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Hackett JC, Krueger S, Urban VS, Zárate-Pérez F. Small angle scattering reveals the orientation of cytochrome P450 19A1 in lipoprotein nanodiscs. J Inorg Biochem 2024; 257:112579. [PMID: 38703512 DOI: 10.1016/j.jinorgbio.2024.112579] [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: 02/13/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
Human aromatase (CYP19A1), the cytochrome P450 enzyme responsible for conversion of androgens to estrogens, was incorporated into lipoprotein nanodiscs (NDs) and interrogated by small angle X-ray and neutron scattering (SAXS/SANS). CYP19A1 was associated with the surface and centered at the edge of the long axis of the ND membrane. In the absence of the N-terminal anchor, the amphipathic A'- and G'-helices were predominately buried in the lipid head groups, with the possibly that their hydrophobic side chains protrude into the hydrophobic, aliphatic tails. The prediction is like that for CYP3A4 based on SAXS employing a similar modeling approach. The orientation of CYP19A1 in a ND is consistent with our previous predictions based on molecular dynamics simulations and lends additional credibility to the notion that CYP19A1 captures substrates from the membrane.
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Affiliation(s)
- John C Hackett
- Department of Chemistry and Biochemistry and the Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States.
| | - Susan Krueger
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, MD 20899, United States; Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Francisco Zárate-Pérez
- Department of Chemistry and Biochemistry and the Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
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Dalal V, Arcario MJ, Petroff JT, Tan BK, Dietzen NM, Rau MJ, Fitzpatrick JAJ, Brannigan G, Cheng WWL. Lipid nanodisc scaffold and size alter the structure of a pentameric ligand-gated ion channel. Nat Commun 2024; 15:25. [PMID: 38167383 PMCID: PMC10762164 DOI: 10.1038/s41467-023-44366-w] [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: 11/20/2022] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Lipid nanodiscs have become a standard tool for studying membrane proteins, including using single particle cryo-electron microscopy (cryo-EM). We find that reconstituting the pentameric ligand-gated ion channel (pLGIC), Erwinia ligand-gated ion channel (ELIC), in different nanodiscs produces distinct structures by cryo-EM. The effect of the nanodisc on ELIC structure extends to the extracellular domain and agonist binding site. Additionally, molecular dynamic simulations indicate that nanodiscs of different size impact ELIC structure and that the nanodisc scaffold directly interacts with ELIC. These findings suggest that the nanodisc plays a crucial role in determining the structure of pLGICs, and that reconstitution of ion channels in larger nanodiscs may better approximate a lipid membrane environment.
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Affiliation(s)
- Vikram Dalal
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Mark J Arcario
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John T Petroff
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Brandon K Tan
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Noah M Dietzen
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael J Rau
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
- Department of Physics, Rutgers University, Camden, NJ, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
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Sweeney DT, Zárate-Pérez F, Stokowa-Sołtys K, Hackett JC. Induced Fit Describes Ligand Binding to Membrane-Associated Cytochrome P450 3A4. Mol Pharmacol 2023; 104:154-163. [PMID: 37536953 PMCID: PMC10506697 DOI: 10.1124/molpharm.123.000698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/06/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Cytochrome P450 3A4 (CYP3A4) is the dominant P450 involved in human xenobiotic metabolism. Competition for CYP3A4 therefore underlies several adverse drug-drug interactions. Despite its clinical significance, the mechanisms CYP3A4 uses to bind diverse ligands remain poorly understood. Highly monodisperse CYP3A4 embedded in anionic lipoprotein nanodiscs containing an equal mixture of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) were used to determine which of the limiting kinetic schemes that include protein conformational change, conformational selection (CS) or induced fit (IF), best described the binding of four known irreversible inhibitors. Azamulin, retapamulin, pleuromutilin, and mibrefadil binding to CYP3A4 nanodiscs conformed to a single-site binding model. Exponential fits of stopped-flow UV-visible absorption spectroscopy data supported multiple-step binding mechanisms. Trends in the rates of relaxation to equilibrium with increasing ligand concentrations were ambiguous as to whether IF or CS was involved; however, global fitting and consideration of the rate constants favored an IF mechanism. In the case of mibrefadil, a transient complex was observed in the stopped-flow UV-visible experiment, definitively assigning the presence of IF in ligand binding. While these studies only consider a small region of CYP3A4's vast ligand space, they provide kinetic evidence that CYP3A4 can use an IF mechanism. SIGNIFICANCE STATEMENT: CYP3A4 is capable of oxidizing numerous xenobiotics, including many drugs. Such promiscuity could not be achieved without conformational changes to accommodate diverse substrates. It is unknown whether conformational heterogeneity is present before (conformational selection) or after (induced fit) ligand binding. Stopped-flow measurements of suicide inhibitors binding to nanodisc-embedded CYP3A4 combined with sophisticated numerical analyses support that induced fit better describes ligand binding to this important enzyme.
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Affiliation(s)
- David Tyler Sweeney
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida (J.C.H., K.S.S., F.Z.P.); Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia (D.T.S.); and Department of Biological and Medicinal Chemistry, Faculty of Chemistry, University of Wroclaw, Wroclaw, Poland (K.S.S.)
| | - Francisco Zárate-Pérez
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida (J.C.H., K.S.S., F.Z.P.); Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia (D.T.S.); and Department of Biological and Medicinal Chemistry, Faculty of Chemistry, University of Wroclaw, Wroclaw, Poland (K.S.S.)
| | - Kamila Stokowa-Sołtys
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida (J.C.H., K.S.S., F.Z.P.); Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia (D.T.S.); and Department of Biological and Medicinal Chemistry, Faculty of Chemistry, University of Wroclaw, Wroclaw, Poland (K.S.S.)
| | - John C Hackett
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida (J.C.H., K.S.S., F.Z.P.); Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia (D.T.S.); and Department of Biological and Medicinal Chemistry, Faculty of Chemistry, University of Wroclaw, Wroclaw, Poland (K.S.S.)
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Sumangala N, Im SC, Valentín-Goyco J, Auchus RJ. Influence of cholesterol on kinetic parameters for human aromatase (P450 19A1) in phospholipid nanodiscs. J Inorg Biochem 2023; 247:112340. [PMID: 37544101 DOI: 10.1016/j.jinorgbio.2023.112340] [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: 03/29/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 08/08/2023]
Abstract
Cholesterol, a significant constituent of the endoplasmic reticulum membrane, exerts a substantial effect on the membrane's biophysical and mechanical properties. Cholesterol, however, is often neglected in model systems used to study membrane-bound proteins. For example, the influence of cholesterol on the enzymatic functions of type 2 cytochromes P450, which require a phospholipid bilayer and the redox partner P450-oxidoreductase (POR) for activity, are rarely investigated. Human aromatase (P450 19A1) catalyzes three sequential oxygenations of 19‑carbon steroids to estrogens and is widely expressed across various tissues, which are characterized by varying cholesterol compositions. Our study examined the impact of cholesterol on the functionality of the P450 19A1 complex with POR. Nanodiscs containing P450 19A1 with 20% cholesterol/80% phospholipid had similar rates and affinity of androstenedione binding as phospholipid-only P450 19A1 nanodiscs, and rates of product formation were indistinguishable among these conditions. In contrast, the rate of the first electron transfer from POR to P450 19A1 was 3-fold faster in cholesterol-containing nanodiscs than in phospholipid-only nanodiscs. These results suggest that cholesterol influences some aspects of POR interaction with P450 19A1 and might serve as an additional regulatory mechanism in this catalytic system.
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Affiliation(s)
- Nirupama Sumangala
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, Ann Arbor, MI 48109, USA; Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sang-Choul Im
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; Veterans Affairs Medical Center, Ann Arbor, MI 48105, United States
| | - Juan Valentín-Goyco
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard J Auchus
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, Ann Arbor, MI 48109, USA; Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; Veterans Affairs Medical Center, Ann Arbor, MI 48105, United States.
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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