Heterogeneous and rate-dependent streptavidin-biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations

TL;DR

This study combines molecular dynamics and high-speed force spectroscopy to reveal the complex, multistate unbinding pathways of the streptavidin-biotin complex, showing how unbinding involves multiple energy barriers and rate-dependent conformational changes.

Contribution

It provides the first atomistic, dynamic picture of the unbinding process, demonstrating multiple pathways and induced-fit motions that depend on loading rate.

Findings

Biotin crosses multiple energy barriers during unbinding.

Streptavidin undergoes transient induced fits.

Unbinding involves many routes, not just a two-state process.

Abstract

Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular complementarity. However, detailed information of the full unbinding pathway is often lacking due, in part, to the static nature of atomic structures and ensemble averaging inherent to bulk biophysics approaches. Here we combine molecular dynamics and high-speed force spectroscopy on the streptavidin-biotin complex to determine the binding strength and unbinding pathways over the widest dynamic range. Experiment and simulation show excellent agreement at overlapping velocities and provided evidence of the unbinding mechanisms. During unbinding, biotin crosses multiple energy barriers and visits various intermediate states far from the binding pocket while streptavidin undergoes transient induced fits, all varying with loading rate. This multistate process slows down the transition to the unbound state and favors rebinding, thus explaining the long lifetime of the complex. We provide an atomistic, dynamic picture of the unbinding process, replacing a simple two-state picture with one that involves many routes to the lock and rate-dependent induced-fit motions for intermediates, which might be relevant for other receptor-ligand bonds.