Exploring the Aggregation Propensity of PHF6 Peptide Segments of the Tau Protein Using Ion Mobility Mass Spectrometry Techniques.

Peptide and protein aggregation involves the formation of oligomeric species, but the complex interplay between oligomers of different conformations and sizes complicates their structural elucidation. Using ion mobility mass spectrometry (IM-MS), we aim to reveal these early steps of aggregation for the Ac-PHF6-NH2 peptide segment from tau protein, thereby distinguishing between different oligomeric species and gaining an understanding of the aggregation pathway. An important factor that is often neglected, but which can alter the aggregation propensity of peptides, is the terminal capping groups. Here, we demonstrate the use of IM-MS to probe the early stages of aggregate formation of Ac-PHF6-NH2, Ac-PHF6, PHF6-NH2, and uncapped PHF6 peptide segments. The aggregation propensity of the four PHF6 segments is confirmed using thioflavin T fluorescence assays and transmission electron microscopy. A novel approach based on post-IM fragmentation and quadrupole selection on the TIMS-Qq-ToF (trapped ion mobility) spectrometer was developed to enhance oligomer assignment, especially for the higher-order aggregates. This approach pushes the limits of IM identification of isobaric species, whose signatures appear closer to each other with increasing oligomer size, and provides new insights into the interpretation of IM-MS data. In addition, TIMS collision cross section values are compared with traveling wave ion mobility (TWIMS) data to evaluate potential instrumental bias in the trapped ion mobility results. The two IM-MS instrumental platforms are based on different ion mobility principles and have different configurations, thereby providing us with valuable insight into the preservation of weakly bound biomolecular complexes such as peptide aggregates.

Covalent bicyclization of protein complexes yields durable quaternary structures.

Proteins are essential biomolecules and central to biotechnological applications. In many cases, assembly into higher-order structures is a prerequisite for protein function. Under conditions relevant for applications, protein integrity is often challenged, resulting in disassembly, aggregation, and loss of function. The stabilization of quaternary structure has proven challenging, particularly for trimeric and higher-order complexes, given the complexity of involved inter- and intramolecular interaction networks. Here, we describe the chemical bicyclization of homotrimeric protein complexes, thereby increasing protein resistance toward thermal and chemical stress. This approach involves the structure-based selection of cross-linking sites, their variation to cysteine, and a subsequent reaction with a triselectrophilic agent to form a protein assembly with bicyclic topology. Besides overall increased stability, we observe resistance toward aggregation and greatly prolonged shelf life. This bicyclization strategy gives rise to unprecedented protein chain topologies and can enable new biotechnological and biomedical applications.

Size distribution of polycyclic aromatic hydrocarbons in space: an old new light on the 11.2/3.3 µm intensity ratio.

The intensity ratio of the 11.2/3.3 µm emission bands is considered to be a reliable tracer of the size distribution of polycyclic aromatic hydrocarbons (PAHs) in the interstellar medium (ISM). This paper describes the validation of the calculated intrinsic infrared (IR) spectra of PAHs that underlie the interpretation of the observed ratio. The comparison of harmonic calculations from the NASA Ames PAH IR spectroscopic database to gas-phase experimental absorption IR spectra reveals a consistent underestimation of the 11.2/3.3 µm intensity ratio by 34%. IR spectra based on higher level anharmonic calculations, on the other hand, are in very good agreement with the experiments. While there are indications that the 11.2/3.3 µm ratio increases systematically for PAHs in the relevant size range when using a larger basis set, it is unfortunately not yet possible to reliably calculate anharmonic spectra for large PAHs. Based on these considerations, we have adjusted the intrinsic ratio of these modes and incorporated this in an interstellar PAH emission model. This corrected model implies that typical PAH sizes in reflection nebulae such as NGC 7023 - previously inferred to be in the range of 50 to 70 carbon atoms per PAH are actually in the range of 40 to 55 carbon atoms. The higher limit of this range is close to the size of the C60 fullerene (also detected in reflection nebulae), which would be in line with the hypothesis that, under appropriate conditions, large PAHs are converted into the more stable fullerenes in the ISM.

Developments in Trapped Ion Mobility Mass Spectrometry to Probe the Early Stages of Peptide Aggregation.

Ion mobility mass spectrometry (IM-MS) has proven to be an excellent method to characterize the structure of amyloidogenic protein and peptide aggregates, which are formed in coincidence with the development of neurodegenerative diseases. However, it remains a challenge to obtain detailed structural information on all conformational intermediates, originating from the early onset of those pathologies, due to their complex and heterogeneous environment. One way to enhance the insights and the identification of these early stage oligomers is by employing high resolution ion mobility mass spectrometry experiments. This would allow us to enhance the mobility separation and MS characterization. Trapped ion mobility spectrometry (TIMS) is an ion mobility technique known for its inherently high resolution and has successfully been applied to the analysis of protein conformations among others. To obtain conformational information on fragile peptide aggregates, the instrumental parameters of the TIMS-Quadrupole-Time-of-Flight mass spectrometer (TIMS-qToF-MS) have to be optimized to allow the study of intact aggregates and ensure their transmission toward the detector. Here, we investigate the suitability and application of TIMS to probe the aggregation process, targeting the well-characterized M307-N319 peptide segment of the TDP-43 protein, which is involved in the development of amyotrophic lateral sclerosis. By studying the influence of key parameters over the full mass spectrometer, such as source temperature, applied voltages or RFs among others, we demonstrate that by using an optimized instrumental method TIMS can be used to probe peptide aggregation.

IR/UV Double Resonance Study of the 2-Phenylallyl Radical and its Pyrolysis Products.

Isolated 2-phenylallyl radicals (2-PA), generated by pyrolysis from a nitrite precursor, have been investigated by IR/UV ion dip spectroscopy using free electron laser radiation. 2-PA is a resonance-stabilized radical that is considered to be involved in the formation of polycyclic aromatic hydrocarbons (PAH) in combustion, but also in interstellar space. The radical is identified based on its gas-phase IR spectrum. Furthermore, a number of bimolecular reaction products are identified, showing that the self-reaction as well as reactions with unimolecular decomposition products of 2-PA form several PAH efficiently. Possible mechanisms are discussed and the chemistry of 2-PA is compared with the one of the related 2-methylallyl and phenylpropargyl radicals.

Competing C-4 and C-5-Acyl Stabilization of Uronic Acid Glycosyl Cations.

Uronic acids are carbohydrates carrying a terminal carboxylic acid and have a unique reactivity in stereoselective glycosylation reactions. Herein, the competing intramolecular stabilization of uronic acid cations by the C-5 carboxylic acid or the C-4 acetyl group was studied with infrared ion spectroscopy (IRIS). IRIS reveals that a mixture of bridged ions is formed, in which the mixture is driven towards the C-1,C-5 dioxolanium ion when the C-5,C-2-relationship is cis, and towards the formation of the C-1,C-4 dioxepanium ion when this relation is trans. Isomer-population analysis and interconversion barrier computations show that the two bridged structures are not in dynamic equilibrium and that their ratio parallels the density functional theory computed stability of the structures. These studies reveal how the intrinsic interplay of the different functional groups influences the formation of the different regioisomeric products.

The kinetic energy of PAH dication and trication dissociation determined by recoil-frame covariance map imaging.

We investigated the dissociation of dications and trications of three polycyclic aromatic hydrocarbons (PAHs), fluorene, phenanthrene, and pyrene. PAHs are a family of molecules ubiquitous in space and involved in much of the chemistry of the interstellar medium. In our experiments, ions are formed by interaction with 30.3 nm extreme ultraviolet (XUV) photons, and their velocity map images are recorded using a PImMS2 multi-mass imaging sensor. Application of recoil-frame covariance analysis allows the total kinetic energy release (TKER) associated with multiple fragmentation channels to be determined to high precision, ranging 1.94-2.60 eV and 2.95-5.29 eV for the dications and trications, respectively. Experimental measurements are supported by Born-Oppenheimer molecular dynamics (BOMD) simulations.

Polycyclic aromatic hydrocarbon growth in a benzene discharge explored by IR-UV action spectroscopy.

Infrared signatures of polycyclic aromatic hydrocarbons (PAHs) are detected towards many phases of stellar evolution. PAHs are major players in the carbon chemistry of the interstellar medium, forming the connection between small hydrocarbons and large fullerenes. However, as details on the formation of PAHs in these environments are still unclear, modeling their abundance and chemistry has remained far from trivial. By combining molecular beam mass-selective IR spectroscopy and calculated IR spectra, we analyze the discharge of benzene and identify resulting products including larger PAHs, radicals and intermediates that serve as promising candidates for radio astronomical searches. The identification of various reaction products indicates that different gas-phase reaction mechanisms leading to PAH growth must occur under the same conditions to account for all observed PAH-related species, thereby revealing the complex and interconnected network of PAH formation pathways. The results of this study highlight key (exothermic) reactions that need to be included in astrochemical models describing the carbon chemistry in our universe.

Using a Caenorhabditis elegans Parkinson's Disease Model to Assess Disease Progression and Therapy Efficiency.

Despite Parkinson's Disease (PD) being the second most common neurodegenerative disease, treatment options are limited. Consequently, there is an urgent need to identify and screen new therapeutic compounds that slow or reverse the pathology of PD. Unfortunately, few new therapeutics are being produced, partly due to the low throughput and/or poor predictability of the currently used model organisms and in vivo screening methods. Our objective was to develop a simple and affordable platform for drug screening utilizing the nematode Caenorhabditis elegans. The effect of Levodopa, the "Gold standard" of PD treatment, was explored in nematodes expressing the disease-causing α-synuclein protein. We focused on two key hallmarks of PD: plaque formation and mobility. Exposure to Levodopa ameliorated the mobility defect in C. elegans, similar to people living with PD who take the drug. Further, long-term Levodopa exposure was not detrimental to lifespan. This C. elegans-based method was used to screen a selection of small-molecule drugs for an impact on α-synuclein aggregation and mobility, identifying several promising compounds worthy of further investigation, most notably Ambroxol. The simple methodology means it can be adopted in many labs to pre-screen candidate compounds for a positive impact on disease progression.

Gas-Phase Infrared Spectra of the C7H5 Radical and Its Bimolecular Reaction Products.

Resonance-stabilized radicals are considered as possible intermediates in the formation of polycyclic aromatic hydrocarbons (PAHs) in interstellar space. Here, we investigate the fulvenallenyl radical, the most stable C7H5 isomer by IR/UV ion dip spectroscopy employing free electron laser radiation in the mid-infrared region between 550 and 1750 cm-1. The radical is generated by pyrolysis from phthalide. Various jet-cooled reaction products are identified by their mass-selective IR spectra in the fingerprint region, based on a comparison with computed spectra. Interestingly, benzyl is present as a second resonance-stabilized radical. It is connected to fulvenallenyl by a sequence of two H atom losses or additions. Among the identified aromatic hydrocarbons are toluene and styrene, as well as polycyclic molecules, such as indene, naphthalene, fluorene and phenanthrene. Mechanisms for the formation of PAH from C7H5 have already been suggested in previous computational work. In particular, the radical/radical reaction of two fulvenallenyl radicals provides an efficient route to phenanthrene in one bimolecular step and might be relevant for PAH formation under astrochemical conditions.

Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy.

Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds.

The gas-phase infrared spectra of the 2-methylallyl radical and its high-temperature reaction products.

The resonance-stabilized 2-methylallyl radical, 2-MA, is considered as a possible intermediate in the formation of polycyclic aromatic hydrocarbons (PAHs) in combustion processes. In this work, we report on its contribution to molecular growth in a high-temperature microreactor and provide mass-selective IR/UV ion dip spectra of the radical, as well as the various jet-cooled reaction products, employing free electron laser radiation in the mid-infrared region. Small (aromatic) hydrocarbons such as fulvene, benzene, styrene, or para-xylene, as well as polycyclic molecules, like (methylated) naphthalene, were identified with the aid of ab initio DFT computations. Several reaction products differ by one or more methyl groups, suggesting that molecular growth is dominated by (de)methylation in the reactor.

Probing the formation of isolated cyclo-FF peptide clusters by far-infrared action spectroscopy.

Small cyclic peptides containing phenylalanine residues are prone to aggregate in the gas phase into highly hydrophobic chains. A combination of laser desorption, mass spectrometry and conformational selective IR-UV action spectroscopy allows us to obtain detailed structural insights into the formation processes of the cyclic L-phenylalanyl-L-phenylalanine dipeptide (named cyclo-FF) aggregates. The rigid properties of cyclo-FF result in highly resolved IR spectra for the smaller clusters (n ≤ 3) and corresponding conformational assignments. For the higher order clusters (n > 3) the spectra are less resolved, however the observed ratios, peak positions and trends in IR shifts are key to make predictions on their structural details. Whereas the mid-IR spectral region between 1000-1800 cm-1 turns out to be undiagnostic for these small aggregates and the 3 µm region only for specific calculated structures, the far-IR contains valuable information that allows for clear assignments.

How does the composition of a PAH influence its microsolvation? A rotational spectroscopy study of the phenanthrene-water and phenanthridine-water clusters.

We report on the noncovalent intermolecular interactions established between the polycyclic aromatic hydrocarbons phenanthrene and phenanthridine with water. Such noncovalent interactions involving extended aromatic systems and water molecules are ubiquitous in a variety of chemical and biological systems. Our study provides spectroscopic results on simple model systems to understand the impact that an extended aromatic surface and the presence of a heteroatom have on the nature of the noncovalent interactions established with the solvent. Microhydrated phenanthrene and phenanthridine clusters with up to three water molecules have been observed and unambiguously characterised by means of broadband rotational spectroscopy and quantum chemical calculations. The presence of a nitrogen atom in the backbone of phenanthridine remarkably affects the geometries of the water clusters and the interaction networks at play, with O-HN and C-HO interactions becoming preferred in the phenanthridine-water clusters over the O-Hπ interactions seen in the phenanthrene-water clusters. The presence of this heteroatom induces nuclear quadrupole coupling, which was used to understand the cooperativity effects found with increasing cluster size. Our results provide important insight to draw a more complete picture of the noncovalent interactions involving solvent molecules and aromatic systems larger than benzene, and they can be significant to enhance our understanding of the aromatic-polar interactions at play in a myriad of chemical and biological contexts.

Metabolomics of sebum reveals lipid dysregulation in Parkinson's disease.

Parkinson's disease (PD) is a progressive neurodegenerative disorder, which is characterised by degeneration of distinct neuronal populations, including dopaminergic neurons of the substantia nigra. Here, we use a metabolomics profiling approach to identify changes to lipids in PD observed in sebum, a non-invasively available biofluid. We used liquid chromatography-mass spectrometry (LC-MS) to analyse 274 samples from participants (80 drug naïve PD, 138 medicated PD and 56 well matched control subjects) and detected metabolites that could predict PD phenotype. Pathway enrichment analysis shows alterations in lipid metabolism related to the carnitine shuttle, sphingolipid metabolism, arachidonic acid metabolism and fatty acid biosynthesis. This study shows sebum can be used to identify potential biomarkers for PD.

Validating Differential Volatilome Profiles in Parkinson's Disease.

Parkinson's disease (PD) is a progressive neurodegenerative disorder that does not currently have a robust clinical diagnostic test. Nonmotor symptoms such as skin disorders have long since been associated with the disease, and more recently a characteristic odor emanating from the skin of people with Parkinson's has been identified. Here, dynamic head space (DHS) thermal desorption (TD) gas chromatography-mass spectrometry (GC-MS) is implemented to directly measure the volatile components of sebum on swabs sampled from people with Parkinson's-both drug naïve and those on PD medications (n = 100) and control subjects (n = 29). Supervised multivariate analyses of data showed 84.4% correct classification of PD cases using all detected volatile compounds. Variable importance in projection (VIP) scores were generated from these data, which revealed eight features with VIP > 1 and p < 0.05 which all presented a downregulation within the control cohorts. Purified standards based on previously annotated analytes of interest eicosane and octadecanal did not match to patient sample data, although multiple metabolite features are annotated with these compounds all with high spectral matches indicating the presence of a series of similar structured species. DHS-TD-GC-MS analysis of a range of lipid standards has revealed the presence of common hydrocarbon species rather than differentiated intact compounds which are hypothesized to be breakdown products of lipids. This replication study validates that a differential volatile profile between control and PD cohorts can be measured using an analytical method that measures volatile compounds directly from skin swabs.

Far-IR Absorption of Neutral Polycyclic Aromatic Hydrocarbons (PAHs): Light on the Mechanism of IR-UV Ion Dip Spectroscopy.

Gas-phase IR-UV double-resonance laser spectroscopy is an IR absorption technique that bridges the gap between experimental IR spectroscopy and theory. The IR experiments are used to directly evaluate predicted frequencies and potential energy surfaces as well as to probe the structure of isolated molecules. However, a detailed understanding of the underlying mechanisms is, especially in the far-IR regime, still far from complete, even though this is crucial for properly interpreting the recorded IR absorption spectra. Here, events occurring upon excitation to vibrational levels of polycyclic aromatic hydrocarbons by far-IR radiation from the FELIX free electron laser are followed using resonance-enhanced multiphoton ionization spectroscopy. These studies provide detailed insight into how ladder climbing and anharmonicity influence IR-UV spectroscopy and therefore the resulting IR signatures in the far-IR region. Moreover, the potential energy surfaces of these low-frequency delocalized modes are investigated and shown to have a strong harmonic character.

Sodium cationization can disrupt the intramolecular hydrogen bond that mediates the sunscreen activity of oxybenzone.

A key decay pathway by which organic sunscreen molecules dissipate harmful UV energy involves excited-state hydrogen atom transfer between proximal enol and keto functional groups. Structural modifications of this molecular architecture have the potential to block ultrafast decay processes, and hence promote direct excited-state molecular dissociation, profoundly affecting the efficiency of an organic sunscreen. Herein, we investigate the binding of alkali metal cations to a prototype organic sunscreen molecule, oxybenzone, using IR characterization. Mass-selective IR action spectroscopy was conducted at the free electron laser for infrared experiments, FELIX (600-1800 cm-1), on complexes of Na+, K+ and Rb+ bound to oxybenzone. The IR spectra reveal that K+ and Rb+ adopt binding positions away from the key OH intermolecular hydrogen bond, while the smaller Na+ cation binds directly between the keto and enol oxygens, thus breaking the intramolecular hydrogen bond. UV laser photodissociation spectroscopy was also performed on the series of complexes, with the Na+ complex displaying a distinctive electronic spectrum compared to those of K+ and Rb+, in line with the IR spectroscopy results. TD-DFT calculations reveal that the origin of the changes in the electronic spectra can be linked to rupture of the intramolecular bond in the sodium cationized complex. The implications of our results for the performance of sunscreens in mixtures and environments with high concentrations of metal cations are discussed.

Do Xylylenes Isomerize in Pyrolysis?

We report infrared spectra of xylylene isomers in the gas phase, using free electron laser (FEL) radiation. All xylylenes were generated by flash pyrolysis. The IR spectra were obtained by monitoring the ion dip signal, using a IR/UV double resonance scheme. A gas phase IR spectrum of para-xylylene  was recorded, whereas ortho- and meta-xylylene were found to partially rearrange to benzocyclobutene and styrene. Computations of the UV oscillator strength  for all molecules were carried out and provde an explanation for the observation of the isomerization products.

Characterization of glycosyl dioxolenium ions and their role in glycosylation reactions.

Controlling the chemical glycosylation reaction remains the major challenge in the synthesis of oligosaccharides. Though 1,2-trans glycosidic linkages can be installed using neighboring group participation, the construction of 1,2-cis linkages is difficult and has no general solution. Long-range participation (LRP) by distal acyl groups may steer the stereoselectivity, but contradictory results have been reported on the role and strength of this stereoelectronic effect. It has been exceedingly difficult to study the bridging dioxolenium ion intermediates because of their high reactivity and fleeting nature. Here we report an integrated approach, using infrared ion spectroscopy, DFT computations, and a systematic series of glycosylation reactions to probe these ions in detail. Our study reveals how distal acyl groups can play a decisive role in shaping the stereochemical outcome of a glycosylation reaction, and opens new avenues to exploit these species in the assembly of oligosaccharides and glycoconjugates to fuel biological research.