Reconsideration of dynamic force spectroscopy analysis of streptavidin-biotin interactions

International Journal of Molecular Sciences

Volumn 11, Issue 5, 2010, Pages 2135-2151

  Taninaka, Atsushi ^a   Takeuchi, Osamu ^a   Shigekawa, Hidemi ^a  

^a UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

Atomic force microscopy; Dynamic force spectroscopy; Site selective analysis; Streptavidin biotin interaction

Indexed keywords

BIOTIN; STREPTAVIDIN;

ACCURACY; ARTICLE; ATOMIC FORCE MICROSCOPY; CONTROLLED STUDY; CROSS LINKING; DYNAMIC FORCE SPECTROSCOPY; MEASUREMENT; MOLECULAR INTERACTION; MOLECULAR PROBE; PREDICTION; PROTEIN ANALYSIS; PROTEIN INTERACTION; SPECTROSCOPY; CHEMISTRY; PROCEDURES;

BIOTIN; MICROSCOPY, ATOMIC FORCE; SPECTRUM ANALYSIS; STREPTAVIDIN;

EID: 77953399255     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms11052134     Document Type: Article

References (31)

1. Badjić, J.D.; Balzani, V.; Credi, A.; Silvi, S.; Stoddart, J.F. A molecular elevator. Science 2004, 303, 1845-1849.
2. Kay, E.R.; Leigh, D.A.; Zerbetto, F. Synthetic molecular motors and mechanical machines. Angew. Chem.: Int. Ed. 2007, 46, 72-192.
3. Ariga, K.; Hill, J.P.; Endo, H. Developments in molecular recognition and sensing at interfaces. Int. J. Mol. Sci. 2007, 8, 864-883.
4. Vestergaard, M.; Kerman, K.; Tamiya, E. An overview of label-free electrochemical protein. Sensors 2007, 7, 3442-3458.
5. Yasuda, S.; Okutsu, Y.; Suzuki, I.; Shinohara, K.; Komiyama, M.; Takeuchi O.; Shigekawa, H. Single molecular anatomy of host-guest chemistry based on atomic force microscopy study of cyclodextrin-ferrocene molecular interaction. Jpn. J. Appl. Phys. 2007, 46, 5614-5616.
6. Yasuda, S.; Suzuki, I.; Shinohara, K.; Shigekawa, H. Single molecular anatomy of solvophobic effects in host-guest interactions based on surface tension using atomic force microscopy. Phys. Rev. Lett. 2006, 96, 228303:1-228303:4.
7. Sulchek, T.A.; Friddle, R.W.; Langry, K.; Lau, E.Y.; Albrecht, H.; Ratto, T.V.; DeNardo, S.J.; Colvin, M.E.; Noy, A. Dynamic force spectroscopy of parallel individual Mucin1-antibody bonds Proc. Natl. Acad. Sci. 2005, 102, 16638-16643.
8. Neuert, G.; Albrecht, C.; Pamir, E.; Gaub, H.E. Dynamic force spectroscopy of the digoxigenin-antibody complex. FEBS Lett. 2006, 580, 505-509.
9. Merkel, R.; Nassoy, P.; Leung, A.; Ritchie, K.; Evans, E. Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy. Nature 1999, 397, 50-53.
10. Evans, E. Introductory Lecture Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectroscopy. Faraday Discuss. 1998, 111, 1.
11. Yuan, C.; Chen, A.; Kolb, R.; Moy, V.T. Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy. Biochemistry 2000, 39, 10219-10223.
12. Patel, A.B.; Allen, S.; Davies, M.C.; Roberts, C.J.; Tendler, S.J.B.; Williams, P. M. Influence of architecture on the kinetic stability of molecular assemblies. J. Am. Chem. Soc. 2004, 126, 1318-1319.
13. Piramowicz, M.O.; Czuba, P.; Targosz, M.; Burda, K.; Szymo ski, M. Dynamic force measurements of avidin-biotin and streptavdin-biotin interactions using AFM. Acta Biochim. Polon. 2006, 53, 93-100.
14. Wong, J.; Chilkoti, A.; Moy. V.T. Direct force measurements of the streptavidin-biotin interaction. Biomol. Eng. 1999, 16, 45-55.
15. Taninaka, A.; Takeuchi, O.; Shigekawa, H. Site-selective anatomy of step-by-step reactions in ligand-receptor bonding processes using dynamic force spectroscopy. Appl. Phys. Express 2009, 2, 085002:1-085002:3.
16. Takeuchi, O.; Miyakoshi, T.; Taninaka, A.; Tanaka, K.; Cho, D.; Fujita, M.; Yasuda, S.; Jarvis, S.P.; Shigekawa, H. Dynamic-force spectroscopy measurement with precise force control using atomic-force microscopy probe. J. Appl. Phys. 2006, 100, 074315:1-074315:6.
17. Oberhauser, A.F.; Hansma, P.K.; Vazquez, M.C.; Fernandez, J.M. Stepwise unfolding of titin under force-clamp atomic force microscopy. Proc. Natl. Acad. Sci. 2001, 98, 468-472.
18. Marszalek, P.E.; Li, H.; Oberhauser, A.F.; Fernandez J.M. Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM. Proc. Natl. Acad. Sci. 2002, 99, 4278-4283.
19. Evans, E.; Ritchie, K. Dynamic strength of molecular adhesion bonds. Biophys. J. 1999, 72, 1541-1555
20. Evans, E.; Ritchie, K. Strength of a weak bond connecting flexible polymer chains. Biophys. J. 1999, 76, 2439-2447.
21. Pierres, A.; Touchard, D.; Benoliel, A.-M.; Bongrand, P. Dissecting streptavidin-biotin interaction with a laminar flow chamber. Biophys. J. 2002, 82, 3214-3223.
22. Friedsam, C.; Wehle, A.K.; Kühner, F.; Gaub, H.E. Dynamic single-molecule force spectroscopy: bond rupture analysis with variable spacer length. J. Phys: Condens. Matter 2003, 15, S1709-S1723.
23. Pincet, F.; Husson, J. The solution to the streptavidin-biotin paradox: The influence of history on the strength of single molecular bonds. Biophys. J. 2005, 89, 4374-4381.
24. Husson, J.; Pincet, F. Analyzing single-bond experiments: Influence of the shape of the energy landscape and universal law between the width, depth, and force spectrum of the bond. Phys. Rev. E 2008, 77, 026108:1-026108:14.
25. Strunz, T.; Oroszlan, K.; Schumakovitch, I.; Güntherodt, H.-J.; Hegner, M. Model energy landscapes and the force-induced dissociation of ligand-receptor bonds. Biophys. J. 2000, 79, 1206-1212.
26. Björnham, O.; Schedin, S. Methods and estimations of uncertainties in single-molecule dynamic force spectroscopy. Eur. Biophys. J. 2009, 38, 911-922.
27. We investigated the sampling rate dependence of the DFS analysis. Particularly for avidin-biotin bonding, the shape of the histogram of rupture force was severely deformed at the sampling rate of 1 kHz in comparison with that at the sampling rate of 100 kHz.
28. Weber, P.C.; Ohlendorf, D.H.; Wendoloski, J.J.; Salemme, F.R. Structural origins of high-affinity biotin binding to streptavidin. Science 1989, 243, 85-88.
29. Katz, B.A. Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH. J. Mol. Biol. 1997, 274, 776-800.
30. Grubmüller, H.; Heymann, B.; Tavan, P. Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force. Science 1996, 271, 997-999.
31. Zhou, J.; Zhang, L.; Yongsheng, L.; Tsao, H.-K.; Sheng, Y.-J.; Jiang, S. Unbinding of the streptavidin-biotin complex by atomic force microscopy: A hybrid simulation study. J. Chem. Phys. 2006, 125, 104905:1-104905:7.