Activation loop plasticity and active site coupling in the MAP kinase, ERK2.

Area of Science:

• Biochemistry and structural biology
• Molecular dynamics simulations
• Protein dynamics and regulation

Background:

• Dual phosphorylation activates the protein kinase ERK2, inducing conformational changes.
• Previous studies suggested ERK2's activation loop (A-loop) motions are coupled to active site regions.
• Understanding ERK2's conformational dynamics is crucial for deciphering its activation mechanisms.

Approach:

• Utilized extensive molecular dynamics (MD) simulations (727 µs total) from crystal structures of active (2P) and inactive (0P) ERK2.
• Analyzed the flexibility and conformational states of the A-loop in both phosphorylated and unphosphorylated ERK2.
• Investigated allosteric coupling between the A-loop and active site via the C-terminal L16 segment.

Key Points:

• The ERK2 A-loop exhibits unexpected flexibility, adopting multiple long-lived conformational states in both active and inactive forms.
• Simulations revealed distinct A-loop conformations: restrained dynamics in the active state (2P-ERK2) and increased dynamics in the inactive state (0P-ERK2).
• Crystal packing may influence observed A-loop structures, suggesting MD simulations offer more biologically relevant insights.

Conclusions:

• ERK2's A-loop dynamically switches between states, allosterically coupled to the active site, likely through the L16 segment.
• The active kinase state is characterized by reduced A-loop dynamics and increased compaction around the catalytic site.
• These findings enhance the understanding of ERK2 regulation by linking conformational dynamics to kinase activation.