Redox potentials of protein disulfide bonds from free-energy calculations.
Identifieur interne : 000514 ( Main/Exploration ); précédent : 000513; suivant : 000515Redox potentials of protein disulfide bonds from free-energy calculations.
Auteurs : Wenjin Li [Allemagne] ; Ilona B. Baldus [Allemagne] ; Frauke Gr Ter [Allemagne]Source :
- The journal of physical chemistry. B [ 1520-5207 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
- composition chimique : Disulfures, Thiorédoxines.
- Modèles moléculaires, Motifs d'acides aminés, Oxydoréduction, Thermodynamique.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Disulfides, Thioredoxins.
- Amino Acid Motifs, Models, Molecular, Oxidation-Reduction, Thermodynamics.
Abstract
Thiol/disulfide exchange in proteins is a vital process in all organisms. To ensure specificity, the involved thermodynamics and kinetics are believed to be tailored by the structure and dynamics of the protein hosting the thiol/disulfide pair. We here aim at predicting the thermodynamics of thiol/disulfide pairs in proteins. We devise a free-energy calculation scheme, which makes use of the Crooks Gaussian intersection method to estimate the redox potential of thiol/disulfide pairs in 12 proteins belonging to the thioredoxin superfamily, namely, thioredoxins, glutaredoxins, and thiol-disulfide oxidoreductases in disulfide bond formation systems. We obtained a satisfying correlation of computed with experimental redox potentials (varying by 160 mV), with a residual error of ∼40 mV (8 kJ/mol), which drastically reduces when considering a less diverse set of only thioredoxins. Our simple and transferrable approach provides a route toward estimating redox potentials of any disulfide-containing protein given that its (reduced or oxidized) structure is known and thereby represents a step toward a rational design of redox proteins.
DOI: 10.1021/acs.jpcb.5b01051
PubMed: 25856548
Affiliations:
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Baldus</name><affiliation wicri:level="3"><nlm:affiliation>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Gr Ter, Frauke" sort="Gr Ter, Frauke" uniqKey="Gr Ter F" first="Frauke" last="Gr Ter">Frauke Gr Ter</name><affiliation wicri:level="3"><nlm:affiliation>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25856548</idno><idno type="pmid">25856548</idno><idno type="doi">10.1021/acs.jpcb.5b01051</idno><idno type="wicri:Area/Main/Corpus">000540</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000540</idno><idno type="wicri:Area/Main/Curation">000540</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000540</idno><idno type="wicri:Area/Main/Exploration">000540</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Redox potentials of protein disulfide bonds from free-energy calculations.</title><author><name sortKey="Li, Wenjin" sort="Li, Wenjin" uniqKey="Li W" first="Wenjin" last="Li">Wenjin Li</name><affiliation wicri:level="3"><nlm:affiliation>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Baldus, Ilona B" sort="Baldus, Ilona B" uniqKey="Baldus I" first="Ilona B" last="Baldus">Ilona B. Baldus</name><affiliation wicri:level="3"><nlm:affiliation>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Gr Ter, Frauke" sort="Gr Ter, Frauke" uniqKey="Gr Ter F" first="Frauke" last="Gr Ter">Frauke Gr Ter</name><affiliation wicri:level="3"><nlm:affiliation>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>†Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author></analytic><series><title level="j">The journal of physical chemistry. B</title><idno type="eISSN">1520-5207</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Motifs (MeSH)</term><term>Disulfides (chemistry)</term><term>Models, Molecular (MeSH)</term><term>Oxidation-Reduction (MeSH)</term><term>Thermodynamics (MeSH)</term><term>Thioredoxins (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Disulfures (composition chimique)</term><term>Modèles moléculaires (MeSH)</term><term>Motifs d'acides aminés (MeSH)</term><term>Oxydoréduction (MeSH)</term><term>Thermodynamique (MeSH)</term><term>Thiorédoxines (composition chimique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Disulfides</term><term>Thioredoxins</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Disulfures</term><term>Thiorédoxines</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Motifs</term><term>Models, Molecular</term><term>Oxidation-Reduction</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Modèles moléculaires</term><term>Motifs d'acides aminés</term><term>Oxydoréduction</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Thiol/disulfide exchange in proteins is a vital process in all organisms. To ensure specificity, the involved thermodynamics and kinetics are believed to be tailored by the structure and dynamics of the protein hosting the thiol/disulfide pair. We here aim at predicting the thermodynamics of thiol/disulfide pairs in proteins. We devise a free-energy calculation scheme, which makes use of the Crooks Gaussian intersection method to estimate the redox potential of thiol/disulfide pairs in 12 proteins belonging to the thioredoxin superfamily, namely, thioredoxins, glutaredoxins, and thiol-disulfide oxidoreductases in disulfide bond formation systems. We obtained a satisfying correlation of computed with experimental redox potentials (varying by 160 mV), with a residual error of ∼40 mV (8 kJ/mol), which drastically reduces when considering a less diverse set of only thioredoxins. Our simple and transferrable approach provides a route toward estimating redox potentials of any disulfide-containing protein given that its (reduced or oxidized) structure is known and thereby represents a step toward a rational design of redox proteins. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25856548</PMID><DateCompleted><Year>2016</Year><Month>01</Month><Day>26</Day></DateCompleted><DateRevised><Year>2015</Year><Month>04</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1520-5207</ISSN><JournalIssue CitedMedium="Internet"><Volume>119</Volume><Issue>17</Issue><PubDate><Year>2015</Year><Month>Apr</Month><Day>30</Day></PubDate></JournalIssue><Title>The journal of physical chemistry. B</Title><ISOAbbreviation>J Phys Chem B</ISOAbbreviation></Journal><ArticleTitle>Redox potentials of protein disulfide bonds from free-energy calculations.</ArticleTitle><Pagination><MedlinePgn>5386-91</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/acs.jpcb.5b01051</ELocationID><Abstract><AbstractText>Thiol/disulfide exchange in proteins is a vital process in all organisms. To ensure specificity, the involved thermodynamics and kinetics are believed to be tailored by the structure and dynamics of the protein hosting the thiol/disulfide pair. We here aim at predicting the thermodynamics of thiol/disulfide pairs in proteins. We devise a free-energy calculation scheme, which makes use of the Crooks Gaussian intersection method to estimate the redox potential of thiol/disulfide pairs in 12 proteins belonging to the thioredoxin superfamily, namely, thioredoxins, glutaredoxins, and thiol-disulfide oxidoreductases in disulfide bond formation systems. We obtained a satisfying correlation of computed with experimental redox potentials (varying by 160 mV), with a residual error of ∼40 mV (8 kJ/mol), which drastically reduces when considering a less diverse set of only thioredoxins. 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Baldus</name><name sortKey="Gr Ter, Frauke" sort="Gr Ter, Frauke" uniqKey="Gr Ter F" first="Frauke" last="Gr Ter">Frauke Gr Ter</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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