Structure-Preserving Coarse-Grained Simulationof Proteins in Explicit Solvent
KOLE, K.; GHOSH MOULICK, A.; Chakrabarti, J.
Show abstract
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 residues 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.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.