About: Mapping a Neutralizing Epitope on the SARS Coronavirus Spike Protein: Computational Prediction Based on Affinity-selected Peptides

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About: Mapping a Neutralizing Epitope on the SARS Coronavirus Spike Protein: Computational Prediction Based on Affinity-selected Peptides Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Mapping a Neutralizing Epitope on the SARS Coronavirus Spike Protein: Computational Prediction Based on Affinity-selected Peptides
Creator	Sui, Jianhua Gershoni, Jonathan Marasco, Wayne Matthews, Leslie Tarnovitski, Natalia
topic	covid:1c83c94fe6d2c6af6cb07d183cc5a53d925590e7#this
Source	Elsevier; Medline; PMC
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.
has issue date	2006-05-26(xsd:dateTime)
bibo:doi	10.1016/j.jmb.2006.03.008
bibo:pmid	16630634
has license	els-covid
sha1sum (hex)	1c83c94fe6d2c6af6cb07d183cc5a53d925590e7
schema:url	https://doi.org/10.1016/j.jmb.2006.03.008
resource representing a document's title	Mapping a Neutralizing Epitope on the SARS Coronavirus Spike Protein: Computational Prediction Based on Affinity-selected Peptides
has PubMed Central identifier	PMC7094247
has PubMed identifier	16630634
schema:publication	Journal of Molecular Biology
resource representing a document's body	covid:1c83c94fe6d2c6af6cb07d183cc5a53d925590e7#body_text
is http://vocab.deri.ie/void#inDataset of	proxy:http/ns.inria.fr/covid19/1c83c94fe6d2c6af6cb07d183cc5a53d925590e7
is schema:about of	named entity 'PEPTIDES' named entity 'protein' named entity 'epitopes' named entity 'phage display' named entity 'random' named entity 'peptides' named entity 'crystal structure' named entity 'Spike' named entity 'Computational' named entity 'SPIKE PROTEIN' named entity 'HIGHEST' named entity 'MODELS' named entity 'VIRUSES' named entity 'EPITOPES' named entity 'LINEAR' named entity 'PAIRS' named entity 'PERFORMED' named entity 'H5N1 VIRUS' named entity 'PEPTIDE LIBRARIES' named entity 'SARS' named entity 'TYPES' named entity 'PANELS' named entity 'RAPID' named entity 'NOVEL' named entity 'CONTAINING' named entity 'CONSTRAINED' named entity 'ANALYSIS' named entity 'TO IDENTIFY' named entity 'PREDICT' named entity 'MOTIF' named entity 'GREAT' named entity 'VACCINES' named entity 'LATER' named entity 'NEUTRALIZING ANTIBODY' named entity 'HOMOLOGOUS' named entity 'CYSTEINE' named entity 'DEFINED' named entity 'CRYSTAL STRUCTURE' named entity 'ISOLATED' named entity 'RANDOM' named entity 'PROTEIN ' named entity 'LOOPS' named entity 'STATISTICALLY SIGNIFICANT' named entity 'ALGORITHM' named entity 'AMINO ACID' named entity 'STUDY' named entity 'MODEL OF' named entity 'HIGHLY PATHOGENIC AVIAN INFLUENZA' named entity 'CORONAVIRUS' named entity 'MAPPING' named entity 'PREDICTION' named entity 'FUNCTIONS' named entity 'MONOCLONAL ANTIBODY' named entity 'PEPTIDES' named entity 'ITS' named entity 'SITES' named entity 'SCREENING' named entity 'RECEPTOR' named entity 'RAPIDLY' named entity 'APPARENT' named entity 'USING' named entity 'SEVERE ACUTE RESPIRATORY SYNDROME' named entity 'INDEPENDENT' named entity 'ABSENCE OF' named entity 'DISPLAY' named entity 'COMBINED' named entity 'RANKED' named entity 'POOLS' named entity 'CLUSTERS' named entity 'DIFFERENT' named entity 'THESE' named entity 'EPITOPE' named entity 'BASED' named entity 'AFFINITY' named entity 'COMPUTATIONAL'

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