ArticleBiochemistry2017
Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).
Article in Biochemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- A closely related pair of superoxide dismutase isozymes from Staphylococcus aureus show distinct stabilities and proton-exchange dynamics.The Journal of biological chemistry · 2026Article
- Structural basis of p53 inactivation by cavity-creating cancer mutations and its implications for the development of mutant p53 reactivators.Cell death & disease · 2024Article
- Article
- Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10.Nature communications · 2024Article
- Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10.bioRxiv : the preprint server for biology · 2024Article
- Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods.Journal of chemical information and modeling · 2023Article
- Simulations suggest double sodium binding induces unexpected conformational changes in thrombin.Journal of molecular modeling · 2022Article
- Molecular insights into the interaction of HPV-16 E6 variants against MAGI-1 PDZ1 domain.Scientific reports · 2022Article
- Light Chain Mutation Effects on the Dynamics of Thrombin.Journal of chemical information and modeling · 2021Article
- Targeting Cavity-Creating p53 Cancer Mutations with Small-Molecule Stabilizers: the Y220X Paradigm.ACS chemical biology · 2020Article
- Arterivirus nsp4 Antagonizes Interferon Beta Production by Proteolytically Cleaving NEMO at Multiple Sites.Journal of virology · 2019Article
- Using correlated motions to determine sufficient sampling times for molecular dynamics.Physical review. E · 2018Article
- All-atom molecular dynamics comparison of disease-associated zinc fingers.Journal of biomolecular structure & dynamics · 2018Article
- Visualizing correlated motion with HDBSCAN clustering.Protein science : a publication of the Protein Society · 2018Article
- Mechanistic insights into thrombin's switch between "slow" and "fast" forms.Physical chemistry chemical physics : PCCP · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.
Indexed as
Identifiers
What OpenQuestion holds
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.