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Registering alpha-Helices and beta-Strands Using Backbone C-H…O Interactions

Singh, Kumar S and Babu, Madan M and Balaram, P (2003) Registering alpha-Helices and beta-Strands Using Backbone C-H…O Interactions. In: Proteins: Structure, Function, and Genetics, 51 (2). pp. 167-171.


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The possible occurrence of a novel helix terminating structural motif in proteins involving a stabilizing short C-H...O interaction has been examined using a dataset of 634 non-homologous protein structures (\leq 2.0 \AA). The search for this motif was prompted by the crystallographic characterization of a novel structural feature in crystals of a synthetic decapeptide in which extension of a Schellman motif led to the formation of a C-H...O hydrogen bond between the T-4 $C^ \alpha H$ and the T+1 C=O groups, where T is the helix terminator adopting a left handed $(\alpha_L)$ conformation. More than 100 such motifs with backbone conformation superposing well with the peptide examples were identified. In several examples, formation of this motif led to an approximately antiparallel arrangement of a helical segment with an extended \beta-strand. Careful examination of these examples suggested the possibility of registering antiparallel arrangement of helices and strands by means of backbone C-H...O interactions with a regular periodicity. Model building resulted in the generation of idealized \alpha \beta and \beta \alpha motifs, which can then be generalized to higher order repetitive structures. Inspection of the antiparallel \alpha \beta motif revealed a significant propensity for Ser, Glu, and Gln residues at the T-4 position resulting in further stabilization using an O...H-N side chain-backbone hydrogen bond. Modeling studies revealed ready accommodation of serine residues along the helix face that contacts the strand. The theoretically generated folds correspond to "open" polypeptide structures.

Item Type: Journal Article
Publication: Proteins: Structure, Function, and Genetics
Publisher: John Wiley & Sons, Inc
Additional Information: Copyright for this article belongs to John Wiley & Sons, Inc
Keywords: Polypeptide folds;hydrogen bonds;Helix termination;Alpha beta motifs
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 03 Aug 2004
Last Modified: 19 Sep 2010 04:14
URI: http://eprints.iisc.ac.in/id/eprint/1227

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