Date of Award
Doctor of Philosophy (PhD)
Biochemistry & Molecular Biophysics
A J. Wand
As the universal solvent, water is unquestionably essential to most aspects of protein biophysics from protein folding to enzymatic activity. Much has been learned about the relationship between proteins and surrounding solvent waters; however, it is often difficult to experimentally examine these interactions in a site-specific manner without perturbing molecular structure. Furthermore, the effect of nearby hydration dynamics on protein dynamics (and, in effect, protein conformational entropy) is poorly understood at atomic resolution. With the use of a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and protein reverse micelle (RM) encapsulation, it is possible to examine both the dynamic behavior of waters in the protein hydration layer as well as protein dynamics for the same sample without physically altering the protein. The goal of this work is to use these complementary techniques in order to better understand the interplay between hydration and protein dynamics. First, we demonstrate the utility of NMR spectroscopy in monitoring and controlling the pH of the aqueous interior of reverse micelle ensembles. This leads to the ability to reliably confirm sample pH and structural fidelity upon RM encapsulation which is often difficult to accomplish using other techniques. Next we propose a novel approach to collecting and analyzing NMR hydration dynamics experiments with the use of non-uniform sampling (NUS) and nuclear Overhauser effect (NOE) mixing time buildup experiments. We examine factors contributing to the reproducibility and reliability of hydration ratios. Using these NOE-based hydration experiments, we then examine the hydration dynamics of hen egg-white lysozyme (HEWL) with and without a bound inhibitor. We find minimal retardation of hydration dynamics within a partially hydrophilic binding cleft; we detect waters within an internal pocket which are relatively fast; and we inspect trapped interfacial waters upon ligand binding. Finally, we use RM encapsulation to examine the effect of changes in solvent dynamics on fast (ps-ns) protein dynamics. While retardation of hydration dynamics seems to affect dynamics of aromatic side chains, it has little to no effect on other fast protein dynamics effectively confirming that protein conformational entropy is not slaved to solvent. This work represents a large leap forward in our understanding of the relationship between proteins and their hydrating environment.
Marques, Bryan Stephen, "Reverse Micelle Encapsulation And Its Use In Examining The Interplay Between Hydration And Protein Dynamics" (2018). Publicly Accessible Penn Dissertations. 3015.