NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics.
Identifieur interne : 002B07 ( Ncbi/Curation ); précédent : 002B06; suivant : 002B08NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics.
Auteurs : Garvita Gupta [Singapour] ; Liangzhong Lim [Singapour] ; Jianxing Song [Singapour]Source :
- PloS one [ 1932-6203 ] ; 2015.
Descripteurs français
- KwdFr :
- Chymotrypsine (), Dengue (virologie), Dichroïsme circulaire, Endopeptidases (), Escherichia coli (métabolisme), Génome viral, Liaison aux protéines, Marqueurs de spin, Micelles, Mutagenèse dirigée, Pliage des protéines, Protéines virales non structurales (), RNA helicases (), Relation structure-activité, Serine endopeptidases (), Simulation de dynamique moléculaire, Spectroscopie par résonance magnétique, Structure secondaire des protéines, Virus de la dengue ().
- MESH :
- métabolisme : Escherichia coli.
- virologie : Dengue.
- Chymotrypsine, Dichroïsme circulaire, Endopeptidases, Génome viral, Liaison aux protéines, Marqueurs de spin, Micelles, Mutagenèse dirigée, Pliage des protéines, Protéines virales non structurales, RNA helicases, Relation structure-activité, Serine endopeptidases, Simulation de dynamique moléculaire, Spectroscopie par résonance magnétique, Structure secondaire des protéines, Virus de la dengue.
English descriptors
- KwdEn :
- Chymotrypsin (chemistry), Circular Dichroism, Dengue (virology), Dengue Virus (chemistry), Endopeptidases (chemistry), Escherichia coli (metabolism), Genome, Viral, Magnetic Resonance Spectroscopy, Micelles, Molecular Dynamics Simulation, Mutagenesis, Site-Directed, Protein Binding, Protein Folding, Protein Structure, Secondary, RNA Helicases (chemistry), Serine Endopeptidases (chemistry), Spin Labels, Structure-Activity Relationship, Viral Nonstructural Proteins (chemistry).
- MESH :
- chemical , chemistry : Chymotrypsin, Endopeptidases, RNA Helicases, Serine Endopeptidases, Viral Nonstructural Proteins.
- chemistry : Dengue Virus.
- metabolism : Escherichia coli.
- virology : Dengue.
- Circular Dichroism, Genome, Viral, Magnetic Resonance Spectroscopy, Micelles, Molecular Dynamics Simulation, Mutagenesis, Site-Directed, Protein Binding, Protein Folding, Protein Structure, Secondary, Spin Labels, Structure-Activity Relationship.
Abstract
Dengue genome encodes a two component protease complex (NS2B-NS3pro) essential for the viral maturation/infectivity, thus representing a key drug target. Previously, due to its "complete insolubility", the isolated NS3pro could not be experimentally studied and it remains elusive what structure it adopts without NS2B and why NS2B is indispensable. Here as facilitated by our previous discovery, the isolated NS3pro has been surprisingly deciphered by NMR to be the first intrinsically-disordered chymotrypsin-like fold, which exists in a loosely-packed state with non-native long-range interactions as revealed by paramagnetic relaxation enhancement (PRE). The disordered NS3pro appears to be needed for binding a human host factor to trigger the membrane remodeling. Moreover, we have in vitro refolded the NS3pro in complex with either NS2B (48-100) or the full-length NS2B (1-130) anchored into the LMPC micelle, and the two complexes have similar activities but different dynamics. We also performed molecular dynamics (MD) simulations and the results revealed that NS2B shows the highest structural fluctuations in the complex, thus providing the dynamic basis for the observation on its conformational exchange between open and closed states. Remarkably, the NS2B cofactor plays a central role in maintaining the correlated motion network required for the catalysis as we previously decoded for the SARS 3CL protease. Indeed, a truncated NS2B (48-100;Δ77-84) with the flexible loop deleted is able to trap the NS2B-NS3pro complex in a highly dynamic and catalytically-impotent state. Taken together, our study implies potential strategies to perturb the NS2B-NS3pro interface for design of inhibitors for treating dengue infection.
DOI: 10.1371/journal.pone.0134823
PubMed: 26258523
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000D87
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :000D87
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000D84
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :002B07
Links to Exploration step
pubmed:26258523Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics.</title><author><name sortKey="Gupta, Garvita" sort="Gupta, Garvita" uniqKey="Gupta G" first="Garvita" last="Gupta">Garvita Gupta</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Lim, Liangzhong" sort="Lim, Liangzhong" uniqKey="Lim L" first="Liangzhong" last="Lim">Liangzhong Lim</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Song, Jianxing" sort="Song, Jianxing" uniqKey="Song J" first="Jianxing" last="Song">Jianxing Song</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26258523</idno><idno type="pmid">26258523</idno><idno type="doi">10.1371/journal.pone.0134823</idno><idno type="wicri:Area/PubMed/Corpus">000D87</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000D87</idno><idno type="wicri:Area/PubMed/Curation">000D87</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000D87</idno><idno type="wicri:Area/PubMed/Checkpoint">000D84</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000D84</idno><idno type="wicri:Area/Ncbi/Merge">002B07</idno><idno type="wicri:Area/Ncbi/Curation">002B07</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics.</title><author><name sortKey="Gupta, Garvita" sort="Gupta, Garvita" uniqKey="Gupta G" first="Garvita" last="Gupta">Garvita Gupta</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Lim, Liangzhong" sort="Lim, Liangzhong" uniqKey="Lim L" first="Liangzhong" last="Lim">Liangzhong Lim</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Song, Jianxing" sort="Song, Jianxing" uniqKey="Song J" first="Jianxing" last="Song">Jianxing Song</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chymotrypsin (chemistry)</term><term>Circular Dichroism</term><term>Dengue (virology)</term><term>Dengue Virus (chemistry)</term><term>Endopeptidases (chemistry)</term><term>Escherichia coli (metabolism)</term><term>Genome, Viral</term><term>Magnetic Resonance Spectroscopy</term><term>Micelles</term><term>Molecular Dynamics Simulation</term><term>Mutagenesis, Site-Directed</term><term>Protein Binding</term><term>Protein Folding</term><term>Protein Structure, Secondary</term><term>RNA Helicases (chemistry)</term><term>Serine Endopeptidases (chemistry)</term><term>Spin Labels</term><term>Structure-Activity Relationship</term><term>Viral Nonstructural Proteins (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chymotrypsine ()</term><term>Dengue (virologie)</term><term>Dichroïsme circulaire</term><term>Endopeptidases ()</term><term>Escherichia coli (métabolisme)</term><term>Génome viral</term><term>Liaison aux protéines</term><term>Marqueurs de spin</term><term>Micelles</term><term>Mutagenèse dirigée</term><term>Pliage des protéines</term><term>Protéines virales non structurales ()</term><term>RNA helicases ()</term><term>Relation structure-activité</term><term>Serine endopeptidases ()</term><term>Simulation de dynamique moléculaire</term><term>Spectroscopie par résonance magnétique</term><term>Structure secondaire des protéines</term><term>Virus de la dengue ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Chymotrypsin</term><term>Endopeptidases</term><term>RNA Helicases</term><term>Serine Endopeptidases</term><term>Viral Nonstructural Proteins</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Dengue Virus</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Escherichia coli</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Escherichia coli</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Dengue</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Dengue</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Circular Dichroism</term><term>Genome, Viral</term><term>Magnetic Resonance Spectroscopy</term><term>Micelles</term><term>Molecular Dynamics Simulation</term><term>Mutagenesis, Site-Directed</term><term>Protein Binding</term><term>Protein Folding</term><term>Protein Structure, Secondary</term><term>Spin Labels</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Chymotrypsine</term><term>Dichroïsme circulaire</term><term>Endopeptidases</term><term>Génome viral</term><term>Liaison aux protéines</term><term>Marqueurs de spin</term><term>Micelles</term><term>Mutagenèse dirigée</term><term>Pliage des protéines</term><term>Protéines virales non structurales</term><term>RNA helicases</term><term>Relation structure-activité</term><term>Serine endopeptidases</term><term>Simulation de dynamique moléculaire</term><term>Spectroscopie par résonance magnétique</term><term>Structure secondaire des protéines</term><term>Virus de la dengue</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Dengue genome encodes a two component protease complex (NS2B-NS3pro) essential for the viral maturation/infectivity, thus representing a key drug target. Previously, due to its "complete insolubility", the isolated NS3pro could not be experimentally studied and it remains elusive what structure it adopts without NS2B and why NS2B is indispensable. Here as facilitated by our previous discovery, the isolated NS3pro has been surprisingly deciphered by NMR to be the first intrinsically-disordered chymotrypsin-like fold, which exists in a loosely-packed state with non-native long-range interactions as revealed by paramagnetic relaxation enhancement (PRE). The disordered NS3pro appears to be needed for binding a human host factor to trigger the membrane remodeling. Moreover, we have in vitro refolded the NS3pro in complex with either NS2B (48-100) or the full-length NS2B (1-130) anchored into the LMPC micelle, and the two complexes have similar activities but different dynamics. We also performed molecular dynamics (MD) simulations and the results revealed that NS2B shows the highest structural fluctuations in the complex, thus providing the dynamic basis for the observation on its conformational exchange between open and closed states. Remarkably, the NS2B cofactor plays a central role in maintaining the correlated motion network required for the catalysis as we previously decoded for the SARS 3CL protease. Indeed, a truncated NS2B (48-100;Δ77-84) with the flexible loop deleted is able to trap the NS2B-NS3pro complex in a highly dynamic and catalytically-impotent state. Taken together, our study implies potential strategies to perturb the NS2B-NS3pro interface for design of inhibitors for treating dengue infection. </div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002B07 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 002B07 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= SrasV1
|flux= Ncbi
|étape= Curation
|type= RBID
|clé= pubmed:26258523
|texte= NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:26258523" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \
| NlmPubMed2Wicri -a SrasV1
| This area was generated with Dilib version V0.6.33. |  |