1
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Bizet M, Byrne D, Biaso F, Gerbaud G, Etienne E, Briola G, Guigliarelli B, Urban P, Dorlet P, Kalai T, Truan G, Martinho M. Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid. Chemistry 2024; 30:e202304307. [PMID: 38277424 DOI: 10.1002/chem.202304307] [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: 12/22/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/28/2024]
Abstract
The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.
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Affiliation(s)
- Maxime Bizet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix Marseille Univ, CNRS, IMM, 13402, Marseille, France
| | - Frédéric Biaso
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Giuseppina Briola
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Philippe Urban
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Pierre Dorlet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Tamas Kalai
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, PO Box 99 Szigeti st. 12, H-7602 7624, Pécs, Hungary
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Marlène Martinho
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
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2
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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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3
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Sutinen A, Jones NC, Hoffmann SV, Ruskamo S, Kursula P. Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane. Biophys Chem 2023; 303:107113. [PMID: 37778197 DOI: 10.1016/j.bpc.2023.107113] [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: 07/10/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
The mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-Tooth disease (CMT). GDAP1 is a distant member of the glutathione-S-transferase (GST) superfamily, with unknown enzymatic properties or functions at the molecular level. The structure of the cytosol-facing GST-like domain has been described, but there is no consensus on how the protein interacts with the mitochondrial outer membrane. Here, we describe a model for GDAP1 assembly on the membrane using peptides vicinal to the GDAP1 transmembrane domain. We used oriented circular dichroism spectroscopy (OCD) with synchrotron radiation to study the secondary structure and orientation of GDAP1 segments at the outer and inner surfaces of the outer mitochondrial membrane. These experiments were complemented by small-angle X-ray scattering, providing the first experimental structural models for full-length human GDAP1. The results indicate that GDAP1 is bound into the membrane via a single transmembrane helix, flanked by two peripheral helices interacting with the outer and inner leaflets of the mitochondrial outer membrane in different orientations. Impairment of these interactions could be a mechanism for CMT in the case of missense mutations affecting these segments instead of the GST-like domain.
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Affiliation(s)
- Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland; Department of Biomedicine, University of Bergen, Bergen, Norway.
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4
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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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5
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Suzuki S, Kumagai S, Nagashima T, Yamazaki T, Okitsu T, Wada A, Naito A, Katayama K, Inoue K, Kandori H, Kawamura I. Characterization of retinal chromophore and protonated Schiff base in Thermoplasmatales archaeon heliorhodopsin using solid-state NMR spectroscopy. Biophys Chem 2023; 296:106991. [PMID: 36905840 DOI: 10.1016/j.bpc.2023.106991] [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: 12/25/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Heliorhodopsin (HeR) is a seven-helical transmembrane protein with a retinal chromophore that corresponds to a new rhodopsin family. HeR from the archaebacterium Thermoplasmatales archaeon (TaHeR) exhibits unique features, such as the inverted protein orientation in the membrane compared to other rhodopsins and a long photocycle. Here, we used solid-state nuclear magnetic resonance (NMR) spectroscopy to investigate the 13C and 15N NMR signals of the retinal chromophore and protonated Schiff base (RPSB) in TaHeR embedded in POPE/POPG membrane. Although the 14- and 20-13C retinal signals indicated 13-trans/15-anti (all-trans) configurations, the 20-13C chemical shift value was different from that of other microbial rhodopsins, indicating weakly steric hinderance between Phe203 and the C20 methyl group. 15N RPSB/λmax plot deviated from the linear correlation based on retinylidene-halide model compounds. Furthermore, 15N chemical shift anisotropy (CSA) suggested that Ser112 and Ser234 polar residues distinguish the electronic environment tendencies of RPSB from those of other microbial rhodopsins. Our NMR results revealed that the retinal chromophore and the RPSB in TaHeR exhibit unique electronic environments.
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Affiliation(s)
- Shibuki Suzuki
- Graduate School of Engineering Science, Yokohama National University, Yokohama 240-8501, Japan
| | - Sari Kumagai
- Graduate School of Engineering Science, Yokohama National University, Yokohama 240-8501, Japan
| | - Toshio Nagashima
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Toshio Yamazaki
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Takashi Okitsu
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan; Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Akira Naito
- Graduate School of Engineering Science, Yokohama National University, Yokohama 240-8501, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Yokohama 240-8501, Japan.
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6
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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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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: 33] [Impact Index Per Article: 16.5] [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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Farrelly MD, Martin LL, Thang SH. Polymer Nanodiscs and Their Bioanalytical Potential. Chemistry 2021; 27:12922-12939. [PMID: 34180107 DOI: 10.1002/chem.202101572] [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] [Received: 05/03/2021] [Indexed: 12/21/2022]
Abstract
Membrane proteins (MPs) play a pivotal role in cellular function and are therefore predominant pharmaceutical targets. Although detailed understanding of MP structure and mechanistic activity is invaluable for rational drug design, challenges are associated with the purification and study of MPs. This review delves into the historical developments that became the prelude to currently available membrane mimetic technologies before shining a spotlight on polymer nanodiscs. These are soluble nanosized particles capable of encompassing MPs embedded in a phospholipid ring. The expanding range of reported amphipathic polymer nanodisc materials is presented and discussed in terms of their tolerance to different solution conditions and their nanodisc properties. Finally, the analytical scope of polymer nanodiscs is considered in both the demonstration of basic nanodisc parameters as well as in the elucidation of structures, lipid-protein interactions, and the functional mechanisms of reconstituted membrane proteins. The final emphasis is given to the unique benefits and applications demonstrated for native nanodiscs accessed through a detergent free process.
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Affiliation(s)
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton, 3800, Vic, Australia
| | - San H Thang
- School of Chemistry, Monash University, Clayton, 3800, Vic, Australia
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10
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Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High-Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021; 60:14960-14966. [PMID: 33595173 DOI: 10.1002/anie.202101149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/13/2022]
Abstract
Metalloproteins constitute a significant fraction of the proteome of all organisms and their characterization is critical for both basic sciences and biomedical applications. A large portion of metalloproteins bind paramagnetic metal ions, and paramagnetic NMR spectroscopy has been widely used in their structural characterization. However, the signals of nuclei in the immediate vicinity of the metal center are often broadened beyond detection. In this work, we show that it is possible to determine the coordination environment of the paramagnetic metal in the protein at a resolution inaccessible to other techniques. Taking the structure of a diamagnetic analogue as a starting point, a geometry optimization is carried out by fitting the pseudocontact shifts obtained from first principles quantum chemical calculations to the experimental ones.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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11
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Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High‐Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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12
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Krishnarjuna B, Yamazaki T, Anantharamaiah GM, Ramamoorthy A. Nanodisc reconstitution of flavin mononucleotide binding domain of cytochrome-P450-reductase enables high-resolution NMR probing. Chem Commun (Camb) 2021; 57:4819-4822. [PMID: 33982687 PMCID: PMC8136615 DOI: 10.1039/d1cc01018b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cytochrome-P450-reductase transfers electrons to cytochrome-P450 through its flavin mononucleotide binding domain (FBD). Despite the importance of membrane-anchoring for FBD function, studies have focused on its soluble domain lacking the transmembrane-domain. Here we demonstrate that the reconstitution of FBD in nanodiscs enables high-resolution NMR measurements and renders a stable conformation.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Arbor, MI 48109, USA.
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13
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Yano Y, Watanabe Y, Matsuzaki K. Thermodynamic and kinetic stabilities of transmembrane helix bundles as revealed by single-pair FRET analysis: Effects of the number of membrane-spanning segments and cholesterol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183532. [PMID: 33316240 DOI: 10.1016/j.bbamem.2020.183532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022]
Abstract
The tertiary structures and conformational dynamics of transmembrane (TM) helical proteins are maintained by the interhelical interaction network in membranes, although it is complicated to analyze the underlying driving forces because the amino acid sequences can involve multiple and various types of interactions. To obtain insights into basal and common effects of the number of membrane-spanning segments and membrane cholesterol, we measured stabilities of helix bundles composed of simple TM helices (AALALAA)3 (1TM) and (AALALAA)3-G5-(AALALAA)3 (2TM). Association-dissociation dynamics for 1TM-1TM, 1TM-2TM, and 2TM-2TM pairs were monitored to compare stabilities of 2-, 3-, and 4-helical bundles, respectively, with single-pair fluorescence resonance energy transfer (sp-FRET) in liposome membranes. Both thermodynamic and kinetic stabilities of the helix bundles increased with a greater number of membrane-spanning segments in POPC. The presence of 30 mol% cholesterol strongly enhanced the formation of 1TM-1TM and 1TM-2TM bundles (~ - 9 kJ mol-1), whereas it only weakly stabilized the 2TM-2TM bundle (~ - 3 kJ mol-1). Fourier transform infrared-polarized attenuated total reflection (ATR-FTIR) spectroscopy revealed an ~30° tilt of the helix axis relative to bilayer normal for the 1TM-2TM pair in the presence of cholesterol, suggesting the formation of a tilted helix bundle to release high lateral pressure at the center of cholesterol-containing membranes. These results demonstrate that the number of membrane-spanning segments affects the stability and structure of the helix bundle, and their cholesterol-dependences. Such information is useful to understand the basics of folding and assembly of multispanning TM proteins.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuta Watanabe
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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14
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Lang L, Ravera E, Parigi G, Luchinat C, Neese F. Solution of a Puzzle: High-Level Quantum-Chemical Treatment of Pseudocontact Chemical Shifts Confirms Classic Semiempirical Theory. J Phys Chem Lett 2020; 11:8735-8744. [PMID: 32930598 PMCID: PMC7584370 DOI: 10.1021/acs.jpclett.0c02462] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
A recently popularized approach for the calculation of pseudocontact shifts (PCSs) based on first-principles quantum chemistry (QC) leads to different results than the classic "semiempirical" equation involving the susceptibility tensor. Studies that attempted a comparison of theory and experiment led to conflicting conclusions with respect to the preferred theoretical approach. In this Letter, we show that after inclusion of previously neglected terms in the full Hamiltonian, one can deduce the semiempirical equations from a rigorous QC-based treatment. It also turns out that in the long-distance limit, one can approximate the complete A tensor in terms of the g tensor. By means of Kohn-Sham density functional theory calculations, we numerically confirm the long-distance expression for the A tensor and the theoretically predicted scaling behavior of the different terms. Our derivation suggests a computational strategy in which one calculates the susceptibility tensor and inserts it into the classic equation for the PCS.
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Affiliation(s)
- Lucas Lang
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Enrico Ravera
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), via Sacconi
6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Giacomo Parigi
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), via Sacconi
6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Claudio Luchinat
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), via Sacconi
6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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15
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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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16
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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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17
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Cerofolini L, Silva JM, Ravera E, Romanelli M, Geraldes CFGC, Macedo AL, Fragai M, Parigi G, Luchinat C. How Do Nuclei Couple to the Magnetic Moment of a Paramagnetic Center? A New Theory at the Gauntlet of the Experiments. J Phys Chem Lett 2019; 10:3610-3614. [PMID: 31181162 DOI: 10.1021/acs.jpclett.9b01128] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The recent derivation, based on pure quantum chemistry (QC) first-principles, of the pseudocontact shifts (PCSs) caused by a paramagnetic metal center on far away nuclei has cast doubts on the validity of the semiempirical (SE) theory, predicting PCSs to arise from the metal magnetic susceptibility anisotropy. The SE theory has been used and applied countless times, especially in the last 2 decades, to obtain structural information on proteins containing paramagnetic metal ions. We show here that the QC and SE predictions can be directly tested against experiments, provided a suitable macromolecular system is used. The SE approach yields a good prediction of the experimental PCSs while the QC one does not. It appears that the classic theory is able to grasp satisfactorily the underlying physics.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
| | - José Malanho Silva
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Life Sciences and Coimbra Chemistry Center , University of Coimbra , Coimbra 3004-531 , Portugal
- UCIBIO-Requimte, Faculty of Sciences and Technology , Universidade NOVA de Lisboa , Caparica 2829-516 , Portugal
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Maurizio Romanelli
- Department of Earth Sciences , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Carlos F G C Geraldes
- Department of Life Sciences and Coimbra Chemistry Center , University of Coimbra , Coimbra 3004-531 , Portugal
| | - Anjos L Macedo
- UCIBIO-Requimte, Faculty of Sciences and Technology , Universidade NOVA de Lisboa , Caparica 2829-516 , Portugal
| | - Marco Fragai
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
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18
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Boulton S, Selvaratnam R, Ahmed R, Van K, Cheng X, Melacini G. Mechanisms of Specific versus Nonspecific Interactions of Aggregation-Prone Inhibitors and Attenuators. J Med Chem 2019; 62:5063-5079. [PMID: 31074269 PMCID: PMC7255057 DOI: 10.1021/acs.jmedchem.9b00258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A common source of false positives in drug discovery is ligand self-association into large colloidal assemblies that nonspecifically inhibit target proteins. However, the mechanisms of aggregation-based inhibition (ABI) and ABI-attenuation by additives, such as Triton X-100 (TX) and human serum albumin (HSA), are not fully understood. Here, we investigate the molecular basis of ABI and ABI-attenuation through the lens of NMR and coupled thermodynamic cycles. We unexpectedly discover a new class of aggregating ligands that exhibit negligible interactions with proteins but act as competitive sinks for the free inhibitor, resulting in bell-shaped dose-response curves. TX attenuates ABI by converting inhibitory, protein-binding aggregates into nonbinding coaggregates, whereas HSA minimizes nonspecific ligand interactions by functioning as a reservoir for free inhibitor and preventing self-association. Hence, both TX and HSA are useful tools to minimize false positives arising from nonspecific binding but at the cost of potentially introducing false negatives due to suppression of specific interactions.
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Affiliation(s)
- Stephen Boulton
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Rajeevan Selvaratnam
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department of Laboratory Medicine, University Health Network, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 2C4, Canada
| | - Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Katherine Van
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Xiaodong Cheng
- Department of Integrative Biology and Pharmacology and Texas Therapeutics Institute, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
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19
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Lapin J, Nevzorov AA. Validation of protein backbone structures calculated from NMR angular restraints using Rosetta. JOURNAL OF BIOMOLECULAR NMR 2019; 73:229-244. [PMID: 31076969 DOI: 10.1007/s10858-019-00251-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Multidimensional solid-state NMR spectra of oriented membrane proteins can be used to infer the backbone torsion angles and hence the overall protein fold by measuring dipolar couplings and chemical shift anisotropies, which depend on the orientation of each peptide plane with respect to the external magnetic field. However, multiple peptide plane orientations can be consistent with a given set of angular restraints. This ambiguity is further exacerbated by experimental uncertainty in obtaining and interpreting such restraints. The previously developed algorithms for structure calculations using angular restraints typically involve a sequential walkthrough along the backbone to find the torsion angles between the consecutive peptide plane orientations that are consistent with the experimental data. This method is sensitive to experimental uncertainty in interpreting the peak positions of as low as ± 10 Hz, often yielding high structural RMSDs for the calculated structures. Here we present a significantly improved version of the algorithm which includes the fitting of several peptide planes at once in order to prevent propagation of error along the backbone. In addition, a protocol has been devised for filtering the structural solutions using Rosetta scoring functions in order to find the structures that both fit the spectrum and satisfy bioinformatics restraints. The robustness of the new algorithm has been tested using synthetic angular restraints generated from the known structures for two proteins: a soluble protein 2gb1 (56 residues), chosen for its diverse secondary structure elements, i.e. an alpha-helix and two beta-sheets, and a membrane protein 4a2n, from which the first two transmembrane helices (having a total of 64 residues) have been used. Extensive simulations have been performed by varying the number of fitted planes, experimental error, and the number of NMR dimensions. It has been found that simultaneously fitting two peptide planes always shifted the distribution of the calculated structures toward lower structural RMSD values as compared to fitting a single torsion-angle pair. For each protein, irrespective of the simulation parameters, Rosetta was able to distinguish the most plausible structures, often having structural RMSDs lower than 2 Å with respect to the original structure. This study establishes a framework for de-novo protein structure prediction using a combination of solid-state NMR angular restraints and bioinformatics.
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Affiliation(s)
- Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA.
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20
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Mustafa G, Nandekar PP, Camp TJ, Bruce NJ, Gregory MC, Sligar SG, Wade RC. 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: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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Affiliation(s)
- Ghulam Mustafa
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Prajwal P Nandekar
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Tyler J Camp
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Michael C Gregory
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Chemistry, University of Illinois, Urbana, Illinois
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany.
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21
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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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22
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Metal centers in biomolecular solid-state NMR. J Struct Biol 2018; 206:99-109. [PMID: 30502494 DOI: 10.1016/j.jsb.2018.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/25/2018] [Accepted: 11/27/2018] [Indexed: 01/03/2023]
Abstract
Solid state NMR (SSNMR) has earned a substantial success in the characterization of paramagnetic systems over the last decades. Nowadays, the resolution and sensitivity of solid state NMR in biological molecules has improved significantly and these advancements can be translated into the study of paramagnetic biomolecules. However, the electronic properties of different metal centers affect the quality of their SSNMR spectra differently, and not all systems turn out to be equally easy to approach by this technique. In this review we will try to give an overview of the properties of different paramagnetic centers and how they can be used to increase the chances of experimental success.
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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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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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25
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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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26
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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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27
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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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28
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Galiakhmetov AR, Kovrigina EA, Xia C, Kim JJP, Kovrigin EL. Application of methyl-TROSY to a large paramagnetic membrane protein without perdeuteration: 13C-MMTS-labeled NADPH-cytochrome P450 oxidoreductase. JOURNAL OF BIOMOLECULAR NMR 2018; 70:21-31. [PMID: 29168021 PMCID: PMC5820150 DOI: 10.1007/s10858-017-0152-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/11/2017] [Indexed: 05/03/2023]
Abstract
NMR spectroscopy of membrane proteins involved in electron transport is difficult due to the presence of both the lipids and paramagnetic centers. Here we report the solution NMR study of the NADPH-cytochrome P450 oxidoreductase (POR) in its reduced and oxidized states. We interrogate POR, first, in its truncated soluble form (70 kDa), which is followed by experiments with the full-length protein incorporated in a lipid nanodisc (240 kDa). To overcome paramagnetic relaxation in the reduced state of POR as well as the signal broadening due to its high molecular weight, we utilized the methyl-TROSY approach. Extrinsic 13C-methyl groups were introduced by modifying the engineered surface-exposed cysteines with methyl-methanethiosulfonate. Chemical shift dispersion of the resonances from different sites in POR was sufficient to monitor differential effects of the reduction-oxidation process and conformation changes in the POR structure related to its function. Despite the high molecular weight of the POR-nanodisc complex, the surface-localized 13C-methyl probes were sufficiently mobile to allow for signal detection at 600 MHz without perdeuteration. This work demonstrates a potential of the solution methyl-TROSY in analysis of structure, dynamics, and function of POR, which may also be applicable to similar paramagnetic and flexible membrane proteins.
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Affiliation(s)
| | | | - Chuanwu Xia
- Biochemistry Department, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jung-Ja P Kim
- Biochemistry Department, Medical College of Wisconsin, Milwaukee, WI, USA.
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29
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Ravera E, Parigi G, Luchinat C. Perspectives on paramagnetic NMR from a life sciences infrastructure. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 282:154-169. [PMID: 28844254 DOI: 10.1016/j.jmr.2017.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 05/17/2023]
Abstract
The effects arising in NMR spectroscopy because of the presence of unpaired electrons, collectively referred to as "paramagnetic NMR" have attracted increasing attention over the last decades. From the standpoint of the structural and mechanistic biology, paramagnetic NMR provides long range restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements through NMR and X-ray data. These restraints also provide information on structure rearrangements and conformational variability in biomolecular systems. Theoretical improvements in quantum chemistry calculations can nowadays allow for accurate calculations of the paramagnetic data from a molecular structural model, thus providing a tool to refine the metal coordination environment by matching the paramagnetic effects observed far away from the metal. Furthermore, the availability of an improved technology (higher fields and faster magic angle spinning) has promoted paramagnetic NMR applications in the fast-growing area of biomolecular solid-state NMR. Major improvements in dynamic nuclear polarization have been recently achieved, especially through the exploitation of the Overhauser effect occurring through the contact-driven relaxation mechanism: the very large enhancement of the 13C signal observed in a variety of liquid organic compounds at high fields is expected to open up new perspectives for applications of solution NMR.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy.
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30
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Yamamoto K, Caporini MA, Im SC, Waskell L, Ramamoorthy A. Transmembrane Interactions of Full-length Mammalian Bitopic Cytochrome-P450-Cytochrome-b 5 Complex in Lipid Bilayers Revealed by Sensitivity-Enhanced Dynamic Nuclear Polarization Solid-state NMR Spectroscopy. Sci Rep 2017; 7:4116. [PMID: 28646173 PMCID: PMC5482851 DOI: 10.1038/s41598-017-04219-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/11/2017] [Indexed: 01/12/2023] Open
Abstract
The dynamic protein-protein and protein-ligand interactions of integral bitopic membrane proteins with a single membrane-spanning helix play a plethora of vital roles in the cellular processes associated with human health and diseases, including signaling and enzymatic catalysis. While an increasing number of high-resolution structural studies of membrane proteins have successfully manifested an in-depth understanding of their biological functions, intact membrane-bound bitopic protein-protein complexes pose tremendous challenges for structural studies by crystallography or solution NMR spectroscopy. Therefore, there is a growing interest in developing approaches to investigate the functional interactions of bitopic membrane proteins embedded in lipid bilayers at atomic-level. Here we demonstrate the feasibility of dynamic nuclear polarization (DNP) magic-angle-spinning NMR techniques, along with a judiciously designed stable isotope labeling scheme, to measure atomistic-resolution transmembrane-transmembrane interactions of full-length mammalian ~72-kDa cytochrome P450-cytochrome b5 complex in lipid bilayers. Additionally, the DNP sensitivity-enhanced two-dimensional 13C/13C chemical shift correlations via proton driven spin diffusion provided distance constraints to characterize protein-lipid interactions and revealed the transmembrane topology of cytochrome b5. The results reported in this study would pave ways for high-resolution structural and topological investigations of membrane-bound full-length bitopic protein complexes under physiological conditions.
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Affiliation(s)
- Kazutoshi Yamamoto
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Marc A Caporini
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, USA
| | - Sang-Choul Im
- Department of Anesthesiology, VA Medical Center, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Lucy Waskell
- Department of Anesthesiology, VA Medical Center, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA.
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31
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Bhatt MR, Khatri Y, Rodgers RJ, Martin LL. Role of cytochrome b5 in the modulation of the enzymatic activities of cytochrome P450 17α-hydroxylase/17,20-lyase (P450 17A1). J Steroid Biochem Mol Biol 2017; 170:2-18. [PMID: 26976652 DOI: 10.1016/j.jsbmb.2016.02.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 12/13/2022]
Abstract
Cytochrome b5 (cyt b5) is a small hemoprotein that plays a significant role in the modulation of activities of an important steroidogenic enzyme, cytochrome P450 17α-hydroxylase/17,20-lyase (P450 17A1, CYP17A1). Located in the zona fasciculata and zona reticularis of the adrenal cortex and in the gonads, P450 17A1 catalyzes two different reactions in the steroidogenic pathway; the 17α-hydroxylation and 17,20-lyase, in the endoplasmic reticulum of these respective tissues. The activities of P450 17A1 are regulated by cyt b5 that enhances the 17,20-lyase reaction by promoting the coupling of P450 17A1 and cytochrome P450 reductase (CPR), allosterically. Cyt b5 can also act as an electron donor to enhance the 16-ene-synthase activity of human P450 17A1. In this review, we discuss the many roles of cyt b5 and focus on the modulation of CYP17A1 activities by cyt b5 and the mechanisms involved.
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Affiliation(s)
- Megh Raj Bhatt
- Everest Biotech Pvt. Ltd., Khumaltar, Lalitpur, P.O. Box 21608, Kathmandu 44600, Nepal
| | - Yogan Khatri
- Institute of Biochemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Raymond J Rodgers
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide SA 5005, Australia
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton, 3800, Victoria, Australia.
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32
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Bertarello A, Schubeis T, Fuccio C, Ravera E, Fragai M, Parigi G, Emsley L, Pintacuda G, Luchinat C. Paramagnetic Properties of a Crystalline Iron–Sulfur Protein by Magic-Angle Spinning NMR Spectroscopy. Inorg Chem 2017; 56:6624-6629. [DOI: 10.1021/acs.inorgchem.7b00674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Andrea Bertarello
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Carmelo Fuccio
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Lyndon Emsley
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Guido Pintacuda
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Claudio Luchinat
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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33
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Barnaba C, Gentry K, Sumangala N, Ramamoorthy A. The catalytic function of cytochrome P450 is entwined with its membrane-bound nature. F1000Res 2017; 6:662. [PMID: 28529725 PMCID: PMC5428493 DOI: 10.12688/f1000research.11015.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2017] [Indexed: 12/21/2022] Open
Abstract
Cytochrome P450, a family of monooxygenase enzymes, is organized as a catalytic metabolon, which requires enzymatic partners as well as environmental factors that tune its complex dynamic. P450 and its reducing counterparts—cytochrome P450-reductase and cytochrome
b
5—are membrane-bound proteins located in the cytosolic side of the endoplasmic reticulum. They are believed to dynamically associate to form functional complexes. Increasing experimental evidence signifies the role(s) played by both protein-protein and protein-lipid interactions in P450 catalytic function and efficiency. However, the biophysical challenges posed by their membrane-bound nature have severely limited high-resolution understanding of the molecular interfaces of these interactions. In this article, we provide an overview of the current knowledge on cytochrome P450, highlighting the environmental factors that are entwined with its metabolic function. Recent advances in structural biophysics are also discussed, setting up the bases for a new paradigm in the study of this important class of membrane-bound enzymes.
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Affiliation(s)
- Carlo Barnaba
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| | - Katherine Gentry
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| | - Nirupama Sumangala
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
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34
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Saurel O, Iordanov I, Nars G, Demange P, Le Marchand T, Andreas LB, Pintacuda G, Milon A. Local and Global Dynamics in Klebsiella pneumoniae Outer Membrane Protein a in Lipid Bilayers Probed at Atomic Resolution. J Am Chem Soc 2017; 139:1590-1597. [DOI: 10.1021/jacs.6b11565] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olivier Saurel
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Iordan Iordanov
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Guillaume Nars
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Pascal Demange
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Tanguy Le Marchand
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Loren B. Andreas
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Guido Pintacuda
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Alain Milon
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
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35
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Navrátilová V, Paloncýová M, Berka K, Otyepka M. Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4. J Phys Chem B 2016; 120:11205-11213. [DOI: 10.1021/acs.jpcb.6b10108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Veronika Navrátilová
- Regional
Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Markéta Paloncýová
- Regional
Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Karel Berka
- Regional
Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
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36
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Matsui R, Uchida N, Ohtani M, Yamada K, Shigeta A, Kawamura I, Aida T, Ishida Y. Magnetically Alignable Bicelles with Unprecedented Stability Using Tunable Surfactants Derived from Cholic Acid. Chemphyschem 2016; 17:3916-3922. [DOI: 10.1002/cphc.201600897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Ryoichi Matsui
- Department of Chemistry and Biotechnology; School of Engineering, the; University of Tokyo; Hongo 7-3-1, Bunkyo-ku Tokyo 113-8656 Japan
| | - Noriyuki Uchida
- Department of Chemistry and Biotechnology; School of Engineering, the; University of Tokyo; Hongo 7-3-1, Bunkyo-ku Tokyo 113-8656 Japan
| | - Masataka Ohtani
- RIKEN Center for Emergent Matter Science; Hirosawa 2-1, Wako Saitama 351-0198 Japan
| | - Kuniyo Yamada
- RIKEN Center for Emergent Matter Science; Hirosawa 2-1, Wako Saitama 351-0198 Japan
| | - Arisu Shigeta
- Graduate School of Engineering; Yokohama National University; Tokiwadai 79-5, Hodogaya-ku Yokohama 240-8501 Japan
| | - Izuru Kawamura
- Graduate School of Engineering; Yokohama National University; Tokiwadai 79-5, Hodogaya-ku Yokohama 240-8501 Japan
| | - Takuzo Aida
- RIKEN Center for Emergent Matter Science; Hirosawa 2-1, Wako Saitama 351-0198 Japan
- Department of Chemistry and Biotechnology; School of Engineering, the; University of Tokyo; Hongo 7-3-1, Bunkyo-ku Tokyo 113-8656 Japan
| | - Yasuhiro Ishida
- RIKEN Center for Emergent Matter Science; Hirosawa 2-1, Wako Saitama 351-0198 Japan
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Jeřábek P, Florián J, Martínek V. Membrane-Anchored Cytochrome P450 1A2–Cytochrome b5 Complex Features an X-Shaped Contact between Antiparallel Transmembrane Helices. Chem Res Toxicol 2016; 29:626-36. [DOI: 10.1021/acs.chemrestox.5b00349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Petr Jeřábek
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, Albertov 2030, 128 43 Prague 2, Czech Republic
| | - Jan Florián
- Department
of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
| | - Václav Martínek
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, Albertov 2030, 128 43 Prague 2, Czech Republic
- Department of Teaching and Didactics of Chemistry, Faculty of Science, Charles University in Prague, Albertov 3, 128 43 Prague 2, Czech Republic
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38
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Li Y, Liew LSY, Li Q, Kang C. Structure of the transmembrane domain of human nicastrin-a component of γ-secretase. Sci Rep 2016; 6:19522. [PMID: 26776682 PMCID: PMC4726005 DOI: 10.1038/srep19522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/09/2015] [Indexed: 02/04/2023] Open
Abstract
Nicastrin is the largest component of γ-secretase that is an intramembrane protease important in the development of Alzheimer's disease. Nicastrin contains a large extracellular domain, a single transmembrane (TM) domain, and a short C-terminus. Its TM domain is important for the γ-secretase complex formation. Here we report nuclear magnetic resonance (NMR) studies of the TM and C-terminal regions of human nicastrin in both sodium dodecyl sulfate (SDS) and dodecylphosphocholine (DPC) micelles. Structural study and dynamic analysis reveal that the TM domain is largely helical and stable under both SDS and DPC micelles with its N-terminal region undergoing intermediate time scale motion. The TM helix contains a hydrophilic patch that is important for TM-TM interactions. The short C-terminus is not structured in solution and a region formed by residues V697-A702 interacts with the membrane, suggesting that these residues may play a role in the γ-secretase complex formation. Our study provides structural insight into the function of the nicastrin TM domain and the C-terminus in γ-secretase complex.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Lynette Sin Yee Liew
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Qingxin Li
- Institute of Chemical &Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
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39
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Salnikov ES, Sarrouj H, Reiter C, Aisenbrey C, Purea A, Aussenac F, Ouari O, Tordo P, Fedotenko I, Engelke F, Bechinger B. Solid-State NMR/Dynamic Nuclear Polarization of Polypeptides in Planar Supported Lipid Bilayers. J Phys Chem B 2015; 119:14574-83. [PMID: 26487390 DOI: 10.1021/acs.jpcb.5b07341] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Dynamic nuclear polarization has been developed to overcome the limitations of the inherently low signal intensity of NMR spectroscopy. This technique promises to be particularly useful for solid-state NMR spectroscopy where the signals are broadened over a larger frequency range and most investigations rely on recording low gamma nuclei. To extend the range of possible investigations, a triple-resonance flat-coil solid-state NMR probe is presented with microwave irradiation capacities allowing the investigation of static samples at temperatures of 100 K, including supported lipid bilayers. The probe performance allows for two-dimensional separated local field experiments with high-power Lee-Goldberg decoupling and cross-polarization under simultaneous irradiation from a gyrotron microwave generator. Efficient cooling of the sample turned out to be essential for best enhancements and line shape and necessitated the development of a dedicated cooling chamber. Furthermore, a new membrane-anchored biradical is presented, and the geometry of supported membranes was optimized not only for good membrane alignment, handling, stability, and filling factor of the coil but also for heat and microwave dissipation. Enhancement factors of 17-fold were obtained, and a two-dimensional PISEMA spectrum of a transmembrane helical peptide was obtained in less than 2 h.
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Affiliation(s)
- Evgeniy S Salnikov
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177 , 67070 Strasbourg, France
| | - Hiba Sarrouj
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177 , 67070 Strasbourg, France.,Bruker BioSpin, Silberstreifen, 76287 Rheinstetten, Germany
| | | | - Christopher Aisenbrey
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177 , 67070 Strasbourg, France
| | - Armin Purea
- Bruker BioSpin, Silberstreifen, 76287 Rheinstetten, Germany
| | - Fabien Aussenac
- Bruker BioSpin, 34, rue de l'Industrie, 67166 Wissembourg, France
| | - Olivier Ouari
- Aix Marseille Université, CNRS , Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille, France
| | - Paul Tordo
- Aix Marseille Université, CNRS , Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille, France
| | - Illya Fedotenko
- Aix Marseille Université, CNRS , Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille, France
| | - Frank Engelke
- Bruker BioSpin, Silberstreifen, 76287 Rheinstetten, Germany
| | - Burkhard Bechinger
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177 , 67070 Strasbourg, France
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40
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Inhibition of cytochrome P450 2B4 by environmentally persistent free radical-containing particulate matter. Biochem Pharmacol 2015; 95:126-32. [PMID: 25817938 DOI: 10.1016/j.bcp.2015.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/17/2015] [Indexed: 01/18/2023]
Abstract
Combustion processes generate particulate matter (PM) that can affect human health. The presence of redox-active metals and aromatic hydrocarbons in the post-combustion regions results in the formation of air-stable, environmentally persistent free radicals (EPFRs) on entrained particles. Exposure to EPFRs has been shown to negatively influence pulmonary and cardiovascular functions. Cytochromes P450 (P450/CYP) are endoplasmic reticulum resident proteins that are responsible for the metabolism of foreign compounds. Previously, it was shown that model EPFRs, generated by exposure of silica containing 5% copper oxide (CuO-Si) to either dicholorobenzene (DCB230) or 2-monochlorophenol (MCP230) at ≥ 230 °C, inhibited six forms of P450 in rat liver microsomes (Toxicol. Appl. Pharmacol. (2014) 277:200-209). In this study, the inhibition of P450 by MCP230 was examined in more detail by measuring its effect on the rate of metabolism of 7-ethoxy-4-trifluoromethylcoumarin (7EFC) and 7-benzyloxyresorufin (7BRF) by the purified, reconstituted CYP2B4 system. MCP230 inhibited the CYP2B4-mediated metabolism of 7EFC at least 10-fold more potently than non-EPFR controls (CuO-Si, silica, and silica generated from heating silica and MCP at 50 °C, so that EPFRs were not formed (MCP50)). The inhibition by EPFRs was specific for the P450 and did not affect the ability of the redox partner, P450 reductase (CPR) from reducing cytochrome c. All of the PM inhibited CYP2B4-mediated metabolism noncompetitively with respect to substrate. When CYP2B4-mediated metabolism of 7EFC was measured as a function of the CPR concentration, the mechanism of inhibition was competitive. EPFRs likely inhibit CYP2B4-mediated substrate metabolism by physically disrupting the CPR·P450 complex.
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41
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Zhang M, Huang R, Im SC, Waskell L, Ramamoorthy A. Effects of membrane mimetics on cytochrome P450-cytochrome b5 interactions characterized by NMR spectroscopy. J Biol Chem 2015; 290:12705-18. [PMID: 25795780 DOI: 10.1074/jbc.m114.597096] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Indexed: 01/08/2023] Open
Abstract
Mammalian cytochrome P450 (P450) is a membrane-bound monooxygenase whose catalytic activities require two electrons to be sequentially delivered from its redox partners: cytochrome b5 (cytb5) and cytochrome P450 reductase, both of which are membrane proteins. Although P450 functional activities are known to be affected by lipids, experimental evidence to reveal the effect of membrane on P450-cytb5 interactions is still lacking. Here, we present evidence for the influence of phospholipid bilayers on complex formation between rabbit P450 2B4 (CYP2B4) and rabbit cytb5 at the atomic level, utilizing NMR techniques. General line broadening and modest chemical shift perturbations of cytb5 resonances characterize CYP2B4-cytb5 interactions on the intermediate time scale. More significant intensity attenuation and a more specific protein-protein binding interface are observed in bicelles as compared with lipid-free solution, highlighting the importance of the lipid bilayer in stabilizing stronger and more specific interactions between CYP2B4 and cytb5, which may lead to a more efficient electron transfer. Similar results observed for the interactions between CYP2B4 lacking the transmembrane domain (tr-CYP2B4) and cytb5 imply interactions between tr-CYP2B4 and the membrane surface, which might assist in CYP2B4-cytb5 complex formation by orienting tr-CYP2B4 for efficient contact with cytb5. Furthermore, the observation of weak and nonspecific interactions between CYP2B4 and cytb5 in micelles suggests that lipid bilayer structures and low curvature membrane surface are preferable for CYP2B4-cytb5 complex formation. Results presented in this study provide structural insights into the mechanism behind the important role that the lipid bilayer plays in the interactions between P450s and their redox partners.
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Affiliation(s)
- Meng Zhang
- From the Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055 and
| | - Rui Huang
- From the Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055 and
| | - Sang-Choul Im
- the Department of Anesthesiology, University of Michigan and Veterans Affairs Medical Center, Ann Arbor, Michigan 48105
| | - Lucy Waskell
- the Department of Anesthesiology, University of Michigan and Veterans Affairs Medical Center, Ann Arbor, Michigan 48105
| | - Ayyalusamy Ramamoorthy
- From the Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055 and
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42
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Navrátilová V, Paloncýová M, Kajšová M, Berka K, Otyepka M. Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. J Chem Inf Model 2015; 55:628-35. [DOI: 10.1021/ci500645k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Veronika Navrátilová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Markéta Paloncýová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michaela Kajšová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
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Basudhar D, Madrona Y, Kandel S, Lampe JN, Nishida CR, de Montellano PRO. Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography. J Biol Chem 2015; 290:10000-17. [PMID: 25670859 DOI: 10.1074/jbc.m114.627935] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 01/04/2023] Open
Abstract
Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional (1)H,(15)N HSQC chemical shift perturbation mapping of (15)N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.
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Affiliation(s)
- Debashree Basudhar
- From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158
| | - Yarrow Madrona
- From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158
| | | | - Jed N Lampe
- the Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Clinton R Nishida
- From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158
| | - Paul R Ortiz de Montellano
- From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158,
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44
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Zhang R, Damron J, Vosegaard T, Ramamoorthy A. A cross-polarization based rotating-frame separated-local-field NMR experiment under ultrafast MAS conditions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 250:37-44. [PMID: 25486635 PMCID: PMC4286468 DOI: 10.1016/j.jmr.2014.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/16/2014] [Accepted: 10/26/2014] [Indexed: 05/04/2023]
Abstract
Rotating-frame separated-local-field solid-state NMR experiments measure highly resolved heteronuclear dipolar couplings which, in turn, provide valuable interatomic distances for structural and dynamic studies of molecules in the solid-state. Though many different rotating-frame SLF sequences have been put forth, recent advances in ultrafast MAS technology have considerably simplified pulse sequence requirements due to the suppression of proton-proton dipolar interactions. In this study we revisit a simple two-dimensional (1)H-(13)C dipolar coupling/chemical shift correlation experiment using (13)C detected cross-polarization with a variable contact time (CPVC) and systematically study the conditions for its optimal performance at 60 kHz MAS. In addition, we demonstrate the feasibility of a proton-detected version of the CPVC experiment. The theoretical analysis of the CPVC pulse sequence under different Hartmann-Hahn matching conditions confirms that it performs optimally under the ZQ (w1H-w1C=±wr) condition for polarization transfer. The limits of the cross polarization process are explored and precisely defined as a function of offset and Hartmann-Hahn mismatch via spin dynamics simulation and experiments on a powder sample of uniformly (13)C-labeled L-isoleucine. Our results show that the performance of the CPVC sequence and subsequent determination of (1)H-(13)C dipolar couplings are insensitive to (1)H/(13)C frequency offset frequency when high RF fields are used on both RF channels. Conversely, the CPVC sequence is quite sensitive to the Hartmann-Hahn mismatch, particularly for systems with weak heteronuclear dipolar couplings. We demonstrate the use of the CPVC based SLF experiment as a tool to identify different carbon groups, and hope to motivate the exploration of more sophisticated (1)H detected avenues for ultrafast MAS.
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Affiliation(s)
- Rongchun Zhang
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Joshua Damron
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States.
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45
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Probing the transmembrane structure and dynamics of microsomal NADPH-cytochrome P450 oxidoreductase by solid-state NMR. Biophys J 2014; 106:2126-33. [PMID: 24853741 DOI: 10.1016/j.bpj.2014.03.051] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/02/2014] [Accepted: 03/19/2014] [Indexed: 10/25/2022] Open
Abstract
NADPH-cytochrome P450 oxidoreductase (CYPOR) is an essential redox partner of the cytochrome P450 (cyt P450) superfamily of metabolic enzymes. In the endoplasmic reticulum of liver cells, such enzymes metabolize ~75% of the pharmaceuticals in use today. It is known that the transmembrane domain of CYPOR plays a crucial role in aiding the formation of a complex between CYPOR and cyt P450. Here we present the transmembrane structure, topology, and dynamics of the FMN binding domain of CYPOR in a native membrane-like environment. Our solid-state NMR results reveal that the N-terminal transmembrane domain of CYPOR adopts an α-helical conformation in the lipid membrane environment. Most notably, we also show that the transmembrane helix is tilted ~13° from the lipid bilayer normal, and exhibits motions on a submillisecond timescale including rotational diffusion of the whole helix and fluctuation of the helical director axis. The approaches and the information reported in this study would enable further investigations on the structure and dynamics of the full-length NADPH-cytochrome P450 oxidoreductase and its interaction with other membrane proteins in a membrane environment.
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46
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Kandel SE, Lampe JN. Role of protein-protein interactions in cytochrome P450-mediated drug metabolism and toxicity. Chem Res Toxicol 2014; 27:1474-86. [PMID: 25133307 PMCID: PMC4164225 DOI: 10.1021/tx500203s] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
![]()
Through their unique oxidative chemistry,
cytochrome P450 monooxygenases
(CYPs) catalyze the elimination of most drugs and toxins from the
human body. Protein–protein interactions play a critical role
in this process. Historically, the study of CYP–protein interactions
has focused on their electron transfer partners and allosteric mediators,
cytochrome P450 reductase and cytochrome b5. However, CYPs can bind
other proteins that also affect CYP function. Some examples include
the progesterone receptor membrane component 1, damage resistance
protein 1, human and bovine serum albumin, and intestinal fatty acid
binding protein, in addition to other CYP isoforms. Furthermore, disruption
of these interactions can lead to altered paths of metabolism and
the production of toxic metabolites. In this review, we summarize
the available evidence for CYP protein–protein interactions
from the literature and offer a discussion of the potential impact
of future studies aimed at characterizing noncanonical protein–protein
interactions with CYP enzymes.
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Affiliation(s)
- Sylvie E Kandel
- XenoTech, LLC , 16825 West 116th Street, Lenexa, Kansas 66219, United States
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47
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Abstract
Membrane proteins have always presented technical challenges for structural studies because of their requirement for a lipid environment. Multiple approaches exist including X-ray crystallography and electron microscopy that can give significant insights into their structure and function. However, nuclear magnetic resonance (NMR) is unique in that it offers the possibility of determining the structures of unmodified membrane proteins in their native environment of phospholipid bilayers under physiological conditions. Furthermore, NMR enables the characterization of the structure and dynamics of backbone and side chain sites of the proteins alone and in complexes with both small molecules and other biopolymers. The learning curve has been steep for the field as most initial studies were performed under non-native environments using modified proteins until ultimately progress in both techniques and instrumentation led to the possibility of examining unmodified membrane proteins in phospholipid bilayers under physiological conditions. This review aims to provide an overview of the development and application of NMR to membrane proteins. It highlights some of the most significant structural milestones that have been reached by NMR spectroscopy of membrane proteins, especially those accomplished with the proteins in phospholipid bilayer environments where they function.
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48
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Cellular solid-state NMR investigation of a membrane protein using dynamic nuclear polarization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:342-9. [PMID: 25017802 DOI: 10.1016/j.bbamem.2014.07.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/30/2014] [Accepted: 07/02/2014] [Indexed: 12/16/2022]
Abstract
While an increasing number of structural biology studies successfully demonstrate the power of high-resolution structures and dynamics of membrane proteins in fully understanding their function, there is considerable interest in developing NMR approaches to obtain such information in a cellular setting. As long as the proteins inside the living cell tumble rapidly in the NMR timescale, recently developed in-cell solution NMR approaches can provide 3D structural information. However, there are numerous challenges to study membrane proteins inside a cell. Research in our laboratory is focused on developing a combination of solid-state NMR and biological approaches to overcome these challenges in order to obtain high-resolution structural insights into electron transfer processes mediated by membrane-bound proteins like mammalian cytochrome-b5, cytochrome-P450 and cytochrome-P450-reductase. In this study, we demonstrate the feasibility of using dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR spectroscopy for in-cell studies on a membrane-anchored protein. Our experimental results obtained from ¹³C-labeled membrane-anchored cytochrome-b5 in native Escherichia coli cells show a ~16-fold DNP signal enhancement. Further, results obtained from a 2D ¹³C/¹³C chemical shift correlation MAS experiment demonstrate the feasibility of suppressing the background signals from other cellular contents for high-resolution structural studies on membrane proteins. We believe that this study would pave new avenues for high-resolution structural studies on a variety of membrane-associated proteins and their complexes in the cellular context to fully understand their functional roles in physiological processes.
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49
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Zhang R, Ramamoorthy A. Performance of RINEPT is amplified by dipolar couplings under ultrafast MAS conditions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 243:85-92. [PMID: 24792960 PMCID: PMC4057659 DOI: 10.1016/j.jmr.2014.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/27/2014] [Accepted: 03/31/2014] [Indexed: 05/04/2023]
Abstract
The refocused insensitive nuclei enhanced by polarization transfer (RINEPT) technique is commonly used for heteronuclear polarization transfer in solution and solid-state NMR spectroscopy. Suppression of dipolar couplings, either by fast molecular motions in solution or by a combination of MAS and multiple pulse sequences in solids, enables the polarization transfer via scalar couplings. However, the presence of unsuppressed dipolar couplings could alter the functioning of RINEPT, particularly under fast/ultrafast MAS conditions. In this study, we demonstrate, through experiments on rigid solids complemented by numerical simulations, that the polarization transfer efficiency of RINEPT is dependent on the MAS frequency. In addition, we show that heteronuclear dipolar coupling is the dominant factor in the polarization transfer, which is strengthened by the presence of (1)H-(1)H dipolar couplings. In fact, the simultaneous presence of homonuclear and heteronuclear dipolar couplings is the premise for the polarization transfer by RINEPT, whereas the scalar coupling plays an insignificant role under ultrafast MAS conditions on rigid solids. Our results additionally reveal that the polarization transfer efficiency decreases with the increasing duration of RF pulses used in the RINEPT sequence.
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Affiliation(s)
- Rongchun Zhang
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, USA; School of Physics, Nankai University, Tianjin 300071, PR China
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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50
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Pandey MK, Vivekanandan S, Yamamoto K, Im S, Waskell L, Ramamoorthy A. Proton-detected 2D radio frequency driven recoupling solid-state NMR studies on micelle-associated cytochrome-b(5). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 242:169-79. [PMID: 24657390 PMCID: PMC4020179 DOI: 10.1016/j.jmr.2014.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/06/2014] [Accepted: 02/10/2014] [Indexed: 05/08/2023]
Abstract
Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled ((13)C, (15)N and (2)H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged (1)H-(1)H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross-peak intensities against the mixing time - obtained from 2D (1)H-(1)H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure (1)H-(1)H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent (1)H-(1)H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from (1)H-(1)H RFDR experiments. The appearance of resonances with distinct chemical shift values in (1)H-(1)H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles.
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Affiliation(s)
- Manoj Kumar Pandey
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Subramanian Vivekanandan
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Kazutoshi Yamamoto
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Sangchoul Im
- Department of Anesthesiology, University of Michigan, VA Medical Center, Ann Arbor, MI 48105, United States
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, VA Medical Center, Ann Arbor, MI 48105, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States.
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