Single-Molecule Protein Unfolding and Refolding Using Atomic Force Microscopy

Methods in Molecular Biology

Volumn 783, Issue , 2011, Pages 233-250

  Bornschlögl, Thomas ^a   Rief, Matthias ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Atomic force microscopy; Coiled coil engineering; Cystein engineering; Mechanical protein unfolding and refolding; Polyprotein design; Single molecule technique

Indexed keywords

PROTEIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMISTRY; METHODOLOGY; PROTEIN FOLDING; PROTEIN UNFOLDING;

MICROSCOPY, ATOMIC FORCE; PROTEIN FOLDING; PROTEIN UNFOLDING; PROTEINS;

EID: 80054722087     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-282-3_13     Document Type: Chapter

References (33)

1. Carrion-Vazquez, M., Oberhauser, A.F., Fisher, T.E., Marszalek, P.E., Li, H., and Fernandez, J.M., (2000) Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. Prog Biophys Mol Biol 74, 63–91.
2. Dietz, H., Bornschlögl, T., Heym, R., König, F., and Rief, M., (2007) Programming protein self assembly with coiled coils. New J. Phys 9, 424.
3. Dietz, H., Bertz, M., Schlierf, M., Berkemeier, F., Bornschlögl, T., Junker, J.P., and Rief, M., (2006) Cysteine engineering of polyproteins for single-molecule force spectroscopy. Nat Protoc 1, 80–84.
4. Fucini, P., Koppel, B., Schleicher, M., Lustig, A., Holak, T.A., Muller, R., Stewart, M., and Noegel, A.A., (1999) Molecular architecture of the rod domain of the Dictyostelium gelation factor (ABP120). J Mol Biol 291, 1017–1023.
5. Bornschlogl, T., and Rief, M., (2006) Single molecule unzipping of coiled coils: sequence resolved stability profiles. Phys Rev Lett 96, 118102.
6. Zitzewitz, J.A., Ibarra-Molero, B., Fishel, D. R., Terry, K.L., and Matthews, C.R., (2000) Preformed secondary structure drives the association reaction of GCN4-p1, a model coiled-coil system. J Mol Biol 296, 1105–1116.
7. Lupas, A., Van Dyke, M., and Stock, J., (1991) Predicting coiled coils from protein sequences. Science 252, 1162–1164.
8. Berger, B., Wilson, D.B., Wolf, E., Tonchev, T., Milla, M., and Kim, P.S., (1995) Predicting coiled coils by use of pairwise residue correlations. Proc Natl Acad Sci U S A 92, 8259–8263.
9. Hutter, J.L., and Bechhoefer, J., (1993) Calibration of atomic-force microscope tips. Rev. Sci. Instrum. 64, 1868.
10. Butt, H.J., and Jaschke, M., (1995) Calculation of thermal noise in atomic force microscopy. Nanotechnology 6, 1.
11. Burnham, N.A., Chen, X., Hodges, C.S., Matei, G.A., Thoreson, E.J., Roberts, C.J., Davies, M.C., and Tendler, S.J.B., (2003) Comparison of calibration methods for atomic-force microscopy cantilevers. Nanotechnology 14, 1.
12. Walters, D.A., Cleveland, J.P., Thomson, N. H., Hansma, P.K., Wendman, M.A., Gurley, G., and Elings. V., (1996) Short cantilevers for atomic force microscopy. Rev. Sci. Instrum. 67, 3583.
13. Dietz, H., and Rief, M., (2007) Detecting molecular fingerprints in single molecule force spectroscopy using pattern recognition. Jap J Appl Phys 46-8B, 5540.
14. Bustamante, C., Marko, J.F., Siggia, E.D., and Smith, S., (1994) Entropic elasticity of lambda-phage DNA. Science 265, 1599–1600.
15. Dietz, H., and Rief, M., (2006) Protein structure by mechanical triangulation. Proc Natl Acad Sci U S A 103, 1244–1247.
16. Bertz, M., and Rief, M., (2008) Mechanical unfoldons as building blocks of maltose-bind-ing protein. J Mol Biol 378, 447–458.
17. Schwaiger, I., Schleicher, M., Noegel, A.A., and Rief, M., (2005) The folding pathway of a fast-folding immunoglobulin domain revealed by single-molecule mechanical experiments. EMBO Rep 6, 46–51.
18. Izrailev, S., Stepaniants, S., Balsera, M., Oono, Y., and Schulten, K., (1997) Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J 72, 1568–1581.
19. Rounsevell, R., Forman, J.R., and Clarke, J., (2004) Atomic force microscopy: mechanical unfolding of proteins. Methods 34, 100–111.
20. Fernandez, J.M., and Li, H., (2004) Force-clamp spectroscopy monitors the folding trajectory of a single protein. Science 303, 1674–1678.
21. Schlierf, M., Berkemeier, F., and Rief, M., (2007) Direct observation of active protein folding using lock-in force spectroscopy. Biophys J 93, 3989–3998.
22. Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J.M., and Gaub, H.E., (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276, 1109–1112.
23. Junker, J.P., Ziegler, F., and Rief, M., (2009) Ligand-dependent equilibrium fluctuations of single calmodulin molecules. Science 323, 633–637.
24. Lee, G., Abdi, K., Jiang, Y., Michaely, P., Bennett, V., and Marszalek, P.E., (2006) Nano-spring behaviour of ankyrin repeats. Nature 440, 246–249.
25. Bustamante, C., Macosko, J.C., and Wuite, G. J., (2000) Grabbing the cat by the tail: manipulating molecules one by one. Nat Rev Mol Cell Biol 1, 130–136.
26. Tinoco, I., Jr., and Bustamante, C., (2002) The effect of force on thermodynamics and kinetics of single molecule reactions. Biophys Chem 101–102, 513–533.
27. Bornschlogl, T., and Rief, M., (2008) Single-molecule dynamics of mechanical coiled-coil unzipping. Langmuir 24, 1338–1342.
28. Politou, A.S., Gautel, M., Improta, S., Vange-lista, L., and Pastore, A., (1996) The elastic I-band region of titin is assembled in a “mod-ular” fashion by weakly interacting Ig-like domains. J Mol Biol 255, 604–616.
29. Borgia, A., Williams, P.M., and Clarke, J., (2008) Single-molecule studies of protein folding. Annu Rev Biochem 77, 101–125.
30. Linke, W.A., and Grutzner, A., (2008) Pulling single molecules of titin by AFM–recent advances and physiological implications. Pflu-gers Arch 456, 101–115.
31. Zhuang, X., and Rief, M., (2003) Single-molecule folding. Curr Opin Struct Biol 13, 88–97.
32. Clausen-Schaumann, H., Seitz, M., Kraut-bauer, R., and Gaub, H.E., (2000) Force spectroscopy with single bio-molecules. Curr Opin Chem Biol 4, 524–530.
33. Oberhauser, A.F., and Carrion-Vazquez, M., (2008) Mechanical biochemistry of proteins one molecule at a time. J Biol Chem 283, 6617–6621.