Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Progress Article
  • Published:

Polymer physics of intracellular phase transitions

Abstract

Intracellular organelles are either membrane-bound vesicles or membrane-less compartments that are made up of proteins and RNA. These organelles play key biological roles, by compartmentalizing the cell to enable spatiotemporal control of biological reactions. Recent studies suggest that membrane-less intracellular compartments are multicomponent viscous liquid droplets that form via phase separation. Proteins that have an intrinsic tendency for being conformationally heterogeneous seem to be the main drivers of liquid–liquid phase separation in the cell. These findings highlight the relevance of classical concepts from the physics of polymeric phase transitions for understanding the assembly of intracellular membrane-less compartments. However, applying these concepts is challenging, given the heteropolymeric nature of protein sequences, the complex intracellular environment, and non-equilibrium features intrinsic to cells. This provides new opportunities for adapting established theories and for the emergence of new physics.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Examples of membrane-less bodies in cells.
Figure 2: Molecular interactions underlying intracellular phase transitions.

Similar content being viewed by others

References

  1. Lu, A. et al. Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes. Cell 156, 1193–1206 (2014).

    Google Scholar 

  2. Li, J. et al. The RIP1/RIP3 necrosome forms a functional amyloid signaling complex required for programmed necrosis. Cell 150, 339–350 (2012).

    Google Scholar 

  3. An, S., Kumar, R., Sheets, E. D. & Benkovic, S. J. Reversible compartmentalization of de novo purine biosynthetic complexes in living cells. Science 320, 103–106 (2008).

    ADS  Google Scholar 

  4. Zwicker, D., Decker, M., Jaensch, S., Hyman, A. A. & Julicher, F. Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles. Proc. Natl Acad. Sci. USA 111, E2636–E2645 (2014).

    ADS  Google Scholar 

  5. Baron, M. K. et al. An architectural framework that may lie at the core of the postsynaptic density. Science 311, 531–535 (2006).

    ADS  Google Scholar 

  6. Ogrodnik, M. et al. Dynamic JUNQ inclusion bodies are asymmetrically inherited in mammalian cell lines through the asymmetric partitioning of vimentin. Proc. Natl Acad. Sci. USA 111, 8049–8054 (2014).

    ADS  Google Scholar 

  7. Mao, Y. S., Zhang, B. & Spector, D. L. Biogenesis and function of nuclear bodies. Trends Genet. 27, 295–306 (2011).

    Google Scholar 

  8. Ramaswami, M., Taylor, J. P. & Parker, R. Altered ribostasis: RNA-protein granules in degenerative disorders. Cell 154, 727–736 (2013).

    Google Scholar 

  9. Brangwynne, C. P. et al. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324, 1729–1732 (2009).

    Article  ADS  Google Scholar 

  10. Lee, C. F., Brangwynne, C. P., Gharakhani, J., Hyman, A. A. & Julicher, F. Spatial organization of the cell cytoplasm by position-dependent phase separation. Phys. Rev. Lett. 111, 088101 (2013).

    ADS  Google Scholar 

  11. Elbaum-Garfinkle, S. et al. The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics. Proc. Natl Acad. Sci. USA 112, 7189–7194 (2015).

    ADS  Google Scholar 

  12. Hubstenberger, A., Noble, S. L., Cameron, C. & Evans, T. C. Translation repressors, an RNA helicase, and developmental cues control RNP phase transitions during early development. Dev. Cell 27, 161–173 (2013).

    Google Scholar 

  13. Brangwynne, C. P., Mitchison, T. J. & Hyman, A. A. Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proc. Natl Acad. Sci. USA 108, 4334–4339 (2011).

    ADS  Google Scholar 

  14. Feric, M. & Brangwynne, C. P. A nuclear F-actin scaffold stabilizes RNP droplets against gravity in large cells. Nature Cell Biol. 15, 1253–1259 (2013).

    Google Scholar 

  15. Weber, S. C. & Brangwynne, C. P. Inverse size scaling of the nucleolus by a concentration-dependent phase transition. Curr. Biol. 25, 641–646 (2015).

    Google Scholar 

  16. Berry, J., Weber, S. C., Vaidya, N., Haataja, M. & Brangwynne, C. P. RNA transcription modulates phase transition-driven nuclear body assembly. Proc. Natl Acad. Sci. USA 112, E5237–E5245 (2015).

    ADS  Google Scholar 

  17. Wippich, F. et al. Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling. Cell 152, 791–805 (2013).

    Google Scholar 

  18. Sear, R. P. Dishevelled: A protein that functions in living cells by phase separating. Soft Matter 3, 680–684 (2006).

    ADS  Google Scholar 

  19. Li, P. et al. Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336–340 (2012).

    ADS  Google Scholar 

  20. Singer, A. B. & Gall, J. G. An inducible nuclear body in the Drosophila germinal vesicle. Nucleus 2, 403–409 (2011).

    Google Scholar 

  21. Altmeyer, M. et al. Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose). Nature Commun. 6, 8088 (2015).

    ADS  Google Scholar 

  22. Nott, T. et al. Phase transition of a disordered Nuage protein generates environmentally responsive membraneless organelles. Mol. Cell 57, 936–947 (2015).

    Google Scholar 

  23. Fromm, S. A. et al. In vitro reconstitution of a cellular phase-transition process that involves the mRNA decapping machinery. Angew. Chem. 53, 7354–7359 (2014).

    Google Scholar 

  24. Hennig, S. et al. Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles. J. Cell Biol. 210, 529–539 (2015).

    Google Scholar 

  25. Banjade, S. & Rosen, M. K. Phase transitions of multivalent proteins can promote clustering of membrane receptors. eLife 3, e04123 (2014).

    Google Scholar 

  26. van der Lee, R. et al. Classification of intrinsically disordered regions and proteins. Chem. Rev. 114, 6589–6631 (2014).

    Google Scholar 

  27. Wright, P. E. & Dyson, H. J. Intrinsically disordered proteins in cellular signalling and regulation. Nature Rev. Mol. Cell Biol. 16, 18–29 (2015).

    Google Scholar 

  28. Uversky, V. N., Kuznetsova, I. M., Turoverov, K. K. & Zaslavsky, B. Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates. FEBS Lett. 589, 15–22 (2015).

    Google Scholar 

  29. Wang, J. T. et al. Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans. eLife 3, e04591 (2014).

    Google Scholar 

  30. Holehouse, A. S., Garai, K., Lyle, N., Vitalis, A. & Pappu, R. V. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. J. Am. Chem. Soc. 137, 2984–2995 (2015).

    Google Scholar 

  31. Crick, S. L., Jayaraman, M., Frieden, C., Wetzel, R. & Pappu, R. V. Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions. Proc. Natl Acad. Sci. USA 103, 16764–16769 (2006).

    ADS  Google Scholar 

  32. Mukhopadhyay, S., Krishnan, R., Lemke, E. A., Lindquist, S. & Deniz, A. A. A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proc. Natl Acad. Sci. USA 104, 2649–2654 (2007).

    ADS  Google Scholar 

  33. Tran, H. T., Mao, A. & Pappu, R. V. Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins. J. Am. Chem. Soc. 130, 7380–7392 (2008).

    Google Scholar 

  34. Crick, S. L., Ruff, K. M., Garai, K., Frieden, C. & Pappu, R. V. Unmasking the roles of N- and C-terminal flanking sequences from exon 1 of huntingtin as modulators of polyglutamine aggregation. Proc. Natl Acad. Sci. USA 110, 20075–20080 (2013).

    ADS  Google Scholar 

  35. Lai, J. et al. Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity. Proc. Natl Acad. Sci. USA 109, 15781–15786 (2012).

    ADS  Google Scholar 

  36. Srinivasan, N., Bhagawati, M., Ananthanarayanan, B. & Kumar, S. Stimuli-sensitive intrinsically disordered protein brushes. Nature Commun. 5, 5145 (2014).

    ADS  Google Scholar 

  37. Das, R. K. & Pappu, R. V. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues. Proc. Natl Acad. Sci. USA 110, 13392–13397 (2013).

    ADS  Google Scholar 

  38. Schmidt, H. B. & Gorlich, D. Nup98 FG domains from diverse species spontaneously phase-separate into particles with nuclear pore-like permselectivity. eLife 4, e04251 (2015).

    Google Scholar 

  39. Alberti, S., Halfmann, R., King, O., Kapila, A. & Lindquist, S. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137, 146–158 (2009).

    Google Scholar 

  40. Kim, H. J. et al. Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature 495, 467–473 (2013).

    ADS  Google Scholar 

  41. Kato, M. et al. Cell-free formation of RNA granules: Low complexity sequence domains form dynamic fibers within hydrogels. Cell 149, 753–767 (2012).

    Google Scholar 

  42. Li, Y. R., King, O. D., Shorter, J. & Gitler, A. D. Stress granules as crucibles of ALS pathogenesis. J. Cell Biol. 201, 361–372 (2013).

    Google Scholar 

  43. Weber, S. C. & Brangwynne, C. P. Getting RNA and protein in phase. Cell 149, 1188–1191 (2012).

    Google Scholar 

  44. Patel, A. et al. A liquid-to-solid phase transition of the ALS ProteinFUS accelerated by disease mutation. Cell 162, 1066–1077 (2015).

    Google Scholar 

  45. Molliex, A. et al. Phase separation by low-complexity domains promotes stress granule assembly and drives pathological fibrillization. Cell 163, 123–133 (2015).

    Google Scholar 

  46. Lin, Y., Protter, D. S. W., Rosen, M. K. & Parker, R. Formation and maturation of phase separated liquid droplets by RNA binding proteins. Mol. Cell 60, 1–12 (2015).

    Google Scholar 

  47. Zhang, H. et al. RNA controls PolyQ protein phase transitions. Mol. Cell 60, 220–230 (2015).

    Google Scholar 

  48. Galkin, O., Chen, K., Nagel, R. L., Hirsch, R. E. & Vekilov, P. G. Liquid–liquid separation in solutions of normal and sickle cell hemoglobin. Proc. Natl Acad. Sci. USA 99, 8479–8483 (2002).

    ADS  Google Scholar 

  49. Liu, C. et al. Phase separation in aqueous solutions of lens gamma-crystallins: Special role of gamma s. Proc. Natl Acad. Sci. USA 93, 377–382 (1996).

    ADS  Google Scholar 

  50. ten Wolde, P. R. & Frenkel, D. Enhancement of protein crystal nucleation by critical density fluctuations. Science 277, 1975–1978 (1997).

    Google Scholar 

  51. Kroschwald, S. et al. Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules. eLife 4, e06807 (2015).

    Google Scholar 

  52. Buchan, J. R., Kolaitis, R. M., Taylor, J. P. & Parker, R. Eukaryotic stress granules are cleared by autophagy and Cdc48/VCP function. Cell 153, 1461–1474 (2013).

    Google Scholar 

  53. Sweeny, E. A. et al. The Hsp104 N-terminal domain enables disaggregase plasticity and potentiation. Mol. Cell 57, 836–849 (2015).

    Google Scholar 

  54. Parry, B. R. et al. The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity. Cell 156, 183–194 (2014).

    Google Scholar 

  55. Weber, S. C., Spakowitz, A. J. & Theriot, J. A. Nonthermal ATP-dependent fluctuations contribute to the in vivo motion of chromosomal loci. Proc. Natl Acad. Sci. USA 109, 7338–7343 (2012).

    ADS  Google Scholar 

  56. Guo, M. et al. Probing the stochastic, motor-driven properties of the cytoplasm using force spectrum microscopy. Cell 158, 822–832 (2014).

    Google Scholar 

  57. Bursac, P. et al. Cytoskeletal remodelling and slow dynamics in the living cell. Nature Mater. 4, 557–561 (2005).

    ADS  Google Scholar 

  58. Sollich, P., Lequeux, F., Hebraud, P. & Cates, M. E. Rheology of soft glassy materials. Phys. Rev. Lett. 78, 2020 (1997).

    ADS  Google Scholar 

  59. Stillinger, F. H. & Debenedetti, P. G. Glass transition thermodynamics and kinetics. Annu. Rev. Condens. Matter Phys. 4, 263–285 (2013).

    ADS  Google Scholar 

  60. Jack, R. L., Hedges, L. O., Garrahan, J. P. & Chandler, D. Preparation and relaxation of very stable glassy states of a simulated liquid. Phys. Rev. Lett. 107, 275702 (2011).

    ADS  Google Scholar 

  61. Weber, J. K., Jack, R. L., Schwantes, C. R. & Pande, V. S. Dynamical phase transitions reveal amyloid-like states on protein folding landscapes. Biophys. J. 107, 974–982 (2014).

    ADS  Google Scholar 

  62. Griffin, E. E., Odde, D. J. & Seydoux, G. Regulation of the MEX-5 gradient by a spatially segregated kinase/phosphatase cycle. Cell 146, 955–968 (2011).

    Google Scholar 

  63. Tritschler, F., Huntzinger, E. & Izaurralde, E. Role of GW182 proteins and PABPC1 in the miRNA pathway: A sense of déjà vu. Nature Rev. Mol. Cell Biol. 11, 379–384 (2010).

    Google Scholar 

  64. Huggins, M. L. Some properties of solutions of long-chain compounds. J. Phys. Chem. 46, 151–158 (1942).

    Google Scholar 

  65. Flory, P. J. Thermodynamics of high polymer solutions. J. Chem. Phys. 10, 51–61 (1942).

    ADS  Google Scholar 

  66. Das, R. K., Ruff, K. M. & Pappu, R. V. Relating sequence encoded information to form and function of intrinsically disordered proteins. Curr. Opin. Struct. Biol. 32, 102–112 (2015).

    Google Scholar 

  67. Overbeek, J. T. G. & Voorn, M. J. Phase separation in polyelectrolyte solutions. Theory of complex coacervation. J. Cell. Comp. Physiol. 49, 7–26 (1957).

    Google Scholar 

Download references

Acknowledgements

We thank Y. Shin and S. E.-Garfinkle for helpful comments on the manuscript. This work was supported by grants 1DP2GM105437-01 from NIH and 1253035 from NSF to C.P.B., Odysseus grant G.0029.12 from FWO to P.T., and 5R01NS056114 from the NIH to R.V.P. We are grateful to A. Holehouse for assistance with Fig. 2.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Clifford P. Brangwynne.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Brangwynne, C., Tompa, P. & Pappu, R. Polymer physics of intracellular phase transitions. Nature Phys 11, 899–904 (2015). https://doi.org/10.1038/nphys3532

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nphys3532

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing