The Conformational Transition Pathways and Hidden Intermediates in DFG-Flip Process of c-Met Kinase Revealed by...

Area of Science:

• Structural Biology
• Computational Biophysics
• Enzymology

Background:

• Protein kinases regulate cellular processes through conformational changes.
• The Asp-Phe-Gly (DFG) motif's flip between "DFG-in" and "DFG-out" states is critical for kinase activity.
• Understanding DFG flipping dynamics is key to kinase conformation-activity relationships.

Purpose of the Study:

• To elucidate the conformational transition pathways of DFG flipping in c-Met kinase.
• To characterize the dynamical and thermodynamical features of these pathways.
• To identify potential new drug targets based on kinase conformational states.

Main Methods:

• Metadynamics simulations, an enhanced sampling technique, were employed.
• Conformational transition pathways of DFG flipping in c-Met were analyzed.
• Path Collective Variable (PCV) metadynamics was used to calculate free energies.

Main Results:

• Two distinct pathways, "DFG-up" and "DFG-down", were identified for the DFG flip in c-Met.
• The "DFG-up" path involves a commonly observed transition state.
• The "DFG-down" path is a unique pathway with a two-step transition mechanism, distinct from the one-step "DFG-up" path, despite similar free energy barriers.

Conclusions:

• The study reveals a novel intermediate state in the "DFG-down" pathway.
• These findings deepen the understanding of c-Met's conformation-activity relationship.
• The identified conformational states may serve as potential drug targets for c-Met and related kinases.