Estimation of peptide hormone noncovalent binding site functionality from frequencies of interaction of amino acid side chains in proteins.
A method is described for estimating the amino acid side chain functional groups most likely to occur at a receptor site (or other protein-type binding site) given a particular peptide hormone sequence. The predictions are based on mutual affinities of amino acid side chains, as manifested in the frequencies of side chain contacts occurring in proteins. The relative merits of various measures of these affinities are discussed, and a new set of contact frequency data based on 36 proteins (coordinate data taken from the Brookhaven Protein Data Bank) is presented. Evaluation of predictions was carried out using subunit-subunit interfaces as models for peptide-receptor association; accuracy of guesses was found to be 3-4 times better than random, according to this measure. Computer programs for carrying out all requisite data manipulations are described.
D000596:Amino Acids / Q000032:analysis*; D055598:Chemical Phenomena; D002621:Chemistry; D002627:Chemistry, Physical; D008956:Models, Chemical; D011506:Proteins / Q000378:metabolism; D011956:Receptors, Cell Surface / Q000378:metabolism*; D013223:Statistics as Topic
D000596:Amino Acids; D011506:Proteins; D011956:Receptors, Cell Surface