Conformational change coupled to ligand binding

Conformational selection, or induced fit?

Molecular recognition carries a long-running debate. Does a ligand bind a high-affinity shape the protein already samples on its own — conformational selection, binding after folding — or does it bind first and pull the protein into shape — induced fit, binding before folding? The two are usually argued as mutually exclusive.

RNase P's P protein is an ideal place to settle it: folding and pyrophosphate (PP_i) binding are tightly coupled, with ligand able to bind at multiple sites across multiple folding states.

One model, fit to everything at once

We built a ten-state kinetic network — every combination of folding state and ligand-bound state — and fit it globally across stopped-flow experiments spanning a range of ligand concentrations. Every rate constant was constrained to be consistent across all conditions simultaneously, so the mechanism had to explain the full dataset, not one curve at a time.

Because the fit returns every microscopic rate constant, we could compute the fractional flux through all 18 folding-and-binding pathways as a function of [PP_i] — turning “which mechanism?” into a direct, per-pathway accounting.

A mixed mechanism tuned by ligand concentration

Flux is continuously partitioned between the two mechanisms, with pyrophosphate concentration setting the balance. At low [PP_i], ~90% of it runs through conformational selection — the protein folds on its own and PP_i binds the already-folded state. Near the apparent K_d, the two run side by side; well above it, induced-fit and mixed routes take over. The mechanism isn't a fixed property of the protein, nor a binary choice between the two — it's a continuously shifting balance set by the conditions.

Conformational selection and induced fit aren't rival answers — they're two ends of a continuum, and ligand concentration sets where you sit on it.