Probing Structural Information of Gas-Phase Peptides by Near-Edge X-ray Absorption Mass Spectrometry

X-ray spectroscopy meets native mass spectrometry: probing gas-phase protein complexes

Gas-phase activation and dissociation studies of biomolecules, proteins and their non-covalent complexes using X-rays hold great promise for revealing new insights into the structure and function of biological samples. This is due to the unique properties of X-ray molecular interactions, such as site-specific and rapid ionization. In this perspective, we report and discuss the promise of first proof-of-principle studies of X-ray-induced dissociation of native (structurally preserved) biological samples ranging from small 17 kDa monomeric proteins up to large 808 kDa non-covalent protein assemblies conducted at a synchrotron (PETRA III) and a free-electron laser (FLASH2). A commercially available quadrupole time-of-flight mass spectrometer (Q-Tof Ultima US, Micromass/Waters), modified for high-mass analysis by MS Vision, was further adapted for integration with the open ports at the corresponding beamlines. The protein complexes were transferred natively into the gas phase via nano-electrospray ionization and subsequently probed by extreme ultraviolet (FLASH2) or soft X-ray (PETRA III) radiation, in either their folded state or following collision-induced activation in the gas phase. Depending on the size of the biomolecule and the activation method, protein fragmentation, dissociation, or enhanced ionization were observed. Additionally, an extension of the setup by ion mobility is described, which can serve as a powerful tool for structural separation of biomolecules prior to X-ray probing. The first experimental results are discussed in the broader context of current and upcoming X-ray sources, highlighting their potential for advancing structural biology in the future.

Photolysis of the peptide bond at 193 and 222 nm

Ultraviolet (UV) light is a well-established tool for fragmenting peptides in vacuum. This study investigates the fragmentation of peptides using 193 and 222 nm light in aqueous solution. Changes in the absorption spectra of solutions of the model dipeptide glycylglycine are monitored using a combination of real-time in situ transmission measurements and UV-Vis spectroscopy to report peptide bond scission following UV irradiation. Irradiation by a broadband ultraviolet light source flattens the absorbance peak centered near 193 nm, indicating cleavage of peptide bonds. Irradiation with low-intensity, monochromatic 193 and 222 nm light enabled measurements of the single-photon quantum yield of peptide bond scission, found to be (1.50 ± 0.12)% at 193 nm and (0.16 ± 0.03)% at 222 nm. These findings indicate that peptides may be fragmented in solution prior to emission into a mass spectrometer for new types of single-molecule analyses. The susceptibility of peptide bonds to ultraviolet radiation also suggests limited lifetimes for peptides on the early Earth's surface, which are relevant to theories of the origins-of-life, and suggests a role for protein damage in explanations of the germicidal effect of 222 nm light exposure.

X-ray absorption spectroscopy reveals charge transfer in π-stacked aromatic amino acids

X-ray absorption spectroscopy (XAS) and quantum mechanical calculations bear great potential to unravel π stacking side-chain interaction properties and structure in, e.g., proteins. However, core-excited state calculations for proteins and their associated interpretation for π-π interactions are challenging due to the complexity of the non-covalent interactions involved. A theoretical analysis is developed to decompose the core-to-valence transitions into their atomic contributions in order to characterize the π stacking of aromatic amino acids as a function of their non-covalent distance change. Three models were studied as a non-covalent mixed dimers of the phenylalanine, tyrosine and tryptophan amino acids. We found that there are carbon 1s → π* charge transfer transitions associated with the non-covalently paired aromatic amino acids through their side chains. The atomic-centered contributions to the electronic transition density quantify the excited state charge transfer of the pairing amino acid models, highlighting the π stacking interactions between their aromatic side chains.

Tautomerism of a backbone protonated peptide revealed by soft X-ray action spectroscopy

The structure and reactivity of peptides can be influenced by their protonation state. Notably, protonation of the backbone can induce structural changes, such as tautomerism, shifting from the stable keto form to the enol form. This phenomenon, particularly in the backbone protonated peptide acetyl-pentaglycine, was examined using a combination of soft X-ray action spectroscopy at the nitrogen K-edge and theoretical calculations based on density functional theory (DFT). We identified a resonance at 400 eV that can be clearly attributed to π*(CN) transitions, linked exclusively to the enol form, as no keto form structures could replicate this resonance. These findings enhanced our understanding of the effect of protonation on the structure of peptides and could be employed for future dynamic studies.

Structures of Gas-Phase Hydrated Phosphotyrosine Revealed by Soft X-ray Action Spectroscopy

Gas-phase near-edge X-ray absorption mass spectrometry (NEXAMS) was employed at the carbon and oxygen K-edges to probe the influence of a single water molecule on the protonated phosphotyrosine molecule. The results of the photodissociation experiments revealed that the water molecule forms two bonds, with the phosphate group and another chemical group. By comparing the NEXAMS spectra at the carbon and oxygen K-edges with density functional theory calculations, we attributed the electronic transitions responsible for the observed resonances, especially the transitions due to the presence of the water molecule. We showed that the water molecule leads to a specific spectral feature in the partial ion yield of hydrated fragments at 536.4 eV. Moreover, comparing the NEXAMS spectra with the calculated structures allowed us to identify three possible structures for singly hydrated phosphotyrosine that agree with the observed fragmentation and resonances.

Integrating Explainability into Graph Neural Network Models for the Prediction of X-ray Absorption Spectra

The use of sophisticated machine learning (ML) models, such as graph neural networks (GNNs), to predict complex molecular properties or all kinds of spectra has grown rapidly. However, ensuring the interpretability of these models' predictions remains a challenge. For example, a rigorous understanding of the predicted X-ray absorption spectrum (XAS) generated by such ML models requires an in-depth investigation of the respective black-box ML model used. Here, this is done for different GNNs based on a comprehensive, custom-generated XAS data set for small organic molecules. We show that a thorough analysis of the different ML models with respect to the local and global environments considered in each ML model is essential for the selection of an appropriate ML model that allows a robust XAS prediction. Moreover, we employ feature attribution to determine the respective contributions of various atoms in the molecules to the peaks observed in the XAS spectrum. By comparing this peak assignment to the core and virtual orbitals from the quantum chemical calculations underlying our data set, we demonstrate that it is possible to relate the atomic contributions via these orbitals to the XAS spectrum.

Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy

Near-edge X-ray absorption mass spectrometry (NEXAMS) around the nitrogen and oxygen K-edges was employed on gas-phase peptides to probe the electronic transitions related to their protonation sites, namely at basic side chains, the N-terminus and the amide oxygen. The experimental results are supported by replica exchange molecular dynamics and density-functional theory and restricted open-shell configuration with single calculations to attribute the transitions responsible for the experimentally observed resonances. We studied five tailor-made glycine-based pentapeptides, where we identified the signature of the protonation site of N-terminal proline, histidine, lysine and arginine, at 406 eV, corresponding to N 1s → σ*(NHx+) (x = 2 or 3) transitions, depending on the peptides. We compared the spectra of pentaglycine and triglycine to evaluate the sensitivity of NEXAMS to protomers. Separate resonances have been identified to distinguish two protomers in triglycine, the protonation site at the N-terminus at 406 eV and the protonation site at the amide oxygen characterized by a transition at 403.1 eV.

Electron and ion spectroscopy of azobenzene in the valence and core shells

Azobenzene is a prototype and a building block of a class of molecules of extreme technological interest as molecular photo-switches. We present a joint experimental and theoretical study of its response to irradiation with light across the UV to x-ray spectrum. The study of valence and inner shell photo-ionization and excitation processes combined with measurement of valence photoelectron-photoion coincidence and mass spectra across the core thresholds provides a detailed insight into the site- and state-selected photo-induced processes. Photo-ionization and excitation measurements are interpreted via the multi-configurational restricted active space self-consistent field method corrected by second order perturbation theory. Using static modeling, we demonstrate that the carbon and nitrogen K edges of azobenzene are suitable candidates for exploring its photoinduced dynamics thanks to the transient signals appearing in background-free regions of the NEXAFS and XPS.

Breaking inversion symmetry by protonation: experimental and theoretical NEXAFS study of the diazynium ion, N2H. Phys Chem Chem Phys 2021;23:17166-17176. [PMID: 34346432 DOI: 10.1039/d1cp02002a]

As an example of symmetry breaking in NEXAFS spectra of protonated species we present a high resolution NEXAFS spectrum of protonated dinitrogen, the diazynium ion N₂H⁺. By ab initio calculations we show that the spectrum consists of a superposition of two nitrogen 1s absorption spectra, each including a π* band, and a nitrogen 1s to H⁺ charge transfer band followed by a weak irregular progression of high energy excitations. Calculations also show that, as an effect of symmetry breaking by protonation, the π* transitions are separated by 0.23 eV, only slightly exceeding the difference in the corresponding dark (symmetry forbidden) and bright (symmetry allowed) core excitations of neutral N₂. By DFT and calculations and vibrational analysis, the complex π* excitation band of N₂H⁺ is understood as due to the superposition of the significantly different vibrational progressions of excitations from terminal and central nitrogen atoms, both leading to bent final state geometries. We also show computationally that the electronic structure of the charge transfer excitation smoothly depends on the nitrogen-proton distance and that there is a clear extension of the spectra going from infinity to close nitrogen-proton distance where fine structures show some, although not fully detailed, similarities. An interesting feature of partial localization of the nitrogen core orbitals, with a strong, non-monotonous, variation with nitrogen-proton distance could be highlighted. Specific effects could be unraveled when comparing molecular cation NEXAFS spectra, as represented by recently recorded spectra of N₂⁺ and CO⁺, and spectra of protonated molecules as represented here by the N₂H⁺ ion. Both types containing rich physical effects not represented in NEXAFS of neutral molecules because of the positive charge, whereas protonation also breaks the symmetry. The effect of the protonation on dinitrogen can be separated in charge, which extends the high-energy part of the spectrum, and symmetry-breaking, which is most clearly seen in the low-energy π* transition.