The Depletion Attraction: an Underappreciated Force Driving Cellular Organization

Overview

Journal J Cell Biol

Specialty Cell Biology

Date 2006 Dec 6

PMID 17145959

Citations 117

Authors

Davide Marenduzzo

Kieran Finan

Peter R Cook

Affiliations

Soon will be listed here.

Abstract

Cellular structures are shaped by hydrogen and ionic bonds, plus van der Waals and hydrophobic forces. In cells crowded with macromolecules, a little-known and distinct force-the "depletion attraction"-also acts. We review evidence that this force assists in the assembly of a wide range of cellular structures, ranging from the cytoskeleton to chromatin loops and whole chromosomes.

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References

Ellis R . Protein folding: inside the cage. Nature. 2006; 442(7101):360-2. DOI: 10.1038/442360a. View

Jackson D, McCready S, Cook P . Replication and transcription depend on attachment of DNA to the nuclear cage. J Cell Sci Suppl. 1984; 1:59-79. DOI: 10.1242/jcs.1984.supplement_1.5. View

Faro-Trindade I, Cook P . A conserved organization of transcription during embryonic stem cell differentiation and in cells with high C value. Mol Biol Cell. 2006; 17(7):2910-20. PMC: 1483028. DOI: 10.1091/mbc.e05-11-1024. View

Chandler D . Hydrophobicity: two faces of water. Nature. 2002; 417(6888):491. DOI: 10.1038/417491a. View

Manders E, Kimura H, Cook P . Direct imaging of DNA in living cells reveals the dynamics of chromosome formation. J Cell Biol. 1999; 144(5):813-21. PMC: 2148202. DOI: 10.1083/jcb.144.5.813. View

Bohrmann B, Haider M, Kellenberger E . Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM. Ultramicroscopy. 1993; 49(1-4):235-51. DOI: 10.1016/0304-3991(93)90230-u. View

Sept D, McCammon J . Thermodynamics and kinetics of actin filament nucleation. Biophys J. 2001; 81(2):667-74. PMC: 1301543. DOI: 10.1016/S0006-3495(01)75731-1. View

Minton A . Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. Methods Enzymol. 1998; 295:127-49. DOI: 10.1016/s0076-6879(98)95038-8. View

Bates D, Kleckner N . Chromosome and replisome dynamics in E. coli: loss of sister cohesion triggers global chromosome movement and mediates chromosome segregation. Cell. 2005; 121(6):899-911. PMC: 2973560. DOI: 10.1016/j.cell.2005.04.013. View

10.

Osborne C, Chakalova L, Brown K, Carter D, Horton A, Debrand E . Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet. 2004; 36(10):1065-71. DOI: 10.1038/ng1423. View

11.

Misteli T . The concept of self-organization in cellular architecture. J Cell Biol. 2001; 155(2):181-5. PMC: 2198832. DOI: 10.1083/jcb.200108110. View

12.

Ellis R, Minton A . Protein aggregation in crowded environments. Biol Chem. 2006; 387(5):485-97. DOI: 10.1515/BC.2006.064. View

13.

Goobes R, Kahana N, Cohen O, Minsky A . Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance. Biochemistry. 2003; 42(8):2431-40. DOI: 10.1021/bi026775x. View

14.

Parsegian V, Rand R, Rau D . Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives. Proc Natl Acad Sci U S A. 2000; 97(8):3987-92. PMC: 18129. DOI: 10.1073/pnas.97.8.3987. View

15.

Cheung M, Klimov D, Thirumalai D . Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Natl Acad Sci U S A. 2005; 102(13):4753-8. PMC: 555696. DOI: 10.1073/pnas.0409630102. View

16.

Hatters D, Minton A, Howlett G . Macromolecular crowding accelerates amyloid formation by human apolipoprotein C-II. J Biol Chem. 2001; 277(10):7824-30. DOI: 10.1074/jbc.M110429200. View

17.

Maritan A, Micheletti C, Trovato A, Banavar J . Optimal shapes of compact strings. Nature. 2000; 406(6793):287-90. DOI: 10.1038/35018538. View

18.

Zimmerman S, Trach S . Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J Mol Biol. 1991; 222(3):599-620. DOI: 10.1016/0022-2836(91)90499-v. View

19.

Kinjo A, Takada S . Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: statics. Phys Rev E Stat Nonlin Soft Matter Phys. 2002; 66(3 Pt 1):031911. DOI: 10.1103/PhysRevE.66.031911. View

20.

Adams M, Fraden S . Phase behavior of mixtures of rods (tobacco mosaic virus) and spheres (polyethylene oxide, bovine serum albumin). Biophys J. 1998; 74(1):669-77. PMC: 1299420. DOI: 10.1016/S0006-3495(98)77826-9. View