Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws

Prog Biophys Mol Biol. 2004 Jun-Jul;85(2-3):235-60. doi: 10.1016/j.pbiomolbio.2004.01.012.

Abstract

We review recent evidence illustrating the fundamental difference between cytoplasmic and test tube biochemical kinetics and thermodynamics, and showing the breakdown of the law of mass action and power-law approximation in in vivo conditions. Simulations of biochemical reactions in non-homogeneous media show that as a result of anomalous diffusion and mixing of the biochemical species, reactions follow a fractal-like kinetics. Consequently, the conventional equations for biochemical pathways fail to describe the reactions in in vivo conditions. We present a modification to fractal-like kinetics following the Zipf-Mandelbrot distribution which will enable the modelling and analysis of biochemical reactions occurring in crowded intracellular environments.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Biopolymers / metabolism*
  • Computer Simulation
  • Intracellular Space / metabolism*
  • Kinetics
  • Macromolecular Substances*
  • Models, Biological*
  • Models, Chemical*
  • Models, Statistical*
  • Multienzyme Complexes / metabolism*

Substances

  • Biopolymers
  • Macromolecular Substances
  • Multienzyme Complexes