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Inferring ideal amino acid interaction forms from statistical protein contact potentials
Author(s) -
Pokarowski Piotr,
Kloczkowski Andrzej,
Jernigan Robert L.,
Kothari Neha S.,
Pokarowska Maria,
Kolinski Andrzej
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20380
Subject(s) - isoelectric point , chemistry , residue (chemistry) , amino acid , electrostatics , amino acid residue , hydrophobic effect , statistical potential , pairwise comparison , type (biology) , crystallography , protein structure , mathematics , peptide sequence , protein structure prediction , enzyme , biochemistry , statistics , gene , ecology , biology
We have analyzed 29 different published matrices of protein pairwise contact potentials (CPs) between amino acids derived from different sets of proteins, either crystallographic structures taken from the Protein Data Bank (PDB) or computer‐generated decoys. Each of the CPs is similar to 1 of the 2 matrices derived in the work of Miyazawa and Jernigan (Proteins 1999;34:49–68). The CP matrices of the first class can be approximated with a correlation of order 0.9 by the formula e ij = h i + h j , 1 ≤ i , j ≤ 20, where the residue‐type dependent factor h is highly correlated with the frequency of occurrence of a given amino acid type inside proteins. Electrostatic interactions for the potentials of this class are almost negligible. In the potentials belonging to this class, the major contribution to the potentials is the one‐body transfer energy of the amino acid from water to the protein environment. Potentials belonging to the second class can be approximated with a correlation of 0.9 by the formula e ij = c 0 − h i h j + q i q j , where c 0 is a constant, h is highly correlated with the Kyte–Doolittle hydrophobicity scale, and a new, less dominant, residue‐type dependent factor q is correlated (∼0.9) with amino acid isoelectric points pI. Including electrostatic interactions significantly improves the approximation for this class of potentials. While, the high correlation between potentials of the first class and the hydrophobic transfer energies is well known, the fact that this approximation can work well also for the second class of potentials is a new finding. We interpret potentials of this class as representing energies of contact of amino acid pairs within an average protein environment. Proteins 2005. © 2005 Wiley‐Liss, Inc.