Literature DB >> 29397728

A Lattice Model of Charge-Pattern-Dependent Polyampholyte Phase Separation.

Suman Das1, Adam Eisen1,2,3, Yi-Hsuan Lin1,4, Hue Sun Chan1,2.   

Abstract

In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding walks on the simple cubic lattice are constructed to study how phase behaviors depend on the sequence of monomers along the chains. To address pertinent general principles, we focus primarily on two fully charged 50-monomer sequences with significantly different charge patterns. Each monomer in our models occupies a single lattice site, and all monomers interact via a screened pairwise Coulomb potential. Phase diagrams are obtained by extensive Monte Carlo sampling performed at multiple temperatures on ensembles of 300 chains in boxes of sizes ranging from 52 × 52 × 52 to 246 × 246 × 246 to simulate a large number of different systems with the overall polymer volume fraction ϕ in each system varying from 0.001 to 0.1. Phase separation in the model systems is characterized by the emergence of a large cluster connected by intermonomer nearest-neighbor lattice contacts and by large fluctuations in local polymer density. The simulated critical temperatures, Tcr, of phase separation for the two sequences differ significantly, whereby the sequence with a more "blocky" charge pattern exhibits a substantially higher propensity to phase separate. The trend is consistent with our sequence-specific random-phase-approximation (RPA) polymer theory, but the variation of the simulated Tcr with a previously proposed "sequence charge decoration" pattern parameter is milder than that predicted by RPA. Ramifications of our findings for the development of analytical theory and simulation protocols of IDP LLPS are discussed.

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Year:  2018        PMID: 29397728     DOI: 10.1021/acs.jpcb.7b11723

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  25 in total

1.  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

2.  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

3.  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

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

Authors:  Yi-Hsuan Lin; Jacob P Brady; Hue Sun Chan; Kingshuk Ghosh
Journal:  J Chem Phys       Date:  2020-01-31       Impact factor: 3.488

5.  Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions.

Authors:  Yanxian Lin; James McCarty; Jennifer N Rauch; Kris T Delaney; Kenneth S Kosik; Glenn H Fredrickson; Joan-Emma Shea; Songi Han
Journal:  Elife       Date:  2019-04-05       Impact factor: 8.140

6.  'RNA modulation of transport properties and stability in phase-separated condensates.

Authors:  Andrés R Tejedor; Adiran Garaizar; Jorge Ramírez; Jorge R Espinosa
Journal:  Biophys J       Date:  2021-11-09       Impact factor: 4.033

7.  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

8.  Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants.

Authors:  Abhinaw Kumar; Debayan Chakraborty; Mauro Lorenzo Mugnai; John E Straub; D Thirumalai
Journal:  J Phys Chem Lett       Date:  2021-09-13       Impact factor: 6.888

9.  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

10.  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

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