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[Advances in Targeted Protein Degradation Technology].

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Related Experiment Video

Updated: Jul 3, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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[Dynamic Oligomerization Processes and Functional Characterization of Bacterial ClpP Protease].

Fumihiro Ishikawa1,2

  • 1Faculty of Pharmaceutical, Kindai University.

Yakugaku Zasshi : Journal of the Pharmaceutical Society of Japan
|July 1, 2026
PubMed
Summary

Acyldepsipeptide (ADEP) antibiotics activate bacterial ClpP protease, leading to degradation of key proteins like SrfAA and SrfAB. This process, visualized by HS-AFM, reveals ClpP

Keywords:
AAA+ ATPaseClpP proteaseacyldepsipeptide (ADEP)high-speed atomic force microscopy (HS-AFM)protein degradationsubstrate protein

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Published on: September 2, 2019

Area of Science:

  • Bacterial protein degradation
  • Molecular mechanisms of enzyme activation
  • Antibiotic development

Background:

  • ClpP protease is vital for bacterial protein quality control, working with AAA+ ATPases.
  • Acyldepsipeptide (ADEP) antibiotics activate ClpP independently of ATP, causing cell death by degrading essential proteins.
  • The ClpP system regulates surfactin biosynthesis in Bacillus subtilis via nonribosomal peptide synthetases.

Purpose of the Study:

  • To investigate the role of ADEP-activated ClpP in degrading Bacillus subtilis nonribosomal peptide synthetases.
  • To elucidate the dynamic assembly and activation mechanism of ClpP upon ADEP binding.
  • To provide a molecular basis for designing novel ClpP-targeting antibiotics.

Main Methods:

  • Biochemical assays to study ClpP activity and substrate degradation.
  • High-speed atomic force microscopy (HS-AFM) to visualize ClpP oligomerization.
  • In vivo and in vitro degradation studies of SrfAA and SrfAB.

Main Results:

  • ADEP1-activated ClpP directly degraded Bacillus subtilis SrfAA and SrfAB, key enzymes in surfactin biosynthesis.
  • HS-AFM revealed stepwise ClpP oligomerization from monomers to tetradecamers upon ADEP1 binding.
  • These findings identify new physiological substrates for the ADEP-ClpP complex and detail its activation dynamics.

Conclusions:

  • ADEP-activated ClpP degrades essential protein substrates, including SrfAA and SrfAB, impacting bacterial survival.
  • The dynamic assembly of ClpP, visualized by HS-AFM, is crucial for its activation and function.
  • Understanding these mechanisms offers a foundation for developing new antibiotics targeting bacterial proteolysis.