Network approach for capturing ligand-induced subtle global changes in protein structures

Sukhwal, Anshul and Bhattacharyya, Moitrayee and Vishveshwara, Saraswathi (2011) Network approach for capturing ligand-induced subtle global changes in protein structures. In: Acta Crystallographica Section D, 67 (Part 5). pp. 429-439.

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Abstract

Ligand-induced conformational changes in proteins are of immense functional relevance. It is a major challenge to elucidate the network of amino acids that are responsible for the percolation of ligand-induced conformational changes to distal regions in the protein from a global perspective. Functionally important subtle conformational changes (at the level of side-chain noncovalent interactions) upon ligand binding or as a result of environmental variations are also elusive in conventional studies such as those using root-mean-square deviations (r.m.s.d.s). In this article, the network representation of protein structures and their analyses provides an efficient tool to capture these variations (both drastic and subtle) in atomistic detail in a global milieu. A generalized graph theoretical metric, using network parameters such as cliques and/or communities, is used to determine similarities or differences between structures in a rigorous manner. The ligand-induced global rewiring in the protein structures is also quantified in terms of network parameters. Thus, a judicious use of graph theory in the context of protein structures can provide meaningful insights into global structural reorganizations upon perturbation and can also be helpful for rigorous structural comparison. Data sets for the present study include high-resolution crystal structures of serine proteases from the S1A family and are probed to quantify the ligand-induced subtle structural variations.

Item Type:	Journal Article
Publication:	Acta Crystallographica Section D
Publisher:	International Union of Crystallography
Additional Information:	Copyright of this article belongs to International Union of Crystallography.
Keywords:	noncovalent interactions;protein structure graph;serine proteases;cliques/communities;low r.m.s.d.;conformational changes.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	01 Jun 2011 12:09
Last Modified:	01 Jun 2011 12:09
URI:	http://eprints.iisc.ac.in/id/eprint/37814

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