Article

Stochastic theory of large-scale enzyme-reaction networks: finite copy number corrections to rate equation models.

Department of Physics, Humboldt University of Berlin, Newtonstr. 15, D-12489 Berlin, Germany.
The Journal of chemical physics (impact factor: 3.09). 11/2010; 133(19):195101. DOI:10.1063/1.3505552 pp.195101
Source: PubMed

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.

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Keywords

actual steady-state substrate concentrations
 
chemical reaction networks
 
Chemical reactions
 
compact expressions
 
compartment volumes
 
constant macroscopic concentrations
 
decreasing Michaelis-Menten constants
 
decreasing subcellular volume
 
enzyme saturation
 
enzyme-catalyzed reactions
 
enzyme-reaction network
 
finite copy number corrections
 
finite-volume corrections
 
finite-volume corrections increase
 
infinite volumes
 
infinitely large numbers
 
mesoscopic version
 
Physiological concentrations
 
small subcellular compartment
 
small volumes