1
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Sahoo BR, Ramamoorthy A. Direct interaction between the transmembrane helices stabilize cytochrome P450 2B4 and cytochrome b5 redox complex. Biophys Chem 2023; 301:107092. [PMID: 37586236 PMCID: PMC10838600 DOI: 10.1016/j.bpc.2023.107092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023]
Abstract
The catalytic activity of cytochrome P450 2B4 (CYP2B4) is moderated by its cognate redox partner cytochrome b5 (Cyt-b5). The endoplasmic reticulum (ER) membrane and intermolecular transmembrane (TM) interaction between CYP2B4 and Cyt-b5 regulate the substrate catalysis and the reaction rate. This emphasizes the significance of elucidating the molecular basis of CYP2B4 and Cyt-b5 complexation in a membrane environment to better understand the enzymatic activity of CYP2B4. Our previous solid-state NMR studies revealed the membrane topology of the transmembrane domains of these proteins in the free and complex forms. Here, we show the cross-angle complex formation by the single-pass TM domains of CYP2B4 and Cyt-b5, which is mainly driven by several salt-bridges (E2-R128, R21-D104 and K25-D104), using a multi-microsecond molecular dynamic simulation. Additionally, the leucine-zipper residues (L8, L12, L15, L18 and L19 from CYP2B4) and π-stacking between H23 and F20 residues of CYP2B4 and W110 of Cyt-b5 are identified to stabilize the TM-TM complex in the ER membrane. The simulated tilts of the helices in the free and in the complex are in excellent agreement with solid-state NMR results. The TM-TM packing influences a higher order structural stability when compared to the complex formed by the truncated soluble domains of these two proteins. MM/PBSA based binding free energy estimates nearly 100-fold higher binding affinity (ΔG = -2810.68 ± 696.44 kJ/mol) between the soluble domains of the full-length CYP2B4 and Cyt-b5 when embedded in lipid membrane as compared to the TM-domain-truncated soluble domains (ΔG = -27.406 ± 10.32 kJ/mol). The high-resolution full-length CYP2B4-Cyt-b5 complex structure and its dynamics in a native ER membrane environment reported here could aid in the development of approaches to effectively modulate the drug-metabolism activity of CYP2B4.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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2
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Denisov IG, Sligar SG. Solvent isotope effects in the catalytic cycle of P450 CYP17A1: Computational modeling of the hydroxylation and lyase reactions. J Inorg Biochem 2023; 243:112202. [PMID: 37004494 PMCID: PMC10128154 DOI: 10.1016/j.jinorgbio.2023.112202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/13/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
The catalytic cycle of the cytochromes P450 (CYP) requires two electrons from a protein redox partner and two protons from water to generate the main catalytic intermediate, a ferryl-oxo complex with π-cation on the heme porphyrin ring, termed Compound 1. The protonation steps are at least partially rate-limiting, therefore the steady-state rates of P450 catalysis are usually slower in deuterated solvent (D2O) by a factor of 1.5-3. However, in several P450 systems a pronounced inverse kinetic solvent isotope effect (KSIE ∼0.4-0.7) is observed, where the reaction is faster in D2O. This raises an important mechanistic question: Is this inverse solvent isotope effect compatible with Compound 1 catalyzed reactions, or is it indicative of another catalytic intermediate being involved? In this communication we use exhaustive numerical modeling of the P450 steady-state kinetics to demonstrate that a significant inverse KSIE cannot be obtained for a pure Compound 1 driven catalytic cycle of P450. Rather, an alternative, protonation independent, catalytic intermediate needs to be introduced. This result is applicable to the broad spectrum of P450s in nature, but as an example we use the extensively documented inverse isotope effect in the human steroid biosynthetic P450 CYP17A1 where the involvement of a heme peroxo anion intermediate has been characterized. Based on this analysis, we show that the observation of an inverse KSIE can be used as a general mechanistic probe for reaction cycle intermediates in the cytochromes P450.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America.
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3
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Liu Y, Denisov I, Gregory M, Sligar SG, Kincaid JR. Importance of Asparagine 202 in Manipulating Active Site Structure and Substrate Preference for Human CYP17A1. Biochemistry 2022; 61:583-594. [PMID: 35287432 PMCID: PMC9972851 DOI: 10.1021/acs.biochem.2c00023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The multifunctional cytochrome P450 17A1 (CYP17A1) plays a crucial role in human steroid hormone synthesis (UniProtKB─P05093). It first carries out standard monooxygenase chemistry, converting pregnenolone (PREG) and progesterone (PROG) into 17OH-PREG and 17OH-PROG, utilizing a "Compound I" to initiate hydrogen abstraction and radical recombination in the classic "oxygen rebound" mechanism. Additionally, these hydroxylated products also serve as substrates in a second oxidative cycle which cleaves the 17-20 carbon-carbon bond to form dehydroepiandrosterone and androstenedione, which are key precursors in the generation of powerful androgens and estrogens. Interestingly, in humans, with 17OH-PREG, this so-called lyase reaction is more efficient than with 17OH-PROG, based on Kcat/Km values. In the present work, the asparagine residue at 202 position was replaced by serine, an alteration which can affect substrate orientation and control substrate preference for the lyase reaction. First, we report studies of solvent isotope effects for the N202S CYP17A1 mutant in the presence of 17OH-PREG and 17OH-PROG, which suggest that the ferric peroxo species is the predominant catalytically active intermediate in the lyase step. This conclusion is further supported by employing a combination of cryoradiolysis and resonance Raman techniques to successfully trap and structurally characterize the key reaction intermediates, including the peroxo, the hydroperoxo, and the crucial peroxo-hemiketal intermediate. Collectively, these studies show that the mutation causes active site structural changes that alter the H-bonding interactions with the key Fe-O-O fragment and the degree of protonation of the reactive ferric peroxo intermediate, thereby impacting lyase efficiency.
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Affiliation(s)
- Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Ilia Denisov
- Departments of Chemistry and Biochemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Michael Gregory
- Departments of Chemistry and Biochemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Departments of Chemistry and Biochemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
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4
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Structural Features of Cytochrome b5–Cytochrome b5 Reductase Complex Formation and Implications for the Intramolecular Dynamics of Cytochrome b5 Reductase. Int J Mol Sci 2021; 23:ijms23010118. [PMID: 33918863 PMCID: PMC8745658 DOI: 10.3390/ijms23010118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/10/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
Membrane cytochrome b5 reductase is a pleiotropic oxidoreductase that uses primarily soluble reduced nicotinamide adenine dinucleotide (NADH) as an electron donor to reduce multiple biological acceptors localized in cellular membranes. Some of the biological acceptors of the reductase and coupled redox proteins might eventually transfer electrons to oxygen to form reactive oxygen species. Additionally, an inefficient electron transfer to redox acceptors can lead to electron uncoupling and superoxide anion formation by the reductase. Many efforts have been made to characterize the involved catalytic domains in the electron transfer from the reduced flavoprotein to its electron acceptors, such as cytochrome b5, through a detailed description of the flavin and NADH-binding sites. This information might help to understand better the processes and modifications involved in reactive oxygen formation by the cytochrome b5 reductase. Nevertheless, more than half a century since this enzyme was first purified, the one-electron transfer process toward potential electron acceptors of the reductase is still only partially understood. New advances in computational analysis of protein structures allow predicting the intramolecular protein dynamics, identifying potential functional sites, or evaluating the effects of microenvironment changes in protein structure and dynamics. We applied this approach to characterize further the roles of amino acid domains within cytochrome b5 reductase structure, part of the catalytic domain, and several sensors and structural domains involved in the interactions with cytochrome b5 and other electron acceptors. The computational analysis results allowed us to rationalize some of the available spectroscopic data regarding ligand-induced conformational changes leading to an increase in the flavin adenine dinucleotide (FAD) solvent-exposed surface, which has been previously correlated with the formation of complexes with electron acceptors.
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5
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Rwere F, Im S, Waskell L. The FMN "140s Loop" of Cytochrome P450 Reductase Controls Electron Transfer to Cytochrome P450. Int J Mol Sci 2021; 22:ijms221910625. [PMID: 34638963 PMCID: PMC8508823 DOI: 10.3390/ijms221910625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/25/2021] [Accepted: 09/25/2021] [Indexed: 11/29/2022] Open
Abstract
Cytochrome P450 reductase (CYPOR) provides electrons to all human microsomal cytochrome P450s (cyt P450s). The length and sequence of the “140s” FMN binding loop of CYPOR has been shown to be a key determinant of its redox potential and activity with cyt P450s. Shortening the “140s loop” by deleting glycine-141(ΔGly141) and by engineering a second mutant that mimics flavo-cytochrome P450 BM3 (ΔGly141/Glu142Asn) resulted in mutants that formed an unstable anionic semiquinone. In an attempt to understand the molecular basis of the inability of these mutants to support activity with cyt P450, we expressed, purified, and determined their ability to reduce ferric P450. Our results showed that the ΔGly141 mutant with a very mobile loop only reduced ~7% of cyt P450 with a rate similar to that of the wild type. On the other hand, the more stable loop in the ΔGly141/Glu142Asn mutant allowed for ~55% of the cyt P450 to be reduced ~60% faster than the wild type. Our results reveal that the poor activity of the ΔGly141 mutant is primarily accounted for by its markedly diminished ability to reduce ferric cyt P450. In contrast, the poor activity of the ΔGly141/Glu142Asn mutant is presumably a consequence of the altered structure and mobility of the “140s loop”.
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Affiliation(s)
- Freeborn Rwere
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI 48105, USA; (S.I.); (L.W.)
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
- Correspondence:
| | - Sangchoul Im
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI 48105, USA; (S.I.); (L.W.)
- Department of Internal Medicine, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI 48105, USA
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI 48105, USA; (S.I.); (L.W.)
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6
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Cheng S, Bo Z, Hollenberg P, Osawa Y, Zhang H. Amphipol-facilitated elucidation of the functional tetrameric complex of full-length cytochrome P450 CYP2B4 and NADPH-cytochrome P450 oxidoreductase. J Biol Chem 2021; 296:100645. [PMID: 33839156 PMCID: PMC8113742 DOI: 10.1016/j.jbc.2021.100645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 10/27/2022] Open
Abstract
Interactions of membrane-bound mammalian cytochromes P450 (CYPs) with NADPH-cytochrome P450 oxidoreductase (POR), which are required for metabolism of xenobiotics, are facilitated by membrane lipids. A variety of membrane mimetics, such as phospholipid liposomes and nanodiscs, have been used to simulate the membrane to form catalytically active CYP:POR complexes. However, the exact mechanism(s) of these interactions are unclear because of the absence of structural information of full-length mammalian CYP:POR complexes in membranes. Herein, we report the use of amphipols (APols) to form a fully functional, soluble, homogeneous preparation of full-length CYP:POR complexes amenable to biochemical and structural study. Incorporation of CYP2B4 and POR into APols resulted in a CYP2B4:POR complex with a stoichiometry of 1:1, which was fully functional in demethylating benzphetamine at a turnover rate of 37.7 ± 2.2 min-1, with a coupling efficiency of 40%. Interestingly, the stable complex had a molecular weight (Mw) of 338 ± 22 kDa determined by multiangle light scattering, suggestive of a tetrameric complex of 2CYP2B4:2POR embedded in one APol nanoparticle. Moreover, negative stain electron microscopy (EM) validated the homogeneity of the complex and allowed us to generate a three-dimensional EM map and model consistent with the tetramer observed in solution. This first report of the full-length mammalian CYP:POR complex by transmission EM not only reveals the architecture that facilitates electron transfer but also highlights a potential use of APols in biochemical and structural studies of functional CYP complexes with redox partners.
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Affiliation(s)
- Shen Cheng
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Zhiyuan Bo
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Paul Hollenberg
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Yoichi Osawa
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Haoming Zhang
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, Michigan, USA.
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7
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Liu Y, Denisov IG, Sligar SG, Kincaid JR. Substrate-Specific Allosteric Effects on the Enhancement of CYP17A1 Lyase Efficiency by Cytochrome b5. J Am Chem Soc 2021; 143:3729-3733. [PMID: 33656879 DOI: 10.1021/jacs.1c00581] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
CYP17A1 is an essential human steroidogenic enzyme, which catalyzes two sequential reactions leading to the formation of androstenedione from progesterone and dehydroepiandrosterone from pregnenolone. The second reaction is the C17-C20 bond scission, which is strongly dependent on the presence of cytochrome b5 and displays a heretofore unexplained more pronounced acceleration when 17OH-progesteone (17OH-PROG) is a substrate. The origin of the stimulating effect of cytochrome b5 on C-C bond scission catalyzed by CYP17A1 is still debated as mostly due to either the acceleration of the electron transfer to the P450 oxy complex or allosteric effects of cytochrome b5 favoring active site conformations that promote lyase activity. Using resonance Raman spectroscopy, we compared the effect of Mn-substituted cytochrome b5 (Mn-Cytb5) on the oxy complex of CYP17A1 with both proteins co-incorporated in lipid nanodiscs. For CYP17A1 with 17OH-PROG, a characteristic shift of the Fe-O mode is observed in the presence of Mn-b5, indicating reorientation of a hydrogen bond between the 17OH group of the substrate from the terminal to the proximal oxygen atom of the Fe-O-O moiety, a configuration favorable for the lyase catalysis. For 17OH-pregnenolone, no such shift is observed, the favorable H-bonding orientation being present even without Mn-Cytb5. These new data provide a precise allosteric interpretation for the more pronounced acceleration seen for the 17OH-PROG substrate.
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Affiliation(s)
- Yilin Liu
- Department of Chemistry, Marquette University, 1414W Clybourn Street, Milwaukee, Wisconsin 53233, United States
| | | | | | - James R Kincaid
- Department of Chemistry, Marquette University, 1414W Clybourn Street, Milwaukee, Wisconsin 53233, United States
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8
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An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase. Commun Biol 2021; 4:55. [PMID: 33420418 PMCID: PMC7794467 DOI: 10.1038/s42003-020-01568-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/06/2020] [Indexed: 01/29/2023] Open
Abstract
Cytochrome P450 (CYP) heme monooxygenases require two electrons for their catalytic cycle. For mammalian microsomal CYPs, key enzymes for xenobiotic metabolism and steroidogenesis and important drug targets and biocatalysts, the electrons are transferred by NADPH-cytochrome P450 oxidoreductase (CPR). No structure of a mammalian CYP-CPR complex has been solved experimentally, hindering understanding of the determinants of electron transfer (ET), which is often rate-limiting for CYP reactions. Here, we investigated the interactions between membrane-bound CYP 1A1, an antitumor drug target, and CPR by a multiresolution computational approach. We find that upon binding to CPR, the CYP 1A1 catalytic domain becomes less embedded in the membrane and reorients, indicating that CPR may affect ligand passage to the CYP active site. Despite the constraints imposed by membrane binding, we identify several arrangements of CPR around CYP 1A1 that are compatible with ET. In the complexes, the interactions of the CPR FMN domain with the proximal side of CYP 1A1 are supplemented by more transient interactions of the CPR NADP domain with the distal side of CYP 1A1. Computed ET rates and pathways agree well with available experimental data and suggest why the CYP-CPR ET rates are low compared to those of soluble bacterial CYPs.
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9
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Wright AM, Pahls DR, Gary JB, Warner T, Williams JZ, M Knapp SM, Allen KE, Landis CR, Cundari TR, Goldberg KI. Experimental and Computational Investigation of the Aerobic Oxidation of a Late Transition Metal-Hydride. J Am Chem Soc 2019; 141:10830-10843. [PMID: 31259542 DOI: 10.1021/jacs.9b04706] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The rational development of homogeneous catalytic systems for selective aerobic oxidations of organics has been hampered by the limited available knowledge of how oxygen reacts with important organometallic intermediates. Recently, several mechanisms for oxygen insertion into late transition metal-hydride bonds have been described. Contributing to this nascent understanding of how oxygen reacts with metal-hydrides, a detailed mechanistic study of the reaction of oxygen with the IrIII hydride complex (dmPhebox)Ir(OAc)(H) (1) in the presence of acetic acid, which proceeds to form the IrIII complex (dmPhebox)Ir(OAc)2(OH2) (2), is described. The evidence supports a multifaceted mechanism wherein a small amount of an initially formed metal hydroperoxide proceeds to generate a metal-oxyl species that then initiates a radical chain reaction to rapidly convert the remaining IrIII-H. Insight into the initiation step was gained through kinetic and mechanistic studies of the radical chain inhibition by BHT (butylated hydroxytoluene). Computational studies were employed to contribute to a further understanding of initiation and propagation in this system.
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Affiliation(s)
- Ashley M Wright
- Department of Chemistry , University of Washington , Box 351700, Seattle , Washington 98195-1700 , United States
| | - Dale R Pahls
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM) , University of North Texas , 1155 Union Circle, #305070 , Denton , Texas 76203-5017 , United States
| | - J Brannon Gary
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM) , University of North Texas , 1155 Union Circle, #305070 , Denton , Texas 76203-5017 , United States.,Department of Chemistry and Biochemistry , Stephen F. Austin State University , P.O. Box 13006, SFA Station , Nacogdoches , Texas 75962-3006 , United States
| | - Theresa Warner
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM) , University of North Texas , 1155 Union Circle, #305070 , Denton , Texas 76203-5017 , United States
| | - Jacob Z Williams
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM) , University of North Texas , 1155 Union Circle, #305070 , Denton , Texas 76203-5017 , United States
| | - Spring Melody M Knapp
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53719 , United States
| | - Kate E Allen
- Department of Chemistry , University of Washington , Box 351700, Seattle , Washington 98195-1700 , United States
| | - Clark R Landis
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53719 , United States
| | - Thomas R Cundari
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM) , University of North Texas , 1155 Union Circle, #305070 , Denton , Texas 76203-5017 , United States
| | - Karen I Goldberg
- Department of Chemistry , University of Washington , Box 351700, Seattle , Washington 98195-1700 , United States.,Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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10
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Abstract
Enzymes are complex biological catalysts and are critical to life. Most oxidations of chemicals are catalyzed by cytochrome P450 (P450, CYP) enzymes, which generally utilize mixed-function oxidase stoichiometry, utilizing pyridine nucleotides as electron donors: NAD(P)H + O2 + R → NAD(P)+ + RO + H2O (where R is a carbon substrate and RO is an oxidized product). The catalysis of oxidations is largely understood in the context of the heme iron-oxygen complex generally referred to as Compound I, formally FeO3+, whose basis was in peroxidase chemistry. Many X-ray crystal structures of P450s are now available (≥ 822 structures from ≥146 different P450s) and have helped in understanding catalytic specificity. In addition to hydroxylations, P450s catalyze more complex oxidations, including C-C bond formation and cleavage. Enzymes derived from P450s by directed evolution can even catalyze more unusual reactions, e.g. cyclopropanation. Current P450 questions under investigation include the potential role of the intermediate Compound 0 (formally FeIII-O2 -) in catalysis of some reactions, the roles of high- and low-spin forms of Compound I, the mechanism of desaturation, the roles of open and closed structures of P450s in catalysis, the extent of processivity in multi-step oxidations, and the role of the accessory protein cytochrome b 5. More global questions include exactly how structure drives function, prediction of catalysis, and roles of multiple protein conformations.
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Affiliation(s)
- F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
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11
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Gentry KA, Zhang M, Im SC, Waskell L, Ramamoorthy A. Substrate mediated redox partner selectivity of cytochrome P450. Chem Commun (Camb) 2018; 54:5780-5783. [PMID: 29781479 DOI: 10.1039/c8cc02525h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Investigating the interplay between cytochrome-P450 and its redox partners (CPR and cytochrome-b5) is vital for understanding the metabolism of most hydrophobic drugs. Dynamic structural interactions with the ternary complex, with and without substrates, captured by NMR reveal a gating mechanism for redox partners to promote P450 function.
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Affiliation(s)
- Katherine A Gentry
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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12
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Prade E, Mahajan M, Im S, Zhang M, Gentry KA, Anantharamaiah GM, Waskell L, Ramamoorthy A. A Minimal Functional Complex of Cytochrome P450 and FBD of Cytochrome P450 Reductase in Nanodiscs. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elke Prade
- Biophysics and Department of Chemistry University of Michigan Ann Arbor MI 48109-1055 USA
| | - Mukesh Mahajan
- Biophysics and Department of Chemistry University of Michigan Ann Arbor MI 48109-1055 USA
| | - Sang‐Choul Im
- Department of Anesthesiology University of Michigan and VA Medical Center Ann Arbor MI 48105-1055 USA
| | - Meng Zhang
- Biophysics and Department of Chemistry University of Michigan Ann Arbor MI 48109-1055 USA
| | - Katherine A. Gentry
- Biophysics and Department of Chemistry University of Michigan Ann Arbor MI 48109-1055 USA
| | | | - Lucy Waskell
- Department of Anesthesiology University of Michigan and VA Medical Center Ann Arbor MI 48105-1055 USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry University of Michigan Ann Arbor MI 48109-1055 USA
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13
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Guengerich FP, Yoshimoto FK. Formation and Cleavage of C-C Bonds by Enzymatic Oxidation-Reduction Reactions. Chem Rev 2018; 118:6573-6655. [PMID: 29932643 DOI: 10.1021/acs.chemrev.8b00031] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many oxidation-reduction (redox) enzymes, particularly oxygenases, have roles in reactions that make and break C-C bonds. The list includes cytochrome P450 and other heme-based monooxygenases, heme-based dioxygenases, nonheme iron mono- and dioxygenases, flavoproteins, radical S-adenosylmethionine enzymes, copper enzymes, and peroxidases. Reactions involve steroids, intermediary metabolism, secondary natural products, drugs, and industrial and agricultural chemicals. Many C-C bonds are formed via either (i) coupling of diradicals or (ii) generation of unstable products that rearrange. C-C cleavage reactions involve several themes: (i) rearrangement of unstable oxidized products produced by the enzymes, (ii) oxidation and collapse of radicals or cations via rearrangement, (iii) oxygenation to yield products that are readily hydrolyzed by other enzymes, and (iv) activation of O2 in systems in which the binding of a substrate facilitates O2 activation. Many of the enzymes involve metals, but of these, iron is clearly predominant.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
| | - Francis K Yoshimoto
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
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14
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Prade E, Mahajan M, Im SC, Zhang M, Gentry KA, Anantharamaiah GM, Waskell L, Ramamoorthy A. A Minimal Functional Complex of Cytochrome P450 and FBD of Cytochrome P450 Reductase in Nanodiscs. Angew Chem Int Ed Engl 2018; 57:8458-8462. [PMID: 29722926 DOI: 10.1002/anie.201802210] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/18/2018] [Indexed: 01/08/2023]
Abstract
Structural interactions that enable electron transfer to cytochrome-P450 (CYP450) from its redox partner CYP450-reductase (CPR) are a vital prerequisite for its catalytic mechanism. The first structural model for the membrane-bound functional complex to reveal interactions between the full-length CYP450 and a minimal domain of CPR is now reported. The results suggest that anchorage of the proteins in a lipid bilayer is a minimal requirement for CYP450 catalytic function. Akin to cytochrome-b5 (cyt-b5 ), Arg 125 on the C-helix of CYP450s is found to be important for effective electron transfer, thus supporting the competitive behavior of redox partners for CYP450s. A general approach is presented to study protein-protein interactions combining the use of nanodiscs with NMR spectroscopy and SAXS. Linking structural details to the mechanism will help unravel the xenobiotic metabolism of diverse microsomal CYP450s in their native environment and facilitate the design of new drug entities.
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Affiliation(s)
- Elke Prade
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Mukesh Mahajan
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Sang-Choul Im
- Department of Anesthesiology, University of Michigan and VA Medical Center, Ann Arbor, MI, 48105-1055, USA
| | - Meng Zhang
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Katherine A Gentry
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | | | - Lucy Waskell
- Department of Anesthesiology, University of Michigan and VA Medical Center, Ann Arbor, MI, 48105-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
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15
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Mak PJ, Duggal R, Denisov IG, Gregory MC, Sligar SG, Kincaid JR. Human Cytochrome CYP17A1: The Structural Basis for Compromised Lyase Activity with 17-Hydroxyprogesterone. J Am Chem Soc 2018; 140:7324-7331. [PMID: 29758981 DOI: 10.1021/jacs.8b03901] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The multifunctional enzyme, cytochrome P450 (CYP17A1), plays a crucial role in the production of androgens, catalyzing two key reactions on pregnenolone (PREG) and progesterone (PROG), the first being a 17-hydroxylation to generate 17-OH PREG and 17-OH PROG, with roughly equal efficiencies. The second is a C-C bond scission or "lyase" reaction in which the C17-C20 bond is cleaved, leading to the eventual production of powerful androgens, whose involvement in the proliferation of prostate cancer has generated intense interest in developing inhibitors of CYP17A1. For humans, the significance of the C-C bond cleavage of 17-OH PROG is lessened, because it is about 50 times less efficient than for 17-OH PREG in terms of kcat/Km. Recognizing the need to clarify relevant reaction mechanisms involved with such transformations, we first report studies of solvent isotope effects, results of which are consistent with a Compound I mediated PROG hydroxylase activity, yet exclude this intermediate as a participant in the formation of androstenedione (AD) via the lyase reaction. This finding is also supported by a combination of cryoreduction and resonance Raman spectroscopy that traps and structurally characterizes the key hemiketal reaction intermediates. Adding to a previous study of PREG and 17-OH PREG metabolism, the current work provides definitive evidence for a more facile protonation of the initially formed ferric peroxo-intermediate for 17-OH PROG-bound CYP17A1, compared to the complex with 17-OH PREG. Importantly, Raman characterization also reveals an H-bonding interaction with the terminal oxygen of the peroxo fragment, rather than with the proximal oxygen, as is present for 17-OH PREG. These factors would favor a diminished lyase activity of the sample with 17-OH PROG relative to the complex with 17-OH PREG, thereby providing a convincing structural explanation for the dramatic differences in activity for these lyase substrates in humans.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Ruchia Duggal
- Department of Biochemistry , University of Illinois at Urbana-Champaign , 505 S. Goodwin , Urbana , Illinois 61801 , United States
| | - Ilia G Denisov
- Department of Biochemistry , University of Illinois at Urbana-Champaign , 505 S. Goodwin , Urbana , Illinois 61801 , United States
| | - Michael C Gregory
- Department of Biochemistry , University of Illinois at Urbana-Champaign , 505 S. Goodwin , Urbana , Illinois 61801 , United States
| | - Stephen G Sligar
- Department of Biochemistry , University of Illinois at Urbana-Champaign , 505 S. Goodwin , Urbana , Illinois 61801 , United States.,Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - James R Kincaid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
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16
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Gentry KA, Prade E, Barnaba C, Zhang M, Mahajan M, Im SC, Anantharamaiah GM, Nagao S, Waskell L, Ramamoorthy A. Kinetic and Structural Characterization of the Effects of Membrane on the Complex of Cytochrome b 5 and Cytochrome c. Sci Rep 2017; 7:7793. [PMID: 28798301 PMCID: PMC5552742 DOI: 10.1038/s41598-017-08130-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/04/2017] [Indexed: 12/13/2022] Open
Abstract
Cytochrome b5 (cytb5) is a membrane protein vital for the regulation of cytochrome P450 (cytP450) metabolism and is capable of electron transfer to many redox partners. Here, using cyt c as a surrogate for cytP450, we report the effect of membrane on the interaction between full-length cytb5 and cyt c for the first time. As shown through stopped-flow kinetic experiments, electron transfer capable cytb5 - cyt c complexes were formed in the presence of bicelles and nanodiscs. Experimentally measured NMR parameters were used to map the cytb5-cyt c binding interface. Our experimental results identify differences in the binding epitope of cytb5 in the presence and absence of membrane. Notably, in the presence of membrane, cytb5 only engaged cyt c at its lower and upper clefts while the membrane-free cytb5 also uses a distal region. Using restraints generated from both cytb5 and cyt c, a complex structure was generated and a potential electron transfer pathway was identified. These results demonstrate the importance of studying protein-protein complex formation in membrane mimetic systems. Our results also demonstrate the successful preparation of novel peptide-based lipid nanodiscs, which are detergent-free and possesses size flexibility, and their use for NMR structural studies of membrane proteins.
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Affiliation(s)
| | - Elke Prade
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carlo Barnaba
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meng Zhang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mukesh Mahajan
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sang-Choul Im
- Department of Anesthesiology, University of Michigan, and Veterans Affairs Medical Center, Ann Arbor, Michigan, 48105, USA
| | - G M Anantharamaiah
- Department of Medicine, UAB Medical Center, Birmingham, Alabama, 35294, USA
| | - Satoshi Nagao
- Graduate School of Material Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, and Veterans Affairs Medical Center, Ann Arbor, Michigan, 48105, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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