Michaelis–Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion

Abstract

The investigation of enzymatic reaction under stochastic effect and spatial effect is an interesting problem. By virtue of Monte Carlo simulation, the stochastic dynamic of enzyme and the related Michaelis–Menten mechanism with stochastic internal noise and spatial diffusion are explored in this article. (i) For the single-enzyme system, two cases, including the fast phosphorylation case [X. S. Xie, et al., J. Phys. Chem. B 109 (2005) 19068] and slow phosphorylation case [X. S. Xie, et al., Nat. Chem. Biol. 2 (2006) 87] are considered. It is found the micro enzymatic velocity rate shows a rough hyperbolic dependence on the substrate concentration, hence obeys the Michaelis–Menten law qualitatively. In addition, our result reveals that diffusion rate can adjust the Michaelis–Menten curve; especially, it is shown that increasing diffusion rate enhances the micro enzyme rate. (ii) For the multi-enzyme system, a typical example, i.e., MAPK signaling pathway is used. We apply the Michaelis–Menten mechanism to the MAPK cascade and give a simple comparison for the signaling ability between the Michaelis–Menten mechanism and the single collision mechanism [J. W. Locasale et al., PLOS Comput. Biol. 4 (2008) e1000099].