Dissecting alpha-helices: Position-specific analysis of alpha-helices in globular proteins

Kumar, S and Bansal, M (1998) Dissecting alpha-helices: Position-specific analysis of alpha-helices in globular proteins. In: Proteins: Structure, Funcaction, and Bioinformatics, 31 (4). pp. 460-470.

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Abstract

An analysis of the amino acid distributions at 15 positions, viz., N", N', Ncap, N1, N2, N3, N4, Mid, C4, C3, C2, C1, Ccap, C', and C" in 1,131 alpha-helices reveals that each position has its own unique characteristics. In general, natural helix sequences optimize by identifying the residues to be avoided at a given position and minimizing the occurrence of these avoided residues rather than by maximizing the preferred residues at various positions. Ncap is most selective in its choice of residues, with six amino acids (S, D, T, N, G, and P) being preferred at this position and another 11 (V, I-,F,A,K,L,Y,R,E,M, and Q) being strongly avoided. Ser, Asp, and Thr are all more preferred at Ncap position than Asn, whose role at helix N-terminus has been highlighted by earlier analyses. Furthermore, Asn is also found to be almost equally preferred at helix C-terminus and a novel structural motif is identified, involving a hydrogen bond formed by N-62 of Asn at Ccap or C1 position, with the backbone carbonyl oxygen four residues inside the helix. His also forms a similar motif at the C-terminus. Pro is the most avoided residue in the main body (N4 to C4 positions) and at C-terminus, including Ccap of an alpha-helix. In 1,131 alpha-helices, no helix contains Pro at C3 or C2 positions. However, Pro is highly favoured at N1 and C'. The doublet X-Pro, with Pro at C' position and extended backbone conformation for the X residue at Ccap, appears to be a common structural motif for termination of alpha-helices, in addition to the Schellman motif. Main body of the helix shows a high preference for aliphatic residues Ala, Leu, Val, and ne, while these are avoided at helix termini. A propensity scale for amino acids to occur in the middle of helices has been obtained. Comparison of this scale with several previously reported scales shows that this scale correlates best with the experimentally determined values.

Item Type:	Journal Article
Publication:	Proteins: Structure, Funcaction, and Bioinformatics
Publisher:	John Wiley and Sons
Additional Information:	Copyright of this article belongs to John Wiley and Sons.
Keywords:	alpha-helix;sequence; structure;database;amino acid; secondary structure.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	18 May 2009 09:20
Last Modified:	19 Sep 2010 05:01
URI:	http://eprints.iisc.ac.in/id/eprint/18417

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