Protein Dynamics: Molecular simulations of RNase A and related proteins

Abstract

Proteins have unique structures. At equilibrium, the atoms in these molecules fluctuate around a mean structure and the extent of fluctuation is determined by the force acting on each atom of the molecule. The motion of atoms about the mean position can elucidate a number of features of proteins such as: which of the non covalent interactions are rigid, which ones are flexible, what kind of conformational change the protein undergoes when it binds to its ligands, how does protein dynamics change when mutations occur at specific positions in the protein and so on. Elucidation of such properties ultimately gives an in-sight into the basic problems of protein folding and the mechanism of action of proteins. In our laboratory, we have carried out molecular dynamics simulations on the protein Ribonuclease A (RNase A), its complexes, fragments and mutants in order to address problems such as protein-ligand interaction and protein dynamics in fragment complemented systems using the computational facilities at the SERC, IISc. The results of some of these investigations are presented below.