Mapping a neutralizing epitope on the SARS coronavirus spike protein: computational prediction based on affinity-selected peptides.
Identifieur interne : 003E24 ( Main/Exploration ); précédent : 003E23; suivant : 003E25Mapping a neutralizing epitope on the SARS coronavirus spike protein: computational prediction based on affinity-selected peptides.
Auteurs : Natalia Tarnovitski [Israël] ; Leslie J. Matthews ; Jianhua Sui ; Jonathan M. Gershoni ; Wayne A. MarascoSource :
- Journal of molecular biology [ 0022-2836 ] ; 2006.
Descripteurs français
- KwdFr :
- Algorithmes, Animaux, Anticorps monoclonaux (immunologie), Banque de peptides, Cartographie épitopique (), Conformation des protéines, Cristallographie aux rayons X, Données de séquences moléculaires, Glycoprotéine de spicule des coronavirus, Glycoprotéines membranaires (), Glycoprotéines membranaires (génétique), Glycoprotéines membranaires (immunologie), Humains, Modèles moléculaires, Peptides (), Peptides (génétique), Peptides (immunologie), Protéines de l'enveloppe virale (), Protéines de l'enveloppe virale (génétique), Protéines de l'enveloppe virale (immunologie), Séquence d'acides aminés, Tests de neutralisation, Virus du SRAS (), Virus du SRAS (génétique), Virus du SRAS (immunologie).
- MESH :
- génétique : Glycoprotéines membranaires, Peptides, Protéines de l'enveloppe virale, Virus du SRAS.
- immunologie : Anticorps monoclonaux, Glycoprotéines membranaires, Peptides, Protéines de l'enveloppe virale, Virus du SRAS.
- Algorithmes, Animaux, Banque de peptides, Cartographie épitopique, Conformation des protéines, Cristallographie aux rayons X, Données de séquences moléculaires, Glycoprotéine de spicule des coronavirus, Glycoprotéines membranaires, Humains, Modèles moléculaires, Peptides, Protéines de l'enveloppe virale, Séquence d'acides aminés, Tests de neutralisation, Virus du SRAS.
English descriptors
- KwdEn :
- Algorithms, Amino Acid Sequence, Animals, Antibodies, Monoclonal (immunology), Crystallography, X-Ray, Epitope Mapping (methods), Humans, Membrane Glycoproteins (chemistry), Membrane Glycoproteins (genetics), Membrane Glycoproteins (immunology), Models, Molecular, Molecular Sequence Data, Neutralization Tests, Peptide Library, Peptides (chemistry), Peptides (genetics), Peptides (immunology), Protein Conformation, SARS Virus (chemistry), SARS Virus (genetics), SARS Virus (immunology), Spike Glycoprotein, Coronavirus, Viral Envelope Proteins (chemistry), Viral Envelope Proteins (genetics), Viral Envelope Proteins (immunology).
- MESH :
- chemical , chemistry : Membrane Glycoproteins, Peptides, Viral Envelope Proteins.
- chemical , genetics : Membrane Glycoproteins, Peptides, Viral Envelope Proteins.
- chemical , immunology : Antibodies, Monoclonal, Membrane Glycoproteins, Peptides, Viral Envelope Proteins.
- chemistry : SARS Virus.
- genetics : SARS Virus.
- immunology : SARS Virus.
- methods : Epitope Mapping.
- Algorithms, Amino Acid Sequence, Animals, Crystallography, X-Ray, Humans, Models, Molecular, Molecular Sequence Data, Neutralization Tests, Peptide Library, Protein Conformation, Spike Glycoprotein, Coronavirus.
Abstract
Rapid elucidation of neutralizing antibody epitopes on emerging viral pathogens like severe acute respiratory syndrome (SARS) coronavirus (CoV) or highly pathogenic avian influenza H5N1 virus is of great importance for rational design of vaccines against these viruses. Here we combined screening of phage display random peptide libraries with a unique computer algorithm "Mapitope" to identify the discontinuous epitope of 80R, a potent neutralizing human anti-SARS monoclonal antibody against the spike protein. Using two different types of random peptide libraries which display cysteine-constrained loops or linear 13-15-mer peptides, independent panels containing 42 and 18 peptides were isolated, respectively. These peptides, which had no apparent homologous motif within or between the peptide pools and spike protein, were deconvoluted into amino acid pairs (AAPs) by Mapitope and the statistically significant pairs (SSPs) were defined. Mapitope analysis of the peptides was first performed on a theoretical model of the spike and later on the genuine crystal structure. Three clusters (A, B and C) were predicted on both structures with remarkable overlap. Cluster A ranked the highest in the algorithm in both models and coincided well with the sites of spike protein that are in contact with the receptor, consistent with the observation that 80R functions as a potent entry inhibitor. This study demonstrates that by using this novel strategy one can rapidly predict and identify a neutralizing antibody epitope, even in the absence of the crystal structure of its target protein.
DOI: 10.1016/j.jmb.2006.03.008
PubMed: 16630634
Affiliations:
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Le document en format XML
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Marasco</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="ISSN">0022-2836</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Animals</term><term>Antibodies, Monoclonal (immunology)</term><term>Crystallography, X-Ray</term><term>Epitope Mapping (methods)</term><term>Humans</term><term>Membrane Glycoproteins (chemistry)</term><term>Membrane Glycoproteins (genetics)</term><term>Membrane Glycoproteins (immunology)</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Neutralization Tests</term><term>Peptide Library</term><term>Peptides (chemistry)</term><term>Peptides (genetics)</term><term>Peptides (immunology)</term><term>Protein Conformation</term><term>SARS Virus (chemistry)</term><term>SARS Virus (genetics)</term><term>SARS Virus (immunology)</term><term>Spike Glycoprotein, Coronavirus</term><term>Viral Envelope Proteins (chemistry)</term><term>Viral Envelope Proteins (genetics)</term><term>Viral Envelope Proteins (immunology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Anticorps monoclonaux (immunologie)</term><term>Banque de peptides</term><term>Cartographie épitopique ()</term><term>Conformation des protéines</term><term>Cristallographie aux rayons X</term><term>Données de séquences moléculaires</term><term>Glycoprotéine de spicule des coronavirus</term><term>Glycoprotéines membranaires ()</term><term>Glycoprotéines membranaires (génétique)</term><term>Glycoprotéines membranaires (immunologie)</term><term>Humains</term><term>Modèles moléculaires</term><term>Peptides ()</term><term>Peptides (génétique)</term><term>Peptides (immunologie)</term><term>Protéines de l'enveloppe virale ()</term><term>Protéines de l'enveloppe virale (génétique)</term><term>Protéines de l'enveloppe virale (immunologie)</term><term>Séquence d'acides aminés</term><term>Tests de neutralisation</term><term>Virus du SRAS ()</term><term>Virus du SRAS (génétique)</term><term>Virus du SRAS (immunologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Membrane Glycoproteins</term><term>Peptides</term><term>Viral Envelope Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Membrane Glycoproteins</term><term>Peptides</term><term>Viral Envelope Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="immunology" xml:lang="en"><term>Antibodies, Monoclonal</term><term>Membrane Glycoproteins</term><term>Peptides</term><term>Viral Envelope Proteins</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Glycoprotéines membranaires</term><term>Peptides</term><term>Protéines de l'enveloppe virale</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Anticorps monoclonaux</term><term>Glycoprotéines membranaires</term><term>Peptides</term><term>Protéines de l'enveloppe virale</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Epitope Mapping</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Animals</term><term>Crystallography, X-Ray</term><term>Humans</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Neutralization Tests</term><term>Peptide Library</term><term>Protein Conformation</term><term>Spike Glycoprotein, Coronavirus</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Banque de peptides</term><term>Cartographie épitopique</term><term>Conformation des protéines</term><term>Cristallographie aux rayons X</term><term>Données de séquences moléculaires</term><term>Glycoprotéine de spicule des coronavirus</term><term>Glycoprotéines membranaires</term><term>Humains</term><term>Modèles moléculaires</term><term>Peptides</term><term>Protéines de l'enveloppe virale</term><term>Séquence d'acides aminés</term><term>Tests de neutralisation</term><term>Virus du SRAS</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Rapid elucidation of neutralizing antibody epitopes on emerging viral pathogens like severe acute respiratory syndrome (SARS) coronavirus (CoV) or highly pathogenic avian influenza H5N1 virus is of great importance for rational design of vaccines against these viruses. Here we combined screening of phage display random peptide libraries with a unique computer algorithm "Mapitope" to identify the discontinuous epitope of 80R, a potent neutralizing human anti-SARS monoclonal antibody against the spike protein. Using two different types of random peptide libraries which display cysteine-constrained loops or linear 13-15-mer peptides, independent panels containing 42 and 18 peptides were isolated, respectively. These peptides, which had no apparent homologous motif within or between the peptide pools and spike protein, were deconvoluted into amino acid pairs (AAPs) by Mapitope and the statistically significant pairs (SSPs) were defined. Mapitope analysis of the peptides was first performed on a theoretical model of the spike and later on the genuine crystal structure. Three clusters (A, B and C) were predicted on both structures with remarkable overlap. Cluster A ranked the highest in the algorithm in both models and coincided well with the sites of spike protein that are in contact with the receptor, consistent with the observation that 80R functions as a potent entry inhibitor. This study demonstrates that by using this novel strategy one can rapidly predict and identify a neutralizing antibody epitope, even in the absence of the crystal structure of its target protein.</div></front></TEI><affiliations><list><country><li>Israël</li></country></list><tree><noCountry><name sortKey="Gershoni, Jonathan M" sort="Gershoni, Jonathan M" uniqKey="Gershoni J" first="Jonathan M" last="Gershoni">Jonathan M. Gershoni</name><name sortKey="Marasco, Wayne A" sort="Marasco, Wayne A" uniqKey="Marasco W" first="Wayne A" last="Marasco">Wayne A. Marasco</name><name sortKey="Matthews, Leslie J" sort="Matthews, Leslie J" uniqKey="Matthews L" first="Leslie J" last="Matthews">Leslie J. Matthews</name><name sortKey="Sui, Jianhua" sort="Sui, Jianhua" uniqKey="Sui J" first="Jianhua" last="Sui">Jianhua Sui</name></noCountry><country name="Israël"><noRegion><name sortKey="Tarnovitski, Natalia" sort="Tarnovitski, Natalia" uniqKey="Tarnovitski N" first="Natalia" last="Tarnovitski">Natalia Tarnovitski</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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