Automated alignment and pattern recognition of single-molecule force spectroscopy data

Journal of Microscopy

Volumn 218, Issue 2, 2005, Pages 125-132

  Kuhn, M ^a,b   Janovjak, H ^b   Hubain, M ^b   Müller, Daniel J ^b  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Molecular interactions; Protein folding; Statistical analysis

Indexed keywords

C++ (PROGRAMMING LANGUAGE); LIGANDS; MOLECULES; NANOCANTILEVERS; OPEN SOURCE SOFTWARE; OPEN SYSTEMS; PATTERN RECOGNITION; PROTEINS;

ATOMIC FORCE; AUTOMATED ALIGNMENTS; DIRECT MEASUREMENT; FORCE SPECTRA; MEASUREMENTS OF; PROTEIN FOLDINGS; SINGLE MOLECULE FORCE SPECTROSCOPY; SPECTRA'S; SPECTROSCOPY DATA; UNFOLDINGS;

ATOMIC FORCE MICROSCOPY;

BACTERIORHODOPSIN; MEMBRANE PROTEIN; NHAA PROTEIN; POLYMER; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; ATOMIC FORCE MICROSCOPY; AUTOMATION; CALCULATION; CHEMICAL BOND; COMPUTER PROGRAM; DATA ANALYSIS; FORCE; MEASUREMENT; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PARAMETER; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; SPECTROSCOPY; SPECTRUM; STATISTICAL ANALYSIS; SURFACE PROPERTY; TECHNIQUE;

EID: 18444364820     PISSN: 00222720     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2818.2005.01478.x     Document Type: Article

References (20)

1. Albrecht, C., Blank, K., Lalic-Multhaler, M., et al. (2003) DNA: a programmable force sensor. Science, 301, 367-370.
2. Benoit, M., Gabriel, D., Gerisch, G. & Gaub, H. (2000) Discrete interactions in cell adhesion measured by single-molecule force spectroscopy. Nat Cell Biol. 2, 313-317.
3. Carl, P. & Dalhaimer, P. (2004) http://www.mpikg-golm.mpg.de/gf/ people/fery/techniques/PUNIAS/.
4. Carl, P., Kwok, C.H., Manderson, G., Speicher, D.W. & Discher, D.E. (2001) Forced unfolding modulated by disulflde bonds in the Ig domains of a cell adhesion molecule. Proc. Natl Acad. Sci. USA. 98, 1565-1570.
5. Dammer, U., Hegner, M., Anselmetti, D., Wagner, P., Dreier, M., Huber, W. & Güntherodt, H. (1996) Specific antigen/antibody interactions measured by force microscopy. Biophys. J. 70, 2437-2441.
6. Fritz, J., Katopodis, A.G., Kolbinger, F. & Anselmetti, D. (1998) Force-mediated kinetics of single P-selectin/ligand complexes observed by atomic force microscopy. Proc. Natl Acad. Sci. USA. 95, 12283-12288.
7. Gergely, C., Senger, B., Voegel, J.C., Horber, J.K.H., Schaaf, P. & Hemmerle, J. (2001) Semi-automatized processing of AFM force-spectroscopy data. Ultramicroscopy. 87, 67-78.
8. Janovjak, H., Kessler, M., Oesterhelt, D., Gaub, H. & Müller, D.J. (2003) Unfolding pathways of native bacteriorhodopsin depend on temperature. EMBO J. 22, 5220-5229.
9. Kasas, S., Riederer, B.M., Catsicas, S., Cappella, B. & Dietler, G. (2000) Fuzzy logic algorithm to extract specific interaction forces from atomic force microscopy data. Rev. Sci. Instrum. 71, 2082-2086.
10. Kedrov, A., Ziegler, C., Janovjak, H., Kühlbrandt, W. & Müller, D.J. (2004) Controlled unfolding and refolding of a single sodium-proton antiporter using atomic force microscopy. J. Mol. Biol. 340, 1143-1152.
11. Leckband, D. & Israelachvili, J. (2001) Intermolecular forces in biology. Quart. Rev. Biophys. 34, 105-267.
12. Möller, C., Fotiadis, D., Suda, K., Engel, A., Kessler, M. & Müller. D.J. (2003) Determining molecular forces that stabilize human aquaporin-1. J. Struct. Biol. 142, 369-378.
13. Müller, D.J., 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.
14. Oberhauser, A.F., Marszalek, P.E., Erickson, H.P. & Fernandez, J.M. (1998) The molecular elasticity of the extracellular matrix protein tenascin. Nature. 393, 181-185.
15. Oesterhelt, F., Oesterhelt, D., Pfeiffer, M., Engel, A., Gaub, H.E. & Müller, D.J. (2000) Unfolding pathways of individual bacteriorhodopsins. Science, 288, 143-146.
16. Rief, M., Gautel, M., Oesterhelt, E. Fernandez, J.M. & Gaub, H.E. (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science. 276, 1109-1112.
17. Rief, M., Gautel, M., Schemmel, A. & Gaub, H.E. (1998) The mechanical stability of immunoglobulin and fibronectin III domains in the muscle protein titin measured by atomic force microscopy. Biophys. J. 75. 3008-3014.
18. Saxton, W.O. (1996) Semper: Distortion compensation, selective averaging, 3-D reconstruction, and transfer function correction in a highly programmable system. J. Struct. Biol. 116, 230-236.
19. Williams, P.M., Fowler, S.B., Best, R.B., LuisToca-Herrera, J., Scott, K.A., Steward, A. & Clarke, J. (2003) Hidden complexity in the mechanical properties of titin. Nature, 422, 446-449.
20. Yeung, K., Medvedovic, M. & Bumgarner, R. (2003) Clustering gene-expression data with repeated measurements. Genome Biol. 4, R34.