Responses to ligand binding in the bacterial DNA sliding clamp β-clamp manifest in dynamic allosteric effects

The homo-dimeric, ring-shaped bacterial DNA sliding clamp, β-clamp, is a central hub in DNA replication and repair. It interacts with a plethora of proteins via short linear motifs, which bind to the same hydrophobic binding pocket on β-clamp. Although the structure, functions and interactions of β-clamp have been amply studied, less focus has been on understanding its dynamics and how this is influenced by ligand binding. In this work, we have made a backbone nuclear magnetic resonance (NMR) assignment of the 83 kDa dimeric β-clamp and used NMR in combination with hydrogen-deuterium exchange mass spectrometry to scrutinize the dynamics of β-clamp and how different ligands affect this. We found that binding of a small peptide from the polymerase III α subunit affects the dynamics and stability of β-clamp. This effect not only appears locally around the binding pocket, but also globally through dynamic allosteric connections to distant regions of the protein, including the dimer interface. This dissipated dynamic effect is likely a consequence of the binding pocket architecture and may reflect a common mechanism of structural plasticity, where different ligands impose differential responses in the structure and dynamics of β-clamp.

Highlights

• NMR spectroscopy of β-clamp revealed its inherent dynamics

• A peptide ligand from polymerase III stabilizes β-clamp from global unfolding

• Peptide binding causes allosteric effects that manifest in changes in dynamics

• Dynamic changes occur distant to the binding pocket in the dimer interface

• Allostery may be a mechanism for differential responses to interaction partners