ArticleThe journal of physical chemistry letters2020
Hydropathy Patterning Complements Charge Patterning to Describe Conformational Preferences of Disordered Proteins.
Article in The journal of physical chemistry letters, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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75 citing papers in PubMed.
- Designed IDPs phase separate and mix or demix according to sequence designed parameters.bioRxiv : the preprint server for biology · 2026Article
- AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level.Protein science : a publication of the Protein Society · 2026Article
- Topological Entanglement in Intrinsically Disordered Proteins: Sequence, Structural, and Functional Determinants.The journal of physical chemistry. B · 2026Article
- Molecular Origins of pH Gradients in Charge-Regulated Biomolecular Condensates.bioRxiv : the preprint server for biology · 2026Article
- Analysis and design of disordered polypeptides with optimized sequence patterning properties.PLoS computational biology · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- De novo design of peptides localizing at the interface of biomolecular condensates.Nature communications · 2026Article
- A composition-matching algorithm, MatchIDR, identifies prion-like domains that localize to stress granules.Protein science : a publication of the Protein Society · 2026Article
- Generative design of intrinsically disordered protein regions with IDiom.bioRxiv : the preprint server for biology · 2026Article
- Topological Entanglement in Intrinsically Disordered Proteins: Sequence, Structural, and Functional Determinants.bioRxiv : the preprint server for biology · 2026Article
- Positive Selection Targeted Primate Genes that Encode Transposable Element Repressors.Genome biology and evolution · 2026Article
- Mapping Charge Interactions in Intrinsically Disordered Proteins.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Analysis and design of disordered polypeptides with optimized sequence patterning properties.bioRxiv : the preprint server for biology · 2026Article
- Molecular grammars of predicted intrinsically disordered regions that span the human proteome.Cell · 2026Article
- Mycobacterium tuberculosis uses intrinsically disordered, fast evolving proteins to interact with conserved host factors.Genome biology · 2025Article
- Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction.Journal of chemical theory and computation · 2025Article
- Statistical Physics-Based Approaches to Model the Function and Complexation of Disordered Proteins.The journal of physical chemistry. B · 2025Article
- Cross-species rescue reveals sequence requirements for a rapidly evolving intrinsically disordered region.PLoS biology · 2025Article
- Systematic analysis of structural disorder in the minimal proteome ofMicrobiology spectrum · 2025Article
- Structural and Functional Relevance of Charge-Based Transient Interactions inside Intrinsically Disordered Proteins.ACS physical chemistry Au · 2025Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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Abstract
Understanding the conformational ensemble of an intrinsically disordered protein (IDP) is of great interest due to its relevance to critical intracellular functions and diseases. It is now well established that the polymer scaling behavior can provide a great deal of information about the conformational properties as well as liquid-liquid phase separation of an IDP. It is, therefore, extremely desirable to be able to predict an IDP's scaling behavior from the protein sequence itself. The work in this direction so far has focused on highly charged proteins and how charge patterning can perturb their structural properties. As naturally occurring IDPs are composed of a significant fraction of uncharged amino acids, the rules based on charge content and patterning are only partially helpful in solving the problem. Here, we propose a new order parameter, sequence hydropathy decoration, which can provide a near-quantitative understanding of scaling and structural properties of IDPs devoid of charged residues. We combine this with a charge patterning parameter, sequence charge decoration, to obtain a general equation, parametrized from extensive coarse-grained simulation data, for predicting protein dimensions from the sequence. We finally test this equation against available experimental data and find a semiquantitative match in predicting the scaling behavior. We also provide guidance on how to extend this approach to experimental data, which should be feasible in the near future.
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