Department of Immunology, School of Medicine, Complutense University of Madrid, Madrid, Spain.
Methods Mol Biol. 2020;2131:399-406. doi: 10.1007/978-1-0716-0389-5_23.
The proteasome complex is mainly responsible for proteolytic degradation of cytosolic proteins, generating the C-terminus of MHC I-restricted peptide ligands and CD8 T cell epitopes. Therefore, prediction of proteasomal cleavage sites is relevant for anticipating CD8 T-cell epitopes. There are two different proteasomes, the constitutive proteasome, expressed in all types of cells, and the immunoproteasome, constitutively expressed in dendritic cells. Although both proteasome forms generate peptides for presentation by MHC I molecules, the immunoproteasome is the main form involved in providing peptide fragments for priming CD8 T cells. On the contrary, the proteasome provides peptides for presentation by MHC I molecules that can be targeted by already primed CD8 T cells. Proteasome cleavage prediction server (PCPS) is a server for predicting cleavage sites generated by both the constitutive proteasome and the immunoproteasome. Here, we illustrate the usage of PCPS to predict proteasome and immunoproteasome cleavage sites and compare the results with those provided by NetChop, a related tool available online. PCPS is implemented for free public use available online at http://imed.med.ucm.es/Tools/pcps/ .
蛋白酶体复合物主要负责细胞溶质蛋白的蛋白水解降解，产生 MHC I 限制性肽配体和 CD8 T 细胞表位的 C 末端。因此，蛋白酶体切割位点的预测对于预测 CD8 T 细胞表位是相关的。有两种不同的蛋白酶体，即组成型蛋白酶体，在所有类型的细胞中表达，和免疫蛋白酶体，在树突状细胞中组成型表达。尽管两种蛋白酶体形式都产生用于 MHC I 分子呈递的肽，但免疫蛋白酶体是主要参与提供用于启动 CD8 T 细胞的肽片段的形式。相反，蛋白酶体提供用于由已经启动的 CD8 T 细胞靶向的 MHC I 分子呈递的肽。蛋白酶体切割预测服务器（PCPS）是一个用于预测由组成型蛋白酶体和免疫蛋白酶体产生的切割位点的服务器。在这里，我们说明使用 PCPS 来预测蛋白酶体和免疫蛋白酶体切割位点，并将结果与在线提供的相关工具 NetChop 的结果进行比较。PCPS 是免费的公共使用的，可在线获得，网址为 http://imed.med.ucm.es/Tools/pcps/ 。
