Backbone cluster identification in proteins by a graph theoretical method

Patra, SM and Vishveshwara, S (2000) Backbone cluster identification in proteins by a graph theoretical method. In: Biophysical Chemistry, 84 (1). pp. 13-25.

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Abstract

A graph theoretical algorithm has been developed to identify backbone clusters of residues in proteins. The identified clusters show protein sites with the highest degree of interactions. An adjacency matrix is constructed from the non-bonded connectivity information in proteins. The diagonalization of such a matrix yields eigenvalues and eigenvectors, which contain the information on clusters. In graph theory, distinct clusters can be obtained from the second lowest eigenvector components of the matrix. However, in an interconnected graph, all the points appear as one single cluster. We have developed a method of identifying highly interacting centers (clusters) in proteins by truncating the vector components of high eigenvalues. This paper presents in detail the method adopted for identifying backbone clusters and the application of the algorithm to families of proteins like RNase-A and globin. The objective of this study was to show the efficiency of the algorithm as well as to detect conserved or similar backbone packing regions in a particular protein family. Three clusters in topologically similar regions in the case of the RNase-A family and three clusters around the porphyrin ring in the globin family were observed. The predicted clusters are consistent with the features of the family of proteins such as the topology and packing density. The method can be applied to problems such as identification of domains and recognition of structural similarities in proteins.

Item Type:	Journal Article
Publication:	Biophysical Chemistry
Publisher:	Elsevier
Additional Information:	Copyright of this article belongs to Elsevier.
Keywords:	Non-covalent interaction;Adjacency matrix;Eigenvalue and eigenvector;Cluster;RNase-A family;Globin family;Domains
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	15 Oct 2007
Last Modified:	19 Sep 2010 04:39
URI:	http://eprints.iisc.ac.in/id/eprint/12001

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