Highly Dynamic Interactions Maintain Kinetic Stability of the ClpXP Protease During the ATP-Fueled Mechanical Cycle

ACS Chem Biol. 2016 Jun 17;11(6):1552-1560. doi: 10.1021/acschembio.6b00083. Epub 2016 Mar 30.

Abstract

The ClpXP protease assembles in a reaction in which an ATP-bound ring hexamer of ClpX binds to one or both heptameric rings of the ClpP peptidase. Contacts between ClpX IGF-loops and clefts on a ClpP ring stabilize the complex. How ClpXP stability is maintained during the ATP-hydrolysis cycle that powers mechanical unfolding and translocation of protein substrates is poorly understood. Here, we use a real-time kinetic assay to monitor the effects of nucleotides on the assembly and disassembly of ClpXP. When ATP is present, complexes containing single-chain ClpX assemble via an intermediate and remain intact until transferred into buffers containing ADP or no nucleotides. ATP binding to high-affinity subunits of the ClpX hexamer prevents rapid dissociation, but additional subunits must be occupied to promote assembly. Small-molecule acyldepsipeptides, which compete with the IGF loops of ClpX for ClpP-cleft binding, cause exceptionally rapid dissociation of otherwise stable ClpXP complexes, suggesting that the IGF-loop interactions with ClpP must be highly dynamic. Our results indicate that the ClpX hexamer spends almost no time in an ATP-free state during the ATPase cycle, allowing highly processive degradation of protein substrates.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATPases Associated with Diverse Cellular Activities
  • Adenosine Diphosphate / chemistry
  • Adenosine Triphosphatases / chemistry*
  • Adenosine Triphosphate / analogs & derivatives
  • Adenosine Triphosphate / chemistry*
  • Biosensing Techniques
  • Depsipeptides / chemistry
  • Endopeptidase Clp / chemistry*
  • Escherichia coli Proteins / chemistry*
  • Hydrolysis
  • Kinetics
  • Models, Chemical
  • Molecular Chaperones / chemistry*
  • Protein Multimerization
  • Protein Stability
  • Protein Structure, Quaternary
  • Streptavidin / chemistry

Substances

  • ADEP-2B depsipeptide
  • Depsipeptides
  • Escherichia coli Proteins
  • Molecular Chaperones
  • adenosine 5'-O-(3-thiotriphosphate)
  • Adenosine Diphosphate
  • Adenosine Triphosphate
  • Streptavidin
  • ClpP protease, E coli
  • ClpXP protease, E coli
  • Endopeptidase Clp
  • Adenosine Triphosphatases
  • ClpX protein, E coli
  • ATPases Associated with Diverse Cellular Activities