Correction: Single-conformation spectroscopy of cold, protonated DPG-containing peptides: switching ß-turn types and formation of a sequential type II/II' double ß-turn.

Correction for 'Single-conformation spectroscopy of cold, protonated DPG-containing peptides: switching ß-turn types and formation of a sequential type II/II' double ß-turn' by John T. Lawler et al., Phys. Chem. Chem. Phys., 2022, 24, 2095-2109, https://doi.org/10.1039/D1CP04852J.

Single-conformation spectroscopy of cold, protonated DPG-containing peptides: switching ß-turn types and formation of a sequential type II/II' double ß-turn.

D-Proline (DPro, DP) is widely utilized to form ß-hairpin loops in engineered peptides that would otherwise be unstructured, most often as part of a DPG sub-unit that forms a ß-turn. To observe whether DPG facilitated this effect in short protonated peptides, conformation specific IR-UV double resonance photofragment spectra of the cold (∼10 K) protonated DP and LP diastereomers of the pentapeptide YAPGA was carried out in the hydride stretch (2800-3700 cm-1) and amide I/II (1400-1800 cm-1) regions. A model localized Hamiltonian was developed to better describe the 1600-1800 cm-1 region commonly associated with the amide I vibrations. The CO stretch fundamentals experience extensive mixing with the N-H bending fundamentals of the NH3+ group in these protonated peptides. The model Hamiltonian accounts for experiment in quantitative detail. In the DP diastereomer, all the population is funneled into a single conformer which presented as a type II ß-turn with A and DP in the i + 1 and i + 2 positions, respectively. This structure was not the anticipated type II' ß-turn across DPG that we had hypothesized based on solution-phase propensities. Analysis of the conformational energy landscape shows that both steric and charge-induced effects play a role in the preferred formation of the type II ß-turn. In contrast, the LP isomer forms three conformations with very different structures, none of which were type II/II' ß-turns, confirming that LPG is not a ß-turn former. Finally, single-conformation spectroscopy was also carried out on the extended peptide [YAADPGAAA + H]+ to determine whether moving the protonated N-terminus further from DPG would lead to ß-hairpin formation. Despite funneling its entire population into a single peptide backbone structure, the assigned structure is not a ß-hairpin, but a concatenated type II/type II' double ß-turn that displaces the peptide backbone laterally by about 7.5 Å, but leaves the backbone oriented in its original direction.

Gas-Phase Sequencing of Cyclotides: Introduction of Selective Ring Opening at Dehydroalanine via Ion/Ion Reaction.

The gas-phase linearization of cyclotides via site-selective ring opening at dehydroalanine residues and its application to cyclotide sequencing is presented. This strategy relies on the ability to incorporate dehydroalanine into macrocyclic peptide ions, which is easily accomplished through an ion/ion reaction. Triply protonated cyclotide cations are transformed into radical cations via ion/ion reaction with the sulfate radical anion. Subsequent activation of the cyclotide radical cation generates dehydroalanine at a single cysteine residue, which is easily identified by the odd-electron loss of ·SCH2CONH2. The presence of dehydroalanine in cyclotides provides a site-selective ring-opening pathway that, in turn, generates linear cyclotide analogues in the gas phase. Unlike cyclic variants, product ions derived from the linear peptides provide rich sequence information. The sequencing capability of this strategy is demonstrated with four known cyclotides found in Viola inconspicua, where, in each case, greater than 93% sequence coverage was observed. Furthermore, the utility of this method is highlighted by the partial de novo sequencing of an unknown cyclotide with much greater sequence coverage than that obtained with a conventional Glu-C digestion approach. This method is particularly well-suited for cyclotide species that are not abundant enough to characterize with traditional methods.

Gold(I) Cationization Promotes Ring Opening in Lysine-Containing Cyclic Peptides.

A strategy to sequence lysine-containing cyclic peptides by MSn is presented. Doubly protonated cyclic peptides ions are transformed into gold (I) cationized peptide ions via cation switching ion/ion reaction. Gold(I) cationization facilitates the oxidation of neutral lysine residues in the gas phase, weakening the adjacent amide bond. Upon activation, facile cleavage N-terminal to the oxidized lysine residue provides a site-specific ring opening pathway that converts cyclic peptides into acyclic analogs. The ensuing ion contains a cyclic imine as the new N-terminus and an oxazolone, or structural equivalent, as the new C-terminus. Product ions are formed from subsequent fragmentation events of the linearized peptide ion. Such an approach simplifies MS/MS data interpretation as a series of fragment ions with common N- and C-termini are generated. Results are presented for two cyclic peptides, sunflower trypsin inhibitor and the model cyclic peptide, ß-Loop. The power of this strategy lies in the ability to generate the oxidized peptide, which is easily identified via the loss of HAuNH3 from [M + Au]+. While some competitive processes are observed, the site of ring opening can be pinpointed to the lysine residue upon MS4 enabling the unambiguous sequencing of cyclic peptides.

Infrared Population Transfer Spectroscopy of Cryo-Cooled Ions: Quantitative Tests of the Effects of Collisional Cooling on the Room Temperature Conformer Populations.

The single-conformation spectroscopy and infrared-induced conformational isomerization of a model protonated pentapeptide [YGPAA + H]+ is studied under cryo-cooled conditions in the gas phase. Building on recent results ( DeBlase , A. F. ; J. Am. Chem. Soc. 2017 , 139 , 5481 - 5493 ), firm assignments are established for the presence of two conformer families with distinct infrared and ultraviolet spectra, using IR-UV depletion spectroscopy. Families (A and B) share a similar structure near the N-terminus but differ in the way that the C-terminal COOH group configures itself (cis versus trans) in forming H-bonds with the peptide backbone. Infrared population transfer (IR-PT) spectroscopy is used to study the IR-induced conformational isomerization following single-conformer infrared excitation. IR-induced isomerization is accomplished in both directions (A → B and B → A) in the hydride stretch region and is used to determine fractional abundances for the two conformer families (FA = 0.65 ± 0.04, FB = 0.35 ± 0.04, 2σ error bars). The time scale for collisional cooling of the room-temperature ions to Tvib = 10 K by cold helium in the octupole trap is established as 1.0 ms. Key stationary points on the isomerization potential energy surface are calculated at the DFT B3LYP/6-31+G(d) G3DBJ level of theory. Using RRKM theory, the energy-dependent isomerization rates and populations are calculated as a function of energy. According to the model, the observed population distribution after collisional cooling is close to that of the 298 K Boltzmann distribution and is in near-quantitative agreement with experiment. On the basis of this success, inferences are drawn for the circumstances that govern the population distribution in the trap, concluding that, in ions the size of [YGPAA + H]+ and larger, the observed distributions will be near those at 298 K.

Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]+ and [YGPAA+H]+ Ions: A Stereochemical "Twist" on the ß-Hairpin Turn.

Incorporation of the unnatural d-proline (DP) stereoisomer into a polypeptide sequence is a typical strategy to encourage formation of ß-hairpin loops because natural sequences are often unstructured in solution. Using conformation-specific IR and UV spectroscopy of cold (≈10 K) gas-phase ions, we probe the inherent conformational preferences of the DP and LP diastereomers in the protonated peptide [YAPAA+H]+, where only intramolecular interactions are possible. Consistent with the solution-phase studies, one of the conformers of [YADPAA+H]+ is folded into a charge-stabilized ß-hairpin turn. However, a second predominant conformer family containing two sequential γ-turns is also identified, with similar energetic stability. A single conformational isomer of the LP diastereomer, [YALPAA+H]+, is found and assigned to a structure that is not the anticipated "mirror image" ß-turn. Instead, the LP stereocenter promotes a cis-alanine-proline amide bond. The assigned structures contain clues that the preference of the DP diastereomer to support a trans-amide bond and the proclivity of LP for a cis-amide bond is sterically driven and can be reversed by substituting glycine for alanine in position 2, forming [YGLPAA+H]+. These results provide a basis for understanding the residue-specific and stereospecific alterations in the potential energy surface that underlie these changing preferences, providing insights to the origin of ß-hairpin formation.

Cytosine Radical Cations: A Gas-Phase Study Combining IRMPD Spectroscopy, UVPD Spectroscopy, Ion-Molecule Reactions, and Theoretical Calculations.

The radical cation of cytosine (Cyt.+ ) is generated by dissociative oxidation from a ternary CuII complex in the gas phase. The radical cation is characterized by infrared multiple photon dissociation (IRMPD) spectroscopy in the fingerprint region, UV/Vis photodissociation (UVPD) spectroscopy, ion-molecule reactions, and theoretical calculations (density functional theory and ab initio). The experimental IRMPD spectrum features diagnostic bands for two enol-amino and two keto-amino tautomers of Cyt.+ that are calculated to be among the lowest energy isomers, in agreement with a previous study. Although the UVPD action spectrum can also be matched to a combination of the four lowest energy tautomers, the presence of a nonclassical distonic radical cation cannot be ruled out. Its formation is, however, unlikely due to the high energy of this isomer and the respective ternary CuII complex. Gas-phase ion-molecule reactions showed that Cyt.+ undergoes hydrogen-atom abstraction from 1-propanethiol, radical recombination reactions with nitric oxide, and electron transfer from dimethyl disulfide.

Alkali-Metal-Ion-Assisted Hydrogen Atom Transfer in the Homocysteine Radical.

Intramolecular hydrogen atom transfer (HAT) was examined in homocysteine (Hcy) thiyl radical/alkali metal ion complexes in the gas phase by combination of experimental techniques (ion-molecule reactions and infrared multiple photon dissociation spectroscopy) and theoretical calculations. The experimental results unequivocally show that metal ion complexation (as opposed to protonation) of the regiospecifically generated Hcy thiyl radical promotes its rapid isomerisation into an α-carbon radical via HAT. Theoretical calculations were employed to calculate the most probable HAT pathway and found that in alkali metal ion complexes the activation barrier is significantly lower, in full agreement with the experimental data. This is, to our knowledge, the first example of a gas-phase thiyl radical thermal rearrangement into an α-carbon species within the same amino acid residue and is consistent with the solution phase behaviour of Hcy radical.

Cysteine Radical/Metal Ion Adducts: A Gas-Phase Structural Elucidation and Reactivity Study.

The formation and investigation of sulfur-based cysteine radicals cationized by a group 1A metal ion or Ag+ in the gas phase are reported. Gas-phase ion-molecule reactions (IMR) and infrared multiple-photon dissociation (IRMPD) spectroscopy revealed that the Li+ , Na+ , and K+ adducts of the cysteine radical remain S-based radicals as initially formed. Theoretical calculations for the three alkali metal ions found that the lowest-energy isomers are Cα -based radicals, but they are not observed experimentally owing to the barriers associated with the hydrogen-atom transfer. A mechanism for the S-to-Cα radical rearrangement in the metal ion complexes was proposed, and the relative energies of the associated energy barriers were found to be Li+ >Na+ >K+ at all levels of theory. Relative to the B3LYP functional, other levels of calculation gave significantly higher barriers (by 35-40 kJ mol-1 at MP2 and 44-47 kJ mol-1 at the CCSD level) using the same basis set. Unlike the alkali metal adducts, the cysteine radical/Ag+ complex rearranged from the S-based radical to an unreactive species as indicated by IMRs and IRMPD spectroscopy. This is consistent with the Ag+ /cysteine radical complex having a lower S-to-Cα radical conversion barrier, as predicted by the MP2 and CCSD levels of theory.