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

Journal Article · · PLoS Computational Biology (Online)
ORCiD logo [1];  [2];  [3];  [4]; ORCiD logo [1];  [5]
  1. Lehigh Univ., Bethlehem, PA (United States)
  2. National Inst. of Health (NIH), Bethesda, MD (United States); ; Arizona State Univ., Mesa, AZ (United States)
  3. Naval Research Lab. (NRL), Washington, DC (United States)
  4. National Inst. of Health (NIH), Bethesda, MD (United States)
  5. Bar Ilan Univ., Ramat Gan, Tel Aviv (Israel)

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. Moreover, 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.

Research Organization:
Lehigh Univ., Bethlehem, PA (United States); University of California, Berkeley, CA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
SC0013979; AC02-05CH11231
OSTI ID:
1419611
Alternate ID(s):
OSTI ID: 1417943; OSTI ID: 1499874
Journal Information:
PLoS Computational Biology (Online), Vol. 14, Issue 1; ISSN 1553-7358
Publisher:
Public Library of ScienceCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 268 works
Citation information provided by
Web of Science

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Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters journal May 2016
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Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment text January 2016
Consistent view of polypeptide chain expansion in chemical denaturants from multiple experimental methods text January 2016
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Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling text January 2013
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How accurate are polymer models in the analysis of Forster resonance energy transfer experiments on proteins? text January 2009
Sequence-specific polyampholyte phase separation in membraneless organelles text January 2016
Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins text January 2016
In Vitro Reconstitution of a Cellular Phase-Transition Process that Involves the mRNA Decapping Machinery journal May 2014
Comparative Protein Modelling by Satisfaction of Spatial Restraints journal December 1993
A simple method for displaying the hydropathic character of a protein journal May 1982
Protein Composition Determines the Effect of Crowding on the Properties of Disordered Proteins journal July 2016
To Mix, or To Demix, That Is the Question journal February 2017
SAXS versus FRET: A Matter of Heterogeneity? journal September 2017
Structural Basis for RNA Unwinding by the DEAD-Box Protein Drosophila Vasa journal April 2006
Bent out of Shape: RNA Unwinding by the DEAD-Box Helicase Vasa journal April 2006
Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels journal May 2012
Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling journal February 2013
Phase Transition of Spindle-Associated Protein Regulate Spindle Apparatus Assembly journal September 2015
Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization journal September 2015
The LC Domain of hnRNPA2 Adopts Similar Conformations in Hydrogel Polymers, Liquid-like Droplets, and Nuclei journal November 2015
Coexisting Liquid Phases Underlie Nucleolar Subcompartments journal June 2016
Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets journal January 2017
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Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates journal November 2014
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Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II journal October 2015
Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein journal July 2016
RNA Remodeling Activity of DEAD Box Proteins Tuned by Protein Concentration, RNA Length, and ATP journal September 2016
ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain journal September 2016
A New Phase in ALS Research journal September 2016
The salting-out behavior of amides and its relation to the denaturation of proteins by salts journal May 1967
Effects of salts on the free energy of the peptide group journal February 1972
Effects of salts on the free energies of nonpolar groups in model peptides journal February 1972
Natively Unfolded Protein Stability as a Coil-to-Globule Transition in Charge/Hydropathy Space journal July 2008
Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment journal September 2016
Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods journal September 2016
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States journal April 2015
Phase transitions in the assembly of multivalent signalling proteins journal March 2012
Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters journal May 2016
Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles journal June 2017
Thermodynamics of High Polymer Solutions journal January 1942
Net charge per residue modulates conformational ensembles of intrinsically disordered proteins journal April 2010
Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes journal February 2011
Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy journal September 2012
The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics journal May 2015
RNA transcription modulates phase transition-driven nuclear body assembly journal September 2015
Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements journal July 2017
Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation journal September 2017
Nuclear Stress Bodies journal April 2010
Reversible Compartmentalization of de Novo Purine Biosynthetic Complexes in Living Cells journal April 2008
Mutations in the FUS/TLS Gene on Chromosome 16 Cause Familial Amyotrophic Lateral Sclerosis journal February 2009
Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation journal May 2009
Atomic-Level Characterization of the Structural Dynamics of Proteins journal October 2010
Polymer-Polymer Phase Behavior journal February 1991
Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water journal October 2017
An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function journal April 2017
The Role of Nuclear Bodies in Gene Expression and Disease journal July 2013

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Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation journal April 2018
Phase behavior of blocky charge lattice polymers: Crystals, liquids, sheets, filaments, and clusters journal November 2019
Loop formation and translational diffusion of intrinsically disordered proteins journal November 2019
Colloidal hydrodynamics of biological cells: A frontier spanning two fields journal November 2019
Phospho‐regulation of intrinsically disordered proteins for actin assembly and endocytosis journal May 2018
Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins journal April 2019
Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications journal August 2019
Evolution of protein interfaces in multimers and fibrils journal June 2019
Relation between single-molecule properties and phase behavior of intrinsically disordered proteins journal September 2018
Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins journal March 2019
Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid–Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications journal August 2019
Thermodynamically driven assemblies and liquid–liquid phase separations in biology journal January 2019
Recent Advances in Machine Learning Based Prediction of RNA-protein Interactions journal September 2019
Coarse-grained residue-based models of disordered protein condensates: utility and limitations of simple charge pattern parameters journal January 2018
Biomolecular Chemistry in Liquid Phase Separated Compartments journal April 2019
Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain journal July 2019
A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes journal January 2020
LASSI: A lattice model for simulating phase transitions of multivalent proteins journal October 2019
Thermodynamically Driven Assemblies and Liquid-liquid Phase Separations in Biology text January 2018
Phase behavior of blocky charge lattice polymers: Crystals, liquids, sheets, filaments and clusters text January 2019
Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range journal August 2022
Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review journal January 2019
Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain journal July 2019
A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes journal January 2020
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level journal February 2019

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