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Galluccio M, Mazza T, Scalise M, Tripicchio M, Scarpelli M, Tolomeo M, Pochini L, Indiveri C. Over-Production of the Human SLC7A10 in E. coli and Functional Assay in Proteoliposomes. Int J Mol Sci 2023; 25:536. [PMID: 38203703 PMCID: PMC10779382 DOI: 10.3390/ijms25010536] [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: 11/30/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The human SLC7A10 transporter, also known as ASC-1, catalyzes the transport of some neutral amino acids. It is expressed in astrocytes, neurons, and adipose tissues, playing roles in learning, memory processes, and lipid metabolism, thus being involved in neurological and metabolic pathologies. Structure/function studies on this transporter are still in their infancy. In this study, we present a methodology for producing the recombinant human transporter in E. coli. Its transport function was assayed in proteoliposomes following the uptake of radiolabeled L-serine. After the testing of several growth conditions, the hASC-1 transporter was successfully expressed in BL21(DE3) codon plus RIL in the presence of 0.5% glucose and induced with 0.05 mM IPTG. After solubilization with C12E8 and cholesteryl hemisuccinate and purification by Ni-chelating chromatography, hASC-1 was reconstituted in proteoliposomes. In this experimental system it was able to catalyze an Na+-independent homologous antiport of L-serine. A Km for L-serine transport of 0.24 mM was measured. The experimental model developed in this work represents a reproducible system for the transport assay of hASC-1 in the absence of interferences. This tool will be useful to unveil unknown transport properties of hASC-1 and for testing ligands with possible application in human pharmacology.
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Affiliation(s)
- Michele Galluccio
- Laboratory of Biochemistry, Molecular Biotechnology, and Molecular Biology, Department DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Via Bucci 4C, 6C, 87036 Arcavacata di Rende, Italy; (T.M.); (M.S.); (M.T.); (M.S.); (M.T.); (L.P.)
| | - Tiziano Mazza
- Laboratory of Biochemistry, Molecular Biotechnology, and Molecular Biology, Department DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Via Bucci 4C, 6C, 87036 Arcavacata di Rende, Italy; (T.M.); (M.S.); (M.T.); (M.S.); (M.T.); (L.P.)
| | - Mariafrancesca Scalise
- Laboratory of Biochemistry, Molecular Biotechnology, and Molecular Biology, Department DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Via Bucci 4C, 6C, 87036 Arcavacata di Rende, Italy; (T.M.); (M.S.); (M.T.); (M.S.); (M.T.); (L.P.)
| | - Martina Tripicchio
- Laboratory of Biochemistry, Molecular Biotechnology, and Molecular Biology, Department DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Via Bucci 4C, 6C, 87036 Arcavacata di Rende, Italy; (T.M.); (M.S.); (M.T.); (M.S.); (M.T.); (L.P.)
| | - Martina Scarpelli
- Laboratory of Biochemistry, Molecular Biotechnology, and Molecular Biology, Department DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Via Bucci 4C, 6C, 87036 Arcavacata di Rende, Italy; (T.M.); (M.S.); (M.T.); (M.S.); (M.T.); (L.P.)
| | - Maria Tolomeo
- Laboratory of Biochemistry, Molecular Biotechnology, and Molecular Biology, Department DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Via Bucci 4C, 6C, 87036 Arcavacata di Rende, Italy; (T.M.); (M.S.); (M.T.); (M.S.); (M.T.); (L.P.)
| | - Lorena Pochini
- Laboratory of Biochemistry, Molecular Biotechnology, and Molecular Biology, Department DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Via Bucci 4C, 6C, 87036 Arcavacata di Rende, Italy; (T.M.); (M.S.); (M.T.); (M.S.); (M.T.); (L.P.)
- National Research Council (CNR), Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy
| | - Cesare Indiveri
- Laboratory of Biochemistry, Molecular Biotechnology, and Molecular Biology, Department DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Via Bucci 4C, 6C, 87036 Arcavacata di Rende, Italy; (T.M.); (M.S.); (M.T.); (M.S.); (M.T.); (L.P.)
- National Research Council (CNR), Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy
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2
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Bruni R, Laguerre A, Kaminska A, McSweeney S, Hendrickson WA, Liu Q. High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics. Protein Sci 2022; 31:639-651. [PMID: 34910339 PMCID: PMC8862427 DOI: 10.1002/pro.4259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/16/2022]
Abstract
Membrane proteins play essential roles in cellular function and metabolism. Nonetheless, biophysical and structural studies of membrane proteins are impeded by the difficulty of their expression in and purification from heterologous cell-based systems. As an alternative to these cell-based systems, cell-free protein synthesis has proven to be an exquisite method for screening membrane protein targets in a variety of lipidic mimetics. Here we report a high-throughput screening workflow and apply it to screen 61 eukaryotic membrane protein targets. For each target, we tested its expression in lipidic mimetics: two detergents, two liposomes, and two nanodiscs. We show that 35 membrane proteins (57%) can be expressed in a soluble fraction in at least one of the mimetics with the two detergents performing significantly better than nanodiscs and liposomes, in that order. Using the established cell-free workflow, we studied the production and biophysical assays for mitochondrial pyruvate carrier (MPC) complexes. Our studies show that the complexes produced in cell-free are functionally competent in complex formation and substrate binding. Our results highlight the utility of using cell-free systems for screening and production of eukaryotic membrane proteins.
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Affiliation(s)
- Renato Bruni
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA
| | - Aisha Laguerre
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Present address:
Roche DiagnosticsSanta ClaraCaliforniaUSA
| | - Anna‐Maria Kaminska
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Present address:
New York Blood CenterNew YorkNew YorkUSA
| | | | - Wayne A. Hendrickson
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
| | - Qun Liu
- NSLS‐II, Brookhaven National LaboratoryUptonNew YorkUSA,Biology DepartmentBrookhaven National LaboratoryUptonNew YorkUSA
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3
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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4
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Drew D, North RA, Nagarathinam K, Tanabe M. Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS). Chem Rev 2021; 121:5289-5335. [PMID: 33886296 PMCID: PMC8154325 DOI: 10.1021/acs.chemrev.0c00983] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is the largest known superfamily of secondary active transporters. MFS transporters are responsible for transporting a broad spectrum of substrates, either down their concentration gradient or uphill using the energy stored in the electrochemical gradients. Over the last 10 years, more than a hundred different MFS transporter structures covering close to 40 members have provided an atomic framework for piecing together the molecular basis of their transport cycles. Here, we summarize the remarkable promiscuity of MFS members in terms of substrate recognition and proton coupling as well as the intricate gating mechanisms undergone in achieving substrate translocation. We outline studies that show how residues far from the substrate binding site can be just as important for fine-tuning substrate recognition and specificity as those residues directly coordinating the substrate, and how a number of MFS transporters have evolved to form unique complexes with chaperone and signaling functions. Through a deeper mechanistic description of glucose (GLUT) transporters and multidrug resistance (MDR) antiporters, we outline novel refinements to the rocker-switch alternating-access model, such as a latch mechanism for proton-coupled monosaccharide transport. We emphasize that a full understanding of transport requires an elucidation of MFS transporter dynamics, energy landscapes, and the determination of how rate transitions are modulated by lipids.
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Affiliation(s)
- David Drew
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Rachel A. North
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Kumar Nagarathinam
- Center
of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, D-23538, Lübeck, Germany
| | - Mikio Tanabe
- Structural
Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
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5
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Bada Juarez JF, Muñoz-García JC, Inácio Dos Reis R, Henry A, McMillan D, Kriek M, Wood M, Vandenplas C, Sands Z, Castro L, Taylor R, Watts A. Detergent-free extraction of a functional low-expressing GPCR from a human cell line. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183152. [PMID: 31843475 DOI: 10.1016/j.bbamem.2019.183152] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/21/2019] [Accepted: 12/05/2019] [Indexed: 01/02/2023]
Abstract
Dopamine receptors (DRs) are class A G-Protein Coupled Receptors (GPCRs) prevalent in the central nervous system (CNS). These receptors mediate physiological functions ranging from voluntary movement and reward recognition to hormonal regulation and hypertension. Drugs targeting dopaminergic neurotransmission have been employed to treat several neurological and psychiatric disorders, including Parkinson's disease, schizophrenia, Huntington's disease, attention deficit hyperactivity disorder (ADHD), and Tourette's syndrome. In vivo, incorporation of GPCRs into lipid membranes is known to be key to their biological function and, by inference, maintenance of their tertiary structure. A further significant challenge in the structural and biochemical characterization of human DRs is their low levels of expression in mammalian cells. Thus, the purification and enrichment of DRs whilst retaining their structural integrity and function is highly desirable for biophysical studies. A promising new approach is the use of styrene-maleic acid (SMA) copolymer to solubilize GPCRs directly in their native environment, to produce polymer-assembled Lipodisqs (LQs). We have developed a novel methodology to yield detergent-free D1-containing Lipodisqs directly from HEK293f cells expressing wild-type human dopamine receptor 1 (D1). We demonstrate that D1 in the Lipodisq retains activity comparable to that in the native environment and report, for the first time, the affinity constant for the interaction of the peptide neurotransmitter neurotensin (NT) with D1, in the native state.
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Affiliation(s)
| | - Juan C Muñoz-García
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, UK; School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | | | | | | | - Marco Kriek
- UCB Celltech, 216 Bath Road, Slough SL1 3WE, UK
| | - Martyn Wood
- UCB BioPharma SPRL, Braine-l'Alleud, Belgium
| | | | - Zara Sands
- UCB Celltech, 216 Bath Road, Slough SL1 3WE, UK
| | - Luis Castro
- UCB Celltech, 216 Bath Road, Slough SL1 3WE, UK
| | | | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, UK.
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6
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Nji E, Chatzikyriakidou Y, Landreh M, Drew D. An engineered thermal-shift screen reveals specific lipid preferences of eukaryotic and prokaryotic membrane proteins. Nat Commun 2018; 9:4253. [PMID: 30315156 PMCID: PMC6185904 DOI: 10.1038/s41467-018-06702-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 09/19/2018] [Indexed: 12/11/2022] Open
Abstract
Membrane bilayers are made up of a myriad of different lipids that regulate the functional activity, stability, and oligomerization of many membrane proteins. Despite their importance, screening the structural and functional impact of lipid–protein interactions to identify specific lipid requirements remains a major challenge. Here, we use the FSEC-TS assay to show cardiolipin-dependent stabilization of the dimeric sodium/proton antiporter NhaA, demonstrating its ability to detect specific protein-lipid interactions. Based on the principle of FSEC-TS, we then engineer a simple thermal-shift assay (GFP-TS), which facilitates the high-throughput screening of lipid- and ligand- interactions with membrane proteins. By comparing the thermostability of medically relevant eukaryotic membrane proteins and a selection of bacterial counterparts, we reveal that eukaryotic proteins appear to have evolved to be more dependent to the presence of specific lipids. Membrane bilayers are made up of a myriad of different lipids that affect membrane proteins, but identifying those specific lipid requirements remains a challenge. Here authors present an engineered thermal-shift screen which reveals specific lipid preferences of eukaryotic and prokaryotic membrane proteins.
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Affiliation(s)
- Emmanuel Nji
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Yurie Chatzikyriakidou
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Michael Landreh
- SciLifeLab and Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - David Drew
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden.
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7
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Boland C, Olatunji S, Bailey J, Howe N, Weichert D, Fetics SK, Yu X, Merino-Gracia J, Delsaut C, Caffrey M. Membrane (and Soluble) Protein Stability and Binding Measurements in the Lipid Cubic Phase Using Label-Free Differential Scanning Fluorimetry. Anal Chem 2018; 90:12152-12160. [DOI: 10.1021/acs.analchem.8b03176] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Coilín Boland
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Samir Olatunji
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Jonathan Bailey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Nicole Howe
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Dietmar Weichert
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Susan Kathleen Fetics
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Xiaoxiao Yu
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Javier Merino-Gracia
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Clement Delsaut
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
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8
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Purification of Histidine-Tagged Membrane-Bound Catechol-O-Methyltransferase from Detergent-Solubilized Pichia pastoris Membranes. Chromatographia 2018. [DOI: 10.1007/s10337-017-3453-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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9
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Veith K, Martinez Molledo M, Almeida Hernandez Y, Josts I, Nitsche J, Löw C, Tidow H. Lipid-like Peptides can Stabilize Integral Membrane Proteins for Biophysical and Structural Studies. Chembiochem 2017; 18:1735-1742. [PMID: 28603929 PMCID: PMC5601290 DOI: 10.1002/cbic.201700235] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Indexed: 12/30/2022]
Abstract
A crucial bottleneck in membrane protein structural biology is the difficulty in identifying a detergent that can maintain the stability and functionality of integral membrane proteins (IMPs). Detergents are poor membrane mimics, and their common use in membrane protein crystallography may be one reason for the challenges in obtaining high-resolution crystal structures of many IMP families. Lipid-like peptides (LLPs) have detergent-like properties and have been proposed as alternatives for the solubilization of G protein-coupled receptors and other membrane proteins. Here, we systematically analyzed the stabilizing effect of LLPs on integral membrane proteins of different families. We found that LLPs could significantly stabilize detergent-solubilized IMPs in vitro. This stabilizing effect depended on the chemical nature of the LLP and the intrinsic stability of a particular IMP in the detergent. Our results suggest that screening a subset of LLPs is sufficient to stabilize a particular IMP, which can have a substantial impact on the crystallization and quality of the crystal.
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Affiliation(s)
- Katharina Veith
- The Hamburg Centre for Ultrafast ImagingDepartment of ChemistryInstitute for Biochemistry and Molecular BiologyUniversity of HamburgMartin-Luther-King-Platz 620146HamburgGermany
| | - Maria Martinez Molledo
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Yasser Almeida Hernandez
- The Hamburg Centre for Ultrafast ImagingDepartment of ChemistryInstitute for Biochemistry and Molecular BiologyUniversity of HamburgMartin-Luther-King-Platz 620146HamburgGermany
| | - Inokentijs Josts
- The Hamburg Centre for Ultrafast ImagingDepartment of ChemistryInstitute for Biochemistry and Molecular BiologyUniversity of HamburgMartin-Luther-King-Platz 620146HamburgGermany
| | - Julius Nitsche
- The Hamburg Centre for Ultrafast ImagingDepartment of ChemistryInstitute for Biochemistry and Molecular BiologyUniversity of HamburgMartin-Luther-King-Platz 620146HamburgGermany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetScheeles väg 217177StockholmSweden
| | - Henning Tidow
- The Hamburg Centre for Ultrafast ImagingDepartment of ChemistryInstitute for Biochemistry and Molecular BiologyUniversity of HamburgMartin-Luther-King-Platz 620146HamburgGermany
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10
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Pollock NL, Lee SC, Patel JH, Gulamhussein AA, Rothnie AJ. Structure and function of membrane proteins encapsulated in a polymer-bound lipid bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:809-817. [PMID: 28865797 DOI: 10.1016/j.bbamem.2017.08.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 12/14/2022]
Abstract
New technologies for the purification of stable membrane proteins have emerged in recent years, in particular methods that allow the preparation of membrane proteins with their native lipid environment. Here, we look at the progress achieved with the use of styrene-maleic acid copolymers (SMA) which are able to insert into biological membranes forming nanoparticles containing membrane proteins and lipids. This technology can be applied to membrane proteins from any host source, and, uniquely, allows purification without the protein ever being removed from a lipid bilayer. Not only do these SMA lipid particles (SMALPs) stabilise membrane proteins, allowing structural and functional studies, but they also offer opportunities to understand the local lipid environment of the host membrane. With any new or different method, questions inevitably arise about the integrity of the protein purified: does it retain its activity; its native structure; and ability to perform its function? How do membrane proteins within SMALPS perform in existing assays and lend themselves to analysis by established methods? We outline here recent work on the structure and function of membrane proteins that have been encapsulated like this in a polymer-bound lipid bilayer, and the potential for the future with this approach. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Naomi L Pollock
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jaimin H Patel
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | | | - Alice J Rothnie
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK.
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11
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Abstract
To study integral membrane proteins, one has to extract them from the membrane—the step that is typically achieved by the application of detergents. In this mini-review, we summarize the top 10 detergents used for the structural analysis of membrane proteins based on the published results. The aim of this study is to provide the reader with an overview of the main properties of available detergents (critical micelle concentration (CMC) value, micelle size, etc.) and provide an idea of what detergents to may merit further study. Furthermore, we briefly discuss alternative solubilization and stabilization agents, such as polymers.
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12
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Saidijam M, Karimi Dermani F, Sohrabi S, Patching SG. Efflux proteins at the blood-brain barrier: review and bioinformatics analysis. Xenobiotica 2017; 48:506-532. [PMID: 28481715 DOI: 10.1080/00498254.2017.1328148] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
1. Efflux proteins at the blood-brain barrier provide a mechanism for export of waste products of normal metabolism from the brain and help to maintain brain homeostasis. They also prevent entry into the brain of a wide range of potentially harmful compounds such as drugs and xenobiotics. 2. Conversely, efflux proteins also hinder delivery of therapeutic drugs to the brain and central nervous system used to treat brain tumours and neurological disorders. For bypassing efflux proteins, a comprehensive understanding of their structures, functions and molecular mechanisms is necessary, along with new strategies and technologies for delivery of drugs across the blood-brain barrier. 3. We review efflux proteins at the blood-brain barrier, classified as either ATP-binding cassette (ABC) transporters (P-gp, BCRP, MRPs) or solute carrier (SLC) transporters (OATP1A2, OATP1A4, OATP1C1, OATP2B1, OAT3, EAATs, PMAT/hENT4 and MATE1). 4. This includes information about substrate and inhibitor specificity, structural organisation and mechanism, membrane localisation, regulation of expression and activity, effects of diseases and conditions and the principal technique used for in vivo analysis of efflux protein activity: positron emission tomography (PET). 5. We also performed analyses of evolutionary relationships, membrane topologies and amino acid compositions of the proteins, and linked these to structure and function.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics , Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan , Iran and
| | - Fatemeh Karimi Dermani
- a Department of Molecular Medicine and Genetics , Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan , Iran and
| | - Sareh Sohrabi
- a Department of Molecular Medicine and Genetics , Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan , Iran and
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds , UK
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13
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Christensen U, Vazquez-Albacete D, Søgaard KM, Hobel T, Nielsen MT, Harrison SJ, Hansen AH, Møller BL, Seppälä S, Nørholm MHH. De-bugging and maximizing plant cytochrome P450 production in Escherichia coli with C-terminal GFP fusions. Appl Microbiol Biotechnol 2017; 101:4103-4113. [DOI: 10.1007/s00253-016-8076-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/17/2016] [Accepted: 12/18/2016] [Indexed: 11/30/2022]
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14
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Yang Y, Ke N, Liu S, Li W. Methods for Structural and Functional Analyses of Intramembrane Prenyltransferases in the UbiA Superfamily. Methods Enzymol 2016; 584:309-347. [PMID: 28065269 DOI: 10.1016/bs.mie.2016.10.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The UbiA superfamily is a group of intramembrane prenyltransferases that generate lipophilic compounds essential in biological membranes. These compounds, which include various quinones, hemes, chlorophylls, and vitamin E, participate in electron transport and function as antioxidants, as well as acting as structural lipids of microbial cell walls and membranes. Prenyltransferases producing these compounds are involved in important physiological processes and human diseases. These UbiA superfamily members differ significantly in their enzymatic activities and substrate selectivities. This chapter describes examples of methods that can be used to group these intramembrane enzymes, analyze their activity, and screen and crystallize homolog proteins for structure determination. Recent structures of two archaeal homologs are compared with structures of soluble prenyltransferases to show distinct mechanisms used by the UbiA superfamily to control enzymatic activity in membranes.
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Affiliation(s)
- Y Yang
- Washington University School of Medicine, St. Louis, MO, United States
| | - N Ke
- New England Biolabs, Ipswich, MA, United States
| | - S Liu
- Washington University School of Medicine, St. Louis, MO, United States
| | - W Li
- Washington University School of Medicine, St. Louis, MO, United States.
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15
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Parker JL, Newstead S. Membrane Protein Crystallisation: Current Trends and Future Perspectives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:61-72. [PMID: 27553235 PMCID: PMC5033070 DOI: 10.1007/978-3-319-35072-1_5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alpha helical membrane proteins are the targets for many pharmaceutical drugs and play important roles in physiology and disease processes. In recent years, substantial progress has been made in determining their atomic structure using X-ray crystallography. However, a major bottleneck still remains; the identification of conditions that give crystals that are suitable for structure determination. Over the past 10 years we have been analysing the crystallisation conditions reported for alpha helical membrane proteins with the aim to facilitate a rational approach to the design and implementation of successful crystallisation screens. The result has been the development of MemGold, MemGold2 and the additive screen MemAdvantage. The associated analysis, summarised and updated in this chapter, has revealed a number of surprisingly successfully strategies for crystallisation and detergent selection.
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Affiliation(s)
- Joanne L. Parker
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
| | - Simon Newstead
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
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16
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Nomura N, Verdon G, Kang HJ, Shimamura T, Nomura Y, Sonoda Y, Hussien SA, Qureshi AA, Coincon M, Sato Y, Abe H, Nakada-Nakura Y, Hino T, Arakawa T, Kusano-Arai O, Iwanari H, Murata T, Kobayashi T, Hamakubo T, Kasahara M, Iwata S, Drew D. Structure and mechanism of the mammalian fructose transporter GLUT5. Nature 2015; 526:397-401. [PMID: 26416735 PMCID: PMC4618315 DOI: 10.1038/nature14909] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/14/2015] [Indexed: 02/02/2023]
Abstract
The altered activity of the fructose transporter GLUT5, an isoform of the facilitated-diffusion glucose transporter family, has been linked to disorders such as type 2 diabetes and obesity. GLUT5 is also overexpressed in certain tumor cells and inhibitors are potential drugs for these conditions. Here, we describe the crystal structure of GLUT5 from Rattus norvegicus and Bos taurus in open outward- and open inward-facing conformations, respectively. GLUT5 has a major facilitator superfamily fold like other homologous monosaccharide transporters. Based on a comparison of the inward-facing structures of GLUT5 and human GLUT1, a ubiquitous glucose transporter, we show that a single point mutation is enough to switch the substrate binding preference of GLUT5 from fructose to glucose. A comparison of the substrate-free structures of GLUT5 with occluded substrate-bound structures of XylE suggests that, besides global rocker-switch like re-orientation of the bundles, local asymmetric rearrangements of C-terminal bundle helices TMs 7 and 10 underlie a “gated-pore” transport mechanism in such monosaccharide transporters.
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Affiliation(s)
- Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Grégory Verdon
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire, OX11 0DE, U.K.,Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire, OX11 0FA, U.K
| | - Hae Joo Kang
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire, OX11 0DE, U.K.,Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire, OX11 0FA, U.K
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yayoi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yo Sonoda
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K
| | - Saba Abdul Hussien
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Aziz Abdul Qureshi
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mathieu Coincon
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Yumi Sato
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hitomi Abe
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoya Hino
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takatoshi Arakawa
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Osamu Kusano-Arai
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroko Iwanari
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takeshi Murata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Systems and Structural Biology Center, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takuya Kobayashi
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takao Hamakubo
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Michihiro Kasahara
- Laboratory of Biophysics, School of Medicine, Teikyo University, Hachioji, Tokyo 192-0395, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire, OX11 0DE, U.K.,Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire, OX11 0FA, U.K.,Systems and Structural Biology Center, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - David Drew
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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17
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Quantification of detergent using colorimetric methods in membrane protein crystallography. Methods Enzymol 2015; 557:95-116. [PMID: 25950961 DOI: 10.1016/bs.mie.2014.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Membrane protein crystallography has the potential to greatly aid our understanding of membrane protein biology. Yet, membrane protein crystals remain challenging to produce. Although robust methods for the expression and purification of membrane proteins continue to be developed, the detergent component of membrane protein samples is equally important to crystallization efforts. This chapter describes the development of three colorimetric assays for the quantitation of detergent in membrane protein samples and provides detailed protocols. All of these techniques use small sample volumes and have potential applications in crystallography. The application of these techniques in crystallization prescreening, detergent concentration modification, and detergent exchange experiments is demonstrated. It has been observed that the concentration of detergent in a membrane protein sample can be just as important as the protein concentration when attempting to reproduce crystallization lead conditions.
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18
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19
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MemStar: A one-shotEscherichia coli-based approach for high-level bacterial membrane protein production. FEBS Lett 2014; 588:3761-9. [DOI: 10.1016/j.febslet.2014.08.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/21/2014] [Accepted: 08/21/2014] [Indexed: 01/22/2023]
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20
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Kumazaki K, Tsukazaki T, Nishizawa T, Tanaka Y, Kato HE, Nakada-Nakura Y, Hirata K, Mori Y, Suga H, Dohmae N, Ishitani R, Nureki O. Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans. Acta Crystallogr F Struct Biol Commun 2014; 70:1056-60. [PMID: 25084381 PMCID: PMC4118803 DOI: 10.1107/s2053230x14012540] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 05/29/2014] [Indexed: 12/02/2022] Open
Abstract
YidC, a member of the YidC/Oxa1/Alb3 family, inserts proteins into the membrane and facilitates membrane-protein folding in bacteria. YidC plays key roles in both Sec-mediated integration and Sec-independent insertion of membrane proteins. Here, Bacillus halodurans YidC2, which has five transmembrane helices conserved among the other family members, was identified as a target protein for structure determination by a fluorescent size-exclusion chromatography analysis. The protein was overexpressed, purified and crystallized in the lipidic cubic phase. The crystals diffracted X-rays to 2.4 Å resolution and belonged to space group P21, with unit-cell parameters a = 43.9, b = 60.6, c = 58.9 Å, β = 100.3°. The experimental phases were determined by the multiwavelength anomalous diffraction method using a mercury-derivatized crystal.
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Affiliation(s)
- Kaoru Kumazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Tomoya Tsukazaki
- Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Yoshiki Tanaka
- Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan
| | - Hideaki E. Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshihiro Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Naoshi Dohmae
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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21
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Emmerstorfer A, Wriessnegger T, Hirz M, Pichler H. Overexpression of membrane proteins from higher eukaryotes in yeasts. Appl Microbiol Biotechnol 2014; 98:7671-98. [PMID: 25070595 DOI: 10.1007/s00253-014-5948-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 02/08/2023]
Abstract
Heterologous expression and characterisation of the membrane proteins of higher eukaryotes is of paramount interest in fundamental and applied research. Due to the rather simple and well-established methods for their genetic modification and cultivation, yeast cells are attractive host systems for recombinant protein production. This review provides an overview on the remarkable progress, and discusses pitfalls, in applying various yeast host strains for high-level expression of eukaryotic membrane proteins. In contrast to the cell lines of higher eukaryotes, yeasts permit efficient library screening methods. Modified yeasts are used as high-throughput screening tools for heterologous membrane protein functions or as benchmark for analysing drug-target relationships, e.g., by using yeasts as sensors. Furthermore, yeasts are powerful hosts for revealing interactions stabilising and/or activating membrane proteins. We also discuss the stress responses of yeasts upon heterologous expression of membrane proteins. Through co-expression of chaperones and/or optimising yeast cultivation and expression strategies, yield-optimised hosts have been created for membrane protein crystallography or efficient whole-cell production of fine chemicals.
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Affiliation(s)
- Anita Emmerstorfer
- ACIB-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
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22
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Yang Z, Wang C, Zhou Q, An J, Hildebrandt E, Aleksandrov LA, Kappes JC, DeLucas LJ, Riordan JR, Urbatsch IL, Hunt JF, Brouillette CG. Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains. Protein Sci 2014; 23:769-89. [PMID: 24652590 PMCID: PMC4093953 DOI: 10.1002/pro.2460] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 03/07/2014] [Accepted: 03/17/2014] [Indexed: 11/06/2022]
Abstract
Detergent interaction with extramembranous soluble domains (ESDs) is not commonly considered an important determinant of integral membrane protein (IMP) behavior during purification and crystallization, even though ESDs contribute to the stability of many IMPs. Here we demonstrate that some generally nondenaturing detergents critically destabilize a model ESD, the first nucleotide-binding domain (NBD1) from the human cystic fibrosis transmembrane conductance regulator (CFTR), a model IMP. Notably, the detergents show equivalent trends in their influence on the stability of isolated NBD1 and full-length CFTR. We used differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy to monitor changes in NBD1 stability and secondary structure, respectively, during titration with a series of detergents. Their effective harshness in these assays mirrors that widely accepted for their interaction with IMPs, i.e., anionic > zwitterionic > nonionic. It is noteworthy that including lipids or nonionic detergents is shown to mitigate detergent harshness, as will limiting contact time. We infer three thermodynamic mechanisms from the observed thermal destabilization by monomer or micelle: (i) binding to the unfolded state with no change in the native structure (all detergent classes); (ii) native state binding that alters thermodynamic properties and perhaps conformation (nonionic detergents); and (iii) detergent binding that directly leads to denaturation of the native state (anionic and zwitterionic). These results demonstrate that the accepted model for the harshness of detergents applies to their interaction with an ESD. It is concluded that destabilization of extramembranous soluble domains by specific detergents will influence the stability of some IMPs during purification.
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Affiliation(s)
- Zhengrong Yang
- Department of Chemistry, University of Alabama at BirminghamBirmingham, Alabama
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Chi Wang
- Department of Biological Sciences, Columbia UniversityNew York, New York
| | - Qingxian Zhou
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Jianli An
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Ellen Hildebrandt
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, Texas
| | - Luba A Aleksandrov
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel HillChapel Hill, North Carolina
- Cystic Fibrosis Treatment and Research Center, The University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - John C Kappes
- Department of Medicine, University of Alabama at BirminghamBirmingham, Alabama
- Birmingham Veterans Affairs Medical Center, Research ServiceBirmingham, Alabama
| | - Lawrence J DeLucas
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
- Department of Optometry, University of Alabama at BirminghamBirmingham, Alabama
| | - John R Riordan
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel HillChapel Hill, North Carolina
- Cystic Fibrosis Treatment and Research Center, The University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, Texas
- Center for Membrane Protein Research, Texas Tech University Health Sciences CenterLubbock, TX
| | - John F Hunt
- Department of Biological Sciences, Columbia UniversityNew York, New York
| | - Christie G Brouillette
- Department of Chemistry, University of Alabama at BirminghamBirmingham, Alabama
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
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23
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L. Pollock N, Moran O, Baroni D, Zegarra-Moran O, C. Ford R. Characterisation of the salmon cystic fibrosis transmembrane conductance regulator protein for structural studies. AIMS MOLECULAR SCIENCE 2014. [DOI: 10.3934/molsci.2014.4.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Detergent quantification in membrane protein samples and its application to crystallization experiments. Amino Acids 2013; 45:1293-302. [PMID: 24105076 DOI: 10.1007/s00726-013-1600-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
The structural characterization of membrane proteins remains a challenging field, largely because the use of stabilizing detergents is required. Researchers must first select a suitable detergent for the solubility and stability of their protein during in vitro studies. In addition, an appropriate concentration of detergent in membrane protein samples can be essential for protein solubility, stability, and experimental success. For example, in membrane protein crystallography, detergent concentration in the crystallization drop can be a critical parameter influencing crystal growth. Over the past decade, multiple techniques have been developed for the measurement of detergent concentration using a wide variety of strategies. These methods include colorimetric reactions, which target specific detergent classes, and analytical techniques applicable to a wide variety of detergents. This review will summarize and discuss the available options. It will be a useful resource to those selecting a strategy that best fits their experimental requirements and available instruments.
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25
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Scharff-Poulsen P, Pedersen PA. Saccharomyces cerevisiae-based platform for rapid production and evaluation of eukaryotic nutrient transporters and transceptors for biochemical studies and crystallography. PLoS One 2013; 8:e76851. [PMID: 24124599 PMCID: PMC3790737 DOI: 10.1371/journal.pone.0076851] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/02/2013] [Indexed: 11/19/2022] Open
Abstract
To produce large quantities of high quality eukaryotic membrane proteins in Saccharomyces cerevisiae, we modified a high-copy vector to express membrane proteins C-terminally-fused to a Tobacco Etch Virus (TEV) protease detachable Green Fluorescent Protein (GFP)-8His tag, which facilitates localization, quantification, quality control, and purification. Using this expression system we examined the production of a human glucose transceptor and 11 nutrient transporters and transceptors from S. cerevisiae that have not previously been overexpressed in S. cerevisiae and purified. Whole-cell GFP-fluorescence showed that induction of GFP-fusion synthesis from a galactose-inducible promoter at 15°C resulted in stable accumulation of the fusions in the plasma membrane and in intracellular membranes. Expression levels of the 12 fusions estimated by GFP-fluorescence were in the range of 0.4 mg to 1.7 mg transporter pr. liter cell culture. A detergent screen showed that n-dodecyl-ß-D-maltopyranoside (DDM) is acceptable for solubilization of the membrane-integrated fusions. Extracts of solubilized membranes were prepared with this detergent and used for purifications by Ni-NTA affinity chromatography, which yielded partially purified full-length fusions. Most of the fusions were readily cleaved at a TEV protease site between the membrane protein and the GFP-8His tag. Using the yeast oligopeptide transporter Ptr2 as an example, we further demonstrate that almost pure transporters, free of the GFP-8His tag, can be achieved by TEV protease cleavage followed by reverse immobilized metal-affinity chromatography. The quality of the GFP-fusions was analysed by fluorescence size-exclusion chromatography. Membranes solubilized in DDM resulted in preparations containing aggregated fusions. However, 9 of the fusions solubilized in DDM in presence of cholesteryl hemisuccinate and specific substrates, yielded monodisperse preparations with only minor amounts of aggregated membrane proteins. In conclusion, we developed a new effective S. cerevisiae expression system that may be used for production of high-quality eukaryotic membrane proteins for functional and structural analysis.
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Affiliation(s)
- Peter Scharff-Poulsen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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26
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Parker JL, Newstead S. Phasing statistics for alpha helical membrane protein structures. Protein Sci 2013; 22:1664-8. [PMID: 23963889 DOI: 10.1002/pro.2341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 07/28/2013] [Accepted: 08/12/2013] [Indexed: 11/05/2022]
Abstract
In this report we highlight the latest trends in phasing methods used to solve alpha helical membrane protein structures and analyze the use of heavy atom metals for the purpose of experimental phasing. Our results reveal that molecular replacement is emerging as the most successful method for phasing alpha helical membrane proteins, with the notable exception of the transporter family, where experimentally derived phase information still remains the most effective method. To facilitate selection of heavy atoms salts for experimental phasing an analysis of these was undertaken and indicates that organic mercury salts are still the most successful heavy atoms reagents. Interestingly the use of seleno-L-methionine incorporated protein has increased since earlier studies into membrane protein phasing, so too the use of SAD and MAD as techniques for phase determination. Taken together this study provides a brief snapshot of phasing methods for alpha helical membrane proteins and suggests possible routes for heavy atom selection and phasing methods based on currently available data.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, UK
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27
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Nørholm MH, Toddo S, Virkki MT, Light S, von Heijne G, Daley DO. Improved production of membrane proteins in Escherichia coli
by selective codon substitutions. FEBS Lett 2013; 587:2352-8. [DOI: 10.1016/j.febslet.2013.05.063] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 05/24/2013] [Accepted: 05/27/2013] [Indexed: 11/29/2022]
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28
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McNeely PM, Naranjo AN, Robinson AS. Structure-function studies with G protein-coupled receptors as a paradigm for improving drug discovery and development of therapeutics. Biotechnol J 2013; 7:1451-61. [PMID: 23213015 DOI: 10.1002/biot.201200076] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 10/07/2012] [Accepted: 10/10/2012] [Indexed: 12/21/2022]
Abstract
There are a great variety of human membrane proteins, and these currently form the largest group of targets for marketed drugs. Despite the advances in drug design, however, promiscuity between drug molecules and targets often leads to undesired signaling effects, which result in unintended side effects. In this review, one family of membrane proteins - the G protein-coupled receptors (GPCRs) - is used as a model to review experimental techniques that may be used to examine the activity of membrane proteins. As these receptors are highly relevant to healthy human physiology and represent the largest family of drug targets, they represent an excellent model for membrane proteins in general. We also review experimental evidence that suggests there may be multiple ways to target a GPCR - and by extension, membrane proteins - to more effectively target unhealthy phenotypes while reducing the occurrence and severity of side effects.
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Affiliation(s)
- Patrick M McNeely
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
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Kang HJ, Lee C, Drew D. Breaking the barriers in membrane protein crystallography. Int J Biochem Cell Biol 2013; 45:636-44. [DOI: 10.1016/j.biocel.2012.12.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 12/03/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
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High-throughput analytical gel filtration screening of integral membrane proteins for structural studies. Biochim Biophys Acta Gen Subj 2013; 1830:3497-508. [PMID: 23403133 DOI: 10.1016/j.bbagen.2013.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/21/2013] [Accepted: 02/04/2013] [Indexed: 11/23/2022]
Abstract
BACKGROUND Structural studies of integral membrane proteins (IMPs) are often hampered by difficulties in producing stable homogenous samples for crystallization. To overcome this hurdle it has become common practice to screen large numbers of target proteins to find suitable candidates for crystallization. For such an approach to be effective, an efficient screening strategy is imperative. To this end, strategies have been developed that involve the use of green fluorescent protein (GFP) fusion constructs. However, these approaches suffer from two drawbacks; proteins with a translocated C-terminus cannot be tested and scale-up from analytical to preparative purification is often non-trivial and may require re-cloning. METHODS Here we present a screening approach that prioritizes IMP targets based on three criteria: expression level, detergent solubilization yield and homogeneity as determined by high-throughput small-scale immobilized metal affinity chromatography (IMAC) and automated size-exclusion chromatography (SEC). RESULTS To validate the strategy, we screened 48 prokaryotic IMPs in two different vectors and two Escherichia coli strains. A set of 11 proteins passed all preset quality control checkpoints and was subjected to crystallization trials. Four of these crystallized directly in initial sparse matrix screens, highlighting the robustness of the strategy. CONCLUSIONS We have developed a rapid and cost efficient screening strategy that can be used for all IMPs regardless of topology. The analytical steps have been designed to be a good mimic of preparative purification, which greatly facilitates scale-up. GENERAL SIGNIFICANCE The screening approach presented here is intended and expected to help drive forward structural biology of membrane proteins.
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Prince C, Jia Z. Measurement of detergent concentration using 2,6-dimethylphenol in membrane-protein crystallization. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1694-6. [DOI: 10.1107/s0907444912040176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/21/2012] [Indexed: 11/10/2022]
Abstract
Methods have previously been developed to measure detergent concentration in membrane-protein samples, but most have significant limitations, such as requiring specialized equipment or consuming a significant amount of precious sample. This work explores the use of 2,6-dimethylphenol in a phenol–sulfuric acid assay to accurately measure the concentration of common glycosidic-based detergents used in crystallization. This method is amenable to routine laboratory use, provides excellent sensitivity and significantly reduces the sample volume required. Using anEscherichia colityrosine kinase (Etk) construct as an example, it is shown that the crystallization potential of Etk is directly influenced by measurable changes in detergent concentration.
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Kellosalo J, Kajander T, Honkanen R, Goldman A. Crystallization and preliminary X-ray analysis of membrane-bound pyrophosphatases. Mol Membr Biol 2012; 30:64-74. [DOI: 10.3109/09687688.2012.712162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Parker JL, Newstead S. Current trends in α-helical membrane protein crystallization: an update. Protein Sci 2012; 21:1358-65. [PMID: 22811290 DOI: 10.1002/pro.2122] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/22/2012] [Accepted: 07/05/2012] [Indexed: 11/10/2022]
Abstract
α-Helical membrane proteins (MPs) are the targets for many pharmaceutical drugs and play important roles in human physiology. In recent years, significant progress has been made in determining their atomic structure using X-ray crystallography. However, a major bottleneck in MP crystallography still remains, namely, the identification of conditions that give crystals that are suitable for structural determination. In 2008, we undertook an analysis of the crystallization conditions for 121 α-helical MPs to design a rationalized sparse matrix crystallization screen, MemGold. We now report an updated analysis that includes a further 133 conditions. The results reveal the current trends in α-helical MP crystallization with notable differences since 2008. The updated information has been used to design new crystallization and additive screens that should prove useful for both initial crystallization scouting and subsequent crystal optimization.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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Drew D, Kim H. Large-scale production of membrane proteins in Saccharomyces cerevisiae: using a green fluorescent protein fusion strategy in the production of membrane proteins. Methods Mol Biol 2012; 866:209-16. [PMID: 22454126 DOI: 10.1007/978-1-61779-770-5_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The production of membrane proteins in the large quantities necessary for structural analysis requires many optimization steps. The GFP-fusion-based scheme described in earlier chapters ( Chapters 4 , 8 , and 16 ) facilitates these steps by allowing the selection of high yielding clones that produce detergent-stable membrane proteins. Here, we describe the experimental steps required to establish the reproducible, large-scale production and purification of membrane protein-GFP fusions using S. cerevisiae.
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Affiliation(s)
- David Drew
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London, UK
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Drew D, Kim H. Screening for high-yielding Saccharomyces cerevisiae clones: using a green fluorescent protein fusion strategy in the production of membrane proteins. Methods Mol Biol 2012; 866:75-86. [PMID: 22454116 DOI: 10.1007/978-1-61779-770-5_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The overproduction of eukaryotic membrane proteins in milligram quantities is a major bottleneck for their further biochemical and structural investigation. Production trials exploring a range of input factors can be rationalized to improve the likelihood of success. Here we discuss some of these factors in combination with the use of a GFP-based Saccharomyces cerevisiae system that enables a quick turnaround time from clone construction to production trials. Since membrane-integrated levels do not necessarily correlate with the amount of functional recombinant protein, we also include the use of fluorescence-detection size exclusion chromatography (FSEC). Using FSEC, the quality of the recombinant material can also be rapidly evaluated as demonstrated for the functional production of the rat vesicular glutamate transporter (VGLUT2) and the human glucose transporter (GLUT1) (5).
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Affiliation(s)
- David Drew
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London, UK
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36
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Abstract
Recombinant membrane protein yields can be optimized in Saccharomyces cerevisiae by adjusting the induction time and temperature and/or by the addition of chemical chaperones. Here we describe a protocol for assessing the importance of these parameters.
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Affiliation(s)
- David Drew
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London, UK
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Franks WT, Linden AH, Kunert B, van Rossum BJ, Oschkinat H. Solid-state magic-angle spinning NMR of membrane proteins and protein-ligand interactions. Eur J Cell Biol 2011; 91:340-8. [PMID: 22019511 DOI: 10.1016/j.ejcb.2011.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 09/09/2011] [Accepted: 09/09/2011] [Indexed: 10/15/2022] Open
Abstract
Structural biology is developing into a universal tool for visualizing biological processes in space and time at atomic resolution. The field has been built by established methodology like X-ray crystallography, electron microscopy and solution NMR and is now incorporating new techniques, such as small-angle X-ray scattering, electron tomography, magic-angle-spinning solid-state NMR and femtosecond X-ray protein nanocrystallography. These new techniques all seek to investigate non-crystalline, native-like biological material. Solid-state NMR is a relatively young technique that has just proven its capabilities for de novo structure determination of model proteins. Further developments promise great potential for investigations on functional biological systems such as membrane-integrated receptors and channels, and macromolecular complexes attached to cytoskeletal proteins. Here, we review the development and applications of solid-state NMR from the first proof-of-principle investigations to mature structure determination projects, including membrane proteins. We describe the development of the methodology by looking at examples in detail and provide an outlook towards future 'big' projects.
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Affiliation(s)
- W Trent Franks
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert Rössle Str. 10, 13125 Berlin, Germany
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Heterologous expression and purification of membrane-bound pyrophosphatases. Protein Expr Purif 2011; 79:25-34. [DOI: 10.1016/j.pep.2011.05.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 05/20/2011] [Accepted: 05/26/2011] [Indexed: 12/18/2022]
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39
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Sonoda Y, Newstead S, Hu NJ, Alguel Y, Nji E, Beis K, Yashiro S, Lee C, Leung J, Cameron AD, Byrne B, Iwata S, Drew D. Benchmarking membrane protein detergent stability for improving throughput of high-resolution X-ray structures. Structure 2011; 19:17-25. [PMID: 21220112 PMCID: PMC3111809 DOI: 10.1016/j.str.2010.12.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/30/2010] [Accepted: 12/06/2010] [Indexed: 12/31/2022]
Abstract
Obtaining well-ordered crystals is a major hurdle to X-ray structure determination of membrane proteins. To facilitate crystal optimization, we investigated the detergent stability of 24 eukaryotic and prokaryotic membrane proteins, predominantly transporters, using a fluorescent-based unfolding assay. We have benchmarked the stability required for crystallization in small micelle detergents, as they are statistically more likely to lead to high-resolution structures. Using this information, we have been able to obtain well-diffracting crystals for a number of sodium and proton-dependent transporters. By including in the analysis seven membrane proteins for which structures are already known, AmtB, GlpG, Mhp1, GlpT, EmrD, NhaA, and LacY, it was further possible to demonstrate an overall trend between protein stability and structural resolution. We suggest that by monitoring membrane protein stability with reference to the benchmarks described here, greater efforts can be placed on constructs and conditions more likely to yield high-resolution structures.
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Affiliation(s)
- Yo Sonoda
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
| | - Simon Newstead
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - Nien-Jen Hu
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
| | - Yilmaz Alguel
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
- Japan Science and Technology Agency, ERATO, Human Receptor Crystallography Project, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Emmanuel Nji
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - Konstantinos Beis
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
| | - Shoko Yashiro
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
- Japan Science and Technology Agency, ERATO, Human Receptor Crystallography Project, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Chiara Lee
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - James Leung
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - Alexander D. Cameron
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
- Japan Science and Technology Agency, ERATO, Human Receptor Crystallography Project, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Bernadette Byrne
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - So Iwata
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
- Japan Science and Technology Agency, ERATO, Human Receptor Crystallography Project, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - David Drew
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
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