Date of Defense
14-4-2026 11:00 AM
Location
Microsoft Teams
Document Type
Thesis Defense
Degree Name
Master of Science (MS)
College
College of Science
Department
Biology
First Advisor
Ranjit Vijayan
Keywords
Molecular docking, molecular dynamics, Halobacterium salinarum, glutamate dehydrogenase, NAD, NADP
Abstract
Glutamate dehydrogenase (GDH) is a hexameric enzyme. GDH is involved in several pathways and cellular processes such as oxidation-reduction homeostasis, ammonia metabolism, lipid biosynthesis, insulin and lactate production, and acid-base equilibrium. The main objective of this thesis is to understand the structural and biochemical properties of this enzyme and why some organisms, for e.g., Halobacterium salinarum, have more than one GDH with different coenzyme specificities. The catabolism of glutamate is linked to NAD+-specific GDHs, meanwhile, NADP+-specific GDHs play an anabolic role in ammonia assimilation. Molecular docking and binding free energy calculations were employed followed by long-scale (500 nanoseconds) comparative molecular dynamics (MD) simulations using Halobacterium salinarum GDH protein structures to understand how these enzymes behave in the presence of different cofactors. The study elucidated the vital role of conserved aspartic acid or glutamic acid in the determination of GDH coenzyme specificity. In summary, this study provides insights into the overall structural and biochemical properties of Halobacterium salinarum GDH. These findings enhance our understanding of GDH coenzyme specificity.
Included in
A Computational Assessment of Halobacterium Salinarum Glutamate Dehydrogenase Enzymes
Microsoft Teams
Glutamate dehydrogenase (GDH) is a hexameric enzyme. GDH is involved in several pathways and cellular processes such as oxidation-reduction homeostasis, ammonia metabolism, lipid biosynthesis, insulin and lactate production, and acid-base equilibrium. The main objective of this thesis is to understand the structural and biochemical properties of this enzyme and why some organisms, for e.g., Halobacterium salinarum, have more than one GDH with different coenzyme specificities. The catabolism of glutamate is linked to NAD+-specific GDHs, meanwhile, NADP+-specific GDHs play an anabolic role in ammonia assimilation. Molecular docking and binding free energy calculations were employed followed by long-scale (500 nanoseconds) comparative molecular dynamics (MD) simulations using Halobacterium salinarum GDH protein structures to understand how these enzymes behave in the presence of different cofactors. The study elucidated the vital role of conserved aspartic acid or glutamic acid in the determination of GDH coenzyme specificity. In summary, this study provides insights into the overall structural and biochemical properties of Halobacterium salinarum GDH. These findings enhance our understanding of GDH coenzyme specificity.