title: Comparative studies on the discrepant fragmentation mechanisms of the GLy-Asp-Gly-Arg and Arg-Gly-Asp-Gly: evidence for the mobile proton model.
abstract: The fragmentation mechanisms of singly protonated Gly-Asp-Gly-Arg (GDGRI and Arg-Gly-Asp-Gly (RGDGJ were investigated by mass spectrometry and theoretical methods. Both protonated molecules are fragmented mainly at the Asp-Gly amide bond C-terminal to Asp, as supported by quantum chemical calculations. Charge distributions of C and N atoms (Qc + QN) on the amide bonds were collected when the ionizing proton was fixed at different nitrogen atoms along the backbone for each peptide. Compared with the neutral molecules, the total charges of C and N atoms (Qc + QN] for the singly charged peptides tended to be negative when the proton was located at the backbone nitrogen atoms. A relatively larger value of QC + QN corresponds to a higher trend of fragmentation, which is consistent with the experimental relative abundances data that the predominant ions are y2 for [GDGR + H]+ and b3 for [RGDG + H]+. Also, the anhydride mechanism driven by the C-terminal COOH for [RGDG + H]+ was explored by a quantum-mechanical/molecular-mechanical method. Calculations indicate that the protonated peptide can be cleaved through an unusual charge-directed pathway by forming a salt bridge at the C-termini. The formation of the anhydride linkage is much more feasible since this process needs very little energy and is exother- mic, though the subsequent nucleophilic attack on the Asp carbonyl carbon is more difficult. The combined experimental and theoretical methods substantiate the mobile proton model, which opens a way to analyze quantitatively the discrepant fragmentation of dissociated peptides in peptide/protein identification.
mesh_terms: D000577:Amides / Q000737:chemistry; D002244:Carbon / Q000737:chemistry; D008956:Models, Chemical; D009584:Nitrogen / Q000737:chemistry; D009842:Oligopeptides / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011522:Protons; D011789:Quantum Theory; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods
chemical_list: D000577:Amides; C000597871:Arg-Gly-Asp-Gly; C000597869:Gly-Asp-Gly-Arg; D009842:Oligopeptides; D010446:Peptide Fragments; D010455:Peptides; D011522:Protons; D002244:Carbon; D009584:Nitrogen