Shake it off: Abl kinase regulatory domain dynamics explain conformational 1 changes upon activation 2

Abstract

Abstract

Abl kinase is a major molecular target for chronic myeloid leukemia therapy. Its activity is tightly controlled by a regulatory module composed of the SH3 and SH2 domains and the SH2–kinase linker. Although the assembled autoinhibited and extended active conformations have been structurally characterized, the molecular pathway connecting these states remains poorly understood. Simulations initiated from the endpoint structures failed to sample the complete transition, even when Gaussian accelerated molecular dynamics (GaMD) was employed to enhance conformational sampling. To overcome this limitation, we combined multiscale modeling with extensive molecular dynamics simulations and Markov state modeling to reconstruct the Abl disassembly pathway. The resulting kinetic landscape revealed two coupled conformational equilibria: a faster exchange between the canonical assembled state and an intermediate ensemble that captures the initial rotation of the regulatory module, and a slower transition toward the extended state, characterized by migration of the regulatory module atop the kinase domain N-lobe. The canonical assembled autoinhibited state is strongly favored, accounting for approximately 60% of the equilibrium population, while early disassembly disrupts the E98-K294 and SH3-inker interactions and promotes exposure of Y226 and Y70. By revealing how these phosphorylation-sensitive residues become accessible during the earliest stages of disassembly, our model provides a mechanistic framework for Abl activation and identifies regulatory interfaces as potential targets for allosteric stabilization of the autoinhibited state.