Analyzing the Effects of Conformational Fluctuations on Protein-Water Interactions in Barnase-Barstar Using All Atom Molecular Dynamics Simulations

Barnase-Barstar is a protein complex that has a strong association constant. The purpose of this research is to investigate the effects of conformational fluctuations on protein-water interactions, resulting water-mediated interactions, and the binding free energy of the protein complex. Using all-atom molecular dynamics simulations, the sets of simulations for flexible and rigid proteins to identify the effects on water-mediated interactions were prepared for analysis. To analyze the properties and interactions that result in the strong association of the Barnase-Barstar protein complex, the molecular dynamics simulations were prepared. A thorough review of the GROMACS manual and completion of the GROMACS Lysozyme in Water tutorial was completed to understand the steps and commands to write and run molecular dynamics simulations. The preliminary data investigated the impact of water-mediated interactions on the solvation free energy in the Barnase-Barstar protein complex where the proteins are kept rigid. This was achieved by observing the change in solvation free energy with respect to separation distance. From the data obtained, it is concluded that solvent-mediated interactions do not contribute to the negative binding free energy. With increasing separation distance, the change in solvation free energy decreased. Therefore, thermodynamically, water-mediated interactions destabilize the protein complex, while the binding free energy is dominated by direct protein-protein interactions. The follow-up simulations of flexible proteins with controlled protein-protein separation distances, for which a fully automated simulation and analysis protocol has been prepared in this project, will allow us to quantify the impact of conformational fluctuations on water-mediated interactions and the binding free energy of the protein complex by comparison to the simulations of rigid proteins.