Gas Phase Hydrogen/Deuterium Exchange of Arginine and Arginine Dipeptides Complexed with Alkali Metals

Hydrogen/deuterium exchange mass spectrometry in the world of small molecules

The combined use of hydrogen/deuterium exchange (HDX) and mass spectrometry (MS), referred to as HDX-MS, is a powerful tool for exploring molecular edifices and has been used for over 60 years. Initially for structural and mechanistic investigation of low-molecular weight organic compounds, then to study protein structure and dynamics, then, the craze to study small molecules by HDX-MS accelerated and has not stopped yet. The purpose of this review is to present its different facets with particular emphasis on recent developments and applications. Reversible H/D exchanges of mobilizable protons as well as stable exchanges of non-labile hydrogen are considered whether they are taking place in solution or in the gas phase, or enzymatically in a biological media. Some fundamental principles are restated, especially for gas-phase processes, and an overview of recent applications, ranging from identification to quantification through the study of metabolic pathways, is given.

Gas-Phase Ion/Ion Chemistry as a Probe for the Presence of Carboxylate Groups in Polypeptide Cations

The reactivity of 1-hydroxybenzoyl triazole (HOBt) esters with the carboxylate functionality present in peptides is demonstrated in the gas phase with a doubly deprotonated dianion. The reaction forms an anhydride linkage at the carboxylate site. Upon ion trap collisional-induced dissociation (CID) of the modified peptide, the resulting spectrum shows a nominal loss of the mass of the reagent and a water molecule. Analogous phenomenology was also noted for model peptide cations that likely contain zwitterionic/salt-bridged motifs in reactions with a negatively charged HOBt ester. Control experiments indicate that a carboxylate group is the likely reactive site, rather than other possible nucleophilic sites present in the peptide. These observations suggest that HOBt ester chemistry may be used as a chemical probe for the presence and location of carboxylate groups in net positively charged polypeptide ions. As an illustration, deprotonated sulfobenzoyl HOBt was reacted with the [M+7H]⁷⁺ ion of ubiquitin. The ion was shown to react with the reagent and CID of the covalent reaction product yielded an abundant [M+6H-H₂O]⁶⁺ ion. Comparison of the CID product ion spectrum of this ion with that of the water loss product generated from CID of the unmodified [M+6H]⁶⁺ ion revealed the glutamic acid at residue 64 as a reactive site, suggesting that it is present in the deprotonated form. Graphical Abstract ᅟ.

Probing the mechanisms and dynamics of gas phase hydrogen-deuterium exchange reactions of sodiated polyglycines

The rate constants for H-D exchange reactions of sodiated polyglycines (GnNa(+), n = 2-8) and polyalanines (AnNa(+), n = 2, 3 and 5) with ND3 have been measured in the cell of an FT-ICR mass spectrometer. All peptides except G2Na(+) are found to undergo three exchange reactions, all of which are consecutive with no sign of multiple exchanges within a single collision event. This information has been used to construct full mechanistic scenarios with the help of detailed quantum chemical calculations of the possible reaction paths for H-D exchange. The first exchange is always located at the C terminus however with different mechanisms depending upon whether the peptide termini can (larger peptides) or cannot (smaller peptides) interact directly without strong energy penalty. The most favourable mechanisms for the second and third exchanges of the N terminus protons, are found to be different from those for the first for all peptide sizes. The peptide distortions that are necessary in order for some of these reactions to occur are made possible by the energy reservoir provided by the favorable interaction of the peptide ion with ND3. Their occurrence and variety preclude any general relationship between H-D exchange kinetics and the most stable ion structures. There is however a break at G7Na(+) in the kinetics trend, with a first exchange rate which is much smaller than for all other peptide sizes. This break can be directly related to a different structural type in which the C terminus is neither free nor close to the N terminus.

Performance of M06, M06-2X, and M06-HF density functionals for conformationally flexible anionic clusters: M06 functionals perform better than B3LYP for a model system with dispersion and ionic hydrogen-bonding interactions

We present a comparative assessment of the performance of the M06 suite of density functionals (M06, M06-2X, and M06-HF) against an MP2 benchmark for calculating the relative energies and geometric structures of the Cl(-)·arginine and Br(-)·arginine halide ion-amino acid clusters. Additional results are presented for the popular B3LYP density functional. The Cl(-)·arginine and Br(-)·arginine complexes are important prototypes for the phenomenon of anion-induced zwitterion formation. Results are presented for the canonical (noncharge separated) and zwitterionic (charge separated) tautomers of the clusters, as well as the numerous conformational isomers of the clusters. We find that all of the M06 functions perform well in terms of predicting the general trends in the conformer relative energies and identifying the global minimum conformer. This is in contrast to the B3LYP functional, which performed significantly less well for the canonical tautomers of the clusters where dispersion interactions contribute more significantly to the conformer energetics. We find that the M06 functional gave the lowest mean unsigned error for the relative energies of the canonical conformers (2.10 and 2.36 kJ/mol for Br(-)·arginine and Cl(-)·arginine), while M06-2X gave the lowest mean unsigned error for the zwitterionic conformers (0.85 and 1.23 kJ/mol for Br(-)·arginine and Cl(-)·arginine), thus providing insight into the types of physical systems where each of these functionals should perform best.

Effects of alkali metal ion cationization on fragmentation pathways of triazole-epothilone

The collisionally activated dissociation mass spectra of the protonated and alkali metal cationized ions of a triazole-epothilone analogue were studied in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation pathway of the protonated ion was characterized by the loss of the unit of C(3)H(4)O(3). However, another fragmentation pathway with the loss of C(3)H(2)O(2) was identified for the complex ions with Na(+), K(+), Rb(+), and Cs(+). The branching ratio of the second pathway increases with the increment of the size of alkali metal ions. Theoretical calculations based on density functional theory (DFT) method show the difference in the binding position of the proton and the metal ions. With the increase of the radii of the metal ions, progressive changes in the macrocycle of the compound are induced, which cause the corresponding change in their fragmentation pathways. It has also been found that the interaction energy between the compound and the metal ion decreases with increase in the size of the latter. This is consistent with the experimental results, which show that cesiated complexes readily eject Cs(+) when subject to collisions.