Does the folding type of a protein depend on its amino acid composition?

Abstract

Proteins of known structures are generally classified into one of the following four folding types: alpha, beta, alpha + beta, and alpha/beta proteins. Recent findings [Muskal and Kim (1992) J. Mol. Biol. 225, 713-727] suggested that the folding type of a protein might basically depend on its amino acid composition. If this is true, why is that the predicted results of the protein folding type from amino acid composition always failed to reach the desired accuracy? An examination of the prediction approach indicates that none of the previous algorithms has ever taken into account the coupling effect among different amino acid components. In view of this, a new algorithm has been developed which distinguishes itself from the previous ones by incorporating such a coupling effect. The very high rates, 99.2% and 95.3%, of correct predictions thus obtained for a recently constructed training set of 120 proteins and testing set of 64 proteins, respectively, provide confirmation of the above suggestion.