The long-term objective of the proposed research is to better understand how enzymes activate stable covalent bonds. A mechanistic investigation of C-H bond activation in alternative dihydrofolate reductases (DHFRs) and thymidylate synthase (TSase) will be conducted. These enzymes play crucial roles in DNA biosynthesis and thus serve as targets for antibiotic and chemotherapeutic drugs. They are also model systems used to address fundamental issues in enzymology, such as the role of protein dynamics and environmentally coupled quantum mechanical hydrogen tunneling in bond activation.
Aim 1 : The FolA encoded chromosomal DHFR (cDHFR) is a small protein that catalyzes a single chemical transformation and has been studied extensively during the previous grant period. Methods were developed to study the physical nature of the C-H-C transfer. It has been demonstrated that the cDHFR reaction coordinate is perfectly arranged for H-tunneling, and that mutants far from the active site can synergistically disturb the H-transfer process. These findings suggested a network of coupled motions across the enzyme that enhance the catalyzed reaction. The proposed studies will extend these studies to compare the effects of different protein scaffolds, dynamics, and reactants orientation on the physical nature of the C-H-C transfer.
Aim 2 : TSase is larger than cDHFR and catalyzes the making and breaking of multiple covalent bonds. We will examine different C-H activation steps in the complex TSase catalyzed reaction. These studies will include the examination of kinetic and dynamic effects of controlled active site mutations on different H- transfer steps. We will also examine the effect of altered networks of coupled motions on kinetics and dynamics using mutations distal to the active site. The findings from kinetic methods that can expose the nature of specific H-transfer steps will be correlated to measurements of protein dynamics, to assess the role of motions in enhancing C-H bond activation, in both fast and rate-limiting chemical steps.
Two families of enzymes that are essential for DNA biosynthesis, and hence targets for antibiotic and chemotherapeutic drugs, will be studied. The investigation aims for a better understanding of how the dynamics of enzymes affect the chemistry they catalyze. The potential impact of including protein dynamics in drug design is far-reaching, and may boost practice of rational design in a field dominated by combinatorial approaches.
|Singh, P; Islam, Z; Kohen, A (2016) Examinations of the Chemical Step in Enzyme Catalysis. Methods Enzymol 577:287-318|
|Kholodar, Svetlana A; Kohen, Amnon (2016) Noncovalent Intermediate of Thymidylate Synthase: Fact or Fiction? J Am Chem Soc 138:8056-9|
|KrzemiÅ„ska, Agnieszka; Moliner, Vicent; Åšwiderek, Katarzyna (2016) Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease. J Am Chem Soc 138:16283-16298|
|Åšwiderek, Katarzyna; Moliner, Vicent (2016) Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point To Redesign New Diels-Alderases. J Phys Chem B 120:2053-70|
|Francis, Kevin; Sapienza, Paul J; Lee, Andrew L et al. (2016) The Effect of Protein Mass Modulation on Human Dihydrofolate Reductase. Biochemistry 55:1100-6|
|Abeysinghe, Thelma; Hong, Baoyu; Wang, Zhen et al. (2016) Preserved hydride transfer mechanism in evolutionarily divergent thymidylate synthases. Curr Top Biochem Res 17:19-30|
|Guo, Qi; Gakhar, Lokesh; Wickersham, Kyle et al. (2016) Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii. Biochemistry 55:2760-71|
|Singh, Priyanka; Morris, Holly; Tivanski, Alexei V et al. (2015) Determination of concentration and activity of immobilized enzymes. Anal Biochem 484:169-72|
|Singh, Priyanka; Francis, Kevin; Kohen, Amnon (2015) Network of remote and local protein dynamics in dihydrofolate reductase catalysis. ACS Catal 5:3067-3073|
|Singh, Priyanka; Abeysinghe, Thelma; Kohen, Amnon (2015) Linking protein motion to enzyme catalysis. Molecules 20:1192-209|
Showing the most recent 10 out of 82 publications