The broad, long-term objectives of this research are to elucidate the fundamental principles and mechanisms of hydrogen transfer in both protein and RNA enzyme catalysis. These objectives will be accomplished with a wide range of theoretical and computational methods, including classical molecular dynamics simulations and mixed quantum mechanical/molecular mechanical simulations that provide atomic-level information about Structural rearrangements and conformational motions. These calculations will probe the roles of hydrogen bonding, active site reorganization, hydrogen tunneling, active site water molecules, electrostatics, and conformational motions in both protein and RNA enzyme catalysis. These theoretical studies will be performed in close collaboration with experimental groups, assisting in the interpretation of experimental data and providing experimentally testable predictions. The protein enzyme projects will focus on soybean lipoxygenase and human DNA polymerase eta, and the RNA enzyme projects will focus on the gImS and twister ribozymes. Soybean lipoxygenase serves as a prototype for investigating hydrogen tunneling in enzymes because it exhibits unusually large hydrogen/deuterium kinetic isotope effects. Theoretical investigations of the temperature and pressure dependence of the rates and kinetic isotope effects of wild- type and mutant enzymes will provide insight into the motions that impact hydrogen tunneling. Human DNA polymerase eta enables the replication of DNA that has been damaged by exposure to ultraviolet rays, and understanding its mechanism has significant implications for skin cancer prevention and treatment. Simulations of this enzyme will provide insight into the mechanism of this biomedically important enzyme. The gImS and twister ribozymes catalyze self-cleavage reactions that are essential for modulating protein synthesis and various RNA processing reactions. Theoretical studies of these ribozymes will illuminate their mechanisms and may assist in the development of ribozymes for use as therapeutic agents to cleave pathogenic RNAs. All of these studies are relevant to public health because the resulting fundamental insights could facilitate the design of more effective drugs for a wide range of diseases.

Public Health Relevance

These studies are relevant to public health because the elucidation of fundamental principles of enzyme catalysis will facilitate the design of more efficient enzymes, thereby potentially assisting in the development of more effective drugs for a broad range of diseases, including skin cancer. Insights into RNA catalysis may assist in the development of RNA enzymes for use as therapeutic agents to cleave pathogenic RNAs.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Method to Extend Research in Time (MERIT) Award (R37)
Project #
5R37GM056207-26
Application #
9926260
Study Section
Special Emphasis Panel (NSS)
Program Officer
Lyster, Peter
Project Start
1998-05-01
Project End
2021-04-30
Budget Start
2020-05-01
Budget End
2021-04-30
Support Year
26
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Yale University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
043207562
City
New Haven
State
CT
Country
United States
Zip Code
06520
Li, Pengfei; Soudackov, Alexander V; Hammes-Schiffer, Sharon (2018) Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations. J Am Chem Soc 140:3068-3076
Ucisik, Melek N; Hammes-Schiffer, Sharon (2017) Effects of Active Site Mutations on Specificity of Nucleobase Binding in Human DNA Polymerase ?. J Phys Chem B 121:3667-3675
Hammes-Schiffer, Sharon (2017) Catalysts by Design: The Power of Theory. Acc Chem Res 50:561-566
Bingaman, Jamie L; Zhang, Sixue; Stevens, David R et al. (2017) The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. Nat Chem Biol 13:439-445
Horitani, Masaki; Offenbacher, Adam R; Carr, Cody A Marcus et al. (2017) 13C ENDOR Spectroscopy of Lipoxygenase-Substrate Complexes Reveals the Structural Basis for C-H Activation by Tunneling. J Am Chem Soc 139:1984-1997
Hu, Shenshen; Soudackov, Alexander V; Hammes-Schiffer, Sharon et al. (2017) Enhanced Rigidification within a Double Mutant of Soybean Lipoxygenase Provides Experimental Support for Vibronically Nonadiabatic Proton-Coupled Electron Transfer Models. ACS Catal 7:3569-3574
Zhang, Sixue; Stevens, David R; Goyal, Puja et al. (2016) Assessing the Potential Effects of Active Site Mg2+ Ions in the glmS Ribozyme-Cofactor Complex. J Phys Chem Lett 7:3984-3988
Ucisik, Melek N; Bevilacqua, Philip C; Hammes-Schiffer, Sharon (2016) Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site. Biochemistry 55:3834-46
Soudackov, Alexander V; Hammes-Schiffer, Sharon (2016) Proton-coupled electron transfer reactions: analytical rate constants and case study of kinetic isotope effects in lipoxygenase. Faraday Discuss 195:171-189
Yu, Tao; Soudackov, Alexander V; Hammes-Schiffer, Sharon (2016) Computational Insights into Five- versus Six-Coordinate Iron Center in Ferrous Soybean Lipoxygenase. J Phys Chem Lett 7:3429-33

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