Valence and Patterning of Aromatic Residues Determine the Phase Behavior of Prion-like Domains

Overview

Journal Science

Specialty Science

Date 2020 Feb 8

PMID 32029630

Citations 442

Authors

Erik W Martin

Alex S Holehouse

Ivan Peran

Mina Farag

J Jeremias Incicco

Anne Bremer

Christy R Grace

Andrea Soranno

Rohit V Pappu

Tanja Mittag

Affiliations

Soon will be listed here.

Abstract

Prion-like domains (PLDs) can drive liquid-liquid phase separation (LLPS) in cells. Using an integrative biophysical approach that includes nuclear magnetic resonance spectroscopy, small-angle x-ray scattering, and multiscale simulations, we have uncovered sequence features that determine the overall phase behavior of PLDs. We show that the numbers (valence) of aromatic residues in PLDs determine the extent of temperature-dependent compaction of individual molecules in dilute solutions. The valence of aromatic residues also determines full binodals that quantify concentrations of PLDs within coexisting dilute and dense phases as a function of temperature. We also show that uniform patterning of aromatic residues is a sequence feature that promotes LLPS while inhibiting aggregation. Our findings lead to the development of a numerical stickers-and-spacers model that enables predictions of full binodals of PLDs from their sequences.

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References

Nott T, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A . Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell. 2015; 57(5):936-947. PMC: 4352761. DOI: 10.1016/j.molcel.2015.01.013. View

Holehouse A, Garai K, Lyle N, Vitalis A, Pappu R . Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. J Am Chem Soc. 2015; 137(8):2984-95. PMC: 4418562. DOI: 10.1021/ja512062h. View

Wei M, Elbaum-Garfinkle S, Holehouse A, Chen C, Feric M, Arnold C . Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles. Nat Chem. 2017; 9(11):1118-1125. PMC: 9719604. DOI: 10.1038/nchem.2803. View

Hopkins J, Gillilan R, Skou S . : improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis. J Appl Crystallogr. 2017; 50(Pt 5):1545-1553. PMC: 5627684. DOI: 10.1107/S1600576717011438. View

Dignon G, Zheng W, Best R, Kim Y, Mittal J . Relation between single-molecule properties and phase behavior of intrinsically disordered proteins. Proc Natl Acad Sci U S A. 2018; 115(40):9929-9934. PMC: 6176625. DOI: 10.1073/pnas.1804177115. View

Marsh J, Singh V, Jia Z, Forman-Kay J . Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation. Protein Sci. 2006; 15(12):2795-804. PMC: 2242444. DOI: 10.1110/ps.062465306. View

Quiroz F, Chilkoti A . Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers. Nat Mater. 2015; 14(11):1164-71. PMC: 4618764. DOI: 10.1038/nmat4418. View

Franzmann T, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse A, Nuske E . Phase separation of a yeast prion protein promotes cellular fitness. Science. 2018; 359(6371). DOI: 10.1126/science.aao5654. View

Das R, Pappu R . Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues. Proc Natl Acad Sci U S A. 2013; 110(33):13392-7. PMC: 3746876. DOI: 10.1073/pnas.1304749110. View

10.

Boke E, Ruer M, Wuhr M, Coughlin M, Lemaitre R, Gygi S . Amyloid-like Self-Assembly of a Cellular Compartment. Cell. 2016; 166(3):637-650. PMC: 5082712. DOI: 10.1016/j.cell.2016.06.051. View

11.

Evans P, Topping K, Woolfson D, Dobson C . Hydrophobic clustering in nonnative states of a protein: interpretation of chemical shifts in NMR spectra of denatured states of lysozyme. Proteins. 1991; 9(4):248-66. DOI: 10.1002/prot.340090404. View

12.

Conicella A, Zerze G, Mittal J, Fawzi N . ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain. Structure. 2016; 24(9):1537-49. PMC: 5014597. DOI: 10.1016/j.str.2016.07.007. View

13.

Patel A, Lee H, Jawerth L, Maharana S, Jahnel M, Hein M . A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation. Cell. 2015; 162(5):1066-77. DOI: 10.1016/j.cell.2015.07.047. View

14.

Holehouse A, Das R, Ahad J, Richardson M, Pappu R . CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins. Biophys J. 2017; 112(1):16-21. PMC: 5232785. DOI: 10.1016/j.bpj.2016.11.3200. View

15.

Burke K, Janke A, Rhine C, Fawzi N . Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II. Mol Cell. 2015; 60(2):231-41. PMC: 4609301. DOI: 10.1016/j.molcel.2015.09.006. View

16.

Gui X, Luo F, Li Y, Zhou H, Qin Z, Liu Z . Structural basis for reversible amyloids of hnRNPA1 elucidates their role in stress granule assembly. Nat Commun. 2019; 10(1):2006. PMC: 6494871. DOI: 10.1038/s41467-019-09902-7. View

17.

Hughes M, Sawaya M, Boyer D, Goldschmidt L, Rodriguez J, Cascio D . Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks. Science. 2018; 359(6376):698-701. PMC: 6192703. DOI: 10.1126/science.aan6398. View

18.

Warner 4th J, Ruff K, Tan P, Lemke E, Pappu R, Lashuel H . Monomeric Huntingtin Exon 1 Has Similar Overall Structural Features for Wild-Type and Pathological Polyglutamine Lengths. J Am Chem Soc. 2017; 139(41):14456-14469. PMC: 5677759. DOI: 10.1021/jacs.7b06659. View

19.

Klein-Seetharaman J, Oikawa M, Grimshaw S, Wirmer J, Duchardt E, Ueda T . Long-range interactions within a nonnative protein. Science. 2002; 295(5560):1719-22. DOI: 10.1126/science.1067680. View

20.

Strom A, Emelyanov A, Mir M, Fyodorov D, Darzacq X, Karpen G . Phase separation drives heterochromatin domain formation. Nature. 2017; 547(7662):241-245. PMC: 6022742. DOI: 10.1038/nature22989. View