Simulation of Protein Structure using a Coarse-Grained Potential incorporating the Backbone Dihedral Interactions

Abstract

Many biologically relevant processes occur on time and length scales which are far beyond the reach of atomistic simulations. These processes include large protein dynamics and the self-assembly of biological materials. Coarse-grained molecular modeling allows computer simulations on length and time scales 2-3 orders of magnitude larger than atomistic simulations, bridging the gap between the atomistic and mesoscopic scales. However, the structural information involving the dihedral angles is lost in coarse-graining. We develop a simple coarse-grained protein model with structural information in explicit solvent. We represent the center of mass of each residue as a polymer bead and water oxygen as a solvent bead. Each polymer bead has five degrees of freedom: position of the center and two additional variables for the backbone dihedral angles. All interaction parameters for bonded, non-bonded, dihedral coupling and bead-solvent interactions are derived from the equilibrated all-atom molecular dynamics simulation trajectory. We find that our coarse-grained approach reproduces residue-level structural information that closely matches the crystal structures and all-atom simulation results.