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Investigating Diproline Segments in Proteins: Occurrences, Conformation and Classification

Saha, Indranil and Shamala, Narayanaswamy (2012) Investigating Diproline Segments in Proteins: Occurrences, Conformation and Classification. In: Biopolymers, 97 (1). pp. 54-64.

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Official URL: http://onlinelibrary.wiley.com/doi/10.1002/bip.217...

Abstract

The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle phi to values of -60 degrees +/- 30 degrees for the L-proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment ((L)Pro-(L)Pro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro-Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa-Pro-Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residues by the diproline segment and the single proline residue. The study indicates that P(II)-P(II) and P(II)-alpha are the most favorable conformational states for the diproline segment. The analysis on Xaa-Pro-Yaa sequences reveals that the XaaPro peptide bond exists preferably as the trans conformer rather than the cis conformer. The present study may lead to a better understanding of the behavior of proline occurring in diproline segments which can facilitate various designed diproline-based synthetic templates for biological and structural studies. (C) 2011 Wiley Periodicals, Inc. Biopolymers 97: 54-64, 2012.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to John Wiley & Sons.
Keywords: diproline segments;conformational states;cis Pro-Pro peptide bond;trans Pro-Pro peptide bond;flanking residue conformation
Department/Centre: Division of Physical & Mathematical Sciences > Physics
Date Deposited: 05 Dec 2011 08:59
Last Modified: 05 Dec 2011 08:59
URI: http://eprints.iisc.ernet.in/id/eprint/42519

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