A predictive coarse-grained model for position-specific effects of post-translational modifications
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Title
A predictive coarse-grained model for position-specific effects of post-translational modifications
Authors
Keywords
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Journal
BIOPHYSICAL JOURNAL
Volume -, Issue -, Pages -
Publisher
Elsevier BV
Online
2021-02-12
DOI
10.1016/j.bpj.2021.01.034
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Note: Only part of the references are listed.- Model for disordered proteins with strongly sequence-dependent liquid phase behavior
- (2020) Antonia Statt et al. JOURNAL OF CHEMICAL PHYSICS
- Effect of Phosphorylation and O-GlcNAcylation on Proline-Rich Domains of Tau
- (2020) Lata Rani et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Biomolecular Phase Separation: From Molecular Driving Forces to Macroscopic Properties
- (2020) Gregory L. Dignon et al. Annual Review of Physical Chemistry
- Hydropathy Patterning Complements Charge Patterning to Describe Conformational Preferences of Disordered Proteins
- (2020) Wenwei Zheng et al. Journal of Physical Chemistry Letters
- Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior
- (2020) Benjamin S. Schuster et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Analytical Theory for Sequence-Specific Binary Fuzzy Complexes of Charged Intrinsically Disordered Proteins
- (2020) Alan N. Amin et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Tyrosine phosphorylation regulates hnRNPA2 granule protein partitioning and reduces neurodegeneration
- (2020) Veronica H Ryan et al. EMBO JOURNAL
- Phosphoregulated FMRP phase separation models activity-dependent translation through bidirectional control of mRNA granule formation
- (2019) Brian Tsang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties
- (2019) Gül H. Zerze et al. Journal of Physical Chemistry Letters
- Simulation methods for liquid–liquid phase separation of disordered proteins
- (2019) Gregory L Dignon et al. Current Opinion in Chemical Engineering
- Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes
- (2019) Adam K. Sieradzan et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain
- (2019) Anastasia C. Murthy et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Inhibition of Axon Regeneration by Liquid-like TIAR-2 Granules
- (2019) Matthew G. Andrusiak et al. NEURON
- Phospho-dependent phase separation of FMRP and CAPRIN1 recapitulates regulation of translation and deadenylation
- (2019) Tae Hun Kim et al. SCIENCE
- The Control Centers of Biomolecular Phase Separation: How Membrane Surfaces, PTMs, and Active Processes Regulate Condensation
- (2019) Wilton T. Snead et al. MOLECULAR CELL
- Physiological, Pathological, and Targetable Membraneless Organelles in Neurons
- (2019) Veronica H. Ryan et al. TRENDS IN NEUROSCIENCES
- LASSI: A lattice model for simulating phase transitions of multivalent proteins
- (2019) Jeong-Mo Choi et al. PLoS Computational Biology
- FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions
- (2018) Seema Qamar et al. CELL
- Tau protein liquid–liquid phase separation can initiate tau aggregation
- (2018) Susanne Wegmann et al. EMBO JOURNAL
- Acetylation Disfavors Tau Phase Separation
- (2018) Josephine Ferreon et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- The Role of Post-Translational Modifications on Prion-Like Aggregation and Liquid-Phase Separation of FUS
- (2018) Shannon Rhoads et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins
- (2018) Taylor Firman et al. JOURNAL OF CHEMICAL PHYSICS
- Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions
- (2018) Carolina Cragnell et al. JOURNAL OF MOLECULAR BIOLOGY
- Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation
- (2018) Veronica H. Ryan et al. MOLECULAR CELL
- Sequence determinants of protein phase behavior from a coarse-grained model
- (2018) Gregory L. Dignon et al. PLoS Computational Biology
- Pi-Pi contacts are an overlooked protein feature relevant to phase separation
- (2018) Robert McCoy Vernon et al. eLife
- Dual roles for ATP in the regulation of phase separated protein aggregates in Xenopus oocyte nucleoli
- (2018) Michael H Hayes et al. eLife
- Acetylation of C-terminal lysines modulates protein turnover and stability of Connexin-32
- (2018) Sarah R. Alaei et al. BMC CELL BIOLOGY
- Modulating charge patterning and ionic strength as a strategy to induce conformational changes in intrinsically disordered proteins
- (2018) Jonathan Huihui et al. JOURNAL OF CHEMICAL PHYSICS
- Who's In and Who's Out—Compositional Control of Biomolecular Condensates
- (2018) Jonathon A. Ditlev et al. JOURNAL OF MOLECULAR BIOLOGY
- Relation between single-molecule properties and phase behavior of intrinsically disordered proteins
- (2018) Gregory L. Dignon et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Controllable protein phase separation and modular recruitment to form responsive membraneless organelles
- (2018) Benjamin S. Schuster et al. Nature Communications
- A Chemical Chaperone Decouples TDP-43 Disordered Domain Phase Separation from Fibrillation
- (2018) Kyoung-Jae Choi et al. BIOCHEMISTRY
- Friend or foe — post-translational modifications as regulators of phase separation and RNP granule dynamics
- (2018) Mario Hofweber et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation
- (2018) Jiří Vymětal et al. Journal of Chemical Theory and Computation
- Acetylation of intrinsically disordered regions regulates phase separation
- (2018) Makoto Saito et al. Nature Chemical Biology
- Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
- (2018) Elizabeth Brunk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations
- (2018) Kiersten M Ruff et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Biomolecular condensates: organizers of cellular biochemistry
- (2017) Salman F. Banani et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins
- (2017) Yi-Hsuan Lin et al. NEW JOURNAL OF PHYSICS
- Intrinsically Disordered Proteome of Human Membrane-Less Organelles
- (2017) April L. Darling et al. PROTEOMICS
- Liquid phase condensation in cell physiology and disease
- (2017) Yongdae Shin et al. SCIENCE
- Protein post-translational modifications: In silico prediction tools and molecular modeling
- (2017) Martina Audagnotto et al. Computational and Structural Biotechnology Journal
- Coexisting Liquid Phases Underlie Nucleolar Subcompartments
- (2016) Marina Feric et al. CELL
- Modulation of Intrinsically Disordered Protein Function by Post-translational Modifications
- (2016) Alaji Bah et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation
- (2016) Erik W. Martin et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The C-Terminal RGG Domain of Human Lsm4 Promotes Processing Body Formation Stimulated by Arginine Dimethylation
- (2016) Marcos Arribas-Layton et al. MOLECULAR AND CELLULAR BIOLOGY
- Vapour–liquid phase equilibrium and surface tension of fully flexible Lennard–Jones chains
- (2016) Kevin S. Silmore et al. MOLECULAR PHYSICS
- Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization
- (2015) Amandine Molliex et al. CELL
- A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins
- (2015) Lucas Sawle et al. JOURNAL OF CHEMICAL PHYSICS
- Effect of O-Linked Glycosylation on the Equilibrium Structural Ensemble of Intrinsically Disordered Polypeptides
- (2015) Gül H. Zerze et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II
- (2015) Kathleen A. Burke et al. MOLECULAR CELL
- Nuclear Magnetic Resonance Analysis of the Acetylation Pattern of the Neuronal Tau Protein
- (2014) Amina Kamah et al. BIOCHEMISTRY
- Forcefield_NCAA: Ab Initio Charge Parameters to Aid in the Discovery and Design of Therapeutic Proteins and Peptides with Unnatural Amino Acids and Their Application to Complement Inhibitors of the Compstatin Family
- (2014) George A. Khoury et al. ACS Synthetic Biology
- Coarse-Graining Methods for Computational Biology
- (2013) Marissa G. Saunders et al. Annual Review of Biophysics
- Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications
- (2013) George A. Khoury et al. Journal of Chemical Theory and Computation
- A Simple Atomic-Level Hydrophobicity Scale Reveals Protein Interfacial Structure
- (2013) Lauren H. Kapcha et al. JOURNAL OF MOLECULAR BIOLOGY
- Mapping and analysis of phosphorylation sites: a quick guide for cell biologists
- (2013) Noah Dephoure et al. MOLECULAR BIOLOGY OF THE CELL
- Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications
- (2013) Christian Margreitter et al. NUCLEIC ACIDS RESEARCH
- Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
- (2013) R. K. Das et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- RNA Seeds Higher-Order Assembly of FUS Protein
- (2013) Jacob C. Schwartz et al. Cell Reports
- Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
- (2012) H. Hofmann et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- PRMT1 is required for RAP55 to localize to processing bodies
- (2012) Ken Matsumoto et al. RNA Biology
- Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database
- (2011) George A. Khoury et al. Scientific Reports
- Regulation of TDP-43 aggregation by phosphorylation andp62/SQSTM1
- (2010) Owen A. Brady et al. JOURNAL OF NEUROCHEMISTRY
- A Variant Mimicking Hyperphosphorylated 4E-BP Inhibits Protein Synthesis in a Sea Urchin Cell-Free, Cap-Dependent Translation System
- (2009) Nathalie Oulhen et al. PLoS One
- Vapor-liquid interfacial properties of fully flexible Lennard-Jones chains
- (2008) Felipe J. Blas et al. JOURNAL OF CHEMICAL PHYSICS
- ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions
- (2008) Andreas Vitalis et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- General purpose molecular dynamics simulations fully implemented on graphics processing units
- (2008) Joshua A. Anderson et al. JOURNAL OF COMPUTATIONAL PHYSICS
- Natively Unfolded Protein Stability as a Coil-to-Globule Transition in Charge/Hydropathy Space
- (2008) Henry S. Ashbaugh et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
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