Paper Citing NAMD - Abstract
Moss, Christopher L.; Turecek, Frantisek
Protonation sites in peptide dications and cation-radicalls containing beta-amino acid residues
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 316:57-67, APR 15 2012
Protonation sites in a model pentapeptide Ala-Ala-beta Ab-Ala-Ala, where beta Ab was beta-aminobutyric acid, were studied by ab initio and density functional theory calculations. Gas-phase dication tautomers protonated at the N-terminus and amide oxygens were found to be substantially more stable than tautomers protonated at amide nitrogens. This order of ion stability did not change upon solvation with methanol. Conformational analysis of dication tautomers indicated similar degrees of internal solvation by hydrogen bonding in amide O- and N-protonated ions in the gas phase. Because of the low stability of amide N-protonated tautomers, their formation by electrospray of non-basic peptides is highly unlikely. Computational analysis of Ala-Ala-beta Ab-Ala-Ala cation-radicals indicated substantially lower transition-state energies for N-C-alpha bond dissociations at Ala residues than for the N-C-beta bond dissociation at beta Ab. The formation of beta-radicals as z(center dot) fragments was found to require a high threshold energy. Cleavage of the CO-NH2 bond leading to b and y fragments was hampered by a high-energy transition state for the formation of an N-protonated cation-radical intermediate as well as by a high threshold energy for the fragment formation. The calculated energies for transition states and dissociation thresholds explain the less efficient N-C-beta bond dissociation upon electron capture or transfer in peptide ions containing beta-amino acid residues. (c) 2011 Elsevier B.V. All rights reserved.
