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Detecting Molecular Fingerprints in Single Molecule Force Spectroscopy Using Pattern Recognition

Hendrik Dietz, Matthias Rief
2007 Japanese Journal of Applied Physics  
Single molecule force spectroscopy has given experimental access to the mechanical properties of protein molecules.  ...  A key issue in single molecule force spectroscopy is thus to identify the characteristic mechanical "fingerprint" of a specific protein in noisy data sets.  ...  Acknowledgments Financial support of the German Excellence Initiative via the Nanosystems Initiative Munich (NIM) is gratefully acknowledged.  ... 
doi:10.1143/jjap.46.5540 fatcat:u7sq2tvkcjbzjiktcwuop5bux4

A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy

A. Marsico, D. Labudde, T. Sapra, D. J. Muller, M. Schroeder
2007 Bioinformatics  
Singlemolecule force spectroscopy is a novel technique, which measures the force necessary to pull a protein out of a membrane.  ...  Manual analysis of these data is a bottleneck and source of inconsistent and subjective annotation.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btl293 pmid:17237097 fatcat:hvxju4dspvawzhppw4p75igpxy

Nanomechanical Recognition Measurements of Individual DNA Molecules Reveal Epigenetic Methylation Patterns

Rong Zhu, Stefan Howorka, Johannes Pröll, Ferry Kienberger, Johannes Preiner, Jan Hesse, Andreas Ebner, Vassilli Ph Pastushenko, Hermann J. Gruber, Peter Hinterdorfer
2011 Biophysical Journal  
[6] Gutierrez-Medina, B., et al. in Methods in Enzymology: Single Molecule Tools, Pt B. 474: pp. 377-404 (2010). 828 - 828 Pos Board B628 Simultaneous AFM Force Spectroscopy and FRET Measurements  ...  We have built a novel magnetic force transducer or ''tweezer'' that can apply a wide range of pico-newton scale forces on single DNA molecules in the horizontal plane.  ... 
doi:10.1016/j.bpj.2010.12.1041 fatcat:bokorinh5jhivpyk4kbecif56q

Analysis of DNA interactions using single-molecule force spectroscopy

Markus Ritzefeld, Volker Walhorn, Dario Anselmetti, Norbert Sewald
2013 Amino Acids  
AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions.  ...  This review article focusses on atomic force microscopy (AFM)-based singlemolecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation  ...  in single-molecule force spectroscopy.  ... 
doi:10.1007/s00726-013-1474-4 pmid:23468137 fatcat:vi7atfy7pnfjfj4iwl3dchsr6m

Combined Recognition Imaging and Force Spectroscopy: A New Mode for Mapping and Studying Interaction Sites at Low Lateral Density

Melanie Koehler, Gabriel Macher, Anne Rupprecht, Rong Zhu, HermannJ. Gruber, ElenaE. Pohl, Peter Hinterdorfer
2017 Science of Advanced Materials  
We combined recognition imaging and force spectroscopy to study the interactions between receptors and ligands on the single molecule level.  ...  This method allowed the selection of a single receptor molecule reconstituted in a supported lipid membrane at low density, with the subsequent quantification of the receptor-ligand unbinding force.  ...  for exploring such forces on the single molecule level by employing the force spectroscopy mode. 3 This technique has been widely used to gain new insights into the molecular principles of many biological  ... 
doi:10.1166/sam.2017.3066 pmid:29743989 pmcid:PMC5937678 fatcat:lurhzrfcpzdmrjebr5i5ifehdi

Detection and localization of single molecular recognition events using atomic force microscopy

Peter Hinterdorfer, Yves F Dufrêne
2006 Nature Methods  
) forces associated with single molecules 5,6 thereby providing fundamental insights into the molecular basis of biological phenomena and properties as diverse as molecular recognition 7-9 , protein folding  ...  and localizing single molecular recognition events.  ...  Here we describe current methodologies for sensing single molecular recognition events using AFM force spectroscopy.  ... 
doi:10.1038/nmeth871 pmid:16628204 fatcat:glvzw7g6pbhyrhcqhvjqq4fwum

Simultaneous AFM Force Spectroscopy and FRET Measurements on Single Biological Molecules

Hui Li, Chi-Fu Yen, Sanjeevi Sivasankar
2011 Biophysical Journal  
[6] Gutierrez-Medina, B., et al. in Methods in Enzymology: Single Molecule Tools, Pt B. 474: pp. 377-404 (2010). 828 - 828 Pos Board B628 Simultaneous AFM Force Spectroscopy and FRET Measurements  ...  We have built a novel magnetic force transducer or ''tweezer'' that can apply a wide range of pico-newton scale forces on single DNA molecules in the horizontal plane.  ... 
doi:10.1016/j.bpj.2010.12.1040 fatcat:lprwhsl4xjf6bhlsyskwh6llde

Atomic Force Microscopy and Quartz Crystal Microbalance Study of the Lectin-Carbohydrate Interaction Kinetics

K. Lebed, A.J. Kulik, L. Forró, M. Lekka
2007 Acta Physica Polonica. A  
Atomic force microscopy in force spectroscopy mode enabled the determination of the energy barrier position of r = 2.29 ± 0.04Å characterizing the dissociation of concanavalin Acarboxypeptidase Y molecular  ...  specific lectin-carbohydrate recognition.  ...  Results Force spectroscopy Prior to force spectroscopy measurements, the spatial distribution of studied proteins on the micro-sized area was made via molecular patterning.  ... 
doi:10.12693/aphyspola.111.273 fatcat:gj3bzbeznfdtnpfnrisfltot6e

Covalent immobilization of recombinant fusion proteins with hAGT for single molecule force spectroscopy

Stefan K. Kufer, Hendrik Dietz, Christian Albrecht, Kerstin Blank, Angelika Kardinal, Matthias Rief, Hermann E. Gaub
2005 European Biophysics Journal  
Individual fusion proteins were unfolded by single molecule force spectroscopy corroborating the selectivity of the covalent attachment.  ...  Anchoring was characterized and quantified with surface plasmon resonance, atomic force microscope and fluorescence measurements.  ...  It is clearly visible that at the BG activated spot the frequency of partial (c>0.2) and good matching (c>0.35) with the three Titin domain-unfolding pattern is by far higher than at the non-activated  ... 
doi:10.1007/s00249-005-0010-1 pmid:16160825 fatcat:afnh4iuzhfgj5esv7qlqiiaieu

Proteoglycan Mechanics Studied by Single-molecule Force Spectroscopy of Allotypic Cell Adhesion Glycans

Sergi Garcia-Manyes, Iwona Bucior, Robert Ros, Dario Anselmetti, Fausto Sanz, Max M. Burger, Xavier Fernàndez-Busquets
2005 Journal of Biological Chemistry  
Singlemolecule force spectroscopy studies of the mechanics of aggregation factor self-binding indicate the existence of intermolecular carbohydrate adhesion domains.  ...  We have purified two of these g200 distinct forms from two individuals of the same sponge species. Comparison of allotypic versus isotypic g200 binding forces reveals significant differences.  ...  Stefan Vinzelberg (Atomic Force, Germany) for help in software development.  ... 
doi:10.1074/jbc.m507878200 pmid:16373355 fatcat:d7l5szn3nffl7kplr6ssbp4gn4

Atomic Force Microscopy: A New Look at Pathogens

David Alsteens, Audrey Beaussart, Sofiane El-Kirat-Chatel, Ruby May A. Sullan, Yves F. Dufrêne, Joseph Heitman
2013 PLoS Pathogens  
Figure 1 . 1 Single-molecule force spectroscopy experiments unravel the nanomechanics of microbial adhesins.  ...  Series of force-distance profiles obtained by stretching adhesins from various microbial species (see text for details): single adhesion peaks reflecting specific recognition (A), sawtooth patterns with  ... 
doi:10.1371/journal.ppat.1003516 pmid:24039570 pmcid:PMC3764196 fatcat:txsixyycxnhftjcxusvtgzxspy

Comparing Proteins by Their Unfolding Pattern

Elias M. Puchner, Gereon Franzen, Mathias Gautel, Hermann E. Gaub
2008 Biophysical Journal  
Single molecule force spectroscopy has evolved into an important and extremely powerful technique for investigating the folding potentials of biomolecules.  ...  The potential of this new method for accurate and automated analysis of force spectroscopy data and for novel automated screening techniques is shown with bacteriorhodopsin and with protein constructs  ...  In this article, we describe a solution for single molecule force spectroscopy.  ... 
doi:10.1529/biophysj.108.129999 pmid:18550806 pmcid:PMC2426622 fatcat:el2gmkqdjzal7a5j2mgquap3lq

Network theory approach for data evaluation in the dynamic force spectroscopy of biomolecular interactions

J. Živković, M. Mitrović, L. Janssen, H. A. Heus, B. Tadić, S. Speller
2010 Europhysics letters  
Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding,  ...  Within our data sets the methodology systematically separates subgroups of curves which are related to different intermolecular interactions and to spatial arrangements in which the molecules are brought  ...  Abstract -Investigations of bonds between single molecules and molecular complexes by dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible aspecific binding, which mask  ... 
doi:10.1209/0295-5075/89/68004 fatcat:oun2ocl3unhpdeqvxmk7xvgxqq

Using Single Molecule Force Spectroscopy to Probe Proteins from Extremophiles

Lorna Dougan
2015 Biophysical Journal  
Here, we report the first structure of "open" and assembled ESCRT-III proteins.  ...  The ESCRT pathway mediates a series of important cellular membrane remodeling and fission events, including cytokinetic abscission.  ...  We use single molecule force spectroscopy to measure the mechanical stability and flexibility of proteins derived from extremophile organisms.  ... 
doi:10.1016/j.bpj.2014.11.1966 fatcat:dyhznb27zfb3dblvru7hfgf6pa

Droplet Tracking for Single Molecule Confinement

Benjamin D. Gamari, Mark E. Arsenault, Peker Milas, Richard E. Buckman, Christophe Wilhelm, Lori S. Goldner
2011 Biophysical Journal  
[6] Gutierrez-Medina, B., et al. in Methods in Enzymology: Single Molecule Tools, Pt B. 474: pp. 377-404 (2010). 828 - 828 Pos Board B628 Simultaneous AFM Force Spectroscopy and FRET Measurements  ...  We have built a novel magnetic force transducer or ''tweezer'' that can apply a wide range of pico-newton scale forces on single DNA molecules in the horizontal plane.  ... 
doi:10.1016/j.bpj.2010.12.1042 fatcat:snor2vuo4bdwjdmwjxmzieepi4
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