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Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates

https://doi.org/10.1021/acs.jctc.4c01646
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Outgoing claims: the papers this work cites, builds on, or argues with.

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RNA-Mediated Feedback Control of Transcriptional Condensates
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The Role of RNA in Biological Phase Separations
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Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins
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Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation
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RNA-driven phase transitions in biomolecular condensates
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Physics-based computational and theoretical approaches to intrinsically disordered proteins
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Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation
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Modeling Concentration-dependent Phase Separation Processes Involving Peptides and RNA via Residue-Based Coarse-Graining
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Coarse-Grained Models to Study Protein–DNA Interactions and Liquid–Liquid Phase Separation
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Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA−Protein Complexes
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Hierarchical Assembly of Single-Stranded RNA
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Accelerated Simulations Reveal Physicochemical Factors Governing Stability and Composition of RNA Clusters
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Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations
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A Data-Driven Hydrophobicity Scale for Predicting Liquid–Liquid Phase Separation of Proteins
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Effect of RNA on Morphology and Dynamics of Membraneless Organelles
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Tuning Formation of Protein–DNA Coacervates by Sequence and Environment
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Quantifying Protein–Protein Interactions in Molecular Simulations
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Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences
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Coarse-Grained Structure-Based Model for RNA-Protein Complexes Developed by Fluctuation Matching
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Convergence of Sampling Kirkwood–Buff Integrals of Aqueous Solutions with Molecular Dynamics Simulations
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The Dielectric Constant of Water at High Temperatures and in Equilibrium with its Vapor
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Natively Unfolded Protein Stability as a Coil-to-Globule Transition in Charge/Hydropathy Space
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Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein–RNA Complexes
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Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics
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Coarse-Grained Model for Predicting RNA Folding Thermodynamics
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RNA phase transitions in repeat expansion disorders
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Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters
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Biomolecular condensates: organizers of cellular biochemistry
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Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies
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Phase separation of protein mixtures is driven by the interplay of homotypic and heterotypic interactions
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An architectural role of specific RNA–RNA interactions in oskar granules
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Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics
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RNAs undergo phase transitions with lower critical solution temperatures
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RNA modulates hnRNPA1A amyloid formation mediated by biomolecular condensates
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The molecular basis for cellular function of intrinsically disordered protein regions
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Extreme dynamics in a biomolecular condensate
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Martini 3: a general purpose force field for coarse-grained molecular dynamics
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Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy
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An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
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Coarse-grained modeling of DNA curvature
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Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach
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Ionic strength-dependent persistence lengths of single-stranded RNA and DNA
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The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics
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Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation
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Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties
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Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations
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Driving forces of RNA condensation revealed through coarse-grained modeling with explicit Mg 2+
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Physical principles of intracellular organization via active and passive phase transitions
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Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations
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A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
inferredcites →https://doi.org/10.1101/2024.01.09.574811openalex-snapshot
RNA regulates cohesiveness and porosity of a biological condensate
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Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering
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DNA Nanotweezers Studied with a Coarse-Grained Model of DNA
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Tie-Line Analysis Reveals Interactions Driving Heteromolecular Condensate Formation
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Liquid phase condensation in cell physiology and disease
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Imaging dynamic and selective low-complexity domain interactions that control gene transcription
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Coactivator condensation at super-enhancers links phase separation and gene control
inferredcites →https://doi.org/10.1126/science.aar4199openalex-snapshot
Mediator and RNA polymerase II clusters associate in transcription-dependent condensates
inferredcites →https://doi.org/10.1126/science.aar7366openalex-snapshot
RNA buffers the phase separation behavior of prion-like RNA binding proteins
inferredcites →https://doi.org/10.1126/science.aaw8653openalex-snapshot
Valence and patterning of aromatic residues determine the phase behavior of prion-like domains
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Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments
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Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
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Experimental Parameterization of an Energy Function for the Simulation of Unfolded Proteins

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Molecular simulations of chromatin-associated biomolecular condensates
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Molecular View on the Heterogeneous Structure and Dynamics of a P-Body Condensate
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Sequence-based prediction of condensate composition reveals that specificity can emerge from multivalent interactions among disordered regions
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Potential structure induced effects of the hairpin motif in RNA to form the phase separated droplet like associate in different solution condition
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Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations
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Driving forces of RNA condensation revealed through coarse-grained modeling with explicit Mg 2+
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StruCloze: A Unified Framework for Backmapping and Inpainting of Biomolecules
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