Ligand Concentration Regulates the Pathways of Coupled Protein Folding and Binding

Coupled ligand binding and conformational
change plays a central
role in biological regulation. Ligands often regulate protein function
by modulating conformational dynamics, yet the order in which binding
and conformational change occurs are often hotly debated. Here we
show that the “conformational selection versus induced fit”
distinction on which this debate is based is a false dichotomy because
the mechanism depends on ligand concentration. Using the binding of
pyrophosphate (PPi) to Bacillus subtilis RNase P
protein as a model, we show that coupled reactions are best understood
as a change in flux between competing pathways with
distinct orders of binding and conformational change. The degree of
partitioning through each pathway depends strongly on PPi concentration,
with ligand binding redistributing the conformational ensemble toward
the folded state by both increasing folding rates and decreasing unfolding
rates. These results indicate that ligand binding induces marked and
varied changes in protein conformational dynamics, and that the order
of binding and conformational change is ligand concentration dependent.