23andMe, Inc. Therapeutics, 349 Oyster Point Boulevard, South San Francisco, CA, 94080, USA.
Commun Biol. 2023 Aug 19;6(1):864. doi: 10.1038/s42003-023-05241-y.
VHHs or nanobodies are single antigen binding domains originating from camelid heavy-chain antibodies. They are used as diagnostic and research tools and in a variety of therapeutic molecules. Analyzing variable domain structures from llama and alpaca we found that VHHs can be classified into two large structural clusters based on their CDR-H3 conformation. Extended CDR-H3 loops protrude into the solvent, whereas kinked CDR-H3 loops fold back onto framework regions. Both major families have distinct properties in terms of their CDR-H3 secondary structure, how their CDR-H3 interacts with the framework region and how they bind to antigens. We show that the CDR-H3 conformation of VHHs correlates with the germline from which the antibodies are derived: IGHV3-3 derived antibodies almost exclusively adopt a kinked CDR-H3 conformation while the CDR-H3 adopts an extended structure in most IGHV3S53 derived antibodies. We do not observe any bias stemming from V(D)J recombination in llama immune repertoires, suggesting that the correlation is the result of selection processes during B-cell development. Our findings demonstrate a previously undescribed impact of germline usage on antigen interaction and contribute to a better understanding on how properties of the antibody framework shape the immune repertoire.
VHHs 或纳米抗体是源自骆驼重链抗体的单抗原结合结构域。它们被用作诊断和研究工具，以及各种治疗分子。分析来自美洲驼和羊驼的可变域结构，我们发现 VHHs 可以根据它们的 CDR-H3 构象分为两个大的结构簇。扩展的 CDR-H3 环突入溶剂中，而扭曲的 CDR-H3 环折叠回框架区域。这两个主要家族在 CDR-H3 二级结构、CDR-H3 与框架区域的相互作用方式以及与抗原的结合方式方面都具有不同的特性。我们表明，VHHs 的 CDR-H3 构象与抗体来源的胚系相关：源自 IGHV3-3 的抗体几乎完全采用扭曲的 CDR-H3 构象，而大多数源自 IGHV3S53 的抗体的 CDR-H3 则采用扩展结构。我们在美洲驼免疫库中没有观察到任何源自 V(D)J 重组的偏向性，这表明这种相关性是 B 细胞发育过程中选择的结果。我们的发现表明，胚系使用对抗原相互作用有以前未描述的影响，并有助于更好地理解抗体框架的特性如何塑造免疫库。
