Intramolecular backbone center dot center dot center dot backbone hydrogen bonds in polypeptide conformations. The other way around: epsilon-turn

Toniolo, Claudio and Crisma, Marco and Formaggio, Fernando and Aleman, Carlos and Ramakrishnan, Chandrasekharan and Kalmankar, Neha and Balaram, Padmanabhan (2017) Intramolecular backbone center dot center dot center dot backbone hydrogen bonds in polypeptide conformations. The other way around: epsilon-turn. In: BIOPOLYMERS, 108 (1, SI).

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Abstract

In this study, we performed a detailed literature survey of the E-turn in peptides and proteins. This three-dimensional structural feature is characterized by an eleven-membered pseudo-cycle closed by an intramolecular backbone center dot center dot center dot backbone H-bond. Interestingly, in this motif the direction of the N-H center dot center dot center dot O=C H-bond runs opposite to that of the much more popular and extensively investigated alpha-, beta-, and gamma-turns. We did not authenticate unequivocally the epsilon-turn main-chain reversal topology in any linear short peptide. However, it is frequently observed in small cyclic peptides formed by four, five, and six amino acid residues with stringent geometric requirements. Rather surprisingly, epsilon-turns do occur in proteins, although to a relatively moderate extent, as an isolated feature or in the turn segment of hairpin motifs based on two antiparallel, pleated beta-strands. Moreover, the E-turn may also host not only the seven-membered, intramolecularly H-bonded, pseudo-cycle termed gamma-turn, either of the classic or inverse type, but also one (or even two) cis peptide bond(s) or a beta-bulge conformation. Based on their phi, psi backbone torsion angles, we were able to classify the protein E-turns in six different families. Conformational energy computations using the DFT methodology were also performed on the E-turns adopted by the amino acid triplet -Gly-Gly-Gly- (Gly is the most commonly found residue at each of the three positions in our analysis of proteins). Again, in this computational study, six families of turns were identified, but only some of them resemble rather closely those extracted from our investigation on proteins.

Item Type:	Journal Article
Publication:	BIOPOLYMERS
Additional Information:	Copy right for this article belongs to the WILEY, 111 RIVER ST, HOBOKEN 07030-5774, NJ USA
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	16 Sep 2017 05:49
Last Modified:	04 Oct 2018 15:33
URI:	http://eprints.iisc.ac.in/id/eprint/57839

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