Discrimination of Aspartic and Isoaspartic Acid Residues in Peptides by Tandem Mass Spectrometry with Hydrogen Attachment Dissociation.

Long-lived proteins undergo chemical modifications that can cause age-related diseases. Among these chemical modifications, isomerization is the most difficult to identify. Isomerization often occurs at the aspartic acid (Asp) residues. In this study, we used tandem mass spectrometry equipped with a newly developed ion activation method, hydrogen attachment dissociation (HAD), to analyze peptides containing Asp isomers. Although HAD preferentially produces [cn + 2H]+ and [zm + 2H]+ via N-Cα bond cleavage, [cn + 58 + 2H]+ and [zm - 58 + 2H]+ originate from the fragmentation of the isoAsp residue. Notably, [cn + 58 + 2H]+ and [zm - 58 + 2H]+ could be used as diagnostic fragment ions for the isoAsp residue because these fragment ions did not originate from the Asp residue. The detailed fragmentation mechanism was investigated by computational analysis using density functional theory. According to the results, hydrogen attachment to the carbonyl oxygen in the isoAsp residue results in the Cα-Cß bond cleavage. The experimental and theoretical joint study indicates that the present method allows us to discriminate Asp and isoAsp residues, including site identification of the isoAsp residue. Moreover, we demonstrated that the molar ratio of peptide isomers in the mixture could be estimated from their fragment ion abundance. Therefore, tandem mass spectrometry with HAD is a useful method for the rapid discrimination and semiquantitative analysis of peptides containing isoAsp residues.

A dopamine D1-like receptor-specific agonist improves the survival of septic mice.

In this study, a murine sepsis model was developed using the cecum ligation and puncture (CLP) technique. The expression of the proinflammatory cytokines tumor necrosis factor alpha (TNF-α) and interleukin-1ß (IL-1ß) in the brain increased 6 h after CLP but decreased 24 h later when elevated endogenous dopamine levels in the brain were sustained. Methyl-4-phenyl-1,2,3,6-tetrahydropyridine hydrochloride reduced dopamine levels in the striatum and increased mortality in septic mice. Dopamine D1-like receptors were significantly expressed in the brain, but not in the lungs. Intraperitoneally administered SKF-81297 (SKF), a blood-brain barrier-permeable D1-like receptor agonist, prevented CLP-induced death of septic mice with ameliorated acute lung injury and cognitive dysfunction and suppressed TNF-α and IL-1ß expression. The D1-like receptor antagonist SCH-23390 abolished the anti-inflammatory effects of SKF. These data suggest that D1-like receptor-mediated signals in the brain prevent CLP-induced inflammation in both the brain and the periphery.

Nanocavity-Mediated Purcell Enhancement of Er in TiO2 Thin Films Grown via Atomic Layer Deposition.

The use of trivalent erbium (Er3+), typically embedded as an atomic defect in the solid-state, has widespread adoption as a dopant in telecommunication devices and shows promise as a spin-based quantum memory for quantum communication. In particular, its natural telecom C-band optical transition and spin-photon interface make it an ideal candidate for integration into existing optical fiber networks without the need for quantum frequency conversion. However, successful scaling requires a host material with few intrinsic nuclear spins, compatibility with semiconductor foundry processes, and straightforward integration with silicon photonics. Here, we present Er-doped titanium dioxide (TiO2) thin film growth on silicon substrates using a foundry-scalable atomic layer deposition process with a wide range of doping controls over the Er concentration. Even though the as-grown films are amorphous after oxygen annealing, they exhibit relatively large crystalline grains, and the embedded Er ions exhibit the characteristic optical emission spectrum from anatase TiO2. Critically, this growth and annealing process maintains the low surface roughness required for nanophotonic integration. Finally, we interface Er ensembles with high quality factor Si nanophotonic cavities via evanescent coupling and demonstrate a large Purcell enhancement (≈300) of their optical lifetime. Our findings demonstrate a low-temperature, nondestructive, and substrate-independent process for integrating Er-doped materials with silicon photonics. At high doping densities this platform can enable integrated photonic components such as on-chip amplifiers and lasers, while dilute concentrations can realize single ion quantum memories.

Growth of Highly Oriented (VNbMoTaW)S2 Layers.

Compositional tunability, an indispensable parameter for modifying the properties of materials, can open up new applications for van der Waals (vdW) layered materials such as transition-metal dichalcogenides (TMDCs). To date, multielement alloy TMDC layers are obtained via exfoliation from bulk polycrystalline powders. Here, we demonstrate direct deposition of high-entropy alloy disulfide, (VNbMoTaW)S2, layers with controllable thicknesses on free-standing graphene membranes and on bare and hBN-covered Al2O3(0001) substrates via ultra-high-vacuum reactive dc magnetron sputtering of the VNbMoTaW target in Kr and H2S gas mixtures. Using a combination of density functional theory calculations, Raman spectroscopy, X-ray diffraction, scanning transmission electron microscopy coupled with energy dispersive X-ray spectroscopy, and X-ray photoelectron spectroscopy, we determine that the as-deposited layers are single-phase, 2H-structured, and 0001-oriented (V0.10Nb0.16Mo0.19Ta0.28W0.27)S2.44. Our synthesis route is general and applicable for heteroepitaxial growth of a wide variety of TMDC alloys and potentially other multielement alloy vdW compounds with the desired compositions.

A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry.

MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum identification of bacterial and archaeal isolates by MALDI-TOF MS using a large-scale database of protein masses predicted from nearly 200,000 publicly available genomes. We verify the ability of the database to identify microorganisms at the species level and below, achieving correct identification for > 90% of measured spectra. We further demonstrate its utility by identifying uncultured strains from mouse feces with metagenomics, allowing the identification of new strains by customizing the database with metagenome-assembled genomes.

Highly Efficient Light Helicity Detection of Enantiomers by Chiral Metal-Organic Framework Thin Films.

The potential of chiral metal-organic frameworks (MOFs) for circularly polarized (CP) optics has been largely unexplored. Herein, we have successfully deposited monolithic and highly oriented chiral MOF thin films prepared by a layer-by-layer method (referred to as surface-coordinated MOF thin films, SURMOF) to fabricate CP photodetection devices and distinguish enantiomers. The helicity-sensitive absorption induced by a pair of enantiopure oriented SURMOF was found to be excellent, with an anisotropy factor reaching 0.41. Moreover, the chiral SURMOFs exhibited a pronounced difference in the uptake of the l- and d-tryptophan enantiomers. To demonstrate the potential of these novel MOF thin films for chirality analysis, we fabricated a portable sensor device that allows for chiral recognition by monitoring the photocurrent signals. Our findings not only introduce a new concept of using chiral building blocks for realizing direct CP photodetectors but also provide a blueprint for novel devices in chiral optics.

Borazine Promoted Growth of Highly Oriented Thin Films.

We report on a phenomenon, where thin films sputter-deposited on single-crystalline Al2O3(0001) substrates exposed to borazine─a precursor commonly used for the synthesis of hexagonal boron nitride layers─are more highly oriented than those grown on bare Al2O3(0001) under the same conditions. We observed this phenomenon in face-centered cubic Pd, body-centered cubic Mo, and trigonal Ta2C thin films grown on Al2O3(0001). Interestingly, intermittent exposure to borazine during the growth of Ta2C thin films on Ta2C yields better crystallinity than direct deposition of monolithic Ta2C. We attribute these rather unusual results to a combination of both enhanced adatom mobilities on, and epitaxial registry with, surfaces exposed to borazine during the deposition. We expect that our approach can potentially help improve the crystalline quality of thin films deposited on a variety of substrates.

Characterisation of an Escherichia coli line that completely lacks ribonucleotide reduction yields insights into the evolution of parasitism and endosymbiosis.

Life requires ribonucleotide reduction for de novo synthesis of deoxyribonucleotides. As ribonucleotide reduction has on occasion been lost in parasites and endosymbionts, which are instead dependent on their host for deoxyribonucleotide synthesis, it should in principle be possible to knock this process out if growth media are supplemented with deoxyribonucleosides. We report the creation of a strain of Escherichia coli where all three ribonucleotide reductase operons have been deleted following introduction of a broad spectrum deoxyribonucleoside kinase from Mycoplasma mycoides. Our strain shows slowed but substantial growth in the presence of deoxyribonucleosides. Under limiting deoxyribonucleoside levels, we observe a distinctive filamentous cell morphology, where cells grow but do not appear to divide regularly. Finally, we examined whether our lines can adapt to limited supplies of deoxyribonucleosides, as might occur in the switch from de novo synthesis to dependence on host production during the evolution of parasitism or endosymbiosis. Over the course of an evolution experiment, we observe a 25-fold reduction in the minimum concentration of exogenous deoxyribonucleosides necessary for growth. Genome analysis reveals that several replicate lines carry mutations in deoB and cdd. deoB codes for phosphopentomutase, a key part of the deoxyriboaldolase pathway, which has been hypothesised as an alternative to ribonucleotide reduction for deoxyribonucleotide synthesis. Rather than complementing the loss of ribonucleotide reduction, our experiments reveal that mutations appear that reduce or eliminate the capacity for this pathway to catabolise deoxyribonucleotides, thus preventing their loss via central metabolism. Mutational inactivation of both deoB and cdd is also observed in a number of obligate intracellular bacteria that have lost ribonucleotide reduction. We conclude that our experiments recapitulate key evolutionary steps in the adaptation to life without ribonucleotide reduction.

ADAMTS4 is involved in the production of the Alzheimer disease amyloid biomarker APP669-711.

Amyloid-ß (Aß) deposition in the brain parenchyma is one of the pathological hallmarks of Alzheimer disease (AD). We have previously identified amyloid precursor protein (APP)669-711 (a.k.a. Aß(-3)-40) in human plasma using immunoprecipitation combined with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (IP-MALDI-MS). Furthermore, we found that the level of a composite biomarker, i.e., a combination of APP669-711/Aß1-42 ratio and Aß1-40/Aß1-42 ratio in human plasma, correlates with the amyloid PET status of AD patients. However, the production mechanism of APP669-711 has remained unclear. Using in vitro and in vivo assays, we identified A Disintegrin and Metalloproteinase with a Thrombospondin type 1 motif, type 4 (ADAMTS4) as a responsible enzyme for APP669-711 production. ADAMTS4 cleaves APP directly to generate the C-terminal stub c102, which is subsequently proteolyzed by γ-secretase to release APP669-711. Genetic knockout of ADAMTS4 reduced the production of endogenous APP669-711 by 30% to 40% in cultured cells as well as mouse plasma, irrespectively of Aß levels. Finally, we found that the endogenous murine APP669-711/Aß1-42 ratio was increased in aged AD model mice, which shows Aß deposition as observed in human patients. These data suggest that ADAMTS4 is involved in the production of APP669-711, and a plasma biomarker determined by IP-MALDI-MS can be used to estimate the level of Aß deposition in the brain of mouse models.

SIG-1451, a Novel, Non-Steroidal Anti-Inflammatory Compound, Attenuates Light-Induced Photoreceptor Degeneration by Affecting the Inflammatory Process.

Age-related macular degeneration is a progressive retinal disease that is associated with factors such as oxidative stress and inflammation. In this study, we evaluated the protective effects of SIG-1451, a non-steroidal anti-inflammatory compound developed for treating atopic dermatitis and known to inhibit Toll-like receptor 4, in light-induced photoreceptor degeneration. SIG-1451 was intraperitoneally injected into rats once per day before exposure to 1000 lx light for 24 h; one day later, optical coherence tomography showed a decrease in retinal thickness, and electroretinogram (ERG) amplitude was also found to have decreased 3 d after light exposure. Moreover, SIG-1451 partially protected against this decrease in retinal thickness and increase in ERG amplitude. One day after light exposure, upregulation of inflammatory response-related genes was observed, and SIG-1451 was found to inhibit this upregulation. Iba-1, a microglial marker, was suppressed in SIG-1451-injected rats. To investigate the molecular mechanism underlying these effects, we used lipopolysaccharide (LPS)-stimulated rat immortalised Müller cells. The upregulation of C-C motif chemokine 2 by LPS stimulation was significantly inhibited by SIG-1451 treatment, and Western blot analysis revealed a decrease in phosphorylated I-κB levels. These results indicate that SIG-1451 indirectly protects photoreceptor cells by attenuating light damage progression, by affecting the inflammatory responses.

Hot Hydrogen Atom Irradiation of Protonated/Deprotonated Peptide in an Ion Trap Facilitates Fragmentation through Heated Radical Formation.

Tandem mass spectrometry with fragmentation involving the reaction with hydrogen atoms is expected to be useful for the analysis of peptides and proteins. In general, hydrogen atoms preferentially react with odd-electron radicals. The attachment of hydrogen atoms to even-electron peptide ions is barely observed because of their low reaction rate. To date, only the methodology developed by our group has successfully induced the fragmentation of even-electron peptide ions by reacting with hydrogen atoms. In the present study, we focused on the temperature of the peptide ions and hydrogen atoms in an ion trap mass spectrometer to understand the mechanism of the corresponding reaction. Because the reaction between even-electron peptide ions and hydrogen atoms has a significant transition state barrier, the use of hot hydrogen atoms is required to initiate the reaction. The reaction contributes to increase the internal energy of the resultant peptide radicals because the heat of reaction and kinetic energy of the hydrogen atom are converted to the internal energy of the product. The resultant oxygen- and carbon-centered peptide radicals undergo radical-induced fragmentation with sub-picosecond and sub-millisecond time scales, respectively.

Self-Organized Growth of 111-Oriented (VNbTaMoW)N Nanorods on MgO(001).

Refractory high-entropy alloy nitride, (VNbTaMoW)N, layers are grown on single-crystalline MgO(001) via ultrahigh vacuum direct current magnetron sputtering of a VNbTaMoW target in Kr/N2 gas mixtures at 1073 K. X-ray diffraction, scanning and transmission electron microscopy, and energy dispersive X-ray spectroscopy characterizations revealed the formation of B1-structured, 111-textured (V0.21Nb0.18Ta0.19Mo0.21W0.21)N1.05 with lattice parameter a = 0.4249 nm. The alloy nitride film exhibits dense columnar microstructure near the substrate-film interface with coherent 001 grain growth limited to a few tens of nanometers, followed by an outgrowth of quasi one-dimensional nanorods with 3-fold symmetric facets. We attribute the self-organized growth of rather unusual 111-textured nanorods on isostructural MgO(001) to kinetic limitations of the sputter-deposition process exacerbated by the sluggish diffusion of the multicomponent adspecies and the preferential growth of {111} crystals.

Gas-Phase Peptide Fragmentation Induced by Hydrogen Attachment, from Principle to Sequencing of Amide Nitrogen-Methylated Peptides.

Tandem mass spectrometry (MS/MS) with radical-based fragmentation was developed recently, which involves the reaction of hydrogen atoms and peptides in a process called hydrogen attachment/abstraction dissociation (HAD). HAD mainly produces [cn + 2H]+ and [zm + 2H]+ via hydrogen attachment to the carbonyl oxygen on the peptide backbone. In addition, HAD often generates [an + 2H]+ and [xm + 2H]+. To explain the formation of [an + 2H]+ and [xm + 2H]+, hydrogen attachment to the carbonyl carbon atom on the peptide backbone is proposed to initiate Cα-C bond cleavage. The resultant hydrogen-abundant oxygen-centered radical intermediate undergoes radical-induced dissociation to give [an + H]+• and [xm + 2H]+. Subsequently, [an + 2H]+ was produced by the reaction of [an + H]+• and a hydrogen atom. The fragment ions formed by the cleavage of N-Cα and Cα-C bonds are observed in the HAD-MS/MS spectra, and the mass differences of these fragment ions correspond to the mass of peptide bonds. Consequently, HAD-MS/MS allows the identification of post-translational modifications on the peptide backbone. In addition, HAD-MS/MS provides a consecutive series of [cn + 2H]+ and [an + 2H]+ as the N-terminal fragments, as well as [zm + 2H]+ and [xm + 2H]+, which enables the sequencing of peptides with post-translational modification, including the discrimination of modifications on the side chain and backbone.

Lactone-Driven Ester-to-Amide Derivatization for Sialic Acid Linkage-Specific Alkylamidation.

Sialic acid attached to nonreducing ends of glycan chains via different linkages is associated with specific interactions and physiological events. Linkage-specific derivatization of sialic acid is of great interest for distinguishing sialic acids by mass spectrometry, specifically for events governed by sialyl linkage types. In the present study, we demonstrate that α-2,3/8-sialyl linkage-specific amidation of esterified sialyloligosaccharides can be achieved via an intramolecular lactone. The method of lactone-driven ester-to-amide derivatization for sialic acid linkage-specific alkylamidation, termed LEAD-SALSA, employs in-solution ester-to-amide conversion to directly generate stable and sialyl linkage-specific glycan amides from their ester form by mixing with a preferred amine, resulting in the easy assignments of sialyl linkages by comparing the signals of esterified and amidated glycan. Using this approach, we demonstrate the accumulation of altered N-glycans in cardiac muscle tissue during mouse aging. Furthermore, we find that the stability of lactone is important for ester-to-amide conversion based on experiments and density functional theory calculations of reaction energies for lactone formation. By using energy differences of lactone formation, the LEAD-SALSA method can be used not only for the sialyl linkage-specific derivatization but also for distinguishing the branching structure of galactose linked to sialic acid. This simplified and direct sialylglycan discrimination will facilitate important studies on sialylated glycoconjugates.

Plasma Amyloid-ß Biomarker Associated with Cognitive Decline in Preclinical Alzheimer's Disease.

BACKGROUND: Using immunoprecipitation-mass spectrometry, we recently developed and validated a plasma composite biomarker for the assessment of amyloid-ß (Aß) levels. However, as yet, its relationship with clinical outcomes remains unclear. OBJECTIVE: We aimed to examine the relationship between this plasma Aß composite biomarker and cognitive function in cognitively normal older adults in two independent cohorts. METHODS: Participants enrolled in the Australian Imaging, Biomarkers and Lifestyle (AIBL) study and the National Centre for Geriatrics and Gerontology (NCGG) study had undergone Aß neuroimaging using positron emission tomography (PET), cognitive assessments and provided blood samples. We derived a high-performance plasma Aß composite biomarker by immunoprecipitation with mass-spectrometry. RESULTS: Both continuous and categorical measures of the plasma Aß composite biomarker were significantly related to decline in episodic memory and executive function. The magnitude of effects of the plasma Aß composite on episodic memory and executive function were comparable to that observed for the effects of PET Aß levels on these same outcome measures. CONCLUSION: Several plasma Aß biomarkers have been developed, but none have yet been applied to investigate their relationship with cognitive outcomes. Our results have important implications for the use of this biomarker in the detection of at-risk individuals.

Acyltransferase that catalyses the condensation of polyketide and peptide moieties of goadvionin hybrid lipopeptides.

Fusions of fatty acids and peptides expand the structural diversity of natural products; however, polyketide/ribosomally synthesized and post-translationally modified peptides (PK/RiPPs) hybrid lipopeptides are relatively rare. Here we report a family of PK/RiPPs called goadvionins, which inhibit the growth of Gram-positive bacteria, and an acyltransferase, GdvG, which catalyses the condensation of the PK and RiPP moieties. Goadvionin comprises a trimethylammonio 32-carbon acyl chain and an eight-residue RiPP with an avionin structure. The positions of six hydroxyl groups and one double bond in the very-long acyl chain were determined by radical-induced dissociation tandem mass spectrometry, which collides radical ion species to generate C-C bond cleavage fragments. GdvG belongs to the Gcn5-related N-acetyltransferase superfamily. Unlike conventional acyltransferases, GdvG transfers a very long acyl chain that is tethered to an acyl carrier protein to the N-terminal amino group of the RiPP moiety. gdvG homologues flanked by PK/fatty acid and RiPP biosynthesis genes are widely distributed in microbial species, suggesting that acyltransferase-catalysed condensation of PKs and RiPPs is a general strategy in biosynthesis of similar lipopeptides.

Characterization of Polyethers Using Tandem Mass Spectrometry with Hydrogen Abstraction Dissociation and Thermal Activation.

The recently developed hydrogen radical-mediated fragmentation technique using an ion trap involving hydrogen attachment/abstraction dissociation-tandem mass spectrometry (HAD-MS/MS) was applied to the analysis of polyethylene glycol (PEG) and its derivatives. HAD was found to be initiated by hydrogen abstraction from carbon atoms in the polyether. Subsequently, the produced carbon-centered radical intermediates underwent radical-induced cleavage of their C-O bonds, with this process being facilitated by heating of the ion trap. The bond cleavage resulted in the formation of b fragments containing double bonds between carbon atoms. A counterpart c• alkoxy radical was discovered to be a fragile radical species. Consequently, c• underwent further radical-induced dissociation to produce small fragments during HAD-MS/MS with thermal activation. As a result, HAD-MS/MS with thermal activation through ion trap heating preferentially provided b fragments, facilitating identification of repeating units and individual end groups of the polyether analytes.

Ultra-high vacuum dc magnetron sputter-deposition of 0001-textured trigonal α-Ta2C/Al2O3(0001) thin films.

We report on the effects of substrate temperature (1073 K ≤ T s ≤ 1373 K) and deposition time t (= 3 ~ 30 min.) on the crystallinity of Ta2C/Al2O3(0001) thin films grown via ultra-high vacuum direct current magnetron sputtering of TaC target in 20 mTorr (2.7 Pa) pure Ar atmospheres. Using X-ray diffraction and transmission electron microscopy, we determine that the layers are 0001-oriented, trigonal-structured α-Ta2C at all T s. With increasing T s, we obtain smoother and thinner layers with enhanced out-of-plane coherency and decreasing unit cell volume. Interestingly, the Ta2C 0001 texture improves with increasing T s up to 1273 K above which the layers are relatively more polycrystalline. At T s = 1373 K, during early stages of deposition, the Ta2C layers grow heteroepitaxially on Al2O3(0001) with ( 0001 ) Ta 2 C ‖ ( 0001 ) Al 2 O 3 and [ 10 1 ¯ 0 ] Ta 2 C ‖ [ 11 2 ¯ 0 ] Al 2 O 3 . With increasing t, we observe the formation of anti-phase domains and misoriented grains resulting in polycrystalline layers. We attribute the observed enhancement in 0001 texture to increased surface adatom mobilities and the development of polycrystallinity to reduced incorporation of C in the lattice with increasing T s. We expect that our results help develop methods for the synthesis of high-quality Ta2C thin films.

Classification of Cutibacterium acnes at phylotype level by MALDI-MS proteotyping.

Cutibacterium acnes is a major commensal human skin bacteria. It is a producer of propionic acids that maintain skin acidic pH to inhibit the growth of pathogens. On the other hand, it is also associated with diseases such as acne vulgaris and sarcoidosis. C. acnes strains have been classified into six phylotypes using DNA-based approaches. Because several characteristic features of C. acnes vary according to the phylotype, the development of a practical method to identify these phylotypes is needed. For rapid identification of phylotypes for C. acnes strains, a matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) fingerprinting technique has been applied; however, some phylotypes have not been discriminated. We developed a high-throughput protein purification method to detect biomarker proteins by ultrafiltration. MALDI-MS proteotyping using profiling of identified biomarker peaks was applied for the classification of 24 strains of C. acnes, and these were successfully classified into the correct phylotypes. This is a promising method that allows the discrimination of C. acnes phylotypes independent of a DNA-based approach.

Hydrogen attachment dissociation of peptides containing disulfide bonds.

A combination of tandem mass spectrometry (MS/MS) and hydrogen attachment dissociation (HAD) is a useful method for peptide sequence analysis. In this study, gas-phase fragmentation induced by the attachment of hydrogen to peptides containing disulfide bonds was investigated. Hydrogen attachment induced the cleavage of either the disulfide or N-Cα bond, which competitively occurred during HAD. The disulfide bond cleavage proceeded through an intermediate, which contains a thiyl radical (-S˙) and a thiol group (-SH). In contrast, N-Cα bond cleavage produced an intermediate containing an enol-imine group and α-carbon radical. The intermediate α-carbon radical then attacked the disulfide bond, resulting in a cyclic [z]+ fragment. The counterpart, [c + H]+˙ with a thiyl radical underwent further hydrogen attachment, producing [c + 2H]+. Because both disulfide and N-Cα bonds were cleaved by a single hydrogen attachment event, HAD-MS/MS can provide sequence information for the backbone region in the disulfide loop.