Stability of polypeptide conformational states. II. Folding of a polypeptide chain by the scanning simulation method, and calculation of the free energy of the statistical coil

The scanning simulation method suggested by Meirovitch is extended to a study of the stability of decaglycine at 100 and 300 K. The model is based on the potential energy function ECEPP (Empirical Conformational Energy Program for Peptides) with rigid geometry and without solvent. The free energy of the statistical coil, which is defined over the whole phase space excluding the region of the right-handed α-helix, is calculated. At 100 K, the molecule is found to be unstable in the statistical coil region, and the method generates (i.e., “folds”) conformations that are left-handed or right-handed α-helices with very high preference. Their free energy is found to be comparable with that obtained by another method developed in our previous paper (paper I) [H. Meirovitch, M. Vásquez, and H. A. Scheraga, (1987) Biopolymers 26 , 651–671]. At 300 K the statistical coil becomes the most stable state; sample conformations of the coil are generated efficiently with the scanning method and the free energy is calculated. It appears that both the scanning method and the method of paper I can be used to carry out a complete analysis of the stability of a polypeptide based on free energy considerations.