Activation of ClpP protease by ADEP antibiotics: insights from hydrogen exchange mass spectrometry.
The bacterial protease ClpP consists of 14 subunits that assemble into two stacked heptameric rings. The central degradation chamber can be accessed via axial pores. In free ClpP, these pores are obstructed by the N-terminal regions of the seven subunits at either end of the barrel. Acyldepsipeptides (ADEPs) are antibacterial compounds that bind in hydrophobic clefts surrounding the pore region, causing the pores to open up. The ensuing uncontrolled degradation of intracellular proteins is responsible for the antibiotic activity of ADEPs. Recently published X-ray structures yielded conflicting models regarding the conformation adopted by the N-terminal regions in the open state. Here, we use hydrogen/deuterium exchange (HDX) mass spectrometry to obtain complementary insights into the ClpP behavior with and without ADEP1. Ligand binding causes rigidification of the equatorial belt, accompanied by destabilization in the vicinity of the binding clefts. The N-terminal regions undergo rapid deuteration with only minor changes after ADEP1 binding, revealing a lack of stable H-bonding. Our data point to a mechanism where the pore opening mechanism is mediated primarily by changes in the packing of N-terminal nonpolar side chains. We propose that a "hydrophobic plug" causes pore blockage in ligand-free ClpP. ADEP1 binding provides new hydrophobic anchor points that nonpolar N-terminal residues can interact with. In this way, ADEP1 triggers the transition to an open conformation, where nonpolar moieties are clustered around the rim of the pore. This proposed mechanism helps reconcile the conflicting models that had been put forward earlier.
Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada.
Modupeola A
MA
Sowole
John A
JA
Alexopoulos
Yi-Qiang
YQ
Cheng
Joaquin
J
Ortega
Lars
L
Konermann
D000494:Allosteric Regulation; D000595:Amino Acid Sequence; D047630:Depsipeptides / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D049071:Endopeptidase Clp / Q000737:chemistry* / Q000378:metabolism; D004789:Enzyme Activation / Q000187:drug effects; D006859:Hydrogen / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D013058:Mass Spectrometry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization
C584118:ADEP1 compound; D047630:Depsipeptides; D006859:Hydrogen; D049071:Endopeptidase Clp
ADEP; ClpP; EM; HDX; MS; acyldepsipeptide; caseinolytic protease P; conformational dynamics; electron microscopy; electrospray ionization; hydrogen/deuterium exchange; hydrophobic clustering; ligand binding; mass spectrometry