Berretta F, Butler R H, Diaz G, Sanarico N, Arroyo J, Fraziano M, Aichinger G, Wucherpfennig K W, Colizzi V, Saltini C, Amicosante M
Department of Internal Medicine, University of Tor Vergata, Rome, Italy.
Tissue Antigens. 2003 Dec;62(6):459-71. doi: 10.1046/j.1399-0039.2003.00131.x.
The polymorphism at position beta69 of the human leukocyte antigen (HLA)-DP molecule has been associated with susceptibility to several immune disorders and alloreactivity. Using molecular modeling, we have predicted a detailed structure of the HLA-DP2 molecule (carrying Glubeta69) complexed with class II associated invariant chain derived peptide (CLIP) and compared it with the form carrying Lys at beta69 (HLA-DP2K69). Major changes between the two models were observed in the shape and charge distribution of pocket 4 and of the nearby pocket 6. Consequently, we analyzed in detail the peptide-binding specificities of both HLA-DP molecules expressed as recombinant proteins. We first determined that the minimum peptide-binding core of CLIP for both HLA-DP2 and DP2K69 is represented by nine aminoacids corresponding to the sequence 91-99 of invariant chain (Ii). We then assessed the peptide-binding specificities of the two pockets and determined the role of position beta69, using competition tests with the Ii-derived peptide CLIP and its mutated forms carrying all the aminoacidic substitutions in P4 and P6. Pocket 4 of HLA-DP2 showed high affinity for positively charged, aromatic, and polar residues, whereas aliphatic residues were disfavored. Pocket 4 of the DP2K69 variant showed a reduced aminoacid selectivity with aromatic residues most preferred. Pocket 6 of HLA-DP2 showed high affinity for aromatic residues, which was increased in DP2K69 and extended to arginine. Finally, we used the experimental data to determine the best molecular-modeling approach for assessing aminoacid selectivity of the two pockets. The results with best predictive value were obtained when single aminoacids were evaluated inside each single pocket, thus, reducing the influence of the overall peptide/ major histocompatibility complex interaction. In conclusion, the HLA-DPbeta69 polymorphism plays a fundamental role in the peptide-binding selectivity of HLA-DP. Furthermore, as this polymorphism is the main change in the pocket 4 area of HLA-DP, it could represent a supertype among HLA-DP molecules significantly contributing to the selection of epitopes presented in the context of this HLA isotype.
人类白细胞抗原（HLA）-DP分子β69位的多态性与多种免疫疾病易感性及同种异体反应性相关。通过分子建模，我们预测了与II类相关恒定链衍生肽（CLIP）复合的HLA-DP2分子（携带β69位的Glu）的详细结构，并将其与β69位携带Lys的形式（HLA-DP2K69）进行比较。在两个模型之间，观察到口袋4及附近口袋6的形状和电荷分布有重大变化。因此，我们详细分析了两种作为重组蛋白表达的HLA-DP分子的肽结合特异性。我们首先确定，对于HLA-DP2和DP2K69，CLIP的最小肽结合核心由对应于恒定链（Ii）序列91-99的九个氨基酸代表。然后，我们评估了两个口袋的肽结合特异性，并使用Ii衍生肽CLIP及其在P4和P6中携带所有氨基酸取代的突变形式进行竞争试验，确定了β69位的作用。HLA-DP2的口袋4对带正电荷、芳香族和极性残基表现出高亲和力，而脂肪族残基则不受青睐。DP2K69变体的口袋4显示出降低的氨基酸选择性，最偏好芳香族残基。HLA-DP2的口袋6对芳香族残基表现出高亲和力，在DP2K69中有所增加并扩展至精氨酸。最后，我们利用实验数据确定评估两个口袋氨基酸选择性的最佳分子建模方法。当在每个单个口袋内评估单个氨基酸时，获得了具有最佳预测价值的结果，从而减少了整体肽/主要组织相容性复合体相互作用的影响。总之，HLA-DPβ69多态性在HLA-DP的肽结合选择性中起基本作用。此外，由于这种多态性是HLA-DP口袋4区域的主要变化，它可能代表HLA-DP分子中的一个超型，对在该HLA同种型背景下呈递的表位选择有显著贡献。
