Electron cryomicroscopy of membrane proteins: Specimen preparation for two-dimensional crystals and single particles

Micron - Tập 42 - Trang 107-116 - 2011
Ingeborg Schmidt-Krey1, John L. Rubinstein2
1Georgia Institute of Technology, School of Biology, School of Chemistry and Biochemistry, 310 Ferst Drive, Rm. A118, Atlanta, GA 30332-0230, USA
2Molecular Structure and Function Program, The Hospital for Sick Children, and Departments of Biochemistry and Medical Biophysics, The University of Toronto, 555 University Avenue, Rm. 3330, Toronto, ON, Canada, M5G 1X8

Tài liệu tham khảo

Abrahams, 1994, Structure at 2.8Å resolution of F1 ATPase from bovine heart mitochondria, Nature, 370, 621, 10.1038/370621a0 Appel, 2009, Conformations of NhaA, the Na/H exchanger from Escherichia coli, in the pH-activated and ion-translocating states, J. Mol. Biol., 388, 659, 10.1016/j.jmb.2009.03.010 Arnold, 1998, Yeast mitochondrial F1F0-ATP synthase exists as a dimer: identification of three dimer-specific subunits, EMBO J., 17, 7170, 10.1093/emboj/17.24.7170 Auer, 1998, Three-dimensional map of the plasma membrane H+-ATPase in the open conformation, Nature, 392, 840, 10.1038/33967 Auer, 1999, Surface crystallisation of the plasma membrane H+-ATPase on a carbon support film for electron crystallography, J. Mol. Biol., 287, 961, 10.1006/jmbi.1999.2652 Avila-Sakar, 1994, Electron cryomicroscopy of Bacillus stearothermophilus 50 S ribosomal subunits crystallized on phospholipid monolayers, J. Mol. Biol., 239, 689, 10.1006/jmbi.1994.1406 Baker, 2010, The resolution dependence of optimal exposures in liquid nitrogen temperature electron cryomicroscopy of catalase crystals, J. Struct. Biol., 169, 431, 10.1016/j.jsb.2009.11.014 Berriman, 1994, Analysis of transient structures by cryo-microscopy combined with rapid mixing of spray droplets, Ultramicroscopy, 56, 241, 10.1016/0304-3991(94)90012-4 Brink, 1998, Evaluation of charging on macromolecules in electron cryomicroscopy, Ultramicroscopy, 72, 41, 10.1016/S0304-3991(97)00126-5 Brisson, 1999, Two-dimensional crystallization of proteins on lipid monolayers at the air–water interface and transfer to an electron microscopy grid, J. Cryst. Growth, 196, 456, 10.1016/S0022-0248(98)00834-3 Bueler, 2008, Location of subunit d in the peripheral stalk of the ATP synthase from Saccharomyces cerevisiae, Biochemistry, 47, 11804, 10.1021/bi801665x Cheng, 2007, Toward automated screening of two-dimensional crystals, J. Struct. Biol., 160, 324, 10.1016/j.jsb.2007.09.012 Chiu, 1997, Electron crystallography of macromolecular periodic arrays on phospholipid monolayers, Adv. Biophys., 34, 161, 10.1016/S0065-227X(97)89638-4 Crowther, 1996, MRC image processing programs, J. Struct. Biol., 116, 9, 10.1006/jsbi.1996.0003 Downing, 1992, Automatic focus correction for spot-scan imaging of tilted specimens, Ultramicroscopy, 46, 199, 10.1016/0304-3991(92)90015-C Downing, 1986, Improvement in high resolution image quality of radiation-sensitive specimens achieved with reduced spot size of the electron beam, Ultramicroscopy, 20, 269, 10.1016/0304-3991(86)90191-9 Dryden, 2009, Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals, Protein Sci., 18, 2629, 10.1002/pro.272 Fezoua-Boubegtiten, 2010, Determination of molecular groups involved in the interaction of Annexin A5 with lipid membrane models at the air-water interface, Biochim. Biophys. Act. - Biomembr., 1798, 1204, 10.1016/j.bbamem.2010.03.014 Fischer, 2004, Average protein density is a molecular-weight-dependent function, Protein Sci., 13, 2825, 10.1110/ps.04688204 Fromherz, 1971, Electron microscopic studies of lipid protein films, Nature, 231, 267, 10.1038/231267a0 Fujiyoshi, 1998, The structural study of membrane proteins by electron crystallography, Adv. Biophys., 35, 25, 10.1016/S0065-227X(98)80003-8 Fujiyoshi, 2008, Electron crystallography of proteins in membranes, Curr. Opin. Struct. Biol., 18, 587, 10.1016/j.sbi.2008.07.005 Ganong, 1989, Application of nonionic polyoxyethylebe detergents in studies of phosphatidylionsitol kinase, Anal. Biochem., 179, 66, 10.1016/0003-2697(89)90201-7 Gibbons, 2000, The structure of the central stalk in bovine F1-ATPase at 2.4Å resolution, Nat. Struct. Biol., 7, 1055, 10.1038/80981 Gipson, 2007, 2dx – User-friendly image processing for 2D crystals, J. Struct. Biol., 157, 64, 10.1016/j.jsb.2006.07.020 Glaeser, 1992, Specimen flatness of thin crystalline arrays: influence of the substrate, Ultramicroscopy, 46, 33, 10.1016/0304-3991(92)90006-6 Glaeser, 2008, Retrospective: radiation damage and its associated “Information Limitations”, J. Struct. Biol., 163, 271, 10.1016/j.jsb.2008.06.001 Glaeser, 2008, Cryo-electron microscopy of biological nanostructures, Phys. Today, 61, 48, 10.1063/1.2835153 Gonen, 2005, Lipid–protein interactions in double layered two dimensional crystals of AQP0, Nature, 438, 633, 10.1038/nature04321 Gyobu, 2004, Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich technique, J. Struct. Biol., 146, 325, 10.1016/j.jsb.2004.01.012 Han, 1994, Specimen flatness of glucose-embedded biological materials for electron crystallography is affected significantly by the choice of carbon evaporation stock, Ultramicroscopy, 55, 1, 10.1016/0304-3991(94)90073-6 Hankamer, 2007, Electron crystallography of membrane proteins, J. Struct. Biol., 160, 263, 10.1016/j.jsb.2007.11.001 Henderson, 1975, Three-dimensional model of purple membrane obtained by electron microscopy, Nature, 257, 28, 10.1038/257028a0 Henderson, 1986, Structure of purple membrane from halobacterium halobium: recording, measurement and evaluation of electron micrographs at 3.5Å resolution, Ultramicroscopy, 19, 147, 10.1016/0304-3991(86)90203-2 Henderson, 1990, Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy, J. Mol. Biol., 213, 899, 10.1016/S0022-2836(05)80271-2 Hite, 2007, Revival of electron crystallography, Curr. Opin. Struct. Biol., 17, 389, 10.1016/j.sbi.2007.06.006 Isoda, 2004, A self-assembled molecular rectifier: two-dimensional crystals of cytochrome c formed on a flavolipid monolayer, Thin Solid Films, 468, 255, 10.1016/j.tsf.2004.04.027 Jap, 1991, Structural architecture of an outer membrane channel as determined by electron crystallography, Nature, 350, 167, 10.1038/350167a0 Kelly, 2008, The affinity grid: a pre-fabricated EM grid for monolayer purification, J. Mol. Biol., 382, 423, 10.1016/j.jmb.2008.07.023 Kelly, 2008, Monolayer purification: a rapid method for isolating protein complexes for single-particle electron microscopy, Proc. Natl. Acad. Sci. USA, 105, 4703, 10.1073/pnas.0800867105 Koning, 2003, Preparation of flat carbon support films, Ultramicroscopy, 94, 183, 10.1016/S0304-3991(02)00263-2 Kubalek, 1991, Improved transfer of two-dimensional crystals from the air/water interface to specimen support grids for high-resolution analysis by electron microscopy, Ultramicroscopy, 35, 295, 10.1016/0304-3991(91)90082-H Kühlbrandt, 1989, Two-dimensional structure of plant light-harvesting complex at 3.7Å resolution by electron crystallography, J. Mol. Biol., 207, 823, 10.1016/0022-2836(89)90247-7 Kühlbrandt, 2003, 253 Lau, 2008, Cryo-EM structure of the yeast ATP synthase, J. Mol. Biol., 382, 1256, 10.1016/j.jmb.2008.08.014 Lau, 2010, Structure of intact Thermus thermophilus V-ATPase by cryo-EM reveals organization of the membrane-bound VO motor, Proc. Natl. Acad. Sci. USA, 107, 1367, 10.1073/pnas.0911085107 le Maire, 2000, Interaction of membrane proteins and lipids with solubilizing detergents, Biochim. Biophys. Acta, 1508, 86, 10.1016/S0304-4157(00)00010-1 Lebeau, 2001, Two-dimensional crystallization of a membrane protein on a detergent-resistant monolayer, J. Mol. Biol., 308, 639, 10.1006/jmbi.2001.4629 Mancheño, 2006, A complementary microscopy analysis of Sticholysin II crystals on lipid films: atomic force and transmission electron characterizations, Biophys. Chem., 119, 219, 10.1016/j.bpc.2005.09.021 Meier, 2005, Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus, Science, 308, 659, 10.1126/science.1111199 Mishima, 1985, An apparent first-order transition between two amorphous phases of ice induced by pressure, Nature, 314, 76, 10.1038/314076a0 Mitra, 2005, Structure of the E. coli protein-conducting channel bound to a translating ribosome, Nature, 438, 318, 10.1038/nature04133 Müller, 2008, What transmission electron microscopes can visualize now and in the future, J. Struct. Biol., 163, 235, 10.1016/j.jsb.2008.05.008 Norville, 2007, 7Å projection map of the S-layer protein sbpA obtained with trehalose-embedded monolayer crystals, J. Struct. Biol., 160, 313, 10.1016/j.jsb.2007.06.002 Oesterhelt, 1971, Rhodposin-like protein from the purple membrane of Halobacterium halobium, Nat. New Biol., 233, 149, 10.1038/newbio233149a0 Pomfret, 2007, Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases, J. Struct. Biol., 157, 106, 10.1016/j.jsb.2006.05.012 Reichow, 2009, Lipid–protein interactions probed by electron crystallography, Curr. Opin. Struct. Biol., 19, 560, 10.1016/j.sbi.2009.07.012 Ren, 2000, Three-dimensional fold of the human AQP1 water channel determined at 4Å resolution by electron crystallography of two-dimensional crystals embedded in ice, J. Mol. Biol., 301, 369, 10.1006/jmbi.2000.3949 Rhinow, 2008, Electron cryo-microscopy of biological specimens on conductive titanium–silicon metal glass films, Ultramicroscopy, 108, 698, 10.1016/j.ultramic.2007.11.005 Richter, 2005, Following the formation of supported lipid bilayers on mica: a study combining AFM, QCM-D, and Ellipsometry, Biophys. J., 88, 3422, 10.1529/biophysj.104.053728 Rubinstein, 2005, ATP synthase from Saccharomyces cerevisiae: location of subunit h in the peripheral stalk region, J. Mol. Biol., 345, 513, 10.1016/j.jmb.2004.10.060 Rubinstein, 2002, ATP synthase from Saccharomyces cerevisiae: location of the OSCP subunit in the peripheral stalk region, J. Mol. Biol., 321, 613, 10.1016/S0022-2836(02)00671-X Rubinstein, 2003, Structure of the mitochondrial ATP synthase by electron cryomicroscopy, EMBO J., 22, 6182, 10.1093/emboj/cdg608 Rubinstein, 2007, Structural analysis of membrane protein complexes by single particle electron microscopy, Methods, 41, 409, 10.1016/j.ymeth.2006.07.019 Serysheva, 2008, Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel, Proc. Natl. Acad. Sci. USA, 105, 9610, 10.1073/pnas.0803189105 Schmidt-Krey, 2007, Electron crystallography of membrane proteins: two-dimensional crystallization and screening by electron microscopy, Methods, 41, 417, 10.1016/j.ymeth.2006.07.011 Schmidt-Krey, 2004, Human leukotriene C4 synthase at 4.5Å resolution in projection, Structure, 12, 2009, 10.1016/j.str.2004.08.008 Schmidt-Krey, 2007, Two-dimensional crystallization of human vitamin K-dependent γ-glutamyl carboxylase, J. Struct. Biol., 157, 437, 10.1016/j.jsb.2006.08.002 Stahlberg, 2001, Twod-imensional crystals: a powerful approach to assess structure, function and dynamics of membrane proteins, FEBS Lett., 504, 166, 10.1016/S0014-5793(01)02746-6 Stock, 1999, Molecular architecture of the rotary motor in ATP synthase, Science, 286, 1700, 10.1126/science.286.5445.1700 Subramaniam, 2000, Crystallographic analysis of protein conformational changes in the bacteriorhodopsin photocycle, Biochim. Biophys. Acta, 1460, 157, 10.1016/S0005-2728(00)00136-5 Tani, 2009, Mechanism of aquaporin-4's fast and highly selective water conduction and proton exclusion, J. Mol. Biol., 389, 694, 10.1016/j.jmb.2009.04.049 Taylor, 1974, Electron diffraction of frozen hydrated protein crystals, Science, 186, 1036, 10.1126/science.186.4168.1036 Taylor, 2008, Retrospective on the early development of cryoelectron microscopy of macromolecules and a prospective on opportunities for the future, J. Struct. Biol., 163, 214, 10.1016/j.jsb.2008.06.004 Timmins, 1988, A physical characterization of some detergents of potential use for membrane protein crystallization, FEBS Lett., 238, 361, 10.1016/0014-5793(88)80513-1 Tocilj, 2008, Bacterial polysaccharide co-polymerases share a common framework for control of polymer length, Nat. Struct. Mol. Biol., 15, 130, 10.1038/nsmb.1374 Tribet, 1996, Amphipols: polymers that keep membrane proteins soluble in aqueous solutions, Proc. Natl. Acad. Sci. USA, 93, 15047, 10.1073/pnas.93.26.15047 Unger, 1999, Three-dimensional structure of a recombinant gap junction membrane channel, Science, 283, 1176, 10.1126/science.283.5405.1176 Unwin, 1975, Molecular structure determination by electron microscope of unstained specimens, J. Mol. Biol., 94, 425, 10.1016/0022-2836(75)90212-0 Unwin, 2005, Refined structure of the nicotinic acetylcholine receptor at 4Å resolution, J. Mol. Biol., 346, 967, 10.1016/j.jmb.2004.12.031 Uzgiris, 1983, Two-dimensional crystallization technique for imaging macromolecules, with application to antigen-antibody-complement complexes, Nature, 301, 125, 10.1038/301125a0 Vénien-Bryan, 1998, Characterization of the growth of 2D protein crystals on a lipid monolayer by ellipsometry and rigidity measurements coupled to electron microscopy, Biophys. J., 74, 2649, 10.1016/S0006-3495(98)77970-6 Vonck, 2002, Molecular architecture of the undecameric rotor of a bacterial Na+-ATP synthase, J. Mol. Biol., 321, 307, 10.1016/S0022-2836(02)00597-1 Walian, 1990, Three-dimensional electron diffraction of PhoE porin to 2.8resolution, J. Mol. Biol., 215, 429, 10.1016/S0022-2836(05)80362-6 Wang, 1991, High-resolution electron crystallography of light-harvesting chlorophyll a/b-protein complex in three different media, J. Mol. Biol., 217, 691, 10.1016/0022-2836(91)90526-C Wang, 2009, Structure of the BK potassium channel in a lipid membrane from electron cryomicroscopy, Nature, 461, 292, 10.1038/nature08291 Wilkens, 2000, F1F0-ATP synthase-stalking mind and imagination, J. Bioenerg. Biomembr., 32, 333, 10.1023/A:1005567717821 Williams, 2008, Cryo-EM structure of the DNA-dependent protein kinase catalytic subunit at subnanometer resolution reveals α helices and insight into DNA binding, Strucutre, 15, 468, 10.1016/j.str.2007.12.014 Zeng, 2007, Automatic lattice determination for two-dimensional crystal images, J. Struct. Biol., 160, 353, 10.1016/j.jsb.2007.08.008