Molecular Dynamics Simulations of Cosolvent Effects on Protein Stability

Angel Garcia, Rensselaer Polytechnic Institute

Usage Details

The student will study short amino acid sequences that serve as stabilizing cosolvents in protein solutions. In this project he will conduct molecular dynamics simulations of four co-solvents (Arg, Pro, Glu and Gly) at various concentrations and calculate the osmotic pressure of the solution. These values will be compared to the known experimental results and it is expected that small changes in the co-solvent force field will be needed to reproduce the data. The changes in the force field for the co-solvent will also be implemented in the protein force field. Validation of the resulting force field will tested by studying the radius of gyration of intrinsically disordered peptides. The simulations of osmotic pressure require multiple calculations at various concentrations and for different trial parameters. Simulations of the IDP require multi-processor parallel computations using enhanced sampling methods.