Regulation of LRRK2 dynamics and conformation states by small molecules.

Abstract

Mutations in LRRK2 is a risk factor for Parkinson's disease (PD), and the aberrant kinase activity is the main cause for pathological functions of LRRK2. Research have been focused on developing selective inhibitors for the LRRK2 kinase. However, we now know that in addition to the intrinsic kinase activity, the conformation of the LRRK2 protein plays important roles in regulate LRRK2 function. We have shown that the kinase domain serves as a central hub for inter-domain communication, and is the major driver for LRRK2 conformation transitions. In this study, we used GaMD simulations coupled with HDX-MS to analyze the dynamic changes and the inter-domain allosteric communications of C-terminal half of the LRRK2, LRRK2RCKW. Specifically, when the kinase domain is locked into a closed, active conformation or an open, inactive conformation by binding of the type I (MLi-2) and type II (Rebastinib) inhibitors, respectively. While both type I and type II inhibitor reduced the kinase activity effectively, they drive the LRRK2 in different conformation. Binding of MLi-2 stabilizes the kinase domain, and reduces the dynamic of LRRK2RCKW globally, thus stabilizes the compact domain orientations of LRRK2RCKW. In contrast, binding of Rebastinib resulted in a more dynamic kinase domain, which promoted the extended conformation of LRRK2RCKW. We also reveal the importance of the Dk-helix, which plays crucial roles in bridging the kinase and GTPase domain. The dynamic changes in the kinase domain that propagate through the DK-helix would lead to different conformations of the ROC domain, which potentially affect the GTPase activity, which is crucial for the cellular function of LRRK2.