AUTOMATIC RECOGNITION OF HYDROPHOBIC CLUSTERS AND THEIR CORRELATION WITH PROTEIN-FOLDING UNITS

A method is described to objectively identify hydrophobic clusters in proteins of known structure. Clusters are found by examining a protein for compact groupings of side chains. Compact clusters contain seven or more residues, have an average of 65% hydrophobic residues, and usu ally occur in protein interiors. Although smaller clusters contain onl y side-chain moieties, larger clusters enclose significant portions of the peptide backbone in regular secondary structure. These clusters a gree well with hydrophobic regions assigned by more intuitive methods and many larger clusters correlate with protein domains. These results are in striking contrast with the clustering algorithm of J. Heringa and P. Argos (1991, J Mol Biol 220: 151-171). That method finds that c lusters located on a protein's surface are not especially hydrophobic and average only 3-4 residues in size. Hydrophobic clusters can be cor related with experimental evidence on early folding intermediates. Thi s correlation is optimized when clusters with less than nine hydrophob ic residues are removed from the data set. This suggests that hydropho bic dusters are important in the folding process only if they have eno ugh hydrophobic residues.