Institute for Research in Biomedicine, Via Vela 6, 6500 Bellinzona, Switzerland.
J Mol Biol. 2010 Mar 12;396(5):1491-507. doi: 10.1016/j.jmb.2009.12.053. Epub 2010 Jan 4.
If we understand the structural rules governing antibody (Ab)-antigen (Ag) interactions in a given virus, then we have the molecular basis to attempt to design and synthesize new epitopes to be used as vaccines or optimize the antibodies themselves for passive immunization. Comparing the binding of several different antibodies to related Ags should also further our understanding of general principles of recognition. To obtain and compare the three-dimensional structure of a large number of different complexes, however, we need a faster method than traditional experimental techniques. While biocomputational docking is fast, its results might not be accurate. Combining experimental validation with computational prediction may be a solution. As a proof of concept, here we isolated a monoclonal Ab from the blood of a human donor recovered from dengue virus infection, characterized its immunological properties, and identified its epitope on domain III of dengue virus E protein through simple and rapid NMR chemical shift mapping experiments. We then obtained the three-dimensional structure of the Ab/Ag complex by computational docking, using the NMR data to drive and validate the results. In an attempt to represent the multiple conformations available to flexible Ab loops, we docked several different starting models and present the result as an ensemble of models equally agreeing with the experimental data. The Ab was shown to bind a region accessible only in part on the viral surface, explaining why it cannot effectively neutralize the virus.
如果我们了解给定病毒中抗体（Ab）-抗原（Ag）相互作用的结构规则，那么我们就有了分子基础，可以尝试设计和合成新的表位，用作疫苗，或者优化自身抗体用于被动免疫。比较几种不同抗体与相关 Ag 的结合情况，也应该进一步加深我们对识别一般原理的理解。然而，为了获得和比较大量不同复合物的三维结构，我们需要一种比传统实验技术更快的方法。虽然生物计算对接速度很快，但结果可能不够准确。将实验验证与计算预测相结合可能是一种解决方案。作为概念验证，我们从从登革热病毒感染中恢复的人类供体血液中分离出一种单克隆抗体，对其免疫学特性进行了表征，并通过简单快速的 NMR 化学位移映射实验鉴定了其在登革病毒 E 蛋白结构域 III 上的表位。然后，我们通过计算对接获得了 Ab/Ag 复合物的三维结构，利用 NMR 数据来驱动和验证结果。为了表示柔性 Ab 环的多种构象，我们对接了几个不同的起始模型，并将结果表示为与实验数据一致的模型集合。该抗体被证明能结合病毒表面部分暴露的区域，这解释了为什么它不能有效地中和病毒。
