Literature DB >> 27669651

Macromolecular Crowding In Vitro, In Vivo, and In Between.

Germán Rivas1, Allen P Minton2.   

Abstract

Biochemical processes take place in heterogeneous and highly volume-occupied or crowded environments that can considerably influence the reactivity and distribution of participating macromolecules. We summarize here the thermodynamic consequences of excluded-volume and long-range nonspecific intermolecular interactions for macromolecular reactions in volume-occupied media. In addition, we summarize and compare the information content of studies of crowding in vitro and in vivo. We emphasize the importance of characterizing the behavior not only of labeled tracer macromolecules but also the composition and behavior of unlabeled macromolecules in the immediate vicinity of the tracer. Finally, we propose strategies for extending quantitative analyses of crowding in simple model systems to increasingly complex media up to and including intact cells. Published by Elsevier Ltd.

Entities:  

Keywords:  crowding theory; in-cell experiments; long-range interactions; nonspecific interactions; steric interactions

Mesh:

Substances:

Year:  2016        PMID: 27669651      PMCID: PMC5804487          DOI: 10.1016/j.tibs.2016.08.013

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  85 in total

1.  Macromolecular crowding effects on protein-protein binding affinity and specificity.

Authors:  Young C Kim; Robert B Best; Jeetain Mittal
Journal:  J Chem Phys       Date:  2010-11-28       Impact factor: 3.488

2.  Mixed macromolecular crowding inhibits amyloid formation of hen egg white lysozyme.

Authors:  Bing-Rui Zhou; Zheng Zhou; Qing-Lian Hu; Jie Chen; Yi Liang
Journal:  Biochim Biophys Acta       Date:  2008-01-18

3.  Protein stability and folding kinetics in the nucleus and endoplasmic reticulum of eucaryotic cells.

Authors:  A Dhar; K Girdhar; D Singh; H Gelman; S Ebbinghaus; M Gruebele
Journal:  Biophys J       Date:  2011-07-20       Impact factor: 4.033

4.  Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding.

Authors:  Allen P Minton
Journal:  Biopolymers       Date:  2013-04       Impact factor: 2.505

Review 5.  Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs).

Authors:  Francois-Xavier Theillet; Andres Binolfi; Tamara Frembgen-Kesner; Karan Hingorani; Mohona Sarkar; Ciara Kyne; Conggang Li; Peter B Crowley; Lila Gierasch; Gary J Pielak; Adrian H Elcock; Anne Gershenson; Philipp Selenko
Journal:  Chem Rev       Date:  2014-06-05       Impact factor: 60.622

6.  Cooperative adsorption of ezrin on PIP2-containing membranes.

Authors:  Alexander Herrig; Matthias Janke; Judith Austermann; Volker Gerke; Andreas Janshoff; Claudia Steinem
Journal:  Biochemistry       Date:  2006-10-31       Impact factor: 3.162

7.  Separating chemical and excluded volume interactions of polyethylene glycols with native proteins: Comparison with PEG effects on DNA helix formation.

Authors:  Irina A Shkel; D B Knowles; M Thomas Record
Journal:  Biopolymers       Date:  2015-09       Impact factor: 2.505

8.  Molecular evolution, intracellular organization, and the quinary structure of proteins.

Authors:  E H McConkey
Journal:  Proc Natl Acad Sci U S A       Date:  1982-05       Impact factor: 11.205

9.  Effect of nonadditive repulsive intermolecular interactions on the light scattering of concentrated protein-osmolyte mixtures.

Authors:  Cristina Fernández; Allen P Minton
Journal:  J Phys Chem B       Date:  2010-12-22       Impact factor: 2.991

10.  The effect of macromolecular crowding on protein aggregation and amyloid fibril formation.

Authors:  Larissa A Munishkina; Elisa M Cooper; Vladimir N Uversky; Anthony L Fink
Journal:  J Mol Recognit       Date:  2004 Sep-Oct       Impact factor: 2.137

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  94 in total

1.  Anomalous and heterogeneous DNA transport in biomimetic cytoskeleton networks.

Authors:  Jonathan Garamella; Kathryn Regan; Gina Aguirre; Ryan J McGorty; Rae M Robertson-Anderson
Journal:  Soft Matter       Date:  2020-06-19       Impact factor: 3.679

2.  Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.

Authors:  Andrew Keller; Juan D Chavez; Kevin C Felt; James E Bruce
Journal:  J Proteome Res       Date:  2019-07-17       Impact factor: 4.466

3.  Physical biology of the cancer cell glycocalyx.

Authors:  Joe Chin-Hun Kuo; Jay G Gandhi; Roseanna N Zia; Matthew J Paszek
Journal:  Nat Phys       Date:  2018-07-04       Impact factor: 20.034

4.  Proteolysis mediated by the membrane-integrated ATP-dependent protease FtsH has a unique nonlinear dependence on ATP hydrolysis rates.

Authors:  Yiqing Yang; Mihiravi Gunasekara; Shaima Muhammednazaar; Zhen Li; Heedeok Hong
Journal:  Protein Sci       Date:  2019-05-08       Impact factor: 6.725

5.  Bacterial FtsZ protein forms phase-separated condensates with its nucleoid-associated inhibitor SlmA.

Authors:  Begoña Monterroso; Silvia Zorrilla; Marta Sobrinos-Sanguino; Miguel A Robles-Ramos; Marina López-Álvarez; William Margolin; Christine D Keating; Germán Rivas
Journal:  EMBO Rep       Date:  2018-12-06       Impact factor: 8.807

Review 6.  Microorganisms maintain crowding homeostasis.

Authors:  Jonas van den Berg; Arnold J Boersma; Bert Poolman
Journal:  Nat Rev Microbiol       Date:  2017-03-27       Impact factor: 60.633

7.  Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding.

Authors:  Boqun Liu; Christoffer Åberg; Floris J van Eerden; Siewert J Marrink; Bert Poolman; Arnold J Boersma
Journal:  Biophys J       Date:  2017-05-09       Impact factor: 4.033

8.  Weak protein-protein interactions in live cells are quantified by cell-volume modulation.

Authors:  Shahar Sukenik; Pin Ren; Martin Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-12       Impact factor: 11.205

Review 9.  To be disordered or not to be disordered: is that still a question for proteins in the cell?

Authors:  Kris Pauwels; Pierre Lebrun; Peter Tompa
Journal:  Cell Mol Life Sci       Date:  2017-06-13       Impact factor: 9.261

10.  Physicochemical code for quinary protein interactions in Escherichia coli.

Authors:  Xin Mu; Seongil Choi; Lisa Lang; David Mowray; Nikolay V Dokholyan; Jens Danielsson; Mikael Oliveberg
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-23       Impact factor: 11.205

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