Investigations of Ramachandran disallowed conformations in protein domain families

Lakshmi, B and Ramakrishnan, C and Archunan, G and Sowdhamini, R and Srinivasan, N (2014) Investigations of Ramachandran disallowed conformations in protein domain families. In: INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 63 . pp. 119-125.

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Abstract

In peptide and protein structures, occurrence of (phi,psi.) angles in the disallowed region of the Ramachandran map almost always suggests local regions of error or poor accuracy. However, very rarely genuine disallowed conformations occur as noted in the current study in proteins of known structure available at ultra-high resolution (<= 1.2 (A) over circle). In the current work, extent of conservation of genuine disallowed conformations in homologous proteins of known structures has been analyzed. From a dataset of 124 protein domain families, with structure of at least one constituent member in each family available at a resolution of 1.2 (A) over circle or better, we have analyzed the conservation of 221 disallowed conformations. It is observed that the disallowed conformation is only moderately conservedin protein domain families. In the gross dataset no particular residue type adopting disallowed conformation elicit high conservation of residue type though there are alignment positions in the dataset with complete conservation of both the residue type and the disallowed conformation. Conserved disallowed conformation in protein domain families play biologically significant role in roughly 50% of the cases. The residues with the disallowed conformation or its flanking residues are often located within or around the functional site of the protein. (C) 2013 Elsevier B.V. All rights reserved.

Item Type:	Journal Article
Publication:	INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
Publisher:	ELSEVIER SCIENCE BV
Additional Information:	Copyright for this article belongs to the ELSEVIER SCIENCE BV, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS
Keywords:	Disallowed conformations; Protein evolution; Protein structures; Ramachandran map; Steric clash
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	11 Mar 2014 10:46
Last Modified:	11 Mar 2014 10:46
URI:	http://eprints.iisc.ac.in/id/eprint/48547

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