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Biomedical subjects

J Moult

Publications and source records attributed to J Moult.

At least 19 recordsLinked to original sources
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↗
PubMed1987

Bacterial resistance to beta-lactam antibiotics: crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.5 A resolution.

beta-lactamases are enzymes that protect bacteria from the lethal effects of beta-lactam antibiotics, and are therefore of considerable clinical importance. The crystal structure of beta-lactamase from the Gram-positive bacterium Staphylococcus aureus PC1 has been determined at 2.5 angstrom resolution. It reveals a molecule of novel topology, made up of two closely associated domains. The active site is located at the interface between the domains, with the key catalytic residue Ser70 at the amino terminus of a buried helix. Examination of the disposition of the functionally important residues within the active site depression leads to a model for the binding of a substrate and a functional analogy to the serine proteases. The unusual topology of the secondary structure units is relevant to questions concerning the evolutionary relation to the beta-lactam target enzymes of the bacterial cell wall.

Anti-Bacterial Agents↗
PubMed1986

A model for the Ca2+-induced conformational transition of troponin C. A trigger for muscle contraction.

The initial contractile event in muscle is the binding of Ca2+ ions to troponin C of the troponin complex, leading to a series of conformational changes in the members of the thin and thick filaments. Knowledge of the crystal structure of turkey skeletal muscle troponin C has provided a structural basis for the modeling of the first stage of this process in atomic detail. This crystal structure probably represents the molecule in the relaxed state of muscle, with two of the maximum of 4 Ca2+ ions bound. The basis for the model presented here is that upon binding of the additional two Ca2+ ions, the regulatory domain of the molecule undergoes a conformational transition to become closely similar in structure to the domain which always binds Ca2+ or Mg2+ under physiological conditions. The root mean square discrepancy in atomic coordinates between the apo and the modeled Ca2+-bound states of the regulatory domain is 4.8 A, with some shifts as large as 10-15 A in the region near the linker between the two Ca2+ binding sites. It is demonstrated that this Ca2+-bound conformation of the regulatory domain conforms to accepted protein structure rules and that the change in conformation can be accomplished without encountering any barriers too high to be surmounted on the physiological time scale.

Amino Acid Sequence↗
PubMed1986

Calcium binding to skeletal muscle troponin C and the regulation of muscle contraction.

Skeletal muscle contraction is initiated by Ca2+ ion binding to troponin C (TnC), a protein of the thin filament. Our three-dimensional structure determination of turkey skeletal TnC at 2.8 A resolution revealed an extended molecule consisting of two domains connected through a long nine-turn alpha-helix. The C-terminal domain has two Ca2+ ions bound in the expected manner of EF hands, whereas the N-terminal regulatory domain is Ca2+-free with a helix-loop-helix conformation different from that of an EF hand. The refinement of TnC at 2.2 A resolution highlights the intricate hydrogen-bonded network common to the Ca2+-bound loops and provides an explanation for the presence of a water molecule in the 5th coordination position of the Ca2+ ion. We propose that Ca2+ binding to the regulatory domain is accompanied by a conformational transition by which its structure becomes similar to that of the C-terminal domain. Dramatic movements of residues in the B and C helices and the connecting peptide of up to 14 A constitute the bulk of this change. A hydrophobic site that could be the site of interaction with troponin I is thereby exposed. We have also demonstrated that this model of the Ca2+-bound conformation can be reached from the Ca2+-free state without having to surmount large energy barriers.

Amino Acid Sequence↗
PubMed1986

An algorithm for determining the conformation of polypeptide segments in proteins by systematic search.

The feasibility of determining the conformation of segments of a polypeptide chain up to six residues in length in globular proteins by means of a systematic search through the possible conformations has been investigated. Trial conformations are generated by using representative sets of phi, psi, and chi angles that have been derived from an examination of the distributions of these angles in refined protein structures. A set of filters based on simple rules that protein structures obey is used to reduce the number of conformations to a manageable total. The most important filters are the maintenance of chain integrity and the avoidance of too-short van der Waals contacts with the rest of the protein and with other portions of the segment under construction. The procedure is intended to be used with approximate models so that allowance is made throughout for errors in the rest of the structure. All possible main chains are first constructed and then all possible side-chain conformations are built onto each of these. The electrostatic energy, including a solvent screening term, and the exposed hydrophobic area are evaluated for each accepted conformation. The method has been tested on two segments of chain in the trypsin like enzyme from Streptomyces griseus. It is found that there is a wide spread of energies among the accepted conformations, and the lowest energy ones have satisfactorily small root mean square deviations from the X-ray structure.

Algorithms↗
PubMed1985

Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution.

Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis. Atomic co-ordinates from the 1.8 A and 1.5 A resolution refinements of the crystal structure of protease A from Streptomyces griseus have been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (N epsilon 2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the N epsilon 2-H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the N epsilon 2 into the pi bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it.

Amino Acid Sequence↗