Fuzzy cluster analysis of simple physicochemical properties of amino acids for recognizing secondary structure in proteins.
Fuzzy cluster analysis has been applied to the 20 amino acids by using 65 physicochemical properties as a basis for classification. The clustering products, the fuzzy sets (i.e., classical sets with associated membership functions), have provided a new measure of amino acid similarities for use in protein folding studies. This work demonstrates that fuzzy sets of simple molecular attributes, when assigned to amino acid residues in a protein's sequence, can predict the secondary structure of the sequence with reasonable accuracy. An approach is presented for discriminating standard folding states, using near-optimum information splitting in half-overlapping segments of the sequence of assigned membership functions. The method is applied to a nonredundant set of 252 proteins and yields approximately 73% matching for correctly predicted and correctly rejected residues with approximately 60% overall success rate for the correctly recognized ones in three folding states: alpha-helix, beta-strand, and coil. The most useful attributes for discriminating these states appear to be related to size, polarity, and thermodynamic factors. Van der Waals volume, apparent average thickness of surrounding molecular free volume, and a measure of dimensionless surface electron density can explain approximately 95% of prediction results. hydrogen bonding and hydrophobicity induces do not yet enable clear clustering and prediction.
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Pacific Biomedical Research Center, University of Hawaii, Honolulu 96822, USA.
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D016000:Cluster Analysis; D016208:Databases, Factual; D005418:Flavodoxin / Q000737:chemistry; D017143:Fuzzy Logic; D008956:Models, Chemical; D017510:Protein Folding; D017433:Protein Structure, Secondary
D000596:Amino Acids; D005418:Flavodoxin