1
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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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2
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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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3
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Kaluzhskiy L, Yablokov E, Gnedenko O, Burkatovskii D, Maslov I, Bogorodskiy A, Ershov P, Tsybruk T, Zelepuga E, Rutckova T, Kozlovskaya E, Dmitrenok P, Gilep A, Borshchevskiy V, Strushkevich N, Ivanov A. The effect of membrane composition on the interaction between human CYP51 and its flavonoid inhibitor - luteolin 7,3'-disulfate. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184286. [PMID: 38272204 DOI: 10.1016/j.bbamem.2024.184286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
Cytochromes P450 (CYP) are a family of membrane proteins involved in the production of endogenous molecules and the metabolism of xenobiotics. It is well-known that the composition of the membrane can influence the activity and orientation of CYP proteins. However, little is known about how membrane composition affects the ligand binding properties of CYP. In this study, we utilized surface plasmon resonance and fluorescence lifetime analysis to examine the impact of membrane micro-environment composition on the interaction between human microsomal CYP51 (CYP51A1) and its inhibitor, luteolin 7,3'-disulphate (LDS). We observed that membranes containing cholesterol or sphingomyelin exhibited the lowest apparent equilibrium dissociation constant for the CYP51A1-LDS complex. Additionally, the tendency for relation between kinetic parameters of the CYP51A1-LDS complex and membrane viscosity and overall charge was observed. These findings suggest that the specific composition of the membrane, particularly the presence of cholesterol and sphingomyelin, plays a vital role in regulating the interaction between CYP enzymes and their ligands.
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Affiliation(s)
- Leonid Kaluzhskiy
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.
| | - Evgeniy Yablokov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.
| | - Oksana Gnedenko
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.
| | - Dmitrii Burkatovskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia.
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia.
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Pavel Ershov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia
| | - Tatsiana Tsybruk
- Institute of Bioorganic Chemistry NASB, 5 Building 2, V.F. Kuprevich Street, 220141 Minsk, Belarus
| | - Elena Zelepuga
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 159 Prospect 100-letiya Vladivostoka, 690022 Vladivostok, Russia.
| | - Tatyana Rutckova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 159 Prospect 100-letiya Vladivostoka, 690022 Vladivostok, Russia
| | - Emma Kozlovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 159 Prospect 100-letiya Vladivostoka, 690022 Vladivostok, Russia
| | - Pavel Dmitrenok
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 159 Prospect 100-letiya Vladivostoka, 690022 Vladivostok, Russia.
| | - Andrei Gilep
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; Institute of Bioorganic Chemistry NASB, 5 Building 2, V.F. Kuprevich Street, 220141 Minsk, Belarus.
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Natallia Strushkevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia.
| | - Alexis Ivanov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.
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4
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Iqbal T, Das D. Biochemical Investigation of Membrane-Bound Cytochrome b5 and the Catalytic Domain of Cytochrome b5 Reductase from Arabidopsis thaliana. Biochemistry 2022; 61:909-921. [PMID: 35475372 DOI: 10.1021/acs.biochem.2c00002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The endoplasmic reticulum (ER) membrane of plant cells contains several enzymes responsible for the biosynthesis of a diverse range of molecules essential for plant growth and holds potential for industrial applications. Many of these enzymes are dependent on electron transfer proteins to sustain their catalytic cycles. In plants, two crucial ER-bound electron transfer proteins are cytochrome b5 and cytochrome b5 reductase, which catalyze the stepwise transfer of electrons from NADH to redox enzymes such as fatty acid desaturases, cytochrome P450s, and plant aldehyde decarbonylase. Despite the high significance of plant cytochrome b5 and cytochrome b5 reductase, they have eluded detailed characterization to date. Here, we overexpressed the full-length membrane-bound cytochrome b5 isoform B from the model plant Arabidopsis thaliana in Escherichia coli, purified the protein employing detergents as well as styrene-maleic acid (SMA) copolymers, and biochemically characterized the protein. The SMA-encapsulated cytochrome b5 exhibits a discoidal shape and the characteristic features of the active heme-bound state. We also overexpressed and purified the soluble domain of cytochrome b5 reductase from A. thaliana, establishing its activity, stability, and kinetic parameters. Further, we demonstrated that the plant cytochrome b5, purified in detergents and styrene maleic acid lipid particles (SMALPs), readily accepts electrons from the cognate plant cytochrome b5 reductase and distant electron mediators such as plant NADPH-cytochrome P450 oxidoreductase and cyanobacterial NADPH-ferredoxin reductase. We also measured the kinetic parameters of cytochrome b5 reductase for cytochrome b5. Our studies are the first to report the purification and detailed biochemical characterization of the plant cytochrome b5 and cytochrome b5 reductase from the bacterial overexpression system.
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Affiliation(s)
- Tabish Iqbal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Debasis Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
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5
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Ravula T, Dai X, Ramamoorthy A. Solid-State NMR Study to Probe the Effects of Divalent Metal Ions (Ca 2+ and Mg 2+) on the Magnetic Alignment of Polymer-Based Lipid Nanodiscs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7780-7788. [PMID: 34129342 PMCID: PMC8587631 DOI: 10.1021/acs.langmuir.1c01018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Divalent cations, especially Ca2+ and Mg2+, play a vital role in the function of biomolecules and making them important to be constituents in samples for in vitro biophysical and biochemical characterizations. Although lipid nanodiscs are becoming valuable tools for structural biology studies on membrane proteins and for drug delivery, most types of nanodiscs used in these studies are unstable in the presence of divalent metal ions. To avoid the interaction of divalent metal ions with the belt of the nanodiscs, synthetic polymers have been designed and demonstrated to form stable lipid nanodiscs under such unstable conditions. Such polymer-based nanodiscs have been shown to provide an ideal platform for structural studies using both solid-state and solution NMR spectroscopies because of the near-native cell-membrane environment they provide and the unique magnetic-alignment behavior of large-size nanodiscs. In this study, we report an investigation probing the effects of Ca2+ and Mg2+ ions on the formation of polymer-based lipid nanodiscs and the magnetic-alignment properties using a synthetic polymer, styrene maleimide quaternary ammonium (SMA-QA), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids. Phosphorus-31 NMR experiments were used to evaluate the stability of the magnetic-alignment behavior of the nanodiscs for varying concentrations of Ca2+ or Mg2+ at different temperatures. It is remarkable that the interaction of divalent cations with lipid headgroups promotes the stacking up of nanodiscs that results in the enhanced magnetic alignment of nanodiscs. Interestingly, the reported results show that both the temperature and the concentration of divalent metal ions can be optimized to achieve the optimal alignment of nanodiscs in the presence of an applied magnetic field. We expect the reported results to be useful in the design of nanodisc-based nanoparticles for various applications in addition to atomic-resolution structural and dynamics studies using NMR and other biophysical techniques.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Xiaofeng Dai
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
- Xiaofeng Dai was a visiting student from the College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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6
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Kruyer NS, Sugianto W, Tickman BI, Alba Burbano D, Noireaux V, Carothers JM, Peralta-Yahya P. Membrane Augmented Cell-Free Systems: A New Frontier in Biotechnology. ACS Synth Biol 2021; 10:670-681. [PMID: 33749249 DOI: 10.1021/acssynbio.0c00625] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Membrane proteins are present in a wide array of cellular processes from primary and secondary metabolite synthesis to electron transport and single carbon metabolism. A key barrier to applying membrane proteins industrially is their difficult functional production. Beyond expression, folding, and membrane insertion, membrane protein activity is influenced by the physicochemical properties of the associated membrane, making it difficult to achieve optimal membrane protein performance outside the endogenous host. In this review, we highlight recent work on production of membrane proteins in membrane augmented cell-free systems (CFSs) and applications thereof. CFSs lack membranes and can thus be augmented with user-specified, tunable, mimetic membranes to generate customized environments for production of functional membrane proteins of interest. Membrane augmented CFSs would enable the synthesis of more complex plant secondary metabolites, the growth and division of synthetic cells for drug delivery and cell therapeutic applications, as well as enable green energy applications including methane capture and artificial photosynthesis.
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Affiliation(s)
- Nicholas S. Kruyer
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Widianti Sugianto
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Benjamin I. Tickman
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
| | - Diego Alba Burbano
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - James M. Carothers
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Pamela Peralta-Yahya
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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7
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Biochemical and NMR characterization of the interactions of Vav2-SH2 domain with lipids and the EphA2 juxtamembrane region on membrane. Biochem J 2021; 477:3791-3801. [PMID: 32897354 DOI: 10.1042/bcj20200300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Vav2 is a ubiquitous guanine nucleotide exchange factor (GEF) for Rho family GTPases that is involved in regulating a wide range of biological processes. It interacts with several tyrosine-phosphorylated cell surface receptors, including the Eph family receptors, through its SH2 domain. The interaction of Vav2 with EphA2 is crucial for EphA2-mediated tumor angiogenesis. Here we show that Vav2-SH2 domain is a lipid-binding module that can recognize PI(4,5)P2 and PI(3,4,5)P3 lipids weakly but specifically. The specific lipid-binding site in Vav2-SH2 domain was identified by NMR chemical shift perturbation experiments using the head groups of PI(4,5)P2 and PI(3,4,5)P3, both of which bind to Vav2-SH2 with millimolar binding affinities. In addition, the interaction between Vav2-SH2 and the phosphorylated juxtamembrane region (JM) of EphA2 (Y594 phosphorylated) was investigated using NMR techniques. Furthermore, by using a nickel-lipid containing peptide-based nanodiscs system, we studied the binding of Vav2-SH2 to the phosphorylated JM region of EphA2 on lipid membrane and uncovered a role of membrane environment in modulating this protein-protein recognition.
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8
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Functional Assembly of Caenorhabditis elegans Cytochrome b-2 (Cecytb-2) into Phospholipid Bilayer Nanodisc with Enhanced Iron Reductase Activity. Biomolecules 2021; 11:biom11010096. [PMID: 33451048 PMCID: PMC7828500 DOI: 10.3390/biom11010096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
Among seven homologs of cytochrome b561 in a model organism C. elegans, Cecytb-2 was confirmed to be expressed in digestive organs and was considered as a homolog of human Dcytb functioning as a ferric reductase. Cecytb-2 protein was expressed in Pichia pastoris cells, purified, and reconstituted into a phospholipid bilayer nanodisc. The reconstituted Cecytb-2 in nanodisc environments was extremely stable and more reducible with ascorbate than in a detergent-micelle state. We confirmed the ferric reductase activity of Cecytb-2 by analyzing the oxidation of ferrous heme upon addition of ferric substrate under anaerobic conditions, where clear and saturable dependencies on the substrate concentrations following the Michaelis–Menten equation were observed. Further, we confirmed that the ferric substrate was converted to a ferrous state by using a nitroso-PSAP assay. Importantly, we observed that the ferric reductase activity of Cecytb-2 became enhanced in the phospholipid bilayer nanodisc.
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9
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Rangubpit W, Paritanon P, Pandey RB, Sompornpisut P. Thermally induced structural organization of nanodiscs by coarse-grained molecular dynamics simulations. Biophys Chem 2020; 267:106464. [PMID: 32927312 DOI: 10.1016/j.bpc.2020.106464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
Membrane scaffold proteins (MSP) nanodiscs have been extensively used in structural study of membrane proteins. In cryo-EM, an incorporation of target proteins into nanodiscs is conducted under a rapid change from cryogenic to ambient temperatures. We present a coarse-grained molecular dynamics (CGMD) study for investigating an effect of temperature on the structural organization of DPPC-nanodisc and POPC-nanodisc. A non-monotonic response of physical quantities (i.e. the lipid order parameter, nanodisc flatness, structural change, solvation property, radius of gyration) with increase in temperature (T = 200-350 K) is found to be associated with the gel-ripple-liquid crystalline phase change within nanodiscs. The reorganization of lipids upon temperature variation induced conformational changes of MSP to minimize hydrophobic exposure of the lipid membrane to an aqueous environment. Structural response to temperature is different to a certain extent between the saturated DPPC and unsaturated POPC.
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Affiliation(s)
- Warin Rangubpit
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, 10330, Thailand
| | - Pasawan Paritanon
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, 10330, Thailand
| | - Ras B Pandey
- School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Pornthep Sompornpisut
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, 10330, Thailand.
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10
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Lee KY, Fang Z, Enomoto M, Gasmi-Seabrook G, Zheng L, Koide S, Ikura M, Marshall CB. Two Distinct Structures of Membrane-Associated Homodimers of GTP- and GDP-Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2020; 59:11037-11045. [PMID: 32227412 PMCID: PMC7395670 DOI: 10.1002/anie.202001758] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Indexed: 11/07/2022]
Abstract
KRAS homo-dimerization has been implicated in the activation of RAF kinases, however, the mechanism and structural basis remain elusive. We developed a system to study KRAS dimerization on nanodiscs using paramagnetic relaxation enhancement (PRE) NMR spectroscopy, and determined distinct structures of membrane-anchored KRAS dimers in the active GTP- and inactive GDP-loaded states. Both dimerize through an α4-α5 interface, but the relative orientation of the protomers and their contacts differ substantially. Dimerization of KRAS-GTP, stabilized by electrostatic interactions between R135 and E168, favors an orientation on the membrane that promotes accessibility of the effector-binding site. Remarkably, "cross"-dimerization between GTP- and GDP-bound KRAS molecules is unfavorable. These models provide a platform to elucidate the structural basis of RAF activation by RAS and to develop inhibitors that can disrupt the KRAS dimerization. The methodology is applicable to many other farnesylated small GTPases.
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Affiliation(s)
- Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Zhenhao Fang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | | | - Le Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Shohei Koide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, and Perlmutter Cancer Center, New York University Langone Health, New York, NY, 10016, USA
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
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11
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Lee K, Fang Z, Enomoto M, Gasmi‐Seabrook G, Zheng L, Koide S, Ikura M, Marshall CB. Two Distinct Structures of Membrane‐Associated Homodimers of GTP‐ and GDP‐Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ki‐Young Lee
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
| | - Zhenhao Fang
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
| | | | - Le Zheng
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
| | - Shohei Koide
- Department of Biochemistry and Molecular PharmacologyNew York University School of Medicine, and Perlmutter Cancer CenterNew York University Langone Health New York NY 10016 USA
| | - Mitsuhiko Ikura
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
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12
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Bai J, Wang J, Ravula T, Im SC, Anantharamaiah GM, Waskell L, Ramamoorthy A. Expression, purification, and functional reconstitution of 19F-labeled cytochrome b5 in peptide nanodiscs for NMR studies. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183194. [PMID: 31953231 PMCID: PMC7050362 DOI: 10.1016/j.bbamem.2020.183194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
Microsomal cytochrome b5 (cytb5) is a membrane-bound protein capable of donating the second electron to cytochrome P450s (cytP450s) in the cytP450s monooxygenase reactions. Recent studies have demonstrated the importance of the transmembrane domain of cytb5 in the interaction with cytP450 by stabilizing its monomeric structure. While recent NMR studies have provided high-resolution insights into the structural interactions between the soluble domains of ~16-kDa cytb5 and ~57-kDa cytP450 in a membrane environment, there is need for studies to probe the residues in the transmembrane region as well as to obtain intermolecular distance constraints to better understand the very large size cytb5-cytP450 complex structure in a near native membrane environment. In this study, we report the expression, purification, functional reconstitution of 19F-labeled full-length rabbit cytb5 in peptide based nanodiscs for structural studies using NMR spectroscopy. Size exclusion chromatography, dynamic light scattering, transmission electron microscopy, and NMR experiments show a stable reconstitution of cytb5 in 4F peptide-based lipid-nanodiscs. The reported results demonstrate the use of 19F NMR experiments to study 19F-labeled (with 5-fluorotryptophan (5FW)) cytb5 reconstituted in peptide-nanodiscs and the detection of residues from the transmembrane domain by solution 19F NMR experiments. 19F NMR results revealing the interaction of the transmembrane domain of cytb5 with the full-length rabbit cytochrome P450 2B4 (CYP2B4) are also presented. We expect the results presented in this study to be useful to devise approaches to probe the structure, dynamics and functional roles of transmembrane domains of a membrane protein, and also to measure intermolecular 19F-19F distance constraints to determine the structural interactions between the transmembrane domains.
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Affiliation(s)
- Jia Bai
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Jian Wang
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Sang-Choul Im
- Department of Internal Medicine, The University of Michigan, and VA Medical Center, Ann Arbor, MI 48105, USA
| | | | - Lucy Waskell
- Department of Anesthesiology, The University of Michigan, and VA Medical Center, Ann Arbor, MI 48105, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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13
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Ravula T, Kim J, Lee DK, Ramamoorthy A. Magnetic Alignment of Polymer Nanodiscs Probed by Solid-State NMR Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1258-1265. [PMID: 31961695 PMCID: PMC7414804 DOI: 10.1021/acs.langmuir.9b03538] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The ability of amphipathic polymers to self-assemble with lipids and form nanodiscs has been a boon for the field of functional reconstitution of membrane proteins. In a field dominated by detergent micelles, a unique feature of polymer nanodiscs is their much-desired ability to align in the presence of an external magnetic field. Magnetic alignment facilitates the application of solid-state nuclear magnetic resonance (NMR) spectroscopy and aids in the measurement of residual dipolar couplings via well-established solution NMR spectroscopy. In this study, we comprehensively investigate the magnetic alignment properties of styrene maleimide quaternary ammonium (SMA-QA) polymer-based nanodiscs by using 31P and 14N solid-state NMR experiments under static conditions. The results reported herein demonstrate the spontaneous magnetic alignment of large-sized (≥20 nm diameter) SMA-QA nanodiscs (also called as macro-nanodiscs) with the lipid bilayer normal perpendicular to the magnetic field direction. Consequently, the orientation of macro-nanodiscs is further shown to flip the alignment axis parallel to the magnetic field direction upon the addition of a paramagnetic lanthanide salt. These results demonstrate the use of SMA-QA polymer nanodiscs for solid-state NMR applications including structural studies on membrane proteins.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics Program and Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - JaeWoong Kim
- Department of Fine Chemistry , Seoul National University of Science and Technology , Seoul 01811 , Republic of Korea
| | - Dong-Kuk Lee
- Department of Fine Chemistry , Seoul National University of Science and Technology , Seoul 01811 , Republic of Korea
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
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14
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Kiriakidi S, Chatzigiannis C, Papaemmanouil C, Tzakos AG, Mavromoustakos T. Exploring the role of the membrane bilayer in the recognition of candesartan by its GPCR AT1 receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183142. [PMID: 31830465 DOI: 10.1016/j.bbamem.2019.183142] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/13/2019] [Accepted: 11/28/2019] [Indexed: 01/20/2023]
Abstract
Cardiovascular diseases and hypertension in particular are major health risks worldwide and the improvement on their treatment will be beneficial for the human health. AT1R antagonists belong to the sartans family that targets the renin-angiotensin aldosterone system (RAAS) through blocking the hormone angiotensin II to exert its detrimental effects in pathological states. As a consequence, they are beneficial to treat hypertension, diabetes related kidney failure and hyperaemic episodes. Long unbiased Molecular Dynamics (MD) simulations are performed in order to explore candesartan's possible 2D and 3D diffusion mechanisms towards AT1R receptor. 3D diffusion mechanism is referred to the direct binding of the AT1 antagonist candesartan to the AT1R 3D structure (PDB ID: 4YAY). 2D diffusion mechanism involves first, the incorporation of candesartan in the bilayer core and then its localization on the AT1R binding cavity, through a diffusion mechanism. The obtained results indicate that membranes interact significantly with the neutral form of candesartan, which is indeed approaching the receptors' active site through diffusion via the lipids. On the other hand, the deprotonated form of the drug is interacting with AT1R's extracellular loop and fails to enter the membrane, pointing out the importance of the pH microenvironment around the receptor. To validate the calculated diffusion coefficients of the drug in the lipid bilayers 2D DOSY NMR experiments were recorded and they were in good agreement. Information on the impact that has the interaction of candesartan with the membrane is very important for the rationally design and development of potent ARBs. Thus, its conformational features as well as its localization in the membrane core have to be thoroughly explored.
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Affiliation(s)
- Sofia Kiriakidi
- National and Kapodistrian University of Athens, Department of Chemistry, Athens, Greece
| | - Christos Chatzigiannis
- University of Ioannina, Department of Chemistry, Section of Organic Chemistry and Biochemistry, Ioannina, Greece
| | - Christina Papaemmanouil
- University of Ioannina, Department of Chemistry, Section of Organic Chemistry and Biochemistry, Ioannina, Greece
| | - Andreas G Tzakos
- University of Ioannina, Department of Chemistry, Section of Organic Chemistry and Biochemistry, Ioannina, Greece
| | - Thomas Mavromoustakos
- National and Kapodistrian University of Athens, Department of Chemistry, Athens, Greece.
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15
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Gentry KA, Anantharamaiah GM, Ramamoorthy A. Probing protein-protein and protein-substrate interactions in the dynamic membrane-associated ternary complex of cytochromes P450, b 5, and reductase. Chem Commun (Camb) 2019; 55:13422-13425. [PMID: 31638629 PMCID: PMC6879317 DOI: 10.1039/c9cc05904k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytochrome P450 (cytP450) interacts with two redox partners, cytP450 reductase and cytochrome-b5, to metabolize substrates. Using NMR, we reveal changes in the dynamic interplay when all three proteins are incorporated into lipid nanodiscs in the absence and presence of substrates.
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Affiliation(s)
- Katherine A Gentry
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - G M Anantharamaiah
- Department of Medicine, UAB Medical Center, Birmingham, Alabama 35294, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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16
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Conformational turn triggers regio-selectivity in the bioactivation of thiophene-contained compounds mediated by cytochrome P450. J Biol Inorg Chem 2019; 24:1023-1033. [PMID: 31506822 DOI: 10.1007/s00775-019-01699-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/24/2019] [Indexed: 10/26/2022]
Abstract
In the present work, we performed Density Functional Theory calculations to explore the bioactivation mechanism of thiophene-containing molecules mediated by P450s. For this purpose, relatively large size compounds, 2,5-diaminothiophene derivatives were selected particularly for this investigation. Here we found the successive regio-selectivity triggered by conformational turn played a significant role in the occurrence of bioactivation. 2,5-Diaminothiophene was oxidized to a 2,5-diimine thiophene-reactive intermediate by Compound I (Cpd I) through successive activations of two N-H bonds (H3-N11 and H1-N6). This reaction exhibited three special characteristics: (1) self-controlled regio-selectivity during the oxidation process. There was a large scale of conformational turn in the abstraction of the first H atom which triggers the selection of the second H for abstraction. (2) Proton-shuttle mechanism. In high spin (HS) state, proton-shuttle mechanism was observed for the abstraction of the second H atom. (3) Spin-selective manner. In protein environment, the energy barrier in HS state was much lower than that in low spin state. The novel proposed bioactivation mechanism of 2,5-diaminothiophene compounds can help us in rational design of thiophene-contained drugs avoiding the occurrence of bioactivation.
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17
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Parui PP, Sarakar Y, Majumder R, Das S, Yang H, Yasuhara K, Hirota S. Determination of proton concentration at cardiolipin-containing membrane interfaces and its relation with the peroxidase activity of cytochrome c. Chem Sci 2019; 10:9140-9151. [PMID: 31827756 PMCID: PMC6889831 DOI: 10.1039/c9sc02993a] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/03/2019] [Indexed: 01/04/2023] Open
Abstract
The interface –log[H+] defined as pH′ of a mimic inner mitochondrial membrane is ∼3.9 at bulk pH ∼ 6.8, which affects cytochrome c activity.
The activities of biomolecules are affected by the proton concentrations at biological membranes. Here, we succeeded in evaluating the interface proton concentration (–log[H+] defined as pH′) of cardiolipin (CL)-enriched membrane models of the inner mitochondrial membrane (IMM) using a spiro-rhodamine-glucose molecule (RHG). According to fluorescence microscopy and 1H-NMR studies, RHG interacted with the Stern layer of the membrane. The acid/base equilibrium of RHG between its protonated open form (o-RHG) and deprotonated closed spiro-form (c-RHG) at the membrane interface was monitored with UV-vis absorption and fluorescence spectra. The interface pH′ of 25% cardiolipin (CL)-containing large unilamellar vesicles (LUVs), which possess similar lipid properties to those of the IMM, was estimated to be ∼3.9, when the bulk pH was similar to the mitochondrial intermembrane space pH (6.8). However, for the membranes containing mono-anionic lipids, the interface pH′ was estimated to be ∼5.3 at bulk pH 6.8, indicating that the local negative charges of the lipid headgroups in the lipid membranes are responsible for the deviation of the interface pH′ from the bulk pH. The peroxidase activity of cyt c increased 5–7 fold upon lowering the pH to 3.9–4.3 or adding CL-containing (10–25% of total lipids) LUVs compared to that at bulk pH 6.8, indicating that the pH′ decrease at the IMM interface from the bulk pH enhances the peroxidase activity of cyt c. The peroxidase activity of cyt c at the membrane interface of tetraoleoyl CL (TOCL)-enriched (50% of total lipids) LUVs was higher than that estimated from the interface pH′, while the peroxidase activity was similar to that estimated from the interface pH′ for tetramyristoyl CL (TMCL)-enriched LUVs, supporting the hypothesis that when interacting with TOCL (not TMCL), cyt c opens the heme crevice to substrates. The present simple methodology allows us to estimate the interface proton concentrations of complex biological membranes.
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Affiliation(s)
- Partha Pratim Parui
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492.,Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
| | - Yeasmin Sarakar
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492
| | - Rini Majumder
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492
| | - Sanju Das
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492.,Department of Chemistry , Maulana Azad College , Kolkata 700013 , India
| | - Hongxu Yang
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
| | - Kazuma Yasuhara
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
| | - Shun Hirota
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
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18
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Mahajan M, Ravula T, Prade E, Anantharamaiah GM, Ramamoorthy A. Probing membrane enhanced protein-protein interactions in a minimal redox complex of cytochrome-P450 and P450-reductase. Chem Commun (Camb) 2019; 55:5777-5780. [PMID: 31041432 PMCID: PMC7467500 DOI: 10.1039/c9cc01630a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Investigating the interplay in a minimal redox complex of cytochrome-P450 and its reductase is crucial for understanding cytochrome-P450's enzymatic activity. Probing the hotspots of dynamic structural interactions using NMR revealed the engagement of loop residues from P450-reductase to be responsible for the enhanced affinity of CYP450 towards its obligate redox partner.
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Affiliation(s)
- Mukesh Mahajan
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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19
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Xia C, Shen AL, Duangkaew P, Kotewong R, Rongnoparut P, Feix J, Kim JJP. Structural and Functional Studies of the Membrane-Binding Domain of NADPH-Cytochrome P450 Oxidoreductase. Biochemistry 2019; 58:2408-2418. [PMID: 31009206 PMCID: PMC6873807 DOI: 10.1021/acs.biochem.9b00130] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NADPH-cytochrome P450 oxidoreductase (CYPOR), the essential flavoprotein of the microsomal cytochrome P450 monooxygenase system, is anchored in the phospholipid bilayer by its amino-terminal membrane-binding domain (MBD), which is necessary for efficient electron transfer to cytochrome P450. Although crystallographic and kinetic studies have established the structure of the soluble catalytic domain and the role of conformational motions in the control of electron transfer, the role of the MBD is largely unknown. We examined the role of the MBD in P450 catalysis through studies of amino-terminal deletion mutants and site-directed spin labeling. We show that the MBD spans the membrane and present a model for the orientation of CYPOR on the membrane capable of forming a complex with cytochrome P450. EPR power saturation measurements of CYPOR mutants in liposomes containing a lipid/Ni(II) chelate identified a region of the soluble domain interacting with the membrane. The deletion of more than 29 residues from the N-terminus of CYPOR decreases cytochrome P450 activity concomitant with alterations in electrophoretic mobility and an increased resistance to protease digestion. The altered kinetic properties of these mutants are consistent with electron transfer through random collisions rather than via formation of a stable CYPOR-P450 complex. Purified MBD binds weakly to cytochrome P450, suggesting that other interactions are also required for CYPOR-P450 complex formation. We propose that the MBD and flexible tether region of CYPOR, residues 51-63, play an important role in facilitating the movement of the soluble domain relative to the membrane and in promoting multiple orientations that permit specific interactions of CYPOR with its varied partners.
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Affiliation(s)
- Chuanwu Xia
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Anna L Shen
- McArdle Laboratory for Cancer Research , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Panida Duangkaew
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
- Department of Biochemistry, Faculty of Science , Mahidol University , Bangkok 10400 , Thailand
| | - Rattanawadee Kotewong
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
- Department of Biochemistry, Faculty of Science , Mahidol University , Bangkok 10400 , Thailand
| | - Pornpimol Rongnoparut
- Department of Biochemistry, Faculty of Science , Mahidol University , Bangkok 10400 , Thailand
| | - Jimmy Feix
- Department of Biophysics , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Jung-Ja P Kim
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
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20
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Huff HC, Maroutsos D, Das A. Lipid composition and macromolecular crowding effects on CYP2J2-mediated drug metabolism in nanodiscs. Protein Sci 2019; 28:928-940. [PMID: 30861250 DOI: 10.1002/pro.3603] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023]
Abstract
Lipid composition and macromolecular crowding are key external effectors of protein activity and stability whose role varies between different proteins. Therefore, it is imperative to study their effects on individual protein function. CYP2J2 is a membrane-bound cytochrome P450 in the heart involved in the metabolism of fatty acids and xenobiotics. In order to facilitate this metabolism, cytochrome P450 reductase (CPR), transfers electrons to CYP2J2 from NADPH. Herein, we use nanodiscs to show that lipid composition of the membrane bilayer affects substrate metabolism of the CYP2J2-CPR nanodisc (ND) system. Differential effects on both NADPH oxidation and substrate metabolism by CYP2J2-CPR are dependent on the lipid composition. For instance, sphingomyelin containing nanodiscs produced more secondary substrate metabolites than discs of other lipid compositions, implying a possible conformational change leading to processive metabolism. Furthermore, we demonstrate that macromolecular crowding plays a role in the lipid-solubilized CYP2J2-CPR system by increasing the Km and decreasing the Vmax , and effect that is size-dependent. Crowding also affects the CYP2J2-CPR-ND system by decreasing both the Km and Vmax for Dextran-based macromolecular crowding agents, implying an increase in substrate affinity but a lack of metabolism. Finally, protein denaturation studies show that crowding agents destabilize CYP2J2, while the multidomain protein CPR is stabilized. Overall, these studies are the first report on the role of the surrounding lipid environment and macromolecular crowding in modulating enzymatic function of CYP2J2-CPR membrane protein system.
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Affiliation(s)
- Hannah C Huff
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Demetri Maroutsos
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Aditi Das
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Beckman Institute for Advanced Science and Technology, Division of Nutritional Science, Neuroscience Program, and Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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21
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Salnikov ES, Aisenbrey C, Anantharamaiah G, Bechinger B. Solid-state NMR structural investigations of peptide-based nanodiscs and of transmembrane helices in bicellar arrangements. Chem Phys Lipids 2019; 219:58-71. [DOI: 10.1016/j.chemphyslip.2019.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 02/08/2023]
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22
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Jiang L, Wang K, Zhang F, Zhang Y, Wang H, Liu S. Enhanced Metabolic Activity of Cytochrome P450 via Carbon Nanocage-Based Photochemical Bionanoreactor. ACS APPLIED MATERIALS & INTERFACES 2018; 10:41956-41961. [PMID: 30422622 DOI: 10.1021/acsami.8b14810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recently, the early screening of the genotoxicity of new chemicals and drugs calls for the envelope of micro-/nanoreactors for metabolic study. Herein, a novel light-driven enzymatic bionanoreactor is designed with the gold nanoparticle (NP)-modified carbon nanocage (Au@CNC) as a nanoreactor and meso-tetrakis(4-carboxyphenyl)porphyrin (TCPP) as a photosensitizer for cytochrome P450-mediated drug metabolism. By confining the cytochrome P450 3A4 (CYP3A4) enzyme and TCPP inside the pores of Au@CNC, a high metabolic activity is achieved by using 7-ethoxytrifluoromethyl coumarin as the substrate because of the three-dimensional hierarchical porous structure, large surface area, and fast electron transfer capacity of Au@CNC. It is noted that owing to the presence of AuNPs inside CNC, the surface hydrophilicity of CNC is much improved, which further promotes the catalytic activity of the CYP3A4 enzyme. To our knowledge, this is the first attempt to apply CNC as a bionanoreactor for NADPH-free and light-driven in vitro drug metabolism. In addition, the presented bionanoreactor exhibits a variety of advantages in terms of fast response, short assay time (10 min), high sensitivity, and good selectivity, which are expected to expedite drug screening and render potential advances in drug discovery and development.
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Affiliation(s)
- Ling Jiang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering , Southeast University , Nanjing 210096 , PR China
| | - Kan Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering , Southeast University , Nanjing 210096 , PR China
| | - Fen Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering , Southeast University , Nanjing 210096 , PR China
| | - Yuanjian Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering , Southeast University , Nanjing 210096 , PR China
| | - Huaisheng Wang
- Department of Chemistry , Liaocheng University , Liaocheng , Shandong 252059 , China
| | - Songqin Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering , Southeast University , Nanjing 210096 , PR China
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23
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Molecular mechanism of metabolic NAD(P)H-dependent electron-transfer systems: The role of redox cofactors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:233-258. [PMID: 30419202 DOI: 10.1016/j.bbabio.2018.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 12/14/2022]
Abstract
NAD(P)H-dependent electron-transfer (ET) systems require three functional components: a flavin-containing NAD(P)H-dehydrogenase, one-electron carrier and metal-containing redox center. In principle, these ET systems consist of one-, two- and three-components, and the electron flux from pyridine nucleotide cofactors, NADPH or NADH to final electron acceptor follows a linear pathway: NAD(P)H → flavin → one-electron carrier → metal containing redox center. In each step ET is primarily controlled by one- and two-electron midpoint reduction potentials of protein-bound redox cofactors in which the redox-linked conformational changes during the catalytic cycle are required for the domain-domain interactions. These interactions play an effective ET reactions in the multi-component ET systems. The microsomal and mitochondrial cytochrome P450 (cyt P450) ET systems, nitric oxide synthase (NOS) isozymes, cytochrome b5 (cyt b5) ET systems and methionine synthase (MS) ET system include a combination of multi-domain, and their organizations display similarities as well as differences in their components. However, these ET systems are sharing of a similar mechanism. More recent structural information obtained by X-ray and cryo-electron microscopy (cryo-EM) analysis provides more detail for the mechanisms associated with multi-domain ET systems. Therefore, this review summarizes the roles of redox cofactors in the metabolic ET systems on the basis of one-electron redox potentials. In final Section, evolutionary aspects of NAD(P)H-dependent multi-domain ET systems will be discussed.
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24
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Ravula T, Hardin NZ, Di Mauro GM, Ramamoorthy A. Styrene maleic acid derivates to enhance the applications of bio-inspired polymer based lipid-nanodiscs. Eur Polym J 2018; 108:597-602. [PMID: 31105326 PMCID: PMC6516473 DOI: 10.1016/j.eurpolymj.2018.09.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Membrane mimetics are essential to study the structure, dynamics and function of membrane-associated proteins by biophysical and biochemical approaches. Among various membrane mimetics that have been developed and demonstrated for studies on membrane proteins, lipid nanodiscs are the latest developments in the field and are increasingly used for various applications. While lipid-nanodiscs can be formed using an amphipathic membrane scaffold protein (MSP), peptide, or synthetic polymer, the synthetic polymer based nanodiscs exhibit unique advantages because of the ability to functionalize them for various applications. In addition to the use of synthetic polymers to extract membrane proteins directly from the cell membranes, recent advances in the development of polymers used for nanodiscs formation are attracting new attention to the field of nanodiscs technology. Here we review the developments of novel polymer modifications that overcome the current limitations and enhance the applications of polymer based nanodiscs to a wider variety of biophysical techniques used to study membrane proteins. A summary of the functionalization of poly(Styrene-co-Maleic Acid), SMA, polymers developed by our research and their advantages are also covered in this review article.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | - Nathaniel. Z Hardin
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | - Giacomo M. Di Mauro
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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25
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Sahoo BR, Genjo T, Cox SJ, Stoddard AK, Anantharamaiah GM, Fierke C, Ramamoorthy A. Nanodisc-Forming Scaffold Protein Promoted Retardation of Amyloid-Beta Aggregation. J Mol Biol 2018; 430:4230-4244. [PMID: 30170005 DOI: 10.1016/j.jmb.2018.08.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/23/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Peptidic nanodiscs are useful membrane mimetic tools for structural and functional studies of membrane proteins, and membrane interacting peptides including amyloids. Here, we demonstrate anti-amyloidogenic activities of a nanodisc-forming 18-residue peptide (denoted as 4F), both in lipid-bound and lipid-free states by using Alzheimer's amyloid-beta (Aβ40) peptide as an example. Fluorescence-based amyloid fibrillation kinetic assays showed a significant delay in Aβ40 amyloid aggregation by the 4F peptide. In addition, 4F-encased lipid nanodiscs, at an optimal concentration of 4F (>20 μM) and nanodisc size (<10 nm), significantly affect amyloid fibrillation. A comparison of experimental results obtained from nanodiscs with that obtained from liposomes revealed a substantial inhibitory efficacy of 4F-lipid nanodiscs against Aβ40 aggregation and were also found to be suitable to trap Aβ40 intermediates. A combination of atomistic molecular dynamics simulations with NMR and circular dichroism experimental results exhibited a substantial change in Aβ40 conformation upon 4F binding through electrostatic and π-π interactions. Specifically, the 4F peptide was found to interfere with the central β-sheet-forming residues of Aβ40 through substantial hydrogen, π-π, and π-alkyl interactions. Fluorescence experiments and coarse-grained molecular dynamics simulations showed the formation of a ternary complex, where Aβ40 binds to the proximity of peptidic belt and membrane surface that deaccelerate amyloid fibrillation. Electron microscopy images revealed short and thick amyloid fibers of Aβ40 formed in the presence of 4F or 4F-lipid nanodsics. These findings could aid in the development of amyloid inhibitors as well as in stabilizing Aβ40 intermediates for high-resolution structural and neurobiological studies.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Biophysics Program, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Takuya Genjo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Biophysics Program, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Sarah J Cox
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Andrea K Stoddard
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | | | - Carol Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department of Chemistry, University of Texas A&M, College Station, TX 77843-3255, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Biophysics Program, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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26
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Ravula T, Hardin NZ, Bai J, Im SC, Waskell L, Ramamoorthy A. Effect of polymer charge on functional reconstitution of membrane proteins in polymer nanodiscs. Chem Commun (Camb) 2018; 54:9615-9618. [PMID: 30094448 DOI: 10.1039/c8cc04184a] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although there is a growing interest in using polymer lipid-nanodiscs, the polymer charge poses limitations for studies on membrane proteins. Here, we demonstrate the functional reconstitution of a large soluble-domain containing positively-charged ∼57 kDa cytochrome-P450 and negatively-charged ∼16 kDa cytochrome-b5 in lipid-nanodiscs, and the role of the polymer charge for high-resolution studies on membrane proteins.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics and Department of Chemistry, University of Michigan Ann Arbor, Ann Arbor, MI 48109-1055, USA.
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27
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Barnaba C, Ramamoorthy A. Picturing the Membrane-assisted Choreography of Cytochrome P450 with Lipid Nanodiscs. Chemphyschem 2018; 19:2603-2613. [DOI: 10.1002/cphc.201800444] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Carlo Barnaba
- Biophysics and Department of Chemistry; University of Michigan; Ann Arbor, MI 48109-1055 USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry; University of Michigan; Ann Arbor, MI 48109-1055 USA
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28
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Supramolecular Organization of Apolipoprotein-A-I-Derived Peptides within Disc-like Arrangements. Biophys J 2018; 115:467-477. [PMID: 30054032 DOI: 10.1016/j.bpj.2018.06.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 01/05/2023] Open
Abstract
Apolipoprotein A-I is the major protein component of high-density lipoproteins and fulfils important functions in lipid metabolism. Its structure consists of a chain of tandem domains of amphipathic helices. Using this protein as a template membrane scaffolding protein, class A amphipathic helical peptides were designed to support the amphipathic helix theory and later as therapeutic tools in biomedicine. Here, we investigated the lipid interactions of two apolipoprotein-A-I-derived class A amphipathic peptides, 14A (Ac-DYLKA FYDKL KEAF-NH2) and 18A (Ac-DWLKA FYDKV AEKLK EAF- NH2), including the disc-like supramolecular structures they form with phospholipids. Thus, the topologies of 14A and 18A in phospholipid bilayers have been determined by oriented solid-state NMR spectroscopy. Whereas at a peptide-to-lipid ratio of 2 mol% the peptides align parallel to the bilayer surface, at 7.5 mol% disc-like structures are formed that spontaneously orient in the magnetic field of the NMR spectrometer. From a comprehensive data set of four 15N- or 2H-labeled positions of 14A, a tilt angle, which deviates from perfectly in-planar by 14°, and a model for the peptidic rim structure have been obtained. The tilt and helical pitch angles are well suited to cover the hydrophobic chain region of the bilayer when two peptide helices form a head-to-tail dimer. Thus, the detailed topology found in this work agrees with the peptides forming the rim of nanodiscs in a double belt arrangement.
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29
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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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30
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Barnaba C, Ravula T, Medina-Meza IG, Im SC, Anantharamaiah GM, Waskell L, Ramamoorthy A. Lipid-exchange in nanodiscs discloses membrane boundaries of cytochrome-P450 reductase. Chem Commun (Camb) 2018; 54:6336-6339. [PMID: 29863198 PMCID: PMC6022741 DOI: 10.1039/c8cc02003e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lipids are critical for the function of membrane proteins. NADPH-cytochrome-P450-reductase, the sole electron transferase for microsomal oxygenases, possesses a conformational dynamics entwined with its topology. Here, we use peptide-nanodiscs to unveil cytochrome-P450-reductase's lipid boundaries, demonstrating a protein-driven enrichment of ethanolamine lipids (by 25%) which ameliorates by 3-fold CPR's electron-transfer ability.
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Affiliation(s)
- Carlo Barnaba
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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31
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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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32
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Hall SCL, Tognoloni C, Charlton J, Bragginton ÉC, Rothnie AJ, Sridhar P, Wheatley M, Knowles TJ, Arnold T, Edler KJ, Dafforn TR. An acid-compatible co-polymer for the solubilization of membranes and proteins into lipid bilayer-containing nanoparticles. NANOSCALE 2018; 10:10609-10619. [PMID: 29845165 PMCID: PMC5996351 DOI: 10.1039/c8nr01322e] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/23/2018] [Indexed: 05/20/2023]
Abstract
The fundamental importance of membrane proteins in drug discovery has meant that membrane mimetic systems for studying membrane proteins are of increasing interest. One such system has been the amphipathic, negatively charged poly(styrene-co-maleic acid) (SMA) polymer to form "SMA Lipid Particles" (SMALPs) which have been widely adopted to solubilize membrane proteins directly from the cell membrane. However, SMALPs are only soluble under basic conditions and precipitate in the presence of divalent cations required for many downstream applications. Here, we show that the positively charged poly(styrene-co-maleimide) (SMI) forms similar nanoparticles with comparable efficiency to SMA, whilst remaining functional at acidic pH and compatible with high concentrations of divalent cations. We have performed a detailed characterization of the performance of SMI that enables a direct comparison with similar data published for SMA. We also demonstrate that SMI is capable of extracting proteins directly from the cell membrane and can solubilize functional human G-protein coupled receptors (GPCRs) expressed in cultured HEK 293T cells. "SMILPs" thus provide an alternative membrane solubilization method that successfully overcomes some of the limitations of the SMALP method.
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Affiliation(s)
- Stephen C. L. Hall
- School of Biosciences
, University of Birmingham
,
Edgbaston
, Birmingham
, B15 2TT
, UK
.
- Diamond Light Source
, Harwell Science and Innovation Campus
,
Didcot
, OX11 ODE
, UK
.
;
| | - Cecilia Tognoloni
- Department of Chemistry
, University of Bath
,
Claverton Down
, Bath
, BA2 7AY
, UK
| | - Jack Charlton
- School of Biosciences
, University of Birmingham
,
Edgbaston
, Birmingham
, B15 2TT
, UK
.
| | - Éilís C. Bragginton
- School of Cellular and Molecular Medicine
, University of Bristol
, University Walk
,
Bristol
, BS8 1TD
, UK
| | - Alice J. Rothnie
- School of Life & Health Sciences
, Aston University
,
Aston Triangle
, Birmingham B4 7ET
, UK
| | - Pooja Sridhar
- School of Biosciences
, University of Birmingham
,
Edgbaston
, Birmingham
, B15 2TT
, UK
.
| | - Mark Wheatley
- School of Biosciences
, University of Birmingham
,
Edgbaston
, Birmingham
, B15 2TT
, UK
.
- Centre of Membrane and Protein and Receptors (COMPARE)
, University of Birmingham and University of Nottingham
,
Midlands
, UK
| | - Timothy J. Knowles
- School of Biosciences
, University of Birmingham
,
Edgbaston
, Birmingham
, B15 2TT
, UK
.
| | - Thomas Arnold
- Diamond Light Source
, Harwell Science and Innovation Campus
,
Didcot
, OX11 ODE
, UK
.
;
- Department of Chemistry
, University of Bath
,
Claverton Down
, Bath
, BA2 7AY
, UK
- European Spallation Source ERIC
,
P.O Box 176
, SE-221 00 Lund
, Sweden
| | - Karen J. Edler
- Department of Chemistry
, University of Bath
,
Claverton Down
, Bath
, BA2 7AY
, UK
| | - Tim R. Dafforn
- School of Biosciences
, University of Birmingham
,
Edgbaston
, Birmingham
, B15 2TT
, UK
.
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33
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Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M. Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem 2018; 183:117-136. [DOI: 10.1016/j.jinorgbio.2018.03.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/16/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023]
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34
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Li Q, Han X. Self-Assembled "Breathing" Grana-Like Cisternae Stacks. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707482. [PMID: 29707837 DOI: 10.1002/adma.201707482] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Membranes in cells display elaborate, dynamic morphologies intimately tied to defined cellular functions. Cisternae stacks are a common membrane morphology in cells widely found in organelles. However, compared with the well-studied spherical cell membrane mimics, cisternae stacks as organelle membrane mimics are greatly neglected because of the difficulty of fabricating this unique structure. Herein, the grana-like cisternae stacks are assembled via the reorganization of stacked microsized bicelles to mimic grana functions. The cisternae stacks are connected by fusion regions between adjacent cisternae. The number of cisternae can be controlled from ≈4 to 15 by the variation of ethanol volume percentage. Under the stimulation of solvent or negatively charged nanoparticles, the cisternae stacks can reversibly compress and expand, similar to the "breathing" property of natural grana. During the "breathing" process, nanoparticles are reversibly captured and released. Frequency resonance energy transfer is realized on the cisternae stacks trapped with two kinds of quantum dots. The cisternae stacks provide advanced membrane model for cell biotechnology, and clues for the shaping of organelles composed of cisternae. The ability of the cisternae stacks to capture materials enables them to possibly be applied in biomimetics and the design of advanced functional materials.
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Affiliation(s)
- Qingchuan Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
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35
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Barnaba C, Sahoo BR, Ravula T, Medina-Meza IG, Im SC, Anantharamaiah GM, Waskell L, Ramamoorthy A. Cytochrome-P450-Induced Ordering of Microsomal Membranes Modulates Affinity for Drugs. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carlo Barnaba
- Biophysics and Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
| | - Bikash Ranjan Sahoo
- Biophysics and Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
| | - Thirupathi Ravula
- Biophysics and Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
| | - Ilce G. Medina-Meza
- Department of Biosystems and Agricultural Engineering; Michigan State University; East Lansing MI 48824-1323 USA
| | - Sang-Choul Im
- Department of Anesthesiology; University of Michigan and VA Medical Center; Ann Arbor MI 48105-1055 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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36
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Barnaba C, Sahoo BR, Ravula T, Medina-Meza IG, Im SC, Anantharamaiah GM, Waskell L, Ramamoorthy A. Cytochrome-P450-Induced Ordering of Microsomal Membranes Modulates Affinity for Drugs. Angew Chem Int Ed Engl 2018; 57:3391-3395. [PMID: 29385304 DOI: 10.1002/anie.201713167] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/16/2018] [Indexed: 11/08/2022]
Abstract
Although membrane environment is known to boost drug metabolism by mammalian cytochrome P450s, the factors that stabilize the structural folding and enhance protein function are unclear. In this study, we use peptide-based lipid nanodiscs to "trap" the lipid boundaries of microsomal cytochrome P450 2B4. We report the first evidence that CYP2B4 is able to induce the formation of raft domains in a biomimetic compound of the endoplasmic reticulum. NMR experiments were used to identify and quantitatively determine the lipids present in nanodiscs. A combination of biophysical experiments and molecular dynamics simulations revealed a sphingomyelin binding region in CYP2B4. The protein-induced lipid raft formation increased the thermal stability of P450 and dramatically altered ligand binding kinetics of the hydrophilic ligand BHT. These results unveil membrane/protein dynamics that contribute to the delicate mechanism of redox catalysis in lipid membrane.
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Affiliation(s)
- Carlo Barnaba
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Bikash Ranjan Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Thirupathi Ravula
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Ilce G Medina-Meza
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI, 48824-1323, USA
| | - Sang-Choul Im
- Department of Anesthesiology, University of Michigan and VA Medical Center, Ann Arbor, MI, 48105-1055, USA
| | - G M Anantharamaiah
- Department of Medicine, UAB Medical Center, Birmingham, Alabama, 35294, 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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37
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Rumpel S, Ravera E, Sommer C, Reijerse E, Farès C, Luchinat C, Lubitz W. 1H NMR Spectroscopy of [FeFe] Hydrogenase: Insight into the Electronic Structure of the Active Site. J Am Chem Soc 2018; 140:131-134. [PMID: 29211457 PMCID: PMC5765528 DOI: 10.1021/jacs.7b11196] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The [FeFe] hydrogenase
HydA1 from Chlamydomonas reinhardtii has been studied
using 1H NMR spectroscopy identifying
the paramagnetically shifted 1H resonances associated with
both the [4Fe-4S]H and the
[2Fe]H subclusters of the active site “H-cluster”.
The signal pattern of the unmaturated HydA1 containing only [4Fe-4S]H is reminiscent of bacterial-type ferredoxins. The spectra
of maturated HydA1, with a complete H-cluster in the active Hox and the CO-inhibited Hox–CO state, reveal
additional upfield and downfield shifted 1H resonances
originating from the four methylene protons of the azadithiolate ligand
in the [2Fe]H subsite. The two axial protons are affected
by positive spin density, while the two equatorial protons experience
negative spin density. These protons can be used as important probes
sensing the effects of ligand-binding to the catalytic site of the
H-cluster.
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Affiliation(s)
- Sigrun Rumpel
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Enrico Ravera
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Constanze Sommer
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Claudio Luchinat
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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