Proteasomes are known to be the main suppliers of MHC class I (MHC-I) ligands. In an attempt to identify coxsackievirus B3 (CVB3)-MHC-I epitopes, a combined approach of in silico MHC-I/transporters associated with antigen processing (TAP)-binding and proteasomal cleavage prediction was applied. Accordingly, 13 potential epitopes originating from the structural and non-structural protein region of CVB3 were selected for further in vitro processing analysis by proteasomes. Mass spectrometry demonstrated the generation of seven of the 13 predicted MHC-I ligands or respective ligand precursors by proteasomes. Detailed processing analysis of three adjacent MHC-I ligands with partially overlapping sequences, i.e. VP2(273–281), VP2(284–292) and VP2(285–293), revealed the preferential generation predominantly of the VP2(285–293) epitope by immunoproteasomes due to altered cleavage site preferences. The VP2(285–293) peptide was identified to be a high affinity binder, rendering VP2(285–293) a likely candidate for CD8 T cell immunity in CVB3 infection. In conclusion, the concerted usage of different in silico prediction methods and in vitro epitope processing/presentation studies was supportive in the identification of CVB3 MHC-I epitopes.

中文翻译：

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蛋白酶体产生计算机预测的柯萨奇病毒B3感染的计算机预测的I类MHC表位

已知蛋白酶体是MHC I类（MHC-1）配体的主要供应商。为了鉴定柯萨奇病毒B3（CVB3）-MHC-1表位，使用了与抗原加工（TAP）结合和蛋白酶体切割预测相关的计算机MHC-1 /转运蛋白的组合方法。因此，选择了来自CVB3的结构和非结构蛋白区域的13个潜在表位用于蛋白酶体的进一步体外加工分析。质谱证明了蛋白酶体产生了13种预测的MHC-1配体或相应配体前体中的7种。对具有部分重叠序列的三个相邻MHC-1配体的详细加工分析，即VP2（273-281），VP2（284-292）和VP2（285-293），揭示了由于切割位点偏好的改变，免疫蛋白酶体优先产生了VP2（285-293）表位。VP2（285-293）肽被鉴定为高亲和力结合剂，使VP2（285-293）可能成为CVB3感染CD8 T细胞免疫的候选者。总之，不同计算机预测方法和体外表位加工/表现研究的协同使用为CVB3 MHC-1表位的鉴定提供了支持。