1
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Selenourea for Experimental Phasing of Membrane Protein Crystals Grown in Lipid Cubic Phase. CRYSTALS 2022. [DOI: 10.3390/cryst12070976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Heavy-atom soaking has been a major method for experimental phasing, but it has been difficult for membrane proteins, partly owing to the lack of available sites in the scarce soluble domain for non-invasive heavy-metal binding. The lipid cubic phase (LCP) has proven to be a successful method for membrane protein crystallization, but experimental phasing with LCP-grown crystals remains difficult, and so far, only 68 such structures were phased experimentally. Here, the selenourea was tested as a soaking reagent for the single-wavelength anomalous dispersion (SAD) phasing of crystals grown in LCP. Using a single crystal, the structure of the glycerol 3-phosphate acyltransferase (PlsY, ~21 kDa), a very hydrophobic enzyme with 80% membrane-embedded residues, was solved. Remarkably, a total of 15 Se sites were found in the two monomers of PlsY, translating to one selenourea-binding site per every six residues in the accessible extramembrane protein. Structure analysis reveals that surface-exposed selenourea sites are mostly contributed by mainchain amides and carbonyls. This low-specificity binding pattern may explain its high loading ratio. Importantly, both the crystal diffraction quality and the LCP integrity were unaffected by selenourea soaking. Taken together, selenourea presents a promising and generally useful reagent for heavy-atom soaking of membrane protein crystals grown in LCP.
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2
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Vlasov AV, Osipov SD, Bondarev NA, Uversky VN, Borshchevskiy VI, Yanyushin MF, Manukhov IV, Rogachev AV, Vlasova AD, Ilyinsky NS, Kuklin AI, Dencher NA, Gordeliy VI. ATP synthase F OF 1 structure, function, and structure-based drug design. Cell Mol Life Sci 2022; 79:179. [PMID: 35253091 PMCID: PMC11072866 DOI: 10.1007/s00018-022-04153-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/26/2021] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
Abstract
ATP synthases are unique rotatory molecular machines that supply biochemical reactions with adenosine triphosphate (ATP)-the universal "currency", which cells use for synthesis of vital molecules and sustaining life. ATP synthases of F-type (FOF1) are found embedded in bacterial cellular membrane, in thylakoid membranes of chloroplasts, and in mitochondrial inner membranes in eukaryotes. The main functions of ATP synthases are control of the ATP synthesis and transmembrane potential. Although the key subunits of the enzyme remain highly conserved, subunit composition and structural organization of ATP synthases and their assemblies are significantly different. In addition, there are hypotheses that the enzyme might be involved in the formation of the mitochondrial permeability transition pore and play a role in regulation of the cell death processes. Dysfunctions of this enzyme lead to numerous severe disorders with high fatality levels. In our review, we focus on FOF1-structure-based approach towards development of new therapies by using FOF1 structural features inherited by the representatives of this enzyme family from different taxonomy groups. We analyzed and systematized the most relevant information about the structural organization of FOF1 to discuss how this approach might help in the development of new therapies targeting ATP synthases and design tools for cellular bioenergetics control.
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Affiliation(s)
- Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, 141980, Dubna, Russia
| | - Stepan D Osipov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Nikolay A Bondarev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Mikhail F Yanyushin
- Institute of Basic Biological Problems, Russian Academy of Sciences, 142290, Pushchino, Moscow region, Russia
| | - Ilya V Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Andrey V Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, 141980, Dubna, Russia
| | - Anastasiia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Alexandr I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, 141980, Dubna, Russia
| | - Norbert A Dencher
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Physical Biochemistry, Department Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia.
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425, Jülich, Germany.
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428, Jülich, Germany.
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027, Grenoble, France.
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Structure and Functional Characterization of Membrane Integral Proteins in the Lipid Cubic Phase. J Mol Biol 2020; 432:5104-5123. [PMID: 32113953 DOI: 10.1016/j.jmb.2020.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
The lipid cubic phase (LCP) has been used extensively as a medium for crystallizing membrane proteins. It is an attractive environment in which to perform such studies because it incorporates a lipid bilayer. It is therefore considered a useful and a faithful biomembrane mimetic. Here, we bring together evidence that supports this view. Biophysical characterizations are described demonstrating that the cubic phase is a porous medium into and out of which water-soluble molecules can diffuse for binding to and reaction with reconstituted proteins. The proteins themselves are shown to be functionally reconstituted into and to have full mobility in the bilayered membrane, a prerequisite for LCP crystallogenesis. Spectroscopic methods have been used to characterize the conformation and disposition of proteins in the mesophase. Procedures for performing activity assays on enzymes directly in the cubic phase have been reported. Specific examples described here include a kinase and two transferases, where quantitative kinetics and mechanism-defining measurements were performed directly or via a coupled assay system. Finally, ligand-binding assays are described, where binding to proteins in the mesophase membrane was monitored directly by eye and indirectly by fluorescence quenching, enabling binding constant determinations for targets with affinity values in the micromolar and nanomolar range. These results make a convincing case that the lipid bilayer of the cubic mesophase is an excellent membrane mimetic and a suitable medium in which to perform not only crystallogenesis but also biochemical and biophysical characterizations of membrane proteins.
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Cai H, Yao H, Li T, Tang Y, Li D. High-level heterologous expression of the human transmembrane sterol Δ8,Δ7-isomerase in Pichia pastoris. Protein Expr Purif 2019; 164:105463. [DOI: 10.1016/j.pep.2019.105463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 07/30/2019] [Indexed: 01/11/2023]
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5
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Nam KH. Sample Delivery Media for Serial Crystallography. Int J Mol Sci 2019; 20:ijms20051094. [PMID: 30836596 PMCID: PMC6429298 DOI: 10.3390/ijms20051094] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 01/19/2023] Open
Abstract
X-ray crystallographic methods can be used to visualize macromolecules at high resolution. This provides an understanding of molecular mechanisms and an insight into drug development and rational engineering of enzymes used in the industry. Although conventional synchrotron-based X-ray crystallography remains a powerful tool for understanding molecular function, it has experimental limitations, including radiation damage, cryogenic temperature, and static structural information. Serial femtosecond crystallography (SFX) using X-ray free electron laser (XFEL) and serial millisecond crystallography (SMX) using synchrotron X-ray have recently gained attention as research methods for visualizing macromolecules at room temperature without causing or reducing radiation damage, respectively. These techniques provide more biologically relevant structures than traditional X-ray crystallography at cryogenic temperatures using a single crystal. Serial femtosecond crystallography techniques visualize the dynamics of macromolecules through time-resolved experiments. In serial crystallography (SX), one of the most important aspects is the delivery of crystal samples efficiently, reliably, and continuously to an X-ray interaction point. A viscous delivery medium, such as a carrier matrix, dramatically reduces sample consumption, contributing to the success of SX experiments. This review discusses the preparation and criteria for the selection and development of a sample delivery medium and its application for SX.
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Affiliation(s)
- Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea.
- Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Korea.
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6
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Enzymatic preparation and facile purification of medium-chain, and medium- and long-chain fatty acid diacylglycerols. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.02.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Li Z, Tang Y, Wu Y, Zhao S, Bao J, Luo Y, Li D. Structural insights into the committed step of bacterial phospholipid biosynthesis. Nat Commun 2017; 8:1691. [PMID: 29167463 PMCID: PMC5700162 DOI: 10.1038/s41467-017-01821-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/18/2017] [Indexed: 11/09/2022] Open
Abstract
The membrane-integral glycerol 3-phosphate (G3P) acyltransferase PlsY catalyses the committed and essential step in bacterial phospholipid biosynthesis by acylation of G3P, forming lysophosphatidic acid. It contains no known acyltransferase motifs, lacks eukaryotic homologs, and uses the unusual acyl-phosphate as acyl donor, as opposed to acyl-CoA or acyl-carrier protein for other acyltransferases. Previous studies have identified several PlsY inhibitors as potential antimicrobials. Here we determine the crystal structure of PlsY at 1.48 Å resolution, revealing a seven-transmembrane helix fold. Four additional substrate- and product-bound structures uncover the atomic details of its relatively inflexible active site. Structure and mutagenesis suggest a different acylation mechanism of ‘substrate-assisted catalysis’ that, unlike other acyltransferases, does not require a proteinaceous catalytic base to complete. The structure data and a high-throughput enzymatic assay developed in this work should prove useful for virtual and experimental screening of inhibitors against this vital bacterial enzyme. The first step in bacterial phospholipid biosynthesis is the acylation of glycerol 3-phosphate to form lysophosphatidic acid. Here, the authors present the high resolution crystal structure of the glycerol 3-phosphate acyltransferase PlsY, a membrane protein and give insights into its catalytical mechanism.
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Affiliation(s)
- Zhenjian Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yannan Tang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yitian Luo
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.
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8
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The cubicon method for concentrating membrane proteins in the cubic mesophase. Nat Protoc 2017; 12:1745-1762. [DOI: 10.1038/nprot.2017.057] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Nagarathinam K, Jaenecke F, Nakada-Nakura Y, Hotta Y, Liu K, Iwata S, Stubbs MT, Nomura N, Tanabe M. The multidrug-resistance transporter MdfA from Escherichia coli: crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun 2017; 73:423-430. [PMID: 28695852 PMCID: PMC5505248 DOI: 10.1107/s2053230x17008500] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/07/2017] [Indexed: 01/03/2023] Open
Abstract
The active efflux of antibiotics by multidrug-resistance (MDR) transporters is a major pathway of drug resistance and complicates the clinical treatment of bacterial infections. MdfA is a member of the major facilitator superfamily (MFS) from Escherichia coli and provides resistance to a wide variety of dissimilar toxic compounds, including neutral, cationic and zwitterionic substances. The 12-transmembrane-helix MdfA was expressed as a GFP-octahistidine fusion protein with a TEV protease cleavage site. Following tag removal, MdfA was purified using two chromatographic steps, complexed with a Fab fragment and further purified using size-exclusion chromatography. MdfA and MdfA-Fab complexes were subjected to both vapour-diffusion and lipidic cubic phase (LCP) crystallization techniques. Vapour-diffusion-grown crystals were of type II, with poor diffraction behaviour and weak crystal contacts. LCP lipid screening resulted in type I crystals that diffracted to 3.4 Å resolution and belonged to the hexagonal space group P6122.
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Affiliation(s)
- Kumar Nagarathinam
- ZIK HALOmem, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, 06120 Halle (Saale), Germany
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, 06120 Halle (Saale), Germany
| | - Frank Jaenecke
- ZIK HALOmem, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, 06120 Halle (Saale), Germany
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yunhon Hotta
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kehong Liu
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Research Acceleration Program, Membrane Protein Crystallography Project, Japan Science and Technology Agency, Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- SPring-8 Center, RIKEN, Sayo, Kohto 1-1-1, Hyogo 679-5148, Japan
| | - Milton T. Stubbs
- ZIK HALOmem, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, 06120 Halle (Saale), Germany
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, 06120 Halle (Saale), Germany
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Research Acceleration Program, Membrane Protein Crystallography Project, Japan Science and Technology Agency, Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mikio Tanabe
- ZIK HALOmem, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, 06120 Halle (Saale), Germany
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Ishchenko A, Peng L, Zinovev E, Vlasov A, Lee SC, Kuklin A, Mishin A, Borshchevskiy V, Zhang Q, Cherezov V. Chemically Stable Lipids for Membrane Protein Crystallization. CRYSTAL GROWTH & DESIGN 2017; 17:3502-3511. [PMID: 29290736 PMCID: PMC5743208 DOI: 10.1021/acs.cgd.7b00458] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Lipidic cubic phase (LCP) has been widely recognized as a promising membrane-mimicking matrix for biophysical studies of membrane proteins and their crystallization in a lipidic environment. Application of this material to a wide variety of membrane proteins, however, is hindered due to a limited number of available host lipids, mostly monoacylglycerols (MAGs). Here, we designed, synthesized and characterized a series of chemically stable lipids resistant to hydrolysis, with properties complementary to the widely used MAGs. In order to assess their potential to serve as host lipids for crystallization, we characterized the phase properties and lattice parameters of mesophases made of two most promising lipids at a variety of different conditions by polarized light microscopy and small-angle X-ray scattering. Both lipids showed remarkable chemical stability and an extended LCP region in the phase diagram covering a wide range of temperatures down to 4 °C. One of these lipids has been used for crystallization and structure determination of a prototypical membrane protein bacteriorhodopsin at 4 °C and 20 °C.
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Affiliation(s)
- Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Lingling Peng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Egor Zinovev
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology (MIPT), Dolgoprudny, Russia
| | - Alexey Vlasov
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology (MIPT), Dolgoprudny, Russia
| | - Sung Chang Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexander Kuklin
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology (MIPT), Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Alexey Mishin
- Laboratory for Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology (MIPT), Dolgoprudny, Russia
- Institute of Complex Systems (ICS-6): Structural Biochemistry, Research Centre Jülich, Germany
| | - Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
- Laboratory for Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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11
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Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs. Structure 2017; 25:384-392. [DOI: 10.1016/j.str.2016.12.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/20/2016] [Accepted: 12/12/2016] [Indexed: 11/20/2022]
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12
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Abstract
Membrane proteins are crucial components of cellular membranes and are responsible for a variety of physiological functions. The advent of new tools and technologies for structural biology of membrane proteins has led to a significant increase in the number of structures deposited to the Protein Data Bank during the past decade. This new knowledge has expanded our fundamental understanding of their mechanism of function and contributed to the drug-design efforts. In this chapter we discuss current approaches for membrane protein expression, solubilization, crystallization, and data collection. Additionally, we describe the protein quality-control assays that are often instrumental as a guideline for a shorter path toward the structure.
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Affiliation(s)
- Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Enrique E Abola
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA.
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13
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Ishchenko A, Cherezov V, Liu W. Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography. J Vis Exp 2016. [PMID: 27683972 PMCID: PMC5092055 DOI: 10.3791/54463] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Membrane proteins (MPs) are essential components of cellular membranes and primary drug targets. Rational drug design relies on precise structural information, typically obtained by crystallography; however MPs are difficult to crystallize. Recent progress in MP structural determination has benefited greatly from the development of lipidic cubic phase (LCP) crystallization methods, which typically yield well-diffracting, but often small crystals that suffer from radiation damage during traditional crystallographic data collection at synchrotron sources. The development of new-generation X-ray free-electron laser (XFEL) sources that produce extremely bright femtosecond pulses has enabled room temperature data collection from microcrystals with no or negligible radiation damage. Our recent efforts in combining LCP technology with serial femtosecond crystallography (LCP-SFX) have resulted in high-resolution structures of several human G protein-coupled receptors, which represent a notoriously difficult target for structure determination. In the LCP-SFX technique, LCP is recruited as a matrix for both growth and delivery of MP microcrystals to the intersection of the injector stream with an XFEL beam for crystallographic data collection. It has been demonstrated that LCP-SFX can substantially improve the diffraction resolution when only sub-10 µm crystals are available, or when the use of smaller crystals at room temperature can overcome various problems associated with larger cryocooled crystals, such as accumulation of defects, high mosaicity and cryocooling artifacts. Future advancements in X-ray sources and detector technologies should make serial crystallography highly attractive and practicable for implementation not only at XFELs, but also at more accessible synchrotron beamlines. Here we present detailed visual protocols for the preparation, characterization and delivery of microcrystals in LCP for serial crystallography experiments. These protocols include methods for conducting crystallization experiments in syringes, detecting and characterizing the crystal samples, optimizing crystal density, loading microcrystal laden LCP into the injector device and delivering the sample to the beam for data collection.
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Affiliation(s)
- Andrii Ishchenko
- The Bridge Institute, University of Southern California; Department of Chemistry, University of Southern California
| | - Vadim Cherezov
- The Bridge Institute, University of Southern California; Department of Chemistry, University of Southern California;
| | - Wei Liu
- School of Molecular Sciences, Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University;
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14
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van 't Hag L, Knoblich K, Seabrook SA, Kirby NM, Mudie ST, Lau D, Li X, Gras SL, Mulet X, Call ME, Call MJ, Drummond CJ, Conn CE. Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0125. [PMID: 27298442 PMCID: PMC4920275 DOI: 10.1098/rsta.2015.0125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 05/19/2023]
Abstract
The proposed mechanism for in meso crystallization of transmembrane proteins suggests that a protein or peptide is initially uniformly dispersed in the lipid self-assembly cubic phase but that crystals grow from a local lamellar phase, which acts as a conduit between the crystal and the bulk cubic phase. However, there is very limited experimental evidence for this theory. We have developed protocols to investigate the lipid mesophase microenvironment during crystal growth using standard procedures readily available in crystallography laboratories. This technique was used to characterize the microenvironment during crystal growth of the DAP12-TM peptide using synchrotron small angle X-ray scattering (SAXS) with a micro-sized X-ray beam. Crystal growth was found to occur from the gyroid cubic mesophase. For one in four crystals, a highly oriented local lamellar phase was observed, providing supporting evidence for the proposed mechanism for in meso crystallization. A new observation of this study was that we can differentiate diffraction peaks from crystals grown in meso, from peaks originating from the surrounding lipid matrix, potentially opening up the possibility of high-throughput SAXS analysis of in meso grown crystals.This article is part of the themed issue 'Soft interfacial materials: from fundamentals to formulation'.
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Affiliation(s)
- Leonie van 't Hag
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Konstantin Knoblich
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Shane A Seabrook
- CSIRO Manufacturing Flagship, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Nigel M Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Stephen T Mudie
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Deborah Lau
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Xu Li
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia
| | - Sally L Gras
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia The ARC Dairy Innovation Hub, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xavier Mulet
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Matthew E Call
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Melissa J Call
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Calum J Drummond
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia School of Applied Sciences, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Charlotte E Conn
- School of Applied Sciences, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
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15
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Membrane protein assembly: two cytoplasmic phosphorylated serine sites of Vpu from HIV-1 affect oligomerization. Sci Rep 2016; 6:28866. [PMID: 27353136 PMCID: PMC4926278 DOI: 10.1038/srep28866] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/06/2016] [Indexed: 11/08/2022] Open
Abstract
Viral protein U (Vpu) encoded by human immunodeficiency virus type 1 (HIV-1) is a short integral membrane protein which is known to self-assemble within the lipid membrane and associate with host factors during the HIV-1 infectivity cycle. In this study, full-length Vpu (M group) from clone NL4-3 was over-expressed in human cells and purified in an oligomeric state. Various single and double mutations were constructed on its phosphorylation sites to mimic different degrees of phosphorylation. Size exclusion chromatography of wild-type Vpu and mutants indicated that the smallest assembly unit of Vpu was a dimer and over time Vpu formed higher oligomers. The rate of oligomerization increased when (i) the degree of phosphorylation at serines 52 and 56 was decreased and (ii) when the ionic strength was increased indicating that the cytoplasmic domain of Vpu affects oligomerization. Coarse-grained molecular dynamic simulations with models of wild-type and mutant Vpu in a hydrated lipid bilayer supported the experimental data in demonstrating that, in addition to a previously known role in downregulation of host factors, the phosphorylation sites of Vpu also modulate oligomerization.
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16
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Ternary structure reveals mechanism of a membrane diacylglycerol kinase. Nat Commun 2015; 6:10140. [PMID: 26673816 PMCID: PMC4703834 DOI: 10.1038/ncomms10140] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 11/09/2015] [Indexed: 11/24/2022] Open
Abstract
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution. Diacylglycerol kinase is a small bacterial membrane-bound trimer that catalyses diacylglycerol conversion to phosphatidic acid. Here, the authors solve the crystal structure of the kinase bound to a lipid substrate and an ATP analogue, and show that the active site arose through convergent evolution.
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17
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Rayan G, Adrien V, Reffay M, Picard M, Ducruix A, Schmutz M, Urbach W, Taulier N. Surfactant bilayers maintain transmembrane protein activity. Biophys J 2015; 107:1129-1135. [PMID: 25185548 DOI: 10.1016/j.bpj.2014.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 06/21/2014] [Accepted: 07/07/2014] [Indexed: 11/26/2022] Open
Abstract
In vitro studies of membrane proteins are of interest only if their structure and function are significantly preserved. One approach is to insert them into the lipid bilayers of highly viscous cubic phases rendering the insertion and manipulation of proteins difficult. Less viscous lipid sponge phases are sometimes used, but their relatively narrow domain of existence can be easily disrupted by protein insertion. We present here a sponge phase consisting of nonionic surfactant bilayers. Its extended domain of existence and its low viscosity allow easy insertion and manipulation of membrane proteins. We show for the first time, to our knowledge, that transmembrane proteins, such as bacteriorhodopsin, sarcoplasmic reticulum Ca(2+)ATPase (SERCA1a), and its associated enzymes, are fully active in a surfactant phase.
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Affiliation(s)
- Gamal Rayan
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France
| | - Vladimir Adrien
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France; Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, UMR 8015, Paris, France
| | - Myriam Reffay
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France
| | - Martin Picard
- Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, UMR 8015, Paris, France
| | - Arnaud Ducruix
- Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, UMR 8015, Paris, France
| | - Marc Schmutz
- Institut Charles Sadron - UPR 022 - CNRS - Unistra, Strasbourg, France
| | - Wladimir Urbach
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France; Sorbonnes Université Univ Paris 6, UMR 7371, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France; CNRS, UMR 7371, Laboratoire d'Imagerie Biomédicale, Paris, France; INSERM, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France
| | - Nicolas Taulier
- Sorbonnes Université Univ Paris 6, UMR 7371, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France; CNRS, UMR 7371, Laboratoire d'Imagerie Biomédicale, Paris, France; INSERM, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France.
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18
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Liu W, Wacker D, Wang C, Abola E, Cherezov V. Femtosecond crystallography of membrane proteins in the lipidic cubic phase. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130314. [PMID: 24914147 DOI: 10.1098/rstb.2013.0314] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite recent technological advances in heterologous expression, stabilization and crystallization of membrane proteins (MPs), their structural studies remain difficult and require new transformative approaches. During the past two years, crystallization in lipidic cubic phase (LCP) has started gaining a widespread acceptance, owing to the spectacular success in high-resolution structure determination of G protein-coupled receptors (GPCRs) and to the introduction of commercial instrumentation, tools and protocols. The recent appearance of X-ray free-electron lasers (XFELs) has enabled structure determination from substantially smaller crystals than previously possible with minimal effects of radiation damage, offering new exciting opportunities in structural biology. The unique properties of LCP material have been exploited to develop special protocols and devices that have established a new method of serial femtosecond crystallography of MPs in LCP (LCP-SFX). In this method, microcrystals are generated in LCP and streamed continuously inside the same media across the intersection with a pulsed XFEL beam at a flow rate that can be adjusted to minimize sample consumption. Pioneering studies that yielded the first room temperature GPCR structures, using a few hundred micrograms of purified protein, validate the LCP-SFX approach and make it attractive for structure determination of difficult-to-crystallize MPs and their complexes with interacting partners. Together with the potential of femtosecond data acquisition to interrogate unstable intermediate functional states of MPs, LCP-SFX holds promise to advance our understanding of this biomedically important class of proteins.
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Affiliation(s)
- Wei Liu
- Marine Drug Research Institute, Huaihai Institute of Technology, Lianyungang 222005, People's Republic of China Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel Wacker
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chong Wang
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Enrique Abola
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vadim Cherezov
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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19
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Barriga HMG, Tyler AII, McCarthy NLC, Parsons ES, Ces O, Law RV, Seddon JM, Brooks NJ. Temperature and pressure tuneable swollen bicontinuous cubic phases approaching nature's length scales. SOFT MATTER 2015; 11:600-607. [PMID: 25430049 DOI: 10.1039/c4sm02343a] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Bicontinuous cubic structures offer enormous potential in applications ranging from protein crystallisation to drug delivery systems and have been observed in cellular membrane structures. One of the current bottlenecks in understanding and exploiting these structures is that cubic scaffolds produced in vitro are considerably smaller in size than those observed in biological systems, differing by almost an order of magnitude in some cases. We have addressed this technological bottleneck and developed a methodology capable of manufacturing highly swollen bicontinuous cubic membranes with length scales approaching those seen in vivo. Crucially, these cubic systems do not require the presence of proteins. We have generated highly swollen Im3m symmetry bicontinuous cubic phases with lattice parameters of up to 480 Å, composed of ternary mixtures of monoolein, cholesterol and negatively charged lipid (DOPS or DOPG) and we have been able to tune their lattice parameters. The swollen cubic phases are highly sensitive to both temperature and pressure; these structural changes are likely to be controlled by a fine balance between lipid headgroup repulsions and lateral pressure in the hydrocarbon chain region.
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Affiliation(s)
- H M G Barriga
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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20
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Caffrey M. A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:3-18. [PMID: 25615961 PMCID: PMC4304740 DOI: 10.1107/s2053230x14026843] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/05/2014] [Indexed: 01/12/2023]
Abstract
A comprehensive and up-to-date review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes is reported. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. The uptake of the method is such that it is experiencing what can only be described as explosive growth. This timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challenges and to their solutions. A model of how crystallization comes about mechanistically is presented for a more rational approach to crystallization. The possible involvement of the lamellar and inverted hexagonal phases in crystallogenesis and the application of the method to water-soluble, monotopic and lipid-anchored proteins are addressed. How to set up trials manually and automatically with a robot is introduced with reference to open-access online videos that provide a practical guide to all aspects of the method. These range from protein reconstitution to crystal harvesting from the hosting mesophase, which is noted for its viscosity and stickiness. The sponge phase, as an alternative medium in which to perform crystallization, is described. The compatibility of the method with additive lipids, detergents, precipitant-screen components and materials carried along with the protein such as denaturants and reducing agents is considered. The powerful host and additive lipid-screening strategies are described along with how samples that have low protein concentration and cell-free expressed protein can be used. Assaying the protein reconstituted in the bilayer of the cubic phase for function is an important element of quality control and is detailed. Host lipid design for crystallization at low temperatures and for large proteins and complexes is outlined. Experimental phasing by heavy-atom derivatization, soaking or co-crystallization is routine and the approaches that have been implemented to date are described. An overview and a breakdown by family and function of the close to 200 published structures that have been obtained using in meso-grown crystals are given. Recommendations for conducting the screening process to give a more productive outcome are summarized. The fact that the in meso method also works with soluble proteins should not be overlooked. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The review ends with a view to the future and to the bright prospects for the method, which continues to contribute to our understanding of the molecular mechanisms of some of nature’s most valued proteinaceous robots.
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Affiliation(s)
- Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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21
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Li D, Pye VE, Caffrey M. Experimental phasing for structure determination using membrane-protein crystals grown by the lipid cubic phase method. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:104-22. [PMID: 25615865 PMCID: PMC4304691 DOI: 10.1107/s1399004714010360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/07/2014] [Indexed: 03/02/2023]
Abstract
Despite the marked increase in the number of membrane-protein structures solved using crystals grown by the lipid cubic phase or in meso method, only ten have been determined by SAD/MAD. This is likely to be a consequence of the technical difficulties associated with handling proteins and crystals in the sticky and viscous hosting mesophase that is usually incubated in glass sandwich plates for the purposes of crystallization. Here, a four-year campaign aimed at phasing the in meso structure of the integral membrane diacylglycerol kinase (DgkA) from Escherichia coli is reported. Heavy-atom labelling of this small hydrophobic enzyme was attempted by pre-labelling, co-crystallization, soaking, site-specific mercury binding to genetically engineered single-cysteine mutants and selenomethionine incorporation. Strategies and techniques for special handling are reported, as well as the typical results and the lessons learned for each of these approaches. In addition, an assay to assess the accessibility of cysteine residues in membrane proteins for mercury labelling is introduced. The various techniques and strategies described will provide a valuable reference for future experimental phasing of membrane proteins where crystals are grown by the lipid cubic phase method.
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Affiliation(s)
- Dianfan Li
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Valerie E. Pye
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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22
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Salvati Manni L, Zabara A, Osornio YM, Schöppe J, Batyuk A, Plückthun A, Siegel JS, Mezzenga R, Landau EM. Phase Behavior of a Designed Cyclopropyl Analogue of Monoolein: Implications for Low-Temperature Membrane Protein Crystallization. Angew Chem Int Ed Engl 2014; 54:1027-31. [DOI: 10.1002/anie.201409791] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 11/12/2022]
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23
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Salvati Manni L, Zabara A, Osornio YM, Schöppe J, Batyuk A, Plückthun A, Siegel JS, Mezzenga R, Landau EM. Phase Behavior of a Designed Cyclopropyl Analogue of Monoolein: Implications for Low-Temperature Membrane Protein Crystallization. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Nji E, Li D, Doyle DA, Caffrey M. Cloning, expression, purification, crystallization and preliminary X-ray diffraction of a lysine-specific permease from Pseudomonas aeruginosa. Acta Crystallogr F Struct Biol Commun 2014; 70:1362-7. [PMID: 25286940 PMCID: PMC4188080 DOI: 10.1107/s2053230x14017865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/02/2014] [Indexed: 11/10/2022] Open
Abstract
The prokaryotic lysine-specific permease (LysP) belongs to the amino acid-polyamine-organocation (APC) transporter superfamily. In the cell, members of this family are responsible for the uptake and recycling of nutrients, for the maintenance of a constant internal ion concentration and for cell volume regulation. The detailed mechanism of substrate selectivity and transport of L-lysine by LysP is not understood. A high-resolution crystal structure would enormously facilitate such an understanding. To this end, LysP from Pseudomonas aeruginosa was recombinantly expressed in Escherichia coli and purified to near homogeneity by immobilized metal ion-affinity chromatography (IMAC) and size-exclusion chromatography (SEC). Hexagonal- and rod-shaped crystals were obtained in the presence of L-lysine and the L-lysine analogue L-4-thialysine by vapour diffusion and diffracted to 7.5 Å resolution. The diffraction data were indexed in space group P21, with unit-cell parameters a = 169.53, b = 169.53, c = 290.13 Å, γ = 120°.
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Affiliation(s)
- Emmanuel Nji
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Dianfan Li
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Declan A. Doyle
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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25
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Liu W, Ishchenko A, Cherezov V. Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography. Nat Protoc 2014; 9:2123-34. [PMID: 25122522 DOI: 10.1038/nprot.2014.141] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have recently established a procedure for serial femtosecond crystallography (SFX) in lipidic cubic phase (LCP) for protein structure determination at X-ray free-electron lasers (XFELs). LCP-SFX uses the gel-like LCP as a matrix for growth and delivery of membrane protein microcrystals for crystallographic data collection. LCP is a liquid-crystalline mesophase composed of lipids and water. It provides a membrane-mimicking environment that stabilizes membrane proteins and supports their crystallization. Here we describe detailed procedures for the preparation and characterization of microcrystals for LCP-SFX applications. The advantages of LCP-SFX over traditional crystallographic methods include the capability of collecting room-temperature high-resolution data with minimal effects of radiation damage from sub-10-μm crystals of membrane and soluble proteins that are difficult to crystallize, while eliminating the need for crystal harvesting and cryo-cooling. Compared with SFX methods for microcrystals in solution using liquid injectors, LCP-SFX reduces protein consumption by 2-3 orders of magnitude for data collection at currently available XFELs. The whole procedure typically takes 3-5 d, including the time required for the crystals to grow.
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Affiliation(s)
- Wei Liu
- 1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening and Marine Drug Research Institute, Huaihai Institute of Technology, Lianyungang, China
| | - Andrii Ishchenko
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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26
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Tan J, Rouse SL, Li D, Pye VE, Vogeley L, Brinth AR, El Arnaout T, Whitney JC, Howell PL, Sansom MSP, Caffrey M. A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2054-68. [PMID: 25084326 PMCID: PMC4118822 DOI: 10.1107/s1399004714001850] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/26/2014] [Indexed: 11/11/2022]
Abstract
The exopolysaccharide alginate is an important component of biofilms produced by Pseudomonas aeruginosa, a major pathogen that contributes to the demise of cystic fibrosis patients. Alginate exits the cell via the outer membrane porin AlgE. X-ray structures of several AlgE crystal forms are reported here. Whilst all share a common β-barrel constitution, they differ in the degree to which loops L2 and T8 are ordered. L2 and T8 have been identified as an extracellular gate (E-gate) and a periplasmic gate (P-gate), respectively, that reside on either side of an alginate-selectivity pore located midway through AlgE. Passage of alginate across the membrane is proposed to be regulated by the sequential opening and closing of the two gates. In one crystal form, the selectivity pore contains a bound citrate. Because citrate mimics the uronate monomers of alginate, its location is taken to highlight a route through AlgE taken by alginate as it crosses the pore. Docking and molecular-dynamics simulations support and extend the proposed transport mechanism. Specifically, the P-gate and E-gate are flexible and move between open and closed states. Citrate can leave the selectivity pore bidirectionally. Alginate docks stably in a linear conformation through the open pore. To translate across the pore, a force is required that presumably is provided by the alginate-synthesis machinery. Accessing the open pore is facilitated by complex formation between AlgE and the periplasmic protein AlgK. Alginate can thread through a continuous pore in the complex, suggesting that AlgK pre-orients newly synthesized exopolysaccharide for delivery to AlgE.
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Affiliation(s)
- Jingquan Tan
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Sarah L. Rouse
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Dianfan Li
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Valerie E. Pye
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Lutz Vogeley
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Alette R. Brinth
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Toufic El Arnaout
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - John C. Whitney
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - P. Lynne Howell
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Martin Caffrey
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
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27
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Renaturing membrane proteins in the lipid cubic phase, a nanoporous membrane mimetic. Sci Rep 2014; 4:5806. [PMID: 25055873 PMCID: PMC4108929 DOI: 10.1038/srep05806] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/23/2014] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins play vital roles in the life of the cell and are important therapeutic targets. Producing them in large quantities, pure and fully functional is a major challenge. Many promising projects end when intractable aggregates or precipitates form. Here we show how such unfolded aggregates can be solubilized and the solution mixed with lipid to spontaneously self-assemble a bicontinuous cubic mesophase into the bilayer of which the protein, in a confined, chaperonin-like environment, reconstitutes with 100% efficiency. The test protein, diacylglycerol kinase, reconstituted in the bilayer of the mesophase, was then crystallized in situ by the in meso or lipid cubic phase method providing an X-ray structure to a resolution of 2.55 Å. This highly efficient, inexpensive, simple and rapid approach should find application wherever properly folded, membrane reconstituted and functional proteins are required where the starting material is a denatured aggregate.
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28
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Caffrey M, Li D, Howe N, Shah STA. 'Hit and run' serial femtosecond crystallography of a membrane kinase in the lipid cubic phase. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130621. [PMID: 24914170 PMCID: PMC4052879 DOI: 10.1098/rstb.2013.0621] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The lipid-based bicontinuous cubic mesophase is a nanoporous membrane mimetic with applications in areas that include medicine, personal care products, foods and the basic sciences. An application of particular note concerns it use as a medium in which to grow crystals of membrane proteins for structure determination by X-ray crystallography. At least two variations of the mesophase exist. One is the highly viscous cubic phase, which has well developed long-range order. The other so-called sponge phase is considerably more fluid and lacks long-range order. The sponge phase has recently been shown to be a convenient vehicle for delivering microcrystals of membrane proteins to an X-ray free-electron laser beam for serial femtosecond crystallography (SFX). Unfortunately, the sponge phase approach calls for large amounts of protein that are not always available in the case of membrane proteins. The cubic phase offers the advantage of requiring significantly less protein for SFX but comes with its own challenges. Here, we describe the physico-chemical bases for these challenges, solutions to them and prospects for future uses of lipidic mesophases in the SFX arena.
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Affiliation(s)
- Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Dianfan Li
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Nicole Howe
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Syed T A Shah
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Republic of Ireland
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29
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Boland C, Li D, Shah STA, Haberstock S, Dötsch V, Bernhard F, Caffrey M. Cell-free expression and in meso crystallisation of an integral membrane kinase for structure determination. Cell Mol Life Sci 2014; 71:4895-4910. [PMID: 25012698 DOI: 10.1007/s00018-014-1655-7] [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: 01/07/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 12/17/2022]
Abstract
Membrane proteins are key elements in cell physiology and drug targeting, but getting a high-resolution structure by crystallographic means is still enormously challenging. Novel strategies are in big demand to facilitate the structure determination process that will ultimately hasten the day when sequence information alone can provide a three-dimensional model. Cell-free or in vitro expression enables rapid access to large quantities of high-quality membrane proteins suitable for an array of applications. Despite its impressive efficiency, to date only two membrane proteins produced by the in vitro approach have yielded crystal structures. Here, we have analysed synergies of cell-free expression and crystallisation in lipid mesophases for generating an X-ray structure of the integral membrane enzyme diacylglycerol kinase to 2.28-Å resolution. The quality of cellular and cell-free-expressed kinase samples has been evaluated systematically by comparing (1) spectroscopic properties, (2) purity and oligomer formation, (3) lipid content and (4) functionality. DgkA is the first membrane enzyme crystallised based on cell-free expression. The study provides a basic standard for the crystallisation of cell-free-expressed membrane proteins and the methods detailed here should prove generally useful and contribute to accelerating the pace at which membrane protein structures are solved.
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Affiliation(s)
- Coilín Boland
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
| | - Dianfan Li
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
| | - Syed Tasadaque Ali Shah
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
| | - Stefan Haberstock
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany
| | - Martin Caffrey
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
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30
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Li D, Howe N, Dukkipati A, Shah ST, Bax BD, Edge C, Bridges A, Hardwicke P, Singh OMP, Giblin G, Pautsch A, Pfau R, Schnapp G, Wang M, Olieric V, Caffrey M. Crystallizing Membrane Proteins in the Lipidic Mesophase. Experience with Human Prostaglandin E2 Synthase 1 and an Evolving Strategy. CRYSTAL GROWTH & DESIGN 2014; 14:2034-2047. [PMID: 24803849 PMCID: PMC3983278 DOI: 10.1021/cg500157x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/04/2014] [Indexed: 05/29/2023]
Abstract
The lipidic mesophase or in meso method for crystallizing membrane proteins has several high profile targets to its credit and is growing in popularity. Despite its success, the method is in its infancy as far as rational crystallogenesis is concerned. Consequently, significant time, effort, and resources are still required to generate structure-grade crystals, especially with a new target type. Therefore, a need exists for crystallogenesis protocols that are effective with a broad range of membrane protein types. Recently, a strategy for crystallizing a prokaryotic α-helical membrane protein, diacylglycerol kinase (DgkA), by the in meso method was reported (Cryst. Growth. Des.2013, 14, 2846-2857). Here, we describe its application to the human α-helical microsomal prostaglandin E2 synthase 1 (mPGES1). While the DgkA strategy proved useful, significant modifications were needed to generate structure-quality crystals of this important therapeutic target. These included protein engineering, using an additive phospholipid in the hosting mesophase, performing multiple rounds of salt screening, and carrying out trials at 4 °C in the presence of a tight binding ligand. The crystallization strategy detailed here should prove useful for generating structures of other integral membrane proteins by the in meso method.
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Affiliation(s)
- Dianfan Li
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
| | - Nicole Howe
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
| | - Abhiram Dukkipati
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
| | - Syed T.
A. Shah
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
| | - Benjamin D. Bax
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Colin Edge
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Angela Bridges
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Phil Hardwicke
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Onkar M. P. Singh
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Ged Giblin
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Alexander Pautsch
- Departments of Lead
Identification and Optimization Support, Boehringer Ingelheim Pharma
GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Roland Pfau
- Departments of Lead
Identification and Optimization Support, Boehringer Ingelheim Pharma
GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Gisela Schnapp
- Departments of Lead
Identification and Optimization Support, Boehringer Ingelheim Pharma
GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Meitian Wang
- Swiss
Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Vincent Olieric
- Swiss
Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Martin Caffrey
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
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31
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Li D, Lyons JA, Pye VE, Vogeley L, Aragão D, Kenyon CP, Shah STA, Doherty C, Aherne M, Caffrey M. Crystal structure of the integral membrane diacylglycerol kinase. Nature 2013; 497:521-4. [PMID: 23676677 PMCID: PMC3740270 DOI: 10.1038/nature12179] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/12/2013] [Indexed: 11/09/2022]
Abstract
Diacylglycerol kinase catalyses the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid for use in shuttling water-soluble components to membrane-derived oligosaccharide and lipopolysaccharide in the cell envelope of Gram-negative bacteria. For half a century, this 121-residue kinase has served as a model for investigating membrane protein enzymology, folding, assembly and stability. Here we present crystal structures for three functional forms of this unique and paradigmatic kinase, one of which is wild type. These reveal a homo-trimeric enzyme with three transmembrane helices and an amino-terminal amphiphilic helix per monomer. Bound lipid substrate and docked ATP identify the putative active site that is of the composite, shared site type. The crystal structures rationalize extensive biochemical and biophysical data on the enzyme. They are, however, at variance with a published solution NMR model in that domain swapping, a key feature of the solution form, is not observed in the crystal structures.
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Affiliation(s)
- Dianfan Li
- School of Biochemistry and Immunology & School of Medicine, Trinity College Dublin, Dublin 2, Ireland
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