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Title: Discovering side-chain correlation in {alpha}-Helices

Using a new representation for interactions in protein sequences based on correlations between pairs of amino acids, we have examined {alpha}-helical segments from known protein structures for important interactions. Traditional techniques for representing protein sequences usually make an explicit assumption of conditional independence of residues in the sequences. Protein structure analyses, however, have repeatedly demonstrated the importance of amino acid interactions for structural stability. We have developed an automated program for discovering sequence correlations in sets of aligned protein sequences using standard statistical tests and for representing them with Bayesian networks. In this paper, we demonstrate the power of our discovery program and representation by analyzing pairs of residues from {alpha}-helices. The sequence correlations we find represent physical and chemical interactions among amino-acid side chains in helical structures. Furthermore, these local interactions are likely to be important for stabilizing and packing {alpha}-helices. Lastly, we have also detect correlations in side-chain conformations that indicate important structural interactions but which don`t appear as sequence correlations.
Authors:
;  [1]
  1. Stanford Univ. School of Medicine, CA (United States)
Publication Date:
OSTI Identifier:
377149
Report Number(s):
CONF-9408117-
CNN: Grant LM05305; TRN: 96:005197-0029
Resource Type:
Technical Report
Resource Relation:
Conference: 2. international conference on intelligent systems for molecular biology, Stanford, CA (United States), 15-17 Aug 1994; Other Information: PBD: [1994]; Related Information: Is Part Of Proceedings: Second international conference on intelligent systems for molecular biology; Altman, R.; Brutlag, D.; Karp, P.; Lathrop, R.; Searls, D. [eds.]; PB: 389 p.
Research Org:
Stanford Univ., CA (United States)
Country of Publication:
United States
Language:
English
Subject:
55 BIOLOGY AND MEDICINE, BASIC STUDIES; 99 MATHEMATICS, COMPUTERS, INFORMATION SCIENCE, MANAGEMENT, LAW, MISCELLANEOUS; PROTEIN STRUCTURE; STATISTICS; AMINO ACID SEQUENCE; STRUCTURAL MODELS; PROBABILITY; MOLECULAR STRUCTURE; HELICAL CONFIGURATION