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Karanth S, Benthin J, Wiesenfarth M, Somoza V, Koehler M. Nanodisc Technology: Direction toward Physicochemical Characterization of Chemosensory Membrane Proteins in Food Flavor Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14521-14529. [PMID: 38906535 PMCID: PMC11228972 DOI: 10.1021/acs.jafc.4c01827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024]
Abstract
Chemosensory membrane proteins such as G-protein-coupled receptors (GPCRs) drive flavor perception of food formulations. To achieve this, a detailed understanding of the structure and function of these membrane proteins is needed, which is often limited by the extraction and purification methods involved. The proposed nanodisc methodology helps overcome some of these existing challenges such as protein stability and solubilization along with their reconstitution from a native cell-membrane environment. Being well-established in structural biology procedures, nanodiscs offer this elegant solution by using, e.g., a membrane scaffold protein (MSP) or styrene-maleic acid (SMA) polymer, which interacts directly with the cell membrane during protein reconstitution. Such derived proteins retain their biophysical properties without compromising the membrane architecture. Here, we seek to show that these lipidic systems can be explored for insights with a focus on chemosensory membrane protein morphology and structure, conformational dynamics of protein-ligand interactions, and binding kinetics to answer pending questions in flavor research. Additionally, the compatibility of nanodiscs across varied (labeled or label-free) techniques offers significant leverage, which has been highlighted here.
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Affiliation(s)
- Sanjai Karanth
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
| | - Julia Benthin
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- TUM
Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354 Freising, Germany
| | - Marina Wiesenfarth
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- TUM
Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354 Freising, Germany
| | - Veronika Somoza
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- Chair
of Nutritional Systems Biology, Technical
University of Munich, 85354 Freising, Germany
- Department
of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Melanie Koehler
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- TUM
Junior Fellow at the Chair of Nutritional Systems Biology, Technical University of Munich, 85354 Freising, Germany
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2
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Kurosawa Y, Otsuka Y, Goto S. Increased selectivity of sodium deoxycholate to around Tryptophan213 in bovine serum albumin upon micellization as revealed by singular value decomposition for excitation emission matrix. Colloids Surf B Biointerfaces 2022; 212:112344. [PMID: 35101827 DOI: 10.1016/j.colsurfb.2022.112344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 11/17/2022]
Abstract
In the present study, we investigated the effect of bile salts (sodium deoxycholate, NaDC) on the conformation of a globular protein (bovine serum albumin, BSA). The two Tryptophan (Trp) residues of BSA and the fluorescence energy of NaDC are in a three-way relationship, and singular value decomposition (SVD) was used to separate each element in the fluorescence spectra. SVD was used to separate the elements in the fluorescence spectra. SVD showed that NaDC had a particularly large effect on the microenvironment around Trp213 and that micellar NaDC enhanced the selectivity for Trp213. In addition, the Stern-Volmer plots of the warfarin (WAR) specific domain (domain I) and ketoprofen (KP) specific domain (domain II) in the presence and absence of NaDC showed that the effect of NaDC was selective for domain II, where Trp213 is located. These results indicate that NaDC induces a localized and selective conformational change in BSA, and that the selectivity varies depending on the aggregation state of NaDC.
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Affiliation(s)
- Yuya Kurosawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamasaki, Noda, Chiba 278-8510, Japan
| | - Yuta Otsuka
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamasaki, Noda, Chiba 278-8510, Japan
| | - Satoru Goto
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamasaki, Noda, Chiba 278-8510, Japan.
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3
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Li M, Heller WT, Liu CH, Gao CY, Cai Y, Hou Y, Nieh MP. Effects of fluidity and charge density on the morphology of a bicellar mixture - A SANS study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183315. [PMID: 32304755 DOI: 10.1016/j.bbamem.2020.183315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 01/28/2023]
Abstract
The spontaneously formed structures of physiologically relevant lipid model membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) and 1,2-hexanoyl-sn-glycero-3-phosphocholine have been evaluated in depth using small angle neutron scattering. Although a common molar ratio of long- to short- chain phospholipids (~4) as reported in many bicellar mixtures was used, discoidal bicelles were not found as the major phase throughout the range of lipid concentration and temperature studied, indicating that the required condition for the formation of bicelle is the immiscibility between the long- and short- chain lipids, which were in the gel and Lα phases, respectively, in previous reports. In this study, all lipids are in the Lα phase. The characterization outcome suggests that the spontaneous structures tie strongly with the physical parameters of the system such as melting transition temperature of the long-chain lipid, total lipid concentration and charge density of the system. Multilamellar vesicles, unilamellar vesicles, ribbons and perforated lamellae can be obtained based on the analysis of the small angle neutron scattering results, leading to the construction of structural diagrams. This report provides the important map to choose suitable lipid systems for the structural study of membrane-associated proteins, design of theranostic nanocarriers or other related research fields.
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Affiliation(s)
- Ming Li
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, 06269, USA
| | - William T Heller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Hao Liu
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, 06269, USA
| | - Carrie Y Gao
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yutian Cai
- Department of Polymer Material Science and Engineering, College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410000, China
| | - Yiming Hou
- Department of Polymer Material Science and Engineering, College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410000, China
| | - Mu-Ping Nieh
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, 06269, USA; Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs 06269, USA; Department of Biomedical Engineering, University of Connecticut, Storrs 06269, USA.
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4
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Chen Y, Krings S, Booth JR, Bon SAF, Hingley-Wilson S, Keddie JL. Introducing Porosity in Colloidal Biocoatings to Increase Bacterial Viability. Biomacromolecules 2020; 21:4545-4558. [DOI: 10.1021/acs.biomac.0c00649] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | | | - Joshua R. Booth
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Stefan A. F. Bon
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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5
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Methods of reconstitution to investigate membrane protein function. Methods 2018; 147:126-141. [DOI: 10.1016/j.ymeth.2018.02.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/13/2018] [Indexed: 02/06/2023] Open
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6
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Rondelli V, Del Favero E, Brocca P, Fragneto G, Trapp M, Mauri L, Ciampa M, Romani G, Braun C, Winterstein L, Schroeder I, Thiel G, Moroni A, Cantu' L. Directional K+ channel insertion in a single phospholipid bilayer: Neutron reflectometry and electrophysiology in the joint exploration of a model membrane functional platform. Biochim Biophys Acta Gen Subj 2018; 1862:1742-1750. [DOI: 10.1016/j.bbagen.2018.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/27/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023]
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7
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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8
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Khadria AS, Senes A. Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET. Biopolymers 2016; 104:247-64. [PMID: 25968159 DOI: 10.1002/bip.22667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/15/2015] [Accepted: 05/04/2015] [Indexed: 12/31/2022]
Abstract
Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations.
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Affiliation(s)
- Ambalika S Khadria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Alessandro Senes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
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9
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Lee SC, Knowles TJ, Postis VLG, Jamshad M, Parslow RA, Lin YP, Goldman A, Sridhar P, Overduin M, Muench SP, Dafforn TR. A method for detergent-free isolation of membrane proteins in their local lipid environment. Nat Protoc 2016; 11:1149-62. [PMID: 27254461 DOI: 10.1038/nprot.2016.070] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the great importance of membrane proteins, structural and functional studies of these proteins present major challenges. A significant hurdle is the extraction of the functional protein from its natural lipid membrane. Traditionally achieved with detergents, purification procedures can be costly and time consuming. A critical flaw with detergent approaches is the removal of the protein from the native lipid environment required to maintain functionally stable protein. This protocol describes the preparation of styrene maleic acid (SMA) co-polymer to extract membrane proteins from prokaryotic and eukaryotic expression systems. Successful isolation of membrane proteins into SMA lipid particles (SMALPs) allows the proteins to remain with native lipid, surrounded by SMA. We detail procedures for obtaining 25 g of SMA (4 d); explain the preparation of protein-containing SMALPs using membranes isolated from Escherichia coli (2 d) and control protein-free SMALPS using E. coli polar lipid extract (1-2 h); investigate SMALP protein purity by SDS-PAGE analysis and estimate protein concentration (4 h); and detail biophysical methods such as circular dichroism (CD) spectroscopy and sedimentation velocity analytical ultracentrifugation (svAUC) to undertake initial structural studies to characterize SMALPs (∼2 d). Together, these methods provide a practical tool kit for those wanting to use SMALPs to study membrane proteins.
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Affiliation(s)
- Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Tim J Knowles
- School of Cancer Sciences, University of Birmingham, Birmingham, UK.,Present address: Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Vincent L G Postis
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds, UK
| | | | | | - Yu-Pin Lin
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Adrian Goldman
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Department of Biosciences, Division of Biochemistry, University of Helsinki, Helsinki, Finland
| | - Pooja Sridhar
- School of Cancer Sciences, University of Birmingham, Birmingham, UK.,Present address: Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Michael Overduin
- School of Biosciences, University of Birmingham, Birmingham, UK.,Department of Biochemistry, Faculty of Medicine &Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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10
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Shirzad-Wasei N, DeGrip WJ. Heterologous expression of melanopsin: Present, problems and prospects. Prog Retin Eye Res 2016; 52:1-21. [DOI: 10.1016/j.preteyeres.2016.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/25/2016] [Accepted: 02/01/2016] [Indexed: 12/12/2022]
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11
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Marmulla R, Šafarić B, Markert S, Schweder T, Harder J. Linalool isomerase, a membrane-anchored enzyme in the anaerobic monoterpene degradation in Thauera linaloolentis 47Lol. BMC BIOCHEMISTRY 2016; 17:6. [PMID: 26979141 PMCID: PMC4791888 DOI: 10.1186/s12858-016-0062-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 03/02/2016] [Indexed: 12/23/2022]
Abstract
Background Thauera linaloolentis 47Lol uses the tertiary monoterpene alcohol (R,S)-linalool as sole carbon and energy source under denitrifying conditions. The conversion of linalool to geraniol had been observed in carbon-excess cultures, suggesting the presence of a 3,1-hydroxyl-Δ1-Δ2-mutase (linalool isomerase) as responsible enzyme. To date, only a single enzyme catalyzing such a reaction is described: the linalool dehydratase/isomerase (Ldi) from Castellaniella defragrans 65Phen acting only on (S)-linalool. Results The linalool isomerase activity was located in the inner membrane. It was enriched by subcellular fractionation and sucrose gradient centrifugation. MALDI-ToF MS analysis of the enriched protein identified the corresponding gene named lis that codes for the protein in the strain with the highest similarity to the Ldi. Linalool isomerase is predicted to have four transmembrane helices at the N-terminal domain and a cytosolic domain. Enzyme activity required a reductant for activation. A specific activity of 3.42 ± 0.28 nkat mg * protein−1 and a kM value of 455 ± 124 μM were determined for the thermodynamically favored isomerization of geraniol to both linalool isomers at optimal conditions of pH 8 and 35 °C. Conclusion The linalool isomerase from T. linaloolentis 47Lol represents a second member of the enzyme class 5.4.4.4, next to the linalool dehydratase/isomerase from C. defragrans 65Phen. Besides considerable amino acid sequence similarity both enzymes share common characteristics with respect to substrate affinity, pH and temperature optima, but differ in the dehydratase activity and the turnover of linalool isomers. Electronic supplementary material The online version of this article (doi:10.1186/s12858-016-0062-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert Marmulla
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Barbara Šafarić
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Stephanie Markert
- Institute for Pharmacy, Department of Pharmaceutical Biotechnology, University of Greifswald, Felix-Hausdorff-Str. 3, D-17487, Greifswald, Germany
| | - Thomas Schweder
- Institute for Pharmacy, Department of Pharmaceutical Biotechnology, University of Greifswald, Felix-Hausdorff-Str. 3, D-17487, Greifswald, Germany
| | - Jens Harder
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
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12
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Jeong JH, Kim JS, Choi SS, Kim Y. NMR Structural Studies of Antimicrobial Peptides: LPcin Analogs. Biophys J 2016; 110:423-430. [PMID: 26789765 PMCID: PMC4724650 DOI: 10.1016/j.bpj.2015.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/30/2015] [Accepted: 12/07/2015] [Indexed: 02/07/2023] Open
Abstract
Lactophoricin (LPcin), a component of proteose peptone (113-135) isolated from bovine milk, is a cationic amphipathic antimicrobial peptide consisting of 23 amino acids. We designed a series of N- or C-terminal truncated variants, mutated analogs, and truncated mutated analogs using peptide-engineering techniques. Then, we selected three LPcin analogs of LPcin-C8 (LPcin-YK1), LPcin-T2WT6W (LPcin-YK2), and LPcin-T2WT6W-C8 (LPcin-YK3), which may have better antimicrobial activities than LPcin, and successfully expressed them in E. coli with high yield. We elucidated the 3D structures and topologies of the three LPcin analogs in membrane environments by conducting NMR structural studies. We investigated the purity of the LPcin analogs and the α-helical secondary structures by performing (1)H-(15)N 2D HSQC and HMQC-NOESY liquid-state NMR spectroscopy using protein-containing micelle samples. We measured the 3D structures and tilt angles in membranes by conducting (15)N 1D and 2D (1)H-(15)N SAMMY type solid-state NMR spectroscopy with an 800 MHz in-house-built (1)H-(15)N double-resonance solid-state NMR probe with a strip-shield coil, using protein-containing large bicelle samples aligned and confirmed by molecular-dynamics simulations. The three LPcin analogs were found to be curved α-helical structures, with tilt angles of 55-75° for normal membrane bilayers, and their enhanced activities may be correlated with these topologies.
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Affiliation(s)
- Ji-Ho Jeong
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In, Korea; Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Ji-Sun Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In, Korea; Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Sung-Sub Choi
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In, Korea; Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Yongae Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In, Korea; Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea.
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13
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Moses M, Hedegård P, Hatzakis N. Quantification of Functional Dynamics of Membrane Proteins Reconstituted in Nanodiscs Membranes by Single Turnover Functional Readout. Methods Enzymol 2016; 581:227-256. [DOI: 10.1016/bs.mie.2016.08.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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14
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Detergents in Membrane Protein Purification and Crystallisation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:13-28. [PMID: 27553232 DOI: 10.1007/978-3-319-35072-1_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Detergents play a significant role in structural and functional characterisation of integral membrane proteins (IMPs). IMPs reside in the biological membranes and exhibit a great variation in their structural and physical properties. For in vitro biophysical studies, structural and functional analyses, IMPs need to be extracted from the membrane lipid bilayer environment in which they are found and purified to homogeneity while maintaining a folded and functionally active state. Detergents are capable of successfully solubilising and extracting the IMPs from the membrane bilayers. A number of detergents with varying structure and physicochemical properties are commercially available and can be applied for this purpose. Nevertheless, it is important to choose a detergent that is not only able to extract the membrane protein but also provide an optimal environment while retaining the correct structural and physical properties of the protein molecule. Choosing the best detergent for this task can be made possible by understanding the physical and chemical properties of the different detergents and their interaction with the IMPs. In addition, understanding the mechanism of membrane solubilisation and protein extraction along with crystallisation requirements, if crystallographic studies are going to be undertaken, can help in choosing the best detergent for the purpose. This chapter aims to present the fundamental properties of detergents and highlight information relevant to IMP crystallisation. The first section of the chapter reviews the physicochemical properties of detergents and parameters essential for predicting their behaviour in solution. The second section covers the interaction of detergents with the biologic membranes and proteins followed by their role in membrane protein crystallisation. The last section will briefly cover the types of detergent and their properties focusing on custom designed detergents for membrane protein studies.
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15
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Watkinson TG, Calabrese AN, Giusti F, Zoonens M, Radford SE, Ashcroft AE. Systematic analysis of the use of amphipathic polymers for studies of outer membrane proteins using mass spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 391:54-61. [PMID: 26869850 PMCID: PMC4708066 DOI: 10.1016/j.ijms.2015.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/19/2015] [Accepted: 06/26/2015] [Indexed: 05/10/2023]
Abstract
Membrane proteins (MPs) are essential for numerous important biological processes. Recently, mass spectrometry (MS), coupled with an array of related techniques, has been used to probe the structural properties of MPs and their complexes. Typically, detergent micelles have been employed for delivering MPs into the gas-phase, but these complexes have intrinsic properties that can limit the utility of structural studies of MPs using MS methods. Amphipols (APols) have advantages over detergent micelles and have been shown to be capable of delivering native MPs into the gas-phase. Comparing six different APols which vary in mass and charge, and the detergent n-dodecyl-β-d-maltopyranoside, we aimed to determine which APols are most efficient for delivery of native outer membrane proteins (OMPs) into the gas-phase. We show that maintaining the solution-phase folding and global structures of three different OMPs (PagP, OmpT and tOmpA) are independent of the APol used, but differences in OMP activity can result from the different APol:OMP complexes. ESI-IMS-MS analysis of OMP:APol complexes shows that the A8-35 APol is most proficient at liberating all three OMPs into the gas-phase, without altering their gas-phase conformations.
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Affiliation(s)
- Thomas G. Watkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Fabrice Giusti
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
| | - Manuela Zoonens
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
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Morris RG, Turner MS. Mobility Measurements Probe Conformational Changes in Membrane Proteins due to Tension. PHYSICAL REVIEW LETTERS 2015; 115:198101. [PMID: 26588417 DOI: 10.1103/physrevlett.115.198101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 05/27/2023]
Abstract
The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such proteins cause local deformations in the membrane, which induce an extra hydrodynamic drag on the protein. Using membrane tension to control the magnitude of the deformations, and hence the drag, measurements of diffusivity can be used to infer-via an elastic model of the protein-how conformation is changed by tension. Motivated by recent experimental results [Quemeneur et al., Proc. Natl. Acad. Sci. U.S.A. 111, 5083 (2014)], we focus on KvAP, a voltage-gated potassium channel from Aeropyrum pernix. The conformation of KvAP is found to change considerably due to tension, with its "walls," where the protein meets the membrane, undergoing significant angular strains. The torsional stiffness is determined to be 26.8k(B)T per radian at room temperature. This has implications for both the structure and the function of such proteins in the environment of a tension-bearing membrane.
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Affiliation(s)
- Richard G Morris
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Matthew S Turner
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
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Giusti F, Kessler P, Hansen RW, Della Pia EA, Le Bon C, Mourier G, Popot JL, Martinez KL, Zoonens M. Synthesis of a Polyhistidine-bearing Amphipol and its Use for Immobilizing Membrane Proteins. Biomacromolecules 2015; 16:3751-61. [DOI: 10.1021/acs.biomac.5b01010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Fabrice Giusti
- Laboratoire de
Biologie Physico-Chimique des Protéines Membranaires, UMR 7099,
CNRS/Université Paris 7, Institut de Biologie Physico-Chimique
(FRC 550), 13 rue Pierre et Marie Curie, F−75005 Paris, France
| | - Pascal Kessler
- CEA, Institut
de Biologie et de Technologies de Saclay, Service d’Ingénierie
Moléculaire des Protéines, 91191 Gif-sur-Yvette, France
| | - Randi Westh Hansen
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Eduardo A. Della Pia
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Christel Le Bon
- Laboratoire de
Biologie Physico-Chimique des Protéines Membranaires, UMR 7099,
CNRS/Université Paris 7, Institut de Biologie Physico-Chimique
(FRC 550), 13 rue Pierre et Marie Curie, F−75005 Paris, France
| | - Gilles Mourier
- CEA, Institut
de Biologie et de Technologies de Saclay, Service d’Ingénierie
Moléculaire des Protéines, 91191 Gif-sur-Yvette, France
| | - Jean-Luc Popot
- Laboratoire de
Biologie Physico-Chimique des Protéines Membranaires, UMR 7099,
CNRS/Université Paris 7, Institut de Biologie Physico-Chimique
(FRC 550), 13 rue Pierre et Marie Curie, F−75005 Paris, France
| | - Karen L. Martinez
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Manuela Zoonens
- Laboratoire de
Biologie Physico-Chimique des Protéines Membranaires, UMR 7099,
CNRS/Université Paris 7, Institut de Biologie Physico-Chimique
(FRC 550), 13 rue Pierre et Marie Curie, F−75005 Paris, France
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18
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Branco MA, Pinheiro L, Faustino C. Amino acid-based cationic gemini surfactant–protein interactions. Colloids Surf A Physicochem Eng Asp 2015. [DOI: 10.1016/j.colsurfa.2014.12.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Mažeika D, Rušinas L, Stupak R, Liesienė J, Valančius Z. Optimization of Crossflow Microfiltration of Disrupted Arthrobacter luteusCells. SEP SCI TECHNOL 2015. [DOI: 10.1080/01496395.2014.990464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Wang L, Tonggu L. Membrane protein reconstitution for functional and structural studies. SCIENCE CHINA-LIFE SCIENCES 2015; 58:66-74. [PMID: 25576454 DOI: 10.1007/s11427-014-4769-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
Abstract
Membrane proteins are involved in various critical biological processes, and studying membrane proteins represents a major challenge in protein biochemistry. As shown by both structural and functional studies, the membrane environment plays an essential role for membrane proteins. In vitro studies are reliant on the successful reconstitution of membrane proteins. This review describes the interaction between detergents and lipids that aids the understanding of the reconstitution processes. Then the techniques of detergent removal and a few useful techniques to refine the formed proteoliposomes are reviewed. Finally the applications of reconstitution techniques to study membrane proteins involved in Ca(2+) signaling are summarized.
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Affiliation(s)
- LiGuo Wang
- Department of Biological Structure, University of Washington, Seattle, Washington, 98195, USA,
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22
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Edwards D, Huber T, Hussain S, Stone K, Kinnebrew M, Kaminker I, Matalon E, Sherwin M, Goldfarb D, Han S. Determining the Oligomeric Structure of Proteorhodopsin by Gd3+-Based Pulsed Dipolar Spectroscopy of Multiple Distances. Structure 2014; 22:1677-86. [DOI: 10.1016/j.str.2014.09.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/15/2014] [Accepted: 09/04/2014] [Indexed: 12/30/2022]
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23
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Abstract
Amphipols (APols) are short amphipathic polymers that can substitute for detergents at the transmembrane surface of membrane proteins (MPs) and, thereby, keep them soluble in detergent free aqueous solutions. APol-trapped MPs are, as a rule, more stable biochemically than their detergent-solubilized counterparts. APols have proven useful to produce MPs, most noticeably by assisting their folding from the denatured state obtained after solubilizing MP inclusion bodies in either SDS or urea. They facilitate the handling in aqueous solution of fragile MPs for the purpose of proteomics, structural and functional studies, and therapeutics. Because APols can be chemically labeled or functionalized, and they form very stable complexes with MPs, they can also be used to functionalize those indirectly, which opens onto many novel applications. Following a brief recall of the properties of APols and MP/APol complexes, an update is provided of recent progress in these various fields.
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Affiliation(s)
- Manuela Zoonens
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
| | - Jean-Luc Popot
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
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Thermal Fluctuations in Amphipol A8-35 Particles: A Neutron Scattering and Molecular Dynamics Study. J Membr Biol 2014; 247:897-908. [DOI: 10.1007/s00232-014-9725-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/26/2014] [Indexed: 01/03/2023]
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25
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Opačić M, Giusti F, Popot JL, Broos J. Isolation of Escherichia coli mannitol permease, EIImtl, trapped in amphipol A8-35 and fluorescein-labeled A8-35. J Membr Biol 2014; 247:1019-30. [PMID: 24952466 DOI: 10.1007/s00232-014-9691-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/22/2014] [Indexed: 12/15/2022]
Abstract
Amphipols (APols) are short amphipathic polymers that keep integral membrane proteins water-soluble while stabilizing them as compared to detergent solutions. In the present work, we have carried out functional and structural studies of a membrane transporter that had not been characterized in APol-trapped form yet, namely EII(mtl), a dimeric mannitol permease from the inner membrane of Escherichia coli. A tryptophan-less and dozens of single-tryptophan (Trp) mutants of this transporter are available, making it possible to study the environment of specific locations in the protein. With few exceptions, the single-Trp mutants show a high mannitol-phosphorylation activity when in membranes, but, as variance with wild-type EII(mtl), some of them lose most of their activity upon solubilization by neutral (PEG- or maltoside-based) detergents. Here, we present a protocol to isolate these detergent-sensitive mutants in active form using APol A8-35. Trapping with A8-35 keeps EII(mtl) soluble and functional in the absence of detergent. The specific phosphorylation activity of an APol-trapped Trp-less EII(mtl) mutant was found to be ~3× higher than the activity of the same protein in dodecylmaltoside. The preparations are suitable both for functional and for fluorescence spectroscopy studies. A fluorescein-labeled version of A8-35 has been synthesized and characterized. Exploratory studies were conducted to examine the environment of specific Trp locations in the transmembrane domain of EII(mtl) using Trp fluorescence quenching by water-soluble quenchers and by the fluorescein-labeled APol. This approach has the potential to provide information on the transmembrane topology of MPs.
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Affiliation(s)
- Milena Opačić
- Unité Mixte de Recherche 7099, Centre National de la Recherche Scientifique and Université Paris 7, Institut de Biologie Physico-Chimique, CNRS FRC 550, 13 rue Pierre-et-Marie Curie, 75005, Paris, France
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26
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Long-term stability of a vaccine formulated with the amphipol-trapped major outer membrane protein from Chlamydia trachomatis. J Membr Biol 2014; 247:1053-65. [PMID: 24942817 DOI: 10.1007/s00232-014-9693-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
Abstract
Chlamydia trachomatis is a major bacterial pathogen throughout the world. Although antibiotic therapy can be implemented in the case of early detection, a majority of the infections are asymptomatic, requiring the development of preventive measures. Efforts have focused on the production of a vaccine using the C. trachomatis major outer membrane protein (MOMP). MOMP is purified in its native (n) trimeric form using the zwitterionic detergent Z3-14, but its stability in detergent solutions is limited. Amphipols (APols) are synthetic polymers that can stabilize membrane proteins (MPs) in detergent-free aqueous solutions. Preservation of protein structure and optimization of exposure of the most effective antigenic regions can avoid vaccination with misfolded, poorly protective protein. Previously, we showed that APols maintain nMOMP secondary structure and that nMOMP/APol vaccine formulations elicit better protection than formulations using either recombinant or nMOMP solubilized in Z3-14. To achieve a greater understanding of the structural behavior and stability of nMOMP in APols, we have used several spectroscopic techniques to characterize its secondary structure (circular dichroism), tertiary and quaternary structures (immunochemistry and gel electrophoresis) and aggregation state (light scattering) as a function of temperature and time. We have also recorded NMR spectra of (15)N-labeled nMOMP and find that the exposed loops are detectable in APols but not in detergent. Our analyses show that APols protect nMOMP much better than Z3-14 against denaturation due to continuous heating, repeated freeze/thaw cycles, or extended storage at room temperature. These results indicate that APols can help improve MP-based vaccine formulations.
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27
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28
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Huynh KW, Cohen MR, Moiseenkova-Bell VY. Application of amphipols for structure-functional analysis of TRP channels. J Membr Biol 2014; 247:843-51. [PMID: 24894720 DOI: 10.1007/s00232-014-9684-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 05/13/2014] [Indexed: 11/25/2022]
Abstract
Amphipathic polymers (amphipols), such as A8-35 and SApol, are a new tool for stabilizing integral membrane proteins in detergent-free conditions for structural and functional studies. Transient receptor potential (TRP) ion channels function as tetrameric protein complexes in a diverse range of cellular processes including sensory transduction. Mammalian TRP channels share ~20 % sequence similarity and are categorized into six subfamilies: TRPC (canonical), TRPV (vanilloid), TRPA (ankyrin), TRPM (melastatin), TRPP (polycystin), and TRPML (mucolipin). Due to the inherent difficulties in purifying eukaryotic membrane proteins, structural studies of TRP channels have been limited. Recently, A8-35 was essential in resolving the molecular architecture of the nociceptor TRPA1 and led to the determination of a high-resolution structure of the thermosensitive TRPV1 channel by cryo-EM. Newly developed maltose-neopentyl glycol (MNG) detergents have also proven to be useful in stabilizing TRP channels for structural analysis. In this review, we will discuss the impacts of amphipols and MNG detergents on structural studies of TRP channels by cryo-EM. We will compare how A8-35 and MNG detergents interact with the hydrophobic transmembrane domains of TRP channels. In addition, we will discuss what these cryo-EM studies reveal on the importance of screening different types of surfactants toward determining high-resolution structures of TRP channels.
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Affiliation(s)
- Kevin W Huynh
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
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29
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Olguín Y, Carrascosa LG, Lechuga LM, Young M. The effects of lipids and surfactants on TLR5-proteoliposome functionality for flagellin detection using surface plasmon resonance biosensing. Talanta 2014; 126:136-44. [PMID: 24881544 DOI: 10.1016/j.talanta.2014.03.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 12/15/2022]
Abstract
The use of proteoliposomes as affinity elements in conjunction with a surface plasmon resonance sensor is a high-sensitivity alternative for the detection of multiple analytes. However, one of the most important aspects of these conformations is maintaining the functionality of the immobilized protein, which is determined by the choice of lipids and surfactants employed in the reconstitutions. Previously, we demonstrated the functionality of TLR5-proteoliposomes as screening affinity elements of bacterial flagellin. In this new study we change the conditions of immobilization of TLR5 and evaluate how the fluidity of the membrane and the final size of the liposomes affect the functionality of the construct and thus increase their utility as an affinity element for design of new biosensors. In particular, we used reconstructions into preformed liposomes composed of the lipids POPC, POPC-DMPC and POPC-POPE mediated by the use of surfactants OG, Triton X100, and DDM, respectively. The affinity results were evaluated by SPR technology proteoliposomes and were correlated with the anisotropic change in the membrane status; the final sizes of the proteoliposomes were estimated. Our results clearly show the dependence of fluidity and final size of the proteoliposomes with surface plasmon resonance affinity measurements.
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Affiliation(s)
- Y Olguín
- Biotechnology Center, Federico Santa Maria Technical University, Valparaíso, Chile.
| | - L G Carrascosa
- Nanobiosensor and Bioanalytical Applications Group, Institut Catàla de Nanociencia i Nanotecnología (ICN2), CSIC and CIBER-BBN, Bellaterra, Barcelona, Spain
| | - L M Lechuga
- Nanobiosensor and Bioanalytical Applications Group, Institut Catàla de Nanociencia i Nanotecnología (ICN2), CSIC and CIBER-BBN, Bellaterra, Barcelona, Spain
| | - M Young
- Biotechnology Center, Federico Santa Maria Technical University, Valparaíso, Chile
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30
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Wang F, Guo J, Bai Q, Wang L. Refolding and purification of recombinant human (Pro)renin receptor fromEscherichia coliby ion exchange chromatography. Biotechnol Prog 2014; 30:864-71. [DOI: 10.1002/btpr.1916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 03/27/2014] [Accepted: 03/29/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Fei Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education; Inst. of Modern Separation Science, Key Lab of Modern Separation Science in Shaanxi Province, Northwest University; Xi'an 710069 China
| | - Jinjin Guo
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education; Inst. of Modern Separation Science, Key Lab of Modern Separation Science in Shaanxi Province, Northwest University; Xi'an 710069 China
| | - Quan Bai
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education; Inst. of Modern Separation Science, Key Lab of Modern Separation Science in Shaanxi Province, Northwest University; Xi'an 710069 China
| | - Lili Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education; Inst. of Modern Separation Science, Key Lab of Modern Separation Science in Shaanxi Province, Northwest University; Xi'an 710069 China
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31
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Tsuruoka K, Tsuneoka H, Kawano M, Yanagihara M, Nojima J, Tanaka T, Yamamoto M, Ichihara K. Evaluation of IgG ELISA using N-lauroyl-sarcosine–soluble proteins of Bartonella henselae for highly specific serodiagnosis of cat scratch disease. Diagn Microbiol Infect Dis 2012; 74:230-5. [DOI: 10.1016/j.diagmicrobio.2012.06.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 06/29/2012] [Accepted: 06/29/2012] [Indexed: 10/28/2022]
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32
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Kyrychenko A, Rodnin MV, Vargas-Uribe M, Sharma SK, Durand G, Pucci B, Popot JL, Ladokhin AS. Folding of diphtheria toxin T-domain in the presence of amphipols and fluorinated surfactants: Toward thermodynamic measurements of membrane protein folding. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1818:1006-12. [PMID: 21945883 PMCID: PMC3261334 DOI: 10.1016/j.bbamem.2011.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/18/2011] [Accepted: 09/12/2011] [Indexed: 11/22/2022]
Abstract
Solubilizing membrane proteins for functional, structural and thermodynamic studies is usually achieved with the help of detergents, which, however, tend to destabilize them. Several classes of non-detergent surfactants have been designed as milder substitutes for detergents, most prominently amphipathic polymers called 'amphipols' and fluorinated surfactants. Here we test the potential usefulness of these compounds for thermodynamic studies by examining their effect on conformational transitions of the diphtheria toxin T-domain. The advantage of the T-domain as a model system is that it exists as a soluble globular protein at neutral pH yet is converted into a membrane-competent form by acidification and inserts into the lipid bilayer as part of its physiological action. We have examined the effects of various surfactants on two conformational transitions of the T-domain, thermal unfolding and pH-induced transition to a membrane-competent form. All tested detergent and non-detergent surfactants lowered the cooperativity of the thermal unfolding of the T-domain. The dependence of enthalpy of unfolding on surfactant concentration was found to be least for fluorinated surfactants, thus making them useful candidates for thermodynamic studies. Circular dichroism measurements demonstrate that non-ionic homopolymeric amphipols (NAhPols), unlike any other surfactants, can actively cause a conformational change of the T-domain. NAhPol-induced structural rearrangements are different from those observed during thermal denaturation and are suggested to be related to the formation of the membrane-competent form of the T-domain. Measurements of leakage of vesicle content indicate that interaction with NAhPols not only does not prevent the T-domain from inserting into the bilayer, but it can make bilayer permeabilization even more efficient, whereas the pH-dependence of membrane permeabilization becomes more cooperative. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160-7421, U.S.A
| | - Mykola V. Rodnin
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160-7421, U.S.A
| | - Mauricio Vargas-Uribe
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160-7421, U.S.A
| | - Shivaji K. Sharma
- Université d’Avignon et des Pays de Vaucluse, Equipe Chimie Bioorganique et Systèmes Amphiphiles, 33 rue Louis Pasteur, F-84000 Avignon, France
| | - Grégory Durand
- Université d’Avignon et des Pays de Vaucluse, Equipe Chimie Bioorganique et Systèmes Amphiphiles, 33 rue Louis Pasteur, F-84000 Avignon, France
- Institut des Biomolécules Max Mousseron (UMR 5247), 15 avenue Charles Flahault, F-34093 Montpellier Cedex 05, France
| | - Bernard Pucci
- Université d’Avignon et des Pays de Vaucluse, Equipe Chimie Bioorganique et Systèmes Amphiphiles, 33 rue Louis Pasteur, F-84000 Avignon, France
- Institut des Biomolécules Max Mousseron (UMR 5247), 15 avenue Charles Flahault, F-34093 Montpellier Cedex 05, France
| | - Jean-Luc Popot
- Institut de Biologie Physico-Chimique, UMR 7099, CNRS and Université Paris-7 F-75005, Paris, France
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160-7421, U.S.A
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Sharma KS, Durand G, Gabel F, Bazzacco P, Le Bon C, Billon-Denis E, Catoire LJ, Popot JL, Ebel C, Pucci B. Non-ionic amphiphilic homopolymers: synthesis, solution properties, and biochemical validation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:4625-4639. [PMID: 22299604 DOI: 10.1021/la205026r] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A novel type of nonionic amphipols for handling membrane proteins in detergent-free aqueous solutions has been obtained through free-radical homo-telomerization of an acrylamide-based monomer comprising a C(11) alkyl chain and two glucose moieties, using a thiol as transfer reagent. By controlling the thiol/monomer ratio, the number-average molecular weight of the polymers was varied from 8 to 63 kDa. Homopolymeric nonionic amphipols were found to be highly soluble in water and to self-organize, within a large concentration range, into small, compact particles of ~6 nm diameter with a narrow size distribution, regardless of the molecular weight of the polymer. They proved able to trap and stabilize two test membrane proteins, bacteriorhodopsin from Halobium salinarum and the outer membrane protein X of Escherichia coli, under the form of small and well-defined complexes, whose size, composition, and shape were studied by aqueous size-exclusion chromatography, analytical ultracentrifugation, and small-angle neutron scattering. As shown in a companion paper, nonionic amphipols can be used for membrane protein folding, cell-free synthesis, and solution NMR studies (Bazzacco et al. 2012, Biochemistry, DOI: 10.1021/bi201862v).
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Affiliation(s)
- K Shivaji Sharma
- Université d'Avignon et des Pays de Vaucluse, Equipe Chimie Bioorganique et Systèmes Amphiphiles, Avignon, France
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Abla M, Durand G, Breyton C, Raynal S, Ebel C, Pucci B. A diglucosylated fluorinated surfactant to handle integral membrane proteins in aqueous solution. J Fluor Chem 2012. [DOI: 10.1016/j.jfluchem.2011.05.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Cvetkov TL, Huynh KW, Cohen MR, Moiseenkova-Bell VY. Molecular architecture and subunit organization of TRPA1 ion channel revealed by electron microscopy. J Biol Chem 2011; 286:38168-38176. [PMID: 21908607 DOI: 10.1074/jbc.m111.288993] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transient receptor potential ankyrin 1 (TRPA1) is a non-selective ion channel, which is expressed in nociceptor sensory neurons and transduces chemical, inflammatory, and neuropathic pain signals. Numerous non-reactive compounds and electrophilic compounds, such as endogenous inflammatory mediators and exogenous pungent chemicals, can activate TRPA1. Here we report a 16-Å resolution structure of purified, functional, amphipol-stabilized TRPA1 analyzed by single-particle EM. Molecular models of the N and C termini of the channel were generated using the I-TASSER protein structure prediction server and docked into the EM density to provide insight into the TRPA1 subunit organization. This structural analysis suggests a location for critical N-terminal cysteine residues involved in electrophilic activation at the interface between neighboring subunits. Our results indicate that covalent modifications within this pocket may alter interactions between subunits and promote conformational changes that lead to channel activation.
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Affiliation(s)
- Teresa L Cvetkov
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Kevin W Huynh
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Matthew R Cohen
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Vera Y Moiseenkova-Bell
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106.
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36
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Popot JL, Althoff T, Bagnard D, Banères JL, Bazzacco P, Billon-Denis E, Catoire LJ, Champeil P, Charvolin D, Cocco MJ, Crémel G, Dahmane T, de la Maza LM, Ebel C, Gabel F, Giusti F, Gohon Y, Goormaghtigh E, Guittet E, Kleinschmidt JH, Kühlbrandt W, Le Bon C, Martinez KL, Picard M, Pucci B, Sachs JN, Tribet C, van Heijenoort C, Wien F, Zito F, Zoonens M. Amphipols from A to Z. Annu Rev Biophys 2011; 40:379-408. [PMID: 21545287 DOI: 10.1146/annurev-biophys-042910-155219] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amphipols (APols) are short amphipathic polymers that can substitute for detergents to keep integral membrane proteins (MPs) water soluble. In this review, we discuss their structure and solution behavior; the way they associate with MPs; and the structure, dynamics, and solution properties of the resulting complexes. All MPs tested to date form water-soluble complexes with APols, and their biochemical stability is in general greatly improved compared with MPs in detergent solutions. The functionality and ligand-binding properties of APol-trapped MPs are reviewed, and the mechanisms by which APols stabilize MPs are discussed. Applications of APols include MP folding and cell-free synthesis, structural studies by NMR, electron microscopy and X-ray diffraction, APol-mediated immobilization of MPs onto solid supports, proteomics, delivery of MPs to preexisting membranes, and vaccine formulation.
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Affiliation(s)
- J-L Popot
- Institut de Biologie Physico-Chimique, CNRS/Université Paris-7 UMR 7099, Paris, France.
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37
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Perlmutter JD, Drasler WJ, Xie W, Gao J, Popot JL, Sachs JN. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:10523-10537. [PMID: 21806035 PMCID: PMC3214636 DOI: 10.1021/la202103v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.
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Affiliation(s)
- Jason D Perlmutter
- Department of Biomedical Engineering, 312 Church Street SE, University of Minnesota, Minneapolis, Minnesota 55455, USA
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38
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Artificial membrane-like environments for in vitro studies of purified G-protein coupled receptors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:225-33. [PMID: 21851807 DOI: 10.1016/j.bbamem.2011.07.047] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 12/31/2022]
Abstract
Functional reconstitution of transmembrane proteins remains a significant barrier to their biochemical, biophysical, and structural characterization. Studies of seven-transmembrane G-protein coupled receptors (GPCRs) in vitro are particularly challenging because, ideally, they require access to the receptor on both sides of the membrane as well as within the plane of the membrane. However, understanding the structure and function of these receptors at the molecular level within a native-like environment will have a large impact both on basic knowledge of cell signaling and on pharmacological research. The goal of this article is to review the main classes of membrane mimics that have been, or could be, used for functional reconstitution of GPCRs. These include the use of micelles, bicelles, lipid vesicles, nanodiscs, lipidic cubic phases, and planar lipid membranes. Each of these approaches is evaluated with respect to its fundamental advantages and limitations and its applications in the field of GPCR research. This article is part of a Special Issue entitled: Membrane protein structure and function.
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39
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Warschawski DE, Arnold AA, Beaugrand M, Gravel A, Chartrand É, Marcotte I. Choosing membrane mimetics for NMR structural studies of transmembrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1957-74. [DOI: 10.1016/j.bbamem.2011.03.016] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 03/28/2011] [Accepted: 03/29/2011] [Indexed: 12/11/2022]
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40
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Janaratne TK, Okach L, Brock A, Lesley SA. Solubilization of native integral membrane proteins in aqueous buffer by noncovalent chelation with monomethoxy poly(ethylene glycol) (mPEG) polymers. Bioconjug Chem 2011; 22:1513-8. [PMID: 21740061 DOI: 10.1021/bc200019x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Highly hydrophobic integral membrane proteins (IMPs)are typically purified in excess detergent media, often resulting in rapid inactivation and denaturation of the protein. One promising approach to solve this problem is to couple hydrophilic polymers, such as monomethoxypolyethylene glycol (mPEG) to IMPs under mild conditions in place of detergents. However, the broad application of this approach is hampered by poor reaction efficiencies, low tolerance of detergent stabilized membrane proteins to reaction conditions, and a lack of proper site-specific reversible approaches. Here, we have developed a straightforward, efficient, and mild approach to site-specific noncovalent binding of long-chain polymers to recombinant IMPs. This method uses the hexa-histidine tag (His-Tag) often used for purification of recombinant proteins as an attachment site for mPEGs. Solubility studies performed using five different IMPs confirmed that all tested mPEG-bound IMPs were completely soluble and stable in detergent free aqueous buffer compared to their precipitated native proteins under the identical circumstances. Activity assays and circular dichroism (CD) spectroscopy confirmed the structural integrity of modified IMPs.
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Affiliation(s)
- Thamara K Janaratne
- The Joint Center for Structural Genomics and The Scripps Research Institute, Department of Molecular Biology, La Jolla, California 92037, United States
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41
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Morgan CR, Hebling CM, Rand KD, Stafford DW, Jorgenson JW, Engen JR. Conformational transitions in the membrane scaffold protein of phospholipid bilayer nanodiscs. Mol Cell Proteomics 2011; 10:M111.010876. [PMID: 21715319 DOI: 10.1074/mcp.m111.010876] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phospholipid bilayer nanodiscs are model membrane systems that provide an environment where membrane proteins are highly stable and monodisperse without the use of detergents or liposomes. Nanodiscs consist of a discoidal phospholipid bilayer encircled by two copies of an amphipathic alpha helical membrane scaffold protein, which is modeled from apolipoprotein A-1. Hydrogen exchange mass spectrometry was used to probe the structure and dynamics of the scaffold protein in the presence and absence of lipid. On nanodisc self-assembly, the entire scaffold protein gained significant protection from exchange, consistent with a large, protein-wide, structural rearrangement. This protection was short-lived and the scaffold protein was highly deuterated within 2 h. Several regions of the scaffold protein, in both the lipid-free and lipid-associated states, displayed EX1 unfolding kinetics. The rapid deuteration of the scaffold protein and the presence of correlated unfolding events both indicate that nanodiscs are dynamic rather than rigid bodies in solution. This work provides a catalog of the expected scaffold protein peptic peptides in a nanodisc-hydrogen exchange mass spectrometry experiment and their deuterium uptake signatures, data that can be used as a benchmark to verify correct assembly and nanodisc structure. Such reference data will be useful control data for all hydrogen exchange mass spectrometry experiments involving nanodiscs in which transmembrane or lipid-associated proteins are the primary molecule(s) of interest.
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Affiliation(s)
- Christopher R Morgan
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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42
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Dahmane T, Giusti F, Catoire LJ, Popot JL. Sulfonated amphipols: synthesis, properties, and applications. Biopolymers 2011; 95:811-23. [PMID: 21638274 DOI: 10.1002/bip.21683] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 05/19/2011] [Accepted: 05/23/2011] [Indexed: 01/20/2023]
Abstract
Amphipols (APols) are amphiphatic polymers that keep membrane proteins (MPs) water-soluble. The best characterized and most widely used APol to date, A8-35, comprises a polyacrylate backbone grafted with octyl- and isopropylamine side chains. The nature of its hydrophilic moieties prevents its use at the slightly acidic pH that is desirable to slow down the rate of amide proton exchange in solution NMR studies. We describe here the synthesis and properties of pH-insensitive APols obtained by replacing isopropyles with taurine. Sulfonated APols (SAPols) can be used to trap MPs in the form of small complexes, to stabilize them, and to keep them water-soluble even at low pH. [(15) N,(1) H]-transverse relaxation-optimized spectroscopy NMR spectra obtained at pH 6.8 of a bacterial outer MP folded in SAPols show that the protein is correctly folded. The spectra have a resolution similar to that achieved with A8-35 and reveal water-exposed amide and indole protons whose resonance peaks are absent at pH 8.0.
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Affiliation(s)
- Tassadite Dahmane
- Laboratoire de Physico-Chimie Moléculaire des Membranes Biologiques, UMR 7099, CNRS and Université Paris-7, Institut de Biologie Physico-Chimique, CNRS IFR 550, 13 rue Pierre et Marie Curie, F-75005 Paris, France
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43
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Patel H, Tscheka C, Edwards K, Karlsson G, Heerklotz H. All-or-none membrane permeabilization by fengycin-type lipopeptides from Bacillus subtilis QST713. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2000-8. [PMID: 21545788 DOI: 10.1016/j.bbamem.2011.04.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 04/19/2011] [Accepted: 04/20/2011] [Indexed: 11/25/2022]
Abstract
The fungicidal activity of Bacillus subtilis QST713 has been utilized for the highly effective and environmentally safe protection of crops against a variety of pathogens. It is based mainly on the production of cyclic lipopeptides of the fengycin (FEs), surfactin, and iturin families. The mixed population of native FEs forms micelles which solubilize individual FEs such as agrastatin 1 (AS1) that are otherwise rather insoluble on their own. Fluorescence lifetime-based calcein efflux measurements and cryo transmission electron microscopy show that these FEs show a unique scenario of membrane permeabilization. Poor miscibility of FEs with lipid probably promotes the formation of pores in 10% of the vesicles at only≈1μM free FE and in 15% of the vesicles at 10 μM. We explain why this limited, all-or-none leakage could nevertheless account for the killing of virtually all fungi whereas the same extent of graded vesicle leakage may be biologically irrelevant. Then, crystallization of AS1 and micellization of plipastatins cause a cut-off in leakage at 15% that might regulate the biological activity of FEs, protecting Bacillus and plant membranes. The fact that FE micelles solubilize only about 10 mol-% fluid lipid resembles the behavior of detergent resistance.
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Affiliation(s)
- Hiren Patel
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada M5S3M2
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44
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Banères JL, Popot JL, Mouillac B. New advances in production and functional folding of G-protein-coupled receptors. Trends Biotechnol 2011; 29:314-22. [PMID: 21497924 DOI: 10.1016/j.tibtech.2011.03.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/25/2011] [Accepted: 03/02/2011] [Indexed: 12/17/2022]
Abstract
G-protein-coupled receptors (GPCRs), the largest family of integral membrane proteins, participate in the regulation of many physiological functions and are the targets of approximately 30% of currently marketed drugs. However, knowledge of the structural and molecular bases of GPCR functions remains limited owing to difficulties related to their overexpression, purification and stabilization. The development of new strategies aimed at obtaining large amounts of functional GPCRs is therefore crucial. Here, we review the most recent advances in the production and functional folding of GPCRs from Escherichia coli inclusion bodies. Major breakthroughs open exciting perspectives for structural and dynamic investigations of GPCRs. In particular, combining targeting to bacterial inclusion bodies with amphipol-assisted folding is emerging as a highly powerful strategy.
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Affiliation(s)
- Jean-Louis Banères
- CNRS, UMR-5247, Institut des Biomolécules Max Mousseron, Faculté de Pharmacie, 15 avenue Charles Flahault, F-34000 Montpellier, France
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45
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Pérez-Victoria I, Pérez-Victoria FJ, Roldán-Vargas S, García-Hernández R, Carvalho L, Castanys S, Gamarro F, Morales JC, Pérez-Victoria JM. Non-reducing trisaccharide fatty acid monoesters: Novel detergents in membrane biochemistry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:717-26. [DOI: 10.1016/j.bbamem.2010.11.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 11/18/2010] [Accepted: 11/22/2010] [Indexed: 11/30/2022]
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46
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Gao T, Blanchette CD, He W, Bourguet F, Ly S, Katzen F, Kudlicki WA, Henderson PT, Laurence TA, Huser T, Coleman MA. Characterizing diffusion dynamics of a membrane protein associated with nanolipoproteins using fluorescence correlation spectroscopy. Protein Sci 2011; 20:437-47. [PMID: 21280134 PMCID: PMC3048428 DOI: 10.1002/pro.577] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 11/29/2010] [Accepted: 12/01/2010] [Indexed: 01/28/2023]
Abstract
Nanolipoprotein particles (NLPs) represent a unique nanometer-sized scaffold for supporting membrane proteins (MP). Characterization of their dynamic shape and association with MP in solution remains a challenge. Here, we present a rapid method of analysis by fluorescence correlation spectroscopy (FCS) to characterize bacteriorhodopsin (bR), a membrane protein capable of forming a NLP complex. By selectively labeling individual components of NLPs during cell-free synthesis, FCS enabled us to measure specific NLP diffusion times and infer size information for different NLP species. The resulting bR-loaded NLPs were shown to be dynamically discoidal in solution with a mean diameter of 7.8 nm. The insertion rate of bR in the complex was ∼55% based on a fit model incorporating two separate diffusion properties to best approximate the FCS data. More importantly, based on these data, we infer that membrane protein associated NLPs are thermodynamically constrained as discs in solution, while empty NLPs appear to be less constrained and dynamically spherical.
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Affiliation(s)
- Tingjuan Gao
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | - Craig D Blanchette
- Lawrence Livermore National Laboratory, Physics and Life SciencesLivermore, California 94550
| | - Wei He
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | - Feliza Bourguet
- Lawrence Livermore National Laboratory, Physics and Life SciencesLivermore, California 94550
| | - Sonny Ly
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | | | | | - Paul T Henderson
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | - Ted A Laurence
- Lawrence Livermore National Laboratory, Physics and Life SciencesLivermore, California 94550
| | - Thomas Huser
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | - Matthew A Coleman
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
- Lawrence Livermore National Laboratory, Physics and Life SciencesLivermore, California 94550
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47
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Hebling CM, Morgan CR, Stafford DW, Jorgenson JW, Rand KD, Engen JR. Conformational analysis of membrane proteins in phospholipid bilayer nanodiscs by hydrogen exchange mass spectrometry. Anal Chem 2010; 82:5415-9. [PMID: 20518534 DOI: 10.1021/ac100962c] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The study of membrane protein structure and enzymology has traditionally been hampered by the inherent insolubility of membrane proteins in aqueous environments and experimental challenges in emulating an in vivo lipid environment. Phospholipid bilayer nanodiscs have recently been shown to be of great use for the study of membrane proteins since they offer a controllable, stable, and monodisperse model membrane with a nativelike lipid bilayer. Here we report the integration of nanodiscs with hydrogen exchange (HX) mass spectrometry (MS) experiments, thereby allowing for analysis of the native conformation of membrane proteins. gamma-Glutamyl carboxylase (GGCX), an approximately 94 kDa transmembrane protein, was inserted into nanodiscs and labeled with deuterium oxide under native conditions. Analytical parameters including sample-handling and chromatographic separation were optimized to measure the incorporation of deuterium into GGCX. Coupling nanodisc technology with HX MS offers an effective approach for investigating the conformation and dynamics of membrane proteins in their native environment and is therefore capable of providing much needed insight into the function of membrane proteins.
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Affiliation(s)
- Christine M Hebling
- Department of Chemistry, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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48
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Park KH, Billon-Denis E, Dahmane T, Lebaupain F, Pucci B, Breyton C, Zito F. In the cauldron of cell-free synthesis of membrane proteins: playing with new surfactants. N Biotechnol 2010; 28:255-61. [PMID: 20800706 DOI: 10.1016/j.nbt.2010.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/22/2010] [Accepted: 08/18/2010] [Indexed: 02/06/2023]
Abstract
Cell-free protein synthesis is a well-known technique for the roles it has played in deciphering the genetic code and in the beginnings of signal sequence studies. Since then, many efforts have been made to optimise this technique and, recently, to adapt it to membrane protein production with yields compatible with structural investigations. The versatility of the method allows membrane proteins to be obtained directly stabilised in surfactant micelles or inserted in a lipidic environment (proteoliposome, bicelle, and nanodisc) at the end of synthesis. Among the surfactants used, non-detergent ones such as fluorinated surfactants proved to be a good alternative in terms of colloidal stability and preservation of the integrity of membrane proteins, as shown for Escherichia coli homo-pentameric channel, MscL (Park et al., Biochem. J., 403: 183-187). Here we report cell-free expression of Escherichia coli leader peptidase (a transmembrane protease), Halobacterium salinarium bacteriorhodopsin (a transmembrane protein binding a hydrophobic cofactor) and E. coli MscL in the presence of non-detergent surfactants, amphipols and fluorinated surfactants in comparison to their expression in classical detergents. The results confirm the potentialities of fluorinated surfactants and, although pointing to limitations in using the first generations amphipols, results are discussed in the light of membrane protein refolding, especially in the case of bacteriorhodopsin. Preliminary experiments using new generations of amphipols supports choices made in developing new molecules.
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Affiliation(s)
- Kyu-Ho Park
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS and Université Paris-7, Institut de Biologie Physico-Chimique, CNRS FRC 550, F-75005 Paris, France
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49
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Popot JL. Amphipols, Nanodiscs, and Fluorinated Surfactants: Three Nonconventional Approaches to Studying Membrane Proteins in Aqueous Solutions. Annu Rev Biochem 2010; 79:737-75. [DOI: 10.1146/annurev.biochem.052208.114057] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jean-Luc Popot
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, Unité Mixte de Recherche 7099, Centre National de la Recherche Scientifique and Université Paris-7 Denis Diderot, Institut de Biologie Physico-Chimique, F-75005 Paris, France; e-mail:
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50
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Amphipols and fluorinated surfactants: Two alternatives to detergents for studying membrane proteins in vitro. Methods Mol Biol 2010; 601:219-45. [PMID: 20099149 DOI: 10.1007/978-1-60761-344-2_14] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Handling integral membrane proteins in aqueous solutions traditionally relies on the use of detergents, which are surfactants capable of dispersing the components of biological membranes into mixed micelles. The dissociating character of detergents, however, most often causes solubilized membrane proteins to be unstable. This has prompted the development of alternative, less-aggressive surfactants designed to keep membrane proteins soluble, after they have been solubilized, under milder conditions. A short overview is presented of the structure, properties, and uses of two families of such surfactants: amphiphilic polymers ("amphipols") and fluorinated surfactants.
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