Specific recognition of ligands including metal ions by proteins is the key of many crucial biological functions and systems. Accurate prediction of the binding strength not only sheds light on the mechanism of the molecular recognition but also provides the most important prerequisite of drug discovery. Computational modeling of molecular binding has gained a great deal of attentions in the last few decades since the advancement of computer power and availability of high-resolution crystal structures. However there still exist two major challenges in the field of molecular modeling, i.e. sampling issue and accuracy of the models. In this work, I have dedicated to tackling these two problems with a noval polarizable force field which is believed to produce more accurate description of molecular interactions than classic non-polarizable force fields. We first developed the model for divalent cations Mg²⁺ and Ca²⁺, deriving the parameters from quantum mechanics. To understand the hydration thermodynamics of these ions we have performed molecular dynamics simulations using our AMOEBA force field. Both the water structures around ions and the solvation free energies were in great accordance with experiment data. We have also simulated and calculated the binding free energies of a series of benzamidine-like inhibitors to trypsin using explicit solvent approach by free energy perturbation. The calculated binding free energies are well within the accuracy of experimental measurement and the direction of change is predicted correctly in all cases. Finally, we computed the hydration free energies of a few organic molecules and automated the calculation procedure. / text

abstract: Na+/H+ antiporters are vital membrane proteins for cell homeostasis, transporting Na+ ions in exchange for H+ across the lipid bilayer. In humans, dysfunction of these transporters are implicated in hypertension, heart failure, epilepsy, and autism, making them well-established drug targets. Although experimental structures for bacterial homologs of the human Na+/H+ have been obtained, the detailed mechanism for ion transport is still not well-understood. The most well-studied of these transporters, Escherichia coli NhaA, known to transport 2 H+ for every Na+ extruded, was recently shown to bind H+ and Na+ at the same binding site, for which the two ion species compete. Using molecular dynamics simulations, the work presented in this dissertation shows that Na+ binding disrupts a previously-unidentified salt bridge between two conserved residues, suggesting that one of these residues, Lys300, may participate directly in transport of H+. This work also demonstrates that the conformational change required for ion translocation in a homolog of NhaA, Thermus thermophilus NapA, thought by some to involve only small helical movements at the ion binding site, is a large-scale, rigid-body movement of the core domain relative to the dimerization domain. This elevator-like transport mechanism translates a bound Na+ up to 10 Å across the membrane. These findings constitute a major shift in the prevailing thought on the mechanism of these transporters, and serve as an exciting launchpad for new developments toward understanding that mechanism in detail. / Dissertation/Thesis / Doctoral Dissertation Physics 2016