Cyclic peptide as reference system for b ion structural analysis in the gas phase

Abstract

Infrared multiple photon dissociation spectroscopy and hydrogen/deuterium exchange methods are used to confirm the macrocylic structure of a b(6) peptide fragment by direct comparison with a synthetically made cyclic peptide. The acetylation of the peptide N-terminus results in the inhibition of the macrocyclic formation, supporting the "head-to-tail" cyclization mechanism. Differences in hydrogen/deuterium exchange rates for macrocyclic and oxazalone structure peptide fragments are interpreted to be a result of the complex interplay of multiple basic sites in the peptide fragment, supporting the relay mechanism for deuterium exchange with CH(3)OD.

Conformation-Specific Spectroscopy of Peptide Fragment Ions in a Low-Temperature Ion Trap

“…Simultaneous investigation of peptide fragment ions and cyclic peptides as well as fragments from acetylated peptide precursors can facilitate systematic comparison of cyclic and non-cyclic structures [44] and thus deliver experimental benchmark data that help to identify fingerprints for the different structures. The possibility to obtain single-photon absorption action spectra in different spectral regions in our approach promises to be particularly beneficial for generating such experimental benchmarks for the structural investigation of peptide fragment ions.…”

“…With increasing complexity of the fragment ion structures, support from other sources of information becomes necessary for unraveling complicated IRMPD spectra. This can be achieved by combining spectroscopy with other techniques [22,31,32] or by comparison of the spectra with chemically modified species in which cyclization is either induced or inhibited [36,38,39,42,44].…”

Disfavoring Macrocycle b Fragments by Constraining Torsional Freedom: The “Twisted” Case of QWFGLM b6

“…A comparison to the synthetically made cyclic peptide reference system, protonated cyclo(QWFGLM), which had been reported previously [18,35], shows that both spectra are nearly identical. There are minor differences in the 1600 cm -1 region, which may suggest some differences in the conformeric structures that are present.…”

“…This study aims at determining how amino acid residues with limited torsional flexibility affect macrocycle formation in the b 6 fragment sequence motif QWFGLM, which has a very high propensity to form macrocycle structures [35]. The residues proline and 4-aminomethylbenzoic acid (4AMBz) were chosen here, in the expectation that their rigid structures may restrict "head-to-tail" cyclization from the N-terminus, as shown in Scheme 1.…”

Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

“…Selective deletion of internal lysine by sequence scrambling following the head-to-tail macrocyclization cannot indeed be completely ruled out in the present case, though no evidence of the deletion of internal alanine as anticipated from the proposed random scrambling [21,[27][28][29][30][31][32] of the peptide sequence was observed in our results. In order to assess whether head-to-tail macrocyclization of the b n -ion (as discussed above) could be a major pathway for the internal lysine deletion, we selectively acetylated the N-terminal α-amine of the peptides since N-acetylation blocks the macrocyclization [28,47]. It is interesting to note that the deletion of internal lysine by collisional activation of the protonated octapeptides as described above (Figure 1 and Figure 3) indeed takes place even after the N-acetylation (see Figures S3, S4, and S5 in the Supporting Information) of the peptides (m/z 742.4, the singly protonated N-acetylated peptides).…”