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

Abstract

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 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 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 {beta}-clamp. HighlightsO_LINMR spectroscopy of {beta}-clamp revealed its inherent dynamics C_LIO_LIA peptide ligand from polymerase III stabilizes {beta}-clamp from global unfolding C_LIO_LIPeptide binding causes allosteric effects that manifest in changes in dynamics C_LIO_LIDynamic changes occur distant to the binding pocket in the dimer interface C_LIO_LIAllostery may be a mechanism for differential responses to interaction partners C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/600769v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1a2fa22org.highwire.dtl.DTLVardef@d40d98org.highwire.dtl.DTLVardef@1c87aaforg.highwire.dtl.DTLVardef@ee8462_HPS_FORMAT_FIGEXP M_FIG C_FIG