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

• Published in: PLoS computational biology 2018-01, Vol.14 (1), p.e1005941-e1005941
• Main Authors: Dignon, Gregory L, Zheng, Wenwei, Kim, Young C, Best, Robert B, Mittal, Jeetain
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Amino acid sequencing; Assemblies; BASIC BIOLOGICAL SCIENCES; Biology and Life Sciences; Coexistence; Computer and Information Sciences; Computer applications; Computer simulation; Contact potentials; Determinants; Diabetes; DNA helicase; Electrostatic properties; Energy; FUS protein; Interaction parameters; Kidney diseases; Laboratories; Mathematical models; Methods; Mutation; Organelles; Phase diagrams; Phase separation; Phase transitions; Phosphorylation; Physical Sciences; Physics; Physiological aspects; Polymers; Protein separation; Proteins; Research and Analysis Methods; Ribonucleic acid; RNA; RNA polymerase; RNA-binding protein; Sampling methods; Simulation; Software; Thermodynamics
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1005941

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.