Amino acid interaction preferences in proteins

Jha, Anupam Nath and Vishveshwara, Saraswathi and Banavar, Jayanth R (2010) Amino acid interaction preferences in proteins. In: Protein Science, 19 (3). pp. 603-616.

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Abstract

Understanding the key factors that influence the interaction preferences of amino acids in the folding of proteins have remained a challenge. Here we present a knowledge-based approach for determining the effective interactions between amino acids based on amino acid type, their secondary structure, and the contact based environment that they find themselves in the native state structure as measured by their number of neighbors. We find that the optimal information is approximately encoded in a 60 x 60 matrix describing the 20 types of amino acids in three distinct secondary structures (helix, beta strand, and loop). We carry out a clustering scheme to understand the similarity between these interactions and to elucidate a nonredundant set. We demonstrate that the inferred energy parameters can be used for assessing the fit of a given sequence into a putative native state structure.

Item Type:	Journal Article
Publication:	Protein Science
Publisher:	Cold Spring Harbor Laboratory Press.
Additional Information:	Copyright of this article belongs to Cold Spring Harbor Laboratory Press.
Keywords:	scoring matrices; secondary structure and contact based environment; hydrophobicity; accessible surface area
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	24 Mar 2010 10:34
Last Modified:	19 Sep 2010 05:57
URI:	http://eprints.iisc.ac.in/id/eprint/26379

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