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Direct prediction of intermolecular interactions driven by disordered regions

https://doi.org/10.1101/2024.06.03.597104
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Uncovering the Contributions of Charge Regulation to the Stability of Single Alpha Helices**
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RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation
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Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient
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Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions
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A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain
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Fuzzy complexes: Specific binding without complete folding
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Uncovering Non-random Binary Patterns Within Sequences of Intrinsically Disordered Proteins
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The Acidic Transcription Activator Gcn4 Binds the Mediator Subunit Gal11/Med15 Using a Simple Protein Interface Forming a Fuzzy Complex
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Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles
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Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins
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Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II
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Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein
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A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning
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Linking folding and binding
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Fold or not to fold upon binding — does it really matter?
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Binding without folding – the biomolecular function of disordered polyelectrolyte complexes
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The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome
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Commonly asked questions about transcriptional activation domains
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ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain
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Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions
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Intrinsically unstructured proteins
inferredcites →https://doi.org/10.1016/s1093-3263(00)00138-8openalex-snapshot
Intrinsically disordered protein
inferredcites →https://doi.org/10.1017/s003358351300005xopenalex-snapshot
Charge regulation in biomolecular solution
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Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model
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Biophysics of Phase Separation of Disordered Proteins Is Governed by Balance between Short- And Long-Range Interactions
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Tuning Formation of Protein–DNA Coacervates by Sequence and Environment
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Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions
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A Lattice Model of Charge-Pattern-Dependent Polyampholyte Phase Separation
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q-Canonical Monte Carlo Sampling for Modeling the Linkage between Charge Regulation and Conformational Equilibria of Peptides
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Analytical Solution to the Flory–Huggins Model
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Complete Phase Diagram for Liquid–Liquid Phase Separation of Intrinsically Disordered Proteins
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Temperature-Controlled Liquid–Liquid Phase Separation of Disordered Proteins
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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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Thermodynamic Origin of Hofmeister Ion Effects
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A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self‐renewal
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Hax1-mediated processing of HtrA2 by Parl allows survival of lymphocytes and neurons
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Extreme disorder in an ultrahigh-affinity protein complex
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Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters
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Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles
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HAX1 deficiency causes autosomal recessive severe congenital neutropenia (Kostmann disease)
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Intrinsically disordered proteins in cellular signalling and regulation
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Phase separation-deficient TDP43 remains functional in splicing
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De novo engineering of intracellular condensates using artificial disordered proteins
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Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains
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RNAs undergo phase transitions with lower critical solution temperatures
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Determinants that enable disordered protein assembly into discrete condensed phases
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Expanding the molecular language of protein liquid–liquid phase separation
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Direct prediction of intrinsically disordered protein conformational properties from sequence
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Conformational buffering underlies functional selection in intrinsically disordered protein regions
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Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy
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The Lennard-Jones potential: when (not) to use it
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Solutions of Long Chain Compounds
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Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures
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Phase separation vs aggregation behavior for model disordered proteins
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Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
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Temperature-dependent solvation modulates the dimensions of disordered proteins
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Selection maintains signaling function of a highly diverged intrinsically disordered region
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Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation
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Relation between single-molecule properties and phase behavior of intrinsically disordered proteins
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Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior
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Comparative roles of charge, π , and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins
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Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase
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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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Connecting sequence features within the disordered C-terminal linker of Bacillus subtilis FtsZ to functions and bacterial cell division
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Prediction of phase-separation propensities of disordered proteins from sequence
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A functional map of the human intrinsically disordered proteome
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Activator Gcn4 Employs Multiple Segments of Med15/Gal11, Including the KIX Domain, to Recruit Mediator to Target Genes in Vivo
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Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs
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Mediator Subunit Gal11p/MED15 Is Required for Fatty Acid-dependent Gene Activation by Yeast Transcription Factor Oaf1p
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SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets
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Transcription factors perform a 2-step search of the nucleus
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Clusters of acidic and hydrophobic residues can predict acidic transcriptional activation domains from protein sequence
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Conservation of Affinity Rather Than Sequence Underlies a Dynamic Evolution of the Motif-Mediated p53/MDM2 Interaction in Ray-Finned Fishes
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Polymer Physics
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Sequence- and chemical specificity define the functional landscape of intrinsically disordered regions
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Aberrant Phase Separation is a Common Killing Strategy of Positively Charged Peptides in Biology and Human Disease
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Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation
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Rational design of disordered proteins for systematic sequence-to-function investigation
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Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
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Natively unfolded proteins: A point where biology waits for physics
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Phase separation of a yeast prion protein promotes cellular fitness
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Valence and patterning of aromatic residues determine the phase behavior of prion-like domains
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Accurate prediction of protein structures and interactions using a three-track neural network
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Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range
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Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range
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Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
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Phosphorylation of the FUS low‐complexity domain disrupts phase separation, aggregation, and toxicity
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Disease‐linked TDP‐43 hyperphosphorylation suppresses TDP‐43 condensation and aggregation
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High‐throughput discovery of functional disordered regions: investigation of transactivation domains
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Interactions by Disorder – A Matter of Context
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Proteome-wide signatures of function in highly diverged intrinsically disordered regions
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Identifying molecular features that are associated with biological function of intrinsically disordered protein regions
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Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

What points at this work

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

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Generalized design of sequence–ensemble–function relationships for intrinsically disordered proteins
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Prediction of phase-separation propensities of disordered proteins from sequence
inferred← citeshttps://doi.org/10.1101/2022.02.10.480018openalex-snapshot
Sequence- and chemical specificity define the functional landscape of intrinsically disordered regions
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Sequence-based prediction of intermolecular interactions driven by disordered regions
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Evolutionary turnover of key amino acids explains conservation of function without conservation of sequence in transcriptional activation domains
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