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

Gomez, D., & Klumpp, S. (2015). Biochemical reactions in crowded environments: Revisiting the effects of volume exclusion with simulations. Frontiers in Physics, 3: 45. doi:10.3389/fphy.2015.00045.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-CF8F-E Version Permalink: http://hdl.handle.net/21.11116/0000-0002-7998-B
Genre: Journal Article

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 Creators:
Gomez, David1, Author              
Klumpp, Stefan1, Author              
Affiliations:
1Stefan Klumpp, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_1863329              

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Free keywords: Open Access, molecular crowding, enzymatic reactions, reaction-diffusion systems, diffusion-limited reactions, gene regulation
 Abstract: 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.

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 Dates: 2015-06-232015
 Publication Status: Published in print
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Title: Frontiers in Physics
Source Genre: Journal
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Publ. Info: Lausanne : Frontiers Media
Pages: - Volume / Issue: 3 Sequence Number: 45 Start / End Page: - Identifier: ISSN: 2296-424X