ArticleBiophysical journal2021
Intrachain interaction topology can identify functionally similar intrinsically disordered proteins.
Article in Biophysical journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 39 citations in OpenAlex.
- Mapping Charge Interactions in Intrinsically Disordered Proteins.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
- Statistical Physics-Based Approaches to Model the Function and Complexation of Disordered Proteins.The journal of physical chemistry. B · 2025Article
- Article
- Physics-Based Machine Learning Trains Hamiltonians and Decodes the Sequence-Conformation Relation in the Disordered Proteome.Journal of chemical theory and computation · 2024Article
- Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins.PNAS nexus · 2024Article
- Protein ensemble modeling and analysis with MMMx.Protein science : a publication of the Protein Society · 2024Article
- The molecular basis for cellular function of intrinsically disordered protein regions.Nature reviews. Molecular cell biology · 2024Review
- Article
- Characterization of Intrinsically Disordered Proteins in Healthy and Diseased States by Nuclear Magnetic Resonance.Reviews on recent clinical trials · 2024Review
- A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation.Nature communications · 2023Article
- Protein intrinsically disordered region prediction by combining neural architecture search and multi-objective genetic algorithm.BMC biology · 2023Article
- Data-Driven Models for Predicting Intrinsically Disordered Protein Polymer Physics Directly from Composition or Sequence.Molecular systems design & engineering · 2023Article
- Circuit Topology Approach for the Comparative Analysis of Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2023Article
- Interpreting Transient Interactions of Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2023Article
- Review
- Rules of Physical Mathematics Govern Intrinsically Disordered Proteins.Annual review of biophysics · 2022Review
- The Protein Folding Problem: The Role of Theory.Journal of molecular biology · 2021Review
- Can sequence-specific and dynamics-based metrics allow us to decipher the function in IDP sequences?Biophysical journal · 2021Article
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2 authors at 1 institution in 1 country.
Funding
Abstract
Functionally similar IDPs (intrinsically disordered proteins) often have little sequence similarity. This is in stark contrast to folded proteins and poses a challenge for the inverse problem, functional classification of IDPs using sequence alignment. The problem is further compounded because of the lack of structure in IDPs, preventing structural alignment as an alternate tool for classification. Recent advances in heteropolymer theory unveiled a powerful set of sequence-patterning metrics bridging molecular interaction with chain conformation. Focusing only on charge patterning, these set of metrics yield a sequence charge decoration matrix (SCDM). SCDMs can potentially identify functionally similar IDPs not apparent from sequence alignment alone. Here, we illustrate how these information-rich "molecular blueprints" encoded in SCDMs can be used for functional classification of IDPs with specific application in three protein families-Ste50, PSC, and RAM-in which electrostatics is known to be important. For both the Ste50 and PSC protein family, the set of metrics appropriately classifies proteins in functional and nonfunctional groups in agreement with experiment. Furthermore, our algorithm groups synthetic variants of the disordered RAM region of the Notch receptor protein-important in gene expression-in reasonable accordance with classification based on experimentally measured binding constants of RAM and transcription factor. Taken together, the novel classification scheme reveals the critical role of a high-dimensional set of metrics-manifest in self-interaction maps and topology-in functional annotation of IDPs even when there is low sequence homology, providing the much-needed alternate to a traditional sequence alignment tool.
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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.