Journal of Chemical Physics, Vol.109, No.4, 1567-1574, 1998
Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method
Ab initio folding of the avian pancreatic polypeptide using a diffusion-process-controlled Monte Carlo method is presented. This method differs from other Monte Carlo methods in that two successive conformations must be kinetically connected in a small period of time. The 36-residue polypeptide is represented using a hybrid level of structure description : the backbone is treated at an all-atom level, while the side chains are modeled as spheres. The conformations are evaluated on the basis of pairwise contact energies between the side chains, a main chain hydrogen bonding potential, and local bonded potentials. Starting from various extended conformations, the chain reaches the basin of lowest energy in similar to 1000-3500 Monte Carlo steps and the predicted conformations deviate by similar to 3.0 Angstrom rms from the x-ray structure. The eight trajectories suggest a three-step mechanism : (1) early formation of the alpha helix in the region 14-33, (2) cooperative formation of long-range interactions, and (3) stabilization of the polyprolinelike conformation in the-region 1-8 in the final steps of folding.
Keywords:PROTEIN CONFORMATION;GLOBULAR-PROTEINS;MODEL PROTEINS;PREDICTION;REPRESENTATION;RESOLUTION;SIMULATION;SEARCH;COIL