Fluorescent Nucleoside Triphosphates for Single-Molecule Enzymology

Methods in Molecular Biology

Volumn 778, Issue , 2011, Pages 161-174

  Toseland, Christopher P ^a,b   Webb, Martin R ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

ATP; Fluorescent nucleotides; GTP; Motor proteins; TIRF microscopy

Indexed keywords

ADENOSINE TRIPHOSPHATE; GUANOSINE TRIPHOSPHATE;

ARTICLE; FLUORESCENCE MICROSCOPY; METABOLISM; METHODOLOGY;

ADENOSINE TRIPHOSPHATE; GUANOSINE TRIPHOSPHATE; MICROSCOPY, FLUORESCENCE;

EID: 80054768852     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-261-8_11     Document Type: Chapter

References (24)

1. Funatsu, T., Harada, Y., Tokunaga, M., Saito, K., and Yanagida, T. (1995) Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous solution. Nature 374, 555–559.
2. Ishijima, A., Kojima, H., Funatsu, T., Tokunaga, M., Higuchi, H., Tanaka, H., and Yanagida, T. (1998) Simultaneous observation of individual ATPase and mechanical events by a single myosin molecule during interaction with actin. Cell 92, 161–171.
3. Oiwa, K., Eccleston, J. F., Anson, M., Kikumoto, M., Davis, C. T., Reid, G. P., Ferenczi, M. A., Corrie, J. E., Yamada, A., Nakayama, H., and Trentham, D. R. (2000) Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives. Biophys. J. 78, 3048–3071.
4. Sakamoto, T., Webb, M. R., Forgacs, E., White, H. D., and Sellers, J. R. (2008) Direct observation of the mechanochemical coupling in myosin Va during processive movement. Nature 455, 128–132.
5. Ha, T. (2001) Single-molecule fluorescencresonance energy transfer. Methods 25, 78–86.
6. Henn, A., Cao, W., Hackney, D. D., and De La Cruz, E. M. (2008) The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA. J. Mol. Biol. 377, 193–205.
7. Moore, K. J., and Lohman, T. M. (1994) Kinetic mechanism of adenine nucleotide binding to and hydrolysis by the Escherichia coli Rep monomer. 2. Application of a kinetic competition approach. Biochemistry 33, 14565–14578.
8. Rossomando, E. F., Jahngen, J. H., and Eccleston, J. F. (1981) Formycin 5¢-triphos-phate, a fluorescent analog of ATP, as a substrate for adenylate cyclase. Proc. Natl. Acad. Sci. USA 78, 2278–2282.
9. Toseland, C. P., Martinez-Senac, M. M., Slatter, A. F., and Webb, M. R. (2009) The ATPase Cycle of PcrA Helicase and Its Coupling to Translocation on DNA. J. Mol. Biol. 392, 1020–1032.
10. Woodward, S. K., Eccleston, J. F., and Geeves, M. A. (1991) Kinetics of the interaction of 2¢(3¢)-O-(N-methylanthraniloyl)-ATP with myosin subfragment 1 and actomyosin subfragment 1: characterization of two acto-S1-ADP complexes. Biochemistry 30, 422–430.
11. Phillips, R. A., Hunter, J. L., Eccleston, J. F., and Webb, M. R. (2003) The mechanism of Ras GTPase activation by neurofibromin. Biochemistry 42, 3956–3965.
12. Cremo, C. R. (2003) Fluorescent nucleotides: synthesis and characterization. Methods Enzymol. 360, 128–177.
13. Jameson, D. M., and Eccleston, J. F. (1997) Fluorescent nucleotide analogs: synthesis and applications. Methods Enzymol. 278, 363–390.
14. Yarbrough, L. R., Schlageck, J. G., and Baughman, M. (1979) Synthesis and properties of fluorescent nucleotide substrates for DNA-dependent RNA polymerases. J. Biol. Chem. 254, 12069–12073.
15. Webb, M. R., Reid, G. P., Munasinghe, V. R., and Corrie, J. E. (2004) A series of related nucleotide analogues that aids optimization of fluorescence signals in probing the mechanism of P-loop ATPases, such as actomyosin. Biochemistry 43, 14463–14471.
16. Webb, M. R., and Corrie, J. E. (2001) Fluorescent coumarin-labeled nucleotides to measure ADP release from actomyosin. Biophys. J. 81, 1562–1569.
17. Cremo, C. R., Neuron, J. M., and Yount, R. G. (1990) Interaction of myosin subfragment 1 with fluorescent ribose-modified nucleotides. A comparison of vanadate trapping and SH1-SH2 cross-linking. Biochemistry 29, 3309–3319.
18. Forgacs, E., Cartwright, S., Kovacs, M., Sakamoto, T., Sellers, J. R., Corrie, J. E., Webb, M. R., and White, H. D. (2006) Kinetic mechanism of myosinV-S1 using a new fluorescent ATP analogue. Biochemistry 45, 13035–13045.
19. Brune, M., Hunter, J. L., Howell, S. A., Martin, S. R., Hazlett, T. L., Corrie, J. E., and Webb, M. R. (1998) Mechanism of inorganic phosphate interaction with phosphate binding protein from Escherichia coli. Biochemistry 37, 10370–10380.
20. Okoh, M. P., Hunter, J. L., Corrie, J. E., and Webb, M. R. (2006) A biosensor for inorganic phosphate using a rhodamine-labeled phosphate binding protein. Biochemistry 45, 14764–14771.
21. Mujumdar, R. B., Ernst, L. A., Mujumdar, S. R., Lewis, C. J., and Waggoner, A. S. (1993) Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters. Bioconjug. Chem. 4, 105–111.
22. Kurzawa-Goertz, S. E., Perreault-Micale, C. L., Trybus, K. M., Szent-Gyorgyi, A. G., and Geeves, M. A. (1998) Loop I can modulate ADP affinity, ATPase activity, and motility of different scallop myosins. Transient kinetic analysis of S1 isoforms. Biochemistry 37, 7517–7525.
23. Talavera, M. A., and De La Cruz, E. M. (2005) Equilibrium and kinetic analysis of nucleotide binding to the DEAD-box RNA helicase DbpA. Biochemistry 44, 959–970.
24. Webb, M. R. (1980) A method for determining the positional isotope exchange in a nucleoside triphosphate: cyclization of nucleoside triphosphate by dicyclohexylcarbodiimide. Biochemistry 19, 4744–4748.