News and Publications

Electronic Structure and Electrostatics Studies of Redox Active Iron and Manganese Metalloenzymes

L. Noodleman, D.A. Case, T. Lovell, W. Han, M.J. Thompson, M. Ullmann, R. Torres, T. Liu, I. Thorpe

We use modern methods of quantum chemistry (density functional methods) to investigate the electronic structures, energetics, and spectroscopic characteristics of transition-metal complexes at the active sites of metalloproteins and of related synthetic analogs. These systems include iron-sulfur and iron-oxo complexes and active-site models for manganese, iron, and copper-zinc superoxide dismutases. Many of these complexes lie at the active sites of important metalloproteins, where the complexes are involved in electron transfer and catalysis.

Two important aspects of our work are the extensive use of quantum mechanical geometry optimization for the active-site quantum cluster and the electrostatic representation of complete protein and solvent environments. The protein electrostatics calculations and analysis are done in collaboration with D. Bashford, V. Spassov, and A. Onufriev, Department of Molecular Biology. We are also involved, through a collaboration with E. Getzoff and M. Thompson, Department of Molecular Biology, in the study of photoactive yellow protein. This protein contains a chromophore that undergoes a light cycle and thus acts as a protein photosensor.

We calculated electronic structures and optimized geometries for the active sites of the iron-oxo enzymes methane monooxygenase and ribonucleotide reductase in both the oxidized and the 2-electron reduced forms of the enzymes. For the 2-electron reduced forms, a comparative study of geometries and energetics of native ribonucleotide reductase, a mutant ribonucleotide reductase, and native methane monooxygenase indicated how the various alternative conformations of the bridging carboxylate ligand (called the carboxylate shift) arise from different protein environments. These alternative structures constitute a "branch point" for the subsequent reactions with molecular oxygen and so influence the different catalytic chemistries of these enzymes.

Because iron-sulfur proteins are often electron-transfer agents, we seek to understand which features of cluster electronic structure and what interactions with the protein environment determine the wide range of redox potentials in these systems. This work was extended to studies in which we used a full self-consistent reaction field method for clusters in protein or solvent environments; redox potential calculations for 2Fe2S clusters in proteins have been completed for phthalate dioxygenase reductase and for Anabena ferredoxin. Working with our collaborators, M. Ludwig and D. Ballou, University of Michigan, we completed a review of the structure, redox energetics, and coenzyme-binding features of phthalate dioxygenase reductase.

The Rieske iron-sulfur protein is an important part of the cytochrome b-c₁ complex, which links electron transfer from ubiquinone to cytochrome c to proton pumping across the inner mitochondrial membrane. We are using density functional and electrostatics methods to study the redox potential of the Rieske iron-sulfur protein.

We are continuing electronic structure calculations for the iron-molybdenum cofactor of the nitrogenase enzyme. This cofactor is the 7Fe1Mo active site of the iron-molybdenum protein that binds molecular nitrogen and protons and catalyzes the multielectron reduction of molecular nitrogen to 2 ammonia molecules and molecular hydrogen. Our first goal is to calculate the active-site geometry, electronic structure, energy, and metal spin alignment for some likely cluster oxidation and electronic states. Using observations from Mossbauer spectroscopy, we are examining which electronic and oxidation states correspond to the "resting form" of the enzyme and which to the 1-electron reduced states. This information is a required starting point for studies of the catalytic cycle of the enzyme.

Manganese, iron, and copper-zinc superoxide dismutases are important detoxifying agents for super-oxide radical anions, converting these anions to molecular oxygen and hydrogen peroxide. Recently, we calculated quantum mechanically optimized geometries and redox potentials, including the coupling between electron transfer and proton transfer, for the active sites of manganese, iron, and copper-zinc superoxide dismutases.

By a systematic study of transition-metal complexes both in aqueous (or organic) solvents and in more complicated protein environments, we are working toward an integrated analysis of the effects of these different environments on catalytic cycles involving electron and proton transfer.

PUBLICATIONS

Case, D.A., Noodleman, L., Li, J. Modern computational approaches to modeling polynuclear transition metal complexes. In: Metal-Ligand Interactions in Chemistry, Physics and Biology. Russo, N., Salahub, D.R. (Eds.). Kluwer, Boston, 2000, p. 19. NATO Series.

Ludwig, M.L., Ballou, D.P., Noodleman, L. Phthalate dioxygenase reductase In: Handbook of Metalloproteins. Wieghardt, K., et al. (Eds.). Wiley & Sons, New York, in press.