ArticleThe journal of physical chemistry. B2023
The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins.
Article in The journal of physical chemistry. B, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Self-Assembly of Peptides and Biomolecular Systems Into Functional Nanomaterials.Journal of peptide science : an official publication of the European Peptide Society · 2026Review
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- Multivariate Chemometric and FTIR Insights Into the Effects of Rice Bran Extracts on Brown Rice Protein Bars.Food science & nutrition · 2026Article
- Protein folding stability estimation with explicit consideration of unfolded states.Nature communications · 2026Article
- Molecular grammars of predicted intrinsically disordered regions that span the human proteome.Cell · 2026Article
- IDPEnsembleTools: An open-source library for analysis of conformational ensembles of disordered proteins.Protein science : a publication of the Protein Society · 2026Article
- Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein A.bioRxiv : the preprint server for biology · 2025Article
- Deep generative modeling of temperature-dependent structural ensembles of proteins.Communications chemistry · 2025Article
- Matrin-3 forms spherical and wormlike assemblies that are modulated by RNA binding and ALS/FTD-associated mutations.Molecular cell · 2025Article
- GSK3β-driven phosphorylation of ABLIM1 regulates its interactions with titin cardiac muscle.The Journal of general physiology · 2025Article
- Noncovalent Lasso Entanglements are Common in Experimentally Derived Intrinsically Disordered Protein Ensembles and Strongly Influenced by Protein Length and Charge.The journal of physical chemistry. B · 2025Article
- Molecular insights into the interaction between a disordered protein and a folded RNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular insights into the interaction between a disordered protein and a folded RNA.bioRxiv : the preprint server for biology · 2024Article
- Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities.Biophysical journal · 2024Article
- Multiphosphorylation-Dependent Recognition of Anti-pS2 Antibodies against RNA Polymerase II C-Terminal Domain Revealed by Chemical Synthesis.Journal of the American Chemical Society · 2024Article
- Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator.Nature communications · 2024Article
- Labile assembly of a tardigrade protein induces biostasis.Protein science : a publication of the Protein Society · 2024Article
- Protein ensemble modeling and analysis with MMMx.Protein science : a publication of the Protein Society · 2024Article
- Direct prediction of intrinsically disordered protein conformational properties from sequence.Nature methods · 2024Article
- SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2023Article
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Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory random coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google Colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.