A conserved protonation-dependent switch controls drug binding in the Abl kinase

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Protein kinases undergo conformational changes, including the DFG flip, switching between active and inactive states.
• Many kinase inhibitors, such as imatinib, target specific DFG conformations, but the flip's mechanism remains elusive.

Purpose of the Study:

• To elucidate the atomic-level mechanism and functional significance of the DFG flip in Abl kinase.
• To develop an energetic model predicting the factors controlling the DFG flip.

Main Methods:

• Long molecular dynamics simulations of Abl kinase to visualize the DFG flip.
• Experimental validation of the model's predictions using pH-dependent binding kinetics and site-directed mutagenesis.

Main Results:

• The DFG flip was visualized in atomic detail, revealing its connection between active and inactive kinase conformations.
• An energetic model was formulated, predicting that protonation of the DFG aspartate controls the flip.
• Experimental data confirmed the pH dependence of imatinib binding to Abl kinase, which was abolished upon mutating the DFG aspartate.

Conclusions:

• Protonation of the DFG aspartate is a key regulator of the DFG flip.
• The DFG flip, modulated by electrostatic changes during the catalytic cycle, facilitates nucleotide binding and release by enabling access to flexible conformations.
• This mechanism may explain the high conservation of the DFG motif across kinases.