Mechanistic Investigations on N–C^α Bond Cleavages in Dibasic Peptides Containing Internal Lys and Arg Residues

Abstract

The model nonapeptide AAARAAKAG* (* indicates amide) is used to explore N–Cα bond fragmentation under CID-MS conditions. Neighboring group participation and the effect of positioning of Lys and Arg residues on N–Cα bond cleavage is established using a library of synthetic peptide analogues. The importance of the Arg residue at position 4 and the i to i+3 spacing between Arg and Lys residues in determining the formation of the N–Cα bond cleaved product ions (c n) is demonstrated by a comparative MS study of positional variants in analogue peptides. The effect of shortening of the Lys side chain has been established using ornithine (Orn) and diaminobutyric acid (Dab) analogues. The involvement of the Lys residue in mediating the N–Cα bond cleavage is further probed using Nε-dimethyl and isotopically labeled 15Nα, ε lysine residues. MSn experiments reveal that the c 6 ion originates from a doubly charged dehydrated b 8 ion [b 8-18]2+. The mechanism of this unusual fragmentation process has been probed by using position 8 analogues (Gly, Ala, and Aib). A plausible mechanism is proposed for the origin of the c 6 ion, which involves C-terminus lactam formation followed by transannular cyclization and dehydration. The results presented in this study highlight the role of reactive side chain functionalities in promoting noncanonical fragmentation pathways.

Screening and Structural Characterization of Heat Shock Response Elements (HSEs) in Entamoeba histolytica Promoters

“…This mechanism has been observed in the HSF1-HSE complex of H. sapiens [84], where amino acids such as Arg71 and Gln72 play a vital role in the formation of salt bridges, thereby increasing the stability of the complex. Furthermore, π-cation interactions are relevant in improving the stability and specificity of ligand-protein complexes, which are formed particularly through the participation of Lys and Arg residues, as reported by Kumar et al [87]. In our analysis, tEhDBD7 exerts π-cation interactions through the Arg72 residue in all dockings carried out with the HSEs, with the exception of the HSE of the Ehpgp5 promoter.…”