101
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Eddy MT, Martin BT, Wüthrich K. A 2A Adenosine Receptor Partial Agonism Related to Structural Rearrangements in an Activation Microswitch. Structure 2020; 29:170-176.e3. [PMID: 33238145 DOI: 10.1016/j.str.2020.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/13/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022]
Abstract
In drug design, G protein-coupled receptor (GPCR) partial agonists enable one to fine-tune receptor output between basal and maximal signaling levels. Here, we add to the structural basis for rationalizing and monitoring partial agonism. NMR spectroscopy of partial agonist complexes of the A2A adenosine receptor (A2AAR) revealed conformations of the P-I-F activation motif that are distinctly different from full agonist complexes. At the intracellular surface, different conformations of helix VI observed for partial and full agonist complexes manifest a correlation between the efficacy-related structural rearrangement of this activation motif and intracellular signaling to partner proteins. While comparisons of A2AAR in complexes with partial and full agonists with different methods showed close similarity of the global folds, this NMR study now reveals subtle but distinct local structural differences related to partial agonism.
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Affiliation(s)
- Matthew T Eddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Departments of Biological Sciences and Chemistry, Bridge Institute, The University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
| | - Bryan T Martin
- Departments of Biological Sciences and Chemistry, Bridge Institute, The University of Southern California, Los Angeles, CA 90089, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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102
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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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103
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Van Drie JH, Tong L. Cryo-EM as a powerful tool for drug discovery. Bioorg Med Chem Lett 2020; 30:127524. [PMID: 32890683 PMCID: PMC7467112 DOI: 10.1016/j.bmcl.2020.127524] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The recent revolution in cryo-EM has produced an explosion of structures at near-atomic or better resolution. This has allowed cryo-EM structures to provide visualization of bound small-molecule ligands in the macromolecules, and these new structures have provided unprecedented insights into the molecular mechanisms of complex biochemical processes. They have also had a profound impact on drug discovery, defining the binding modes and mechanisms of action of well-known drugs as well as driving the design and development of new compounds. This review will summarize and highlight some of these structures. Most excitingly, the latest cryo-EM technology has produced structures at 1.2 Å resolution, further solidifying cryo-EM as a powerful tool for drug discovery. Therefore, cryo-EM will play an ever-increasing role in drug discovery in the coming years.
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Affiliation(s)
- John H Van Drie
- Van Drie Research LLC, 109 Millpond, North Andover, MA 01845, USA.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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104
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Kraus S, Benard O, Naor Z, Seger R. C-Src is Activated by the EGF Receptor in a Pathway that Mediates JNK and ERK Activation by Gonadotropin-Releasing Hormone in COS7 Cells. Int J Mol Sci 2020; 21:ijms21228575. [PMID: 33202981 PMCID: PMC7697137 DOI: 10.3390/ijms21228575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/26/2022] Open
Abstract
The key participants in G-protein-coupled receptor (GPCR) signaling are the mitogen-activated protein kinase (MAPK) signaling cascades. The mechanisms involved in the activation of the above cascades by GPCRs are not fully elucidated. The prototypical GPCR is the receptor for gonadotropin-releasing hormone (GnRHR), which serves as a key regulator of the reproductive system. Here, we expressed GnRHR in COS7 cells and found that GnRHR transmits its signals to MAPKs mainly via Gαi and the EGF receptor, without the involvement of Hb-EGF or PKCs. The main pathway that leads to JNK activation downstream of the EGF receptor involves a sequential activation of c-Src and PI3K. ERK activation by GnRHR is mediated by the EGF receptor, which activates Ras either directly or via c-Src. Beside the main pathway, the dissociated Gβγ and β-arrestin may initiate additional (albeit minor) pathways that lead to MAPK activation in the transfected COS7 cells. The pathways detected are significantly different from those in other GnRHR-bearing cells, indicating that GnRH can utilize various signaling mechanisms for MAPK activation. The unique pathway elucidated here, in which c-Src and PI3K are sequentially activated downstream of the EGF receptor, may serve as a prototype of signaling mechanisms by GnRHR and additional GPCRs in various cell types.
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Affiliation(s)
- Sarah Kraus
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel; (S.K.); (O.B.)
| | - Outhiriaradjou Benard
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel; (S.K.); (O.B.)
| | - Zvi Naor
- Department of Biochemistry, Tel Aviv University, Ramat Aviv 69978, Israel;
| | - Rony Seger
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel; (S.K.); (O.B.)
- Correspondence: ; Tel.: +972-8-9343602
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105
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Yeh V, Goode A, Bonev BB. Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR. BIOLOGY 2020; 9:E396. [PMID: 33198410 PMCID: PMC7697852 DOI: 10.3390/biology9110396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022]
Abstract
Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells.
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Affiliation(s)
| | | | - Boyan B. Bonev
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (V.Y.); (A.G.)
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106
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Dubey A, Takeuchi K, Reibarkh M, Arthanari H. The role of NMR in leveraging dynamics and entropy in drug design. JOURNAL OF BIOMOLECULAR NMR 2020; 74:479-498. [PMID: 32720098 PMCID: PMC7686249 DOI: 10.1007/s10858-020-00335-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/11/2020] [Indexed: 05/03/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has contributed to structure-based drug development (SBDD) in a unique way compared to the other biophysical methods. The potency of a ligand binding to a protein is dictated by the binding free energy, which is an intricate interplay between entropy and enthalpy. In addition to providing the atomic resolution structural information, NMR can help to identify protein-ligand interactions that potentially contribute to the enthalpic component of the free energy. NMR can also illuminate dynamic aspects of the interaction, which correspond to the entropic term of the free energy. The ability of NMR to access both terms in the free energy equation stems from the suite of experiments developed to shed light on various aspects that contribute to both entropy and enthalpy, deepening our understanding of the biological function of macromolecules and assisting to target them in physiological conditions. Here we provide a brief account of the contribution of NMR to SBDD, highlighting hallmark examples and discussing the challenges that demand further method development. In the era of integrated biology, the unique ability of NMR to directly ascertain structural and dynamical aspects of macromolecule and monitor changes in these properties upon engaging a ligand can be combined with computational and other structural and biophysical methods to provide a more complete picture of the energetics of drug engagement with the target. Such efforts can be used to engineer better drugs.
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Affiliation(s)
- Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute & Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan.
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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107
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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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108
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Rößler P, Mathieu D, Gossert AD. NMR‐Studien an biologischen Makromolekülen (>100 kDa) ohne Notwendigkeit der Deuterierung: Das XL‐ALSOFAST Experiment mit verzögerter Entkopplung. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Philip Rößler
- Institut für Molekularbiologie und Biophysik Department Biologie und Biomolekulare NMR Spektroskopie Plattform Department Biologie ETH Zürich Otto-Stern-Weg 5 8093 Zürich Schweiz
| | - Daniel Mathieu
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Deutschland
| | - Alvar D. Gossert
- Institut für Molekularbiologie und Biophysik Department Biologie und Biomolekulare NMR Spektroskopie Plattform Department Biologie ETH Zürich Otto-Stern-Weg 5 8093 Zürich Schweiz
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109
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Rößler P, Mathieu D, Gossert AD. Enabling NMR Studies of High Molecular Weight Systems Without the Need for Deuteration: The XL-ALSOFAST Experiment with Delayed Decoupling. Angew Chem Int Ed Engl 2020; 59:19329-19337. [PMID: 32743971 PMCID: PMC7589290 DOI: 10.1002/anie.202007715] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 11/30/2022]
Abstract
Current biological research increasingly focusses on large human proteins and their complexes. Such proteins are difficult to study by NMR spectroscopy because they often can only be produced in higher eukaryotic expression systems, where deuteration is hardly feasible. Here, we present the XL-ALSOFAST-[13 C,1 H]-HMQC experiment with much improved sensitivity for fully protonated high molecular weight proteins. For the tested systems ranging from 100 to 240 kDa in size, 3-fold higher sensitivity was obtained on average for fast relaxing signals compared to current state-of-the-art experiments. In the XL-ALSOFAST approach, non-observed magnetisation is optimally exploited and transverse relaxation is minimized by the newly introduced concept of delayed decoupling. The combination of high sensitivity and superior artefact suppression makes it ideal for studying inherently unstable membrane proteins or for analysing therapeutic antibodies at natural 13 C abundance. The XL-ALSOFAST and delayed decoupling will therefore expand the range of biomolecular systems accessible to NMR spectroscopy.
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Affiliation(s)
- Philip Rößler
- Institute of Molecular Biology and BiophysicsDepartment of Biology and Biomolecular NMR Spectroscopy PlatformDepartment of BiologyETH ZürichOtto-Stern-Weg 58093ZürichSwitzerland
| | - Daniel Mathieu
- Bruker BioSpin GmbHSilberstreifen 476287RheinstettenGermany
| | - Alvar D. Gossert
- Institute of Molecular Biology and BiophysicsDepartment of Biology and Biomolecular NMR Spectroscopy PlatformDepartment of BiologyETH ZürichOtto-Stern-Weg 58093ZürichSwitzerland
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110
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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111
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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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112
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Nielsen CDT, Dhasmana D, Floresta G, Wohland T, Cilibrizzi A. Illuminating the Path to Target GPCR Structures and Functions. Biochemistry 2020; 59:3783-3795. [PMID: 32956586 DOI: 10.1021/acs.biochem.0c00606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-Protein-coupled receptors (GPCRs) are ubiquitous within eukaryotes, responsible for a wide array of physiological and pathological processes. Indeed, the fact that they are the most drugged target in the human genome is indicative of their importance. Despite the clear interest in GPCRs, most information regarding their activity has been so far obtained by analyzing the response from a "bulk medium". As such, this Perspective summarizes some of the common methods for this indirect observation. Nonetheless, by inspecting approaches applying super-resolution imaging, we argue that imaging is perfectly situated to obtain more detailed structural and spatial information, assisting in the development of new GPCR-targeted drugs and clinical strategies. The benefits of direct optical visualization of GPCRs are analyzed in the context of potential future directions in the field.
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Affiliation(s)
- Christian D-T Nielsen
- Imperial College London, White City Campus, Molecular Sciences Research Hub, 80 Wood Lane, London W12 0BZ, U.K
| | - Divya Dhasmana
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Giuseppe Floresta
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Agostino Cilibrizzi
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
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113
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Yeliseev A, van den Berg A, Zoubak L, Hines K, Stepnowski S, Williston K, Yan W, Gawrisch K, Zmuda J. Thermostability of a recombinant G protein-coupled receptor expressed at high level in mammalian cell culture. Sci Rep 2020; 10:16805. [PMID: 33033368 PMCID: PMC7546613 DOI: 10.1038/s41598-020-73813-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022] Open
Abstract
Rational design of pharmaceutical drugs targeting integral membrane G protein-coupled receptors (GPCR) requires thorough understanding of ligand binding and mechanism of activation through high resolution structural studies of purified proteins. Due to inherent conformational flexibility of GPCR, stabilization of these proteins solubilized from cell membranes into detergents is a challenging task. Here, we take advantage of naturally occurring post-translational modifications for stabilization of purified GPCR in detergent micelles. The recombinant cannabinoid CB2 receptor was expressed at high yield in Expi293F mammalian cell cultures, solubilized and purified in Façade detergent. We report superior stability of the mammalian cell-expressed receptor compared to its E.coli-expressed counterpart, due to contributions from glycosylation of the N terminus and palmitoylation of the C terminus of CB2. Finally, we demonstrate that the mammalian Expi293F amino acid labelling kit is suitable for preparation of multi-milligram quantities of high quality, selectively stable isotope-labeled GPCR for studies by nuclear magnetic resonance.
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Affiliation(s)
- Alexei Yeliseev
- National Institute on Alcoholism and Alcohol Abuse, NIH, Bethesda, MD, 20892, USA.
| | | | - Lioudmila Zoubak
- National Institute on Alcoholism and Alcohol Abuse, NIH, Bethesda, MD, 20892, USA
| | - Kirk Hines
- National Institute on Alcoholism and Alcohol Abuse, NIH, Bethesda, MD, 20892, USA
| | - Sam Stepnowski
- ThermoFisher Scientific, 7335 Executive Way, Frederick, MD, 21704, USA
| | - Kyle Williston
- ThermoFisher Scientific, 7335 Executive Way, Frederick, MD, 21704, USA
| | - Wanhua Yan
- ThermoFisher Scientific, 7335 Executive Way, Frederick, MD, 21704, USA
| | - Klaus Gawrisch
- National Institute on Alcoholism and Alcohol Abuse, NIH, Bethesda, MD, 20892, USA
| | - Jonathan Zmuda
- ThermoFisher Scientific, 7335 Executive Way, Frederick, MD, 21704, USA
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114
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Muratspahić E, Koehbach J, Gruber CW, Craik DJ. Harnessing cyclotides to design and develop novel peptide GPCR ligands. RSC Chem Biol 2020; 1:177-191. [PMID: 34458757 PMCID: PMC8341132 DOI: 10.1039/d0cb00062k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
Cyclotides are plant-derived cyclic, disulfide-rich peptides with a unique cyclic cystine knot topology that confers them with remarkable structural stability and resistance to proteolytic degradation. Recently, cyclotides have emerged as promising scaffold molecules for designing peptide-based therapeutics. Here, we provide examples of how engineering cyclotides using molecular grafting may lead to the development of novel peptide ligands of G protein-coupled receptors (GPCRs), today's most exploited drug targets. Integrating bioactive epitopes into stable cyclotide scaffolds can lead to improved pharmacokinetics and oral activity as well as selectivity and high enzymatic stability. We also discuss and highlight the importance of engineered cyclotides as novel tools to study GPCR signaling.
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Affiliation(s)
- Edin Muratspahić
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Austria
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland 4072 Australia
| | - Johannes Koehbach
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland 4072 Australia
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Austria
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland 4072 Australia
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115
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Paramagnetic NMR Spectroscopy Is a Tool to Address Reactivity, Structure, and Protein–Protein Interactions of Metalloproteins: The Case of Iron–Sulfur Proteins. MAGNETOCHEMISTRY 2020. [DOI: 10.3390/magnetochemistry6040046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The study of cellular machineries responsible for the iron–sulfur (Fe–S) cluster biogenesis has led to the identification of a large number of proteins, whose importance for life is documented by an increasing number of diseases linked to them. The labile nature of Fe–S clusters and the transient protein–protein interactions, occurring during the various steps of the maturation process, make their structural characterization in solution particularly difficult. Paramagnetic nuclear magnetic resonance (NMR) has been used for decades to characterize chemical composition, magnetic coupling, and the electronic structure of Fe–S clusters in proteins; it represents, therefore, a powerful tool to study the protein–protein interaction networks of proteins involving into iron–sulfur cluster biogenesis. The optimization of the various NMR experiments with respect to the hyperfine interaction will be summarized here in the form of a protocol; recently developed experiments for measuring longitudinal and transverse nuclear relaxation rates in highly paramagnetic systems will be also reviewed. Finally, we will address the use of extrinsic paramagnetic centers covalently bound to diamagnetic proteins, which contributed over the last twenty years to promote the applications of paramagnetic NMR well beyond the structural biology of metalloproteins.
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116
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The lysophospholipase D enzyme Gdpd3 is required to maintain chronic myelogenous leukaemia stem cells. Nat Commun 2020; 11:4681. [PMID: 32943626 PMCID: PMC7499193 DOI: 10.1038/s41467-020-18491-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/26/2020] [Indexed: 02/02/2023] Open
Abstract
Although advanced lipidomics technology facilitates quantitation of intracellular lipid components, little is known about the regulation of lipid metabolism in cancer cells. Here, we show that disruption of the Gdpd3 gene encoding a lysophospholipase D enzyme significantly decreased self-renewal capacity in murine chronic myelogenous leukaemia (CML) stem cells in vivo. Sophisticated lipidomics analyses revealed that Gdpd3 deficiency reduced levels of certain lysophosphatidic acids (LPAs) and lipid mediators in CML cells. Loss of Gdpd3 also activated AKT/mTORC1 signalling and cell cycle progression while suppressing Foxo3a/β-catenin interaction within CML stem cell nuclei. Strikingly, CML stem cells carrying a hypomorphic mutation of Lgr4/Gpr48, which encodes a leucine-rich repeat (LRR)-containing G-protein coupled receptor (GPCR) acting downstream of Gdpd3, displayed inadequate disease-initiating capacity in vivo. Our data showing that lysophospholipid metabolism is required for CML stem cell maintenance in vivo establish a new, biologically significant mechanism of cancer recurrence that is independent of oncogene addiction. How lipid metabolism can affect cancer recurrence is still unclear. Here, the authors show that the lysophospholipase D Gdpd3 maintains self-renewal capacity of CML stem cells by regulating the quiescence, and AKT/mTORC1 and Foxo3a/β-catenin signalling in an oncogene-independent manner.
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117
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Kögler LM, Stichel J, Beck-Sickinger AG. Structural investigations of cell-free expressed G protein-coupled receptors. Biol Chem 2020; 401:97-116. [PMID: 31539345 DOI: 10.1515/hsz-2019-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are of great pharmaceutical interest and about 35% of the commercial drugs target these proteins. Still there is huge potential left in finding molecules that target new GPCRs or that modulate GPCRs differentially. For a rational drug design, it is important to understand the structure, binding and activation of the protein of interest. Structural investigations of GPCRs remain challenging, although huge progress has been made in the last 20 years, especially in the generation of crystal structures of GPCRs. This is mostly caused by issues with the expression yield, purity or labeling. Cell-free protein synthesis (CFPS) is an efficient alternative for recombinant expression systems that can potentially address many of these problems. In this article the use of CFPS for structural investigations of GPCRs is reviewed. We compare different CFPS systems, including the cellular basis and reaction configurations, and strategies for an efficient solubilization. Next, we highlight recent advances in the structural investigation of cell-free expressed GPCRs, with special emphasis on the role of photo-crosslinking approaches to investigate ligand binding sites on GPCRs.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
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118
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Mazzolari A, Gervasoni S, Pedretti A, Fumagalli L, Matucci R, Vistoli G. Repositioning Dequalinium as Potent Muscarinic Allosteric Ligand by Combining Virtual Screening Campaigns and Experimental Binding Assays. Int J Mol Sci 2020; 21:ijms21175961. [PMID: 32825082 PMCID: PMC7503225 DOI: 10.3390/ijms21175961] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/14/2020] [Accepted: 08/16/2020] [Indexed: 12/12/2022] Open
Abstract
Structure-based virtual screening is a truly productive repurposing approach provided that reliable target structures are available. Recent progresses in the structural resolution of the G-Protein Coupled Receptors (GPCRs) render these targets amenable for structure-based repurposing studies. Hence, the present study describes structure-based virtual screening campaigns with a view to repurposing known drugs as potential allosteric (and/or orthosteric) ligands for the hM2 muscarinic subtype which was indeed resolved in complex with an allosteric modulator thus allowing a precise identification of this binding cavity. First, a docking protocol was developed and optimized based on binding space concept and enrichment factor optimization algorithm (EFO) consensus approach by using a purposely collected database including known allosteric modulators. The so-developed consensus models were then utilized to virtually screen the DrugBank database. Based on the computational results, six promising molecules were selected and experimentally tested and four of them revealed interesting affinity data; in particular, dequalinium showed a very impressive allosteric modulation for hM2. Based on these results, a second campaign was focused on bis-cationic derivatives and allowed the identification of other two relevant hM2 ligands. Overall, the study enhances the understanding of the factors governing the hM2 allosteric modulation emphasizing the key role of ligand flexibility as well as of arrangement and delocalization of the positively charged moieties.
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Affiliation(s)
- Angelica Mazzolari
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (A.M.); (S.G.); (A.P.); (L.F.)
| | - Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (A.M.); (S.G.); (A.P.); (L.F.)
| | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (A.M.); (S.G.); (A.P.); (L.F.)
| | - Laura Fumagalli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (A.M.); (S.G.); (A.P.); (L.F.)
| | - Rosanna Matucci
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), Sezione di Farmacologia e Tossicologia, Università degli Studi di Firenze, Viale Pieraccini 6, 50139 Firenze, Italy;
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (A.M.); (S.G.); (A.P.); (L.F.)
- Correspondence: ; Tel.: +39-02-5019349
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119
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Goto K, Nishitsuji H, Sugiyama M, Nishida N, Mizokami M, Shimotohno K. Orchestration of Intracellular Circuits by G Protein-Coupled Receptor 39 for Hepatitis B Virus Proliferation. Int J Mol Sci 2020; 21:ijms21165661. [PMID: 32784555 PMCID: PMC7460832 DOI: 10.3390/ijms21165661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV), a highly persistent pathogen causing hepatocellular carcinoma (HCC), takes full advantage of host machinery, presenting therapeutic targets. Here we aimed to identify novel druggable host cellular factors using the reporter HBV we have recently generated. In an RNAi screen of G protein-coupled receptors (GPCRs), GPCR39 (GPR39) appeared as the top hit to facilitate HBV proliferation. Lentiviral overexpression of active GPR39 proteins and an agonist enhanced HBV replication and transcriptional activities of viral promoters, inducing the expression of CCAAT/enhancer binding protein (CEBP)-β (CEBPB). Meanwhile, GPR39 was uncovered to activate the heat shock response, upregulating the expression of proviral heat shock proteins (HSPs). In addition, glioma-associated oncogene homologue signaling, a recently reported target of GPR39, was suggested to inhibit HBV replication and eventually suppress expression of CEBPB and HSPs. Thus, GPR39 provirally governed intracellular circuits simultaneously affecting the carcinopathogenetic gene functions. GPR39 and the regulated signaling networks would serve as antiviral targets, and strategies with selective inhibitors of GPR39 functions can develop host-targeted antiviral therapies preventing HCC.
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Affiliation(s)
- Kaku Goto
- Correspondence: ; Tel.: +81-47-372-3501; Fax: +81-47-375-4766
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120
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Structural biology of human GPCR drugs and endogenous ligands - insights from NMR spectroscopy. Methods 2020; 180:79-88. [PMID: 32911074 DOI: 10.1016/j.ymeth.2020.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest class of "druggable" proteins in the human genome. For more than a decade, crystal structures and, more recently, cryoEM structures of GPCR complexes have provided unprecedented insight into GPCR drug binding and cell signaling. Nevertheless, structure determination of receptors in complexes with weakly binding molecules or complex polypeptides remains especially challenging, including for hormones, many of which have so far eluded researchers. Nuclear magnetic resonance (NMR) spectroscopy has emerged as a promising approach to determine structures of ligands bound to their receptors and to provide insights into the dynamics of GPCR-bound drugs. The capability to investigate compounds with weak binding affinities has also been leveraged in NMR applications to identify novel lead compounds in drug screening campaigns. We review recent structural biology studies of GPCR ligands by NMR, highlighting new methodologies enabling studies of GPCRs with native sequences and in native-like membrane environments that provide insights into important drugs and endogenous ligands.
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121
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Li Q, Kang C. A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery. Molecules 2020; 25:molecules25132974. [PMID: 32605297 PMCID: PMC7411973 DOI: 10.3390/molecules25132974] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/21/2020] [Accepted: 06/26/2020] [Indexed: 11/26/2022] Open
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to study structures and dynamics of biomolecules under physiological conditions. As there are numerous NMR-derived methods applicable to probe protein–ligand interactions, NMR has been widely utilized in drug discovery, especially in such steps as hit identification and lead optimization. NMR is frequently used to locate ligand-binding sites on a target protein and to determine ligand binding modes. NMR spectroscopy is also a unique tool in fragment-based drug design (FBDD), as it is able to investigate target-ligand interactions with diverse binding affinities. NMR spectroscopy is able to identify fragments that bind weakly to a target, making it valuable for identifying hits targeting undruggable sites. In this review, we summarize the roles of solution NMR spectroscopy in drug discovery. We describe some methods that are used in identifying fragments, understanding the mechanism of action for a ligand, and monitoring the conformational changes of a target induced by ligand binding. A number of studies have proven that 19F-NMR is very powerful in screening fragments and detecting protein conformational changes. In-cell NMR will also play important roles in drug discovery by elucidating protein-ligand interactions in living cells.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, China
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore 138670, Singapore
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
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122
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Zsidó BZ, Hetényi C. Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome. Int J Mol Sci 2020; 21:ijms21114134. [PMID: 32531926 PMCID: PMC7311975 DOI: 10.3390/ijms21114134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Development of valid structure–activity relationships (SARs) is a key to the elucidation of pathomechanisms of epigenetic diseases and the development of efficient, new drugs. The present review is based on selected methodologies and applications supplying molecular structure, binding affinity and biological activity data for the development of new SARs. An emphasis is placed on emerging trends and permanent challenges of new discoveries of SARs in the context of proteins as epigenetic drug targets. The review gives a brief overview and classification of the molecular background of epigenetic changes, and surveys both experimental and theoretical approaches in the field. Besides the results of sophisticated, cutting edge techniques such as cryo-electron microscopy, protein crystallography, and isothermal titration calorimetry, examples of frequently used assays and fast screening techniques are also selected. The review features how different experimental methods and theoretical approaches complement each other and result in valid SARs of the epigenome.
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123
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Delgado L, Franke B, Frigård T, Isogai S. Automated multistep column chromatography on ÄKTA pure system using in-line sample dilution. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2020.116556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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124
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Wu FJ, Williams LM, Abdul-Ridha A, Gunatilaka A, Vaid TM, Kocan M, Whitehead AR, Griffin MDW, Bathgate RAD, Scott DJ, Gooley PR. Probing the correlation between ligand efficacy and conformational diversity at the α 1A-adrenoreceptor reveals allosteric coupling of its microswitches. J Biol Chem 2020; 295:7404-7417. [PMID: 32303636 PMCID: PMC7247315 DOI: 10.1074/jbc.ra120.012842] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
G protein-coupled receptors (GPCRs) use a series of conserved microswitches to transmit signals across the cell membrane via an allosteric network encompassing the ligand-binding site and the G protein-binding site. Crystal structures of GPCRs provide snapshots of their inactive and active states, but poorly describe the conformational dynamics of the allosteric network that underlies GPCR activation. Here, we analyzed the correlation between ligand binding and receptor conformation of the α1A-adrenoreceptor, a GPCR that stimulates smooth muscle contraction in response to binding noradrenaline. NMR of [13CϵH3]methionine-labeled α1A-adrenoreceptor variants, each exhibiting differing signaling capacities, revealed how different classes of ligands modulate the conformational equilibria of this receptor. [13CϵH3]Methionine residues near the microswitches exhibited distinct states that correlated with ligand efficacies, supporting a conformational selection mechanism. We propose that allosteric coupling among the microswitches controls the conformation of the α1A-adrenoreceptor and underlies the mechanism of ligand modulation of GPCR signaling in cells.
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Affiliation(s)
- Feng-Jie Wu
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Lisa M Williams
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Alaa Abdul-Ridha
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Avanka Gunatilaka
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Tasneem M Vaid
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Martina Kocan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Alice R Whitehead
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia.
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia.
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125
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Grahl A, Abiko LA, Isogai S, Sharpe T, Grzesiek S. A high-resolution description of β 1-adrenergic receptor functional dynamics and allosteric coupling from backbone NMR. Nat Commun 2020; 11:2216. [PMID: 32371991 PMCID: PMC7200737 DOI: 10.1038/s41467-020-15864-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 04/01/2020] [Indexed: 12/29/2022] Open
Abstract
Signal transmission and regulation of G-protein-coupled receptors (GPCRs) by extra- and intracellular ligands occurs via modulation of complex conformational equilibria, but their exact kinetic details and underlying atomic mechanisms are unknown. Here we quantified these dynamic equilibria in the β1-adrenergic receptor in its apo form and seven ligand complexes using 1H/15N NMR spectroscopy. We observe three major exchanging conformations: an inactive conformation (Ci), a preactive conformation (Cp) and an active conformation (Ca), which becomes fully populated in a ternary complex with a G protein mimicking nanobody. The Ci ↔ Cp exchange occurs on the microsecond scale, the Cp ↔ Ca exchange is slower than ~5 ms and only occurs in the presence of two highly conserved tyrosines (Y5.58, Y7.53), which stabilize the active conformation of TM6. The Cp→Ca chemical shift changes indicate a pivoting motion of the entire TM6 that couples the effector site to the orthosteric ligand pocket. Signal transmission and regulation of G-protein-coupled receptors (GPCRs) by ligands occurs via modulation of complex conformational equilibria. Here authors quantify these equilibria and their dynamics in the β1-adrenergic receptor in its apo form and seven ligand complexes using NMR.
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Affiliation(s)
- Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Shin Isogai
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Timothy Sharpe
- Biophysics Core Facility, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland.
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126
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Lecas L, Hartmann L, Caro L, Mohamed-Bouteben S, Raingeval C, Krimm I, Wagner R, Dugas V, Demesmay C. Miniaturized weak affinity chromatography for ligand identification of nanodiscs-embedded G-protein coupled receptors. Anal Chim Acta 2020; 1113:26-35. [DOI: 10.1016/j.aca.2020.03.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
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127
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Murata T, Yasuda S, Hayashi T, Kinoshita M. Theoretical identification of thermostabilizing amino acid mutations for G-protein-coupled receptors. Biophys Rev 2020; 12:323-332. [PMID: 32270446 DOI: 10.1007/s12551-020-00678-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Thermostabilization of a membrane proteins, especially G-protein-coupled receptors (GPCRs), is often necessary for biochemical applications and pharmaceutical studies involving structure-based drug design. Here we review our theoretical, physics-based method for identifying thermostabilizing amino acid mutations. Its novel aspects are the following: The entropic effect originating from the translational displacement of hydrocarbon groups within the lipid bilayer is treated as a pivotal factor; a reliable measure of thermostability is introduced and a mutation which enlarges the measure to a significant extent is chosen; and all the possible mutations can be examined with moderate computational effort. It was shown that mutating the residue at a position of NBW = 3.39 (NBW is the Ballesteros-Weinstein number) to Arg or Lys leads to the stabilization of significantly many different GPCRs of class A in the inactive state. Up to now, we have been successful in stabilizing several GPCRs and newly solving three-dimensional structures for the muscarinic acetylcholine receptor 2 (M2R), prostaglandin E receptor 4 (EP4), and serotonin 2A receptor (5-HT2AR) using X-ray crystallography. The subjects to be pursued in future studies are also discussed.
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Affiliation(s)
- Takeshi Murata
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan.,Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan
| | - Satoshi Yasuda
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan.,Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan.,Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.,Present address: Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata, 950-2181, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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128
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Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR. Int J Mol Sci 2020; 21:ijms21051829. [PMID: 32155847 PMCID: PMC7084655 DOI: 10.3390/ijms21051829] [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: 02/22/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology.
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129
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Mizumura T, Kondo K, Kurita M, Kofuku Y, Natsume M, Imai S, Shiraishi Y, Ueda T, Shimada I. Activation of adenosine A 2A receptor by lipids from docosahexaenoic acid revealed by NMR. SCIENCE ADVANCES 2020; 6:eaay8544. [PMID: 32206717 PMCID: PMC7080496 DOI: 10.1126/sciadv.aay8544] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/18/2019] [Indexed: 05/05/2023]
Abstract
The lipid composition of the plasma membrane is a key parameter in controlling signal transduction through G protein-coupled receptors (GPCRs). Adenosine A2A receptor (A2AAR) is located in the lipid bilayers of cells, containing acyl chains derived from docosahexaenoic acid (DHA). For the NMR studies, we prepared A2AAR in lipid bilayers of nanodiscs, containing DHA chains and other acyl chains. The DHA chains in nanodiscs enhanced the activation of G proteins by A2AAR. Our NMR studies revealed that the DHA chains redistribute the multiple conformations of A2AAR toward those preferable for G protein binding. In these conformations, the rotational angle of transmembrane helix 6 is similar to that in the A2AAR-G protein complex, suggesting that the population shift of the equilibrium causes the enhanced activation of G protein by A2AAR. These findings provide insights into the control of neurotransmissions by A2AAR and the effects of lipids on various GPCR functions.
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Affiliation(s)
- Takuya Mizumura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Masatoshi Kurita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Mei Natsume
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Corresponding author.
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130
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Routledge SJ, Jamshad M, Little HA, Lin YP, Simms J, Thakker A, Spickett CM, Bill RM, Dafforn TR, Poyner DR, Wheatley M. Ligand-induced conformational changes in a SMALP-encapsulated GPCR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183235. [PMID: 32126232 PMCID: PMC7156913 DOI: 10.1016/j.bbamem.2020.183235] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/27/2022]
Abstract
The adenosine 2A receptor (A2AR), a G-protein-coupled receptor (GPCR), was solubilised and purified encapsulated in styrene maleic acid lipid particles (SMALPs). The purified A2AR-SMALP was associated with phospholipids characteristic of the plasma membrane of Pichia pastoris, the host used for its expression, confirming that the A2AR-SMALP encapsulated native lipids. The fluorescence spectrum of the A2AR-SMALP showed a characteristic broad emission peak at 330 nm, produced by endogenous Trp residues. The inverse agonist ZM241385 caused 30% increase in fluorescence emission, unusually accompanied by a red-shift in the emission wavelength. The emission spectrum also showed sub-peaks at 321 nm, 335 nm and 350 nm, indicating that individual Trp inhabited different environments following ZM241385 addition. There was no effect of the agonist NECA on the A2AR-SMALP fluorescence spectrum. Substitution of two Trp residues by Tyr suggested that ZM241385 affected the environment and mobility of Trp2466.48 in TM6 and Trp2687.33 at the extracellular face of TM7, causing transition to a more hydrophobic environment. The fluorescent moiety IAEDANS was site-specifically introduced at the intracellular end of TM6 (residue 2316.33) to report on the dynamic cytoplasmic face of the A2AR. The inverse agonist ZM241385 caused a concentration-dependent increase in fluorescence emission as the IAEDANS moved to a more hydrophobic environment, consistent with closing the G-protein binding crevice. NECA generated only 30% of the effect of ZM241385. This study provides insight into the SMALP environment; encapsulation supported constitutive activity of the A2AR and ZM241385-induced conformational transitions but the agonist NECA generated only small effects. Conformational changes in the A2AR monitored in a nano-scale membrane disc (SMALP). Profile of phospholipids in A2AR-SMALP similar to the plasma membrane. A partially-active conformation of A2AR is supported in a SMALP. Inverse agonist induced dose-dependent conformational transitions in A2AR-SMALP. In contrast to inverse agonist, agonist induced only small conformational changes.
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Affiliation(s)
| | - Mohammed Jamshad
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Haydn A Little
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Yu-Pin Lin
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - John Simms
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Alpesh Thakker
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | | | - Roslyn M Bill
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - David R Poyner
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK.
| | - Mark Wheatley
- Centre for Sport, Exercise and Life Sciences, Alison Gingell Building, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 2DS, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
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131
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Giusti F, Casiraghi M, Point E, Damian M, Rieger J, Bon CL, Pozza A, Moncoq K, Banères JL, Catoire LJ. Structure of the agonist 12-HHT in its BLT2 receptor-bound state. Sci Rep 2020; 10:2630. [PMID: 32060341 PMCID: PMC7021728 DOI: 10.1038/s41598-020-59571-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/28/2020] [Indexed: 12/25/2022] Open
Abstract
G Protein-Coupled receptors represent the main communicating pathway for signals from the outside to the inside of most of eukaryotic cells. They define the largest family of integral membrane receptors at the surface of the cells and constitute the main target of the current drugs on the market. The low affinity leukotriene receptor BLT2 is a receptor involved in pro- and anti-inflammatory pathways and can be activated by various unsaturated fatty acid compounds. We present here the NMR structure of the agonist 12-HHT in its BLT2-bound state and a model of interaction of the ligand with the receptor based on a conformational homology modeling associated with docking simulations. Put into perspective with the data obtained with leukotriene B4, our results illuminate the ligand selectivity of BLT2 and may help define new molecules to modulate the activity of this receptor.
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Affiliation(s)
- Fabrice Giusti
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Chimie Séparative de Marcoule, ICSM UMR 5257, Site de Marcoule, Bâtiment 426, BP 17171, F-30207, Bagnols sur Cèze Cedex, France
| | - Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, 94305, Stanford California, USA
| | - Elodie Point
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Marjorie Damian
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université Montpellier, ENSCM, , 15 av. Charles Flahault, 34093, Montpellier, France
| | - Jutta Rieger
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, CNRS, UMR 8232, Equipe Chimie des Polymères, 4 place Jussieu, 75252, Paris Cedex, 05, France
| | - Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Alexandre Pozza
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 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 de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France.
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132
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Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the β 1-adrenergic receptor. Nat Commun 2020; 11:669. [PMID: 32015348 PMCID: PMC6997182 DOI: 10.1038/s41467-020-14526-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/10/2020] [Indexed: 01/14/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are allosteric signaling proteins that transmit an extracellular stimulus across the cell membrane. Using 19F NMR and site-specific labelling, we investigate the response of the cytoplasmic region of transmembrane helices 6 and 7 of the β1-adrenergic receptor to agonist stimulation and coupling to a Gs-protein-mimetic nanobody. Agonist binding shows the receptor in equilibrium between two inactive states and a pre-active form, increasingly populated with higher ligand efficacy. Nanobody coupling leads to a fully active ternary receptor complex present in amounts correlating directly with agonist efficacy, consistent with partial agonism. While for different agonists the helix 6 environment in the active-state ternary complexes resides in a well-defined conformation, showing little conformational mobility, the environment of the highly conserved NPxxY motif on helix 7 remains dynamic adopting diverse, agonist-specific conformations, implying a further role of this region in receptor function. An inactive nanobody-coupled ternary receptor form is also observed.
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133
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Boutin JA, Legros C. The five dimensions of receptor pharmacology exemplified by melatonin receptors: An opinion. Pharmacol Res Perspect 2020; 8:e00556. [PMID: 31893125 PMCID: PMC6935684 DOI: 10.1002/prp2.556] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022] Open
Abstract
Receptology has been complicated with enhancements in our knowledge of G-protein-coupled-receptor (GPCR) biochemistry. This complexity is exemplified by the pharmacology of melatonin receptors. Here, we describe the complexity of GPCR biochemistry in five dimensions: (a) receptor expression, particularly in organs/tissues that are only partially understood; (b) ligands and receptor-associated proteins (interactome); (c) receptor function, which might be more complex than the known G-protein-coupled systems; (d) ligand bias, which favors a particular pathway; and (e) receptor dimerization, which might concern all receptors coexpressed in the same cell. Thus, receptor signaling might be modified or modulated, depending on the nature of the receptor complex. Fundamental studies are needed to clarify these points and find new ways to tackle receptor functionality. This opinion article emphasizes the global questions attached to new descriptions of GPCRs and aims to raise our awareness of the tremendous complexity of modern receptology.
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Affiliation(s)
- Jean A. Boutin
- Institut de Recherches Internationales ServierSuresnesFrance
| | - Céline Legros
- Institut de Recherches ServierCroissy‐sur‐SeineFrance
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134
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Ganapathy S, Opdam L, Hontani Y, Frehan S, Chen Q, Hellingwerf KJ, de Groot HJ, Kennis JT, de Grip WJ. Membrane matters: The impact of a nanodisc-bilayer or a detergent microenvironment on the properties of two eubacterial rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183113. [DOI: 10.1016/j.bbamem.2019.183113] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 12/29/2022]
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135
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Structural equilibrium underlying ligand-dependent activation of β2-adrenoreceptor. Nat Chem Biol 2020; 16:430-439. [DOI: 10.1038/s41589-019-0457-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 12/01/2019] [Accepted: 12/17/2019] [Indexed: 11/08/2022]
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136
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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137
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Molecular Basis of Opioid Action: From Structures to New Leads. Biol Psychiatry 2020; 87:6-14. [PMID: 31653480 PMCID: PMC6898784 DOI: 10.1016/j.biopsych.2019.08.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 02/06/2023]
Abstract
Since the isolation of morphine from the opium poppy over 200 years ago, the molecular basis of opioid action has remained the subject of intense inquiry. The identification of specific receptors responsible for opioid function and the discovery of many chemically diverse molecules with unique opioid-like efficacies have provided glimpses into the molecular logic of opioid action. Recent revolutions in the structural biology of transmembrane proteins have, for the first time, yielded high-resolution views into the 3-dimensional shapes of all 4 opioid receptors. These studies have begun to decode the chemical logic that enables opioids to specifically bind and activate their receptor targets. A combination of spectroscopic experiments and computational simulations has provided a view into the molecular movements of the opioid receptors, which itself gives rise to the complex opioid pharmacology observed at the cellular and behavioral levels. Further diversity in opioid receptor structure is driven by both genetic variation and receptor oligomerization. These insights have enabled computational drug discovery efforts, with some evidence of success in the design of completely novel opioids with unique efficacies. The combined progress over the past few years provides hope for new, efficacious opioids devoid of the side effects that have made them the scourge of humanity for millennia.
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138
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Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S. Common activation mechanism of class A GPCRs. eLife 2019; 8:e50279. [PMID: 31855179 PMCID: PMC6954041 DOI: 10.7554/elife.50279] [Citation(s) in RCA: 320] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.
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Affiliation(s)
- Qingtong Zhou
- iHuman InstituteShanghaiTech UniversityShanghaiChina
| | - Dehua Yang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Meng Wu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yu Guo
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Wanjing Guo
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Li Zhong
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Antao Dai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Zhi-Jie Liu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Raymond C Stevens
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ming-Wei Wang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- School of PharmacyFudan UniversityShanghaiChina
| | - Suwen Zhao
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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139
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Conformational equilibrium defines the variable induction of the multidrug-binding transcriptional repressor QacR. Proc Natl Acad Sci U S A 2019; 116:19963-19972. [PMID: 31527244 DOI: 10.1073/pnas.1906129116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
QacR, a multidrug-binding transcriptional repressor in pathogenic bacteria Staphylococcus aureus, modulates the transcriptional level of the multidrug transporter gene, qacA, in response to engaging a set of diverse ligands. However, the structural basis that defines the variable induction level remains unknown. Here, we reveal that the conformational equilibrium between the repressive and inducive conformations in QacR defines the induction level of the transporter gene. In addition, the unligated QacR is already partly populated in the inducive conformation, allowing the basal expression of the transporter. We also showed that, in the known constitutively active QacR mutants, the equilibrium is shifted more toward the inducive conformation, even in the unligated state. These results highlight the unexpected structural mechanism, connecting the promiscuous multidrug binding to the variable transcriptional regulation of QacR, which provide clues to dysfunctioning of the multidrug resistance systems.
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140
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Adikaram PR, Zhang JH, Kittock CM, Pandey M, Hassan SA, Lue NG, Wang G, Gucek M, Simonds WF. Development of R7BP inhibitors through cross-linking coupled mass spectrometry and integrated modeling. Commun Biol 2019; 2:338. [PMID: 31531399 PMCID: PMC6744478 DOI: 10.1038/s42003-019-0585-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/21/2019] [Indexed: 02/08/2023] Open
Abstract
Protein-protein interaction (PPI) networks are known to be valuable targets for therapeutic intervention; yet the development of PPI modulators as next-generation drugs to target specific vertices, edges, and hubs has been impeded by the lack of structural information of many of the proteins and complexes involved. Building on recent advancements in cross-linking mass spectrometry (XL-MS), we describe an effective approach to obtain relevant structural data on R7BP, a master regulator of itch sensation, and its interfaces with other proteins in its network. This approach integrates XL-MS with a variety of modeling techniques to successfully develop antibody inhibitors of the R7BP and RGS7/Gβ5 duplex interaction. Binding and inhibitory efficiency are studied by surface plasmon resonance spectroscopy and through an R7BP-derived dominant negative construct. This approach may have broader applications as a tool to facilitate the development of PPI modulators in the absence of crystal structures or when structural information is limited.
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Affiliation(s)
- Poorni R. Adikaram
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bldg. 10/Rm 8C-101, Bethesda, MD 20892 USA
| | - Jian-Hua Zhang
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bldg. 10/Rm 8C-101, Bethesda, MD 20892 USA
| | - Claire M. Kittock
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bldg. 10/Rm 8C-101, Bethesda, MD 20892 USA
| | - Mritunjay Pandey
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bldg. 10/Rm 8C-101, Bethesda, MD 20892 USA
| | - Sergio A. Hassan
- Center for Molecular Modeling, Center for Information Technology, Bldg. 12/Rm 2049, Bethesda, MD 20892 USA
| | - Nicole G. Lue
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bldg. 10/Rm 8C-101, Bethesda, MD 20892 USA
| | - Guanghui Wang
- Proteomics Core, National Heart Lung and Blood Institute, National Institutes of Health, Bldg. 10/Rm 8C-103A, Bethesda, MD 20892 USA
| | - Marjan Gucek
- Proteomics Core, National Heart Lung and Blood Institute, National Institutes of Health, Bldg. 10/Rm 8C-103A, Bethesda, MD 20892 USA
| | - William F. Simonds
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bldg. 10/Rm 8C-101, Bethesda, MD 20892 USA
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141
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Sahu BS, Rodriguez P, Nguyen ME, Han R, Cero C, Razzoli M, Piaggi P, Laskowski LJ, Pavlicev M, Muglia L, Mahata SK, O'Grady S, McCorvy JD, Baier LJ, Sham YY, Bartolomucci A. Peptide/Receptor Co-evolution Explains the Lipolytic Function of the Neuropeptide TLQP-21. Cell Rep 2019; 28:2567-2580.e6. [PMID: 31484069 PMCID: PMC6753381 DOI: 10.1016/j.celrep.2019.07.101] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/11/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
Structural and functional diversity of peptides and GPCR result from long evolutionary processes. Even small changes in sequence can alter receptor activation, affecting therapeutic efficacy. We conducted a structure-function relationship study on the neuropeptide TLQP-21, a promising target for obesity, and its complement 3a receptor (C3aR1). After having characterized the TLQP-21/C3aR1 lipolytic mechanism, a homology modeling and molecular dynamics simulation identified the TLQP-21 binding motif and C3aR1 binding site for the human (h) and mouse (m) molecules. mTLQP-21 showed enhanced binding affinity and potency for hC3aR1 compared with hTLQP-21. Consistently, mTLQP-21, but not hTLQP-21, potentiates lipolysis in human adipocytes. These findings led us to uncover five mutations in the C3aR1 binding pocket of the rodent Murinae subfamily that are causal for enhanced calculated affinity and measured potency of TLQP-21. Identifying functionally relevant peptide/receptor co-evolution mechanisms can facilitate the development of innovative pharmacotherapies for obesity and other diseases implicating GPCRs.
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Affiliation(s)
- Bhavani S Sahu
- Department of Integrative Biology and Physiology, University of Minnesota, 2231 6(th) St. SE, Minneapolis, MN, USA
| | - Pedro Rodriguez
- Department of Integrative Biology and Physiology, University of Minnesota, 2231 6(th) St. SE, Minneapolis, MN, USA
| | - Megin E Nguyen
- Department of Integrative Biology and Physiology, University of Minnesota, 2231 6(th) St. SE, Minneapolis, MN, USA
| | - Ruijun Han
- Department of Integrative Biology and Physiology, University of Minnesota, 2231 6(th) St. SE, Minneapolis, MN, USA
| | - Cheryl Cero
- Department of Integrative Biology and Physiology, University of Minnesota, 2231 6(th) St. SE, Minneapolis, MN, USA
| | - Maria Razzoli
- Department of Integrative Biology and Physiology, University of Minnesota, 2231 6(th) St. SE, Minneapolis, MN, USA
| | - Paolo Piaggi
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes, Digestive and Kidney Diseases, NIH, Phoenix, AZ, USA
| | - Lauren J Laskowski
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mihaela Pavlicev
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Louis Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sushil K Mahata
- VA San Diego Healthcare System, San Diego, CA, USA; Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Scott O'Grady
- Department of Animal Science, University of Minnesota, 480 Haecker Hall, 1364 Eckles Avenue, St. Paul, MN, USA
| | - John D McCorvy
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Leslie J Baier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes, Digestive and Kidney Diseases, NIH, Phoenix, AZ, USA
| | - Yuk Y Sham
- Department of Integrative Biology and Physiology, University of Minnesota, 2231 6(th) St. SE, Minneapolis, MN, USA; Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Alessandro Bartolomucci
- Department of Integrative Biology and Physiology, University of Minnesota, 2231 6(th) St. SE, Minneapolis, MN, USA.
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142
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Siegal G, Selenko P. Cells, drugs and NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:202-212. [PMID: 31358370 DOI: 10.1016/j.jmr.2019.07.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/08/2019] [Accepted: 07/08/2019] [Indexed: 05/18/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool for investigating cellular structures and their compositions. While in vivo and whole-cell NMR have a long tradition in cell-based approaches, high-resolution in-cell NMR spectroscopy is a new addition to these methods. In recent years, technological advancements in multiple areas provided converging benefits for cellular MR applications, especially in terms of robustness, reproducibility and physiological relevance. Here, we review the use of cellular NMR methods for drug discovery purposes in academia and industry. Specifically, we discuss how developments in NMR technologies such as miniaturized bioreactors and flow-probe perfusion systems have helped to consolidate NMR's role in cell-based drug discovery efforts.
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Affiliation(s)
- Gregg Siegal
- ZoBio B.V., BioPartner 2 Building, J.H. Oortweg 19, 2333 Leiden, the Netherlands
| | - Philipp Selenko
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl Street, 761000 Rehovot, Israel.
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143
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Marx S, Dal Maso T, Chen JW, Bury M, Wouters J, Michiels C, Le Calvé B. Transmembrane (TMEM) protein family members: Poorly characterized even if essential for the metastatic process. Semin Cancer Biol 2019; 60:96-106. [PMID: 31454669 DOI: 10.1016/j.semcancer.2019.08.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 01/02/2023]
Abstract
The majority of cancer-associated deaths are related to secondary tumor formation. This multistep process involves the migration of cancer cells to anatomically distant organs. Metastasis formation relies on cancer cell dissemination and survival in the circulatory system, as well as adaptation to the new tissue notably through genetic and/or epigenetic alterations. A large number of proteins are clearly identified to play a role in the metastatic process but the structures and modes of action of these proteins are essentially unknown or poorly described. In this review, we detail the involvement of members of the transmembrane (TMEM) protein family in the formation of metastases or in the mechanisms leading to cancer cell dissemination such as migration and extra-cellular matrix remodelling. While the phenotype associated with TMEM over or down-expression is clear, the mechanisms by which these proteins allow cancer cell spreading remain, for most of them, unclear. In parallel, the 3D structures of these proteins are presented. Moreover, we proposed that TMEM proteins could be used as prognostic markers in different types of cancers and could represent potential targets for cancer treatment. A better understanding of this heterogeneous family of poorly characterized proteins thus opens perspectives for better cancer patient care.
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Affiliation(s)
- Sébastien Marx
- Department of Chemistry, NAmur MEdicine & Drug Innovation Center (NAMEDIC-NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Thomas Dal Maso
- Department of Chemistry, NAmur MEdicine & Drug Innovation Center (NAMEDIC-NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Jia-Wei Chen
- URBC - NARILIS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Marina Bury
- de Duve Institute, 75 Avenue Hippocrate, 1200 Bruxelles, Belgium
| | - Johan Wouters
- Department of Chemistry, NAmur MEdicine & Drug Innovation Center (NAMEDIC-NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Carine Michiels
- URBC - NARILIS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Benjamin Le Calvé
- URBC - NARILIS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium.
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144
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Xue D, Xu T, Wang H, Wu M, Yuan Y, Wang W, Tan Q, Zhao F, Zhou F, Hu T, Jiang Z, Liu Z, Zhao S, Liu D, Wüthrich K, Tao H. Disulfide‐Containing Detergents (DCDs) for the Structural Biology of Membrane Proteins. Chemistry 2019; 25:11635-11640. [DOI: 10.1002/chem.201903190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Dongxiang Xue
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- Shanghai Institute of Materia Medica Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Tiandan Xu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai 200031 China
| | - Huixia Wang
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai 200031 China
| | - Meng Wu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai 200031 China
| | - Ya Yuan
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
| | - Wei Wang
- Hubei Province Engineering and Technology Research Center, for Fluorinated Pharmaceuticals School of Pharmaceutical Sciences Wuhan University Wuhan 430071 China
| | - Qiwen Tan
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
| | - Fei Zhao
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
| | - Fang Zhou
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- Shanghai Institute of Materia Medica Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Tao Hu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai 200031 China
| | - Zhongxing Jiang
- Hubei Province Engineering and Technology Research Center, for Fluorinated Pharmaceuticals School of Pharmaceutical Sciences Wuhan University Wuhan 430071 China
| | - Zhi‐Jie Liu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Suwen Zhao
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Dongsheng Liu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
| | - Kurt Wüthrich
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Houchao Tao
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
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145
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Golay H, Jurkovic Mlakar S, Mlakar V, Nava T, Ansari M. The Biological and Clinical Relevance of G Protein-Coupled Receptors to the Outcomes of Hematopoietic Stem Cell Transplantation: A Systematized Review. Int J Mol Sci 2019; 20:E3889. [PMID: 31404983 PMCID: PMC6719093 DOI: 10.3390/ijms20163889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 01/04/2023] Open
Abstract
Hematopoietic stem cell transplantation (HSCT) remains the only curative treatment for several malignant and non-malignant diseases at the cost of serious treatment-related toxicities (TRTs). Recent research on extending the benefits of HSCT to more patients and indications has focused on limiting TRTs and improving immunological effects following proper mobilization and engraftment. Increasing numbers of studies report associations between HSCT outcomes and the expression or the manipulation of G protein-coupled receptors (GPCRs). This large family of cell surface receptors is involved in various human diseases. With ever-better knowledge of their crystal structures and signaling dynamics, GPCRs are already the targets for one third of the current therapeutic arsenal. The present paper assesses the current status of animal and human research on GPCRs in the context of selected HSCT outcomes via a systematized survey and analysis of the literature.
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Affiliation(s)
- Hadrien Golay
- Platform of Pediatric Onco-Hematology research (CANSEARCH Laboratory), Department of Pediatrics, Gynecology, and Obstetrics, University of Geneva, Bâtiment La Tulipe, Avenue de la Roseraie 64, 1205 Geneva, Switzerland
| | - Simona Jurkovic Mlakar
- Platform of Pediatric Onco-Hematology research (CANSEARCH Laboratory), Department of Pediatrics, Gynecology, and Obstetrics, University of Geneva, Bâtiment La Tulipe, Avenue de la Roseraie 64, 1205 Geneva, Switzerland
| | - Vid Mlakar
- Platform of Pediatric Onco-Hematology research (CANSEARCH Laboratory), Department of Pediatrics, Gynecology, and Obstetrics, University of Geneva, Bâtiment La Tulipe, Avenue de la Roseraie 64, 1205 Geneva, Switzerland
| | - Tiago Nava
- Platform of Pediatric Onco-Hematology research (CANSEARCH Laboratory), Department of Pediatrics, Gynecology, and Obstetrics, University of Geneva, Bâtiment La Tulipe, Avenue de la Roseraie 64, 1205 Geneva, Switzerland
- Department of Women-Children-Adolescents, Division of General Pediatrics, Pediatric Onco-Hematology Unit, Geneva University Hospitals (HUG), Avenue de la Roseraie 64, 1205 Geneva, Switzerland
| | - Marc Ansari
- Platform of Pediatric Onco-Hematology research (CANSEARCH Laboratory), Department of Pediatrics, Gynecology, and Obstetrics, University of Geneva, Bâtiment La Tulipe, Avenue de la Roseraie 64, 1205 Geneva, Switzerland.
- Department of Women-Children-Adolescents, Division of General Pediatrics, Pediatric Onco-Hematology Unit, Geneva University Hospitals (HUG), Avenue de la Roseraie 64, 1205 Geneva, Switzerland.
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146
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García-Nafría J, Tate CG. Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development. Annu Rev Pharmacol Toxicol 2019; 60:51-71. [PMID: 31348870 DOI: 10.1146/annurev-pharmtox-010919-023545] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein-coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiological heteromeric receptors in a lipid environment have uncovered the molecular basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR-G protein complexes from three different classes of GPCRs have now been determined by cryo-EM. These structures give detailed insights into molecular interactions with drugs, GPCR-G protein selectivity, how accessory membrane proteins alter receptor-ligand pharmacology, and the mechanism by which HIV uses GPCRs to enter host cells.
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Affiliation(s)
- Javier García-Nafría
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; .,Current affiliation: Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopias Avanzadas, University of Zaragoza, 50018 Zaragoza, Spain;
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147
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NMR investigation of protein-ligand interactions for G-protein coupled receptors. Future Med Chem 2019; 11:1811-1825. [PMID: 31287732 DOI: 10.4155/fmc-2018-0312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this review, we report NMR studies of ligand-GPCR interactions, including both ligand-observed and protein-observed NMR experiments. Published studies exemplify how NMR can be used as a powerful tool to design novel GPCR ligands and investigate the ligand-induced conformational changes of GPCRs. The strength of NMR also lies in its capability to explore the diverse signaling pathways and probe the allosteric modulation of these highly dynamic receptors. By offering unique opportunities for the identification, structural and functional characterization of GPCR ligands, NMR will likely play a major role for the generation of novel molecules both as new tools for the understanding of the GPCR function and as therapeutic compounds for a large diversity of pathologies.
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148
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Arimont M, Hoffmann C, de Graaf C, Leurs R. Chemokine Receptor Crystal Structures: What Can Be Learned from Them? Mol Pharmacol 2019; 96:765-777. [PMID: 31266800 DOI: 10.1124/mol.119.117168] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/21/2019] [Indexed: 12/18/2022] Open
Abstract
Chemokine receptors belong to the class A of G protein-coupled receptors (GPCRs) and are implicated in a wide variety of physiologic functions, mostly related to the homeostasis of the immune system. Chemokine receptors are also involved in multiple pathologic processes, including immune and autoimmune diseases, as well as cancer. Hence, several members of this GPCR subfamily are considered to be very relevant therapeutic targets. Since drug discovery efforts can be significantly reinforced by the availability of crystal structures, substantial efforts in the area of chemokine receptor structural biology could dramatically increase the outcome of drug discovery campaigns. This short review summarizes the available data on chemokine receptor crystal structures, discusses the numerous applications from chemokine receptor structures that can enhance the daily work of molecular pharmacologists, and describes the challenges and pitfalls to consider when relying on crystal structures for further research applications. SIGNIFICANCE STATEMENT: This short review summarizes the available data on chemokine receptor crystal structures, discusses the numerous applications from chemokine receptor structures that can enhance the daily work of molecular pharmacologists, and describes the challenges and pitfalls to consider when relying on crystal structures for further research applications.
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Affiliation(s)
- Marta Arimont
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Carsten Hoffmann
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
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149
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Ueda T, Kofuku Y, Okude J, Imai S, Shiraishi Y, Shimada I. Function-related conformational dynamics of G protein-coupled receptors revealed by NMR. Biophys Rev 2019; 11:409-418. [PMID: 31102199 PMCID: PMC6557943 DOI: 10.1007/s12551-019-00539-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/26/2019] [Indexed: 11/26/2022] Open
Abstract
G protein-coupled receptors (GPCRs) function as receptors for various neurotransmitters, hormones, cytokines, and metabolites. GPCR ligands impart differing degrees of signaling in the G protein and arrestin pathways, in phenomena called biased signaling, and each ligand for a given GPCR has a characteristic level of ability to activate or deactivate its target, which is referred to as its efficacy. The ligand efficacies and biased signaling of GPCRs remarkably affect the therapeutic properties of the ligands. However, these features of GPCRs can only be partially understood from the crystallography data, although numerous GPCR structures have been solved. NMR analyses have revealed that GPCRs have multiple interconverting substates, exchanging on various timescales, and that the exchange rates are related to the ligand efficacies and biased signaling. In addition, NMR analyses of GPCRs in the lipid bilayer environment of rHDLs revealed that the exchange rates are modulated by the lipid bilayer environment, highlighting the importance of the function-related dynamics in the lipid bilayer. In this review, we will describe several solution NMR studies that have clarified the conformational dynamics related to the ligand efficacy and biased signaling of GPCRs.
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Affiliation(s)
- Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shunsuke Imai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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150
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Importance of protein dynamics in the structure-based drug discovery of class A G protein-coupled receptors (GPCRs). Curr Opin Struct Biol 2019; 55:147-153. [PMID: 31102980 DOI: 10.1016/j.sbi.2019.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/06/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022]
Abstract
Demand for novel GPCR modulators is increasing as the association between the GPCR signaling pathway and numerous diseases such as cancers, psychological and metabolic disorders continues to be established. In silico structure-based drug design (SBDD) offers an outlet where researchers could exploit the accumulating structural information of GPCR to expedite the process of drug discovery. The coupling of structure-based approaches such as virtual screening and molecular docking with molecular dynamics and/or Monte Carlo simulation aids in reflecting the dynamics of proteins in nature into previously static docking studies, thus enhancing the accuracy of rationally designed ligands. This review will highlight recent computational strategies that incorporate protein flexibility into SBDD of GPCR-targeted ligands.
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