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Computational Insights Into Nitrogen-Related Biocatalysis, Bogdan Florin Ion
Computational Insights Into Nitrogen-Related Biocatalysis, Bogdan Florin Ion
Electronic Theses and Dissertations
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 …
Computational Investigations On Enzymatic Catalysis And Inhibition, Daniel James Simard
Computational Investigations On Enzymatic Catalysis And Inhibition, Daniel James Simard
Electronic Theses and Dissertations
Enzymes are the bimolecular “workhorses” of the cell due to their range of functions and their requirement for cellular success. The atomistic details of how they function can provide key insights into the fundamentals of catalysis and in turn, provide a blueprint for biotechnological advances. A wide range of contemporary computational techniques has been applied with the aim to characterize recently discovered intermediates or to provide insights into enzymatic mechanisms and inhibition. More specifically, an assessment of methods was conducted to evaluate the presence of the growing number 3– and 4–coordinated sulfur intermediates in proteins/enzymes. Furthermore, two mechanisms have been …