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.
%0 Journal Article
%1 Schn_2004_235
%A Schnell, S.
%A Turner, T. E.
%D 2004
%J Prog. Biophys. Mol. Biol.
%K 15142746 Algorithms, Biochemistry, Biological, Biology, Biopolymers, Carlo Chemical, Complexes, Computational Computer Fractals, Gov't, Intracellular Kinetics, Macromolecular Metabolism, Method, Models, Monte Multienzyme Non-U.S. Processes, Research Simulation, Space, Statistical, Stochastic Substances, Support,
%N 2-3
%P 235--260
%R 10.1016/j.pbiomolbio.2004.01.012
%T Reaction kinetics in intracellular environments with macromolecular
crowding: simulations and rate laws.
%U http://dx.doi.org/10.1016/j.pbiomolbio.2004.01.012
%V 85
%X 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.
@article{Schn_2004_235,
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.},
added-at = {2009-06-03T11:20:58.000+0200},
author = {Schnell, S. and Turner, T. E.},
biburl = {https://www.bibsonomy.org/bibtex/205810e15f162de7c963bf6a08df00ee0/hake},
description = {The whole bibliography file I use.},
doi = {10.1016/j.pbiomolbio.2004.01.012},
file = {Schn_2004_235.pdf:Schn_2004_235.pdf:PDF},
interhash = {f358302bc9388da3b165d0af7e0936e5},
intrahash = {05810e15f162de7c963bf6a08df00ee0},
journal = {Prog. Biophys. Mol. Biol.},
key = 171,
keywords = {15142746 Algorithms, Biochemistry, Biological, Biology, Biopolymers, Carlo Chemical, Complexes, Computational Computer Fractals, Gov't, Intracellular Kinetics, Macromolecular Metabolism, Method, Models, Monte Multienzyme Non-U.S. Processes, Research Simulation, Space, Statistical, Stochastic Substances, Support,},
number = {2-3},
pages = {235--260},
pii = {S0079610704000240},
pmid = {15142746},
timestamp = {2009-06-03T11:21:29.000+0200},
title = {Reaction kinetics in intracellular environments with macromolecular
crowding: simulations and rate laws.},
url = {http://dx.doi.org/10.1016/j.pbiomolbio.2004.01.012},
volume = 85,
year = 2004
}