Vishal Koparde, Chemical Engineering, Penn State University, 174 Fenske Lab, University Park, PA 16802 and Kristen A. Fichthorn, Dept. of Chemical Engineering, The Pennsylvania State University, 164 Fenske Laboratory, University Park, PA 16802.
Water is known to play a vital role in the structure and dynamics of proteins, thereby affecting their biological functionality. Similarly, it is believed that protein-protein interactions that lead to self-assembly are governed to a large extent by hydration forces. We are particularly interested in studying the interactions between two insulin hexamers. Insulin is a small protein that is comprised of 51 amino acid residues per monomer. Its hexamer complex includes two zinc ions. In this work, we use molecular dynamics to analyze hexamer-hexamer interactions in water and to evaluate the role of hydration forces in these interactions. We use NAMD, along with the CHARMM force field to model the protein and the TIP3P potential to model the water molecules. Simulations of a single insulin hexamer are carried out to determine the variation of water residence times and water coordination number with protein residues. Simulation results can be directly compared with experiments. Simulations to determine the potential of mean force between two insulin hexamers are performed with hydrophobic and hydrophilic surfaces of the hexamers facing each other. The structure and density of water in the region between the two hexamers is analyzed in detail and linked with the hexamer force profiles. Our simulations show that hydrophobic interactions can be an important driving force to direct protein assembly.