Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America.
Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America.
PLoS Comput Biol. 2021 Jul 26;17(7):e1009168. doi: 10.1371/journal.pcbi.1009168. eCollection 2021 Jul.
In Arabidopsis thaliana, the Light-Oxygen-Voltage (LOV) domain containing protein ZEITLUPE (ZTL) integrates light quality, intensity, and duration into regulation of the circadian clock. Recent structural and biochemical studies of ZTL indicate that the protein diverges from other members of the LOV superfamily in its allosteric mechanism, and that the divergent allosteric mechanism hinges upon conservation of two signaling residues G46 and V48 that alter dynamic motions of a Gln residue implicated in signal transduction in all LOV proteins. Here, we delineate the allosteric mechanism of ZTL via an integrated computational approach that employs atomistic simulations of wild type and allosteric variants of ZTL in the functional dark and light states, together with Markov state and supervised machine learning classification models. This approach has unveiled key factors of the ZTL allosteric mechanisms, and identified specific interactions and residues implicated in functional allosteric changes. The final results reveal atomic level insights into allosteric mechanisms of ZTL function that operate via a non-trivial combination of population-shift and dynamics-driven allosteric pathways.
在拟南芥中，光氧电压（LOV）结构域蛋白 ZEITLUPE（ZTL）将光质、光强和光时整合到生物钟的调控中。最近对 ZTL 的结构和生化研究表明，该蛋白在别构机制上与 LOV 超家族的其他成员不同，而别构机制的分歧取决于两个信号残基 G46 和 V48 的保守性，这两个残基改变了所有 LOV 蛋白中参与信号转导的 Gln 残基的动态运动。在这里，我们通过整合计算方法来描绘 ZTL 的别构机制，该方法采用野生型和别构变体的原子模拟，在功能暗态和光态下，结合 Markov 状态和有监督的机器学习分类模型。这种方法揭示了 ZTL 别构机制的关键因素，并确定了在功能别构变化中涉及的特定相互作用和残基。最终结果揭示了 ZTL 功能的别构机制的原子水平见解，这些机制通过群体转移和动力学驱动的别构途径的非平凡组合起作用。
