  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.
