmetric unit. The crystals are stable to X‐rays and diffract to at least 2.5 Å resolution. © 1995 Wiley‐Liss, Inc.
Prediction of the structure of GroES and its interaction with GroEL
Authors: Valencia Alfonso , Hubbard Tim J. , Muga Arturo , Bañuelos Sonia , Llorca Oscar , Carrascosa José L. , Valpuesta José Marí
Published: May 2005

The three‐dimensional structure of the GroES monomer and its interaction with GroEL has been predicted using a combination of prediction tools and experimental data obtained by biophysical [electron microscope (EM), Fourier transform infrared (FTIR), and nuclear magnetic resonance (NMR)] and biochemical techniques. The GroES monomer, according to the prediction, is composed of eight β‐strands forming a β‐barrel with loose ends. In the model, β‐strands 5–8 run along the outer surface of GroES, forming an antiparallel β‐sheet with β4 loosely bound to one of the edges. β‐strands 1–3 would then be parallel and placed in the interior of the molecule. Loops 1–3 would face the internal cavity of the GroEL–GroES complex, and together with conserved residues in loops 5 and 7, would form the active surface interacting with GroEL. © 1995 Wiley‐Liss, Inc.
The catalytic domain of a bacterial lytic transglycosylase defines a novel class of lysozymes
Authors: Thunnissen Andy‐Mark W. H. , Isaacs Neil W. , Dijkstral Bauke W.
Published: May 2005

The 70‐kDa soluble lytic transglycosylase (SLT70) from Escherichia coli is a bacterial exo‐muramidase that cleaves the cell wall peptidoglycan, producing 1,6‐anhydro‐muropeptides. The X‐ray structure of SLT70 showed that one of its domains is structurally related to lysozyme, although there is no obvious similarity in amino acid sequence. To relate discrete structural features to differences in reaction mechanism and substrate/product specificity, we compared the threedimensional structure of the catalytic domain of SLT70 with the structures of three typical representatives of the lysozyme superfamily: chicken‐type hen egg‐white lysozyme, goosetype swan egg‐white lysozyme, and phage‐type lysozyme from bacteriophage T4. We find a particularly close relationship between the catalytic domain of SLT70 and goose‐type lysozyme, with not only a significant similarity in overall structure, but even a weak homology in amino acid sequence. This finding supports the notion that the goose‐type lysozyme takes up a central position in the lysozyme superfamily and that it is structurally closest to the lysozyme ancestors. The saccharide‐binding groove is the most conserved part in the four structures, but only two residues are absolutely preserved: the “catalytic” glutamic acid and a structurally required glycine. The “catalytic” aspartate is absent in SLT70, a difference that can be related to a different mechanism of cleavage of the β‐1,4‐glycosidic bond. The unique composition of amino acids at the catalytic site, and the observation of a number of differences in the arrangements of secondary structure elements, define the catalytic domain of SLT70 as a novel class of lysozymes. Its fold is expected to be exemplary for other bacterial and bacteriophage muramidases with lytic transglycosylase activity. © 1995 Wiley‐Liss, Inc.
Crystallization of Thermus thermophilus histidyl‐tRNA synthetase and Its complex with tRNAHis
Authors: Yaremchuk A. D. , Cusack S. , Åberg A. , Gudzera O. , Kryklivyi I. , Tukalo M.
Published: May 2005

Histidyl‐tRNA synthetase (HisRS) has been purified from the extreme thermophile Thermus thermophilus. The protein has been crystallized separately with histidine and with its cognate tRNAHis. Both crystals have been obtained using the vapor diffusion method with ammonium sulphate as precipitant. The crystals of HisRS with histidine belong to the spacegroup P21212 with cell parameters a = 171.3 Å, b = 214.7 Å, c = 49.3 Å, α = β = γ = 90°. A complete data set to a resolution of 2.7Å with an Rmerge on intensities of 4.1% has been collected on a single frozen crystal. A partial data set collected on a crystal of HisRS in complex with tRNAHis shows that the crystals are tetragonal with cell parameters a = b = 232 Å, c = 559 Å, α = β = γ = 90° and diffract to about 4.5 Å resolution. © 1995 Wiley‐Liss, Inc.
Rigid domains in proteins: An algorithmic approach to their identification
Authors: Nichols William L. , Rose George D. , Ten Eyck Lynn F. , Zimm Bruno H.
Published: May 2005

A rigid domain, defined here as a tertiary structure common to two or more different protein conformations, can be identified numerically from atomic coordinates by finding sets of residues, one in each conformation, such that the distance between any two residues within the set belonging to one conformation is the same as the distance between the two structurally equivalent residues within the set belonging to any other conformation. The distance between two residues is taken to be the distance between their respective α carbon atoms. With the methods of this paper we have found in the deoxy and oxy conformations of the human hemoglobin α1β1 dimer a rigid domain closely related to that previously identified by Baldwin and Chothia (J. Mol. Biol. 129:175–220,1979). We provide two algorithms, both using the difference‐distance matrix, with which to search for rigid domains directly from atomic coordinates. The first finds all rigid domains in a protein but has storage and processing demands that become prohibitively large with increasing protein size. The second, although not necessarily finding every rigid domain, is computationally tractable for proteins of any size. Because of its efficiency we are able to search protein conformations recursively for groups of non‐intersecting domains. Different protein conformations, when aligned by superimposing their respective domain structures; can be examined for structural differences in regions complementing a rigid domain. © 1995 Wiley‐Liss, Inc.
Characterization of crystals of the thermostable DNA polymerase I from thermus aquaticus
Authors: Urs Usha K. , Sharkey David J. , Peat Thomas S. , Hendrickson Wayne A. , Krishna Murthy H. M.
Published: May 2005

Thermus aquaticus DNA polymerase I is an enzyme that is of both physiological and technological interest. It carries out template‐directed polymerization of DNA at elevated temperatures and is widely used in polymerase chain reaction (PCR). We have obtained crystals of the enzyme that diffracts X‐rays to at least 3.0 Å resolution in a cubic space group. Determination of the three‐dimensional structure of the native enzyme along with those of relevant complexes will greatly enhance our knowledge of molecular events involved in DNA replication, will permit improvements in PCR, and will add to our knowledge of the structural bases of thermo stability in proteins. © 1995 Wiley‐Liss, Inc.
Structural superposition of proteins with unknown alignment and detection of topological similarity using a six‐dimensional search algorithm
Authors: Diederichs Kay
Published: May 2005

An algorithm for the rigid‐body superposition of proteins is described and tested. No prior knowledge of equivalent residues is required. To find the common structural core of two proteins, an exhaustive grid search is conducted in three‐dimensional angle space, and at each grid point a fast translation search in three‐dimensional space is performed. The best superposition at a given angle set is defined by that translation vector which maximizes the weighted number of equivalent Cα atoms. Filters using the information about the sequential character of the polypeptide chain are employed to identify that rotation and translation which yields the highest topological similarity of the two proteins. The algorithm is shown to find the best superposition of distantly related structures, and to be capable of finding similar structures to a given atomic model in the Brookhaven Protein Data Bank. In a search using granulocyte‐macrophage colony‐stimulating factor as a template, all other four‐helix bundle cytokines with up‐up‐down‐down topology were found to give the highest values of a topological similarity score, followed by interferon‐β and ‐γ and those four‐helix bundles with the more common up‐down‐up‐down topology. In another example, the insertion domain of the long variant adenylate kinases is demonstrated to share its fold with rubredoxin. © 1995 Wiley‐Liss, Inc.
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

A 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

Computer 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.