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Currently, animal tests are being used to confirm the potency and lack of toxicity of toxoid vaccines. In a consistency approach, animal tests could be replaced if production consistency (compared to known good products) can be proven in a panel of in vitro assays. By mimicking the in vivo antigen processing in a simplified in vitro approach, it may be possible to distinguish aberrant products from good products. To demonstrate this, heat-exposed diphtheria toxoid was subjected to partial digestion by cathepsin S (an endoprotease involved in antigen processing), and the peptide formation/degradation kinetics were mapped for various heated toxoids. To overcome the limitations associated with the very large number of samples, we used common reference-based tandem mass tag (TMT) labeling. Instead of using one label per condition with direct comparison between the set of labels, we compared multiple labeled samples to a common reference (a pooled sample containing an aliquot of each condition). In this method, the number of samples is not limited by the number of unique TMT labels. This TMT multiplexing strategy allows for a 15-fold reduction of analysis time while retaining the reliability advantage of TMT labeling over label-free quantification. The formation of the most important peptides could be followed over time and compared among several conditions. The changes in enzymatic degradation kinetics of diphtheria toxoid revealed several suitable candidate peptides for use in a quality control assay that can distinguish structurally aberrant diphtheria toxoid from compliant toxoids. [ABSTRACT FROM AUTHOR]

The conformational analysis of glycosidases affords a route to their specific inhibition through transition-state mimicry. Inspired by the rapid reaction rates of cyclophellitol and cyclophellitol aziridineboth covalent retaining β-glucosidase inhibitorswe postulated that the corresponding carba "cyclopropyl" analogue would be a potent retaining β-glucosidase inhibitor for those enzymes reacting through the 4H3 transition-state conformation. Ab initio metadynamics simulations of the conformational free energy landscape for the cyclopropyl inhibitors show a strong bias for the 4H3 conformation, and carba-cyclophellitol, with an N-(4-azidobutyl)carboxamide moiety, proved to be a potent inhibitor (K i = 8.2 nM) of the Thermotoga maritima TmGH1 β-glucosidase. 3-D structural analysis and comparison with unreacted epoxides show that this compound indeed binds in the 4H3 conformation, suggesting that conformational strain induced through a cyclopropyl unit may add to the armory of tight-binding inhibitor designs. [ABSTRACT FROM AUTHOR]

Lysosomal degradation of glycosphingolipids is mediated by the consecutive action of several glycosidases. Malfunctioning of one of these hydrolases can lead to a lysosomal storage disorder such as Fabry disease, which is caused by a deficiency in a-galactosidase A Herein we describe the development of potent and selective activity-based probes that target retaining α-galactosidases. The fluorescently labeled aziridine-based probes 3 and 4 inhibit the two human retaining α-galactosidases αGal A and αGal B covalently and with high affinity. Moreover, they enable the visualization of the endogenous activity of both a-galactosidases in cell extracts, thereby providing a means to study the presence and location of active enzyme levels in different cell types, such as healthy cells versus those derived from Fabry patients. [ABSTRACT FROM AUTHOR]

Formaldehyde-inactivated toxoid vaccines have been in use for almost a century. Despite formaldehyde's deceptively simple structure, its reactions with proteins are complex. Treatment of immunogenic proteins with aqueous formaldehyde results in heterogenous mixtures due to a variety of adducts and cross-links. In this study, we aimed to further elucidate the reaction products of formaldehyde reaction with proteins and report unique modifications in formaldehyde-treated cytochrome c and corresponding synthetic peptides. Synthetic peptides (Ac-GDVEKGAK and Ac-GDVEKGKK) were treated with isotopically labeled formaldehyde ( 13 CH 2 O or CD 2 O) followed by purification of the two main reaction products. This allowed for their structural elucidation by (2D)-nuclear magnetic resonance and nanoscale liquid chromatography-coupled mass spectrometry analysis. We observed modifications resulting from ( i ) formaldehyde-induced deamination and formation of α,β-unsaturated aldehydes and methylation on two adjacent lysine residues and ( ii ) formaldehyde-induced methylation and formylation of two adjacent lysine residues. These products react further to form intramolecular cross-links between the two lysine residues. At higher peptide concentrations, these two main reaction products were also found to subsequently cross-link to lysine residues in other peptides, forming dimers and trimers. The accurate identification and quantification of formaldehyde-induced modifications improves our knowledge of formaldehyde-inactivated vaccine products, potentially aiding the development and registration of new vaccines.

Amorphous network materials are becoming increasingly important with applications, for example, as supercapacitors, battery anodes, and proton conduction membranes. The design of these materials is hampered by the amorphous nature of the structure and sensitivity to synthetic conditions. Here, we show that through artificial synthesis, fully mimicking the catalytic formation cycle, and full synthetic conditions, we can generate structural models that can fully describe the physical properties of these amorphous network materials. This opens up pathways for the rational design where complex structural influences, such as the solvent and catalyst choice, can be taken into account.

Using activity-based protein profiling (ABPP), functional proteins can be interrogated in their native environment. Despite their pharmaceutical relevance, G protein-coupled receptors (GPCRs) have been difficult to address through ABPP. In the current study, we took the prototypical human adenosine A 2A receptor (hA 2A R) as the starting point for the construction of a chemical toolbox allowing two-step affinity-based labeling of GPCRs. First, we equipped an irreversibly binding hA 2A R ligand with a terminal alkyne to serve as probe. We showed that our probe irreversibly and concentration-dependently labeled purified hA 2A R. Click-ligation with a sulfonated cyanine-3 fluorophore allowed us to visualize the receptor on SDS-PAGE. We further demonstrated that labeling of the purified hA 2A R by our probe could be inhibited by selective antagonists. Lastly, we showed successful labeling of the receptor in cell membranes overexpressing hA 2A R, making our probe a promising affinity-based tool compound that sets the stage for the further development of probes for GPCRs.

The conformational analysis of glycosidases affords a route to their specific inhibition through transition-state mimicry. Inspired by the rapid reaction rates of cyclophellitol and cyclophellitol aziridine-both covalent retaining β-glucosidase inhibitors-we postulated that the corresponding carba "cyclopropyl" analogue would be a potent retaining β-glucosidase inhibitor for those enzymes reacting through the 4 H 3 transition-state conformation. Ab initio metadynamics simulations of the conformational free energy landscape for the cyclopropyl inhibitors show a strong bias for the 4 H 3 conformation, and carba-cyclophellitol, with an N-(4-azidobutyl)carboxamide moiety, proved to be a potent inhibitor (K i = 8.2 nM) of the Thermotoga maritima TmGH1 β-glucosidase. 3-D structural analysis and comparison with unreacted epoxides show that this compound indeed binds in the 4 H 3 conformation, suggesting that conformational strain induced through a cyclopropyl unit may add to the armory of tight-binding inhibitor designs.

Twenty years ago, one of us embarked (Bursill, L. A.; Lodge, E. A.; Thomas, J. M. Zeolitic structures as revealed by high-resolution electron microscopy. Nature 1980, 286, 111-113) on the study of zeolites (renowned for their electron-beam sensitivity) by high-resolution transmission electron microscopy (HRTEM). In the ensuing years, high-resolution imaging aided by optical diffractometry has yielded details of the open framework structures of a number of new aluminosilicate and aluminophosphate molecular sieves and catalysts. The nature of intergrowth and recurrently twinned structures, as well as new types of structural imperfection in hitherto uncharacterized materials, has also been elucidated. With continued improvements in instrumental development, encompassing higher accelerating voltages, better objective lenses and vacua, computational advances, and the arrival of slow-scan CCD detectors, electron crystallographic methods and HRTEM imaging now enable the ab initio three-dimensional structures of micro- and mesoporous solids, with their occluded structure-directing organic species, to be determined. High-resolution scanning transmission electron microscopy using subnanometric probes provides supplementary structural and ultramicro analytical information and electron spectroscopic imaging (at the attogram level). In its high-angle annular dark-field mode, it is capable of locating and determining the composition of individual nanoparticle catalysts (consisting of just a few atoms) supported on porous hosts.

X-ray absorption fine structure (XAFS) measurements unambiguously establish the structure of the active centers in high-performance Ti-SiO2 epoxidation catalysts. Subtleties in structural changes in proceeding from the dispersed titanocene dichloride precursor to the anchored Ti(IV) centers are charted, in situ, by both near-edge (XANES) and extended-edge (EXAFS) measurements. The active centers are tripodally attached titanol groups: (Si-O)3-TiOH. These permit facile expansion of the coordination shell (also monitored by in situ XAFS studies) during catalysis, and thereby lead to the formulation of a plausible mechanism of epoxidation of alkenes that is consonant with recent DFT computations. Previously proposed mechanisms, based on a three-coordinated titanyl group (as well as possible five- or six-coordinated active sites), are discounted. Comparable XAFS studies of soluble catalytically active four-coordinated Ti(IV)-containing molecular entities establish that the heterogeneous Ti-SiO2 catalyst has "single-site" active centers. Equipped with such information, minute changes in hydrophobicity and local composition (e.g., replacement of one Si by a Ge) can be wrought so as to boost the performance of the catalyst. The merits of using combined in situ X-ray absorption spectroscopic and X-ray diffractometric measurements are also highlighted.

Framework-substituted, molecular-sieve, aluminophosphate, microporous solids are the centerpieces of a new approach to the aerobic oxyfunctionalization of saturated hydrocarbons. The sieves, and the few percent of the Al(III) sites within them that are replaced by catalytically active, transition-metal ions in high oxidation states (Co(III), Mn(III), Fe(III)), are designed so as to allow free access of oxygen in to and out of the interior of these high-area solids. Certain metal-substituted, molecular sieves permit only end-on approach of linear alkanes to the active centers, thereby favoring enhanced reactivity of the terminal methyl groups. By optimizing cage dimension, with respect to that of the hydrocarbon reactant, as well as adjusting the average separation of active centers within a cage, and by choosing the sieve with the appropriate pore aperture, highly selective conversions such as n-hexane to hexanoic acid or adipic acid, and cyclohexane to cyclohexanol, cyclohexanone, or adipic acid, may be effected at low temperature, heterogeneously in air.

Structural determinants for the glucose transport kinetics of the erythrocyte glucose transporter have not been established. In this work the role of the cytosolic carboxy-terminal tail in the expression and function of the human GLUT1 isoform in Xenopus oocytes was investigated. Oocyte plasma membrane expression of GLUT1 was a saturable function of the amount of mRNA injected. Transport activity increased as a linear function of the amount of immunoreactive transporter in the plasma membrane. Transport kinetics of human GLUT1 expressed in oocytes resembled those of human erythrocyte GLUT1. Addition of up to 31 extra amino acids to the carboxy-terminal tail of GLUT1 was without effect on its function in oocytes. Removal of the carboxy-terminal 21 amino acids also did not affect GLUT1 expression or transport kinetics in oocytes. Removal of the entire carboxy-terminal tail to Phe-450 resulted in a transporter that had moderately decreased plasma membrane expression compared to that of GLUT1. However, transport activity of this construct was less than 5% of that of GLUT1, and was associated with loss of its outward-facing inhibitor binding site. When the carboxy-terminal 29 amino acids of GLUT1 were replaced with the corresponding region of GLUT4, transporter expression in the plasma membrane and the transport Vmax fell to low levels, similar to those of native GLUT4. When the carboxy-terminal 29 or 73 amino acids of GLUT1 were swapped into the corresponding region of GLUT4, the transport Vmax markedly increased to about one-third to one-half that of GLUT1, although the affinity for substrate was halved. These results show that the carboxy-terminal tail of the GLUT1 is not critical for targeting of the protein to the plasma membrane, but that this region is an important determinant of transport function.