title: Quantitative chemical proteomics approach to identify post-translational modification-mediated protein-protein interactions.
abstract: Post-translational modifications (PTMs) (e.g., acetylation, methylation, and phosphorylation) play crucial roles in regulating the diverse protein-protein interactions involved in essentially every cellular process. While significant progress has been made to detect PTMs, profiling protein-protein interactions mediated by these PTMs remains a challenge. Here, we report a method that combines a photo-cross-linking strategy with stable isotope labeling in cell culture (SILAC)-based quantitative mass spectrometry to identify PTM-dependent protein-protein interactions. To develop and apply this approach, we focused on trimethylated lysine-4 at the histone H3 N-terminus (H3K4Me(3)), a PTM linked to actively transcribed gene promoters. Our approach identified proteins previously known to recognize this modification and MORC3 as a new protein that binds H3M4Me(3). This study indicates that our cross-linking-assisted and SILAC-based protein identification (CLASPI) approach can be used to profile protein-protein interactions mediated by PTMs, such as lysine methylation.
authors.affiliation: Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Xiang
authors.initials: X
authors.lastname: Li
authors.forename: Emily A
authors.initials: EA
authors.lastname: Foley
authors.forename: Kelly R
authors.initials: KR
authors.lastname: Molloy
authors.forename: Yinyin
authors.initials: Y
authors.lastname: Li
authors.forename: Brian T
authors.initials: BT
authors.lastname: Chait
authors.forename: Tarun M
authors.initials: TM
authors.lastname: Kapoor
mesh_terms: D002478:Cells, Cultured; D006367:HeLa Cells; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008239:Lysine / Q000737:chemistry / Q000378:metabolism; D013058:Mass Spectrometry; D015394:Molecular Structure; D011485:Protein Binding; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D040901:Proteomics
chemical_list: D006657:Histones; D011506:Proteins; D008239:Lysine