University of Belgrade, Faculty of Mathematics, P.O.B. 550, Studentski trg 16, Belgrade, Serbia.
University of Belgrade, Institute of General and Physical Chemistry, Studentski trg 12/V, Belgrade, Serbia.
J Immunol Methods. 2014 Apr;406:83-103. doi: 10.1016/j.jim.2014.02.012. Epub 2014 Mar 12.
Highly disordered protein regions are prevalently hydrophilic, extremely sensitive to proteolysis in vitro, and are expected to be under-represented as T-cell epitopes. The aim of this research was to find out whether disorder and hydropathy prediction methods could help in understanding epitope processing and presentation. According to the pan-specific T-cell epitope predictors NetMHCpan and NetMHCIIpan and 9 publicly available disorder predictors, frequency of epitopes presented by human leukocyte antigens (HLA) class-I or -II was found to be more than 2.5 times higher in ordered than in disordered protein regions (depending on the disorder predictor). Both HLA class-I and HLA class-II binding epitopes are prevalently hydrophilic in disordered and prevalently hydrophobic in ordered protein regions, whereas epitopes recognized by HLA class-II alleles are more hydrophobic than those recognized by HLA class-I. As regards both classes of HLA molecules, high-affinity binding epitopes display more hydrophobicity than low affinity-binding epitopes (in both ordered and disordered regions). Epitopes belonging to disordered protein regions were not predicted to have poor affinity to HLA class-II molecules, as expected from disorder intrinsic proteolytic instability. The relation of epitope hydrophobicity and order/disorder location was also valid if alleles were grouped according to the HLA class-I and HLA class-II supertypes, except for the class-I supertype A3 in which the main part of recognized epitopes was prevalently hydrophilic. Regarding specific supertypes, the affinity of epitopes belonging to ordered regions varies only slightly (depending on the disorder predictor) compared to the affinity of epitopes in corresponding disordered regions. The distribution of epitopes in ordered and disordered protein regions has revealed that the curves of order-epitope distribution were convex-like while the curves of disorder-epitope distribution were concave-like. The percentage of prevalently hydrophobic epitopes increases with the enhancement of epitope promiscuity level and moving from disordered to ordered regions. These data suggests that reverse vaccinology, oriented towards promiscuous and high-affinity epitopes, is also oriented towards prevalently hydrophobic, ordered regions. The analysis of predicted and experimentally evaluated epitopes of cancer-testis antigen MAGE-A3 has confirmed that the majority of T-cell epitopes, particularly those that are promiscuous or naturally processed, was located in ordered and disorder/order boundary protein regions overlapping hydrophobic regions.
高度无序的蛋白质区域普遍具有亲水性，在体外极易被蛋白水解，因此预计作为 T 细胞表位的可能性较低。本研究旨在探讨无序和疏水性预测方法是否有助于理解表位加工和呈递。根据 pan-specific T 细胞表位预测器 NetMHCpan 和 NetMHCIIpan 以及 9 个公开的无序预测器，与无序蛋白区域相比，人类白细胞抗原 (HLA) Ⅰ类或Ⅱ类呈现的表位频率高出 2.5 倍以上（取决于无序预测器）。无序和有序蛋白区域中，HLA Ⅰ类和 HLA Ⅱ类结合表位普遍具有亲水性，而 HLA Ⅱ类结合表位比 HLA Ⅰ类结合表位更具疏水性。对于这两类 HLA 分子，高亲和力结合表位比低亲和力结合表位（无论是在有序还是无序区域）都具有更高的疏水性。正如预期的那样，无序蛋白区域的表位与 HLA Ⅱ类分子的亲和力预计不会很差，因为无序蛋白的固有蛋白水解不稳定性。如果根据 HLA Ⅰ类和 HLA Ⅱ类超型对等位基因进行分组，那么表位疏水性和有序/无序位置之间的关系仍然有效，除了 HLA Ⅰ类超型 A3，其中识别的表位主要是亲水性的。对于特定的超型，与相应无序区域的表位相比，有序区域的表位亲和力变化很小（取决于无序预测器）。有序和无序蛋白区域的表位分布表明，有序表位分布曲线呈凸形，而无序表位分布曲线呈凹形。亲水性表位的百分比随着表位混杂性水平的提高和从无序区域向有序区域的移动而增加。这些数据表明，以混杂性和高亲和力表位为导向的反向疫苗学也以亲水性为主，以有序区域为导向。对癌症睾丸抗原 MAGE-A3 的预测和实验评估表位的分析证实，大多数 T 细胞表位，特别是那些具有混杂性或自然加工的表位，位于有序和无序/有序边界蛋白区域，与疏水区重叠。
