title: Characterization of native protein complexes using ultraviolet photodissociation mass spectrometry.
abstract: Ultraviolet photodissociation (UVPD) mass spectrometry (MS) was used to characterize the sequences of proteins in native protein-ligand and protein-protein complexes and to provide auxiliary information about the binding sites of the ligands and protein-protein interfaces. UVPD outperformed collisional induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron transfer dissociation (ETD) in terms of yielding the most comprehensive diagnostic primary sequence information about the proteins in the complexes. UVPD also generated noncovalent fragment ions containing a portion of the protein still bound to the ligand which revealed some insight into the nature of the binding sites of myoglobin/heme, eIF4E/m(7)GTP, and human peptidyl-prolyl cis-trans isomerase 1 (Pin1) in complex with the peptide derived from the C-terminal domain of RNA polymerase II (CTD). Noncovalently bound protein-protein fragment ions from oligomeric β-lactoglobulin dimers and hexameric insulin complexes were also produced upon UVPD, providing some illumination of tertiary and quaternary protein structural features.
authors.affiliation: Department of Chemistry, ‡Department of Molecular Biosciences, and §Institute for Cellular and Molecular Biology, The University of Texas at Austin , 105 East 24th Street Stop A5300, Austin, Texas 78712, United States.
authors.forename: John P
authors.initials: JP
authors.lastname: O'Brien
authors.forename: Wenzong
authors.initials: W
authors.lastname: Li
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jennifer S
authors.initials: JS
authors.lastname: Brodbelt
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D018360:Crystallography, X-Ray; D039561:Eukaryotic Initiation Factor-4E / Q000737:chemistry / Q000378:metabolism; D006418:Heme / Q000737:chemistry / Q000378:metabolism; D006736:Horses; D006801:Humans; D007782:Lactoglobulins / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D013058:Mass Spectrometry / Q000379:methods*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009211:Myoglobin / Q000737:chemistry / Q000378:metabolism; D019696:Peptidylprolyl Isomerase / Q000737:chemistry / Q000378:metabolism; D055668:Photochemical Processes; D011485:Protein Binding; D055503:Protein Multimerization; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D014466:Ultraviolet Rays
chemical_list: D039561:Eukaryotic Initiation Factor-4E; D007782:Lactoglobulins; D008024:Ligands; D009211:Myoglobin; D011506:Proteins; D006418:Heme; D019696:Peptidylprolyl Isomerase