Sequence determinants of protein phase behavior from a coarse-grained model
- 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. https://doi.org/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. https://doi.org/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}
}
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https://doi.org/10.1371/journal.pcbi.1005941
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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
- Molliex, Amandine; Temirov, Jamshid; Lee, Jihun
- Cell, Vol. 163, Issue 1
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
RNA Remodeling Activity of DEAD Box Proteins Tuned by Protein Concentration, RNA Length, and ATP
journal, September 2016
- Kim, Younghoon; Myong, Sua
- Molecular Cell, Vol. 63, Issue 5
Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins
journal, October 2015
- Lin, Yuan; Protter, David S. W.; Rosen, Michael K.
- Molecular Cell, Vol. 60, Issue 2
Phase Transition of Spindle-Associated Protein Regulate Spindle Apparatus Assembly
journal, September 2015
- Jiang, Hao; Wang, Shusheng; Huang, Yuejia
- Cell, Vol. 163, Issue 1
Why are ?natively unfolded? proteins unstructured under physiologic conditions?
journal, January 2000
- Uversky, Vladimir N.; Gillespie, Joel R.; Fink, Anthony L.
- Proteins: Structure, Function, and Genetics, Vol. 41, Issue 3
Protein crystallization and phase diagrams
journal, November 2004
- Asherie, N.
- Methods, Vol. 34, Issue 3
Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein
journal, July 2016
- Pak, Chi W.; Kosno, Martyna; Holehouse, Alex S.
- Molecular Cell, Vol. 63, Issue 1
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
How Hofmeister ion interactions affect protein stability
journal, October 1996
- Baldwin, R. L.
- Biophysical Journal, Vol. 71, Issue 4, p. 2056-2063
Atomic-Level Characterization of the Structural Dynamics of Proteins
journal, October 2010
- Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.
- Science, Vol. 330, Issue 6002
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
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
RNA Controls PolyQ Protein Phase Transitions
journal, October 2015
- Zhang, Huaiying; Elbaum-Garfinkle, Shana; Langdon, Erin M.
- Molecular Cell, Vol. 60, Issue 2
How Fast-Folding Proteins Fold
journal, October 2011
- Lindorff-Larsen, K.; Piana, S.; Dror, R. O.
- Science, Vol. 334, Issue 6055
Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995
- Plimpton, Steve
- Journal of Computational Physics, Vol. 117, Issue 1
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
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
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
Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains
journal, November 2013
- Kwon, Ilmin; Kato, Masato; Xiang, Siheng
- Cell, Vol. 155, Issue 5
Generalized Replica Exchange Method
journal, June 2010
- Kim, Jaegil; Keyes, Thomas; Straub, John E.
- The Journal of Chemical Physics, Vol. 132, Issue 22
Conformational Heterogeneity and FRET Data Interpretation for Dimensions of Unfolded Proteins
journal, September 2017
- Song, Jianhui; Gomes, Gregory-Neal; Shi, Tongfei
- Biophysical Journal, Vol. 113, Issue 5
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
Phase Transitions in Biological Systems with Many Components
journal, February 2017
- Jacobs, William M.; Frenkel, Daan
- Biophysical Journal, Vol. 112, Issue 4
Protein intrinsic disorder-based liquid–liquid phase transitions in biological systems: Complex coacervates and membrane-less organelles
journal, January 2017
- Uversky, Vladimir N.
- Advances in Colloid and Interface Science, Vol. 239
ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain
journal, September 2016
- Conicella, Alexander E.; Zerze, Gül H.; Mittal, Jeetain
- Structure, Vol. 24, Issue 9
Polymer-Polymer Phase Behavior
journal, February 1991
- Bates, Frank S.
- Science, Vol. 251, Issue 4996, p. 898-905
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
Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins
journal, February 2017
- Lin, Yi-Hsuan; Song, Jianhui; Forman-Kay, Julie D.
- Journal of Molecular Liquids, Vol. 228
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
Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans
journal, December 2014
- Wang, Jennifer T.; Smith, Jarrett; Chen, Bi-Chang
- eLife, Vol. 3
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
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
Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding
journal, February 2008
- Kim, Young C.; Hummer, Gerhard
- Journal of Molecular Biology, Vol. 375, Issue 5
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
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
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
Mutations in the FUS/TLS Gene on Chromosome 16 Cause Familial Amyotrophic Lateral Sclerosis
journal, February 2009
- Kwiatkowski, T. J.; Bosco, D. A.; LeClerc, A. L.
- Science, Vol. 323, Issue 5918
Vapour–liquid phase equilibrium and surface tension of fully flexible Lennard–Jones chains
journal, December 2016
- Silmore, Kevin S.; Howard, Michael P.; Panagiotopoulos, Athanassios Z.
- Molecular Physics, Vol. 115, Issue 3
Sequence-Specific Polyampholyte Phase Separation in Membraneless Organelles
journal, October 2016
- Lin, Yi-Hsuan; Forman-Kay, Julie D.; Chan, Hue Sun
- Physical Review Letters, Vol. 117, Issue 17
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
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
Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels
journal, May 2012
- Kato, Masato; Han, Tina W.; Xie, Shanhai
- Cell, Vol. 149, Issue 4
Structural Basis for RNA Unwinding by the DEAD-Box Protein Drosophila Vasa
journal, April 2006
- Sengoku, Toru; Nureki, Osamu; Nakamura, Akira
- Cell, Vol. 125, Issue 2
A Phase Separation Model for Transcriptional Control
journal, March 2017
- Hnisz, Denes; Shrinivas, Krishna; Young, Richard A.
- Cell, Vol. 169, Issue 1
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
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
Comparative Protein Modelling by Satisfaction of Spatial Restraints
journal, December 1993
- Šali, Andrej; Blundell, Tom L.
- Journal of Molecular Biology, Vol. 234, Issue 3
Thermodynamics of High Polymer Solutions
journal, January 1942
- Flory, Paul J.
- The Journal of Chemical Physics, Vol. 10, Issue 1
Phase transitions in the assembly of multivalent signalling proteins
journal, March 2012
- Li, Pilong; Banjade, Sudeep; Cheng, Hui-Chun
- Nature, Vol. 483, Issue 7389
Reversible Compartmentalization of de Novo Purine Biosynthetic Complexes in Living Cells
journal, April 2008
- An, S.; Kumar, R.; Sheets, E. D.
- Science, Vol. 320, Issue 5872
The LC Domain of hnRNPA2 Adopts Similar Conformations in Hydrogel Polymers, Liquid-like Droplets, and Nuclei
journal, November 2015
- Xiang, Siheng; Kato, Masato; Wu, Leeju C.
- Cell, Vol. 163, Issue 4
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
Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation
journal, May 2009
- Brangwynne, C. P.; Eckmann, C. R.; Courson, D. S.
- Science, Vol. 324, Issue 5935
A simple method for displaying the hydropathic character of a protein
journal, May 1982
- Kyte, Jack; Doolittle, Russell F.
- Journal of Molecular Biology, Vol. 157, Issue 1, p. 105-132
Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles
journal, March 2015
- Nott, Timothy J.; Petsalaki, Evangelia; Farber, Patrick
- Molecular Cell, Vol. 57, Issue 5
Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates
journal, November 2014
- Uversky, Vladimir N.; Kuznetsova, Irina M.; Turoverov, Konstantin K.
- FEBS Letters, Vol. 589, Issue 1
Polymer physics of intracellular phase transitions
journal, November 2015
- Brangwynne, Clifford P.; Tompa, Peter; Pappu, Rohit V.
- Nature Physics, Vol. 11, Issue 11
Some Properties of Solutions of Long-chain Compounds.
journal, January 1942
- Huggins, Maurice L.
- The Journal of Physical Chemistry, Vol. 46, Issue 1
Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets
journal, January 2017
- Shin, Yongdae; Berry, Joel; Pannucci, Nicole
- Cell, Vol. 168, Issue 1-2
A Simple Atomic-Level Hydrophobicity Scale Reveals Protein Interfacial Structure
journal, January 2014
- Kapcha, Lauren H.; Rossky, Peter J.
- Journal of Molecular Biology, Vol. 426, Issue 2
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
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
Coexisting Liquid Phases Underlie Nucleolar Subcompartments
journal, June 2016
- Feric, Marina; Vaidya, Nilesh; Harmon, Tyler S.
- Cell, Vol. 165, Issue 7
Phase separation of signaling molecules promotes T cell receptor signal transduction
journal, April 2016
- Su, Xiaolei; Ditlev, Jonathon A.; Hui, Enfu
- Science, Vol. 352, Issue 6285
Protein Composition Determines the Effect of Crowding on the Properties of Disordered Proteins
journal, July 2016
- Miller, Cayla M.; Kim, Young C.; Mittal, Jeetain
- Biophysical Journal, Vol. 111, Issue 1
Mutations in FUS, an RNA Processing Protein, Cause Familial Amyotrophic Lateral Sclerosis Type 6
journal, February 2009
- Vance, C.; Rogelj, B.; Hortobagyi, T.
- Science, Vol. 323, Issue 5918
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
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
Nuclear Stress Bodies
journal, April 2010
- Biamonti, G.; Vourc'h, C.
- Cold Spring Harbor Perspectives in Biology, Vol. 2, Issue 6
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
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
The Role of Nuclear Bodies in Gene Expression and Disease
journal, July 2013
- Morimoto, Marie; Boerkoel, Cornelius
- Biology, Vol. 2, Issue 3
Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling
journal, February 2013
- Wippich, Frank; Bodenmiller, Bernd; Trajkovska, Maria Gustafsson
- Cell, Vol. 152, Issue 4
Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II
journal, October 2015
- Burke, Kathleen A.; Janke, Abigail M.; Rhine, Christy L.
- Molecular Cell, Vol. 60, Issue 2
Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response
journal, March 2017
- Riback, Joshua A.; Katanski, Christopher D.; Kear-Scott, Jamie L.
- Cell, Vol. 168, Issue 6
A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation
journal, August 2015
- Patel, Avinash; Lee, Hyun O.; Jawerth, Louise
- Cell, Vol. 162, Issue 5
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
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