Mapping a neutralizing epitope on the SARS coronavirus spike protein: computational prediction based on affinity-selected peptides.

Journal of Molecular Biology
Natalia TarnovitskiWayne A Marasco

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...Continue Reading

Citations

Aug 31, 2006·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Erez M BublilJonathan M Gershoni
May 23, 2007·BioDrugs : Clinical Immunotherapeutics, Biopharmaceuticals and Gene Therapy·Jonathan M GershoniYael Weiss
Nov 6, 2007·Bioinformatics·Itay MayroseTal Pupko
Mar 27, 2010·Journal of Biomedicine & Biotechnology·Jian HuangFeng-Biao Guo
Jan 20, 2011·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Jian HuangPing Dai
Oct 1, 2011·Interdisciplinary Sciences, Computational Life Sciences·Vicente M Reyes
Nov 19, 2013·FEBS Letters·Yael Weiss-Ottolenghi, Jonathan M Gershoni
Feb 9, 2010·Bioinformatics and Biology Insights·Surendra S Negi, Werner Braun
Jul 24, 2008·Archives of Dermatological Research·Limor NaharyItai Benhar
Nov 30, 2007·Bioinformatics·Claus LundegaardMorten Nielsen
Oct 22, 2015·Protein Engineering, Design & Selection : PEDS·Natalia T FreundJonathan M Gershoni
Jul 1, 2007·Expert Opinion on Drug Discovery·Sheng-He HuangAmbrose Jong
Oct 14, 2006·BMC Bioinformatics·Jian HuangMinoru Kanehisa
Mar 10, 2021·Current Microbiology·Taruna AnandBhupendra N Tripathi
May 5, 2011·Journal of Chemical Information and Modeling·Luis F PaciosAraceli Díaz-Perales

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Methods Mentioned

BETA
phage display
ELISA
X-ray

Software Mentioned

FlexProt
SurfRace
Mapitope
Spike
Windows XP
RasTop

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