Mutations in leucine-rich repeat kinase 2 (LRRK2) are recognized as the most frequent cause of Parkinson’s disease (PD). As a multidomain ROCO protein, LRRK2 is characterized by the presence of both a Ras-of-complex (ROC) GTPase domain and a kinase domain connected through the C-terminal of an ROC domain (COR). The bienzymatic ROC–COR–kinase catalytic triad indicated the potential role of GTPase domain in regulating kinase activity. However, as a functional GTPase, the detailed intrinsic regulation of the ROC activation cycle remains poorly understood. Here, combining extensive molecular dynamics simulations and Markov state models, we disclosed the dynamic structural rearrangement of ROC’s homodimer during nucleotide turnover. Our study revealed the coupling between dimerization extent and nucleotide-binding state, indicating a nucleotide-dependent dimerization-based activation scheme adopted by ROC GTPase. Furthermore, inspired by the well-known R1441C/G/H PD-relevant mutations within the ROC domain, we illuminated the potential allosteric molecular mechanism for its pathogenetic effects through enabling faster interconversion between inactive and active states, thus trapping ROC in a prolonged activated state, while the implicated allostery could provide further guidance for identification of regulatory allosteric pockets on the ROC complex. Our investigations illuminated the thermodynamics and kinetics of ROC homodimer during nucleotide-dependent activation for the first time and provided guidance for further exploiting ROC as therapeutic targets for controlling LRRK2 functionality in PD treatment.

中文翻译：

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马尔可夫状态模型和分子动力学模拟提供了对 LRRK2 ROC 域的基于核苷酸的二聚化激活的理解

富含亮氨酸重复激酶 2 (LRRK2) 的突变被认为是帕金森病 (PD) 的最常见原因。作为多域 ROCO 蛋白，LRRK2 的特征在于同时存在 Ras-of-complex (ROC) GTPase 域和通过 ROC 域 (COR) 的 C 端连接的激酶域。双酶促 ROC-COR-激酶催化三联体表明 GTPase 结构域在调节激酶活性中的潜在作用。然而，作为一种功能性 GTPase，对 ROC 激活周期的详细内在调节仍然知之甚少。在这里，结合广泛的分子动力学模拟和马尔可夫状态模型，我们揭示了核苷酸转换过程中 ROC 同源二聚体的动态结构重排。我们的研究揭示了二聚化程度与核苷酸结合状态之间的耦合，表示 ROC GTPase 采用的基于核苷酸的二聚化激活方案。此外，受 ROC 域内众所周知的 R1441C/G/H PD 相关突变的启发，我们通过实现非活动状态和活动状态之间的更快相互转换，阐明了其致病作用的潜在变构分子机制，从而将 ROC 捕获在延长的激活状态中。状态，而所涉及的变构可以为识别 ROC 复合体上的监管变构口袋提供进一步的指导。我们的研究首次阐明了在核苷酸依赖性激活过程中 ROC 同源二聚体的热力学和动力学，并为进一步利用 ROC 作为控制 PD 治疗中 LRRK2 功能的治疗靶点提供了指导。