| Nitrogen-dependent reactions are prevalent and essential in many biochemical systems. These chemical reactions are ensured to occur at physiological rates via the catalytic power of enzymes. Important to some reactions, their catalysis is also dependent on cofactors such as NAD+, metal ions, and active site water molecules. In this dissertation, several nitrogen-related biochemical systems are investigated using complementary computational methods such as docking, molecular dynamics simulations, quantum chemical clusters, and quantum mechanics/molecular mechanics.;The use of this multi-scale computational approach has been successfully applied to investigate the catalytic mechanisms, substrate binding, and roles of key active site residues of both metallo- (e.g., Streptococcus pneumoniae Nicotinamidase) and non-metalloenzymes (e.g., Ornithine Cyclodeaminase). Additionally, in silico mutations were done to examine the impact genetic mutations have on the catalytic site of physiologically important enzymes (e.g., Delta 1-pyrroline-5-carboxylate dehydrogenase). The specificity of enzymes involved in protein synthesis (e.g., L-lysyl-tRNA synthetase) has also been studied along with their ability to discriminate with high-fidelity between chemically and structurally similar ligands.;The application of quantum chemical cluster methods to explore multiple X-ray crystal structures of an enzyme (e.g., pseudouridine-5'-monophosphate glycosidase) provided a greater understanding of its reaction mechanism. Moreover, the importance in carefully selecting a starting point from available crystal structures was shown when applying molecular modeling and simulation methods. |
