The Michaelis-Menten mechanism is an extremely important tool for understanding enzyme-catalyzed transformation of substrates into final products. In this work, a computationally viable, full stochastic description of the Michaelis-Menten kinetic scheme is introduced based on a stochastic equivalent of the steady-state assumption. The full solution derived is free of restrictions on amounts of substance or parameter values and is used to create stochastic maps of the Michaelis-Menten mechanism, which show the regions in the parameter space of the scheme where the use of the stochastic kinetic approach is inevitable. The stochastic aspects of recently published examples of single-enzyme kinetic studies are analyzed using these maps.
REFERENCES
1.
2.
3.
S. J.
Benkovic
and S.
Hammes-Schiffer
, Science
301
, 1196
(2003
).4.
N. G.
Walter
, Nat. Chem. Biol.
2
, 66
(2006
).5.
A. M.
van Oijen
, Nat. Chem. Biol.
4
, 440
(2008
).6.
K.
Svoboda
, P. P.
Mitra
, and S. M.
Block
, Proc. Natl. Acad. Sci. U.S.A.
91
, 11782
(1994
).7.
H. P.
Lu
, L.
Xun
, and X. S.
Xie
, Science
282
, 1877
(1998
).8.
A. M.
van Oijen
, P. C.
Blainey
, D. J.
Crampton
, C. C.
Richardson
, T.
Ellenberger
, and X. S.
Xie
, Science
301
, 1235
(2003
).9.
N. M.
Antikainen
, R. D.
Smiley
, S. J.
Benkovic
, and G. G.
Hammes
, Biochemistry
44
, 16835
(2005
).10.
K.
Velonia
, O.
Flomenbom
, D.
Loos
, S.
Masuo
, M.
Cotlet
, Y.
Engelborghs
, J.
Hofkens
, A. E.
Rowan
, J.
Klafter
, R. J. M.
Nolte
, and F. C.
de Schryver
, Angew. Chem., Int. Ed.
44
, 560
(2005
).11.
B. P.
English
, W.
Min
, A. M.
van Oijen
, K. T.
Lee
, G.
Luo
, H.
Sun
, B.
Cherayil
, S. C.
Kou
, and X. S.
Xie
, Nat. Chem. Biol.
2
, 87
(2006
).12.
D. M.
Rissin
, H. H.
Gorris
, and D. R.
Walt
, J. Am. Chem. Soc.
130
, 5349
(2008
).13.
N. K.
Lee
, H. R.
Koh
, K. Y.
Han
, J.
Lee
, and S. K.
Kim
, Chem. Commun.
46
, 4683
(2010
).14.
P. J.
Staff
, J. Theor. Biol.
27
, 221
(1970
).15.
16.
L.
Edman
, Z.
Foldes-Papp
, S.
Wennmalm
, and R.
Rigler
, Chem. Phys.
247
, 11
(1999
).17.
X. S.
Xie
, Single Mol.
2
, 229
(2001
).18.
A.
Ishijima
and T.
Yanagida
, Trends Biochem. Sci.
26
, 438
(2001
).19.
H.
Qian
and E. L.
Elson
, Biophys. Chem.
101–102
, 565
(2002
).20.
C. V.
Rao
and A. P.
Arkin
, J. Chem. Phys.
118
, 4999
(2003
).21.
T. E.
Turner
, S.
Schnell
, and K.
Burrage
, Comput. Biol. Chem.
28
, 165
(2004
).22.
S. C.
Kou
, B. J.
Cherayil
, W.
Min
, B. P.
English
, and X. S.
Xie
, J. Phys. Chem. B
109
, 19068
(2005
).23.
24.
J. R.
Moffitt
, Y. R.
Chemla
, and C.
Bustamante
, Meth. Enzymol.
475
, 221
(2010
).25.
Frontiers in Computational and Systems Biology
, Computational Biology Vol. 15, edited by P. Z.
Shi
and H.
Qian
(Springer-Verlag
, London
2010
), p. 175
.26.
M.
Yi
and Q.
Liu
, Physica A
389
, 3791
(2010
).27.
K. R.
Sanft
, D. T.
Gillespie
, and L. R.
Petzold
, IET Syst. Biol.
5
, 58
(2011
).28.
D. T.
Gillespie
, J. Phys. Chem.
81
, 2340
(1977
).29.
G.
Lente
, J. Phys. Chem. A
109
, 11058
(2005
).30.
G.
Lente
, Symmetry
2
, 767
(2010
).31.
B.
Barabás
, J.
Tóth
, and G.
Pályi
, J. Math. Chem.
48
, 457
(2010
).32.
See supplementary material at http://dx.doi.org/10.1063/1.3681942 for additional figures and mathematical proofs of the equations appearing in the manuscript.
33.
P.
Érdi
and J.
Tóth
, Mathematical Models of Chemical Reactions
(Manchester University Press
, Manchester, UK
, 1981
), p. 91
.34.
E. A.
Mastny
, E. L.
Haseltine
, and J. B.
Rawlings
, J. Chem. Phys.
127
, 094106
(2007
).35.
D. A.
McQuarrie
, J. Appl. Probab.
4
, 413
(1967
).36.
É.
Dóka
and G.
Lente
, J. Am. Chem. Soc.
133
, 17878
(2011
).37.
M.
Frankowicz
, M.
Moreau
, P. P.
Szczesny
, J.
Tóth
, and L.
Vicente
, J. Phys. Chem.
97
, 1891
(1993
).38.
G.
Lente
, Phys. Chem. Chem. Phys.
9
, 6134
(2007
).39.
T. G.
Kurtz
, J. Chem. Phys.
57
, 2976
(1972
).© 2012 American Institute of Physics.
2012
American Institute of Physics
You do not currently have access to this content.