IronSulferCluV1, Main, Exploration, bibRecord, 000184

A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII.

Identifieur interne : 000184 ( Main/Exploration ); précédent : 000183; suivant : 000185

A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII.

Auteurs : Ayaz Hassan [Brésil] ; Lucyano J A. Macedo [Brésil] ; João C P De Souza [Brésil] ; Filipe C D A. Lima [Brésil] ; Frank N. Crespilho [Brésil]

Source :

Scientific reports [ 2045-2322 ] ; 2020.

RBID : pubmed:32029762

Descripteurs français

English descriptors

KwdEn :
- Binding Sites (physiology), DNA (metabolism), DNA Damage (physiology), DNA Glycosylases (metabolism), DNA Repair (physiology), DNA-Binding Proteins (metabolism), Deoxyribonuclease (Pyrimidine Dimer) (metabolism), Escherichia coli (metabolism), Escherichia coli Proteins (metabolism), Iron-Sulfur Proteins (metabolism), Oxidation-Reduction (MeSH), Spectroscopy, Fourier Transform Infrared (methods).
MESH :
- chemical , metabolism : DNA, DNA Glycosylases, DNA-Binding Proteins, Deoxyribonuclease (Pyrimidine Dimer), Escherichia coli Proteins, Iron-Sulfur Proteins.
- metabolism : Escherichia coli.
- methods : Spectroscopy, Fourier Transform Infrared.
- physiology : Binding Sites, DNA Damage, DNA Repair.
- Oxidation-Reduction.

Abstract

Endonuclease III (EndoIII) is a DNA glycosylase that contains the [4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe-S bonds of the [4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300 cm^-1) were used independently to study the structural changes in EndoIII and the behavior of the [4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe-S (sulfide) and Fe-S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe-S bond lengths upon DNA binding, both of the Fe-S (sulfide) and Fe-S (thiolate) bonds in the [4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix.

DOI: 10.1038/s41598-020-58531-4
PubMed: 32029762
PubMed Central: PMC7005299

Affiliations:

Links toward previous steps (curation, corpus...)

to stream Main, to step Corpus: 000151
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Le document en format XML

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<term>Escherichia coli (métabolisme)</term>
<term>Ferrosulfoprotéines (métabolisme)</term>
<term>Oxydoréduction (MeSH)</term>
<term>Protéines Escherichia coli (métabolisme)</term>
<term>Protéines de liaison à l'ADN (métabolisme)</term>
<term>Réparation de l'ADN (physiologie)</term>
<term>Sites de fixation (physiologie)</term>
<term>Spectroscopie infrarouge à transformée de Fourier (méthodes)</term>
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<term>DNA-Binding Proteins</term>
<term>Deoxyribonuclease (Pyrimidine Dimer)</term>
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<term>Iron-Sulfur Proteins</term>
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<term>DNA Repair</term>
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<front><div type="abstract" xml:lang="en">Endonuclease III (EndoIII) is a DNA glycosylase that contains the [4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe-S bonds of the [4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300 cm<sup>-1</sup>
) were used independently to study the structural changes in EndoIII and the behavior of the [4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe-S (sulfide) and Fe-S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe-S bond lengths upon DNA binding, both of the Fe-S (sulfide) and Fe-S (thiolate) bonds in the [4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix.</div>
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<Abstract><AbstractText>Endonuclease III (EndoIII) is a DNA glycosylase that contains the [4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe-S bonds of the [4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300 cm<sup>-1</sup>
) were used independently to study the structural changes in EndoIII and the behavior of the [4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe-S (sulfide) and Fe-S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe-S bond lengths upon DNA binding, both of the Fe-S (sulfide) and Fe-S (thiolate) bonds in the [4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix.</AbstractText>
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A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII.

A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII.

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