Related Experiment Video
Updated: Jan 1, 2026
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
Published on: May 20, 2020
The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning
Brajesh Narayan1, Arman Fathizadeh2, Clark Templeton3
1School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.
Background:
Kinases are a family of enzymes that catalyze the transfer of the ɤ-phosphate group from ATP to a protein's residue. Malfunctioning kinases are involved in many health problems such as cardiovascular diseases, diabetes, and cancer. Kinases transitions between multiple conformations of inactive to active forms attracted considerable interest.
Method:
A reaction coordinate is computed for the transition between the active to inactive conformation in Abl kinase with a focus on the DFG-in to DFG-out flip. The method of Rock Climbing is used to construct a path locally, which is subsequently optimized using a functional of the entire path. The discrete coordinate sets along the reaction path are used in a Milestoning calculation of the free energy landscape and the rate of the transition.
Results:
The estimated transition times are between a few milliseconds and seconds, consistent with simulations of the kinetics and with indirect experimental data. The activation requires the transient dissociation of the salt bridge between Lys271 and Glu286. The salt bridge reforms once the DFG motif is stabilized by a locked conformation of Phe382. About ten residues are identified that contribute significantly to the process and are included as part of the reaction space.
Conclusions:
The transition from DFG-in to DFG-out in Abl kinase was simulated using atomic resolution of a fully solvated protein yielding detailed description of the kinetics and the mechanism of the DFG flip. The results are consistent with other computational methods that simulate the kinetics and with some indirect experimental measurements.
General Significance:
The activation of kinases includes a conformational transition of the DFG motif that is important for enzyme activity but is not accessible to conventional Molecular Dynamics. We propose a detailed mechanism for the transition, at a timescale longer than conventional MD, using a combination of reaction path and Milestoning algorithms. The mechanism includes local structural adjustments near the binding site as well as collective interactions with more remote residues.
Insights
This study details the DFG flip mechanism in Abl kinase, revealing key salt bridge dynamics and residue interactions. These findings provide insights into kinase activation pathways relevant to diseases like cancer.
Area of Science:
- Biochemistry and Molecular Biology
- Computational Chemistry
- Structural Biology
Background:
- Kinases are enzymes crucial for cellular signaling, transferring phosphate groups from ATP to proteins.
- Dysfunctional kinases are implicated in various diseases, including cancer, cardiovascular conditions, and diabetes.
- Understanding kinase conformational transitions, particularly the inactive to active states, is vital for therapeutic development.
Purpose of the Study:
- To elucidate the atomic-level mechanism and kinetics of the DFG-in to DFG-out conformational transition in Abl kinase.
- To determine the timescale and key molecular events governing kinase activation.
- To identify specific residues and interactions critical for regulating the kinase's active state.
Main Methods:
- Employed the Rock Climbing method to construct a reaction path for the DFG motif transition.
- Utilized Milestoning calculations on discrete coordinate sets to determine the free energy landscape and transition rates.
- Performed all-atom molecular dynamics simulations in a fully solvated system for detailed mechanistic insights.
Main Results:
- Estimated transition times for the DFG flip range from milliseconds to seconds, aligning with experimental data.
- Identified the transient dissociation of a salt bridge between Lys271 and Glu286 as essential for activation.
- Pinpointed approximately ten key residues involved in the conformational change, including Phe382 stabilizing the active conformation.
Conclusions:
- The study provides a detailed atomic-resolution mechanism for the Abl kinase DFG flip, a process challenging for conventional molecular dynamics.
- The findings are consistent with existing computational and indirect experimental data, validating the proposed mechanism.
- The identified mechanism highlights the interplay of local and collective residue interactions in regulating kinase activity.
