牛病毒性腹泻病毒NS3蛋白的生物信息学分析及多表位筛选

doi:10.16431/j.cnki.1671-7236.2019.12.003

Abstract

Abstract: This study was aimed to perform bioinformatics analysis and screening of T cell and B cell epitopes for bovine viral diarrhea virus (BVDV) NS3 protein.First,the amino acid sequence of the NS3 protein was found in GenBank database.The resulting sequence was analyzed for physicochemical properties using an Expasy ProtParam online server.Then TMHMM Server was used to analyze the transmembrane domain.The DNAStar software was used to predict the secondary structure of the NS3 protein.To more accurately predict the secondary structure of a protein,the SOPMA analysis software performed a second prediction.The Phyre2 online server was used to predict the tertiary structure of the NS3 protein,and Raswin software was used to identify the location of each element.Linear B cell epitopes of NS3 protein were analyzed by four predictive software (BCPREDS,ABCpred,BepiPred and SVMTriP),CD4⁺ T cell epitopes were predicted by NetMHCⅡpan,NetBoLApan and IEDB were used to predict CD8⁺ T cell epitopes.Finally,the results obtained were screened for T cell and B cell epitopes.The results showed that the NS3 protein consisted of 683 amino acids,the molecular weight was 75 ku,the theoretical pI value was 8.31,chemical formula was C₃₃₄₇H₅₃₄₆N₉₁₆O₁₀₀₉S₂₈,the instability coefficient was 35.93,the average value of hydrophilicity (GRAVY) was -0.267,it was indicated that NS3 was a stable and hydrophilic protein.The TMHMM results showed that the NS3 protein did not have a transmembrane domain.SOPMA results showed that in the secondary structure of NS3 protein,α-helix β-fold,β-turn and random coil accounted for about 30.75%,22.55%,8.35% and 38.35%,respectively.DNAStar software marked their respective position.Eight linear epitopes were screened using four different B cell prediction software:12-16,289-298,349-360,394-407,421-432,489-498,515-525 and 665-679 amino acids.Four T cell epitopes were screened using NetMHCⅡpan:248-262,315-320,400-414 and 482-496 amino acids.This study provided a theoretical basis for the screening of the dominant antigen of NS3 protein in BVDV.

Key words: bovine viral diarrhea virus (BVDV); NS3 protein; bioinformatics analysis; B cells; T cells; epitope screening

CLC Number:

S852.65⁺3

HE Jinke, YANG Yajun, DENG Xiaoyu, HE Yanhua, ZHANG Chao, MA Zhongchen, WANG Yong, CHEN Chuangfu. Bioinformatics Analysis and Multi-epitope Screening of NS3 Protein of Bovine Viral Diarrhea Virus[J]. China Animal Husbandry and Veterinary Medicine, 2019, 46(12): 3475-3485.

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Bioinformatics Analysis and Multi-epitope Screening of NS3 Protein of Bovine Viral Diarrhea Virus

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