Development of parameters compatible with the CHARMM36 force field for [Fe4S4]2+ clusters and molecular dynamics simulations of adenosine-5'-phosphosulfate reductase in GROMACS 2019.
Identifieur interne : 000145 ( Main/Exploration ); précédent : 000144; suivant : 000146Development of parameters compatible with the CHARMM36 force field for [Fe4S4]2+ clusters and molecular dynamics simulations of adenosine-5'-phosphosulfate reductase in GROMACS 2019.
Auteurs : Talis Uelisson Da Silva [Brésil] ; Karina De Carvalho Pougy [Brésil] ; Magaly Girão Albuquerque [Brésil] ; Camilo Henrique Da Silva Lima [Brésil] ; Sérgio De Paula Machado [Brésil]Source :
- Journal of biomolecular structure & dynamics [ 1538-0254 ] ; 2020.
Abstract
DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [Fe4S4]2+ that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [Fe4S4]2+ through the CHARMM36 force field.
DOI: 10.1080/07391102.2020.1847687
PubMed: 33183173
Affiliations:
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Karina De Carvalho" sort="Pougy, Karina De Carvalho" uniqKey="Pougy K" first="Karina De Carvalho" last="Pougy">Karina De Carvalho Pougy</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro</wicri:regionArea><placeName><settlement type="city">Rio de Janeiro</settlement><region type="state">État de Rio de Janeiro</region></placeName></affiliation></author><author><name sortKey="Albuquerque, Magaly Girao" sort="Albuquerque, Magaly Girao" uniqKey="Albuquerque M" first="Magaly Girão" last="Albuquerque">Magaly Girão Albuquerque</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro</wicri:regionArea><placeName><settlement type="city">Rio de Janeiro</settlement><region type="state">État de Rio de Janeiro</region></placeName></affiliation></author><author><name sortKey="Da Silva Lima, Camilo Henrique" sort="Da Silva Lima, Camilo Henrique" uniqKey="Da Silva Lima C" first="Camilo Henrique" last="Da Silva Lima">Camilo Henrique Da Silva Lima</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro</wicri:regionArea><placeName><settlement type="city">Rio de Janeiro</settlement><region type="state">État de Rio de Janeiro</region></placeName></affiliation></author><author><name sortKey="Machado, Sergio De Paula" sort="Machado, Sergio De Paula" uniqKey="Machado S" first="Sérgio De Paula" last="Machado">Sérgio De Paula Machado</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro</wicri:regionArea><placeName><settlement type="city">Rio de Janeiro</settlement><region type="state">État de Rio de Janeiro</region></placeName></affiliation></author></analytic><series><title level="j">Journal of biomolecular structure & dynamics</title><idno type="eISSN">1538-0254</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">DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [Fe<sub>4</sub>S<sub>4</sub>]<sup>2+</sup> that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [Fe<sub>4</sub>S<sub>4</sub>]<sup>2+</sup> through the CHARMM36 force field.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33183173</PMID><DateRevised><Year>2020</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1538-0254</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Nov</Month><Day>13</Day></PubDate></JournalIssue><Title>Journal of biomolecular structure & dynamics</Title><ISOAbbreviation>J Biomol Struct Dyn</ISOAbbreviation></Journal><ArticleTitle>Development of parameters compatible with the CHARMM36 force field for [Fe<sub>4</sub>S<sub>4</sub>]<sup>2+</sup> clusters and molecular dynamics simulations of adenosine-5'-phosphosulfate reductase in GROMACS 2019.</ArticleTitle><Pagination><MedlinePgn>1-11</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/07391102.2020.1847687</ELocationID><Abstract><AbstractText>DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [Fe<sub>4</sub>S<sub>4</sub>]<sup>2+</sup> that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [Fe<sub>4</sub>S<sub>4</sub>]<sup>2+</sup> through the CHARMM36 force field.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>da Silva</LastName><ForeName>Talis Uelisson</ForeName><Initials>TU</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-0745-0042</Identifier><AffiliationInfo><Affiliation>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pougy</LastName><ForeName>Karina de Carvalho</ForeName><Initials>KC</Initials><AffiliationInfo><Affiliation>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Albuquerque</LastName><ForeName>Magaly Girão</ForeName><Initials>MG</Initials><AffiliationInfo><Affiliation>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>da Silva Lima</LastName><ForeName>Camilo Henrique</ForeName><Initials>CH</Initials><AffiliationInfo><Affiliation>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Machado</LastName><ForeName>Sérgio de Paula</ForeName><Initials>SP</Initials><AffiliationInfo><Affiliation>Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>11</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Biomol Struct Dyn</MedlineTA><NlmUniqueID>8404176</NlmUniqueID><ISSNLinking>0739-1102</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">DFT</Keyword><Keyword MajorTopicYN="N">Dissimilatory adenosine-5’-phosphosulfate reductase</Keyword><Keyword MajorTopicYN="N">force field parametrization</Keyword><Keyword MajorTopicYN="N">iron-sulfur clusters</Keyword><Keyword MajorTopicYN="N">molecular dynamics simulation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>11</Month><Day>13</Day><Hour>5</Hour><Minute>32</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>11</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>11</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33183173</ArticleId><ArticleId IdType="doi">10.1080/07391102.2020.1847687</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Brésil</li></country><region><li>État de Rio de Janeiro</li></region><settlement><li>Rio de Janeiro</li></settlement></list><tree><country name="Brésil"><region name="État de Rio de Janeiro"><name sortKey="Da Silva, Talis Uelisson" sort="Da Silva, Talis Uelisson" uniqKey="Da Silva T" first="Talis Uelisson" last="Da Silva">Talis Uelisson Da Silva</name></region><name sortKey="Albuquerque, Magaly Girao" sort="Albuquerque, Magaly Girao" uniqKey="Albuquerque M" first="Magaly Girão" last="Albuquerque">Magaly Girão Albuquerque</name><name sortKey="Da Silva Lima, Camilo Henrique" sort="Da Silva Lima, Camilo Henrique" uniqKey="Da Silva Lima C" first="Camilo Henrique" last="Da Silva Lima">Camilo Henrique Da Silva Lima</name><name sortKey="Machado, Sergio De Paula" sort="Machado, Sergio De Paula" uniqKey="Machado S" first="Sérgio De Paula" last="Machado">Sérgio De Paula Machado</name><name sortKey="Pougy, Karina De Carvalho" sort="Pougy, Karina De Carvalho" uniqKey="Pougy K" first="Karina De Carvalho" last="Pougy">Karina De Carvalho Pougy</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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