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Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope

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Lipid-Protein Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2003))

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Abstract

The atomic force microscope (AFM) has opened avenues and provided opportunities to investigate biological soft matter and processes ranging from nanometer (nm) to millimeter (mm). The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever—aptly termed as a “lab on a tip”—can be used as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples have convincingly established AFM as a tool to study the mechanical properties and monitor processes of single proteins and cells with high sensitivity, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of transmembrane proteins in a lipid bilayer (reconstituted or native). Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theory and practical skills.

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Notes

  1. 1.

    The cantilever tip can potentially attach to misfolded or unfolded molecules on/in the membrane giving spurious F-D traces.

References

  1. Binnig G, Rohrer H, Gerber C, Weibel E (1982) Surface studies by scanning tunneling microscopy. Phys Rev Lett 49:57–61

    Google Scholar 

  2. Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56:930–933

    CAS  PubMed  Google Scholar 

  3. Muller DJ, Dufrene YF (2011) Force nanoscopy of living cells. Curr Biol 21:R212–R216

    PubMed  Google Scholar 

  4. Muller DJ, Krieg M, Alsteens D, Dufrene YF (2009) New frontiers in atomic force microscopy: analyzing interactions from single-molecules to cells. Curr Opin Biotechnol 20:4–13

    PubMed  Google Scholar 

  5. Alegre-Cebollada J, Perez-Jimenez R, Kosuri P, Fernandez JM (2010) Single-molecule force spectroscopy approach to enzyme catalysis. J Biol Chem 285:18961–18966

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Zhuang X, Rief M (2003) Single-molecule folding. Curr Opin Struct Biol 13:88–97

    CAS  PubMed  Google Scholar 

  7. Brujic J, Hermans R, Walther KA, Fernandez JM (2006) Single molecule force spectroscopy reveals signatures of glassy dynamics in the energy landscape of ubiquitin. Nat Phys 2:282–286

    CAS  Google Scholar 

  8. Cyr DM, Venkataraman B, Flynn GW (1996) STM investigations of organic molecules physisorbed at the liquid−solid interface. Chem Mater 8:1600–1615

    CAS  Google Scholar 

  9. Gross L, Mohn F, Moll N, Liljeroth P, Meyer G (2009) The chemical structure of a molecule resolved by atomic force microscopy. Science 325:1110–1114

    CAS  PubMed  Google Scholar 

  10. Ando T, Kodera N, Takai E, Maruyama D, Saito K, Toda A (2001) A high-speed atomic force microscope for studying biological macromolecules. Proc Natl Acad Sci U S A 98:12468–12472

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Uchihashi T, Iino R, Ando T, Noji H (2011) High-speed atomic force microscopy reveals rotary catalysis of rotorless F1-ATPase. Science 333:755–758

    CAS  PubMed  Google Scholar 

  12. Shibata M, Yamashita H, Uchihashi T, Kandori H, Ando T (2010) High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin. Nat Nanotechnnol 5:208–212

    CAS  Google Scholar 

  13. Puchner EM, Gaub HE (2009) Force and function: probing proteins with AFM-based force spectroscopy. Curr Opin Struct Biol 19:605–614

    CAS  PubMed  Google Scholar 

  14. Newton R, Delguste M, Koehler M, Dumitru AC, Laskowski PR, Müller DJ, Alsteens D (2017) Combining confocal and atomic force microscopy to quantify single-virus binding to mammalian cell surfaces. Nat Protoc 12:2275–2292

    CAS  PubMed  Google Scholar 

  15. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002) Molecular biology of the cell, 4th edn. Garland Science, New York, NY

    Google Scholar 

  16. Bowie JU (2005) Solving the membrane protein folding problem. Nature 438:581–589

    CAS  PubMed  Google Scholar 

  17. White SH (2009) Biophysical dissection of membrane proteins. Nature 459:344–346

    CAS  PubMed  Google Scholar 

  18. Vinothkumar KR (2015) Membrane protein structures without crystals, by single particle electron cryomicroscopy. Curr Opin Struct Biol 33:103–114

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Sachs JN, Engelman DM (2006) Introduction to the membrane protein reviews: the interplay of structure, dynamics, and environment in membrane protein function. Annu Rev Biochem 75:707–712

    CAS  PubMed  Google Scholar 

  20. Seddon AM, Curnow P, Booth PJ (2004) Membrane proteins, lipids and detergents: not just a soap opera. Biochim Biophys Acta 1666:105–117

    CAS  PubMed  Google Scholar 

  21. Engelman DM (2005) Membranes are more mosaic than fluid. Nature 438:578–580

    CAS  PubMed  Google Scholar 

  22. Jefferson RE, Min D, Corin K, Wang JY, Bowie JU (2018) Applications of single-molecule methods to membrane protein folding studies. J Mol Biol 430:424–437

    CAS  PubMed  Google Scholar 

  23. Muller DJ (2008) AFM: a nanotool in membrane biology. Biochemistry 47:7986–7998

    CAS  PubMed  Google Scholar 

  24. Kedrov A, Janovjak H, Sapra KT, Muller DJ (2007) Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy. Annu Rev Biophys Biomol Struct 36:233–260

    CAS  PubMed  Google Scholar 

  25. Engel A, Gaub HE (2008) Structure and mechanics of membrane proteins. Annu Rev Biochem 77:127–148

    CAS  PubMed  Google Scholar 

  26. Bippes CA, Muller DJ (2011) High-resolution atomic force microscopy and spectroscopy of native membrane proteins. Rep Prog Phys 74:086601

    Google Scholar 

  27. Seelert H, Poetsch A, Dencher NA, Engel A, Stahlberg H, Müller DJ (2000) Proton powered turbine of a plant motor. Nature 405:418–419

    CAS  PubMed  Google Scholar 

  28. Scheuring S (2006) AFM studies of the supramolecular assembly of bacterial photosynthetic core-complexes. Curr Opin Chem Biol 10:387–393

    CAS  PubMed  Google Scholar 

  29. Stahlberg H, Muller DJ, Suda K, Fotiadis D, Engel A, Meier T, Matthey U, Dimroth P (2001) Bacterial Na(+)-ATP synthase has an undecameric rotor. EMBO Rep 2:229–233

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Pogoryelov D, Yu J, Meier T, Vonck J, Dimroth P, Müller DJ (2005) The c15 ring of the Spirulina platensis F-ATP synthase: F1/F0 symmetry mismatch is not obligatory. EMBO Rep 6:1040–1044

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Hoogenboom BW, Suda K, Engel A, Fotiadis D (2007) The supramolecular assemblies of voltage-dependent anion channels in the native membrane. J Mol Biol 370:246–255

    CAS  PubMed  Google Scholar 

  32. Müller DJ, Engel A (1999) Voltage and pH-induced channel closure of porin OmpF visualized by atomic force microscopy. J Mol Biol 285:1347–1351

    PubMed  Google Scholar 

  33. Yu J, Bippes CA, Hand GM, Muller DJ, Sosinsky GE (2007) Aminosulfonate modulated pH-induced conformational changes in connexin26 hemichannels. J Biol Chem 282:8895–8904

    CAS  PubMed  Google Scholar 

  34. Kedrov A, Krieg M, Ziegler C, Kuhlbrandt W, Müller DJ (2005) Locating ligand binding and activation of a single antiporter. EMBO Rep 6:668–674

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Park PS, Sapra KT, Kolinski M, Filipek S, Palczewski K, Muller DJ (2007) Stabilizing effect of Zn2+ in native bovine rhodopsin. J Biol Chem 282:11377–11385

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Janovjak H, Kessler M, Oesterhelt D, Gaub HE, Müller DJ (2003) Unfolding pathways of native bacteriorhodopsin depend on temperature. EMBO J 22:5220–5229

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Janovjak H, Knaus H, Muller DJ (2007) Transmembrane helices have rough energy surfaces. J Am Chem Soc 129:246–247

    CAS  PubMed  Google Scholar 

  38. Serdiuk T, Madej MG, Sugihara J, Kawamura S, Mari SA, Kaback HR, Muller DJ (2014) Substrate-induced changes in the structural properties of LacY. Proc Natl Acad Sci U S A 111:E1571–E1580

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Bippes CA, Ge L, Meury M, Harder D, Ucurum Z, Daniel H, Fotiadis D, Muller DJ (2013) Peptide transporter DtpA has two alternate conformations, one of which is promoted by inhibitor binding. Proc Natl Acad Sci U S A 110:E3978–E3986

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Zocher M, Fung JJ, Kobilka BK, Muller DJ (2012) Ligand-specific interactions modulate kinetic, energetic, and mechanical properties of the human beta2 adrenergic receptor. Structure 20:1391–1402

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Serdiuk T, Sugihara J, Mari SA, Kaback HR, Muller DJ (2015) Observing a lipid-dependent alteration in single lactose permeases. Structure 23:754–761

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Zocher M, Zhang C, Rasmussen SG, Kobilka BK, Muller DJ (2012) Cholesterol increases kinetic, energetic, and mechanical stability of the human beta2-adrenergic receptor. Proc Natl Acad Sci U S A 109:E3463–E3472

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Sapra KT, Besir H, Oesterhelt D, Muller DJ (2006) Characterizing molecular interactions in different bacteriorhodopsin assemblies by single-molecule force spectroscopy. J Mol Biol 355:640–650

    CAS  PubMed  Google Scholar 

  44. Cisneros DA, Oberbarnscheidt L, Pannier A, Klare JP, Helenius J, Engelhard M, Oesterhelt F, Muller DJ (2008) Transducer binding establishes localized interactions to tune sensory rhodopsin II. Structure 16:1206–1213

    CAS  PubMed  Google Scholar 

  45. Sapra KT, Doehner J, Renugopalakrishnan V, Padros E, Muller DJ (2008) Role of extracellular glutamic acids in the stability and energy landscape of bacteriorhodopsin. Biophys J 95:3407–3418

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Sapra KT, Balasubramanian GP, Labudde D, Bowie JU, Muller DJ (2008) Point mutations in membrane proteins reshape energy landscape and populate different unfolding pathways. J Mol Biol 376:1076–1090

    CAS  PubMed  Google Scholar 

  47. Serdiuk T, Balasubramaniam D, Sugihara J, Mari SA, Kaback HR, Muller DJ (2016) YidC assists the stepwise and stochastic folding of membrane proteins. Nat Chem Biol 12:911–917

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Kedrov A, Janovjak H, Ziegler C, Kuhlbrandt W, Muller DJ (2006) Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. J Mol Biol 355:2–8

    CAS  PubMed  Google Scholar 

  49. Thoma J, Bosshart P, Pfreundschuh M, Muller DJ (2012) Out but not in: the large transmembrane β-barrel protein FhuA unfolds but cannot refold via β-hairpins. Structure 20:2185–2190

    CAS  PubMed  Google Scholar 

  50. Damaghi M, Koster S, Bippes CA, Yildiz O, Muller DJ (2011) One β-hairpin follows the other: exploring refolding pathways and kinetics of the transmembrane β-barrel protein OmpG. Angew Chem Int Ed Engl 50:7422–7424

    CAS  PubMed  Google Scholar 

  51. Thoma J, Burmann BM, Hiller S, Muller DJ (2015) Impact of holdase chaperones Skp and SurA on the folding of beta-barrel outer-membrane proteins. Nat Struct Mol Biol 22:795–802

    CAS  PubMed  Google Scholar 

  52. Krieg M, Arboleda-Estudillo Y, Puech PH, Kafer J, Graner F, Muller DJ, Heisenberg CP (2008) Tensile forces govern germ-layer organization in zebrafish. Nat Cell Biol 10:429–436

    CAS  PubMed  Google Scholar 

  53. Alsteens D, Newton R, Schubert R, Martinez-Martin D, Delguste M, Roska B, Muller DJ (2017) Nanomechanical mapping of first binding steps of a virus to animal cells. Nat Nanotechnol 12:177–183

    CAS  PubMed  Google Scholar 

  54. Stewart MP, Toyoda Y, Hyman AA, Muller DJ (2011) Force probing cell shape changes to molecular resolution. Trends Biochem Sci 36:444–450

    CAS  PubMed  Google Scholar 

  55. Müller DJ, Dufrêne YF (2011) Atomic force microscopy: a nanoscopic window on the cell surface. Trends Cell Biol 21:461–469

    PubMed  Google Scholar 

  56. Engel A, Müller DJ (2000) Observing single biomolecules at work with the atomic force microscope. Nat Struct Biol 7:715–718

    CAS  PubMed  Google Scholar 

  57. Müller DJ, Hand GM, Engel A, Sosinsky G (2002) Conformational changes in surface structures of isolated connexin26 gap junctions. EMBO J 21:3598–3607

    PubMed  PubMed Central  Google Scholar 

  58. Hoogenboom BW, Hug HJ, Pellmont Y, Martin S, Frederix PLTM, Fotiadis D, Engel A (2006) Quantitative dynamic-mode scanning force microscopy in liquid. Appl Phys Lett 88:193109

    Google Scholar 

  59. Hansma PK, Cleveland JP, Radmacher M, Walters DA, Hillner PE, Bezanilla M, Fritz M, Vie D, Hansma HG, Prater CB, Massie J, Fukunaga L, Gurley J, Elings V (1994) Tapping mode atomic force microscopy in liquids. Appl Phys Lett 64:1738–1740

    CAS  Google Scholar 

  60. Müller DJ, Fotiadis D, Scheuring S, Müller SA, Engel A (1999) Electrostatically balanced subnanometer imaging of biological specimens by atomic force microscope. Biophys J 76:1101–1111

    PubMed  PubMed Central  Google Scholar 

  61. Butt H-J, Jaschke M, Ducker W (1995) Measuring surface forces in aqueous solution with the atomic force microscope. Bioelectrochem Bioenerg 38:191–201

    CAS  Google Scholar 

  62. Butt H-J (1992) Measuring local surface charge densities in electrolyte solutions with a scanning force microscope. Biophys J 63:578–582

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Butt H-J (1992) Electrostatic interaction in scanning probe microscopy when imaging in electrolyte solutions. Nanotechnology 3:60–68

    Google Scholar 

  64. Müller DJ, Engel A (1997) The height of biomolecules measured with the atomic force microscope depends on electrostatic interactions. Biophys J 73:1633–1644

    PubMed  PubMed Central  Google Scholar 

  65. Czajkowsky D, Allen M, Elings V, Shao Z (1998) Direct visualization of surface charge in aqueous solution. Ultramicroscopy 74:1–5

    CAS  PubMed  Google Scholar 

  66. Baker AA, Helbert W, Sugiyama J, Miles MJ (2000) New insight into cellulose structure by atomic force microscopy shows the i(alpha) crystal phase at near-atomic resolution. Biophys J 79:1139–1145

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Müller DJ, Büldt G, Engel A (1995) Force-induced conformational change of bacteriorhodopsin. J Mol Biol 249:239–243

    PubMed  Google Scholar 

  68. Müller DJ, Engel A (2002) Conformations, flexibility, and interactions observed on individual membrane proteins by atomic force microscopy. Methods Cell Biol 68:257–299

    PubMed  Google Scholar 

  69. Karrasch S, Dolder M, Hoh J, Schabert F, Ramsden J, Engel A (1993) Covalent binding of biological samples to solid supports for scanning probe microscopy in buffer solution. Biophys J 65:2437–2446

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Bezanilla M, Drake B, Nudler E, Kashlev M, Hansma PK, Hansma HG (1994) Motion and enzymatic degradation of DNA in the atomic force microscope. Biophys J 67:2454–2459

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Fritz M, Radmacher M, Allersma MW, Cleveland JP, Stewart RJ, Hansma PK, Schmidt CF (1995) Imaging microtubles in buffer solution using tapping mode atomic force microscopy. SPIE 2384:150–157

    CAS  Google Scholar 

  72. Guthold M, Zhu X, Rivetti C, Yang G, Thomson NH, Kasas S, Hansma HG, Smith B, Hansma PK, Bustamante C (1999) Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase. Biophys J 77:2284–2294

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Elie-Caille C, Severin F, Helenius J, Howard J, Muller DJ, Hyman AA (2007) Straight GDP-tubulin protofilaments form in the presence of taxol. Curr Biol 17:1765–1770

    CAS  PubMed  Google Scholar 

  74. Dufrene YF, Martinez-Martin D, Medalsy I, Alsteens D, Muller DJ (2013) Multiparametric imaging of biological systems by force-distance curve-based AFM. Nat Methods 10:847–854

    CAS  PubMed  Google Scholar 

  75. Dufrêne YF, Ando T, Garcia R, Alsteens D, Martinez-Martin D, Engel A, Gerber C, Müller DJ (2017) Imaging modes of atomic force microscopy for application in molecular and cell biology. Nat Nanotechnol 12:295–307

    PubMed  Google Scholar 

  76. Alsteens D, Müller DJ, Dufrene YF (2017) Multiparameteric atomic force microscopy imaging of biomolecular and cellular systems. Acc Chem Res 50:924–931

    CAS  PubMed  Google Scholar 

  77. Viani MB, Pietrasanta LI, Thompson JB, Chand A, Gebeshuber IC, Kindt JH, Richter M, Hansma HG, Hansma PK (2000) Probing protein-protein interactions in real time. Nat Struct Biol 7:644–647

    CAS  PubMed  Google Scholar 

  78. Yamashita H, Voïtchovsky K, Uchihashi T, Contera SA, Ryan JF, Ando T (2009) Dynamics of bacteriorhodopsin 2D crystal observed by high-speed atomic force microscopy. J Struct Biol 167:153–158

    CAS  PubMed  Google Scholar 

  79. Junge W, Muller DJ (2011) Seeing a molecular motor at work. Science 333:704–705

    CAS  PubMed  Google Scholar 

  80. Borgia A, Williams PM, Clarke J (2008) Single-molecule studies of protein folding. Annu Rev Biochem 77:101–125

    CAS  PubMed  Google Scholar 

  81. Hinterdorfer P, Dufrene YF (2006) Detection and localization of single molecular recognition events using atomic force microscopy. Nat Methods 3:347–355

    CAS  PubMed  Google Scholar 

  82. Wiita AP, Perez-Jimenez R, Walther KA, Grater F, Berne BJ, Holmgren A, Sanchez-Ruiz JM, Fernandez JM (2007) Probing the chemistry of thioredoxin catalysis with force. Nature 450:124–127

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Zhang X, Halvorsen K, Zhang CZ, Wong WP, Springer TA (2009) Mechanoenzymatic cleavage of the ultralarge vascular protein von Willebrand factor. Science 324:1330–1334

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Alegre-Cebollada J, Kosuri P, Rivas-Pardo JA, Fernández JM (2011) Direct observation of disulfide isomerization in a single protein. Nat Chem 3:882–887

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Dietz H, Rief M (2004) Exploring the energy landscape of GFP by single-molecule mechanical experiments. Proc Natl Acad Sci U S A 101:16192–16197

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276:1109–1112

    CAS  PubMed  Google Scholar 

  87. Thoma J, Sapra KT, Müller DJ (2018) Single-molecule force spectroscopy of transmembrane β-barrel proteins. Annu Rev Anal Chem 11:375–395

    CAS  Google Scholar 

  88. Evans E (2001) Probing the relation between force-lifetime-and chemistry in single molecular bonds. Annu Rev Biophys Biomol Struct 30:105–128

    CAS  PubMed  Google Scholar 

  89. Evans E (1998) Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectroscopy. Faraday Discuss 111:1–16

    CAS  Google Scholar 

  90. Baldwin RL, Rose GD (1999) Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem Sci 24:77–83

    CAS  PubMed  Google Scholar 

  91. Baldwin RL, Rose GD (1999) Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 24:26–33

    CAS  PubMed  Google Scholar 

  92. Rief M, Fernandez JM, Gaub HE (1998) Elastically coupled two-level-systems as a model for biopolymer extensibility. Phys Rev Lett 81:4764–4767

    CAS  Google Scholar 

  93. Evans E, Ritchie K (1997) Dynamic strength of molecular adhesion bonds. Biophys J 72:1541–1555

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Bell GI (1978) Models for the specific adhesion of cells to cells. Science 200:618–627

    CAS  PubMed  Google Scholar 

  95. Evans E (1999) Looking inside molecular bonds at biological interfaces with dynamic force spectroscopy. Biophys Chem 82:83–97

    CAS  PubMed  Google Scholar 

  96. Ge L, Perez C, Waclawska I, Ziegler C, Muller DJ (2011) Locating an extracellular K+-dependent interaction site that modulates betaine-binding of the Na+-coupled betaine symporter BetP. Proc Natl Acad Sci U S A 108:E890–E898

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Bippes CA, Zeltina A, Casagrande F, Ratera M, Palacin M, Muller DJ, Fotiadis D (2009) Substrate binding tunes conformational flexibility and kinetic stability of an amino acid antiporter. J Biol Chem 284:18651–18663

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Sapra KT, Park PS, Palczewski K, Muller DJ (2008) Mechanical properties of bovine rhodopsin and bacteriorhodopsin: possible roles in folding and function. Langmuir 24:1330–1337

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Damaghi M, Sapra KT, Koster S, Yildiz O, Kuhlbrandt W, Muller DJ (2010) Dual energy landscape: the functional state of the beta-barrel outer membrane protein G molds its unfolding energy landscape. Proteomics 10:4151–4162

    CAS  PubMed  Google Scholar 

  100. Edwards DT, Faulk JK, LeBlanc MA, Perkins TT (2017) Force spectroscopy with 9-μs resolution and sub-pN stability by tailoring AFM cantilever geometry. Biophys J 113:2595–2600

    CAS  PubMed  PubMed Central  Google Scholar 

  101. Schitter G, Stark RW, Stemmer A (2004) Fast contact-mode atomic force microscopy on biological specimen by model-based control. Ultramicroscopy 100:253–257

    CAS  PubMed  Google Scholar 

  102. Mahmood IA, Moheimani SOR (2009) Making a commercial atomic force microscope more accurate and faster using positive position feedback control. Rev Sci Instrum 80:063705

    CAS  PubMed  Google Scholar 

  103. Meyer E, Hug HJ, Bennewitz R (2003) Scanning probe microscopy – the lab on a tip. Advanced text in physics. Springer, Berlin

    Google Scholar 

  104. Yasumura KY, Stowe TD, Chow EM, Pfafman T, Kenny TW, Stipe BC, Rugar D (2000) Quality factors in micron- and submicron-thick cantilevers. J Microelectromech Syst 9:117–125

    CAS  Google Scholar 

  105. Müller DJ, Engel A (2007) Atomic force microscopy and spectroscopy of native membrane proteins. Nat Protoc 2:2191–2197

    PubMed  Google Scholar 

  106. Zong Q, Innis D, Kjoller K, Elings VB (1993) Fractured polymer/silica fiber surface studied by tapping mode atomic force microscopy. Surf Sci Lett 290:L688–L692

    Google Scholar 

  107. Viani MB, Schäffer TE, Paloczi GT, Pietrasanta LI, Smith BL, Thompson JB, Richter M, Rief M, Gaub HE, Plaxco KW, Cleland AN, Hansma HG, Hansma PK (1999) Fast imaging and fast force spectroscopy of single biopolymers with a new atomic force microscope designed for small cantilevers. Rev Sci Ins 70:4300–4303

    CAS  Google Scholar 

  108. Viani MB, Schäfer TE, Chand A, Rief M, Gaub H, Hansma PK (1999) Small cantilevers for force spectroscopy of single molecules. J Appl Phys 86:2258–2262

    CAS  Google Scholar 

  109. Friedrichs J, Helenius J, Muller DJ (2010) Quantifying cellular adhesion to extracellular matrix components by single-cell force spectroscopy. Nat Protoc 5:1353–1361

    CAS  PubMed  Google Scholar 

  110. Cleveland JP, Manne S, Bocek D, Hansma PK (1993) A nondestructive method for determining the spring constant of cantilevers for scanning force microscopy. Rev Sci Instrum 64:403–405

    CAS  Google Scholar 

  111. Sader JE, Larson I, Mulvaney P, White LR (1995) Method for calibration of atomic force cantilevers. Rev Sci Instrum 60:3131–3134

    Google Scholar 

  112. Gibson CT, Watson GS, Myhra S (1996) Determination of the spring constants of probes for force microscopy/spectroscopy. Nanotechnology 7:259–262

    Google Scholar 

  113. Torii A, Sasaki M, Hane K, Okuma S (1996) A method for determining the spring constant of cantilevers for atomic force microscopy. Meas Sci Technol 7:179–184

    CAS  Google Scholar 

  114. Butt H-J, Jaschke M (1995) Calculation of thermal noise in atomic force microscopy. Nanotechnology 6:1–7

    Google Scholar 

  115. Florin E-L, Rief M, Lehmann H, Ludwig M, Dornmair C, Moy VT, Gaub HE (1995) Sensing specific molecular interactions with the atomic force microscope. Biosens Bioelectron 10:895–901

    CAS  Google Scholar 

  116. Howard J (2001) Mechanics of motor proteins and the cytoskeleton. Sinauer Associates Inc., Sunderland, MA

    Google Scholar 

  117. Muller DJ, Engel A (2008) Strategies to prepare and characterize native membrane proteins and protein membranes by AFM. Curr Opin Colloid Int Sci 13:338–350

    CAS  Google Scholar 

  118. Pashley RM (1981) Hydration forces between mica surfaces in Li+, Na+, Na+ and Cs+ electrolyte solutions: a correlation of double layer and hydration forces with surface cation exchange properties. J Colloid Interface Sci 83:531–546

    CAS  Google Scholar 

  119. Müller DJ, Amrein M, Engel A (1997) Adsorption of biological molecules to a solid support for scanning probe microscopy. J Struct Biol 119:172–188

    PubMed  Google Scholar 

  120. Schwarz UD, Haefke H, Reimann P, Guntherodt HJ (1994) Tip artefacts in scanning force microscopy. J Microsc 173:183–197

    CAS  Google Scholar 

  121. Möller C, Allen M, Elings V, Engel A, Müller DJ (1999) Tapping-mode atomic force microscopy produces faithful high-resolution images of protein surfaces. Biophys J 77:1150–1158

    PubMed  PubMed Central  Google Scholar 

  122. Dietz H, Bertz M, Schlierf M, Berkemeier F, Bornschlogl T, Junker JP, Rief M (2006) Cysteine engineering of polyproteins for single-molecule force spectroscopy. Nat Protoc 1:80–84

    CAS  PubMed  Google Scholar 

  123. Cisneros DA, Muller DJ, Daud SM, Lakey JH (2006) An approach to prepare membrane proteins for single-molecule imaging. Angew Chem Int Ed Engl 45:3252–3256

    CAS  PubMed  Google Scholar 

  124. Bosshart PD, Iordanov I, Garzon-Coral C, Demange P, Engel A, Milon A, Muller DJ (2012) The transmembrane protein KpOmpA anchoring the outer membrane of Klebsiella pneumoniae unfolds and refolds in response to tensile load. Structure 20:121–127

    CAS  PubMed  Google Scholar 

  125. Kessler M, Gottschalk KE, Janovjak H, Muller DJ, Gaub HE (2006) Bacteriorhodopsin folds into the membrane against an external force. J Mol Biol 357:644–654

    CAS  PubMed  Google Scholar 

  126. Oesterhelt F, Oesterhelt D, Pfeiffer M, Engel A, Gaub HE, Müller DJ (2000) Unfolding pathways of individual bacteriorhodopsins. Science 288:143–146

    CAS  PubMed  Google Scholar 

  127. Kessler M, Gaub H (2006) Unfolding barriers in bacteriorhodopsin probed from the cytoplasmic and the extracellular side by AFM. Structure 14:521–527

    CAS  PubMed  Google Scholar 

  128. Sapra KT, Damaghi M, Koster S, Yildiz O, Kuhlbrandt W, Muller DJ (2009) One beta hairpin after the other: exploring mechanical unfolding pathways of the transmembrane beta-barrel protein OmpG. Angew Chem Int Ed Engl 48:8306–8308

    CAS  PubMed  Google Scholar 

  129. Müller DJ, Schoenenberger CA, Büldt G, Engel A (1996) Immuno-atomic force microscopy of purple membrane. Biophys J 70:1796–1802

    PubMed  PubMed Central  Google Scholar 

  130. Sapra KT, Park PS, Filipek S, Engel A, Müller DJ, Palczewski K (2006) Detecting molecular interactions that stabilize native bovine rhodopsin. J Mol Biol 358:255–269

    Google Scholar 

  131. Kedrov A, Hellawell AM, Klosin A, Broadhurst RB, Kunji ER, Müller DJ (2010) Probing the interactions of carboxy-atractyloside and atractyloside with the yeast mitochondrial ADP/ATP carrier. Structure 18:39–46

    CAS  PubMed  Google Scholar 

  132. Müller DJ, Kessler M, Oesterhelt F, Möller C, Oesterhelt D, Gaub H (2002) Stability of bacteriorhodopsin alpha-helices and loops analyzed by single-molecule force spectroscopy. Biophys J 83:3578–3588

    PubMed  PubMed Central  Google Scholar 

  133. Spoerri PM, Kato HE, Pfreundschuh M, Mari SA, Serdiuk T, Thoma J, Sapra KT, Zhang C, Kobilka BK, Müller DJ (2018) Structural properties of the human protease-activated receptor 1 changing by a strong antagonist. Structure 26:829–838

    CAS  PubMed  Google Scholar 

  134. Thoma J, Ritzmann N, Wolf D, Mulvihill E, Hiller S, Müller DJ (2017) Maltoporin LamB unfolds β-hairpins along mechanical stress-dependent unfolding pathways. Structure 25:1139–1144

    CAS  PubMed  Google Scholar 

  135. Bosshart PD, Casagrande F, Frederix PL, Ratera M, Bippes CA, Muller DJ, Palacin M, Engel A, Fotiadis D (2008) High-throughput single-molecule force spectroscopy for membrane proteins. Nanotechnology 19:384014

    PubMed  Google Scholar 

  136. Bustamante C, Marko JF, Siggia ED, Smith S (1994) Entropic elasticity of lambda-phage DNA. Science 265:1599–1600

    CAS  PubMed  Google Scholar 

  137. Scheuring S, Sturgis JN (2005) Chromatic adaptation of photosynthetic membranes. Science 309:484–487

    CAS  PubMed  Google Scholar 

  138. Czajkowsky DM, Hotze EM, Shao Z, Tweten RK (2004) Vertical collapse of a cytolysin prepore moves its transmembrane beta-hairpins to the membrane. EMBO J 23:3206–3215

    CAS  PubMed  PubMed Central  Google Scholar 

  139. Fotiadis D, Liang Y, Filipek S, Saperstein DA, Engel A, Palczewski K (2003) Atomic-force microscopy: rhodopsin dimers in native disc membranes. Nature 421:127–128

    CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland

    K. Tanuj Sapra

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  1. K. Tanuj Sapra
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Correspondence to K. Tanuj Sapra .

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  1. Department of Biophysics, Institute of Biology, FB10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany

    Jörg H. Kleinschmidt

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Sapra, K.T. (2019). Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope. In: Kleinschmidt, J. (eds) Lipid-Protein Interactions. Methods in Molecular Biology, vol 2003. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9512-7_6

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  • DOI: https://doi.org/10.1007/978-1-4939-9512-7_6

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