Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited

Nature Chemical Biology

Volumn 2, Issue 2, 2006, Pages 87-94

  English, Brian P ^a   Min, Wei ^a   Van Oijen, Antoine M ^a,c   Kang, Taek Lee ^a,d   Luo, Guobin ^a   Sun, Hongye ^a,e   Cherayil, Binny J ^a,b   Kou, S C ^a   Xie, X Sunney ^a  

^a HARVARD UNIVERSITY   (United States)

^b INDIAN INSTITUTE OF SCIENCE   (India)

^c HARVARD MEDICAL SCHOOL   (United States)

^d UNIVERSITY OF CHICAGO   (United States)

^e APPLIED BIOSYSTEMS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GALACTOSIDASE; ENZYME; GALACTOSIDE; OXAZINE DERIVATIVE; RESORUFIN GALACTOPYRANOSIDE;

ARTICLE; CATALYST; ENZYME KINETICS; ENZYME MECHANISM; ENZYME METABOLISM; ENZYME SUBSTRATE; MICHAELIS MENTEN KINETICS; MOLECULE; PRIORITY JOURNAL; CATALYSIS; CHEMISTRY; CONFORMATION; FLUORESCENCE MICROSCOPY; KINETICS; METABOLISM;

BETA-GALACTOSIDASE; CATALYSIS; GALACTOSIDES; KINETICS; MICROSCOPY, FLUORESCENCE; MOLECULAR CONFORMATION; OXAZINES;

EID: 33644910749     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio759     Document Type: Article

References (45)

1. Michaelis, L. & Menten, M.L. Kinetics of invertase action. Biochem. Z. 49, 333-369 (1913).
2. Moerner, W.E. & Orrit, M. Illuminating single molecules in condensed matter. Science 283, 1670-1676 (1999).
3. Xie, X.S. & Trautman, J.K. Optical studies of single molecules at room temperature. Annu. Rev. Phys. Chem. 49, 441-480 (1998).
4. Ishijima, A. & Yanagida, T. Single molecule nanobioscience. Trends Biochem. Sci. 26, 438-444 (2001).
5. Weiss, S. Fluorescence spectroscopy of single biomolecules. Science 283, 1676-1683 (1999).
6. Bustamante, C., Bryant, Z. & Smith, S.B. Ten years of tension: single-molecule DNA mechanics. Nature 421, 423-427 (2003).
7. Lu, H.P., Xun, L. & Xie, X.S. Single-molecule enzymatic dynamics. Science 282, 1877-1882 (1998).
8. Zhuang, X. et al. Correlating structural dynamics and function in single ribozyme molecules. Science 296, 1473-1476 (2002).
9. van Oijen, A.M. et al. Single-molecule kinetics of λ exonuclease reveal base dependence and dynamic disorder. Science 301, 1235-1239 (2003).
10. Velonia, K. et al. Single-enzyme kinetics of CALB-catalyzed hydrolysis. Angew. Chem. Intl. Edn. 44, 560-564 (2005).
11. Flomenbom, O. et al. Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules. Proc. Natl. Acad. Sci. USA 102, 2368-2372 (2005).
12. Yang, H. et al. Protein conformational dynamics probed by single-molecule electron transfer. Science 302, 262-266 (2003).
13. Min, W., Luo, G., Cherayil, B.J., Kou, S.C. & Xie, X.S. Observation of a power-law memory kernel for fluctuations within a single protein molecule. Phys. Rev. Lett. 94, 198302/1-198302/4 (2005).
14. Segel, I.H. Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady State Enzyme Systems (Wiley, New York, 1993).
15. Xie, X.S. Single-molecule approach to enzymology. Single Molecules 2, 229-236 (2001).
16. Qian, H. & Elson, E.L. Single-molecule enzymology: stochastic Michaelis-Menten kinetics. Biophys. Chem. 101-102, 565-576 (2002).
17. Kou, S.C., Cherayil, B.J., Min, W., English, B.P. & Xie, S.X. Single-molecule Michaelis-Menten equations. J. Phys. Chem. B 109, 19068-19081 (2005).
18. Fersht, A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (Freeman, New York, 1999).
19. Edman, L., Foldes-Papp, Z., Wennmalm, S. & Rigler, R. The fluctuating enzyme: a single molecule approach. Chem. Phys. 247, 11-22 (1999).
20. Jacobson, R.H., Zhang, X.J., DuBose, R.F. & Matthews, B.W. Three-dimensional structure of β-galactosidase from E. coli. Nature 369, 761-766 (1994).
21. Richard, J.P., Huber, R.E., Heo, C., Amyes, T.L. & Lin, S. Structure-reactivity relationships for β-galactosidase (Escherichia coli, lacZ). 4. Mechanism for reaction of nucleophiles with the galactosyl-enzyme intermediates of E461G and E461Q β-galactosidases. Biochemistry 35, 12387-12401 (1996).
22. Marchesi, S.L., Steers, E., Jr. & Shifrin, S. Purification and characterization of the multiple forms of β-galactosidase of Escherichia coli. Biochim. Biophys. Acta 181, 20-34 (1969).
23. Seong, G.H., Heo, J. & Crooks, R.M. Measurement of enzyme kinetics using a continuous-flow microfluidic system. Anal. Chem. 75, 3161-3167 (2003).
24. Hadd, A.G., Raymond, D.E., Halliwell, J.W., Jacobson, S.C. & Ramsey, J.M. Microchip device for performing enzyme assays. Anal. Chem. 69, 3407-3412 (1997).
25. Matthews, B.W. The structure of E. coli β-galactosidase. C. R. Biol. 328, 549-556 (2005).
26. Hofmann, J. & Sernetz, M. Immobilized enzyme kinetics analyzed by flow-through microfluorimetry. Resorufin-β-D-galactopyranoside as a new fluorogenic substrate for β-galactosidase. Anal. Chim. Acta 163, 67-72 (1984).
27. Ha, T. et al. Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419, 638-641 (2002).
28. Zwanzig, R. Rate processes with dynamical disorder. Acc. Chem. Res. 23, 148-152 (1990).
29. Karplus, M. Aspects of protein reaction dynamics: deviations from simple behavior. J. Phys. Chem. B 104, 11-27 (2000).
30. Mesecar, A.D., Stoddard, B.L. & Koshland, D.E., Jr. Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences. Science 277, 202-206 (1997).
31. Hammes, G.G. Multiple conformational changes in enzyme catalysis. Biochemistry 41, 8221-8228 (2002).
32. Austin, R.H., Beeson, K.W., Eisenstein, L., Frauenfelder, H. & Gunsalus, I.C. Dynamics of ligand binding to myoglobin. Biochemistry 14, 5355-5373 (1975).
33. Frauenfelder, H., Sligar, S.G. & Wolynes, P.G. The energy landscapes and motions of proteins. Science 254, 1598-1603 (1991).
34. Sakmann, B. & Neher, E. Single-Channel Recording 2nd. edn. (Plenum, New York and London, 1995).
35. Benkovic Stephen, J. & Hammes-Schiffer, S. A perspective on enzyme catalysis. Science 301, 1196-1202 (2003).
36. Kohen, A., Cannio, R., Bartolucci, S. & Klinman, J.P. Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase. Nature 399, 496-499 (1999).
37. Schnitzer, M.J. & Block, S.M. Statistical kinetics of processive enzymes. Cold Spring Harb. Symp. Quant. Biol. 60, 793-802 (1995).
38. Svoboda, K., Mitra, P.P. & Block, S.M. Fluctuation analysis of motor protein movement and single enzyme kinetics. Proc. Natl. Acad. Sci. USA 91, 11782-11786 (1994).
39. Yang, S. & Cao, J. Two-event echos in single-molecule kinetics: a signature of conformational fluctuations. J. Phys. Chem. B 105, 6536-6549 (2001).
40. Lippitz, M., Kulzer, F. & Orrit, M. Statistical evaluation of single nano-object fluorescence. ChemPhysChem 6, 770-789 (2005).
41. Lerch, H.-P., Rigler, R. & Mikhailov, A.S. Functional conformational motions in the turnover cycle of cholesterol oxidase. Proc. Natl. Acad. Sci. USA 102, 10807-10812 (2005).
42. Flomenbom, O., Klafter, J. & Szabo, A. What can one learn from two-state single-molecule trajectories? Biophys. J. 88, 3780-3783 (2005).
43. Barsegov, V., Chernyak, V. & Mukamel, S. Multitime correlation functions for single molecule kinetics with fluctuating bottlenecks. J. Chem. Phys. 116, 4240-4251 (2002).
44. Magde, D., Elson, E. & Webb, W.W. Thermodynamic fluctations in a reacting system. Measurement by fluorescence correlation spectroscopy. Phys. Rev. Lett. 29, 705-708 (1972).
45. Yang, S. & Cao, J. Direct measurements of memory effects in single-molecule kinetics. J. Chem. Phys. 117, 10996-11009 (2002).