1
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Kupče Ē, Mote KR, Webb A, Madhu PK, Claridge TDW. Multiplexing experiments in NMR and multi-nuclear MRI. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 124-125:1-56. [PMID: 34479710 DOI: 10.1016/j.pnmrs.2021.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 05/22/2023]
Abstract
Multiplexing NMR experiments by direct detection of multiple free induction decays (FIDs) in a single experiment offers a dramatic increase in the spectral information content and often yields significant improvement in sensitivity per unit time. Experiments with multi-FID detection have been designed with both homonuclear and multinuclear acquisition, and the advent of multiple receivers on commercial spectrometers opens up new possibilities for recording spectra from different nuclear species in parallel. Here we provide an extensive overview of such techniques, designed for applications in liquid- and solid-state NMR as well as in hyperpolarized samples. A brief overview of multinuclear MRI is also provided, to stimulate cross fertilization of ideas between the two areas of research (NMR and MRI). It is shown how such techniques enable the design of experiments that allow structure elucidation of small molecules from a single measurement. Likewise, in biomolecular NMR experiments multi-FID detection allows complete resonance assignment in proteins. Probes with multiple RF microcoils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems, effectively reducing the cost of NMR analysis and increasing the information content at the same time. Solid-state NMR experiments have also benefited immensely from both parallel and sequential multi-FID detection in a variety of multi-dimensional pulse schemes. We are confident that multi-FID detection will become an essential component of future NMR methodologies, effectively increasing the sensitivity and information content of NMR measurements.
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Affiliation(s)
- Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, United Kingdom.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research-Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Andrew Webb
- Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Perunthiruthy K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research-Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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2
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Krug U, Gloge A, Schmidt P, Becker‐Baldus J, Bernhard F, Kaiser A, Montag C, Gauglitz M, Vishnivetskiy SA, Gurevich VV, Beck‐Sickinger AG, Glaubitz C, Huster D. The Conformational Equilibrium of the Neuropeptide Y2 Receptor in Bilayer Membranes. Angew Chem Int Ed Engl 2020; 59:23854-23861. [PMID: 32790043 PMCID: PMC7736470 DOI: 10.1002/anie.202006075] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/13/2020] [Indexed: 12/23/2022]
Abstract
Dynamic structural transitions within the seven-transmembrane bundle represent the mechanism by which G-protein-coupled receptors convert an extracellular chemical signal into an intracellular biological function. Here, the conformational dynamics of the neuropeptide Y receptor type 2 (Y2R) during activation was investigated. The apo, full agonist-, and arrestin-bound states of Y2R were prepared by cell-free expression, functional refolding, and reconstitution into lipid membranes. To study conformational transitions between these states, all six tryptophans of Y2R were 13 C-labeled. NMR-signal assignment was achieved by dynamic-nuclear-polarization enhancement and the individual functional states of the receptor were characterized by monitoring 13 C NMR chemical shifts. Activation of Y2R is mediated by molecular switches involving the toggle switch residue Trp2816.48 of the highly conserved SWLP motif and Trp3277.55 adjacent to the NPxxY motif. Furthermore, a conformationally preserved "cysteine lock"-Trp11623.50 was identified.
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Affiliation(s)
- Ulrike Krug
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Anika Gloge
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Peter Schmidt
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Johanna Becker‐Baldus
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Frank Bernhard
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Anette Kaiser
- Institute of BiochemistryUniversity of LeipzigLeipzigGermany
| | - Cindy Montag
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Marcel Gauglitz
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
- Berlin Joint Electron Paramagnetic Resonance LaboratoryFree University BerlinGermany
| | | | | | | | - Clemens Glaubitz
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Daniel Huster
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
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3
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Krug U, Gloge A, Schmidt P, Becker‐Baldus J, Bernhard F, Kaiser A, Montag C, Gauglitz M, Vishnivetskiy SA, Gurevich VV, Beck‐Sickinger AG, Glaubitz C, Huster D. Das Konformationsgleichgewicht des Neuropeptid‐Y2‐Rezeptors in Lipidmembranen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ulrike Krug
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Anika Gloge
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Peter Schmidt
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Johanna Becker‐Baldus
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Frank Bernhard
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Anette Kaiser
- Institut für Biochemie Universität Leipzig Deutschland
| | - Cindy Montag
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Marcel Gauglitz
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
- Berlin Joint Electron Paramagnetic Resonance Laboratory Freie Universität Berlin Deutschland
| | | | | | | | - Clemens Glaubitz
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Daniel Huster
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
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4
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Vogel A, Bosse M, Gauglitz M, Wistuba S, Schmidt P, Kaiser A, Gurevich VV, Beck-Sickinger AG, Hildebrand PW, Huster D. The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation. Molecules 2020; 25:E5489. [PMID: 33255213 PMCID: PMC7727705 DOI: 10.3390/molecules25235489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 01/08/2023] Open
Abstract
We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using 15N-NMR and quantitative determination of 1H-13C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH2 and 0.18 for the CH3 groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.
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Affiliation(s)
- Alexander Vogel
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Mathias Bosse
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Marcel Gauglitz
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Sarah Wistuba
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Peter Schmidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Anette Kaiser
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany; (A.K.); (A.G.B.-S.)
| | - Vsevolod V. Gurevich
- Vanderbilt University Medical Center, 2200 Pierce Avenue, Nashville, TN 37232, USA;
| | - Annette G. Beck-Sickinger
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany; (A.K.); (A.G.B.-S.)
| | - Peter W. Hildebrand
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
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5
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Pacull EM, Sendker F, Bernhard F, Scheidt HA, Schmidt P, Huster D, Krug U. Integration of Cell-Free Expression and Solid-State NMR to Investigate the Dynamic Properties of Different Sites of the Growth Hormone Secretagogue Receptor. Front Pharmacol 2020; 11:562113. [PMID: 33324203 PMCID: PMC7723455 DOI: 10.3389/fphar.2020.562113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023] Open
Abstract
Cell-free expression represents an attractive method to produce large quantities of selectively labeled protein for NMR applications. Here, cell-free expression was used to label specific regions of the growth hormone secretagogue receptor (GHSR) with NMR-active isotopes. The GHSR is a member of the class A family of G protein-coupled receptors. A cell-free expression system was established to produce the GHSR in the precipitated form. The solubilized receptor was refolded in vitro and reconstituted into DMPC lipid membranes. Methionines, arginines, and histidines were chosen for 13C-labeling as they are representative for the transmembrane domains, the loops and flanking regions of the transmembrane α-helices, and the C-terminus of the receptor, respectively. The dynamics of the isotopically labeled residues was characterized by solid-state NMR measuring motionally averaged 1H-13C dipolar couplings, which were converted into molecular order parameters. Separated local field DIPSHIFT experiments under magic-angle spinning conditions using either varying cross polarization contact times or direct excitation provided order parameters for these residues showing that the C-terminus was the segment with the highest motional amplitude. The loop regions and helix ends as well as the transmembrane regions of the GHSR represent relatively rigid segments in the overall very flexible receptor molecule. Although no site resolution could be achieved in the experiments, the previously reported highly dynamic character of the receptor concluded from uniformly 13C labeled receptor samples could be further specified by this segmental labeling approach, leading to a more diversified understanding of the receptor dynamics under equilibrium conditions.
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Affiliation(s)
- Emelyne M Pacull
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Franziska Sendker
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Peter Schmidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Ulrike Krug
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
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6
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Engberg O, Bochicchio A, Brandner AF, Gupta A, Dey S, Böckmann RA, Maiti S, Huster D. Serotonin Alters the Phase Equilibrium of a Ternary Mixture of Phospholipids and Cholesterol. Front Physiol 2020; 11:578868. [PMID: 33192582 PMCID: PMC7645218 DOI: 10.3389/fphys.2020.578868] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Unsaturated and saturated phospholipids tend to laterally segregate, especially in the presence of cholesterol. Small molecules such as neurotransmitters, toxins, drugs etc. possibly modulate this lateral segregation. The small aromatic neurotransmitter serotonin (5-HT) has been found to bind to membranes. We studied the lipid structure and packing of a ternary membrane mixture consisting of palmitoyl-oleoyl-phosphatidylcholine, palmitoyl-sphingomyelin, and cholesterol at a molar ratio of 4/4/2 in the absence and in the presence of 5-HT, using a combination of solid-state 2H NMR, atomic force microscopy, and atomistic molecular dynamics (MD) simulations. Both NMR and MD report formation of a liquid ordered (L o ) and a liquid disordered (L d ) phase coexistence with small domains. Lipid exchange between the domains was fast such that single component 2H NMR spectra are detected over a wide temperature range. A drastic restructuring of the domains was induced when 5-HT is added to the membranes at a 9 mol% concentration relative to the lipids. 2H NMR spectra of all components of the mixture showed two prominent contributions indicative of molecules of the same kind residing both in the disordered and the ordered phase. Compared to the data in the absence of 5-HT, the lipid chain order in the disordered phase was further decreased in the presence of 5-HT. Likewise, addition of serotonin increased lipid chain order within the ordered phase. These characteristic lipid chain order changes were confirmed by MD simulations. The 5-HT-induced larger difference in lipid chain order results in more pronounced differences in the hydrophobic thickness of the individual membrane domains. The correspondingly enlarged hydrophobic mismatch between ordered and disordered phases is assumed to increase the line tension at the domain boundary, which drives the system into formation of larger size domains. These results not only demonstrate that small membrane binding molecules such as neurotransmitters have a profound impact on essential membrane properties. It also suggests a mechanism by which the interaction of small molecules with membranes can influence the function of membrane proteins and non-cognate receptors. Altered membrane properties may modify lateral sorting of membrane protein, membrane protein conformation, and thus influence their function as suspected for neurotransmitters, local anesthetics, and other small drug molecules.
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Affiliation(s)
- Oskar Engberg
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Anna Bochicchio
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Astrid F. Brandner
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Ankur Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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7
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Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
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8
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Casiraghi M, Damian M, Lescop E, Banères JL, Catoire LJ. Illuminating the Energy Landscape of GPCRs: The Key Contribution of Solution-State NMR Associated with Escherichia coli as an Expression Host. Biochemistry 2018; 57:2297-2307. [PMID: 29607648 DOI: 10.1021/acs.biochem.8b00035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Conformational dynamics of GPCRs are central to their function but are difficult to explore at the atomic scale. Solution-state NMR has provided the major contribution in that area of study during the past decade, despite nonoptimized labeling schemes due to the use of insect cells and, to a lesser extent, yeast as the main expression hosts. Indeed, the most efficient isotope-labeling scheme ever to address energy landscape issues for large proteins or protein complexes relies on the use of 13CH3 probes immersed in a perdeuterated dipolar environment, which is essentially out of reach of eukaryotic expression systems. In contrast, although its contribution has been underestimated because of technical issues, Escherichia coli is by far the best-adapted host for such labeling. As it is now tightly controlled, we show in this review that bacterial expression can provide an NMR spectral resolution never achieved in the GPCR field.
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Affiliation(s)
- Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires , UMR 7099, CNRS/Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550) , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Marjorie Damian
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, Université Montpellier, ENSCM , 15 av. Charles Flahault , 34093 Montpellier , France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay , 1 av. de la Terrasse , 91198 Gif-sur-Yvette , France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, Université Montpellier, ENSCM , 15 av. Charles Flahault , 34093 Montpellier , France
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires , UMR 7099, CNRS/Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550) , 13 rue Pierre et Marie Curie , 75005 Paris , France
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9
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McKay MJ, Afrose F, Koeppe RE, Greathouse DV. Helix formation and stability in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2108-2117. [PMID: 29447916 DOI: 10.1016/j.bbamem.2018.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 01/05/2023]
Abstract
In this article we review current understanding of basic principles for the folding of membrane proteins, focusing on the more abundant alpha-helical class. Membrane proteins, vital to many biological functions and implicated in numerous diseases, fold into their active conformations in the complex environment of the cell bilayer membrane. While many membrane proteins rely on the translocon and chaperone proteins to fold correctly, others can achieve their functional form in the absence of any translation apparatus or other aides. Nevertheless, the spontaneous folding process is not well understood at the molecular level. Recent findings suggest that helix fraying and loop formation may be important for overall structure, dynamics and regulation of function. Several types of membrane helices with ionizable amino acids change their topology with pH. Additionally we note that some peptides, including many that are rich in arginine, and a particular analogue of gramicidin, are able passively to translocate across cell membranes. The findings indicate that a final protein structure in a lipid-bilayer membrane is sequence-based, with lipids contributing to stability and regulation. While much progress has been made toward understanding the folding process for alpha-helical membrane proteins, it remains a work in progress. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Fahmida Afrose
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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10
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Schmidt P, Bender BJ, Kaiser A, Gulati K, Scheidt HA, Hamm HE, Meiler J, Beck-Sickinger AG, Huster D. Improved in Vitro Folding of the Y 2 G Protein-Coupled Receptor into Bicelles. Front Mol Biosci 2018; 4:100. [PMID: 29387686 PMCID: PMC5776092 DOI: 10.3389/fmolb.2017.00100] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/28/2017] [Indexed: 12/26/2022] Open
Abstract
Prerequisite for structural studies on G protein-coupled receptors is the preparation of highly concentrated, stable, and biologically active receptor samples in milligram amounts of protein. Here, we present an improved protocol for Escherichia coli expression, functional refolding, and reconstitution into bicelles of the human neuropeptide Y receptor type 2 (Y2R) for solution and solid-state NMR experiments. The isotopically labeled receptor is expressed in inclusion bodies and purified using SDS. We studied the details of an improved preparation protocol including the in vitro folding of the receptor, e.g., the native disulfide bridge formation, the exchange of the denaturating detergent SDS, and the functional reconstitution into bicelle environments of varying size. Full pharmacological functionality of the Y2R preparation was shown by a ligand affinity of 4 nM and G-protein activation. Further, simple NMR experiments are used to test sample quality in high micromolar concentration.
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Affiliation(s)
- Peter Schmidt
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Brian J Bender
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Anette Kaiser
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Leipzig, Germany
| | - Khushboo Gulati
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Holger A Scheidt
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Heidi E Hamm
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, United States
| | | | - Daniel Huster
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
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11
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Expression, Functional Characterization, and Solid-State NMR Investigation of the G Protein-Coupled GHS Receptor in Bilayer Membranes. Sci Rep 2017; 7:46128. [PMID: 28387359 PMCID: PMC5384189 DOI: 10.1038/srep46128] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/13/2017] [Indexed: 01/14/2023] Open
Abstract
The expression, functional reconstitution and first NMR characterization of the human growth hormone secretagogue (GHS) receptor reconstituted into either DMPC or POPC membranes is described. The receptor was expressed in E. coli. refolded, and reconstituted into bilayer membranes. The molecule was characterized by 15N and 13C solid-state NMR spectroscopy in the absence and in the presence of its natural agonist ghrelin or an inverse agonist. Static 15N NMR spectra of the uniformly labeled receptor are indicative of axially symmetric rotational diffusion of the G protein-coupled receptor in the membrane. In addition, about 25% of the 15N sites undergo large amplitude motions giving rise to very narrow spectral components. For an initial quantitative assessment of the receptor mobility, 1H-13C dipolar coupling values, which are scaled by molecular motions, were determined quantitatively. From these values, average order parameters, reporting the motional amplitudes of the individual receptor segments can be derived. Average backbone order parameters were determined with values between 0.56 and 0.69, corresponding to average motional amplitudes of 40–50° of these segments. Differences between the receptor dynamics in DMPC or POPC membranes were within experimental error. Furthermore, agonist or inverse agonist binding only insignificantly influenced the average molecular dynamics of the receptor.
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Vogel A, Scheidt HA, Baek DJ, Bittman R, Huster D. Structure and dynamics of the aliphatic cholesterol side chain in membranes as studied by (2)H NMR spectroscopy and molecular dynamics simulation. Phys Chem Chem Phys 2016; 18:3730-8. [PMID: 26762541 DOI: 10.1039/c5cp05084g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cholesterol is an evolutionarily highly optimized molecule particularly known for its ability to condense the phospholipids in cellular membranes. Until recently, the accompanying increase in the chain order of the surrounding phospholipids was attributed to the planar and rigid tetracyclic ring structure of cholesterol. However, detailed investigations of cholesterol's aliphatic side chain demonstrated that this side chain is responsible for approximately half of the condensation effect. Therefore, we investigated the structure and dynamics of the aliphatic side chain of cholesterol using (2)H solid-state nuclear magnetic resonance (NMR) spectroscopy and microsecond timescale all-atom molecular dynamics (MD) simulations in four different model membranes: POPC, DPPC, PSM, and POPC/PSM (1 : 1 mol/mol) and at three different temperatures: 5 °C, 37 °C, and 50 °C. A cholesterol variant, in which 11 hydrogens of the aliphatic side chain were exchanged for deuterium, was used and the respective (2)H NMR spectra confirmed the axially asymmetric rotational diffusion of cholesterol in DPPC and PSM. Furthermore, NMR spectra indicated that some hydrogens showed an unexpected magnetic inequivalency. This finding was confirmed by all-atom molecular dynamics simulations and detailed analysis revealed that the hydrogens of the methylene groups at C22, C23, and C24 are magnetically inequivalent. This inequivalency is caused by steric clashes of the aliphatic side chain with the ring structure of cholesterol as well as the branched C21 methyl group. These excluded volume effects result in reduced conformational flexibility of the aliphatic side chain of cholesterol and explain its high order (order parameter of 0.78 for chain motions) and large contribution to the condensation effect. Additionally, the motional pattern of the side chain becomes highly anisotropic such that it shows larger fluctuations perpendicular to the ring plane of cholesterol with a biaxiality of the distribution of 0.046. Overall, our results shed light on the mechanism how the aliphatic side chain is able to contribute about half of the condensation effect of cholesterol.
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Affiliation(s)
- Alexander Vogel
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany.
| | - Holger A Scheidt
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany.
| | - Dong Jae Baek
- College of Pharmacy and Natural Medicine Research Institute, Mokpo National University, Jeonnam, Republic of Korea and Department of Chemistry and Biochemistry, Queens College of the City University of New York, Flushing, NY 11367-1597, USA
| | - Robert Bittman
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, Flushing, NY 11367-1597, USA
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany.
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Schanda P, Ernst M. Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:1-46. [PMID: 27110043 PMCID: PMC4836562 DOI: 10.1016/j.pnmrs.2016.02.001] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution.
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Affiliation(s)
- Paul Schanda
- CEA, Institut de Biologie Structurale (IBS), 38027 Grenoble, France ; CNRS, Institut de Biologie Structurale (IBS), 38027 Grenoble, France ; Université Grenoble Alpes, IBS, 38027 Grenoble, France
| | - Matthias Ernst
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Mortazavi A, Rajagopalan V, Sparks KA, Greathouse DV, Koeppe RE. Juxta-terminal Helix Unwinding as a Stabilizing Factor to Modulate the Dynamics of Transmembrane Helices. Chembiochem 2016; 17:462-5. [PMID: 26749271 PMCID: PMC4820057 DOI: 10.1002/cbic.201500656] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Indexed: 12/24/2022]
Abstract
Transmembrane helices of integral membrane proteins often are flanked by interfacial aromatic residues that can serve as anchors to aid the stabilization of a tilted transmembrane orientation. Yet, physical factors that govern the orientation or dynamic averaging of individual transmembrane helices are not well understood and have not been adequately explained. Using solid-state (2) H NMR spectroscopy to examine lipid bilayer-incorporated model peptides of the GWALP23 (acetyl-GGALW(LA)6 LWLAGA-amide) family, we observed substantial unwinding at the terminals of several tilted helices spanning the membranes of DLPC, DMPC, or DOPC lipid bilayers. The fraying of helix ends might be vital for defining the dynamics and orientations of transmembrane helices in lipid bilayer membranes.
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Affiliation(s)
- Armin Mortazavi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Venkatesan Rajagopalan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Kelsey A Sparks
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA.
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Okude J, Ueda T, Kofuku Y, Sato M, Nobuyama N, Kondo K, Shiraishi Y, Mizumura T, Onishi K, Natsume M, Maeda M, Tsujishita H, Kuranaga T, Inoue M, Shimada I. Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ-Opioid Receptor. Angew Chem Int Ed Engl 2015; 54:15771-6. [PMID: 26568421 PMCID: PMC4722849 DOI: 10.1002/anie.201508794] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 10/19/2015] [Indexed: 12/13/2022]
Abstract
G-protein-coupled receptor (GPCR) ligands impart differing degrees of signaling in the G-protein and arrestin pathways, in phenomena called "biased signaling". However, the mechanism underlying the biased signaling of GPCRs is still unclear, although crystal structures of GPCRs bound to the G protein or arrestin are available. In this study, we observed the NMR signals from methionine residues of the μ-opioid receptor (μOR) in the balanced- and biased-ligand-bound states. We found that the intracellular cavity of μOR exists in an equilibrium between closed and multiple open conformations with coupled conformational changes on the transmembrane helices 3, 5, 6, and 7, and that the population of each open conformation determines the G-protein- and arrestin-mediated signaling levels in each ligand-bound state. These findings provide insight into the biased signaling of GPCRs and will be helpful for development of analgesics that stimulate μOR with reduced tolerance and dependence.
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Affiliation(s)
- Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0075 (Japan)
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Motohiko Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Naoyuki Nobuyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Takuya Mizumura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Kento Onishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Mei Natsume
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Masahiro Maeda
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561-0825 (Japan)
| | - Hideki Tsujishita
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561-0825 (Japan)
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan).
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16
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Okude J, Ueda T, Kofuku Y, Sato M, Nobuyama N, Kondo K, Shiraishi Y, Mizumura T, Onishi K, Natsume M, Maeda M, Tsujishita H, Kuranaga T, Inoue M, Shimada I. Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ‐Opioid Receptor. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508794] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Chiyoda‐ku, Tokyo 102‐0075 (Japan)
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Motohiko Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Naoyuki Nobuyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takuya Mizumura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Kento Onishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Mei Natsume
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Masahiro Maeda
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561‐0825 (Japan)
| | - Hideki Tsujishita
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561‐0825 (Japan)
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
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Affiliation(s)
- Rob Kaptein
- Bijvoet Centre, Utrecht University, 3584 CH, Utrecht, The Netherlands
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