ArticleBiophysical journal2016
On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- Molecular Cloning, Optimization of Expression and Functional Characterization of the Global Transcriptional Regulator MosR (Rv0348) of Mycobacterium tuberculosis.Applied biochemistry and biotechnology · 2025Article
- Distant ribose 2'-O-methylation of 23S rRNA helix 69 pre-orders the capreomycin drug binding pocket at the ribosome subunit interface.Nucleic acids research · 2025Article
- A perspective on the molecular simulation of DNA from structural and functional aspects.Chemical science · 2021Review
- Synergy between Protein Positioning and DNA Elasticity: Energy Minimization of Protein-Decorated DNA Minicircles.The journal of physical chemistry. B · 2021Article
- Statistical mechanics of a double-stranded rod model for DNA melting and elasticity.Soft matter · 2020Article
- Elasticity as the Basis of Allostery in DNA.The journal of physical chemistry. B · 2019Article
- Stacking-induced fluorescence increase reveals allosteric interactions through DNA.Nucleic acids research · 2018Article
- Allosteric interactions in a birod model of DNA.Proceedings. Mathematical, physical, and engineering sciences · 2018Article
- The temperature dependence of the helical twist of DNA.Nucleic acids research · 2018Article
- Allosterism and signal transfer in DNA.Nucleic acids research · 2018Article
- Sequential eviction of crowded nucleoprotein complexes by the exonuclease RecBCD molecular motor.Proceedings of the National Academy of Sciences of the United States of America · 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A recent study described an allosteric effect in which the binding of a protein to DNA is influenced by another protein bound nearby. The effect shows a periodicity of ∼10 basepairs and decays with increasing protein-protein distance. As a mechanistic explanation, the authors reported a similar periodic, decaying pattern of the correlation coefficient between major groove widths inferred from a shorter molecular dynamics simulation. Here we show that in a state-of-the-art, microsecond-long simulation of the same DNA sequence, the periodicity of the correlation coefficient is not observed. To study the problem further, we extend an earlier mechanical model of DNA allostery based on constrained minimization of effective quadratic deformation energy of the DNA. We demonstrate that, if the constraints mimicking the bound proteins are properly applied, the periodicity in the binding energy is indeed recovered.
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.