Coarse grain molecular dynamics simulation for the prediction of tertiary conformation of lysozyme adsorbed on silica surface

Abstract

A coarse-grain (CG) algorithm is developed for molecular dynamics (MD) simulation of proteins in which the polypeptide backbone as well as side chains were mapped into spherical interaction centres. The force field parameters for non-bonded interaction between these centres (beads) were evaluated from the interaction of all atoms corresponding to these beads using pairwise additivity. The validity of CG algorithm was demonstrated by comparing the potential energy, radius of gyration (RG), end-to-end distance and root-mean-square deviation with those obtained by all-atom (AA) simulation for a small protein molecule Trp-cage as well as for lysozyme in solution. The CG simulation for lysozyme in solution requires less than 1/50 CPU-time compared to that for the AA method. Also, the CG method converges to equilibrium potential energy much faster than AA simulation. CG simulation for lysozyme adsorbed on silica surface showed that the molecule is more unfolded with a less compact tertiary structure compared to that in the solution (with higher RG, end-to-end distance and the projected area on silica surface), this effect being more pronounced at higher temperature. A higher ionic strength resulted in a more extended structure for the lysozyme on silica surface.