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

Gregory L. Dignon, Wenwei Zheng, Young C. Kim, Robert B. Best, Jeetain Mittal

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

Membraneless organelles important to intracellular compartmentalization have recently been shown to comprise assemblies of proteins which undergo liquid-liquid phase separation (LLPS). However, many proteins involved in this phase separation are at least partially disordered. The molecular mechanism and the sequence determinants of this process are challenging to determine experimentally owing to the disordered nature of the assemblies, motivating the use of theoretical and simulation methods. This work advances a computational framework for conducting simulations of LLPS with residue-level detail, and allows for the determination of phase diagrams and coexistence densities of proteins in the two phases. The model includes a short-range contact potential as well as a simplified treatment of electrostatic energy. Interaction parameters are optimized against experimentally determined radius of gyration data for multiple unfolded or intrinsically disordered proteins (IDPs). These models are applied to two systems which undergo LLPS: the low complexity domain of the RNA-binding protein FUS and the DEAD-box helicase protein LAF-1. We develop a novel simulation method to determine thermodynamic phase diagrams as a function of the total protein concentration and temperature. We show that the model is capable of capturing qualitative changes in the phase diagram due to phosphomimetic mutations of FUS and to the presence or absence of the large folded domain in LAF-1. We also explore the effects of chain-length, or multivalency, on the phase diagram, and obtain results consistent with Flory-Huggins theory for polymers. Most importantly, the methodology presented here is flexible so that it can be easily extended to other pair potentials, be used with other enhanced sampling methods, and may incorporate additional features for biological systems of interest.

Original languageEnglish (US)
Article numbere1005941
JournalPLoS Computational Biology
Volume14
Issue number1
DOIs
StatePublished - Jan 1 2018
Externally publishedYes

Fingerprint

Phase behavior
Determinant
Proteins
Protein
Phase separation
Phase Separation
Liquid
Phase diagrams
protein
liquids
Liquids
Phase Diagram
liquid
diagram
proteins
RNA-Binding Protein FUS
Intrinsically Disordered Proteins
Simulation Methods
Model
RNA-binding proteins

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

Cite this

Sequence determinants of protein phase behavior from a coarse-grained model. / Dignon, Gregory L.; Zheng, Wenwei; Kim, Young C.; Best, Robert B.; Mittal, Jeetain.

In: PLoS Computational Biology, Vol. 14, No. 1, e1005941, 01.01.2018.

Research output: Contribution to journalArticle

Dignon, Gregory L. ; Zheng, Wenwei ; Kim, Young C. ; Best, Robert B. ; Mittal, Jeetain. / Sequence determinants of protein phase behavior from a coarse-grained model. In: PLoS Computational Biology. 2018 ; Vol. 14, No. 1.
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