Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses
Identifieur interne : 001365 ( Main/Exploration ); précédent : 001364; suivant : 001366Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses
Auteurs : Jordon Rahaman [États-Unis] ; Jessica Siltberg-Liberles [États-Unis]Source :
- Genome Biology and Evolution [ 1759-6653 ] ; 2016.
Descripteurs français
- KwdFr :
- Antiviraux (pharmacologie), Coronavirus du syndrome respiratoire du Moyen-Orient (), Coronavirus du syndrome respiratoire du Moyen-Orient (génétique), Génome viral, Liaison aux protéines, Motifs nucléotidiques, Protéines intrinsèquement désordonnées (), Protéines intrinsèquement désordonnées (génétique), Protéines virales (), Protéines virales (génétique), Sites de fixation, Séquence conservée, Virus du SRAS (), Virus du SRAS (génétique), Évolution moléculaire.
- MESH :
- génétique : Coronavirus du syndrome respiratoire du Moyen-Orient, Protéines intrinsèquement désordonnées, Protéines virales, Virus du SRAS.
- pharmacologie : Antiviraux.
- Coronavirus du syndrome respiratoire du Moyen-Orient, Génome viral, Liaison aux protéines, Motifs nucléotidiques, Protéines intrinsèquement désordonnées, Protéines virales, Sites de fixation, Séquence conservée, Virus du SRAS, Évolution moléculaire.
English descriptors
- KwdEn :
- Antiviral Agents (pharmacology), Binding Sites, Conserved Sequence, Evolution, Molecular, Genome, Viral, Intrinsically Disordered Proteins (chemistry), Intrinsically Disordered Proteins (genetics), Middle East Respiratory Syndrome Coronavirus (drug effects), Middle East Respiratory Syndrome Coronavirus (genetics), Nucleotide Motifs, Protein Binding, SARS Virus (drug effects), SARS Virus (genetics), Viral Proteins (chemistry), Viral Proteins (genetics).
- MESH :
- chemical , chemistry : Intrinsically Disordered Proteins, Viral Proteins.
- chemical , genetics : Intrinsically Disordered Proteins, Viral Proteins.
- chemical , pharmacology : Antiviral Agents.
- drug effects : Middle East Respiratory Syndrome Coronavirus, SARS Virus.
- genetics : Middle East Respiratory Syndrome Coronavirus, SARS Virus.
- Binding Sites, Conserved Sequence, Evolution, Molecular, Genome, Viral, Nucleotide Motifs, Protein Binding.
Abstract
Within the last 15 years, two related coronaviruses (Severe Acute Respiratory Syndrome [SARS]-CoV and Middle East Respiratory Syndrome [MERS]-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared with many other virus families. Because intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context. We found that regions of intrinsic disorder are rarely conserved among different coronavirus protein families, with the primary exception of the nucleocapsid. Also, secondary structure predictions are only conserved across 50–80% of sites for most protein families, with the implication that 20–50% of sites do not have conserved secondary structure prediction. Furthermore, nonconserved structure sites are significantly less constrained in sequence divergence than either sites conserved in the secondary structure or sites conserved in loop. Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the >10,000 starting sites across all coronaviruses in this study. The identified sequence motif is found within the nonstructural protein (NSP) 12 and constitutes an antiviral target potentially effective against the present day and future coronaviruses. On shorter evolutionary timescales, the SARS and MERS clades have more sequence motifs fulfilling the criteria applied. Interestingly, many motifs map to NSP12 making this a prime target for coronavirus antivirals.
Url:
DOI: 10.1093/gbe/evw246
PubMed: 27797946
PubMed Central: 5203785
Affiliations:
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Sciences, Florida International University, Miami</wicri:cityArea></affiliation></author><author><name sortKey="Siltberg Liberles, Jessica" sort="Siltberg Liberles, Jessica" uniqKey="Siltberg Liberles J" first="Jessica" last="Siltberg-Liberles">Jessica Siltberg-Liberles</name><affiliation wicri:level="2"><nlm:aff id="evw246-aff1">Department of Biological Sciences, Florida International University, Miami, FL</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Department of Biological Sciences, Florida International University, Miami</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="evw246-aff2">Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami</wicri:cityArea></affiliation></author></analytic><series><title level="j">Genome Biology and Evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Antiviral Agents (pharmacology)</term><term>Binding Sites</term><term>Conserved Sequence</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Intrinsically Disordered Proteins (chemistry)</term><term>Intrinsically Disordered Proteins (genetics)</term><term>Middle East Respiratory Syndrome Coronavirus (drug effects)</term><term>Middle East Respiratory Syndrome Coronavirus (genetics)</term><term>Nucleotide Motifs</term><term>Protein Binding</term><term>SARS Virus (drug effects)</term><term>SARS Virus (genetics)</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Antiviraux (pharmacologie)</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient ()</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient (génétique)</term><term>Génome viral</term><term>Liaison aux protéines</term><term>Motifs nucléotidiques</term><term>Protéines intrinsèquement désordonnées ()</term><term>Protéines intrinsèquement désordonnées (génétique)</term><term>Protéines virales ()</term><term>Protéines virales (génétique)</term><term>Sites de fixation</term><term>Séquence conservée</term><term>Virus du SRAS ()</term><term>Virus du SRAS (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Intrinsically Disordered Proteins</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Intrinsically Disordered Proteins</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Antiviral Agents</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term><term>Protéines intrinsèquement désordonnées</term><term>Protéines virales</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antiviraux</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Conserved Sequence</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Nucleotide Motifs</term><term>Protein Binding</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term><term>Génome viral</term><term>Liaison aux protéines</term><term>Motifs nucléotidiques</term><term>Protéines intrinsèquement désordonnées</term><term>Protéines virales</term><term>Sites de fixation</term><term>Séquence conservée</term><term>Virus du SRAS</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Within the last 15 years, two related coronaviruses (Severe Acute Respiratory Syndrome [SARS]-CoV and Middle East Respiratory Syndrome [MERS]-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared with many other virus families. Because intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context. We found that regions of intrinsic disorder are rarely conserved among different coronavirus protein families, with the primary exception of the nucleocapsid. Also, secondary structure predictions are only conserved across 50–80% of sites for most protein families, with the implication that 20–50% of sites do not have conserved secondary structure prediction. Furthermore, nonconserved structure sites are significantly less constrained in sequence divergence than either sites conserved in the secondary structure or sites conserved in loop. Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the >10,000 starting sites across all coronaviruses in this study. The identified sequence motif is found within the nonstructural protein (NSP) 12 and constitutes an antiviral target potentially effective against the present day and future coronaviruses. On shorter evolutionary timescales, the SARS and MERS clades have more sequence motifs fulfilling the criteria applied. Interestingly, many motifs map to NSP12 making this a prime target for coronavirus antivirals.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Anderson, Lj" uniqKey="Anderson L">LJ Anderson</name></author><author><name sortKey="Tong, S" uniqKey="Tong S">S. 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Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woo, Pc" uniqKey="Woo P">PC Woo</name></author><author><name sortKey="Lau, Sk" uniqKey="Lau S">SK Lau</name></author><author><name sortKey="Li, Ks" uniqKey="Li K">KS Li</name></author><author><name sortKey="Tsang, Ak" uniqKey="Tsang A">AK Tsang</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K-Y. Yuen</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Xue, B" uniqKey="Xue B">B Xue</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, H" uniqKey="Yang H">H Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, C" uniqKey="Yu C">C Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Shen, L" uniqKey="Shen L">L Shen</name></author><author><name sortKey="Gu, X" uniqKey="Gu X">X. Gu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zheng, A" uniqKey="Zheng A">A Zheng</name></author><author><name sortKey="Yuan, F" uniqKey="Yuan F">F Yuan</name></author><author><name sortKey="Kleinfelter, Lm" uniqKey="Kleinfelter L">LM Kleinfelter</name></author><author><name sortKey="Kielian, M" uniqKey="Kielian M">M. Kielian</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Floride</li></region></list><tree><country name="États-Unis"><region name="Floride"><name sortKey="Rahaman, Jordon" sort="Rahaman, Jordon" uniqKey="Rahaman J" first="Jordon" last="Rahaman">Jordon Rahaman</name></region><name sortKey="Siltberg Liberles, Jessica" sort="Siltberg Liberles, Jessica" uniqKey="Siltberg Liberles J" first="Jessica" last="Siltberg-Liberles">Jessica Siltberg-Liberles</name><name sortKey="Siltberg Liberles, Jessica" sort="Siltberg Liberles, Jessica" uniqKey="Siltberg Liberles J" first="Jessica" last="Siltberg-Liberles">Jessica Siltberg-Liberles</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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