Nanosolvation-Induced Stabilization of a Protonated Peptide Dimer Isolated in the Gas Phase

Oxygen K-shell spectroscopy of isolated progressively solvated peptide

X-ray spectroscopy of an isolated controllably hydrated peptide: core excitation of the first solvation shell enhances peptide backbone fragmentation.

Installation, validation, and application examples of two instrumental setups for gas-phase HDX-MS analysis of peptides and proteins

Gas-phase hydrogen/deuterium exchange measured by mass spectrometry in a millisecond timeframe after ESI (gas-phase HDX-MS) is a fast and sensitive, yet unharnessed method to analyze the primary- and higher-order structure, intramolecular and intermolecular interactions, surface properties, and charge location of peptides and proteins. During a gas-phase HDX-MS experiment, heteroatom-bound non-amide hydrogens are made to exchange with deuterium during a millisecond timespan after electrospray ionization (ESI) by reaction with the highly basic reagent ND₃, enabling conformational analysis of protein states that are pertinent to the native solution-phase. Here, we describe two different instrumental approaches to enable gas-phase HDX-MS for analysis of peptides and proteins on high-resolution Q-TOF mass spectrometers. We include a description of the procedure and equipment required for successful installation as well as suggested procedures for testing, validation, and troubleshooting of a gas-phase HDX-MS setup. In the two described approaches, gas-phase HDX-MS are performed either immediately after ESI in the cone exit region by leading N₂-gas over a deuterated ND₃/D₂O solution, or by leading purified ND₃-gas into different traveling wave ion guides (TWIG) of the mass spectrometer. We envision that a detailed description of the two gas-phase HDX-MS setups and their practical implementation and validation can pave the way for gas-phase HDX-MS to become a more routinely used MS technique for structural analysis of peptides and proteins.

A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy

The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic level. We employ density functional calculations to compute a large pool of structures and vibrational spectra for a gas-phase complex, in which a doubly protonated decapeptide, gramicidin S, is solvated by two water molecules. Though most vibrations of this large complex are treated in a harmonic approximation, the water molecules and the vibrations of the host ion coupled to them are locally described by a quantum mechanical vibrational self-consistent field theory with second-order perturbation correction (VSCF-PT2). Guided and validated by the available cold ion spectroscopy data, the computational analysis identifies structures of the three experimentally observed conformers of the complex. They, mainly, differ by the hydration sites, of which the one at the Orn side chain is the most important for reshaping the peptide toward its native structure. The study demonstrates the ability of a quantum chemistry approach that intelligently combines the semiempirical and ab initio computations to disentangle a complex interplay of intra- and intermolecular hydrogen bonds in large molecular systems.

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

By monitoring ionization and fragmentation after single-photon absorption, we show that an isolated collagen triple helix model is stabilized by proline hydroxylation.

Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments

The fragmentation of the isolated 5-bromouracil (5BrU) molecule and pure and nano-hydrated 5BrU clusters induced by low energy ¹²C⁴⁺ ions has been studied.

The role of the environment in the ion induced fragmentation of uracil

The fragmentation of uracil molecules and pure and nano-hydrated uracil clusters by ¹²C⁴⁺ ion impact is investigated.

Action spectroscopy of a protonated peptide in the ultraviolet range

Action spectroscopy of substance P, a model undecapeptide, has been probed from 5.2 eV to 20 eV.

Energy-Dependent UV Photodissociation of Gas-Phase Adenosine Monophosphate Nucleotide Ions: The Role of a Single Solvent Molecule

The photodissociation of gaseous protonated adenosine 5'-monophosphate (AMP) and the same system hydrated with one water molecule has been investigated in the 4 to 13 eV photon energy range by coupling a linear quadrupole ion trap with a synchrotron radiation beamline. The dissociation of the bare AMP cation upon absorption of a single ultraviolet (UV) photon below the ionization energy (IE) almost exclusively produces the protonated adenine base, with a measured photodissociation yield showing spectroscopic features with dominant absorption bands located at 4.75 and 6.5 eV, found in agreement with TD-DFT calculations. Nevertheless, the addition of a single water molecule to the system modifies the dissociation energy dependence and strongly suppresses the cleavage of the glycosidic CN bond below the IE. Both the experimental and theoretical results suggest that a single solvent molecule can intrinsically influence the structure and physicochemical properties of the AMP cation, including its UV induced dissociation pattern, beyond the simple water evaporation.