ArticleNucleic acids research2018
Tunable order-disorder continuum in protein-DNA interactions.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 33 citations in OpenAlex.
- Prediction of Intrinsically Disordered Regions That Bind RNA with DisoRDPbind.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Marginal Stability of the YB1 Cold-Shock Domain in Cells Enables Binding of Multiple Nucleic Acids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Solution structure of the Sox2 DNA-binding domain reveals conformational selection in DNA binding.Nucleic acids research · 2025Article
- Article
- Prediction of Disordered Linear Interacting Peptides with CLIP.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences.Briefings in bioinformatics · 2024Review
- HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins.Nucleic acids research · 2024Article
- Functional regulation of an intrinsically disordered protein via a conformationally excited state.Science advances · 2023Article
- Flexible Target Recognition of the Intrinsically Disordered DNA-Binding Domain of CytR Monitored by Single-Molecule Fluorescence Spectroscopy.The journal of physical chemistry. B · 2022Article
- The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics.Molecules (Basel, Switzerland) · 2022Review
- Quantification of Entropic Excluded Volume Effects Driving Crowding-Induced Collapse and Folding of a Disordered Protein.The journal of physical chemistry letters · 2022Article
- Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4.Acta crystallographica. Section F, Structural biology communications · 2021Article
- A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures.Current research in structural biology · 2021Review
- Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape?The journal of physical chemistry. B · 2020Article
- Phase Separation and Disorder-to-Order Transition of Human Brain Expressed X-Linked 3 (hBEX3) in the Presence of Small Fragments of tRNA.Journal of molecular biology · 2020Article
- Controlling Structure and Dimensions of a Disordered Protein via Mutations.Biochemistry · 2020Article
- Thermodynamics and folding landscapes of large proteins from a statistical mechanical model.Current research in structural biology · 2019Article
- Engineering Order and Cooperativity in a Disordered Protein.Biochemistry · 2019Article
- Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential.The Journal of biological chemistryArticle
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
DNA-binding protein domains (DBDs) sample diverse conformations in equilibrium facilitating the search and recognition of specific sites on DNA over millions of energetically degenerate competing sites. We hypothesize that DBDs have co-evolved to sense and exploit the strong electric potential from the array of negatively charged phosphate groups on DNA. We test our hypothesis by employing the intrinsically disordered DBD of cytidine repressor (CytR) as a model system. CytR displays a graded increase in structure, stability and folding rate on increasing the osmolarity of the solution that mimics the non-specific screening by DNA phosphates. Electrostatic calculations and an Ising-like statistical mechanical model predict that CytR exhibits features of an electric potential sensor modulating its dimensions and landscape in a unique distance-dependent manner, while DNA plays the role of a non-specific macromolecular chaperone. Accordingly, CytR binds its natural half-site faster than the diffusion-controlled limit and even random DNA conforming to an electrostatic-steering binding mechanism. Our work unravels for the first time the synergistic features of a natural electrostatic potential sensor, a novel binding mechanism driven by electrostatic frustration and disorder, and the role of DNA in promoting distance-dependent protein structural transitions critical for switching between specific and non-specific DNA-binding modes.
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Registered trials
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.