DMCA
DM: Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions
| Venue: | J Mol Biol |
| Citations: | 84 - 9 self |
BibTeX
@ARTICLE{Senes_dm:statistical,
author = {Ro Senes and Mark Gerstein and Donald M. Engelman},
title = {DM: Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions},
journal = {J Mol Biol},
year = {},
pages = {296--921}
}
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Abstract
To ®nd motifs that mediate helix-helix interactions in membrane proteins, we have analyzed frequently occurring combinations of residues in a database of transmembrane domains. Our analysis was performed with a novel formalism, which we call TMSTAT, for exactly calculating the expectancies of all pairs and triplets of residues in individual sequences, taking into account differential sequence composition and the substantial effect of ®nite length in short segments. We found that the number of signi®cantly over and under-represented pairs and triplets was much greater than the random expectation. Isoleucine, glycine and valine were the most common residues in these extreme cases. The main theme observed is patterns of small residues (Gly, Ala and Ser) at i and i ‡ 4 found in association with large aliphatic residues (Ile, Val and Leu) at neighboring positions (i.e. i 1 and i 2). The most over-represented pair is formed by two glycine residues at i and i ‡ 4 (GxxxG, 31.6 % above expectation, p <1 10�33) and it is strongly associated with the
Keyphrases
gxxxg motif statistical analysis transmembrane helix amino acid pattern beta-branched residue account differential sequence composition membrane protein glycine residue helix-helix interaction nite length large aliphatic residue transmembrane domain over-represented pair main theme novel formalism extreme case substantial effect common residue small residue random expectation individual sequence under-represented pair short segment
