1
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Weinstein JJ, Saikia C, Karbat I, Goldenzweig A, Reuveny E, Fleishman SJ. One-shot design elevates functional expression levels of a voltage-gated potassium channel. Protein Sci 2024; 33:e4995. [PMID: 38747377 PMCID: PMC11094769 DOI: 10.1002/pro.4995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/19/2024]
Abstract
Membrane proteins play critical physiological roles as receptors, channels, pumps, and transporters. Despite their importance, however, low expression levels often hamper the experimental characterization of membrane proteins. We present an automated and web-accessible design algorithm called mPROSS (https://mPROSS.weizmann.ac.il), which uses phylogenetic analysis and an atomistic potential, including an empirical lipophilicity scale, to improve native-state energy. As a stringent test, we apply mPROSS to the Kv1.2-Kv2.1 paddle chimera voltage-gated potassium channel. Four designs, encoding 9-26 mutations relative to the parental channel, were functional and maintained potassium-selective permeation and voltage dependence in Xenopus oocytes with up to 14-fold increase in whole-cell current densities. Additionally, single-channel recordings reveal no significant change in the channel-opening probability nor in unitary conductance, indicating that functional expression levels increase without impacting the activity profile of individual channels. Our results suggest that the expression levels of other dynamic channels and receptors may be enhanced through one-shot design calculations.
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Affiliation(s)
- Jonathan Jacob Weinstein
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Scala Biodesign LtdTel AvivIsrael
| | - Chandamita Saikia
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Institute for BiochemistryUniversity of LübeckLübeckGermany
| | - Izhar Karbat
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | | | - Eitan Reuveny
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
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2
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Jones AJY, Harman TH, Harris M, Lewis OE, Ladds G, Nietlispach D. Binding kinetics drive G protein subtype selectivity at the β 1-adrenergic receptor. Nat Commun 2024; 15:1334. [PMID: 38351103 PMCID: PMC10864275 DOI: 10.1038/s41467-024-45680-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
G protein-coupled receptors (GPCRs) bind to different G protein α-subtypes with varying degrees of selectivity. The mechanism by which GPCRs achieve this selectivity is still unclear. Using 13C methyl methionine and 19F NMR, we investigate the agonist-bound active state of β1AR and its ternary complexes with different G proteins in solution. We find the receptor in the ternary complexes adopts very similar conformations. In contrast, the full agonist-bound receptor active state assumes a conformation differing from previously characterised activation intermediates or from β1AR in ternary complexes. Assessing the kinetics of binding for the agonist-bound receptor with different G proteins, we find the increased affinity of β1AR for Gs results from its much faster association with the receptor. Consequently, we suggest a kinetic-driven selectivity gate between canonical and secondary coupling which arises from differential favourability of G protein binding to the agonist-bound receptor active state.
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Affiliation(s)
- Andrew J Y Jones
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Thomas H Harman
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Matthew Harris
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Oliver E Lewis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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3
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Hoare BL, Tippett DN, Kaur A, Cullum SA, Miljuš T, Koers EJ, Harwood CR, Dijon N, Holliday ND, Sykes DA, Veprintsev DB. ThermoBRET: A Ligand-Engagement Nanoscale Thermostability Assay Applied to GPCRs. Chembiochem 2024; 25:e202300459. [PMID: 37872746 DOI: 10.1002/cbic.202300459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Measurements of membrane protein thermostability reflect ligand binding. Current thermostability assays often require protein purification or rely on pre-existing radiolabelled or fluorescent ligands, limiting their application to established targets. Alternative methods, such as fluorescence-detection size exclusion chromatography thermal shift, detect protein aggregation but are not amenable to high-throughput screening. Here, we present a ThermoBRET method to quantify the relative thermostability of G protein coupled receptors (GPCRs), using cannabinoid receptors (CB1 and CB2 ) and the β2 -adrenoceptor (β2 AR) as model systems. ThermoBRET reports receptor unfolding, does not need labelled ligands and can be used with non-purified proteins. It uses Bioluminescence Resonance Energy Transfer (BRET) between Nanoluciferase (Nluc) and a thiol-reactive fluorescent dye that binds cysteines exposed by unfolding. We demonstrate that the melting point (Tm ) of Nluc-fused GPCRs can be determined in non-purified detergent solubilised membrane preparations or solubilised whole cells, revealing differences in thermostability for different solubilising conditions and in the presence of stabilising ligands. We extended the range of the assay by developing the thermostable tsNLuc by incorporating mutations from the fragments of split-Nluc (Tm of 87 °C versus 59 °C). ThermoBRET allows the determination of GPCR thermostability, which is useful for protein purification optimisation and drug discovery screening.
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Affiliation(s)
- Bradley L Hoare
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - David N Tippett
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Amandeep Kaur
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Sean A Cullum
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Tamara Miljuš
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Eline J Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicola Dijon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicholas D Holliday
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
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4
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Watanabe A, Nakajima A, Shiroishi M. Recovery of the histamine H 3 receptor activity lost in yeast cells through error-prone PCR and in vivo selection. Sci Rep 2023; 13:16127. [PMID: 37752220 PMCID: PMC10522717 DOI: 10.1038/s41598-023-43389-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest protein family in humans and are important drug targets. Yeast, especially Saccharomyces cerevisiae, is a useful host for modifying the function and stability of GPCRs through protein engineering, which is advantageous for mammalian cells. When GPCRs are expressed in yeast, their function is often impaired. In this study, we performed random mutagenesis using error-prone PCR and then an in vivo screening to obtain mutants that recovered the activity of the human histamine H3 receptor (H3R), which loses its signaling function when expressed in yeast. Four mutations with recovered activity were identified after screening. Three of the mutations were identified near the DRY and NPxxY motifs of H3R, which are important for activation and are commonly found in class A GPCRs. The mutants responded exclusively to the yeast YB1 strain harboring Gi-chimera proteins, showing retention of G protein specificity. Analysis of one of the mutants with recovered activity, C415R, revealed that it maintained its ligand-binding characteristics. The strategy used in this study may enable the recovery of the activity of other GPCRs that do not function in S. cerevisiae and may be useful in creating GPCRs mutants stabilized in their active conformations.
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Affiliation(s)
- Ayami Watanabe
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Ami Nakajima
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Mitsunori Shiroishi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan.
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5
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Amer M, Leka O, Jasko P, Frey D, Li X, Kammerer RA. A coiled-coil-based design strategy for the thermostabilization of G-protein-coupled receptors. Sci Rep 2023; 13:10159. [PMID: 37349348 PMCID: PMC10287670 DOI: 10.1038/s41598-023-36855-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/11/2023] [Indexed: 06/24/2023] Open
Abstract
Structure elucidation of inactive-state GPCRs still mostly relies on X-ray crystallography. The major goal of our work was to create a new GPCR tool that would provide receptor stability and additional soluble surface for crystallization. Towards this aim, we selected the two-stranded antiparallel coiled coil as a domain fold that satisfies both criteria. A selection of antiparallel coiled coils was used for structure-guided substitution of intracellular loop 3 of the β3 adrenergic receptor. Unexpectedly, only the two GPCR variants containing thermostable coiled coils were expressed. We showed that one GPCR chimera is stable upon purification in detergent, retains ligand-binding properties, and can be crystallized. However, the quality of the crystals was not suitable for structure determination. By using two other examples, 5HTR2C and α2BAR, we demonstrate that our approach is generally suitable for the stabilization of GPCRs. To provide additional surface for promoting crystal contacts, we replaced in a structure-based approach the loop connecting the antiparallel coiled coil by T4L. We found that the engineered GPCR is even more stable than the coiled-coil variant. Negative-staining TEM revealed a homogeneous distribution of particles, indicating that coiled-coil-T4L receptor variants might also be promising candidate proteins for structure elucidation by cryo-EM. Our approach should be of interest for applications that benefit from stable GPCRs.
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Affiliation(s)
- Marwa Amer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Oneda Leka
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Piotr Jasko
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Daniel Frey
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Xiaodan Li
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland.
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6
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Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W. Conformational Dynamics of the Activated GLP-1 Receptor-G s Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling. ACS CENTRAL SCIENCE 2023; 9:992-1007. [PMID: 37252352 PMCID: PMC10214531 DOI: 10.1021/acscentsci.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Indexed: 05/31/2023]
Abstract
Despite advances in characterizing the structures and functions of G protein-coupled receptors (GPCRs), our understanding of GPCR activation and signaling is still limited by the lack of information on conformational dynamics. It is particularly challenging to study the dynamics of GPCR complexes with their signaling partners because of their transient nature and low stability. Here, by combining cross-linking mass spectrometry (CLMS) with integrative structure modeling, we map the conformational ensemble of an activated GPCR-G protein complex at near-atomic resolution. The integrative structures describe heterogeneous conformations for a high number of potential alternative active states of the GLP-1 receptor-Gs complex. These structures show marked differences from the previously determined cryo-EM structure, especially at the receptor-Gs interface and in the interior of the Gs heterotrimer. Alanine-scanning mutagenesis coupled with pharmacological assays validates the functional significance of 24 interface residue contacts only observed in the integrative structures, yet absent in the cryo-EM structure. Through the integration of spatial connectivity data from CLMS with structure modeling, our study provides a new approach that is generalizable to characterizing the conformational dynamics of GPCR signaling complexes.
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Affiliation(s)
- Shijia Yuan
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Lisha Xia
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Wang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Wu
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Bingjie Zhang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Chen Pan
- National
Facility for Protein Science in Shanghai, Shanghai Advanced Research
Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Zhiran Fan
- Biocreater
(WuHan) Biotechnology Co., Ltd, Wuhan 430075, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Department of
Chemical Biology, College of Chemistry and Molecular Engineering,
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Raymond C. Stevens
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Andrej Sali
- Quantitative
Biosciences Institute, University of California,
San Francisco, San Francisco, California 94143, United States
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, United States
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, San
Francisco, California 94143, United States
| | - Liping Sun
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Shui
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
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7
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Ma C, Gong C. Considerations in production of the prokaryotic ZIP family transporters for structural and functional studies. Methods Enzymol 2023; 687:1-30. [PMID: 37666628 DOI: 10.1016/bs.mie.2023.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Zinc ions play essential roles as components of enzymes and many other important biomolecules, and are associated with numerous diseases. The uptake of Zn2+ and other metal ions require a widely distributed transporter protein family called Zrt/Irt-like Proteins (ZIP family), the majority members of which tend to have eight transmembrane helices with both N- and C- termini located on the extracellular or periplasmic side. Their small sizes and dynamic conformations bring many difficulties in their production for structural studies either by crystallography or Cryo-EM. Here, we summarize the problems that may encounter at the various steps of processing the ZIP proteins from gene to structural and functional studies, and provide some solutions and examples from our and other labs for the cloning, expression, purification, stability screening, metal ion transport assays and structural studies of prokaryotic ZIP family transporters using Escherichia coli as a heterologous host.
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Affiliation(s)
- Cheng Ma
- Protein Facility, Zhejiang University School of Medicine, Hangzhou, P.R. China; The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, P.R. China.
| | - Caixia Gong
- The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, P.R. China; Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-chemical Injury Diseases, Hangzhou, P.R. China.
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8
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Mattheisen JM, Limberakis C, Ruggeri RB, Dowling MS, Am Ende CW, Ceraudo E, Huber T, McClendon CL, Sakmar TP. Bioorthogonal Tethering Enhances Drug Fragment Affinity for G Protein-Coupled Receptors in Live Cells. J Am Chem Soc 2023; 145:11173-11184. [PMID: 37116188 DOI: 10.1021/jacs.3c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
G protein-coupled receptors (GPCRs) modulate diverse cellular signaling pathways and are important drug targets. Despite the availability of high-resolution structures, the discovery of allosteric modulators remains challenging due to the dynamic nature of GPCRs in native membranes. We developed a strategy to covalently tether drug fragments adjacent to allosteric sites in GPCRs to enhance their potency and enable fragment-based drug screening in cell-based systems. We employed genetic code expansion to site-specifically introduce noncanonical amino acids with reactive groups in C-C chemokine receptor 5 (CCR5) near an allosteric binding site for the drug maraviroc. We then used molecular dynamics simulations to design heterobifunctional maraviroc analogues consisting of a drug fragment connected by a flexible linker to a reactive moiety capable of undergoing a bioorthogonal coupling reaction. We synthesized a library of these analogues and employed the bioorthogonal inverse electron demand Diels-Alder reaction to couple the analogues to the engineered CCR5 in live cells, which were then assayed using cell-based signaling assays. Tetherable low-affinity maraviroc fragments displayed an increase in potency for CCR5 engineered with reactive unnatural amino acids that were adjacent to the maraviroc binding site. The strategy we describe to tether novel drug fragments to GPCRs should prove useful to probe allosteric or cryptic binding site functionality in fragment-based GPCR-targeted drug discovery.
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Affiliation(s)
- Jordan M Mattheisen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
| | - Chris Limberakis
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Roger B Ruggeri
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Matthew S Dowling
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Christopher W Am Ende
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Emilie Ceraudo
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
| | - Christopher L McClendon
- Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts 02139, United States
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
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9
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Ghani L, Zhang X, Munk CF, Hariharan P, Lan B, Yun HS, Byrne B, Guan L, Loland CJ, Liu X, Chae PS. Tris(hydroxymethyl)aminomethane Linker-Bearing Triazine-Based Triglucosides for Solubilization and Stabilization of Membrane Proteins. Bioconjug Chem 2023; 34:739-747. [PMID: 36919927 PMCID: PMC10145683 DOI: 10.1021/acs.bioconjchem.3c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/21/2023] [Indexed: 03/16/2023]
Abstract
High-resolution membrane protein structures are essential for a fundamental understanding of the molecular basis of diverse cellular processes and for drug discovery. Detergents are widely used to extract membrane-spanning proteins from membranes and maintain them in a functional state for downstream characterization. Due to limited long-term stability of membrane proteins encapsulated in conventional detergents, development of novel agents is required to facilitate membrane protein structural study. In the current study, we designed and synthesized tris(hydroxymethyl)aminomethane linker-bearing triazine-based triglucosides (TTGs) for solubilization and stabilization of membrane proteins. When these glucoside detergents were evaluated for four membrane proteins including two G protein-coupled receptors, a few TTGs including TTG-C10 and TTG-C11 displayed markedly enhanced behaviors toward membrane protein stability relative to two maltoside detergents [DDM (n-dodecyl-β-d-maltoside) and LMNG (lauryl maltose neopentyl glycol)]. This is a notable feature of the TTGs as glucoside detergents tend to be inferior to maltoside detergents at stabilizing membrane proteins. The favorable behavior of the TTGs for membrane protein stability is likely due to the high hydrophobicity of the lipophilic groups, an optimal range of hydrophilic-lipophilic balance, and the absence of cis-trans isomerism.
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Affiliation(s)
- Lubna Ghani
- Department
of Bionano Engineering, Hanyang University, Ansan 155-88, South Korea
| | - Xiang Zhang
- Tsinghua-Peking
Center for Life Sciences, Beijing Frontier Research Center for Biological
Structure, Beijing Advanced Innovation Center for Structural Biology,
School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Chastine F. Munk
- Department
of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Parameswaran Hariharan
- Department
of Cell Physiology and Molecular Biophysics, Center for Membrane Protein
Research, School of Medicine, Texas Tech
University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Baoliang Lan
- Tsinghua-Peking
Center for Life Sciences, Beijing Frontier Research Center for Biological
Structure, Beijing Advanced Innovation Center for Structural Biology,
School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Hong Sik Yun
- Department
of Bionano Engineering, Hanyang University, Ansan 155-88, South Korea
| | - Bernadette Byrne
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Lan Guan
- Department
of Cell Physiology and Molecular Biophysics, Center for Membrane Protein
Research, School of Medicine, Texas Tech
University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Claus J. Loland
- Department
of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Xiangyu Liu
- Tsinghua-Peking
Center for Life Sciences, Beijing Frontier Research Center for Biological
Structure, Beijing Advanced Innovation Center for Structural Biology,
School of Medicine, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Pil Seok Chae
- Department
of Bionano Engineering, Hanyang University, Ansan 155-88, South Korea
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10
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- 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.
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11
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Sugaya K, Yasuda S, Sato S, Sisi C, Yamamoto T, Umeno D, Matsuura T, Hayashi T, Ogasawara S, Kinoshita M, Murata T. A methodology for creating thermostabilized mutants of G‐protein coupled receptors by combining statistical thermodynamics and evolutionary molecular engineering. Protein Sci 2022. [DOI: 10.1002/pro.4404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kanna Sugaya
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
| | - Shingo Sato
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Chen Sisi
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
| | - Taisei Yamamoto
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Daisuke Umeno
- Department of Applied Chemistry Waseda University Tokyo Japan
| | - Tomoaki Matsuura
- Earth‐Life Science Institute Tokyo Institute of Technology Tokyo Japan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering Niigata University Niigata Japan
- Institute of Advanced Energy Kyoto University Kyoto Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
- Institute for Advanced Academic Research Chiba University Chiba Japan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Institute of Advanced Energy Kyoto University Kyoto Japan
- Center for the Promotion of Interdisciplinary Education and Research Kyoto University Kyoto‐shi Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
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12
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Köck Z, Ermel U, Martin J, Morgner N, Achilleas Frangakis S, Dötsch V, Hilger D, Bernhard F. Biochemical characterization of cell-free synthesized human β 1 adrenergic receptor cotranslationally inserted into nanodiscs. J Mol Biol 2022; 434:167687. [PMID: 35717996 DOI: 10.1016/j.jmb.2022.167687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022]
Abstract
Cell-free expression enables direct cotranslational insertion of G protein coupled receptors (GPCRs) and other membrane proteins into the defined membrane environments of nanodiscs. This technique avoids GPCR contacts with detergents and allows rapid identification of lipid effects on GPCR function as well as fast screening of receptor derivatives. Critical steps of conventional GPCR preparation from cellular membranes followed by detergent-based reconstitution into nanodisc membranes are thus eliminated. We report the efficient cotranslational insertion of full-length human β1-adrenergic receptor and of a truncated derivative into preformed nanodisc membranes. Their biochemical characterization revealed significant differences in lipid requirements, dimer formation and ligand binding activity. The truncated receptor showed a higher affinity to most tested ligands, in particular in presence of choline-containing lipids. However, introducing the naturally occurring G389R polymorphism in the full-length receptor resulted into an increased affinity to the antagonists alprenolol and carvedilol. Receptor quality was generally improved by coexpression with the agonist isoproterenol and the percentage of the ligand binding active fraction was twofold increased. Specific coupling of full-length and truncated human receptors in nanodisc membranes to Mini-Gαs protein as well as to purified Gs heterotrimer could be demonstrated and homogeneity of purified GPCR/Gs protein complexes in nanodiscs was demonstrated by negative stain single particle analysis.
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Affiliation(s)
- Zoe Köck
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main
| | - Utz Ermel
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University of Frankfurt/Main
| | - Janosch Martin
- Institute of Physical and Theoretical Chemistry, Goethe University of Frankfurt/Main
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University of Frankfurt/Main
| | - S Achilleas Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University of Frankfurt/Main
| | - Volker Dötsch
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main
| | - Daniel Hilger
- Department of Pharmaceutical Chemistry, Philipps-University Marburg
| | - Frank Bernhard
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main.
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13
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Shepherd C, Robinson S, Berizzi A, Thompson LEJ, Bird L, Culurgioni S, Varzandeh S, Rawlins PB, Olsen RHJ, Navratilova IH. Surface Plasmon Resonance Screening to Identify Active and Selective Adenosine Receptor Binding Fragments. ACS Med Chem Lett 2022; 13:1172-1181. [DOI: 10.1021/acsmedchemlett.2c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Claire Shepherd
- University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Sean Robinson
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Alice Berizzi
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Laura E. J. Thompson
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Louise Bird
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Simone Culurgioni
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Simon Varzandeh
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Philip B. Rawlins
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Reid H. J. Olsen
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Iva Hopkins Navratilova
- University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
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14
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Yeast-based directed-evolution for high-throughput structural stabilization of G protein-coupled receptors (GPCRs). Sci Rep 2022; 12:8657. [PMID: 35606532 PMCID: PMC9126886 DOI: 10.1038/s41598-022-12731-2] [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: 01/24/2022] [Accepted: 05/10/2022] [Indexed: 11/08/2022] Open
Abstract
The immense potential of G protein-coupled receptors (GPCRs) as targets for drug discovery is not fully realized due to the enormous difficulties associated with structure elucidation of these profoundly unstable membrane proteins. The existing methods of GPCR stability-engineering are cumbersome and low-throughput; in addition, the scope of GPCRs that could benefit from these techniques is limited. Here, we present a yeast-based screening platform for a single-step isolation of GRCR variants stable in the presence of short-chain detergents, a feature essential for their successful crystallization using vapor diffusion method. The yeast detergent-resistant cell wall presents a unique opportunity for compartmentalization, to physically link the receptor's phenotype to its encoding DNA, and thus enable discovery of stable GPCR variants with unprecedent efficiency. The scope of mutations identified by the method reveals a surprising amenability of the GPCR scaffold to stabilization, and suggests an intriguing possibility of amending the stability properties of GPCR by varying the structural status of the C-terminus.
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15
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Lee HJ, Ehsan M, Zhang X, Katsube S, Munk CF, Wang H, Ahmed W, Kumar A, Byrne B, Loland CJ, Guan L, Liu X, Chae PS. Development of 1,3-acetonedicarboxylate-derived glucoside amphiphiles (ACAs) for membrane protein study. Chem Sci 2022; 13:5750-5759. [PMID: 35694361 PMCID: PMC9116450 DOI: 10.1039/d2sc00539e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/02/2022] [Indexed: 12/31/2022] Open
Abstract
Detergents are extensively used for membrane protein manipulation. Membrane proteins solubilized in conventional detergents are prone to denaturation and aggregation, rendering downstream characterization of these bio-macromolecules difficult. Although many amphiphiles have been developed to overcome the limited efficacy of conventional detergents for protein stabilization, only a handful of novel detergents have so far proved useful for membrane protein structural studies. Here, we introduce 1,3-acetonedicarboxylate-derived amphiphiles (ACAs) containing three glucose units and two alkyl chains as head and tail groups, respectively. The ACAs incorporate two different patterns of alkyl chain attachment to the core detergent unit, generating two sets of amphiphiles: ACA-As (asymmetrically alkylated) and ACA-Ss (symmetrically alkylated). The difference in the attachment pattern of the detergent alkyl chains resulted in minor variation in detergent properties such as micelle size, critical micelle concentration, and detergent behaviors toward membrane protein extraction and stabilization. In contrast, the impact of the detergent alkyl chain length on protein stability was marked. The two C11 variants (ACA-AC11 and ACA-SC11) were most effective at stabilizing the tested membrane proteins. The current study not only introduces new glucosides as tools for membrane protein study, but also provides detergent structure–property relationships important for future design of novel amphiphiles. Newly developed amphiphiles, designated ACAs, are not only efficient at extracting G protein-coupled receptors from the membranes, but also conferred enhanced stability to the receptors compared to the gold standards (DDM and LMNG).![]()
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Affiliation(s)
- Ho Jin Lee
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
| | - Muhammad Ehsan
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
| | - Xiang Zhang
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock TX 79430 USA
| | - Chastine F Munk
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University California 94305 USA
| | - Waqar Ahmed
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
| | - Ashwani Kumar
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock TX 79430 USA
| | - Xiangyu Liu
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University Ansan 155-88 Korea
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16
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Ghani L, Kim S, Wang H, Lee HS, Mortensen JS, Katsube S, Du Y, Sadaf A, Ahmed W, Byrne B, Guan L, Loland CJ, Kobilka BK, Im W, Chae PS. Foldable Detergents for Membrane Protein Study: Importance of Detergent Core Flexibility in Protein Stabilization. Chemistry 2022; 28:e202200116. [PMID: 35238091 PMCID: PMC9007890 DOI: 10.1002/chem.202200116] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 12/30/2022]
Abstract
Membrane proteins are of biological and pharmaceutical significance. However, their structural study is extremely challenging mainly due to the fact that only a small number of chemical tools are suitable for stabilizing membrane proteins in solution. Detergents are widely used in membrane protein study, but conventional detergents are generally poor at stabilizing challenging membrane proteins such as G protein-coupled receptors and protein complexes. In the current study, we prepared tandem triazine-based maltosides (TZMs) with two amphiphilic triazine units connected by different diamine linkers, hydrazine (TZM-Hs) and 1,2-ethylenediamine (TZM-Es). These TZMs were consistently superior to a gold standard detergent (DDM) in terms of stabilizing a few membrane proteins. In addition, the TZM-Es containing a long linker showed more general protein stabilization efficacy with multiple membrane proteins than the TZM-Hs containing a short linker. This result indicates that introduction of the flexible1,2-ethylenediamine linker between two rigid triazine rings enables the TZM-Es to fold into favourable conformations in order to promote membrane protein stability. The novel concept of detergent foldability introduced in the current study has potential in rational detergent design and membrane protein applications.
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Affiliation(s)
- Lubna Ghani
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 024-55, South Korea
| | - Haoqing Wang
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Hyun Sung Lee
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.,Current address: School of Life and Health Sciences, Chinese University of Hong Kong, 2001 Longxiang Ave, Shenzhen, Guangdong, 518172, China
| | - Aiman Sadaf
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Waqar Ahmed
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Pil Seok Chae
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
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17
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Schöppe J, Ehrenmann J, Waltenspühl Y, Plückthun A. Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP. Nat Protoc 2022; 17:698-726. [PMID: 35140409 DOI: 10.1038/s41596-021-00660-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022]
Abstract
Structural studies of G-protein-coupled receptors (GPCRs) are often limited by difficulties in obtaining well-diffracting crystals suitable for high-resolution structure determination. During the past decade, crystallization in lipidic cubic phase (LCP) has become the most successful and widely used technique for obtaining such crystals. Despite often intense efforts, many GPCRs remain refractory to crystallization, even if receptors can be purified in sufficient amounts. To address this issue, we have developed a highly efficient screening and stabilization strategy for GPCRs, based on a fluorescence thermal stability assay readout, which seems to correlate particularly well with those GPCR constructs that remain native during incorporation into the LCP. Detailed protocols are provided for rapid and cost-efficient mutant and construct generation using sequence- and ligation-independent cloning, high-throughput magnetic bead-based protein purification from small-scale expressions in mammalian cells, the screening and optimal combination of mutations for increased receptor thermostability and the rapid identification of suitable chimeric fusion protein constructs for successful crystallization in LCP. We exemplify the method on three receptors from two different classes: the neurokinin 1 receptor, the oxytocin receptor and the parathyroid hormone 1 receptor.
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Affiliation(s)
- Jendrik Schöppe
- Department of Biochemistry, University of Zürich, Zurich, Switzerland.,Novo Nordisk A/S, Måløv, Denmark
| | - Janosch Ehrenmann
- Department of Biochemistry, University of Zürich, Zurich, Switzerland.,leadXpro AG, PARK InnovAARE, Villigen, Switzerland
| | - Yann Waltenspühl
- Department of Biochemistry, University of Zürich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zurich, Switzerland.
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18
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19
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Ehsan M, Wang H, Katsube S, Munk CF, Du Y, Youn T, Yoon S, Byrne B, Loland CJ, Guan L, Kobilka BK, Chae PS. Glyco-steroidal amphiphiles (GSAs) for membrane protein structural study. Chembiochem 2022; 23:e202200027. [PMID: 35129249 PMCID: PMC8986615 DOI: 10.1002/cbic.202200027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/05/2022] [Indexed: 11/08/2022]
Abstract
Integral membrane proteins pose considerable challenges to high resolution structural analysis. Maintaining membrane proteins in their native state during protein isolation is essential for structural study of these bio-macromolecules. Detergents are the most commonly used amphiphilic compounds for stabilizing membrane proteins in solution outside a lipid bilayer. We previously introduced a glyco-diosgenin (GDN) detergent that was shown to be highly effective at stabilizing a wide range of membrane proteins. This steroidal detergent has additionally gained attention due to its compatibility with membrane protein structure study via cryo-EM. However, synthetic inconvenience limits widespread use of GDN in membrane protein study. To improve its synthetic accessibility and to further enhance detergent efficacy for protein stabilization, we designed a new class of glyco-steroid-based detergents using three steroid units: cholestanol, cholesterol and diosgenin. These new detergents were efficiently prepared and showed marked efficacy for protein stabilization in evaluation with a few model membrane proteins including two G protein-coupled receptors. Some new agents were not only superior to a gold standard detergent, DDM, but were also more effective than the original GDN at preserving protein integrity long term. These agents represent valuable alternatives to GDN, and are likely to facilitate structural determination of challenging membrane proteins.
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Affiliation(s)
- Muhammad Ehsan
- Hanyang University, Department of Bionano Engineering, KOREA, REPUBLIC OF
| | - Haoqing Wang
- Stanford University, Department of Molecular and Cellular Physiology, UNITED STATES
| | - Satoshi Katsube
- Texas Tech University, Department of Cell Physiology and Molecular Biophysics, UNITED STATES
| | - Chastine F Munk
- University of Copenhagen: Kobenhavns Universitet, Department of Neuroscience, DENMARK
| | - Yang Du
- Stanford University, Department of Molecular and Cellular Physiology, UNITED STATES
| | - Taeyeol Youn
- Hanyang University, Department of Bionano Engineering, KOREA, REPUBLIC OF
| | - Soyoung Yoon
- Hanyang University, Department of Bionano Engineering, KOREA, REPUBLIC OF
| | - Bernadette Byrne
- Imperial College London, Department of Life Sciences, UNITED KINGDOM
| | - Claus J Loland
- University of Copenhagen: Kobenhavns Universitet, Department of Neurosciences, DENMARK
| | - Lan Guan
- Texas Tech University, Department of Cell Physiology and Molecular Biophysics, UNITED STATES
| | - Brian K Kobilka
- Stanford University, Department of Molecular and Cellular Physiology, UNITED STATES
| | - Pil Seok Chae
- Hanyang University, Department of Bionano Engineering, 55 Hanyangdaehak-ro, 426-791, Ansan, KOREA, REPUBLIC OF
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20
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Chandler B, Todd L, Smith SO. Magic angle spinning NMR of G protein-coupled receptors. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:25-43. [PMID: 35282868 PMCID: PMC10718405 DOI: 10.1016/j.pnmrs.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
G protein-coupled receptors (GPCRs) have a simple seven transmembrane helix architecture which has evolved to recognize a diverse number of chemical signals. The more than 800 GPCRs encoded in the human genome function as receptors for vision, smell and taste, and mediate key physiological processes. Consequently, these receptors are a major target for pharmaceuticals. Protein crystallography and electron cryo-microscopy have provided high resolution structures of many GPCRs in both active and inactive conformations. However, these structures have not sparked a surge in rational drug design, in part because GPCRs are inherently dynamic and the structural changes induced by ligand or drug binding to stabilize inactive or active conformations are often subtle rearrangements in packing or hydrogen-bonding interactions. NMR spectroscopy provides a sensitive probe of local structure and dynamics at specific sites within these receptors as well as global changes in receptor structure and dynamics. These methods can also capture intermediate states and conformations with low populations that provide insights into the activation pathways. We review the use of solid-state magic angle spinning NMR to address the structure and activation mechanisms of GPCRs. The focus is on the large and diverse class A family of receptors. We highlight three specific class A GPCRs in order to illustrate how solid-state, as well as solution-state, NMR spectroscopy can answer questions in the field involving how different GPCR classes and subfamilies are activated by their associated ligands, and how small molecule drugs can modulate GPCR activation.
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Affiliation(s)
- Bianca Chandler
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Lauren Todd
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
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21
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Liu S, Li S, Krezel AM, Li W. Stabilization and structure determination of integral membrane proteins by termini restraining. Nat Protoc 2022; 17:540-565. [PMID: 35039670 DOI: 10.1038/s41596-021-00656-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Integral membrane proteins isolated from cellular environment often lose activity and native conformation required for functional analyses and structural studies. Even in their native state, they lack sufficient surfaces to form crystal contacts. Furthermore, most of them are too small for cryogenic electron microscopy detection and too big for solution NMR. To overcome these difficulties, we recently developed a strategy to stabilize the folded state of membrane proteins by restraining their two termini with a self-assembling protein coupler. The termini-restrained membrane proteins from distinct functional families retain their activities and show increased stability and yield. This strategy enables their structure determination at near-atomic resolution by facilitating the entire pipeline from crystallization, crystal identification, diffraction enhancement and phase determination, to electron density improvement. Furthermore, stabilization of membrane proteins enables their biochemical and biophysical characterization. Here we present the protocol of membrane protein engineering (2 weeks), quality assessment (1-2 weeks), protein production (1-6 weeks), crystallization (1-2 weeks), diffraction improvement (1-3 months) and crystallographic data analysis (1 week). This protocol is intended not only for structural biologists, but also for biochemists, biophysicists and pharmaceutical scientists whose research focuses on membrane proteins.
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Affiliation(s)
- Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Shuang Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrzej M Krezel
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
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22
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Yasuda S, Akiyama T, Kojima K, Ueta T, Hayashi T, Ogasawara S, Nagatoishi S, Tsumoto K, Kunishima N, Sudo Y, Kinoshita M, Murata T. Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations. J Phys Chem B 2022; 126:1004-1015. [PMID: 35089040 DOI: 10.1021/acs.jpcb.1c08684] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We have developed a methodology for identifying further thermostabilizing mutations for an intrinsically thermostable membrane protein. The methodology comprises the following steps: (1) identifying thermostabilizing single mutations (TSSMs) for residues in the transmembrane region using our physics-based method; (2) identifying TSSMs for residues in the extracellular and intracellular regions, which are in aqueous environment, using an empirical force field FoldX; and (3) combining the TSSMs identified in steps (1) and (2) to construct multiple mutations. The methodology is illustrated for thermophilic rhodopsin whose apparent midpoint temperature of thermal denaturation Tm is ∼91.8 °C. The TSSMs previously identified in step (1) were F90K, F90R, and Y91I with ΔTm ∼5.6, ∼5.5, and ∼2.9 °C, respectively, and those in step (2) were V79K, T114D, A115P, and A116E with ΔTm ∼2.7, ∼4.2, ∼2.6, and ∼2.3 °C, respectively (ΔTm denotes the increase in Tm). In this study, we construct triple and quadruple mutants, F90K+Y91I+T114D and F90K+Y91I+V79K+T114D. The values of ΔTm for these multiple mutants are ∼11.4 and ∼13.5 °C, respectively. Tm of the quadruple mutant (∼105.3 °C) establishes a new record in a class of outward proton pumping rhodopsins. It is higher than Tm of Rubrobacter xylanophilus rhodopsin (∼100.8 °C) that was the most thermostable in the class before this study.
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Affiliation(s)
- Satoshi Yasuda
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.,Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Tomoki Akiyama
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Tetsuya Ueta
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan.,Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Satoshi Ogasawara
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.,Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Naoki Kunishima
- RIKEN RSC-Rigaku Collaboration Center, RIKEN SPring-8 Center, Sayo-gun, Hyogo 679-5165, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Masahiro Kinoshita
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.,Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.,Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takeshi Murata
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.,Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
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23
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Mitsumoto M, Sugaya K, Kazama K, Nakano R, Kosugi T, Murata T, Koga N. State-Targeting Stabilization of Adenosine A 2A Receptor by Fusing a Custom-Made De Novo Designed α-Helical Protein. Int J Mol Sci 2021; 22:12906. [PMID: 34884716 PMCID: PMC8657880 DOI: 10.3390/ijms222312906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 01/03/2023] Open
Abstract
G-protein coupled receptors (GPCRs) are known for their low stability and large conformational changes upon transitions between multiple states. A widely used method for stabilizing these receptors is to make chimeric receptors by fusing soluble proteins (i.e., fusion partner proteins) into the intracellular loop 3 (ICL3) connecting the transmembrane helices 5 and 6 (TM5 and TM6). However, this fusion approach requires experimental trial and error to identify appropriate soluble proteins, residue positions, and linker lengths for making the fusion. Moreover, this approach has not provided state-targeting stabilization of GPCRs. Here, to rationally stabilize a class A GPCR, adenosine A2A receptor (A2AR) in a target state, we carried out the custom-made de novo design of α-helical fusion partner proteins, which can fix the conformation of TM5 and TM6 to that in an inactive state of A2AR through straight helical connections without any kinks or intervening loops. The chimeric A2AR fused with one of the designs (FiX1) exhibited increased thermal stability. Moreover, compared with the wild type, the binding affinity of the chimera against the agonist NECA was significantly decreased, whereas that against the inverse agonist ZM241385 was similar, indicating that the inactive state was selectively stabilized. Our strategy contributes to the rational state-targeting stabilization of GPCRs.
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Affiliation(s)
- Masaya Mitsumoto
- Department of Structural Molecular Science, School of Physical Sciences, SOKENDAI, The Graduate University for Advanced Studies, Shonan Village, Hayama 240-0193, Kanagawa, Japan; (M.M.); (T.K.)
- Research Center of Integrative Molecular Systems, Institute for Molecular Science (IMS), National Institutes of Natural Sciences (NINS), Okazaki 444-8585, Aichi, Japan
| | - Kanna Sugaya
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (K.S.); (K.K.); (R.N.)
| | - Kazuki Kazama
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (K.S.); (K.K.); (R.N.)
| | - Ryosuke Nakano
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (K.S.); (K.K.); (R.N.)
| | - Takahiro Kosugi
- Department of Structural Molecular Science, School of Physical Sciences, SOKENDAI, The Graduate University for Advanced Studies, Shonan Village, Hayama 240-0193, Kanagawa, Japan; (M.M.); (T.K.)
- Research Center of Integrative Molecular Systems, Institute for Molecular Science (IMS), National Institutes of Natural Sciences (NINS), Okazaki 444-8585, Aichi, Japan
- Protein Design Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), Okazaki 444-8585, Aichi, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (K.S.); (K.K.); (R.N.)
- Membrane Protein Research Center, Chiba University, Chiba 263-8522, Japan
| | - Nobuyasu Koga
- Department of Structural Molecular Science, School of Physical Sciences, SOKENDAI, The Graduate University for Advanced Studies, Shonan Village, Hayama 240-0193, Kanagawa, Japan; (M.M.); (T.K.)
- Research Center of Integrative Molecular Systems, Institute for Molecular Science (IMS), National Institutes of Natural Sciences (NINS), Okazaki 444-8585, Aichi, Japan
- Protein Design Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), Okazaki 444-8585, Aichi, Japan
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24
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van Aalst E, Wylie BJ. Cholesterol Is a Dose-Dependent Positive Allosteric Modulator of CCR3 Ligand Affinity and G Protein Coupling. Front Mol Biosci 2021; 8:724603. [PMID: 34490352 PMCID: PMC8417553 DOI: 10.3389/fmolb.2021.724603] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 07/14/2021] [Indexed: 01/14/2023] Open
Abstract
Cholesterol as an allosteric modulator of G protein-coupled receptor (GPCR) function is well documented. This quintessential mammalian lipid facilitates receptor–ligand interactions and multimerization states. Functionally, this introduces a complicated mechanism for the homeostatic modulation of GPCR signaling. Chemokine receptors are Class A GPCRs responsible for immune cell trafficking through the binding of endogenous peptide ligands. CCR3 is a CC motif chemokine receptor expressed by eosinophils and basophils. It traffics these cells by transducing the signal stimulated by the CC motif chemokine primary messengers 11, 24, and 26. These behaviors are close to the human immunoresponse. Thus, CCR3 is implicated in cancer metastasis and inflammatory conditions. However, there is a paucity of experimental evidence linking the functional states of CCR3 to the molecular mechanisms of cholesterol–receptor cooperativity. In this vein, we present a means to combine codon harmonization and a maltose-binding protein fusion tag to produce CCR3 from E. coli. This technique yields ∼2.6 mg of functional GPCR per liter of minimal media. We leveraged this protein production capability to investigate the effects of cholesterol on CCR3 function in vitro. We found that affinity for the endogenous ligand CCL11 increases in a dose-dependent manner with cholesterol concentration in both styrene:maleic acid lipid particles (SMALPs) and proteoliposomes. This heightened receptor activation directly translates to increased signal transduction as measured by the GTPase activity of the bound G-protein α inhibitory subunit 3 (Gαi3). This work represents a critical step forward in understanding the role of cholesterol-GPCR allostery in regulation of signal transduction.
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Affiliation(s)
- Evan van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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25
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Bibbe JM, Vriend G. Motions around conserved helical weak spots facilitate GPCR activation. Proteins 2021; 89:1577-1586. [PMID: 34272892 PMCID: PMC9290982 DOI: 10.1002/prot.26179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/03/2021] [Accepted: 07/11/2021] [Indexed: 01/24/2023]
Abstract
G protein‐coupled receptors (GPCRs) participate in most physiological processes and are important drug targets in many therapeutic areas. Recently, many GPCR X‐ray structures became available, facilitating detailed studies of their sequence‐structure‐mobility‐function relations. We show that the functional role of many conserved GPCR sequence motifs is to create weak spots in the transmembrane helices that provide the structural plasticity necessary for ligand binding and signaling. Different receptor families use different conserved sequence motifs to obtain similar helix irregularities that allow for the same motions upon GPCR activation. These conserved motions come together to facilitate the timely release of the conserved sodium ion to the cytosol. Most GPCR crystal structures could be determined only after stabilization of the transmembrane helices by mutations that remove weak spots. These mutations often lead to diminished binding of agonists, but not antagonists, which logically agrees with the fact that large helix rearrangements occur only upon agonist binding. Upon activation, six of the seven TM helices in GPCRs undergo helix motions and/or deformations facilitated by weak spots in these helices. The location of these weak spots is much more conserved than the sequence motifs that cause them. Knowledge about these weak spots helps understand the activation process of GPCRs and thus helps design medicines.
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26
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Sadaf A, Kim S, Bae HE, Wang H, Nygaard A, Uegaki Y, Du Y, Munk CF, Katsube S, Sung Lee H, Bae J, Choi CW, Choi HJ, Byrne B, Gellman SH, Guan L, Loland CJ, Kobilka BK, Im W, Chae PS. Conformationally flexible core-bearing detergents with a hydrophobic or hydrophilic pendant: Effect of pendant polarity on detergent conformation and membrane protein stability. Acta Biomater 2021; 128:393-407. [PMID: 33933694 PMCID: PMC8222176 DOI: 10.1016/j.actbio.2021.04.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/31/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
Membrane protein structures provide atomic level insight into essential biochemical processes and facilitate protein structure-based drug design. However, the inherent instability of these bio-macromolecules outside lipid bilayers hampers their structural and functional study. Detergent micelles can be used to solubilize and stabilize these membrane-inserted proteins in aqueous solution, thereby enabling their downstream characterizations. Membrane proteins encapsulated in detergent micelles tend to denature and aggregate over time, highlighting the need for development of new amphiphiles effective for protein solubility and stability. In this work, we present newly-designed maltoside detergents containing a pendant chain attached to a glycerol-decorated tris(hydroxymethyl)methane (THM) core, designated GTMs. One set of the GTMs has a hydrophobic pendant (ethyl chain; E-GTMs), and the other set has a hydrophilic pendant (methoxyethoxylmethyl chain; M-GTMs) placed in the hydrophobic-hydrophilic interfaces. The two sets of GTMs displayed profoundly different behaviors in terms of detergent self-assembly and protein stabilization efficacy. These behaviors mainly arise from the polarity difference between two pendants (ethyl and methoxyethoxylmethyl chains) that results in a large variation in detergent conformation between these sets of GTMs in aqueous media. The resulting high hydrophobic density in the detergent micelle interior is likely responsible for enhanced efficacy of the M-GTMs for protein stabilization compared to the E-GTMs and a gold standard detergent DDM. A representative GTM, M-GTM-O12, was more effective for protein stability than some recently developed detergents including LMNG. This is the first case study investigating the effect of pendant polarity on detergent geometry correlated with detergent efficacy for protein stabilization. STATEMENT OF SIGNIFICANCE: This study introduces new amphiphiles for use as biochemical tools in membrane protein studies. We identified a few hydrophilic pendant-bearing amphiphiles such as M-GTM-O11 and M-GTM-O12 that show remarkable efficacy for membrane protein solubilization and stabilization compared to a gold standard DDM, the hydrophobic counterparts (E-GTMs) and a significantly optimized detergent LMNG. In addition, detergent results obtained in the current study reveals the effect of detergent pendant polarity on protein solubility and stability. Thus, the current study represents both significant chemical and conceptual advance. The detergent tools and design principle introduced here advance protein science and facilitate structure-based drug design and development.
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Affiliation(s)
- Aiman Sadaf
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Hyoung Eun Bae
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, USA
| | - Andreas Nygaard
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Yuki Uegaki
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, USA
| | - Chastine F Munk
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Hyun Sung Lee
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Jungnam Bae
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Chul Won Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, USA
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Pil Seok Chae
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea.
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27
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Directed evolution for high functional production and stability of a challenging G protein-coupled receptor. Sci Rep 2021; 11:8630. [PMID: 33883583 PMCID: PMC8060309 DOI: 10.1038/s41598-021-87793-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Membrane proteins such as G protein-coupled receptors (GPCRs) carry out many fundamental biological functions, are involved in a large number of physiological responses, and are thus important drug targets. To allow detailed biophysical and structural studies, most of these important receptors have to be engineered to overcome their poor intrinsic stability and low expression levels. However, those GPCRs with especially poor properties cannot be successfully optimised even with the current technologies. Here, we present an engineering strategy, based on the combination of three previously developed directed evolution methods, to improve the properties of particularly challenging GPCRs. Application of this novel combination approach enabled the successful selection for improved and crystallisable variants of the human oxytocin receptor, a GPCR with particularly low intrinsic production levels. To analyse the selection results and, in particular, compare the mutations enriched in different hosts, we developed a Next-Generation Sequencing (NGS) strategy that combines long reads, covering the whole receptor, with exceptionally low error rates. This study thus gave insight into the evolution pressure on the same membrane protein in prokaryotes and eukaryotes. Our long-read NGS strategy provides a general methodology for the highly accurate analysis of libraries of point mutants during directed evolution.
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28
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Waltenspühl Y, Ehrenmann J, Klenk C, Plückthun A. Engineering of Challenging G Protein-Coupled Receptors for Structure Determination and Biophysical Studies. Molecules 2021; 26:molecules26051465. [PMID: 33800379 PMCID: PMC7962830 DOI: 10.3390/molecules26051465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 01/14/2023] Open
Abstract
Membrane proteins such as G protein-coupled receptors (GPCRs) exert fundamental biological functions and are involved in a multitude of physiological responses, making these receptors ideal drug targets. Drug discovery programs targeting GPCRs have been greatly facilitated by the emergence of high-resolution structures and the resulting opportunities to identify new chemical entities through structure-based drug design. To enable the determination of high-resolution structures of GPCRs, most receptors have to be engineered to overcome intrinsic hurdles such as their poor stability and low expression levels. In recent years, multiple engineering approaches have been developed to specifically address the technical difficulties of working with GPCRs, which are now beginning to make more challenging receptors accessible to detailed studies. Importantly, successfully engineered GPCRs are not only valuable in X-ray crystallography, but further enable biophysical studies with nuclear magnetic resonance spectroscopy, surface plasmon resonance, native mass spectrometry, and fluorescence anisotropy measurements, all of which are important for the detailed mechanistic understanding, which is the prerequisite for successful drug design. Here, we summarize engineering strategies based on directed evolution to reduce workload and enable biophysical experiments of particularly challenging GPCRs.
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29
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Errasti-Murugarren E, Bartoccioni P, Palacín M. Membrane Protein Stabilization Strategies for Structural and Functional Studies. MEMBRANES 2021; 11:membranes11020155. [PMID: 33671740 PMCID: PMC7926488 DOI: 10.3390/membranes11020155] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Accounting for nearly two-thirds of known druggable targets, membrane proteins are highly relevant for cell physiology and pharmacology. In this regard, the structural determination of pharmacologically relevant targets would facilitate the intelligent design of new drugs. The structural biology of membrane proteins is a field experiencing significant growth as a result of the development of new strategies for structure determination. However, membrane protein preparation for structural studies continues to be a limiting step in many cases due to the inherent instability of these molecules in non-native membrane environments. This review describes the approaches that have been developed to improve membrane protein stability. Membrane protein mutagenesis, detergent selection, lipid membrane mimics, antibodies, and ligands are described in this review as approaches to facilitate the production of purified and stable membrane proteins of interest for structural and functional studies.
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Affiliation(s)
- Ekaitz Errasti-Murugarren
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
| | - Paola Bartoccioni
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
| | - Manuel Palacín
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
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30
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GPCR Activation States Induced by Nanobodies and Mini-G Proteins Compared by NMR Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25245984. [PMID: 33348734 PMCID: PMC7767065 DOI: 10.3390/molecules25245984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/04/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022]
Abstract
In this work, we examine methyl nuclear magnetic resonance (NMR) spectra of the methionine ε-[13CH3] labelled thermostabilized β1 adrenergic receptor from turkey in association with a variety of different effectors, including mini-Gs and nanobody 60 (Nb60), which have not been previously studied in complex with β1 adrenergic receptor (β1AR) by NMR. Complexes with pindolol and Nb60 induce highly similar inactive states of the receptor, closely resembling the resting state conformational ensemble. We show that, upon binding of mini-Gs or nanobody 80 (Nb80), large allosteric changes throughout the receptor take place. The conformation of tβ1AR stabilized by the native-like mini-Gs protein is highly similar to the conformation induced by the currently used surrogate Nb80. Interestingly, in both cases residual dynamics are present, which were not observed in the resting states. Finally, we reproduce a pharmaceutically relevant situation, where an antagonist abolishes the interaction of the receptor with the mini-G protein in a competitive manner, validating the functional integrity of our preparation. The presented system is therefore well suited for reproducing the individual steps of the activation cycle of a G protein-coupled receptor (GPCR) in vitro and serves as a basis for functional and pharmacological characterizations of more native-like systems in the future.
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31
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Liu S, Li S, Yang Y, Li W. Termini restraining of small membrane proteins enables structure determination at near-atomic resolution. SCIENCE ADVANCES 2020; 6:eabe3717. [PMID: 33355146 PMCID: PMC11205269 DOI: 10.1126/sciadv.abe3717] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
Small membrane proteins are difficult targets for structural characterization. Here, we stabilize their folding by restraining their amino and carboxyl termini with associable protein entities, exemplified by the two halves of a superfolder GFP. The termini-restrained proteins are functional and show improved stability during overexpression and purification. The reassembled GFP provides a versatile scaffold for membrane protein crystallization, enables diffraction to atomic resolution, and facilitates crystal identification, phase determination, and density modification. This strategy gives rise to 14 new structures of five vertebrate proteins from distinct functional families, bringing a substantial expansion to the structural database of small membrane proteins. Moreover, a high-resolution structure of bacterial DsbB reveals that this thiol oxidoreductase is activated through a catalytic triad, similar to cysteine proteases. Overall, termini restraining proves exceptionally effective for stabilization and structure determination of small membrane proteins.
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Affiliation(s)
- Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shuang Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yihu Yang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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32
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Lavington S, Watts A. Lipid nanoparticle technologies for the study of G protein-coupled receptors in lipid environments. Biophys Rev 2020; 12:10.1007/s12551-020-00775-5. [PMID: 33215301 PMCID: PMC7755959 DOI: 10.1007/s12551-020-00775-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are a large family of integral membrane proteins which conduct a wide range of biological roles and represent significant drug targets. Most biophysical and structural studies of GPCRs have been conducted on detergent-solubilised receptors, and it is clear that detergents can have detrimental effects on GPCR function. Simultaneously, there is increasing appreciation of roles for specific lipids in modulation of GPCR function. Lipid nanoparticles such as nanodiscs and styrene maleic acid lipid particles (SMALPs) offer opportunities to study integral membrane proteins in lipid environments, in a form that is soluble and amenable to structural and biophysical experiments. Here, we review the application of lipid nanoparticle technologies to the study of GPCRs, assessing the relative merits and limitations of each system. We highlight how these technologies can provide superior platforms to detergents for structural and biophysical studies of GPCRs and inform on roles for protein-lipid interactions in GPCR function.
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Affiliation(s)
- Steven Lavington
- Biochemistry Department, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony Watts
- Biochemistry Department, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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33
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Jones EM, Lubock NB, Venkatakrishnan AJ, Wang J, Tseng AM, Paggi JM, Latorraca NR, Cancilla D, Satyadi M, Davis JE, Babu MM, Dror RO, Kosuri S. Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. eLife 2020; 9:54895. [PMID: 33084570 PMCID: PMC7707821 DOI: 10.7554/elife.54895] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/16/2020] [Indexed: 01/14/2023] Open
Abstract
The >800 human G protein–coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state- and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it challenging to understand their structure and function. Here, we developed a platform to characterize large libraries of GPCR variants in human cell lines with a barcoded transcriptional reporter of G protein signal transduction. We tested 7800 of 7828 possible single amino acid substitutions to the beta-2 adrenergic receptor (β2AR) at four concentrations of the agonist isoproterenol. We identified residues specifically important for β2AR signaling, mutations in the human population that are potentially loss of function, and residues that modulate basal activity. Using unsupervised learning, we identify residues critical for signaling, including all major structural motifs and molecular interfaces. We also find a previously uncharacterized structural latch spanning the first two extracellular loops that is highly conserved across Class A GPCRs and is conformationally rigid in both the inactive and active states of the receptor. More broadly, by linking deep mutational scanning with engineered transcriptional reporters, we establish a generalizable method for exploring pharmacogenomics, structure and function across broad classes of drug receptors.
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Affiliation(s)
- Eric M Jones
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Nathan B Lubock
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - A J Venkatakrishnan
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Jeffrey Wang
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Alex M Tseng
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Naomi R Latorraca
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Daniel Cancilla
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Megan Satyadi
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Jessica E Davis
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ron O Dror
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
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Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme. Proc Natl Acad Sci U S A 2020; 117:22146-22156. [PMID: 32848056 DOI: 10.1073/pnas.1917770117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Packing interaction is a critical driving force in the folding of helical membrane proteins. Despite the importance, packing defects (i.e., cavities including voids, pockets, and pores) are prevalent in membrane-integral enzymes, channels, transporters, and receptors, playing essential roles in function. Then, a question arises regarding how the two competing requirements, packing for stability vs. cavities for function, are reconciled in membrane protein structures. Here, using the intramembrane protease GlpG of Escherichia coli as a model and cavity-filling mutation as a probe, we tested the impacts of native cavities on the thermodynamic stability and function of a membrane protein. We find several stabilizing mutations which induce substantial activity reduction without distorting the active site. Notably, these mutations are all mapped onto the regions of conformational flexibility and functional importance, indicating that the cavities facilitate functional movement of GlpG while compromising the stability. Experiment and molecular dynamics simulation suggest that the stabilization is induced by the coupling between enhanced protein packing and weakly unfavorable lipid desolvation, or solely by favorable lipid solvation on the cavities. Our result suggests that, stabilized by the relatively weak interactions with lipids, cavities are accommodated in membrane proteins without severe energetic cost, which, in turn, serve as a platform to fine-tune the balance between stability and flexibility for optimal activity.
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Lavington S, Watts A. Detergent-free solubilisation & purification of a G protein coupled receptor using a polymethacrylate polymer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183441. [PMID: 32810489 DOI: 10.1016/j.bbamem.2020.183441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022]
Abstract
G protein coupled receptors (GPCRs) function as guanine nucleotide exchange factors (GEFs) at heterotrimeric G proteins, and conduct this role embedded in a lipid bilayer. Detergents are widely used to solubilise GPCRs for structural and biophysical analysis, but are poor mimics of the lipid bilayer and may be deleterious to protein function. Amphipathic polymers have emerged as promising alternatives to detergents, which maintain a lipid environment around a membrane protein during purification. Of these polymers, the polymethacrylate (PMA) polymers have potential advantages over the most popular styrene maleic acid (SMA) polymer, but to date have not been applied to purification of membrane proteins. Here we use a class A GPCR, neurotensin receptor 1 (NTSR1), to explore detergent-free purification using PMA. By using an NTSR1-eGFP fusion protein expressed in Sf9 cells, a range of solubilisation conditions were screened, demonstrating the importance of solubilisation temperature, pH, NaCl concentration and the relative amounts of polymer and membrane sample. PMA-solubilised NTSR1 displayed compatibility with standard purification protocols and millimolar divalent cation concentrations. Moreover, the receptor in PMA discs showed stimulation of both Gq and Gi1 heterotrimers to an extent that was greater than that for the detergent-solubilised receptor. PMA therefore represents a viable alternative to SMA for membrane protein purification and has a potentially broad utility in studying GPCRs and other membrane proteins.
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Affiliation(s)
- Steven Lavington
- Department of Biochemistry, Oxford University, South Parks Road, OX1 3QU, UK
| | - Anthony Watts
- Department of Biochemistry, Oxford University, South Parks Road, OX1 3QU, UK.
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Bae HE, Cecchetti C, Du Y, Katsube S, Mortensen JS, Huang W, Rehan S, Lee HJ, Loland CJ, Guan L, Kobilka BK, Byrne B, Chae PS. Pendant-bearing glucose-neopentyl glycol (P-GNG) amphiphiles for membrane protein manipulation: Importance of detergent pendant chain for protein stabilization. Acta Biomater 2020; 112:250-261. [PMID: 32522715 PMCID: PMC7366829 DOI: 10.1016/j.actbio.2020.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022]
Abstract
Glucoside detergents are successfully used for membrane protein crystallization mainly because of their ability to form small protein-detergent complexes. In a previous study, we introduced glucose neopentyl glycol (GNG) amphiphiles with a branched diglucoside structure that has facilitated high resolution crystallographic structure determination of several membrane proteins. Like other glucoside detergents, however, these GNGs were less successful than DDM in stabilizing membrane proteins, limiting their wide use in protein structural study. As a strategy to improve GNG efficacy for protein stabilization, we introduced two different alkyl chains (i.e., main and pendant chains) into the GNG scaffold while maintaining the branched diglucoside head group. Of these pendant-bearing GNGs (P-GNGs), three detergents (GNG-2,14, GNG-3,13 and GNG-3,14) were not only notably better than both DDM (a gold standard detergent) and the previously described GNGs at stabilizing all six membrane proteins tested here, but were also as efficient as DDM at membrane protein extraction. The results suggest that the C14 main chain of the P-GNGs is highly compatible with the hydrophobic widths of membrane proteins, while the C2/C3 pendant chain is effective at strengthening detergent hydrophobic interactions. Based on the marked effect on protein stability and solubility, these glucoside detergents hold significant potential for membrane protein structural study. Furthermore, the independent roles of the detergent two alkyl chains first introduced in this study have shed light on new amphiphile design for membrane protein study. STATEMENT OF SIGNIFICANCE: Detergent efficacy for protein stabilization tends to be protein-specific, thus it is challenging to find a detergent that is effective at stabilizing multiple membrane proteins. By incorporating a pendant chain into our previous GNG scaffold, we prepared pendant chain-bearing GNGs (P-GNGs) and identified three P-GNGs that were highly effective at stabilizing all membrane proteins tested here including two GPCRs. In addition, the new detergents were as efficient as DDM at extracting membrane proteins, enabling use of these detergents over the multiple steps of protein isolation. The key difference between the P-GNGs and other glucoside detergents, the presence of a pendant chain, is likely to be responsible for their markedly enhanced protein stabilization behavior.
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Affiliation(s)
- Hyoung Eun Bae
- Department of Bionanotechnology, Hanyang University, Ansan, 15588 (Korea)
| | - Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, CA 94305 (USA)
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430 (USA)
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200 (Denmark)
| | - Weijiao Huang
- Department of Molecular and Cellular Physiology, Stanford University, CA 94305 (USA)
| | - Shahid Rehan
- Institute of Biotechnology, University of Helsinki, Helsinki (Finland); HiLIFE, University of Helsinki, Helsinki (Finland)
| | - Ho Jin Lee
- Department of Bionanotechnology, Hanyang University, Ansan, 15588 (Korea)
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen, DK-2200 (Denmark)
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430 (USA)
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, CA 94305 (USA)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 15588 (Korea).
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37
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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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38
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Murata T, Yasuda S, Hayashi T, Kinoshita M. Theoretical identification of thermostabilizing amino acid mutations for G-protein-coupled receptors. Biophys Rev 2020; 12:323-332. [PMID: 32270446 DOI: 10.1007/s12551-020-00678-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Thermostabilization of a membrane proteins, especially G-protein-coupled receptors (GPCRs), is often necessary for biochemical applications and pharmaceutical studies involving structure-based drug design. Here we review our theoretical, physics-based method for identifying thermostabilizing amino acid mutations. Its novel aspects are the following: The entropic effect originating from the translational displacement of hydrocarbon groups within the lipid bilayer is treated as a pivotal factor; a reliable measure of thermostability is introduced and a mutation which enlarges the measure to a significant extent is chosen; and all the possible mutations can be examined with moderate computational effort. It was shown that mutating the residue at a position of NBW = 3.39 (NBW is the Ballesteros-Weinstein number) to Arg or Lys leads to the stabilization of significantly many different GPCRs of class A in the inactive state. Up to now, we have been successful in stabilizing several GPCRs and newly solving three-dimensional structures for the muscarinic acetylcholine receptor 2 (M2R), prostaglandin E receptor 4 (EP4), and serotonin 2A receptor (5-HT2AR) using X-ray crystallography. The subjects to be pursued in future studies are also discussed.
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Affiliation(s)
- Takeshi Murata
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan.,Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan
| | - Satoshi Yasuda
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan.,Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan.,Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.,Present address: Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata, 950-2181, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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39
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Yasuda S, Akiyama T, Nemoto S, Hayashi T, Ueta T, Kojima K, Tsukamoto T, Nagatoishi S, Tsumoto K, Sudo Y, Kinoshita M, Murata T. Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained. J Chem Inf Model 2020; 60:1709-1716. [PMID: 32155058 DOI: 10.1021/acs.jcim.0c00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We develop a new methodology best suited to the identification of thermostabilizing mutations for an intrinsically stable membrane protein. The recently discovered thermophilic rhodopsin, whose apparent midpoint temperature of thermal denaturation Tm is measured to be ∼91.8 °C, is chosen as a paradigmatic target. In the methodology, we first regard the residues whose side chains are missing in the crystal structure of the wild type (WT) as the "residues with disordered side chains," which make no significant contributions to the stability, unlike the other essential residues. We then undertake mutating each of the residues with disordered side chains to another residue except Ala and Pro, and the resultant mutant structure is constructed by modifying only the local structure around the mutated residue. This construction is based on the postulation that the structure formed by the other essential residues, which is nearly optimized in such a highly stable protein, should not be modified. The stability changes arising from the mutations are then evaluated using our physics-based free-energy function (FEF). We choose the mutations for which the FEF is much lower than for the WT and test them by experiments. We successfully find three mutants that are significantly more stable than the WT. A double mutant whose Tm reaches ∼100 °C is also discovered.
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Affiliation(s)
- Satoshi Yasuda
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.,Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.,Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoki Akiyama
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Sayaka Nemoto
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tetsuya Ueta
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Takashi Tsukamoto
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takeshi Murata
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.,Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
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40
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Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
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41
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Evaluation of chemical cross-linkers for in-depth structural analysis of G protein-coupled receptors through cross-linking mass spectrometry. Anal Chim Acta 2020; 1102:53-62. [DOI: 10.1016/j.aca.2019.12.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/12/2019] [Accepted: 12/15/2019] [Indexed: 01/05/2023]
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42
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Yao H, Cai H, Li D. Thermostabilization of Membrane Proteins by Consensus Mutation: A Case Study for a Fungal Δ8-7 Sterol Isomerase. J Mol Biol 2020; 432:5162-5183. [PMID: 32105736 DOI: 10.1016/j.jmb.2020.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 11/15/2022]
Abstract
Membrane proteins are generally challenging to work with because of their notorious instability. Protein engineering has been used increasingly to thermostabilize labile membrane proteins such as G-protein-coupled receptors for structural and functional studies in recent years. Two major strategies exist. Scanning mutagenesis systematically eliminates destabilizing residues, whereas the consensus approach assembles mutants with the most frequent residues among selected homologs, bridging sequence conservation with stability. Here, we applied the consensus concept to stabilize a fungal homolog of the human sterol Δ8-7 isomerase, a 26.4 kDa protein with five transmembrane helices. The isomerase is also called emopamil-binding protein (EBP), as it binds this anti-ischemic drug with high affinity. The wild-type had an apparent melting temperature (Tm) of 35.9 °C as measured by the fluorescence-detection size-exclusion chromatography-based thermostability assay. A total of 87 consensus mutations sourced from 22 homologs gained expression level and thermostability, increasing the apparent Tm to 69.9 °C at the cost of partial function loss. Assessing the stability and activity of several systematic chimeric constructs identified a construct with an apparent Tm of 79.8 °C and two regions for function rescue. Further back-mutations of the chimeric construct in the two target regions yielded the final construct with similar apparent activity to the wild-type and an elevated Tm of 88.8 °C, totaling an increase of 52.9 °C. The consensus approach is effective and efficient because it involves fewer constructs compared with scanning mutagenesis. Our results should encourage more use of the consensus strategy for membrane protein thermostabilization.
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Affiliation(s)
- Hebang Yao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Hongmin Cai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.
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43
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Gose T, Shafi T, Fukuda Y, Das S, Wang Y, Allcock A, Gavan McHarg A, Lynch J, Chen T, Tamai I, Shelat A, Ford RC, Schuetz JD. ABCG2 requires a single aromatic amino acid to "clamp" substrates and inhibitors into the binding pocket. FASEB J 2020; 34:4890-4903. [PMID: 32067270 DOI: 10.1096/fj.201902338rr] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/26/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022]
Abstract
ATP-binding cassette sub-family G member 2 (ABCG2) is a homodimeric ATP-binding cassette (ABC) transporter that not only has a key role in helping cancer cells to evade the cytotoxic effects of chemotherapy, but also in protecting organisms from multiple xeno- and endobiotics. Structural studies indicate that substrate and inhibitor (ligands) binding to ABCG2 can be differentiated quantitatively by the number of amino acid contacts, with inhibitors displaying more contacts. Although binding is the obligate initial step in the transport cycle, there is no empirical evidence for one amino acid being primarily responsible for ligand binding. By mutagenesis and biochemical studies, we demonstrated that the phylogenetically conserved amino acid residue, F439, was critical for both transport and the binding of multiple substrates and inhibitors. Structural modeling implied that the π-π interactions from each F439 monomer mediated the binding of a surprisingly diverse array of structurally unrelated substrates and inhibitors and that this symmetrical π-π interaction "clamps" the ligand into the binding pocket. Key molecular features of diverse ABCG2 ligands using the π-π clamp along with structural studies created a pharmacophore model. These novel findings have important therapeutic implications because key properties of ligands interacting with ABCG2 have been disovered. Furthermore, mechanistic insights have been revealed by demonstrating that for ABCG2 a single amino acid is essential for engaging and initiating transport of multiple drugs and xenobiotics.
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Affiliation(s)
- Tomoka Gose
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Talha Shafi
- School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Yu Fukuda
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yao Wang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alice Allcock
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ailsa Gavan McHarg
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Lynch
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ikumi Tamai
- Department of Pharmaceutical Sciences, Kanazawa University, Kanazawa, Japan
| | - Anang Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert C Ford
- School of Biological Sciences, The University of Manchester, Manchester, UK
| | - John D Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
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Kooijman L, Ansorge P, Schuster M, Baumann C, Löhr F, Jurt S, Güntert P, Zerbe O. Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs. JOURNAL OF BIOMOLECULAR NMR 2020; 74:45-60. [PMID: 31754899 PMCID: PMC7015963 DOI: 10.1007/s10858-019-00289-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/11/2019] [Indexed: 05/21/2023]
Abstract
Resonance assignments are challenging for membrane proteins due to the size of the lipid/detergent-protein complex and the presence of line-broadening from conformational exchange. As a consequence, many correlations are missing in the triple-resonance NMR experiments typically used for assignments. Herein, we present an approach in which correlations from these solution-state NMR experiments are supplemented by data from 13C unlabeling, single-amino acid type labeling, 4D NOESY data and proximity of moieties to lipids or water in combination with a structure of the protein. These additional data are used to edit the expected peaklists for the automated assignment protocol FLYA, a module of the program package CYANA. We demonstrate application of the protocol to the 262-residue proton pump from archaeal bacteriorhodopsin (bR) in lipid nanodiscs. The lipid-protein assembly is characterized by an overall correlation time of 44 ns. The protocol yielded assignments for 62% of all backbone (H, N, Cα, Cβ, C') resonances of bR, corresponding to 74% of all observed backbone spin systems, and 60% of the Ala, Met, Ile (δ1), Leu and Val methyl groups, thus enabling to assign a large fraction of the protein without mutagenesis data. Most missing resonances stem from the extracellular half, likely due intermediate exchange line-broadening. Further analysis revealed that missing information of the amino acid type of the preceding residue is the largest problem, and that 4D NOESY experiments are particularly helpful to compensate for that information loss.
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Affiliation(s)
- Laurens Kooijman
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Philipp Ansorge
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Matthias Schuster
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christian Baumann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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45
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Pérez-Benito L, Llinas del Torrent C, Pardo L, Tresadern G. The computational modeling of allosteric modulation of metabotropic glutamate receptors. FROM STRUCTURE TO CLINICAL DEVELOPMENT: ALLOSTERIC MODULATION OF G PROTEIN-COUPLED RECEPTORS 2020; 88:1-33. [DOI: 10.1016/bs.apha.2020.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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46
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Ghani L, Munk CF, Zhang X, Katsube S, Du Y, Cecchetti C, Huang W, Bae HE, Saouros S, Ehsan M, Guan L, Liu X, Loland CJ, Kobilka BK, Byrne B, Chae PS. 1,3,5-Triazine-Cored Maltoside Amphiphiles for Membrane Protein Extraction and Stabilization. J Am Chem Soc 2019; 141:19677-19687. [PMID: 31809039 DOI: 10.1021/jacs.9b07883] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Despite their major biological and pharmacological significance, the structural and functional study of membrane proteins remains a significant challenge. A main issue is the isolation of these proteins in a stable and functional state from native lipid membranes. Detergents are amphiphilic compounds widely used to extract membrane proteins from the native membranes and maintain them in a stable form during downstream analysis. However, due to limitations of conventional detergents, it is essential to develop novel amphiphiles with optimal properties for protein stability in order to advance membrane protein research. Here we designed and synthesized 1,3,5-triazine-cored dimaltoside amphiphiles derived from cyanuric chloride. By introducing variations in the alkyl chain linkage (ether/thioether) and an amine-functionalized diol linker (serinol/diethanolamine), we prepared two sets of 1,3,5-triazine-based detergents. When tested with several model membrane proteins, these agents showed remarkable efficacy in stabilizing three transporters and two G protein-coupled receptors. Detergent behavior substantially varied depending on the detergent structural variation, allowing us to explore detergent structure-property-efficacy relationships. The 1,3,5-triazine-based detergents introduced here have significant potential for membrane protein study as a consequence of their structural diversity and universal stabilization efficacy for several membrane proteins.
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Affiliation(s)
- Lubna Ghani
- Department of Bionanotechnology , Hanyang University , Ansan 155-88 , Korea
| | - Chastine F Munk
- Department of Neuroscience , University of Copenhagen , Copenhagen DK-2200 , Denmark
| | - Xiang Zhang
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences , Tsinghua University , 100084 Beijing , China
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine , Texas Tech University Health Sciences Center , Lubbock , Texas 79430 , United States
| | - Yang Du
- Department of Molecular and Cellular Physiology , Stanford University , Stanford , California 94305 , United States
| | - Cristina Cecchetti
- Department of Life Sciences , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Weijiao Huang
- Department of Molecular and Cellular Physiology , Stanford University , Stanford , California 94305 , United States
| | - Hyoung Eun Bae
- Department of Bionanotechnology , Hanyang University , Ansan 155-88 , Korea
| | - Savvas Saouros
- Department of Life Sciences , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Muhammad Ehsan
- Department of Bionanotechnology , Hanyang University , Ansan 155-88 , Korea
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine , Texas Tech University Health Sciences Center , Lubbock , Texas 79430 , United States
| | - Xiangyu Liu
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences , Tsinghua University , 100084 Beijing , China
| | - Claus J Loland
- Department of Neuroscience , University of Copenhagen , Copenhagen DK-2200 , Denmark
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology , Stanford University , Stanford , California 94305 , United States
| | - Bernadette Byrne
- Department of Life Sciences , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Pil Seok Chae
- Department of Bionanotechnology , Hanyang University , Ansan 155-88 , Korea
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47
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Ishchenko A, Stauch B, Han GW, Batyuk A, Shiriaeva A, Li C, Zatsepin N, Weierstall U, Liu W, Nango E, Nakane T, Tanaka R, Tono K, Joti Y, Iwata S, Moraes I, Gati C, Cherezov V. Toward G protein-coupled receptor structure-based drug design using X-ray lasers. IUCRJ 2019; 6:1106-1119. [PMID: 31709066 PMCID: PMC6830214 DOI: 10.1107/s2052252519013137] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.
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Affiliation(s)
- Andrii Ishchenko
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Benjamin Stauch
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anna Shiriaeva
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Vadim Cherezov
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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48
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Muk S, Ghosh S, Achuthan S, Chen X, Yao X, Sandhu M, Griffor MC, Fennell KF, Che Y, Shanmugasundaram V, Qiu X, Tate CG, Vaidehi N. Machine Learning for Prioritization of Thermostabilizing Mutations for G-Protein Coupled Receptors. Biophys J 2019; 117:2228-2239. [PMID: 31703801 DOI: 10.1016/j.bpj.2019.10.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/11/2019] [Accepted: 10/17/2019] [Indexed: 01/01/2023] Open
Abstract
Although the three-dimensional structures of G-protein coupled receptors (GPCRs), the largest superfamily of drug targets, have enabled structure-based drug design, there are no structures available for 87% of GPCRs. This is due to the stiff challenge in purifying the inherently flexible GPCRs. Identifying thermostabilized mutant GPCRs via systematic alanine scanning mutations has been a successful strategy in stabilizing GPCRs, but it remains a daunting task for each GPCR. We developed a computational method that combines sequence-, structure-, and dynamics-based molecular properties of GPCRs that recapitulate GPCR stability, with four different machine learning methods to predict thermostable mutations ahead of experiments. This method has been trained on thermostability data for 1231 mutants, the largest publicly available data set. A blind prediction for thermostable mutations of the complement factor C5a receptor 1 retrieved 36% of the thermostable mutants in the top 50 prioritized mutants compared to 3% in the first 50 attempts using systematic alanine scanning.
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Affiliation(s)
- Sanychen Muk
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California
| | - Soumadwip Ghosh
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California
| | - Srisairam Achuthan
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California
| | | | - XiaoJie Yao
- Discovery Sciences, Pfizer, Groton, Connecticut
| | - Manbir Sandhu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California
| | | | | | - Ye Che
- Discovery Sciences, Pfizer, Groton, Connecticut
| | | | - Xiayang Qiu
- Discovery Sciences, Pfizer, Groton, Connecticut
| | | | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California.
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49
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Méndez M, Matter H, Defossa E, Kurz M, Lebreton S, Li Z, Lohmann M, Löhn M, Mors H, Podeschwa M, Rackelmann N, Riedel J, Safar P, Thorpe DS, Schäfer M, Weitz D, Breitschopf K. Design, Synthesis, and Pharmacological Evaluation of Potent Positive Allosteric Modulators of the Glucagon-like Peptide-1 Receptor (GLP-1R). J Med Chem 2019; 63:2292-2307. [PMID: 31596080 DOI: 10.1021/acs.jmedchem.9b01071] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The therapeutic success of peptidic GLP-1 receptor agonists for treatment of type 2 diabetes mellitus (T2DM) motivated our search for orally bioavailable small molecules that can activate the GLP-1 receptor (GLP-1R) as a well-validated target for T2DM. Here, the discovery and characterization of a potent and selective positive allosteric modulator (PAM) for GLP-1R based on a 3,4,5,6-tetrahydro-1H-1,5-epiminoazocino[4,5-b]indole scaffold is reported. Optimization of this series from HTS was supported by a GLP-1R ligand binding model. Biological in vitro testing revealed favorable ADME and pharmacological profiles for the best compound 19. Characterization by in vivo pharmacokinetic and pharmacological studies demonstrated that 19 activates GLP-1R as positive allosteric modulator (PAM) in the presence of the much less active endogenous degradation product GLP1(9-36)NH2 of the potent endogenous ligand GLP-1(7-36)NH2. While these data suggest the potential of small molecule GLP-1R PAMs for T2DM treatment, further optimization is still required towards a clinical candidate.
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Affiliation(s)
- María Méndez
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Hans Matter
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Elisabeth Defossa
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Sylvain Lebreton
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Ziyu Li
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Matthias Lohmann
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Matthias Löhn
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Hartmut Mors
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Michael Podeschwa
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Nils Rackelmann
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Jens Riedel
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Pavel Safar
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - David S Thorpe
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Matthias Schäfer
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Dietmar Weitz
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Kristin Breitschopf
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany
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50
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Jana S, Ghosh S, Muk S, Levy B, Vaidehi N. Prediction of Conformation Specific Thermostabilizing Mutations for Class A G Protein-Coupled Receptors. J Chem Inf Model 2019; 59:3744-3754. [PMID: 31408606 PMCID: PMC6944194 DOI: 10.1021/acs.jcim.9b00175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G protein-coupled receptors (GPCRs) are highly flexible and prone to denaturation during protein extraction in detergents and purification. This poses a huge challenge to purify a conformationally homogeneous solution of GPCRs. Thermostabilizing mutations have been used widely to purify and obtain crystal structures of several GPCRs. However, identifying thermostabilizing mutations for GPCRs remains a tedious and expensive task as they are not transferable even among closely related GPCRs. Additionally, the mutations stabilizing one conformational state of a GPCR do not always stabilize other conformational state(s) of the same GPCR. Previously we developed a computational method, LiticonDesign, for rapid prediction of thermostabilizing mutations for a specific GPCR conformation. In this study, we have used LiticonDesign to predict thermostabilizing mutations for the agonist bound active-intermediate state of the human adenosine receptor (A2AR) using the structure of the inactive state of the same GPCR and vice versa. Our study shows that the thermostable mutation predictions using LiticonDesign, for an active-intermediate state of a GPCR (A2AR in our case), requires a homology model that is derived from an active/active-intermediate state GPCR structure as a template. Similarly, the homology models derived from inactive state GPCR conformations are better in predicting the thermostable mutations for the inactive state of A2AR. Overall, LiticonDesign method is not only efficient in predicting thermostabilizing mutations for a given GPCR sequence but also can recover conformation specific mutations for a state of interest, if a suitable starting structure of desired conformation is chosen.
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Affiliation(s)
- Suvamay Jana
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| | - Soumadwip Ghosh
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| | - Sanychen Muk
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| | - Benjamin Levy
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| | - Nagarajan Vaidehi
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
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