ABSTRACT
The gas-phase structures of doubly and triply protonated Amyloid-ß12-28 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. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.
Subject(s)
Amyloid beta-Peptides/chemistry , Peptide Fragments/chemistry , Humans , Ions/chemistry , Mass Spectrometry/methods , Models, Molecular , Protein Structure, Secondary , Protons , Spectrophotometry, Infrared/methodsABSTRACT
The N-hexanoyl-homoserine lactone (C6-HSL) molecule has been investigated by means of infrared multiphoton dissociation (IRMPD) and Fourier-transform infrared spectroscopy (FT-IR) under different conditions in an attempt to mimic biological situations encountered in communication between bacteria for quorum sensing. The protonated molecular ion was studied in the gas-phase that corresponds to a solvent-free situation somewhat analogous to that encountered in the receptor. The simulation of the IRMPD spectrum of the isolated ion was then conducted by means of quantum chemistry calculations in vacuum. In the case of the neutral species, the FT-IR spectra were recorded in D(2)O, mimicking the cytosolic and extracellular media as well as in 1-octanol that is often used for simulation of cell membranes. The interpretation was conducted by considering a C6-HSL molecule in its endo or exo conformation hydrogen-bonded to, respectively, six D(2)O and four 1-octanol molecules. A satisfying agreement with the experimental FT-IR studies conducted in solution at room temperature was obtained as long as a continuum IEFPCM model was added to the explicit solvent environment.
Subject(s)
4-Butyrolactone/analogs & derivatives , Molecular Mimicry , Quorum Sensing , Signal Transduction , 1-Octanol/chemistry , 4-Butyrolactone/chemistry , 4-Butyrolactone/pharmacology , Bacteria/metabolism , Bacterial Proteins/metabolism , Deuterium , Gases/chemistry , Hydrogen-Ion Concentration , Models, Molecular , Repressor Proteins/metabolism , Signal Transduction/drug effects , Solutions , Solvents/chemistry , Spectrophotometry, Infrared , Spectroscopy, Fourier Transform Infrared , Trans-Activators/metabolism , Transcription Factors/metabolism , WaterABSTRACT
We studied the single-photon ionization of gas-phase δ-valerolactam (piperidin-2-one) and of its dimer using vacuum-ultraviolet (VUV) synchrotron radiation coupled to a velocity map imaging electron/ion coincidence spectrometer. The slow photoelectron spectrum (SPES) of the monomer is dominated by the vibrational transitions to the Í X state. Moreover, several weaker and complex bands are observed, corresponding to the population of the vibrational bands (pure or combination) of the electronically excited states of the cation arising from their mutual vibronic interactions. For the dimer, we measure a unique large band. These spectra are assigned with the help of theoretical calculations dealing with the equilibrium geometries, electronic-state patterns and evolutions, harmonic and anharmonic wavenumbers of the monomer and dimer, either neutral or positively charged. The state energies of the [δ-valerolactam](+) cation in the Í X ground, Í A, Í B, Í C, excited electronic states, and of the [δ-valerolactam](2) (+) cation's lowest states are determined. After its formation, [δ-valerolactam](2) (+) is subject to intramolecular isomerization, H transfer and then unimolecular fragmentation processes. Close to the ionization thresholds, the photoionization of these molecules is found to be mainly dominated by a direct process whereas the indirect route (autoionization) contributes at higher energies.
Subject(s)
Piperidones/chemistry , Cations/chemistry , Dimerization , Models, Theoretical , Photoelectron Spectroscopy , Quantum Theory , VibrationABSTRACT
In general, radiation-induced fragmentation of small amino acids is governed by the cleavage of the C-C(α) bond. We present results obtained with 300 keV Xe(20+) ions that allow molecules (glycine and valine) to be ionised at large distances without appreciable energy transfer. Also in the present case, the C-C(α) bond turns out to be the weakest link and hence its scission is the dominant fragmentation channel. Intact ionised molecules are observed with very low intensities. When the molecules are embedded in a cluster of amino acids, a protective effect of the environment is observed. The fragmentation pattern changes: the C-C(α) bond becomes more protected and stable amino acid cations are observed as fragments of the molecular clusters. Evidently, the molecular cluster acts as a "buffer" for the excess energy, capable of rapidly redistributing excess energy and charge.
Subject(s)
Glycine/chemistry , Ions/chemistry , Valine/chemistry , Energy Transfer , Hydrogen Bonding , Mass SpectrometryABSTRACT
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. Comparison between deprotonated vancomycin and its non-covalently bound V + Ac(2)(L)K(D)A(D)A complex shows significant spectral shifts of the carboxylate stretches and the Amide I and Amide II modes that are satisfactorily reproduced in the structures known from the condensed phase. Both theoretical and experimental findings provide strong evidence that the native structure of the deprotonated V + Ac(2)(L)K(D)A(D)A complex is preserved in the gas phase.
Subject(s)
Anti-Bacterial Agents/chemistry , Gases , Spectrum Analysis/methods , Vancomycin/chemistry , Crystallography, X-Ray , Molecular Probes , Nuclear Magnetic Resonance, Biomolecular , Spectrophotometry, InfraredABSTRACT
The results from an experimental study of bare and microsolvated peptide monocations in high-energy collisions with cesium vapor are reported. Neutral radicals form after electron capture from cesium, which decay by H loss, NH(3) loss, or N-C(alpha) bond cleavage into characteristic z(*) and c fragments. The neutral fragments are converted into negatively charged species in a second collision with cesium and are identified by means of mass spectrometry. For protonated GA (G = glycine, A = alanine), the branching ratio between NH(3) loss and N-C(alpha) bond cleavage is found to strongly depend on the molecule attached (H(2)O, CH(3)CN, CH(3)OH, and 18-crown-6 ether (CE)). Addition of H(2)O and CH(3)OH increases this ratio whereas CH(3)CN and CE decrease it. For protonated AAA ([AAA+H](+)), a similar effect is observed with methanol, while the ratio between the z(1) and z(2) fragment peaks remains unchanged for the bare and microsolvated species. Density functional theory calculations reveal that in the case of [GA+H](+)(CE), the singly occupied molecular orbital is located mainly on the amide group in accordance with the experimental results.
Subject(s)
Ions/chemistry , Peptides/chemistry , Cations/chemistry , Cesium/chemistry , Crown Ethers/chemistry , Electrons , Mass SpectrometryABSTRACT
Electron-capture induced dissociation of protoporphyrin cations and anions has been studied. The cations captured two electrons in two successive collisions and were converted to the corresponding even-electron anions. About one fifth of the ions lost a hydrogen atom to become radical anions but otherwise very little fragmentation was observed. The anions captured an electron to become dianions. No hydrogen loss occurred, and the only fragmentation channel observed was loss of CO2H, to give a doubly charged carbanion. Our results indicate that protoporphyrin ions are very efficient in accommodating one or even two electrons in the lowest unoccupied molecular orbital of the porphyrin macrocycle, and that electron capture induces only limited dissociation.
Subject(s)
Mass Spectrometry/methods , Models, Chemical , Models, Molecular , Protoporphyrins/chemistry , Computer Simulation , Electrons , Ions , Molecular Conformation/radiation effects , Protoporphyrins/radiation effectsABSTRACT
The authors find even-odd variations as functions of r (
ABSTRACT
A large number of studies are devoted to the investigation of the biomolecular ionization and fragmentation dynamics underlying biological radiation damage. Most of these studies have been based on gas-phase collisions with isolated DNA building blocks. The radiobiological significance of these studies is often questioned because of the lack of a chemical environment. To clarify this aspect, we studied interactions of keV ions with isolated nucleobases and with nucleobase clusters by means of coincidence time-of-flight spectrometry. Significant changes already show up in the molecular fragmentation patterns of very small clusters.