Stranded in isolation: structural role of isolated extended strands in proteins

Eswar, Narayanan and Ramakrishnan, C and Srinivasan, N (2003) Stranded in isolation: structural role of isolated extended strands in proteins. In: Protein Engineering, 16 (5). pp. 331-339.

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Abstract

Reasons for the formation of extended-strands (E-strands) in proteins are often associated with the formation of beta-sheets. However E-strands, not part of beta-sheets, commonly occur in proteins. This raises questions about the structural role and stability of such isolated E-strands. Using a dataset of 250 largely non-homologous and high-resolution (<2 Angstrom) crystal structures of proteins, we have identified 518 isolated E-strands from187 proteins. The two most distinguishing features of isolat ed E-strands from beta-strands in beta-sheets are the high preponderance of prolyl residues occuring in isolated E-strands and their high exposure to the surroundings.Removal of regions with polyproline conformation from the dataset did not significantly reduce the propensity of prolyl residues to occur in isolated E-strands. Isolated E-strands are often characterized by their main-chain amide and carbonyl groups involved in hydrogen bonding with polar side chains or water. They are often flanked by irregular loop structures and are less well conserved, than beta-sheet forming beta-strands, among homologous protein structures. It is suggested that isolated beta-strands have many characteristics of loop segments but with repetitive (phi,psi) values falling within the beta-region of the Ramachandran map.

Item Type:	Journal Article
Publication:	Protein Engineering
Publisher:	Oxford University Press
Additional Information:	Copyright of this article belongs to Oxford University Press.
Keywords:	beta-sheet;beta-strand;extended strand;hydrogen bonding;protein structures.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	05 Nov 2009 07:51
Last Modified:	19 Sep 2010 04:56
URI:	http://eprints.iisc.ac.in/id/eprint/17374

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