Protein Backbone Dynamics Simulations Using Coarse-Grained Bonded Potentials and Simplified Hydrogen Bonds.

A new set of bonded potentials is introduced to model the flexibility of coarse-grained polypeptide chains. Based on a statistical analysis of known structures, the bonded potentials are sequence-dependent, and the secondary-structure propensity of each amino acid is partially reflected in the Si-Bi-Bi+1-Bi+2 pseudotorsion angle, where Si and Bi denote the side-chain and backbone beads, respectively. To stabilize the secondary structures during simulations, the bonded force field must be balanced by a simplified model of the protein hydrogen bonds, based on dipole-dipole interactions. Tested on eight polypeptides with sequence lengths ranging from 17 to 98, using 200-ns molecular dynamics simulations, the coarse-grained model yields trajectories with RMSDs ranging from 3 to 8 Å from the experimental conformations. The less-structured regions of the simulated proteins exhibit the largest-amplitude movements.