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

Authors:
ORCiD logo; ; ; ; ORCiD logo;
Publication Date:
Research Org.:
Lehigh Univ., Bethlehem, PA (United States); Univ. of California, Berkeley, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1419611
Alternate Identifier(s):
OSTI ID: 1417943; OSTI ID: 1499874
Grant/Contract Number:  
SC0013979; AC02-05CH11231
Resource Type:
Published Article
Journal Name:
PLoS Computational Biology (Online)
Additional Journal Information:
Journal Name: PLoS Computational Biology (Online) Journal Volume: 14 Journal Issue: 1; Journal ID: ISSN 1553-7358
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Dignon, Gregory L., Zheng, Wenwei, Kim, Young C., Best, Robert B., Mittal, Jeetain, and Ofran, ed., Yanay. Sequence determinants of protein phase behavior from a coarse-grained model. United States: N. p., 2018. Web. doi:10.1371/journal.pcbi.1005941.
Dignon, Gregory L., Zheng, Wenwei, Kim, Young C., Best, Robert B., Mittal, Jeetain, & Ofran, ed., Yanay. Sequence determinants of protein phase behavior from a coarse-grained model. United States. doi:10.1371/journal.pcbi.1005941.
Dignon, Gregory L., Zheng, Wenwei, Kim, Young C., Best, Robert B., Mittal, Jeetain, and Ofran, ed., Yanay. Wed . "Sequence determinants of protein phase behavior from a coarse-grained model". United States. doi:10.1371/journal.pcbi.1005941.
@article{osti_1419611,
title = {Sequence determinants of protein phase behavior from a coarse-grained model},
author = {Dignon, Gregory L. and Zheng, Wenwei and Kim, Young C. and Best, Robert B. and Mittal, Jeetain and Ofran, ed., Yanay},
abstractNote = {},
doi = {10.1371/journal.pcbi.1005941},
journal = {PLoS Computational Biology (Online)},
number = 1,
volume = 14,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1371/journal.pcbi.1005941

Citation Metrics:
Cited by: 16 works
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Works referenced in this record:

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization
journal, September 2015


The salting-out behavior of amides and its relation to the denaturation of proteins by salts
journal, May 1967

  • Schrier, Eugene E.; Schrier, Evelyn B.
  • The Journal of Physical Chemistry, Vol. 71, Issue 6
  • DOI: 10.1021/j100865a049

RNA Remodeling Activity of DEAD Box Proteins Tuned by Protein Concentration, RNA Length, and ATP
journal, September 2016


Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins
journal, October 2015


Phase Transition of Spindle-Associated Protein Regulate Spindle Apparatus Assembly
journal, September 2015


Why are ?natively unfolded? proteins unstructured under physiologic conditions?
journal, January 2000


Protein crystallization and phase diagrams
journal, November 2004


Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein
journal, July 2016


Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water
journal, October 2017

  • Riback, Joshua A.; Bowman, Micayla A.; Zmyslowski, Adam M.
  • Science, Vol. 358, Issue 6360
  • DOI: 10.1126/science.aan5774

How Hofmeister ion interactions affect protein stability
journal, October 1996


Atomic-Level Characterization of the Structural Dynamics of Proteins
journal, October 2010


Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods
journal, September 2016

  • Borgia, Alessandro; Zheng, Wenwei; Buholzer, Karin
  • Journal of the American Chemical Society, Vol. 138, Issue 36
  • DOI: 10.1021/jacs.6b05917

Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids
journal, June 1971

  • Weeks, John D.; Chandler, David; Andersen, Hans C.
  • The Journal of Chemical Physics, Vol. 54, Issue 12
  • DOI: 10.1063/1.1674820

RNA Controls PolyQ Protein Phase Transitions
journal, October 2015


How Fast-Folding Proteins Fold
journal, October 2011


Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995


How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?
journal, March 2009

  • O’Brien, Edward P.; Morrison, Greg; Brooks, Bernard R.
  • The Journal of Chemical Physics, Vol. 130, Issue 12
  • DOI: 10.1063/1.3082151

Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles
journal, June 2017

  • Wei, Ming-Tzo; Elbaum-Garfinkle, Shana; Holehouse, Alex S.
  • Nature Chemistry, Vol. 9, Issue 11
  • DOI: 10.1038/nchem.2803

RNA transcription modulates phase transition-driven nuclear body assembly
journal, September 2015

  • Berry, Joel; Weber, Stephanie C.; Vaidya, Nilesh
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 38
  • DOI: 10.1073/pnas.1509317112

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains
journal, November 2013


Generalized Replica Exchange Method
journal, June 2010

  • Kim, Jaegil; Keyes, Thomas; Straub, John E.
  • The Journal of Chemical Physics, Vol. 132, Issue 22
  • DOI: 10.1063/1.3432176

Conformational Heterogeneity and FRET Data Interpretation for Dimensions of Unfolded Proteins
journal, September 2017


Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment
journal, September 2016

  • Zheng, Wenwei; Borgia, Alessandro; Buholzer, Karin
  • Journal of the American Chemical Society, Vol. 138, Issue 36
  • DOI: 10.1021/jacs.6b05443

Phase Transitions in Biological Systems with Many Components
journal, February 2017


ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain
journal, September 2016


Polymer-Polymer Phase Behavior
journal, February 1991


Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes
journal, February 2011

  • Brangwynne, C. P.; Mitchison, T. J.; Hyman, A. A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 11
  • DOI: 10.1073/pnas.1017150108

Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins
journal, February 2017


Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
journal, September 2012

  • Hofmann, H.; Soranno, A.; Borgia, A.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 40
  • DOI: 10.1073/pnas.1207719109

Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans
journal, December 2014


Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers
journal, September 2015

  • Quiroz, Felipe García; Chilkoti, Ashutosh
  • Nature Materials, Vol. 14, Issue 11
  • DOI: 10.1038/nmat4418

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
journal, October 2014

  • Best, Robert B.; Zheng, Wenwei; Mittal, Jeetain
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 11
  • DOI: 10.1021/ct500569b

Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding
journal, February 2008


A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins
journal, August 2015

  • Sawle, Lucas; Ghosh, Kingshuk
  • The Journal of Chemical Physics, Vol. 143, Issue 8
  • DOI: 10.1063/1.4929391

Vapor-liquid interfacial properties of fully flexible Lennard-Jones chains
journal, October 2008

  • Blas, Felipe J.; MacDowell, Luis G.; de Miguel, Enrique
  • The Journal of Chemical Physics, Vol. 129, Issue 14
  • DOI: 10.1063/1.2989115

Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation
journal, September 2017

  • Brady, Jacob P.; Farber, Patrick J.; Sekhar, Ashok
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 39
  • DOI: 10.1073/pnas.1706197114

Mutations in the FUS/TLS Gene on Chromosome 16 Cause Familial Amyotrophic Lateral Sclerosis
journal, February 2009


Vapour–liquid phase equilibrium and surface tension of fully flexible Lennard–Jones chains
journal, December 2016


Sequence-Specific Polyampholyte Phase Separation in Membraneless Organelles
journal, October 2016


Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements
journal, July 2017

  • Fuertes, Gustavo; Banterle, Niccolò; Ruff, Kiersten M.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 31
  • DOI: 10.1073/pnas.1704692114

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins
journal, April 2010

  • Mao, A. H.; Crick, S. L.; Vitalis, A.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 18
  • DOI: 10.1073/pnas.0911107107

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels
journal, May 2012


Structural Basis for RNA Unwinding by the DEAD-Box Protein Drosophila Vasa
journal, April 2006


A Phase Separation Model for Transcriptional Control
journal, March 2017


Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose)
journal, August 2015

  • Altmeyer, Matthias; Neelsen, Kai J.; Teloni, Federico
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms9088

General purpose molecular dynamics simulations fully implemented on graphics processing units
journal, May 2008

  • Anderson, Joshua A.; Lorenz, Chris D.; Travesset, A.
  • Journal of Computational Physics, Vol. 227, Issue 10
  • DOI: 10.1016/j.jcp.2008.01.047

Comparative Protein Modelling by Satisfaction of Spatial Restraints
journal, December 1993


Thermodynamics of High Polymer Solutions
journal, January 1942

  • Flory, Paul J.
  • The Journal of Chemical Physics, Vol. 10, Issue 1
  • DOI: 10.1063/1.1723621

Phase transitions in the assembly of multivalent signalling proteins
journal, March 2012

  • Li, Pilong; Banjade, Sudeep; Cheng, Hui-Chun
  • Nature, Vol. 483, Issue 7389
  • DOI: 10.1038/nature10879

Reversible Compartmentalization of de Novo Purine Biosynthetic Complexes in Living Cells
journal, April 2008


The LC Domain of hnRNPA2 Adopts Similar Conformations in Hydrogel Polymers, Liquid-like Droplets, and Nuclei
journal, November 2015


Residue – Residue Potentials with a Favorable Contact Pair Term and an Unfavorable High Packing Density Term, for Simulation and Threading
journal, March 1996

  • Miyazawa, Sanzo; Jernigan, Robert L.
  • Journal of Molecular Biology, Vol. 256, Issue 3
  • DOI: 10.1006/jmbi.1996.0114

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation
journal, May 2009


A simple method for displaying the hydropathic character of a protein
journal, May 1982


Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles
journal, March 2015


Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates
journal, November 2014


Polymer physics of intracellular phase transitions
journal, November 2015

  • Brangwynne, Clifford P.; Tompa, Peter; Pappu, Rohit V.
  • Nature Physics, Vol. 11, Issue 11
  • DOI: 10.1038/nphys3532

Some Properties of Solutions of Long-chain Compounds.
journal, January 1942

  • Huggins, Maurice L.
  • The Journal of Physical Chemistry, Vol. 46, Issue 1
  • DOI: 10.1021/j150415a018

Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets
journal, January 2017


A Simple Atomic-Level Hydrophobicity Scale Reveals Protein Interfacial Structure
journal, January 2014


Polymorphic transitions in single crystals: A new molecular dynamics method
journal, December 1981

  • Parrinello, M.; Rahman, A.
  • Journal of Applied Physics, Vol. 52, Issue 12
  • DOI: 10.1063/1.328693

Natively Unfolded Protein Stability as a Coil-to-Globule Transition in Charge/Hydropathy Space
journal, July 2008

  • Ashbaugh, Henry S.; Hatch, Harold W.
  • Journal of the American Chemical Society, Vol. 130, Issue 29
  • DOI: 10.1021/ja802124e

Coexisting Liquid Phases Underlie Nucleolar Subcompartments
journal, June 2016


Phase separation of signaling molecules promotes T cell receptor signal transduction
journal, April 2016


Protein Composition Determines the Effect of Crowding on the Properties of Disordered Proteins
journal, July 2016


Mutations in FUS, an RNA Processing Protein, Cause Familial Amyotrophic Lateral Sclerosis Type 6
journal, February 2009


The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics
journal, May 2015

  • Elbaum-Garfinkle, Shana; Kim, Younghoon; Szczepaniak, Krzysztof
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 23
  • DOI: 10.1073/pnas.1504822112

In Vitro Reconstitution of a Cellular Phase-Transition Process that Involves the mRNA Decapping Machinery
journal, May 2014

  • Fromm, Simon A.; Kamenz, Julia; Nöldeke, Erik R.
  • Angewandte Chemie International Edition, Vol. 53, Issue 28
  • DOI: 10.1002/anie.201402885

Nuclear Stress Bodies
journal, April 2010


Effects of salts on the free energies of nonpolar groups in model peptides
journal, February 1972

  • Nandi, Pradip K.; Robinson, Dwight R.
  • Journal of the American Chemical Society, Vol. 94, Issue 4
  • DOI: 10.1021/ja00759a043

Effects of salts on the free energy of the peptide group
journal, February 1972

  • Nandi, Pradip K.; Robinson, Dwight R.
  • Journal of the American Chemical Society, Vol. 94, Issue 4
  • DOI: 10.1021/ja00759a042

The Role of Nuclear Bodies in Gene Expression and Disease
journal, July 2013


Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling
journal, February 2013


Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II
journal, October 2015


Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response
journal, March 2017


A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation
journal, August 2015


Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters
journal, May 2016

  • Nott, Timothy J.; Craggs, Timothy D.; Baldwin, Andrew J.
  • Nature Chemistry, Vol. 8, Issue 6
  • DOI: 10.1038/nchem.2519

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
journal, April 2015

  • Piana, Stefano; Donchev, Alexander G.; Robustelli, Paul
  • The Journal of Physical Chemistry B, Vol. 119, Issue 16
  • DOI: 10.1021/jp508971m