Mutations in the leucine-rich repeat kinase 2 gene (LRRK2) have been associated with late-onset Parkinson's disease. The most common and well-studied LRRK2 mutation, G2019S, is in the activation loop of the kinase domain. In this study, we explore the effect of the G2019S mutation on the dynamics and free energy surface of LRRK2 kinase using a combination of homology modeling and metadynamics simulations. Our results suggest that the G2019S mutation results in stabilization of the DYG-in conformation and an energetic increase in the barrier that separates the active (DYG-in) and inactive (DYG-out) conformation. Two key factors contributing to this barrier include the reduction of the conformational space accessible to the loop due to G2019S mutation and hydrogen bonding of the S2019 side chain in the DYG-in state.  We propose that the mutant kinase, once activated, may not be able to switch to an inactive form (DYG-out) as readily as the wild type, thereby making the mutant enzyme appear more active. This is consistent with the biochemical literature and has implications in disease, as an overactive mutant enzyme that has difficulty accessing the inactive state may cause unregulated phosphorylation of LRRK2 substrates, eventually leading to autosomal dominant form of Parkinson's disease. We experimentally validate this hypothesis by testing new compounds and show that the experimental binding affinities are consistent with this hypothesis.

Metadynamics approach to understand the free energy surface of the kinase activation loop transition in Parkinson's disease mutation G2019S in LRRK2

243rd National Meeting (2012)

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