Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria.
MAbs. 2020 Jan-Dec;12(1):1744328. doi: 10.1080/19420862.2020.1744328.
In the past decade, the relevance of antibodies as therapeutics has increased substantially. Therefore, structural and functional characterization, in particular of the complementarity-determining regions (CDRs), is crucial to the design and engineering of antibodies with unique binding properties. Various studies have focused on classifying the CDR loops into a small set of main-chain conformations to facilitate antibody design by assuming that certain sequences can only adopt a limited number of conformations. Here, we present a kinetic classification of CDR loop structures as ensembles in solution. Using molecular dynamics simulations in combination with strong experimental structural information, we observe conformational transitions between canonical clusters and additional dominant solution structures in the micro-to-millisecond timescale for all CDR loops, independent of length and sequence composition. Besides identifying all relevant conformations in solution, our results revealed that various canonical cluster medians actually belong to the same kinetic minimum. Additionally, we reconstruct the kinetics and probabilities of the conformational transitions between canonical clusters, and thereby extend the model of static canonical structures to reveal a dynamic conformational ensemble in solution as a new paradigm in the field of antibody structure design. CDR: Complementary-determining region; Fv: Antibody variable fragment; PCCA: Perron cluster analysis; tICA: Time-lagged independent component analysis; V: Heavy chain variable region; V: Light chain variable region.
在过去的十年中，抗体作为治疗药物的相关性大大增加。因此，结构和功能的表征，特别是互补决定区（CDR）的结构和功能的表征，对于设计和工程具有独特结合特性的抗体至关重要。各种研究都集中在将 CDR 环分类为一小部分主链构象上，以通过假设某些序列只能采用有限数量的构象来促进抗体设计。在这里，我们提出了一种 CDR 环结构的动力学分类方法，将其作为溶液中的集合。我们使用分子动力学模拟结合强实验结构信息，观察到所有 CDR 环在微秒到毫秒时间尺度上从典型簇到额外主导溶液结构的构象转变，而与长度和序列组成无关。除了识别溶液中所有相关的构象外，我们的结果还表明，各种典型簇中位数实际上属于相同的动力学最小值。此外，我们还重建了典型簇之间构象转变的动力学和概率，从而将静态典型结构模型扩展到揭示溶液中动态构象集合，这是抗体结构设计领域的一个新范例。CDR：互补决定区；Fv：抗体可变片段；PCCA：Perron 聚类分析；tICA：时滞独立成分分析；V：重链可变区；V：轻链可变区。
