AAA+ chaperones and acyldepsipeptides activate the ClpP protease via conformational control

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• The Clp protease complex, comprising ClpP and chaperones like ClpX, degrades proteins.
• Acyldepsipeptides (ADEPs) are natural products that activate ClpP for chaperone-independent proteolysis.

Purpose of the Study:

• To investigate the allosteric mechanisms by which protein and small-molecule activators control ClpP conformation.
• To elucidate the catalytic mechanism of ADEP-activated ClpP.
• To determine the effect of ADEPs on ClpX binding and ClpP inhibition.

Main Methods:

• Chemical probing to dissect the catalytic mechanism.
• Analysis of allosteric control of ClpP barrel conformation by activators.
• Investigation of ADEP binding and its impact on ClpX-ClpP interaction.

Main Results:

• Both protein and small-molecule activators allosterically regulate ClpP barrel conformation.
• ADEPs open the axial pore and directly stimulate ClpP activity via cooperative binding, involving conformational control of catalytic residues.
• Substoichiometric ADEPs inhibit ClpP by preventing ClpX binding and inducing conformational changes.

Conclusions:

• The hydrophobic binding pocket is a key allosteric regulatory site for ClpP.
• Understanding ClpP conformational control is crucial for ClpXP proteolysis and ADEP antibiotic development.