Stochastic theory of large-scale enzyme-reaction networks: finite copy number corrections to rate equation models
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Published version
Author(s)
Thomas, P
Straube, AV
Grima, R
Type
Journal Article
Abstract
Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtoliters. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of considerable fluctuations in the concentrations. In contrast, rate equation models are based on the implicit assumption of infinitely large numbers of interacting molecules, or equivalently, that reactions occur in infinite volumes at constant macroscopic concentrations. In this article we compute the finite-volume corrections (or equivalently the finite copy number corrections) to the solutions of the rate equations for chemical reaction networks composed of arbitrarily large numbers of enzyme-catalyzed reactions which are confined inside a small subcellular compartment. This is achieved by applying a mesoscopic version of the quasisteady-state assumption to the exact Fokker-Planck equation associated with the Poisson representation of the chemical master equation. The procedure yields impressively simple and compact expressions for the finite-volume corrections. We prove that the predictions of the rate equations will always underestimate the actual steady-state substrate concentrations for an enzyme-reaction network confined in a small volume. In particular we show that the finite-volume corrections increase with decreasing subcellular volume, decreasing Michaelis-Menten constants, and increasing enzyme saturation. The magnitude of the corrections depends sensitively on the topology of the network. The predictions of the theory are shown to be in excellent agreement with stochastic simulations for two types of networks typically associated with protein methylation and metabolism.
Date Issued
2010-11-18
Date Acceptance
2010-10-05
Citation
Journal of Chemical Physics, 2010, 133 (19)
ISSN
1089-7690
Publisher
AIP Publishing
Journal / Book Title
Journal of Chemical Physics
Volume
133
Issue
19
Copyright Statement
© 2010 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. The following article appeared in Journal of Chemical Physics and may be found at http://dx.doi.org/10.1063/1.3505552.
Subjects
Enzymes
Kinetics
Models, Chemical
Poisson Distribution
Stochastic Processes
cond-mat.stat-mech
physics.chem-ph
q-bio.MN
Chemical Physics
02 Physical Sciences
03 Chemical Sciences
09 Engineering
Publication Status
Published
Article Number
195101