ArticleThe journal of physical chemistry. B2016
PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites.
Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 24 citations in OpenAlex.
- DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins.Nature communications · 2025Article
- Frustration in physiology and molecular medicine.Molecular aspects of medicine · 2025Review
- Fuzzy protein-DNA interactions and beyond: A common theme in transcription?Current opinion in structural biology · 2024Review
- A contact-based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold-switch.Protein science : a publication of the Protein Society · 2024Article
- The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Entropy-driven electrochemiluminescence ultra-sensitive detection strategy of NF-κB p50 as the regulator of cytokine storm.Biosensors & bioelectronics · 2021Article
- Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation.Frontiers in molecular biosciences · 2021Article
- Post-translational Modifications of IκBα: The State of the Art.Frontiers in cell and developmental biology · 2020Review
- Disorder Mediated Oligomerization ofThe journal of physical chemistry. B · 2019Article
- Frustration, function and folding.Current opinion in structural biology · 2018Review
- Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors.Journal of the American Chemical Society · 2017Article
- Stochastic dynamics of genetic broadcasting networks.Physical review. E · 2017Article
- DNA and IκBα Both Induce Long-Range Conformational Changes in NFκB.Journal of molecular biology · 2017Article
- Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Molecular stripping, targets and decoys as modulators of oscillations in the NF-κB/IκBα/DNA genetic network.Journal of the Royal Society, Interface · 2016Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
We recently proposed a model for IκBα-mediated molecular stripping of NFκB from transcription sites. IκBα was shown experimentally to form a transient ternary complex with DNA-bound NFκB, but the mechanism by which the IκBα accelerates dissociation of the NFκB from the DNA was unknown. In this paper we construct and compute free energy profiles for the wild-type IκBα-mediated molecular stripping reaction of NFκB from DNA and compare with that for a mutant of IκBα bearing a charge-neutralized PEST. The differences in the free energy profile for stripping originate from the frustrated electrostatic interactions between the negatively charged PEST and the DNA. The PEST occupies two different conformations in the NFκB-IκBα binary complex, one of which occupies the DNA-binding cavity. Specific interactions with positively charged residues in the N-terminal domains of both p50 and p65 apparently draw the domains closer together hindering reassociation of DNA. Comparison with the charge-neutralized mutant reveals that all of these functional consequences result from the negative charges in the PEST sequence of IκBα.
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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.