OrangerV1, Main, Exploration, bibRecord, 000832

In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour

Identifieur interne : 000832 ( Main/Exploration ); précédent : 000831; suivant : 000833

In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour

Auteurs : Imen Rekik [Tunisie] ; Zayneb Chaabene [Tunisie] ; C. Douglas Grubb [Allemagne] ; Noureddine Drira [Tunisie] ; Foued Cheour [Tunisie] ; Amine Elleuch [Tunisie]

Source :

Theoretical Biology & Medical Modelling [ 1742-4682 ] ; 2015.

RBID : PMC:4635681

Abstract

Background

DNA double-strand breaks (DSBs) are highly cytotoxic and mutagenic. MRE11 plays an essential role in repairing DNA by cleaving broken ends through its 3′ to 5′ exonuclease and single-stranded DNA endonuclease activities.

Methods

The present study aimed to in silico characterization and molecular modeling of MRE11 from Phoenix dactylifera L cv deglet nour (DnMRE11) by various bioinformatic approaches. To identify DnMRE11 cDNA, assembled contigs from our cDNA libraries were analysed using the Blast2GO2.8 program.

Results

The DnMRE11 protein length was 726 amino acids. The results of HUMMER show that DnMRE11 is formed by three domains: the N-terminal core domain containing the nuclease and capping domains, the C-terminal half containing the DNA binding and coiled coil region. The structure of DnMRE11 is predicted using the Swiss-Model server, which contains the nuclease and capping domains. The obtained model was verified with the structure validation programs such as ProSA and QMEAN servers for reliability. Ligand binding studies using COACH indicated the interaction of DnMRE11 protein with two Mn²⁺ ions and dAMP. The ConSurf server predicted that residues of the active site and Nbs binding site have high conservation scores between plant species.

Conclusions

A model structure of DnMRE11 was constructed and validated with various bioinformatics programs which suggested the predicted model to be satisfactory. Further validation studies were conducted by COACH analysis for active site ligand prediction, and revealed the presence of six ligands binding sites and two ligands (2 Mn²⁺ and dAMP).

Electronic supplementary material

The online version of this article (doi:10.1186/s12976-015-0013-2) contains supplementary material, which is available to authorized users.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4635681

DOI: 10.1186/s12976-015-0013-2
PubMed: 26541955
PubMed Central: 4635681

Affiliations:

Allemagne, Tunisie

Le document en format XML

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 characterization and Molecular modeling of double-strand break repair protein <italic>MRE11</italic>
 from <italic>Phoenix dactylifera</italic>
 v deglet nour</title>
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<author><name sortKey="Elleuch, Amine" sort="Elleuch, Amine" uniqKey="Elleuch A" first="Amine" last="Elleuch">Amine Elleuch</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>In silico</italic>
 characterization and Molecular modeling of double-strand break repair protein <italic>MRE11</italic>
 from <italic>Phoenix dactylifera</italic>
 v deglet nour</title>
<author><name sortKey="Rekik, Imen" sort="Rekik, Imen" uniqKey="Rekik I" first="Imen" last="Rekik">Imen Rekik</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax, Tunisia</nlm:aff>
<country xml:lang="fr">Tunisie</country>
<wicri:regionArea>Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax</wicri:regionArea>
<wicri:noRegion>Sfax</wicri:noRegion>
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</author>
<author><name sortKey="Chaabene, Zayneb" sort="Chaabene, Zayneb" uniqKey="Chaabene Z" first="Zayneb" last="Chaabene">Zayneb Chaabene</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax, Tunisia</nlm:aff>
<country xml:lang="fr">Tunisie</country>
<wicri:regionArea>Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax</wicri:regionArea>
<wicri:noRegion>Sfax</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Grubb, C Douglas" sort="Grubb, C Douglas" uniqKey="Grubb C" first="C. Douglas" last="Grubb">C. Douglas Grubb</name>
<affiliation wicri:level="1"><nlm:aff id="Aff2">Leibniz Institute of Plant Biochemistry, Halle, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Leibniz Institute of Plant Biochemistry, Halle</wicri:regionArea>
<wicri:noRegion>Halle</wicri:noRegion>
<wicri:noRegion>Halle</wicri:noRegion>
<wicri:noRegion>Halle</wicri:noRegion>
</affiliation>
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<author><name sortKey="Drira, Noureddine" sort="Drira, Noureddine" uniqKey="Drira N" first="Noureddine" last="Drira">Noureddine Drira</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax, Tunisia</nlm:aff>
<country xml:lang="fr">Tunisie</country>
<wicri:regionArea>Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax</wicri:regionArea>
<wicri:noRegion>Sfax</wicri:noRegion>
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</author>
<author><name sortKey="Cheour, Foued" sort="Cheour, Foued" uniqKey="Cheour F" first="Foued" last="Cheour">Foued Cheour</name>
<affiliation wicri:level="1"><nlm:aff id="Aff3">High Institute of Applied Biology of Medenine, Medenine, Tunisia</nlm:aff>
<country xml:lang="fr">Tunisie</country>
<wicri:regionArea>High Institute of Applied Biology of Medenine, Medenine</wicri:regionArea>
<wicri:noRegion>Medenine</wicri:noRegion>
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</author>
<author><name sortKey="Elleuch, Amine" sort="Elleuch, Amine" uniqKey="Elleuch A" first="Amine" last="Elleuch">Amine Elleuch</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax, Tunisia</nlm:aff>
<country xml:lang="fr">Tunisie</country>
<wicri:regionArea>Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax</wicri:regionArea>
<wicri:noRegion>Sfax</wicri:noRegion>
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<series><title level="j">Theoretical Biology & Medical Modelling</title>
<idno type="eISSN">1742-4682</idno>
<imprint><date when="2015">2015</date>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>DNA double-strand breaks (DSBs) are highly cytotoxic and mutagenic. <italic>MRE11</italic>
 plays an essential role in repairing DNA by cleaving broken ends through its 3′ to 5′ exonuclease and single-stranded DNA endonuclease activities.</p>
</sec>
<sec><title>Methods</title>
<p>The present study aimed to <italic>in silico</italic>
 characterization and molecular modeling of <italic>MRE11</italic>
 from <italic>Phoenix dactylifera</italic>
 L cv deglet nour (<italic>DnMRE11</italic>
) by various bioinformatic approaches. To identify <italic>DnMRE11</italic>
 cDNA, assembled contigs from our cDNA libraries were analysed using the Blast2GO2.8 program.</p>
</sec>
<sec><title>Results</title>
<p>The <italic>DnMRE11</italic>
 protein length was 726 amino acids. The results of HUMMER show that <italic>DnMRE11</italic>
 is formed by three domains: the N-terminal core domain containing the nuclease and capping domains, the C-terminal half containing the DNA binding and coiled coil region. The structure of <italic>DnMRE11</italic>
 is predicted using the Swiss-Model server, which contains the nuclease and capping domains. The obtained model was verified with the structure validation programs such as ProSA and QMEAN servers for reliability. Ligand binding studies using COACH indicated the interaction of <italic>DnMRE11</italic>
 protein with two Mn<sup>2+</sup>
 ions and dAMP. The ConSurf server predicted that residues of the active site and Nbs binding site have high conservation scores between plant species.</p>
</sec>
<sec><title>Conclusions</title>
<p>A model structure of <italic>DnMRE11</italic>
 was constructed and validated with various bioinformatics programs which suggested the predicted model to be satisfactory. Further validation studies were conducted by COACH analysis for active site ligand prediction, and revealed the presence of six ligands binding sites and two ligands (2 Mn<sup>2+</sup>
 and dAMP).</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12976-015-0013-2) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour

In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour

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