Literature DB >> 20867619

Diffusion-limited reactions in crowded environments.

N Dorsaz1, C De Michele, F Piazza, P De Los Rios, G Foffi.   

Abstract

Diffusion-limited reactions are usually described within the Smoluchowski theory, which neglects interparticle interactions. We propose a simple way to incorporate excluded-volume effects building on simulations of hard sphere in the presence of a sink. For large values of the sink-to-particle size ratio R(s), the measured encounter rate is in good agreement with a simple generalization of the Smoluchowski equation at high densities. Reducing R(s), the encounter rate is substantially depressed and becomes even nonmonotonic for R(s)<<1. Concurrently with the saturation of the rate, stationary density waves set in close to the sink. A mean-field analysis helps to shed light on the subtle link between such ordering and the slowing down of the encounter dynamics. Finally, we show how an infinitesimal amount of nonreacting impurities can equally slow down dramatically the reaction.

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Year:  2010        PMID: 20867619     DOI: 10.1103/PhysRevLett.105.120601

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  11 in total

1.  A method for computing association rate constants of atomistically represented proteins under macromolecular crowding.

Authors:  Sanbo Qin; Lu Cai; Huan-Xiang Zhou
Journal:  Phys Biol       Date:  2012-11-29       Impact factor: 2.583

2.  Severe osmotic compression triggers a slowdown of intracellular signaling, which can be explained by molecular crowding.

Authors:  Agnès Miermont; François Waharte; Shiqiong Hu; Megan Nicole McClean; Samuel Bottani; Sébastien Léon; Pascal Hersen
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-14       Impact factor: 11.205

3.  Theory of Crowding Effects on Bimolecular Reaction Rates.

Authors:  Alexander M Berezhkovskii; Attila Szabo
Journal:  J Phys Chem B       Date:  2016-05-02       Impact factor: 2.991

4.  The Impact of Membrane Protein Diffusion on GPCR Signaling.

Authors:  Horst-Holger Boltz; Alexei Sirbu; Nina Stelzer; Primal de Lanerolle; Stefanie Winkelmann; Paolo Annibale
Journal:  Cells       Date:  2022-05-17       Impact factor: 7.666

5.  Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome.

Authors:  Yu Xu; Hong Wang; Ruth Nussinov; Buyong Ma
Journal:  Proteomics       Date:  2013-03-18       Impact factor: 3.984

6.  Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin.

Authors:  Xingcheng Lin; Jeffrey K Noel; Qinghua Wang; Jianpeng Ma; José N Onuchic
Journal:  J Phys Chem B       Date:  2016-09-01       Impact factor: 2.991

7.  Sequential metabolic phases as a means to optimize cellular output in a constant environment.

Authors:  Aljoscha Palinkas; Sascha Bulik; Alexander Bockmayr; Hermann-Georg Holzhütter
Journal:  PLoS One       Date:  2015-03-18       Impact factor: 3.240

8.  Fluorescence Self-Quenching from Reporter Dyes Informs on the Structural Properties of Amyloid Clusters Formed in Vitro and in Cells.

Authors:  WeiYue Chen; Laurence J Young; Meng Lu; Alessio Zaccone; Florian Ströhl; Na Yu; Gabriele S Kaminski Schierle; Clemens F Kaminski
Journal:  Nano Lett       Date:  2016-12-08       Impact factor: 11.189

9.  Trehalose as an osmolyte in Candidatus Accumulibacter phosphatis.

Authors:  Danny R de Graaff; Mark C M van Loosdrecht; Mario Pronk
Journal:  Appl Microbiol Biotechnol       Date:  2020-10-19       Impact factor: 4.813

Review 10.  Structured crowding and its effects on enzyme catalysis.

Authors:  Buyong Ma; Ruth Nussinov
Journal:  Top Curr Chem       Date:  2013
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