Literature DB >> 32007034

A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes.

Yi-Hsuan Lin1, Jacob P Brady1, Hue Sun Chan1, Kingshuk Ghosh2.   

Abstract

The physical chemistry of liquid-liquid phase separation (LLPS) of polymer solutions bears directly on the assembly of biologically functional dropletlike bodies from proteins and nucleic acids. These biomolecular condensates include certain extracellular materials and intracellular compartments that are characterized as "membraneless organelles." Analytical theories are a valuable, computationally efficient tool for addressing general principles. LLPS of neutral homopolymers is quite well described by theory, but it has been a challenge to develop general theories for the LLPS of heteropolymers involving charge-charge interactions. Here, we present a theory that combines a random-phase-approximation treatment of polymer density fluctuations and an account of intrachain conformational heterogeneity based on renormalized Kuhn lengths to provide predictions of LLPS properties as a function of pH, salt, and charge patterning along the chain sequence. Advancing beyond more limited analytical approaches, our LLPS theory is applicable to a wide variety of charged sequences ranging from highly charged polyelectrolytes to neutral or nearly neutral polyampholytes. This theory should be useful in high-throughput screening of protein and other sequences for their LLPS propensities and can serve as a basis for more comprehensive theories that incorporate nonelectrostatic interactions. Experimental ramifications of our theory are discussed.

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Year:  2020        PMID: 32007034      PMCID: PMC7043852          DOI: 10.1063/1.5139661

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  67 in total

1.  Phase Diagram of Colloidal Solutions.

Authors: 
Journal:  Phys Rev Lett       Date:  1996-12-02       Impact factor: 9.161

2.  Binary-liquid phase separation of lens protein solutions.

Authors:  M L Broide; C R Berland; J Pande; O O Ogun; G B Benedek
Journal:  Proc Natl Acad Sci U S A       Date:  1991-07-01       Impact factor: 11.205

3.  Computing protein stabilities from their chain lengths.

Authors:  Kingshuk Ghosh; Ken A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  2009-06-17       Impact factor: 11.205

4.  Pressure-Sensitive and Osmolyte-Modulated Liquid-Liquid Phase Separation of Eye-Lens γ-Crystallins.

Authors:  Süleyman Cinar; Hasan Cinar; Hue Sun Chan; Roland Winter
Journal:  J Am Chem Soc       Date:  2019-04-23       Impact factor: 15.419

5.  Molecular design of self-coacervation phenomena in block polyampholytes.

Authors:  Scott P O Danielsen; James McCarty; Joan-Emma Shea; Kris T Delaney; Glenn H Fredrickson
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-04       Impact factor: 11.205

6.  Dynamic condensates activate transcription.

Authors:  Aaron J Plys; Robert E Kingston
Journal:  Science       Date:  2018-07-27       Impact factor: 47.728

Review 7.  Protein Phase Separation: A New Phase in Cell Biology.

Authors:  Steven Boeynaems; Simon Alberti; Nicolas L Fawzi; Tanja Mittag; Magdalini Polymenidou; Frederic Rousseau; Joost Schymkowitz; James Shorter; Benjamin Wolozin; Ludo Van Den Bosch; Peter Tompa; Monika Fuxreiter
Journal:  Trends Cell Biol       Date:  2018-03-27       Impact factor: 20.808

8.  Phase behavior of polyelectrolyte solutions with salt.

Authors:  Chi-Lun Lee; Murugappan Muthukumar
Journal:  J Chem Phys       Date:  2009-01-14       Impact factor: 3.488

9.  Phase transitions in the assembly of multivalent signalling proteins.

Authors:  Pilong Li; Sudeep Banjade; Hui-Chun Cheng; Soyeon Kim; Baoyu Chen; Liang Guo; Marc Llaguno; Javoris V Hollingsworth; David S King; Salman F Banani; Paul S Russo; Qiu-Xing Jiang; B Tracy Nixon; Michael K Rosen
Journal:  Nature       Date:  2012-03-07       Impact factor: 49.962

10.  Sequence determinants of protein phase behavior from a coarse-grained model.

Authors:  Gregory L Dignon; Wenwei Zheng; Young C Kim; Robert B Best; Jeetain Mittal
Journal:  PLoS Comput Biol       Date:  2018-01-24       Impact factor: 4.475

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  14 in total

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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

2.  An analytical theory to describe sequence-specific inter-residue distance profiles for polyampholytes and intrinsically disordered proteins.

Authors:  Jonathan Huihui; Kingshuk Ghosh
Journal:  J Chem Phys       Date:  2020-04-30       Impact factor: 3.488

3.  Assembly of model postsynaptic densities involves interactions auxiliary to stoichiometric binding.

Authors:  Yi-Hsuan Lin; Haowei Wu; Bowen Jia; Mingjie Zhang; Hue Sun Chan
Journal:  Biophys J       Date:  2021-10-09       Impact factor: 4.033

4.  Numerical Techniques for Applications of Analytical Theories to Sequence-Dependent Phase Separations of Intrinsically Disordered Proteins.

Authors:  Yi-Hsuan Lin; Jonas Wessén; Tanmoy Pal; Suman Das; Hue Sun Chan
Journal:  Methods Mol Biol       Date:  2023

5.  Multiscale Modeling of Protein-RNA Condensation in and Out of Equilibrium.

Authors:  Rabia Laghmach; Isha Malhotra; Davit A Potoyan
Journal:  Methods Mol Biol       Date:  2023

6.  Intrachain interaction topology can identify functionally similar intrinsically disordered proteins.

Authors:  Jonathan Huihui; Kingshuk Ghosh
Journal:  Biophys J       Date:  2021-04-15       Impact factor: 4.033

Review 7.  Physics-based computational and theoretical approaches to intrinsically disordered proteins.

Authors:  Joan-Emma Shea; Robert B Best; Jeetain Mittal
Journal:  Curr Opin Struct Biol       Date:  2021-02-02       Impact factor: 6.809

8.  Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model.

Authors:  Jerelle A Joseph; Jorge R Espinosa; Ignacio Sanchez-Burgos; Adiran Garaizar; Daan Frenkel; Rosana Collepardo-Guevara
Journal:  Biophys J       Date:  2021-02-09       Impact factor: 4.033

Review 9.  The Protein Folding Problem: The Role of Theory.

Authors:  Roy Nassar; Gregory L Dignon; Rostam M Razban; Ken A Dill
Journal:  J Mol Biol       Date:  2021-07-03       Impact factor: 6.151

Review 10.  Rules of Physical Mathematics Govern Intrinsically Disordered Proteins.

Authors:  Kingshuk Ghosh; Jonathan Huihui; Michael Phillips; Austin Haider
Journal:  Annu Rev Biophys       Date:  2022-02-04       Impact factor: 19.763

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