Structure-Preserving Coarse-Grained Simulation of Proteins in Explicit Solvent

Many biologically relevant processes occur on time scales that are 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 atomic planes is lost in coarse-grained. We develop a simple coarse grained protein model with structural information in explicit solvent. We represent each residue’s center of mass as a polymer bead and water oxygen as a solvent bead. Each polymer bead has five degrees of freedom: position of the center and additional two variables, for the backbone dihedral angles. All interaction parameters for bonded, non-bonded and dihedral coupling are derived from the equilibrated all-atom molecular dynamics simulation trajectory. We find that our coarse-grained approach, reproduces residue-level structural features that closely match the crystal structures and all-atom simulation results for both structured and disordered proteins.