Analysis on sliding helices and strands in protein structural comparisons: A case study with protein kinases

Gowri, VS and Anamika, K and Gore, S and Srinivasan, N (2007) Analysis on sliding helices and strands in protein structural comparisons: A case study with protein kinases. In: Journal of Biosciences, 32 (5). pp. 921-928.

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Abstract

Protein structural alignments are generally considered as ‘golden standard’ for the alignment at the level of amino acid residues. In this study we have compared the quality of pairwise and multiple structural alignments of about 5900 homologous proteins from 718 families of known 3-D structures. We observe shifts in the alignment of regular secondary structural elements (helices and strands) between pairwise and multiple structural alignments. The differences between pairwise and multiple structural alignments within helical and \beta-strand regions often correspond to 4 and 2 residue positions respectively. Such shifts correspond approximately to “one turn” of these regular secondary structures. We have performed manual analysis explicitly on the family of protein kinases. We note shifts of one or two turns in helix-helix alignments obtained using pairwise and multiple structural alignments. Investigations on the quality of the equivalent helix-helix, strand-strand pairs in terms of their residue side-chain accessibilities have been made. Our results indicate that the quality of the pairwise alignments is comparable to that of the multiple structural alignments and, in fact, is often better. We propose that pairwise alignment of protein structures should also be used in formulation of methods for structure prediction and evolutionary analysis.

Item Type:	Journal Article
Publication:	Journal of Biosciences
Publisher:	Indian Academy of Sciences
Additional Information:	Copyright of this article belongs to Indian Academy of Sciences.
Keywords:	Protein kinase;shift in secondary structures;structural alignments.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	30 Jul 2008
Last Modified:	19 Sep 2010 04:48
URI:	http://eprints.iisc.ac.in/id/eprint/15357

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