Aldo DeBenedictis Distinguished Professor of Chemistry and Professor of Biochemistry, Biophysics and Structural BiologyLab Homepage: http://www.cchem.berkeley.edu/mmargrp/
Research in this laboratory is focused on structure/function relationships in proteins with a particular emphasis on the catalytic and biological properties of enzymes and signaling proteins. Current emphasis is on nitric oxide signaling (including studies on nitric oxide synthase, guanylate cyclase and S-nitrosation mechanisms), oxygen sensing, pathogen responses to nitric oxide, and enzymology of biofuel utilization.
Nitric oxide (NO) is a freely diffusible gas that functions in cell-to-cell communication regulating processes such as blood vessel homeostasis and neuronal cell function. NO is toxic and chemically reactive, properties that impose stringent demands on the regulation of synthesis and the receptors. NO activates the soluble isoform of guanylate cyclase (sGC) which leads to the synthesis of guanosine 3':5'-cyclic monophosphate, (cGMP) in a target cell. sGC uses a heme cofactor to trap NO. The immune system, on the other hand, uses NO to kill or inhibit the growth of pathogens. NO is made by the enzyme nitric oxide synthase (NOS). In signaling constitutive isoforms of NOS controlled by calcium and calmodulin are responsible for synthesizing NO wheres in killing, an inducible isoform is utilized.
In studies directed toward a molecular understanding of NO signaling, homologues of the sGC heme domain were found in a number of prokaryotes. Some of these heme domains share properties with sGC (they do not bind oxygen), while others do bind oxygen. We have termed this new family of heme-based sensor proteins H-NOX proteins (for Heme-Nitric oxide OXygen). In collaboration with the Kuriyan lab we have solved several H-NOX structures. These structures and subsequent functional studies have uncovered how Nature is able to selectively sense similar ligands such as NO and oxygen.
Nitric Oxide Synthase. NOS catalyzes the conversion of L-arginine to NO and citrulline. NOS contains a reductase domain that shuttles electrons into the P45—heme site where catalysis takes place. We continue to study the mechanism leading to NO formation and the design of selective inhibitors. Our studies to date have involved various aspects of structure and catalysis, and future investigations will continue to explore these areas. NOS has now been found in prokaryotes. Mechanism and functional studies are our current emphasis with the bacterial NOSs.
Soluble Guanylate Cyclase. Activation and deactivations mechanisms sGC are key questions under study. The heme moiety on sGC is an efficient chemical trap for NO because nitrosyl-heme complexes form rapidly and are very stable. However, it is not obvious how catalytic activity and the resulting signal (cGMP) are turned off. We continue to explore the molecular details sGC function with a goal of understanding dysfunction in disease and the development of novel therapeutics.
H-NOX Proteins. H-NOX proteins also exhibit remarkable diatomic ligand selectivity despite a similar protein fold. For example, the H-NOX domain from Vibrio cholera (a facultative aerobe) binds NO in a high spin 5-coordinate complex and excludes oxygen, while the H-NOX domain from Thermoanaerobacter tengcongensis (Tt, obligate anaerobe) has been found to bind oxygen in a low-spin 6-coordinate complex, making it the first member of the family to bind oxygen. Current research is focused on understanding the nature of this ligand selectivity from a molecular level and how this selectivity translates into protein function as sensors in biology. Our lab is currently focused on investigating three main areas pertaining to H-NOXs: 1) How do H-NOX domains control ligand affinity and selectivity?, 2) How do H-NOX domains regulate their associated signaling proteins?, 3) What role do H-NOX domains play in vivo?
S-Nitrosation. Broad details of NO signaling involving NO synthesis by nitric oxide synthase and NO activation of soluble guanylate cyclase (sGC) are reasonably well-understood, though critical molecular aspects of function remain unanswered. On the contrary, relatively little is known about sGC-independent NO signaling. Most sGC- independent hypotheses involve S-nitrosation of low molecular weight thiols or protein thiols. We are currently involved in several aspects of the signaling chemistry.
Cellulose Degradation. Cellulose is the most abundant biopolymer on earth and holds an important biological role in maintaining the structural rigidity of plant cell walls. Cellulosic biomass holds great promise as a feedstock for second generation biofuels and within the Energy Biosciences Institute (EBI) we are part of an interdisciplinary team to make that vision of turning plant biomass into fuels a reality. The bottleneck to make fuels from cellulose is the relatively expensive and slow enzymatic degradation of cellulose to glucose monomers. The extensive hydrogen-bonding network within and between chains makes cellulose an insoluble, and heterogenous substrate. We are exploring novel enzymatic routes to cellulose degradation.
Carlson, H.K., Plate, L., Price, M.S., Allen, J.J., Shokat, K.M., and Marletta, M.A. (2010). Use of a semisynthetic epitope to probe histidine Kinase activity and regulation. Anal. Biochem. 397: 139-143.
Weinert, E.E., Plate, L., Whited, C.A., Olea, C. Jr, and Marletta, M.A. (2010). Determinants of ligand affinity and heme reactivity in H-NOX domains. Angew. Chem. Int. Ed. Engl. 49: 720-723.
Olea, C. Jr, Herzik, M.A. Jr, Kuriyan, J., and Marletta, M.A. (2010). Structural insights into the molecular mechanism of H-NOX activation. Protein Science 19: 881-887.
Woodward, J.J., Nejatyjahromy, Y., Britt, R.D., and Marletta, M.A. (2010). Pterin-Centered Radical as a Mechanistic Probe of the Second Step of Nitric Oxide Synthase. J. Amer. Chem. Soc. 132: 5105-5113.
Wang, Y., Dufour, Y.S., Carlson, H.K., Donohue, T.J., Marletta, M.A., and Ruby, E.G. (2010). H-NOX-mediated NO sensing modulates symbiotic colonization byVibrio fischeri. Proc. Natl. Acad. Sci. USA 107: 8375-8380.
Derbyshire, E.R., Fernhoff, N.B., Deng, S. and Marletta, M. A. (2009). Nucleotide regulation of soluble guanylate cyclase substrate specificity. Biochemistry 48: 7519-7524.
Agapie, T., Suseno, S., Woodward, J.J., Stoll, S., Britt, R.D., and Marletta, M.A. (2009). NO Formation by a Protein from Sorangium cellulosum: A Catalytically Self-Sufficient Bacterial Nitric Oxide Synthase. Proc. Natl. Acad. Sci. USA 106: 16221-16226.
Fernhoff, N.B., Derbyshire, E.R. and Marletta, M.A. (2009). A nitric oxide/cysteine interaction mediates the activation of soluble guanylate cyclase. Proc. Natl. Acad. Sci. USA 106: 21602-22607.
Erbil, W.K., Price, M.S., Wemmer, D.E., and Marletta, M.A. (2009). A structural basis for N-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation. Proc. Natl. Acad. Sci. USA 106: 19753-19760.
Tian, C., Beeson, W.T., Iavarone, A.T., Sun, J., Marletta, M.A., Cate, J.H., and Glass, N.L. (2009). Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Proc. Natl. Acad. Sci. USA. 106: 22157-22162.
Last Updated 2010-07-17