The broad goal of this project is to understand the specific chemical strategies used by enzymes to catalyze phosphoryl transfer reactions, which is one of the most common and essential reaction in biology. The current focus of our research is on enzymes that are prototypes for defining fundamental features of enzymatic catalysis. Because phosphoryl transfer is essential in biology, enzymes of this class are potential therapeutic targets for human diseases. The results from the current project period will increase understanding of the fundamental principles underlying catalysis setting the stage for studies that may lead to new therapeutics. While the study of phosphoryl transfer is decades old, there remain long standing, fundamental questions about the mechanisms of these enzymes. Crystal structures for many of these enzymes have been solved;yet, significant discrepancies between structures and inconsistencies with functional experiments remain. This lack of understanding is a key barrier to discovering the defining features of biological catalysis by this enzyme class and realizing the potential for design of mechanism-based inhibitors. To overcome this barrier, we developed new methods for analyzing enzyme transition state interactions by measuring kinetic isotope effects. In this method the effect on reaction rate of substituting and atom undergoing reaction with a heavier stable isotope is measured. The magnitude of these effects provides detailed information about the transition state structure. These data can be used to interrogate the interactions between diverse biological catalysts and the transition state for phosphoryl transfer reactions. Our current efforts focus on comparing ribozyme and protein phosphoryl transfer enzymes, aiming to understand their underlying unique and idiosyncratic catalytic strategies. The ability to compare catalysis at the level of transition state charge distribution, combined with the ability to manipulate active site interactions in defined ways provides a powerful means to distinguish enzymatic features involved in specific catalytic mechanisms. Although our main focus is on heavy atom isotope effects, the overall approach is multidisciplinary. Information from high resolution structures, steady state and pre-steady state kinetics with wild type and mutant enzymes, and computational simulations will be integrated to obtain information about the reactions'transition states and their interactions with catalysts.

Public Health Relevance

Cell function depends on enzymes to dramatically increase of the rates of biochemical reactions and they are the target of numerous diagnostics, drugs and clinical therapy. The research will for the first time test directly how enzymes that are important for human health and pathogenesis increase rates of reactions involving the formation and breakage of RNA and DNA chains.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function E Study Section (MSFE)
Program Officer
Barski, Oleg
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Case Western Reserve University
Schools of Medicine
United States
Zip Code
Vijayaraghavan, Jagamya; Kramp, Kristopher; Harris, Michael E et al. (2016) Inhibition of soluble guanylyl cyclase by small molecules targeting the catalytic domain. FEBS Lett 590:3669-3680
Zhang, Shuming; Gu, Hong; Chen, Haoyuan et al. (2016) Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+). Chem Commun (Camb) 52:4462-5
Niland, Courtney N; Jankowsky, Eckhard; Harris, Michael E (2016) Optimization of high-throughput sequencing kinetics for determining enzymatic rate constants of thousands of RNA substrates. Anal Biochem 510:1-10
Lee, Tai-Sung; Radak, Brian K; Harris, Michael E et al. (2016) A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation. ACS Catal 6:1853-1869
Dissanayake, Thakshila; Swails, Jason M; Harris, Michael E et al. (2015) Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations. Biochemistry 54:1307-13
Koo, Selene C; Lu, Jun; Li, Nan-Sheng et al. (2015) Transition State Features in the Hepatitis Delta Virus Ribozyme Reaction Revealed by Atomic Perturbations. J Am Chem Soc 137:8973-82
Mojica, Maria F; Mahler, S Graciela; Bethel, Christopher R et al. (2015) Exploring the Role of Residue 228 in Substrate and Inhibitor Recognition by VIM Metallo-β-lactamases. Biochemistry 54:3183-96
Weissman, Benjamin P; Li, Nan-Sheng; York, Darrin et al. (2015) Heavy atom labeled nucleotides for measurement of kinetic isotope effects. Biochim Biophys Acta 1854:1737-45
Jankowsky, Eckhard; Harris, Michael E (2015) Specificity and nonspecificity in RNA-protein interactions. Nat Rev Mol Cell Biol 16:533-44
Radak, Brian K; Lee, Tai-Sung; Harris, Michael E et al. (2015) Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM. RNA 21:1566-77

Showing the most recent 10 out of 25 publications