Molecular dynamics simulation of phosphorylated KID post-translational modification.

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Kinase-inducible domain (KID) acts as a transcriptional activator by interacting with the KID interacting domain (KIX).
• Apo-KID is unstructured, but phosphorylation induces a transition to a well-folded state upon KIX binding.
• The precise mechanism of binding-induced protein folding remains poorly understood.

Purpose of the Study:

• To elucidate the mechanism of binding-induced protein folding of phosphorylated KID (pKID).
• To investigate the conformational changes and folding pathways of pKID upon KIX interaction.

Main Methods:

• Explicit-solvent molecular dynamics (MD) simulations were performed for both bound and apo phosphorylated KID (pKID).
• Ten MD trajectories were utilized for both room-temperature and high-temperature simulations to capture folding and unfolding dynamics.
• Kinetic and free energy landscape analyses were employed to understand the folding process.

Main Results:

• Bound pKID exhibits increased rigidity and stability compared to apo-pKID.
• Apo-pKID unfolds via a two-state process, while bound pKID unfolds through a three-state process.
• Key residues (Asn139, Asp140, Leu141) were identified as crucial for the folding of bound pKID.

Conclusions:

• Binding to KIX induces a specific folding order in pKID, involving KIX access, tertiary folding initiation, and helix formation.
• The folding pathway of apo-pKID differs significantly from the bound state, with swapped helix folding orders.
• The findings provide significant insights into binding-induced protein folding and conformational adjustments in post-translational modifications, aligning with NMR experimental observations.