Exploring dimethylsulfate for in vivo proteome footprinting

TL;DR

This study investigates the use of dimethylsulfate for in vivo protein footprinting, enabling the analysis of protein conformations and interactions within living cells through methylation detection.

Contribution

It demonstrates the feasibility of using DMS for in vivo footprinting of proteins, expanding the methodology from nucleic acids to proteins inside living cells.

Findings

DMS methylates lysine, histidine, and glutamate residues in vivo.

Methylation patterns reveal residue accessibility and protein conformations.

In vivo footprinting distinguishes structural states of proteins in cells.

Abstract

Protein footprinting is a new methodology that is based on probing, typically with the use of mass spectrometry, of reactivity of different aminoacid residues to a modifying reagent. Data thus obtained allow one to make inferences about protein conformations and their intermolecular interactions. Most of the protein footprinting studies so far have been performed on individual proteins in vitro. We explore whether a similar approach is possible with the proteins inside of living cells, employing dimethylsulfate (DMS), a reagent widely used for the in vivo footprinting of nucleic acids. DMS can induce methylation of the lysine, histidine and glutamate residues on proteins. Using models of the histone H2B/H2AZ heterodimer assembled in vitro and from chromatin treated in vivo, we show that the methylation by deuterated DMS allows one to distinguish the accessibility of a particular residue in and out of the protein's environmental/structural context. The detection of changes in protein conformations or their interactions in vivo can provide a new approach to the identification of proteins involved in various intracellular pathways and help in the search for perspective drug targets and biomarkers of diseases.