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Soulié M, Deletraz A, Wehbie M, Mahler F, Chantemargue B, Bouchemal I, Le Roy A, Petit-Härtlein I, Fieschi F, Breyton C, Ebel C, Keller S, Durand G. Rigid Cyclic Fluorinated Detergents: Fine-Tuning the Hydrophilic-Lipophilic Balance Controls Self-Assembling and Biochemical Properties. ACS APPLIED MATERIALS & INTERFACES 2024; 16:32971-32982. [PMID: 38885044 DOI: 10.1021/acsami.4c03359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
We report herein the synthesis of three detergents bearing a perfluorinated cyclohexyl group connected through a short, hydrogenated spacer (i.e., propyl, butyl, or pentyl) to a β-maltoside polar head that are, respectively, called FCymal-3, FCymal-4, and FCymal-5. Increasing the length of the spacer decreased the critical micellar concentration (CMC), as demonstrated by surface tension (SFT) and isothermal titration calorimetry (ITC), from 5 mM for FCymal-3 to 0.7 mM for FCymal-5. The morphology of the micelles was studied by dynamic light scattering (DLS), analytical ultracentrifugation (AUC), and small-angle X-ray scattering (SAXS), indicating heterogeneous rod-like shapes. While micelles of FCymal-3 and -4 have similar hydrodynamic diameters of ∼10 nm, those of FCymal-5 were twice as large. We also investigated the ability of the detergents to solubilize lipid membranes made of 1-palmitoyl-2-oleyl-sn-glycero-3-phosphocholine (POPC). Molecular modeling indicated that the FCymal detergents generate disorder in lipid bilayers, with FCymal-3 being inserted more deeply into bilayers than FCymal-4 and -5. This was experimentally confirmed using POPC vesicles that were completely solubilized within 2 h with FCymal-3, whereas FCymal-5 required >8 h. A similar trend was noticed for the direct extraction of membrane proteins from E. coli membranes, with FCymal-3 being more potent than FCymal-5. An opposite trend was observed in terms of stabilization of the two model membrane proteins bacteriorhodopsin (bR) and SpNOX. In all three FCymal detergents, bR was stable for at least 2 months with no signs of aggregation. However, while the structural integrity of bR was fully preserved in FCymal-4 and -5, minor bleaching was observed in FCymal-3. Similarly, SpNOX exhibited the least activity in FCymal-3 and the highest activity in FCymal-5. By combining solubilizing and stabilizing potency, FCymal detergents push forward our expectations of the usefulness of fluorinated detergents for handling and investigating membrane proteins.
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Affiliation(s)
- Marine Soulié
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
- Avignon Université, Unité Propre de Recherche et d'Innovation, Equipe Synthèse et Systèmes Colloïdaux Bio-organiques, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Anais Deletraz
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Moheddine Wehbie
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Florian Mahler
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | | | - Ilham Bouchemal
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Aline Le Roy
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Christine Ebel
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Sandro Keller
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Grégory Durand
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
- Avignon Université, Unité Propre de Recherche et d'Innovation, Equipe Synthèse et Systèmes Colloïdaux Bio-organiques, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
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Jiko C, Li J, Moon Y, Tanaka Y, Gopalasingam CC, Shigematsu H, Chae PS, Kurisu G, Gerle C. NDT-C11 as a Viable Novel Detergent for Single Particle Cryo-EM. Chempluschem 2024:e202400242. [PMID: 38881532 DOI: 10.1002/cplu.202400242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/31/2024] [Accepted: 06/17/2024] [Indexed: 06/18/2024]
Abstract
Single particle cryo electron microscopy (cryo-EM) is now the major method for the determination of integral membrane protein structure. For the success of a given project the type of membrane mimetic used for extraction from the native cell membrane, purification to homogeneity and finally cryo-grid vitrification is crucial. Although small molecule amphiphiles - detergents - are the most widely used membrane mimetic, specific tailoring of detergent structure for single particle cryo-EM is rare and the demand for effective detergents not satisfied. Here, we compare the popular detergent lauryl maltose-neopentyl glycol (LMNG) with the novel detergent neopentyl glycol-derived triglucoside-C11 (NDT-C11) in its behavior as free detergent and when bound to two types of multisubunit membrane protein complexes - cyanobacterial photosystem I (PSI) and mammalian F-ATP synthase. We conclude that NDT-C11 has high potential to become a very useful detergent for single particle cryo-EM of integral membrane proteins.
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Affiliation(s)
- Chimari Jiko
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka, 590-0494, Japan
| | - Jiannan Li
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Youngsun Moon
- Department of Bionano Engineering, Hanyang University, Ansan, 155-88, South Korea
| | - Yoshito Tanaka
- Graduate School of Life Science, University of Hyogo, Kamigori, 678-1297, Japan
| | - Chai C Gopalasingam
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Sayo, 679-5148, Japan
| | - Hideki Shigematsu
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, 679-5148, Japan
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University, Ansan, 155-88, South Korea
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Christoph Gerle
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Sayo, 679-5148, Japan
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3
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Sawyer TK, Aral E, Staros JV, Bobst CE, Garman SC. Human Saposin B Ligand Binding and Presentation to α-Galactosidase A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.584535. [PMID: 38617236 PMCID: PMC11014568 DOI: 10.1101/2024.04.04.584535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Sphingolipid activator protein B (saposin B; SapB) is an essential activator of globotriaosylceramide (Gb3) catabolism by α-galactosidase A. However, the manner by which SapB stimulates α-galactosidase A activity remains unknown. To uncover the molecular mechanism of SapB presenting Gb3 to α-galactosidase A, we subjected the fluorescent substrate globotriaosylceramide-nitrobenzoxidazole (Gb3-NBD) to a series of biochemical and structural assays involving SapB. First, we showed that SapB stably binds Gb3-NBD using a fluorescence equilibrium binding assay, isolates Gb3-NBD from micelles, and facilitates α-galactosidase A cleavage of Gb3-NBD in vitro. Second, we crystallized SapB in the presence of Gb3-NBD and validated the ligand-bound assembly. Third, we captured transient interactions between SapB and α-galactosidase A by chemical cross-linking. Finally, we determined the crystal structure of SapB bound to α-galactosidase A. These findings establish general principles for molecular recognition in saposin:hydrolase complexes and highlight the utility of NBD reporter lipids in saposin biochemistry and structural biology.
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Affiliation(s)
- Thomas K Sawyer
- Department of Biochemistry & Molecular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Program in Molecular & Cellular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Efecan Aral
- Department of Biochemistry & Molecular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Program in Molecular & Cellular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - James V Staros
- Department of Biochemistry & Molecular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Cedric E Bobst
- Mass Spectrometry Core Facility, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Scott C Garman
- Department of Biochemistry & Molecular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Program in Molecular & Cellular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
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Di Cesare M, Kaplan E, Rendon J, Gerbaud G, Valimehr S, Gobet A, Ngo TAT, Chaptal V, Falson P, Martinho M, Dorlet P, Hanssen E, Jault JM, Orelle C. The transport activity of the multidrug ABC transporter BmrA does not require a wide separation of the nucleotide-binding domains. J Biol Chem 2024; 300:105546. [PMID: 38072053 PMCID: PMC10821409 DOI: 10.1016/j.jbc.2023.105546] [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: 07/07/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
ATP-binding cassette (ABC) transporters are ubiquitous membrane proteins responsible for the translocation of a wide diversity of substrates across biological membranes. Some of them confer multidrug or antimicrobial resistance to cancer cells and pathogenic microorganisms, respectively. Despite a wealth of structural data gained in the last two decades, the molecular mechanism of these multidrug efflux pumps remains elusive, including the extent of separation between the two nucleotide-binding domains (NBDs) during the transport cycle. Based on recent outward-facing structures of BmrA, a homodimeric multidrug ABC transporter from Bacillus subtilis, we introduced a cysteine mutation near the C-terminal end of the NBDs to analyze the impact of disulfide-bond formation on BmrA function. Interestingly, the presence of the disulfide bond between the NBDs did not prevent the ATPase, nor did it affect the transport of Hoechst 33342 and doxorubicin. Yet, the 7-amino-actinomycin D was less efficiently transported, suggesting that a further opening of the transporter might improve its ability to translocate this larger compound. We solved by cryo-EM the apo structures of the cross-linked mutant and the WT protein. Both structures are highly similar, showing an intermediate opening between their NBDs while their C-terminal extremities remain in close proximity. Distance measurements obtained by electron paramagnetic resonance spectroscopy support the intermediate opening found in these 3D structures. Overall, our data suggest that the NBDs of BmrA function with a tweezers-like mechanism distinct from the related lipid A exporter MsbA.
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Affiliation(s)
- Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Elise Kaplan
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Julia Rendon
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | | | - Sepideh Valimehr
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Thu-Anh Thi Ngo
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Vincent Chaptal
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Pierre Falson
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | | | - Pierre Dorlet
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | - Eric Hanssen
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
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Wycisk V, Wagner MC, Urner LH. Trends in the Diversification of the Detergentome. Chempluschem 2024; 89:e202300386. [PMID: 37668309 DOI: 10.1002/cplu.202300386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/06/2023]
Abstract
Detergents are amphiphilic molecules that serve as enabling steps for today's world applications. The increasing diversity of the detergentome is key to applications enabled by detergent science. Regardless of the application, the optimal design of detergents is determined empirically, which leads to failed preparations, and raising costs. To facilitate project planning, here we review synthesis strategies that drive the diversification of the detergentome. Synthesis strategies relevant for industrial and academic applications include linear, modular, combinatorial, bio-based, and metric-assisted detergent synthesis. Scopes and limitations of individual synthesis strategies in context with industrial product development and academic research are discussed. Furthermore, when designing detergents, the selection of molecular building blocks, i. e., head, linker, tail, is as important as the employed synthesis strategy. To facilitate the design of safe-to-use and tailor-made detergents, we provide an overview of established head, linker, and tail groups and highlight selected scopes and limitations for applications. It becomes apparent that most recent contributions to the increasing chemical diversity of detergent building blocks originate from the development of detergents for membrane protein studies. The overview of synthesis strategies and molecular blocks will bring us closer to the ability to predictably design and synthesize optimal detergents for challenging future applications.
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Affiliation(s)
- Virginia Wycisk
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Marc-Christian Wagner
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Leonhard H Urner
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
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Ghani L, Kim S, Ehsan M, Lan B, Poulsen IH, Dev C, Katsube S, Byrne B, Guan L, Loland CJ, Liu X, Im W, Chae PS. Melamine-cored glucosides for membrane protein solubilization and stabilization: importance of water-mediated intermolecular hydrogen bonding in detergent performance. Chem Sci 2023; 14:13014-13024. [PMID: 38023530 PMCID: PMC10664503 DOI: 10.1039/d3sc03543c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Membrane proteins play essential roles in a number of biological processes, and their structures are important in elucidating such processes at the molecular level and also for rational drug design and development. Membrane protein structure determination is notoriously challenging compared to that of soluble proteins, due largely to the inherent instability of their structures in non-lipid environments. Micelles formed by conventional detergents have been widely used for membrane protein manipulation, but they are suboptimal for long-term stability of membrane proteins, making downstream characterization difficult. Hence, there is an unmet need for the development of new amphipathic agents with enhanced efficacy for membrane protein stabilization. In this study, we designed and synthesized a set of glucoside amphiphiles with a melamine core, denoted melamine-cored glucosides (MGs). When evaluated with four membrane proteins (two transporters and two G protein-coupled receptors), MG-C11 conferred notably enhanced stability compared to the commonly used detergents, DDM and LMNG. These promising findings are mainly attributed to a unique feature of the MGs, i.e., the ability to form dynamic water-mediated hydrogen-bond networks between detergent molecules, as supported by molecular dynamics simulations. Thus, MG-C11 is the first example of a non-peptide amphiphile capable of forming intermolecular hydrogen bonds within a protein-detergent complex environment. Detergent micelles formed via a hydrogen-bond network could represent the next generation of highly effective membrane-mimetic systems useful for membrane protein structural studies.
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Affiliation(s)
- Lubna Ghani
- Department of Bionano Engineering, Hanyang University Ansan 155-88 South Korea
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study Seoul 024-55 South Korea
| | - Muhammad Ehsan
- Department of Bionano Engineering, Hanyang University Ansan 155-88 South Korea
| | - Baoliang Lan
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University Beijing 100084 China
| | - Ida H Poulsen
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - Chandra Dev
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock Texas 79430 USA
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock Texas 79430 USA
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock Texas 79430 USA
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - Xiangyu Liu
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University Beijing 100084 China
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, and Bioengineering Lehigh University Bethlehem PA 18015 USA
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University Ansan 155-88 South Korea
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Vénien-Bryan C, Fernandes CAH. Overview of Membrane Protein Sample Preparation for Single-Particle Cryo-Electron Microscopy Analysis. Int J Mol Sci 2023; 24:14785. [PMID: 37834233 PMCID: PMC10573263 DOI: 10.3390/ijms241914785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins (MPs). Indeed, in recent years, huge increase in the number of MPs solved via cryo-EM SPA at a resolution better than 3.0 Å in the Protein Data Bank (PDB) has been observed. However, sample preparation remains a significant challenge in the field. Here, we evaluated the MPs solved using cryo-EM SPA deposited in the PDB in the last two years at a resolution below 3.0 Å. The most critical parameters for sample preparation are as follows: (i) the surfactant used for protein extraction from the membrane, (ii) the surfactant, amphiphiles, nanodiscs or other molecules present in the vitrification step, (iii) the vitrification method employed, and (iv) the type of grids used. The aim is not to provide a definitive answer on the optimal sample conditions for cryo-EM SPA of MPs but rather assess the current trends in the MP structural biology community towards obtaining high-resolution cryo-EM structures.
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Affiliation(s)
| | - Carlos A. H. Fernandes
- Unité Mixte de Recherche (UMR) 7590, Centre National de la Recherche Scientifique (CNRS), Muséum National d’Histoire Naturelle, Institut de Recherche pour le Développement (IRD), Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, 75005 Paris, France;
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8
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Degroux S, Effantin G, Linares R, Schoehn G, Breyton C. Deciphering Bacteriophage T5 Host Recognition Mechanism and Infection Trigger. J Virol 2023; 97:e0158422. [PMID: 36779755 PMCID: PMC10062170 DOI: 10.1128/jvi.01584-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/05/2023] [Indexed: 02/14/2023] Open
Abstract
Bacteriophages, viruses infecting bacteria, recognize their host with high specificity, binding to either saccharide motifs or proteins of the cell wall of their host. In the majority of bacteriophages, this host recognition is performed by receptor binding proteins (RBPs) located at the extremity of a tail. Interaction between the RBPs and the host is the trigger for bacteriophage infection, but the molecular details of the mechanisms are unknown for most bacteriophages. Here, we present the electron cryomicroscopy (cryo-EM) structure of bacteriophage T5 RBPpb5 in complex with its Escherichia coli receptor, the iron ferrichrome transporter FhuA. Monomeric RBPpb5 is located at the extremity of T5's long flexible tail, and its irreversible binding to FhuA commits T5 to infection. Analysis of the structure of RBPpb5 within the complex, comparison with its AlphaFold2-predicted structure, and its fit into a previously determined map of the T5 tail tip in complex with FhuA allow us to propose a mechanism of transmission of the RBPpb5 receptor binding to the straight fiber, initiating the cascade of events that commits T5 to DNA ejection. IMPORTANCE Tailed bacteriophages specifically recognize their bacterial host by interaction of their receptor binding protein(s) (RBPs) with saccharides and/or proteins located at the surface of their prey. This crucial interaction commits the virus to infection, but the molecular details of this mechanism are unknown for the majority of bacteriophages. We determined the structure of bacteriophage T5 RBPpb5 in complex with its E. coli receptor, FhuA, by cryo-EM. This first structure of an RBP bound to its protein receptor allowed us to propose a mechanism of transmission of host recognition to the rest of the phage, ultimately opening the capsid and perforating the cell wall and, thus, allowing safe channeling of the DNA into the host cytoplasm.
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Affiliation(s)
| | | | - Romain Linares
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Guy Schoehn
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Cécile Breyton
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
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9
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Zwitterionic fluorinated detergents: From design to membrane protein applications. Biochimie 2023; 205:40-52. [PMID: 36375632 DOI: 10.1016/j.biochi.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
We report herein the synthesis of zwitterionic sulfobetaine (SB) and dimethylamine oxide (AO) detergents whose alkyl chain is made of either a perfluorohexyl (F6H3) or a perfluoropentyl (F5H5) group linked to a hydrogenated spacer arm. In aqueous solution, the critical micellar concentrations (CMCs) measured by surface tensiometry (SFT) and isothermal titration calorimetry (ITC) were found in the millimolar range (1.3-2.4 mM). The morphologies of the aggregates were evaluated by dynamic light scattering (DLS), analytical ultracentrifugation (AUC), small-angle X-ray scattering (SAXS), and transmission electron microscopy (TEM), demonstrating that the two perfluoropentyl derivatives formed small micelles less than 10 nm in diameter, whereas the perfluorohexyl derivatives formed larger and more heterogeneous micelles. The two SB detergents were able to solubilize synthetic lipid vesicles in a few hours; by contrast, the perfluoropentyl AO induced much faster solubilization, whereas the perfluorohexyl AO did not show any solubilization. All detergents were tested for their abilities to stabilize three membrane proteins, namely, bacteriorhodopsin (bR), the Bacillus subtilis ABC transporter BmrA, and the Streptococcus pneumoniae enzyme SpNOX. The SB detergents outperformed the AO derivatives as well as their hydrogenated analogs in stabilizing these proteins. Among the four new compounds, F5H5SB combines many desirable properties for membrane-protein study, as it is a powerful yet gentle detergent.
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10
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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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11
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Ghani L, Kim S, Wang H, Lee HS, Mortensen JS, Katsube S, Du Y, Sadaf A, Ahmed W, Byrne B, Guan L, Loland CJ, Kobilka BK, Im W, Chae PS. Foldable Detergents for Membrane Protein Study: Importance of Detergent Core Flexibility in Protein Stabilization. Chemistry 2022; 28:e202200116. [PMID: 35238091 PMCID: PMC9007890 DOI: 10.1002/chem.202200116] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 12/30/2022]
Abstract
Membrane proteins are of biological and pharmaceutical significance. However, their structural study is extremely challenging mainly due to the fact that only a small number of chemical tools are suitable for stabilizing membrane proteins in solution. Detergents are widely used in membrane protein study, but conventional detergents are generally poor at stabilizing challenging membrane proteins such as G protein-coupled receptors and protein complexes. In the current study, we prepared tandem triazine-based maltosides (TZMs) with two amphiphilic triazine units connected by different diamine linkers, hydrazine (TZM-Hs) and 1,2-ethylenediamine (TZM-Es). These TZMs were consistently superior to a gold standard detergent (DDM) in terms of stabilizing a few membrane proteins. In addition, the TZM-Es containing a long linker showed more general protein stabilization efficacy with multiple membrane proteins than the TZM-Hs containing a short linker. This result indicates that introduction of the flexible1,2-ethylenediamine linker between two rigid triazine rings enables the TZM-Es to fold into favourable conformations in order to promote membrane protein stability. The novel concept of detergent foldability introduced in the current study has potential in rational detergent design and membrane protein applications.
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Affiliation(s)
- Lubna Ghani
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 024-55, South Korea
| | - Haoqing Wang
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Hyun Sung Lee
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.,Current address: School of Life and Health Sciences, Chinese University of Hong Kong, 2001 Longxiang Ave, Shenzhen, Guangdong, 518172, China
| | - Aiman Sadaf
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Waqar Ahmed
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Brian K Kobilka
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Pil Seok Chae
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, 155-88, South Korea
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12
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Structural insights into the catalytic cycle of a bacterial multidrug ABC efflux pump. J Mol Biol 2022; 434:167541. [DOI: 10.1016/j.jmb.2022.167541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/19/2022]
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13
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14
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Di Cesare M, Diagne AM, Bourgey B, Jault JM, Orelle C. Functional Overexpression of Membrane Proteins in E. coli: The Good, the Bad, and the Ugly. Methods Mol Biol 2022; 2507:41-58. [PMID: 35773576 DOI: 10.1007/978-1-0716-2368-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Overexpression of properly folded membrane proteins is a mandatory step for their functional and structural characterization. One of the most used expression systems for the production of proteins is Escherichia coli. Many advantageous strains combined with T7 expression systems have been developed over the years. Recently, we showed that the choice of the strain is critical for the functionality of membrane proteins, even when the proteins are successfully incorporated in the membrane (Mathieu et al. Sci Rep. 2019; 9(1):2654). Notably, the amount and/or activity of the T7-RNA polymerase, which drives the transcription of the genes of interest, may indirectly affect the folding and functionality of overexpressed membrane proteins. Moreover, we reported a general trend in which mild detergents mainly extract the population of active membrane proteins, whereas a harsher detergent like Fos-choline 12 could solubilize them irrespectively of their functionality. Based on these observations, we provide some guidelines to optimize the quality of membrane proteins overexpressed in E. coli.
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Affiliation(s)
- Margot Di Cesare
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Aissatou Maty Diagne
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Benjamin Bourgey
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France.
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France.
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15
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Flegler VJ, Rasmussen A, Borbil K, Boten L, Chen HA, Deinlein H, Halang J, Hellmanzik K, Löffler J, Schmidt V, Makbul C, Kraft C, Hedrich R, Rasmussen T, Böttcher B. Mechanosensitive channel gating by delipidation. Proc Natl Acad Sci U S A 2021; 118:e2107095118. [PMID: 34376558 PMCID: PMC8379960 DOI: 10.1073/pnas.2107095118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The mechanosensitive channel of small conductance (MscS) protects bacteria against hypoosmotic shock. It can sense the tension in the surrounding membrane and releases solutes if the pressure in the cell is getting too high. The membrane contacts MscS at sensor paddles, but lipids also leave the membrane and move along grooves between the paddles to reside as far as 15 Å away from the membrane in hydrophobic pockets. One sensing model suggests that a higher tension pulls lipids from the grooves back to the membrane, which triggers gating. However, it is still unclear to what degree this model accounts for sensing and what contribution the direct interaction of the membrane with the channel has. Here, we show that MscS opens when it is sufficiently delipidated by incubation with the detergent dodecyl-β-maltoside or the branched detergent lauryl maltose neopentyl glycol. After addition of detergent-solubilized lipids, it closes again. These results support the model that lipid extrusion causes gating: Lipids are slowly removed from the grooves and pockets by the incubation with detergent, which triggers opening. Addition of lipids in micelles allows lipids to migrate back into the pockets, which closes the channel even in the absence of a membrane. Based on the distribution of the aliphatic chains in the open and closed conformation, we propose that during gating, lipids leave the complex on the cytosolic leaflet at the height of highest lateral tension, while on the periplasmic side, lipids flow into gaps, which open between transmembrane helices.
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Affiliation(s)
| | - Akiko Rasmussen
- Lehrstuhl für Botanik I, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Karina Borbil
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Lea Boten
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Hsuan-Ai Chen
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Hanna Deinlein
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Julia Halang
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Kristin Hellmanzik
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Jessica Löffler
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Vanessa Schmidt
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Cihan Makbul
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Christian Kraft
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany
| | - Rainer Hedrich
- Lehrstuhl für Botanik I, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Tim Rasmussen
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany;
| | - Bettina Böttcher
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, 97080 Würzburg, Germany;
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16
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Zampieri V, Hilpert C, Garnier M, Gestin Y, Delolme S, Martin J, Falson P, Launay G, Chaptal V. The Det.Belt Server: A Tool to Visualize and Estimate Amphipathic Solvent Belts around Membrane Proteins. MEMBRANES 2021; 11:459. [PMID: 34206634 PMCID: PMC8307592 DOI: 10.3390/membranes11070459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 11/23/2022]
Abstract
Detergents wrap around membrane proteins to form a belt covering the hydrophobic part of the protein serving for membrane insertion and interaction with lipids. The number of detergent monomers forming this belt is usually unknown to investigators, unless dedicated detergent quantification is undertaken, which for many projects is difficult to setup. Yet, having an approximate knowledge of the amount of detergent forming the belt is extremely useful, to better grasp the protein of interest in interaction with its direct environment rather than picturing the membrane protein "naked". We created the Det.Belt server to dress up membrane proteins and represent in 3D the bulk made by detergent molecules wrapping in a belt. Many detergents are included in a database, allowing investigators to screen in silico the effect of different detergents around their membrane protein. The input number of detergents is changeable with fast recomputation of the belt for interactive usage. Metrics representing the belt are readily available together with scripts to render quality 3D images for publication. The Det.Belt server is a tool for biochemists to better grasp their sample.
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Affiliation(s)
- Veronica Zampieri
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, CEDEX 9, 38042 Grenoble, France;
| | - Cécile Hilpert
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Mélanie Garnier
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Yannick Gestin
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Sébastien Delolme
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Juliette Martin
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Guillaume Launay
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
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17
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Wehbie M, Onyia KK, Mahler F, Le Roy A, Deletraz A, Bouchemal I, Vargas C, Babalola JO, Breyton C, Ebel C, Keller S, Durand G. Maltose-Based Fluorinated Surfactants for Membrane-Protein Extraction and Stabilization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:2111-2122. [PMID: 33539092 DOI: 10.1021/acs.langmuir.0c03214] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Two new surfactants, F5OM and F5DM, were designed as partially fluorinated analogues of n-dodecyl-β-D-maltoside (DDM). The micellization properties and the morphologies of the aggregates formed by the two surfactants in water and phosphate buffer were evaluated by NMR spectroscopy, surface tension measurement, isothermal titration calorimetry, dynamic light scattering, small-angle X-ray scattering, and analytical ultracentrifugation. As expected, the critical micellar concentration (cmc) was found to decrease with chain length of the fluorinated tail from 2.1-2.5 mM for F5OM to 0.3-0.5 mM for F5DM, and micellization was mainly entropy-driven at 25 °C. Close to their respective cmc, the micelle sizes were similar for both surfactants, that is, 7 and 13 nm for F5OM and F5DM, respectively, and both increased with concentration forming 4 nm diameter rods with maximum dimensions of 50 and 70 nm, respectively, at a surfactant concentration of ∼30 mM. The surfactants were found to readily solubilize lipid vesicles and extract membrane proteins directly from Escherichia coli membranes. They were found more efficient than the commercial fluorinated detergent F6H2OM over a broad range of concentrations (1-10 mM) and even better than DDM at low concentrations (1-5 mM). When transferred into the two new surfactants, the thermal stability of the proteins bacteriorhodopsin (bR) and FhuA was higher than in the presence of their solubilization detergents and similar to that in DDM; furthermore, bR was stable over several months. The membrane enzymes SpNOX and BmrA were not as active as in DDM micelles but similarly active as in F6OM. Together, these findings indicate both extracting and stabilizing properties of the new maltose-based fluorinated surfactants, making them promising tools in MP applications.
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Affiliation(s)
- Moheddine Wehbie
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM) & Avignon University, Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 rue Baruch de Spinoza, 84916 cedex 9 Avignon, France
| | - Kenechi Kanayo Onyia
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- Department of Chemistry, University of Ibadan, 200284 Ibadan, Nigeria
| | - Florian Mahler
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Aline Le Roy
- Université Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Anais Deletraz
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM) & Avignon University, Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 rue Baruch de Spinoza, 84916 cedex 9 Avignon, France
| | - Ilham Bouchemal
- Université Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Carolyn Vargas
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | | | - Cécile Breyton
- Université Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Christine Ebel
- Université Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Grégory Durand
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM) & Avignon University, Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 rue Baruch de Spinoza, 84916 cedex 9 Avignon, France
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18
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Olerinyova A, Sonn-Segev A, Gault J, Eichmann C, Schimpf J, Kopf AH, Rudden LSP, Ashkinadze D, Bomba R, Frey L, Greenwald J, Degiacomi MT, Steinhilper R, Killian JA, Friedrich T, Riek R, Struwe WB, Kukura P. Mass Photometry of Membrane Proteins. Chem 2021; 7:224-236. [PMID: 33511302 PMCID: PMC7815066 DOI: 10.1016/j.chempr.2020.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/20/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Abstract
Integral membrane proteins (IMPs) are biologically highly significant but challenging to study because they require maintaining a cellular lipid-like environment. Here, we explore the application of mass photometry (MP) to IMPs and membrane-mimetic systems at the single-particle level. We apply MP to amphipathic vehicles, such as detergents and amphipols, as well as to lipid and native nanodiscs, characterizing the particle size, sample purity, and heterogeneity. Using methods established for cryogenic electron microscopy, we eliminate detergent background, enabling high-resolution studies of membrane-protein structure and interactions. We find evidence that, when extracted from native membranes using native styrene-maleic acid nanodiscs, the potassium channel KcsA is present as a dimer of tetramers—in contrast to results obtained using detergent purification. Finally, using lipid nanodiscs, we show that MP can help distinguish between functional and non-functional nanodisc assemblies, as well as determine the critical factors for lipid nanodisc formation. We introduce a label-free, single molecule approach for membrane-protein characterization Mass photometry quantifies membrane proteins in different membrane-mimetic systems MP reveals carrier and protein heterogeneity It helps distinguish different functional states of membrane proteins
Membrane proteins are some of the most important biological molecules, carrying out vital functions and being frequent drug targets. Yet, preferring lipid environments and so requiring solubilization, they are challenging to study. Here, we show that mass photometry can characterize the heterogeneity of membrane proteins and the carriers in which they are solubilized. It can also distinguish different functional states of membrane proteins. Our approach thus opens the door to more comprehensive studies of function, structure, and interaction of these critical proteins in their native membrane environment at the single-molecule level.
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Affiliation(s)
- Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Adar Sonn-Segev
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Adrian H Kopf
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Lucas S P Rudden
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Dzmitry Ashkinadze
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Radoslaw Bomba
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Matteo T Degiacomi
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Ralf Steinhilper
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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19
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Carvalho V, Prabudiansyah I, Kovacik L, Chami M, Kieffer R, van der Valk R, de Lange N, Engel A, Aubin-Tam ME. The cytoplasmic domain of the AAA+ protease FtsH is tilted with respect to the membrane to facilitate substrate entry. J Biol Chem 2021; 296:100029. [PMID: 33154162 PMCID: PMC7949044 DOI: 10.1074/jbc.ra120.014739] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/28/2020] [Accepted: 11/05/2020] [Indexed: 11/06/2022] Open
Abstract
AAA+ proteases are degradation machines that use ATP hydrolysis to unfold protein substrates and translocate them through a central pore toward a degradation chamber. FtsH, a bacterial membrane-anchored AAA+ protease, plays a vital role in membrane protein quality control. How substrates reach the FtsH central pore is an open key question that is not resolved by the available atomic structures of cytoplasmic and periplasmic domains. In this work, we used both negative stain TEM and cryo-EM to determine 3D maps of the full-length Aquifex aeolicus FtsH protease. Unexpectedly, we observed that detergent solubilization induces the formation of fully active FtsH dodecamers, which consist of two FtsH hexamers in a single detergent micelle. The striking tilted conformation of the cytosolic domain in the FtsH dodecamer visualized by negative stain TEM suggests a lateral substrate entrance between the membrane and cytosolic domain. Such a substrate path was then resolved in the cryo-EM structure of the FtsH hexamer. By mapping the available structural information and structure predictions for the transmembrane helices to the amino acid sequence we identified a linker of ∼20 residues between the second transmembrane helix and the cytosolic domain. This unique polypeptide appears to be highly flexible and turned out to be essential for proper functioning of FtsH as its deletion fully eliminated the proteolytic activity of FtsH.
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Affiliation(s)
- Vanessa Carvalho
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Irfan Prabudiansyah
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Lubomir Kovacik
- BioEM Lab, C-CINA, Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland
| | - Mohamed Chami
- BioEM Lab, C-CINA, Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland
| | - Roland Kieffer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Ramon van der Valk
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nick de Lange
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Andreas Engel
- BioEM Lab, C-CINA, Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland.
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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Vermot A, Petit-Härtlein I, Breyton C, Le Roy A, Thépaut M, Vivès C, Moulin M, Härtlein M, Grudinin S, Smith SME, Ebel C, Martel A, Fieschi F. Interdomain Flexibility within NADPH Oxidase Suggested by SANS Using LMNG Stealth Carrier. Biophys J 2020; 119:605-618. [PMID: 32668232 PMCID: PMC7399496 DOI: 10.1016/j.bpj.2020.06.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/26/2020] [Accepted: 06/23/2020] [Indexed: 11/12/2022] Open
Abstract
Small angle neutron scattering (SANS) provides a method to obtain important low-resolution information for integral membrane proteins (IMPs), challenging targets for structural determination. Specific deuteration furnishes a "stealth" carrier for the solubilized IMP. We used SANS to determine a structural envelope of SpNOX, the Streptococcus pneumoniae NADPH oxidase (NOX), a prokaryotic model system for exploring structure and function of eukaryotic NOXes. SpNOX was solubilized in the detergent lauryl maltose neopentyl glycol, which provides optimal SpNOX stability and activity. Using deuterated solvent and protein, the lauryl maltose neopentyl glycol was experimentally undetected in SANS. This affords a cost-effective SANS approach for obtaining novel structural information on IMPs. Combining SANS data with molecular modeling provided a first, to our knowledge, structural characterization of an entire NOX enzyme. It revealed a distinctly less compact structure than that predicted from the docking of homologous crystal structures of the separate transmembrane and dehydrogenase domains, consistent with a flexible linker connecting the two domains.
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Affiliation(s)
- Annelise Vermot
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | | | - Cécile Breyton
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Aline Le Roy
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Michel Thépaut
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Corinne Vivès
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | | | | | | | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia
| | - Christine Ebel
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | | | - Franck Fieschi
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France.
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Savelyev A, Gorbet GE, Henrickson A, Demeler B. Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment. PLoS Comput Biol 2020; 16:e1007942. [PMID: 32559250 PMCID: PMC7347214 DOI: 10.1371/journal.pcbi.1007942] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/09/2020] [Accepted: 05/11/2020] [Indexed: 01/19/2023] Open
Abstract
Recent advances in instrumentation have moved analytical ultracentrifugation (AUC) closer to a possible validation in a Good Manufacturing Practices (GMP) environment. In order for AUC to be validated for a GMP environment, stringent requirements need to be satisfied; analysis procedures must be evaluated for consistency and reproducibility, and GMP capable data acquisition software needs to be developed and validated. These requirements extend to multiple regulatory aspects, covering documentation of instrument hardware functionality, data handling and software for data acquisition and data analysis, process control, audit trails and automation. Here we review the requirements for GMP validation of data acquisition software and illustrate software solutions based on UltraScan that address these requirements as far as they relate to the operation and data handling in conjunction with the latest analytical ultracentrifuge, the Optima AUC by Beckman Coulter. The software targets the needs of regulatory agencies, where AUC plays a critical role in the solution-based characterization of biopolymers and macromolecular assemblies. Biopharmaceutical and regulatory agencies rely heavily on this technique for characterizations of pharmaceutical formulations, biosimilars, injectables, nanoparticles, and other soluble therapeutics. Because of its resolving power, AUC is a favorite application, despite the current lack of GMP validation. We believe that recent advances in standards, hardware, and software presented in this work manage to bridge this gap and allow AUC to be routinely used in a GMP environment. AUC has great potential to provide more detailed information, at higher resolution, and with greater confidence than other analytical techniques, and our software satisfies an urgent need for AUC operation in the GMP environment. The software, including documentation, are publicly available for free download from Github. The multi-platform software is licensed by the LGPL v.3 open source license and supports Windows, Mac and Linux platforms. Installation instructions and a mailing list are available from ultrascan.aucsolutions.com.
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Affiliation(s)
- Alexey Savelyev
- University of Montana, Dept. of Chemistry, Missoula, Montana, United States of America
| | | | - Amy Henrickson
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
| | - Borries Demeler
- University of Montana, Dept. of Chemistry, Missoula, Montana, United States of America
- AUC Solutions, Houston, Texas, United States of America
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
- * E-mail:
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Guyot L, Hartmann L, Mohammed-Bouteben S, Caro L, Wagner R. Preparation of Recombinant Membrane Proteins from Pichia pastoris for Molecular Investigations. ACTA ACUST UNITED AC 2020; 100:e104. [PMID: 32289210 DOI: 10.1002/cpps.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pichia pastoris is a eukaryotic microorganism reputed for its ability to mass-produce recombinant proteins, including integral membrane proteins, for various applications. This article details a series of protocols that progress towards the production of integral membrane proteins, their extraction and purification in the presence of detergents, and their eventual reconstitution in lipid nanoparticles. These basic procedures can be further optimized to provide integral membrane protein samples that are compatible with a number of structural and/or functional investigations at the molecular level. Each protocol provides general guidelines, technical hints, and specific recommendations, and is illustrated with case studies corresponding to several representative mammalian proteins. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Production of membrane proteins in a P. pastoris recombinant clone using methanol induction Basic Protocol 2: Preparation of whole-membrane fractions Alternate Protocol 1: Preparation of yeast protoplasts Basic Protocol 3: Extraction of membrane proteins from whole-membrane fractions Basic Protocol 4: Purification of membrane proteins Alternate Protocol 2: Purification of membrane proteins from yeast protoplasts Alternate Protocol 3: Simultaneous protoplast preparation and membrane solubilization for purification of membrane proteins Basic Protocol 5: Reconstitution of detergent-purified membrane proteins in lipid nanoparticles.
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Affiliation(s)
- Lucile Guyot
- IMPReSs Facility, Biotechnology and Cell Signaling UMR 7242, CNRS-University of Strasbourg, Illkirch, Cedex, France.,NovAliX, Illkirch, France
| | - Lucie Hartmann
- IMPReSs Facility, Biotechnology and Cell Signaling UMR 7242, CNRS-University of Strasbourg, Illkirch, Cedex, France
| | - Sarah Mohammed-Bouteben
- IMPReSs Facility, Biotechnology and Cell Signaling UMR 7242, CNRS-University of Strasbourg, Illkirch, Cedex, France
| | - Lydia Caro
- IMPReSs Facility, Biotechnology and Cell Signaling UMR 7242, CNRS-University of Strasbourg, Illkirch, Cedex, France
| | - Renaud Wagner
- IMPReSs Facility, Biotechnology and Cell Signaling UMR 7242, CNRS-University of Strasbourg, Illkirch, Cedex, France
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