Biomedical subjects

J Moult

Publications and source records attributed to J Moult.

At least 55 records · Page 3Linked to original sources

PubMed1995

Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms.

Ab initio folding simulations have been performed on three peptides, using a genetic algorithm-based search method which operates on a full atom representation. Conformations are evaluated with an empirical force field parameterized by a potential of mean force analysis of experimental structures. The dominant terms in the force field are local and nonlocal main chain electrostatics and the hydrophobic effect. Two of the simulated structures were for fragments of complete proteins (eosinophil-derived neurotoxin (EDN) and the subtilisin propeptide) that were identified as being likely initiation sites for folding. The experimental structure of one of these (EDN) was subsequently found to be consistent with that prediction (using local hydrophobic burial as the determinant for independent folding). The simulations of the structures of these two peptides were only partly successful. The most successful folding simulation was that of a 22-residue peptide corresponding to the membrane binding domain of blood coagulation factor VIII (Membind). Three simulations were performed on this peptide and the lowest energy conformation was found to be the most similar to the experimental structure. The conformation of this peptide was determined with a C alpha rms deviation of 4.4 A. Although these simulations were partly successful there are still many unresolved problems, which we expect to be able to address in the next structure prediction experiment.

Algorithms↗

PubMed1994

Comparison of systematic search and database methods for constructing segments of protein structure.

Two principal methods of determining the conformation of short pieces of polypeptide backbone in proteins have been developed: using a database of known structures and systematically generating all conformations. In this paper, we compare the effectiveness of these two techniques. The completeness of the database for segments of different lengths is examined and it is found to contain most conformations for segments seven residues long, but to deteriorate rapidly for longer regions. When the database segment is to be incorporated into the rest of a structure, at least seven residues are required to build four new residues, because of the need to position the segment relative to the rest of the structure. It is found that such positioning using flanking residues results in large errors in the inserted region. We conclude that the database method is currently not effective for comparative modeling, even for short segments. The systematic search procedure is found to generate almost all structures of short segments found in proteins. In contrast to the database method, low root mean square error structures are obtained for a set of trial segments embedded in the rest of a protein structure. Thus, it should be considered the method of choice.

Computer Simulation↗

PubMed1993

On achieving better than 1-A accuracy in a simulation of a large protein: Streptomyces griseus protease A.

Computational methods are frequently used to simulate the properties of proteins. In these studies accuracy is clearly important, and the improvement of accuracy of protein simulation methodology is one of the major challenges in the application of theoretical methods, such as molecular dynamics, to structural studies of biological molecules. Much effort is being devoted to such improvements. Here, we present an analysis of a 187-ps molecular dynamics simulation of the serine protease Streptomyces griseus protease A in its crystal environment. The reproduction of the experimental structure is considerably better than has been achieved in earlier simulations--the root mean square deviation of the simulated structure from the x-ray structure being less than 1 A, a significant step toward the goal of simulating proteins to within experimental error. The use of a longer cutoff with truncation rather than a switching function, inclusion of all crystalline water and the counterions in the crystallization medium, and use of the consistent valence force field characterize the differences in this calculation.

Bacterial Proteins↗

PubMed1993

Genetic algorithms for protein folding simulations.

Genetic algorithms methods utilize the same optimization procedures as natural genetic evolution, in which a population is gradually improved by selection. We have developed a genetic algorithm search procedure suitable for use in protein folding simulations. A population of conformations of the polypeptide chain is maintained, and conformations are changed by mutation, in the form of conventional Monte Carlo steps, and crossovers in which parts of the polypeptide chain are interchanged between conformations. For folding on a simple two-dimensional lattice it is found that the genetic algorithm is dramatically superior to conventional Monte Carlo methods.

Algorithms↗

PubMed1993

Troponin-C mutants with increased calcium affinity.

Binding of two Ca2+ to the regulatory sites I and II of troponin C (TnC) induces a conformational transition believed to be responsible for the activation of muscle contraction. Based on the known crystal structure (2Ca2+ state), a model for the transition to the 4Ca2+ state has been proposed [Herzberg, O., Moult, J. & James, M. N. G. (1986) J. Biol. Chem. 261, 2638-2644]. The proposed conformational transition predicts that during Ca2+ binding a number of nonpolar residues become exposed to the solvent, creating a hydrophobic patch. Such a model implies that mutation of the hydrophobic to polar residues should increase the Ca2+ affinity at the regulatory sites and reduce the Ca2+ concentration necessary for muscle activation. To test this prediction, we have constructed and functionally characterized two troponin-C mutants (V45T and M48A mutations). Direct calcium-binding measurements in the mutants demonstrate an increase in the Ca2+ affinity for two low-affinity sites. Replacement of endogenous troponin C in skinned muscle fibers by TnC with mutations V45T or M48A increased the Ca2+ sensitivity of their tension development. These results show that the model can be used to construct mutants that regulate muscle contraction at lower Ca2+ concentrations. They provide further experimental support for the proposed calcium-induced conformational change of troponin C and suggest that the predicted transition plays a central role in the activation of the thin filament.

Animals↗

PubMed1993

Finding the lowest free energy conformation of a protein is an NP-hard problem: proof and implications.

The protein folding problem and the notion of NP-completeness and NP-hardness are discussed. A lattice model is suggested to capture the essence of protein folding. For this model we present a proof that finding the lowest free energy conformation belongs to the class of NP-hard problems. The implications of the proof are discussed and we suggest that the natural folding process cannot be considered as a search for the global free energy minimum. However, we suggest an explanation as to why, for many proteins, the native functional conformation may coincide with the lowest free energy conformation.

Amino Acid Sequence↗

PubMed1992

Construction and characterization of a spectral probe mutant of troponin C: application to analyses of mutants with increased Ca2+ affinity.

A spectral probe mutant (F29W) of chicken skeletal muscle troponin C (TnC) has been prepared in which Phe-29 has been substituted by Trp. Residue 29 is at the COOH-terminal end of the A helix immediately adjacent to the Ca2+ binding loop of site I (residues 30-41) of the regulatory N domain. Since this protein is naturally devoid of Tyr and Trp, spectral features can be assigned unambiguously to the single Trp. The fluorescent quantum yield at 336 nm is increased almost 3-fold in going from the Ca(2+)-free state to the 4Ca2+ state with no change in the wavelength of maximum emission. Comparisons of the Ca2+ titration curves of the change in far-UV CD and fluorescence emission indicated that the latter was associated only with the binding of 2Ca2+ to the regulatory sites I and II. No change in fluorescence was detected by titration with Mg2+. The Ca(2+)-induced transitions of both the N and C domains were highly cooperative. Addition of Ca2+ also produced a red shift in the UV absorbance spectrum and a reduction in positive ellipticity as monitored by near-UV CD measurements. The fluorescent properties of F29W were applied to an investigation of five double mutants: F29W/V45T, F29W/M46Q, F29W/M48A, F29W/L49T, and F29W/M82Q. Ca2+ titration of their fluorescent emissions indicated in each case an increased Ca2+ affinity of their N domains. The magnitude of these changes and the decreased cooperativity observed between Ca2+ binding sites I and II for some of the mutants are discussed in terms of the environment of the mutated residues in the 2Ca2+ and modeled 4Ca2+ states.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1992

Docking by least-squares fitting of molecular surface patterns.

Molecular surfaces are fitted to each other by a new solution to the problem of docking a ligand into the active site of a protein molecule. The procedure constructs patterns of points on the surfaces and superimposes them upon each other using a least-squares best-fit algorithm. This brings the surfaces into contact and provides a direct measure of their local complementarity. The search over the ligand surface produces a large number of dockings, of which a small fraction having the best complementarity and the least steric hindrance are evaluated for electrostatic interaction energy. When applied to molecules taken from crystallographically observed complexes, this procedure consistently assigns the lowest electrostatic energies to correct dockings. On independently determined structures, the ability of the method to discern correct dockings depends on how much conformational difference there is between the free and complexed forms of the molecules. The procedure is found to be fast enough on contemporary workstation computers to permit many conformations to be considered, and tolerant enough to make rather coarse bond dihedral sampling a practicable way to overcome the problem of structural flexibility.

Binding Sites↗

PubMed1992

Fitting electron density by systematic search.

A systematic search approach to the automatic refinement of protein structures could reduce the need for manual intervention. In this approach, possible conformations for a segment of the polypeptide chain are generated systematically and the trial segments are scored for their agreement with the observed diffraction data. The sampling of conformational space is sufficiently exhaustive that reasonable conformations should be included. A number of score functions have been tested, including local electron-density correlations and global structure-factor agreements. The score functions vary in their predictive power as well as in their bias toward the conformation found in the current refined model, but the best score functions have reasonable predictive power. Related functions can be used to indicate which regions of the model fit poorly, reducing the need for manual inspection of models in electron density.

Algorithms↗

PubMed1991

An analysis of protein folding pathways.

We have developed a model of the protein folding process based on three primary assumptions: that burying of hydrophobic area is the dominant contribution to the relative free energy of a conformation, that a record of the folding process is largely preserved in the final structure, and that the denatured state is a random coil. Detailed folding pathways are identified for 19 protein structures. The picture of the folding process that emerges from this analysis is one of nucleation by regions of 8-16 residues. Nucleation sites then lead to larger structures by two mechanisms: propagation and diffusion/collision. A Monte Carlo simulation is used to follow the folding pathway when propagation is the dominant mechanism. Because detailed pathways are derived for each protein, the models are susceptible to experimental verification.

Amino Acid Sequence↗

PubMed1991

Analysis of the steric strain in the polypeptide backbone of protein molecules.

The extent to which local strain is present in the polypeptide backbone of folded protein molecules has been examined. The occurrence of steric strain associated with nonproline cis peptide bonds and energetically unfavorable main chain dihedral angles can be identified reliably from the well ordered parts of high resolution, refined crystal structures. The analysis reveals that there are relatively few sterically strained features. Those that do occur are located overwhelmingly in regions concerned with function. We attribute this to the greater precision necessary for ligand binding and catalysis, compared with the requirements of satisfactory folding.

Binding Sites↗

PubMed1990

Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A.

A large-scale molecular dynamics simulation of the behavior of a serine protease (Streptomyces griseus protease A) in a crystalline environment has been performed. All atoms (including hydrogens) of two protein molecules and the surrounding solvent of crystallization, consisting of both water and salt ions, were explicitly represented, and a relatively long range of interactions (up to 15 A) were included. The simulation is the longest so far reported for a protein in such an environment (60 ps). The use of the full crystalline environment allows a direct comparison of the structure and dynamic properties of the protein and surrounding solvent to be made with the experimental X-ray structure. Here we report the comparison of the protein structures and analyze the energetics of the system, including interaction with the aqueous environment. Subsequent papers will deal with other aspects of the simulation. The overall root mean square differences between the time-averaged molecular dynamics structure and that from crystallography, for all well-ordered, non-hydrogen atoms, are 1.67 and 1.25 A for the two molecules taken as the asymmetric unit. An extensive analysis of the conformation of substructural elements and individual residues and their deviation from experiment has revealed a strong influence of the ionic medium on their behavior. Implications of the results for free energy calculations and for future directions are also discussed.

Algorithms↗

PubMed1990

Probing the calcium-induced conformational transition of troponin C with site-directed mutants.

The contraction of skeletal muscle is regulated by calcium binding to troponin C (TnC). TnC consists of two spatially independent domains, each of which contains two metal ion binding sites. Calcium binding to the regulatory sites of the N-terminal domain triggers muscle contraction by a series of conformational changes. Site-directed mutagenesis offers a means of elucidating the links in this signal path between TnC and actin-myosin crossbridges. Such mapping is possible if the mutants shift the equilibrium between 'on' and 'off' states of the regulatory complex while maintaining the coupling between calcium binding and tension development. Candidate amino-acid residues for yielding this information would be in positions remote from the calcium-binding sites and from the site of development of tension. Analysis of the crystal structure of TnC and of the model of the calcium-activated molecule has enabled us to identify two such residues: Glu 57 and Glu 88. In separate experiments we have replaced each of these residues by lysines. The resulting reduction in calcium affinity indicates that these residues have a long-range effect on calcium binding. This result may reflect the formation of a salt bridge between positions 57 and 88 that is not present in the native molecule. Moreover, the level of tension recovery when the mutants are incorporated into muscle suggests that the interaction between TnC and other muscle components has also been altered. Thus, these residues may participate in the contraction signal transmission.

Animals↗

PubMed1989

Prostacyclin production by human umbilical vein endothelium in response to serum from patients with systemic sclerosis.

Sera from 29 patients with systemic sclerosis and 30 normal controls were examined for their effect on prostacyclin release by human umbilical vein endothelial cells during periods of response of 15 min and 72 h and for their effect on endothelial growth and 3H-thymidine uptake during a 72-h culture period. In contrast to previous reports, no significant differences were detected between patient and control sera in their effect on endothelial cell prostacyclin release, growth or 3H-thymidine uptake.

Adult↗

PubMed1989

Antibody-dependent cellular cytotoxicity of vascular endothelium: characterization and pathogenic associations in systemic sclerosis.

Ten sera from 48 patients with systemic sclerosis were found to be capable of producing cytotoxicity of human umbilical venous and arterial endothelium when co-cultured with peripheral blood mononuclear cells. Fractionation of sera on Ultrogel and the preparation of monomeric IgG by ion exchange and affinity chromatography suggested that the cytotoxicity was mediated by anti-endothelial antibodies capable of pre-sensitizing target cells in a mechanism that resembled antibody-dependent cellular cytotoxicity. These anti-endothelial antibodies together with C1q-binding immune complexes and anti-cardiolipin antibodies were found in 18 of 28 patients so investigated, suggesting that multiple immunological mechanisms may be involved in the pathogenesis of the vascular lesion of systemic sclerosis.

Antibody-Dependent Cell Cytotoxicity↗

PubMed1988

Comparative molecular model building of two serine proteinases from cytotoxic T lymphocytes.

Two genes that are expressed when precursor cytotoxic T lymphocytes are transformed to T killer cells have been cloned and sequenced. The derived amino acid sequences, coding for cytotoxic cell protease 1 (CCP1) and Hannuka factor (HF) are highly homologous to members of the serine proteinase family. Comparative molecular model building using the known three-dimensional structures and the derived amino acid sequences of the lymphocyte enzymes has provided useful structural information, especially in predicting the conformations of the substrate binding sites. In applying this modelling procedure, we used the X-ray structures of four serine proteinases to provide a structurally based sequence alignment: alpha-chymotrypsin (CHT), bovine trypsin (BT), Streptomyces griseus trypsin (SGT), and rat mast cell protease 2 (RMCP2). The root mean square differences in alpha-carbon atom positions among these four structures when compared in a pairwise fashion range from 0.79 to 0.97 A for structurally equivalent residues. The sequences of the two lymphocyte enzymes were then aligned to these proteinases using chemical criteria and the superimposed X-ray structures as guides. The alignment showed that the sequence of CCP1 was most similar to RMCP2, whereas HF has regions of homology with both RMCP2 and BT. With RMCP2 as a template for CCP1 and the two enzymes RMCP2 and BT as templates for HF, the molecular models were constructed. Intramolecular steric clashes that resulted from the replacement of amino acid side chains of the templates by the aligned residues of CCP1 and HF were relieved by adjustment of the side chain conformational angles in an interactive computer graphics device. This process was followed by energy minimization of the enzyme model to optimize the stereochemical geometry and to relieve any remaining unacceptably close nonbonded contacts. The resulting model of CCP1 has an arginine residue at position 226 in the specificity pocket, thereby predicting a substrate preference for P1 aspartate or glutamate residues. The model also predicts favorable binding for a small hydrophobic residue at the P2 position of the substrate. The primary specificity pocket of HF resembles that of BT and therefore predicts a lysine or arginine preference for the P1 residue. The arginine at position 99 in the model of HF suggests a preference for aspartate or glutamate side chains in the P2 position of the substrate. Both CCP1 and HF have a free cysteine in the segment of polypeptide 88 to 93.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed1988

Elevated von Willebrand factor antigen in systemic sclerosis: relationship to visceral disease.

Plasma levels of the factor VIII complex (von Willebrand factor antigen, factor VIII coagulant and ristocetin co-factor) were measured in 28 patients with systemic sclerosis. Elevated von Willebrand factor antigen was found in 12 patients overall and in 10 of 16 patients characterized by severe extensive visceral disease, with a resulting positive correlation between the extent of visceral involvement and the plasma level of von Willebrand factor antigen (r = 0.60, p less than 0.001). Factor VIII coagulant and ristocetin co-factor levels, however, frequently failed to parallel the increases of von Willebrand factor antigen, supporting the view that these increases were due to in vivo endothelial damage. The findings suggest that vascular damage is an important aspect of the visceral lesions of systemic sclerosis.

Adult↗

PubMed1988

Anticardiolipin antibodies in systemic sclerosis: immunological and clinical associations.

Anticardiolipin antibodies of IgG/IgM class were detected in seven of 28 patients with systemic sclerosis including five of 16 patients severely affected by extensive visceral disease. This severely affected sub-group also showed significant elevations of plasma levels of von Willebrand factor antigen in 10 cases and serum C1q binding activity in seven cases respectively. This triple association raises the possibility that multiple immunological mechanisms are involved in the pathogenesis of systemic sclerosis and its vascular lesions.

Adult↗