A METHOD FOR DETECTING HYDROPHOBIC PATCHES PROTEIN

A method for the detection of hydrophobic patches on the surfaces of p rotein tertiary structures is presented, it delineates explicit contig uous pieces of surface of arbitrary size and shape that consist solely of carbon and sulphur atoms using a dot representation of the solvent -accessible surface, The technique is also useful in detecting surface segments with other characteristics, such as polar patches, Its poten tial as a tool in the study of protein-protein interactions and substr ate recognition is demonstrated by applying the method to myoglobin, L eu/Ile/Val-bonding protein, lipase, lysozyme, azurin, triose phosphate isomerase, carbonic anhydrase, and phosphoglycerate kinase. Only the largest patches, having sizes exceeding random expectation, are deemed meaningful, in addition to well-known hydrophobic patches on these pr oteins, a number of other patches are found, and their significance is discussed, The method is simple, fast, and robust. The program text i s obtainable by anonymous ftp. (C) 1996 Wiley-Liss, Inc.