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Sparsely populated residue conformations in protein structures: Revisiting ``experimental'' Ramachandran maps

Kalmankar, Neha V and Ramakrishnan, C and Balaram, P (2014) Sparsely populated residue conformations in protein structures: Revisiting ``experimental'' Ramachandran maps. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82 (7). pp. 1101-1112.

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Official URL: http://dx.doi.org/10.1002/prot.24384

Abstract

The Ramachandran map clearly delineates the regions of accessible conformational (phi-) space for amino acid residues in proteins. Experimental distributions of phi, values in high-resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely arid, fully allowed region in the top left quadrant establishes that side-chain and backbone interactions may provide the energetic compensation necessary for populating this region of phi- space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II turns (Bin 13). Of the 516 non-Gly residues in Bin 13, 384 occupied the i + 1 position of Type II turns. Further examination of these turn segments revealed a high propensity to occur at the N-terminus of helices and as a tight turn in hairpins. The strand-helix motif with the Type II turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101-1112. (c) 2013 Wiley Periodicals, Inc.

Item Type: Journal Article
Additional Information: Copyright for this article belongs to the WILEY-BLACKWELL, 111 RIVER ST, HOBOKEN 07030-5774, NJ USA
Keywords: Ramachandran map; protein conformation; secondary structural motifs; amino acid conformational propensities; Type II ` beta turn
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Depositing User: Id for Latest eprints
Date Deposited: 22 Jul 2014 11:53
Last Modified: 22 Jul 2014 11:53
URI: http://eprints.iisc.ac.in/id/eprint/49507

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