ArticleJournal of the American Chemical Society2013
Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed, 30 citations in OpenAlex.
- London dispersion forces and steric effects within nanocomposites tune interaction energies and chain conformation.Communications chemistry · 2025Article
- AsJournal of the American Chemical Society · 2024Article
- Article
- Calorimetric analysis of AdcR and its interactions with zinc(II) and DNA.Journal of inorganic biochemistry · 2023Article
- Direct C-H amination reactions of arenes withBeilstein journal of organic chemistry · 2022Article
- NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes.Biophysical reviews · 2020Review
- Tuning site-specific dynamics to drive allosteric activation in a pneumococcal zinc uptake regulator.eLife · 2018Article
- Functional Role of Solvent Entropy and Conformational Entropy of Metal Binding in a Dynamically Driven Allosteric System.Journal of the American Chemical Society · 2018Article
- Negative regulation of daptomycin production by DepR2, an ArsR-family transcriptional factor.Journal of industrial microbiology & biotechnology · 2017Article
- Metallochaperones and metalloregulation in bacteria.Essays in biochemistry · 2017Review
- Solution NMR Spectroscopy for the Study of Enzyme Allostery.Chemical reviews · 2016Review
- Role of substrate dynamics in protein prenylation reactions.Accounts of chemical research · 2015Review
- Characterizing solution surface loop conformational flexibility of the GM2 activator protein.The journal of physical chemistry. B · 2014Article
- Recent developments in copper and zinc homeostasis in bacterial pathogens.Current opinion in chemical biology · 2014Review
- Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent.Journal of chemical theory and computation · 2013Article
- Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.Journal of biomolecular NMR · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
A metal-mediated interprotomer hydrogen bond has been implicated in the allosteric mechanism of DNA operator binding in several metal-sensing proteins. Using computational methods, we investigate the energetics of such zinc-mediated interactions in members of the ArsR/SmtB family of proteins (CzrA, SmtB, CadC, and NmtR) and the MarR family zinc-uptake repressor AdcR, which feature similar interactions, but in sites that differ widely in their allosteric responsiveness. We provide novel structural insight into previously uncharacterized allosteric forms of these proteins using computational methodologies. We find this metal-mediated interaction to be significantly stronger (∼8 kcal/mol) at functional allosteric metal binding sites compared to a nonresponsive site (CadC) and the apo-proteins. Simulations of the apo-proteins further reveal that the high interaction energy works to overcome the considerable disorder at these hydrogen-bonding sites and functions as a "switch" to lock in a weak DNA-binding conformation once metal is bound. These findings suggest a conserved functional role of metal-mediated second coordination shell hydrogen bonds at allosterically responsive sites in zinc-sensing transcription regulators.
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.