Linked Life Data

9626705

Source:http://linkedlifedata.com/resource/pubmed/id/9626705

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
1998-9-15
pubmed:abstractText
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 delta 2 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 Ile, 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.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Jun
pubmed:issn
0887-3585
pubmed:author
pubmed:issnType
Print
pubmed:day
1
pubmed:volume
31
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
460-76
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed:year
1998
pubmed:articleTitle
Dissecting alpha-helices: position-specific analysis of alpha-helices in globular proteins.
pubmed:affiliation
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't