Biomedical subjects

A Vinayagam

Publications and source records attributed to A Vinayagam.

5 recordsLinked to original sources

PubMed2005

Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides.

Structure prediction and three-dimensional modeling of disulfide-rich systems are challenging due to the limited number of such folds in the structural databank. We exploit the stereochemical compatibility of substructures in known protein structures to accommodate disulfide bonds in predicting the structures of disulfide-rich polypeptides directly from disulfide connectivity pattern and amino acid sequence in the absence of structural homologs and any other structural information. This knowledge-based approach is illustrated using structure prediction of 40 nonredundant bioactive disulfide-rich polypeptides such as toxins, growth factors, and endothelins available in the structural databank. The polypeptide conformation could be predicted in 35 out of 40 nonredundant entries (87%). Nonhomologous templates could be identified and models could be obtained within 2 A deviation from the query in 29 peptides (72%). This procedure can be accessed from the World Wide Web (http://www.ncbs.res.in/ approximately faculty/mini/dsdbase/dsdbase.html).

Algorithms↗

PubMed2004

DSDBASE: a consortium of native and modelled disulphide bonds in proteins.

DSDBASE is a database of disulphide bonds in proteins, which provides information on native disulphides and those that are stereochemically possible between pairs of residues for all known protein structural entries. The modelling of disulphides has been performed, using MODIP, by the identification of residue pairs that can strainlessly accommodate a covalent cross-link. We also assess the stereochemical quality of the covalent cross-link and grade them appropriately. One of the potential uses of the database is to design site-directed mutants in order to enhance the thermal stability of a protein. The proposed sites of mutations can be viewed specifically with respect to active sites of enzymes and across physiological dimers. The occurrence of native and modelled disulphides increases the dimensions of the database enormously. This database can also be employed for proposing three-dimensional models of disulphide-rich short polypeptides. The database can be accessed from http://www.ncbs.res.in/ approximately faculty/mini/dsdbase/dsdbase.html. Supplementary information can be accessed from http://www.ncbs.res.in/ approximately faculty/mini/dsdbase/nar/suppl.htm.

Animals↗

PubMed2003

DDBASE2.0: updated domain database with improved identification of structural domains.

MOTIVATION: Although many methods are available for the identification of structural domains from protein three-dimensional structures, accurate definition of protein domains and the curation of such data for a large number of proteins are often possible only after manual intervention. The availability of domain definitions for protein structural entries is useful for the sequence analysis of aligned domains, structure comparison, fold recognition procedures and understanding protein folding, domain stability and flexibility. RESULTS: We have improved our method of domain identification starting from the concept of clustering secondary structural elements, but with an intention of reducing the number of discontinuous segments in identified domains. The results of our modified and automatic approach have been compared with the domain definitions from other databases. On a test data set of 55 proteins, this method acquires high agreement (88%) in the number of domains with the crystallographers' definition and resources such as SCOP, CATH, DALI, 3Dee and PDP databases. This method also obtains 98% overlap score with the other resources in the definition of domain boundaries of the 55 proteins. We have examined the domain arrangements of 4592 non-redundant protein chains using the improved method to include 5409 domains leading to an update of the structural domain database. AVAILABILITY: The latest version of the domain database and online domain identification methods are available from http://www.ncbs.res.in/~faculty/mini/ddbase/ddbase.html SUPPLEMENTARY INFORMATION: http://www.ncbs.res.in/~faculty/mini/ddbase/supplementary/supplementary.html

Amino Acid Sequence↗

PubMed1989

Electrophoretic pattern of blood and cuticular phenoloxidase of different crustaceans.

A 7% sodium dodecyl sulfate (SDS) polyacrylamide slab gel electrophoresis was carried out to study the molecular weight of blood and cuticular phenoloxidase from different crustaceans. In Uca lacteus de Haan, Scylla serrata Forskal and Ocypode platytarsis Milne Edwards, the apparent molecular weight of cuticular phenoloxidase is higher than that of blood phenoloxidase, whereas the molecular weights of cuticular phenoloxidase isozymes of Emerita emeritus L. are lower than those of blood phenoloxidase isozymes. In Metapenaeus monoceros Fabricius, the blood phenoloxidase shows a molecular weight of 250,000 and the cuticular phenoloxidase shows two isozymes with molecular weights of 350,000 and 250,000. The individuality of blood phenoloxidase and cuticular phenoloxidase and their roles are discussed.

Animals↗

PubMed1986

A rapid method for detection of tyrosinase activity in electrophoresis.

This rapid and sensitive method for localizing tyrosinase in polyacrylamide slab gels is based on the condensation of Bestthorn's hydrazone (3 methyl-2-benzothiazolinone hydrazone hydrochloride) with the quinone obtained by enzymatic oxidation of phenol. Both monophenolase and diphenolase activities are localized by this method.

Animals↗