Literature DB >> 32029630

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains.

Erik W Martin1, Alex S Holehouse2,3, Ivan Peran1, Mina Farag2,3, J Jeremias Incicco4, Anne Bremer1, Christy R Grace1, Andrea Soranno3,4, Rohit V Pappu5,3, Tanja Mittag6.   

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.
Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2020        PMID: 32029630      PMCID: PMC7297187          DOI: 10.1126/science.aaw8653

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  52 in total

1.  Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.

Authors:  Alex S Holehouse; Kanchan Garai; Nicholas Lyle; Andreas Vitalis; Rohit V Pappu
Journal:  J Am Chem Soc       Date:  2015-02-23       Impact factor: 15.419

2.  Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues.

Authors:  Rahul K Das; Rohit V Pappu
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-30       Impact factor: 11.205

3.  Relation between single-molecule properties and phase behavior of intrinsically disordered proteins.

Authors:  Gregory L Dignon; Wenwei Zheng; Robert B Best; Young C Kim; Jeetain Mittal
Journal:  Proc Natl Acad Sci U S A       Date:  2018-09-14       Impact factor: 11.205

4.  Phase separation of a yeast prion protein promotes cellular fitness.

Authors:  Titus M Franzmann; Marcus Jahnel; Andrei Pozniakovsky; Julia Mahamid; Alex S Holehouse; Elisabeth Nüske; Doris Richter; Wolfgang Baumeister; Stephan W Grill; Rohit V Pappu; Anthony A Hyman; Simon Alberti
Journal:  Science       Date:  2018-01-05       Impact factor: 47.728

5.  Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles.

Authors:  Ming-Tzo Wei; Shana Elbaum-Garfinkle; Alex S Holehouse; Carlos Chih-Hsiung Chen; Marina Feric; Craig B Arnold; Rodney D Priestley; Rohit V Pappu; Clifford P Brangwynne
Journal:  Nat Chem       Date:  2017-06-26       Impact factor: 24.427

6.  Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation.

Authors:  Joseph A Marsh; Vinay K Singh; Zongchao Jia; Julie D Forman-Kay
Journal:  Protein Sci       Date:  2006-11-06       Impact factor: 6.725

7.  ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions.

Authors:  Andreas Vitalis; Rohit V Pappu
Journal:  J Comput Chem       Date:  2009-04-15       Impact factor: 3.376

8.  Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles.

Authors:  Timothy J Nott; Evangelia Petsalaki; Patrick Farber; Dylan Jervis; Eden Fussner; Anne Plochowietz; Timothy D Craggs; David P Bazett-Jones; Tony Pawson; Julie D Forman-Kay; Andrew J Baldwin
Journal:  Mol Cell       Date:  2015-03-05       Impact factor: 17.970

9.  Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers.

Authors:  Felipe García Quiroz; Ashutosh Chilkoti
Journal:  Nat Mater       Date:  2015-09-21       Impact factor: 43.841

10.  BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis.

Authors:  Jesse Bennett Hopkins; Richard E Gillilan; Soren Skou
Journal:  J Appl Crystallogr       Date:  2017-09-05       Impact factor: 3.304

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  162 in total

Review 1.  RNA contributions to the form and function of biomolecular condensates.

Authors:  Christine Roden; Amy S Gladfelter
Journal:  Nat Rev Mol Cell Biol       Date:  2020-07-06       Impact factor: 94.444

2.  LCD-Composer: an intuitive, composition-centric method enabling the identification and detailed functional mapping of low-complexity domains.

Authors:  Sean M Cascarina; David C King; Erin Osborne Nishimura; Eric D Ross
Journal:  NAR Genom Bioinform       Date:  2021-05-26

3.  Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase.

Authors:  Tae Hun Kim; Brandon J Payliss; Michael L Nosella; Ian T W Lee; Yuki Toyama; Julie D Forman-Kay; Lewis E Kay
Journal:  Proc Natl Acad Sci U S A       Date:  2021-06-08       Impact factor: 11.205

4.  Comparative roles of charge, π, and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins.

Authors:  Suman Das; Yi-Hsuan Lin; Robert M Vernon; Julie D Forman-Kay; Hue Sun Chan
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-02       Impact factor: 11.205

5.  Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment.

Authors:  David Moses; Feng Yu; Garrett M Ginell; Nora M Shamoon; Patrick S Koenig; Alex S Holehouse; Shahar Sukenik
Journal:  J Phys Chem Lett       Date:  2020-11-16       Impact factor: 6.475

6.  Microfluidic characterization of macromolecular liquid-liquid phase separation.

Authors:  Anne Bremer; Tanja Mittag; Michael Heymann
Journal:  Lab Chip       Date:  2020-11-10       Impact factor: 6.799

Review 7.  Emerging Roles for Phase Separation in Plants.

Authors:  Ryan J Emenecker; Alex S Holehouse; Lucia C Strader
Journal:  Dev Cell       Date:  2020-10-12       Impact factor: 12.270

Review 8.  Biomolecular Condensates in the Nucleus.

Authors:  Benjamin R Sabari; Alessandra Dall'Agnese; Richard A Young
Journal:  Trends Biochem Sci       Date:  2020-07-17       Impact factor: 13.807

9.  Ubiquitin-Modulated Phase Separation of Shuttle Proteins: Does Condensate Formation Promote Protein Degradation?

Authors:  Thuy P Dao; Carlos A Castañeda
Journal:  Bioessays       Date:  2020-09-03       Impact factor: 4.345

10.  Properties of protein unfolded states suggest broad selection for expanded conformational ensembles.

Authors:  Micayla A Bowman; Joshua A Riback; Anabel Rodriguez; Hongyu Guo; Jun Li; Tobin R Sosnick; Patricia L Clark
Journal:  Proc Natl Acad Sci U S A       Date:  2020-09-02       Impact factor: 11.205

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