Abstract
Atomic force microscopy (AFM) is a form of contact microscopy that uses a very sharp tip to scan the surface of a sample. It provides a 3D image of the surface structure and in the force mode it can also be used to test the mechanical properties of the sample. AFM has been successfully applied to study the molecular mechanism of pore-forming proteins on model membranes. It gives information about both the structural reorganization of the membrane surface and the changes in the force required for membrane piercing upon incubation with this special type of proteins. Here we describe robust protocols to investigate the effect of pore-forming proteins in supported lipid bilayers .
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Morris VJ, Kirby AR, Gunning AP (2010) Atomic force microscopy for biologists, 2nd edn. Imperial College Press, London
Hansma PK, Elings VB, Marti O, Bracker CE (1988) Scanning tunneling microscopy and atomic force microscopy: application to biology and technology. Science 242:209–216. https://doi.org/10.1126/science.3051380
Goksu EI, Vanegas JM, Blanchette CD, Lin W-C, Longo ML (2009) AFM for structure and dynamics of biomembranes. BBA-Biomembranes 1788(1):254–266. https://doi.org/10.1016/j.bbamem.2008.08.021
Muller DJ (2008) AFM: a nanotool in membrane biology. Biochemistry-US 47:7986–7998. https://doi.org/10.1021/bi800753x
Fradin C, Satsoura D, Andrews DW (2009) Punching holes in membranes: how oligomeric pore-forming proteins and lipids cooperate to form aqueous channels in membranes, Handbook of modern biophysics, vol vol. 2. Humana Press, New York, pp 223–262. https://doi.org/10.1007/978-1-60761-314-5_9
Bischofberger M, Iacovache I, van der Goot FG (2012) Pathogenic pore-forming proteins: function and host response. Cell Host Microbe 12(3):266–275. https://doi.org/10.1016/j.chom.2012.08.005
Iacovache I, Bischofberger M, van der Goot FG (2010) Structure and assembly of pore-forming proteins. Curr Opin Struct Biol 20(2):241–246. https://doi.org/10.1016/j.sbi.2010.01.013
Pipkin ME, Lieberman J (2007) Delivering the kiss of death: progress on understanding how perforin works. Curr Opin Immunol 19(3):301–308. https://doi.org/10.1016/j.coi.2007.04.011
Bubeck D (2014) The making of a macromolecular machine: assembly of the membrane attack complex. Biochemistry-US 53(12):1908–1915. https://doi.org/10.1021/bi500157z
Serna M, Giles JL, Morgan BP, Bubeck D (2016) Structural basis of complement membrane attack complex formation. Nat Commun 7:10587. https://doi.org/10.1038/ncomms10587
Cosentino K, Garcia-Saez AJ (2014) Mitochondrial alterations in apoptosis. Chem Phys Lipids 181:62–75. https://doi.org/10.1016/j.chemphyslip.2014.04.001
Gross A, McDonnell JM, Korsmeyer SJ (1999) Bcl-2 family members and the mitochondria in apoptosis. Genes Dev 13:1899–1911
Suen DF, Norris KL, Youle RJ (2008) Mitochondrial dynamics and apoptosis. Genes Dev 22(12):1577–1590. https://doi.org/10.1101/gad.1658508
Cosentino K, Ros U, Garcia-Saez AJ (2016) Assembling the puzzle: oligomerization of alpha-pore forming proteins in membranes. Biochim Biophys Acta 1858(3):457–466. https://doi.org/10.1016/j.bbamem.2015.09.013
Ros U, Garcia-Saez AJ (2015) More than a pore: the interplay of pore-forming proteins and lipid membranes. J Membr Biol 248(3):545–561. https://doi.org/10.1007/s00232-015-9820-y
Huang HW (2000) Action of antimicrobial peptides: two-state model. Biochemistry-US 39:8347–8352
Xu XP, Zhai D, Kim E, Swift M, Reed JC, Volkmann N, Hanein D (2013) Three-dimensional structure of Bax-mediated pores in membrane bilayers. Cell Death Dis 4:e683. https://doi.org/10.1038/cddis.2013.210
Parker MW, Feil SC (2005) Pore-forming protein toxins: from structure to function. Prog Biophys Mol Biol 88(1):91–142. https://doi.org/10.1016/j.pbiomolbio.2004.01.009
Sonnen AF, Plitzko JM, Gilbert RJ (2014) Incomplete pneumolysin oligomers form membrane pores. Open Biol 4:140044. https://doi.org/10.1098/rsob.140044
Metkar SS, Marchioretto M, Antonini V, Lunelli L, Wang B, Gilbert RJ, Anderluh G, Roth R, Pooga M, Pardo J, Heuser JE, Serra MD, Froelich CJ (2015) Perforin oligomers form arcs in cellular membranes: a locus for intracellular delivery of granzymes. Cell Death Differ 22(1):74–85. https://doi.org/10.1038/cdd.2014.110
Salvador-Gallego R, Mund M, Cosentino K, Schneider J, Unsay J, Schraermeyer U, Engelhardt J, Ries J, Garcia-Saez AJ (2016) Bax assembly into rings and arcs in apoptotic mitochondria is linked to membrane pores. EMBO J 35(4):389–401. https://doi.org/10.15252/embj.201593384
Castellana ET, Cremer PS (2006) Solid supported lipid bilayers: from biophysical studies to sensor design. Surf Sci Rep 61(10):429–444. https://doi.org/10.1016/j.surfrep.2006.06.001
Frederix PLTM, Bosshart PD, Engel A (2009) Atomic force microscopy of biological membranes. Biophys J 96(2):329–338. https://doi.org/10.1016/j.bpj.2008.09.046
Mennicke U, Salditt T (2002) Preparation of solid-supported lipid bilayers by spin-coating. Langmuir 18:8172–8177. https://doi.org/10.1021/la025863f
Yilmaz N, Kobayashi T (2016) Assemblies of pore-forming toxins visualized by atomic force microscopy. Biochim Biophys Acta 1858(3):500–511. https://doi.org/10.1016/j.bbamem.2015.11.005
Mou J, Yang J, Shao Z (1995) Atomic force microscopy of cholera toxin B-oligomers bound to bilayers of biologically relevant lipids. J Mol Biol 248:507–512
Epand RF, Martinou J-C, Montessuit S, Epand RM, Yip CM (2002) Direct evidence of membrane pore formation by the apoptotic protein Bax. Biochem Biophys Res Commun 298:744–749
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. https://doi.org/10.1038/sj.emboj.7600350
Yilmaz N, Kobayashi T (2015) Visualization of lipid membrane reorganization induced by a pore-forming toxin using high-speed atomic force microscopy. ACS Nano 9:7960–7967
Unsay J, Cosentino K, Garcia-Saez AJ (2015) Atomic force microscopy imaging and force spectroscopy of supported lipid bilayers. J Vis Exp 101:e52867. https://doi.org/10.3791/52867
Canale C, Jacono M, Diaspro A, Dante S (2010) Force spectroscopy as a tool to investigate the properties of supported lipid membranes. Microsc Res Tech 73(10):965–972. https://doi.org/10.1002/jemt.20834
Redondo-Morata L, Giannotti MI, Sanz F (2012) Stability of lipid bilayers as model membranes: atomic force microscopy and spectroscopy approach. In: Baró AM, Reifenberger RG (eds) Atomic force microscopy in liquid: biological applications, 1st edn. Wiley-VCH Verlag GmbH, Weinheim. https://doi.org/10.1002/9783527649808.ch10
Butt H-J, Franz V (2002) Rupture of molecular thin films observed in atomic force microscopy I. Theory Phys Rev E 66:031601. https://doi.org/10.1103/PhysRevE.66.031601
Unsay JD, Cosentino K, Sporbeck K, Garcia-Saez AJ (2017) Pro-apoptotic cBid and Bax exhibit distinct membrane remodeling activities: an AFM study. BBA-Biomembranes 1859:17–27. https://doi.org/10.1016/j.bbamem.2016.10.007
Gräslund S, Nordlund P, Weigelt J, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, Dhe-Paganon S, Park H-W, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim S-H, Rao Z, Shi Y, Terwilliger TC, Kim C-Y, Hung L-W, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC (2008) Protein production and purification. Nat Methods 5(2):135–146. https://doi.org/10.1038/nmeth.f.202
Subburaj Y, Cosentino K, Axmann M, Pedrueza-Villalmanzo E, Hermann E, Bleicken S, Spatz J, Garcia-Saez AJ (2015) Bax monomers form dimer units in the membrane that further self-assemble into multiple oligomeric species. Nat Commun 6:8042. https://doi.org/10.1038/ncomms9042
Bleicken S, Jeschke G, Stegmueller C, Salvador-Gallego R, García-Sáez Ana J, Bordignon E (2014) Structural model of active Bax at the membrane. Mol Cell 56:496. https://doi.org/10.1016/j.molcel.2014.09.022
Desagher S, Osen-Sand A, Nichols A, Eskes R, Montessuit S, Lauper S, Maundrell K, Antonsson B, Martinou J-C (1999) Bid-induced conformational change of Bax is responsible for mitochondrial cytochrome c release during apoptosis. J Cell Biol 144:891–901
Subburaj Y (2014) Single particle tracking to characterize the mechanism of pore formation by pore-forming proteins. University of Tübingen, Tübingen
Shamas-Din A, Binder S, Zhu W, Zaltsman Y, Campbell C, Gross A, Leber B, Andrews DW, Fradin C (2013) tBid undergoes multiple conformational changes at the membrane required for Bax activation. J Biol Chem 288(30):22111–22127. https://doi.org/10.1074/jbc.M113.482109
Lovell JF, Billen LP, Bindner S, Shamas-Din A, Fradin C, Leber B, Andrews DW (2008) Membrane binding by tBid initiates an ordered series of events culminating in membrane permeabilization by Bax. Cell 135(6):1074–1084. https://doi.org/10.1016/j.cell.2008.11.010
Burnham NA, Chen X, Hodges CS, Matei GA, Thoreson EJ, Roberts CJ, Davies MC, Tendler SJB (2002) Comparison of calibration methods for atomic-force microscopy. Nanotechnology 14:1–6
Sader JE, Larson I, Mulvaney P, White LR (1995) Method for the calibration of atomic force microscope cantilevers. Rev Sci Instrum 66(7):3789. https://doi.org/10.1063/1.1145439
Miller EJ, Trewby W, Payam AF, Piantanida L, Cafolla C, Voitchovsky K (2016) Sub-nanometer resolution imaging with amplitude-modulation atomic force microscopy in liquid. J Vis Exp:e54924. https://doi.org/10.3791/54924
Alessandrini A, Seeger Heiko M, Caramaschi T, Facci P (2012) Dynamic force spectroscopy on supported lipid bilayers: effect of temperature and sample preparation. Biophys J 103(1):38–47. https://doi.org/10.1016/j.bpj.2012.05.039
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Unsay, J.D., García-Sáez, A.J. (2019). AFM to Study Pore-Forming Proteins. In: Santos, N., Carvalho, F. (eds) Atomic Force Microscopy. Methods in Molecular Biology, vol 1886. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8894-5_10
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8894-5_10
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8893-8
Online ISBN: 978-1-4939-8894-5
eBook Packages: Springer Protocols