Literature DB >> 25643150

A sensor for quantification of macromolecular crowding in living cells.

Arnold J Boersma1, Inge S Zuhorn2, Bert Poolman1.   

Abstract

Macromolecular crowding in cells influences processes such as folding, association and diffusion of proteins and polynucleic acids. Direct spatiotemporal readout of crowding would be a powerful approach for unraveling the structure of the cytoplasm and determining the impact of excluded volume on protein function in living cells. Here, we introduce a genetically encodable fluorescence resonance energy transfer (FRET) sensor for quantifying macromolecular crowding and discuss our application of the sensor in bacterial and mammalian cells.

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Year:  2015        PMID: 25643150     DOI: 10.1038/nmeth.3257

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  21 in total

1.  Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells.

Authors:  David A Zacharias; Jonathan D Violin; Alexandra C Newton; Roger Y Tsien
Journal:  Science       Date:  2002-05-03       Impact factor: 47.728

2.  Compression of random coils due to macromolecular crowding: scaling effects.

Authors:  C Le Coeur; J Teixeira; P Busch; S Longeville
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-06-11

3.  Crowding and confinement effects on protein diffusion in vivo.

Authors:  Michael C Konopka; Irina A Shkel; Scott Cayley; M Thomas Record; James C Weisshaar
Journal:  J Bacteriol       Date:  2006-09       Impact factor: 3.490

Review 4.  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

5.  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

6.  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

7.  Direct observation of protein unfolded state compaction in the presence of macromolecular crowding.

Authors:  Therese Mikaelsson; Jörgen Adén; Lennart B-Å Johansson; Pernilla Wittung-Stafshede
Journal:  Biophys J       Date:  2013-02-05       Impact factor: 4.033

Review 8.  Ficoll and dextran vs. globular proteins as probes for testing glomerular permselectivity: effects of molecular size, shape, charge, and deformability.

Authors:  Daniele Venturoli; Bengt Rippe
Journal:  Am J Physiol Renal Physiol       Date:  2005-04

9.  The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity.

Authors:  Bradley R Parry; Ivan V Surovtsev; Matthew T Cabeen; Corey S O'Hern; Eric R Dufresne; Christine Jacobs-Wagner
Journal:  Cell       Date:  2013-12-19       Impact factor: 41.582

10.  Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo.

Authors:  S Cayley; B A Lewis; H J Guttman; M T Record
Journal:  J Mol Biol       Date:  1991-11-20       Impact factor: 5.469

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  54 in total

Review 1.  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

2.  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

3.  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

4.  Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome.

Authors:  Fabai Wu; Pinaki Swain; Louis Kuijpers; Xuan Zheng; Kevin Felter; Margot Guurink; Jacopo Solari; Suckjoon Jun; Thomas S Shimizu; Debasish Chaudhuri; Bela Mulder; Cees Dekker
Journal:  Curr Biol       Date:  2019-05-30       Impact factor: 10.834

5.  Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage.

Authors:  Rebecca Smith; Théo Lebeaupin; Szilvia Juhász; Catherine Chapuis; Ostiane D'Augustin; Stéphanie Dutertre; Peter Burkovics; Christian Biertümpfel; Gyula Timinszky; Sébastien Huet
Journal:  Nucleic Acids Res       Date:  2019-12-02       Impact factor: 16.971

Review 6.  Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria.

Authors:  Alexander Cambré; Abram Aertsen
Journal:  Microbiol Mol Biol Rev       Date:  2020-10-28       Impact factor: 11.056

7.  Cell volume change through water efflux impacts cell stiffness and stem cell fate.

Authors:  Ming Guo; Adrian F Pegoraro; Angelo Mao; Enhua H Zhou; Praveen R Arany; Yulong Han; Dylan T Burnette; Mikkel H Jensen; Karen E Kasza; Jeffrey R Moore; Frederick C Mackintosh; Jeffrey J Fredberg; David J Mooney; Jennifer Lippincott-Schwartz; David A Weitz
Journal:  Proc Natl Acad Sci U S A       Date:  2017-09-25       Impact factor: 11.205

Review 8.  Toward an understanding of biochemical equilibria within living cells.

Authors:  Germán Rivas; Allen P Minton
Journal:  Biophys Rev       Date:  2017-12-12

Review 9.  Macromolecular Crowding In Vitro, In Vivo, and In Between.

Authors:  Germán Rivas; Allen P Minton
Journal:  Trends Biochem Sci       Date:  2016-09-23       Impact factor: 13.807

10.  Deamidation of Human γS-Crystallin Increases Attractive Protein Interactions: Implications for Cataract.

Authors:  Ajay Pande; Natalya Mokhor; Jayanti Pande
Journal:  Biochemistry       Date:  2015-07-29       Impact factor: 3.162

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