# Local and Global Breathing Motions Prime the Access to Buried Binding Site in an Antibiotic-Sequestering Protein

## TL;DR

This paper studies how a protein from a gut microbe opens up to allow antibiotic binding by changing its shape.

## Contribution

The study reveals how local and global breathing motions in AlbAS protein enable access to a buried binding site.

## Key findings

- AlbAS undergoes large-scale conformational changes to expose a buried binding site for albicidin.
- The N-terminal subdomain partially unlocks in 6 ms, aiding ligand binding.
- Hydrogen–deuterium exchange shows anisotropic stability distributions in the protein.

## Abstract

Proteins frequently undergo large-scale conformational
excursions
in their native ensemble. Such structural transitions are particularly
critical for enabling access to binding sites when they are buried
in the protein interior. Here, we map the conformational landscape
of AlbAS, a natural isoform of the transcription factor AlbA from
the gut microbe Klebsiella oxytoca,
which sequesters the antibiotic albicidin in a solvent-inaccessible
binding tunnel. Combining equilibrium, time-resolved experiments,
structural mass spectrometry and calorimetry with statistical modeling,
we show that AlbAS displays large differences in local and global
stability and dynamics, with ∼600-fold difference in unfolding
rates across different parts of the structure. Several residues lining
the ligand-binding pocket and the inter-sub-domain residues rapidly
exchange protons with the solvent in hydrogen–deuterium exchange
mass spectrometry experiments, indicative of anisotropic distributions
of local stabilities, with the N-terminal subdomain being less stable.
The AlbAS conformational landscape is thus quite rugged, encompassing
numerous partially structured states in equilibrium, including partial
unlocking of the N-terminal subdomain at a time-constant of 6 ms that
exposes the binding sites to aid in albicidin binding.