Evidence map›Paper›PMID 28374217›Full record

ArticleJournal of molecular modeling2017

Methylation-targeted specificity of the DNA binding proteins R.DpnI and MeCP2 studied by molecular dynamics simulations.

Siba Shanak, Ozlem Ulucan, Volkhard Helms

Abstract read
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In one paragraph

Article in Journal of molecular modeling, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.4field-weighted citation impact, top 29% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 5 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors at 2 institutions in 2 countries.

Siba ShanakCenter for Bioinformatics, Saarland University, PO Box/15 11 50, 66041, Saarbrücken, Germany.
Ozlem UlucanCenter for Bioinformatics, Saarland University, PO Box/15 11 50, 66041, Saarbrücken, Germany.
Volkhard HelmsCenter for Bioinformatics, Saarland University, PO Box/15 11 50, 66041, Saarbrücken, Germany. volkhard.helms@bioinformatik.uni-saarland.de.ORCID http://orcid.org/0000-0002-2180-9154
Saarland University · DEArab American University · PS

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

DNA methylation plays a major role in organismal development and the regulation of gene expression. Methylation of cytosine bases and the cellular roles of methylated cytosine in eukaryotes are well established, as well as methylation of adenine bases in bacterial genomes. Still lacking, however, is a general mechanistic understanding, in structural and thermodynamic terms, of how proteins recognize methylated DNA. Toward this aim, we present the results of molecular dynamics simulations, alchemical free energy perturbation, and MM-PBSA calculations to explain the specificity of the R.DpnI enzyme from Streptococcus pneumonia in binding to adenine-methylated DNA with both its catalytic and winged-helix domains. We found that adenine-methylated DNA binds more favorably to the catalytic subunit of R.DpnI (-4 kcal mol

Indexed as

AdenineCatalytic DomainCytosineDNADNA-Binding ProteinsDNA MethylationDNA Restriction EnzymesHumansMethyl-CpG-Binding Protein 2Molecular Dynamics SimulationStreptococcus pneumoniaeThermodynamicsAdenineCytosineDNADNA-Binding ProteinsDNA Restriction EnzymesMECP2 protein, humanMethyl-CpG-Binding Protein 2Binding free energyConformational entropyDNA methylationFree energy perturbationm5Cm6AMM-PBSARestriction endonucleaseSequence specificity

Identifiers

PMID28374217
OpenAlexW2605093393

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.