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An automated approach to network features of protein structure ensembles

Bhattacharyya, Moitrayee and Bhat, Chanda R and Vishveshwara, Saraswathi (2013) An automated approach to network features of protein structure ensembles. In: PROTEIN SCIENCE, 22 (10). pp. 1399-1416.

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Official URL: http://dx.doi.org/10.1002/pro.2333


Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

Item Type: Journal Article
Additional Information: copyright for this article belongs to WILEY-BLACKWELL
Keywords: PSN-Ensemble program; network features; protein structure network; weighted network; MD; NMR ensemble; UbcH5b; beta2-adrenergic receptor; tRNA synthetases
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 14 Nov 2013 10:44
Last Modified: 14 Nov 2013 10:44
URI: http://eprints.iisc.ac.in/id/eprint/47752

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