1
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Amaya JA, Manley OM, Bian JC, Rutland CD, Leschinsky N, Ratigan SC, Makris TM. Enhancing ferryl accumulation in H 2O 2-dependent cytochrome P450s. J Inorg Biochem 2024; 252:112458. [PMID: 38141432 DOI: 10.1016/j.jinorgbio.2023.112458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 12/25/2023]
Abstract
A facile strategy is presented to enhance the accumulation of ferryl (iron(IV)-oxo) species in H2O2 dependent cytochrome P450s (CYPs) of the CYP152 family. We report the characterization of a highly chemoselective CYP decarboxylase from Staphylococcus aureus (OleTSA) that is soluble at high concentrations. Examination of OleTSA Compound I (CpdI) accumulation with a variety of fatty acid substrates reveals a dependence on resting spin-state equilibrium. Alteration of this equilibrium through targeted mutagenesis of the proximal pocket favors the high-spin form, and as a result, enhances Cpd-I accumulation to nearly stoichiometric yields.
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Affiliation(s)
- Jose A Amaya
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Olivia M Manley
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America; Department of Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Julia C Bian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Cooper D Rutland
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Nicholas Leschinsky
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Steven C Ratigan
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America; Department of Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC 27695, United States of America; Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America.
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2
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Schmitz F, Röder A, Hoffrogge M, Urlacher VB, Koschorreck K. Agar plate-based activity assay for easy and fast screening of recombinant Pichia pastoris expressing unspecific peroxygenases. Biotechnol J 2024; 19:e2300421. [PMID: 38044796 DOI: 10.1002/biot.202300421] [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: 08/18/2023] [Revised: 11/14/2023] [Accepted: 11/30/2023] [Indexed: 12/05/2023]
Abstract
Unspecific peroxygenases (UPOs) are promising biocatalysts that catalyze oxyfunctionalization reactions without the need for costly cofactors. Pichia pastoris (reclassified as Komagataella phaffii) is considered an attractive host for heterologous expression of UPOs. However, integration of UPO-expression cassettes into the genome via a single cross-over yields recombinant Pichia transformants with different UPO gene copy numbers resulting in different expression levels. Selection of the most productive Pichia transformants by a commonly used screening in liquid medium in 96-well plates is laborious and lasts up to 5 days. In this work, we developed a simple two-step agar plate-based assay to screen P. pastoris transformants for UPO activity with less effort, within shorter time, and without automated screening devices. After cell growth and protein expression on agar plates supplemented with methanol and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), an additional top agar layer supplemented with ABTS and peroxide is added. UPO activity is visualized within 15 min by formation of green zones around UPO-secreting P. pastoris transformants. The assay was validated with two UPOs, AbrUPO from Aspergillus brasiliensis and evolved PaDa-I from Agrocybe aegerita. The assay results were confirmed in a quantitative 96-deep well plate screening in liquid medium.
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Affiliation(s)
- Fabian Schmitz
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
| | - Annika Röder
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
| | - Maike Hoffrogge
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
| | - Katja Koschorreck
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
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3
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Hirao H, Zhang E. Bidirectional Charge Transfer at the Heme Iron in Reversible and Quasi-irreversible Cytochrome P450 Inhibition. Inorg Chem 2023; 62:16599-16608. [PMID: 37737847 DOI: 10.1021/acs.inorgchem.3c02541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
The coordination bonding between inhibitor ligands and heme iron plays a critical role in disrupting the essential catalytic functions of cytochrome P450 enzymes (P450s). Despite its intrinsic importance and consequential implications for human health, our current understanding of coordination bonding in P450 inhibition remains limited. To address this knowledge gap, we conducted a systematic theoretical analysis of the complexes between a ferric or a ferrous heme model and representative inhibitor ligands. Specifically, we evaluated the charge-transfer (CT) effect within these complexes by employing a series of theoretical methods based on density functional theory (DFT). Through a comprehensive analysis, we unveiled the relative significance of ligand-to-heme forward CT in the ferric and ferrous complexes of reversible inhibitors. In contrast, backward CT dominates over forward CT in the ferrous heme complexes of quasi-irreversible inhibitors. Further analysis using the compact frontier orbital method underscores the elevated electron-accepting abilities of quasi-irreversible inhibitors for π backdonation, which greatly amplifies their binding affinity for the ferrous heme. This study sheds light on the intricate mechanisms underlying P450 inhibition and provides valuable insights for future inhibitor design and development.
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Affiliation(s)
- Hajime Hirao
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong 518172, P. R. China
| | - Enhua Zhang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong 518172, P. R. China
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4
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Liu S, Xia S, Yue D, Sun H, Hirao H. The Bonding Nature of Fe–CO Complexes in Heme Proteins. Inorg Chem 2022; 61:17494-17504. [DOI: 10.1021/acs.inorgchem.2c02387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Shuyang Liu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
| | - Songyan Xia
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
| | - Dongxiao Yue
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
| | - Haoran Sun
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
| | - Hajime Hirao
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
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5
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Metabolism of 8-aminoquinoline (8AQ) primaquine via aromatic hydroxylation step mediated by cytochrome P450 enzyme using density functional theory. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2021.122154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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6
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Mukherjee M, Dey A. Rejigging Electron and Proton Transfer to Transition between Dioxygenase, Monooxygenase, Peroxygenase, and Oxygen Reduction Activity: Insights from Bioinspired Constructs of Heme Enzymes. JACS AU 2021; 1:1296-1311. [PMID: 34604840 PMCID: PMC8479764 DOI: 10.1021/jacsau.1c00100] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 05/10/2023]
Abstract
Nature has employed heme proteins to execute a diverse set of vital life processes. Years of research have been devoted to understanding the factors which bias these heme enzymes, with all having a heme cofactor, toward distinct catalytic activity. Among them, axial ligation, distal super structure, and substrate binding pockets are few very vividly recognized ones. Detailed mechanistic investigation of these heme enzymes suggested that several of these enzymes, while functionally divergent, use similar intermediates. Furthermore, the formation and decay of these intermediates depend on proton and electron transfer processes in the enzyme active site. Over the past decade, work in this group, using in situ surface enhanced resonance Raman spectroscopy of synthetic and biosynthetic analogues of heme enzymes, a general idea of how proton and electron transfer rates relate to the lifetime of different O2 derived intermediates has been developed. These findings suggest that the enzymatic activities of all these heme enzymes can be integrated into one general cycle which can be branched out to different catalytic pathways by regulating the lifetime and population of each of these intermediates. This regulation can further be achieved by tuning the electron and proton transfer steps. By strategically populating one of these intermediates during oxygen reduction, one can navigate through different catalytic processes to a desired direction by altering proton and electron transfer steps.
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Affiliation(s)
- Manjistha Mukherjee
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India, 700032
| | - Abhishek Dey
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India, 700032
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7
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Mukherjee G, Satpathy JK, Bagha UK, Mubarak MQE, Sastri CV, de Visser SP. Inspiration from Nature: Influence of Engineered Ligand Scaffolds and Auxiliary Factors on the Reactivity of Biomimetic Oxidants. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01993] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Jagnyesh K. Satpathy
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Umesh K. Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Fakulti Sains dan Teknologi, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan Malaysia
| | - Chivukula V. Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Sam P. de Visser
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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8
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Mammoser CC, Ramos S, Thielges MC. Active Site Hydrogen Bonding Induced in Cytochrome P450cam by Effector Putidaredoxin. Biochemistry 2021; 60:1699-1707. [PMID: 34006086 DOI: 10.1021/acs.biochem.1c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome P450s are diverse and powerful catalysts that can activate molecular oxygen to oxidize a wide variety of substrates. Catalysis relies on effective uptake of two electrons and two protons. For cytochrome P450cam, an archetypal member of the superfamily, the second electron must be supplied by the redox partner putidaredoxin (Pdx). Pdx also plays an effector role beyond electron transfer, but after decades the mechanism remains under investigation. We applied infrared spectroscopy to heme-ligated CN- to examine the influence of Pdx binding. The results indicate that Pdx induces the population of a conformation wherein the CN- ligand forms a strong hydrogen bond to a solvent water molecule, experimentally corroborating the formation of a proposed proton delivery network. Further, characterization of T252A P450cam implicates the side chain of Thr252 in regulating the population equilibrium of hydrogen-bonded states within the P450cam/Pdx complex, which could underlie its role in directing activated oxygen toward product formation and preventing reaction uncoupling through peroxide release.
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Affiliation(s)
- Claire C Mammoser
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Sashary Ramos
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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9
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Yang Y, Arnold FH. Navigating the Unnatural Reaction Space: Directed Evolution of Heme Proteins for Selective Carbene and Nitrene Transfer. Acc Chem Res 2021; 54:1209-1225. [PMID: 33491448 PMCID: PMC7931446 DOI: 10.1021/acs.accounts.0c00591] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Despite the astonishing diversity of naturally
occurring biocatalytic
processes, enzymes do not catalyze many of the transformations favored
by synthetic chemists. Either nature does not care about the specific
products, or if she does, she has adopted a different synthetic strategy.
In many cases, the appropriate reagents used by synthetic chemists
are not readily accessible to biological systems. Here, we discuss
our efforts to expand the catalytic repertoire of enzymes to encompass
powerful reactions previously known only in small-molecule catalysis:
formation and transfer of reactive carbene and nitrene intermediates
leading to a broad range of products, including products with bonds
not known in biology. In light of the structural similarity of iron
carbene (Fe=C(R1)(R2)) and iron nitrene
(Fe=NR) to the iron oxo (Fe=O) intermediate involved
in cytochrome P450-catalyzed oxidation, we have used synthetic carbene
and nitrene precursors that biological systems have not encountered
and repurposed P450s to catalyze reactions that are not known in the
natural world. The resulting protein catalysts are fully genetically
encoded and function in intact microbial cells or cell-free lysates,
where their performance can be improved and optimized by directed
evolution. By leveraging the catalytic promiscuity of P450 enzymes,
we evolved a range of carbene and nitrene transferases exhibiting
excellent activity toward these new-to-nature reactions. Since our
initial report in 2012, a number of other heme proteins including
myoglobins, protoglobins, and cytochromes c have
also been found and engineered to promote unnatural carbene and nitrene
transfer. Due to the altered active-site environments, these heme
proteins often displayed complementary activities and selectivities
to P450s. Using wild-type and engineered heme proteins, we and
others have
described a range of selective carbene transfer reactions, including
cyclopropanation, cyclopropenation, Si–H insertion, B–H
insertion, and C–H insertion. Similarly, a variety of asymmetric
nitrene transfer processes including aziridination, sulfide imidation,
C–H amidation, and, most recently, C–H amination have
been demonstrated. The scopes of these biocatalytic carbene and nitrene
transfer reactions are often complementary to the state-of-the-art
processes based on small-molecule transition-metal catalysts, making
engineered biocatalysts a valuable addition to the synthetic chemist’s
toolbox. Moreover, enabled by the exquisite regio- and stereocontrol
imposed by the enzyme catalyst, this biocatalytic platform provides
an exciting opportunity to address challenging problems in modern
synthetic chemistry and selective catalysis, including ones that have
eluded synthetic chemists for decades.
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Affiliation(s)
- Yang Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 210-41, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 210-41, 1200 East California Boulevard, Pasadena, California 91125, United States
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10
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Hunt AP, Samanta S, Dent MR, Milbauer MW, Burstyn JN, Lehnert N. Model Complexes Elucidate the Role of the Proximal Hydrogen-Bonding Network in Cytochrome P450s. Inorg Chem 2020; 59:8034-8043. [DOI: 10.1021/acs.inorgchem.0c00245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew P. Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Subhra Samanta
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Matthew R. Dent
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Michael W. Milbauer
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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11
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Mayers JM, Larsen RW. Vibrational spectroscopy of Fe tetrakis(4-sulphonatophenyl) porphyrin encapsulated within the metal organic framework HKUST-1. INORG CHEM COMMUN 2019. [DOI: 10.1016/j.inoche.2019.107457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Ramos S, Basom EJ, Thielges MC. Conformational Change Induced by Putidaredoxin Binding to Ferrous CO-ligated Cytochrome P450cam Characterized by 2D IR Spectroscopy. Front Mol Biosci 2018; 5:94. [PMID: 30483514 PMCID: PMC6243089 DOI: 10.3389/fmolb.2018.00094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/22/2018] [Indexed: 11/16/2022] Open
Abstract
The importance of conformational dynamics to protein function is now well-appreciated. An outstanding question is whether they are involved in the effector role played by putidaredoxin (Pdx) in its reduction of the O2 complex of cytochrome P450cam (P450cam), an archetypical member of the cytochrome P450 superfamily. Recent studies have reported that binding of Pdx induces a conformational change from a closed to an open state of ferric P450cam, but a similar conformational change does not appear to occur for the ferrous, CO-ligated enzyme. To better understand the effector role of Pdx when binding the ferrous, CO-ligated P450cam, we applied 2D IR spectroscopy to compare the conformations and dynamics of the wild-type (wt) enzyme in the absence and presence of Pdx, as well as of L358P P450cam (L358P), which has served as a putative model for the Pdx complex. The CO vibrations of the Pdx complex and L358P report population of two conformational states in which the CO experiences distinct environments. The dynamics among the CO frequencies indicate that the energy landscape of substates within one conformation are reflective of the closed state of P450cam, and for the other conformation, differ from the free wt enzyme, but are equivalent between the Pdx complex and L358P. The two states co-populated by the Pdx complex are postulated to reflect a loosely bound encounter complex and a more tightly bound state, as is commonly observed for the dynamic complexes of redox partners. Significantly, this study shows that the binding of Pdx to ferrous, CO-ligated P450cam does perturb the conformational ensemble in a way that might underlie the effector role of Pdx.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Edward J Basom
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, IN, United States
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13
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Chatfield DC, Morozov AN. Proximal Pocket Controls Alkene Oxidation Selectivity of Cytochrome P450 and Chloroperoxidase toward Small, Nonpolar Substrates. J Phys Chem B 2018; 122:7828-7838. [PMID: 30052045 DOI: 10.1021/acs.jpcb.8b04279] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This paper examines the influence of the proximal pockets of cytochrome P450CAM and chloroperoxidase (CPO) on the relative favorability of catalytic epoxidation and allylic hydroxylation of olefins, a type of alkene oxidation selectivity. The study employs quantum mechanical models of the active site to isolate the proximal pocket's influence on the barrier for the selectivity-determining step for each reaction, using cyclohexene and cis-β-methylstyrene as substrates. The proximal pocket is found to preference epoxidation by 2-5 kcal/mol, the largest value being for CPO, converting the active heme-thiolate moiety from being intrinsically hydroxylation-selective to being intrinsically epoxidation-selective. This theoretical study, the first to correctly predict these enzymes' preference for epoxidation of allylic substrates, strongly suggests that the proximal pocket is the key determinant of alkene oxidation selectivity. The selectivity for epoxidation can be rationalized in terms of the proximal pocket's modulation of the thiolate's electron "push" and consequent influence on the heme redox potential and the basicity of the trans ligand.
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Affiliation(s)
- David C Chatfield
- Department of Chemistry and Biochemistry , Florida International University , 11200 8th Street , Miami , Florida 33199 , United States
| | - Alexander N Morozov
- Department of Chemistry and Biochemistry , Florida International University , 11200 8th Street , Miami , Florida 33199 , United States
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14
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Enzymatic Activation of the Emerging Drug Resveratrol. Appl Biochem Biotechnol 2017; 185:248-256. [PMID: 29124656 DOI: 10.1007/s12010-017-2645-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
Abstract
The plant originated stilbene "resveratrol" (3,4',5-trans-trihydroxystilbene) is well known for its diverse health benefits including anti-tumor, anti-inflammatory, anti-microbial, and anti-oxidant properties. Besides a significant amount of reports on different aspects of its application as prodrug in the last 50 years, still, a strategy leading to the production of the active drug is missing. The aim of this work was to evaluate the enzymatic activation of prodrug resveratrol to the effective drug piceatannol, without engaging expensive cofactors. Five different heme proteins were analyzed for the transformation of resveratrol. Kinetic parameters of resveratrol transformation and analysis of the transformed products were conducted through HPLC and GC-MS. Effect of pH and organic solvent on the transformation process had also been evaluated. Among all tested heme proteins, only a variant of cytochrome P450BM3 from Bacillus megaterium (CYPBM3F87A) was found suitable for piceatannol production. The most suitable pH for the reaction conditions was 8.5, while organic solvents did not show any effect on transformation. For resveratrol transformation, the turnover rate (k cat) was 21.7 (± 0.6) min-1, the affinity constant (K M) showed a value of 55.7 (± 16.7) μM for a catalytic efficiency (k cat/K M) of 389 min-1 mM-1. GC-MS analysis showed that the only product from resveratrol transformation by cytochrome P450BM3 is the biologically active piceatannol. The enzymatic transformation of resveratrol, an emerging compound with medical interest, to active product piceatannol by a variant of cytochrome P450BM3 in the absence of expensive NADPH cofactor is demonstrated. This enzymatic process is economically attractive and can be scaled up to cover the increasing medical demand for piceatannol.
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15
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Batabyal D, Richards LS, Poulos TL. Effect of Redox Partner Binding on Cytochrome P450 Conformational Dynamics. J Am Chem Soc 2017; 139:13193-13199. [PMID: 28823160 DOI: 10.1021/jacs.7b07656] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Previous crystal structures of cytochrome P450cam complexed with its redox partner, putidaredoxin (Pdx), shows that P450cam adopts the open conformation. It has been hypothesized that the Pdx-induced shift toward the open state frees the essential Asp251 from salt bridges with Arg186 and Lys178 so that Asp251 can participate in a proton relay network required for O2 activation. This in part explains why P450cam has such a strict requirement for Pdx. One problem with this view is that looser substrate-protein interactions in the open state may not be compatible with the observed regio- and stereoselective hydroxylation. In the present study, molecular dynamics simulations show that Pdx binding favors a conformation that stabilizes the active site and decreases camphor mobility yet retains a partially open conformation compatible with the required proton relay network. The R186A mutant which frees Asp251 in the absence of Pdx retains good enzyme activity, and the crystal structure shows that product, 5-exo-hydroxycamphor, is bound. This indicates that rupture of the Asp251-Arg186 relaxes selectivity with respect to source of electrons and enables X-ray generated reducing equivalents to support substrate hydroxylation. These combined computational and experimental results are consistent with the proposed role of Pdx in assisting the release of Asp251 from ion pairs so that it can participate in proton-coupled electron transfer.
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Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Logan S Richards
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
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16
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Identification of productive and futile encounters in an electron transfer protein complex. Proc Natl Acad Sci U S A 2017; 114:E1840-E1847. [PMID: 28223532 DOI: 10.1073/pnas.1616813114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Well-defined, stereospecific states in protein complexes are often in exchange with an ensemble of more dynamic orientations: the encounter states. The structure of the stereospecific complex between cytochrome P450cam and putidaredoxin was solved recently by X-ray diffraction as well as paramagnetic NMR spectroscopy. Other than the stereospecific complex, the NMR data clearly show the presence of additional states in the complex in solution. In these encounter states, populated for a small percentage of the time, putidaredoxin assumes multiple orientations and samples a large part of the surface of cytochrome P450cam. To characterize the nature of the encounter states, an extensive paramagnetic NMR dataset has been analyzed using the Maximum Occurrence of Regions methodology. The analysis reveals the location and maximal spatial extent of the additional states needed to fully explain the NMR data. Under the assumption of sparsity of the size of the conformational ensemble, several minor states can be located quite precisely. The distribution of these minor states correlates with the electrostatic potential map around cytochrome P450cam. Whereas some minor states are on isolated positively charged patches, others are connected to the stereospecific site via positively charged paths. The existence of electrostatically favorable pathways between the stereospecific interaction site and the different minor states or lack thereof suggests a means to discriminate between productive and futile encounter states.
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17
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Morozov AN, Chatfield DC. How the Proximal Pocket May Influence the Enantiospecificities of Chloroperoxidase-Catalyzed Epoxidations of Olefins. Int J Mol Sci 2016; 17:E1297. [PMID: 27517911 PMCID: PMC5000694 DOI: 10.3390/ijms17081297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/28/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022] Open
Abstract
Chloroperoxidase-catalyzed enantiospecific epoxidations of olefins are of significant biotechnological interest. Typical enantiomeric excesses are in the range of 66%-97% and translate into free energy differences on the order of 1 kcal/mol. These differences are generally attributed to the effect of the distal pocket. In this paper, we show that the influence of the proximal pocket on the electron transfer mechanism in the rate-limiting event may be just as significant for a quantitatively accurate account of the experimentally-measured enantiospecificities.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
| | - David C Chatfield
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
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18
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Cook D, Finnigan J, Cook K, Black G, Charnock S. Cytochromes P450. INSIGHTS INTO ENZYME MECHANISMS AND FUNCTIONS FROM EXPERIMENTAL AND COMPUTATIONAL METHODS 2016; 105:105-26. [DOI: 10.1016/bs.apcsb.2016.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Morozov AN, Pardillo AD, Chatfield DC. Chloroperoxidase-Catalyzed Epoxidation of Cis-β-Methylstyrene: NH-S Hydrogen Bonds and Proximal Helix Dipole Change the Catalytic Mechanism and Significantly Lower the Reaction Barrier. J Phys Chem B 2015; 119:14350-63. [PMID: 26452587 DOI: 10.1021/acs.jpcb.5b06731] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH-S) is a conserved feature of heme-thiolate enzymes such as chloroperoxidase (CPO) and cytochrome P450 (P450). In CPO, the effect of NH-S bonds is amplified by the dipole moment of the proximal helix. Our gas-phase DFT studies show that the proximal pocket effect significantly enhances CPO's reactivity toward the epoxidation of olefinic substrates. Comparison of models with and without proximal pocket residues shows that with them, the barrier for Cβ-O bond formation is lowered by about ∼4.6 kcal/mol, while Cα-O-Cβ ring closure becomes barrierless. The dipole moment of the proximal helix was estimated to contribute 1/3 of the decrease, while the rest is attributed to the effect of NH-S bonds. The decrease of the reaction barrier correlates with increased electron density transfer to residues of the proximal pocket. The effect is most pronounced on the doublet spin surface and involves a change in the electron-transfer mechanism. A full enzyme QMMM study on the doublet spin surface gives about the same barrier as the gas-phase DFT study. The free-energy barrier was estimated to be in agreement with the experimental results for the CPO-catalyzed epoxidation of styrene.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - Armando D Pardillo
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - David C Chatfield
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
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20
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Vandemeulebroucke A, Aldag C, Stiebritz MT, Reiher M, Hilvert D. Kinetic Consequences of Introducing a Proximal Selenocysteine Ligand into Cytochrome P450cam. Biochemistry 2015; 54:6692-703. [DOI: 10.1021/acs.biochem.5b00939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- An Vandemeulebroucke
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Caroline Aldag
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin T. Stiebritz
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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21
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Abstract
Nitric oxide synthases (NOSs) are haem-thiolate enzymes that catalyse the conversion of L-arginine (L-Arg) into NO and citrulline. Inducible NOS (iNOS) is responsible for delivery of NO in response to stressors during inflammation. The catalytic performance of iNOS is proposed to rely mainly on the haem midpoint potential and the ability of the substrate L-Arg to provide a hydrogen bond for oxygen activation (O-O scission). We present a study of native iNOS compared with iNOS-mesohaem, and investigate the formation of a low-spin ferric haem-aquo or -hydroxo species (P) in iNOS mutant W188H substituted with mesohaem. iNOS-mesohaem and W188H-mesohaem were stable and dimeric, and presented substrate-binding affinities comparable to those of their native counterparts. Single turnover reactions catalysed by iNOSoxy with L-Arg (first reaction step) or N-hydroxy-L-arginine (second reaction step) showed that mesohaem substitution triggered higher rates of Fe(II)O₂ conversion and altered other key kinetic parameters. We elucidated the first crystal structure of a NOS substituted with mesohaem and found essentially identical features compared with the structure of iNOS carrying native haem. This facilitated the dissection of structural and electronic effects. Mesohaem substitution substantially reduced the build-up of species P in W188H iNOS during catalysis, thus increasing its proficiency towards NO synthesis. The marked structural similarities of iNOSoxy containing native haem or mesohaem indicate that the kinetic behaviour observed in mesohaem-substituted iNOS is most heavily influenced by electronic effects rather than structural alterations.
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22
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Smith AT, Pazicni S, Marvin KA, Stevens DJ, Paulsen KM, Burstyn JN. Functional divergence of heme-thiolate proteins: a classification based on spectroscopic attributes. Chem Rev 2015; 115:2532-58. [PMID: 25763468 DOI: 10.1021/cr500056m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aaron T Smith
- †Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208, United States
| | - Samuel Pazicni
- ‡Department of Chemistry, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Katherine A Marvin
- §Department of Chemistry, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032, United States
| | - Daniel J Stevens
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Katherine M Paulsen
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Judith N Burstyn
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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23
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Zhang A, Zhang T, Hall EA, Hutchinson S, Cryle MJ, Wong LL, Zhou W, Bell SG. The crystal structure of the versatile cytochrome P450 enzyme CYP109B1 from Bacillus subtilis. MOLECULAR BIOSYSTEMS 2015; 11:869-81. [PMID: 25587700 DOI: 10.1039/c4mb00665h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The crystal structure of the versatile CYP109B1 enzyme from Bacillus subtilis has been solved at 1.8 Å resolution. This is the first structure of an enzyme from this CYP family, whose members are prevalent across diverse species of bacteria. In the crystal structure the enzyme has an open conformation with an access channel leading from the heme to the surface. The substrate-free structure reveals the location of the key residues in the active site that are responsible for binding the substrate in the correct orientation for regioselective oxidation. Importantly, there are significant differences among these residues in members of the CYP109 and closely related CYP106 families and these likely account for the variations in substrate binding and oxidation profiles observed with these enzymes. A whole-cell oxidation biosystem was developed, which contains CYP109B1 and a phthalate family oxygenase reductase (PFOR), from Pseudomonas putida KT24440, as the electron transfer partner. This electron transfer system is able to support CYP109B1 activity resulting in the regioselective hydroxylation of both α- and β-ionone in vivo and in vitro. The PFOR is therefore a versatile electron transfer partner that is able to support the activity of CYP enzymes from other bacterium. The crystal structure of CYP109B1 has a positively charged proximal face and this explains why it can interact with PFOR and adrenodoxin which are predominantly negatively charged around their [2Fe-2S] clusters.
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Affiliation(s)
- Aili Zhang
- College of Life Sciences, Nankai University, Tianjin 300071, China.
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24
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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: 67] [Impact Index Per Article: 7.4] [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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25
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Larsen RW, Wojtas L. Fixed distance photoinduced electron transfer between Fe and Zn porphyrins encapsulated within the Zn HKUST-1 metal organic framework. Dalton Trans 2015; 44:2959-63. [DOI: 10.1039/c4dt02685c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An attractive strategy for the development of photocatalytic metal organic framework (MOF) materials is to co-encapsulate a photoactive electron donor with a catalytic electron acceptor within the MOF.
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Affiliation(s)
| | - Lukasz Wojtas
- Department of Chemistry
- University of South Florida
- Tampa
- USA
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26
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Sainna MA, Kumar S, Kumar D, Fornarini S, Crestoni ME, de Visser SP. A comprehensive test set of epoxidation rate constants for iron(iv)-oxo porphyrin cation radical complexes. Chem Sci 2014; 6:1516-1529. [PMID: 29560240 PMCID: PMC5811088 DOI: 10.1039/c4sc02717e] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022] Open
Abstract
Trends in oxygen atom transfer to Compound I of the P450 models with an extensive test set have been studied and show a preferred regioselectivity of epoxidation over hydroxylation in the gas-phase for the first time.
Cytochrome P450 enzymes are heme based monoxygenases that catalyse a range of oxygen atom transfer reactions with various substrates, including aliphatic and aromatic hydroxylation as well as epoxidation reactions. The active species is short-lived and difficult to trap and characterize experimentally, moreover, it reacts in a regioselective manner with substrates leading to aliphatic hydroxylation and epoxidation products, but the origin of this regioselectivity is poorly understood. We have synthesized a model complex and studied it with low-pressure Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry (MS). A novel approach was devised using the reaction of [FeIII(TPFPP)]+ (TPFPP = meso-tetrakis(pentafluorophenyl)porphinato dianion) with iodosylbenzene as a terminal oxidant which leads to the production of ions corresponding to [FeIV(O)(TPFPP+˙)]+. This species was isolated in the gas-phase and studied in its reactivity with a variety of olefins. Product patterns and rate constants under Ideal Gas conditions were determined by FT-ICR MS. All substrates react with [FeIV(O)(TPFPP+˙)]+ by a more or less efficient oxygen atom transfer process. In addition, substrates with low ionization energies react by a charge-transfer channel, which enabled us to determine the electron affinity of [FeIV(O)(TPFPP+˙)]+ for the first time. Interestingly, no hydrogen atom abstraction pathways are observed for the reaction of [FeIV(O)(TPFPP+˙)]+ with prototypical olefins such as propene, cyclohexene and cyclohexadiene and also no kinetic isotope effect in the reaction rate is found, which suggests that the competition between epoxidation and hydroxylation – in the gas-phase – is in favour of substrate epoxidation. This notion further implies that P450 enzymes will need to adapt their substrate binding pocket, in order to enable favourable aliphatic hydroxylation over double bond epoxidation pathways. The MS studies yield a large test-set of experimental reaction rates of iron(iv)–oxo porphyrin cation radical complexes, so far unprecedented in the gas-phase, providing a benchmark for calibration studies using computational techniques. Preliminary computational results presented here confirm the observed trends excellently and rationalize the reactivities within the framework of thermochemical considerations and valence bond schemes.
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Affiliation(s)
- Mala A Sainna
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , UK .
| | - Suresh Kumar
- Department of Applied Physics , School for Physical Sciences , Babasaheb Bhimrao Ambedkar University , Vidya Vihar, Rai Bareilly Road , Lucknow 226 025 , India .
| | - Devesh Kumar
- Department of Applied Physics , School for Physical Sciences , Babasaheb Bhimrao Ambedkar University , Vidya Vihar, Rai Bareilly Road , Lucknow 226 025 , India .
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco , Università di Roma "La Sapienza" , P.le A. Moro 5 , 00185 , Roma , Italy . ;
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco , Università di Roma "La Sapienza" , P.le A. Moro 5 , 00185 , Roma , Italy . ;
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , UK .
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27
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Rydberg P, Lonsdale R, Harvey JN, Mulholland AJ, Olsen L. Trends in predicted chemoselectivity of cytochrome P450 oxidation: B3LYP barrier heights for epoxidation and hydroxylation reactions. J Mol Graph Model 2014; 52:30-5. [PMID: 25000094 DOI: 10.1016/j.jmgm.2014.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 01/19/2023]
Abstract
Prediction of epoxide formation in drug metabolism is a difficult but important task, as epoxide formation is linked to drug toxicity. A comparison of the energy barriers for cytochrome P450 mediated epoxidation of alkenes to the barriers for the hydroxylation of an aliphatic carbon atom next to a double bond has been performed using B3LYP and B3LYP-D3. Relevant experimental data on oxidation selectivity has also been assessed. The results show that density functional theory, when using B3LYP-D3, does well in reproducing the experimental trends. Considering that the comparison involves chemical steps with quite different features this is remarkable. We also find that B3LYP consistently underestimates the hydrogen abstraction barriers relative to the epoxidation barriers, and that including a dispersion correction reduces this problem.
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Affiliation(s)
- Patrik Rydberg
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Jeremy N Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Lars Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
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28
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Hong S, Lee YM, Cho KB, Seo MS, Song D, Yoon J, Garcia-Serres R, Clémancey M, Ogura T, Shin W, Latour JM, Nam W. Conversion of high-spin iron(iii)–alkylperoxo to iron(iv)–oxo species via O–O bond homolysis in nonheme iron models. Chem Sci 2014. [DOI: 10.1039/c3sc52236a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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29
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Electrochemistry of mammalian cytochrome P450 2B4 indicates tunable thermodynamic parameters in surfactant films. J Inorg Biochem 2013; 129:30-4. [PMID: 24013063 DOI: 10.1016/j.jinorgbio.2013.07.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/28/2013] [Accepted: 07/29/2013] [Indexed: 11/23/2022]
Abstract
Electrochemical methods continue to present an attractive means for achieving in vitro biocatalysis with cytochromes P450; however understanding fully the nature of electrode-bound P450 remains elusive. Herein we report thermodynamic parameters using electrochemical analysis of full-length mammalian microsomal cytochrome P450 2B4 (CYP 2B4) in didodecyldimethylammonium bromide (DDAB) surfactant films. Electronic absorption spectra of CYP 2B4-DDAB films on silica slides reveal an absorption maximum at 418nm, characteristic of low-spin, six-coordinate, water-ligated Fe(III) heme in P450. The Fe(III/II) and Fe(II/I) redox couples (E1/2) of substrate-free CYP 2B4 measured by cyclic voltammetry are -0.23V and -1.02V (vs. SCE, or 14mV and -776mV vs. NHE) at 21°C. The standard heterogeneous rate constant for electron transfer from the electrode to the heme for the Fe(III/II) couple was estimated at 170s(-1). Experiments indicate that the system is capable of catalytic reduction of dioxygen, however substrate oxidation was not observed. From the variation of E1/2 with temperature (18-40°C), we have measured entropy and enthalpy changes that accompany heme reduction, -151Jmol(-1)K(-1) and -46kJmol(-1), respectfully. The corresponding entropy and enthalpy values are less for the six-coordinate low-spin, imidazole-ligated enzyme (-59Jmol(-1)K(-1) and -18kJmol(-1)), consistent with limited conformational changes upon reduction. These thermodynamic parameters are comparable to those measured for bacterial P450 from Bacillus megaterium (CYP BM3), confirming our prior reports that the surfactant environment exerts a strong influence on the redox properties of the heme.
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30
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Batabyal D, Li H, Poulos TL. Synergistic effects of mutations in cytochrome P450cam designed to mimic CYP101D1. Biochemistry 2013; 52:5396-402. [PMID: 23865948 PMCID: PMC3790332 DOI: 10.1021/bi400676d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A close orthologue to cytochrome P450cam (CYP101A1) that catalyzes the same hydroxylation of camphor to 5-exo-hydroxycamphor is CYP101D1. There are potentially important differences in and around the active site that could contribute to subtle functional differences. Adjacent to the heme iron ligand, Cys357, is Leu358 in P450cam, whereas this residue is Ala in CYP101D1. Leu358 plays a role in binding of the P450cam redox partner, putidaredoxin (Pdx). On the opposite side of the heme, about 15-20 Å away, Asp251 in P450cam plays a critical role in a proton relay network required for O2 activation but forms strong ion pairs with Arg186 and Lys178. In CYP101D1 Gly replaces Lys178. Thus, the local electrostatic environment and ion pairing are substantially different in CYP101D1. These sites have been systematically mutated in P450cam to the corresponding residues in CYP101D1 and the mutants analyzed by crystallography, kinetics, and UV-vis spectroscopy. Individually, the mutants have little effect on activity or structure, but in combination there is a major drop in enzyme activity. This loss in activity is due to the mutants being locked in the low-spin state, which prevents electron transfer from the P450cam redox partner, Pdx. These studies illustrate the strong synergistic effects on well-separated parts of the structure in controlling the equilibrium between the open (low-spin) and closed (high-spin) conformational states.
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Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697-3900
| | - Huiying Li
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697-3900
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697-3900
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31
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Rebouças JS, James BR. Molecular Recognition Using Ruthenium(II) Porphyrin Thiol Complexes as Probes. Inorg Chem 2013; 52:1084-98. [DOI: 10.1021/ic302401m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Júlio S. Rebouças
- Departamento de Química, CCEN, Universidade Federal da Paraíba, João Pessoa, PB 58.051-900,
Brazil
| | - Brian R. James
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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32
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Sabat J, Egawa T, Lu C, Stuehr DJ, Gerfen GJ, Rousseau DL, Yeh SR. Catalytic intermediates of inducible nitric-oxide synthase stabilized by the W188H mutation. J Biol Chem 2012; 288:6095-106. [PMID: 23269673 DOI: 10.1074/jbc.m112.403238] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitric-oxide synthase (NOS) catalyzes nitric oxide (NO) synthesis via a two-step process: L-arginine (L-Arg) → N-hydroxy-L-arginine → citrulline + NO. In the active site the heme is coordinated by a thiolate ligand, which accepts a H-bond from a nearby tryptophan residue, Trp-188. Mutation of Trp-188 to histidine in murine inducible NOS was shown to retard NO synthesis and allow for transient accumulation of a new intermediate with a Soret maximum at 420 nm during the L-Arg hydroxylation reaction (Tejero, J., Biswas, A., Wang, Z. Q., Page, R. C., Haque, M. M., Hemann, C., Zweier, J. L., Misra, S., and Stuehr, D. J. (2008) J. Biol. Chem. 283, 33498-33507). However, crystallographic data showed that the mutation did not perturb the overall structure of the enzyme. To understand how the proximal mutation affects the oxygen chemistry, we carried out biophysical studies of the W188H mutant. Our stopped-flow data showed that the 420-nm intermediate was not only populated during the L-Arg reaction but also during the N-hydroxy-L-arginine reaction. Spectroscopic data and structural analysis demonstrated that the 420-nm intermediate is a hydroxide-bound ferric heme species that is stabilized by an out-of-plane distortion of the heme macrocycle and a cation radical centered on the tetrahydrobiopterin cofactor. The current data add important new insights into the previously proposed catalytic mechanism of NOS (Li, D., Kabir, M., Stuehr, D. J., Rousseau, D. L., and Yeh, S. R. (2007) J. Am. Chem. Soc. 129, 6943-6951).
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Affiliation(s)
- Joseph Sabat
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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33
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Iyanagi T, Xia C, Kim JJP. NADPH-cytochrome P450 oxidoreductase: prototypic member of the diflavin reductase family. Arch Biochem Biophys 2012; 528:72-89. [PMID: 22982532 PMCID: PMC3606592 DOI: 10.1016/j.abb.2012.09.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 09/01/2012] [Accepted: 09/03/2012] [Indexed: 12/31/2022]
Abstract
NADPH-cytochrome P450 oxidoreductase (CYPOR) and nitric oxide synthase (NOS), two members of the diflavin oxidoreductase family, are multi-domain enzymes containing distinct FAD and FMN domains connected by a flexible hinge. FAD accepts a hydride ion from NADPH, and reduced FAD donates electrons to FMN, which in turn transfers electrons to the heme center of cytochrome P450 or NOS oxygenase domain. Structural analysis of CYPOR, the prototype of this enzyme family, has revealed the exact nature of the domain arrangement and the role of residues involved in cofactor binding. Recent structural and biophysical studies of CYPOR have shown that the two flavin domains undergo large domain movements during catalysis. NOS isoforms contain additional regulatory elements within the reductase domain that control electron transfer through Ca(2+)-dependent calmodulin (CaM) binding. The recent crystal structure of an iNOS Ca(2+)/CaM-FMN construct, containing the FMN domain in complex with Ca(2+)/CaM, provided structural information on the linkage between the reductase and oxgenase domains of NOS, making it possible to model the holo iNOS structure. This review summarizes recent advances in our understanding of the dynamics of domain movements during CYPOR catalysis and the role of the NOS diflavin reductase domain in the regulation of NOS isozyme activities.
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Affiliation(s)
- Takashi Iyanagi
- Department of Biochemistry, Medical College of Wisconsin, USA
- Department of Life Science, The Himeji Institute of Technology, University of Hyogo, Japan
| | - Chuanwu Xia
- Department of Biochemistry, Medical College of Wisconsin, USA
| | - Jung-Ja P. Kim
- Department of Biochemistry, Medical College of Wisconsin, USA
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Lonsdale R, Harvey JN, Mulholland AJ. Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions. J Chem Theory Comput 2012; 8:4637-45. [PMID: 26605619 DOI: 10.1021/ct300329h] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory (DFT) based quantum mechanical/molecular mechanical (QM/MM) calculations have provided valuable insight into the reactivity of the cytochrome P450 family of enzymes (P450s). A failure of commonly used DFT methods, such as B3LYP, is the neglect of dispersion interactions. An empirical dispersion correction has been shown to improve the accuracy of gas phase DFT calculations of P450s. The current work examines the effect of the dispersion correction in QM/MM calculations on P450s. The hydrogen abstraction from camphor, and hydrogen abstraction and C-O addition of cyclohexene and propene by P450cam have been modeled, along with the addition of benzene to Compound I in CYP2C9, at the B3LYP-D2/CHARMM27 level of theory. Single point energy calculations were also performed at the B3LYP-D3//B3LYP-D2/CHARMM27 level. The dispersion corrections lower activation energy barriers significantly (by ∼5 kcal/mol), as seen for gas phase calculations, but has a small effect on optimized geometries.These effects are likely to be important in modeling reactions catalyzed by other enzymes also. Given the low computational cost of including such dispersion corrections, we recommend doing so in all B3LYP based QM/MM calculations.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Jeremy N Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
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Madrona Y, Tripathi S, Li H, Poulos TL. Crystal structures of substrate-free and nitrosyl cytochrome P450cin: implications for O(2) activation. Biochemistry 2012; 51:6623-31. [PMID: 22775403 DOI: 10.1021/bi300666u] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The crystal structure of the P450cin substrate-bound nitric oxide complex and the substrate-free form have been determined revealing a substrate-free structure that adopts an open conformation relative to the substrate-bound structure. The region of the I helix that forms part of the O(2) binding pocket shifts from an α helix in the substrate-free form to a π helix in the substrate-bound form. Unique to P450cin is an active site residue, Asn242, in the I helix that H-bonds with the substrate. In most other P450s this residue is a Thr and plays an important role in O(2) activation by participating in an H-bonding network required for O(2) activation. The π/α I helix transition results in the carbonyl O atom of Gly238 moving in to form an H-bond with the water/hydroxide ligand in the substrate-free form. The corresponding residue, Gly248, in the substrate-free P450cam structure experiences a similar motion. Most significantly, in the oxy-P450cam complex Gly248 adopts a position midway between the substrate-free and -bound states. A comparison between these P450cam and the new P450cin structures provides insights into differences in how the two P450s activate O(2). The structure of P450cin complexed with nitric oxide, a close mimic of the O(2) complex, shows that Gly238 is likely to form tighter interactions with ligands than the corresponding Gly248 in P450cam. Having a close interaction between an H-bond acceptor, the Gly238 carbonyl O atom, and the distal oxygen atom of O(2) will promote protonation and hence further reduction of the oxy complex to the hydroperoxy intermediate resulting in heterolytic cleavage of the peroxide O-O bond and formation of the active ferryl intermediate required for substrate hydroxylation.
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Affiliation(s)
- Yarrow Madrona
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
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Smith AT, Su Y, Stevens DJ, Majtan T, Kraus JP, Burstyn JN. Effect of the disease-causing R266K mutation on the heme and PLP environments of human cystathionine β-synthase. Biochemistry 2012; 51:6360-70. [PMID: 22738154 DOI: 10.1021/bi300421z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cystathionine β-synthase (CBS) is an essential pyridoxal 5'-phosphate (PLP)-dependent enzyme of the transsulfuration pathway that condenses serine with homocysteine to form cystathionine; intriguingly, human CBS also contains a heme b cofactor of unknown function. Herein we describe the enzymatic and spectroscopic properties of a disease-associated R266K hCBS variant, which has an altered hydrogen-bonding environment. The R266K hCBS contains a low-spin, six-coordinate Fe(III) heme bearing a His/Cys ligation motif, like that of WT hCBS; however, there is a geometric distortion that exists at the R266K heme. Using rR spectroscopy, we show that the Fe(III)-Cys(thiolate) bond is longer and weaker in R266K, as evidenced by an 8 cm(-1) downshift in the ν(Fe-S) resonance. Presence of this longer and weaker Fe(III)-Cys(thiolate) bond is correlated with alteration of the fluorescence spectrum of the active PLP ketoenamine tautomer. Activity data demonstrate that, relative to WT, the R266K variant is more impaired in the alternative cysteine-synthesis reaction than in the canonical cystathionine-synthesis reaction. This diminished cysteine synthesis activity and a greater sensitivity to exogenous PLP correlate with the change in PLP environment. Fe-S(Cys) bond weakening causes a nearly 300-fold increase in the rate of ligand switching upon reduction of the R266K heme. Combined, these data demonstrate cross talk between the heme and PLP active sites, consistent with previous proposals, revealing that alteration of the Arg(266)-Cys(52) interaction affects PLP-dependent activity and dramatically destabilizes the ferrous thiolate-ligated heme complex, underscoring the importance of this hydrogen-bonding residue pair.
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Affiliation(s)
- Aaron T Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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Usharani D, Zazza C, Lai W, Chourasia M, Waskell L, Shaik S. A single-site mutation (F429H) converts the enzyme CYP 2B4 into a heme oxygenase: a QM/MM study. J Am Chem Soc 2012; 134:4053-6. [PMID: 22356576 DOI: 10.1021/ja211905e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The intriguing deactivation of the cytochrome P450 (CYP) 2B4 enzyme induced by mutation of a single residue, Phe429 to His, is explored by quantum mechanical/molecular mechanical calculations of the O-OH bond activation of the (Fe(3+)OOH)(-) intermediate. It is found that the F429H mutant of CYP 2B4 undergoes homolytic instead of heterolytic O-OH bond cleavage. Thus, the mutant acquires the following characteristics of a heme oxygenase enzyme: (a) donation by His429 of an additional NH---S H-bond to the cysteine ligand combined with the presence of the substrate retards the heterolytic cleavage and gives rise to homolytic O-OH cleavage, and (b) the Thr302/water cluster orients nascent OH(•) and ensures efficient meso hydroxylation.
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Affiliation(s)
- Dandamudi Usharani
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Hannibal L, Somasundaram R, Tejero J, Wilson A, Stuehr DJ. Influence of heme-thiolate in shaping the catalytic properties of a bacterial nitric-oxide synthase. J Biol Chem 2011; 286:39224-35. [PMID: 21921039 PMCID: PMC3234747 DOI: 10.1074/jbc.m111.286351] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 08/26/2011] [Indexed: 12/26/2022] Open
Abstract
Nitric-oxide synthases (NOS) are heme-thiolate enzymes that generate nitric oxide (NO) from L-arginine. Mammalian and bacterial NOSs contain a conserved tryptophan (Trp) that hydrogen bonds with the heme-thiolate ligand. We mutated Trp(66) to His and Phe (W66H, W66F) in B. subtilis NOS to investigate how heme-thiolate electronic properties control enzyme catalysis. The mutations had opposite effects on heme midpoint potential (-302, -361, and -427 mV for W66H, wild-type (WT), and W66F, respectively). These changes were associated with rank order (W66H < WT < W66F) changes in the rates of oxygen activation and product formation in Arg hydroxylation and N-hydroxyarginine (NOHA) oxidation single turnover reactions, and in the O(2) reactivity of the ferrous heme-NO product complex. However, enzyme ferrous heme-O(2) autoxidation showed an opposite rank order. Tetrahydrofolate supported NO synthesis by WT and the mutant NOS. All three proteins showed similar extents of product formation (L-Arg → NOHA or NOHA → citrulline) in single turnover studies, but the W66F mutant showed a 2.5 times lower activity when the reactions were supported by flavoproteins and NADPH. We conclude that Trp(66) controls several catalytic parameters by tuning the electron density of the heme-thiolate bond. A greater electron density (as in W66F) improves oxygen activation and reactivity toward substrate, but decreases heme-dioxy stability and lowers the driving force for heme reduction. In the WT enzyme the Trp(66) residue balances these opposing effects for optimal catalysis.
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Affiliation(s)
- Luciana Hannibal
- From the Department of Pathobiology, Lerner
Research Institute, Cleveland Clinic, Cleveland, Ohio 44195 and
| | - Ramasamy Somasundaram
- From the Department of Pathobiology, Lerner
Research Institute, Cleveland Clinic, Cleveland, Ohio 44195 and
| | - Jesús Tejero
- From the Department of Pathobiology, Lerner
Research Institute, Cleveland Clinic, Cleveland, Ohio 44195 and
| | - Adjele Wilson
- the Laboratoire Stress Oxidant et Detoxication
(LSOD), CEA-IBITEC-S, Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Dennis J. Stuehr
- From the Department of Pathobiology, Lerner
Research Institute, Cleveland Clinic, Cleveland, Ohio 44195 and
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Lang J, Santolini J, Couture M. The conserved Trp-Cys hydrogen bond dampens the "push effect" of the heme cysteinate proximal ligand during the first catalytic cycle of nitric oxide synthase. Biochemistry 2011; 50:10069-81. [PMID: 22023145 DOI: 10.1021/bi200965e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Residues surrounding and interacting with the heme proximal ligand are important for efficient catalysis by heme proteins. The nitric oxide synthases (NOSs) are thiolate-coordinated enzymes that catalyze the hydroxylation of l-Arg in the first of the two catalytic cycles needed to synthesize nitric oxide. In NOSs, the indole NH group of a conserved tryptophan [W56 of the bacterial NOS-like protein from Staphylococcus aureus (saNOS)] forms a hydrogen bond with the heme proximal cysteinate ligand. The purpose of this study was to determine the impact of increasing (W56F and W56Y variants) or decreasing (W56H variant) the electron density of the proximal cysteinate ligand on molecular oxygen (O(2)) activation using saNOS as a model. We show that the removal of the indole NH···S(-) bond for W56F and W56Y caused an increase in the electron density of the cysteinate. This was probed by the decrease of the midpoint reduction potential (E(1/2)) along with weakened σ-bonding and strengthened π-backbonding with distal ligands (CO and O(2)). On the other hand, the W56H variant showed stronger Fe-OO and Fe-CO bonds (strengthened σ-bonding) along with an elevated E(1/2), which is consistent with the formation of a strong NH···S(-) hydrogen bond from H56. We also show here that changing the electron density of the proximal thiolate controls its "push effect"; whereas the rates of both O(2) activation and autoxidation of the Fe(II)O(2) complex increase with the stronger push effect created by removing the indole NH···S(-) hydrogen bond (W56F and W56Y variants), the W56H variant showed an increased stability of the complex against autoxidation and a slower rate of O(2) activation. These results are discussed with regard to the roles played by the conserved tryptophan-cysteinate interaction in the first catalytic cycle of NOS.
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Affiliation(s)
- Jérôme Lang
- Département de biochimie, de microbiologie et de bioinformatique, PROTEO and IBIS, pavillon Charles-Eugène Marchand, room 3163, Université Laval, Québec, Canada G1V 0A6
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Karunakaran V, Denisov I, Sligar SG, Champion PM. Investigation of the low frequency dynamics of heme proteins: native and mutant cytochrome P450(cam) and redox partner complexes. J Phys Chem B 2011; 115:5665-77. [PMID: 21391540 DOI: 10.1021/jp112298y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Vibrational coherence spectroscopy (VCS) is used to investigate the low-frequency dynamics of camphor-free and camphor-bound cytochrome P450(cam) (CYP 101) and its L358P mutant. The low-frequency heme vibrations are found to be perturbed upon binding to the electron transfer partner putidaredoxin (Pdx). A strong correlation between the "detuned" vibrational coherence spectrum, which monitors frequencies between 100 and 400 cm(-1), and the lower frequency part of the Raman spectrum is also demonstrated. The very low frequency region ≤200 cm(-1), uniquely accessed by open-band VCS measurements, reveals a mode near 103 cm(-1) in P450(cam) when camphor is not present in the distal pocket. This reflects the presence of a specific heme distortion, such as saddling or ruffling, in the substrate-free state where water is coordinated to the low-spin iron atom. Such distortions are likely to retard the rate of electron transfer to the substrate-free protein. The presence of strong mode near ∼33 cm(-1) in the camphor-bound form suggests a significant heme-doming distortion, which is supported by analysis using normal coordinate structural decomposition. Pdx also displays a strong coherent vibration near 30 cm(-1) that in principle could be involved in vibrational resonance with its electron transfer target. A splitting of the 33 cm(-1) feature and intensification of a mode near 78 cm(-1) appear when the P450(cam)/Pdx complex is formed. These observations are consistent with vibrational mixing and heme geometric distortions upon Pdx binding that are coincident with the increased thiolate electron donation to the heme. The appearance of a mode near 65 cm(-1) in the coherence spectra of the L358P mutant is comparable to the mode at 78 cm(-1) seen in the P450(cam)/Pdx complex and is consistent with the view that the heme and its environment in the L358P mutant are similar to the Pdx-bound native protein. Resonance Raman spectra are presented for both P450(cam) and the L358P mutant and the changes are correlated with an increased amount of thiolate electron donation to the heme in the mutant sample.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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41
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Mesohaem substitution reveals how haem electronic properties can influence the kinetic and catalytic parameters of neuronal NO synthase. Biochem J 2011; 433:163-74. [PMID: 20950274 DOI: 10.1042/bj20101353] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NOSs (NO synthases, EC 1.14.13.39) are haem-thiolate enzymes that catalyse a two-step oxidation of L-arginine to generate NO. The structural and electronic features that regulate their NO synthesis activity are incompletely understood. To investigate how haem electronics govern the catalytic properties of NOS, we utilized a bacterial haem transporter protein to overexpress a mesohaem-containing nNOS (neuronal NOS) and characterized the enzyme using a variety of techniques. Mesohaem-nNOS catalysed NO synthesis and retained a coupled NADPH consumption much like the wild-type enzyme. However, mesohaem-nNOS had a decreased rate of Fe(III) haem reduction and had increased rates for haem-dioxy transformation, Fe(III) haem-NO dissociation and Fe(II) haem-NO reaction with O2. These changes are largely related to the 48 mV decrease in haem midpoint potential that we measured for the bound mesohaem cofactor. Mesohaem nNOS displayed a significantly lower Vmax and KmO2 value for its NO synthesis activity compared with wild-type nNOS. Computer simulation showed that these altered catalytic behaviours of mesohaem-nNOS are consistent with the changes in the kinetic parameters. Taken together, the results of the present study reveal that several key kinetic parameters are sensitive to changes in haem electronics in nNOS, and show how these changes combine to alter its catalytic behaviour.
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42
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Biological Outer-Sphere Coordination. MOLECULAR ELECTRONIC STRUCTURES OF TRANSITION METAL COMPLEXES I 2011. [DOI: 10.1007/430_2011_49] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Molecular basis for the inability of an oxygen atom donor ligand to replace the natural sulfur donor heme axial ligand in cytochrome P450 catalysis. Spectroscopic characterization of the Cys436Ser CYP2B4 mutant. Arch Biochem Biophys 2010; 507:119-25. [PMID: 21147058 DOI: 10.1016/j.abb.2010.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/06/2010] [Accepted: 12/07/2010] [Indexed: 11/21/2022]
Abstract
All cytochrome P450s (CYPs) contain a cysteinate heme iron proximal ligand that plays a crucial role in their mechanism of action. Conversion of the proximal Cys436 to Ser in NH(2)-truncated microsomal CYP2B4 (ΔCYP2B4) transforms the enzyme into a two-electron NADPH oxidase producing H(2)O(2) without monooxygenase activity [K.P. Vatsis, H.M. Peng, M.J. Coon, J. Inorg. Biochem. 91 (2002) 542-553]. To examine the effects of this ligation change on the heme iron spin-state and coordination structure of ΔC436S CYP2B4, the magnetic circular dichroism and electronic absorption spectra of several oxidation/ligation states of the variant have been measured and compared with those of structurally defined heme complexes. The spectra of the substrate-free ferric mutant are indicative of a high-spin five-coordinate structure ligated by anionic serinate. The spectroscopic properties of the dithionite-reduced (deoxyferrous) protein are those of a five-coordinate (high-spin) state, and it is concluded that the proximal ligand has been protonated to yield neutral serine (ROH-donor). Low-spin six-coordinate ferrous complexes of the mutant with neutral sixth ligands (NO, CO, and O(2)) examined are also likely ligated by neutral serine, as would be expected for ferric complexes with anionic sixth ligands such as the hydroperoxo-ferric catalytic intermediate. Ligation of the heme iron by neutral serine vs. deprotonated cysteine is likely the result of the large difference in their acidity. Thus, without the necessary proximal ligand push of the cysteinate, although the ΔC436S mutant can accept two electrons and two protons, it is unable to heterolytically cleave the O-O bond of the hydroperoxo-ferric species to generate Compound I and hydroxylate the substrate.
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Lai W, Chen H, Cho KB, Shaik S. Effects of substrate, protein environment, and proximal ligand mutation on compound I and compound 0 of chloroperoxidase. J Phys Chem A 2010; 113:11763-71. [PMID: 19572690 DOI: 10.1021/jp902898s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper investigates the enzyme chloroperoxidase (CPO) by means of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. The effects of anionic substrate, protein environment, and proximal ligand mutation on the high-valent iron-oxo species, compound I (Cpd I), and the ferric hydroperoxide complex, compound 0 (Cpd 0), are studied. The results indicate that the presence of an anionic substrate (acetate) and the protonation state of one critical residue (Glu104) have a considerable impact on the relative stabilities of Cpd I and Cpd 0. In the absence of the substrate or when the substrate is protonated, Cpd I is considerably more stable, and its formation barrier is smaller than in the case where the substrate is in its anionic state and when Glu104 is deprotonated. This trend, which is shown to be a simple manifestation of the Hammond principle, reproduces the experimental observation that the working pH of the enzyme is acidic. Furthermore, in the absence of substrate (or when it is protonated), the relative Cpd 0/Cpd I energies are found to be a good index of Cpd I stability in heme enzymes and to follow the experimental order: horseradish peroxidase (HRP) > CPO > P450. In silico mutation of the proximal ligand from cysteine to selenocysteine was found to have no effect at all on the properties of Cpd I (e.g., spin density on the chalcogen, Mössbauer parameters, etc.) and its relative stability to Cpd 0 or on the corresponding barrier for formation. This surprising finding shows that the polar CPO pocket applies a leveling effect that stabilizes the anionic forms of the proximal ligands (CysS(-) and CysSe(-)). This in turn means that the Se-Cpd I of the mutant CPO is observable.
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Affiliation(s)
- Wenzhen Lai
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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Martell JD, Li H, Doukov T, Martásek P, Roman LJ, Soltis M, Poulos TL, Silverman RB. Heme-coordinating inhibitors of neuronal nitric oxide synthase. Iron-thioether coordination is stabilized by hydrophobic contacts without increased inhibitor potency. J Am Chem Soc 2010; 132:798-806. [PMID: 20014790 PMCID: PMC2826131 DOI: 10.1021/ja908544f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The heme-thioether ligand interaction often occurs between heme iron and native methionine ligands, but thioether-based heme-coordinating (type II) inhibitors are uncommon due to the difficulty in stabilizing the Fe-S bond. Here, a thioether-based inhibitor (3) of neuronal nitric oxide synthase (nNOS) was designed, and its binding was characterized by spectrophotometry and crystallography. A crystal structure of inhibitor 3 coordinated to heme iron was obtained, representing, to our knowledge, the first crystal structure of a thioether inhibitor complexed to any heme enzyme. A series of related potential inhibitors (4-8) also were evaluated. Compounds 4-8 were all found to be type I (non-heme-coordinating) inhibitors of ferric nNOS, but 4 and 6-8 were found to switch to type II upon heme reduction to the ferrous state, reflecting the higher affinity of thioethers for ferrous heme than for ferric heme. Contrary to what has been widely thought, thioether-heme ligation was found not to increase inhibitor potency, illustrating the intrinsic weakness of the thioether-ferric heme linkage. Subtle changes in the alkyl groups attached to the thioether sulfur caused drastic changes in the binding conformation, indicating that hydrophobic contacts play a crucial role in stabilizing the thioether-heme coordination.
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Affiliation(s)
- Jeffrey D. Martell
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, and Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3113
| | - Huiying Li
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Chemistry, and Chemistry, University of California, Irvine, California 92697-3900
| | - Tzanko Doukov
- Macromolecular Crystallographic Group, Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Stanford, California 94309
| | - Pavel Martásek
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78384-7760
| | - Linda J. Roman
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78384-7760
| | - Michael Soltis
- Macromolecular Crystallographic Group, Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Stanford, California 94309
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Chemistry, and Chemistry, University of California, Irvine, California 92697-3900
| | - Richard B. Silverman
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, and Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3113
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46
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Lonsdale R, Harvey JN, Mulholland AJ. Compound I Reactivity Defines Alkene Oxidation Selectivity in Cytochrome P450cam. J Phys Chem B 2009; 114:1156-62. [DOI: 10.1021/jp910127j] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Jeremy N. Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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Shaik S, Cohen S, Wang Y, Chen H, Kumar D, Thiel W. P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations. Chem Rev 2009; 110:949-1017. [DOI: 10.1021/cr900121s] [Citation(s) in RCA: 791] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sason Shaik
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Shimrit Cohen
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Yong Wang
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Hui Chen
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Devesh Kumar
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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48
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Whitehouse CJC, Bell SG, Yang W, Yorke JA, Blanford CF, Strong AJF, Morse EJ, Bartlam M, Rao Z, Wong LL. A Highly Active Single-Mutation Variant of P450BM3(CYP102A1). Chembiochem 2009; 10:1654-6. [DOI: 10.1002/cbic.200900279] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Wu KY, Hsieh CC, Horng YC. Mononuclear zinc(II) and mercury(II) complexes of Schiff bases derived from pyrrolealdehyde and cysteamine containing intramolecular NH⋯S hydrogen bonds. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2009.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Probing the role of the proximal heme ligand in cytochrome P450cam by recombinant incorporation of selenocysteine. Proc Natl Acad Sci U S A 2009; 106:5481-6. [PMID: 19293375 DOI: 10.1073/pnas.0810503106] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The unique monooxygenase activity of cytochrome P450cam has been attributed to coordination of a cysteine thiolate to the heme cofactor. To investigate this interaction, we replaced cysteine with the more electron-donating selenocysteine. Good yields of the selenoenzyme were obtained by bacterial expression of an engineered gene containing the requisite UGA codon for selenocysteine and a simplified yet functional selenocysteine insertion sequence (SECIS). The sulfur-to-selenium substitution subtly modulates the structural, electronic, and catalytic properties of the enzyme. Catalytic activity decreases only 2-fold, whereas substrate oxidation becomes partially uncoupled from electron transfer, implying a more complex role for the axial ligand than generally assumed.
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