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Abstract
The interactions between lipids and proteins are one of the most fundamental processes in living organisms, responsible for critical cellular events ranging from replication, cell division, signaling, and movement. Enabling the central coupling responsible for maintaining the functionality of the breadth of proteins, receptors, and enzymes that find their natural home in biological membranes, the fundamental mechanisms of recognition of protein for lipid, and vice versa, have been a focal point of biochemical and biophysical investigations for many decades. Complexes of lipids and proteins, such as the various lipoprotein factions, play central roles in the trafficking of important proteins, small molecules and metabolites and are often implicated in disease states. Recently an engineered lipoprotein particle, termed the nanodisc, a modified form of the human high density lipoprotein fraction, has served as a membrane mimetic for the investigation of membrane proteins and studies of lipid-protein interactions. In this review, we summarize the current knowledge regarding this self-assembling lipid-protein complex and provide examples for its utility in the investigation of a large number of biological systems.
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Haffke M, Duckely M, Bergsdorf C, Jaakola VP, Shrestha B. Development of a biochemical and biophysical suite for integral membrane protein targets: A review. Protein Expr Purif 2020; 167:105545. [DOI: 10.1016/j.pep.2019.105545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/18/2019] [Accepted: 11/24/2019] [Indexed: 12/11/2022]
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Kalienkova V, Alvadia C, Clerico Mosina V, Paulino C. Single-Particle Cryo-EM of Membrane Proteins in Lipid Nanodiscs. Methods Mol Biol 2020; 2127:245-273. [PMID: 32112327 DOI: 10.1007/978-1-0716-0373-4_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single-particle cryo-electron microscopy has become an indispensable technique in structural biology. In particular when studying membrane proteins, it allows the use of membrane-mimicking tools, which can be crucial for a comprehensive understanding of the structure-function relationship of the protein in its native environment. In this chapter we focus on the application of nanodiscs and use our recent studies on the TMEM16 family as an example.
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Affiliation(s)
- Valeria Kalienkova
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Carolina Alvadia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Vanessa Clerico Mosina
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Cristina Paulino
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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54
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Klöpfer K, Hagn F. Beyond detergent micelles: The advantages and applications of non-micellar and lipid-based membrane mimetics for solution-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:271-283. [PMID: 31779883 DOI: 10.1016/j.pnmrs.2019.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Membrane proteins are important players in signal transduction and the exchange of metabolites within or between cells. Thus, this protein class is the target of around 60 % of currently marketed drugs, emphasizing their essential biological role. Besides functional assays, structural and dynamical investigations on this protein class are crucial to fully understanding their functionality. Even though X-ray crystallography and electron microscopy are the main methods to determine structures of membrane proteins and their complexes, NMR spectroscopy can contribute essential information on systems that (a) do not crystallize and (b) are too small for EM. Furthermore, NMR is a versatile tool for monitoring functional dynamics of biomolecules at various time scales. A crucial aspect of such studies is the use of a membrane mimetic that resembles a native environment and thus enables the extraction of functional insights. In recent decades, the membrane protein NMR community has moved from rather harsh detergents to membrane systems having more native-like properties. In particular, most recently phospholipid nanodiscs have been developed and optimized mainly for solution-state NMR but are now also being used for solid-state NMR spectroscopy. Nanodiscs consist of a patch of a planar lipid bilayer that is encircled by different (bio-)polymers to form particles of defined and tunable size. In this review, we provide an overview of available membrane mimetics, including nanodiscs, amphipols and bicelles, that are suitable for high-resolution NMR spectroscopy and describe how these advanced membrane mimetics can facilitate NMR studies on the structure and dynamics of membrane proteins. Since the stability of membrane proteins depends critically on the chosen membrane mimetic, we emphasize the importance of a suitable system that is not necessarily developed for solution-state NMR applications and hence requires optimization for each membrane protein. However, lipid-based membrane mimetics offer the possibility of performing NMR experiments at elevated temperatures and studying ligand and partner protein complexes as well as their functional dynamics in a realistic membrane environment. In order to be able to make an informed decision during the selection of a suitable membrane system, we provide a detailed overview of the available options for various membrane protein classes and thereby facilitate this often-difficult selection process for a broad range of desired NMR applications.
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Affiliation(s)
- Kai Klöpfer
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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55
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Reading E. Assessing Membrane Protein Structural Dynamics within Lipid Nanodiscs. Trends Biochem Sci 2019; 44:989-990. [PMID: 31521386 DOI: 10.1016/j.tibs.2019.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Eamonn Reading
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, SE1 1DB, UK.
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56
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Kostelic MM, Ryan AM, Reid DJ, Noun JM, Marty MT. Expanding the Types of Lipids Amenable to Native Mass Spectrometry of Lipoprotein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1416-1425. [PMID: 30972726 PMCID: PMC6675625 DOI: 10.1007/s13361-019-02174-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 05/12/2023]
Abstract
Native mass spectrometry (MS) has become an important tool for the analysis of membrane proteins. Although detergent micelles are the most commonly used method for solubilizing membrane proteins for native MS, nanoscale lipoprotein complexes such as nanodiscs are emerging as a promising complementary approach because they solubilize membrane proteins in a lipid bilayer environment. However, prior native MS studies of intact nanodiscs have employed only a limited set of phospholipids that are similar in mass. Here, we extend the range of lipids that are amenable to native MS of nanodiscs by combining lipids with masses that are simple integer multiples of each other. Although these lipid combinations create complex distributions, overlap between resonant peak series allows interpretation of nanodisc spectra containing glycolipids, sterols, and cardiolipin. We also investigate the gas-phase stability of nanodiscs with these new lipids towards collisional activation. We observe that negative ionization mode or charge reduction stabilizes nanodiscs and is essential to preserving labile lipids such as sterols. These new approaches to native MS of nanodiscs will enable future studies of membrane proteins embedded in model membranes that more accurately mimic natural bilayers. Graphical Abstract.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Alex M Ryan
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Jibriel M Noun
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA.
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57
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Kostelic MM, Ryan AM, Reid DJ, Noun JM, Marty MT. Expanding the Types of Lipids Amenable to Native Mass Spectrometry of Lipoprotein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1416-1425. [PMID: 30972726 DOI: 10.1007/s13361-13019-02174-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 05/26/2023]
Abstract
Native mass spectrometry (MS) has become an important tool for the analysis of membrane proteins. Although detergent micelles are the most commonly used method for solubilizing membrane proteins for native MS, nanoscale lipoprotein complexes such as nanodiscs are emerging as a promising complementary approach because they solubilize membrane proteins in a lipid bilayer environment. However, prior native MS studies of intact nanodiscs have employed only a limited set of phospholipids that are similar in mass. Here, we extend the range of lipids that are amenable to native MS of nanodiscs by combining lipids with masses that are simple integer multiples of each other. Although these lipid combinations create complex distributions, overlap between resonant peak series allows interpretation of nanodisc spectra containing glycolipids, sterols, and cardiolipin. We also investigate the gas-phase stability of nanodiscs with these new lipids towards collisional activation. We observe that negative ionization mode or charge reduction stabilizes nanodiscs and is essential to preserving labile lipids such as sterols. These new approaches to native MS of nanodiscs will enable future studies of membrane proteins embedded in model membranes that more accurately mimic natural bilayers. Graphical Abstract.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Alex M Ryan
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Jibriel M Noun
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA.
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58
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High-throughput stability screening for detergent-solubilized membrane proteins. Sci Rep 2019; 9:10379. [PMID: 31316088 PMCID: PMC6637136 DOI: 10.1038/s41598-019-46686-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/03/2019] [Indexed: 01/08/2023] Open
Abstract
Protein stability in detergent or membrane-like environments is the bottleneck for structural studies on integral membrane proteins (IMP). Irrespective of the method to study the structure of an IMP, detergent solubilization from the membrane is usually the first step in the workflow. Here, we establish a simple, high-throughput screening method to identify optimal detergent conditions for membrane protein stabilization. We apply differential scanning fluorimetry in combination with scattering upon thermal denaturation to study the unfolding of integral membrane proteins. Nine different prokaryotic and eukaryotic membrane proteins were used as test cases to benchmark our detergent screening method. Our results show that it is possible to measure the stability and solubility of IMPs by diluting them from their initial solubilization condition into different detergents. We were able to identify groups of detergents with characteristic stabilization and destabilization effects for selected targets. We further show that fos-choline and PEG family detergents may lead to membrane protein destabilization and unfolding. Finally, we determined thenmodynamic parameters that are important indicators of IMP stability. The described protocol allows the identification of conditions that are suitable for downstream handling of membrane proteins during purification.
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59
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Frick M, Schmidt C. Mass spectrometry—A versatile tool for characterising the lipid environment of membrane protein assemblies. Chem Phys Lipids 2019; 221:145-157. [DOI: 10.1016/j.chemphyslip.2019.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 01/02/2023]
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Functional Reconstitution of HlyB, a Type I Secretion ABC Transporter, in Saposin-A Nanoparticles. Sci Rep 2019; 9:8436. [PMID: 31182729 PMCID: PMC6558041 DOI: 10.1038/s41598-019-44812-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/23/2019] [Indexed: 11/08/2022] Open
Abstract
Type I secretion systems (T1SS) are ubiquitous transport machineries in Gram-negative bacteria. They comprise a relatively simple assembly of three membrane-localised proteins: an inner-membrane complex composed of an ABC transporter and a membrane fusion protein, and a TolC-like outer membrane component. T1SS transport a wide variety of substrates with broad functional diversity. The ABC transporter hemolysin B (HlyB), for example, is part of the hemolysin A-T1SS in Escherichia coli. In contrast to canonical ABC transporters, an accessory domain, a C39 peptidase-like domain (CLD), is located at the N-terminus of HlyB and is essential for secretion. In this study, we have established an optimised purification protocol for HlyB and the subsequent reconstitution employing the saposin-nanoparticle system. We point out the negative influence of free detergent on the basal ATPase activity of HlyB, studied the influence of a lysolipid or lipid matrix on activity and present functional studies with the full-length substrate proHlyA in its folded and unfolded states, which both have a stimulatory effect on the ATPase activity.
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61
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Ural-Blimke Y, Flayhan A, Strauss J, Rantos V, Bartels K, Nielsen R, Pardon E, Steyaert J, Kosinski J, Quistgaard EM, Löw C. Structure of Prototypic Peptide Transporter DtpA from E. coli in Complex with Valganciclovir Provides Insights into Drug Binding of Human PepT1. J Am Chem Soc 2019; 141:2404-2412. [DOI: 10.1021/jacs.8b11343] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yonca Ural-Blimke
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Ali Flayhan
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Jan Strauss
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Vasileios Rantos
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Kim Bartels
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Rolf Nielsen
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Jan Kosinski
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Esben M. Quistgaard
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177 Stockholm, Sweden
- Department of Molecular Biology and Genetics − DANDRITE, Gustav Wieds Vej 10, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177 Stockholm, Sweden
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62
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iNEXT: a European facility network to stimulate translational structural biology. FEBS Lett 2018; 592:1909-1917. [DOI: 10.1002/1873-3468.13062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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