Literature DB >> 27096470

Theory of Crowding Effects on Bimolecular Reaction Rates.

Alexander M Berezhkovskii1, Attila Szabo2.   

Abstract

An analytical expression for the rate constant of a diffusion-influenced bimolecular reaction in a crowded environment is derived in the framework of a microscopic model that accounts for: (1) the slowdown of diffusion due to crowding and the dependence of the diffusivity on the distance between the reactants, (2) a crowding-induced attractive short-range potential of mean force, and (3) nonspecific reversible binding to the crowders. This expression spans the range from reaction to diffusion control. Crowding can increase the reaction-controlled rate by inducing an effective attraction between reactants but decrease the diffusion-controlled rate by reducing their relative diffusivity.

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Year:  2016        PMID: 27096470      PMCID: PMC5577823          DOI: 10.1021/acs.jpcb.6b01892

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  22 in total

1.  Cell biology: join the crowd.

Authors:  R John Ellis; Allen P Minton
Journal:  Nature       Date:  2003-09-04       Impact factor: 49.962

2.  Protein folding and binding in confined spaces and in crowded solutions.

Authors:  Huan-Xiang Zhou
Journal:  J Mol Recognit       Date:  2004 Sep-Oct       Impact factor: 2.137

3.  Diffusion-limited reactions in crowded environments.

Authors:  N Dorsaz; C De Michele; F Piazza; P De Los Rios; G Foffi
Journal:  Phys Rev Lett       Date:  2010-09-13       Impact factor: 9.161

4.  Diffusion-limited reactions in crowded environments: a local density approximation.

Authors:  F Piazza; N Dorsaz; C De Michele; P De Los Rios; G Foffi
Journal:  J Phys Condens Matter       Date:  2013-09-18       Impact factor: 2.333

Review 5.  Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences.

Authors:  Huan-Xiang Zhou; Germán Rivas; Allen P Minton
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

6.  Diffusion-limited encounter rate in a three-dimensional lattice of connected compartments studied by Brownian-dynamics simulations.

Authors:  Ran Li; Brian A Todd
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2015-03-04

7.  Calculated rates of diffusion-limited reactions in a three-dimensional network of connected compartments: application to porous catalysts and biological systems.

Authors:  Ran Li; Justin A Fowler; Brian A Todd
Journal:  Phys Rev Lett       Date:  2014-07-10       Impact factor: 9.161

8.  Effects of macromolecular crowding on intracellular diffusion from a single particle perspective.

Authors:  Damien Hall; Masaru Hoshino
Journal:  Biophys Rev       Date:  2010-02-06

9.  Speeding by a crowd.

Authors:  Huan-Xiang Zhou
Journal:  Physics (College Park Md)       Date:  2010-09-13

Review 10.  Fundamental aspects of protein-protein association kinetics.

Authors:  G Schreiber; G Haran; H-X Zhou
Journal:  Chem Rev       Date:  2009-03-11       Impact factor: 60.622

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  4 in total

1.  Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules.

Authors:  Shane Scott; Cynthia Shaheen; Brendon McGuinness; Kimberly Metera; Fedor Kouzine; David Levens; Craig J Benham; Sabrina Leslie
Journal:  Nucleic Acids Res       Date:  2019-07-09       Impact factor: 16.971

2.  Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism.

Authors:  Daniel R Weilandt; Vassily Hatzimanikatis
Journal:  Biophys J       Date:  2019-06-25       Impact factor: 4.033

3.  Depletion interactions modulate the binding between disordered proteins in crowded environments.

Authors:  Franziska Zosel; Andrea Soranno; Karin J Buholzer; Daniel Nettels; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-02       Impact factor: 11.205

4.  Transcription and Translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions.

Authors:  Mahesh A Vibhute; Mark H Schaap; Roel J M Maas; Frank H T Nelissen; Evan Spruijt; Hans A Heus; Maike M K Hansen; Wilhelm T S Huck
Journal:  ACS Synth Biol       Date:  2020-10-05       Impact factor: 5.110

  4 in total

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