Simulation of Proton and Hydride Transfer in Enzymes

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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. RELEVANCE (See instructions): 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.