Myristoyl's dual role in allosterically regulating and localizing Abl kinase

c-Abl kinase, a key signalling hub in many biological processes ranging from cell development to proliferation, is tightly regulated by two inhibitory Src homology domains. An N-terminal myristoyl-modification can bind to a hydrophobic pocket in the kinase C-lobe, which stabilizes the auto-inhibitory assembly. Activation is triggered by myristoyl release. We used molecular dynamics simulations to show how both myristoyl and the Src homology domains are required to impose the full inhibitory effect on the kinase domain, and reveal the allosteric transmission pathway at residue-level resolution. Importantly, we find myristoyl insertion into a membrane to thermodynamically compete with binding to c-Abl. Myristoyl thus not only localizes the protein to the cellular membrane, but membrane attachment at the same time enhances activation of c-Abl by stabilizing its pre-activated state. Our data put forward a model in which lipidation tightly couples kinase localization and regulation, a scheme that currently appears to be unique for this non-receptor tyrosine kinase.

Methods
Data was generated using Gromacs 2020 and 2018 and Plumed v2.5.2

Data was analyzed using Gromacs tools, Force Distribution Analysis (FDA) and ConAn

We performed extensive Molecular Dynamics simulations under equilibrium conditions to compare the dynamics of different protein models and enhanced sampling methods such as Metadynamics to study helix conformational changes and Umbrella Sampling for Free Energy calculations of unbinding events. We analyzed contacts between protein domains and deciphered allosteric networks by looking at the forces between residue pairs.