Responses to Ligand Binding in the Bacterial DNA Sliding Clamp "β-Clamp" Manifest in Dynamic Allosteric Effects.

Abstract

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 their short linear motifs, binding 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 ligand binding affects this. We found that the binding of a short peptide from the polymerase III α subunit affects the dynamics and stability of β-clamp. The 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. The dissipated dynamic effect from ligand binding is likely a consequence of a unique binding pocket architecture that connects distant parts of the structure and may reflect a mechanism of structural plasticity in protein hubs, where different ligands impose differential responses in the structure and dynamics of β-clamp, resulting in diverse functional responses.