A general screened Coulomb potential based implicit solvent model: Calculation of secondary structure of small peptides

The screened Coulomb potential based implicit solvent model (SCP-ISM) was r ecently proposed to describe bulk solvent effects in proteins. In this work it is combined with the Monte Carlo approach of conformational memories (C M) and the PAR22 force field of CHARMM to carry out sequence to structure c alculations on peptides that have been shown to adopt alpha -helix and beta -hairpin conformations. Simulations at 270 K and 300 K on the peptide, CH3 CO-(AAQAA)(3)-NHCH3, result in a-helix containing populations of 60% and 53 % at these two temperatures, respectively. The residue helicities were foun d to change dramatically between these two temperatures, and at the lower t emperature are in good agreement with the experimental helicities estimated at 274 K. CM simulations on the second peptide, CH3CO-V(5)(D)PGV(5)-NH2, w ere carried out to study the beta -hairpin forming propensity of (D)Pro. Th e calculations gave a population of about 40% beta -hairpin conformations a t 300 K with the residues (D)Pro-Gly forming all or part of the loop. Four main subfamilies of different beta -hairpin/beta -turn structures were foun d. It was observed that hydrophobic interactions between specific side chai ns play a fundamental role in the formation and stabilization of the differ ent types of beta -turns. For both peptides, populations of about 40% rando m coil structures were found. Comparison with available theoretical and exp erimental results is presented and discussed. (C) 2001 John Wiley & Sons, I nc.