Evidence map›Paper›PMID 26254213›Full record

ArticleEuropean biophysics journal : EBJ2015

Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

Mustafa Tekpinar, Ahmet Yildirim, Tsjerk A Wassenaar

Abstract read
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In one paragraph

Article in European biophysics journal : EBJ, 2015. 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
0.3field-weighted citation impact, top 39% 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, 7 citations in OpenAlex.

  1. Towards EffectiveInternational journal of molecular sciences · 2025
    Review
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 3 institutions in 2 countries.

Mustafa TekpinarDepartment of Physics, Faculty of Science, Yüzüncü Yıl University, 65100, Van, Turkey. tekpinar@buffalo.edu.
Ahmet YildirimDepartment of Physics, Faculty of Science and Art, Siirt University, 56100, Siirt, Turkey.
Tsjerk A WassenaarDepartment of Biology, University of Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
Friedrich-Alexander-Universität Erlangen-Nürnberg · DESiirt Üniversitesi · TRVan Yüzüncü Yıl Üniversitesi · TR

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is involved in the quorum sensing of several bacterial species, including Helicobacter pylori. In particular, these bacteria depend on MTAN for synthesis of vitamin K2 homologs. The residue D198 in the active site of MTAN seems to be of crucial importance, by acting as a hydrogen-bond acceptor for the ligand. In this study, we investigated the conformation and dynamics of apo and holo H. pylori MTAN (HpMTAN), and assessed the effect of protonation of D198 by use of molecular dynamics simulations. Our results show that protonation of the active site of HpMTAN can cause a conformational transition from a closed state to an open state even in the absence of substrate, via inter-chain mechanical coupling.

Indexed as

Molecular Dynamics SimulationProtonsAmino Acid SequenceBacterial ProteinsCatalytic DomainHelicobacter pyloriHydrogen BondingMolecular Sequence DataN-Glycosyl HydrolasesProtein Bindingadenosylhomocysteine nucleosidaseBacterial ProteinsN-Glycosyl HydrolasesProtonsD198 protonationHelicobacter pyloriMolecular dynamics simulationMTAN

Identifiers

PMID26254213
OpenAlexW1091218568

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.