(232e) Coarse Grain Molecular Dynamics Simulation for the Prediction of Conformation of Lysozyme Adsorbed on Silica Surface

All-atoms molecular dynamics (AAMD) simulation is an effective tool for the prediction of conformation of polypeptides. However, it is computationally intensive to predict folding kinetics for a larger protein molecule using AAMD. Therefore, a simplified and more efficient simulation algorithm, coarse-grain molecular dynamics (CGMD), was developed to investigate the equilibrium conformation of lysozyme both in solution as well as on silica surface. The CGMD method is a mesoscopic simulation technique in which groups of atoms are mapped to beads based on a four-to-one rule. This systematic reduction of the degrees of freedom allows for computationally efficient calculation of the dynamics of conformational changes of lysozyme for larger time and length scales than all atoms models, thus providing important information on protein folding in solution and its interaction with the surface. To validate this CGMD method, a comparison of AAMD and CGMD on the folding kinetics of a small protein Trp-cage (consisting of twenty amino acids) in solution, which is initially fully unfolded, was carried out with AMBER version 8.0. The results shows that the equilibrium state of the Trp-cage obtained by CGMD is comparable to that obtained by AAMD as indicated by the analysis of the potential energy, root mean square deviation, end-to-end distance, radius of gyration, and overall structure comparison. The CGMD results also show that the equilibrium structure of Trp-cage forms stable folded structure with a hydrophobic core in the cage regions in agreement with experimentally reported NMR structure. A topology and force fields of the Lysozyme by CGMD was developed. The folding kinetics of lysozyme in solution was evaluated using CGMD. The equilibrium conformation as obtained by CGMD was compared with published NMR structure. In addition, the kinetics of conformational changes of lysozyme adsorbed on silica surface was also evaluated.