Antigen processing in the class II MHC pathway depends on conventional proteolytic enzymes, potentially acting on antigens in native-like conformational states. CD4+ epitope dominance arises from a competition between antigen folding, proteolysis, and MHCII binding. Protease-sensitive sites, linear antibody epitopes, and CD4+ T-cell epitopes were mapped in the plague vaccine candidate F1-V to evaluate the various contributions to CD4+ epitope dominance. Using X-ray crystal structures, antigen processing likelihood (APL) predicts CD4+ epitopes with significant accuracy without considering peptide-MHCII binding affinity. The profiles of conformational flexibility derived from the X-ray crystal structures of the F1-V proteins, Caf1 and LcrV, were similar to the biochemical profiles of linear antibody epitope reactivity and protease-sensitivity, suggesting that the role of structure in proteolysis was captured by the analysis of the crystal structures. The patterns of CD4+ T-cell epitope dominance in C57BL/6, CBA, and BALB/c mice were compared to epitope predictions based on APL, peptide binding to MHCII proteins, or both. For a sample of 13 diverse antigens larger than 200 residues, accuracy of epitope prediction by the combination of APL and I-A^b-MHCII-peptide affinity approached 40%. When MHCII allele specificity is also diverse, such as in human immunity, prediction of dominant epitopes by APL alone approached 40%. Since dominant CD4+ epitopes tend to occur in conformationally stable antigen domains, crystal structures typically are available for analysis by APL; and thus, the requirement for a crystal structure is not a severe limitation.

中文翻译：

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通过抗原构象柔性和肽-MHCII结合亲和力的组合分析预测CD4 + T细胞表位

II类MHC途径中的抗原加工取决于常规的蛋白水解酶，可能以天然样构象状态作用于抗原。CD4 +表位的优势来自抗原折叠，蛋白水解和MHCII结合之间的竞争。将蛋白酶敏感位点，线性抗体表位和CD4 + T细胞表位绘制在瘟疫疫苗候选F1-V中，以评估对CD4 +表位优势的各种贡献。使用X射线晶体结构，抗原加工可能性（APL）可以非常准确地预测CD4 +表位，而无需考虑肽-MHCII结合亲和力。从F1-V蛋白Caf1和LcrV的X射线晶体结构得出的构象柔韧性曲线类似于线性抗体表位反应性和蛋白酶敏感性的生化曲线，这表明结构在蛋白水解中的作用是通过分析晶体结构来捕获的。将C57BL / 6，CBA和BALB / c小鼠的CD4 + T细胞表位优势模式与基于APL，与MHCII蛋白结合的肽或两者的表位预测进行了比较。对于13个大于200个残基的多种抗原的样本，通过APL和IA的组合预测表位的准确性^b -MHCII-肽亲和力接近40％。当MHCII等位基因特异性也不同时，例如在人类免疫中，仅APL对优势表位的预测就接近40％。由于主要的CD4 +表位倾向于出现在构象稳定的抗原结构域中，因此晶体结构通常可用于APL分析。因此，对晶体结构的要求不是严格的限制。