COMPARISON OF A NEW MONTE-CARLO PEPTIDE CONFORMATIONAL SEARCH PROCEDURE WITH HIGH-TEMPERATURE MOLECULAR-DYNAMICS

In an accompanying paper (1) a new Monte Carlo simulation method for exploring the potential energy surface of oligopeptides is described. In the present article the method is applied to generate configurations of penta-alanine. The simulations were performed at 300K and 1000K, and are compared with two 1000K molecular dynamics (MD) simulations; a 200 ps trajectory starting from an alpha-helical conformation and a 100 ps trajectory starting from an extended (beta) structure. Configurations obtained were energy-minimised and the resulting structures and energies compared. The Monte Carlo simulations and the MD run that started from the extended configuration found the same minimum-energy conformer. The MD trajectory starting from the helical configuration sampled a different region of configurational space, associated with a conformer of 0.5 kcals/mol higher energy.