PROTEIN SECONDARY STRUCTURE CONFORMATIONS AND ASSOCIATED HYDROPHOBICITY SCALES

We have developed conformational preference functions and a hierarchy of algorithms that can evaluate the success of each hydrophobicity sca le in predicting protein secondary conformation. The results of such e valuation are shown for fiftyfive different scales with respect to the ir ability to predict alpha-helix, beta-sheet and coil structure in th ree testing sets of proteins: five integral membrane proteins, twelve alpha-class and sixteen beta-class soluble proteins. Our scale of conf ormational parameters is the best predictor of secondary structure seg ments in membrane proteins and alpha-class proteins. The success rate and correlation coefficient for alpha-helix conformation in membrane p roteins are 76% and 0.46 respectively, which is superior to the perfor mance measures attained with other prediction schemes. Evaluation of s olution hydrophobicity scales, often used to predict transmembrane seg ments in membrane proteins, indicated absence of correlation in predic tion of helix segments and experimental results for the conformation o f membrane proteins. Such scales have better performance (correlation coefficient around 0.30) in predicting sheet conformation in the beta- class proteins.