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.Abbreviations: CDR: Complementary-determining region; Fv: Antibody variable fragment; PCCA: Perron cluster analysis; tICA: Time-lagged independent component analysis; VH: Heavy chain variable region; VL: Light chain variable region.

中文翻译：

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抗体CDR环在溶液中与X射线结构的规范簇形成整体。

在过去的十年中，抗体作为治疗剂的相关性已大大提高。因此，结构和功能表征，特别是互补决定区（CDR）的表征，对于具有独特结合特性的抗体的设计和工程化至关重要。各种研究集中于通过假设某些序列只能采用有限数量的构象，将CDR环分类为一小组主链构象，以促进抗体设计。在这里，我们提出了解决方案中的CDR环结构的动力学分类。结合分子动力学模拟和强大的实验结构信息，我们观察到所有CDR环的微距到毫秒级时标簇与其他优势溶液结构之间的构象转变，而与长度和序列组成无关。除了确定溶液中所有相关构象之外，我们的结果还表明，各种规范的簇中位数实际上属于同一动力学最小值。此外，我们重建了规范簇之间构象转变的动力学和概率，从而扩展了静态规范结构的模型以揭示溶液中的动态构象集合，这是抗体结构设计领域中的一种新范式。缩写：CDR：Complementary -确定区域；Fv：抗体可变片段；PCCA：Perron聚类分析；tICA：时滞独立成分分析；VH：重链可变区；VL：轻链可变区。