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Trinh TKH, Cabezas AJ, Joshi S, Catalano C, Siddique AB, Qiu W, Deshmukh S, des Georges A, Guo Y. pH-tunable membrane-active polymers, NCMNP2a- x, and their potential membrane protein applications. Chem Sci 2023; 14:7310-7326. [PMID: 37416719 PMCID: PMC10321531 DOI: 10.1039/d3sc01890c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Accurate 3D structures of membrane proteins are essential for comprehending their mechanisms of action and designing specific ligands to modulate their activities. However, these structures are still uncommon due to the involvement of detergents in the sample preparation. Recently, membrane-active polymers have emerged as an alternative to detergents, but their incompatibility with low pH and divalent cations has hindered their efficacy. Herein, we describe the design, synthesis, characterization, and application of a new class of pH-tunable membrane-active polymers, NCMNP2a-x. The results demonstrated that NCMNP2a-x could be used for high-resolution single-particle cryo-EM structural analysis of AcrB in various pH conditions and can effectively solubilize BcTSPO with the function preserved. Molecular dynamic simulation is consistent with experimental data that shed great insights into the working mechanism of this class of polymers. These results demonstrated that NCMNP2a-x might have broad applications in membrane protein research.
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Affiliation(s)
- Thi Kim Hoang Trinh
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Andres Jorge Cabezas
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York New York New York 10017 USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York New York New York 10017 USA
| | - Soumil Joshi
- Department of Chemical Engineering, Virginia Tech Blacksburg VA2 4060 USA
| | - Claudio Catalano
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Abu Bakkar Siddique
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Weihua Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Sanket Deshmukh
- Department of Chemical Engineering, Virginia Tech Blacksburg VA2 4060 USA
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York New York New York 10017 USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York New York New York 10017 USA
- Department of Chemistry & Biochemistry, City College of New York New York New York 10017 USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
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2
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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3
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Najbauer EE, Becker S, Giller K, Zweckstetter M, Lange A, Steinem C, de Groot BL, Griesinger C, Andreas LB. Structure, gating and interactions of the voltage-dependent anion channel. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:159-172. [PMID: 33782728 PMCID: PMC8071794 DOI: 10.1007/s00249-021-01515-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 02/19/2021] [Accepted: 03/08/2021] [Indexed: 12/14/2022]
Abstract
The voltage-dependent anion channel (VDAC) is one of the most highly abundant proteins found in the outer mitochondrial membrane, and was one of the earliest discovered. Here we review progress in understanding VDAC function with a focus on its structure, discussing various models proposed for voltage gating as well as potential drug targets to modulate the channel's function. In addition, we explore the sensitivity of VDAC structure to variations in the membrane environment, comparing DMPC-only, DMPC with cholesterol, and near-native lipid compositions, and use magic-angle spinning NMR spectroscopy to locate cholesterol on the outside of the β-barrel. We find that the VDAC protein structure remains unchanged in different membrane compositions, including conditions with cholesterol.
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Affiliation(s)
- Eszter E Najbauer
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Markus Zweckstetter
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- Senior Research Group of Translational Structural Biology in Dementia, Deutsches Zentrum Für Neurodegenerative Erkrankungen (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
- Department of Neurology, University Medical Center Göttingen, University of Göttingen, Waldweg 33, 37073, Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut Für Molekulare Pharmakologie, 13125, Berlin, Germany
- Institut Für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Göttingen, Germany
- Max-Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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4
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Johnson MC, Uddin YM, Neselu K, Schmidt-Krey I. 2D Electron Crystallography of Membrane Protein Single-, Double-, and Multi-Layered Ordered Arrays. Methods Mol Biol 2021; 2215:227-245. [PMID: 33368006 DOI: 10.1007/978-1-0716-0966-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The electron cryo-microscopy (cryo-EM) approach of 2D electron crystallography allows for structure determination of two-dimensional (2D) crystals of soluble and membrane proteins, employing identical principles and methods once 2D crystals are obtained. Two-dimensional crystallization trials of membrane proteins can result in multiple outcomes of ordered arrays, which may be suited for either 2D electron crystallography, helical analysis, or MicroED.The membrane protein 2D crystals used for 2D electron crystallography are either single- or double-layered ordered proteoliposome vesicles or sheet-like membranes. We have developed a cryo-EM grid preparation approach, which allows for the analysis of stacked 2D crystals that are neither suitable for MicroED nor for directly applying 2D electron crystallography. This new grid preparation approach, the peel-blot, uses the capillary force generated by submicron filter paper and mechanical means for the separation of stacked 2D crystals into single-layered 2D crystals, for which standard 2D electron crystallography can then be employed. The preparation of 2D crystals, the peel-blot grid preparation, and the structure determination by 2D electron crystallography are described here.
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Affiliation(s)
| | - Yusuf M Uddin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kasahun Neselu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ingeborg Schmidt-Krey
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
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5
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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6
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Casadei CM, Nass K, Barty A, Hunter MS, Padeste C, Tsai CJ, Boutet S, Messerschmidt M, Sala L, Williams GJ, Ozerov D, Coleman M, Li XD, Frank M, Pedrini B. Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals. IUCRJ 2019; 6:34-45. [PMID: 30713701 PMCID: PMC6327180 DOI: 10.1107/s2052252518014641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/16/2018] [Indexed: 06/09/2023]
Abstract
Serial femtosecond crystallography of two-dimensional membrane-protein crystals at X-ray free-electron lasers has the potential to address the dynamics of functionally relevant large-scale motions, which can be sterically hindered in three-dimensional crystals and suppressed in cryocooled samples. In previous work, diffraction data limited to a two-dimensional reciprocal-space slice were evaluated and it was demonstrated that the low intensity of the diffraction signal can be overcome by collecting highly redundant data, thus enhancing the achievable resolution. Here, the application of a newly developed method to analyze diffraction data covering three reciprocal-space dimensions, extracting the reciprocal-space map of the structure-factor amplitudes, is presented. Despite the low resolution and completeness of the data set, it is shown by molecular replacement that the reconstructed amplitudes carry meaningful structural information. Therefore, it appears that these intrinsic limitations in resolution and completeness from two-dimensional crystal diffraction may be overcome by collecting highly redundant data along the three reciprocal-space axes, thus allowing the measurement of large-scale dynamics in pump-probe experiments.
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Affiliation(s)
| | - Karol Nass
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mark S. Hunter
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | | | - Ching-Ju Tsai
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Leonardo Sala
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Garth J. Williams
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- NSLS-II, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973, USA
| | - Dmitry Ozerov
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Matthew Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Xiao-Dan Li
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Bill Pedrini
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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7
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Ge Y, Gu Y, Wang J, Zhang Z. Membrane topology of rat sodium-coupled neutral amino acid transporter 2 (SNAT2). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1460-1469. [PMID: 29678469 DOI: 10.1016/j.bbamem.2018.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/24/2018] [Accepted: 04/15/2018] [Indexed: 11/19/2022]
Abstract
Sodium-coupled neutral amino acid transporter 2 (SNAT2) is a subtype of the amino acid transport system A that is widely expressed in mammalian tissues. It plays critical roles in glutamic acid-glutamine circulation, liver gluconeogenesis and other biological pathway. However, the topology of the SNAT2 amino acid transporter is unknown. Here we identified the topological structure of SNAT2 using bioinformatics analysis, Methoxy-polyethylene glycol maleimide (mPEG-Mal) chemical modification, protease cleavage assays, immunofluorescence and examination of glycosylation. Our results show that SNAT2 contains 11 transmembrane domains (TMDs) with an intracellular N terminus and an extracellular C terminus. Three N-glycosylation sites were verified at the largest extracellular loop. This model is consistent with the previous model of SNAT2 with the exception of a difference in number of glycosylation sites. This is the first time to confirm the SNAT2 membrane topology using experimental methods. Our study on SNAT2 topology provides valuable structural information of one of the solute carrier family 38 (SLC38) members.
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Affiliation(s)
- Yudan Ge
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Yanting Gu
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Jiahong Wang
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Zhou Zhang
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China.
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8
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Polymer Nanodiscs: Discoidal Amphiphilic Block Copolymer Membranes as a New Platform for Membrane Proteins. Sci Rep 2017; 7:15227. [PMID: 29123151 PMCID: PMC5680229 DOI: 10.1038/s41598-017-15151-9] [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: 08/04/2017] [Accepted: 10/18/2017] [Indexed: 12/23/2022] Open
Abstract
Lipid nanodiscs are playing increasingly important roles in studies of the structure and function of membrane proteins. Development of lipid nanodiscs as a membrane-protein-supporting platform, or a drug targeting and delivery vehicle in general, is undermined by the fluidic and labile nature of lipid bilayers. Here, we report the discovery of polymer nanodiscs, i.e., discoidal amphiphilic block copolymer membrane patches encased within membrane scaffold proteins, as a novel two-dimensional nanomembrane that maintains the advantages of lipid nanodiscs while addressing their weaknesses. Using MsbA, a bacterial ATP-binding cassette transporter as a membrane protein prototype, we show that the protein can be reconstituted into the polymer nanodiscs in an active state. As with lipid nanodiscs, reconstitution of detergent-solubilized MsbA into the polymer nanodiscs significantly enhances its activity. In contrast to lipid nanodiscs that undergo time- and temperature-dependent structural changes, the polymer nanodiscs experience negligible structural evolution under similar environmental stresses, revealing a critically important property for the development of nanodisc-based characterization methodologies or biotechnologies. We expect that the higher mechanical and chemical stability of block copolymer membranes and their chemical versatility for adaptation will open new opportunities for applications built upon diverse membrane protein functions, or involved with drug targeting and delivery.
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9
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Polymer-encased nanodiscs with improved buffer compatibility. Sci Rep 2017; 7:7432. [PMID: 28785023 PMCID: PMC5547149 DOI: 10.1038/s41598-017-07110-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/23/2017] [Indexed: 01/07/2023] Open
Abstract
Styrene-maleic acid copolymers allow for solubilization and reconstitution of membrane proteins into nanodiscs. These polymer-encased nanodiscs are promising platforms for studies of membrane proteins in a near-physiologic environment without the use of detergents. However, current styrene-maleic acid copolymers display severe limitations in terms of buffer compatibility and ensued flexibility for various applications. Here, we present a new family of styrene-maleic acid copolymers that do not aggregate at low pH or in the presence of polyvalent cations, and can be used to solubilize membrane proteins and produce nanodiscs of controlled sizes.
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10
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Suzuki Y, Cardone G, Restrepo D, Zavattieri PD, Baker TS, Tezcan FA. Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals. Nature 2016; 533:369-73. [PMID: 27135928 PMCID: PMC4991361 DOI: 10.1038/nature17633] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 03/01/2016] [Indexed: 12/25/2022]
Abstract
Two-dimensional (2D) crystalline materials possess unique structural, mechanical and electronic properties that make them highly attractive in many applications. Although there have been advances in preparing 2D materials that consist of one or a few atomic or molecular layers, bottom-up assembly of 2D crystalline materials remains a challenge and an active area of development. More challenging is the design of dynamic 2D lattices that can undergo large-scale motions without loss of crystallinity. Dynamic behaviour in porous three-dimensional (3D) crystalline solids has been exploited for stimuli-responsive functions and adaptive behaviour. As in such 3D materials, integrating flexibility and adaptiveness into crystalline 2D lattices would greatly broaden the functional scope of 2D materials. Here we report the self-assembly of unsupported, 2D protein lattices with precise spatial arrangements and patterns using a readily accessible design strategy. Three single- or double-point mutants of the C4-symmetric protein RhuA were designed to assemble via different modes of intermolecular interactions (single-disulfide, double-disulfide and metal-coordination) into crystalline 2D arrays. Owing to the flexibility of the single-disulfide interactions, the lattices of one of the variants ((C98)RhuA) are essentially defect-free and undergo substantial, but fully correlated, changes in molecular arrangement, yielding coherently dynamic 2D molecular lattices. (C98)RhuA lattices display a Poisson's ratio of -1-the lowest thermodynamically possible value for an isotropic material-making them auxetic.
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Affiliation(s)
- Yuta Suzuki
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Giovanni Cardone
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - David Restrepo
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, USA
| | - Pablo D. Zavattieri
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, USA
| | - Timothy S. Baker
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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11
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Multifrequency Force Microscopy of Helical Protein Assembly on a Virus. Sci Rep 2016; 6:21899. [PMID: 26915629 PMCID: PMC4768132 DOI: 10.1038/srep21899] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/01/2016] [Indexed: 01/09/2023] Open
Abstract
High-resolution microscopy techniques have been extensively used to investigate the structure of soft, biological matter at the nanoscale, from very thin membranes to small objects, like viruses. Electron microscopy techniques allow for obtaining extraordinary resolution by averaging signals from multiple identical structures. In contrast, atomic force microscopy (AFM) collects data from single entities. Here, it is possible to finely modulate the interaction with the samples, in order to be sensitive to their top surface, avoiding mechanical deformations. However, most biological surfaces are highly curved, such as fibers or tubes, and ultimate details of their surface are in the vicinity of steep height variations. This limits lateral resolution, even when sharp probes are used. We overcome this problem by using multifrequency force microscopy on a textbook example, the Tobacco Mosaic Virus (TMV). We achieved unprecedented resolution in local maps of amplitude and phase shift of the second excited mode, recorded together with sample topography. Our data, which combine multifrequency imaging and Fourier analysis, confirm the structure deduced from averaging techniques (XRD, cryoEM) for surface features of single virus particles, down to the helical pitch of the coat protein subunits, 2.3 nm. Remarkably, multifrequency AFM images do not require any image postprocessing.
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12
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van Genderen E, Li YW, Nederlof I, Abrahams JP. Lattice filter for processing image data of three-dimensional protein nanocrystals. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:34-9. [PMID: 26894532 PMCID: PMC4756612 DOI: 10.1107/s205979831502149x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 11/12/2015] [Indexed: 11/28/2022]
Abstract
A specialized filter for finding lattices in images of three-dimensional nanocrystals devoid of any contrast is described. When 300 kV cryo-EM images at Scherzer focus are acquired from ∼100 nm thick three-dimensional protein nanocrystals using a Falcon 2 direct electron detector, Fourier transformation can reveal the crystalline lattice to surprisingly high resolutions, even though the images themselves seem to be devoid of any contrast. Here, it is reported how this lattice information can be enhanced by means of a wave finder in combination with Wiener-type maximum-likelihood filtering. This procedure paves the way towards full three-dimensional structure determination at high resolution for protein crystals.
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Affiliation(s)
- E van Genderen
- Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Y W Li
- Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - I Nederlof
- Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - J P Abrahams
- Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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13
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Preiner J, Horner A, Karner A, Ollinger N, Siligan C, Pohl P, Hinterdorfer P. High-speed AFM images of thermal motion provide stiffness map of interfacial membrane protein moieties. NANO LETTERS 2015; 15:759-63. [PMID: 25516527 PMCID: PMC4296598 DOI: 10.1021/nl504478f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/11/2014] [Indexed: 05/20/2023]
Abstract
The flexibilities of extracellular loops determine ligand binding and activation of membrane receptors. Arising from fluctuations in inter- and intraproteinaceous interactions, flexibility manifests in thermal motion. Here we demonstrate that quantitative flexibility values can be extracted from directly imaging the thermal motion of membrane protein moieties using high-speed atomic force microscopy (HS-AFM). Stiffness maps of the main periplasmic loops of single reconstituted water channels (AqpZ, GlpF) revealed the spatial and temporal organization of loop-stabilizing intraproteinaceous H-bonds and salt bridges.
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Affiliation(s)
- Johannes Preiner
- Center
for Advanced Bioanalysis GmbH, Gruberstrasse 40, 4020 Linz, Austria
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
- E-mail:
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Andreas Karner
- Center
for Advanced Bioanalysis GmbH, Gruberstrasse 40, 4020 Linz, Austria
| | - Nicole Ollinger
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Peter Hinterdorfer
- Center
for Advanced Bioanalysis GmbH, Gruberstrasse 40, 4020 Linz, Austria
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
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14
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Bosshart PD, Engel A, Fotiadis D. High-resolution atomic force microscopy imaging of rhodopsin in rod outer segment disk membranes. Methods Mol Biol 2015; 1271:189-203. [PMID: 25697525 DOI: 10.1007/978-1-4939-2330-4_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Atomic force microscopy (AFM) is a powerful imaging technique that allows recording topographical information of membrane proteins under near-physiological conditions. Remarkable results have been obtained on membrane proteins that were reconstituted into lipid bilayers. High-resolution AFM imaging of native disk membranes from vertebrate rod outer segments has unveiled the higher-order oligomeric state of the G protein-coupled receptor rhodopsin, which is highly expressed in disk membranes. Based on AFM imaging, it has been demonstrated that rhodopsin assembles in rows of dimers and paracrystals and that the rhodopsin dimer is the fundamental building block of higher-order structures.
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Affiliation(s)
- Patrick D Bosshart
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, Bern, CH-3012, Switzerland
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15
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Armstrong PB. Comparative Biology of the Pentraxin Protein Family: Evolutionarily Conserved Component of Innate Immune System. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 316:1-47. [DOI: 10.1016/bs.ircmb.2015.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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16
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Makky A, Viel P, Chen SWW, Berthelot T, Pellequer JL, Polesel-Maris J. Piezoelectric tuning fork probe for atomic force microscopy imaging and specific recognition force spectroscopy of an enzyme and its ligand. J Mol Recognit 2014; 26:521-31. [PMID: 24089359 DOI: 10.1002/jmr.2294] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/13/2013] [Accepted: 06/17/2013] [Indexed: 11/12/2022]
Abstract
Piezoelectric quartz tuning fork has drawn the attention of many researchers for the development of new atomic force microscopy (AFM) self-sensing probes. However, only few works have been done for soft biological materials imaging in air or aqueous conditions. The aim of this work was to demonstrate the efficiency of the AFM tuning fork probe to perform high-resolution imaging of proteins and to study the specific interaction between a ligand and its receptor in aqueous media. Thus, a new kind of self-sensing AFM sensor was introduced to realize imaging and biochemical specific recognition spectroscopy of glucose oxidase enzyme using a new chemical functionalization procedure of the metallic tips based on the electrochemical reduction of diazonium salt. This scanning probe as well as the functionalization strategy proved to be efficient respectively for the topography and force spectroscopy of soft biological materials in buffer conditions.
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Affiliation(s)
- Ali Makky
- CEA, IRAMIS, Service de Physique et Chimie des Surfaces et Interfaces, Gif-sur-Yvette, France
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17
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The ArrayGrid: A methodology for applying multiple samples to a single TEM specimen grid. Ultramicroscopy 2013; 135:105-12. [DOI: 10.1016/j.ultramic.2013.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/16/2013] [Accepted: 07/19/2013] [Indexed: 11/20/2022]
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18
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Chen SWW, Odorico M, Meillan M, Vellutini L, Teulon JM, Parot P, Bennetau B, Pellequer JL. Nanoscale structural features determined by AFM for single virus particles. NANOSCALE 2013; 5:10877-10886. [PMID: 24056758 DOI: 10.1039/c3nr02706f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this work, we propose "single-image analysis", as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis.
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Affiliation(s)
- Shu-wen W Chen
- CEA, iBEB, Service de Biochimie et Toxicologie Nucléaire, DSV/iBEB/SBTN - Bat 170, BP17171, F-30207 Bagnols sur Cèze, France.
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19
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Marasini C, Jacchetti E, Moretti M, Canale C, Moran O, Vassalli M. Visualization of single proteins from stripped native cell membranes: A protocol for high-resolution atomic force microscopy. Microsc Res Tech 2013; 76:723-32. [DOI: 10.1002/jemt.22223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 04/08/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Carlotta Marasini
- Istituto di Biofisica; Consiglio Nazionale delle Ricerche; Genova; 16149; Italy
| | | | - Manola Moretti
- Nanophysics Dipartimento; Istituto Italiano di Tecnologia; Morego; Genova; 16163; Italy
| | - Claudio Canale
- Nanophysics Dipartimento; Istituto Italiano di Tecnologia; Morego; Genova; 16163; Italy
| | - Oscar Moran
- Istituto di Biofisica; Consiglio Nazionale delle Ricerche; Genova; 16149; Italy
| | - Massimo Vassalli
- Istituto di Biofisica; Consiglio Nazionale delle Ricerche; Genova; 16149; Italy
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20
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Eddy MT, Ong TC, Clark L, Teijido O, van der Wel PCA, Garces R, Wagner G, Rostovtseva TK, Griffin RG. Lipid dynamics and protein-lipid interactions in 2D crystals formed with the β-barrel integral membrane protein VDAC1. J Am Chem Soc 2012; 134:6375-87. [PMID: 22435461 PMCID: PMC3333839 DOI: 10.1021/ja300347v] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We employ a combination of (13)C/(15)N magic angle spinning (MAS) NMR and (2)H NMR to study the structural and functional consequences of different membrane environments on VDAC1 and, conversely, the effect of VDAC1 on the structure of the lipid bilayer. MAS spectra reveal a well-structured VDAC1 in 2D crystals of dimyristoylphosphatidylcholine (DMPC) and diphytanoylphosphatidylcholine (DPhPC), and their temperature dependence suggests that the VDAC structure does not change conformation above and below the lipid phase transition temperature. The same data show that the N-terminus remains structured at both low and high temperatures. Importantly, functional studies based on electrophysiological measurements on these same samples show fully functional channels, even without the presence of Triton X-100 that has been found necessary for in vitro-refolded channels. (2)H solid-state NMR and differential scanning calorimetry were used to investigate the dynamics and phase behavior of the lipids within the VDAC1 2D crystals. (2)H NMR spectra indicate that the presence of protein in DMPC results in a broad lipid phase transition that is shifted from 19 to ~27 °C and show the existence of different lipid populations, consistent with the presence of both annular and bulk lipids in the functionally and structurally homogeneous samples.
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Affiliation(s)
- Matthew T. Eddy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ta-Chung Ong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lindsay Clark
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Oscar Teijido
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Patrick C. A. van der Wel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Garces
- Department of Biological and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Gerhard Wagner
- Department of Biological and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Tatiana K. Rostovtseva
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert G. Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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21
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Egel R. Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life. Life (Basel) 2012; 2:170-212. [PMID: 25382122 PMCID: PMC4187143 DOI: 10.3390/life2010170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 12/29/2011] [Accepted: 01/11/2012] [Indexed: 02/08/2023] Open
Abstract
This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.
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Affiliation(s)
- Richard Egel
- Department of Biology, University of Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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22
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Buzhynskyy N, Salesse C, Scheuring S. Rhodopsin is spatially heterogeneously distributed in rod outer segment disk membranes. J Mol Recognit 2011; 24:483-9. [DOI: 10.1002/jmr.1086] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Abstract
TEM image processing tools are devised for the assessment of 2D-crystallization experiments. The algorithms search for the presence and assess the quality of crystalline membranes. The retained scenario emulates the decisions of a microscopist in selecting targets and assessing the sample. Crystallinity is automatically assessed through the diffraction patterns of high magnification images acquired on pertinent regions selected at lower magnifications. Further algorithms have been developed for membrane characterization. Tests on images of different samples, acquired on different microscopes led to good results.
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24
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Mio K, Maruyama Y, Ogura T, Kawata M, Moriya T, Mio M, Sato C. Single particle reconstruction of membrane proteins: A tool for understanding the 3D structure of disease-related macromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2010; 103:122-30. [DOI: 10.1016/j.pbiomolbio.2010.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 02/06/2010] [Accepted: 03/07/2010] [Indexed: 11/28/2022]
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25
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Schmidt-Krey I, Rubinstein JL. Electron cryomicroscopy of membrane proteins: specimen preparation for two-dimensional crystals and single particles. Micron 2010; 42:107-16. [PMID: 20678942 DOI: 10.1016/j.micron.2010.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 07/08/2010] [Accepted: 07/11/2010] [Indexed: 01/08/2023]
Abstract
Membrane protein structure and function can be studied by two powerful and highly complementary electron cryomicroscopy (cryo-EM) methods: electron crystallography of two-dimensional (2D) crystals and single particle analysis of detergent-solubilized protein complexes. To obtain the highest-possible resolution data from membrane proteins, whether prepared as 2D crystals or single particles, cryo-EM samples must be vitrified with great care. Grid preparation for cryo-EM of 2D crystals is possible by back-injection, the carbon sandwich technique, drying in sugars before cooling in the electron microscope, or plunge-freezing. Specimen grids for single particle cryo-EM studies of membrane proteins are usually produced by plunge-freezing protein solutions, supported either by perforated or a continuous carbon film substrate. This review outlines the different techniques available and the suitability of each method for particular samples and studies. Experimental considerations in sample preparation and preservation include the protein itself and the presence of lipid or detergent. The appearance of cryo-EM samples in different conditions is also discussed.
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Affiliation(s)
- Ingeborg Schmidt-Krey
- Georgia Institute of Technology, School of Biology, School of Chemistry and Biochemistry, 310 Ferst Drive, Rm. A118, Atlanta, GA 30332-0230, USA.
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26
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Mus-Veteau I. Heterologous expression and purification systems for structural proteomics of mammalian membrane proteins. Comp Funct Genomics 2010; 3:511-7. [PMID: 18629259 PMCID: PMC2448422 DOI: 10.1002/cfg.218] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2002] [Accepted: 10/14/2002] [Indexed: 01/14/2023] Open
Abstract
Membrane proteins (MPs) are responsible for the interface between the exterior and the interior of the cell. These proteins are implicated in numerous diseases,
such as cancer, cystic fibrosis, epilepsy, hyperinsulinism, heart failure, hypertension
and Alzheimer's disease. However, studies on these disorders are hampered by
a lack of structural information about the proteins involved. Structural analysis
requires large quantities of pure and active proteins. The majority of medically and
pharmaceutically relevant MPs are present in tissues at very low concentration, which
makes heterologous expression in large-scale production-adapted cells a prerequisite
for structural studies. Obtaining mammalian MP structural data depends on the
development of methods that allow the production of large quantities of MPs.
This review focuses on the different heterologous expression systems, and the
purification strategies, used to produce large amounts of pure mammalian MPs for
structural proteomics.
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Affiliation(s)
- Isabelle Mus-Veteau
- Laboratoire de Physiologie Cellulaire et Moléculaire, UMR-CNRS 6548, Université de Nice-Sophia Antipolis, Parc Valrose Nice cedex 2, 06108 France.
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27
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Bahar I, Lezon TR, Bakan A, Shrivastava IH. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 2010; 110:1463-97. [PMID: 19785456 PMCID: PMC2836427 DOI: 10.1021/cr900095e] [Citation(s) in RCA: 377] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA.
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28
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AFM study of the interaction of cytochrome P450 2C9 with phospholipid bilayers. Chem Phys Lipids 2010; 163:182-9. [DOI: 10.1016/j.chemphyslip.2009.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 08/07/2009] [Accepted: 11/09/2009] [Indexed: 11/18/2022]
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29
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Two-dimensional crystallization of integral membrane proteins for electron crystallography. Methods Mol Biol 2010; 654:187-205. [PMID: 20665267 DOI: 10.1007/978-1-60761-762-4_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although membrane proteins make up 30% of the proteome and are a common target for therapeutic drugs, determination of their atomic structure remains a technical challenge. Electron crystallography represents an alternative to the conventional methods of X-ray diffraction and NMR and relies on the formation of two-dimensional crystals. These crystals are produced by reconstituting purified, detergent-solubilized membrane proteins back into the native environment of a lipid bilayer. This chapter reviews methods for producing two-dimensional crystals and for screening them by negative stain electron microscopy. In addition, we show examples of the different morphologies that are commonly obtained and describe basic image analysis procedures that can be used to evaluate their promise for structure determination by cryoelectron microscopy.
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30
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Ubarretxena-Belandia I, Stokes DL. Present and future of membrane protein structure determination by electron crystallography. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 81:33-60. [PMID: 21115172 DOI: 10.1016/b978-0-12-381357-2.00002-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins.
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Affiliation(s)
- Iban Ubarretxena-Belandia
- Department of Structural and Chemical Biology, Mt. Sinai School of Medicine, New York, New York, USA
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31
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Krishnaswamy S, Verdile G, Groth D, Kanyenda L, Martins RN. The structure and function of Alzheimer’s gamma secretase enzyme complex. Crit Rev Clin Lab Sci 2009; 46:282-301. [DOI: 10.3109/10408360903335821] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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32
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Zhao G, Johnson MC, Schnell JR, Kanaoka Y, Haase W, Irikura D, Lam BK, Schmidt-Krey I. Two-dimensional crystallization conditions of human leukotriene C4 synthase requiring adjustment of a particularly large combination of specific parameters. J Struct Biol 2009; 169:450-4. [PMID: 19903529 DOI: 10.1016/j.jsb.2009.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 11/03/2009] [Accepted: 11/05/2009] [Indexed: 11/29/2022]
Abstract
Human leukotriene C(4) synthase (LTC(4)S) forms highly ordered two-dimensional (2D) crystals under specific reconstitution conditions. It was found that control of a larger number of parameters than is usually observed for 2D crystallization of membrane proteins was necessary to induce crystal formation of LTC(4)S. Here, we describe the parameters that were optimized to yield large and well-ordered 2D crystals of LTC(4)S. Careful fractioning of eluates during the protein purification was essential for obtaining crystals. While the lipid-to-protein ratio was critical in obtaining order, four parameters were decisive in inducing growth of crystals that were up to several microns in size. To obtain a favorable diameter, salt, temperature, glycerol, and initial detergent concentration had to be controlled with great care. Interestingly, several crystal forms could be grown, namely the plane group symmetries of p2, p3, p312, and two different unit cell sizes of plane group symmetry p321.
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Affiliation(s)
- G Zhao
- Georgia Institute of Technology, School of Biology, School of Chemistry and Biochemistry, 310 Ferst Drive, Atlanta, GA 30332, USA
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33
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Casagrande F, Harder D, Schenk A, Meury M, Ucurum Z, Engel A, Weitz D, Daniel H, Fotiadis D. Projection structure of DtpD (YbgH), a prokaryotic member of the peptide transporter family. J Mol Biol 2009; 394:708-17. [PMID: 19782088 DOI: 10.1016/j.jmb.2009.09.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 09/09/2009] [Accepted: 09/18/2009] [Indexed: 10/20/2022]
Abstract
Cellular uptake of di- and tripeptides has been characterized in numerous organisms, and various transporters have been identified. In contrast, structural information on peptide transporters is very sparse. Here, we have cloned, overexpressed, purified, and biochemically characterized DtpD (YbgH) from Escherichia coli, a prokaryotic member of the peptide transporter family. Its homologues in mammals, PEPT1 (SLC15A1) and PEPT2 (SLC15A2), not only transport peptides but also are of relevance for uptake of drugs as they accept a large spectrum of peptidomimetics such as beta-lactam antibiotics, antivirals, peptidase inhibitors, and others as substrates. Uptake experiments indicated that DtpD functions as a canonical peptide transporter and is, therefore, a valid model for structural studies of this family of proteins. Blue native polyacrylamide gel electrophoresis, gel filtration, and transmission electron microscopy of single-DtpD particles suggest that the transporter exists in a monomeric form when solubilized in detergent. Two-dimensional crystallization of DtpD yielded first tubular crystals that allowed the determination of a projection structure at better than 19 A resolution. This structure of DtpD represents the first structural view of a member of the peptide transporter family.
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Affiliation(s)
- Fabio Casagrande
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, San Diego, La Jolla, CA 92093, USA
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34
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Arinaminpathy Y, Khurana E, Engelman DM, Gerstein MB. Computational analysis of membrane proteins: the largest class of drug targets. Drug Discov Today 2009; 14:1130-5. [PMID: 19733256 DOI: 10.1016/j.drudis.2009.08.006] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Revised: 08/15/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
Abstract
Given the key roles of integral membrane proteins as transporters and channels, it is necessary to understand their structures and, hence, mechanisms and regulation at the molecular level. Membrane proteins represent approximately 30% of all proteins of currently sequenced genomes. Paradoxically, however, only approximately 2% of crystal structures deposited in the protein data bank are of membrane proteins, and very few of these are at high resolution (better than 2A). The great disparity between our understanding of soluble proteins and our understanding of membrane proteins is because of the practical problems of working with membrane proteins - specifically, difficulties in expression, purification and crystallization. Thus, computational modeling has been utilized extensively to make crucial advances in understanding membrane protein structure and function.
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Affiliation(s)
- Yalini Arinaminpathy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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35
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Fechner P, Boudier T, Mangenot S, Jaroslawski S, Sturgis JN, Scheuring S. Structural information, resolution, and noise in high-resolution atomic force microscopy topographs. Biophys J 2009; 96:3822-31. [PMID: 19413988 PMCID: PMC2711429 DOI: 10.1016/j.bpj.2009.02.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 12/10/2008] [Accepted: 02/04/2009] [Indexed: 11/22/2022] Open
Abstract
AFM has developed into a powerful tool in structural biology, providing topographs of proteins under close-to-native conditions and featuring an outstanding signal/noise ratio. However, the imaging mechanism exhibits particularities: fast and slow scan axis represent two independent image acquisition axes. Additionally, unknown tip geometry and tip-sample interaction render the contrast transfer function nondefinable. Hence, the interpretation of AFM topographs remained difficult. How can noise and distortions present in AFM images be quantified? How does the number of molecule topographs merged influence the structural information provided by averages? What is the resolution of topographs? Here, we find that in high-resolution AFM topographs, many molecule images are only slightly disturbed by noise, distortions, and tip-sample interactions. To identify these high-quality particles, we propose a selection criterion based on the internal symmetry of the imaged protein. We introduce a novel feature-based resolution analysis and show that AFM topographs of different proteins contain structural information beginning at different resolution thresholds: 10 A (AqpZ), 12 A (AQP0), 13 A (AQP2), and 20 A (light-harvesting-complex-2). Importantly, we highlight that the best single-molecule images are more accurate molecular representations than ensemble averages, because averaging downsizes the z-dimension and "blurs" structural details.
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Key Words
- 2d, two-dimensional
- 3d, three-dimensional
- acv, auto-correlation value
- afm, atomic force microscopy
- aqp0, aquaporin-0
- aqp2, aquaporin-2
- aqpz, aquaporin-z
- br, bacteriorhodopsin
- ccv, cross-correlation value
- ctf, contrast transfer function
- dpr, differential phase residual
- em, electron microscopy
- frc, fourier ring correlation
- fsc, fourier shell correlation
- is, internal symmetry
- lh2, light-harvesting-complex 2
- rmsd, root mean-square deviation
- sd, standard deviation
- snr, signal/noise ratio
- ssnr, spectral signal/noise ratio
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Affiliation(s)
- Peter Fechner
- Institut Curie, Équipe Institut National de la Santé et de la Recherche Médicale Avenir, 75248 Paris, France
| | - Thomas Boudier
- Institut de Biologie Intégrative, Institut Fédératif de Recherche 83, Université Pierre et Marie Curie, Paris, France
| | - Stéphanie Mangenot
- Institut Curie, Équipe Institut National de la Santé et de la Recherche Médicale Avenir, 75248 Paris, France
- Université Paris-Sud, 91405 Orsay, France
| | - Szymon Jaroslawski
- Institut Curie, Équipe Institut National de la Santé et de la Recherche Médicale Avenir, 75248 Paris, France
| | - James N. Sturgis
- UPR-9027 Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique–Aix-Marseille Université, 13402 Marseille, France
| | - Simon Scheuring
- Institut Curie, Équipe Institut National de la Santé et de la Recherche Médicale Avenir, 75248 Paris, France
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36
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Casagrande F, Ratera M, Schenk AD, Chami M, Valencia E, Lopez JM, Torrents D, Engel A, Palacin M, Fotiadis D. Projection structure of a member of the amino acid/polyamine/organocation transporter superfamily. J Biol Chem 2008; 283:33240-8. [PMID: 18819925 DOI: 10.1074/jbc.m806917200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The L-arginine/agmatine antiporter AdiC is a key component of the arginine-dependent extreme acid resistance system of Escherichia coli. Phylogenetic analysis indicated that AdiC belongs to the amino acid/polyamine/organocation (APC) transporter superfamily having sequence identities of 15-17% to eukaryotic and human APC transporters. For functional and structural characterization, we cloned, overexpressed, and purified wild-type AdiC and the point mutant AdiC-W293L, which is unable to bind and consequently transport L-arginine. Purified detergent-solubilized AdiC particles were dimeric. Reconstitution experiments yielded two-dimensional crystals of AdiC-W293L diffracting beyond 6 angstroms resolution from which we determined the projection structure at 6.5 angstroms resolution. The projection map showed 10-12 density peaks per monomer and suggested mainly tilted helices with the exception of one distinct perpendicular membrane spanning alpha-helix. Comparison of AdiC-W293L with the projection map of the oxalate/formate antiporter from Oxalobacter formigenes, a member from the major facilitator superfamily, indicated different structures. Thus, two-dimensional crystals of AdiC-W293L yielded the first detailed view of a transport protein from the APC superfamily at sub-nanometer resolution.
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Affiliation(s)
- Fabio Casagrande
- M. E. Müller Institute for Structural Biology, Biozentrum of the University of Basel, CH-4056 Basel, Switzerland
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37
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Abstract
Aquaporins are a family of ubiquitous membrane proteins that form a pore for the permeation of water. Both electron and X-ray crystallography played major roles in determining the atomic structures of a number of aquaporins. This review focuses on electron crystallography, and its contribution to the field of aquaporin biology. We briefly discuss electron crystallography and the two-dimensional crystallization process. We describe features of aquaporins common to both electron and X-ray crystallographic structures; as well as some structural insights unique to electron crystallography, including aquaporin junction formation and lipid-protein interactions.
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Affiliation(s)
- Simeon Andrews
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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38
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Liu LN, Aartsma TJ, Frese RN. Dimers of light-harvesting complex 2 from Rhodobacter sphaeroides characterized in reconstituted 2D crystals with atomic force microscopy. FEBS J 2008; 275:3157-66. [DOI: 10.1111/j.1742-4658.2008.06469.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Müller DJ, Wu N, Palczewski K. Vertebrate membrane proteins: structure, function, and insights from biophysical approaches. Pharmacol Rev 2008; 60:43-78. [PMID: 18321962 DOI: 10.1124/pr.107.07111] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Membrane proteins are key targets for pharmacological intervention because they are vital for cellular function. Here, we analyze recent progress made in the understanding of the structure and function of membrane proteins with a focus on rhodopsin and development of atomic force microscopy techniques to study biological membranes. Membrane proteins are compartmentalized to carry out extra- and intracellular processes. Biological membranes are densely populated with membrane proteins that occupy approximately 50% of their volume. In most cases membranes contain lipid rafts, protein patches, or paracrystalline formations that lack the higher-order symmetry that would allow them to be characterized by diffraction methods. Despite many technical difficulties, several crystal structures of membrane proteins that illustrate their internal structural organization have been determined. Moreover, high-resolution atomic force microscopy, near-field scanning optical microscopy, and other lower resolution techniques have been used to investigate these structures. Single-molecule force spectroscopy tracks interactions that stabilize membrane proteins and those that switch their functional state; this spectroscopy can be applied to locate a ligand-binding site. Recent development of this technique also reveals the energy landscape of a membrane protein, defining its folding, reaction pathways, and kinetics. Future development and application of novel approaches during the coming years should provide even greater insights to the understanding of biological membrane organization and function.
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Affiliation(s)
- Daniel J Müller
- Biotechnology Center, University of Technology, Dresden, Germany
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40
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Liang H, Whited G, Nguyen C, Okerlund A, Stucky GD. Inherently tunable electrostatic assembly of membrane proteins. NANO LETTERS 2008; 8:333-339. [PMID: 18052232 DOI: 10.1021/nl0729173] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Membrane proteins are a class of nanoscopic entities that control the matter, energy, and information transport across cellular boundaries. Electrostatic interactions are shown to direct the rapid co-assembly of proteorhodopsin (PR) and lipids into long-range crystalline arrays. The roles of inherent charge variations on lipid membranes and PR variants with different compositions are examined by tuning recombinant PR variants with different extramembrane domain sizes and charged amino acid substitutions, lipid membrane compositions, and lipid-to-PR stoichiometric ratios. Rational control of this predominantly electrostatic assembly for PR crystallization is demonstrated, and the same principles should be applicable to the assembly and crystallization of other integral membrane proteins.
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Affiliation(s)
- Hongjun Liang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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41
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Imaging CFTR in its native environment. Pflugers Arch 2007; 456:163-77. [DOI: 10.1007/s00424-007-0399-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2007] [Accepted: 11/09/2007] [Indexed: 12/18/2022]
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42
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Reconstitution of mitochondrial ATP synthase into lipid bilayers for structural analysis. J Struct Biol 2007; 160:287-94. [PMID: 17959389 DOI: 10.1016/j.jsb.2007.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 07/10/2007] [Accepted: 09/12/2007] [Indexed: 11/21/2022]
Abstract
Mitochondrial F(1)F(o)-ATP synthase is a molecular motor that couples the energy generated by oxidative metabolism to the synthesis of ATP. Direct visualization of the rotary action of the bacterial ATP synthase has been well characterized. However, direct observation of rotation of the mitochondrial enzyme has not been reported yet. Here, we describe two methods to reconstitute mitochondrial F(1)F(o)-ATP synthase into lipid bilayers suitable for structure analysis by electron and atomic force microscopy (AFM). Proteoliposomes densely packed with bovine heart mitochondria F(1)F(o)-ATP synthase were obtained upon detergent removal from ternary mixtures (lipid, detergent and protein). Two-dimensional crystals of recombinant hexahistidine-tagged yeast F(1)F(o)-ATP synthase were grown using the supported monolayer technique. Because the hexahistidine-tag is located at the F(1) catalytic subcomplex, ATP synthases were oriented unidirectionally in such two-dimensional crystals, exposing F(1) to the lipid monolayer and the F(o) membrane region to the bulk solution. This configuration opens a new avenue for the determination of the c-ring stoichiometry of unknown hexahistidine-tagged ATP synthases and the organization of the membrane intrinsic subunits within F(o) by electron microscopy and AFM.
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43
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Liang H, Whited G, Nguyen C, Stucky GD. The directed cooperative assembly of proteorhodopsin into 2D and 3D polarized arrays. Proc Natl Acad Sci U S A 2007; 104:8212-7. [PMID: 17488827 PMCID: PMC1895931 DOI: 10.1073/pnas.0702336104] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteorhodopsin is the membrane protein used by marine bacterioplankton as a light-driven proton pump. Here, we describe a rapid cooperative assembly process directed by universal electrostatic interactions that spontaneously organizes proteorhodopsin molecules into ordered arrays with well defined orientation and packing density. We demonstrate the charge density-matching mechanism that selectively controls the assembly process. The interactions among different components in the system are tuned by varying their charge densities to yield different organized transmembrane protein arrays: (i) a bacteriorhodopsin purple membrane-like structure where proteorhodopsin molecules are cooperatively arranged with charged lipids into a 2D hexagonal lattice; (ii) selected liquid-crystalline states in which crystalline lamellae made up of the coassembled proteorhodopsin and charged lipid molecules are coupled three-dimensionally with polarized proteorhodopsin orientation persisting through the macroscopic scale. Understanding this rapid electrostatically driven assembly process sheds light on organizing membrane proteins in general, which is a prerequisite for membrane protein structural and mechanistic studies as well as in vitro applications.
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Affiliation(s)
- Hongjun Liang
- *Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106; and
| | - Gregg Whited
- Genencor International, Inc., Palo Alto, CA 94304
| | - Chi Nguyen
- *Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106; and
| | - Galen D. Stucky
- *Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106; and
- To whom correspondence should be addressed. E-mail:
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44
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Madden DR, Safferling M. Baculoviral expression of an integral membrane protein for structural studies. Methods Mol Biol 2007; 363:39-57. [PMID: 17272836 DOI: 10.1007/978-1-59745-209-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The baculovirus system has proven successful for the expression of integral membrane proteins for structural studies. A recombinant baculovirus, in which the gene of interest is placed under the control of the late-stage polyhedrin promoter, serves as the starting point for viral expansion and protein expression studies. Using large-scale insect cell culture techniques together with a filter-binding assay for protein function, the conditions of expression, purification, and solubilization can be optimized. As applied to the glutamate receptor ion channel subunit GluR2, this approach yields milligram quantities of pure, active protein, which have been used for single-particle electron microscopic analysis of the receptor structure. Detergent exchange protocols are also discussed, as a prerequisite for two-dimensional crystallization trials.
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Affiliation(s)
- Dean R Madden
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH, USA
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45
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Schmidt-Krey I, Haase W, Mutucumarana V, Stafford DW, Kühlbrandt W. Two-dimensional crystallization of human vitamin K-dependent γ-glutamyl carboxylase. J Struct Biol 2007; 157:437-42. [PMID: 16979907 DOI: 10.1016/j.jsb.2006.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 08/08/2006] [Accepted: 08/08/2006] [Indexed: 10/24/2022]
Abstract
Planar-tubular two-dimensional (2D) crystals of human vitamin K-dependent gamma-glutamyl carboxylase grow in the presence of dimyristoyl phosphatidylcholine (DMPC). Surprisingly, these crystals form below the phase transition temperature of DMPC and at the unusually low molar lipid-to-protein (LPR) ratio of 1, while 2D crystals are conventionally grown above the phase transition temperature of the reconstituting lipid and significantly higher LPRs. The crystals are up to 0.75 microm in the shorter dimension of the planar tubes and at least 1 microm in length. Due to the planar-tubular nature of the crystals, two lattices are present. These are rotated by nearly 90 degrees in respect to each other. The ordered arrays exhibit p12(1) plane group symmetry with unit cell dimensions of a=83.7 A, b=76.6 A, gamma=91 degrees. Projection maps calculated from images of negatively stained and electron cryo-microscopy samples reveal the human vitamin K-dependent gamma-glutamyl carboxylase to be a monomer.
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Affiliation(s)
- Ingeborg Schmidt-Krey
- Georgia Institute of Technology, School of Biology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA.
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46
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Abstract
Although the examination of the protein data bank reveals an important backlog in the number of three-dimensional structures of membrane proteins, several recent successes are serving as preludes to what will become a very prosperous decade in this field. Systematic investigations of various factors affecting the stability of membrane proteins, as well as their potential to crystallize three dimensionally, have paved the way for such achievements. The importance of the role of detergents both at the level of purification and crystallization is now well established. In addition, the recognition of the protein-detergent complex as the entity to crystallize, as well as the understanding of its physical-chemical properties and discovery of factors affecting these, have permitted the design of better crystallization strategies. As a consequence of the various efforts in the field, new crystallization methods for membrane proteins are being implemented. These have already been successful and are expected to contribute significantly to the future successes. This chapter will review some basic principles in membrane protein crystallization and give an overview of the current state of the art in the field. Some practical guidelines to help the novice approach the problem of membrane protein crystallization from the initial step of protein purification to crystallogenesis will also be given.
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Affiliation(s)
- James Féthière
- European Molecular Biology Laboratory, Heidelberg, Germany
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47
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Gonçalves RP, Agnus G, Sens P, Houssin C, Bartenlian B, Scheuring S. Two-chamber AFM: probing membrane proteins separating two aqueous compartments. Nat Methods 2006; 3:1007-12. [PMID: 17060909 DOI: 10.1038/nmeth965] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 09/20/2006] [Indexed: 11/08/2022]
Abstract
Biological membranes compartmentalize and define physical borders of cells. They are crowded with membrane proteins that fulfill diverse crucial functions. About one-third of all genes in organisms code for, and the majority of drugs target, membrane proteins. To combine structure and function analysis of membrane proteins, we designed a two-chamber atomic force microscopy (AFM) setup that allows investigation of membranes spanned over nanowells, therefore separating two aqueous chambers. We imaged nonsupported surface layers (S layers) of Corynebacterium glutamicum at sufficient resolution to delineate a 15 A-wide protein pore. We probed the elastic and yield moduli of nonsupported membranes, giving access to the lateral interaction energy between proteins. We combined AFM and fluorescence microscopy to demonstrate the functionality of proteins in the setup by documenting proton pumping by Halobacterium salinarium purple membranes.
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48
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Tsai CJ, Ziegler C. Structure Determination of Secondary Transport Proteins by Electron Crystallography: Two-Dimensional Crystallization of the Betaine Uptake System BetP. J Mol Microbiol Biotechnol 2006; 10:197-207. [PMID: 16645315 DOI: 10.1159/000091565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Structure determination at high resolution is still a challenge for membrane proteins in general, but in particular for secondary transporters due to their highly dynamic nature. X-ray structures of ten secondary transporters have recently been determined, but a thorough understanding of transport mechanisms necessitates structures at different functional states. Electron cryo-microscopy of two-dimensional (2D) crystals offers an alternative to obtain structural information at intermediate resolution. Electron crystallography is a sophisticated way to study proteins in a natural membrane environment and to track conformational changes in situ. Furthermore, basic interactions between protein and lipids can be investigated. Projection and 3-dimensional maps of six secondary transporters from different families have been determined by electron crystallography of 2D crystals at a resolution of 8 A and better. In this review, we give an overview about the principles of 2D crystallization, in particular of secondary transporters, and summarize the important steps successfully applied to establish and improve the 2D crystallization of the high-affinity glycine betaine uptake system from Corynebacterium glutamicum, BetP.
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Affiliation(s)
- Ching-Ju Tsai
- Max Planck Institute of Biophysics Frankfurt, Department of Structural Biology, Frankfurt a. Main, Germany
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49
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Merino-Montero S, Domènech O, Montero MT, Hernández-Borrell J. Preliminary atomic force microscopy study of two-dimensional crystals of lactose permease from Escherichia coli. Biophys Chem 2006; 119:78-83. [PMID: 16098656 DOI: 10.1016/j.bpc.2005.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 07/15/2005] [Accepted: 07/15/2005] [Indexed: 10/25/2022]
Abstract
Lactose permease (LacY) of Escherichia coli is not only a paradigm for secondary transporters but also for difficulties in two-dimensional (2D) crystallization. In this work we present the progresses achieved in the observation of 2D crystals of wild-type LacY by atomic force microscopy (AFM). Crystals were obtained following reconstitution of LacY in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) liposomes. Proteolipid sheets (PLSs) 6.4 nm in height were obtained after spreading the samples onto mica. Observations were carried out in liquid medium and in contact mode (CM-AFM). When the crystalline surfaces of the PLSs were imaged regular packing arrangements were observed. The back-Fourier transformation revealed the existence of various orientations mostly consistent with crystals possessing p2 symmetry and unit-cell dimensions: a=13.15 nm, b=16.74 nm, gamma=116 degrees. The characteristics, size, and shape of the repetitive motif could be compatible with dimers of this protein. These preliminary results are compared and discussed with previously reported 2D crystals observed by electron microscopy.
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50
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Merino S, Domènech O, Díez-Pérez I, Sanz F, Montero MT, Hernández-Borrell J. Surface thermodynamic properties of monolayers versus reconstitution of a membrane protein in solid-supported bilayers. Colloids Surf B Biointerfaces 2005; 44:93-8. [PMID: 16023838 DOI: 10.1016/j.colsurfb.2005.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 05/31/2005] [Accepted: 06/02/2005] [Indexed: 10/25/2022]
Abstract
Atomic force microscopy (AFM) was used to study the influence of a membrane protein, lactose permease of Escherichia coli (LacY), on the surface spreading behavior and the features of self-assembled phospholipids bilayers on mica. The miscibility of phospholipids used, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), was investigated by surface pressure area isotherm measurements at the air-water interface. A composition with an equimolar proportion of POPC and DMPC was used to form the liposomes. Surface layers formed with DMPC:POPC (0.5:0.5, mol/mol) or LacY reconstituted in proteoliposomes with the same phospholipid composition were imaged by using AFM. When lactose permease was reconstituted in DMPC:POPC (0.5:0.5, mol/mol), self-assembled structures that remained firmly adsorbed onto the mica surface were observed. These sheets had an irregular shape and their upper layer was more corrugated than that obtained for the phospholipid matrix.
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Affiliation(s)
- Sandra Merino
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Spain
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