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Investigating proline puckering states in diproline segments in proteins

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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Correspondence to: N. Shamala; e-mail: shamala@physics.iisc.ernet.in

ABSTRACT

In the current study, the puckering states of the Proline ring occurring in diproline segments (LPro-LPro) in proteins has been investigated with a segregation made on the basis of cis and trans states for the Pro-Pro peptide bond and the conformational states for the diproline segment to investigate the effects of conformation of the diproline segment on the corresponding puckering state of the Proline ring in the segment if any. The value of the endocyclic ring torsional angles of the pyrrolidine ring has been used for calculating and visualizing various puckering states using a proposed new sign convention (+/−) nomenclature. The results have been compared to that obtained in a previous study on peptides from this group. In this study, quite interestingly, the Planar (G) conformation that was present in 14.3% of the cases in peptides, appears to be nearly a rare conformation in the case of proteins (1.9%). The present study indicates that the (Cγ-exo/Cγ-exo), (Cγ-exo/Twisted Cγ-exo-Cβ-endo) and (Twisted Cγ-endo-Cβ-exo/Twisted Cγ-endo-Cβ-exo) categories are the most preferred combinations. For Proline rings in proteins, the states Cγ-exo, Twisted Cγ-exo-Cβ-endo and Twisted Cγ-endo-Cβ-exo are the most preferred states. Within diproline segments, the pyrrolidine ring conformations do not show a strong co-relation to the backbone conformation in which they are observed. It is likely that five-membered rings have a considerable plasticity of structure and are readily deformed to accommodate a variety of energetically preferred backbone conformations. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 605–610, 2013.

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