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Preparation of Proteins and Macromolecular Assemblies for Cryo-electron Microscopy

  • Lou Brillault
  • Michael J. LandsbergEmail author
Protocol
  • 920 Downloads
Part of the Methods in Molecular Biology book series (MIMB, volume 2073)

Abstract

Cryo-electron microscopy has become popular as the penultimate step on the road to structure determination for many proteins and macromolecular assemblies. The process of obtaining high-resolution images of a purified biomolecular complex in an electron microscope often follows a long, and in many cases exhaustive screening process in which many iterative rounds of protein purification are employed and the sample preparation procedure progressively re-evaluated in order to improve the distribution of particles visualized under the electron microscope, and thus maximize the opportunity for high-resolution structure determination. Typically, negative stain electron microscopy is employed to obtain a preliminary assessment of the sample quality, followed by cryo-EM which first requires the identification of optimal vitrification conditions. The original methods for frozen-hydrated specimen preparation developed over 40 years ago still enjoy widespread use today, although recent developments have set the scene for a future where more systematic and high-throughput approaches to the preparation of vitrified biomolecular complexes may be routinely employed. Here we summarize current approaches and ongoing innovations for the preparation of frozen-hydrated single particle specimens for cryo-EM, highlighting some of the commonly encountered problems and approaches that may help overcome these.

Key words

Macromolecular assemblies Protein complexes Negative staining Cryo-EM Plunge-freezing Frozen-hydrated specimens 

References

  1. 1.
    Ruska H, Borries BY, Ruska E (1939) Die Bedeutung der Ubermikrokopie fur die Virusforschung. Arch Gesanch Virusforsh 1:155–169CrossRefGoogle Scholar
  2. 2.
    Luria SE, Delbruck M, Anderson TF (1943) Electron microscope studies of bacterial viruses. J Bacteriol 46(1):57–77CrossRefGoogle Scholar
  3. 3.
    Brenner S, Horne RW (1959) A negative staining method for high resolution electron microscopy of viruses. Biochim Biophys Acta 34:103–110.  https://doi.org/10.1016/0006-3002(59)90237-9CrossRefGoogle Scholar
  4. 4.
    Bremer A, Henn C, Engel A, Baumeister W, Aebi U (1992) Has negative staining still a place in biomacromolecular electron microsocpy? Ultamicroscopy 46(1–4):85–111CrossRefGoogle Scholar
  5. 5.
    Scarff CA, Fuller MJG, Thompson RF, Iadaza MG (2018) Variations on negative stain electron microscopy methods: tools for tackling challenging systems. J Vis Exp 132.  https://doi.org/10.3791/57199
  6. 6.
    Frank J (1996) Electron microscopy of macromolecular assemblies. In: Three-dimensional electron microscopy of macromolecular assemblies, vol 1. Science Direct, Academic, Cambridge, MA, pp 12–53CrossRefGoogle Scholar
  7. 7.
    Dubochet J, Chang JJ, Freeman R, Lepault J, McDowall AW (1982) Frozen aqueous suspensions. Ultramicroscopy 10(1–2):55–62.  https://doi.org/10.1016/0304-3991(82)90187-5CrossRefGoogle Scholar
  8. 8.
    Taylor KA, Glaeser RM (1976) Electron microscopy of frozen hydrated biological specimens. J Ultra Mol Struct Res 55:448–456CrossRefGoogle Scholar
  9. 9.
    Dubochet J, Adrian M, Chang JJ, Homo JC, Lepault J, McDowall AW, Schultz P (1988) Cryo-electron microscopy of vitrified specimens. Q Rev Biophys 21(2):129–228CrossRefGoogle Scholar
  10. 10.
    Adrian M, Dubochet J, Lepault J, McDowall AW (1984) Cryo-electron microscopy of viruses. Nature 308:32–36.  https://doi.org/10.1038/308032a0CrossRefGoogle Scholar
  11. 11.
    Downing KH, McCartney MR, Glaeser RM (2004) Experimental characterization and mitigation of specimen charging on thin films with one conducting layer. Microsc Microanal 10(06):783–789.  https://doi.org/10.1017/s143192760404067xCrossRefGoogle Scholar
  12. 12.
    Glaeser RM, Downing KH (2004) Specimen charging on thin films with one conducting layer: discussion of physical principles. Microsc Microanal 10(06):790–796.  https://doi.org/10.1017/s1431927604040668CrossRefGoogle Scholar
  13. 13.
    Brink J, Gross H, Tittmann P, Sherman MB, Chiu W (1998) Reduction of charging in protein electron cryomicroscopy. J Microsc 191(1):67–73CrossRefGoogle Scholar
  14. 14.
    Brink J, Sherman MB, Berriman J, Chiu W (1998) Evalution of charging on macromolecules in electron cryomicroscopy. Ultamicroscopy 72(1–2):41–52CrossRefGoogle Scholar
  15. 15.
    Karuppasamy M, Karimi Nejadasl F, Vulovic M, Koster AJ, Ravelli RB (2011) Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate. J Synchrotron Radiat 18(3):398–412.  https://doi.org/10.1107/S090904951100820XCrossRefGoogle Scholar
  16. 16.
    Glaeser RM (2008) Retrospective: radiation damage and its associated “information limitations”. J Struct Biol 163(3):271–276.  https://doi.org/10.1016/j.jsb.2008.06.001CrossRefGoogle Scholar
  17. 17.
    Henderson R, Glaeser RM (1985) Quantitative analysis of image contrast in electron micrographs of beam-sensitive crystals. Ultamicroscopy 16(2):139–150CrossRefGoogle Scholar
  18. 18.
    Chiu W, Downing KH, Dubochet J, Glaeser RM, Heide HG, Knapek E, Kopf D, Lamvik MK, Lepault J, Robertson JD, Zemlin F (1987) Cryoprotection in electron microscopy. J Microsc 141(3):385–391Google Scholar
  19. 19.
    Carlson DB, Evans JE (2012) Low-dose imaging techniques for transmission electron microscopy. In: Khan M (ed) The transmission electron microscope, vol 1. InTechGoogle Scholar
  20. 20.
    Sun J, Li H (2010) How to operate a cryo-electron microscope. In: Cryo-EM part A sample preparation and data collection. Methods Enzymol 481:231–249.  https://doi.org/10.1016/S0076-6879(10)81010-9CrossRefGoogle Scholar
  21. 21.
    Vinothkumar KR, Henderson R (2016) Single particle electron cryomicroscopy: trends, issues and future perspective. Q Rev Biophys 49:e13.  https://doi.org/10.1017/S0033583516000068CrossRefGoogle Scholar
  22. 22.
    Isakozawa S, Nagaoki I, Watabe A, Nagakubo Y, Saito N, Matsumoto H, Zhang XF, Taniguchi Y, Baba N (2016) Design of a 300-kV gas environmental transmission electron microscope equipped with a cold field emission gun. Microscopy (Oxf) 65(4):353–362.  https://doi.org/10.1093/jmicro/dfw015CrossRefGoogle Scholar
  23. 23.
    Kohno Y, Okunishi E, Tomita T, Ishikawa I, Kaneyama T, Ohkura Y, Kondo Y, Isabell TC (2010) Development of a cold field-emission gun for a 200kV atomic resolution electron microscope. Microsc Microanal 27(7):S9–S13Google Scholar
  24. 24.
    Grimm R, Typke D, Baumeister W (1998) Improving image quality by zero-loss energy filtering: quantitative assessment by menas of image cross-correlation. J Microsc 190(3):339–349CrossRefGoogle Scholar
  25. 25.
    Grogger W, Varela M, Ristau R, Schaffer B, Hofer F, Krishnan KM (2005) Energy-filtering transmission electron microscopy on the nanometer length scale. J Electron Spectrosc Relat Phenom 143(2–3):139–147.  https://doi.org/10.1016/j.elspec.2004.09.028CrossRefGoogle Scholar
  26. 26.
    Gubbens A, Barfels M, Trevor C, Twesten R, Mooney P, Thomas PJ, Menon N, Kraus B, Mao C, McGinn B (2010) The GIF quantum, a next generation post-column imaging energy filter. Ultramicroscopy 110(8):962–970.  https://doi.org/10.1016/j.ultramic.2010.01.009CrossRefGoogle Scholar
  27. 27.
    Rhinow D, Buenfeld M, Weber NE, Beyer A, Golzhauser A, Kuhlbrandt W, Hampp N, Turchanin A (2011) Energy-filtered transmission electron microscopy of biological samples on highly transparent carbon nanomembranes. Ultramicroscopy 111(5):342–349.  https://doi.org/10.1016/j.ultramic.2011.01.028CrossRefGoogle Scholar
  28. 28.
    Schroder RR, Hofmann W, Menetret JF (1990) Zero-loss energy filtering as improved imaging mode in cryoelectronmicroscopy of frozen-hydrated specimens. J Struct Biol 105(1–3):28–34CrossRefGoogle Scholar
  29. 29.
    Tsuno K (2004) Evaluation of in-column energy filters for analytical electron microscopes. Nucl Instrum Methods 519(1–2):286–296.  https://doi.org/10.1016/j.nima.2003.11.165CrossRefGoogle Scholar
  30. 30.
    Danev R, Baumeister W (2016) Cryo-EM single particle analysis with the volta phase plate. elife 5.  https://doi.org/10.7554/eLife.13046
  31. 31.
    Nagayama K, Danev R (2008) Phase contrast electron microscopy: development of thin-film phase plates and biological applications. Philos Trans R Soc Lond Ser B Biol Sci 363(1500):2153–2162.  https://doi.org/10.1098/rstb.2008.2268CrossRefGoogle Scholar
  32. 32.
    McMullan G, Faruqi AR, Clare D, Henderson R (2014) Comparison of optimal performance at 300 keV of three direct electron detectors for use in low dose electron microscopy. Ultramicroscopy 147:156–163.  https://doi.org/10.1016/j.ultramic.2014.08.002CrossRefGoogle Scholar
  33. 33.
    McMullan G, Faruqi AR, Henderson R, Guerrini N, Turchetta R, Jacobs A, van Hoften G (2009) Experimental observation of the improvement in MTF from backthinning a CMOS direct electron detector. Ultramicroscopy 109(9):1144–1147.  https://doi.org/10.1016/j.ultramic.2009.05.005CrossRefGoogle Scholar
  34. 34.
    Ruskin RS, Yu Z, Grigorieff N (2013) Quantitative characterization of electron detectors for transmission electron microscopy. J Struct Biol 184(3):385–393.  https://doi.org/10.1016/j.jsb.2013.10.016CrossRefGoogle Scholar
  35. 35.
    Brilot AF, Chen JZ, Cheng A, Pan J, Harrison SC, Potter CS, Carragher B, Henderson R, Grigorieff N (2012) Beam-induced motion of vitrified specimen on holey carbon film. J Struct Biol 177(3):630–637.  https://doi.org/10.1016/j.jsb.2012.02.003CrossRefGoogle Scholar
  36. 36.
    Moreau MJJ, Morin I, Askin SP, Cooper A, Moreland NJ, Vasudevan SG, Schaeffer PM (2012) Rapid determination of protein stability and ligand binding by differential scanning fluorimetry of GFP-tagged proteins. RSC Adv 2(31).  https://doi.org/10.1039/c2ra22368f
  37. 37.
    Ericsson UB, Hallberg BM, Detitta GT, Dekker N, Nordlund P (2006) Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal Biochem 357(2):289–298.  https://doi.org/10.1016/j.ab.2006.07.027CrossRefGoogle Scholar
  38. 38.
    Chari A, Haselbach D, Kirves JM, Ohmer J, Paknia E, Fischer N, Ganichkin O, Moller V, Frye JJ, Petzold G, Jarvis M, Tietzel M, Grimm C, Peters JM, Schulman BA, Tittmann K, Markl J, Fischer U, Stark H (2015) ProteoPlex: stability optimization of macromolecular complexes by sparse-matrix screening of chemical space. Nat Methods 12(9):859–865.  https://doi.org/10.1038/nmeth.3493CrossRefGoogle Scholar
  39. 39.
    He Y, Fang J, Taatjes DJ, Nogales E (2013) Structural visualization of key steps in human transcription initiation. Nature 495(7442):481–486.  https://doi.org/10.1038/nature11991CrossRefGoogle Scholar
  40. 40.
    Monroe N, Han H, Shen PS, Sundquist WI, Hill CP (2017) Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase. elife 6.  https://doi.org/10.7554/eLife.24487
  41. 41.
    Kastner B, Fischer N, Golas MM, Sander B, Dube P, Boehringer D, Hartmuth K, Deckert J, Hauer F, Wolf E, Uchtenhagen H, Urlaub H, Herzog F, Peters JM, Poerschke D, Luhrmann R, Stark H (2008) GraFix: sample preparation for single-particle electron cryomicroscopy. Nat Methods 5(1):53–55.  https://doi.org/10.1038/nmeth1139CrossRefGoogle Scholar
  42. 42.
    Stark H (2010) GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM. Methos Enzymol 481:109–126.  https://doi.org/10.1016/s0076-6879(10)81005-5CrossRefGoogle Scholar
  43. 43.
    Singh SK, Sigworth FJ (2015) Cryo-EM: spinning the micelles away. Structure 23(9):1561.  https://doi.org/10.1016/j.str.2015.08.001CrossRefGoogle Scholar
  44. 44.
    Hauer F, Gerle C, Fischer N, Oshima A, Shinzawa-Itoh K, Shimada S, Yokoyama K, Fujiyoshi Y, Stark H (2015) GraDeR: membrane protein complex preparation for single-particle cryo-EM. Structure 23(9):1769–1775.  https://doi.org/10.1016/j.str.2015.06.029CrossRefGoogle Scholar
  45. 45.
    Gewering T, Januliene D, Ries AB, Moeller A (2018) Know your detergents: a case study on detergent background in negative stain electron microscopy. J Struct Biol 203(3):242–246.  https://doi.org/10.1016/j.jsb.2018.05.008CrossRefGoogle Scholar
  46. 46.
    Tribet C, Mills DJ, Haider M, Popot J-L (1998) Scanning transmission electron microscopy study of the molecular mass of amphipol/cytochrome b6f complexes. Biochimie 80(5–6):475–482.  https://doi.org/10.1016/S0300-9084(00)80014-0CrossRefGoogle Scholar
  47. 47.
    Popot J-L (2018) The use of amphipols for electron microscopy. In: Membrane proteins in aqueous solutions: from detergents to amphipols. Springer, Cham.  https://doi.org/10.1007/978-3-319-73148-3_12CrossRefGoogle Scholar
  48. 48.
    Liao M, Cao E, Julius D, Cheng Y (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504(7478):107–112.  https://doi.org/10.1038/nature12822CrossRefGoogle Scholar
  49. 49.
    Gao Y, Cao E, Julius D, Cheng Y (2016) TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. Nature 534(7607):347–351.  https://doi.org/10.1038/nature17964CrossRefGoogle Scholar
  50. 50.
    Civjan NR, Bayburt TH, Schuler MA, Sligar SG (2003) Direct solubilization of heterologously expressed membrane proteins by incorporation into nanoscale lipid bilayers. BioTechniques 35(3):556–560CrossRefGoogle Scholar
  51. 51.
    Bayburt TH, Carlson JW, Sligar SG (1998) Reconstitution and imaging of a membrane protein in a nanometer-size phospholipid bilayer. J Struct Biol 123(1):37–44CrossRefGoogle Scholar
  52. 52.
    Machen AJ, Akkaladevi N, Trecazzi C, O’Neil PT, Mukherjee S, Qi Y, Dillard R, Im W, Gogol EP, White TA, Fisher MT (2017) Asymmetric cryo-EM structure of anthrax toxin protective antigen pore with lethal factor N-terminal domain. Toxins (Basel) 9(10):E298.  https://doi.org/10.3390/toxins9100298CrossRefGoogle Scholar
  53. 53.
    Zhang S, Li N, Zeng W, Gao N, Yang M (2017) Cryo-EM structures of the mammalian endo-lysosomal TRPML1 channel elucidate the combined regulation mechanism. Protein Cell 8(11):834–847.  https://doi.org/10.1007/s13238-017-0476-5CrossRefGoogle Scholar
  54. 54.
    Martinez D, Decossas M, Kowal J, Frey L, Stahlberg H, Dufourc EJ, Riek R, Habenstain B, Bibow S, Loquet A (2017) Lipid internal dynamics probed in nanodiscs. ChemPhysChem 18(19):2651–2657.  https://doi.org/10.1002/cphc.201700450CrossRefGoogle Scholar
  55. 55.
    Stam NJ, Wilkens S (2017) Structure of the lipid nanodisc-reconstituted vacuolar ATPase proton channel: definition of the interaction of rotor and stator and implication for enzyme regulation by reversible dissociation. J Biol Chem 292(5):1749–1761.  https://doi.org/10.1074/jbc.M116.766790CrossRefGoogle Scholar
  56. 56.
    Gatsogiannis C, Merino F, Prumbaum D, Roderer D, Leidreiter F, Meusch D, Raunser S (2016) Membrane insertion of a Tc toxin in near-atomic detail. Nat Struct Mol Biol 23(10):884–890.  https://doi.org/10.1038/nsmb.3281CrossRefGoogle Scholar
  57. 57.
    Frauenfeld J, Loving R, Armache JP, Sonnen AF, Guettou F, Moberg P, Zhu L, Jegerschold C, Flayhan A, Briggs JA, Garoff H, Low C, Cheng Y, Nordlund P (2016) A saposin-lipoprotein nanoparticle system for membrane proteins. Nat Methods 13(4):345–351.  https://doi.org/10.1038/nmeth.3801CrossRefGoogle Scholar
  58. 58.
    Lee SC, Knowles TJ, Postis VL, Jamshad M, Parslow RA, Lin YP, Goldman A, Sridhar P, Overduin M, Muench SP, Dafforn TR (2016) A method for detergent-free isolation of membrane proteins in their local lipid environment. Nat Protoc 11(7):1149–1162.  https://doi.org/10.1038/nprot.2016.070CrossRefGoogle Scholar
  59. 59.
    Thompson RF, Walker M, Siebert CA, Muench SP, Ranson NA (2016) An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology. Methods 100:3–15.  https://doi.org/10.1016/j.ymeth.2016.02.017CrossRefGoogle Scholar
  60. 60.
    Marlon L (1976) Early application of electron microscopy to biology. Ultamicroscopy 1:281–296CrossRefGoogle Scholar
  61. 61.
    Bradley DE (1954) Evaporated carbon films for use in electron microscopy. Br J Appl Phys 5:65CrossRefGoogle Scholar
  62. 62.
    Russo CJ, Passmore LA (2016) Progress towards an optimal specimen support for electron cryomicroscopy. Curr Opin Struct Biol 37:81–89.  https://doi.org/10.1016/j.sbi.2015.12.007CrossRefGoogle Scholar
  63. 63.
    Tivol WF, Briegel A, Jensen GJ (2008) An improved cryogen for plunge freezing. Microsc Microanal 14(5):375–379.  https://doi.org/10.1017/S1431927608080781CrossRefGoogle Scholar
  64. 64.
    Dobro MJ, Melanson LA, Jensen GJ, McDowall AW (2010) Plunge freezing for electron cryomicroscopy. Methods Enzymol 481:63–82.  https://doi.org/10.1016/s0076-6879(10)81003-1CrossRefGoogle Scholar
  65. 65.
    Trurnit HJ (1960) A theory and method for the spreading of protein monolayers. J Colloid Sci 15(1):1–13CrossRefGoogle Scholar
  66. 66.
    Glaeser RM, Han BG, Csencsits R, Killilea A, Pulk A, Cate JH (2016) Factors that influence the formation and stability of thin, cryo-EM specimens. Biophys J 110(4):749–755.  https://doi.org/10.1016/j.bpj.2015.07.050CrossRefGoogle Scholar
  67. 67.
    Kemmerling S, Ziegler J, Schweighauser G, Arnold SA, Giss D, Muller SA, Ringler P, Goldie KN, Goedecke N, Hierlemann A, Stahlberg H, Engel A, Braun T (2012) Connecting mu-fluidics to electron microscopy. J Struct Biol 177(1):128–134.  https://doi.org/10.1016/j.jsb.2011.11.001CrossRefGoogle Scholar
  68. 68.
    Isabell TC, Fischione PE, O’Keefe C, Guruz MU, Dravid VP (1999) Plasma cleaning and its applications for electron microscopy. Microsc Microanal 5(2):126–135.  https://doi.org/10.1017/S1431927699000094CrossRefGoogle Scholar
  69. 69.
    Quispe J, Damiano J, Mick SE, Nackashi DP, Fellmann D, Ajero TG, Carragher B, Potter CS (2007) An improved holey carbon film for cryo-electron microscopy. Microsc Microanal 13(5):365–371.  https://doi.org/10.1017/S1431927607070791CrossRefGoogle Scholar
  70. 70.
    Russo CJ, Passmore LA (2014) Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas. Nat Methods 11(6):649–652.  https://doi.org/10.1038/nmeth.2931CrossRefGoogle Scholar
  71. 71.
    Grassucci RA, Taylor DJ, Frank J (2007) Preparation of macromolecular complexes for cryo-electron microscopy. Nat Protoc 2(12):3239–3246.  https://doi.org/10.1038/nprot.2007.452CrossRefGoogle Scholar
  72. 72.
    Frank J (1996) Introduction. In: Three-dimensional electron microscopy of macromolecular assemblies, vol 1. Science Direct, Academic, Cambridge, MA, pp 1–11Google Scholar
  73. 73.
    Sauerwald A, Sandin S, Cristofari G, Scheres SHW, Lingner J, Rhodes D (2013) Structure of active dimeric human telomerase. Nat Struct Mol Biol 20(4):454–460.  https://doi.org/10.1038/nsmb.2530CrossRefGoogle Scholar
  74. 74.
    Chen PH, Unger V, He X (2015) Structure of full-length human PDGFRbeta bound to its activating ligand PDGF-B as determined by negative-stain electron microscopy. J Mol Biol 427(24):3921–3934.  https://doi.org/10.1016/j.jmb.2015.10.003CrossRefGoogle Scholar
  75. 75.
    Tegunov D, Cramer P (2018) Real-time cryo-EM data pre-processing with Warp. BioRxiv.  https://doi.org/10.1101/338558
  76. 76.
    Reboul CF, Kiesewetter S, Eager M, Belousoff M, Cui T, De Sterck H, Elmlund D, Elmlund H (2018) Rapid near-atomic resolution single-particle 3D reconstruction with SIMPLE. J Struct Biol.  https://doi.org/10.1016/j.jsb.2018.08.005
  77. 77.
    Penczek PA, Radermacher M, Frank J (1992) Three-dimensional reconstruction of single particles embedded in ice. Ultamicroscopy 40(1):33–53.  https://doi.org/10.1016/0304-3991(92)90233-ACrossRefGoogle Scholar
  78. 78.
    Frank J (1996) Three-dimensional reconstruction. In: Three-dimensional electron microscopy of macromolecular assemblies, vol 1. Science Direct, Academic, Cambridge, MAGoogle Scholar
  79. 79.
    D’Imprima E, Floris D, Joppe M, Sánchez R, Grininger M, Kühlbrandt W (2018) The deadly touch: protein denaturation at the water-air interface and how to prevent it. BioRxiv.  https://doi.org/10.1101/400432
  80. 80.
    Noble AJ, Wei H, Dandey VP, Zhang Z, Potter CS, Carragher B (2018) Reducing effects of particle adsorption to the air-water interface in cryoEM. BioRxiv.  https://doi.org/10.1101/288340
  81. 81.
    Raffaini G, Ganazzoli F (2010) Protein adsorption on a hydrophobic surface: a molecular dynamics study of lysozyme on graphite. Langmuir 26(8):5679–5689.  https://doi.org/10.1021/la903769cCrossRefGoogle Scholar
  82. 82.
    Glaeser RM (2018) Proteins, interfaces, and cryo-Em grids. Curr Opin Colloid Interface Sci 34:1–8.  https://doi.org/10.1016/j.cocis.2017.12.009CrossRefGoogle Scholar
  83. 83.
    Glaeser RM, Han BG (2017) Opinion: hazards faced by macromolecules when confined to thin aqueous films. Biophys Rep 3(1):1–7.  https://doi.org/10.1007/s41048-016-0026-3CrossRefGoogle Scholar
  84. 84.
    Taylor KA, Glaeser RM (2008) Retrospective on the early development of cryoelectron microscopy of macromolecules and a prospective on opportunities for the future. J Struct Biol 163(3):214–223.  https://doi.org/10.1016/j.jsb.2008.06.004CrossRefGoogle Scholar
  85. 85.
    Schwalbe H, Fiebig KM, Buck M, Jones AJ, Grimshaw SB, Spencer A, Glaser SJ, Smith LJ, Dobson CM (1997) Structural and dynamical properties of a denaturated protein. Heteronuclear 3D NMR experiments and theoretical simulation of lysozyme in 8 M Urea. Biochemist 36:8977–8991CrossRefGoogle Scholar
  86. 86.
    Agard DA, Cheng Y, Glaeser RM, Subramaniam S (2014) Single-particle cryo-electron microscopy (Cryo-EM): progress, challenges and prespectives for further improvement. Adv Imag Electron Phys 185:113–137.  https://doi.org/10.1016/b978-0-12-800144-8.00002-1CrossRefGoogle Scholar
  87. 87.
    Tabor RF, Manica R, Chan DY, Grieser F, Dagastine RR (2011) Repulsive van der Waals forces in soft matter: why bubbles do not stick to walls. Phys Rev Lett 106(6):064501.  https://doi.org/10.1103/PhysRevLett.106.064501CrossRefGoogle Scholar
  88. 88.
    Jensen GJ, Kornberg RD (2000) Defocus-gradient corrected back-projection. Ultramicroscopy 84(1–2):57–64.  https://doi.org/10.1016/S0304-3991(00)00005-XCrossRefGoogle Scholar
  89. 89.
    Tan YZ, Aiyer S, Mietzsch M, Hull JA, McKenna R, Grieger J, Samulski RJ, Baker TS, Agbandje-McKenna M, Lyumkis D (2018) Sub-2 Å Ewald curvature corrected single-particle cryo-EM.  https://doi.org/10.1101/305599
  90. 90.
    Cavadini S, Fischer ES, Bunker RD, Potenza A, Lingaraju GM, Goldie KN, Mohamed WI, Faty M, Petzold G, Beckwith RE, Tichkule RB, Hassiepen U, Abdulrahman W, Pantelic RS, Matsumoto S, Sugasawa K, Stahlberg H, Thoma NH (2016) Cullin-RING ubiquitin E3 ligase regulation by the COP9 signalosome. Nature 531(7596):598–603.  https://doi.org/10.1038/nature17416CrossRefGoogle Scholar
  91. 91.
    Bokori-Brown M, Martin TG, Naylor CE, Basak AK, Titball RW, Savva CG (2016) Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein. Nat Commun 7:11293.  https://doi.org/10.1038/ncomms11293CrossRefGoogle Scholar
  92. 92.
    Rhinow D, Kuhlbrandt W (2008) Electron cryo-microscopy of biological specimens on conductive titanium-silicon metal glass films. Ultramicroscopy 108(7):698–705.  https://doi.org/10.1016/j.ultramic.2007.11.005CrossRefGoogle Scholar
  93. 93.
    Rhinow D, Weber NE, Turchanin A, Gölzhäuser A, Kühlbrandt W (2011) Single-walled carbon nanotubes and nanocrystalline graphene reduce beam-induced movements in high-resolution electron cryo-microscopy of ice-embedded biological samples. Appl Phys Lett 99(13):133701.  https://doi.org/10.1063/1.3645010CrossRefGoogle Scholar
  94. 94.
    Pantelic RS, Meyer JC, Kaiser U, Baumeister W, Plitzko JM (2010) Graphene oxide: a substrate for optimizing preparations of frozen-hydrated samples. J Struct Biol 170(1):152–156.  https://doi.org/10.1016/j.jsb.2009.12.020CrossRefGoogle Scholar
  95. 95.
    Pantelic RS, Suk JW, Magnuson CW, Meyer JC, Wachsmuth P, Kaiser U, Ruoff RS, Stahlberg H (2011) Graphene: substrate preparation and introduction. J Struct Biol 174(1):234–238.  https://doi.org/10.1016/j.jsb.2010.10.002CrossRefGoogle Scholar
  96. 96.
    Palovcak E, Wang F, Zheng SQ, Yu Z, Li S, Bulkley D, Agard DA, Cheng Y (2018) A simple and robust procedure for preparing graphene-oxide cryo-EM grids. BioRxiv.  https://doi.org/10.1101/290197
  97. 97.
    Pantelic RS, Fu W, Schoenenberger C, Stahlberg H (2014) Rendering graphene supports hydrophilic with non-covalent aromatic functionalization for transmission electron microscopy. Appl Phys Lett 104(13):134103CrossRefGoogle Scholar
  98. 98.
    Elias DC, Nair RR, Mohiuddin TMG, Morozov SV, Blake P, Halsall MP, Ferrari AC, Boukhvalov DW, Katsnelson MI, Geim AK, Novoselov KS (2009) Control of graphene’s properties by reversible hydrogeneation evidence for graphane. Science 323(5914):610–613CrossRefGoogle Scholar
  99. 99.
    Wang Y-F, You Y-S, Tsai C-H, Wang L-C (2010) Production of hydrogen by plasma-reforming of methanol. Int J Hydrog Energy 35(18):9637–9640.  https://doi.org/10.1016/j.ijhydene.2010.06.104CrossRefGoogle Scholar
  100. 100.
    Lima LM, Fu W, Jiang L, Kros A, Schneider GF (2016) Graphene-stabilized lipid monolayer heterostructures: a novel biomembrane superstructure. Nanoscale 8(44):18646–18653.  https://doi.org/10.1039/c6nr05706cCrossRefGoogle Scholar
  101. 101.
    Levy D, Mosser AG, Lambert O, Moeck GS, Bald D, Rigaud JL (1999) Two-dimensional crystallization on lipid layer: a successful approach for membrane proteins. J Struct Biol 127(1):44–52CrossRefGoogle Scholar
  102. 102.
    Uzgiris EE, Kornberg RD (1983) Two-dimensional crystalisation technique for imaging macromolecules, with application to antigen-antibody-complement complexes. Nature 301:125–129CrossRefGoogle Scholar
  103. 103.
    Kelly DF, Dukovski D, Walz T (2010) A practical guide to the use of monolayer purification and affinity grids. Methods Enzymol 481:83–107.  https://doi.org/10.1016/s0076-6879(10)81004-3CrossRefGoogle Scholar
  104. 104.
    Kelly DF, Dukovski D, Walz T (2008) Monolayer purification: a rapid method for isolating protein complexes for single-aprticle electron microscopy. Proc Natl Acad Sci 105(12):4703–4708CrossRefGoogle Scholar
  105. 105.
    Kelly DF, Abeyrathne PD, Dukovski D, Walz T (2008) The affinity grid: a pre-fabricated EM grid for monolayer purification. J Mol Biol 382(2):423–433.  https://doi.org/10.1016/j.jmb.2008.07.023CrossRefGoogle Scholar
  106. 106.
    Kelly DF, Dukovski D, Walz T (2010) Strategy for the use of affinity grids to prepare non-His-tagged macromolecular complexes for single-particle electron microscopy. J Mol Biol 400(4):675–681.  https://doi.org/10.1016/j.jmb.2010.05.045CrossRefGoogle Scholar
  107. 107.
    Yu G, Vago F, Zhang D, Snyder JE, Yan R, Zhang C, Benjamin C, Jiang X, Kuhn RJ, Serwer P, Thompson DH, Jiang W (2014) Single-step antibody-based affinity cryo-electron microscopy for imaging and structural analysis of macromolecular assemblies. J Struct Biol 187(1):1–9.  https://doi.org/10.1016/j.jsb.2014.04.006CrossRefGoogle Scholar
  108. 108.
    Yu G, Li K, Jiang W (2016) Antibody-based affinity cryo-EM grid. Methods 100:16–24.  https://doi.org/10.1016/j.ymeth.2016.01.010CrossRefGoogle Scholar
  109. 109.
    Johnson ZL, Chen J (2017) Structural basis of substrate recognition by the multidrug resistance protein MRP1. Cell 168(6):1075–1085.  https://doi.org/10.1016/j.cell.2017.01.041CrossRefGoogle Scholar
  110. 110.
    Zhang Z, Chen J (2016) Atomic structure of the cystic fibrosis transmembrane conductance regulator. Cell 167(6):1586–1597.  https://doi.org/10.1016/j.cell.2016.11.014CrossRefGoogle Scholar
  111. 111.
    Efremov RG, Leitner A, Aebersold R, Raunser S (2015) Architecture and conformational switch mechanism of the ryanodine receptor. Nature 517(7532):39–43.  https://doi.org/10.1038/nature13916CrossRefGoogle Scholar
  112. 112.
    Chiu PL, Kelly DF, Walz T (2011) The use of trehalose in the preparation of specimens for molecular electron microscopy. Micron 42(8):762–772.  https://doi.org/10.1016/j.micron.2011.06.005CrossRefGoogle Scholar
  113. 113.
    Bosch S, de Beaurepaire L, Allard M, Mosser M, Heichette C, Chretien D, Jegou D, Bach JM (2016) Trehalose prevents aggregation of exosomes and cryodamage. Sci Rep 6:36162.  https://doi.org/10.1038/srep36162CrossRefGoogle Scholar
  114. 114.
    Arnold SA, Albiez S, Bieri A, Syntychaki A, Adaixo R, McLeod RA, Goldie KN, Stahlberg H, Braun T (2017) Blotting-free and lossless cryo-electron microscopy grid preparation from nanoliter-sized protein samples and single-cell extracts. J Struct Biol 197(3):220–226.  https://doi.org/10.1016/j.jsb.2016.11.002CrossRefGoogle Scholar
  115. 115.
    Dandey VP, Wei H, Zhang Z, Tan YZ, Acharya P, Eng ET, Rice WJ, Kahn PA, Potter CS, Carragher B (2018) Spotiton: new features and applications. J Struct Biol 202(2):161–169.  https://doi.org/10.1016/j.jsb.2018.01.002CrossRefGoogle Scholar
  116. 116.
    Jain T, Sheehan P, Crum J, Carragher B, Potter CS (2012) Spotiton: a prototype for an integrated inkjet dispense and vitrification system for cryo-TEM. J Struct Biol 179(1):68–75.  https://doi.org/10.1016/j.jsb.2012.04.020CrossRefGoogle Scholar
  117. 117.
    Patwardhan A (2017) Trends in the electron microscopy data bank (EMDB). Acta Crystallogr D Struct Biol 73(6):503–508.  https://doi.org/10.1107/S2059798317004181CrossRefGoogle Scholar
  118. 118.
    Feng X, Fu Z, Kaledhonkar S, Jia Y, Shah B, Jin A, Liu Z, Sun M, Chen B, Grassucci RA, Ren Y, Jiang H, Frank J, Lin Q (2017) A fast and effective microfluidic spraying-plunging method for high-resolution single-particle cryo-EM. Structure 25(4):663–670.  https://doi.org/10.1016/j.str.2017.02.005CrossRefGoogle Scholar
  119. 119.
    Razinkov I, Dandey V, Wei H, Zhang Z, Melnekoff D, Rice WJ, Wigge C, Potter CS, Carragher B (2016) A new method for vitrifying samples for cryoEM. J Struct Biol 195(2):190–198.  https://doi.org/10.1016/j.jsb.2016.06.001CrossRefGoogle Scholar
  120. 120.
    Drulyte I, Johnson RM, Hesketh EL, Hurdiss DL, Scarff CA, Porav SA, Ranson NA, Muench SP, Thompson RF (2018) Approaches to altering particle distributions in cryo-electron microscopy sample preparation. Acta Crystallogr D Struct Biol 74(6):560–571.  https://doi.org/10.1107/S2059798318006496CrossRefGoogle Scholar
  121. 121.
    Tan YZ, Baldwin PR, Davis JH, Williamson JR, Potter CS, Carragher B, Lyumkis D (2017) Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat Methods 14(8):793–796.  https://doi.org/10.1038/nmeth.4347CrossRefGoogle Scholar
  122. 122.
    Naydenova K, Russo CJ (2017) Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy. Nat Commun 8(1):629.  https://doi.org/10.1038/s41467-017-00782-3CrossRefGoogle Scholar
  123. 123.
    Glaeser RM (1992) Specimen flatness of thin crystalline arrays: influence of the substrate. Ultamicroscopy 46:33–43CrossRefGoogle Scholar
  124. 124.
    Booy FP, Pawley JB (1993) Cryo-crinkling: what happens to carbon films on copper grids at low temperature. Ultamicroscopy 48:273–280CrossRefGoogle Scholar
  125. 125.
    Glaeser RM, McMullan G, Faruqi AR, Henderson R (2011) Images of paraffin monolayer crystals with perfect contrast: minimization of beam-induced specimen motion. Ultramicroscopy 111(2):90–100.  https://doi.org/10.1016/j.ultramic.2010.10.010CrossRefGoogle Scholar
  126. 126.
    Yoshioka C, Carragher B, Potter CS (2010) Cryomesh: a new substrate for cryo-electron microscopy. Microsc Microanal 16(1):43–53.  https://doi.org/10.1017/S1431927609991310CrossRefGoogle Scholar
  127. 127.
    Russo CJ, Passmore LA (2014) Ultrastable gold substrates for electron cryomicroscopy. Science 346(6215):1377–1380CrossRefGoogle Scholar
  128. 128.
    Russo CJ, Passmore LA (2016) Ultrastable gold substrates: properties of a support for high-resolution electron cryomicroscopy of biological specimens. J Struct Biol 193(1):33–44.  https://doi.org/10.1016/j.jsb.2015.11.006CrossRefGoogle Scholar
  129. 129.
    Meyerson JR, Rao P, Kumar J, Chittori S, Banerjee S, Pierson J, Mayer ML, Subramaniam S (2014) Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports. Sci Rep 4:7084.  https://doi.org/10.1038/srep07084CrossRefGoogle Scholar
  130. 130.
    Martin TG, Bharat TAM, Joerger AC, Bai X, Praetorius F, Fersht AR, Dietz H, Scheres SHW (2016) Design of a molecular support for cryo-EM structure determination. Proc Natl Acad Sci 113(47):7456–7463.  https://doi.org/10.1073/pnas.1612720113CrossRefGoogle Scholar

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© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.School of Chemistry and Molecular BiosciencesThe University of QueenslandSt. LuciaAustralia

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