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Sterically hindered imine-based non-heme complexes 4 and 5 rapidly self-assemble in acetonitrile at 25 °C, when the corresponding building blocks are added in solution in the proper ratios. Such complexes are investigated as catalysts for the H2O2 oxidation of a series of substrates in order to ascertain the role and the importance of the ligand steric hindrance on the action of the catalytic core 1, previously shown to be an efficient catalyst for aliphatic and aromatic C–H bond oxidation. The study reveals a modest dependence of the output of the oxidation reactions on the presence of bulky substituents in the backbone of the catalyst, both in terms of activity and selectivity. This result supports a previously hypothesized catalytic mechanism, which is based on the hemi-lability of the metal complex. In the active form of the catalyst, one of the pyridine arms temporarily leaves the iron centre, freeing up a lot of room for the access of the substrate.

Pompe disease (PD) is caused by deficiency of the enzyme acid α-glucosidase resulting in glycogen accumulation in lysosomes. Clinical symptoms include skeletal myopathy, respiratory failure, and cardiac hypertrophy. We studied plasma proteomic and lipidomic profiles in 12 PD patients compared to age-matched controls. The proteomic profiles were analyzed by nLC-MS/MS SWATH method. Wide-targeted lipidomic analysis was performed by LC-IMS/MS, allowing to quantify >1100 lipid species, spanning 13 classes. Significant differences were found for 16 proteins, with four showing the most relevant changes (GPLD1, PON1, LDHB, PKM). Lipidomic analysis showed elevated levels of three phosphatidylcholines and of the free fatty acid 22:4, and reduced levels of six lysophosphatidylcholines. Up-regulated glycolytic enzymes (LDHB and PKM) are involved in autophagy and glycogen metabolism, while down-regulated PON1 and GPLD1 combined with lipidomic data indicate an abnormal phospholipid metabolism. Reduced GPLD1 and dysregulation of lipids with acyl-chains characteristic of GPI-anchor structure suggest the potential involvement of GPI-anchor system in PD. Results of proteomic analysis displayed the involvement of multiple cellular functions affecting inflammatory, immune and antioxidant responses, autophagy, Ca2+ -homeostasis, and cell adhesion. The combined multi-omic approach revealed new biosignatures in PD, providing novel insights in disease pathophysiology with potential future clinical application.

Cystic fibrosis (CF) is the most common rare disease caused by a mutation of the

Extremely sensitive food-allergic patients may react to very small amounts of allergenic foods. Precautionary allergen labelling (PAL) warns from possible allergenic contaminations. We explored the ability of proteomic methods to identify minute amounts of milk/egg allergens in a brand of PAL-labelled milk- and egg-free biscuits. We evaluated the reactivity of children with severe milk and egg allergy, by oral food challenge. Traces of milk and/or egg allergens in biscuits were measured by two different liquid-chromatography-mass spectrometry methods. The binding of patient's serum with egg/milk proteins was assessed at immunoblotting. None of the patients reacted to biscuits. Egg and milk proteins were found under the limit of detection of 0.6 µg/g for milk and egg (method A), and of 0.1 and 0.3 µg /g for milk and egg, respectively (method B). The immunoblots did not show milk/egg proteins in the studied biscuits. Our biscuits did not contain allergens of clinical significance. Their milk/egg content is far lower than 4 µg of milk or egg protein per gram of product, the minimal doses considered theoretically capable of causing reactions. With high sensitivity, proteomic assessments predict the harmlessness of very small amount of allergenic foods and can be used to avoid unnecessary PAL.

Background Hepatocellular carcinoma (HCC) is one of the most common and lethal malignant tumours worldwide. Sorafenib (SOR) is one of the most effective single-drug systemic therapy against advanced HCC, but the identification of novel combination regimens for a continued improvement in overall survival is a big challenge. Recent studies highlighted the crucial role of focal adhesion kinase (FAK) in HCC growth. The aim of this study was to investigate the antitumor effects of three different FAK inhibitors (FAKi), alone or in combination with SOR, using in vitro and in vivo models of HCC. Methods The effect of PND1186, PF431396, TAE226 on cell viability was compared to SOR. Among them TAE226, emerging as the most effective FAKi, was tested alone or in combination with SOR using 2D/3D human HCC cell line cultures and HCC xenograft murine models. The mechanisms of action were assessed by gene/protein expression and imaging approaches, combined with high-throughput methods. Results TAE226 was the more effective FAKi to be combined with SOR against HCC. Combined TAE226 and SOR treatment reduced HCC growth both in vitro and in vivo by affecting tumour-promoting gene expression and inducing epigenetic changes via dysregulation of FAK nuclear interactome. We characterized a novel nuclear functional interaction between FAK and the NuRD complex. TAE226-mediated FAK depletion and SOR-promoted MAPK down-modulation caused a decrease in the nuclear amount of HDAC1/2 and a consequent increase of the histone H3 lysine 27 acetylation, thus counteracting histone H3 lysine 27 trimethylation. Conclusions Altogether, our findings provide the first evidence that TAE226 combined with SOR efficiently reduces HCC growth in vitro and in vivo. Also, our data highlight that deep analysis of FAK nuclear interactome may lead to the identification of new promising targets for HCC therapy.

Autism spectrum disorders (ASDs) are neurodevelopmental disorders characterized by behavioral alterations and currently affect about 1% of children. Significant genetic factors and mechanisms underline the causation of ASD. Indeed, many affected individuals are diagnosed with chromosomal abnormalities, submicroscopic deletions or duplications, single-gene disorders or variants. However, a range of metabolic abnormalities has been highlighted in many patients, by identifying biofluid metabolome and proteome profiles potentially usable as ASD biomarkers. Indeed, next-generation sequencing and other omics platforms, including proteomics and metabolomics, have uncovered early age disease biomarkers which may lead to novel diagnostic tools and treatment targets that may vary from patient to patient depending on the specific genomic and other omics findings. The progressive identification of new proteins and metabolites acting as biomarker candidates, combined with patient genetic and clinical data and environmental factors, including microbiota, would bring us towards advanced clinical decision support systems (CDSSs) assisted by machine learning models for advanced ASD-personalized medicine. Herein, we will discuss novel computational solutions to evaluate new proteome and metabolome ASD biomarker candidates, in terms of their recurrence in the reviewed literature and laboratory medicine feasibility. Moreover, the way to exploit CDSS, performed by artificial intelligence, is presented as an effective tool to integrate omics data to electronic health/medical records (EHR/EMR), hopefully acting as added value in the near future for the clinical management of ASD.

Food allergy is the disease where the immune system is elicited by antigens in food. Although innocuous for immune-tolerant individuals, an ever-growing number of food allergenic people are being registered worldwide. To date, no treatment to cure food allergy is available and the disease management relies on the careful exclusion of the allergenic food from the diet of the allergic individuals. Great efforts are ongoing to clarify the allergenic mechanisms of the diverse allergenic proteins of food origin, aimed to both designing suitable therapies and for a timely and precise diagnosis of the allergic condition. Among the other omics sciences, mass spectrometry (MS)-based proteomics is gaining a steadily increasing interest by the whole scientific community acknowledged its high versatility. In the present work, the latest proteomics based-studies on allergenic proteins are reviewed to provide guidance on the different MS-based methodologies adopted in the research on food allergens. Our review points to highlight the strengths of the MS-based proteomics and how these have been exploited to address specific research questions. Also, the most common drawbacks encountered in a proteomic study are discussed, providing an overview that helps novel researchers in choosing the more suitable experimental workflow. SIGNIFICANCE: Wide wealth of knowledge arising from the various MS-based proteomic investigations is improving our understanding of food allergy through molecular characterization of food allergens. The present work reviews the key aspects to be evaluated while investigating food allergens by means of MS-based proteomics and provide guidance to the novel research groups approaching to the fascinating world of MS-based food allergens detection.

Carbapenem-resistant Acinetobacter baumannii strains cause life-threatening infections due to the lack of therapeutic options. Although the main mechanisms underlying antibiotic-resistance have been extensively studied, the general response to maintain bacterial viability under antibiotic exposure deserves to be fully investigated. Since the periplasmic space contains several proteins with crucial cellular functions, besides carbapenemases, we decided to study the periplasmic proteome of the multidrug-resistant (MDR) A. baumannii AB5075 strain, grown in the absence and presence of imipenem (IMP). Through the proteomic approach, 65 unique periplasmic proteins common in both growth conditions were identified: eight proteins involved in protein fate, response to oxidative stress, energy metabolism, antibiotic-resistance, were differentially expressed. Among them, ABUW_1746 and ABUW_2363 gene products presented the tetratricopeptide repeat motif, mediating protein-protein interactions. The expression switch of these proteins might determine specific protein interactions to better adapt to changing environmental conditions. ABUW_2868, encoding a heat shock protein likely involved in protection against oxidative stress, was upregulated in IMP-exposed bacteria. Accordingly, the addition of periplasmic proteins from A. baumannii cultured with IMP increased bacterial viability in an antioxidant activity assay. Overall, this study provides the first insights about the composition of the periplasmic proteins of a MDR A. baumannii strain, its biological response to IMP and suggests possible new targets to develop alternative antibiotic drugs.

Lam et al. characterize a novel hematological/autoinflammatory disorder due to a de novo recurrent missense mutation of CDC42. The authors use in silico, in vitro, and in vivo analyses to correlate the molecular mechanisms altering CDC42 function to the observed phenotype., Hemophagocytic lymphohistiocytosis (HLH) is characterized by immune dysregulation due to inadequate restraint of overactivated immune cells and is associated with a variable clinical spectrum having overlap with more common pathophysiologies. HLH is difficult to diagnose and can be part of inflammatory syndromes. Here, we identify a novel hematological/autoinflammatory condition (NOCARH syndrome) in four unrelated patients with superimposable features, including neonatal-onset cytopenia with dyshematopoiesis, autoinflammation, rash, and HLH. Patients shared the same de novo CDC42 mutation (Chr1:22417990C>T, p.R186C) and altered hematopoietic compartment, immune dysregulation, and inflammation. CDC42 mutations had been associated with syndromic neurodevelopmental disorders. In vitro and in vivo assays documented unique effects of p.R186C on CDC42 localization and function, correlating with the distinctiveness of the trait. Emapalumab was critical to the survival of one patient, who underwent successful bone marrow transplantation. Early recognition of the disorder and establishment of treatment followed by bone marrow transplant are important to survival., Graphical Abstract

Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition. SIGNIFICANCE: This paper would represent a reference work for investigations on gut microbiota in early life, from both a microbiological and a functional proteomic point of view. We focused on the shaping of the mouse gut microbiota in dependence on the feeding modality, defining a reliable taxonomic description, highlighting some functional characteristics of the microbial community, and performing a first quantitative evaluation by data independent analysis in metaproteomics.

Diffuse intrinsic pontine glioma (DIPG) and pediatric glioblastoma (pGBM) are heterogeneous brain tumors characterized by different anatomical and molecular subgroups and the presence of genetically and phenotypically distinct subclonal cell populations. It is recognized that exosomes mediate cross-talk among tumor cells. We hypothesize that there are different exosome-mediated paracrine signaling promoting tumour progression in DIPG and pGBM. Our aim was to determine the specific DIPG and pGBM-derived exosome oncogenic signatures. We used a panel of fifteen patient primary-derived cell lines, which included nine DIPG (seven H3.3 K27M, one H3.3 K27M/ACVR1 and one H3.1 K27M/ACVR1), one diffuse midline glioma H3.3 K27M and three GBM (one H3.3 G34R and two histone WT). Conditioned medium was collected from cells maintained under stem-cell culture condition, adherent on laminin and/or as neurospheres (NS), and exosomes harvested through serial centrifugations. Electron microscopy demonstrated that the isolated microvescicles are exosomes sized between 50–80 nm. DIPG derived-exosomes appeared to have a variable cargo of total protein (µg)/10(6) cells, which was higher than for pGBM-exosomes. Proteomic analysis revealed that proteins associated with vesicle docking, exocytosis and synaptic transmission were exclusively enriched in pontine-derived exosomes, while cell-cell and cell-matrix interaction proteinswere exclusive tohemispheric ones. Proteins in common to the two locations were involved in metabolism and energy pathways. Interestingly, principle component analysis on the different molecular subgroups suggests that ACVR1 may be not implicated in the exosomal proteomic signature. Exosomal miRNA profile appeared to be driven by the two main histone mutated subgroups H3.3 K27M and H3.1 K27M with the latter overexpressing hypoxia and angiogenic-associated miRNAs, leading to distinct oncogenic programs with different specific potential therapeutic targets. This study aimed to development new diagnostic/prognostic tools for DIPG and pGBM patients. Further investigations are aimed to identify new therapeutic strategies to inhibit the cross-talk among glioma subpopulations.

The full development of the mammalian immune system occurs after birth upon exposure to non self-antigens. The gut is the first site of bacterial colonization where it is crucial to create the appropriate microenvironment able to balance effector or tolerogenic responses to external stimuli. It is a well-established fact that at mucosal sites bacteria play a key role in developing the immune system but we ignore how colonising bacteria impact the maturation of the spleen. Here we addressed this issue. Taking advantage of the fact that milk SIgA regulates bacterial colonization of the newborn intestine, we generated immunocompetent mice born either from IgA pro-efficient or IgA deficient females. Having demonstrated that SIgA in maternal milk modulates neonatal gut microbiota by promoting an increased diversity of the colonizing species we also found that immunocompetent pups, not exposed to milk SIgA, fail to properly develop the FDC network and primary follicles in the spleen compromising the response to T-dependent antigens. The presence of a less diverse microbiota with a higher representation of pathogenic species leads to a fast replenishment of the marginal zone and the IgM plasma cell compartment of the spleen as well as IgA plasma cells in the gut.

The exposure of blood to an artificial surface such as the haemodialysis membrane results in the nearly instantaneous deposition of a layer of plasma proteins. The composition of the protein layer profoundly influences all subsequent events, and to a large extent determines the biocompatibility of the biomaterial. In the present study, we examine the protein adsorption capacity and coagulation profiles of the polysulfone-based helixone material in comparison to cellulose triacetate. A differential profiling investigation using shotgun proteomics data-independent analysis was applied to eluates obtained with each membrane after a dialysis session, in order to assess the function of desorbed proteins. Functional classification and network analysis performed using bioinformatics tools shed light on the involvement of adsorbed proteins into important molecular processes, such as lipid transport and metabolism, cell growth differentiation and communication, and the coagulation cascade. The collected evidence was further validated by targeted mass spectrometry using selected reaction monitoring on proteotypic transitions of key protein effectors, confirming the different panels of adsorbed protein on each membrane. The coagulation profile during haemodialysis of patients under polysulfone-based helixone filter cartridges was also assessed showing a slightly higher platelet activation profile after the dialysis session. The overall collected evidence highlights a modulation of the coagulation biological pathway during haemodialysis, which is largely influenced by the biomaterial used. Refereed/Peer-reviewed

The tissue inhibitor of metalloproteinase TIMP3 is a stromal protein that restrains the activity of both protease and receptor in the extracellular matrix and has been found to be down-regulated in diabetic nephropathy (DN), the leading cause of end-stage renal disease in developed countries. In order to gain deeper insights on the association of loss of TIMP3 and DN, we performed differential proteomic analysis of kidney and blood metabolic profiling of wild-type and Timp3-knockout mice before and after streptozotocin (STZ) treatment, widely used to induce insulin deficiency and hyperglycemia. Kidney proteomic data and blood metabolic profiles suggest significant alterations of peroxisomal and mitochondrial fatty acids β-oxidation in Timp3-knockout mice compared to wild-type mice under basal condition. These alterations were exacerbated in response to STZ treatment. Proteomic and metabolomic approaches showed that loss of TIMP3 alone or in combination with STZ treatment results in significant alterations of kidney lipid metabolism and peripheral acylcarnitine levels, supporting the idea that loss of TIMP3 may generate a phenotype more prone to DN.

Among the most common stable-isotope labeling strategies, the reaction of formaldehyde with peptides in the presence of NaCNBH₃ features many attractive aspects that are conducive to its employment in quantitation experiments in proteomics. Reductive amination, with formaldehyde and d(2)-formaldehyde, is reported to be a fast, easy, and specific reaction, undoubtedly inexpensive if compared with commercially available kits for differential isotope coding. Acetaldehyde and d(4)-acetaldehyde could be employed as well without a substantial increase in terms of cost, and should provide a wider spacing between the differentially tagged peptides in the mass spectrum. Nevertheless, only a single paper reports about a diethylation approach for quantitation. We undertook a systematic analytical investigation on the reductive amination of some standard peptides pointing out the occasional occurrence of side reactions in dependence of pH or reagents order of addition, particularly observing the formation of cyclic adducts ascribable to rearrangements involving the generated Schiff-base and all the nucleophilic sites of its chemical environment. We also tried to evaluate how much this side-products amount may impair isotope coded relative quantitation.

In order to characterize newborn mouse gut microbiota phylotypes in very early-life stages, an original metaproteomic pipeline, based on LC–MS 2 -spectra and Mascot driven NCBI non-redundant repository database interrogation was developed. An original computational analysis assisted in the generation of a taxonomic gut architecture from protein hits to operational taxonomic units (OTUs) and related functional categories. Regardless of the mouse's genetic background, a prevalence of Firmicutes (Lactobacillaceae) and Proteobacteria (Enterobacteriaceae) was observed among the entire Eubacteria taxonomic node. However, a higher abundance of Firmicutes was retrieved for Balb/c gut microbiota compared to Rag2 ko mice, the latter was mainly characterized by a Proteobacteria enriched microbiota. The metaproteomic-obtained OTUs were supported, for the identification (ID) of the cultivable bacteria fraction, corroborated by axenic culture-based MALDI-TOF MS IDs. Particularly, functional analysis of Rag2 ko mice gut microbiota proteins revealed the presence of abundant glutathione, riboflavin metabolism and pentose phosphate pathway components, possibly related to genetic background. The metaproteomic pipeline herein presented may represent a useful tool to investigate the highly debated onset of the human gut microbiota in the first days of life, when the bacterial composition, despite its very low diversity (complexity), is still very far from an exhaustive description and other complex microbial consortia. Biological significance The manuscript deals with a “frontier” topic regarding the study of the gut microbiota and the application of a metaproteomic pipeline to unveil the complexity of this fascinating ecosystem at the very early stages of life. Indeed during these phases, its diversity is very low but the bacterial content is highly “instable”, and the relative balance between mucosal and fecal bacteria starts its dynamics of “fight” to get homeostasis. However, in the neonatal period, especially immediately after birth, a comprehensive description of this microbial eco-organ is still lacking, while it should be mandatory to highlight its first mechanisms of homeostasis and perturbation, while it co-develops with and within the host species. In order to unravel its low but almost unknown microbial community multiplicity, the newborn mouse gut, characterized by a “very” low complexity, was herein selected as model to design a LC–MS 2 -based shotgun metaproteomic approach, potentially suitable to study onset and shaping in human newborns. A microbiological semi-automatic computational analysis was performed to infer gut phylotypes; such as proof of evidence, related OTUs were compared to axenic-culture-based MALDI-TOF MS IDs showing consistency at family and phyla levels for the bacterial cultivable fraction. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

Grana Padano is a typical Italian Protected Designation of Origin (PDO) hard cheese largely consumed all over the world. The major problem during its production is represented by late blowing. Clostridia are gasogen bacteria responsible of the swelling during ripening, and they are partially counteracted by the use of egg white lysozyme as additive. In this work was applied, for the first time in cheese, a metaproteomic approach that identified the functional dynamics of microbial consortia in relation to the number of clostridial spores and lysozyme treatment using experimental samples of Grana Padano cheese. We used a combined custom BLAST +/MEGAN/STAMP approach to obtain a global taxonomic view associated to low and high clostridial spores cheese without and with lysozyme. Main differences were highlighted in the bacilli class. Functional analysis with SEED provided a deep view into several metabolic pathways, highlighting the subsystems “amino acid and derivatives” and “clustering-based subsystem” as the targeted subsystems during lysozyme treatment in the high spore group. In these subsystems, acetate kinase from clostridia was one of the main enzymes affected by the lysozyme treatment. Biological significance Metaproteomics is a very promising and useful technique in the control of food safety and quality, from fresh products until ‘ready to eat’ food. Tools able to identify at molecular level the dynamic fingerprinting of food microbiota could be of great help to improve food safety and quality.

A new team player: The "three-point interaction" model, which is usually employed to rationalize chiral recognition, does not account for the amazing enantioselectivity measured for the receptors of many proteic acceptors. Gas-phase experiments have indicated that at least a fourth "player" must be considered: the rigidity that a receptor opposes to distortions of its cavity resulting from noncovalent interactions with a chiral molecule (see picture).

Human medulloblastoma (MB) is a malignant brain tumor that comprises four distinct molecular subgroups including the Sonic Hedgehog (SHH)-MB group. A leading cause of the SHH subgroup is an aberrant activation of the SHH pathway, a developmental signaling that regulates postnatal development of the cerebellum by promoting the mitotic expansion of granule neural precursors (GNPs) in the external granule layer (EGL). The abnormal SHH signaling pathway drives not only SHH-MB but also its cancer stem-like cells (SLCs), which represent a fraction of the tumor cell population that maintain cancer growth and have been associated with high grade tumors. Here, we report the first proteomic analysis of human SHH-MB SLCs before and after Retinoic Acid (RA)-induced differentiation. A total of 994 nLC-MS buckets were statistically analysed returning 68 modulated proteins between SLCs and their differentiated counterparts. Heat Shock Protein 70 (Hsp70) was one of the proteins that characterized the protein profile of SLCs. By means of Ingenuity Pathway Analysis (IPA), Genomatix analysis and extending the network obtained using the differentially expressed proteins we found a correlation between Hsp70 and the NF-κB complex. A key driver of the SHH-MB group is cMET whose downstream proliferation/survival signalling is indeed via PI3K/Akt/NF-κB. We confirmed the results of the proteomic analysis by western blot, underlining that a P-p65/NF-κB activatory complex is highly expressed in SLCs. Taking together these results we define a new protein feature of SHH-MB SLCs. Refereed/Peer-reviewed

In the acetylation of an oxygenated calix[4]arene homologue in the presence of CsF as a base, relaxation of the reaction system to the equilibrium composition takes place through several intra- and intermolecular steps that can be easily controlled to obtain the various acetyl derivatives. The effect of different bases is also discussed.

[structure: see text] The whole set (five compounds) of partially O-methylated products of p-tert-butyl[3.1.3.1]homooxacalixarene, currently named p-tert-butyltetrahomodioxacalix[4]arene, have been prepared. Their structure has been investigated in solution through NMR techniques and in the solid state by single-crystal X-ray diffraction. A systematic investigation, extended to the parent tetraphenol and to the tetramethyl ether derivative, has been carried out on the complexation of tetramethylammonium, acetylcholine, N-methylpyridinium, and tetraethylammonium picrate in CDCl3. The observed trends in the binding and in the selectivity of the strictly related hosts could be analyzed on the basis of the varying importance of intramolecular hydrogen bonding and its effects on the conformation of the free and of the complexed ligands. On increasing the number of methyl ether functions, the cone conformation appears to be relatively less stable but deeper, so small organic cations can be more effectively encircled.

Reaction of the expanded calixarenes p-R-tetrahomodioxacalix[4]arenes (R=methyl, phenyl) with uranyl ions in the presence of amines (butylamine, pyrrolidine, triethylamine) gives complexes in which the metal ion is in a distorted square-planar, tetra-phenoxide, equatorial environment. Changes in para-substituents and/or in the amine lead to different supramolecular assemblies, resulting in sheets or columns held by hydrogen bonds and cation–π interactions. The importance of primary or secondary amines, able to give divergent hydrogen bonds, to promote such structures, is evidenced.

Among the most common stable-isotope labeling strategies, the reaction of formaldehyde with peptides in the presence of NaCNBH₃ features many attractive aspects that are conducive to its employment in quantitation experiments in proteomics. Reductive amination, with formaldehyde and d(2)-formaldehyde, is reported to be a fast, easy, and specific reaction, undoubtedly inexpensive if compared with commercially available kits for differential isotope coding. Acetaldehyde and d(4)-acetaldehyde could be employed as well without a substantial increase in terms of cost, and should provide a wider spacing between the differentially tagged peptides in the mass spectrum. Nevertheless, only a single paper reports about a diethylation approach for quantitation. We undertook a systematic analytical investigation on the reductive amination of some standard peptides pointing out the occasional occurrence of side reactions in dependence of pH or reagents order of addition, particularly observing the formation of cyclic adducts ascribable to rearrangements involving the generated Schiff-base and all the nucleophilic sites of its chemical environment. We also tried to evaluate how much this side-products amount may impair isotope coded relative quantitation.

In the title compound, 4,7,13,16,21,24-hexaoxa-1,10-diazoniabicyclo[8.8.8]hexacosane dioxo[7,13,21,27-tetraphenyl-3,17-dioxapentacyclo[23.3.1.1 5,9 .1 11,15 .1 19,23 ]ditriaconta-1(29),5,7,-9(30),11(31),12,14,19(32),20,22,25,27-dodecaene-29,30,31,32-tetraolato] uranium dimethyl sulfoxide trisolvate, (C 18 H 38 -N 2 O 6 )[U(C 54 H 40 O 6 )O 2 ].3C 2 H 6 OS, the uranyl ion is bound to the four phenoxide groups of the deprotonated p-phenyl-tetrahomodioxacalix[4]arene ligand in a cone conformation, resulting in a dianionic complex. The diprotonated [2.2.2]cryptand counter-ion is located in the cavity defined by the eight aromatic rings of the homooxacalixarene, where it is held by cation-anion, cation-π and possibly C-H...π interactions. Dimerization in the packing leads to the formation of sandwich assemblages in which two diprotonated [2.2.2]cryptands are encompassed by two uranyl complexes.

Two related compounds containing p-tert-butyl-o-methyl­ene-linked phenol or phenol-derived subunits are described, namely 5,5′-di-tert-butyl-2,2′-di­hydroxy-3,3′-methyl­ene­di­benz­aldehyde, C23H28O4, (I), and 6,6′-di-tert-butyl-8,8′-methyl­ene­bis­(spiro­[4H-1,3-benzo­di­oxin-2,1′-cyclo­hexane]), C35H48O4, (II). Both compounds adopt a `butterfly' shape, with the two phenol or phenol-derived O atoms in distal positions. Phenol and aldehyde groups in (I) are involved in intramolecular hydrogen bonds and the two dioxin rings in (II) are in distorted half-chair conformations.

The enantioselective interactions between chiral tetra-amidic receptors and nucleosides have been investigated by the ESI-IT-MS and ESI-FT-ICR-MS methodologies. Configurational effects on the CID fragmentation of diastereomeric [M(H)(2)•H•A](+) aggregates (A = 2'-deoxycytidine dC, citarabine (ara-C) were found to be mostly offset by isotope effect in [S(X)(2)•H•A](+) (X = H, D) differently from the results obtained on the analogues (A = cytidine C and gemcitabine G). This result points the involvement of two different nucleoside/tetraamide isoforms. The structural differences of the [M(H)(2)•H•A](+) (A = C and G) complexes vs. the [M(H)(2)•H•A](+) (dC and ara-C) ones is fully confirmed by the kinetics of their uptake of the 2-aminobutane enantiomers, measured by FT-ICR mass spectrometry. Indeed, uptake of the 2-aminobutane enantiomers by [M(H)(n)•H•A](+) (n = 1,2; A = dC and ara-C) complexes is reversible, while that by [M(H)(n)•H•A](+) (n = 1,2; A = C and G) is not. The most encouraging result concerning the measured fragmentation and kinetic differences between C and ara-C, that are just epimers, indicates the possibility to subtly modulate the non-covalent drug/receptor interactions, through the electronic properties of the 2'-substituent on the nucleoside furanose ring, and furthermore on its three-dimensional position.

The interconverting stereoisomers of tri-o-thymotide have been separated by HPLC on chiral stationary phases and the temperature dependence of the dynamic chromatographic patterns has been interpreted in terms of exchange between enantiomeric propeller and helical conformations. Computed low energy structures and CD spectra were used in absolute configuration assignment.

The reactivity of proton-bound diastereomeric [M·H·A]+ complexes (A = amino acid; M = “strapped” tetra-amide macrocycle) towards the 2-aminobutane enantiomers (B) has been investigated in the gas phase by ESI-FT-ICR mass spectrometry. The displacement of the A guest from the diastereomeric [M·H·A]+ complexes by reaction with B exhibits a distinct enantioselectivity which markedly depend upon the presence of a π ring in A and on the nature of the intramolecular chain in the strapped macrocycle, whether –(CH2)10– (II) or –(C2H4O)5– (III). The emerging picture confirms the view that the chiral tetra-amide macrocycle II, characterized by an intramolecular decamethylene chain, may acquire in the gas phase a different conformation by induced fit on complexation of the selected A guests on the convex face of the host. This leads to the coexistence in the gas phase of stable diastereomeric [M·H·A]+ eq–eq and ax–ax structures, in proportions depending on the configuration of A and M and characterized by different stability and reactivity towards the 2-aminobutane enantiomers. When the decamethylene chain of the host is replaced by the –(CH2CH2O)5– chain, as in III, the guest A is blocked on the concave face of the host by complexation of its ammonium group by the “crown-ether”-like chain of the host and, therefore, the B-to-A displacement exhibits a more pronounced enantioselectivity.

Platelets, the smallest human blood cells component, have a key role in the control of haemostasis and thrombosis but they have also been shown to be implicated in a number of different pathological states because of their involvement also in the process of inflammation end its resolution. Their peculiar anucleated morphology render the proteomics an intriguing approach to understand their biology. Given the high impact of platelet in different diseases we have started a systematic investigation of protein repertoire in controlled platelet preparation.Platelets have been extracted from blood of healthy donors (n=6) collected by venipuncture in Vacutainer. The quality of the preparation was assessed by observation and enumeration in a Bürker chamber with a conventional tissue culture microscope. To characterize human platelets proteome we analysed the pool of purified platelets combining two proteomic approaches: 2-DE separation combined with Mass Spectrometry and nanoscale ultra performances LC-MS(E) shotgun proteomics experiments.The 2D gel analysis leads an average of 1900 protein spots, after the filtering of "noise" and "false positive" spots, over 500 were selected to be eligible for further analysis given their optimal spot quality value. To perform the analysis by ion accounting shotgun proteomic approach, based on nano ultra performance liquid chromatography (nUPLC) coupled to MS(E) processing of continuum LC-MS data, the same pool of samples was subject to liquid phase tryptic digestion and the peptide obtained used for the experiments. All the data obtained were analysed using ProteinLynx GlobalServer v2.3 (PLGS, Waters). Three analytical replicates run were acquire in high/low energy modes and associated to a human protein database returning the identification of 100 distinct genes. Comparative analysis of the Gene Ontology has been performed to evaluate the differential functional representation of the molecular repertoire investigated with these two orthogonal approaches.The overall molecular function classification revealed differences between the two proteomic approaches. In particular, we found significant differences in cytoskeletal proteins (19.65% 2-DE versus 45.60 Shotgun) and receptors (0,92% 2-DE versus 6.90% Shotgun).

The aggregates of three new isomeric chiral bola-amphiphiles have been taken into consideration as models for investigating chiral recognition in biological membranes. The recognition capabilities of the aggregates were explored following (by CD and HPLC experiments) the shift in the equilibrium between the inter-converting enantiomers of a biphenylic derivative and bilirubin, used as markers of chirality. The chiral recognition experiments were performed under different pH and concentration conditions. The results were compared with those relative to the aggregates formed by an equimolar mixture of single head/single chain amphiphiles that mimic the structure of the bola surfactant devoid of a covalent link.

Conformational factors in self-assembled chiral tetraamide macrocycles control their gas-phase enantioselectivity towards the ethyl ester of naphthylalanine to levels typical of enzymes.

A series of chiral tris-(1,10)-phenanthroline iron(II) complexes have been resolved by HPLC on chiral stationary phases based on either cellulose tris-(3,5-dimethylphenylcarbamate) or teicoplanin. At sub ambient temperatures, baseline separation of the enantiomers was observed for five different iron(II) complexes featuring substituted phenanthroline ligands. Dynamic HPLC profiles were observed near or above room temperature, indicating on-column Delta/Lambda enantiomerization. Rate constants for the Delta/Lambda interconversion in free solution and during chromatography were obtained by thermal racemization experiments and by computer simulation of the HPLC dynamic plots, respectively.

Simple biomembrane models, namely micellar aggregates formed by enantiopure sodium N-acylprolinates, are able to convert the racemic mixture of bilirubin-IXalpha into an enantiomerically enriched mixture, thus suggesting a possible role of chirality in bilirubin toxicity due to the perturbation of neuron membrane dynamics. The length of alkyl chain does not influence the extent of equilibrium displacement, however, it affects the conformation of bilirubin, thus confirming the role of lipid structure in the membrane/bilirubin interaction, and suggesting a non-superficial main site of association.

The chirality of micellar aggregates formed by surfactants derived from l -proline was investigated by using two chiral biphenylic derivatives as probes of chirality. The investigation carried out by 1H NMR, circular dichroism, and HPLC on chiral phase demonstrates that chiral recognition may occur in sites of the aggregates far from the head-group stereogenic centers and it is due to interaction with a whole region of the aggregate rather than with a single monomer in the aggregate. Subtle changes of the structure of the monomer influence the aggregation properties of the surfactants and its expression of chirality.

Two compounds containing 1,3-benzodioxin groups are reported, namely (+/-)-6-tert-butyl-8-hydroxymethyl-2-phenyl-4H-1,3-benzodioxin, C(19)H(22)O(3), (I), and 2,2,2',2',6,6'-hexamethyl-8,8'-methylenebis(4H-1,3-benzodioxin), C(23)H(28)O(4), (II). The hydroxy groups of neighbouring molecules in (I) are hydrogen bonded to each other, giving rise to double-row chains. The molecule in (II) adopts a 'butterfly' conformation, with the O atoms in distal positions. In both compounds, the dioxin rings are in distorted half-chair conformations.