1
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Khorn PA, Luginina AP, Pospelov VA, Dashevsky DE, Khnykin AN, Moiseeva OV, Safronova NA, Belousov AS, Mishin AV, Borshchevsky VI. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:747-764. [PMID: 38831510 DOI: 10.1134/s0006297924040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor-ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.
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Affiliation(s)
- Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Valentin I Borshchevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Moscow Region, 141980, Russia
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2
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Yen HY, Liko I, Song W, Kapoor P, Almeida F, Toporowska J, Gherbi K, Hopper JTS, Charlton SJ, Politis A, Sansom MSP, Jazayeri A, Robinson CV. Mass spectrometry captures biased signalling and allosteric modulation of a G-protein-coupled receptor. Nat Chem 2022; 14:1375-1382. [PMID: 36357787 PMCID: PMC9758051 DOI: 10.1038/s41557-022-01041-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 08/09/2022] [Indexed: 11/12/2022]
Abstract
G-protein-coupled receptors signal through cognate G proteins. Despite the widespread importance of these receptors, their regulatory mechanisms for G-protein selectivity are not fully understood. Here we present a native mass spectrometry-based approach to interrogate both biased signalling and allosteric modulation of the β1-adrenergic receptor in response to various ligands. By simultaneously capturing the effects of ligand binding and receptor coupling to different G proteins, we probed the relative importance of specific interactions with the receptor through systematic changes in 14 ligands, including isoprenaline derivatives, full and partial agonists, and antagonists. We observed enhanced dynamics of the intracellular loop 3 in the presence of isoprenaline, which is capable of acting as a biased agonist. We also show here that endogenous zinc ions augment the binding in receptor-Gs complexes and propose a zinc ion-binding hotspot at the TM5/TM6 intracellular interface of the receptor-Gs complex. Further interrogation led us to propose a mechanism in which zinc ions facilitate a structural transition of the intermediate complex towards the stable state.
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Affiliation(s)
- Hsin-Yung Yen
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- OMass Therapeutics, Oxford, UK.
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
| | - Idlir Liko
- Chemical Research Laboratory, University of Oxford, Oxford, UK
- OMass Therapeutics, Oxford, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford, UK
- Rahko, London, UK
| | | | | | | | | | | | - Steven J Charlton
- OMass Therapeutics, Oxford, UK
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, London, UK
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Carol V Robinson
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, Oxford, UK.
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3
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Saumell-Esnaola M, Elejaga-Jimeno A, Echeazarra L, Borrega-Román L, Barrondo S, López de Jesús M, González-Burguera I, Gómez-Caballero A, Goicolea MA, Sallés J, García del Caño G. Design and validation of recombinant protein standards for quantitative Western blot analysis of cannabinoid CB1 receptor density in cell membranes: an alternative to radioligand binding methods. Microb Cell Fact 2022; 21:192. [PMID: 36109736 PMCID: PMC9479267 DOI: 10.1186/s12934-022-01914-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Background Replacement of radioligand binding assays with antibody-antigen interaction-based approaches for quantitative analysis of G protein-coupled receptor (GPCR) levels requires the use of purified protein standards containing the antigen. GPCRs in general and cannabinoid CB1 receptor in particular show a progressive tendency to aggregate and precipitate in aqueous solution outside of their biological context due to the low solubility that the hydrophobic nature imprinted by their seven transmembrane domains. This renders full-length recombinant GPCRs useless for analytical purposes, a problem that can be overcome by engineering soluble recombinant fragments of the receptor containing the antigen. Results Here we generated highly soluble and stable recombinant protein constructs GST-CB1414–472 and GST-CB1414-442 containing much of the human CB1 receptor C-terminal tail for use as standard and negative control, respectively, in quantitative Western blot analysis of CB1 receptor expression on crude synaptosomes of the adult rat brain cortex. To this end we used three different antibodies, all raised against a peptide comprising the C-terminal residues 443–473 of the mouse CB1 receptor that corresponds to residues 442–472 in the human homolog. Estimated values of CB1 receptor density obtained by quantitative Western blot were of the same order of magnitude but slightly higher than values obtained by the radioligand saturation binding assay. Conclusions Collectively, here we provide a suitable Western blot-based design as a simple, cost-effective and radioactivity-free alternative for the quantitative analysis of CB1 receptor expression, and potentially of any GPCR, in a variety of biological samples. The discrepancies between the results obtained by quantitative Western blot and radioligand saturation binding techniques are discussed in the context of their particular theoretical bases and methodological constraints. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01914-1.
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4
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Abiko LA, Dias Teixeira R, Engilberge S, Grahl A, Mühlethaler T, Sharpe T, Grzesiek S. Filling of a water-free void explains the allosteric regulation of the β 1-adrenergic receptor by cholesterol. Nat Chem 2022; 14:1133-1141. [PMID: 35953642 DOI: 10.1038/s41557-022-01009-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 06/24/2022] [Indexed: 11/09/2022]
Abstract
Recent high-pressure NMR results indicate that the preactive conformation of the β1-adrenergic receptor (β1AR) harbours completely empty cavities of ~100 Å3 volume, which disappear in the active conformation of the receptor. Here we have localized these cavities using X-ray crystallography of xenon-derivatized β1AR crystals. One of the cavities is in direct contact with the cholesterol-binding pocket. Solution NMR shows that addition of the cholesterol analogue cholesteryl hemisuccinate impedes the formation of the active conformation of detergent-solubilized β1AR by blocking conserved G protein-coupled receptor microswitches, concomitant with an affinity reduction of both isoprenaline and G protein-mimicking nanobody Nb80 for β1AR detected by isothermal titration calorimetry. This wedge-like action explains the function of cholesterol as a negative allosteric modulator of β1AR. A detailed understanding of G protein-coupled receptor regulation by cholesterol by filling of a dry void and the easy scouting for such voids by xenon may provide new routes for the development of allosteric drugs.
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Affiliation(s)
| | | | - Sylvain Engilberge
- Paul Scherrer Institut, Villigen, Switzerland.,European Synchrotron Radiation Facility, Grenoble, France
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
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5
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Jansen M, Beaumelle B. How palmitoylation affects trafficking and signaling of membrane receptors. Biol Cell 2021; 114:61-72. [PMID: 34738237 DOI: 10.1111/boc.202100052] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/06/2021] [Accepted: 10/19/2021] [Indexed: 01/10/2023]
Abstract
S-acylation (or palmitoylation) is a reversible post-translational modification (PTM) that modulates protein activity, signalization and trafficking. Palmitoylation was found to significantly impact the activity of various membrane receptors involved in either pathogen entry, such as CCR5 (for HIV) and anthrax toxin receptors, cell proliferation (epidermal growth factor receptor), cardiac function (β-Adrenergic receptor), or synaptic function (AMPA receptor). Palmitoylation of these membrane receptors indeed affects not only their internalization, localization, and activation, but also other PTMs such as phosphorylation. In this review, we discuss recent results showing how palmitoylation differently affects the biology of these membrane receptors.
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Affiliation(s)
- Maxime Jansen
- Institut de Recherche en Infectiologie de Montpellier (IRIM), UMR9004-Université de Montpellier-CNRS, Montpellier, France
| | - Bruno Beaumelle
- Institut de Recherche en Infectiologie de Montpellier (IRIM), UMR9004-Université de Montpellier-CNRS, Montpellier, France
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6
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García-Nafría J, Tate CG. Structure determination of GPCRs: cryo-EM compared with X-ray crystallography. Biochem Soc Trans 2021; 49:2345-2355. [PMID: 34581758 PMCID: PMC8589417 DOI: 10.1042/bst20210431] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/19/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest single family of cell surface receptors encoded by the human genome and they play pivotal roles in co-ordinating cellular systems throughout the human body, making them ideal drug targets. Structural biology has played a key role in defining how receptors are activated and signal through G proteins and β-arrestins. The application of structure-based drug design (SBDD) is now yielding novel compounds targeting GPCRs. There is thus significant interest from both academia and the pharmaceutical industry in the structural biology of GPCRs as currently only about one quarter of human non-odorant receptors have had their structure determined. Initially, all the structures were determined by X-ray crystallography, but recent advances in electron cryo-microscopy (cryo-EM) now make GPCRs tractable targets for single-particle cryo-EM with comparable resolution to X-ray crystallography. So far this year, 78% of the 99 GPCR structures deposited in the PDB (Jan-Jul 2021) were determined by cryo-EM. Cryo-EM has also opened up new possibilities in GPCR structural biology, such as determining structures of GPCRs embedded in a lipid nanodisc and multiple GPCR conformations from a single preparation. However, X-ray crystallography still has a number of advantages, particularly in the speed of determining many structures of the same receptor bound to different ligands, an essential prerequisite for effective SBDD. We will discuss the relative merits of cryo-EM and X-ray crystallography for the structure determination of GPCRs and the future potential of both techniques.
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Affiliation(s)
- Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018 Zaragoza, Spain
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7
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Abiko LA, Rogowski M, Gautier A, Schertler G, Grzesiek S. Efficient production of a functional G protein-coupled receptor in E. coli for structural studies. JOURNAL OF BIOMOLECULAR NMR 2021; 75:25-38. [PMID: 33501610 PMCID: PMC7897205 DOI: 10.1007/s10858-020-00354-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/08/2020] [Indexed: 05/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are transmembrane signal transducers which regulate many key physiological process. Since their discovery, their analysis has been limited by difficulties in obtaining sufficient amounts of the receptors in high-quality, functional form from heterologous expression hosts. Albeit highly attractive because of its simplicity and the ease of isotope labeling for NMR studies, heterologous expression of functional GPCRs in E. coli has proven particularly challenging due to the absence of the more evolved protein expression and folding machinery of higher eukaryotic hosts. Here we first give an overview on the previous strategies for GPCR E. coli expression and then describe the development of an optimized robust protocol for the E. coli expression and purification of two mutants of the turkey β1-adrenergic receptor (β1AR) uniformly or selectively labeled in 15N or 2H,15N. These mutants had been previously optimized for thermal stability using insect cell expression and used successfully in crystallographic and NMR studies. The same sequences were then used for E. coli expression. Optimization of E. coli expression was achieved by a quantitative analysis of losses of receptor material at each step of the solubilization and purification procedure. Final yields are 0.2-0.3 mg receptor per liter culture. Whereas both expressed mutants are well folded and competent for orthosteric ligand binding, the less stable YY-β1AR mutant also comprises the two native tyrosines Y5.58 and Y7.53, which enable G protein binding. High-quality 1H-15N TROSY spectra were obtained for E. coli-expressed YY-β1AR in three different functional states (antagonist, agonist, and agonist + G protein-mimicking nanobody-bound), which are identical to spectra obtained of the same forms of the receptor expressed in insect cells. NdeI and AgeI restriction sites introduced into the expression plasmid allow for the easy replacement of the receptor gene by other GPCR genes of interest, and the provided quantitative workflow analysis may guide the respective adaptation of the purification protocol.
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Affiliation(s)
- Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland.
| | - Marco Rogowski
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Antoine Gautier
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | | | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland.
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8
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Deshpande CN, Azucenas CR, Qiao B, Nomura N, Xin V, Font J, Iwata S, Ganz T, Nemeth E, Mackenzie B, Jormakka M. Isolation and thermal stabilization of mouse ferroportin. FEBS Open Bio 2020; 11:26-34. [PMID: 33190422 PMCID: PMC7780100 DOI: 10.1002/2211-5463.13039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 12/03/2022] Open
Abstract
Ferroportin (Fpn) is an essential mammalian iron transporter that is negatively regulated by the hormone hepcidin. Our current molecular understanding of Fpn‐mediated iron efflux and regulation is limited due to a lack of biochemical, biophysical and high‐resolution structural studies. A critical step towards understanding the transport mechanism of Fpn is to obtain sufficient quantities of pure and stable protein for downstream studies. As such, we detail here an expression and purification protocol for mouse Fpn yielding milligram quantities of pure protein. We have generated deletion constructs exhibiting enhanced thermal stability and which retained iron‐transport activity and hepcidin responsiveness, providing a platform for further biophysical studies of Fpn.
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Affiliation(s)
| | - Corbin R Azucenas
- Department of Pharmacology & Systems Physiology, University of Cincinnati College of Medicine, OH.,Medical Sciences Baccalaureate Program, University of Cincinnati College of Medicine, OH, USA
| | - Bo Qiao
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Japan
| | - Vicky Xin
- Structural Biology Program, Centenary Institute, Sydney, NSW, Australia
| | - Josep Font
- Structural Biology Program, Centenary Institute, Sydney, NSW, Australia
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Japan
| | - Tomas Ganz
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Elizabeta Nemeth
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Bryan Mackenzie
- Medical Sciences Baccalaureate Program, University of Cincinnati College of Medicine, OH, USA.,Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Mika Jormakka
- Structural Biology Program, Centenary Institute, Sydney, NSW, Australia
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9
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IMPROvER: the Integral Membrane Protein Stability Selector. Sci Rep 2020; 10:15165. [PMID: 32938971 PMCID: PMC7495477 DOI: 10.1038/s41598-020-71744-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 08/04/2020] [Indexed: 01/20/2023] Open
Abstract
Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of \documentclass[12pt]{minimal}
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\begin{document}$$\upalpha$$\end{document}α-helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/.
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10
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Lee Y, Warne T, Nehmé R, Pandey S, Dwivedi-Agnihotri H, Chaturvedi M, Edwards PC, García-Nafría J, Leslie AGW, Shukla AK, Tate CG. Molecular basis of β-arrestin coupling to formoterol-bound β 1-adrenoceptor. Nature 2020; 583:862-866. [PMID: 32555462 DOI: 10.1038/s41586-020-2419-1] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/07/2020] [Indexed: 12/15/2022]
Abstract
The β1-adrenoceptor (β1AR) is a G-protein-coupled receptor (GPCR) that couples1 to the heterotrimeric G protein Gs. G-protein-mediated signalling is terminated by phosphorylation of the C terminus of the receptor by GPCR kinases (GRKs) and by coupling of β-arrestin 1 (βarr1, also known as arrestin 2), which displaces Gs and induces signalling through the MAP kinase pathway2. The ability of synthetic agonists to induce signalling preferentially through either G proteins or arrestins-known as biased agonism3-is important in drug development, because the therapeutic effect may arise from only one signalling cascade, whereas the other pathway may mediate undesirable side effects4. To understand the molecular basis for arrestin coupling, here we determined the cryo-electron microscopy structure of the β1AR-βarr1 complex in lipid nanodiscs bound to the biased agonist formoterol5, and the crystal structure of formoterol-bound β1AR coupled to the G-protein-mimetic nanobody6 Nb80. βarr1 couples to β1AR in a manner distinct to that7 of Gs coupling to β2AR-the finger loop of βarr1 occupies a narrower cleft on the intracellular surface, and is closer to transmembrane helix H7 of the receptor when compared with the C-terminal α5 helix of Gs. The conformation of the finger loop in βarr1 is different from that adopted by the finger loop of visual arrestin when it couples to rhodopsin8. β1AR coupled to βarr1 shows considerable differences in structure compared with β1AR coupled to Nb80, including an inward movement of extracellular loop 3 and the cytoplasmic ends of H5 and H6. We observe weakened interactions between formoterol and two serine residues in H5 at the orthosteric binding site of β1AR, and find that formoterol has a lower affinity for the β1AR-βarr1 complex than for the β1AR-Gs complex. The structural differences between these complexes of β1AR provide a foundation for the design of small molecules that could bias signalling in the β-adrenoceptors.
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Affiliation(s)
- Yang Lee
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Tony Warne
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Rony Nehmé
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Creoptix AG, Wädenswil, Switzerland
| | - Shubhi Pandey
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | | | - Madhu Chaturvedi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | | | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC), Zaragoza, Spain.,Laboratorio de Microscopías Avanzadas, University of Zaragoza, Zaragoza, Spain
| | | | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
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11
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Gault J, Liko I, Landreh M, Shutin D, Bolla JR, Jefferies D, Agasid M, Yen HY, Ladds MJGW, Lane DP, Khalid S, Mullen C, Remes PM, Huguet R, McAlister G, Goodwin M, Viner R, Syka JEP, Robinson CV. Combining native and 'omics' mass spectrometry to identify endogenous ligands bound to membrane proteins. Nat Methods 2020; 17:505-508. [PMID: 32371966 PMCID: PMC7332344 DOI: 10.1038/s41592-020-0821-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/25/2020] [Indexed: 02/08/2023]
Abstract
Ligands bound to protein assemblies provide critical information for function, yet are often difficult to capture and define. Here we develop a top-down method, 'nativeomics', unifying 'omics' (lipidomics, proteomics, metabolomics) analysis with native mass spectrometry to identify ligands bound to membrane protein assemblies. By maintaining the link between proteins and ligands, we define the lipidome/metabolome in contact with membrane porins and a mitochondrial translocator to discover potential regulators of protein function.
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Affiliation(s)
- Joseph Gault
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Idlir Liko
- Department of Chemistry, University of Oxford, Oxford, UK
- OMass Therapeutics, Oxford, UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Denis Shutin
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | - Mark Agasid
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
| | | | | | | | | | | | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, USA
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12
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Errey JC, Fiez-Vandal C. Production of membrane proteins in industry: The example of GPCRs. Protein Expr Purif 2020; 169:105569. [DOI: 10.1016/j.pep.2020.105569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 01/08/2023]
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13
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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: 322] [Impact Index Per Article: 64.4] [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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14
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Hot CoFi Blot: A High-Throughput Colony-Based Screen for Identifying More Thermally Stable Protein Variants. Methods Mol Biol 2019. [PMID: 31267459 DOI: 10.1007/978-1-4939-9624-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Highly soluble and stable proteins are desirable for many different applications, from basic science to reaching a cancer patient in the form of a biological drug. For X-ray crystallography-where production of a protein crystal might take weeks and even months-a stable protein sample of high purity and concentration can greatly increase the chances of producing a well-diffracting crystal. For a patient receiving a specific protein drug, its safety, efficacy, and even cost are factors affected by its solubility and stability. Increased protein expression and protein stability can be achieved by randomly altering the coding sequence. As the number of mutants generated might be overwhelming, a powerful protein expression and stability screen is required. In this chapter, we describe a colony filtration technology, which allows us to screen random mutagenesis libraries for increased thermal stability-the Hot CoFi blot. We share how to create the random mutagenesis library, how to perform the Hot CoFi blot, and how to identify more thermally stable clones. We use the Tobacco Etch Virus protease as a target to exemplify the procedure.
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15
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Warne T, Edwards PC, Doré AS, Leslie AGW, Tate CG. Molecular basis for high-affinity agonist binding in GPCRs. Science 2019; 364:775-778. [PMID: 31072904 PMCID: PMC6586556 DOI: 10.1126/science.aau5595] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 04/29/2019] [Indexed: 12/22/2022]
Abstract
G protein-coupled receptors (GPCRs) in the G protein-coupled active state have higher affinity for agonists as compared with when they are in the inactive state, but the molecular basis for this is unclear. We have determined four active-state structures of the β1-adrenoceptor (β1AR) bound to conformation-specific nanobodies in the presence of agonists of varying efficacy. Comparison with inactive-state structures of β1AR bound to the identical ligands showed a 24 to 42% reduction in the volume of the orthosteric binding site. Potential hydrogen bonds were also shorter, and there was up to a 30% increase in the number of atomic contacts between the receptor and ligand. This explains the increase in agonist affinity of GPCRs in the active state for a wide range of structurally distinct agonists.
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Affiliation(s)
- Tony Warne
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Patricia C Edwards
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew S Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6GT, UK
| | - Andrew G W Leslie
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher G Tate
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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16
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EMC Is Required to Initiate Accurate Membrane Protein Topogenesis. Cell 2018; 175:1507-1519.e16. [PMID: 30415835 PMCID: PMC6269167 DOI: 10.1016/j.cell.2018.10.009] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/15/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
Mammals encode ∼5,000 integral membrane proteins that need to be inserted in a defined topology at the endoplasmic reticulum (ER) membrane by mechanisms that are incompletely understood. Here, we found that efficient biogenesis of β1-adrenergic receptor (β1AR) and other G protein-coupled receptors (GPCRs) requires the conserved ER membrane protein complex (EMC). Reconstitution studies of β1AR biogenesis narrowed the EMC requirement to the co-translational insertion of the first transmembrane domain (TMD). Without EMC, a proportion of TMD1 inserted in an inverted orientation or failed altogether. Purified EMC and SRP receptor were sufficient for correctly oriented TMD1 insertion, while the Sec61 translocon was necessary for insertion of the next TMD. Enforcing TMD1 topology with an N-terminal signal peptide bypassed the EMC requirement for insertion in vitro and restored efficient biogenesis of multiple GPCRs in EMC-knockout cells. Thus, EMC inserts TMDs co-translationally and cooperates with the Sec61 translocon to ensure accurate topogenesis of many membrane proteins. Efficient biogenesis of many GPCRs requires EMC, the ER membrane protein complex Without EMC, correct topology and insertion of the first transmembrane domain fails Purified EMC is sufficient for insertion of the first transmembrane domain of GPCRs The Sec61 complex is required for insertion of subsequent transmembrane domains
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17
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Ghosh S, Bierig T, Lee S, Jana S, Löhle A, Schnapp G, Tautermann CS, Vaidehi N. Engineering Salt Bridge Networks between Transmembrane Helices Confers Thermostability in G-Protein-Coupled Receptors. J Chem Theory Comput 2018; 14:6574-6585. [PMID: 30359017 DOI: 10.1021/acs.jctc.8b00602] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction of specific point mutations has been an effective strategy in enhancing the thermostability of G-protein-coupled receptors (GPCRs). Our previous work showed that a specific residue position on transmembrane helix 6 (TM6) in class A GPCRs consistently yields thermostable mutants. The crystal structure of human chemokine receptor CCR5 also showed increased thermostability upon mutation of two positions, A233D6.33 and K303E7.59. With the goal of testing the transferability of these two thermostabilizing mutations in other chemokine receptors, we tested the mutations A237D6.33 and R307E7.59 in human CCR3 for thermostability and aggregation properties in detergent solution. Interestingly, the double mutant exhibited a 6-10-fold decrease in the aggregation propensity of the wild-type protein. This is in stark contrast to the two single mutants whose aggregation properties resemble the wild type (WT). Moreover, unlike in CCR5, the two single mutants separately showed no increase in thermostability compared to the wild-type CCR3, while the double-mutant A237D6.33/R307E7.59 confers an increase of 2.6 °C in the melting temperature compared to the WT. Extensive all-atom molecular dynamics (MD) simulations in detergent micelles show that a salt bridge network between transmembrane helices TM3, TM6, and TM7 that is absent in the two single mutants confers stability in the double mutant. The free energy surface of the double mutant shows conformational homogeneity compared to the single mutants. An annular n-dodecyl maltoside detergent layer packs tighter to the hydrophobic surface of the double-mutant CCR3 compared to the single mutants providing additional stability. The purification of other C-C chemokine receptors lacking such stabilizing residues may benefit from the incorporation of these two point mutations.
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Affiliation(s)
- Soumadwip Ghosh
- Department of Molecular Imaging and Therapy , Beckman Research Institute of the City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Tobias Bierig
- Department of Medicinal Chemistry , Boehringer Ingelheim Pharma GmbH & Company KG , Birkendorfer Strasse 65 , D-88397 Biberach an der Riss , Germany
| | | | | | | | - Gisela Schnapp
- Department of Medicinal Chemistry , Boehringer Ingelheim Pharma GmbH & Company KG , Birkendorfer Strasse 65 , D-88397 Biberach an der Riss , Germany
| | - Christofer S Tautermann
- Department of Medicinal Chemistry , Boehringer Ingelheim Pharma GmbH & Company KG , Birkendorfer Strasse 65 , D-88397 Biberach an der Riss , Germany
| | - Nagarajan Vaidehi
- Department of Molecular Imaging and Therapy , Beckman Research Institute of the City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
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18
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Biomimetic Membranes as a Technology Platform: Challenges and Opportunities. MEMBRANES 2018; 8:membranes8030044. [PMID: 30018213 PMCID: PMC6161077 DOI: 10.3390/membranes8030044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 01/08/2023]
Abstract
Biomimetic membranes are attracting increased attention due to the huge potential of using biological functional components and processes as an inspirational basis for technology development. Indeed, this has led to several new membrane designs and applications. However, there are still a number of issues which need attention. Here, I will discuss three examples of biomimetic membrane developments within the areas of water treatment, energy conversion, and biomedicine with a focus on challenges and applicability. While the water treatment area has witnessed some progress in developing biomimetic membranes of which some are now commercially available, other areas are still far from being translated into technology. For energy conversion, there has been much focus on using bacteriorhodopsin proteins, but energy densities have so far not reached sufficient levels to be competitive with state-of-the-art photovoltaic cells. For biomedical (e.g., drug delivery) applications the research focus has been on the mechanism of action, and much less on the delivery 'per se'. Thus, in order for these areas to move forward, we need to address some hard questions: is bacteriorhodopsin really the optimal light harvester to be used in energy conversion? And how do we ensure that biomedical nano-carriers covered with biomimetic membrane material ever reach their target cells/tissue in sufficient quantities? In addition to these area-specific questions the general issue of production cost and scalability must also be treated in order to ensure efficient translation of biomimetic membrane concepts into reality.
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19
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Yen HY, Hoi KK, Liko I, Hedger G, Horrell MR, Song W, Wu D, Heine P, Warne T, Lee Y, Carpenter B, Plückthun A, Tate CG, Sansom MSP, Robinson CV. PtdIns(4,5)P 2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling. Nature 2018; 559:423-427. [PMID: 29995853 PMCID: PMC6059376 DOI: 10.1038/s41586-018-0325-6] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 05/14/2018] [Indexed: 11/21/2022]
Abstract
G-protein-coupled receptors (GPCRs) are involved in many physiological processes and are therefore key drug targets1. Although detailed structural information is available for GPCRs, the effects of lipids on the receptors, and on downstream coupling of GPCRs to G proteins are largely unknown. Here we use native mass spectrometry to identify endogenous lipids bound to three class A GPCRs. We observed preferential binding of phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) over related lipids and confirm that the intracellular surface of the receptors contain hotspots for PtdIns(4,5)P2 binding. Endogenous lipids were also observed bound directly to the trimeric Gαsβγ protein complex of the adenosine A2A receptor (A2AR) in the gas phase. Using engineered Gα subunits (mini-Gαs, mini-Gαi and mini-Gα12)2, we demonstrate that the complex of mini-Gαs with the β1 adrenergic receptor (β1AR) is stabilized by the binding of two PtdIns(4,5)P2 molecules. By contrast, PtdIns(4,5)P2 does not stabilize coupling between β1AR and other Gα subunits (mini-Gαi or mini-Gα12) or a high-affinity nanobody. Other endogenous lipids that bind to these receptors have no effect on coupling, highlighting the specificity of PtdIns(4,5)P2. Calculations of potential of mean force and increased GTP turnover by the activated neurotensin receptor when coupled to trimeric Gαiβγ complex in the presence of PtdIns(4,5)P2 provide further evidence for a specific effect of PtdIns(4,5)P2 on coupling. We identify key residues on cognate Gα subunits through which PtdIns(4,5)P2 forms bridging interactions with basic residues on class A GPCRs. These modulating effects of lipids on receptors suggest consequences for understanding function, G-protein selectivity and drug targeting of class A GPCRs.
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MESH Headings
- Animals
- GTP-Binding Protein alpha Subunits, Gi-Go/metabolism
- GTP-Binding Protein alpha Subunits, Gs/metabolism
- Heterotrimeric GTP-Binding Proteins/metabolism
- Humans
- Molecular Dynamics Simulation
- Phosphatidylinositol 4,5-Diphosphate/metabolism
- Protein Stability
- Rats
- Receptors, Adrenergic, alpha-2/chemistry
- Receptors, Adrenergic, alpha-2/genetics
- Receptors, Adrenergic, alpha-2/metabolism
- Receptors, Adrenergic, beta-1/chemistry
- Receptors, Adrenergic, beta-1/genetics
- Receptors, Adrenergic, beta-1/metabolism
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Neurotensin/chemistry
- Receptors, Neurotensin/genetics
- Receptors, Neurotensin/metabolism
- Single-Chain Antibodies/chemistry
- Single-Chain Antibodies/metabolism
- Substrate Specificity
- Turkeys
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Affiliation(s)
- Hsin-Yung Yen
- Chemical Research Laboratory, University of Oxford, Oxford, UK
- OMass Technologies, Kidlington, UK
| | - Kin Kuan Hoi
- Chemical Research Laboratory, University of Oxford, Oxford, UK
| | - Idlir Liko
- Chemical Research Laboratory, University of Oxford, Oxford, UK
- OMass Technologies, Kidlington, UK
| | - George Hedger
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Di Wu
- Chemical Research Laboratory, University of Oxford, Oxford, UK
| | - Philipp Heine
- Biochemisches Institut, Universität Zürich, Zurich, Switzerland
| | - Tony Warne
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Yang Lee
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Byron Carpenter
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, The University of Warwick, Coventry, UK
| | | | | | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK.
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20
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Popov P, Peng Y, Shen L, Stevens RC, Cherezov V, Liu ZJ, Katritch V. Computational design of thermostabilizing point mutations for G protein-coupled receptors. eLife 2018; 7:34729. [PMID: 29927385 PMCID: PMC6013254 DOI: 10.7554/elife.34729] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/05/2018] [Indexed: 12/02/2022] Open
Abstract
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational approach to effective prediction of stabilizing mutations in GPCRs, named CompoMug, which employs sequence-based analysis, structural information, and a derived machine learning predictor. Tested experimentally on the serotonin 5-HT2C receptor target, CompoMug predictions resulted in 10 new stabilizing mutations, with an apparent thermostability gain ~8.8°C for the best single mutation and ~13°C for a triple mutant. Binding of antagonists confers further stabilization for the triple mutant receptor, with total gains of ~21°C as compared to wild type apo 5-HT2C. The predicted mutations enabled crystallization and structure determination for the 5-HT2C receptor complexes in inactive and active-like states. While CompoMug already shows high 25% hit rate and utility in GPCR structural studies, further improvements are expected with accumulation of structural and mutation data. The trillions of cells in the human body rely on receptors that sit in their cell membranes to communicate with each other. Hundreds of different receptors belong to the G protein-coupled receptor superfamily (called GPCRs for short) and play vital roles in the all organs and bodily systems. Indeed, GPCRs are the targets for almost 40% of therapeutic drugs. As such, deciphering the shape and activity of GPCRs is key to understanding the normal workings of the human biology and could help scientists discover new treatments for various diseases, from depression to high blood pressure to cancer. These receptors, however, are notoriously flimsy and unstable, making them difficult to work with in the laboratory. Different approaches have been developed to make GPCRs more stable, usually by swapping one or a few of the amino acid building blocks in the protein for other amino acids. Currently, this requires a costly and slow trial-and-error approach in which each amino acid out of 300-400 in the protein is mutated and tested experimentally. To speed up and reduce the cost of the process, Popov et al. asked if a computer could predict which mutations in the protein would stabilize it, meaning that fewer proteins would actually need to be tested. Four computer algorithms based on four different principles were developed and verified. The first one compares the target GPCR to other closely related receptors, trying to detect variations that cause the instability. The second tries to build in specific stabilizing interactions, or “bridges”, between different parts of the receptor. The third algorithm searches the known structures of other GPCRs for useful mutations. Finally, the fourth one uses accumulated data on the stability of hundreds of mutations in different GPCRs to train a machine learning predictor to recognize stabilizing mutations. All four algorithms produced useful predictions in a real-life project. Indeed, when combined in one computational tool, named CompoMug, the algorithms made it possible to detect optimal mutations in a human GPCR called 5-HT2C. This made the protein much easier to work with in the laboratory, and ultimately helped to solve its three-dimensional structure (which was reported in a separate study, published earlier in 2018) The 5-HT2C receptor is involved in regulating, among other things, mood and appetite. Details of its structure might therefore help researchers to design new antidepressants and obesity treatments. Moreover, CompoMug is already helping structural biologists to solve the structures of other GPCRs, which will further facilitate many aspects of GPCR drug discovery.
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Affiliation(s)
- Petr Popov
- Department of Biological Sciences, University of Southern California, Los Angeles, Los Angeles, United States.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Yao Peng
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Ling Shen
- iHuman Institute, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Raymond C Stevens
- Department of Biological Sciences, University of Southern California, Los Angeles, Los Angeles, United States.,iHuman Institute, ShanghaiTech University, Shanghai, China.,Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, United States.,Bridge Institute, University of Southern California, Los Angeles, Los Angeles, United States
| | - Vadim Cherezov
- Department of Biological Sciences, University of Southern California, Los Angeles, Los Angeles, United States.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, United States.,Bridge Institute, University of Southern California, Los Angeles, Los Angeles, United States
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Insititute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China
| | - Vsevolod Katritch
- Department of Biological Sciences, University of Southern California, Los Angeles, Los Angeles, United States.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, United States.,Bridge Institute, University of Southern California, Los Angeles, Los Angeles, United States
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21
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Lee S, Mao A, Bhattacharya S, Robertson N, Grisshammer R, Tate CG, Vaidehi N. How Do Short Chain Nonionic Detergents Destabilize G-Protein-Coupled Receptors? J Am Chem Soc 2016; 138:15425-15433. [PMID: 27792324 PMCID: PMC5148649 DOI: 10.1021/jacs.6b08742] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stability of detergent-solubilized G-protein-coupled receptors (GPCRs) is crucial for their purification in a biologically relevant state, and it is well-known that short chain detergents such as octylglucoside are more denaturing than long chain detergents such as dodecylmaltoside. However, the molecular basis for this phenomenon is poorly understood. To gain insights into the mechanism of detergent destabilization of GPCRs, we used atomistic molecular dynamics simulations of thermostabilized adenosine receptor (A2AR) mutants embedded in either a lipid bilayer or detergent micelles of alkylmaltosides and alkylglucosides. A2AR mutants in dodecylmaltoside or phospholipid showed low flexibility and good interhelical packing. In contrast, A2AR mutants in either octylglucoside or nonylglucoside showed decreased α-helicity in transmembrane regions, decreased α-helical packing, and the interpenetration of detergent molecules between transmembrane α-helices. This was not observed in octylglucoside containing phospholipid. Cholesteryl hemisuccinate in dodecylmaltoside increased the energetic stability of the receptor by wedging into crevices on the hydrophobic surface of A2AR, increasing packing interactions within the receptor and stiffening the detergent micelle. The data suggest a three-stage process for the initial events in the destabilization of GPCRs by octylglucoside: (i) highly mobile detergent molecules form small micelles around the receptor; (ii) loss of α-helicity and decreased interhelical packing interactions in transmembrane regions are promoted by increased receptor thermal motion; (iii) transient separation of transmembrane helices allowed penetration of detergent molecules into the core of the receptor. The relative hydration of the headgroup and alkyl chain correlates with detergent harshness and suggests new avenues to develop milder versions of octylglucoside for receptor crystallization.
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Affiliation(s)
- Sangbae Lee
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Allen Mao
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Supriyo Bhattacharya
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Nathan Robertson
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, AL7 3AX, UK
| | - Reinhard Grisshammer
- Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, USA
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Nagarajan Vaidehi
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
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22
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Carpenter B, Tate CG. Engineering a minimal G protein to facilitate crystallisation of G protein-coupled receptors in their active conformation. Protein Eng Des Sel 2016; 29:583-594. [PMID: 27672048 PMCID: PMC5181381 DOI: 10.1093/protein/gzw049] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/01/2016] [Accepted: 08/23/2016] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) modulate cytoplasmic signalling in response to extracellular stimuli, and are important therapeutic targets in a wide range of diseases. Structure determination of GPCRs in all activation states is important to elucidate the precise mechanism of signal transduction and to facilitate optimal drug design. However, due to their inherent instability, crystallisation of GPCRs in complex with cytoplasmic signalling proteins, such as heterotrimeric G proteins and β-arrestins, has proved challenging. Here, we describe the design of a minimal G protein, mini-Gs, which is composed solely of the GTPase domain from the adenylate cyclase stimulating G protein Gs. Mini-Gs is a small, soluble protein, which efficiently couples GPCRs in the absence of Gβγ subunits. We engineered mini-Gs, using rational design mutagenesis, to form a stable complex with detergent-solubilised β1-adrenergic receptor (β1AR). Mini G proteins induce similar pharmacological and structural changes in GPCRs as heterotrimeric G proteins, but eliminate many of the problems associated with crystallisation of these complexes, specifically their large size, conformational dynamics and instability in detergent. They are therefore novel tools, which will facilitate the biochemical and structural characterisation of GPCRs in their active conformation.
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Affiliation(s)
- Byron Carpenter
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus , Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus , Francis Crick Avenue, Cambridge CB2 0QH, UK
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23
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Magnani F, Serrano-Vega MJ, Shibata Y, Abdul-Hussein S, Lebon G, Miller-Gallacher J, Singhal A, Strege A, Thomas JA, Tate CG. A mutagenesis and screening strategy to generate optimally thermostabilized membrane proteins for structural studies. Nat Protoc 2016; 11:1554-71. [PMID: 27466713 PMCID: PMC5268090 DOI: 10.1038/nprot.2016.088] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The thermostability of an integral membrane protein (MP) in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals that are suitable for structure determination. However, many mammalian MPs are too unstable for crystallization. We developed a thermostabilization strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes ∼6-12 months to thermostabilize a G-protein-coupled receptor (GPCR) containing 300 amino acid (aa) residues. The resulting thermostabilized MPs are more easily crystallized and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs because it is possible to determine multiple structures of the thermostabilized receptors bound to low-affinity ligands. Protocols and advice are given on how to develop thermostability assays for MPs and how to combine mutations to make an optimally stable mutant suitable for structural studies. The steps in the procedure include the generation of ∼300 site-directed mutants by Ala/Leu scanning mutagenesis, the expression of each mutant in mammalian cells by transient transfection and the identification of thermostable mutants using a thermostability assay that is based on binding of an (125)I-labeled radioligand to the unpurified, detergent-solubilized MP. Individual thermostabilizing point mutations are then combined to make an optimally stable MP that is suitable for structural biology and other biophysical studies.
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Affiliation(s)
| | | | | | | | | | | | - Ankita Singhal
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Annette Strege
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jennifer A. Thomas
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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24
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Di Bartolo N, Compton ELR, Warne T, Edwards PC, Tate CG, Schertler GFX, Booth PJ. Complete Reversible Refolding of a G-Protein Coupled Receptor on a Solid Support. PLoS One 2016; 11:e0151582. [PMID: 26982879 PMCID: PMC4794186 DOI: 10.1371/journal.pone.0151582] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 03/01/2016] [Indexed: 12/22/2022] Open
Abstract
The factors defining the correct folding and stability of integral membrane proteins are poorly understood. Folding of only a few select membrane proteins has been scrutinised, leaving considerable deficiencies in knowledge for large protein families, such as G protein coupled receptors (GPCRs). Complete reversible folding, which is problematic for any membrane protein, has eluded this dominant receptor family. Moreover, attempts to recover receptors from denatured states are inefficient, yielding at best 40–70% functional protein. We present a method for the reversible unfolding of an archetypal family member, the β1-adrenergic receptor, and attain 100% recovery of the folded, functional state, in terms of ligand binding, compared to receptor which has not been subject to any unfolding and retains its original, folded structure. We exploit refolding on a solid support, which could avoid unwanted interactions and aggregation that occur in bulk solution. We determine the changes in structure and function upon unfolding and refolding. Additionally, we employ a method that is relatively new to membrane protein folding; pulse proteolysis. Complete refolding of β1-adrenergic receptor occurs in n-decyl-β-D-maltoside (DM) micelles from a urea-denatured state, as shown by regain of its original helical structure, ligand binding and protein fluorescence. The successful refolding strategy on a solid support offers a defined method for the controlled refolding and recovery of functional GPCRs and other membrane proteins that suffer from instability and irreversible denaturation once isolated from their native membranes.
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Affiliation(s)
- Natalie Di Bartolo
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Emma L. R. Compton
- Organisational and Staff Development Unit, University of Strathclyde, Glasgow, United Kingdom
| | - Tony Warne
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Patricia C. Edwards
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Paula J. Booth
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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25
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Kane Dickson V. Phasing and structure of bestrophin-1: a case study in the use of heavy-atom cluster compounds with multi-subunit transmembrane proteins. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:319-25. [PMID: 26960119 PMCID: PMC4784663 DOI: 10.1107/s2059798315022524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 11/25/2015] [Indexed: 11/16/2022]
Abstract
The structure of a eukaryotic ion channel solved using tantalum bromide SAD phasing is discussed in the context of basic challenges common to membrane proteins. The purification and three-dimensional crystallization of membrane proteins are commonly affected by a cumulation of pathologies that are less prevalent in their soluble counterparts. This may include severe anisotropy, poor spot shape, poor to moderate-resolution diffraction, crystal twinning, translational pseudo-symmetry and poor uptake of heavy atoms for derivatization. Such challenges must be circumvented by adaptations in the approach to crystallization and/or phasing. Here, an example of a protein that exhibited all of the above-mentioned complications is presented. Bestrophin-1 is a eukaryotic calcium-activated chloride channel, the structure of which was recently determined in complex with monoclonal antibody fragments using SAD phasing with tantalum bromide clusters (Ta6Br12·Br2). Some of the obstacles to obtaining improved diffraction and phasing for this particular channel are discussed, as well as the approach and adaptations that were key to determining the structure.
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Affiliation(s)
- Veronica Kane Dickson
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
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26
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Snijder HJA, Hakulinen J. Membrane Protein Production in E. coli for Applications in Drug Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:59-77. [PMID: 27165319 DOI: 10.1007/978-3-319-27216-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Producing high quality purified membrane proteins for structure-based drug design and biophysical assays compatible with typical timelines in drug discovery is a significant challenge. Escherichia coli has been an expression host of the utmost importance for soluble proteins and has applications for membrane proteins as well. However, membrane protein overexpression in E. coli may lead to toxicity and low yields of functional product. Here, we review the challenges encountered with heterologous overproduction of α-helical membrane proteins in E. coli and a range of strategies to overcome them. A detailed protocol is also provided for expression and screening of membrane proteins in E. coli using a His-specific fluorescent probe and fluorescent size-exclusion chromatography.
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Affiliation(s)
| | - Jonna Hakulinen
- Discovery Sciences, AstraZeneca R&D, SE-43183, Mölndal, Sweden
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27
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Characterizing diverse orthologues of the cystic fibrosis transmembrane conductance regulator protein for structural studies. Biochem Soc Trans 2015; 43:894-900. [DOI: 10.1042/bst20150081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As an ion channel, the cystic fibrosis transmembrane conductance regulator (CFTR) protein occupies a unique niche within the ABC family. Orthologues of CFTR are extant throughout the animal kingdom from sharks to platypods to sheep, where the osmoregulatory function of the protein has been applied to differing lifestyles and diverse organ systems. In humans, loss-of-function mutations to CFTR cause the disease cystic fibrosis, which is a significant health burden in populations of white European descent. Orthologue screening has proved fruitful in the pursuit of high-resolution structural data for several membrane proteins, and we have applied some of the princples developed in previous studies to the expression and purification of CFTR. We have overexpressed this protein, along with evolutionarily diverse orthologues, in Saccharomyces cerevisiae and developed a purification to isolate it in quantities sufficient for structural and functional studies.
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28
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Sato T, Baker J, Warne T, Brown GA, Leslie AGW, Congreve M, Tate CG. Pharmacological Analysis and Structure Determination of 7-Methylcyanopindolol-Bound β1-Adrenergic Receptor. Mol Pharmacol 2015; 88:1024-34. [PMID: 26385885 DOI: 10.1124/mol.115.101030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/17/2015] [Indexed: 11/22/2022] Open
Abstract
Comparisons between structures of the β1-adrenergic receptor (AR) bound to either agonists, partial agonists, or weak partial agonists led to the proposal that rotamer changes of Ser(5.46), coupled to a contraction of the binding pocket, are sufficient to increase the probability of receptor activation. (RS)-4-[3-(tert-butylamino)-2-hydroxypropoxy]-1H-indole-2-carbonitrile (cyanopindolol) is a weak partial agonist of β1AR and, based on the hypothesis above, we predicted that the addition of a methyl group to form 4-[(2S)-3-(tert-butylamino)-2-hydroxypropoxy]-7-methyl-1H-indole-2-carbonitrile (7-methylcyanopindolol) would dramatically reduce its efficacy. An eight-step synthesis of 7-methylcyanopindolol was developed and its pharmacology was analyzed. 7-Methylcyanopindolol bound with similar affinity to cyanopindolol to both β1AR and β2AR. As predicted, the efficacy of 7-methylcyanopindolol was reduced significantly compared with cyanopindolol, acting as a very weak partial agonist of turkey β1AR and an inverse agonist of human β2AR. The structure of 7-methylcyanopindolol-bound β1AR was determined to 2.4-Å resolution and found to be virtually identical to the structure of cyanopindolol-bound β1AR. The major differences in the orthosteric binding pocket are that it has expanded by 0.3 Å in 7-methylcyanopindolol-bound β1AR and the hydroxyl group of Ser(5.46) is positioned 0.8 Å further from the ligand, with respect to the position of the Ser(5.46) side chain in cyanopindolol-bound β1AR. Thus, the molecular basis for the reduction in efficacy of 7-methylcyanopindolol compared with cyanopindolol may be regarded as the opposite of the mechanism proposed for the increase in efficacy of agonists compared with antagonists.
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Affiliation(s)
- Tomomi Sato
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Jillian Baker
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Tony Warne
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Giles A Brown
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Andrew G W Leslie
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Miles Congreve
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
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29
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Structural dynamics and energetics underlying allosteric inactivation of the cannabinoid receptor CB1. Proc Natl Acad Sci U S A 2015; 112:8469-74. [PMID: 26100912 DOI: 10.1073/pnas.1500895112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are surprisingly flexible molecules that can do much more than simply turn on G proteins. Some even exhibit biased signaling, wherein the same receptor preferentially activates different G-protein or arrestin signaling pathways depending on the type of ligand bound. Why this behavior occurs is still unclear, but it can happen with both traditional ligands and ligands that bind allosterically outside the orthosteric receptor binding pocket. Here, we looked for structural mechanisms underlying these phenomena in the marijuana receptor CB1. Our work focused on the allosteric ligand Org 27569, which has an unusual effect on CB1-it simultaneously increases agonist binding, decreases G--protein activation, and induces biased signaling. Using classical pharmacological binding studies, we find that Org 27569 binds to a unique allosteric site on CB1 and show that it can act alone (without need for agonist cobinding). Through mutagenesis studies, we find that the ability of Org 27569 to bind is related to how much receptor is in an active conformation that can couple with G protein. Using these data, we estimated the energy differences between the inactive and active states. Finally, site-directed fluorescence labeling studies show the CB1 structure stabilized by Org 27569 is different and unique from that stabilized by antagonist or agonist. Specifically, transmembrane helix 6 (TM6) movements associated with G-protein activation are blocked, but at the same time, helix 8/TM7 movements are enhanced, suggesting a possible mechanism for the ability of Org 27569 to induce biased signaling.
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30
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To J, Yeo CY, Soon CH, Torres J. A generic high-throughput assay to detect aquaporin functional mutants: Potential application to discovery of aquaporin inhibitors. Biochim Biophys Acta Gen Subj 2015; 1850:1869-76. [PMID: 26028295 DOI: 10.1016/j.bbagen.2015.05.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 05/13/2015] [Accepted: 05/27/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND The discovery of stable, yet functional, protein mutants is a limiting factor in the development of biotechnological applications, structural studies or in drug discovery. Rapid detection of functional mutants is especially challenging for water channel aquaporins, as they do not have a directly measurable enzymatic or binding activity. Current methods available are time consuming and only applicable to specific aquaporins. METHODS Herein we describe an assay based on the protective effect of aquaporins on yeast S. cerevisiae in response to rapid freezing. RESULTS Yeast overexpressing a functional water-permeable aquaporin of choice are rescued after the challenge, while inactive or blocked aquaporins confer no protection and lead to cell death. The potential of this assay is shown by screening a small number of E. coli aquaporin Z (AQPZ) mutants. Additionally, a library of ~10,000 drug-like compounds was tested against human AQP1 (hAQP1). CONCLUSIONS Since rescue is only dependent on transmembrane water flux, the assay is applicable to water-permeable aquaporins of any origin. GENERAL SIGNIFICANCE Mapping of permissive mutations on the aquaporin structure can help delineate the minimal requirements for effective water transport. Alternatively, the assay can be potentially used to discover compounds that inhibit aquaporin water transport. When additionally screened for thermostability, functional aquaporin mutants can be useful in the development of biomimetic membranes for water purification, or to improve the likelihood of producing well-diffracting crystals, enabling rational design of much needed aquaporin inhibitors.
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Affiliation(s)
- Janet To
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Chiew Ying Yeo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Cin Huang Soon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.
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31
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Heydenreich FM, Vuckovic Z, Matkovic M, Veprintsev DB. Stabilization of G protein-coupled receptors by point mutations. Front Pharmacol 2015; 6:82. [PMID: 25941489 PMCID: PMC4403299 DOI: 10.3389/fphar.2015.00082] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/31/2015] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are flexible integral membrane proteins involved in transmembrane signaling. Their involvement in many physiological processes makes them interesting targets for drug development. Determination of the structure of these receptors will help to design more specific drugs, however, their structural characterization has so far been hampered by the low expression and their inherent instability in detergents which made protein engineering indispensable for structural and biophysical characterization. Several approaches to stabilize the receptors in a particular conformation have led to breakthroughs in GPCR structure determination. These include truncations of the flexible regions, stabilization by antibodies and nanobodies, fusion partners, high affinity and covalently bound ligands as well as conformational stabilization by mutagenesis. In this review we focus on stabilization of GPCRs by insertion of point mutations, which lead to increased conformational and thermal stability as well as improved expression levels. We summarize existing mutagenesis strategies with different coverage of GPCR sequence space and depth of information, design and transferability of mutations and the molecular basis for stabilization. We also discuss whether mutations alter the structure and pharmacological properties of GPCRs.
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Affiliation(s)
- Franziska M Heydenreich
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Ziva Vuckovic
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Milos Matkovic
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
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32
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Thomas JA, Tate CG. Quality control in eukaryotic membrane protein overproduction. J Mol Biol 2015; 426:4139-4154. [PMID: 25454020 PMCID: PMC4271737 DOI: 10.1016/j.jmb.2014.10.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/12/2014] [Accepted: 10/13/2014] [Indexed: 10/25/2022]
Abstract
The overexpression of authentically folded eukaryotic membrane proteins in milligramme quantities is a fundamental prerequisite for structural studies. One of the most commonly used expression systems for the production of mammalian membrane proteins is the baculovirus expression system in insect cells. However, a detailed analysis by radioligand binding and comparative Western blotting of G protein-coupled receptors and a transporter produced in insect cells showed that a considerable proportion of the expressed protein was misfolded and incapable of ligand binding. In contrast, production of the same membrane proteins in stable inducible mammalian cell lines suggested that the majority was folded correctly. It was noted that detergent solubilisation of the misfolded membrane proteins using either digitonin or dodecylmaltoside was considerablyless efficient than using sodium dodecyl sulfate or foscholine-12, whilst these detergents were equally efficient at solubilising correctly folded membrane proteins. This provides a simple and rapid test to suggest whether heterologously expressed mammalian membrane proteins are indeed correctly folded, without requiring radioligand binding assays. This will greatly facilitate the high-throughput production of fully functional membrane proteins for structural studies.
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Affiliation(s)
- Jennifer A Thomas
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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33
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Milić D, Veprintsev DB. Large-scale production and protein engineering of G protein-coupled receptors for structural studies. Front Pharmacol 2015; 6:66. [PMID: 25873898 PMCID: PMC4379943 DOI: 10.3389/fphar.2015.00066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 03/13/2015] [Indexed: 01/26/2023] Open
Abstract
Structural studies of G protein-coupled receptors (GPCRs) gave insights into molecular mechanisms of their action and contributed significantly to molecular pharmacology. This is primarily due to technical advances in protein engineering, production and crystallization of these important receptor targets. On the other hand, NMR spectroscopy of GPCRs, which can provide information about their dynamics, still remains challenging due to difficulties in preparation of isotopically labeled receptors and their low long-term stabilities. In this review, we discuss methods used for expression and purification of GPCRs for crystallographic and NMR studies. We also summarize protein engineering methods that played a crucial role in obtaining GPCR crystal structures.
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Affiliation(s)
- Dalibor Milić
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland ; Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich Switzerland
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34
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Miller DM, Gulbis JM. Engineering protocells: prospects for self-assembly and nanoscale production-lines. Life (Basel) 2015; 5:1019-53. [PMID: 25815781 PMCID: PMC4500129 DOI: 10.3390/life5021019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic "organisms" with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. Until now, artificial cell technology has been largely restricted to the modification and metabolic engineering of living unicellular organisms. This review discusses emerging possibilities for developing synthetic protocell "machines" assembled entirely from individual biological components. We describe a host of recent technological advances that could potentially be harnessed in design and construction of synthetic protocells, some of which have already been utilized toward these ends. More elaborate designs include options for building self-assembling machines by incorporating cellular transport and assembly machinery. We also discuss production in miniature, using microfluidic production lines. While there are still many unknowns in the design, engineering and optimization of protocells, current technologies are now tantalizingly close to the capabilities required to build the first prototype protocells with potential real-world applications.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
| | - Jacqueline M Gulbis
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
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35
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Methodological advances: the unsung heroes of the GPCR structural revolution. Nat Rev Mol Cell Biol 2015; 16:69-81. [DOI: 10.1038/nrm3933] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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36
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Kouvatsos N, Niarchos A, Zisimopoulou P, Eliopoulos E, Poulas K, Tzartos S. Purification and functional characterization of a truncated human α4β2 nicotinic acetylcholine receptor. Int J Biol Macromol 2014; 70:320-6. [PMID: 25014634 DOI: 10.1016/j.ijbiomac.2014.06.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 10/25/2022]
Abstract
Nicotinic acetylcholine receptors (nAChR) are abundant in the brain and are essential in cognitive function, learning and memory. Previous efforts on α4β2 nAChR had been focused on functional and pharmacological characterization, where high expression yield is not essential. For structural studies though, large amounts of pure protein is important but heterologous overexpression of membrane proteins can be a burdensome task, especially if high amounts are required. In the current study, a truncated mutant of the human α4β2 nAChR was designed in order to improve expression and solubility and to obtain material suitable for high resolution structural studies. We showed that the wild type α4β2 nAChR presented low expression and solubilization yield both of which were improved with the truncated construct. The truncated nAChR showed similar binding profile to the wild type, was purified by a two-step chromatography and isolated in high purity and adequate quantity.
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Affiliation(s)
- Nikolaos Kouvatsos
- Department of Neurobiology, Hellenic Pasteur Institute, 127 Vass. Sofias Avenue, GR11521 Athens, Greece
| | | | - Paraskevi Zisimopoulou
- Department of Neurobiology, Hellenic Pasteur Institute, 127 Vass. Sofias Avenue, GR11521 Athens, Greece
| | - Elias Eliopoulos
- Department of Agricultural Biotechnology, Agricultural University of Athens, Holy Street 75, GR11855 Athens, Greece
| | | | - Socrates Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute, 127 Vass. Sofias Avenue, GR11521 Athens, Greece; Department of Pharmacy, University of Patras, GR26500 Patras, Greece.
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37
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Miller-Gallacher JL, Nehmé R, Warne T, Edwards PC, Schertler GFX, Leslie AGW, Tate CG. The 2.1 Å resolution structure of cyanopindolol-bound β1-adrenoceptor identifies an intramembrane Na+ ion that stabilises the ligand-free receptor. PLoS One 2014; 9:e92727. [PMID: 24663151 PMCID: PMC3963952 DOI: 10.1371/journal.pone.0092727] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/25/2014] [Indexed: 12/30/2022] Open
Abstract
The β1-adrenoceptor (β1AR) is a G protein-coupled receptor (GPCR) that is activated by the endogenous agonists adrenaline and noradrenaline. We have determined the structure of an ultra-thermostable β1AR mutant bound to the weak partial agonist cyanopindolol to 2.1 Å resolution. High-quality crystals (100 μm plates) were grown in lipidic cubic phase without the assistance of a T4 lysozyme or BRIL fusion in cytoplasmic loop 3, which is commonly employed for GPCR crystallisation. An intramembrane Na+ ion was identified co-ordinated to Asp872.50, Ser1283.39 and 3 water molecules, which is part of a more extensive network of water molecules in a cavity formed between transmembrane helices 1, 2, 3, 6 and 7. Remarkably, this water network and Na+ ion is highly conserved between β1AR and the adenosine A2A receptor (rmsd of 0.3 Å), despite an overall rmsd of 2.4 Å for all Cα atoms and only 23% amino acid identity in the transmembrane regions. The affinity of agonist binding and nanobody Nb80 binding to β1AR is unaffected by Na+ ions, but the stability of the receptor is decreased by 7.5°C in the absence of Na+. Mutation of amino acid side chains that are involved in the co-ordination of either Na+ or water molecules in the network decreases the stability of β1AR by 5–10°C. The data suggest that the intramembrane Na+ and associated water network stabilise the ligand-free state of β1AR, but still permits the receptor to form the activated state which involves the collapse of the Na+ binding pocket on agonist binding.
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Affiliation(s)
| | - Rony Nehmé
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire, United Kingdom
| | - Tony Warne
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire, United Kingdom
| | - Patricia C. Edwards
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire, United Kingdom
| | - Gebhard F. X. Schertler
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire, United Kingdom
| | - Andrew G. W. Leslie
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire, United Kingdom
| | - Christopher G. Tate
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire, United Kingdom
- * E-mail:
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38
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L. Pollock N, Moran O, Baroni D, Zegarra-Moran O, C. Ford R. Characterisation of the salmon cystic fibrosis transmembrane conductance regulator protein for structural studies. AIMS MOLECULAR SCIENCE 2014. [DOI: 10.3934/molsci.2014.4.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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39
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Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell. Nat Commun 2013; 4:2901. [DOI: 10.1038/ncomms3901] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/08/2013] [Indexed: 11/08/2022] Open
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40
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Boivin S, Kozak S, Meijers R. Optimization of protein purification and characterization using Thermofluor screens. Protein Expr Purif 2013; 91:192-206. [DOI: 10.1016/j.pep.2013.08.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/29/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
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41
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Pollock NL, McDevitt CA, Collins R, Niesten PHM, Prince S, Kerr ID, Ford RC, Callaghan R. Improving the stability and function of purified ABCB1 and ABCA4: the influence of membrane lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:134-47. [PMID: 24036079 DOI: 10.1016/j.bbamem.2013.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 08/27/2013] [Accepted: 09/03/2013] [Indexed: 12/17/2022]
Abstract
ATP Binding Cassette (ABC) transporters play prominent roles in numerous cellular processes and many have been implicated in human diseases. Unfortunately, detailed mechanistic information on the majority of ABC transporters has not yet been elucidated. The slow rate of progress of molecular and high resolution structural studies may be attributed to the difficulty in the investigation of integral membrane proteins. These difficulties include the expression of functional, non-aggregated protein in heterologous systems. Furthermore, the extraction of membrane proteins from source material remains a major bottle-neck in the process since there are relatively few guidelines for selection of an appropriate detergent to achieve optimal extraction. Whilst affinity tag strategies have simplified the purification of membrane proteins; many challenges remain. For example, the chromatographic process and associated steps can rapidly lead to functional inactivation, random aggregation, or even precipitation of the target protein. Furthermore, optimisation of high yield and purity, does not guarantee successful structure determination. Based on this series of potential issues, any investigation into structure-function of membrane proteins requires a systematic evaluation of preparation quality. In particular, the evaluation should focus on function, homogeneity and mono-dispersity. The present investigation provides a detailed assessment of the quality of purified ATP Binding Cassette (ABC) transporters; namely ABCB1 (P-gp) and ABCA4 (ABCR). A number of suggestions are provided to facilitate the production of functional, homogeneous and mono-disperse preparations using the insect cell expression system. Finally, the ABCA4 samples have been used to provide structural insights into this essential photo-receptor cell protein.
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Affiliation(s)
- Naomi L Pollock
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
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42
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The importance of interactions with helix 5 in determining the efficacy of β-adrenoceptor ligands. Biochem Soc Trans 2013; 41:159-65. [PMID: 23356277 DOI: 10.1042/bst20120228] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Structures of the inactive state of the thermostabilized β1-adrenoceptor have been determined bound to eight different ligands, including full agonists, partial agonists, inverse agonists and biased agonists. Comparison of the structures shows distinct differences within the binding pocket that correlate with the pharmacological properties of the ligands. These data suggest that full agonists stabilize a structure with a contracted binding pocket and a rotamer change of serine (5.46) compared with when antagonists are bound. Inverse agonists may prevent both of these occurrences, whereas partial agonists stabilize a contraction of the binding pocket but not the rotamer change of serine (5.46). It is likely that subtle changes in the interactions between transmembrane helix 5 (H5) and H3/H4 on agonist binding promote the formation of the activated state.
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43
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Royle K, Kontoravdi C. A systems biology approach to optimising hosts for industrial protein production. Biotechnol Lett 2013; 35:1961-9. [DOI: 10.1007/s10529-013-1297-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 07/01/2013] [Indexed: 02/07/2023]
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44
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Backmark AE, Olivier N, Snijder A, Gordon E, Dekker N, Ferguson AD. Fluorescent probe for high-throughput screening of membrane protein expression. Protein Sci 2013; 22:1124-32. [PMID: 23776061 DOI: 10.1002/pro.2297] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 06/02/2013] [Accepted: 06/06/2013] [Indexed: 12/20/2022]
Abstract
Screening of protein variants requires specific detection methods to assay protein levels and stability in crude mixtures. Many strategies apply fluorescence-detection size-exclusion chromatography (FSEC) using green fluorescent protein (GFP) fusion proteins to qualitatively monitor expression, stability, and monodispersity. However, GFP fusion proteins have several important disadvantages; including false-positives, protein aggregation after proteolytic removal of GFP, and reductions in protein yields without the GFP fusion. Here we describe a FSEC screening strategy based on a fluorescent multivalent NTA probe that interacts with polyhistidine-tags on target proteins. This method overcomes the limitations of GFP fusion proteins, and can be used to rank protein production based on qualitative and quantitative parameters. Domain boundaries of the human G-protein coupled adenosine A2a receptor were readily identified from crude detergent-extracts of a library of construct variants transiently produced in suspension-adapted HEK293-6E cells. Well expressing clones of MraY, an important bacterial infection target, could be identified from a library of 24 orthologs. This probe provides a highly sensitive tool to detect target proteins to expression levels down to 0.02 mg/L in crude lysate, and requires minimal amounts of cell culture.
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Affiliation(s)
- A E Backmark
- Discovery Sciences, Reagents and Assay Development, AstraZeneca Pharmaceuticals, Mölndal, Sweden
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45
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Gorrec F. The current approach to initial crystallization screening of proteins is under-sampled. J Appl Crystallogr 2013; 46:795-797. [PMID: 23682195 PMCID: PMC3654315 DOI: 10.1107/s0021889813008030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/23/2013] [Indexed: 11/20/2022] Open
Abstract
Protein crystallization conditions that resulted in crystal structures published by scientists at the MRC Laboratory of Molecular Biology (MRC-LMB, Cambridge, UK) have been analysed. It was observed that the more often a crystallization reagent had been used to formulate the initial conditions, the more often it was found in the reported conditions that yielded diffraction quality crystals. The present analysis shows that, despite the broad variety of reagents, they have the same impact overall on the yield of crystal structures. More interestingly, the correlation implies that, although the initial crystallization screen may be considered very large, it is an under-sampled combinatorial approach.
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Affiliation(s)
- Fabrice Gorrec
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
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46
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Cordomí A, Gómez-Tamayo JC, Gigoux V, Fourmy D. Sulfur-containing amino acids in 7TMRs: molecular gears for pharmacology and function. Trends Pharmacol Sci 2013; 34:320-31. [PMID: 23611707 DOI: 10.1016/j.tips.2013.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/14/2013] [Accepted: 03/25/2013] [Indexed: 11/17/2022]
Abstract
Seven-transmembrane receptors (7TMRs) mediate the majority of physiological responses to hormones and neurotransmitters in higher organisms. Tertiary structure stability and activation of these versatile membrane proteins require formation or disruption of complex networks of well-recognized interactions (such as H-bonds, ionic, or aromatic-aromatic) but also of other type of interactions which have been less studied. In this review, we compile evidence from crystal structure, biophysical, and site-directed mutagenesis data that indicate or support the importance of interactions involving Met and Cys in 7TMRs in terms of pharmacology and function. We show examples of Met/Cys-aromatic and Met-Met interactions participating in ligand binding, in tuning the orientation of functionally important aromatic residues during activation or even in modulating the type of signaling response. Collectively, data presented enlarge the repertoire of interactions governing 7TMR functioning.
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Affiliation(s)
- Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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47
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Christopher JA, Brown J, Doré AS, Errey JC, Koglin M, Marshall FH, Myszka DG, Rich RL, Tate CG, Tehan B, Warne T, Congreve M. Biophysical fragment screening of the β1-adrenergic receptor: identification of high affinity arylpiperazine leads using structure-based drug design. J Med Chem 2013; 56:3446-55. [PMID: 23517028 PMCID: PMC3654563 DOI: 10.1021/jm400140q] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biophysical fragment screening of a thermostabilized β1-adrenergic receptor (β1AR) using surface plasmon resonance (SPR) enabled the identification of moderate affinity, high ligand efficiency (LE) arylpiperazine hits 7 and 8. Subsequent hit to lead follow-up confirmed the activity of the chemotype, and a structure-based design approach using protein-ligand crystal structures of the β1AR resulted in the identification of several fragments that bound with higher affinity, including indole 19 and quinoline 20. In the first example of GPCR crystallography with ligands derived from fragment screening, structures of the stabilized β1AR complexed with 19 and 20 were determined at resolutions of 2.8 and 2.7 Å, respectively.
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Affiliation(s)
- John A Christopher
- Heptares Therapeutics Ltd. , BioPark, Welwyn Garden City, Hertfordshire, AL7 3AX, U.K.
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Brueckner F, Piscitelli CL, Tsai CJ, Standfuss J, Deupi X, Schertler GFX. Structure of β-adrenergic receptors. Methods Enzymol 2013; 520:117-51. [PMID: 23332698 DOI: 10.1016/b978-0-12-391861-1.00006-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
β-Adrenergic receptors (βARs) control key physiological functions by transducing signals encoded in catecholamine hormones and neurotransmitters to activate intracellular signaling pathways. As members of the large family of G protein-coupled receptors (GPCRs), βARs have a seven-transmembrane helix topology and signal via G protein- and arrestin-dependent pathways. Until 2007, three-dimensional structural information of GPCRs activated by diffusible ligands, including βARs, was limited to homology models that used the related photoreceptor rhodopsin as a template. Over many years, several labs have developed strategies that have finally allowed the structures of the turkey β(1)AR and the human β(2)AR to be determined experimentally. The challenges to overcome included heterologous receptor overexpression, design of stabilized and crystallizable modified receptor constructs, ligand-affinity purification of active receptor and the development of novel techniques in crystallization and microcrystallography. The structures of βARs in complex with inverse agonists, antagonists, and agonists have revealed the binding mode of ligands with different efficacies, have allowed to obtain insights into ligand selectivity, and have provided better templates for drug design. Also, the structures of β(2)AR in complex with a G protein and a G protein-mimicking nanobody have provided important insights into the mechanism of receptor activation and G protein coupling. This chapter summarizes the strategies and methods that have been successfully applied to the structural studies of βARs. These are exemplified with detailed protocols toward the structure determination of stabilized turkey β(1)AR-ligand complexes. We also discuss the spectacular insights into adrenergic receptor function that were obtained from the structures.
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Affiliation(s)
- Florian Brueckner
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzerland
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49
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Andrews SP, Tehan B. Stabilised G protein-coupled receptors in structure-based drug design: a case study with adenosine A2A receptor. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20164j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The first example of structure-based drug design with stabilised GPCRs has enabled the identification of a preclinical candidate for the treatment of Parkinson's disease.
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Affiliation(s)
| | - Benjamin Tehan
- Heptares Therapeutics Limited
- BioPark
- Welwyn Garden City
- UK
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50
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Katritch V, Cherezov V, Stevens RC. Structure-function of the G protein-coupled receptor superfamily. Annu Rev Pharmacol Toxicol 2012; 53:531-56. [PMID: 23140243 DOI: 10.1146/annurev-pharmtox-032112-135923] [Citation(s) in RCA: 783] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
During the past few years, crystallography of G protein-coupled receptors (GPCRs) has experienced exponential growth, resulting in the determination of the structures of 16 distinct receptors-9 of them in 2012 alone. Including closely related subtype homology models, this coverage amounts to approximately 12% of the human GPCR superfamily. The adrenergic, rhodopsin, and adenosine receptor systems are also described by agonist-bound active-state structures, including a structure of the receptor-G protein complex for the β(2)-adrenergic receptor. Biochemical and biophysical techniques, such as nuclear magnetic resonance and hydrogen-deuterium exchange coupled with mass spectrometry, are providing complementary insights into ligand-dependent dynamic equilibrium between different functional states. Additional details revealed by high-resolution structures illustrate the receptors as allosteric machines that are controlled not only by ligands but also by ions, lipids, cholesterol, and water. This wealth of data is helping redefine our knowledge of how GPCRs recognize such a diverse array of ligands and how they transmit signals 30 angstroms across the cell membrane; it also is shedding light on a structural basis of GPCR allosteric modulation and biased signaling.
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Affiliation(s)
- Vsevolod Katritch
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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