Single-molecule enzymology: Stochastic Michaelis-Menten kinetics

Biophysical Chemistry

Volumn 101-102, Issue , 2002, Pages 565-576

  Qian, Hong ^a   Elson, Elliot L ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Deterministic kinetics; Enzyme dynamics; Non equilibrium; Oscillatory behaviour; Stochastic analysis

Indexed keywords

ENZYME;

ARTICLE; ENZYME CONFORMATION; ENZYME METABOLISM; ENZYME SUBSTRATE; ENZYMOLOGY; KINETICS; MICHAELIS CONSTANT; MOLECULAR DYNAMICS; OSCILLATION; PRIORITY JOURNAL; STEADY STATE; STOCHASTIC MODEL; TIME; ENZYME SPECIFICITY; METABOLISM;

ENZYMES; KINETICS; SUBSTRATE SPECIFICITY;

EID: 0037058951     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(02)00145-X     Document Type: Article

References (43)

1. Schellman J.A. Solvent denaturation. Biopolymers. 17:1978;1305-1322.
2. Schellman J.A. Fluctuation and linkage relations in macromolecular solution. Biopolymers. 29:1990;215-224.
3. Bai C.-L., Wang C., Xie X.S., Wolynes P.G. Single molecule physics and chemistry. Proc. Natl. Acad. Sci. USA. 96:1999;11075-11076.
4. Elson E.L., Webb W.W. Fluorescence correlation spectroscopy: a new biophysical probe based on occupation number fluctuations. Ann. Rev. Biophys. Bioeng. 4:1975;311-334.
5. Nie S., Chiu D.T., Zare R.N. Probing individual molecules with confocal fluorescence microscopy. Science. 266:1994;1018-1021.
6. Xie X.S., Trautman J.K. Optical studies of single-molecule at room temperature. Ann. Rev. Phys. Chem. 49:1998;441-480.
7. Edman L., Rigler R. Memory landscapes of single-enzyme molecules. Proc. Natl. Acad. Sci. USA. 97:2000;8266-8271.
8. Heikal A.A., Hess S.T., Baird G.S., Tsien R.Y., Webb W.W. Molecular spectroscopy and dynamics of intrinsically fluorescent proteins: Coral red (dsRed) and yellow (Citrine). Proc. Natl. Acad. Sci. USA. 97:2000;11996-12001.
9. Xie X.S., Lu H.P. Single-molecule enzymology. J. Biol. Chem. 274:1999;15967-15970.
10. Sakmann B., Neher E. Single-Channel Recording. 2nd Edition :1995;Plenum Press, New York.
11. Ball F.G., Rice J.A. Stochastic models for ion channels: introduction and bibliography. Math. Biosci. 112:1992;189-206.
12. Agmon N., Hopfield J.J. Transient kinetics of chemical reactions with bounded diffusion perpendicular to the reaction coordinate: intramolecular processes with slow conformational changes. J. Chem. Phys. 78:1983;6947-6959.
13. Qian H. Equations for stochastic macromolecular mechanics of single proteins: equilibrium fluctuations, transient kinetics and non-equilibrium steady-state. J. Phys. Chem. 106:2002;2065-2073.
14. Lu H.P., Xun L.-Y., Xie X.S. Single-molecule enzymatic dynamics. Science. 282:1998;1877-1882.
15. Hammes G.G. Enzyme Catalysis and Regulation. 2nd Edition :1982;Academic Press, New York.
16. Arkin A., Shen P., Ross J. A test case of correlation metric construction of a reaction pathway from measurements. Science. 29:1997;1275-1279.
17. Svoboda K., Mitra P.P., Block S.M. Fluctuation analysis of motor protein movement and single enzyme kinetics. Proc. Natl. Acad. Sci. USA. 91:1994;11782-11786.
18. Wang J., Wolynes P.G. Intermittency of single molecular reaction dynamics in fluctuating environments. Phys. Rev. Lett. 74:1995;4317-4320.
19. Qian H. A simple theory of motor protein kinetics and energetics II. Biophys. Chem. 83:2000;35-43.
20. Li G.P., Qian H. Kinetic timing: a novel mechanism for improving the accuracy of GTPase timers in endosome fusion and other biological processes. Traffic. 3:2002;249-255.
21. Schenter G.K., Lu H.P., Xie X.S. Statistical analysis and theoretical models of single-molecule enzymatic dynamics. J. Phys. Chem. 103:1999;10477-10488.
22. Segel I.H. Enzyme Kinetics. 1993;John Wiley & Sons, New York.
23. Nitzan A., Ross J. Oscillations, multiple steady-states, and instabilities in illuminated systems. J. Chem. Phys. 59:1973;241-250.
24. Hill T.L. Free Energy Transduction and Biochemical Cycle Kinetics. 1989;Springer-Verlag, New York.
25. Taylor H.M., Karlin S. An Introduction to Stochastic Modeling. 3rd Edition :1998;Academic Press, New York.
26. Hopfield J.J. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl. Acad. Sci. USA. 71:1974;4135-4139.
27. Qian H., Qian M. Pumped biochemical reactions, non-equilibrium circulation, and stochastic resonance. Phys. Rev. Lett. 84:2000;2271-2274.
28. Hahn H.-S., Nitzan A., Ortoleva P., Ross J. Threshold excitations, relaxation oscillations, and effect of noise in an enzyme reaction. Proc. Natl. Acad. Sci. USA. 71:1974;4067-4071.
29. Palmer A.G., Thompson N.L. High-order fluorescence fluctuation analysis of model protein clusters. Proc. Natl. Acad. Sci. USA. 52:1989;6148-6152.
30. Qian H. On the statistics of fluorescence correlation speetroscopy. Biophys. Chem. 38:1990;49-57.
31. Keizer J. Statistical Thermodynamics of non-equilibrium Processes. 1987;Springer-Verlag, New York.
32. Haberman R. Mathematical Models: Mechanical Vibrations, Population Dynamics, and Traffic Flow. 1998;SIAM Press, Philadelphia.
33. Kramers H.A. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica. 7:1940;284-304.
34. Hänggi P., Talkner P., Borkovec M. Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62:1990;251-341.
35. Delbrück M. Statistical fluctuations in autocatalytic reactions. J. Chem. Phys. 8:1940;120-124.
36. Jachimowski C.J., McQuarrie D.A., Russell M.E. A stochastic approach to enzyme-substrate reactions. Biochemistry. 3:1964;1732-1736.
37. Darvey I.G., Ninham B.W., Staff P.J. Stochastic models for second-order chemical reaction kinetics: the equilibrium state. J. Chem. Phys. 45:1966;2145-2155.
38. Darvey I.G., Staff P.J. The application of the theory of Markov processes to the reversible one substrate-one intermediate-one product enzymic mechanism. J. Theor. Biol. 14:1967;157-172.
39. Staff P.J. Approximation method for equilibrium distributions in second-order chemical reaction kinetics. J. Chem. Phys. 46:1967;2209-2212.
40. McQuarrie D.A. Stochastic Approach to Chemical Kinetics. 1968;Methuen, London.
41. Gillespie D.T. Markov Processes: An Introduction for Physical Scientists. 1992;Academic Press, San Diego.
42. van Kampen N.G. Stochastic Processes in Physics and Chemistry. 1992;Elsevier, Amsterdam.
43. Conti F. Noise analysis and single-channel recordings. Curr. Top. Membr. Transp. 22:1984;371-405.