Assistant Professor
Department of Chemistry
Krieger School of Arts & Sciences

jproth@jhu.edu

121 Remsen Hall
3400 N. Charles Street
Baltimore, MD 21218

Office: 410-516-7835

The Roth group pursues problems at the interface of biological, inorganic and physical chemistry. Our goal is to understand how enzymes are involved in the oxidative processes which underlie aging and age-related disease. The enzymes of greatest interest influence cellular redox status through reactions with molecular oxygen and hydrogen peroxide.

In certain classes of enzymes, the oxidation of protein residues is of physiological significance. Amino acid radicals formed by specific oxidation mechanisms carry out transformations during the enzyme's catalytic cycle. In contrast, protein radicals may also form non-specifically as the result of oxidative damage, when reactions of oxygen and peroxides go awry.

The coupled transfer of electrons and protons is indicated in enzymes that use amino acid radicals for catalysis. Though multiple types of coupled electron/proton transfer (cEPT) have been demonstrated in solution, it is unclear whether similar mechanisms occur in biological environments where highly structured networks of dipoles and hydrogen bonds are present. By investigating amino acid radical formation in ancestrally related proteins, we are asking how conserved structural elements influence oxidation mechanisms. We are also attempting to elucidate the quantum mechanical phenomena which allow reactions to occur over large distances site-specifically. The emerging model provides a foundation for predicting rates of electron and proton translocations in a variety of biomolecules under physiological conditions.

The interaction of oxygen and hydrogen peroxide with metal ions (e.g. copper, iron and manganese) is the primary step in sensing of cellular redox state and the ensuing cascade of oxidative events which sustain life. A significant portion of our research is, therefore, dedicated to exploring the reactivity patterns of metal-activated oxygen species. Because of their transient natures, metal-activated oxygen intermediates are extremely challenging to detect in enzymes and have only rarely been characterized using conventional spectroscopy.

New probes are being developed in the Roth laboratories to probe the identities of metal-activated oxygen intermediates formed during respiration, detoxification and inflammation, among other normal and pathological cellular events. These probes are based on the experimental as well as computational determination of oxygen isotope effects which arise from changes in bond stretching frequencies. Analyzing oxygen isotope distributions in the context of the appropriate theory allows use to deduce the structures and mechanisms of reactive intermediates which would escape detection otherwise.

An overriding objective of our work is to understand the strategies used by enzymes to catalyze difficult chemical transformations, such that they occur selectively and at rates which are accelerated relative to the un-catalyzed reaction. To this end, we compare reactions in proteins to those which occur by the same mechanism in solution, under carefully controlled conditions. Through the application of theory we evaluate the importance of intrinsic and thermodynamic factors in determining reaction rates. This approach allows us to also assess the probability of quantum mechanical events which in some instances manifest differently in the active site than in solution.

Selected Publications
Gupta, A., A. Mukherjee, K. Matsui, and J.P. Roth. (2008) Evidence for protein radical-mediated nuclear tunneling in fatty acid alpha-oxygenase. J. Am. Chem. Soc. ASAP 10.1021/ja8042273.

Mukherjee, A., V.V. Smirnov, M.P. Lanci, D.E. Brown, E.M. Shepard, D.M. Dooley, and J.P. Roth. (2008) Inner-sphere mechanism for molecular oxygen reduction catalyzed by copper amine oxidases. J. Am. Chem. Soc. 130:9459-9473. 

Roth, J.P., and C.J. Cramer. (2008) Direct examination of H₂O₂ activation by a heme peroxidase. J. Am. Chem. Soc. 130:7802-7803. 

Mukherjee, A., D.W. Brinkley, K-M. Chang, J.P. Roth. (2007) Molecular oxygen dependent steps in fatty acid oxidation by cyclooxygenase-1 (COX-1). Biochemistry 46:3975-3989.

Roth, J.P. (2007) Advances in studying bioinorganic reaction mechanisms: Isotopic probes of activated oxygen intermediates in metalloenzymes. Curr. Opin. Chem. Biol. 11:142-150.

Smirnov, V.V., and J.P. Roth. (2006) Mechanisms of electron transfer in catalysis by copper zinc superoxide dismutase. J. Am. Chem. Soc. 128:16424-16425.

Brinkley, D.W., and J.P. Roth. (2005) Determination of a large reorganization energy barrier for hydride abstraction by glucose oxidase. J. Am. Chem. Soc. 127:15720-15721.