title: Exploring the use of dimethylsulfate for in vivo proteome footprinting.
abstract: Protein footprinting is a new methodology that is based on probing, typically with the use of MS, of reactivity of different amino acid 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.
authors.affiliation: Università G.D'Annunzio, Facolta' di Medicina e Chirurgia, Dipartamento Scienze Biomediche Sez. Biochimica e Biochimica Clinica, Chieti, Italy.
authors.forename: Pasquale
authors.initials: P
authors.lastname: Moio
authors.forename: Arman
authors.initials: A
authors.lastname: Kulyyassov
authors.forename: Damien
authors.initials: D
authors.lastname: Vertut
authors.forename: Luc
authors.initials: L
authors.lastname: Camoin
authors.forename: Erlan
authors.initials: E
authors.lastname: Ramankulov
authors.forename: Marc
authors.initials: M
authors.lastname: Lipinski
authors.forename: Vasily
authors.initials: V
authors.lastname: Ogryzko
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002843:Chromatin / Q000378:metabolism; D018698:Glutamic Acid / Q000378:metabolism; D006367:HeLa Cells; D006639:Histidine / Q000378:metabolism; D006657:Histones / Q000378:metabolism*; D006801:Humans; D008239:Lysine / Q000378:metabolism; D008745:Methylation; D008969:Molecular Sequence Data; D017510:Protein Folding; D055503:Protein Multimerization; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D013463:Sulfuric Acid Esters / Q000378:metabolism*; D014981:Xenopus
chemical_list: D002843:Chromatin; D006657:Histones; D020543:Proteome; D013463:Sulfuric Acid Esters; D018698:Glutamic Acid; D006639:Histidine; C007482:dimethyl sulfate; D008239:Lysine