Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification.
Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification.
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DOI：
10.3389/fimmu.2018.00413
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发表时间：
2018
影响因子：
7.3
通讯作者：
Gray JJ
中科院分区：
文献类型：
--
作者：
Jeliazkov JR;Sljoka A;Kuroda D;Tsuchimura N;Katoh N;Tsumoto K;Gray JJ
抗体可以针对抗原的特异性反应快速进化。亲和力成熟通过突变和选择循环驱动这种进化，从而增强抗体特异性和亲和力。阐明亲和力成熟背后的生物物理机制是理解 B 细胞免疫的基础。一个新的假设是，亲和力成熟降低了抗体抗原结合互补位的构象灵活性，以最大限度地减少结合时产生的熵损失。近年来，计算和实验方法已经在少量抗体上测试了这一假设，经常观察到通常包含互补位的互补决定区（CDR）环的灵活性下降，特别是贡献多个抗原接触的CDR-H3环。然而，也有一些例外，之前的研究仅限于少数案例。在这里，我们使用刚性理论确定了数千个最新的人外周血细胞抗体库同源模型的 CDR-H3 环的结构灵活性。我们发现天然抗体和抗原经历过的抗体的灵活性没有明确的界限。为了解释可能的错误来源，我们还通过刚性理论和 B 因子分析分析了蛋白质数据库中的数百种人类和小鼠抗体。通过这两个指标，当将亲和力成熟的抗体与初始抗体进行比较时，我们观察到 CDR-H3 环灵活性仅略有下降，并且下降幅度并不像之前报道的那么剧烈。结合分子动力学模拟的进一步分析揭示了灵活性的一系列变化。我们的结果表明，刚性化可能只是增加亲和力的众多生物物理机制之一。
Antibodies can rapidly evolve in specific response to antigens. Affinity maturation drives this evolution through cycles of mutation and selection leading to enhanced antibody specificity and affinity. Elucidating the biophysical mechanisms that underlie affinity maturation is fundamental to understanding B-cell immunity. An emergent hypothesis is that affinity maturation reduces the conformational flexibility of the antibody’s antigen-binding paratope to minimize entropic losses incurred upon binding. In recent years, computational and experimental approaches have tested this hypothesis on a small number of antibodies, often observing a decrease in the flexibility of the complementarity determining region (CDR) loops that typically comprise the paratope and in particular the CDR-H3 loop, which contributes a plurality of antigen contacts. However, there were a few exceptions and previous studies were limited to a small handful of cases. Here, we determined the structural flexibility of the CDR-H3 loop for thousands of recent homology models of the human peripheral blood cell antibody repertoire using rigidity theory. We found no clear delineation in the flexibility of naïve and antigen-experienced antibodies. To account for possible sources of error, we additionally analyzed hundreds of human and mouse antibodies in the Protein Data Bank through both rigidity theory and B-factor analysis. By both metrics, we observed only a slight decrease in the CDR-H3 loop flexibility when comparing affinity matured antibodies to naïve antibodies, and the decrease was not as drastic as previously reported. Further analysis, incorporating molecular dynamics simulations, revealed a spectrum of changes in flexibility. Our results suggest that rigidification may be just one of many biophysical mechanisms for increasing affinity.