2020
DOI: 10.1101/2020.06.12.148650
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A predictive coarse-grained model for position-specific effects of post-translational modifications on disordered protein phase separation

Abstract: Biomolecules undergo liquid-liquid phase separation (LLPS) resulting in the formation of multicomponent protein-RNA membraneless organelles in cells. However, the physiological and pathological role of post translational modifications (PTMs) on the biophysics of phase behavior is only beginning to be probed. To study the effect of PTMs on LLPS in silico, we extend our transferable coarse-grained model of intrinsically disordered proteins to include phosphorylated and acetylated amino acids. Using the parameter… Show more

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Cited by 10 publications
(10 citation statements)
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“…The attractiveness between the particles is scaled based on a common hydrophobicity scale (Kapcha & Rossky, 2014). The hydrophobicity of phosphorylated tyrosine was calculated from ab‐initio‐derived partial charges (Khoury et al , 2013; preprint: Perdikari et al , 2020).…”
Section: Methodsmentioning
confidence: 99%
“…The attractiveness between the particles is scaled based on a common hydrophobicity scale (Kapcha & Rossky, 2014). The hydrophobicity of phosphorylated tyrosine was calculated from ab‐initio‐derived partial charges (Khoury et al , 2013; preprint: Perdikari et al , 2020).…”
Section: Methodsmentioning
confidence: 99%
“…The HPS model is based on defining nonbonded interactions between amino acid pairs using the hydropathy values of the naturally occurring twenty amino acids ( 33 , 35 ). This model was recently extended to post-translationally modified amino acids as well ( 36 ).…”
Section: Introductionmentioning
confidence: 99%
“…We have previously overcome this difficulty by developing coarse-grained (CG) simulation models for LLPS. 29,31,[40][41][42][43] We have complemented CG simulations of LLPS with atomistic simulations of smaller fragments of the IDPs, 5,22,24,35,44 which yield detailed interactions occurring between the relevant proteins in dilute solution, and in principle, within the condensed phase. 31 In this work, we unify these two approaches, by using CG simulations to generate an initial, equilibrated configuration of phase-separated proteins, which is then mapped back to all-atom coordinates to investigate the details of atomic interactions occurring within a protein condensate.…”
Section: Introductionmentioning
confidence: 99%