Pilot screening of potential matrikines resulting from collagen breakages through ionizing radiation.

Little is known regarding radiation-induced matrikines and the possible degradation of extracellular matrix following therapeutic irradiation. The goal of this study was to determine if irradiation can cut collagen proteins at specific sites, inducing potentially biologically active peptides against cartilage cells. Chondrocytes cultured as 3D models were evaluated for extracellular matrix production.

Radiation-Induced Molecular Processes in DNA: A Perspective on Gas-Phase Interaction Studies.

Studying the direct effects of DNA irradiation is essential for understanding the impact of radiation on biological systems. Gas-phase interactions are especially well suited to uncover the molecular mechanisms underlying these direct effects. Only relatively recently, isolated DNA oligonucleotides were irradiated by ionizing particles such as VUV or X-ray photons or ion beams, and ionic products were analyzed by mass spectrometry.

Ionizing radiation induces cross-linking of two noncovalently bound collagen mimetic peptide triple helices in the absence of a molecular environment.

Cross-linking is a fundamental molecular process that is highly important for many applications, in particular, to tune the properties of collagen-based biomaterials. Chemical reagents, the action of enzymes or physical factors such as heat or radiation can facilitate collagen cross-linking. Ionizing radiation has the advantages of being fast, efficient and free from potentially toxic reagents.

Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems.

In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy.

Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides.

Understanding how charge and energy, as well as protons and hydrogen atoms, are transferred in molecular systems as a result of an electronic excitation is fundamental for understanding the interaction between ionizing radiation and biological matter on the molecular level. To localize the excitation at the atomic scale, it was chosen to target phosphorus atoms in the backbone of gas-phase oligonucleotide anions and cations, by means of resonant photoabsorption at the L- and K-edges. The ionic photoproducts of the excitation process were studied by a combination of mass spectrometry and X-ray spectroscopy.

UV-VUV Photofragmentation Spectroscopy of Isolated Neutral Fragile Macromolecules: A Proof-of-Principle Based on a Deprotonated Vancomycin-Peptide Noncovalent Complex.

The gas phase offers the possibility to analyze organic molecules by ultraviolet-vacuum ultraviolet (UV-VUV) spectroscopy without any solvent effect or limitation in terms of spectral range due to absorption by the solvent. Up to now, the size and chemical composition of neutral molecular systems under study have been limited by the use of vaporization methods based on thermal heating. Soft sources of gas-phase thermolabile molecular systems such as electrospray or matrix-assisted laser desorption ionization are appealing alternatives to heating-based techniques, but they lead to the production of ions.

A velocity map imaging spectrometer for measuring absolute differential cross sections for ion-induced electron emission from molecules.

In this paper, we present a newly developed crossed beam experimental setup that utilizes the velocity map imaging (VMI) technique to simultaneously measure both the kinetic energy and emission angle of electrons emitted from atoms or molecules upon ion collision. The projectile ion beam with keV to MeV kinetic energy orthogonally crosses the neutral target beam produced by an effusion cell. The emitted electrons are extracted and analyzed by a multi-electrode VMI spectrometer.

Thermal desorption effects on fragment ion production from multi-photon ionized uridine and selected analogues.

Experiments on neutral gas-phase nucleosides are often complicated by thermal lability. Previous mass spectrometry studies of nucleosides have identified enhanced relative production of nucleobase ions ( uracil from uridine) as a function of desorption temperature to be the critical indicator of thermal decomposition. On this basis, the present multi-photon ionization (MPI) experiments demonstrate that laser-based thermal desorption is effective for producing uridine, 5-methyluridine, and 2'-deoxyuridine targets without thermal decomposition.

Multiple valence electron detachment following Auger decay of inner-shell vacancies in gas-phase DNA.

We have studied soft X-ray photoabsorption in the doubly deprotonated gas-phase oligonucleotide [dTGGGGT-2H]. The dominating decay mechanism of the X-ray induced inner shell vacancy was found to be Auger decay with detachment of at least three electrons, leading to charge reversal of the anionic precursor and the formation of positively charged photofragment ions. The same process is observed in heavy ion (12 MeV C) collisions with [dTGGGGT-2H] where inner shell vacancies are generated as well, but with smaller probability.

Chemical Processes Involving 18-Crown-6-Ether in Activated Noncovalent Complexes with Protonated Peptides.

These last decades, it has been widely assumed that 18-crown-6-ether (CE) plays a spectator role during the chemical processes occurring in isolated host-guest complexes between peptides or proteins and CE after activation in mass spectrometers. Our present experimental and theoretical results challenge this hypothesis by showing that CE can abstract a proton or a protonated molecule from protonated peptides after activation by collisions in argon or electron capture/transfer. Furthermore, thanks to comparison between experimental and calculated values of collision cross-sections, we demonstrate that CE can change binding site after electron transfer.

Mass Spectral Signatures of Complex Post-Translational Modifications in Proteins: A Proof-of-Principle Based on X-ray Irradiated Vancomycin.

Characterizing post-translational modifications (PTM) of proteins is of key relevance for the understanding of many biological processes, as these covalent modifications strongly influence or even determine protein function. Among the different analytical techniques available, mass spectrometry is attracting growing attention because recent instrumental and computational improvements have led to a massive rise of the number of PTM sites that can be identified and quantified. However, multiple PTM occurring at adjacent amino acid residues can lead to complex and dense chemical patterns that are a challenge to characterize.

Photoinduced Processes within Noncovalent Complexes Involved in Molecular Recognition.

Investigating the intrinsic properties of molecular complexes is crucial for understanding the influence of noncovalent interactions on fundamental chemical reactions. Moreover, specific molecular recognition between a ligand and its receptor is a highly important biological process, but little is known about the effects of ionizing radiation on ligand-receptor complexes. The processes triggered by VUV photoabsorption on isolated noncovalent complexes between the glycopeptide antibiotic vancomycin and a mimic of its receptor have been probed by means of mass spectrometry and synchrotron radiation.

Hole Migration in Telomere-Based Oligonucleotide Anions and G-Quadruplexes.

Vacuum ultraviolet photoionization of a gas-phase oligonucleotide anion leads to the formation of a valence hole. This hole migrates towards an energetically favorable site where it can weaken bonds and ultimately lead to bond cleavage. We have studied Vacuum UV photoionization of deprotonated oligonucleotides containing the human telomere sequence dTTAGGG and G-quadruplex structures consisting of four dTGGGGT single strands, stabilized by NH counter ions.

Direct Radiation Effects on the Structure and Stability of Collagen and Other Proteins.

In this review, recent progress in understanding the direct effects of radiation on the structure and stability of collagen, the most abundant protein in the human body, and other proteins is surveyed. Special emphasis is placed on the triple-helical structure of collagen, as studied by means of collagen mimetic peptides. The emerging patterns are the dose dependence of radiation processes and their abundance, the crucial role of radicals in covalent-bond formation (crosslinking) or cleavage, and the influence of the radiation energy and nature.

Isolated Collagen Mimetic Peptide Assemblies Have Stable Triple-Helix Structures.

The origin of the triple-helix structure and high stability of collagen has been debated for many years. As models of the triple helix and building blocks for new biomaterials, collagen mimetic peptide (CMP) assemblies have been deeply studied in the condensed phase. In particular, it was found that hydroxylation of proline, an abundant post-translational modification in collagen, increases its stability.

A tandem mass spectrometer for crossed-beam irradiation of mass-selected molecular systems by keV atomic ions.

In the present paper, we describe a new home-built crossed-beam apparatus devoted to ion-induced ionization and fragmentation of isolated biologically relevant molecular systems. The biomolecular ions are produced by an electrospray ionization source, mass-over-charge selected, accumulated in a 3D ion trap, and then guided to the extraction region of an orthogonal time-of-flight mass spectrometer. Here, the target molecular ions interact with a keV atomic ion beam produced by an electron cyclotron resonance ion source.

Radical-driven processes within a peptidic sequence of type I collagen upon single-photon ionisation in the gas phase.

We report on an experimental single-photon absorption study on gas-phase protonated collagen peptides employing a combination of mass spectrometry and synchrotron radiation. Partial ion yields for the main photoabsorption products vary steadily with photon energy over the range from 14 to 545 eV. At low energy, non-dissociative photoionisation competes with neutral molecule loss from the precursor ion, whereas fragmentation of the peptide backbone dominates at soft X-ray energies.

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

Cartilage and tendons owe their special mechanical properties to the fibrous collagen structure. These strong fibrils are aggregates of a sub-unit consisting of three collagen proteins wound around each other in a triple helix. Even though collagen is the most abundant protein in the human body, the response of this protein complex to ionizing radiation has never been studied.

Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase.

Collisions between O(3+) ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum-chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non-negligible amount of the radical cation monomer is observed.

Proton irradiation of DNA nucleosides in the gas phase.

The four DNA nucleosides guanosine, adenosine, cytidine and thymidine have been produced in the gas phase by a laser thermal desorption source, and irradiated by a beam of protons with 5 keV kinetic energy. The molecular ions as well as energetic neutrals formed have been analyzed by mass spectrometry in order to shed light on the ionization and fragmentation processes triggered by proton collision. A range of 8-20 eV has been estimated for the binding energy of the electron captured by the proton.

Gas-phase structure of amyloid-β (12-28) peptide investigated by infrared spectroscopy, electron capture dissociation and ion mobility mass spectrometry.

The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level.

Ions colliding with clusters of fullerenes--decay pathways and covalent bond formations.

We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C60 molecules following collisions with Ar(2+), He(2+), and Xe(20+) at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C60 monomers are the dominant reaction products in all three cases and this is accounted for by means of Monte Carlo calculations of energy transfer processes and a simple Arrhenius-type [C60]n(+) → C60(+)+(n-1)C60 evaporation model.

Formations of dumbbell C118 and C119 inside clusters of C60 molecules by collision with α particles.

We report highly selective covalent bond modifications in collisions between keV alpha particles and van der Waals clusters of C(60) fullerenes. Surprisingly, C(119)(+) and C(118)(+) are the dominant molecular fusion products. We use molecular dynamics simulations to show that C(59)(+) and C(58)(+) ions--effectively produced in prompt knockout processes with He(2+)--react rapidly with C(60) to form dumbbell C(119)(+) and C(118)(+).

A multicoincidence study of fragmentation dynamics in collision of γ-aminobutyric acid with low-energy ions.

Fragmentation of the γ-aminobutyric acid molecule (GABA, NH(2)(CH(2))(3)COOH) following collisions with slow O(6+) ions (v≈0.3 a.u.

Probing the specific interactions and structures of gas-phase vancomycin antibiotics with cell-wall precursor through IRMPD spectroscopy.

Biomolecular recognition of vancomycin antibiotics with its cell-wall precursor analogue Ac(2)(L)K(D)A(D)A has been investigated in the gas phase through a combined laser spectroscopy/mass spectrometry approach. The mid-IR spectra (1100-1800 cm(-1)) of these mass-selected anionic species have been recorded by means of resonant infrared multiphoton dissociation (IRMPD) spectroscopy performed with the free-electron laser CLIO. Structural assignment has been achieved through comparisons with the low-energy conformers obtained from replica-exchange molecular dynamics simulations, for which IR spectra were calculated using a hybrid quantum mechanics/semi-empirical (QM/SE) method at the DFT/B3LYP/6-31+G*/AM1 level.