Simonsen, S.; Prestel, A.; Oesterlund, E. C.; Otterlei, M.; Jorgensen, T. J. D.; Kragelund, B. B.

The homo-dimeric, ring-shaped bacterial DNA sliding clamp, beta-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 beta-clamp. Although the structure, functions and interactions of beta-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 beta-clamp and used NMR in combination with hydrogen-deuterium exchange mass spectrometry to scrutinize the dynamics of beta-clamp and how different ligands affect this. We found that binding of a small peptide from the polymerase III alpha subunit affects the dynamics and stability of beta-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 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 beta-clamp.