Amino acid interaction preferences in proteins
Open Access
- 13 January 2010
- journal article
- research article
- Published by Wiley in Protein Science
- Vol. 19 (3), 603-616
- https://doi.org/10.1002/pro.339
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 × 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.Keywords
Funding Information
- Supercomputer Education and Research Center
- Indian Institute of Science, Bangalore, Mathematical Biology Project
- Department of Science and Technology (DST), India
This publication has 55 references indexed in Scilit:
- Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoysBMC Structural Biology, 2008
- AAindex: amino acid index database, progress report 2008Nucleic Acids Research, 2007
- OPUS‐Ca: A knowledge‐based potential function requiring only Cα positionsProtein Science, 2007
- Four-body contact potentials derived from two protein datasets to discriminate native structures from decoysProteins: Structure, Function, and Bioinformatics, 2007
- Inferring ideal amino acid interaction forms from statistical protein contact potentialsProteins: Structure, Function, and Bioinformatics, 2005
- The Protein Data BankNucleic Acids Research, 2000
- Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemesProtein Science, 1999
- Are proteins ideal mixtures of amino acids? Analysis of energy parameter setsProtein Science, 1995
- One thousand families for the molecular biologistNature, 1992
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresPeptide Science, 1983