Ontology type: schema:ScholarlyArticle
2011-05
AUTHORSE. Thiriot, G. Monard, S. Boschi-Muller, G. Branlant, M. F. Ruiz-López
ABSTRACTAb initio calculations at the B3LYP/6–311 ++G(2df,2p) and B3LYP/6–31G(d) level have been carried out to investigate the reaction mechanism of methionine sulfoxide reductases of class A. These enzymes reduce oxidized methionine in vivo and therefore play an important role in repairing protein damage caused by the oxidative stress. Our calculations have been carried out for a model reaction in a model active site. Several reaction mechanisms have been explored that can roughly be described as (2H+ + 2e−) or (H+ + e−). The results suggest that the actual reaction mechanism is of the (2H+ + 2e−) type corresponding to a more or less asynchronous-concerted double-proton transfer reaction leading to the formation of methionine (dimethylthioether in our model) and a sulfenic acid Cys-SOH. The Michaelis complex would involve one deprotonated Cys and one protonated Glu residues in the active site, this protonation state being mandatory to stabilize the sulfoxide substrate. Then, proton transfer from Glu to the substrate takes place, followed by proton transfer from one Tyr residue and fast reorganization of the system. The overall activation energy barrier is estimated to fall in the range 7–9 kcal/mol, much lower than the predicted barrier in DMSO solution (29.6 kcal/mol) reported before. More... »
PAGES93-103
http://scigraph.springernature.com/pub.10.1007/s00214-011-0901-4
DOIhttp://dx.doi.org/10.1007/s00214-011-0901-4
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1007614585
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biochemistry and Cell Biology",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"name": [
"Theoretical Chemistry and Biochemistry Group, SRSMC, Nancy University, CNRS, BP 70239, 54506, Vandoeuvre-l\u00e8s-Nancy, France"
],
"type": "Organization"
},
"familyName": "Thiriot",
"givenName": "E.",
"id": "sg:person.011742667041.26",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011742667041.26"
],
"type": "Person"
},
{
"affiliation": {
"name": [
"Theoretical Chemistry and Biochemistry Group, SRSMC, Nancy University, CNRS, BP 70239, 54506, Vandoeuvre-l\u00e8s-Nancy, France"
],
"type": "Organization"
},
"familyName": "Monard",
"givenName": "G.",
"id": "sg:person.0575563033.20",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0575563033.20"
],
"type": "Person"
},
{
"affiliation": {
"name": [
"Molecular and Structural Enzymology Group, AREMS, Nancy University, CNRS, BP 70239, 54506, Vandoeuvre-l\u00e8s-Nancy, France"
],
"type": "Organization"
},
"familyName": "Boschi-Muller",
"givenName": "S.",
"id": "sg:person.0752337723.27",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0752337723.27"
],
"type": "Person"
},
{
"affiliation": {
"name": [
"Molecular and Structural Enzymology Group, AREMS, Nancy University, CNRS, BP 70239, 54506, Vandoeuvre-l\u00e8s-Nancy, France"
],
"type": "Organization"
},
"familyName": "Branlant",
"givenName": "G.",
"id": "sg:person.0777076244.60",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777076244.60"
],
"type": "Person"
},
{
"affiliation": {
"name": [
"Theoretical Chemistry and Biochemistry Group, SRSMC, Nancy University, CNRS, BP 70239, 54506, Vandoeuvre-l\u00e8s-Nancy, France"
],
"type": "Organization"
},
"familyName": "Ruiz-L\u00f3pez",
"givenName": "M. F.",
"id": "sg:person.01133440365.30",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01133440365.30"
],
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1002/jcc.540110311",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004779307"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nsb783",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004990844",
"https://doi.org/10.1038/nsb783"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0020-1693(02)01434-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005225066"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0020-1693(02)01434-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005225066"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/cphc.200400568",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1006465709"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/cphc.200400568",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1006465709"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1074/jbc.m110.134528",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1006634712"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1074/jbc.m307471200",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008869081"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s10858-005-1059-y",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009611772",
"https://doi.org/10.1007/s10858-005-1059-y"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0040-4020(01)90096-1",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018289759"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.231472998",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020000782"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1074/jbc.m608844200",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020671290"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1074/jbc.m112350200",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024754799"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/0166-1280(91)89026-w",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024856440"
],
"type": "CreativeWork"
},
{
"id": "https://app.dimensions.ai/details/publication/pub.1025319891",
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-94-009-5883-8",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1025319891",
"https://doi.org/10.1007/978-94-009-5883-8"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-94-009-5883-8",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1025319891",
"https://doi.org/10.1007/978-94-009-5883-8"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1074/jbc.m203496200",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1028544377"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.abb.2008.02.007",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030906955"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.jmb.2008.01.021",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031928864"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0969-2126(00)00526-8",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038137187"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1074/jbc.m006137200",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1040432623"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1091/mbc.e03-08-0629",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1040621004"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.bbapap.2004.09.016",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041972942"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1063/1.464913",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042899913"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/0009-2614(83)80005-0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046035962"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1110/ps.10701",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047983512"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.0703774104",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050329185"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1042/bj2400897",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051077054"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1042/bj2400897",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051077054"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/jb.185.14.4119-4126.2003",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051311266"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/cr60247a001",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1053786099"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/cr00031a013",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1053853829"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/bi0020269",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055165038"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/bi0020269",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055165038"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/bi049306z",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055199671"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/bi049306z",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055199671"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ed081p1265.1",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055467743"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ed081p596",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055468095"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ed084p934.1",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055470003"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ic980348j",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055588722"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ic980348j",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055588722"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja01064a022",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055765315"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja01073a039",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055765994"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja972013r",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055867947"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja972013r",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055867947"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jo00873a048",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055989402"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jo00902a019",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055990645"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jo01016a039",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055995143"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jo01046a528",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055998570"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jp0573036",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1056064409"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jp0573036",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1056064409"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jp065403l",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1056068132"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jp065403l",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1056068132"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jp0658445",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1056068397"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jp0658445",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1056068397"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1070/rc2008v077n10abeh003805",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1058192965"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1103/physrevb.37.785",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1060546104"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1103/physrevb.37.785",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1060546104"
],
"type": "CreativeWork"
}
],
"datePublished": "2011-05",
"datePublishedReg": "2011-05-01",
"description": "Ab initio calculations at the B3LYP/6\u2013311 ++G(2df,2p) and B3LYP/6\u201331G(d) level have been carried out to investigate the reaction mechanism of methionine sulfoxide reductases of class A. These enzymes reduce oxidized methionine in vivo and therefore play an important role in repairing protein damage caused by the oxidative stress. Our calculations have been carried out for a model reaction in a model active site. Several reaction mechanisms have been explored that can roughly be described as (2H+ + 2e\u2212) or (H+ + e\u2212). The results suggest that the actual reaction mechanism is of the (2H+ + 2e\u2212) type corresponding to a more or less asynchronous-concerted double-proton transfer reaction leading to the formation of methionine (dimethylthioether in our model) and a sulfenic acid Cys-SOH. The Michaelis complex would involve one deprotonated Cys and one protonated Glu residues in the active site, this protonation state being mandatory to stabilize the sulfoxide substrate. Then, proton transfer from Glu to the substrate takes place, followed by proton transfer from one Tyr residue and fast reorganization of the system. The overall activation energy barrier is estimated to fall in the range 7\u20139 kcal/mol, much lower than the predicted barrier in DMSO solution (29.6 kcal/mol) reported before.",
"genre": "research_article",
"id": "sg:pub.10.1007/s00214-011-0901-4",
"inLanguage": [
"en"
],
"isAccessibleForFree": false,
"isPartOf": [
{
"id": "sg:journal.1134081",
"issn": [
"1432-881X",
"1432-2234"
],
"name": "Theoretical Chemistry Accounts",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "129"
}
],
"name": "Reduction mechanism in class A methionine sulfoxide reductases: a theoretical chemistry investigation",
"pagination": "93-103",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"2445388e03eafa7728556cd324065f7e27792a75fd04cffddcd9e667de8d1d44"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1007/s00214-011-0901-4"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1007614585"
]
}
],
"sameAs": [
"https://doi.org/10.1007/s00214-011-0901-4",
"https://app.dimensions.ai/details/publication/pub.1007614585"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-10T19:08",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8678_00000510.jsonl",
"type": "ScholarlyArticle",
"url": "http://link.springer.com/10.1007%2Fs00214-011-0901-4"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s00214-011-0901-4'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s00214-011-0901-4'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00214-011-0901-4'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00214-011-0901-4'
This table displays all metadata directly associated to this object as RDF triples.
239 TRIPLES
21 PREDICATES
74 URIs
19 LITERALS
7 BLANK NODES