Profiling of Substrate Specificities of 3C-Like Proteases from Group 1, 2a, 2b, and 3 Coronaviruses
Identifieur interne : 002063 ( Main/Curation ); précédent : 002062; suivant : 002064Profiling of Substrate Specificities of 3C-Like Proteases from Group 1, 2a, 2b, and 3 Coronaviruses
Auteurs : Chi-Pang Chuck [République populaire de Chine] ; Hak-Fun Chow [République populaire de Chine] ; David Chi-Cheong Wan [République populaire de Chine] ; Kam-Bo Wong [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
- enzymologie : Coronavirus.
- génétique : Peptide hydrolases.
- métabolisme : Peptide hydrolases.
- Clonage moléculaire, Coronavirus, Données de séquences moléculaires, Modèles moléculaires, Spécificité du substrat.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Peptide Hydrolases.
- classification : Coronavirus.
- enzymology : Coronavirus.
- chemical , metabolism : Peptide Hydrolases.
- Cloning, Molecular, Models, Molecular, Molecular Sequence Data, Substrate Specificity.
Abstract
Coronaviruses (CoVs) can be classified into alphacoronavirus (group 1), betacoronavirus (group 2), and gammacoronavirus (group 3) based on diversity of the protein sequences. Their 3C-like protease (3CLpro), which catalyzes the proteolytic processing of the polyproteins for viral replication, is a potential target for anti-coronaviral infection.
Here, we profiled the substrate specificities of 3CLpro from human CoV NL63 (group 1), human CoV OC43 (group 2a), severe acute respiratory syndrome coronavirus (SARS-CoV) (group 2b) and infectious bronchitis virus (IBV) (group 3), by measuring their activity against a substrate library of 19×8 of variants with single substitutions at P5 to P3' positions. The results were correlated with structural properties like side chain volume, hydrophobicity, and secondary structure propensities of substituting residues. All 3CLpro prefer Gln at P1 position, Leu at P2 position, basic residues at P3 position, small hydrophobic residues at P4 position, and small residues at P1' and P2' positions. Despite 3CLpro from different groups of CoVs share many similarities in substrate specificities, differences in substrate specificities were observed at P4 positions, with IBV 3CLpro prefers P4-Pro and SARS-CoV 3CLpro prefers P4-Val. By combining the most favorable residues at P3 to P5 positions, we identified super-active substrate sequences ‘VARLQ↓SGF’ that can be cleaved efficiently by all 3CLpro with relative activity of 1.7 to 3.2, and ‘VPRLQ↓SGF’ that can be cleaved specifically by IBV 3CLpro with relative activity of 4.3.
The comprehensive substrate specificities of 3CLpro from each of the group 1, 2a, 2b, and 3 CoVs have been profiled in this study, which may provide insights into a rational design of broad-spectrum peptidomimetic inhibitors targeting the proteases.
Url:
DOI: 10.1371/journal.pone.0027228
PubMed: 22073294
PubMed Central: 3206940
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PMC:3206940Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Profiling of Substrate Specificities of 3C-Like Proteases from Group 1, 2a, 2b, and 3 Coronaviruses</title>
<author><name sortKey="Chuck, Chi Pang" sort="Chuck, Chi Pang" uniqKey="Chuck C" first="Chi-Pang" last="Chuck">Chi-Pang Chuck</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China</addr-line>
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<country xml:lang="fr">République populaire de Chine</country>
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<orgName type="university">Université chinoise de Hong Kong</orgName>
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<author><name sortKey="Chow, Hak Fun" sort="Chow, Hak Fun" uniqKey="Chow H" first="Hak-Fun" last="Chow">Hak-Fun Chow</name>
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<term>Coronavirus (classification)</term>
<term>Coronavirus (enzymology)</term>
<term>Models, Molecular</term>
<term>Molecular Sequence Data</term>
<term>Peptide Hydrolases (genetics)</term>
<term>Peptide Hydrolases (metabolism)</term>
<term>Substrate Specificity</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Clonage moléculaire</term>
<term>Coronavirus ()</term>
<term>Coronavirus (enzymologie)</term>
<term>Données de séquences moléculaires</term>
<term>Modèles moléculaires</term>
<term>Peptide hydrolases (génétique)</term>
<term>Peptide hydrolases (métabolisme)</term>
<term>Spécificité du substrat</term>
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<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Coronavirus</term>
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<keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Coronavirus</term>
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<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Peptide hydrolases</term>
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<keywords scheme="MESH" xml:lang="en"><term>Cloning, Molecular</term>
<term>Models, Molecular</term>
<term>Molecular Sequence Data</term>
<term>Substrate Specificity</term>
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<term>Coronavirus</term>
<term>Données de séquences moléculaires</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Coronaviruses (CoVs) can be classified into alphacoronavirus (group 1), betacoronavirus (group 2), and gammacoronavirus (group 3) based on diversity of the protein sequences. Their 3C-like protease (3CL<sup>pro</sup>
), which catalyzes the proteolytic processing of the polyproteins for viral replication, is a potential target for anti-coronaviral infection.</p>
</sec>
<sec><title>Methodology/Principal Findings</title>
<p>Here, we profiled the substrate specificities of 3CL<sup>pro</sup>
from human CoV NL63 (group 1), human CoV OC43 (group 2a), severe acute respiratory syndrome coronavirus (SARS-CoV) (group 2b) and infectious bronchitis virus (IBV) (group 3), by measuring their activity against a substrate library of 19×8 of variants with single substitutions at P5 to P3' positions. The results were correlated with structural properties like side chain volume, hydrophobicity, and secondary structure propensities of substituting residues. All 3CL<sup>pro</sup>
prefer Gln at P1 position, Leu at P2 position, basic residues at P3 position, small hydrophobic residues at P4 position, and small residues at P1' and P2' positions. Despite 3CL<sup>pro</sup>
from different groups of CoVs share many similarities in substrate specificities, differences in substrate specificities were observed at P4 positions, with IBV 3CL<sup>pro</sup>
prefers P4-Pro and SARS-CoV 3CL<sup>pro</sup>
prefers P4-Val. By combining the most favorable residues at P3 to P5 positions, we identified super-active substrate sequences ‘VARLQ↓SGF’ that can be cleaved efficiently by all 3CL<sup>pro</sup>
with relative activity of 1.7 to 3.2, and ‘VPRLQ↓SGF’ that can be cleaved specifically by IBV 3CL<sup>pro</sup>
with relative activity of 4.3.</p>
</sec>
<sec><title>Conclusions/Significance</title>
<p>The comprehensive substrate specificities of 3CL<sup>pro</sup>
from each of the group 1, 2a, 2b, and 3 CoVs have been profiled in this study, which may provide insights into a rational design of broad-spectrum peptidomimetic inhibitors targeting the proteases.</p>
</sec>
</div>
</front>
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