1
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Waeterschoot J, Barniol-Xicota M, Verhelst S, Baatsen P, Koos E, Lammertyn J, Casadevall i Solvas X. Lipid vesicle formation by encapsulation of SMALPs in surfactant-stabilised droplets. Heliyon 2024; 10:e37915. [PMID: 39347415 PMCID: PMC11437848 DOI: 10.1016/j.heliyon.2024.e37915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 09/12/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024] Open
Abstract
Understanding the intricate functions of membrane proteins is pivotal in cell biology and drug discovery. The composition of the cell membrane is highly complex, with different types of membrane proteins and lipid species. Hence, studying cellular membranes in a complexity-reduced context is important to enhance our understanding of the roles of these different elements. However, reconstitution of membrane proteins in an environment that closely mimics the cell, like giant unilamellar vesicles (GUVs), remains challenging, often requiring detergents that compromise protein function. To address this challenge, we present a novel strategy to manufacture GUVs from styrene maleic acid lipid particles (SMALPs) that utilises surfactant-stabilised droplets as a template. As a first step towards the incorporation of membrane proteins, this work focusses on the conversion of pure lipid SMALPs in GUVs. To evaluate the method, we produced a new form of SMA linked to fluorescein, referred to as FSMA. We demonstrate the assembly of SMALPs at the surfactant-stabilised droplet interface, resulting in the formation of GUVs when released upon addition of a demulsifying agent. The released vesicles appear similar to electroformed vesicles imaged with confocal light microscopy, but a fluorescein leakage assay and cryo-TEM imaging reveal their porous nature, potentially as a result of residual interactions of SMA with the lipid bilayer. Our study represents a significant step towards opening new avenues for comprehensive protein research in a complexity-reduced, yet biologically relevant, setting.
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Affiliation(s)
- Jorik Waeterschoot
- Biomimetics Group, Division of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Marta Barniol-Xicota
- Department of Medicine and Life Sciences (MELIS), Barcelona Biomedical Research Park, Universitat Pompeu Fabra, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Steven Verhelst
- Department of Cellular and Molecular Medicine, KU Leuven – University of Leuven, Herestraat 49, box 901b, 3000 Leuven, Belgium
| | - Pieter Baatsen
- Center for the Biology of Disease, VIB, Herestraat 49, Leuven, 3000, Belgium
| | - Erin Koos
- Soft Matter, Rheology and Technology (SMaRT) at KU Leuven, Celestijnenlaan 200J, 3000 Leuven, Belgium
| | - Jeroen Lammertyn
- Biosensors Group, Division of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Heverlee, Belgium
| | - Xavier Casadevall i Solvas
- Biomimetics Group, Division of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
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2
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Agyemang E, Gonneville AN, Tiruvadi-Krishnan S, Lamichhane R. Exploring GPCR conformational dynamics using single-molecule fluorescence. Methods 2024; 226:35-48. [PMID: 38604413 PMCID: PMC11098685 DOI: 10.1016/j.ymeth.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are membrane proteins that transmit specific external stimuli into cells by changing their conformation. This conformational change allows them to couple and activate G-proteins to initiate signal transduction. A critical challenge in studying and inferring these structural dynamics arises from the complexity of the cellular environment, including the presence of various endogenous factors. Due to the recent advances in cell-expression systems, membrane-protein purification techniques, and labeling approaches, it is now possible to study the structural dynamics of GPCRs at a single-molecule level both in vitro and in live cells. In this review, we discuss state-of-the-art techniques and strategies for expressing, purifying, and labeling GPCRs in the context of single-molecule research. We also highlight four recent studies that demonstrate the applications of single-molecule microscopy in revealing the dynamics of GPCRs. These techniques are also useful as complementary methods to verify the results obtained from other structural biology tools like cryo-electron microscopy and x-ray crystallography.
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Affiliation(s)
- Eugene Agyemang
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Alyssa N Gonneville
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sriram Tiruvadi-Krishnan
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
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3
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Ayub H, Murray RJ, Kuyler GC, Napier-Khwaja F, Gunner J, Dafforn TR, Klumperman B, Poyner DR, Wheatley M. GPCRs in the round: SMA-like copolymers and SMALPs as a platform for investigating GPCRs. Arch Biochem Biophys 2024; 754:109946. [PMID: 38395122 DOI: 10.1016/j.abb.2024.109946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/21/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
G-protein-coupled receptors (GPCRs) are the largest family of membrane proteins, regulate a plethora of physiological responses and are the therapeutic target for 30-40% of clinically-prescribed drugs. They are integral membrane proteins deeply embedded in the plasma membrane where they activate intracellular signalling via coupling to G-proteins and β-arrestin. GPCRs are in intimate association with the bilayer lipids and that lipid environment regulates the signalling functions of GPCRs. This complex lipid 'landscape' is both heterogeneous and dynamic. GPCR function is modulated by bulk membrane properties including membrane fluidity, microdomains, curvature, thickness and asymmetry but GPCRs are also regulated by specific lipid:GPCR binding, including cholesterol and anionic lipids. Understanding the molecular mechanisms whereby GPCR signalling is regulated by lipids is a very active area of research currently. A major advance in membrane protein research in recent years was the application of poly(styrene-co-maleic acid) (SMA) copolymers. These spontaneously generate SMA lipid particles (SMALPs) encapsulating membrane protein in a nano-scale disc of cell membrane, thereby removing the historical need for detergent and preserving lipid:GPCR interaction. The focus of this review is how GPCR-SMALPs are increasing our understanding of GPCR structure and function at the molecular level. Furthermore, an increasing number of 'second generation' SMA-like copolymers have been reported recently. These are reviewed from the context of increasing our understanding of GPCR molecular mechanisms. Moreover, their potential as a novel platform for downstream biophysical and structural analyses is assessed and looking ahead, the translational application of SMA-like copolymers to GPCR drug discovery programmes in the future is considered.
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Affiliation(s)
- Hoor Ayub
- Centre for Health and Life Sciences, Coventry University, Coventry, CV1 2DS, UK.
| | - Rebecca J Murray
- Centre for Health and Life Sciences, Coventry University, Coventry, CV1 2DS, UK; Department of Chemistry and Polymer Sciences, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Gestél C Kuyler
- Centre for Health and Life Sciences, Coventry University, Coventry, CV1 2DS, UK; Department of Chemistry and Polymer Sciences, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | | | - Joseph Gunner
- School of Life and Health Sciences, Aston University, Birmingham, B4 7ET, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Bert Klumperman
- Department of Chemistry and Polymer Sciences, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - David R Poyner
- School of Life and Health Sciences, Aston University, Birmingham, B4 7ET, UK
| | - Mark Wheatley
- Centre for Health and Life Sciences, Coventry University, Coventry, CV1 2DS, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
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4
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Mamatkulov K, Zavatski S, Arynbek Y, Esawii HA, Burko A, Bandarenka H, Arzumanyan G. Conformational analysis of lipid membrane mimetics modified with A β42 peptide by Raman spectroscopy and computer simulations. J Biomol Struct Dyn 2024:1-14. [PMID: 38520152 DOI: 10.1080/07391102.2024.2330706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024]
Abstract
Peptide-lipid interactions play an important role in maintaining the integrity and function of the cell membrane. Even slight changes in these interactions can induce the development of various diseases. Specifically, peptide misfolding and aggregation in the membrane is considered to be one of the triggers of Alzheimer's disease (AD), however its exact mechanism is still unclear. To this end, an increase of amyloid-beta (Aβ) peptide concentration in the human brain is widely accepted to gradually produce cytotoxic Aβ aggregates (plaques). These plaques initiate a sequence of pathogenic events ending up in observable symptoms of dementia. Understanding the mechanism of the Aβ interaction with cells is crucial for early detection and prevention of Alzheimer's disease. Hence, in this work, a comprehensive Raman analysis of the Aβ42 conformational dynamics in water and in liposomes and lipodiscs that mimic the membrane system is presented. The obtained results show that the secondary structure of Aβ42 in liposomes is dominated by the α-helix conformation, which remains stable over time. However, it comes as a surprise to reveal that the lipodisc environment induces the transformation of the Aβ42 secondary structure to a β-turn/random coil. Our Raman spectroscopy findings are supported with molecular dynamics (MD) and density functional theory (DFT) simulations, showing their good agreement.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kahramon Mamatkulov
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
| | - Siarhei Zavatski
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Yersultan Arynbek
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Faculty of Physics and Technology, al-Farabi, Kazakh National University, Almaty, Kazakhstan
| | - Heba A Esawii
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Biophysics Department, Faculty of Science, Cairo University, Egypt
| | - Aliaksandr Burko
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Hanna Bandarenka
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Grigory Arzumanyan
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
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5
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Addis P, Bali U, Baron F, Campbell A, Harborne S, Jagger L, Milne G, Pearce M, Rosethorne EM, Satchell R, Swift D, Young B, Unitt JF. Key aspects of modern GPCR drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:1-22. [PMID: 37625784 DOI: 10.1016/j.slasd.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/07/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest and most versatile cell surface receptor family with a broad repertoire of ligands and functions. We've learned an enormous amount about discovering drugs of this receptor class since the first GPCR was cloned and expressed in 1986, such that it's now well-recognized that GPCRs are the most successful target class for approved drugs. Here we take the reader through a GPCR drug discovery journey from target to the clinic, highlighting the key learnings, best practices, challenges, trends and insights on discovering drugs that ultimately modulate GPCR function therapeutically in patients. The future of GPCR drug discovery is inspiring, with more desirable drug mechanisms and new technologies enabling the delivery of better and more successful drugs.
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Affiliation(s)
- Phil Addis
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Utsav Bali
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Frank Baron
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Adrian Campbell
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Steven Harborne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Liz Jagger
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Gavin Milne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Martin Pearce
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Elizabeth M Rosethorne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Rupert Satchell
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Denise Swift
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Barbara Young
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - John F Unitt
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK.
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6
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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7
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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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8
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Cary BP, Zhang X, Cao J, Johnson RM, Piper SJ, Gerrard EJ, Wootten D, Sexton PM. New insights into the structure and function of class B1 GPCRs. Endocr Rev 2022; 44:492-517. [PMID: 36546772 PMCID: PMC10166269 DOI: 10.1210/endrev/bnac033] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/07/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors. Class B1 GPCRs constitute a subfamily of 15 receptors that characteristically contain large extracellular domains (ECDs) and respond to long polypeptide hormones. Class B1 GPCRs are critical regulators of homeostasis, and as such, many are important drug targets. While most transmembrane proteins, including GPCRs, are recalcitrant to crystallization, recent advances in electron cryo-microscopy (cryo-EM) have facilitated a rapid expansion of the structural understanding of membrane proteins. As a testament to this success, structures for all the class B1 receptors bound to G proteins have been determined by cryo-EM in the past five years. Further advances in cryo-EM have uncovered dynamics of these receptors, ligands, and signalling partners. Here, we examine the recent structural underpinnings of the class B1 GPCRs with an emphasis on structure-function relationships.
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Affiliation(s)
- Brian P Cary
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Xin Zhang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Jianjun Cao
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Rachel M Johnson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Sarah J Piper
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Elliot J Gerrard
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
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9
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Li S. Detergents and alternatives in cryo-EM studies of membrane proteins. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1049-1056. [PMID: 35866608 PMCID: PMC9828306 DOI: 10.3724/abbs.2022088] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/28/2022] [Indexed: 11/25/2022] Open
Abstract
Structure determination of membrane proteins has been a long-standing challenge to understand the molecular basis of life processes. Detergents are widely used to study the structure and function of membrane proteins by various experimental methods, and the application of membrane mimetics is also a prevalent trend in the field of cryo-EM analysis. This review focuses on the widely-used detergents and corresponding properties and structures, and also discusses the growing interests in membrane mimetic systems used in cryo-EM studies, providing insights into the role of detergent alternatives in structure determination.
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Affiliation(s)
- Shuo Li
- />Department of Life ScienceNational Natural Science Foundation of ChinaBeijing100085China
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10
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Zhu L, Zhao H, Wang Y, Yu C, Liu J, Li L, Li Z, Zhang J, Dai H, Wang J, Zhu L. Solubilization, purification, and ligand binding characterization of G protein-coupled receptor SMO in native membrane bilayer using styrene maleic acid copolymer. PeerJ 2022; 10:e13381. [PMID: 35529497 PMCID: PMC9074879 DOI: 10.7717/peerj.13381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 01/13/2023] Open
Abstract
Smoothened (SMO) protein is a member of the G protein-coupled receptor (GPCR) family that is involved in the Hedgehog (Hh) signaling pathway. It is a putative target for treating various cancers, including medulloblastoma and basal cell carcinoma (BCC). Characterizing membrane proteins such as SMO in their native state is highly beneficial for the development of effective pharmaceutical drugs, as their structures and functions are retained to the highest extent in this state. Therefore, although SMO protein is conventionally solubilized in detergent micelles, incorporating the protein in a lipid-based membrane mimic is still required. In this study, we used styrene maleic acid (SMA) copolymer that directly extracted membrane protein and surrounding lipids as well as formed the so-called polymer nanodiscs, to solubilize and purify the SMO transmembrane domain encapsulated by SMA-nanodiscs. The obtained SMA-nanodiscs showed high homogeneity and maintained the physiological activity of SMO protein, thereby enabling the measurement of the dissociation constant (Kd) for SMO ligands SMO-ligands Shh Signaling Antagonist V (SANT-1) and Smoothened Agonist (SAG) using ligand-based solution nuclear magnetic resonance spectroscopy. This work paves the way for investigating the structure, function, and drug development of SMO proteins in a native-like lipid environment.
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Affiliation(s)
- Lina Zhu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China,High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hongxin Zhao
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Yizhuo Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Chuandi Yu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Juanjuan Liu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Ling Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Zehua Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Han Dai
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Junfeng Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China,High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Lei Zhu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
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11
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Morrison KA, Wood L, Edler KJ, Doutch J, Price GJ, Koumanov F, Whitley P. Membrane extraction with styrene-maleic acid copolymer results in insulin receptor autophosphorylation in the absence of ligand. Sci Rep 2022; 12:3532. [PMID: 35241773 PMCID: PMC8894449 DOI: 10.1038/s41598-022-07606-5] [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: 09/24/2021] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
Extraction of integral membrane proteins with poly(styrene-co-maleic acid) provides a promising alternative to detergent extraction. A major advantage of extraction using copolymers rather than detergent is the retention of the lipid bilayer around the proteins. Here we report the first functional investigation of the mammalian insulin receptor which was extracted from cell membranes using poly(styrene-co-maleic acid). We found that the copolymer efficiently extracted the insulin receptor from 3T3L1 fibroblast membranes. Surprisingly, activation of the insulin receptor and proximal downstream signalling was detected upon copolymer extraction even in the absence of insulin stimulation. Insulin receptor and IRS1 phosphorylations were above levels measured in the control extracts made with detergents. However, more distal signalling events in the insulin signalling cascade, such as the phosphorylation of Akt were not observed. Following copolymer extraction, in vitro addition of insulin had no further effect on insulin receptor or IRS1 phosphorylation. Therefore, under our experimental conditions, the insulin receptor is not functionally responsive to insulin. This study is the first to investigate receptor tyrosine kinases extracted from mammalian cells using a styrene-maleic acid copolymer and highlights the importance of thorough functional characterisation when using this method of protein extraction.
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Affiliation(s)
- Kerrie A Morrison
- Department of Biology and Biochemistry, University of Bath, Bath, UK.,Department of Chemistry, University of Bath, Bath, UK.,Centre for Sustainable Circular Technologies, University of Bath, Bath, UK
| | - Laura Wood
- Department of Biology and Biochemistry, University of Bath, Bath, UK.,Department for Health, Centre for Nutrition, Exercise and Metabolism, University of Bath, Bath, UK
| | - Karen J Edler
- Department of Chemistry, University of Bath, Bath, UK
| | - James Doutch
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
| | - Gareth J Price
- Department of Chemistry, University of Bath, Bath, UK.,Department of Chemistry, Khalifa University, Abu Dhabi, UAE
| | - Francoise Koumanov
- Department for Health, Centre for Nutrition, Exercise and Metabolism, University of Bath, Bath, UK.
| | - Paul Whitley
- Department of Biology and Biochemistry, University of Bath, Bath, UK.
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12
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Conformational trapping of an ABC transporter in polymer lipid nanoparticles. Biochem J 2022; 479:145-159. [PMID: 35050326 PMCID: PMC8883494 DOI: 10.1042/bcj20210312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
Abstract
ATP-binding cassette (ABC) proteins play important roles in cells as importers and exporters but as membrane proteins they are subject to well-known challenges of isolating pure and stable samples for study. One solution to this problem is to use styrene-maleic acid lipid particles (SMALPs). Styrene-maleic acid (SMA) can be added directly to membranes, forming stable nanoparticles incorporating membrane proteins and lipids. Here we use Sav1866, a well-characterised bacterial protein, as a proxy for ABC proteins in general. We show that stable and monodispersed Sav1866 can be purified at high yield using SMA. This protein can be used for biophysical characterisations showing that its overall structure is consistent with existing evidence. However, like other ABC proteins in SMALPs it does not hydrolyse ATP. The lack of ATPase activity in ABC–SMALPs may result from conformational trapping of the proteins in SMALPs. Undertaken in a controlled manner, conformational trapping is a useful tool to stabilise protein samples into a single conformation for structural studies. Due to their inability to hydrolyse ATP, the conformation of Sav1866–SMALPs cannot be altered using ATP and vanadate after purification. To achieve controlled trapping of Sav1866–SMALPs we show that Sav1866 in crude membranes can be incubated with ATP, magnesium and sodium orthovanadate. Subsequent solubilisation and purification with SMA produces a sample of Sav1866–SMALPs with enhanced stability, and in a single conformational state. This method may be generally applicable to vanadate-sensitive ABC proteins and overcomes a limitation of the SMALP system for the study of this protein family.
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13
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Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Karlova MG, Yudenko A, Remeeva A, Ryzhykau YL, Gushchin I, Gordeliy VI, Sokolova OS, Steinhoff HJ, Kirpichnikov MP, Shaitan KV. Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:361. [PMID: 35159706 PMCID: PMC8838559 DOI: 10.3390/nano12030361] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene-maleic acid (SMA), diisobutylene-maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.
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Affiliation(s)
- Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
| | - Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia Voskoboynikova
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Karlova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Valentin I. Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
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14
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Morrison KA, Heesom KJ, Edler KJ, Doutch J, Price GJ, Koumanov F, Whitley P. Development of Methodology to Investigate the Surface SMALPome of Mammalian Cells. Front Mol Biosci 2021; 8:780033. [PMID: 34869600 PMCID: PMC8637157 DOI: 10.3389/fmolb.2021.780033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
Extraction of membrane proteins from biological membranes has traditionally involved detergents. In the past decade, a new technique has been developed, which uses styrene maleic acid (SMA) copolymers to extract membrane proteins into nanodiscs without the requirement of detergents. SMA nanodiscs are compatible with analytical techniques, such as small-angle scattering, NMR spectroscopy, and DLS, and are therefore an attractive medium for membrane protein characterization. While mass spectrometry has also been reported as a technique compatible with copolymer extraction, most studies have focused on lipidomics, which involves solvent extraction of lipids from nanodiscs prior to mass-spectrometry analysis. In this study, mass spectrometry proteomics was used to investigate whether there are qualitative or quantitative differences in the mammalian plasma membrane proteins extracted with SMA compared to a detergent control. For this, cell surface proteins of 3T3L1 fibroblasts were biotinylated and extracted using either SMA or detergent. Following affinity pull-down of biotinylated proteins with NeutrAvidin beads, samples were analyzed by nanoLC-MS. Here, we report for the first time, a global proteomics protocol for detection of a mammalian cell "SMALPome", membrane proteins incorporated into SMA nanodiscs. Removal of SMA from samples prior to processing of samples for mass spectrometry was a crucial step in the protocol. The reported surface SMALPome of 3T3L1 fibroblasts consists of 205 integral membrane proteins. It is apparent that the detergent extraction method used is, in general, quantitatively more efficient at extracting proteins from the plasma membrane than SMA extraction. However, samples prepared following detergent extraction contained a greater proportion of proteins that were considered to be "non-specific" than in samples prepared from SMA extracts. Tantalizingly, it was also observed that proteins detected uniquely or highly preferentially in pull-downs from SMA extracts were primarily multi-spanning membrane proteins. These observations hint at qualitative differences between SMA and detergent extraction that are worthy of further investigation.
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Affiliation(s)
- Kerrie A. Morrison
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Department of Chemistry, University of Bath, Bath, United Kingdom
- Centre for Sustainable Circular Technologies, University of Bath, Bath, United Kingdom
| | - Kate J. Heesom
- University of Bristol, Proteomics Facility, Bristol, United Kingdom
| | - Karen J. Edler
- Department of Chemistry, University of Bath, Bath, United Kingdom
| | - James Doutch
- Rutherford Appleton Laboratory, ISIS Pulsed Neutron and Muon Source, Harwell Oxford, United Kingdom
| | - Gareth J. Price
- Department of Chemistry, University of Bath, Bath, United Kingdom
- Department of Chemistry, Khalifa University, Abu Dhabi, United Arab Emirates
| | | | - Paul Whitley
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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15
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Farrelly MD, Martin LL, Thang SH. Polymer Nanodiscs and Their Bioanalytical Potential. Chemistry 2021; 27:12922-12939. [PMID: 34180107 DOI: 10.1002/chem.202101572] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/21/2022]
Abstract
Membrane proteins (MPs) play a pivotal role in cellular function and are therefore predominant pharmaceutical targets. Although detailed understanding of MP structure and mechanistic activity is invaluable for rational drug design, challenges are associated with the purification and study of MPs. This review delves into the historical developments that became the prelude to currently available membrane mimetic technologies before shining a spotlight on polymer nanodiscs. These are soluble nanosized particles capable of encompassing MPs embedded in a phospholipid ring. The expanding range of reported amphipathic polymer nanodisc materials is presented and discussed in terms of their tolerance to different solution conditions and their nanodisc properties. Finally, the analytical scope of polymer nanodiscs is considered in both the demonstration of basic nanodisc parameters as well as in the elucidation of structures, lipid-protein interactions, and the functional mechanisms of reconstituted membrane proteins. The final emphasis is given to the unique benefits and applications demonstrated for native nanodiscs accessed through a detergent free process.
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Affiliation(s)
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton, 3800, Vic, Australia
| | - San H Thang
- School of Chemistry, Monash University, Clayton, 3800, Vic, Australia
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16
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Grime RL, Logan RT, Nestorow SA, Sridhar P, Edwards PC, Tate CG, Klumperman B, Dafforn TR, Poyner DR, Reeves PJ, Wheatley M. Differences in SMA-like polymer architecture dictate the conformational changes exhibited by the membrane protein rhodopsin encapsulated in lipid nano-particles. NANOSCALE 2021; 13:13519-13528. [PMID: 34477756 PMCID: PMC8359648 DOI: 10.1039/d1nr02419a] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Membrane proteins are of fundamental importance to cellular processes and nano-encapsulation strategies that preserve their native lipid bilayer environment are particularly attractive for studying and exploiting these proteins. Poly(styrene-co-maleic acid) (SMA) and related polymers poly(styrene-co-(N-(3-N',N'-dimethylaminopropyl)maleimide)) (SMI) and poly(diisobutylene-alt-maleic acid) (DIBMA) have revolutionised the study of membrane proteins by spontaneously solubilising membrane proteins direct from cell membranes within nanoscale discs of native bilayer called SMA lipid particles (SMALPs), SMILPs and DIBMALPs respectively. This systematic study shows for the first time, that conformational changes of the encapsulated protein are dictated by the solubilising polymer. The photoactivation pathway of rhodopsin (Rho), a G-protein-coupled receptor (GPCR), comprises structurally-defined intermediates with characteristic absorbance spectra that revealed conformational restrictions with styrene-containing SMA and SMI, so that photoactivation proceeded only as far as metarhodopsin-I, absorbing at 478 nm, in a SMALP or SMILP. In contrast, full attainment of metarhodopsin-II, absorbing at 382 nm, was observed in a DIBMALP. Consequently, different intermediate states of Rho could be generated readily by simply employing different SMA-like polymers. Dynamic light-scattering and analytical ultracentrifugation revealed differences in size and thermostability between SMALP, SMILP and DIBMALP. Moreover, encapsulated Rho exhibited different stability in a SMALP, SMILP or DIBMALP. Overall, we establish that SMA, SMI and DIBMA constitute a 'toolkit' of solubilising polymers, so that selection of the appropriate solubilising polymer provides a spectrum of useful attributes for studying membrane proteins.
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Affiliation(s)
- Rachael L Grime
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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17
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Elgeti M, Hubbell WL. DEER Analysis of GPCR Conformational Heterogeneity. Biomolecules 2021; 11:778. [PMID: 34067265 PMCID: PMC8224605 DOI: 10.3390/biom11060778] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent a large class of transmembrane helical proteins which are involved in numerous physiological signaling pathways and therefore represent crucial pharmacological targets. GPCR function and the action of therapeutic molecules are defined by only a few parameters, including receptor basal activity, ligand affinity, intrinsic efficacy and signal bias. These parameters are encoded in characteristic receptor conformations existing in equilibrium and their populations, which are thus of paramount interest for the understanding of receptor (mal-)functions and rational design of improved therapeutics. To this end, the combination of site-directed spin labeling and EPR spectroscopy, in particular double electron-electron resonance (DEER), is exceedingly valuable as it has access to sub-Angstrom spatial resolution and provides a detailed picture of the number and populations of conformations in equilibrium. This review gives an overview of existing DEER studies on GPCRs with a focus on the delineation of structure/function frameworks, highlighting recent developments in data analysis and visualization. We introduce "conformational efficacy" as a parameter to describe ligand-specific shifts in the conformational equilibrium, taking into account the loose coupling between receptor segments observed for different GPCRs using DEER.
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Affiliation(s)
- Matthias Elgeti
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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18
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Pitch SG, Yao W, Szundi I, Fay J, Chen E, Shumate A, Kliger DS, Farrens DL. Functional integrity of membrane protein rhodopsin solubilized by styrene-maleic acid copolymer. Biophys J 2021; 120:3508-3515. [PMID: 34022241 DOI: 10.1016/j.bpj.2021.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/18/2021] [Accepted: 05/13/2021] [Indexed: 11/25/2022] Open
Abstract
Membrane proteins often require solubilization to study their structure or define the mechanisms underlying their function. In this study, the functional properties of the membrane protein rhodopsin in its native lipid environment were investigated after being solubilized with styrene-maleic acid (SMA) copolymer. The static absorption spectra of rhodopsin before and after the addition of SMA were recorded at room temperature to quantify the amount of membrane protein solubilized. The samples were then photobleached to analyze the functionality of rhodopsin upon solubilization. Samples with low or high SMA/rhodopsin ratios were compared to find a threshold in which the maximal amount of active rhodopsin was solubilized from membrane suspensions. Interestingly, whereas the highest SMA/rhodopsin ratios yielded the most solubilized rhodopsin, the rhodopsin produced under these conditions could not reach the active (Meta II) state upon photoactivation. The results confirm that SMA is a useful tool for membrane protein research, but SMA added in excess can interfere with the dynamics of protein activation.
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Affiliation(s)
- Stephanie G Pitch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Weekie Yao
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Jonathan Fay
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - David L Farrens
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon.
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19
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Abstract
The biological process of photosynthesis was critical in catalyzing the oxygenation of Earth’s atmosphere 2.5 billion years ago, changing the course of development of life on Earth. Recently, the fields of applied and synthetic photosynthesis have utilized the light-driven protein–pigment supercomplexes central to photosynthesis for the photocatalytic production of fuel and other various valuable products. The reaction center Photosystem I is of particular interest in applied photosynthesis due to its high stability post-purification, non-geopolitical limitation, and its ability to generate the greatest reducing power found in nature. These remarkable properties have been harnessed for the photocatalytic production of a number of valuable products in the applied photosynthesis research field. These primarily include photocurrents and molecular hydrogen as fuels. The use of artificial reaction centers to generate substrates and reducing equivalents to drive non-photoactive enzymes for valuable product generation has been a long-standing area of interest in the synthetic photosynthesis research field. In this review, we cover advances in these areas and further speculate synthetic and applied photosynthesis as photocatalysts for the generation of valuable products.
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20
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Hothersall JD, Jones AY, Dafforn TR, Perrior T, Chapman KL. Releasing the technical 'shackles' on GPCR drug discovery: opportunities enabled by detergent-free polymer lipid particle (PoLiPa) purification. Drug Discov Today 2020; 25:S1359-6446(20)30337-8. [PMID: 32835806 DOI: 10.1016/j.drudis.2020.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/04/2020] [Accepted: 08/13/2020] [Indexed: 12/19/2022]
Abstract
G-protein-coupled receptor (GPCR) drug research is presently hindered by the technical challenges associated with generating purified receptors. Consequently, the application of critical modern discovery technologies has been limited, and the vast untapped opportunity for new GPCR-directed medicines is not being realised. A simple but transformative solution is to purify receptors without removing them from their native phospholipid environment by using polymer lipid particle (PoLiPa) technology, with reagents such as styrene-maleic acid co-polymer (SMA). Compared with contemporary detergent-based and stabilising mutagenesis methods, the PoLiPa approach is simple and generic and, therefore, offers huge advantages, with the potential to revolutionise GPCR research by facilitating the availability of the purified receptors that are required for structural biology, biophysical, and panning technologies.
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Affiliation(s)
- J Daniel Hothersall
- Domainex Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden, CB10 1XL, UK.
| | - Andrew Y Jones
- Domainex Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden, CB10 1XL, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Trevor Perrior
- Domainex Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden, CB10 1XL, UK
| | - Kathryn L Chapman
- Domainex Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden, CB10 1XL, UK
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21
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Synthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical Production. Trends Biotechnol 2020; 38:766-778. [DOI: 10.1016/j.tibtech.2019.12.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 01/26/2023]
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22
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Grime RL, Goulding J, Uddin R, Stoddart LA, Hill SJ, Poyner DR, Briddon SJ, Wheatley M. Single molecule binding of a ligand to a G-protein-coupled receptor in real time using fluorescence correlation spectroscopy, rendered possible by nano-encapsulation in styrene maleic acid lipid particles. NANOSCALE 2020; 12:11518-11525. [PMID: 32428052 DOI: 10.1039/d0nr01060j] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The fundamental importance of membrane proteins in cellular processes has driven a marked increase in the use of membrane mimetic approaches for studying and exploiting these proteins. Nano-encapsulation strategies which preserve the native lipid bilayer environment are particularly attractive. Consequently, the use of poly(styrene co-maleic acid) (SMA) has been widely adopted to solubilise proteins directly from cell membranes by spontaneously forming "SMA Lipid Particles" (SMALPs). G-protein-coupled receptors (GPCRs) are ubiquitous "chemical switches", are central to cell signalling throughout the evolutionary tree, form the largest family of membrane proteins in humans and are a major drug discovery target. GPCR-SMALPs that retain binding capability would be a versatile platform for a wide range of down-stream applications. Here, using the adenosine A2A receptor (A2AR) as an archetypical GPCR, we show for the first time the utility of fluorescence correlation spectroscopy (FCS) to characterise the binding capability of GPCRs following nano-encapsulation. Unbound fluorescent ligand CA200645 exhibited a monophasic autocorrelation curve (dwell time, τD = 68 ± 2 μs; diffusion coefficient, D = 287 ± 15 μm2 s-1). In the presence of A2AR-SMALP, bound ligand was also evident (τD = 625 ± 23 μs; D = 30 ± 4 μm2 s-1). Using a non-receptor control (ZipA-SMALP) plus competition binding confirmed that this slower component represented binding to the encapsulated A2AR. Consequently, the combination of GPCR-SMALP and FCS is an effective platform for the quantitative real-time characterisation of nano-encapsulated receptors, with single molecule sensitivity, that will have widespread utility for future exploitation of GPCR-SMALPs in general.
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Affiliation(s)
- Rachael L Grime
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Joelle Goulding
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Romez Uddin
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Leigh A Stoddart
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Stephen J Hill
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David R Poyner
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Stephen J Briddon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Mark Wheatley
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Alison Gingell Building, Coventry University, Coventry, CV1 2DS, UK.
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23
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Wiseman DN, Otchere A, Patel JH, Uddin R, Pollock NL, Routledge SJ, Rothnie AJ, Slack C, Poyner DR, Bill RM, Goddard AD. Expression and purification of recombinant G protein-coupled receptors: A review. Protein Expr Purif 2020; 167:105524. [PMID: 31678667 PMCID: PMC6983937 DOI: 10.1016/j.pep.2019.105524] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 01/15/2023]
Abstract
Given their extensive role in cell signalling, GPCRs are significant drug targets; despite this, many of these receptors have limited or no available prophylaxis. Novel drug design and discovery significantly rely on structure determination, of which GPCRs are typically elusive. Progress has been made thus far to produce sufficient quantity and quality of protein for downstream analysis. As such, this review highlights the systems available for recombinant GPCR expression, with consideration of their advantages and disadvantages, as well as examples of receptors successfully expressed in these systems. Additionally, an overview is given on the use of detergents and the styrene maleic acid (SMA) co-polymer for membrane solubilisation, as well as purification techniques.
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Affiliation(s)
- Daniel N Wiseman
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Abigail Otchere
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Jaimin H Patel
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Romez Uddin
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | | | - Sarah J Routledge
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Alice J Rothnie
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Cathy Slack
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - David R Poyner
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Roslyn M Bill
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Alan D Goddard
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
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24
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Routledge SJ, Jamshad M, Little HA, Lin YP, Simms J, Thakker A, Spickett CM, Bill RM, Dafforn TR, Poyner DR, Wheatley M. Ligand-induced conformational changes in a SMALP-encapsulated GPCR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183235. [PMID: 32126232 PMCID: PMC7156913 DOI: 10.1016/j.bbamem.2020.183235] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/27/2022]
Abstract
The adenosine 2A receptor (A2AR), a G-protein-coupled receptor (GPCR), was solubilised and purified encapsulated in styrene maleic acid lipid particles (SMALPs). The purified A2AR-SMALP was associated with phospholipids characteristic of the plasma membrane of Pichia pastoris, the host used for its expression, confirming that the A2AR-SMALP encapsulated native lipids. The fluorescence spectrum of the A2AR-SMALP showed a characteristic broad emission peak at 330 nm, produced by endogenous Trp residues. The inverse agonist ZM241385 caused 30% increase in fluorescence emission, unusually accompanied by a red-shift in the emission wavelength. The emission spectrum also showed sub-peaks at 321 nm, 335 nm and 350 nm, indicating that individual Trp inhabited different environments following ZM241385 addition. There was no effect of the agonist NECA on the A2AR-SMALP fluorescence spectrum. Substitution of two Trp residues by Tyr suggested that ZM241385 affected the environment and mobility of Trp2466.48 in TM6 and Trp2687.33 at the extracellular face of TM7, causing transition to a more hydrophobic environment. The fluorescent moiety IAEDANS was site-specifically introduced at the intracellular end of TM6 (residue 2316.33) to report on the dynamic cytoplasmic face of the A2AR. The inverse agonist ZM241385 caused a concentration-dependent increase in fluorescence emission as the IAEDANS moved to a more hydrophobic environment, consistent with closing the G-protein binding crevice. NECA generated only 30% of the effect of ZM241385. This study provides insight into the SMALP environment; encapsulation supported constitutive activity of the A2AR and ZM241385-induced conformational transitions but the agonist NECA generated only small effects. Conformational changes in the A2AR monitored in a nano-scale membrane disc (SMALP). Profile of phospholipids in A2AR-SMALP similar to the plasma membrane. A partially-active conformation of A2AR is supported in a SMALP. Inverse agonist induced dose-dependent conformational transitions in A2AR-SMALP. In contrast to inverse agonist, agonist induced only small conformational changes.
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Affiliation(s)
| | - Mohammed Jamshad
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Haydn A Little
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Yu-Pin Lin
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - John Simms
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Alpesh Thakker
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | | | - Roslyn M Bill
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - David R Poyner
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK.
| | - Mark Wheatley
- Centre for Sport, Exercise and Life Sciences, Alison Gingell Building, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 2DS, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
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25
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Miljus T, Sykes DA, Harwood CR, Vuckovic Z, Veprintsev DB. GPCR Solubilization and Quality Control. Methods Mol Biol 2020; 2127:105-127. [PMID: 32112318 DOI: 10.1007/978-1-0716-0373-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
G protein-coupled receptors (GPCRs) are versatile membrane proteins involved in the regulation of many physiological processes and pathological conditions, making them interesting pharmacological targets. In order to study their structure and function, GPCRs are traditionally extracted from membranes using detergents. However, due to their hydrophobic nature, intrinsic instability in aqueous solutions, and their denaturing effects, the isolation of properly folded and functional GPCRs is not trivial. Therefore, it is of crucial importance to solubilize receptors under mild conditions and control the sample quality subsequently. Here we describe widely used methods for small-scale GPCR solubilization, followed by quality control based on fluorescence size-exclusion chromatography, SDS-PAGE, temperature-induced protein unfolding (CPM dye binding) and fluorescent ligand binding assay. These methods can easily be used to assess the thermostability and functionality of a GPCR sample exposed to different conditions, such as the use of various detergents, addition of lipids and ligands, making them valuable for obtaining an optimal sample quality for structural and functional studies.
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Affiliation(s)
- Tamara Miljus
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Zürich, Switzerland
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, 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, 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, UK
| | - Ziva Vuckovic
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Zürich, Switzerland
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
- Department of Biology, ETH Zürich, Zürich, Switzerland.
- 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, UK.
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26
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Brady NG, Qian S, Bruce BD. Analysis of styrene maleic acid alternating copolymer supramolecular assemblies in solution by small angle X-ray scattering. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2018.11.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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The lipid environment of Escherichia coli Aquaporin Z. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:431-440. [DOI: 10.1016/j.bbamem.2018.10.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 11/22/2022]
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28
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Brady NG, Li M, Ma Y, Gumbart JC, Bruce BD. Non-detergent isolation of a cyanobacterial photosystem I using styrene maleic acid alternating copolymers. RSC Adv 2019; 9:31781-31796. [PMID: 35527920 PMCID: PMC9072662 DOI: 10.1039/c9ra04619d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/02/2019] [Indexed: 11/21/2022] Open
Abstract
Trimeric Photosystem I (PSI) from the thermophilic cyanobacteriumThermosynechococcus elongatus(Te) is the largest membrane protein complex to be encapsulated within a SMALP to date.
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Affiliation(s)
- Nathan G. Brady
- Department of Biochemistry & Cellular and Molecular Biology
- University of Tennessee at Knoxville
- Knoxville
- USA
| | - Meng Li
- Department of Biochemistry & Cellular and Molecular Biology
- University of Tennessee at Knoxville
- Knoxville
- USA
- Bredesen Center for Interdisciplinary Research and Education
| | - Yue Ma
- Department of Biochemistry & Cellular and Molecular Biology
- University of Tennessee at Knoxville
- Knoxville
- USA
| | | | - Barry D. Bruce
- Department of Biochemistry & Cellular and Molecular Biology
- University of Tennessee at Knoxville
- Knoxville
- USA
- Bredesen Center for Interdisciplinary Research and Education
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29
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Membrane protein nanoparticles: the shape of things to come. Biochem Soc Trans 2018; 46:1495-1504. [PMID: 30464048 PMCID: PMC6299238 DOI: 10.1042/bst20180139] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/23/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022]
Abstract
The use of styrene–maleic acid (SMA) for the purification of a wide range of membrane proteins (MPs) from both prokaryotic and eukaryotic sources has begun to make an impact in the field of MP biology. This method is growing in popularity as a means to purify and thoroughly investigate the structure and function of MPs and biological membranes. The amphiphilic SMA copolymer can effectively extract MPs directly from a native lipid bilayer to form discs ∼10 nm in diameter. The resulting lipid particles, or styrene–maleic acid lipid particles (SMALPs), contain SMA, protein and membrane lipid. MPs purified in SMALPs are able to retain their native structure and, in many cases, functional activity, and growing evidence suggests that MPs purified using SMA have enhanced thermal stability compared with detergent-purified proteins. The SMALP method is versatile and is compatible with a wide range of cell types across taxonomic domains. It can readily be adapted to replace detergent in many protein purification methods, often with only minor changes made to the existing protocol. Moreover, biophysical analysis and structural determination may now be a possibility for many large, unstable MPs. Here, we review recent advances in the area of SMALP purification and how it is affecting the field of MP biology, critically assess recent progress made with this method, address some of the associated technical challenges which may remain unresolved and discuss opportunities for exploiting SMALPs to expand our understanding of structural and functional properties of MPs.
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30
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Thonghin N, Kargas V, Clews J, Ford RC. Cryo-electron microscopy of membrane proteins. Methods 2018; 147:176-186. [DOI: 10.1016/j.ymeth.2018.04.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022] Open
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31
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Stroud Z, Hall SCL, Dafforn TR. Purification of membrane proteins free from conventional detergents: SMA, new polymers, new opportunities and new insights. Methods 2018; 147:106-117. [PMID: 29608964 DOI: 10.1016/j.ymeth.2018.03.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/19/2018] [Accepted: 03/26/2018] [Indexed: 11/17/2022] Open
Abstract
Membrane proteins remain a somewhat enigmatic group of biomolecules. On the one hand they mediate some of the most important processes in biology with molecular mechanisms that are often elegantly complex. On the other hand they are exceptionally challenging to produce, making studies of membrane protein structure and function among the most difficult projects undertaken by biochemists. The central issue with studies of a membrane protein has been the need to extract them from their native lipid environment before purification and production of a homogenous sample. Historical approaches have utilized detergent solubilisation but these often lead to a sample with low activity and stability. In the past 15 years a new approach that focuses on preserving the local lipid environment surrounding the membrane proteins has been developed. The latest, and perhaps most complete, incarnation of this method has been the use of polymers based on styrene maleic acid (SMA) to stabilise nanoscale discs of lipid that contain membrane proteins. In this review we examine the range of SMA-related polymers that have now been shown to have utility in the production of membrane proteins. We discuss the differences between the polymers and attempt to discover rules and trends that explain their behavior.
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Affiliation(s)
- Zoe Stroud
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Stephen C L Hall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK.
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32
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Fungal G-protein-coupled receptors: mediators of pathogenesis and targets for disease control. Nat Microbiol 2018; 3:402-414. [DOI: 10.1038/s41564-018-0127-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/09/2018] [Indexed: 12/31/2022]
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33
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Swainsbury DJK, Scheidelaar S, Foster N, van Grondelle R, Killian JA, Jones MR. The effectiveness of styrene-maleic acid (SMA) copolymers for solubilisation of integral membrane proteins from SMA-accessible and SMA-resistant membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2017; 1859:2133-2143. [PMID: 28751090 PMCID: PMC5593810 DOI: 10.1016/j.bbamem.2017.07.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/14/2017] [Accepted: 07/23/2017] [Indexed: 11/27/2022]
Abstract
Solubilisation of biological lipid bilayer membranes for analysis of their protein complement has traditionally been carried out using detergents, but there is increasing interest in the use of amphiphilic copolymers such as styrene maleic acid (SMA) for the solubilisation, purification and characterisation of integral membrane proteins in the form of protein/lipid nanodiscs. Here we survey the effectiveness of various commercially-available formulations of the SMA copolymer in solubilising Rhodobacter sphaeroides reaction centres (RCs) from photosynthetic membranes. We find that formulations of SMA with a 2:1 or 3:1 ratio of styrene to maleic acid are almost as effective as detergent in solubilising RCs, with the best solubilisation by short chain variants (<30kDa weight average molecular weight). The effectiveness of 10kDa 2:1 and 3:1 formulations of SMA to solubilise RCs gradually declined when genetically-encoded coiled-coil bundles were used to artificially tether normally monomeric RCs into dimeric, trimeric and tetrameric multimers. The ability of SMA to solubilise reaction centre-light harvesting 1 (RC-LH1) complexes from densely packed and highly ordered photosynthetic membranes was uniformly low, but could be increased through a variety of treatments to increase the lipid:protein ratio. However, proteins isolated from such membranes comprised clusters of complexes in small membrane patches rather than individual proteins. We conclude that short-chain 2:1 and 3:1 formulations of SMA are the most effective in solubilising integral membrane proteins, but that solubilisation efficiencies are strongly influenced by the size of the target protein and the density of packing of proteins in the membrane.
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Affiliation(s)
- David J K Swainsbury
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Stefan Scheidelaar
- Membrane Biochemistry & Biophysics, Utrecht University, Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands
| | - Nicholas Foster
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Rienk van Grondelle
- Division of Physics and Astronomy, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Utrecht University, Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands
| | - Michael R Jones
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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34
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Hu Z, Ho JC, Nallani M. Synthetic (polymer) biology (membrane): functionalization of polymer scaffolds for membrane proteins. Curr Opin Biotechnol 2017; 46:51-56. [DOI: 10.1016/j.copbio.2016.10.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/24/2016] [Indexed: 12/13/2022]
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35
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Abstract
The use of styrene maleic acid lipid particles (SMALPs) for the purification of membrane proteins (MPs) is a rapidly developing technology. The amphiphilic copolymer of styrene and maleic acid (SMA) disrupts biological membranes and can extract membrane proteins in nanodiscs of approximately 10 nm diameter. These discs contain SMA, protein and membrane lipids. There is evidence that MPs in SMALPs retain their native structures and functions, in some cases with enhanced thermal stability. In addition, the method is compatible with biological buffers and a wide variety of biophysical and structural analysis techniques. The use of SMALPs to solubilize and stabilize MPs offers a new approach in our attempts to understand, and influence, the structure and function of MPs and biological membranes. In this review, we critically assess progress with this method, address some of the associated technical challenges, and discuss opportunities for exploiting SMA and SMALPs to expand our understanding of MP biology.
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36
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Opportunities for therapeutic antibodies directed at G-protein-coupled receptors. Nat Rev Drug Discov 2017; 16:787-810. [PMID: 28706220 DOI: 10.1038/nrd.2017.91] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-protein-coupled receptors (GPCRs) are activated by a diverse range of ligands, from large proteins and proteases to small peptides, metabolites, neurotransmitters and ions. They are expressed on all cells in the body and have key roles in physiology and homeostasis. As such, GPCRs are one of the most important target classes for therapeutic drug discovery. The development of drugs targeting GPCRs has therapeutic value across a wide range of diseases, including cancer, immune and inflammatory disorders as well as neurological and metabolic diseases. The progress made by targeting GPCRs with antibody-based therapeutics, as well as technical hurdles to overcome, are presented and discussed in this Review. Antibody therapeutics targeting C-C chemokine receptor type 4 (CCR4), CCR5 and calcitonin gene-related peptide (CGRP) are used as illustrative clinical case studies.
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37
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Rehan S, Paavilainen VO, Jaakola VP. Functional reconstitution of human equilibrative nucleoside transporter-1 into styrene maleic acid co-polymer lipid particles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1059-1065. [DOI: 10.1016/j.bbamem.2017.02.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/30/2017] [Accepted: 02/26/2017] [Indexed: 12/14/2022]
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38
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Scheidelaar S, Koorengevel MC, van Walree CA, Dominguez JJ, Dörr JM, Killian JA. Effect of Polymer Composition and pH on Membrane Solubilization by Styrene-Maleic Acid Copolymers. Biophys J 2016; 111:1974-1986. [PMID: 27806279 PMCID: PMC5103014 DOI: 10.1016/j.bpj.2016.09.025] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/21/2016] [Accepted: 09/21/2016] [Indexed: 11/28/2022] Open
Abstract
The styrene-maleic acid (SMA) copolymer is rapidly gaining attention as a tool in membrane research, due to its ability to directly solubilize lipid membranes into nanodisk particles without the requirement of conventional detergents. Although many variants of SMA are commercially available, so far only SMA variants with a 2:1 and 3:1 styrene-to-maleic acid ratio have been used in lipid membrane studies. It is not known how SMA composition affects the solubilization behavior of SMA. Here, we systematically investigated the effect of varying the styrene/maleic acid on the properties of SMA in solution and on its interaction with membranes. Also the effect of pH was studied, because the proton concentration in the solution will affect the charge density and thereby may modulate the properties of the polymers. Using model membranes of 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipids at pH > pHagg, we found that membrane solubilization is promoted by a low charge density and by a relatively high fraction of maleic acid units in the polymer. Furthermore, it was found that a collapsed conformation of the polymer is required to ensure efficient insertion into the lipid membrane and that efficient solubilization may be improved by a more homogenous distribution of the maleic acid monomer units along the polymer chain. Altogether, the results show large differences in behavior between the SMA variants tested in the various steps of solubilization. The main conclusion is that the variant with a 2:1 styrene-to-maleic acid ratio is the most efficient membrane solubilizer in a wide pH range.
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Affiliation(s)
- Stefan Scheidelaar
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
| | - Martijn C Koorengevel
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Cornelius A van Walree
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Juan J Dominguez
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Jonas M Dörr
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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