Bioinformatic analysis of non-VP1 capsid protein of coxsackievirus A6
Bioinformatic analysis of non-VP1 capsid protein of coxsackievirus A6
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柯萨奇病毒A6非VP1衣壳蛋白的生物信息学分析
DOI：
10.1007/s11596-016-1633-4
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发表时间：
2016-08-01
影响因子：
--
通讯作者：
Lin, Jun
中科院分区：
文献类型：
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作者：
Liu, Hong-bo;Yang, Guang-fei;Lin, Jun
利用生物信息学方法对柯萨奇病毒A 6型（CVA 6）的非VP 1衣壳蛋白（VP 2-VP 4）进行分析，预测其基本理化性质、结构/功能特征和线性B细胞表位。利用来自ExPASy Bioinformatics Resource Portal的在线工具SubLoc、TargetP和其他工具以及SWISS-MODEL（在线蛋白质结构建模服务器）来分析CVA 6的VP 2-VP 4蛋白的氨基酸（AA）序列。结果表明，CVA 6的VP蛋白均为亲水性蛋白，含有磷酸化和糖基化位点，不含信号肽序列和乙酰化位点。除VP 3外，其余蛋白均不具有跨膜螺旋结构和核定位信号序列。无规卷曲是衣壳蛋白二级结构的主要构象。Bepipred分析线性B细胞表位结果表明，VP蛋白的平均抗原指数（AI）均大于0，其中VP 4的AI明显高于VP 2和VP 3。VP蛋白均含有大量潜在的B细胞表位，有些表位位于病毒衣壳的内侧或被掩埋。我们成功地预测了VP蛋白的基本理化性质、结构/功能特征和线性B细胞表位，发现不同VP蛋白具有一些共同的特征，并且每个蛋白都有其独特的属性。这些发现将有助于我们了解CVA 6的致病性，并开发相关的疫苗和免疫诊断试剂。
This study bioinformatically analyzed the non-VP1 capsid proteins (VP2-VP4) of Coxasckievirus A6 (CVA6), with an attempt to predict their basic physicochemical properties, structural/functional features and linear B cell eiptopes. The online tools SubLoc, TargetP and the others from ExPASy Bioinformatics Resource Portal, and SWISS-MODEL (an online protein structure modeling server), were utilized to analyze the amino acid (AA) sequences of VP2-VP4 proteins of CVA6. Our results showed that the VP proteins of CVA6 were all of hydrophilic nature, contained phosphorylation and glycosylation sites and harbored no signal peptide sequences and acetylation sites. Except VP3, the other proteins did not have transmembrane helix structure and nuclear localization signal sequences. Random coils were the major conformation of the secondary structure of the capsid proteins. Analysis of the linear B cell epitopes by employing Bepipred showed that the average antigenic indices (AI) of individual VP proteins were all greater than 0 and the average AI of VP4 was substantially higher than that of VP2 and VP3. The VP proteins all contained a number of potential B cell epitopes and some eiptopes were located at the internal side of the viral capsid or were buried. We successfully predicted the fundamental physicochemical properties, structural/functional features and the linear B cell eiptopes and found that different VP proteins share some common features and each has its unique attributes. These findings will help us understand the pathogenicity of CVA6 and develop related vaccines and immunodiagnostic reagents.