UV Photodissociation of Proline-containing Peptide Ions: Insights from Molecular Dynamics

Abstract

Abstract. UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of prolinecontaining peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S 2 and S 3 , lie close to 213 nm. Non-adiabatic MD simulation starting from S 2 and S 3 shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.

Single-photon absorption of isolated collagen mimetic peptides and triple-helix models in the VUV-X energy range

“…Most single backbone cleavages occur N-terminal to proline residues. This preferential cleavage site (the so-called proline effect) has been observed previously in CID or UV photofragmentation of proline-containing peptides [31][32][33] . This is consistent with the fact that in our experiment, these fragments are mainly formed at low energy when photoexcitation without ionization dominates.…”

The Mechanism Behind Top-Down UVPD Experiments: Making Sense of Apparent Contradictions

“…At 266 nm, 11,12 absorption in peptides occurs at primarily at tyrosine and tryptophan sidechains. At 193 nm 13,14 and 213 nm, 15 which correspond to higher energy photons, excitation of the peptide backbone is also possible. At 157 nm, 16 excitation of most bonds becomes feasible, including molecules in the air, requiring transmission of the laser beam in vacuo .…”

Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry

“…35 In instances where a +2 ions were observed, typically entailing cleavages adjacent to Pro residues, the a +2 population was included in the fit but the contributions of the a +2 population were not included in the α a value as production of these ions follows an alternate mechanism unrelated to a ion formation. 25,38 Reported values are the average of duplicate data, and fragments having isotopes that overlapped with other fragments are not reported. Criteria for S/N and fragment ion size are discussed in the text.…”