Literature DB >> 26080429

Analysis of the size dependence of macromolecular crowding shows that smaller is better.

Kim A Sharp1.   

Abstract

The aqueous milieu inside cells contains as much as 30-40% dissolved protein and RNA by volume. This large concentration of macromolecules is expected to cause significant deviations from solution ideality. In vivo biochemical reaction rates and equilibria might differ significantly from those measured in the majority of in vitro experiments that are performed at much lower macromolecule concentrations. Consequently crowding, a nonspecific phenomenon believed to arise from the large excluded volume of these macromolecules, has been studied extensively by experimental and theoretical methods. However, the relevant theory has not been applied consistently. When the steric effects of macromolecular crowders and small molecules like water and ions are treated on an equal footing, the effect of the macromolecules is opposite to that commonly believed. Large molecules are less effective at crowding than water and ions. There is also a surprisingly weak dependence on crowder size. Molecules of medium size, ∼5 Å radius, have the same effect as much larger macromolecules like proteins and RNA. These results require a reassessment of observed high-concentration effects and of strategies to mimic in vivo conditions with in vitro experiments.

Entities:  

Keywords:  depletion effects; exclusion effects; hard sphere fluids; macromolecular crowding

Mesh:

Substances:

Year:  2015        PMID: 26080429      PMCID: PMC4491746          DOI: 10.1073/pnas.1505396112

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  24 in total

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Journal:  Annu Rev Biophys Biomol Struct       Date:  2001

2.  Enthalpically driven peptide stabilization by protective osmolytes.

Authors:  Regina Politi; Daniel Harries
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3.  Origin of Enthalpic Depletion Forces.

Authors:  Liel Sapir; Daniel Harries
Journal:  J Phys Chem Lett       Date:  2014-03-13       Impact factor: 6.475

Review 4.  Protein aggregation in crowded environments.

Authors:  R John Ellis; Allen P Minton
Journal:  Biol Chem       Date:  2006-05       Impact factor: 3.915

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.  Unexpected effects of macromolecular crowding on protein stability.

Authors:  Laura A Benton; Austin E Smith; Gregory B Young; Gary J Pielak
Journal:  Biochemistry       Date:  2012-11-27       Impact factor: 3.162

7.  Protein stabilization by macromolecular crowding through enthalpy rather than entropy.

Authors:  Michael Senske; Lisa Törk; Benjamin Born; Martina Havenith; Christian Herrmann; Simon Ebbinghaus
Journal:  J Am Chem Soc       Date:  2014-06-16       Impact factor: 15.419

8.  Denaturant-induced movement of the transition state of protein folding revealed by high-pressure stopped-flow measurements.

Authors:  G Pappenberger; C Saudan; M Becker; A E Merbach; T Kiefhaber
Journal:  Proc Natl Acad Sci U S A       Date:  2000-01-04       Impact factor: 11.205

9.  Macromolecular crowding fails to fold a globular protein in cells.

Authors:  Alexander P Schlesinger; Yaqiang Wang; Xavier Tadeo; Oscar Millet; Gary J Pielak
Journal:  J Am Chem Soc       Date:  2011-05-10       Impact factor: 15.419

10.  An upper limit for macromolecular crowding effects.

Authors:  Andrew C Miklos; Conggang Li; Courtney D Sorrell; L Andrew Lyon; Gary J Pielak
Journal:  BMC Biophys       Date:  2011-05-31       Impact factor: 4.778

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  30 in total

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Authors:  Austin E Smith; Larry Z Zhou; Annelise H Gorensek; Michael Senske; Gary J Pielak
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-11       Impact factor: 11.205

2.  Unpacking the origins of in-cell crowding.

Authors:  Kim A Sharp
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-09       Impact factor: 11.205

3.  Quantifying enzyme activity in living cells.

Authors:  Agnes Zotter; Felix Bäuerle; Debabrata Dey; Vladimir Kiss; Gideon Schreiber
Journal:  J Biol Chem       Date:  2017-08-07       Impact factor: 5.157

4.  Protein shape modulates crowding effects.

Authors:  Alex J Guseman; Gerardo M Perez Goncalves; Shannon L Speer; Gregory B Young; Gary J Pielak
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-09       Impact factor: 11.205

Review 5.  Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo.

Authors:  Alexander V Fonin; April L Darling; Irina M Kuznetsova; Konstantin K Turoverov; Vladimir N Uversky
Journal:  Cell Mol Life Sci       Date:  2018-07-31       Impact factor: 9.261

6.  Computational Study of the Forces Driving Aggregation of Ultrasmall Nanoparticles in Biological Fluids.

Authors:  Sergio A Hassan
Journal:  ACS Nano       Date:  2017-03-21       Impact factor: 15.881

7.  Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.

Authors:  Tadashi Ando; Isseki Yu; Michael Feig; Yuji Sugita
Journal:  J Phys Chem B       Date:  2016-11-15       Impact factor: 2.991

8.  The intracellular environment affects protein-protein interactions.

Authors:  Shannon L Speer; Wenwen Zheng; Xin Jiang; I-Te Chu; Alex J Guseman; Maili Liu; Gary J Pielak; Conggang Li
Journal:  Proc Natl Acad Sci U S A       Date:  2021-03-16       Impact factor: 11.205

9.  Cosolutes, Crowding, and Protein Folding Kinetics.

Authors:  Annelise H Gorensek-Benitez; Austin E Smith; Samantha S Stadmiller; Gerardo M Perez Goncalves; Gary J Pielak
Journal:  J Phys Chem B       Date:  2017-06-29       Impact factor: 2.991

10.  Biointeractions of ultrasmall glutathione-coated gold nanoparticles: effect of small size variations.

Authors:  Alioscka A Sousa; Sergio A Hassan; Luiza L Knittel; Andrea Balbo; Maria A Aronova; Patrick H Brown; Peter Schuck; Richard D Leapman
Journal:  Nanoscale       Date:  2016-03-28       Impact factor: 7.790

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