1
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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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2
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Saad A, Bechinger B. Solid-state NMR spectroscopy for structural studies of polypeptides and lipids in extended physiological membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184162. [PMID: 37949788 DOI: 10.1016/j.bbamem.2023.184162] [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: 04/06/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 11/12/2023]
Abstract
Solid-state NMR is a quickly developing technique that allows one to obtain structural information at atomic resolution in extended lipid bilayers in a rather unique manner. Two approaches have been developed for membrane proteins and peptides namely magic angle sample spinning and the use of uniaxially oriented membrane samples. The state-of-the-art of both approaches will be introduced and the perspectives of solid-state NMR spectroscopy in the context of other structural biology techniques, pressing biomedical questions and membrane biophysics will be discussed.
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Affiliation(s)
- Ahmad Saad
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France; Institut Universitaire de France, 75005 Paris, France.
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3
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Sahoo BR, Ramamoorthy A. Direct interaction between the transmembrane helices stabilize cytochrome P450 2B4 and cytochrome b5 redox complex. Biophys Chem 2023; 301:107092. [PMID: 37586236 PMCID: PMC10838600 DOI: 10.1016/j.bpc.2023.107092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023]
Abstract
The catalytic activity of cytochrome P450 2B4 (CYP2B4) is moderated by its cognate redox partner cytochrome b5 (Cyt-b5). The endoplasmic reticulum (ER) membrane and intermolecular transmembrane (TM) interaction between CYP2B4 and Cyt-b5 regulate the substrate catalysis and the reaction rate. This emphasizes the significance of elucidating the molecular basis of CYP2B4 and Cyt-b5 complexation in a membrane environment to better understand the enzymatic activity of CYP2B4. Our previous solid-state NMR studies revealed the membrane topology of the transmembrane domains of these proteins in the free and complex forms. Here, we show the cross-angle complex formation by the single-pass TM domains of CYP2B4 and Cyt-b5, which is mainly driven by several salt-bridges (E2-R128, R21-D104 and K25-D104), using a multi-microsecond molecular dynamic simulation. Additionally, the leucine-zipper residues (L8, L12, L15, L18 and L19 from CYP2B4) and π-stacking between H23 and F20 residues of CYP2B4 and W110 of Cyt-b5 are identified to stabilize the TM-TM complex in the ER membrane. The simulated tilts of the helices in the free and in the complex are in excellent agreement with solid-state NMR results. The TM-TM packing influences a higher order structural stability when compared to the complex formed by the truncated soluble domains of these two proteins. MM/PBSA based binding free energy estimates nearly 100-fold higher binding affinity (ΔG = -2810.68 ± 696.44 kJ/mol) between the soluble domains of the full-length CYP2B4 and Cyt-b5 when embedded in lipid membrane as compared to the TM-domain-truncated soluble domains (ΔG = -27.406 ± 10.32 kJ/mol). The high-resolution full-length CYP2B4-Cyt-b5 complex structure and its dynamics in a native ER membrane environment reported here could aid in the development of approaches to effectively modulate the drug-metabolism activity of CYP2B4.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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4
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Becker-Baldus J, Yeliseev A, Joseph TT, Sigurdsson ST, Zoubak L, Hines K, Iyer MR, van den Berg A, Stepnowski S, Zmuda J, Gawrisch K, Glaubitz C. Probing the Conformational Space of the Cannabinoid Receptor 2 and a Systematic Investigation of DNP-Enhanced MAS NMR Spectroscopy of Proteins in Detergent Micelles. ACS OMEGA 2023; 8:32963-32976. [PMID: 37720784 PMCID: PMC10500644 DOI: 10.1021/acsomega.3c04681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/09/2023] [Indexed: 09/19/2023]
Abstract
Tremendous progress has been made in determining the structures of G-protein coupled receptors (GPCR) and their complexes in recent years. However, understanding activation and signaling in GPCRs is still challenging due to the role of protein dynamics in these processes. Here, we show how dynamic nuclear polarization (DNP)-enhanced magic angle spinning nuclear magnetic resonance in combination with a unique pair labeling approach can be used to study the conformational ensemble at specific sites of the cannabinoid receptor 2. To improve the signal-to-noise, we carefully optimized the DNP sample conditions and utilized the recently introduced AsymPol-POK as a polarizing agent. We could show qualitatively that the conformational space available to the protein backbone is different in different parts of the receptor and that a site in TM7 is sensitive to the nature of the ligand, whereas a site in ICL3 always showed large conformational freedom.
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Affiliation(s)
- Johanna Becker-Baldus
- Institute
of Biophysical Chemistry and Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Alexei Yeliseev
- National
Institute on Alcohol Abuse and Alcoholism, National Institutes of
Health, Bethesda, Maryland 20852, United States
| | - Thomas T. Joseph
- Department
of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Snorri Th. Sigurdsson
- Department
of Chemistry, Science Institute, University
of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - Lioudmila Zoubak
- National
Institute on Alcohol Abuse and Alcoholism, National Institutes of
Health, Bethesda, Maryland 20852, United States
| | - Kirk Hines
- National
Institute on Alcohol Abuse and Alcoholism, National Institutes of
Health, Bethesda, Maryland 20852, United States
| | - Malliga R. Iyer
- Section
on Medicinal Chemistry, National Institute
on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Arjen van den Berg
- ThermoFisher
Scientific, 7335 Executive
Way, Frederick, Maryland 21704, United States
| | - Sam Stepnowski
- ThermoFisher
Scientific, 7335 Executive
Way, Frederick, Maryland 21704, United States
| | - Jon Zmuda
- ThermoFisher
Scientific, 7335 Executive
Way, Frederick, Maryland 21704, United States
| | - Klaus Gawrisch
- National
Institute on Alcohol Abuse and Alcoholism, National Institutes of
Health, Bethesda, Maryland 20852, United States
| | - Clemens Glaubitz
- Institute
of Biophysical Chemistry and Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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5
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Shen J, Wu G, Tsai AL, Zhou M. Transmembrane helices mediate the formation of a stable ternary complex of b 5R, cyt b 5, and SCD1. Commun Biol 2022; 5:956. [PMID: 36097052 PMCID: PMC9468158 DOI: 10.1038/s42003-022-03882-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022] Open
Abstract
Mammalian cytochrome b5 (cyt b5) and cytochrome b5 reductase (b5R) are electron carrier proteins for membrane-embedded oxidoreductases. Both b5R and cyt b5 have a cytosolic domain and a single transmembrane (TM) helix. The cytosolic domains of b5R and cyt b5 contain cofactors required for electron transfer, but it is not clear if the TM helix has function beyond being an anchor to the membrane. Here we show that b5R and cyt b5 form a stable binary complex, and so do cyt b5 and stearoyl-CoA desaturase-1 (SCD1). We also show that b5R, cyt b5 and SCD1 form a stable ternary complex. We demonstrate that the TM helices are required for the assembly of stable binary and ternary complexes where electron transfer rates are greatly enhanced. These results reveal a role of the TM helix in cyt b5 and b5R, and suggest that an electron transport chain composed of a stable ternary complex may be a general feature in membrane-embedded oxidoreductases that require cyt b5 and b5R. The transmembrane domains of mammalian cytochrome b5 (cyt b5), cyt b5 reductase (b5R), and stearoyl-CoA desaturase-1 (SCD1) form stable binary complexes between cyt b5/b5R or cyt b5/SCD1 and a ternary complex, which enhance electron transfer rates.
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Affiliation(s)
- Jiemin Shen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gang Wu
- Division of Hematology-Oncology, University of Texas McGovern Medical School, Houston, TX, 77030, USA
| | - Ah-Lim Tsai
- Division of Hematology-Oncology, University of Texas McGovern Medical School, Houston, TX, 77030, USA
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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6
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Krishnarjuna B, Im SC, Ravula T, Marte J, Auchus RJ, Ramamoorthy A. Non-Ionic Inulin-Based Polymer Nanodiscs Enable Functional Reconstitution of a Redox Complex Composed of Oppositely Charged CYP450 and CPR in a Lipid Bilayer Membrane. Anal Chem 2022; 94:11908-11915. [PMID: 35977417 PMCID: PMC10851674 DOI: 10.1021/acs.analchem.2c02489] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Although polymer-based lipid nanodiscs are increasingly used in the structural studies of membrane proteins, the charge of the belt-forming polymer is a major limitation for functional reconstitution of membrane proteins possessing an opposite net charge to that of the polymer. This limitation also rules out the reconstitution of a protein-protein complex composed of oppositely charged membrane proteins. In this study, we report the first successful functional reconstitution of a membrane-bound redox complex constituting a cationic cytochrome P450 (CYP450) and an anionic cytochrome P450 reductase (CPR) in non-ionic inulin-based lipid nanodiscs. The gel-to-liquid-crystalline phase-transition temperature (Tm) of DMPC:DMPG (7:3 w/w) lipids in polymer nanodiscs was determined by differential scanning calorimetry (DSC) and 31P NMR experiments. The CYP450-CPR redox complex reconstitution in polymer nanodiscs was characterized by size-exclusion chromatography (SEC), and the electron transfer kinetics was carried out using the stopped-flow technique under anaerobic conditions. The Tm of DMPC:DMPG (7:3 w/w) in polymer nanodiscs measured from 31P NMR agrees with that obtained from DSC and was found to be higher than that for liposomes due to the decreased cooperativity of lipids present in the nanodiscs. The stopped-flow measurements revealed the CYP450-CPR redox complex reconstituted in nanodiscs to be functional, and the electron transfer kinetics was found to be temperature-dependent. Based on the successful demonstration of the use of non-ionic inulin-based polymer nanodiscs reported in this study, we expect them to be useful in studying the function and structures of a variety of membrane proteins/complexes irrespective of the charge of the molecular components. Since the polymer nanodiscs were shown to align in an externally applied magnetic field, they can also be used to measure residual dipolar couplings (RDCs) and residual quadrupolar couplings (RQCs) for various molecules ranging from small molecules to soluble proteins and nucleic acids.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Sang-Choul Im
- Department of Pharmacology and Internal Medicine, Division of Metabolism, Endocrinology, & Diabetes, University of Michigan, Ann Arbor, MI 48109
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Joseph Marte
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Richard J. Auchus
- Department of Pharmacology and Internal Medicine, Division of Metabolism, Endocrinology, & Diabetes, University of Michigan, Ann Arbor, MI 48109
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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7
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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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8
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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9
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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10
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Khazen G, Gyulkhandanian A, Issa T, Maroun RC. Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. Comput Struct Biotechnol J 2021; 19:5184-5197. [PMID: 34630938 PMCID: PMC8476896 DOI: 10.1016/j.csbj.2021.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/23/2021] [Accepted: 09/12/2021] [Indexed: 02/03/2023] Open
Abstract
Because of their considerable number and diversity, membrane proteins and their macromolecular complexes represent the functional units of cells. Their quaternary structure may be stabilized by interactions between the α-helices of different proteins in the hydrophobic region of the cell membrane. Membrane proteins equally represent potential pharmacological targets par excellence for various diseases. Unfortunately, their experimental 3D structure and that of their complexes with other intramembrane protein partners are scarce due to technical difficulties. To overcome this key problem, we devised PPIMem, a computational approach for the specific prediction of higher-order structures of α-helical transmembrane proteins. The novel approach involves proper identification of the amino acid residues at the interface of molecular complexes with a 3D structure. The identified residues compose then nonlinear interaction motifs that are conveniently expressed as mathematical regular expressions. These are efficiently implemented for motif search in amino acid sequence databases, and for the accurate prediction of intramembrane protein-protein complexes. Our template interface-based approach predicted 21,544 binary complexes between 1,504 eukaryotic plasma membrane proteins across 39 species. We compare our predictions to experimental datasets of protein-protein interactions as a first validation method. The online database that results from the PPIMem algorithm with the annotated predicted interactions are implemented as a web server and can be accessed directly at https://transint.univ-evry.fr.
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Affiliation(s)
- Georges Khazen
- Computer Science and Mathematics Department, Lebanese American University, Byblos, Lebanon
| | - Aram Gyulkhandanian
- Inserm U1204/Université d'Evry/Université Paris-Saclay, Structure-Activité des Biomolécules Normales et Pathologiques, 91025 Evry, France
| | - Tina Issa
- Computer Science and Mathematics Department, Lebanese American University, Byblos, Lebanon
| | - Rachid C Maroun
- Inserm U1204/Université d'Evry/Université Paris-Saclay, Structure-Activité des Biomolécules Normales et Pathologiques, 91025 Evry, France
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11
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Laursen T, Lam HYM, Sørensen KK, Tian P, Hansen CC, Groves JT, Jensen KJ, Christensen SM. Membrane anchoring facilitates colocalization of enzymes in plant cytochrome P450 redox systems. Commun Biol 2021; 4:1057. [PMID: 34504298 PMCID: PMC8429664 DOI: 10.1038/s42003-021-02604-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 08/25/2021] [Indexed: 01/03/2023] Open
Abstract
Plant metabolism depends on cascade reactions mediated by dynamic enzyme assemblies known as metabolons. In this context, the cytochrome P450 (P450) superfamily catalyze key reactions underpinning the unique diversity of bioactive compounds. In contrast to their soluble bacterial counterparts, eukaryotic P450s are anchored to the endoplasmic reticulum membrane and serve as metabolon nucleation sites. Hence, membrane anchoring appears to play a pivotal role in the evolution of complex biosynthetic pathways. Here, a model membrane assay enabled characterization of membrane anchor dynamics by single molecule microscopy. As a model system, we reconstituted the membrane anchor of cytochrome P450 oxidoreductase (POR), the ubiquitous electron donor to all microsomal P450s. The transmembrane segment in the membrane anchor of POR is relatively conserved, corroborating its functional importance. We observe dynamic colocalization of the POR anchors in our assay suggesting that membrane anchoring might promote intermolecular interactions and in this way impact assembly of metabolic multienzyme complexes.
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Affiliation(s)
- Tomas Laursen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Cecilie Cetti Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA, USA
| | | | - Sune M Christensen
- Department of Chemistry, University of California, Berkeley, CA, USA. .,Enzyme Research, Lyngby, Denmark.
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12
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Hale LL, Harris CT, Luk TS, Addamane SJ, Reno JL, Brener I, Mitrofanov O. Highly efficient terahertz photoconductive metasurface detectors operating at microwatt-level gate powers. OPTICS LETTERS 2021; 46:3159-3162. [PMID: 34197405 DOI: 10.1364/ol.427798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
Despite their wide use in terahertz (THz) research and technology, the application spectra of photoconductive antenna (PCA) THz detectors are severely limited due to the relatively high optical gating power requirement. This originates from poor conversion efficiency of optical gate beam photons to photocurrent in materials with sub-picosecond carrier lifetimes. Here we show that using an ultra-thin (160 nm), perfectly absorbing low-temperature grown GaAs metasurface as the photoconductive channel drastically improves the efficiency of THz PCA detectors. This is achieved through perfect absorption of the gate beam in a significantly reduced photoconductive volume, enabled by the metasurface. This Letter demonstrates that sensitive THz PCA detection is possible using optical gate powers as low as 5 µW-three orders of magnitude lower than gating powers used for conventional PCA detectors. We show that significantly higher optical gate powers are not necessary for optimal operation, as they do not improve the sensitivity to the THz field. This class of efficient PCA THz detectors opens doors for THz applications with low gate power requirements.
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13
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Phạm TTT, Rainey JK. On-cell nuclear magnetic resonance spectroscopy to probe cell surface interactions. Biochem Cell Biol 2021; 99:683-692. [PMID: 33945753 DOI: 10.1139/bcb-2021-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy allows determination of atomic-level information about intermolecular interactions, molecular structure, and molecular dynamics in the cellular environment. This may be broadly divided into studies focused on obtaining detailed molecular information in the intracellular context ("in-cell") or those focused on characterizing molecules or events at the cell surface ("on-cell"). In this review, we outline some key NMR techniques applied for on-cell NMR studies through both solution-state and solid-state NMR and survey studies that have used these techniques to uncover key information. We particularly focus on application of on-cell NMR spectroscopy to characterize ligand interactions with cell surface membrane proteins such as G-protein coupled receptors (GPCRs), receptor tyrosine kinases, etc. These techniques allow for quantification of binding affinities, competitive binding assays, delineation of portions of ligands involved in binding, ligand bound-state conformational determination, evaluation of receptor structuring and dynamics, and inference of distance constraints characteristic of the ligand-receptor bound state. Excitingly, it is possible to avoid the barriers of production and purification of membrane proteins while obtaining directly physiologically-relevant information through on-cell NMR. We also provide a briefer survey of the applicability of on-cell NMR approaches to other classes of cell surface molecule.
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Affiliation(s)
- Trần Thanh Tâm Phạm
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Nova Scotia, Canada;
| | - Jan K Rainey
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Canada;
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14
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Sun SC, Huang HW, Lo YT, Chuang MC, Hsu YHH. Unraveling cardiolipin-induced conformational change of cytochrome c through H/D exchange mass spectrometry and quartz crystal microbalance. Sci Rep 2021; 11:1090. [PMID: 33441668 PMCID: PMC7806790 DOI: 10.1038/s41598-020-79905-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/04/2020] [Indexed: 11/21/2022] Open
Abstract
Cardiolipin (CL), a crucial component in inner mitochondrial membranes, interacts with cytochrome c (cyt c) to form a peroxidase complex for the catalysis of CL oxidation. Such interaction is pivotal to the mitochondrial regulation of apoptosis and is affected by the redox state of cyt c. In the present study, the redox-dependent interaction of cyt c with CL was investigated through amide hydrogen/deuterium exchange coupled with mass spectrometry (HDXMS) and quartz crystal microbalance with dissipation monitoring (QCM-D). Ferrous cyt c exhibited a more compact conformation compared with its ferric form, which was supported by the lower number of deuterons accumulated and the greater amplitude reduction on dissipation. Upon association with CL, ferrous cyt c resulted in a moderate increase in deuteration, whereas the ferric form caused a drastic increase of deuteration, which indicated that CL-bound ferric cyt c formed an extended conformation. These results were consistent with those of the frequency (f) − dissipation (D) experiments, which revealed that ferric cyt c yielded greater values of |ΔD/Δf| within the first minute. Further fragmentation analysis based on HDXMS indicated that the effect of CL binding was considerably different on ferric and ferrous cyt c in the C-helix and the Loop 9–24. In ferric cyt c, CL binding affected Met80 and destabilized His18 interaction with heme, which was not observed with ferrous cyt c. An interaction model was proposed to explain the aforementioned results.
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Affiliation(s)
- Sin-Cih Sun
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Hung-Wei Huang
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Yi-Ting Lo
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Min-Chieh Chuang
- Department of Chemistry, Tunghai University, Taichung, Taiwan. .,Department of Environmental Science and Engineering, Taichung, Taiwan.
| | - Yuan-Hao Howard Hsu
- Department of Chemistry, Tunghai University, Taichung, Taiwan. .,Biological Science Center, Tunghai University, Taichung, Taiwan.
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15
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Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
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16
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Di Mauro GM, Hardin NZ, Ramamoorthy A. Lipid-nanodiscs formed by paramagnetic metal chelated polymer for fast NMR data acquisition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183332. [PMID: 32360741 PMCID: PMC7340147 DOI: 10.1016/j.bbamem.2020.183332] [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: 02/18/2020] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
Lipid-nanodiscs have been shown to be an exciting innovation as a membrane-mimicking system for studies on membrane proteins by a variety of biophysical techniques, including NMR spectroscopy. Although NMR spectroscopy is unique in enabling the atomic-resolution investigation of dynamic structures of membrane-associated molecules, it, unfortunately, suffers from intrinsically low sensitivity. The long data acquisition often used to enhance the sensitivity is not desirable for sensitive membrane proteins. Instead, paramagnetic relaxation enhancement (PRE) has been used to reduce NMR data acquisition time or to reduce the amount of sample required to acquire an NMR spectra. However, the PRE approach involves the introduction of external paramagnetic probes in the system, which can induce undesired changes in the sample and on the observed NMR spectra. For example, the addition of paramagnetic ions, as frequently used, can denature the protein via direct interaction and also through sample heating. In this study, we show how the introduction of paramagnetic tags on the outer belt of polymer-nanodiscs can be used to speed-up data acquisition by significantly reducing the spin-lattice relaxation (T1) times with minimum-to-no alteration of the spectral quality. Our results also demonstrate the feasibility of using different types of paramagnetic ions (Eu3+, Gd3+, Dy3+, Er3+, Yb3+) for NMR studies on lipid-nanodiscs. Experimental results characterizing the formation of lipid-nanodiscs by the metal-chelated polymer, and their increased tolerance toward metal ions are also reported.
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Affiliation(s)
- Giacomo M Di Mauro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nathaniel Z Hardin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Biophysics and Chemistry Department, The University of Michigan, Ann Arbor, MI 48109-1055, USA; Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA; Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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17
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Tran NT, Mentink-Vigier F, Long JR. Dynamic Nuclear Polarization of Biomembrane Assemblies. Biomolecules 2020; 10:E1246. [PMID: 32867275 PMCID: PMC7565305 DOI: 10.3390/biom10091246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 01/02/2023] Open
Abstract
While atomic scale structural and dynamic information are hallmarks of nuclear magnetic resonance (NMR) methodologies, sensitivity is a fundamental limitation in NMR studies. Fully exploiting NMR capabilities to study membrane proteins is further hampered by their dilution within biological membranes. Recent developments in dynamic nuclear polarization (DNP), which can transfer the relatively high polarization of unpaired electrons to nuclear spins, show promise for overcoming the sensitivity bottleneck and enabling NMR characterization of membrane proteins under native-like conditions. Here we discuss fundamental aspects of DNP-enhanced solid-state NMR spectroscopy, experimental details relevant to the study of lipid assemblies and incorporated proteins, and sensitivity gains which can be realized in biomembrane-based samples. We also present unique insights which can be gained from DNP measurements and prospects for further development of the technique for elucidating structures and orientations of membrane proteins in native lipid environments.
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Affiliation(s)
- Nhi T. Tran
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA;
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA;
| | - Joanna R. Long
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA;
- Department of Biochemistry & Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
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18
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Zhang C, Catucci G, Di Nardo G, Gilardi G. Effector role of cytochrome P450 reductase for androstenedione binding to human aromatase. Int J Biol Macromol 2020; 164:510-517. [PMID: 32698066 DOI: 10.1016/j.ijbiomac.2020.07.163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/04/2020] [Accepted: 07/15/2020] [Indexed: 10/23/2022]
Abstract
Cytochromes P450 constitute a large superfamily of monooxygenases involved in many metabolic pathways. Most of them are not self-sufficient and need a reductase protein to provide the electrons necessary for catalysis. It was shown that the redox partner plays a role in the modulation of the structure and function of some bacterial P450 enzymes. Here, the effect of NADPH-cytochrome reductase (CPR) on human aromatase (Aro) is studied for what concerns its role in substrate binding. Pre-steady-state kinetic experiments indicate that both the substrate binding rates and the percentage of spin shift detected for aromatase are increased when CPR is present. Moreover, aromatase binds the substrate through a conformational selection mechanism, suggesting a possible effector role of CPR. The thermodynamic parameters for the formation of the CPR-Aro complex were studied by isothermal titration calorimetry. The dissociation constant of the complex formation is 4.5 folds lower for substrate-free compared to the substrate-bound enzyme. The enthalpy change observed when the CPR-Aro complex forms in the absence of the substrate are higher than in its presence, indicating that more interactions are formed/broken in the former case. Taken together, our data confirm that CPR has a role in promoting aromatase conformation optimal for substrate binding.
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Affiliation(s)
- Chao Zhang
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy.
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy.
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19
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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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20
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Mustafa G, Nandekar PP, Mukherjee G, Bruce NJ, Wade RC. The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics. Sci Rep 2020; 10:7284. [PMID: 32350331 PMCID: PMC7190701 DOI: 10.1038/s41598-020-64129-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 04/13/2020] [Indexed: 11/24/2022] Open
Abstract
The simulation of membrane proteins requires compatible protein and lipid force fields that reproduce the properties of both the protein and the lipid bilayer. Cytochrome P450 enzymes are bitopic membrane proteins with a transmembrane helical anchor and a large cytosolic globular domain that dips into the membrane. As such, they are representative and challenging examples of membrane proteins for simulations, displaying features of both peripheral and integral membrane proteins. We performed molecular dynamics simulations of three cytochrome P450 isoforms (2C9, 2C19 and 1A1) in a 2-oleoyl-1-palmitoyl-sn-glycerol-3-phosphocholine bilayer using two AMBER force field combinations: GAFF-LIPID with ff99SB for the protein, and LIPID14 with ff14SB for the protein. Comparison of the structural and dynamic properties of the proteins, the lipids and the protein-membrane interactions shows differing sensitivity of the cytochrome P450 isoforms to the choice of force field, with generally better agreement with experiment for the LIPID14 + ff14SB combination.
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Affiliation(s)
- Ghulam Mustafa
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,B-Zell-Immunologie (D130), German Cancer Research Center, Deutsches Krebsforschungszentrum (DKF), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Prajwal P Nandekar
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120, Heidelberg, Germany.,Schrodinger Inc. #147, 3rd Floor, Jawaharlal Nehru main road, Above State Bank of India, Channasandra, 5th Stage, RR Nagar, Bengaluru, 560098, India
| | - Goutam Mukherjee
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120, Heidelberg, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. .,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120, Heidelberg, Germany. .,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, INF 368, 69120, Heidelberg, Germany.
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21
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McKay MJ, Fu R, Greathouse DV, Koeppe RE. Breaking the Backbone: Central Arginine Residues Induce Membrane Exit and Helix Distortions within a Dynamic Membrane Peptide. J Phys Chem B 2019; 123:8034-8047. [PMID: 31483653 DOI: 10.1021/acs.jpcb.9b06034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane domains of membrane proteins sometimes contain conserved charged or ionizable residues which may be essential for protein function and regulation. This work examines the molecular interactions of single Arg residues within a highly dynamic transmembrane peptide helix. To this end, we have modified the GW4,20ALP23 (acetyl-GGAW4(AL)7AW20AGA-amide) model peptide framework to incorporate Arg residues near the center of the peptide. Peptide helix formation, orientation and dynamics were analyzed by means of solid-state NMR spectroscopy to monitor specific 2H- or 15N-labeled residues. GW4,20ALP23 itself adopts a tilted orientation within lipid bilayer membranes. Nevertheless, the GW4,20ALP23 helix exhibits moderate to high dynamic averaging of NMR observables, such as 2H quadrupolar splittings or 15N-1H dipolar couplings, due to competition between the interfacial Trp residues on opposing helix faces. Here we examine how the helix dynamics are impacted by the introduction of a single Arg residue at position 12 or 14. Residue R14 restricts the helix to low dynamic averaging and a well-defined tilt that varies inversely with the lipid bilayer thickness. To compensate for the dominance of R14, the competing Trp residues cause partial unwinding of the helix at the C-terminal. By contrast, R12GW4,20ALP23 exits the DOPC bilayer to an interfacial surface-bound location. Interestingly, multiple orientations are exhibited by a single residue, Ala-9. Quadrupolar splittings generated by 2H-labeled residues A3, A5, A7, and A9 do not fit to the α-helical quadrupolar wave plot defined by residues A11, A13, A15, A17, A19, and A21. The discontinuity at residue A9 implicates a helical swivel distortion and an apparent 310-helix involving the N-terminal residues preceding A11. These molecular features suggest that, while arginine residues are prominent factors controlling transmembrane helix dynamics, the influence of interfacial tryptophan residues cannot be ignored.
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Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University , Tallahassee , Florida 32310 , United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
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22
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Salnikov ES, Aussenac F, Abel S, Purea A, Tordo P, Ouari O, Bechinger B. Dynamic Nuclear Polarization / solid-state NMR of membranes. Thermal effects and sample geometry. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 100:70-76. [PMID: 30995597 DOI: 10.1016/j.ssnmr.2019.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Whereas specially designed dinitroxide biradicals, reconstitution protocols, oriented sample geometries and NMR probes have helped to much increase the DNP enhancement factors of membrane samples they still lag considerably behind those obtained from glasses made of protein solutions. Here we show that not only the MAS rotor material but also the distribution of the membrane samples within the NMR rotor have a pronounced effect on the DNP enhancement. These observations are rationalized with the cooling efficiency and the internal properties of the sample, monitored by their T1 relaxation, microwave ON versus OFF signal intensities and DNP effect. The data are suggestive that for membranes the speed of cooling has a pronounced effect on the membrane properties and concomitantly the distribution of biradicals within the sample.
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Affiliation(s)
| | | | - Sebastian Abel
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | | | - Paul Tordo
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | - Olivier Ouari
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | - Burkhard Bechinger
- Institute of Chemistry, University of Strasbourg / CNRS, UMR7177, 67070, Strasbourg, France.
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23
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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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24
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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25
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Influence of Transmembrane Helix Mutations on Cytochrome P450-Membrane Interactions and Function. Biophys J 2019; 116:419-432. [PMID: 30658838 PMCID: PMC6369400 DOI: 10.1016/j.bpj.2018.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/01/2018] [Accepted: 12/17/2018] [Indexed: 11/22/2022] Open
Abstract
Human cytochrome P450 (CYP) enzymes play an important role in the metabolism of drugs, steroids, fatty acids, and xenobiotics. Microsomal CYPs are anchored in the endoplasmic reticulum membrane by an N-terminal transmembrane (TM) helix that is connected to the globular catalytic domain by a flexible linker sequence. However, the structural and functional importance of the TM-helix is unclear because it has been shown that CYPs can still associate with the membrane and have enzymatic activity in reconstituted systems after truncation or modification of the N-terminal sequence. Here, we investigated the effect of mutations in the N-terminal TM-helix residues of two human steroidogenic enzymes, CYP 17A1 and CYP 19A1, that are major drug targets for cancer therapy. These mutations were originally introduced to increase the expression of the proteins in Escherichia coli. To investigate the effect of the mutations on protein-membrane interactions and function, we carried out coarse-grained and all-atom molecular dynamics simulations of the CYPs in a phospholipid bilayer. We confirmed the orientations of the globular domain in the membrane observed in the simulations by linear dichroism measurements in a Nanodisc. Whereas the behavior of CYP 19A1 was rather insensitive to truncation of the TM-helix, mutations in the TM-helix of CYP 17A1, especially W2A and E3L, led to a gradual drifting of the TM-helix out of the hydrophobic core of the membrane. This instability of the TM-helix could affect interactions with the allosteric redox partner, cytochrome b5, required for CYP 17A1’s lyase activity. Furthermore, the simulations showed that the mutant TM-helix influenced the membrane interactions of the CYP 17A1 globular domain. In some simulations, the mutated TM-helix obstructed the substrate access tunnel from the membrane to the CYP active site, indicating a possible effect on enzyme function.
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26
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Tsujita M, Wolska A, Gutmann DAP, Remaley AT. Reconstituted Discoidal High-Density Lipoproteins: Bioinspired Nanodiscs with Many Unexpected Applications. Curr Atheroscler Rep 2018; 20:59. [PMID: 30397748 DOI: 10.1007/s11883-018-0759-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
PURPOSE OF REVIEW Summarize the initial discovery of discoidal high-density lipoprotein (HDL) in human plasma and review more recent innovations that span the use of reconstituted nanodisc HDL for membrane protein characterization to its use as a drug carrier and a novel therapeutic agent for cardiovascular disease. RECENT FINDINGS Using a wide variety of biophysical techniques, the structure and composition of endogenous discoidal HDL have now largely been solved. This has led to the development of new methods for the in vitro reconstitution of nanodisc HDL, which have proven to have a wide variety of biomedical applications. Nanodisc HDL has been used as a platform for mimicking the plasma membrane for the reconstitution and investigation of the structures of several plasma membrane proteins, such as cytochrome P450s and ABC transporters. Nanodisc HDL has also been designed as drug carriers to transport amphipathic, as well as hydrophobic small molecules, and has potential therapeutic applications for several diseases. Finally, nanodisc HDL itself like native discoidal HDL can mediate cholesterol efflux from cells and are currently being tested in late-stage clinical trials for cardiovascular disease. The discovery of the characterization of native discoidal HDL has inspired a new field of synthetic nanodisc HDL, which has offered a growing number of unanticipated biomedical applications.
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Affiliation(s)
- Maki Tsujita
- Department of Biochemistry, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan.
| | - Anna Wolska
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Alan T Remaley
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, 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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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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29
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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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30
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Barnaba C, Taylor E, Brozik JA. Dissociation Constants of Cytochrome P450 2C9/Cytochrome P450 Reductase Complexes in a Lipid Bilayer Membrane Depend on NADPH: A Single-Protein Tracking Study. J Am Chem Soc 2017; 139:17923-17934. [PMID: 29148818 DOI: 10.1021/jacs.7b08750] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome P450-reductase (CPR) is a versatile NADPH-dependent electron donor located in the cytoplasmic side of the endoplasmic reticulum. It is an electron transferase that is able to deliver electrons to a variety of membrane-bound oxidative partners, including the drug-metabolizing enzymes of the cytochrome P450s (P450). CPR is also stoichiometrically limited compared to its oxidative counterparts, and hypotheses have arisen about possible models that can overcome the stoichiometric imbalance, including quaternary organization of P450 and diffusion-limited models. Described here are results from a single-protein tracking study of fluorescently labeled CPR and cytochrome P450 2C9 (CYP2C9) molecules in which stochastic analysis was used to determine the dissociation constants of CPR/CYP2C9 complexes in a lipid bilayer membrane for the first time. Single-protein trajectories demonstrate the transient nature of these CPR-CYP2C9 interactions, and the measured Kd values are highly dependent on the redox state of CPR. It is shown that CPRox/CYP2C9 complexes have a much higher dissociation constant than CPR2-/CYP2C9 or CPR4-/CYP2C9 complexes, and a model is presented to account for these results. An Arrhenius analysis of diffusion constants was also carried out, demonstrating that the reduced forms of CPR and CYP2C9 interact differently with the biomimetic ER and may, in addition to protein conformational changes, contribute to the observed NADPH-dependent shift in Kd. Finally, it is also shown that the CPRox/CYP2C9 affinity depends on the nature of the ligand, being higher when a substrate is bound, compared to an inhibitor.
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Affiliation(s)
- Carlo Barnaba
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164-4630, United States
| | - Evan Taylor
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164-4630, United States
| | - James A Brozik
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164-4630, United States
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