Dissecting contact potentials for proteins: Relative contributions of individual amino acids
Corresponding Author
N.-V. Buchete
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
Laboratory of Chemical Physics, NIDDK, National Institutes of Health, 9000 Rockville Pike, Bldg. 5, Rm. 137A, Bethesda, Maryland, 20892-0520===Search for more papers by this authorJ. E. Straub
Department of Chemistry, Boston University, Boston, Massachusetts 02215
Search for more papers by this authorD. Thirumalai
Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742
Search for more papers by this authorCorresponding Author
N.-V. Buchete
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
Laboratory of Chemical Physics, NIDDK, National Institutes of Health, 9000 Rockville Pike, Bldg. 5, Rm. 137A, Bethesda, Maryland, 20892-0520===Search for more papers by this authorJ. E. Straub
Department of Chemistry, Boston University, Boston, Massachusetts 02215
Search for more papers by this authorD. Thirumalai
Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742
Search for more papers by this authorAbstract
Knowledge-based contact potentials are routinely used in fold recognition, binding of peptides to proteins, structure prediction, and coarse-grained models to probe protein folding kinetics. The dominant physical forces embodied in the contact potentials are revealed by eigenvalue analysis of the matrices, whose elements describe the strengths of interaction between amino acid side chains. We propose a general method to rank quantitatively the importance of various inter-residue interactions represented in the currently popular pair contact potentials. Eigenvalue analysis and correlation diagrams are used to rank the inter-residue pair interactions with respect to the magnitude of their relative contributions to the contact potentials. The amino acid ranking is shown to be consistent with a mean field approximation that is used to reconstruct the original contact potentials from the most relevant amino acids for several contact potentials. By providing a general, relative ranking score for amino acids, this method permits a detailed, quantitative comparison of various contact interaction schemes. For most contact potentials, between 7 and 9 amino acids of varying chemical character are needed to accurately reconstruct the full matrix. By correlating the identified important amino acid residues in contact potentials and analysis of about 7800 structural domains in the CATH database we predict that it is important to model accurately interactions between small hydrophobic residues. In addition, only potentials that take interactions involving the protein backbone into account can predict dense packing in protein structures. Proteins 2008. © 2007 Wiley-Liss, Inc.
Supporting Information
The Supplementary Material referred to in this article can be found online at http://www.interscience.wiley.com/jpages/0887-3585/suppmat/
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