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Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers

Gunasekaran, K and Gomathi, L and Ramakrishnan, C and Chandrasekhar, J and Balaram, P (1998) Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers. In: Journal of Molecular Biology, 284 (5). pp. 1505-15016.

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Abstract

The two most important beta-turn features in peptides and proteins are the type I and type II turns, which differ mainly in the orientation of the central peptide unit. Facile conformational interconversion is possible, in principle, by a flip of the central peptide unit. Homologous crystal structures afford an opportunity to structurally characterize both possible conformational states, thus allowing identification of sites that are potentially stereochemically mobile. A representative data set of 250 high-resolution (less than or equal to 2.0 Angstrom), non-homologous protein crystal structures and corresponding variant and homologous entries, obtained from the Brookhaven Protein Data Bank, was examined to identify turns that are assigned different conformational types (type I/type II) in related structures. A total of 55 examples of beta-turns were identified as possible candidates for a stereochemically mobile site. Of the 55 examples, 45 could be classified as a potential site for interconversion between type I and type II beta-turns, while ten correspond to flips from type I' to type II' structures. As a further check, the temperature factors of the central peptide unit carbonyl oxygen atom of the 55 examples were examined. The analysis reveals that the turn assignments ape indeed reliable. Examination of the secondary structures at the flanking positions of the flippable beta-turns reveals that seven examples occur in the loop region of beta-hairpins, indicating that the formation of ordered secondary structures on either side of the beta-turn does not preclude local conformational variations. In these beta-turns, Pro (11 examples), Lys (nine examples) and Ser (seven examples) were most often found at the i + 1 position. Glycine was found to occur overwhelmingly at position i + 2 (28 examples), while Ser (seven examples) and Asn (six examples) were amongst the most frequent residues. Activation energy barriers for the interconversion between type I and type II beta-turns were computed using the peptide models Ac-Pro-Aib-NHMe and Ac-Pro-Gly-NHMe within the framework of the AM1 semi-empirical molecular orbital procedure. In order to have a uniform basis for comparison and to eliminate the distracting influence of the deviation of backbone dihedral angles from that expected for ideal beta-turns, the dihedral angles phi(i+1) and psi(i+2) were fixed at the ideal values (phi(i+1) = -60 degrees and psi(i+2) = 0 degrees). The other two angles (psi(i+1) and phi(i+2)) were varied systematically to go from type II to type I beta-turn structures. The computational results suggest that there exists one stereospecific, concerted flip of the central peptide unit involving correlated single bond rotation that can occur with an activation barrier of the order of 3 kcal/mol. The results presented here suggest that conformational variations in beta-turns are observed in protein crystal structures and such changes may be an important dynamic feature in solution.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Academic Press.
Keywords: beta-turns;conformational interconversions;energy barrier computation;protein mobility;protein structure analysis.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Division of Chemical Sciences > Organic Chemistry
Date Deposited: 18 May 2009 04:41
Last Modified: 03 May 2011 05:21
URI: http://eprints.iisc.ernet.in/id/eprint/18309

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