Lai Jennifer I, Verma Deeptak, Bailey-Kellogg Chris, Ackerman Margaret E
Thayer School of Engineering, Dartmouth College, 14 Engineering Dr, Hanover NH, USA.
Department of Computer Science, Dartmouth College, 9 Maynard St, Hanover NH, USA.
Protein Eng Des Sel. 2018 Apr 1;31(4):121-133. doi: 10.1093/protein/gzy010.
Structure-based approaches to antigen design utilize insights from antibody (Ab):antigen interactions and a refined understanding of protective Ab responses to engineer novel antigens presenting epitopes with conformations relevant to eliciting or discovering protective humoral responses. For human immunodeficiency virus-1 (HIV-1), one model of protection is provided by broadly neutralizing Abs (bnAbs) against epitopes present in the closed prefusion trimeric conformation of HIV-1 envelope glycoprotein, such as the variable loops 1-2 (V1V2) apex. Here, computational design and directed evolution yielded a novel V1V2 sequence variant with potential utility for inclusion in an immunogen for eliciting bnAbs, or as an epitope probe for their detection. The computational design goal was to engineer a minimal single-chain antigen with three copies of the V1V2 loops to support maintenance of closed prefusion V1V2 trimeric conformation and presentation of bnAb epitopes. Via directed evolution of this computationally designed single-chain antigen, we isolated a V1V2 sequence variant that in monomeric form exhibited preferential recognition by quaternary-preferring and conformation-dependent mAbs. Structural context and transferability of this phenotype to V1V2 sequences from all strains of HIV-1 tested suggest a conformation-stabilizing effect. This example demonstrates the potential utility of computational design and directed evolution-based protein engineering strategies to develop minimal, conformation-stabilized epitope-specific antigens.
基于结构的抗原设计方法利用了抗体（Ab）与抗原相互作用的相关见解，以及对保护性Ab反应的深入理解，来设计新型抗原，这些抗原呈现出与引发或发现保护性体液反应相关构象的表位。对于人类免疫缺陷病毒1型（HIV-1），一种保护模型由针对HIV-1包膜糖蛋白封闭预融合三聚体构象中存在的表位的广泛中和抗体（bnAbs）提供，例如可变环1-2（V1V2）顶端。在此，通过计算设计和定向进化产生了一种新型V1V2序列变体，它有可能用于包含在免疫原中以引发bnAbs，或作为检测它们的表位探针。计算设计的目标是设计一种最小的单链抗原，其具有三个V1V2环拷贝，以支持维持封闭预融合V1V2三聚体构象并呈现bnAb表位。通过对这种通过计算设计的单链抗原进行定向进化，我们分离出一种V1V2序列变体，其单体形式表现出被优先识别四级结构且依赖构象的单克隆抗体的特性。这种表型的结构背景及其对所有测试的HIV-1毒株的V1V2序列的可转移性表明存在构象稳定作用。这个例子证明了基于计算设计和定向进化的蛋白质工程策略在开发最小的、构象稳定的表位特异性抗原方面的潜在效用。
