Biochemical reactions in crowded environments: revisiting the effects of volume exclusion with simulations

Frontiers in Physics

Klumpp, Stefan¹  Gomez, David² 

[1] Bio-Systems, Science Park Golm, Potsdam, 14476, Germany;Max Planck Institute of Colloids and Interfaces, Theory &

关键词: molecular crowding;    enzymatic reactions;    Reaction-diffusion systems;    Diffusion-limited reactions;    gene regulation;   

DOI  :  10.3389/fphy.2015.00045

学科分类：物理（综合）

来源: Frontiers

【 摘 要 】

Molecular crowding is ubiquitous within cells and affects many biological processes including protein-protein binding, enzyme activities and gene regulation. Here we revisit some generic effects of crowding using a combination of lattice simulations and reaction-diffusion simulations with the program ReaDDy. Specifically, we implement three reactions, simple binding, a diffusion-limited reaction and a reaction with Michaelis-Menten kinetics. Histograms of binding and unbinding times provide a detailed picture how crowding affects these reactions and how the separate effects of crowding on binding equilibrium and on diffusion act together. In addition, we discuss how crowding affects processes related to gene expression such as RNA polymerase-promoter binding and translation elongation.

【 授权许可】

CC BY