Importance of the iron-sulfur component and of the siroheme modification in the resting state of sulfite reductase.
Identifieur interne : 000105 ( Main/Exploration ); précédent : 000104; suivant : 000106Importance of the iron-sulfur component and of the siroheme modification in the resting state of sulfite reductase.
Auteurs : Adrian M V. Brânzanic [Roumanie] ; Ulf Ryde [Suède] ; Radu Silaghi-Dumitrescu [Roumanie]Source :
- Journal of inorganic biochemistry [ 1873-3344 ] ; 2020.
Abstract
The active site of sulfite reductase (SiR) consists of an unusual siroheme-Fe4S4 assembly coupled via a cysteinate sulfur, and serves for multi-electron reduction reactions. Clear explanations have not been demonstrated for the reasons behind the choice of siroheme (vs. other types of heme) or for the single-atom coupling to an Fe4S4 center (as opposed to simple adjacency or to coupling via chains consisting of more than one atom). Possible explanations for these choices have previously been invoked, relating to the control of the spin state of the substrate-binding (siro)heme iron, modulation of the trans effect of the (Fe4S4-bound) cysteinate, or modulation of the redox potential. Reported here is a density functional theory (DFT) investigation of the structural interplay (in terms of geometry, molecular orbitals and magnetic interactions) between the siroheme and the Fe4S4 center as well as the importance of the covalent modifications within siroheme compared to the more common heme b, aiming to verify the role of the siroheme modification and of the Fe4S4 cluster at the SiR active site, with focus on previously-formulated hypotheses (geometrical/sterics, spin state, redox and electron-transfer control). A calibration of various DFT methods/variants for the correct description of ground state spin multiplicity is performed using a set of problematic cases of bioinorganic Fe centers; out of 11 functionals tested, M06-L and B3LYP offer the best results - though none of them correctly predict the spin state for all test cases. Upon examination of the relative energies of spin states, reduction potentials, energy decomposition (electrostatic, exchange-repulsion, orbital relaxation, correlation and dispersion interactions) and Mayer bond indices in SiR models, the following main roles of the siroheme and cubane are identified: (1) the cubane cofactor decreases the reduction potential of the siroheme and stabilizes the siroheme-cysteine bond interaction, and (2) the siroheme removes the quasi-degeneracy between the intermediate and high-spin states found in ferrous systems by preserving the latter as ground state; the higher-spin preference and the increased accessibility of multiple spin states are likely to be important in selective binding of the substrate and of the subsequent reaction intermediates, and in efficient changes in redox states throughout the catalytic cycle.
DOI: 10.1016/j.jinorgbio.2019.110928
PubMed: 31756559
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Brânzanic</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Babeș-Bolyai University, Cluj-Napoca, Romania; Institute of Interdisciplinary Research in Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca, Romania.</nlm:affiliation><country xml:lang="fr">Roumanie</country><wicri:regionArea>Department of Chemistry, Babeș-Bolyai University, Cluj-Napoca, Romania; Institute of Interdisciplinary Research in Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca</wicri:regionArea><wicri:noRegion>Cluj-Napoca</wicri:noRegion></affiliation></author><author><name sortKey="Ryde, Ulf" sort="Ryde, Ulf" uniqKey="Ryde U" first="Ulf" last="Ryde">Ulf Ryde</name><affiliation wicri:level="1"><nlm:affiliation>Department of Theoretical Chemistry, Lund University, Lund, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Theoretical Chemistry, Lund University, Lund</wicri:regionArea><wicri:noRegion>Lund</wicri:noRegion></affiliation></author><author><name sortKey="Silaghi Dumitrescu, Radu" sort="Silaghi Dumitrescu, Radu" uniqKey="Silaghi Dumitrescu R" first="Radu" last="Silaghi-Dumitrescu">Radu Silaghi-Dumitrescu</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Babeș-Bolyai University, Cluj-Napoca, Romania. 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Brânzanic</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Babeș-Bolyai University, Cluj-Napoca, Romania; Institute of Interdisciplinary Research in Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca, Romania.</nlm:affiliation><country xml:lang="fr">Roumanie</country><wicri:regionArea>Department of Chemistry, Babeș-Bolyai University, Cluj-Napoca, Romania; Institute of Interdisciplinary Research in Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca</wicri:regionArea><wicri:noRegion>Cluj-Napoca</wicri:noRegion></affiliation></author><author><name sortKey="Ryde, Ulf" sort="Ryde, Ulf" uniqKey="Ryde U" first="Ulf" last="Ryde">Ulf Ryde</name><affiliation wicri:level="1"><nlm:affiliation>Department of Theoretical Chemistry, Lund University, Lund, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Theoretical Chemistry, Lund University, Lund</wicri:regionArea><wicri:noRegion>Lund</wicri:noRegion></affiliation></author><author><name sortKey="Silaghi Dumitrescu, Radu" sort="Silaghi Dumitrescu, Radu" uniqKey="Silaghi Dumitrescu R" first="Radu" last="Silaghi-Dumitrescu">Radu Silaghi-Dumitrescu</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Babeș-Bolyai University, Cluj-Napoca, Romania. Electronic address: rsilaghi@chem.ubbcluj.ro.</nlm:affiliation><country xml:lang="fr">Roumanie</country><wicri:regionArea>Department of Chemistry, Babeș-Bolyai University, Cluj-Napoca</wicri:regionArea><wicri:noRegion>Cluj-Napoca</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of inorganic biochemistry</title><idno type="eISSN">1873-3344</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The active site of sulfite reductase (SiR) consists of an unusual siroheme-Fe<sub>4</sub>S<sub>4</sub> assembly coupled via a cysteinate sulfur, and serves for multi-electron reduction reactions. Clear explanations have not been demonstrated for the reasons behind the choice of siroheme (vs. other types of heme) or for the single-atom coupling to an Fe<sub>4</sub>S<sub>4</sub> center (as opposed to simple adjacency or to coupling via chains consisting of more than one atom). Possible explanations for these choices have previously been invoked, relating to the control of the spin state of the substrate-binding (siro)heme iron, modulation of the trans effect of the (Fe<sub>4</sub>S<sub>4</sub>-bound) cysteinate, or modulation of the redox potential. Reported here is a density functional theory (DFT) investigation of the structural interplay (in terms of geometry, molecular orbitals and magnetic interactions) between the siroheme and the Fe<sub>4</sub>S<sub>4</sub> center as well as the importance of the covalent modifications within siroheme compared to the more common heme b, aiming to verify the role of the siroheme modification and of the Fe<sub>4</sub>S<sub>4</sub> cluster at the SiR active site, with focus on previously-formulated hypotheses (geometrical/sterics, spin state, redox and electron-transfer control). A calibration of various DFT methods/variants for the correct description of ground state spin multiplicity is performed using a set of problematic cases of bioinorganic Fe centers; out of 11 functionals tested, M06-L and B3LYP offer the best results - though none of them correctly predict the spin state for all test cases. Upon examination of the relative energies of spin states, reduction potentials, energy decomposition (electrostatic, exchange-repulsion, orbital relaxation, correlation and dispersion interactions) and Mayer bond indices in SiR models, the following main roles of the siroheme and cubane are identified: (1) the cubane cofactor decreases the reduction potential of the siroheme and stabilizes the siroheme-cysteine bond interaction, and (2) the siroheme removes the quasi-degeneracy between the intermediate and high-spin states found in ferrous systems by preserving the latter as ground state; the higher-spin preference and the increased accessibility of multiple spin states are likely to be important in selective binding of the substrate and of the subsequent reaction intermediates, and in efficient changes in redox states throughout the catalytic cycle.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">31756559</PMID><DateRevised><Year>2020</Year><Month>03</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1873-3344</ISSN><JournalIssue CitedMedium="Internet"><Volume>203</Volume><PubDate><Year>2020</Year><Month>02</Month></PubDate></JournalIssue><Title>Journal of inorganic biochemistry</Title><ISOAbbreviation>J Inorg Biochem</ISOAbbreviation></Journal><ArticleTitle>Importance of the iron-sulfur component and of the siroheme modification in the resting state of sulfite reductase.</ArticleTitle><Pagination><MedlinePgn>110928</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0162-0134(19)30340-X</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jinorgbio.2019.110928</ELocationID><Abstract><AbstractText>The active site of sulfite reductase (SiR) consists of an unusual siroheme-Fe<sub>4</sub>S<sub>4</sub> assembly coupled via a cysteinate sulfur, and serves for multi-electron reduction reactions. Clear explanations have not been demonstrated for the reasons behind the choice of siroheme (vs. other types of heme) or for the single-atom coupling to an Fe<sub>4</sub>S<sub>4</sub> center (as opposed to simple adjacency or to coupling via chains consisting of more than one atom). Possible explanations for these choices have previously been invoked, relating to the control of the spin state of the substrate-binding (siro)heme iron, modulation of the trans effect of the (Fe<sub>4</sub>S<sub>4</sub>-bound) cysteinate, or modulation of the redox potential. Reported here is a density functional theory (DFT) investigation of the structural interplay (in terms of geometry, molecular orbitals and magnetic interactions) between the siroheme and the Fe<sub>4</sub>S<sub>4</sub> center as well as the importance of the covalent modifications within siroheme compared to the more common heme b, aiming to verify the role of the siroheme modification and of the Fe<sub>4</sub>S<sub>4</sub> cluster at the SiR active site, with focus on previously-formulated hypotheses (geometrical/sterics, spin state, redox and electron-transfer control). A calibration of various DFT methods/variants for the correct description of ground state spin multiplicity is performed using a set of problematic cases of bioinorganic Fe centers; out of 11 functionals tested, M06-L and B3LYP offer the best results - though none of them correctly predict the spin state for all test cases. Upon examination of the relative energies of spin states, reduction potentials, energy decomposition (electrostatic, exchange-repulsion, orbital relaxation, correlation and dispersion interactions) and Mayer bond indices in SiR models, the following main roles of the siroheme and cubane are identified: (1) the cubane cofactor decreases the reduction potential of the siroheme and stabilizes the siroheme-cysteine bond interaction, and (2) the siroheme removes the quasi-degeneracy between the intermediate and high-spin states found in ferrous systems by preserving the latter as ground state; the higher-spin preference and the increased accessibility of multiple spin states are likely to be important in selective binding of the substrate and of the subsequent reaction intermediates, and in efficient changes in redox states throughout the catalytic cycle.</AbstractText><CopyrightInformation>Copyright © 2019 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Brânzanic</LastName><ForeName>Adrian M V</ForeName><Initials>AMV</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Babeș-Bolyai University, Cluj-Napoca, Romania; Institute of Interdisciplinary Research in Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca, Romania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ryde</LastName><ForeName>Ulf</ForeName><Initials>U</Initials><AffiliationInfo><Affiliation>Department of Theoretical Chemistry, Lund University, Lund, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Silaghi-Dumitrescu</LastName><ForeName>Radu</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Babeș-Bolyai University, Cluj-Napoca, Romania. Electronic address: rsilaghi@chem.ubbcluj.ro.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>11</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Inorg Biochem</MedlineTA><NlmUniqueID>7905788</NlmUniqueID><ISSNLinking>0162-0134</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><CoiStatement>Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>05</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>11</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>11</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>11</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>11</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>11</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31756559</ArticleId><ArticleId IdType="pii">S0162-0134(19)30340-X</ArticleId><ArticleId IdType="doi">10.1016/j.jinorgbio.2019.110928</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Roumanie</li><li>Suède</li></country></list><tree><country name="Roumanie"><noRegion><name sortKey="Branzanic, Adrian M V" sort="Branzanic, Adrian M V" uniqKey="Branzanic A" first="Adrian M V" last="Brânzanic">Adrian M V. Brânzanic</name></noRegion><name sortKey="Silaghi Dumitrescu, Radu" sort="Silaghi Dumitrescu, Radu" uniqKey="Silaghi Dumitrescu R" first="Radu" last="Silaghi-Dumitrescu">Radu Silaghi-Dumitrescu</name></country><country name="Suède"><noRegion><name sortKey="Ryde, Ulf" sort="Ryde, Ulf" uniqKey="Ryde U" first="Ulf" last="Ryde">Ulf Ryde</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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