Activation of Abl1 Kinase Explored Using Well-Tempered Metadynamics Simulations on an Essential Dynamics Sampled Path.

Well-tempered metadynamics (wT-metaD) simulations using path collective variables (CVs) have been successfully applied in recent years to explore conformational transitions in protein kinases and other biomolecular systems. While this methodology has the advantage of describing the transitions with a limited number of predefined path CVs, it requires as an input a reference path connecting the initial and target states of the system. It is desirable to automate the path generation using approaches that do not rely on the choice of geometric CVs to describe the transition of interest. To this end, we developed an approach that couples essential dynamics sampling with wT-metaD simulations. We used this newly developed procedure to explore the activation mechanism of Abl1 kinase and compute the associated free energy barriers. Through these simulations, we identified a three-step mechanism for the activation that involved two metastable intermediates that possessed a partially open activation loop and differed primarily in the "in" or "out" conformation of the aspartate residue of the DFG motif. One of these states is similar to a conformation that was detected in previous spectroscopic studies of Abl1 kinase, albeit its mechanistic role in the activation was hitherto not well understood. The present study establishes its intermediary role in the activation and predicts a rate-determining free energy barrier of 13.8 kcal/mol that is in good agreement with previous experimental and computational estimates. Overall, our study demonstrates the usability of essential dynamics sampling as a path CV in wT-metaD to conveniently study conformational transitions and accurately calculate the associated barriers.