Wu Di, Sun Jing, Xu Tianlei, Wang Shuning, Li Guoqing, Li Yixue, Cao Zhiwei
Department of Biomedical Engineering, College Life Science and Technology, Tongji University, Shanghai, 200092, China.
Immunome Res. 2010 Sep 27;6 Suppl 1(Suppl 1):S1. doi: 10.1186/1745-7580-6-S1-S1.
The enrichment and importance of some aromatic residues, such as Tyr and Trp, have been widely noticed at the binding interfaces of antibodies from many experimental and statistical results, some of which were even identified as "hot spots" contributing significantly greater to the binding affinity than other amino acids. However, how these aromatic residues influence the immune binding still deserves further investigation. A large-scale examination was done regarding the local spatial environment around the interfacial Tyr or Trp residues. Energetic contribution of these Tyr and Trp residues to the binding affinity was then studied regarding 82 representative antibody interfaces covering 509 immune complexes from the PDB database and IMGT/3Dstructure-DB.
The connectivity analysis of interfacial residues showed that Tyr and Trp tended to cluster into the spatial Aromatic Islands (AI) rather than being distributed randomly at the antibody interfaces. Out of 82 antibody-antigen complexes, 72% (59) interfaces were found to contain AI with more than 3 aromatic residues. The statistical test against an empirical distribution indicated that the existence of AI was significant in about 60% representative antibody interfaces. Secondly, the loss of solvent accessible surface area (SASA) for side chains of aromatic residues between actually crowded state and independent state was nicely correlated with the AI size increasing in a linearly positive way which indicated that the aromatic side chains in AI tended to take a compact and ordered stacking conformation at the interfaces. Interestingly, the SASA loss of AI was also correlated roughly with the averaged gap of binding free energy between the theoretical and experimental data for immune complexes.
The results of our study revealed the wide existence and statistical significance of "Aromatic Island" (AI) composed of the spatially clustered Tyr and Trp residues at the antibody interfaces. The regular arrangement and stacking of aromatic side chains in AI could probably produce extra cooperative effects to the binding affinity which was firstly observed through the large-scale data analysis. The finding in this work not only provides insights into the functional role of aromatic residues in the antibody-antigen interaction, but also may facilitate the antibody engineering and potential clinical applications.
从许多实验和统计结果来看，一些芳香族残基，如酪氨酸（Tyr）和色氨酸（Trp）在抗体结合界面的富集及其重要性已受到广泛关注，其中一些甚至被确定为“热点”，对结合亲和力的贡献比其他氨基酸显著更大。然而，这些芳香族残基如何影响免疫结合仍值得进一步研究。我们针对界面酪氨酸或色氨酸残基周围的局部空间环境进行了大规模检测。随后，结合来自蛋白质数据库（PDB）和国际免疫基因组数据库（IMGT）/3D结构数据库中涵盖509个免疫复合物的82个代表性抗体界面，研究了这些酪氨酸和色氨酸残基对结合亲和力的能量贡献。
界面残基的连通性分析表明，酪氨酸和色氨酸倾向于聚集成空间芳香岛（AI），而非随机分布在抗体界面。在82个抗体 - 抗原复合物中，发现72%（59个）界面含有超过3个芳香族残基的芳香岛。针对经验分布的统计检验表明，芳香岛的存在在约60%的代表性抗体界面中具有显著性。其次，芳香族残基侧链在实际拥挤状态和独立状态之间的可及溶剂表面积（SASA）损失与芳香岛大小呈线性正相关增加，这表明芳香岛中的芳香族侧链在界面处倾向于采取紧凑且有序的堆积构象。有趣的是，芳香岛的SASA损失也大致与免疫复合物理论和实验数据之间结合自由能的平均差距相关。
我们的研究结果揭示了由空间聚集的酪氨酸和色氨酸残基组成的“芳香岛”（AI）在抗体界面广泛存在且具有统计学意义。芳香岛中芳香族侧链的规则排列和堆积可能对结合亲和力产生额外的协同效应，这是首次通过大规模数据分析观察到的。本研究中的发现不仅为芳香族残基在抗体 - 抗原相互作用中的功能作用提供了见解，还可能促进抗体工程及潜在的临床应用。
