Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, New York, USA.
Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
J Virol. 2018 Aug 29;92(18). doi: 10.1128/JVI.00641-18. Print 2018 Sep 15.
Elucidating the structural basis of antibody (Ab) gene usage and affinity maturation of vaccine-induced Abs can inform the design of immunogens for inducing desired Ab responses in HIV vaccine development. Analyses of monoclonal Abs (MAbs) encoded by the same immunoglobulin genes at different stages of maturation can help to elucidate the maturation process. We have analyzed four human anti-V3 MAbs with the same VH1-301 and VL3-1001 gene usage. Two MAbs, TA6 and TA7, were developed from a vaccinee in the HIV vaccine phase I trial DP6-001 with a polyvalent DNA prime/protein boost regimen, and two others, 311-11D and 1334, were developed from HIV-infected patients. The somatic hypermutation (SHM) rates in VH of vaccine-induced MAbs are lower than in chronic HIV infection-induced MAbs, while those in VL are comparable. Crystal structures of the antigen-binding fragments (Fabs) in complex with V3 peptides show that these MAbs bind the V3 epitope with a new cradle-binding mode and that the V3 β-hairpin lies along the antigen-binding groove, which consists of residues from both heavy and light chains. Residues conserved from the germ line sequences form specific binding pockets accommodating conserved structural elements of the V3 crown hairpin, predetermining the Ab gene selection, while somatically mutated residues create additional hydrogen bonds, electrostatic interactions, and van der Waals contacts, correlating with an increased binding affinity. Our data provide a unique example of germ line sequences determining the primordial antigen-binding sites and SHMs correlating with affinity maturation of Abs induced by vaccine and natural HIV infection. Understanding the structural basis of gene usage and affinity maturation for anti-HIV-1 antibodies may help vaccine design and development. Antibodies targeting the highly immunogenic third variable loop (V3) of HIV-1 gp120 provide a unique opportunity for detailed structural investigations. By comparing the sequences and structures of four anti-V3 MAbs at different stages of affinity maturation but of the same V gene usage, two induced by vaccination and another two by chronic infection, we provide a fine example of how germ line sequence determines the essential elements for epitope recognition and how affinity maturation improves the antibody's recognition of its epitope.
阐明抗体（Ab）基因使用和疫苗诱导 Ab 亲和力成熟的结构基础，可以为 HIV 疫苗开发中诱导所需 Ab 反应的免疫原设计提供信息。分析在成熟的不同阶段由相同免疫球蛋白基因编码的单克隆抗体（MAb）有助于阐明成熟过程。我们分析了具有相同 VH1-301 和 VL3-1001 基因使用的四种人抗 V3 MAb。两种 MAb，TA6 和 TA7，是从 DP6-001 HIV 疫苗 I 期试验中的疫苗接种者中开发的，采用多价 DNA 初免/蛋白加强方案，另外两种，311-11D 和 1334，是从 HIV 感染者中开发的。疫苗诱导的 MAb 中 VH 的体细胞超突变（SHM）率低于慢性 HIV 感染诱导的 MAb，而 VL 中的则相当。与 V3 肽复合物的抗原结合片段（Fab）的晶体结构表明，这些 MAb 以一种新的摇篮结合模式结合 V3 表位，V3 β-发夹沿着由重链和轻链的残基组成的抗原结合槽排列。从种系序列保守的残基形成容纳 V3 冠发夹保守结构元件的特定结合口袋，预先确定 Ab 基因选择，而体细胞突变残基则产生额外的氢键、静电相互作用和范德华接触，与结合亲和力增加相关。我们的数据提供了一个独特的例子，即种系序列决定原始抗原结合位点，并且 SHM 与疫苗和自然 HIV 感染诱导的 Ab 亲和力成熟相关。了解抗 HIV-1 抗体的基因使用和亲和力成熟的结构基础可能有助于疫苗设计和开发。针对 HIV-1 gp120 的高度免疫原性第三可变环（V3）的抗体提供了详细结构研究的独特机会。通过比较处于不同亲和力成熟阶段但具有相同 V 基因使用的四种抗 V3 MAb 的序列和结构，两种由疫苗诱导，另两种由慢性感染诱导，我们提供了一个很好的例子，说明种系序列如何决定表位识别的基本要素，以及亲和力成熟如何提高抗体对其表位的识别。
