Antibodies have the ability to bind various types of antigens and to recognize different antibody-binding sites (epitopes) of the same antigen with different binding affinities. Due to the conserved structural framework of antibodies, their specificity to antigens is mainly determined by their antigen-binding site (paratope). Therefore, characterization of epitopes in combination with describing the involved conformational changes of the paratope upon binding is crucial in understanding and predicting antibody-antigen binding. Using molecular dynamics simulations complemented with strong experimental structural information, we investigated the underlying binding mechanism and the resulting local and global surface plasticity in the binding interfaces of distinct antibody-antigen complexes. In all studied allergen-antibody complexes, we clearly observe that experimentally suggested epitopes reveal less plasticity, while non-epitope regions show high surface plasticity. Surprisingly, the paratope shows higher conformational diversity reflected in substantially higher surface plasticity, compared to the epitope. This work allows a visualization and characterization of antibody-antigen interfaces and might have strong implications for antibody-antigen docking and in the area of epitope prediction.

中文翻译：

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过敏原-抗体复合物的构象选择-互补位和表位的表面可塑性。


抗体能够结合各种类型的抗原，并以不同的结合亲和力识别同一抗原的不同抗体结合位点（表位）。由于抗体的结构框架保守，其对抗原的特异性主要由其抗原结合位点（互补位）决定。因此，表位的表征以及结合时互补位所涉及的构象变化的描述对于理解和预测抗体-抗原结合至关重要。利用分子动力学模拟并辅以强大的实验结构信息，我们研究了不同抗体-抗原复合物结合界面中潜在的结合机制以及由此产生的局部和全局表面可塑性。在所有研究的过敏原-抗体复合物中，我们清楚地观察到实验表明的表位显示出较低的可塑性，而非表位区域则显示出较高的表面可塑性。令人惊讶的是，与表位相比，互补位显示出更高的构象多样性，这反映在显着更高的表面可塑性上。这项工作可以实现抗体-抗原界面的可视化和表征，并且可能对抗体-抗原对接和表位预测领域产生重大影响。