Understanding the diverse chemistry displayed by P450s is a central issue in biomedical science and requires understanding their notorious propensity for specificity and promiscuity. Drug metabolizing P450s display a remarkable promiscuity in substrate recognition, while enzymes involved in steroid biosynthesis are often very specific with respect to substrate binding and catalysis. However, the molecular mechanism by which these different forms control this promiscuity or specificity is not well understood. How does structure encode such diversity? It is known that significant conformational changes occur in many, if not all, P450s during substrate recognition. These changes may also play a role in gating the reactions following O2 activation to produce reactive intermediates. However, we know very little about how substrates are recognized by a particular P450 or how these changes are coupled to function. Does a P450 recognize its substrate by induced fit or by dynamically sampling only a few preferred conformations? Results in the past period have produced significant insights into the conformational changes that occur upon substrate binding to P450, they suggest how these changes may be coupled to function, and they provide a platform for development of novel catalysts with designed specificity. The current aims will use a library of molecular probes for the P450 active site to control the formation and properties of proposed reactive intermediates. These studies will test specific hypotheses, based on our recent progress, about how conformational changes at the active site may help control the O2 activation step. We will develop these approaches to investigate the electrochemical behavior of P450s specifically wired to electrode surfaces. Finally, we will explore the potential for using specific probes for molecular evolution of novel catalysts with designed substrate specificity. These studies will contribute to a better understanding how the protein structure of these important enzymes is coupled to function and substrate specificity.

Public Health Relevance

P450s are a diverse class of enzymes of critical importance to human health because they are responsible for the biosynthesis of important compounds and drug metabolism. Our long term goal is to develop a general method for introducing new activities into these enzymes, as evolved P450 catalysts have the potential for producing novel drugs and antibiotics. In the process, we will gain a deeper understanding of how the substrates are recognized and how the enzymatic reactions are controlled.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM041049-26
Application #
8462621
Study Section
Macromolecular Structure and Function A Study Section (MSFA)
Program Officer
Anderson, Vernon
Project Start
1989-01-01
Project End
2015-04-30
Budget Start
2013-05-01
Budget End
2014-04-30
Support Year
26
Fiscal Year
2013
Total Cost
$330,802
Indirect Cost
$113,677
Name
University of California Davis
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
047120084
City
Davis
State
CA
Country
United States
Zip Code
95618
Spradlin, Jessica; Lee, Diana; Mahadevan, Sruthi et al. (2016) Insights into an efficient light-driven hybrid P450 BM3 enzyme from crystallographic, spectroscopic and biochemical studies. Biochim Biophys Acta 1864:1732-1738
Barelier, Sarah; Boyce, Sarah E; Fish, Inbar et al. (2013) Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities. PLoS One 8:e69153
Myers, William K; Lee, Young-Tae; Britt, R David et al. (2013) The conformation of P450cam in complex with putidaredoxin is dependent on oxidation state. J Am Chem Soc 135:11732-5
Stoll, Stefan; Lee, Young-Tae; Zhang, Mo et al. (2012) Double electron-electron resonance shows cytochrome P450cam undergoes a conformational change in solution upon binding substrate. Proc Natl Acad Sci U S A 109:12888-93
Lee, Young-Tae; Glazer, Edith C; Wilson, Richard F et al. (2011) Three clusters of conformational states in p450cam reveal a multistep pathway for closing of the substrate access channel. Biochemistry 50:693-703
Markwick, Phineus R L; Pierce, Levi C T; Goodin, David B et al. (2011) Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam. J Phys Chem Lett 2:158-164
Jensen, G M; Goodin, D B (2011) Impact of Proximal and Distal Pocket Site-Directed Mutations on the Ferric/Ferrous Heme Redox Potential of Yeast Cytochrome-c-Peroxidase. Theor Chem Acc 130:1185-1196
Lee, Young-Tae; Wilson, Richard F; Rupniewski, Igor et al. (2010) P450cam visits an open conformation in the absence of substrate. Biochemistry 49:3412-9
Annalora, Andrew J; Goodin, David B; Hong, Wen-Xu et al. (2010) Crystal structure of CYP24A1, a mitochondrial cytochrome P450 involved in vitamin D metabolism. J Mol Biol 396:441-51
Nigro, Alycen Pond; Goodin, David B (2010) Reaction of N-hydroxyguanidine with the ferrous-oxy state of a heme peroxidase cavity mutant: a model for the reactions of nitric oxide synthase. Arch Biochem Biophys 500:66-73

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