Date of Award
Free energy calculations for the transfer of a water molecule from the pure liquid to an interior cavity site in a protein are presented. Three different protein cavities, in bovine pancreatic trypsin inhibitor (BPTI), the I106A mutant of lysozyme, and in the I76A mutant of barnase, represent very different environments for the water molecule, one which is polar, forming four water-protein hydrogen bonds, and two which are more hydrophobic, only forming one or two water-protein hydrogen bonds. The calculations give very different free energies for the different cavities, with only the polar BPTI cavity predicted to be hydrated. The corresponding entropies for the transfer to the interior cavities are calculated as well and show that the transfer to the polar cavity is significantly entropically unfavorable while the transfer to the non-polar cavity is entropically favorable. For all proteins an analysis of the fluctuations in the positions of the protein atoms shows that the addition of a water molecule makes the protein more flexible. This increased flexibility appears to be due to an increase length and weakened strength of protein-protein hydrogen bonds near the cavity. Similar free energy studies are performed on the three proteins at high pressure, 3 kbar. As in the 1 atm studies BPTI is the only protein that should be hydrated at 3 kbar, however the protein free energy changes appear to be not strongly dependent on the number of hydrogen bonds available. Changes in protein structure and flexibility are analyzed in an attempt to more fully understand the changes proteins undergo prior to pressure induced denaturation. These changes can help understand the forces at work in the last stages of protein folding. The role of interior water in this process is also analyzed. Changes to the fluctuating charge algorithm that handles polarizability in molecular dynamics simulations were performed to allow for longer time steps. The fluctuating charge model treats partial charges as variables which are propagated using Lagrangian dynamics. A coordinate transform to normal mode charge variables is applied to the TIP4P-FQ model of water to decrease the coupling between the atomic and charge degrees of freedom.
Olano, Lisa Renee, "Thermodynamics of Buried Water in Protein Cavities and Revised Algorithms for Introducing Polarizability to Molecular Dynamics Simulations" (2006). University of New Orleans Theses and Dissertations. 387.