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.配体结合与构象变化在生物调控中占据核心地位。配体通常通过调节构象动力学来调控蛋白质功能，然而，结合与构象变化发生的顺序往往引发激烈的争议。本研究揭示了基于“构象选择与诱导契合”这一争议的区分实为一种错误的二分法，因为其机制取决于配体浓度。以焦磷酸盐（PPi）与枯草芽孢杆菌RNase P蛋白质的结合为模型，我们表明耦合反应最好理解为竞争路径间通量变化的过程，这些路径具有不同的结合和构象变化顺序。通过每条路径的分配程度强烈依赖于PPi浓度，配体结合通过增加折叠速率和降低展开速率，将构象集合体重新分配向折叠状态。这些结果指出，配体结合可引起蛋白质构象动力学的显著和多样的变化，并且结合与构象变化的顺序依赖于配体浓度。