Abstract
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.
Highlights
The rapidly ageing population has imposed challenging public health crises in dealing with age-associated neurodegenerative afflictions with effective treatments [1,2,3]
The simulation trajectories of both ROCs-GDP and ROCs-GTP were first featurized with inter-residue distances to describe the overall ROCs topology, and the resulting dynamics data were subjected to principal component analysis (PCA) from scikit-learn for dimensionality reduction to preserve the first two components (PC1 and PC2) with the greatest contribution to kinetic variance [43]
While a plethora of pathogenic mutations are found within the ROC domain, considerably less attention has been paid to understanding the importance of GTPase activity in regulating leucine-rich repeat kinase 2 (LRRK2) function, and we do not know anything regarding the regulation of the ROC GTPase cycle associated with activation [14]
Summary
The rapidly ageing population has imposed challenging public health crises in dealing with age-associated neurodegenerative afflictions with effective treatments [1,2,3]. As a functional GTPase, the detailed mode of action of ROC remains elusive, but studies on LRRK2 homologs from prokaryotes have suggested that LRRK2 ROC is likely to function as a G protein activated by nucleotide-dependent dimerization (GAD) [31], which relies mainly on spontaneous nucleotide turnover and dimerization for the regulation of the activation cycle [32,33] (Figure 1C) Under this circumstance, exploration of the conformational dynamics relevant to the dimerization and nucleotide turnover of LRRK2 ROC is of primary importance for further investigations into its contribution to the overall functional output of LRRK2 under both physiological and pathological conditions
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