A C-H…O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus helices in proteins.

Madan Babu, M and Kumar Singh , S and Balaram, Padmanabhan (2002) A C-H…O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus helices in proteins. In: Journal of Molecular Biology, 322 (4). 871-880 .

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Abstract

The serendipitous observation of a C–Hcdots, three dots, centeredO 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–Hcdots, three dots, centeredO interaction between the T−4 CαH and T+1 C=O group (Ccdots, three dots, centeredO≤3.5 Å) becomes possible only when the T+1 residue adopts an extended β conformation (T is defined as the helix terminating residue adopting an αL 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 β conformation. In a majority of these cases, the succeeding β strand lies approximately antiparallel with the helix, suggesting that the backbone C–Hcdots, three dots, centeredO 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–Hcdots, three dots, centeredO hydrogen bonds between (T−4) CαHcdots, three dots, centeredC=O (T+1) and (T−8) CαHcdots, three dots, centeredC=O (T+3).

Item Type:	Journal Article
Publication:	Journal of Molecular Biology
Publisher:	Elsevier Science
Additional Information:	Copyright of this article belongs to Elsevier Science.
Keywords:	C–Hcdots, three dots, centeredO hydrogen bonds; helix termination; Schellman motif; polypeptide chain reversal.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	24 Nov 2010 08:27
Last Modified:	24 Nov 2010 08:27
URI:	http://eprints.iisc.ac.in/id/eprint/33879

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