A C–H...O, Hydrogen Bond Stabilized Polypeptide Chain Reversal Motif at the C Terminus of Helices in Proteins

Babu, Madan M and Singh, Kumar S and Balaram, P (2002) A C–H...O, Hydrogen Bond Stabilized Polypeptide Chain Reversal Motif at the C Terminus of Helices in Proteins. In: Journal of Molecular Biology, 322 (4). pp. 871-880.

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Abstract

The serendipitous observation of a C–H···O, hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C–H···O interaction between the T−4 $C^\alpha H$ and T+1 C=O group $(C...O \leq3.5 \AA)$ becomes possible only when the T+1 residue adopts an extended $\beta$ conformation (T is defined as the helix terminating residue adopting an $\alpha_L $ conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational preferences at positions T−4, T, and T+1 determined. A marked preference for residues like Ser, Glu and Gln is observed at T−4 position with the motif being further stabilized by the formation of a side-chain–backbone Ocdots, three dots, centeredH–N hydrogen bond involving the side-chain of residue T−4 and the N–H group of residue T+3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in $\beta$ conformation. In a majority of these cases, the succeeding $\beta$ strand lies approximately antiparallel with the helix, suggesting that the backbone C–H...O interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C–H...O hydrogen bonds between (T−4) $C^\alpha H...C=O$ (T+1) and (T−8) $C^\alpha H...C=O (T+3)$.

Item Type:	Journal Article
Publication:	Journal of Molecular Biology
Publisher:	Elsevier
Additional Information:	Copyright of this article belongs to Elsevier.
Keywords:	C–H· · ·O hydrogen bonds;Helix termination;Schellman motif;Polypeptide chain reversal
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	23 Oct 2007
Last Modified:	19 Sep 2010 04:40
URI:	http://eprints.iisc.ac.in/id/eprint/12332

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