Patronov Atanas, Dimitrov Ivan, Flower Darren R, Doytchinova Irini
School of Pharmacy, Medical University of Sofia, 2 Dunav st, Sofia 1000, Bulgaria.
BMC Struct Biol. 2012 Aug 5;12:20. doi: 10.1186/1472-6807-12-20.
HLA-DPs are class II MHC proteins mediating immune responses to many diseases. Peptides bind MHC class II proteins in the acidic environment within endosomes. Acidic pH markedly elevates association rate constants but dissociation rates are almost unchanged in the pH range 5.0 - 7.0. This pH-driven effect can be explained by the protonation/deprotonation states of Histidine, whose imidazole has a pK(a) of 6.0. At pH 5.0, imidazole ring is protonated, making Histidine positively charged and very hydrophilic, while at pH 7.0 imidazole is unprotonated, making Histidine less hydrophilic. We develop here a method to predict peptide binding to the four most frequent HLA-DP proteins: DP1, DP41, DP42 and DP5, using a molecular docking protocol. Dockings to virtual combinatorial peptide libraries were performed at pH 5.0 and pH 7.0.
The X-ray structure of the peptide--HLA-DP2 protein complex was used as a starting template to model by homology the structure of the four DP proteins. The resulting models were used to produce virtual combinatorial peptide libraries constructed using the single amino acid substitution (SAAS) principle. Peptides were docked into the DP binding site using AutoDock at pH 5.0 and pH 7.0. The resulting scores were normalized and used to generate Docking Score-based Quantitative Matrices (DS-QMs). The predictive ability of these QMs was tested using an external test set of 484 known DP binders. They were also compared to existing servers for DP binding prediction. The models derived at pH 5.0 predict better than those derived at pH 7.0 and showed significantly improved predictions for three of the four DP proteins, when compared to the existing servers. They are able to recognize 50% of the known binders in the top 5% of predicted peptides.
The higher predictive ability of DS-QMs derived at pH 5.0 may be rationalised by the additional hydrogen bond formed between the backbone carbonyl oxygen belonging to the peptide position before p1 (p-1) and the protonated ε-nitrogen of His79β. Additionally, protonated His residues are well accepted at most of the peptide binding core positions which is in a good agreement with the overall negatively charged peptide binding site of most MHC proteins.
HLA - DP是介导对多种疾病免疫反应的II类主要组织相容性复合体（MHC）蛋白。肽段在内体的酸性环境中与II类MHC蛋白结合。酸性pH值显著提高结合速率常数，但在5.0 - 7.0的pH范围内解离速率几乎不变。这种pH驱动效应可以用组氨酸的质子化/去质子化状态来解释，其咪唑的pK(a)为6.0。在pH 5.0时，咪唑环质子化，使组氨酸带正电且亲水性很强，而在pH 7.0时咪唑未质子化，使组氨酸亲水性降低。我们在此开发了一种使用分子对接协议预测肽段与四种最常见的HLA - DP蛋白（DP1、DP41、DP42和DP5）结合的方法。在pH 5.0和pH 7.0下对虚拟组合肽库进行对接。
肽 - HLA - DP2蛋白复合物的X射线结构被用作起始模板，通过同源性建模四种DP蛋白的结构。所得模型用于生成基于单氨基酸替换（SAAS）原理构建的虚拟组合肽库。使用AutoDock在pH 5.0和pH 7.0下将肽段对接至DP结合位点。对所得分数进行归一化处理，并用于生成基于对接分数的定量矩阵（DS - QM）。使用484个已知DP结合物的外部测试集测试这些QM的预测能力。还将它们与现有的用于DP结合预测的服务器进行比较。在pH 5.0下推导的模型比在pH 7.0下推导的模型预测效果更好，并且与现有服务器相比，对四种DP蛋白中的三种显示出显著改进的预测。它们能够在预测肽段的前5%中识别50%的已知结合物。
在pH 5.0下推导的DS - QM具有更高的预测能力，这可能是由于在p1（p - 1）之前的肽段位置的主链羰基氧与His79β的质子化ε - 氮之间形成了额外的氢键。此外，质子化的His残基在大多数肽结合核心位置都能很好地被接受，这与大多数MHC蛋白的整体带负电的肽结合位点非常一致。
