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Famulari A, Correddu D, Di Nardo G, Gilardi G, Mitrikas G, Chiesa M, García-Rubio I. Heme Spin Distribution in the Substrate-Free and Inhibited Novel CYP116B5hd: A Multifrequency Hyperfine Sublevel Correlation (HYSCORE) Study. Molecules 2024; 29:518. [PMID: 38276601 PMCID: PMC10819608 DOI: 10.3390/molecules29020518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The cytochrome P450 family consists of ubiquitous monooxygenases with the potential to perform a wide variety of catalytic applications. Among the members of this family, CYP116B5hd shows a very prominent resistance to peracid damage, a property that makes it a promising tool for fine chemical synthesis using the peroxide shunt. In this meticulous study, we use hyperfine spectroscopy with a multifrequency approach (X- and Q-band) to characterize in detail the electronic structure of the heme iron of CYP116B5hd in the resting state, which provides structural details about its active site. The hyperfine dipole-dipole interaction between the electron and proton nuclear spins allows for the locating of two different protons from the coordinated water and a beta proton from the cysteine axial ligand of heme iron with respect to the magnetic axes centered on the iron. Additionally, since new anti-cancer therapies target the inhibition of P450s, here we use the CYP116B5hd system-imidazole as a model for studying cytochrome P450 inhibition by an azo compound. The effects of the inhibition of protein by imidazole in the active-site geometry and electron spin distribution are presented. The binding of imidazole to CYP116B5hd results in an imidazole-nitrogen axial coordination and a low-spin heme FeIII. HYSCORE experiments were used to detect the hyperfine interactions. The combined interpretation of the gyromagnetic tensor and the hyperfine and quadrupole tensors of magnetic nuclei coupled to the iron electron spin allowed us to obtain a precise picture of the active-site geometry, including the orientation of the semi-occupied orbitals and magnetic axes, which coincide with the porphyrin N-Fe-N axes. The electronic structure of the iron does not seem to be affected by imidazole binding. Two different possible coordination geometries of the axial imidazole were observed. The angles between gx (coinciding with one of the N-Fe-N axes) and the projection of the imidazole plane on the heme were determined to be -60° and -25° for each of the two possibilities via measurement of the hyperfine structure of the axially coordinated 14N.
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Affiliation(s)
- Antonino Famulari
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Danilo Correddu
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - George Mitrikas
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, 15341 Athens, Greece;
| | - Mario Chiesa
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Inés García-Rubio
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
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2
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Panda S, Phan H, Karlin KD. Heme-copper and Heme O 2-derived synthetic (bioinorganic) chemistry toward an understanding of cytochrome c oxidase dioxygen chemistry. J Inorg Biochem 2023; 249:112367. [PMID: 37742491 PMCID: PMC10615892 DOI: 10.1016/j.jinorgbio.2023.112367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/22/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
Cytochrome c oxidase (CcO), also widely known as mitochondrial electron-transport-chain complex IV, is a multi-subunit transmembrane protein responsible for catalyzing the last step of the electron transport chain, dioxygen reduction to water, which is essential to the establishment and maintenance of the membrane proton gradient that drives ATP synthesis. Although many intermediates in the CcO catalytic cycle have been spectroscopically and/or computationally authenticated, the specifics regarding the IP intermediate, hypothesized to be a heme-Cu (hydro)peroxo species whose O-O bond homolysis is supported by a hydrogen-bonding network of water molecules, are largely obscured by the fast kinetics of the A (FeIII-O2•-/CuI/Tyr) → PM (FeIV=O/CuII-OH/Tyr•) step. In this review, we have focused on the recent advancements in the design, development, and characterization of synthetic heme-peroxo‑copper model complexes, which can circumvent the abovementioned limitation, for the investigation of the formation of IP and its O-O cleavage chemistry. Novel findings regarding (a) proton and electron transfer (PT/ET) processes, together with their contributions to exogenous phenol induced O-O cleavage, (b) the stereo-electronic tunability of the secondary coordination sphere (especially hydrogen-bonding) on the geometric and spin state alteration of the heme-peroxo‑copper unit, and (c) a plausible mechanism for the Tyr-His cofactor biogenesis, are discussed in great detail. Additionally, since the ferric-superoxide and the ferryl-oxo (Compound II) species are critically involved in the CcO catalytic cycle, this review also highlights a few fundamental aspects of these heme-only (i.e., without copper) species, including the structural and reactivity influences of electron-donating trans-axial ligands and Lewis acid-promoted H-bonding.
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Affiliation(s)
- Sanjib Panda
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hai Phan
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
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3
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Nguyen RC, Davis I, Dasgupta M, Wang Y, Simon PS, Butryn A, Makita H, Bogacz I, Dornevil K, Aller P, Bhowmick A, Chatterjee R, Kim IS, Zhou T, Mendez D, Paley D, Fuller F, Alonso-Mori R, Batyuk A, Sauter NK, Brewster AS, Orville AM, Yachandra VK, Yano J, Kern JF, Liu A. In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121. J Am Chem Soc 2023; 145:25120-25133. [PMID: 37939223 PMCID: PMC10799213 DOI: 10.1021/jacs.3c04991] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon-carbon (C-C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. We show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme-substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C-C bond coupling chemistry.
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Affiliation(s)
- Romie C. Nguyen
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Yifan Wang
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Kednerlin Dornevil
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Tiankun Zhou
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Derek Mendez
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Daniel Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Franklin Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jan F. Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
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4
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Vansuch G, Mulder DW, Chica B, Ruzicka JL, Yang ZY, Pellows LM, Willis MA, Brown KA, Seefeldt LC, Peters JW, Dukovic G, King PW. Cryo-annealing of Photoreduced CdS Quantum Dot-Nitrogenase MoFe Protein Complexes Reveals the Kinetic Stability of the E 4(2N2H) Intermediate. J Am Chem Soc 2023; 145:21165-21169. [PMID: 37729189 PMCID: PMC10557137 DOI: 10.1021/jacs.3c06832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Indexed: 09/22/2023]
Abstract
A critical step in the mechanism of N2 reduction to 2NH3 catalyzed by the enzyme nitrogenase is the reaction of the four-electron/four-proton reduced intermediate state of the active-site FeMo-cofactor (E4(4H)). This state is a junction in the catalytic mechanism, either relaxing by the reaction of a metal bound Fe-hydride with a proton forming H2 or going forward with N2 binding coupled to the reductive elimination (re) of two Fe-hydrides as H2 to form the E4(2N2H) state. E4(2N2H) can relax to E4(4H) by the oxidative addition (oa) of H2 and release of N2 or can be further reduced in a series of catalytic steps to release 2NH3. If the H2 re/oa mechanism is correct, it requires that oa of H2 be associative with E4(2N2H). In this report, we have taken advantage of CdS quantum dots in complex with MoFe protein to achieve photodriven electron delivery in the frozen state, with cryo-annealing in the dark, to reveal details of the E-state species and to test the stability of E4(2N2H). Illumination of frozen CdS:MoFe protein complexes led to formation of a population of reduced intermediates. Electron paramagnetic resonance spectroscopy identified E-state signals including E2 and E4(2N2H), as well as signals suggesting the formation of E6 or E8. It is shown that in the frozen state when pN2 is much greater than pH2, the E4(2N2H) state is kinetically stable, with very limited forward or reverse reaction rates. These results establish that the oa of H2 to the E4(2N2H) state follows an associative reaction mechanism.
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Affiliation(s)
- Gregory
E. Vansuch
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - David W. Mulder
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Bryant Chica
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jesse L. Ruzicka
- Department
of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Zhi-Yong Yang
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322, United States
| | - Lauren M. Pellows
- Department
of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Mark A. Willis
- Institute
of Biological Chemistry, Washington State
University, Pullman, Washington 99163, United States
| | - Katherine A. Brown
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Lance C. Seefeldt
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322, United States
| | - John W. Peters
- Institute
of Biological Chemistry, Washington State
University, Pullman, Washington 99163, United States
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Gordana Dukovic
- Department
of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Materials
Science and Engineering, University of Colorado
Boulder, Boulder, Colorado 80303, United States
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Paul W. King
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80303, United States
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5
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Johnson KL, Graves AB, Eckhert K, Liptak MD. Second-sphere tuning of analogues for the ferric-hydroperoxoheme form of Mycobacterium tuberculosis MhuD. J Inorg Biochem 2023; 246:112300. [PMID: 37364353 DOI: 10.1016/j.jinorgbio.2023.112300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023]
Abstract
Mycobacterium tuberculosis MhuD catalyzes the oxygenation of heme to mycobilin; experimental data presented here elucidates the novel hydroxylation reaction catalyzed by this enzyme. Analogues for the critical ferric-hydroperoxoheme (MhuD-heme-OOH) intermediate of this enzyme were characterized using UV/Vis absorption (Abs), circular dichroism (CD), and magnetic CD (MCD) spectroscopies. In order to extract electronic transition energies from these spectroscopic data, a novel global fitting model was developed for analysis of UV/Vis Abs, CD, and MCD data. A variant of MhuD was prepared, N7S, which weakens the affinity of heme-bound enzyme for a hydroperoxo analogue, azide, without significantly altering the protein secondary structure. Global fitting of spectroscopic data acquired in this study revealed that the second-sphere N7S substitution perturbs the electronic structure of two analogues for MhuD-heme-OOH: azide-inhibited MhuD (MhuD-heme-N3) and cyanide-inhibited MhuD (MhuD-heme-CN). The ground state electronic structures of MhuD-heme-N3 and MhuD-heme-CN were assessed using variable-temperature, variable-field MCD. Altogether, these data strongly suggest that there is a hydrogen bond between the Asn7 side-chain and the terminal oxygen of the hydroperoxo ligand in MhuD-heme-OOH. As discussed herein, this finding supports a novel hydroxylation reaction mechanism where the Asn7 side-chain guides a transient hydroxyl radical derived from homolysis of the OO bond in MhuD-heme-OOH to the β- or δ-meso carbon of the porphyrin ligand yielding β- or δ-meso-hydroxyheme, respectively.
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Affiliation(s)
- Kayla L Johnson
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America
| | - Amanda B Graves
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America
| | - Kaitlyn Eckhert
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America
| | - Matthew D Liptak
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America.
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6
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Denisov IG, Sligar SG. Solvent isotope effects in the catalytic cycle of P450 CYP17A1: Computational modeling of the hydroxylation and lyase reactions. J Inorg Biochem 2023; 243:112202. [PMID: 37004494 PMCID: PMC10128154 DOI: 10.1016/j.jinorgbio.2023.112202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/13/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
The catalytic cycle of the cytochromes P450 (CYP) requires two electrons from a protein redox partner and two protons from water to generate the main catalytic intermediate, a ferryl-oxo complex with π-cation on the heme porphyrin ring, termed Compound 1. The protonation steps are at least partially rate-limiting, therefore the steady-state rates of P450 catalysis are usually slower in deuterated solvent (D2O) by a factor of 1.5-3. However, in several P450 systems a pronounced inverse kinetic solvent isotope effect (KSIE ∼0.4-0.7) is observed, where the reaction is faster in D2O. This raises an important mechanistic question: Is this inverse solvent isotope effect compatible with Compound 1 catalyzed reactions, or is it indicative of another catalytic intermediate being involved? In this communication we use exhaustive numerical modeling of the P450 steady-state kinetics to demonstrate that a significant inverse KSIE cannot be obtained for a pure Compound 1 driven catalytic cycle of P450. Rather, an alternative, protonation independent, catalytic intermediate needs to be introduced. This result is applicable to the broad spectrum of P450s in nature, but as an example we use the extensively documented inverse isotope effect in the human steroid biosynthetic P450 CYP17A1 where the involvement of a heme peroxo anion intermediate has been characterized. Based on this analysis, we show that the observation of an inverse KSIE can be used as a general mechanistic probe for reaction cycle intermediates in the cytochromes P450.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America.
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7
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Usai R, Kaluka D, Cai S, Sem DS, Kincaid JR. Solution phase refinement of active site structure using 2D NMR and judiciously 13C-labeled cytochrome P450. J Inorg Biochem 2023; 241:112126. [PMID: 36682280 PMCID: PMC10725731 DOI: 10.1016/j.jinorgbio.2023.112126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
The Cytochrome P450 (CYP450) superfamily has been the subject of intense research for over six decades. Here the HU227 strain of E. coli, lacking the δ-aminolevulinic acid (δ-ALA) synthase gene, was employed, along with [5-13C] δ-ALA, in the heterologous expression of P450cam harboring a prosthetic group labeled with 13C at the four methine carbons (Cm) and pyrrole Cα positions. The product was utilized as a proof of principle strategy for defining and refining solution phase active site structure in cytochrome P450cam, providing proton-to-proton distances from 13CmH to protons on bound substrate or nearby amino acid residues, using short mixing time 2D or 3D NOESY-HMQC methods. The results reveal the interesting finding that 2D 13C-filtered NOESY-HMQC can be used to obtain distances between protons on labeled 13C to positions of protons nearby in the active site, confirming the utility of this NMR-based approach to probing active site structure under physiological conditions. Such 13C-heme-filtered NOE data complement X-ray crystallographic and T1-based NMR measurements; and, may also be of potentially significant utility in furnishing experimental distance constraints in validations of docking routines commonly employed for determining the relative affinities and binding orientations of drug candidates with CYP450s.
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Affiliation(s)
- Remigio Usai
- Department of Chemistry, Marquette University, Wisconsin 53233, United States
| | - Daniel Kaluka
- Department of Chemistry and Biochemistry, Taylor University, Upland, IN 46989, United States
| | - Sheng Cai
- School of Pharmacy, University of Wisconsin Madison, Madison, Wisconsin 53705, United States
| | - Daniel S. Sem
- Department of Pharmaceutical Sciences, Concordia University of Wisconsin, Mequon, WI, 53097, United States
| | - James R. Kincaid
- Department of Chemistry, Marquette University, Wisconsin 53233, United States
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8
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Takeda H, Shimba K, Horitani M, Kimura T, Nomura T, Kubo M, Shiro Y, Tosha T. Trapping of a Mononitrosyl Nonheme Intermediate of Nitric Oxide Reductase by Cryo-Photolysis of Caged Nitric Oxide. J Phys Chem B 2023; 127:846-854. [PMID: 36602896 DOI: 10.1021/acs.jpcb.2c05852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Characterization of short-lived reaction intermediates is essential for elucidating the mechanism of the reaction catalyzed by metalloenzymes. Here, we demonstrated that the photolysis of a caged compound under cryogenic temperature followed by thermal annealing is an invaluable technique for trapping of short-lived reaction intermediates of metalloenzymes through the study of membrane-integrated nitric oxide reductase (NOR) that catalyzes reductive coupling of two NO molecules to N2O at its heme/nonheme FeB binuclear center. Although NO produced by the photolysis of caged NO did not react with NOR under cryogenic temperature, annealing to ∼160 K allowed NO to diffuse and react with NOR, which was evident from the appearance of EPR signals assignable to the S = 3/2 state. This indicates that the nonheme FeB-NO species can be trapped as the intermediate. Time-resolved IR spectroscopy with the use of the photolysis of caged NO as a reaction trigger showed that the intermediate formed at 10 μs gave the NO stretching frequency at 1683 cm-1 typical of nonheme Fe-NO, confirming that the combination of the cryo-photolysis of caged NO and annealing enabled us to trap the reaction intermediate. Thus, the cryo-photolysis of the caged compound has great potential for the characterization of short-lived reaction intermediates.
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Affiliation(s)
- Hanae Takeda
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
| | - Kanji Shimba
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry & Food Science, Saga University, Saga 840-8502, Japan.,The United Graduate School of Agricultural Science, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
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9
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Geeraerts Z, Stiller OR, Lukat-Rodgers GS, Rodgers KR. Roles of High-Valent Hemes and pH Dependence in Halite Decomposition Catalyzed by Chlorite Dismutase from Dechloromonas aromatica. ACS Catal 2022; 12:8641-8657. [DOI: 10.1021/acscatal.2c01428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zachary Geeraerts
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Olivia R. Stiller
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
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10
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Resolution and characterization of contributions of select protein and coupled solvent configurational fluctuations to radical rearrangement catalysis in coenzyme B 12-dependent ethanolamine ammonia-lyase. Methods Enzymol 2022; 669:229-259. [PMID: 35644173 DOI: 10.1016/bs.mie.2021.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Coenzyme B12 (adenosylcobalamin) -dependent ethanolamine ammonia-lyase (EAL) is the signature enzyme in ethanolamine utilization metabolism associated with microbiome homeostasis and disease conditions in the human gut. The enzyme conducts a complex choreography of bond-making/bond-breaking steps that rearrange substrate to products through a radical mechanism, with themes common to other coenzyme B12-dependent and radical enzymes. The methods presented are targeted to test the hypothesis that particular, select protein and coupled solvent configurational fluctuations contribute to enzyme function. The general approach is to correlate enzyme function with an introduced perturbation that alters the properties (for example, degree of concertedness, or collectiveness) of protein and coupled solvent dynamics. Methods for sample preparation and low-temperature kinetic measurements by using temperature-step reaction initiation and time-resolved, full-spectrum electron paramagnetic resonance spectroscopy are detailed. A framework for interpretation of results obtained in ensemble systems under conditions of statistical equilibrium within the reacting, globally unstable state is presented. The temperature-dependence of the first-order rate constants for decay of the cryotrapped paramagnetic substrate radical state in EAL, through the chemical step of radical rearrangement, displays a piecewise-continuous Arrhenius dependence from 203 to 295K, punctuated by a kinetic bifurcation over 219-220K. The results reveal the obligatory contribution of a class of select collective protein and coupled solvent fluctuations to the interconversion of two resolved, sequential configurational substates, on the decay time scale. The select class of collective fluctuations also contributes to the chemical step. The methods and analysis are generally applicable to other coenzyme B12-dependent and related radical enzymes.
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11
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Davydov R, Herzog AE, Jodts RJ, Karlin KD, Hoffman BM. End-On Copper(I) Superoxo and Cu(II) Peroxo and Hydroperoxo Complexes Generated by Cryoreduction/Annealing and Characterized by EPR/ENDOR Spectroscopy. J Am Chem Soc 2022; 144:377-389. [PMID: 34981938 PMCID: PMC8785356 DOI: 10.1021/jacs.1c10252] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this report, we investigate the physical and chemical properties of monocopper Cu(I) superoxo and Cu(II) peroxo and hydroperoxo complexes. These are prepared by cryoreduction/annealing of the parent [LCuI(O2)]+ Cu(I) dioxygen adducts with the tripodal, N4-coordinating, tetradentate ligands L = PVtmpa, DMMtmpa, TMG3tren and are best described as [LCuII(O2•-)]+ Cu(II) complexes that possess end-on (η1-O2•-) superoxo coordination. Cryogenic γ-irradiation (77 K) of the EPR-silent parent complexes generates mobile electrons from the solvent that reduce the [LCuII(O2•-)]+ within the frozen matrix, trapping the reduced form fixed in the structure of the parent complex. Cryoannealing, namely progressively raising the temperature of a frozen sample in stages and then cooling back to low temperature at each stage for examination, tracks the reduced product as it relaxes its structure and undergoes chemical transformations. We employ EPR and ENDOR (electron-nuclear double resonance) as powerful spectroscopic tools for examining the properties of the states that form. Surprisingly, the primary products of reduction of the Cu(II) superoxo species are metastable cuprous superoxo [LCuI(O2•-)]+ complexes. During annealing to higher temperatures this state first undergoes internal electron transfer (IET) to form the end-on Cu(II) peroxo state, which is then protonated to form Cu(II)-OOH species. This is the first time these methods, which have been used to determine key details of metalloenzyme catalytic cycles and are a powerful tools for tracking PCET reactions, have been applied to copper coordination compounds.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201, United States
| | - Austin E Herzog
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Richard J Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201, United States
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201, United States
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12
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Trapping a cross-linked lysine-tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB. Proc Natl Acad Sci U S A 2021; 118:2101571118. [PMID: 34001621 DOI: 10.1073/pnas.2101571118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The radical S-adenosylmethionine (rSAM) enzyme SuiB catalyzes the formation of an unusual carbon-carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the biosynthesis of a ribosomal peptide natural product. Prior work on SuiB has suggested that the Lys-Trp cross-link is formed via radical electrophilic aromatic substitution (rEAS), in which an auxiliary [4Fe-4S] cluster (AuxI), bound in the SPASM domain of SuiB, carries out an essential oxidation reaction during turnover. Despite the prevalence of auxiliary clusters in over 165,000 rSAM enzymes, direct evidence for their catalytic role has not been reported. Here, we have used electron paramagnetic resonance (EPR) spectroscopy to dissect the SuiB mechanism. Our studies reveal substrate-dependent redox potential tuning of the AuxI cluster, constraining it to the oxidized [4Fe-4S]2+ state, which is active in catalysis. We further report the trapping and characterization of an unprecedented cross-linked Lys-Trp radical (Lys-Trp•) in addition to the organometallic Ω intermediate, providing compelling support for the proposed rEAS mechanism. Finally, we observe oxidation of the Lys-Trp• intermediate by the redox-tuned [4Fe-4S]2+ AuxI cluster by EPR spectroscopy. Our findings provide direct evidence for a role of a SPASM domain auxiliary cluster and consolidate rEAS as a mechanistic paradigm for rSAM enzyme-catalyzed carbon-carbon bond-forming reactions.
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Chiura T, Mak PJ. Investigation of Cyanide Ligand as an Active Site Probe of Human Heme Oxygenase. Inorg Chem 2021; 60:4633-4645. [PMID: 33754715 DOI: 10.1021/acs.inorgchem.0c03611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human heme oxygenase (hHO-1) is a physiologically important enzyme responsible for free heme catabolism. The enzyme's high regiospecificity is controlled by the distal site hydrogen bond network that involves water molecules and the D140 amino acid residue. In this work, we probe the active site environment of the wild-type (WT) hHO-1 and its D140 mutants using resonance Raman (rR) spectroscopy. Cyanide ligands are more stable than dioxygen adducts and are an effective probe of active site environment of heme proteins. The inherently linear geometry of the Fe-C-N fragment can be altered by the steric, electrostatic, and H-bonding interactions imposed by the amino acid residues present in the heme distal site, resulting in a tilted or bent configuration. The WT hHO-1 and its D140A, D140N, and D140E mutants were studied in the presence of natural abundance CN- and its isotopic analogues (13CN-, C15N-, and 13C15N-). Deconvolution of spectral data revealed that the ν(Fe-CN) stretching and δ(Fe-CN) bending modes are present at 454 and 376 cm-1, respectively. The rR spectral patterns of the CN- adducts of WT revealed that the Fe-C-N fragment adopts a tilted conformation, with a larger bending contribution for the D140A, D140N, and D140E mutants. These studies suggest that the FeCN fragment in hHO-1 is tilted more strongly toward the porphyrin macrocycle compared to other histidine-ligated proteins, reflecting the propensity of the exogenous hHO-l ligands to position toward the α-meso-carbon, which is crucial for the HO reactivity and essential for regioselectivity.
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Affiliation(s)
- Tapiwa Chiura
- Chemistry Department, Saint Louis University, Saint Louis, Missouri 63103, United States
| | - Piotr J Mak
- Chemistry Department, Saint Louis University, Saint Louis, Missouri 63103, United States
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14
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Petrik ID, Davydov R, Kahle M, Sandoval B, Dwaraknath S, Ädelroth P, Hoffman B, Lu Y. An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network. Biochemistry 2021; 60:346-355. [PMID: 33464878 PMCID: PMC7888536 DOI: 10.1021/acs.biochem.0c00852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Efficiently carrying out the oxygen reduction reaction (ORR) is critical for many applications in biology and chemistry, such as bioenergetics and fuel cells, respectively. In biology, this reaction is carried out by large, transmembrane oxidases such as heme-copper oxidases (HCOs) and cytochrome bd oxidases. Common to these oxidases is the presence of a glutamate residue next to the active site, but its precise role in regulating the oxidase activity remains unclear. To gain insight into its role, we herein report that incorporation of glutamate next to a designed heme-copper center in two biosynthetic models of HCOs improves O2 binding affinity, facilitates protonation of reaction intermediates, and eliminates release of reactive oxygen species. High-resolution crystal structures of the models revealed extended, water-mediated hydrogen-bonding networks involving the glutamate. Electron paramagnetic resonance of the cryoreduced oxy-ferrous centers at cryogenic temperature followed by thermal annealing allowed observation of the key hydroperoxo intermediate that can be attributed to the hydrogen-bonding network. By demonstrating these important roles of glutamate in oxygen reduction biochemistry, this work offers deeper insights into its role in native oxidases, which may guide the design of more efficient artificial ORR enzymes or catalysts for applications such as fuel cells.
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Affiliation(s)
- Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Roman Davydov
- The Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Maximilian Kahle
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Braddock Sandoval
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sudharsan Dwaraknath
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brian Hoffman
- The Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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15
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Sligar SG, Denisov IG. Nanodiscs: A toolkit for membrane protein science. Protein Sci 2020; 30:297-315. [PMID: 33165998 DOI: 10.1002/pro.3994] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
Membrane proteins are involved in numerous vital biological processes, including transport, signal transduction and the enzymes in a variety of metabolic pathways. Integral membrane proteins account for up to 30% of the human proteome and they make up more than half of all currently marketed therapeutic targets. Unfortunately, membrane proteins are inherently recalcitrant to study using the normal toolkit available to scientists, and one is most often left with the challenge of finding inhibitors, activators and specific antibodies using a denatured or detergent solubilized aggregate. The Nanodisc platform circumvents these challenges by providing a self-assembled system that renders typically insoluble, yet biologically and pharmacologically significant, targets such as receptors, transporters, enzymes, and viral antigens soluble in aqueous media in a native-like bilayer environment that maintain a target's functional activity. By providing a bilayer surface of defined composition and structure, Nanodiscs have found great utility in the study of cellular signaling complexes that assemble on a membrane surface. Nanodiscs provide a nanometer scale vehicle for the in vivo delivery of amphipathic drugs, therapeutic lipids, tethered nucleic acids, imaging agents and active protein complexes. This means for generating nanoscale lipid bilayers has spawned the successful use of numerous other polymer and peptide amphipathic systems. This review, in celebration of the Anfinsen Award, summarizes some recent results and provides an inroad into the current and historical literature.
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Affiliation(s)
- Stephen G Sligar
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Ilia G Denisov
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
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16
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Usai R, Kaluka D, Mak PJ, Liu Y, Kincaid JR. Resonance Raman spectroscopic studies of peroxo and hydroperoxo intermediates in lauric acid (LA)-bound cytochrome P450 119. J Inorg Biochem 2020; 208:111084. [PMID: 32470906 DOI: 10.1016/j.jinorgbio.2020.111084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 03/07/2020] [Accepted: 03/29/2020] [Indexed: 11/30/2022]
Abstract
Cytochromes P450 bind and cleave dioxygen to generate a potent intermediate compound I, capable of hydroxylating inert hydrocarbon substrates. Cytochrome P450 119, a bacterial cytochrome P450 that serves as a good model system for the study of the intermediate states in the P450 catalytic cycle. CYP119 is found in high temperature and sulfur rich environments. Though the natural substrate and redox partner are still unknown, a potential application of such thermophilic P450s is utilizing them as biocatalysts in biotechnological industry; e.g., the synthesis of organic compounds otherwise requiring hostile environments like extremes of pH or temperature. In the present work the oxygenated complex of this enzyme bound to lauric acid, a surrogate substrate known to have a good binding affinity, was studied by a combination of cryoradiolysis and resonance Raman spectroscopy, to trap and characterize active site structures of the key fleeting enzymatic intermediates, including the peroxo and hydroperoxo species.
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Affiliation(s)
- Remigio Usai
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - Daniel Kaluka
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - Piotr J Mak
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - Yilin Liu
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - James R Kincaid
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States.
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17
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Kim H, Rogler PJ, Sharma SK, Schaefer AW, Solomon EI, Karlin KD. Heme-Fe III Superoxide, Peroxide and Hydroperoxide Thermodynamic Relationships: Fe III-O 2•- Complex H-Atom Abstraction Reactivity. J Am Chem Soc 2020; 142:3104-3116. [PMID: 31913628 PMCID: PMC7034651 DOI: 10.1021/jacs.9b12571] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Establishing redox and thermodynamic relationships between metal-ion-bound O2 and its reduced (and protonated) derivatives is critically important for a full understanding of (bio)chemical processes involving dioxygen processing. Here, a ferric heme peroxide complex, [(F8)FeIII-(O22-)]- (P) (F8 = tetrakis(2,6-difluorophenyl)porphyrinate), and a superoxide complex, [(F8)FeIII-(O2•-)] (S), are shown to be redox interconvertible. Using Cr(η-C6H6)2, an equilibrium state where S and P are present is established in tetrahydrofuran (THF) at -80 °C, allowing determination of the reduction potential of S as -1.17 V vs Fc+/0. P could be protonated with 2,6-lutidinium triflate, yielding the low-spin ferric hydroperoxide species, [(F8)FeIII-(OOH)] (HP). Partial conversion of HP back to P using a derivatized phosphazene base gave a P/HP equilibrium mixture, leading to the determination of pKa = 28.8 for HP (THF, -80 °C). With the measured reduction potential and pKa, the O-H bond dissociation free energy (BDFE) of hydroperoxide species HP was calculated to be 73.5 kcal/mol, employing the thermodynamic square scheme and Bordwell relationship. This calculated O-H BDFE of HP, in fact, lines up with an experimental demonstration of the oxidizing ability of S via hydrogen atom transfer (HAT) from TEMPO-H (2,2,6,6-tetramethylpiperdine-N-hydroxide, BDFE = 66.5 kcal/mol in THF), forming the hydroperoxide species HP and TEMPO radical. Kinetic studies carried out with TEMPO-H(D) reveal second-order behavior, kH = 0.5, kD = 0.08 M-1 s-1 (THF, -80 °C); thus, the hydrogen/deuterium kinetic isotope effect (KIE) = 6, consistent with H-atom abstraction by S being the rate-determining step. This appears to be the first case where experimentally derived thermodynamics lead to a ferric heme hydroperoxide OO-H BDFE determination, that FeIII-OOH species being formed via HAT reactivity of the partner ferric heme superoxide complex.
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Affiliation(s)
- Hyun Kim
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Patrick J Rogler
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Savita K Sharma
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Andrew W Schaefer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Kenneth D Karlin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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18
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Van Stappen C, Davydov R, Yang ZY, Fan R, Guo Y, Bill E, Seefeldt LC, Hoffman BM, DeBeer S. Spectroscopic Description of the E 1 State of Mo Nitrogenase Based on Mo and Fe X-ray Absorption and Mössbauer Studies. Inorg Chem 2019; 58:12365-12376. [PMID: 31441651 PMCID: PMC6751781 DOI: 10.1021/acs.inorgchem.9b01951] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Indexed: 11/29/2022]
Abstract
Mo nitrogenase (N2ase) utilizes a two-component protein system, the catalytic MoFe and its electron-transfer partner FeP, to reduce atmospheric dinitrogen (N2) to ammonia (NH3). The FeMo cofactor contained in the MoFe protein serves as the catalytic center for this reaction and has long inspired model chemistry oriented toward activating N2. This field of chemistry has relied heavily on the detailed characterization of how Mo N2ase accomplishes this feat. Understanding the reaction mechanism of Mo N2ase itself has presented one of the most challenging problems in bioinorganic chemistry because of the ephemeral nature of its catalytic intermediates, which are difficult, if not impossible, to singly isolate. This is further exacerbated by the near necessity of FeP to reduce native MoFe, rendering most traditional means of selective reduction inept. We have now investigated the first fundamental intermediate of the MoFe catalytic cycle, E1, as prepared both by low-flux turnover and radiolytic cryoreduction, using a combination of Mo Kα high-energy-resolution fluorescence detection and Fe K-edge partial-fluorescence-yield X-ray absorption spectroscopy techniques. The results demonstrate that the formation of this state is the result of an Fe-centered reduction and that Mo remains redox-innocent. Furthermore, using Fe X-ray absorption and 57Fe Mössbauer spectroscopies, we correlate a previously reported unique species formed under cryoreducing conditions to the natively formed E1 state through annealing, demonstrating the viability of cryoreduction in studying the catalytic intermediates of MoFe.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Ruixi Fan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Eckhard Bill
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Serena DeBeer
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
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19
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Xu S, Draksharapu A, Rasheed W, Que L. Acid pKa Dependence in O–O Bond Heterolysis of a Nonheme FeIII–OOH Intermediate To Form a Potent FeV═O Oxidant with Heme Compound I-Like Reactivity. J Am Chem Soc 2019; 141:16093-16107. [DOI: 10.1021/jacs.9b08442] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shuangning Xu
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Apparao Draksharapu
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Waqas Rasheed
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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20
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Davydov RM, Jennings G, Hoffman BM, Podust LM. Short-lived neutral FMN and FAD semiquinones are transient intermediates in cryo-reduced yeast NADPH-cytochrome P450 reductase. Arch Biochem Biophys 2019; 673:108080. [PMID: 31445894 DOI: 10.1016/j.abb.2019.108080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 11/28/2022]
Abstract
The electron configuration of flavin cofactors, FMN and FAD, is a critical factor governing the reactivity of NADPH-cytochrome P450 reductase (CPR). The current view of electron transfer by the mammalian CPR, based on equilibrium redox potentials of the flavin cofactors, is that the two electron-reduced FMN hydroquinone (FMNH2), rather than one electron-reduced FMN semiquinone, serves as electron donor to the terminal protein acceptors. However, kinetic and thermodynamic studies on the CPR species originated from different organisms have shown that redox potentials measured at distinct electron transfer steps differ from redox potentials determined by equilibrium titration. Collectively, previous observations suggest that the short-lived transient semiquinone species may carry electrons in diflavin reductases. In this work, we have investigated spectroscopic properties of the CPR-bound FAD and FMN reduced at 77 K by radiolytically-generated thermalized electrons. Using UV-vis spectroscopy, we demonstrated that upon cryo-reduction of oxidized yeast CPR (yCPR) containing an equimolar ratio of both FAD and FMN, or FAD alone, neutral semiquinones were trapped at 77 K. During annealing at the elevated temperatures, unstable short-lived neutral semiquinones relaxed to spectroscopically distinct air-stable neutral semiquinones. This transition was independent of pH within the 6.0-10.7 range. Our data on yeast CPR are in line with the previous observations of others that the flavin short-lived transient semiquinone intermediates may have a role in the electron transfer by CPR at physiological conditions.
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Affiliation(s)
- Roman M Davydov
- The Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Gareth Jennings
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Brian M Hoffman
- The Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Larissa M Podust
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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21
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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22
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Wise CE, Hsieh CH, Poplin NL, Makris TM. Dioxygen Activation by the Biofuel-Generating Cytochrome P450 OleT. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02631] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Courtney E. Wise
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Chun H. Hsieh
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Nathan L. Poplin
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Thomas M. Makris
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
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23
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Kuzikov AV, Masamrekh RA, Archakov AI, Shumyantseva VV. Methods for Determination of Functional Activity of Cytochrome P450 Isoenzymes. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2018. [DOI: 10.1134/s1990750818030046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Kuzikov AV, Masamrekh RA, Archakov AI, Shumyantseva VV. [Methods for determining of cytochrome P450 isozymes functional activity]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:149-168. [PMID: 29723145 DOI: 10.18097/pbmc20186402149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review is dedicated to modern methods and technologies for determining of cytochrome P450 isozymes functional activity, such as absorbance and fluorescent spectroscopy, electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), Raman, Mossbauer, and X-ray spectroscopy, surface plasmon resonance (SPR), atomic force microscopy (AFM). Methods of molecular genetic analysis were reviewed from personalized medicine point of view. The use of chromate-mass-spectrometric methods for cytochrome P450-dependent catalytic reactions' products was discussed. The review covers modern electrochemical systems based on cytochrome P450 isozymes for their catalytic activity analysis, their use in practice and further development perspectives for experimental pharmacology, biotechnology and translational medicine.
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Affiliation(s)
- A V Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - R A Masamrekh
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - V V Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
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25
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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26
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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27
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Sharma A, Roemelt M, Reithofer M, Schrock RR, Hoffman BM, Neese F. EPR/ENDOR and Theoretical Study of the Jahn-Teller-Active [HIPTN 3N]Mo VL Complexes (L = N -, NH). Inorg Chem 2017; 56:6906-6919. [PMID: 28571321 DOI: 10.1021/acs.inorgchem.7b00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molybdenum trisamidoamine (TAA) complex [Mo] {[3,5-(2,4,6-i-Pr3C6H2)2C6H3NCH2CH2N]Mo} carries out catalytic reduction of N2 to ammonia (NH3) by protons and electrons at room temperature. A key intermediate in the proposed [Mo] nitrogen reduction cycle is nitridomolybdenum(VI), [Mo(VI)]N. The addition of [e-/H+] to [Mo(VI)]N to generate [Mo(V)]NH might, in principle, follow one of three possible pathways: direct proton-coupled electron transfer; H+ first and then e-; e- and then H+. In this study, the paramagnetic Mo(V) intermediate {[Mo]N}- and the [Mo]NH transfer product were generated by irradiating the diamagnetic [Mo]N and {[Mo]NH}+ Mo(VI) complexes, respectively, with γ-rays at 77 K, and their electronic and geometric structures were characterized by electron paramagnetic resonance and electron nuclear double resonance spectroscopies, combined with quantum-chemical computations. In combination with previous X-ray studies, this creates the rare situation in which each one of the four possible states of [e-/H+] delivery has been characterized. Because of the degeneracy of the electronic ground states of both {[Mo(V)]N}- and [Mo(V)]NH, only multireference-based methods such as the complete active-space self-consistent field (CASSCF) and related methods provide a qualitatively correct description of the electronic ground state and vibronic coupling. The molecular g values of {[Mo]N}- and [Mo]NH exhibit large deviations from the free-electron value ge. Their actual values reflect the relative strengths of vibronic and spin-orbit coupling. In the course of the computational treatment, the utility and limitations of a formal two-state model that describes this competition between couplings are illustrated, and the implications of our results for the chemical reactivity of these states are discussed.
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Affiliation(s)
- Ajay Sharma
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Michael Roemelt
- Max-Planck Institut für Chemische Energiekonversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.,Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum , D-44780 Bochum, Germany.,Max-Planck Institut für Kohlenforschung , Kaiser-Wilhelm Platz1, D-45470 Mülheim an der Ruhr, Germany
| | - Michael Reithofer
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Richard R Schrock
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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28
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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29
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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30
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Bhagi-Damodaran A, Petrik I, Lu Y. Using Biosynthetic Models of Heme-Copper Oxidase and Nitric Oxide Reductase in Myoglobin to Elucidate Structural Features Responsible for Enzymatic Activities. Isr J Chem 2016; 56:773-790. [PMID: 27994254 PMCID: PMC5161413 DOI: 10.1002/ijch.201600033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In biology, a heme-Cu center in heme-copper oxidases (HCOs) is used to catalyze the four-electron reduction of oxygen to water, while a heme-nonheme diiron center in nitric oxide reductases (NORs) is employed to catalyze the two-electron reduction of nitric oxide to nitrous oxide. Although much progress has been made in biochemical and biophysical studies of HCOs and NORs, structural features responsible for similarities and differences within the two enzymatic systems remain to be understood. Here, we discuss the progress made in the design and characterization of myoglobin-based enzyme models of HCOs and NORs. In particular, we focus on use of these models to understand the structure-function relations between HCOs and NORs, including the role of nonheme metals, conserved amino acids in the active site, heme types and hydrogen-bonding network in tuning enzymatic activities and total turnovers. Insights gained from these studies are summarized and future directions are proposed.
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Affiliation(s)
| | - Igor Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL. 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL. 61801
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31
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Dong M, Horitani M, Dzikovski B, Pandelia ME, Krebs C, Freed JH, Hoffman BM, Lin H. Organometallic Complex Formed by an Unconventional Radical S-Adenosylmethionine Enzyme. J Am Chem Soc 2016; 138:9755-8. [PMID: 27465315 DOI: 10.1021/jacs.6b04155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pyrococcus horikoshii Dph2 (PhDph2) is an unusual radical S-adenosylmethionine (SAM) enzyme involved in the first step of diphthamide biosynthesis. It catalyzes the reaction by cleaving SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. To probe the reaction mechanism, we synthesized a SAM analogue (SAMCA), in which the ACP group of SAM is replaced with a 3-carboxyallyl group. SAMCA is cleaved by PhDph2, yielding a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, α-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Electron-nuclear double resonance (ENDOR) measurements with (13)C and (2)H isotopically labeled SAMCA support a π-complex between the C═C double bond of α-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster. This is the first example of a radical SAM-related [4Fe-4S](+) cluster forming an organometallic complex with an alkene, shedding additional light on the mechanism of PhDph2 and expanding our current notions for the reactivity of [4Fe-4S] clusters in radical SAM enzymes.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02453, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Howard Hughes Medical Institute, Cornell University , Ithaca, New York 14853, United States
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32
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Davydov R, Khadka N, Yang ZY, Fielding AJ, Lukoyanov D, Dean DR, Seefeldt LC, Hoffman BM. Exploring Electron/Proton Transfer and Conformational Changes in the Nitrogenase MoFe Protein and FeMo-cofactor Through Cryoreduction/EPR Measurements. Isr J Chem 2016; 56:841-851. [PMID: 27777444 DOI: 10.1002/ijch.201600026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We combine cryoreduction/annealing/EPR measurements of nitrogenase MoFe protein with results of earlier investigations to provide a detailed view of the electron/proton transfer events and conformational changes that occur during early stages of [e-/H+] accumulation by the MoFe protein. This includes reduction of (i) the non-catalytic state of the iron-molybdenum cofactor (FeMo-co) active site that is generated by chemical oxidation of the resting-state cofactor (S = 3/2)) within resting MoFe (E0), and (ii) the catalytic state that has accumulated n =1 [e-/H+] above the resting-state level, denoted E1(1H) (S ≥ 1) in the Lowe-Thorneley kinetic scheme. FeMo-co does not undergo a major change of conformation during reduction of oxidized FeMo-co. In contrast, FeMo-co undergoes substantial conformational changes during the reduction of E0 to E1(1H), and of E1(1H) to E2(2H) (n = 2; S = 3/2). The experimental results further suggest that the E1(1H) → E2(2H) step involves coupled delivery of a proton and electron (PCET) to FeMo-co of E1(H) to generate a non-equilibrium S = ½ form E2(2H)*. This subsequently undergoes conformational relaxation and attendant change in FeMo-co spin state, to generate the equilibrium E2(2H) (S = 3/2) state. Unexpectedly, these experiments also reveal conformational coupling between FeMo-co and P-cluster, and between Fe protein binding and FeMo-co, which might play a role in gated ET from reduced Fe protein to FeMo-co.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Andrew J Fielding
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Dmitriy Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, 110 Fralin Hall, Blacksburg, VA 24061
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
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33
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Davydov R, Im S, Shanmugam M, Gunderson WA, Pearl NM, Hoffman BM, Waskell L. Role of the Proximal Cysteine Hydrogen Bonding Interaction in Cytochrome P450 2B4 Studied by Cryoreduction, Electron Paramagnetic Resonance, and Electron-Nuclear Double Resonance Spectroscopy. Biochemistry 2016; 55:869-83. [PMID: 26750753 DOI: 10.1021/acs.biochem.5b00744] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystallographic studies have shown that the F429H mutation of cytochrome P450 2B4 introduces an H-bond between His429 and the proximal thiolate ligand, Cys436, without altering the protein fold but sharply decreases the enzymatic activity and stabilizes the oxyferrous P450 2B4 complex. To characterize the influence of this hydrogen bond on the states of the catalytic cycle, we have used radiolytic cryoreduction combined with electron paramagnetic resonance (EPR) and (electron-nuclear double resonance (ENDOR) spectroscopy to study and compare their characteristics for wild-type (WT) P450 2B4 and the F429H mutant. (i) The addition of an H-bond to the axial Cys436 thiolate significantly changes the EPR signals of both low-spin and high-spin heme-iron(III) and the hyperfine couplings of the heme-pyrrole (14)N but has relatively little effect on the (1)H ENDOR spectra of the water ligand in the six-coordinate low-spin ferriheme state. These changes indicate that the H-bond introduced between His and the proximal cysteine decreases the extent of S → Fe electron donation and weakens the Fe(III)-S bond. (ii) The added H-bond changes the primary product of cryoreduction of the Fe(II) enzyme, which is trapped in the conformation of the parent Fe(II) state. In the wild-type enzyme, the added electron localizes on the porphyrin, generating an S = (3)/2 state with the anion radical exchange-coupled to the Fe(II). In the mutant, it localizes on the iron, generating an S = (1)/2 Fe(I) state. (iii) The additional H-bond has little effect on g values and (1)H-(14)N hyperfine couplings of the cryogenerated, ferric hydroperoxo intermediate but noticeably slows its decay during cryoannealing. (iv) In both the WT and the mutant enzyme, this decay shows a significant solvent kinetic isotope effect, indicating that the decay reflects a proton-assisted conversion to Compound I (Cpd I). (v) We confirm that Cpd I formed during the annealing of the cryogenerated hydroperoxy intermediate and that it is the active hydroxylating species in both WT P450 2B4 and the F429H mutant. (vi) Our data also indicate that the added H-bond of the mutation diminishes the reactivity of Cpd I.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Sangchoul Im
- Department of Anesthesiology, University of Michigan, and VA Medical Center , 2215 Fuller Road, Ann Arbor, Michigan 48105, United States
| | - Muralidharan Shanmugam
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - William A Gunderson
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Naw May Pearl
- Department of Anesthesiology, University of Michigan, and VA Medical Center , 2215 Fuller Road, Ann Arbor, Michigan 48105, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, and VA Medical Center , 2215 Fuller Road, Ann Arbor, Michigan 48105, United States
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34
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Petrik ID, Davydov R, Ross M, Zhao X, Hoffman B, Lu Y. Spectroscopic and Crystallographic Evidence for the Role of a Water-Containing H-Bond Network in Oxidase Activity of an Engineered Myoglobin. J Am Chem Soc 2016; 138:1134-7. [PMID: 26716352 PMCID: PMC4750474 DOI: 10.1021/jacs.5b12004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme-copper oxidases (HCOs) catalyze efficient reduction of oxygen to water in biological respiration. Despite progress in studying native enzymes and their models, the roles of non-covalent interactions in promoting this activity are still not well understood. Here we report EPR spectroscopic studies of cryoreduced oxy-F33Y-CuBMb, a functional model of HCOs engineered in myoglobin (Mb). We find that cryoreduction at 77 K of the O2-bound form, trapped in the conformation of the parent oxyferrous form, displays a ferric-hydroperoxo EPR signal, in contrast to the cryoreduced oxy-wild-type (WT) Mb, which is unable to deliver a proton and shows a signal from the peroxo-ferric state. Crystallography of oxy-F33Y-CuBMb reveals an extensive H-bond network involving H2O molecules, which is absent from oxy-WTMb. This H-bonding proton-delivery network is the key structural feature that transforms the reversible oxygen-binding protein, WTMb, into F33Y-CuBMb, an oxygen-activating enzyme that reduces O2 to H2O. These results provide direct evidence of the importance of H-bond networks involving H2O in conferring enzymatic activity to a designed protein. Incorporating such extended H-bond networks in designing other metalloenzymes may allow us to confer and fine-tune their enzymatic activities.
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Affiliation(s)
- Igor D Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Roman Davydov
- The Department of Chemistry, Northwestern University , Evanston, Illinois 60201, United States
| | - Matthew Ross
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,The Department of Chemistry, Northwestern University , Evanston, Illinois 60201, United States
| | - Xuan Zhao
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Brian Hoffman
- The Department of Chemistry, Northwestern University , Evanston, Illinois 60201, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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35
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Davydov R, Fleischhacker AS, Bagai I, Hoffman BM, Ragsdale SW. Comparison of the Mechanisms of Heme Hydroxylation by Heme Oxygenases-1 and -2: Kinetic and Cryoreduction Studies. Biochemistry 2015; 55:62-8. [PMID: 26652036 DOI: 10.1021/acs.biochem.5b00943] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The two isoforms of human heme oxygenase (HO1 and HO2) catalyze oxidative degradation of heme to biliverdin, Fe, and CO. Unlike HO1, HO2 contains two C-terminal heme regulatory motifs (HRMs) centered at Cys265 and Cys282 that act as redox switches and, in their reduced dithiolate state, bind heme (Fleischhacker et al., Biochemistry , 2015 , 54 , 2693 - 2708 ). Here, we describe cryoreduction/annealing and electron paramagnetic resonance spectroscopic experiments to study the structural features of the oxyheme moiety in HO2 and to elucidate the initial steps in heme degradation. We conclude that the same mechanism of heme hydroxylation to α-meso-hydroxyheme is employed by both isoforms and that the HRMs do not affect the physicochemical properties of the oxy-Fe(II) and HOO-Fe(III) states of HO2. However, the absorption spectrum of oxy-Fe(II)-HO2 is slightly blue-shifted relative to that of HO1. Furthermore, heme hydroxylation proceeds three times more slowly, and the oxy-Fe(II) state is 100-fold less stable in HO2 than in HO1. These distinctions are attributed to slight structural variances in the two proteins, including differences in equilibrium between open versus closed conformations. Kinetic studies revealed that heme oxygenation by HO2 occurs solely at the catalytic core in that a variant of HO2 lacking the C-terminal HRM domain exhibits the same specific activity as one containing both the catalytic core and HRM domain; furthermore, a truncated variant containing only the HRM region binds but cannot oxidize heme. In summary, HO1 and HO2 share similar catalytic mechanisms, and the HRMs do not play a direct role in the HO2 catalytic cycle.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Angela S Fleischhacker
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Ireena Bagai
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
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36
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Abstract
Ablation of androgen production through surgery is one strategy against prostate cancer, with the current focus placed on pharmaceutical intervention to restrict androgen synthesis selectively, an endeavor that could benefit from the enhanced understanding of enzymatic mechanisms that derives from characterization of key reaction intermediates. The multifunctional cytochrome P450 17A1 (CYP17A1) first catalyzes the typical hydroxylation of its primary substrate, pregnenolone (PREG) and then also orchestrates a remarkable C17-C20 bond cleavage (lyase) reaction, converting the 17-hydroxypregnenolone initial product to dehydroepiandrosterone, a process representing the first committed step in the biosynthesis of androgens. Now, we report the capture and structural characterization of intermediates produced during this lyase step: an initial peroxo-anion intermediate, poised for nucleophilic attack on the C20 position by a substrate-associated H-bond, and the crucial ferric peroxo-hemiacetal intermediate that precedes carbon-carbon (C-C) bond cleavage. These studies provide a rare glimpse at the actual structural determinants of a chemical transformation that carries profound physiological consequences.
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Davydov R, Strushkevich N, Smil D, Yantsevich A, Gilep A, Usanov S, Hoffman BM. Evidence That Compound I Is the Active Species in Both the Hydroxylase and Lyase Steps by Which P450scc Converts Cholesterol to Pregnenolone: EPR/ENDOR/Cryoreduction/Annealing Studies. Biochemistry 2015; 54:7089-97. [PMID: 26603348 DOI: 10.1021/acs.biochem.5b00903] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450scc (CYP 11A1) catalyzes the conversion of cholesterol (Ch) to pregnenolone, the precursor to steroid hormones. This process proceeds via three sequential monooxygenation reactions: two hydroxylations of Ch first form 22(R)-hydroxycholesterol (HC) and then 20α,22(R)-dihydroxycholesterol (DHC); a lyase reaction then cleaves the C20-C22 bond to form pregnenolone. Recent cryoreduction/annealing studies that employed electron paramagnetic resonance (EPR)/electron nuclear double resonance (ENDOR) spectroscopy [Davydov, R., et al. (2012) J. Am. Chem. Soc. 134, 17149] showed that compound I (Cpd I) is the active intermediate in the first step, hydroxylation of Ch. Herein, we have employed EPR and ENDOR spectroscopy to characterize the intermediates in the second and third steps of the enzymatic process, as conducted by 77 K radiolytic one-electron cryoreduction and subsequent annealing of the ternary oxy-cytochrome P450scc complexes with HC and DHC. This procedure is validated by showing that the cryoreduced ternary complexes of oxy-cytochrome P450scc with HC and DHC are catalytically competent and during annealing generate DHC and pregnenolone, respectively. Cryoreduction of the oxy-P450scc-HC ternary complex trapped at 77K produces the superoxo-ferrous P450scc intermediate along with a minor fraction of ferric hydroperoxo intermediates. The superoxo-ferrous intermediate converts into a ferric-hydroperoxo species after annealing at 145 K. During subsequent annealing at 170-180 K, the ferric-hydroperoxo intermediate converts to the primary product complex with the large solvent kinetic isotope effect that indicates Cpd I is being formed, and (1)H ENDOR measurements of the primary product formed in D2O demonstrate that Cpd I is the active species. They show that the primary product contains Fe(III) coordinated to the 20-O(1)H of DHC with the (1)H derived from substrate, the signature of the Cpd I reaction. Hydroperoxo ferric intermediates are the primary species formed during cryoreduction of the oxy-P450scc-DHC ternary complex, and they decay at 185 K with a strong solvent kinetic isotope effect to form low-spin ferric P450scc. Together, these observations indicated that Cpd I also is the active intermediate in the C20,22 lyase final step. In combination with our previous results, this study thus indicates that Cpd I is the active species in each of the three sequential monooxygenation reactions by which P450scc catalytically converts Ch to pregnenolone.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208-3113, United States
| | - Natallia Strushkevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus , Kuprevicha Street 5/2, Minsk 220141, Belarus
| | - David Smil
- Structural Genomics Consortium, University of Toronto , 101 College Street, Toronto, ON, Canada M5G 1L7
| | - Aliaksei Yantsevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus , Kuprevicha Street 5/2, Minsk 220141, Belarus
| | - Andrey Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus , Kuprevicha Street 5/2, Minsk 220141, Belarus
| | - Sergey Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus , Kuprevicha Street 5/2, Minsk 220141, Belarus
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208-3113, United States
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Franke A, van Eldik R. Spectroscopic and Kinetic Evidence for the Crucial Role of Compound 0 in the P450cam -Catalyzed Hydroxylation of Camphor by Hydrogen Peroxide. Chemistry 2015; 21:15201-10. [PMID: 26353996 DOI: 10.1002/chem.201501886] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 11/09/2022]
Abstract
The hydroperoxo iron(III) intermediate P450cam Fe(III) -OOH, being the true Compound 0 (Cpd 0) involved in the natural catalytic cycle of P450cam , could be transiently observed in the peroxo-shunt oxidation of the substrate-free enzyme by hydrogen peroxide under mild basic conditions and low temperature. The prolonged lifetime of Cpd 0 enabled us to kinetically examine the formation and reactivity of P450cam Fe(III) -OOH species as a function of varying reaction conditions, such as pH, and concentration of H2 O2 , camphor, and potassium ions. The mechanism of hydrogen peroxide binding to the substrate-free form of P450cam differs completely from that observed for other heme proteins possessing the distal histidine as a general acid-base catalyst and is mainly governed by the ability of H2 O2 to undergo deprotonation at the hydroxo ligand coordinated to the iron(III) center under conditions of pH≥p${K{{{\rm P450}\hfill \atop {\rm a}\hfill}}}$. Notably, no spectroscopic evidence for the formation of either Cpd I or Cpd II as products of heterolytic or homolytic OO bond cleavage, respectively, in Cpd 0 could be observed under the selected reaction conditions. The kinetic data obtained from the reactivity studies involving (1R)-camphor, provide, for the first time, experimental evidence for the catalytic activity of the P450Fe(III) -OOH intermediate in the oxidation of the natural substrate of P450cam .
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Affiliation(s)
- Alicja Franke
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen (Germany)
| | - Rudi van Eldik
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen (Germany). .,Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow (Poland).
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Wang M, Zhu C, Kohne M, Warncke K. Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems. Methods Enzymol 2015; 563:59-94. [PMID: 26478482 PMCID: PMC6186429 DOI: 10.1016/bs.mie.2015.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Approaches to the resolution and characterization of individual chemical steps in enzyme catalytic sequences, by using temperatures in the cryogenic range of 190-250 K, and kinetics measured by time-resolved, full-spectrum electron paramagnetic resonance spectroscopy in fluid cryosolvent and frozen solution systems, are described. The preparation and performance of the adenosylcobalamin-dependent ethanolamine ammonia-lyase enzyme from Salmonella typhimurium in the two systems exemplifies the biochemical and spectroscopic methods. General advantages of low-temperature studies are (1) slowing of reaction steps, so that measurements can be made by using straightforward T-step kinetic methods and commercial instrumentation, (2) resolution of individual reaction steps, so that first-order kinetic analysis can be applied, and (3) accumulation of intermediates that are not detectable at room temperatures. The broad temperature range from room temperature to 190 K encompasses three regimes: (1) temperature-independent mean free energy surface (corresponding to native behavior); (2) the narrow temperature region of a glass-like transition in the protein, over which the free energy surface changes, revealing dependence of the native reaction on collective protein/solvent motions; and (3) the temperature range below the glass transition region, for which persistent reaction corresponds to nonnative, alternative reaction pathways, in the vicinity of the native configurational envelope. Representative outcomes of low-temperature kinetics studies are portrayed on Eyring and free energy surface (landscape) plots, and guidelines for interpretations are presented.
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Affiliation(s)
- Miao Wang
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Chen Zhu
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Meghan Kohne
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Kurt Warncke
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA.
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Lukoyanov D, Yang ZY, Khadka N, Dean DR, Seefeldt LC, Hoffman BM. Identification of a key catalytic intermediate demonstrates that nitrogenase is activated by the reversible exchange of N₂ for H₂. J Am Chem Soc 2015; 137:3610-5. [PMID: 25741750 DOI: 10.1021/jacs.5b00103] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Freeze-quenching nitrogenase during turnover with N2 traps an S = ½ intermediate that was shown by ENDOR and EPR spectroscopy to contain N2 or a reduction product bound to the active-site molybdenum-iron cofactor (FeMo-co). To identify this intermediate (termed here EG), we turned to a quench-cryoannealing relaxation protocol. The trapped state is allowed to relax to the resting E0 state in frozen medium at a temperature below the melting temperature; relaxation is monitored by periodically cooling the sample to cryogenic temperature for EPR analysis. During -50 °C cryoannealing of EG prepared under turnover conditions in which the concentrations of N2 and H2 ([H2], [N2]) are systematically and independently varied, the rate of decay of EG is accelerated by increasing [H2] and slowed by increasing [N2] in the frozen reaction mixture; correspondingly, the accumulation of EG is greater with low [H2] and/or high [N2]. The influence of these diatomics identifies EG as the key catalytic intermediate formed by reductive elimination of H2 with concomitant N2 binding, a state in which FeMo-co binds the components of diazene (an N-N moiety, perhaps N2 and two [e(-)/H(+)] or diazene itself). This identification combines with an earlier study to demonstrate that nitrogenase is activated for N2 binding and reduction through the thermodynamically and kinetically reversible reductive-elimination/oxidative-addition exchange of N2 and H2, with an implied limiting stoichiometry of eight electrons/protons for the reduction of N2 to two NH3.
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Affiliation(s)
- Dmitriy Lukoyanov
- ‡Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Zhi-Yong Yang
- †Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Nimesh Khadka
- †Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dennis R Dean
- §Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lance C Seefeldt
- †Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Brian M Hoffman
- ‡Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
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Monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:1-61. [PMID: 26002730 DOI: 10.1007/978-3-319-16009-2_1] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review examines the monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 (CYP) enzymes in bacterial, archaeal and mammalian systems. CYP enzymes catalyze monooxygenation reactions by inserting one oxygen atom from O2 into an enormous number and variety of substrates. The catalytic versatility of CYP stems from its ability to functionalize unactivated carbon-hydrogen (C-H) bonds of substrates through monooxygenation. The oxidative prowess of CYP in catalyzing monooxygenation reactions is attributed primarily to a porphyrin π radical ferryl intermediate known as Compound I (CpdI) (Por•+FeIV=O), or its ferryl radical resonance form (FeIV-O•). CYP-mediated hydroxylations occur via a consensus H atom abstraction/oxygen rebound mechanism involving an initial abstraction by CpdI of a H atom from the substrate, generating a highly-reactive protonated Compound II (CpdII) intermediate (FeIV-OH) and a carbon-centered alkyl radical that rebounds onto the ferryl hydroxyl moiety to yield the hydroxylated substrate. CYP enzymes utilize hydroperoxides, peracids, perborate, percarbonate, periodate, chlorite, iodosobenzene and N-oxides as surrogate oxygen atom donors to oxygenate substrates via the shunt pathway in the absence of NAD(P)H/O2 and reduction-oxidation (redox) auxiliary proteins. It has been difficult to isolate the historically elusive CpdI intermediate in the native NAD(P)H/O2-supported monooxygenase pathway and to determine its precise electronic structure and kinetic and physicochemical properties because of its high reactivity, unstable nature (t½~2 ms) and short life cycle, prompting suggestions for participation in monooxygenation reactions of alternative CYP iron-oxygen intermediates such as the ferric-peroxo anion species (FeIII-OO-), ferric-hydroperoxo species (FeIII-OOH) and FeIII-(H2O2) complex.
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Salvadori E, Fung MW, Hoffmann M, Anderson HL, Kay CWM. Exploiting the Symmetry of the Resonator Mode to Enhance PELDOR Sensitivity. APPLIED MAGNETIC RESONANCE 2014; 46:359-368. [PMID: 25798030 PMCID: PMC4359710 DOI: 10.1007/s00723-014-0621-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/29/2014] [Indexed: 06/04/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) spectroscopy using microwaves at two frequencies can be employed to measure distances between pairs of paramagnets separated by up to 10 nm. The method, combined with site-directed mutagenesis, has become increasingly popular in structural biology for both its selectivity and capability of providing information not accessible through more standard methods such as nuclear magnetic resonance and X-ray crystallography. Despite these advantages, EPR distance measurements suffer from poor sensitivity. One contributing factor is technical: since 65 MHz typically separates the pump and detection frequencies, they cannot both be located at the center of the pseudo-Lorentzian microwave resonance of a single-mode resonator. To maximize the inversion efficiency, the pump pulse is usually placed at the center of the resonance, while the observer frequency is placed in the wing, with consequent reduction in sensitivity. Here, we consider an alternative configuration: by spacing pump and observer frequencies symmetrically with respect to the microwave resonance and by increasing the quality factor, valuable improvement in the signal-to-noise ratio can be obtained.
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Affiliation(s)
- Enrico Salvadori
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH UK
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Mei Wai Fung
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Markus Hoffmann
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA UK
| | - Harry L. Anderson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA UK
| | - Christopher W. M. Kay
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH UK
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
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Davydov R, Labby KJ, Chobot SE, Lukoyanov DA, Crane BR, Silverman RB, Hoffman BM. Enzymatic and cryoreduction EPR studies of the hydroxylation of methylated N(ω)-hydroxy-L-arginine analogues by nitric oxide synthase from Geobacillus stearothermophilus. Biochemistry 2014; 53:6511-9. [PMID: 25251261 PMCID: PMC4204881 DOI: 10.1021/bi500485z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Nitric
oxide synthase (NOS) catalyzes the conversion of l-arginine
to l-citrulline and NO in a two-step process involving the
intermediate Nω-hydroxy-l-arginine (NHA). It was shown that Cpd I is the oxygenating species
for l-arginine; the hydroperoxo ferric intermediate is the
reactive intermediate with NHA. Methylation of the Nω-OH and Nω-H of NHA significantly inhibits the conversion
of NHA into NO and l-citrulline by mammalian NOS. Kinetic
studies now show that Nω-methylation of NHA has a
qualitatively similar effect on H2O2-dependent
catalysis by bacterial gsNOS. To elucidate the effect of methylating
Nω-hydroxy l-arginine on the properties
and reactivity of the one-electron-reduced oxy-heme center of NOS,
we have applied cryoreduction/annealing/EPR/ENDOR techniques. Measurements
of solvent kinetic isotope effects during 160 K cryoannealing cryoreduced
oxy-gsNOS/NHA confirm the hydroperoxo ferric intermediate as the catalytically
active species of step two. Product analysis for cryoreduced samples
with methylated NHA’s, NHMA, NMOA, and NMMA, annealed to 273
K, show a correlation of yields of l-citrulline with the
intensity of the g 2.26 EPR signal of the peroxo ferric
species trapped at 77 K, which converts to the reactive hydroperoxo
ferric state. There is also a correlation between the yield of l-citrulline in these experiments and kobs for the H2O2-dependent conversion
of the substrates by gsNOS. Correspondingly, no detectable amount
of cyanoornithine, formed when Cpd I is the reactive species, was
found in the samples. Methylation of the NHA guanidinium Nω-OH and Nω-H inhibits the second NO-producing reaction
by favoring protonation of the ferric-peroxo to form unreactive conformers
of the ferric-hydroperoxo state. It is suggested that this is caused
by modification of the distal-pocket hydrogen-bonding network of oxy
gsNOS and introduction of an ordered water molecule that facilitates
delivery of the proton(s) to the one-electron-reduced oxy-heme moiety.
These results illustrate how variations in the properties of the substrate
can modulate the reactivity of a monooxygenase.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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Davydov R, Laryukhin M, Ledbetter-Rogers A, Sono M, Dawson JH, Hoffman BM. Electron paramagnetic resonance and electron-nuclear double resonance studies of the reactions of cryogenerated hydroperoxoferric-hemoprotein intermediates. Biochemistry 2014; 53:4894-903. [PMID: 25046203 PMCID: PMC4144713 DOI: 10.1021/bi500296d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The fleeting ferric peroxo and hydroperoxo
intermediates of dioxygen
activation by hemoproteins can be readily trapped and characterized
during cryoradiolytic reduction of ferrous hemoprotein–O2 complexes at 77 K. Previous cryoannealing studies suggested
that the relaxation of cryogenerated hydroperoxoferric intermediates
of myoglobin (Mb), hemoglobin, and horseradish peroxidase (HRP), either
trapped directly at 77 K or generated by cryoannealing of a trapped
peroxo-ferric state, proceeds through dissociation of bound H2O2 and formation of the ferric heme without formation
of the ferryl porphyrin π-cation radical intermediate, compound
I (Cpd I). Herein we have reinvestigated the mechanism of decays of
the cryogenerated hydroperoxyferric intermediates of α- and
β-chains of human hemoglobin, HRP, and chloroperoxidase (CPO).
The latter two proteins are well-known to form spectroscopically detectable
quasistable Cpds I. Peroxoferric intermediates are trapped during
77 K cryoreduction of oxy Mb, α-chains, and β-chains of
human hemoglobin and CPO. They convert into hydroperoxoferric intermediates
during annealing at temperatures above 160 K. The hydroperoxoferric
intermediate of HRP is trapped directly at 77 K. All studied hydroperoxoferric
intermediates decay with measurable rates at temperatures above 170
K with appreciable solvent kinetic isotope effects. The hydroperoxoferric
intermediate of β-chains converts to the S =
3/2 Cpd I, which in turn decays to an electron paramagnetic resonance
(EPR)-silent product at temperature above 220 K. For all the other
hemoproteins studied, cryoannealing of the hydroperoxo intermediate
directly yields an EPR-silent majority product. In each case, a second
follow-up 77 K γ-irradiation of the annealed samples yields
low-spin EPR signals characteristic of cryoreduced ferrylheme (compound
II, Cpd II). This indicates that in general the hydroperoxoferric
intermediates relax to Cpd I during cryoanealing at low temperatures,
but when this state is not captured by reaction with a bound substrate,
it is reduced to Cpd II by redox-active products of radiolysis.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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Munro AW, Girvan HM, Mason AE, Dunford AJ, McLean KJ. What makes a P450 tick? Trends Biochem Sci 2013; 38:140-50. [DOI: 10.1016/j.tibs.2012.11.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/15/2012] [Accepted: 11/21/2012] [Indexed: 12/31/2022]
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Davydov R, Dawson JH, Perera R, Hoffman BM. The use of deuterated camphor as a substrate in (1)H ENDOR studies of hydroxylation by cryoreduced oxy P450cam provides new evidence of the involvement of compound I. Biochemistry 2013; 52:667-71. [PMID: 23215047 DOI: 10.1021/bi301527c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Electron paramagnetic resonance and (1)H electron nuclear double resonance (ENDOR) spectroscopies have been used to analyze intermediate states formed during the hydroxylation of (1R)-camphor (H(2)-camphor) and (1R)-5,5-dideuterocamphor (D(2)-camphor) as induced by cryoreduction (77 K) and annealing of the ternary ferrous cytochrome P450cam-O(2)-substrate complex. Hydroxylation of H(2)-camphor produced a primary product state in which 5-exo-hydroxycamphor is coordinated with Fe(III). ENDOR spectra contained signals derived from two protons [Fe(III)-bound C5-OH(exo) and C5-H(endo)] from camphor. When D(2)-camphor was hydroxylated under the same condition in H(2)O or D(2)O buffer, both ENDOR H(exo) and H(endo) signals are absent. For D(2)-camphor in H(2)O buffer, H/D exchange causes the C5-OH(exo) signal to reappear during relaxation upon annealing to 230 K; for H(2)-camphor in D(2)O, the magnitude of the C5-OH(exo) signal decreases via H/D exchange. These observations clearly show that Compound I is the reactive species in the hydroxylation of camphor in P450cam.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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Davydov R, Gilep AA, Strushkevich NV, Usanov SA, Hoffman BM. Compound I is the reactive intermediate in the first monooxygenation step during conversion of cholesterol to pregnenolone by cytochrome P450scc: EPR/ENDOR/cryoreduction/annealing studies. J Am Chem Soc 2012; 134:17149-56. [PMID: 23039857 DOI: 10.1021/ja3067226] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome P450scc (CYP11A1) catalyzes conversion of cholesterol (CH) to pregnenolone, the precursor to all steroid hormones. This process proceeds via three sequential monooxygenation reactions: two stereospecific hydroxylations with formation first of 22R-hydroxycholesterol (22-HC) and then 20α,22R-dihydroxycholesterol (20,22-DHC), followed by C20-C22 bond cleavage. Herein we have employed EPR and ENDOR spectroscopy to characterize the intermediates in the first hydroxylation step by 77 K radiolytic one-electron cryoreduction and subsequent annealing of the ternary oxy-cytochrome P450scc-cholesterol complex. This approach is fully validated by the demonstration that the cryoreduced ternary complex of oxy-P450scc-CH is catalytically competent and hydroxylates cholesterol to form 22-HC with no detectable formation of 20-HC, just as occurs under physiological conditions. Cryoreduction of the ternary complex trapped at 77 K produces predominantly the hydroperoxy-ferriheme P450scc intermediate, along with a minor fraction of peroxo-ferriheme intermediate that converts into a new hydroperoxo-ferriheme species at 145 K. This behavior reveals that the distal pocket of the parent oxy-P450scc-cholesterol complex exhibits an efficient proton delivery network, with an ordered water molecule H-bonded to the distal oxygen of the dioxygen ligand. During annealing of the hydroperoxy-ferric P450scc intermediates at 185 K, they convert to the primary product complex in which CH has been converted to 22-HC. In this process, the hydroperoxy-ferric intermediate decays with a large solvent kinetic isotope effect, as expected when proton delivery to the terminal O leads to formation of Compound I (Cpd I). (1)H ENDOR measurements of the primary product formed in deuterated solvent show that the heme Fe(III) is coordinated to the 22R-O(1)H of 22-HC, where the (1)H is derived from substrate and exchanges to D after annealing at higher temperatures. These observations establish that Cpd I is the agent that hydroxylates CH, rather than the hydroperoxy-ferric heme.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
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Shanmugam M, Xue G, Que L, Hoffman BM. 1H-ENDOR evidence for a hydrogen-bonding interaction that modulates the reactivity of a nonheme Fe(IV)═O unit. Inorg Chem 2012; 51:10080-2. [PMID: 22984805 DOI: 10.1021/ic3015783] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report that a novel use of 35 GHz (1)H-ENDOR spectroscopy establishes the presence in 1 of an Fe(IV)═O···H-O-Fe(III) hydrogen bond predicted by density functional theory computations to generate a six-membered-ring core for 1. The hydrogen bond rationalizes the difference in the C-H bond cleavage reactivity between 1 and 4(OCH(3)) (where a CH(3)O group has replaced the HO on the Fe(III) site). This result substantiates the seemingly paradoxical conclusion that the nonheme Fe(IV)═O unit of 1 not only has the electrophilic character required for H-atom abstraction but also retains sufficient nucleophilic character to accept a hydrogen bond from the Fe(III)-OH unit.
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50
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Bernad S, Brunel A, Dorlet P, Sicard-Roselli C, Santolini J. A novel cryo-reduction method to investigate the molecular mechanism of nitric oxide synthases. J Phys Chem B 2012; 116:5595-603. [PMID: 22530945 DOI: 10.1021/jp300749b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitric oxide synthases (NOSs) are hemoproteins responsible for the biosynthesis of NO in mammals. They catalyze two successive oxidation reactions. The mechanism of oxygen activation is based on the transfer of two electrons and two protons. Despite structural analogies with cytochromes P450, the molecular mechanism of NOS remains yet to be elucidated. Because of extremely high reaction rates, conventional kinetics methods failed to trap and characterize the major reaction intermediates. Cryo-reduction methods offer a possibility to circumvent this technological lock, by triggering oxygen activation at cryogenic temperatures by using water radiolysis. However, this method is not adapted to the NOS mechanism because of the high instability of the initial Fe(II)O2 complex (extremely fast autoxidation and/or reaction with the cofactor H4B). This imposed a protocol with a stable Fe(II)O2 complex (observed only for one NOS-like protein) and that excludes any redox role for H4B. A relevant approach to the NOS mechanism would use H4B to provide the (second) electron involved in oxygen activation; water radiolysis would thus provide the first electron (heme reduction). In this context, we report here an investigation of the first electron transfer by this alternative approach, i.e., the reduction of native NOS by water radiolysis. We combined EPR and resonance Raman spectroscopies to analyze NOS reduction for a combination of different substrates, cofactor, and oxygen concentrations, and for different NOS isoforms. Our results show that cryo-reduction of native NOS is achieved for all conditions that are relevant to the investigation of the NOS mechanism.
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Affiliation(s)
- Sophie Bernad
- Laboratoire de Chimie Physique, CNRS UMR 8000, Univ Paris-Sud, 91405 Orsay Cedex, France
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