Apha-Helix Propensities of Nonpolar Amino Acids Predicted by Monte Carlo Simulated Annealing

Monte Carlo simulated annealing is applied to the study of o-helix propensities of seven nonpolar amino acids, Ala, Leu, Met, Phe, Ile, Val, and Gly. Homopolymers of 10 amino acids are used and the propensity is calculated by folding cz-helicies from completely random initial conformations. The results suggest the large differences in propensities between helix former and breaker in agreement with the recent experiments with short peptides. It is argued that enthalpy difference for helix-coil transitions will play a major role in determining the helix propensity. The &strand propensities of the same homopolymers are also considered, and they are shown to agree with the frequencies of amino acids in P-strands.