Formation, Isomerization, and Dissociation of α-Carbon-Centered and π-Centered Glycylglycyltryptophan Radical Cations

Gas phase fragmentations of two isomeric radical cationic tripeptides of glycylglycyltryptophan[G•GW]+ and [GGW]•+with well-defined initial radical sites at the α-carbon atom and the 3-methylindole ring, respectively, have been studied using collision-induced dissociation (CID), density functional theory (DFT), and Rice−Ramsperger−Kassel−Marcus (RRKM) theory. Substantially different low-energy CID spectra were obtained for these two isomeric GGW structures, suggesting that they did not interconvert on the time scale of these experiments. DFT and RRKM calculations were used to investigate the influence of the kinetics, stabilities, and locations of the radicals on the competition between the isomerization and dissociation channels. The calculated isomerization barrier between the GGW radical cations (>35.4 kcal/mol) was slightly higher than the barrier for competitive dissociation of these species (<30.5 kcal/mol); the corresponding microcanonical rate constants for isomerization obtained from RRKM calculations were all considerably lower than the dissociation rates at all internal energies. Thus, interconversion between the GGW isomers examined in this study cannot compete with their fragmentations

Arginine-Facilitated Isomerization: Radical-Induced Dissociation of Aliphatic Radical Cationic Glycylarginyl(iso)leucine Tripeptides

The gas phase fragmentations of aliphatic radical cationic glycylglycyl­(iso)­leucine tripeptides ([G•G­(L/I)]+), with well-defined initial locations of the radical centers at their N-terminal α-carbon atoms, are significantly different from those of their basic glycylarginyl­(iso)­leucine ([G•R­(L/I)]+) counterparts; the former lead predominantly to [b2 – H]•+ fragment ions, whereas the latter result in the formation of characteristic product ions via the losses of •CH­(CH3)2 from [G•RL]+ and •CH2CH3 from [G•RI]+ through Cβ–Cγ side-chain cleavages of the (iso)­leucine residues, making these two peptides distinguishable. The α-carbon-centered radical at the leucine residue is the key intermediate that triggers the subsequent Cβ–Cγ bond cleavage, as supported by the absence of •CH­(CH3)2 loss from the collision-induced dissociation of [G•RLα‑Me]+, a radical cation for which the α-hydrogen atom of the leucine residue had been substituted by a methyl group. Density functional theory calculations at the B3LYP 6-31++G­(d,p) level of theory supported the notion that the highly basic arginine residue could not only increase the energy barriers against charge-induced dissociation pathways but also decrease the energy barriers against hydrogen atom transfers in the GR­(L/I) radical cations by ∼10 kcal mol–1, thereby allowing the intermediate precursors containing α- and γ-carbon-centered radicals at the (iso)­leucine residues to be formed more readily prior to promoting subsequent Cβ–Cγ and Cα–Cβ bond cleavages. The hydrogen atom transfer barriers for the α- and γ-carbon-centered GR­(L/I) radical cations (roughly in the range 29–34 kcal mol–1) are comparable with those of the competitive side-chain cleavage processes. The transition structures for the elimination of •CH­(CH3)2 and •CH2CH3 from the (iso)­leucine side chains possess similar structures, but slightly different dissociation barriers of 31.9 and 34.0 kcal mol–1, respectively; the energy barriers for the elimination of the alkenes CH2CH­(CH3)2 and CH3CHCHCH3 through Cα–Cβ bond cleavages of γ-carbon-centered radicals at the (iso)­leucine side chains are 29.1 and 32.8 kcal mol–1, respectively

Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems

Amidst the proteomes of human tissues lie subsets of proteins that are closely involved in conserved pathophysiological processes. Much of biomedical research concerns interrogating disease signature proteins and defining their roles in disease mechanisms. With advances in proteomics technologies, it is now feasible to develop targeted proteomics assays that can accurately quantify protein abundance as well as their post-translational modifications; however, with rapidly accumulating number of studies implicating proteins in diseases, current resources are insufficient to target every protein without judiciously prioritizing the proteins with high significance and impact for assay development. We describe here a data science method to prioritize and expedite assay development on high-impact proteins across research fields by leveraging the biomedical literature record to rank and normalize proteins that are popularly and preferentially published by biomedical researchers. We demonstrate this method by finding priority proteins across six major physiological systems (cardiovascular, cerebral, hepatic, renal, pulmonary, and intestinal). The described method is data-driven and builds upon the collective knowledge of previous publications referenced on PubMed to lend objectivity to target selection. The method and resulting popular protein lists may also be useful for exploring biological processes associated with various physiological systems and research topics, in addition to benefiting ongoing efforts to facilitate the broad translation of proteomics technologies