Moe, Sarah2020-11-172020-11-172018-08https://hdl.handle.net/11299/217116University of Minnesota M.S. thesis. August 2018. Major: Chemistry. Advisor: Alessandro Cembran. 1 computer file (PDF); vii, 111 pages.Dystrophin is a cytoplasmic protein that provides stability to the membrane of muscle cells by dissipating mechanical stress during muscle contraction and relaxation. Mutations in the dystrophin gene lead to various forms of muscular dystrophy, for which there is currently no cure and in the most severe forms lead to premature death. The design of therapeutics is hindered by the lack of structural information of full dystrophin, and by the fact that dystrophin’s mechanism of function is largely unknown. We hypothesize that dystrophin dissipates mechanical energy by undergoing an order-to-disorder transition, during which buried hydrophobic regions are partially exposed to solvent, and transduction of energy leads to an enhanced local ordering and corresponding decrease in entropy of surrounding water molecules. While it is well-established that protein motion influences the structure and dynamics of hydration shell water, the potential stabilizing effect of water ordering throughout the unfolding pathway of proteins is not fully understood. To test our hypothesis, we have generated a structural model of a large portion of dystrophin using homology modeling. We have investigated the mechanism of unfolding in spectrin monomers using computational pulling with steered molecular dynamic simulations. The evaluation of tetrahedral and Steinhardt order parameters throughout unfolding trajectories suggests enhanced geometrical ordering of water molecules as the protein unfolds. Counterintuitively, this structural ordering is accompanied by faster water dynamics, as indicated by both a smaller water rotational relaxation lifetime and by faster diffusive motion of water in the protein’s vicinity. Overall, the effects appear to offset each other, as the resulting entropy change is small and hardly detectable over the noise level. Together, these results suggest that hydrophobic exposure increases geometrical ordering of hydration shell water while also decreasing the strength of the protein-water interactions. Analysis of these water properties provides insight into the structure and dynamics of hydration shells around dystrophin protein and presents a compelling motif for further mechanistic analysis.enThesis or Dissertation