UC San Diego

A combination of classical and quantum mechanical approaches are described in Chapter 1 and utilized in this dissertation to study catalysis and allostery in the metalloprotein IspH, as well as to probe protonation equilibria in a variety of macromolecules. Chapters 2 and 3 are dedicated to characterizing the oxidized [4Fe-4S] IspH protein, which is biologically important as an antimicrobial drug target. In Chapter 2, the protonation states of active site residues in substrate-bound IspH are characterized using broken-symmetry density functional theory to provide a foundation for exploring IspH catalysis. Subsequently, a more coarse-grained approach is used in Chapter 3 to assess the internal motions of IspH, both with and without its substrate bound, using classical molecular dynamics. Both these studies reveal rational approaches for the design of novel IspH inhibitors. Chapters 4 and 5 deviate from the metalloprotein theme established in Chapters 2 and 3 to consider classical approaches for treating proton binding and unbinding in the context of molecular dynamics simulations. The ability of the constant pH molecular dynamics method to predict protein pKa values is assessed in Chapter 4 using an experimental test set comprising Staphylococcal nuclease variants. Building on this work, Chapter 5 provides proof of concept for the constant pH molecular dynamics method to obtain pH-dependent binding free energies in conjunction with Wyman's binding polynomial formalism