Unraveling Membrane Perturbations Caused by the Bacterial Riboregulator Hfq.

Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNAs. Previously, we showed that the Hfq C-terminal region forms an amyloid-like structure and that these fibrils interact with membranes.

Analysis of Bacterial Amyloid Interaction with Lipidic Membrane by Orientated Circular Dichroism and Infrared Spectroscopies.

Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), and orientated circular dichroism (OCD) are complementary spectroscopies widely used for the analysis of protein samples such as the amyloids commonly renowned as neurodegenerative agents. Determining the secondary structure content of proteins, such as aggregated β-sheets inside the amyloids and in various environments, including membranes and lipids, has made these techniques very valuable and complemental to high-resolution techniques such as nuclear magnetic resonance (NMR), X-ray crystallography, and cryo-electron microscopy. FTIR and CD are extremely sensitive to structural changes of proteins due to environmental changes.

Evaluation of Amyloid Inhibitor Efficiency to Block Bacterial Survival.

Amyloid inhibitors, such as the green tea compound epigallocatechin gallate EGCG, apomorphine or curlicide, have antibacterial properties. Conversely, antibiotics such as tetracycline derivatives or rifampicin also affect eukaryotic amyloids formation and may be used to treat neurodegenerative diseases. This opens the possibility for existing drugs to be repurposed in view of new therapy, targeting amyloid-like proteins from eukaryotes to prokaryotes and conversely.

Characterization of Bacterial Amyloids by Nano-infrared Spectroscopy.

Atomic force microscopy has been used for decades to study the topography of proteins during aggregation but with a lack of information on the secondary structure. On the contrary, infrared spectroscopy was able to study structural changes during the aggregation, but this analysis is complicated due to the presence of different species in mixtures and the poor spatial (~μm) resolution of the FTIR microscopy. Recently, Professor Alexandre Dazzi combined those techniques in the so-called AFM-IR.

Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study.

The import of thiamine pyrophosphate (TPP) through both mitochondrial membranes was studied using a total of 3-µs molecular dynamics simulations. Regarding the translocation through the mitochondrial outer membrane, our simulations support the conjecture that TPP uses the voltage-dependent anion channel, the major pore of this membrane, for its passage to the intermembrane space, as its transport presents significant analogies with that used by other metabolites previously studied, in particular with ATP. As far as passing through the mitochondrial inner membrane is concerned, our simulations show that the specific carrier of TPP has a single binding site that becomes accessible, through an alternating access mechanism.

Characterization by Nano-Infrared Spectroscopy of Individual Aggregated Species of Amyloid Proteins.

Amyloid fibrils are composed of aggregated peptides or proteins in a fibrillar structure with a higher β-sheet content than in their native structure. To characterize them, we used an innovative tool that coupled infrared spectroscopy with atomic force microscopy (AFM-IR). With this method, we show that we can detect different individual aggregated species from oligomers to fibrils and study their morphologies by AFM and their secondary structures based on their IR spectra.

Impact of azole drugs on energetics, kinetics, and ligand migration pathways of CO photo-dissociation in bacterial flavohemoglobins.

Flavohemoglobins (fHbs) are heme proteins found in prokaryotic and eukaryotic microbes. They are involved in NO detoxification through an NO˙ dioxygenase mechanism. The N-terminal heme globin domain allows for binding of gaseous ligands whereas a C-terminal NADH/FADH binding domain facilitates association of redox cofactors necessary for ligand reduction.

Structure of Proton-Bound Methionine and Tryptophan Dimers in the Gas Phase Investigated with IRMPD Spectroscopy and Quantum Chemical Calculations.

The structures of three proton-bound dimers (MetH, MetTrpH, and TrpH) are investigated in the gas phase with infrared multiple photon disassociation (IRMPD) spectroscopy in combination with quantum chemical calculations. Their IRMPD spectra in the range of 600-1850 cm are obtained experimentally using an FT-ICR mass spectrometer and the CLIO free electron laser as an IR light source. The most abundant conformers are elucidated by comparing the IRMPD spectra with harmonic frequencies obtained at the B3LYP-GD3BJ/6-311++G** level of theory.

The Bacterial Amyloid-Like Hfq Promotes DNA Alignment.

The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin.

Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications.

Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment.

Charge-Shift Bonding: A New and Unique Form of Bonding.

Charge-shift bonds (CSBs) constitute a new class of bonds different than covalent/polar-covalent and ionic bonds. Bonding in CSBs does not arise from either the covalent or the ionic structures of the bond, but rather from the resonance interaction between the structures. This Essay describes the reasons why the CSB family was overlooked by valence-bond pioneers and then demonstrates that the unique status of CSBs is not theory-dependent.

Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides.

The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain.

Reactions of Thiiranium and Sulfonium Ions with Alkenes in the Gas Phase.

Ion-molecule reactions between thiiranium ion ( 213) and cyclohexene and -cyclooctene resulted in the formation of addition products and ( 295 and 323, respectively) via an electrophilic addition pathway. Associative π-ligand exchange involving direct transfer of the PhS moiety, which has been observed for analogous seleniranium ions in the gas phase, did not occur despite previous solution experiments suggesting it as a valid pathway. DFT calculations at the M06-2X/def2-TZVP level of theory showed high barriers for the exchange reaction, while the addition pathway was more plausible.

Study of the conformational behaviour of trehalose mycolates by FT-IR spectroscopy.

Mycolic acids are fundamental cell wall components, found in the outer membrane barrier (mycomembrane) of Mycobacterium related genera, that have shown antigenic, murine innate immunity inducting and inflammatory activity triggering action. The mycolic acid derivatives, such as the lipid extractable trehalose monomycolates (TMM) and dimycolates (TDM), have been extensively investigated by several biochemical and biological methods and, more recently, we have performed the first neutron scattering measurements on these molecules in order to characterize their dynamical behavior as well as their rigidity properties. In the present paper, we show the first systematic FT-IR study on TMM, TDM and glucose monomycolate (GMM).

Resolution-elastic neutron scattering by correlation techniques.

Neutron scattering applications often require discriminating the elastic contribution from the inelastic contribution. For this purpose, correlation spectroscopy offers an effective tool with both pulsed and continuous neutron sources as well as several advantages: the analysis of the neutron velocity distribution can be carried out with a duty factor of 50%, independently on the resolution value; the best statistical accuracy for spectra where the elastic part encompasses most of the integrated intensity is provided. Depending on the statistical chopper position, correlation analysis can be used for both incoming and outgoing neutron velocity determination.

A Close-Up View of the Impact of Arachidonic Acid on the Phagocyte NADPH Oxidase.

The NADPH oxidase NOX2 complex consists of assembled cytosolic and redox membrane proteins. In mammalian cells, natural arachidonic acid (cis-AA), released by activated phospholipase-A2, plays an important role in the activation of the NADPH oxidase, but the mechanism of action of cis-AA is still a matter of debate. In cell-free systems, cis-AA is commonly used for activation although its structural effects are still unclear.

Infrared multiple photon dissociation action spectroscopy of protonated glycine, histidine, lysine, and arginine complexed with 18-crown-6 ether.

Complexes of 18-crown-6 ether (18C6) with four protonated amino acids (AAs) are examined using infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by the infrared free electron laser at the Centre Laser Infrarouge d'Orsay (CLIO). The AAs examined in this work include glycine (Gly) and the three basic AAs: histidine (His), lysine (Lys), and arginine (Arg). To identify the (AA)H(18C6) conformations present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at the B3LYP/6-311+G(d,p) level of theory.

Orbitals and the Interpretation of Photoelectron Spectroscopy and (e,2e) Ionization Experiments.

Electron momentum spectroscopy, scanning tunneling microscopy, and photoelectron spectroscopy provide unique information about electronic structure, but their interpretation has been controversial. This essay discusses a framework for interpretation. Although this interpretation is not new, we believe it is important to present this framework in light of recent publications.

Vibrational signatures of curcumin's chelation in copper(II) complexes: An appraisal by IRMPD spectroscopy.

Curcumin (Cur) is a natural polyphenol with a wide spectrum of biological activities and appealing therapeutic potential. Herein, it has been delivered by electrospray ionization as gaseous protonated species, [Cur + H], and as a Cu(ii) complex, [Cu(Cur - H)], a promising antioxidant and radical scavenger. The gas phase structures were assayed by infrared multiple photon dissociation (IRMPD) spectroscopy in both the fingerprint (800-2000 cm) and hydrogen stretching (3100-3750 cm) ranges.

l-Cysteine Modified by S-Sulfation: Consequence on Fragmentation Processes Elucidated by Tandem Mass Spectrometry and Chemical Dynamics Simulations.

Low-energy collision-induced dissociation (CID) of deprotonated l-cysteine S-sulfate, [cysS-SO], delivered in the gas phase by electrospray ionization, has been found to provide a means to form deprotonated l-cysteine sulfenic acid, which is a fleeting intermediate in biological media. The reaction mechanism underlying this process is the focus of the present contribution. At the same time, other novel species are formed, which were not observed in previous experiments.

Sequence Ion Structures and Dissociation Chemistry of Deprotonated Sucrose Anions.

We investigate the tandem mass spectrometry of regiospecifically labeled, deprotonated sucrose analytes. We utilize density functional theory calculations to model the pertinent gas-phase fragmentation chemistry of the prevalent glycosidic bond cleavages (B-Y and C-Z reactions) and compare these predictions to infrared spectroscopy experiments on the resulting B and C product anions. For the C anions, barriers to interconversion of the pyranose [α-glucose-H], C anions to entropically favorable ring-open aldehyde-terminated forms were modest (41 kJ mol) consistent with the observation of a band assigned to a carbonyl stretch at ~ 1680-1720 cm.

Leonardo da Vinci: Cause, effect, linearity, and memory.

In this contribution, some textual portions of the Leonardo da Vinci's work were analyzed with the aim to highlight how, moving from Aristotle and going beyond him, he combines the intermediate positions that, from the Greek philosopher, passing through Buridan, arrive to Newton. This has been performed following a path that passes through the formulation of the principle of causality, the use of the concept of linear relationship (pyramidal law) between cause and effect and the introduction of a duration of the impression (memory) of mechanical systems. In the framework of the studies aimed to a valorization of Leonardo as a scientist, which is a crucial aspect in the analysis of the Leonardo genius, the present work sheds a new light on his intuitions about some fundamental physics concepts as well as about the conceptual model that, several centuries later, will be formalized in the modern linear response theory.

Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Purine Nucleosides.

The chemical difference between DNA and RNA nucleosides is their 2'-hydrogen versus 2'-hydroxyl substituents. Modification of the ribosyl moiety at the 2'-position and 2'-O-methylation in particular, is common among natural post-transcriptional modifications of RNA. 2'-Modification may alter the electronic properties and hydrogen-bonding characteristics of the nucleoside and thus may lead to enhanced stabilization or malfunction.