# Inferring residue level hydrogen deuterium exchange with ReX

## TL;DR

The paper introduces ReX, a new method that improves the resolution of hydrogen-deuterium exchange mass spectrometry by inferring detailed residue-level conformational changes in proteins.

## Contribution

ReX introduces a Bayesian non-parametric framework to infer residue-level HDX significance and outperforms existing methods in prediction accuracy.

## Key findings

- ReX outperforms existing methods in predicting unseen HDX data in a three-way proteolytic digestion experiment.
- ReX reveals distinct residue-level HDX signatures for ligands with different functional outcomes on LXRα and BRD4.
- The method provides global and local resolution metrics aligning HDX-MS with other structural methods.

## Abstract

Hydrogen-Deuterium Exchange Mass-Spectrometry (HDX-MS) has emerged as a powerful technique to explore the conformational dynamics of proteins and protein complexes in solution. The bottom-up approach to MS uses peptides to represent an average of residues, leading to reduced resolution of deuterium exchange and complicates the interpretation of the data. Here, we introduce ReX, a method to infer residue-level uptake patterns leveraging the overlap in peptides, the temporal component of the data and the correlation along the sequence dimension. This approach infers statistical significance for individual residues by treating HDX-MS as a multiple change-point problem. By fitting our model in a Bayesian non-parametric framework, we perform parameter number inference, differential HDX confidence assessments, and uncertainty estimation for temporal kinetics. Benchmarking against existing methods using a three-way proteolytic digestion experiment shows our method’s superior performance at predicting unseen HDX data. Moreover, it aligns HDX-MS with the reporting standards of other structural methods by providing global and local resolution metrics. Using ReX, we analyze the differential flexibility of BRD4’s two Bromodomains in the presence of I-BET151 and quantify the conformational variations induced by a panel of seventeen small molecules on LXRα. Our analysis reveals distinct residue-level HDX signatures for ligands with varied functional outcomes, highlighting the potential of this characterisation to inform mode of action analysis.

Hydrogen-Deuterium Exchange Mass-Spectrometry (HDX-MS) is a powerful method to study protein conformational dynamics, but peptide-level measurements obscure residue-level detail. The authors present ReX, a statistical approach that infers residue-level significance, outperforms existing methods on unseen data, and reveals distinct conformational signatures of ligand binding.