Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed.

[1]  Henning Stahlberg,et al.  Characterization of the motion of membrane proteins using high-speed atomic force microscopy. , 2012, Nature nanotechnology.

[2]  Daniel J. Muller,et al.  Imaging and quantifying chemical and physical properties of native proteins at molecular resolution by force-volume AFM. , 2011, Angewandte Chemie.

[3]  Steve Barrett,et al.  Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy , 2015, Nano letters.

[4]  Manel Puig-Vidal,et al.  High-Speed Force Spectroscopy Unfolds Titin at the Velocity of Molecular Dynamics Simulations , 2013, Science.

[5]  Vamsi K Yadavalli,et al.  Investigating biomolecular recognition at the cell surface using atomic force microscopy. , 2014, Micron.

[6]  Celine Elie-Caille,et al.  Glyphosate-induced stiffening of HaCaT keratinocytes, a Peak Force Tapping study on living cells. , 2012, Journal of structural biology.

[7]  Daniel J. Müller,et al.  Out but not in: the large transmembrane β-barrel protein FhuA unfolds but cannot refold via β-hairpins. , 2012, Structure.

[8]  Laurent Cognet,et al.  A highly specific gold nanoprobe for live-cell single-molecule imaging. , 2013, Nano letters.

[9]  S. Lindsay,et al.  Recent Progress in Molecular Recognition Imaging Using Atomic Force Microscopy. , 2016, Accounts of chemical research.

[10]  Simon Scheuring,et al.  A hybrid high-speed atomic force–optical microscope for visualizing single membrane proteins on eukaryotic cells , 2013, Nature Communications.

[11]  Shuiqing Hu,et al.  PeakForce Tapping resolves individual microvilli on living cells† , 2015, Journal of molecular recognition : JMR.

[12]  Xiaotang Hu,et al.  Direct Observation of the Reversible Two-State Unfolding and Refolding of an α/β Protein by Single-Molecule Atomic Force Microscopy. , 2015, Angewandte Chemie.

[13]  Yves F Dufrêne,et al.  Unfolding individual als5p adhesion proteins on live cells. , 2009, ACS nano.

[14]  Xiaohong Fang,et al.  Living cell study at the single-molecule and single-cell levels by atomic force microscopy. , 2012, Nanomedicine.

[15]  Holger Schönherr,et al.  The effect of PeakForce tapping mode AFM imaging on the apparent shape of surface nanobubbles , 2013, Journal of physics. Condensed matter : an Institute of Physics journal.

[16]  Chanmin Su,et al.  Mechanical mapping of single membrane proteins at submolecular resolution. , 2011, Nano letters.

[17]  N. Santos,et al.  Atomic force microscopy-based molecular recognition of a fibrinogen receptor on human erythrocytes. , 2010, ACS nano.

[18]  Kei Kobayashi,et al.  Immunoactive two-dimensional self-assembly of monoclonal antibodies in aqueous solution revealed by atomic force microscopy. , 2014, Nature materials.

[19]  Y. Dufrêne,et al.  Detection and localization of single molecular recognition events using atomic force microscopy , 2006, Nature Methods.

[20]  T. Ando,et al.  Imaging of Nucleic Acids with Atomic Force Microscopy , 1990 .

[21]  Peter Hinterdorfer,et al.  Single-molecule recognition force spectroscopy of transmembrane transporters on living cells , 2011, Nature Protocols.

[22]  Mi Li,et al.  Nanoscale monitoring of drug actions on cell membrane using atomic force microscopy , 2015, Acta Pharmacologica Sinica.

[23]  N. Santos,et al.  Atomic force microscopy‐based force spectroscopy — biological and biomedical applications , 2012, IUBMB life.

[24]  Toshio Ando,et al.  High-speed atomic force microscopy coming of age , 2012, Nanotechnology.

[25]  Lianqing Liu,et al.  AFM analysis of the multiple types of molecular interactions involved in rituximab lymphoma therapy on patient tumor cells and NK cells. , 2014, Cellular immunology.

[26]  A. Ashworth,et al.  The DNA damage response and cancer therapy , 2012, Nature.

[27]  Xin Shang,et al.  Direct evidence of lipid rafts by in situ atomic force microscopy. , 2012, Small.

[28]  Giovanni Dietler,et al.  Time-lapse AFM imaging of DNA conformational changes induced by daunorubicin. , 2013, Nano letters.

[29]  Christopher Hein,et al.  High-speed atomic force microscopy reveals rotary catalysis of rotor-less F 1 -ATPase , 2011 .

[30]  David Balchin,et al.  In vivo aspects of protein folding and quality control , 2016, Science.

[31]  L. Oddershede,et al.  Force probing of individual molecules inside the living cell is now a reality. , 2012, Nature chemical biology.

[32]  Daniel A. Fletcher,et al.  Cell mechanics and the cytoskeleton , 2010, Nature.

[33]  Qingze Zou,et al.  High-speed adaptive contact-mode atomic force microscopy imaging with near-minimum-force. , 2014, The Review of scientific instruments.

[34]  John A Tainer,et al.  Super-resolution in solution X-ray scattering and its applications to structural systems biology. , 2013, Annual review of biophysics.

[35]  Hiroyuki Noji,et al.  High-Speed Atomic Force Microscopy Reveals Rotary Catalysis of Rotorless F1-ATPase , 2011, Science.

[36]  Andres F Oberhauser,et al.  Tracking unfolding and refolding reactions of single proteins using atomic force microscopy methods. , 2013, Methods.

[37]  Toshio Ando,et al.  Wide-area scanner for high-speed atomic force microscopy. , 2013, The Review of scientific instruments.

[38]  Michael Schmidt,et al.  Structural-mechanical characterization of nanoparticle exosomes in human saliva, using correlative AFM, FESEM, and force spectroscopy. , 2010, ACS nano.

[39]  Cees Dekker,et al.  High-Speed AFM Reveals the Dynamics of Single Biomolecules at the Nanometer Scale , 2011, Cell.

[40]  F. Kienberger,et al.  A new, simple method for linking of antibodies to atomic force microscopy tips. , 2007, Bioconjugate chemistry.

[41]  H Schindler,et al.  Detection and localization of individual antibody-antigen recognition events by atomic force microscopy. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Xiaohong Fang,et al.  Single-molecule force spectroscopy study of interaction between transforming growth factor beta1 and its receptor in living cells. , 2007, The journal of physical chemistry. B.

[43]  Daniel J Müller,et al.  Deciphering teneurin domains that facilitate cellular recognition, cell-cell adhesion, and neurite outgrowth using atomic force microscopy-based single-cell force spectroscopy. , 2013, Nano letters.

[44]  D. Lohr,et al.  Single-molecule recognition imaging microscopy. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Daniel J Müller,et al.  Atomic force microscopy: a nanoscopic window on the cell surface. , 2011, Trends in cell biology.

[46]  Adrian Wiestner,et al.  Unique Cell Surface Expression of Receptor Tyrosine Kinase ROR1 in Human B-Cell Chronic Lymphocytic Leukemia , 2008, Clinical Cancer Research.

[47]  Daniel J Müller,et al.  Quantitative imaging of the electrostatic field and potential generated by a transmembrane protein pore at subnanometer resolution. , 2013, Nano letters.

[48]  Aiko Yoshida,et al.  High-speed atomic force microscopy combined with inverted optical microscopy for studying cellular events , 2013, Scientific Reports.

[49]  Roderick Y. H. Lim,et al.  Spatiotemporal dynamics of the nuclear pore complex transport barrier resolved by high-speed atomic force microscopy. , 2016, Nature nanotechnology.

[50]  J. Hoh,et al.  Surface morphology and mechanical properties of MDCK monolayers by atomic force microscopy , 1996 .

[51]  M. Lekka Discrimination Between Normal and Cancerous Cells Using AFM , 2016, BioNanoScience.

[52]  Lianqing Liu,et al.  Rapid recognition and functional analysis of membrane proteins on human cancer cells using atomic force microscopy. , 2016, Journal of immunological methods.

[53]  Chih-Kung Lee,et al.  Atomic force microscopy: determination of unbinding force, off rate and energy barrier for protein-ligand interaction. , 2007, Micron.

[54]  P. Park,et al.  Atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands. , 2014, Biochimica et biophysica acta.

[55]  A. Fuhrmann,et al.  Single-molecule force spectroscopy: a method for quantitative analysis of ligand-receptor interactions. , 2010, Nanomedicine.

[56]  Peter Hinterdorfer,et al.  Ligands on the string: single-molecule AFM studies on the interaction of antibodies and substrates with the Na+-glucose co-transporter SGLT1 in living cells , 2006, Journal of Cell Science.

[57]  Lianqing Liu,et al.  Mapping CD20 molecules on the lymphoma cell surface using atomic force microscopy , 2013 .

[58]  Lianqing Liu,et al.  Progress of AFM single-cell and single-molecule morphology imaging , 2013 .

[59]  D. Müller,et al.  Multiparametric imaging of biological systems by force-distance curve–based AFM , 2013, Nature Methods.

[60]  Aiko Yoshida,et al.  Probing in vivo dynamics of mitochondria and cortical actin networks using high‐speed atomic force/fluorescence microscopy , 2015, Genes to cells : devoted to molecular & cellular mechanisms.

[61]  Toshio Ando,et al.  High-speed AFM imaging. , 2014, Current opinion in structural biology.

[62]  Douglas J Taatjes,et al.  Atomic force microscopy: High resolution dynamic imaging of cellular and molecular structure in health and disease , 2013, Journal of cellular physiology.

[63]  Boris Mizaikoff,et al.  Combined atomic force microscopy-fluorescence microscopy: analyzing exocytosis in alveolar type II cells. , 2012, Analytical chemistry.

[64]  Jing Zhang,et al.  Nanoscale organization of human GnRH-R on human bladder cancer cells. , 2014, Analytical chemistry.

[65]  Y. WANG,et al.  Nanoscale distribution of CD20 on B‐cell lymphoma tumour cells and its potential role in the clinical efficacy of rituximab , 2014, Journal of microscopy.

[66]  Andreas Ebner,et al.  Mapping the Nucleotide Binding Site of Uncoupling Protein 1 Using Atomic Force Microscopy , 2013, Journal of the American Chemical Society.

[67]  Daniel J. Muller,et al.  Multiparametric high-resolution imaging of native proteins by force-distance curve–based AFM , 2014, Nature Protocols.

[68]  L. Staudt,et al.  Targeting pathological B cell receptor signalling in lymphoid malignancies , 2013, Nature Reviews Drug Discovery.

[69]  T. Ando,et al.  High-speed atomic force microscopy for nano-visualization of dynamic biomolecular processes , 2008 .

[70]  D. Schübeler Function and information content of DNA methylation , 2015, Nature.

[71]  Toshio Ando,et al.  Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells , 2015, Scientific Reports.

[72]  Ilia Loubana,et al.  Corrections , 2016, The Lancet Neurology.

[73]  Sjors H. W. Scheres,et al.  Unravelling biological macromolecules with cryo-electron microscopy , 2016, Nature.

[74]  M. Rief,et al.  Reversible unfolding of individual titin immunoglobulin domains by AFM. , 1997, Science.

[75]  Lianqing Liu,et al.  Nanoscale mapping and organization analysis of target proteins on cancer cells from B-cell lymphoma patients. , 2013, Experimental cell research.

[76]  David Alsteens,et al.  Single-molecule imaging and functional analysis of Als adhesins and mannans during Candida albicans morphogenesis. , 2012, ACS nano.

[77]  Yves F Dufrêne,et al.  Single-molecule imaging of cell surfaces using near-field nanoscopy. , 2012, Accounts of chemical research.

[78]  Evan Evans,et al.  Five challenges to bringing single-molecule force spectroscopy into living cells , 2011, Nature Methods.

[79]  Toshio Ando,et al.  Video imaging of walking myosin V by high-speed atomic force microscopy , 2010, Nature.

[80]  H. Gaub,et al.  Unfolding pathways of individual bacteriorhodopsins. , 2000, Science.

[81]  Yuping Shan,et al.  The structure and function of cell membranes examined by atomic force microscopy and single-molecule force spectroscopy. , 2015, Chemical Society reviews.

[82]  Steven M Block,et al.  Reconstructing folding energy landscapes by single-molecule force spectroscopy. , 2014, Annual review of biophysics.

[83]  B. Druker,et al.  Crosstalk between ROR1 and the Pre-B cell receptor promotes survival of t(1;19) acute lymphoblastic leukemia. , 2012, Cancer cell.

[84]  Liping Xu,et al.  Heterobivalent ligands target cell-surface receptor combinations in vivo , 2012, Proceedings of the National Academy of Sciences.

[85]  H. Gaub,et al.  Adhesion forces between individual ligand-receptor pairs. , 1994, Science.

[86]  I. Martins,et al.  Atomic force microscopy and force spectroscopy on the assessment of protein folding and functionality. , 2013, Archives of biochemistry and biophysics.

[87]  Daniel J Müller,et al.  Atomic force microscopy and spectroscopy of native membrane proteins , 2007, Nature Protocols.

[88]  Andreas Ebner,et al.  IgGs are made for walking on bacterial and viral surfaces , 2014, Nature Communications.

[89]  Kei Kobayashi,et al.  Beyond the helix pitch: direct visualization of native DNA in aqueous solution. , 2013, ACS nano.

[90]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[91]  Patrice Soumillion,et al.  Multiparametric atomic force microscopy imaging of single bacteriophages extruding from living bacteria , 2013, Nature Communications.

[92]  Toshio Ando,et al.  High-speed AFM and nano-visualization of biomolecular processes , 2008, Pflügers Archiv - European Journal of Physiology.

[93]  Yves F Dufrêne,et al.  The yeast Wsc1 cell surface sensor behaves like a nanospring in vivo. , 2009, Nature chemical biology.

[94]  Lianqing Liu,et al.  Progress in measuring biophysical properties of membrane proteins with AFM single-molecule force spectroscopy , 2014 .

[95]  Toshio Ando,et al.  Filming Biomolecular Processes by High-Speed Atomic Force Microscopy , 2014, Chemical reviews.

[96]  Yves F Dufrêne,et al.  Force-induced formation and propagation of adhesion nanodomains in living fungal cells , 2010, Proceedings of the National Academy of Sciences.

[97]  Peter Hinterdorfer,et al.  Detection of HSP60 on the membrane surface of stressed human endothelial cells by atomic force and confocal microscopy , 2005, Journal of Cell Science.

[98]  Masayuki Endo,et al.  Single-molecule imaging of dynamic motions of biomolecules in DNA origami nanostructures using high-speed atomic force microscopy. , 2014, Accounts of chemical research.

[99]  Toshio Ando,et al.  High-speed atomic force microscopy techniques for observing dynamic biomolecular processes. , 2010, Methods in enzymology.

[100]  Lianqing Liu,et al.  Imaging and measuring the biophysical properties of Fc gamma receptors on single macrophages using atomic force microscopy. , 2013, Biochemical and biophysical research communications.

[101]  Lianqing Liu,et al.  Imaging and measuring the rituximab-induced changes of mechanical properties in B-lymphoma cells using atomic force microscopy. , 2011, Biochemical and biophysical research communications.

[102]  Piotr E. Marszalek,et al.  Stretching single molecules into novel conformations using the atomic force microscope , 2000, Nature Structural Biology.

[103]  Yves F Dufrêne,et al.  Atomic force microscopy – looking at mechanosensors on the cell surface , 2012, Journal of Cell Science.