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G Chelvanayagam

Publications and source records attributed to G Chelvanayagam.

44 records · Page 3Linked to original sources
PubMed1995

The phospho-beta-galactosidase and synaptotagmin predictions.

Two bona fide consensus predictions of secondary and tertiary structure in a protein family, made and announced before experimental structures were known, are evaluated in light of the subsequently determined experimental structures. The first, for phospho-beta-galactosidase, identified the core strands of an 8-fold alpha-beta barrel, and identified the 8-fold alpha-beta barrel itself, which was found in the subsequently determined experimental structure to be the core folding domain. The second, for synaptotagmin, identified seven out of eight beta-strands in the structure correctly, missing only a noncore strand. Three preferred "topologies" were selected from several hundred thousand possible topologies of these seven predicted strands using a rule-based analysis. The subsequently determined experimental structure showed that these seven strands in synaptotagmin adopt one of the three preferred topologies. We were unable, however, to identify the correct topology from among these three topologies.

Amino Acid Sequence↗
PubMed1994

Structural characteristics and stabilizing principles of bent beta-strands in protein tertiary architectures.

beta-Strands as constituents of beta-pleated sheets in protein tertiary structures often display considerable distortion from a purely extended conformation. The dislocation types are often characterized as "bulging," "twisting," and "bending." The former 2 properties have been extensively studied and classified. In this work an investigation of bent beta-structures is undertaken. The structural characteristics examined included the bending angles within and out of the principal strand plane, their distribution among various strand types such as parallel and antiparallel, the amino acid preferences at bend sites, and the usage of charged and polar residues for stabilization through interactive anchoring with other atoms of the beta-sheet within which the bent strand lies.

Amino Acids↗
PubMed1994

Easy adaptation of protein structure to sequence.

An investigation into the conservation of coarse, medium and fine grain structural properties has been performed over a data set of 175 protein tertiary structures in 34 different families, each characterized by a common core fold and a library of conserved sites formed for each family. It is shown that, while the conservation of coarse and medium grain properties correlates to the structural deviation between the proteins, fine grain properties are poorly conserved except in functional sites. This flexibility in fine grain properties suggests that folding can be viewed as an optimization process whereby side chains have freedom to position themselves as best as possible given environmental conformational constraints and that given a basic framework, the local structure is able to adapt easily to sequence variation. The conserved cores of the 34 families are used to estimate a minimal core size of 35% of the fold, consistent with buried residue considerations. Finally, conservation in side chain chi 1 torsion angles is combined with structural deviation, sequence deviation and resolution to suggest a set of example structure pairs suitable for testing automatic homology modelling programs.

Hydrogen Bonding↗
PubMed1992

Anatomy and evolution of proteins displaying the viral capsid jellyroll topology.

In this paper the anatomy of 25 structures containing a jellyroll motif, consisting of eight antiparallel beta-strands forming a so-called beta-barrel, was investigated. This involved performing a careful structural alignment based on hydrogen bonds for the equivalent regions of the tertiary folds and a subsequent analysis of conserved amino acids, equivalenced residue-residue contacts, and various parameters describing the size, shape and other geometrical characteristics of these regions. It was found that the jellyroll motif is best viewed as a two-sheet wedge structure rather than a barrel. The more conserved parameters are discussed. A model of evolutionary development for the jellyroll fold in the various protein and viral structures is proposed.

Amino Acid Sequence↗
PubMed1992

Prediction of protein folding pathways.

Recent 1H nuclear magnetic resonance (n.m.r.) hydrogen exchange experiments on five different proteins have delineated the secondary structures formed in trapped, partially folded intermediates. The early forming structural elements are identifiable through a technique described in this work to predict folding pathways. The method assumes that the sequential selection of structural fragments such as alpha-helices and beta-strands involved in the folding process is founded upon the maximal burial of solvent accessible surface from both the formation of internal structure and substructure association. The substructural elements were defined objectively by major changes in main-chain direction. The predicted folding pathways are in complete correspondence with the n.m.r. results in that the formed structural fragments found in the folding intermediates are those predicted earliest in the pathways. The technique was also applied to proteins of known tertiary structure and with fold similar to one of the five proteins examined by 1H n.m.r. The pathways for these structures also showed general consistency with the n.m.r. observations, suggesting conservation of a secondary structural framework or molten globule about which folding nucleates and proceeds.

Amino Acid Sequence↗
PubMed1991

Stereo viewing on the PC/AT with EGA graphics.

Tachystoscopic stereo can be used to greatly enhance the performance and usability of low-cost molecular graphics systems. Here, a simple way to connect and control three-dimensional liquid-crystal glasses from a PC/AT with EGA graphics capabilities is described. The method makes elegant use of the screen's vertical retrace for synchronization purposes, allowing left and right views to be alternated every refresh cycle.

Computer Graphics↗
PubMed1990

PASS: simple molecular graphics system for personal computers.

An interactive tool for displaying and manipulating molecular structures is presented. The system has a user friendly, menu driven interface and provides good quality graphics for viewing proteins. Full screen stereo viewing and a high degree of flexibility in the investigation of specific sites are among its key attributes. The low cost of the system allows it a diverse range of applicability.

Computer Graphics↗