Prediction and Evolution of B Cell Epitopes of Surface Protein in SARS-CoV-2

Jerome R Lon; Yunmeng Bai; Bingxu Zhong; Fuqiang Cai; Hongli Du

Based on the PDB model and the multiple alignment result, we used the Consurf Server to analyze the conservation of amino acid sites of the epitopes online [27] . The conservation of epitopes on the surface protein of SARS-CoV-2 was analyzed by multiple alignment with MAFFT and Logo was drawn with Weblogo [28, 29] . The 3D structure of the S protein predicted by homology modeling. It is a trimer, the head contains RBD (receptor Binding Domain) [24] , the tail contains the basic elements required for the membrane fusion, the end of the tail is a transmembrane region and is embedded in the envelope of SARS-CoV-2. B. The 3D structure of the E protein predicted by homology modeling. It is a pentamer with ion channel activity [25] . Its head is short, the middle of the tail is a transmembrane region which help the E protein embed in the envelope of SARS-CoV-2. C. The Ramachandran plot analysis of the 3D structure of the S protein (without Gly and Pro). Most residues located in the red (core) regions, and few in the white regions. D. The Ramachandran plot analysis of the 3D structure of the E protein (without Gly and Pro). All of the residues located on the red(core) region. Table 1 The plot statistics of the Ramachandran plot Table 2 The composition and the antigenic index of the epitopes of SARS-CoV-2 Table 3A The conservation of the epitopes in SARS-CoV-2 Table 3B The conservation of the epitopes in human coronavirus Table 3C The The online software, ProtScale, was used to predict the hydrophilicity and hydrophobicity of the surface protein deeply. A. The S protein has a maximum score of hydrophobicity, 3.222 at the 7 th site, which revealed a strong hydrophobicity; a minimum score of hydrophobicity, -2.589 at the 679 th site, which revealed a strong author/funder. All rights reserved. No reuse allowed without permission.