Probing the Gate-Opening Transition in the Bacterial ClpP Peptidase Using Molecular Dynamics Simulations and Machine...

Area of Science:

• Biochemistry and Molecular Biology
• Structural Biology
• Computational Biology

Background:

• Proteome integrity is vital for cell viability.
• Bacterial caseinolytic protease (ClpP) maintains protein homeostasis by degrading misfolded or damaged proteins.
• The ClpP N-terminus regulates substrate access to its proteolytic chamber.

Purpose of the Study:

• To investigate the structural determinants controlling the ClpP pore opening transition.
• To understand how ClpP transitions from a closed to an open pore conformation.

Main Methods:

• Molecular dynamics (MD) simulations.
• Machine learning (ML) classification approaches (multiclass and binary).
• SHapley Additive exPlanations (SHAP) analysis.

Main Results:

• Identified stabilizing intraloop interactions (hydrogen bonds, native contacts, salt bridges) as key features of the open/closed pore transition.
• Revealed the impact of perturbations like ADEP removal and specific mutations on the conformational transition.
• Characterized the direction of structural feature changes during pore opening.

Conclusions:

• Stabilizing intraloop interactions in the ClpP N-terminus are critical for regulating pore opening.
• MD simulations and ML provide powerful tools to dissect protein conformational dynamics.
• Understanding ClpP regulation offers insights into bacterial protein homeostasis and potential therapeutic targets.