Structural insight into the role of novel SARS-CoV-2 E protein: A potential target for vaccine development and other therapeutic strategies.
Identifieur interne : 000562 ( Main/Exploration ); précédent : 000561; suivant : 000563Structural insight into the role of novel SARS-CoV-2 E protein: A potential target for vaccine development and other therapeutic strategies.
Auteurs : Manish Sarkar [Inde] ; Soham Saha [France]Source :
- PloS one [ 1932-6203 ] ; 2020.
Descripteurs français
- KwdFr :
- Betacoronavirus (composition chimique), Betacoronavirus (isolement et purification), Conformation des protéines (MeSH), Eau (composition chimique), Humains (MeSH), Hydrogène (MeSH), Infections à coronavirus (prévention et contrôle), Infections à coronavirus (virologie), Liaison hydrogène (MeSH), Modèles moléculaires (MeSH), Mutation ponctuelle (MeSH), Pandémies (prévention et contrôle), Pneumopathie virale (prévention et contrôle), Pneumopathie virale (virologie), Protéines de l'enveloppe virale (composition chimique), Protéines de l'enveloppe virale (génétique), Protéines de l'enveloppe virale (immunologie), Similitude structurale de protéines (MeSH), Simulation numérique (MeSH), Spectroscopie par résonance magnétique (MeSH), Vaccins antiviraux (MeSH), Vaccins atténués (MeSH), Vaccins inactivés (MeSH).
- MESH :
- composition chimique : Betacoronavirus, Eau, Protéines de l'enveloppe virale.
- génétique : Protéines de l'enveloppe virale.
- immunologie : Protéines de l'enveloppe virale.
- isolement et purification : Betacoronavirus.
- prévention et contrôle : Infections à coronavirus, Pandémies, Pneumopathie virale.
- virologie : Infections à coronavirus, Pneumopathie virale.
- Conformation des protéines, Humains, Hydrogène, Liaison hydrogène, Modèles moléculaires, Mutation ponctuelle, Similitude structurale de protéines, Simulation numérique, Spectroscopie par résonance magnétique, Vaccins antiviraux, Vaccins atténués, Vaccins inactivés.
English descriptors
- KwdEn :
- Betacoronavirus (chemistry), Betacoronavirus (isolation & purification), Computer Simulation (MeSH), Coronavirus Infections (prevention & control), Coronavirus Infections (virology), Humans (MeSH), Hydrogen (MeSH), Hydrogen Bonding (MeSH), Magnetic Resonance Spectroscopy (MeSH), Models, Molecular (MeSH), Pandemics (prevention & control), Pneumonia, Viral (prevention & control), Pneumonia, Viral (virology), Point Mutation (MeSH), Protein Conformation (MeSH), Structural Homology, Protein (MeSH), Vaccines, Attenuated (MeSH), Vaccines, Inactivated (MeSH), Viral Envelope Proteins (chemistry), Viral Envelope Proteins (genetics), Viral Envelope Proteins (immunology), Viral Vaccines (MeSH), Water (chemistry).
- MESH :
- chemical , chemistry : Viral Envelope Proteins, Water.
- chemical , genetics : Viral Envelope Proteins.
- chemical , immunology : Viral Envelope Proteins.
- chemical : Hydrogen, Vaccines, Attenuated, Vaccines, Inactivated, Viral Vaccines.
- chemistry : Betacoronavirus.
- isolation & purification : Betacoronavirus.
- prevention & control : Coronavirus Infections, Pandemics, Pneumonia, Viral.
- virology : Coronavirus Infections, Pneumonia, Viral.
- Computer Simulation, Humans, Hydrogen Bonding, Magnetic Resonance Spectroscopy, Models, Molecular, Point Mutation, Protein Conformation, Structural Homology, Protein.
Abstract
The outbreak of COVID-19 across the world has posed unprecedented and global challenges on multiple fronts. Most of the vaccine and drug development has focused on the spike proteins and viral RNA-polymerases and main protease for viral replication. Using the bioinformatics and structural modelling approach, we modelled the structure of the envelope (E)-protein of novel SARS-CoV-2. The E-protein of this virus shares sequence similarity with that of SARS- CoV-1, and is highly conserved in the N-terminus regions. Incidentally, compared to spike proteins, E proteins demonstrate lower disparity and mutability among the isolated sequences. Using homology modelling, we found that the most favorable structure could function as a gated ion channel conducting H+ ions. Combining pocket estimation and docking with water, we determined that GLU 8 and ASN 15 in the N-terminal region were in close proximity to form H-bonds which was further validated by insertion of the E protein in an ERGIC-mimic membrane. Additionally, two distinct "core" structures were visible, the hydrophobic core and the central core, which may regulate the opening/closing of the channel. We propose this as a mechanism of viral ion channeling activity which plays a critical role in viral infection and pathogenesis. In addition, it provides a structural basis and additional avenues for vaccine development and generating therapeutic interventions against the virus.
DOI: 10.1371/journal.pone.0237300
PubMed: 32785274
PubMed Central: PMC7423102
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Most of the vaccine and drug development has focused on the spike proteins and viral RNA-polymerases and main protease for viral replication. Using the bioinformatics and structural modelling approach, we modelled the structure of the envelope (E)-protein of novel SARS-CoV-2. The E-protein of this virus shares sequence similarity with that of SARS- CoV-1, and is highly conserved in the N-terminus regions. Incidentally, compared to spike proteins, E proteins demonstrate lower disparity and mutability among the isolated sequences. Using homology modelling, we found that the most favorable structure could function as a gated ion channel conducting H+ ions. Combining pocket estimation and docking with water, we determined that GLU 8 and ASN 15 in the N-terminal region were in close proximity to form H-bonds which was further validated by insertion of the E protein in an ERGIC-mimic membrane. Additionally, two distinct "core" structures were visible, the hydrophobic core and the central core, which may regulate the opening/closing of the channel. We propose this as a mechanism of viral ion channeling activity which plays a critical role in viral infection and pathogenesis. In addition, it provides a structural basis and additional avenues for vaccine development and generating therapeutic interventions against the virus.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32785274</PMID><DateCompleted><Year>2020</Year><Month>08</Month><Day>28</Day></DateCompleted><DateRevised><Year>2020</Year><Month>08</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><Issue>8</Issue><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>Structural insight into the role of novel SARS-CoV-2 E protein: A potential target for vaccine development and other therapeutic strategies.</ArticleTitle><Pagination><MedlinePgn>e0237300</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0237300</ELocationID><Abstract><AbstractText>The outbreak of COVID-19 across the world has posed unprecedented and global challenges on multiple fronts. Most of the vaccine and drug development has focused on the spike proteins and viral RNA-polymerases and main protease for viral replication. Using the bioinformatics and structural modelling approach, we modelled the structure of the envelope (E)-protein of novel SARS-CoV-2. The E-protein of this virus shares sequence similarity with that of SARS- CoV-1, and is highly conserved in the N-terminus regions. Incidentally, compared to spike proteins, E proteins demonstrate lower disparity and mutability among the isolated sequences. Using homology modelling, we found that the most favorable structure could function as a gated ion channel conducting H+ ions. Combining pocket estimation and docking with water, we determined that GLU 8 and ASN 15 in the N-terminal region were in close proximity to form H-bonds which was further validated by insertion of the E protein in an ERGIC-mimic membrane. Additionally, two distinct "core" structures were visible, the hydrophobic core and the central core, which may regulate the opening/closing of the channel. We propose this as a mechanism of viral ion channeling activity which plays a critical role in viral infection and pathogenesis. In addition, it provides a structural basis and additional avenues for vaccine development and generating therapeutic interventions against the virus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sarkar</LastName><ForeName>Manish</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Bose Institute, Kolkata, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Saha</LastName><ForeName>Soham</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0003-1173-1397</Identifier><AffiliationInfo><Affiliation>Laboratory for Perception and Memory, Institut Pasteur, Paris, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR-3571), Paris, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>08</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C000669933">COVID-19 vaccine</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014613">Vaccines, Attenuated</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015164">Vaccines, Inactivated</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014759">Viral Envelope Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014765">Viral Vaccines</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C000705509">envelope protein, SARS-CoV-2</NameOfSubstance></Chemical><Chemical><RegistryNumber>059QF0KO0R</RegistryNumber><NameOfSubstance UI="D014867">Water</NameOfSubstance></Chemical><Chemical><RegistryNumber>7YNJ3PO35Z</RegistryNumber><NameOfSubstance UI="D006859">Hydrogen</NameOfSubstance></Chemical></ChemicalList><SupplMeshList><SupplMeshName Type="Disease" UI="C000657245">COVID-19</SupplMeshName><SupplMeshName Type="Organism" UI="C000656484">severe acute respiratory syndrome coronavirus 2</SupplMeshName></SupplMeshList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000073640" MajorTopicYN="N">Betacoronavirus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName><QualifierName UI="Q000517" MajorTopicYN="Y">prevention & control</QualifierName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006859" MajorTopicYN="N">Hydrogen</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006860" MajorTopicYN="N">Hydrogen Bonding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009682" MajorTopicYN="N">Magnetic Resonance Spectroscopy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058873" MajorTopicYN="N">Pandemics</DescriptorName><QualifierName UI="Q000517" MajorTopicYN="Y">prevention & control</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011024" MajorTopicYN="N">Pneumonia, Viral</DescriptorName><QualifierName UI="Q000517" MajorTopicYN="Y">prevention & control</QualifierName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017354" MajorTopicYN="N">Point Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D040681" MajorTopicYN="N">Structural Homology, Protein</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014613" MajorTopicYN="N">Vaccines, Attenuated</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015164" MajorTopicYN="N">Vaccines, Inactivated</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014759" MajorTopicYN="N">Viral Envelope Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000276" MajorTopicYN="N">immunology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014765" MajorTopicYN="N">Viral Vaccines</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014867" MajorTopicYN="N">Water</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading></MeshHeadingList><CoiStatement>The authors have declared that no competing interests exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>05</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>07</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>8</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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