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Analysis of Conformational Variation in Macromolecular Structural Models

Srivastava, Sandeep Kumar and Gayathri, Savitha and Manjasetty, Babu A and Gopal, Balasubramanian (2012) Analysis of Conformational Variation in Macromolecular Structural Models. In: PLOS ONE, 7 (7).

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Official URL: http://dx.doi.org/10.1371/journal.pone.0039993

Abstract

Experimental conditions or the presence of interacting components can lead to variations in the structural models of macromolecules. However, the role of these factors in conformational selection is often omitted by in silico methods to extract dynamic information from protein structural models. Structures of small peptides, considered building blocks for larger macromolecular structural models, can substantially differ in the context of a larger protein. This limitation is more evident in the case of modeling large multi-subunit macromolecular complexes using structures of the individual protein components. Here we report an analysis of variations in structural models of proteins with high sequence similarity. These models were analyzed for sequence features of the protein, the role of scaffolding segments including interacting proteins or affinity tags and the chemical components in the experimental conditions. Conformational features in these structural models could be rationalized by conformational selection events, perhaps induced by experimental conditions. This analysis was performed on a non-redundant dataset of protein structures from different SCOP classes. The sequence-conformation correlations that we note here suggest additional features that could be incorporated by in silico methods to extract dynamic information from protein structural models.

Item Type: Journal Article
Additional Information: Copy right for this article belongs to Srivastava et al
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 21 Aug 2012 03:57
Last Modified: 21 Aug 2012 03:59
URI: http://eprints.iisc.ernet.in/id/eprint/44964

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