Mass spectroscopic analysis of Sup35NM prion polymerization.
Ontology highlight
ABSTRACT:
SUBMITTER: Goncharov VA
PROVIDER: S-EPMC1366979 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The innate immune system relies on receptors that sense common signs of infection to trigger a robust host-defense response. Receptors such as RIG-I and NLRP3 activate downstream adaptors mitochondrial antiviral signaling (MAVS) and apoptosis-associated speck-like protein (ASC), respectively, to propagate immune and inflammatory signaling. Recent studies have indicated that both MAVS and ASC form functional prion-like polymers to propagate immune signaling. Here, we summarize the biochemical, genetic, and structural studies that characterize the prion-like behavior of MAVS and ASC in their respective signaling pathways. We then discuss prion-like polymerization as an evolutionarily conserved mechanism of signal transduction in innate immunity in light of the similarity between the NLRP3-ASC, the NLRP3-ASC pathway in mammals, and the NWD2-HET-s pathway in fungi. We conclude by outlining the unique advantages to signaling through functional prions and potential future directions in the field.
| S-EPMC5378051 | biostudies-literature
Project description:The brain functions through chemical interactions between many different cell types, including neurons and glia. Acquiring comprehensive information on complex, heterogeneous systems requires multiple analytical tools, each of which have unique chemical specificity and spatial resolution. Multimodal imaging generates complementary chemical information via spatially localized molecular maps, ideally from the same sample, but requires method enhancements that span from data acquisition to interpretation. We devised a protocol for performing matrix-assisted laser desorption/ionization (MALDI)-Fourier transform ion cyclotron resonance-mass spectrometry imaging (MSI), followed by infrared (IR) spectroscopic imaging on the same specimen. Multimodal measurements from the same tissue provide precise spatial alignment between modalities, enabling more advanced image processing such as image fusion and sharpening. Performing MSI first produces higher quality data from each technique compared to performing IR imaging before MSI. The difference is likely due to fixing the tissue section during MALDI matrix removal, thereby preventing analyte degradation occurring during IR imaging from an unfixed specimen. Leveraging the unique capabilities of each modality, we utilized pan sharpening of MS (mass spectrometry) ion images with selected bands from IR spectroscopy and midlevel data fusion. In comparison to sharpening with histological images, pan sharpening can employ a plethora of IR bands, producing sharpened MS images while retaining the fidelity of the initial ion images. Using Laplacian pyramid sharpening, we determine the localization of several lipids present within the hippocampus with high mass accuracy at 5 ?m pixel widths. Further, through midlevel data fusion of the imaging data sets combined with k-means clustering, the combined data set discriminates between additional anatomical structures unrecognized by the individual imaging approaches. Significant differences between molecular ion abundances are detected between relevant structures within the hippocampus, such as the CA1 and CA3 regions. Our methodology provides high quality multiplex and multimodal chemical imaging of the same tissue sample, enabling more advanced data processing and analysis routines.
| S-EPMC6168410 | biostudies-literature
Project description:Ziegler-Natta polymerization catalysts were characterized by a complex of surface- and bulk-sensitive methods (DRIFTS, XPS, ESR, and XAS = XANES + EXAFS). A diffuse-reflectance Fourier-transform IR spectroscopy (DRIFTS) study showed the presence of strong Lewis acid sites in different concentrations and absence of strong basic sites in the polymerization catalysts. X-ray photoelectron spectroscopy (XPS), electron-spin resonance (ESR), and (X-ray absorption near-edge structure (XANES) analysis revealed the presence of Ti4+, Ti3+, Ti2+, and Ti1+ species in the surface layers and in the bulk of catalysts. The samples under study differ drastically in terms of the number of ESR-visible paramagnetic sites. The EXAFS study shows the presence of a Cl atom as a nearest neighbor of the absorbing Ti atom.
| S-EPMC5459041 | biostudies-literature
Project description:Prions are composed solely of an alternatively folded isoform of the prion protein (PrP), designated PrP(Sc). N-terminally truncated PrP(Sc), denoted PrP 27-30, retains infectivity and polymerizes into rods with the ultrastructural and tinctorial properties of amyloid. We report here that some polyoxometalates (POMs) favor polymerization of PrP 27-30 into prion rods, whereas other POMs promote assembly of the protein into 2D crystals. Antibodies reacting with epitopes in denatured PrP 27-30 also bound to 2D crystals treated with 3 M urea. These same antibodies did not bind to either native PrP(Sc) or untreated 2D crystals. By using small, spherical POMs with Keggin-type structures, the central heteroatom was found to determine whether prion rods or 2D crystals were preferentially formed. An example of a Keggin-type POM with a phosphorous heteroatom is the phosphotungstate anion (PTA). Both PTA and a Keggin-type POM with a silicon heteratom have low-charge densities and favor formation of prion rods. In contrast, POMs with boron or hydrogen heteroatoms exhibiting higher negative charges encouraged 2D crystal formation. The 2D crystals of PrP 27-30 produced by selective precipitation with POMs were larger and more well ordered than those obtained by sucrose gradient centrifugation. Our findings argue that the negative charge of Keggin-type POMs determines the quaternary structure adopted by PrP 27-30. The mechanism by which POMs function in competing prion polymerization pathways--one favoring 2D crystals and the other, amyloid fibrils--remains to be established.
| S-EPMC2656150 | biostudies-literature
Project description:Pathogens and cellular danger signals activate sensors such as RIG-I and NLRP3 to produce robust immune and inflammatory responses through respective adaptor proteins MAVS and ASC, which harbor essential N-terminal CARD and PYRIN domains, respectively. Here, we show that CARD and PYRIN function as bona fide prions in yeast and that their prion forms are inducible by their respective upstream activators. Likewise, a yeast prion domain can functionally replace CARD and PYRIN in mammalian cell signaling. Mutations in MAVS and ASC that disrupt their prion activities in yeast also abrogate their ability to signal in mammalian cells. Furthermore, fibers of recombinant PYRIN can convert ASC into functional polymers capable of activating caspase-1. Remarkably, a conserved fungal NOD-like receptor and prion pair can functionally reconstitute signaling of NLRP3 and ASC PYRINs in mammalian cells. These results indicate that prion-like polymerization is a conserved signal transduction mechanism in innate immunity and inflammation.
| S-EPMC4034535 | biostudies-literature
Project description:The correlation between molecular structure and mechanism of supramolecular polymerizations is a topic of great interest, with a special focus on the pathway complexity of porphyrin assemblies. Their cooperative polymerization typically yields highly ordered, long 1D polymers and is driven by a combination of π-stacking due to solvophobic effects and hydrogen bonding interactions. Subtle changes in molecular structure, however, have significant influence on the cooperativity factor and yield different aggregate types (J- versus H-aggregates) of different lengths. In this study, the influence of amide connectivity on the self-assembly behavior of porphyrin-based supramolecular monomers was investigated. While in nonpolar solvents, C=O centered monomers readily assemble into helical supramolecular polymers via a cooperative mechanism, their NH centered counterparts form short, non-helical J-type aggregates via an isodesmic pathway. A combination of spectroscopy and density functional theory modelling sheds light on the molecular origins causing this stunning difference in assembly properties and demonstrates the importance of molecular connectivity in the design of supramolecular systems. Finally, their mutual interference in copolymerization experiments is presented.
| S-EPMC8362183 | biostudies-literature
Project description:Semiconductor quantum dots (QDs) or nanoparticles (NPs) exhibit very unusual physico-chemcial and optical properties. This review article introduces the applications of semiconductor nanomaterials (NMs) in fluorescence spectroscopy and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for biomolecule analysis. Due to their unique physico-chemical and optical properties, semiconductors NMs have created many new platforms for investigating biomolecular structures and information in modern biology. These semiconductor NMs served as effective fluorescent probes for sensing proteins and cells and acted as affinity or concentrating probes for enriching peptides, proteins and bacteria proteins prior to MALDI-MS analysis.
| S-EPMC5452753 | biostudies-literature
Project description:Chia seeds are becoming more and more popular in modern diets. In this contribution NIR and 2D-fluorescence spectroscopy were used to determine their nutritional values, mainly fat and protein content. 25 samples of chia seeds were analysed, whereof 9 samples were obtained from different regions in Kenya, 16 samples were purchased in stores in Germany and originated mostly from South America. For the purchased samples the nutritional information of the package was taken in addition to the values obtained for fat and protein, which were determined at the Hohenheim Core Facility. For the first time the NIR and fluorescence spectroscopy were used for the analysis of chia. For the spectral evaluation two different pre-processing methods were tested. Baseline correction with subsequent mean-centring lead to the best results for NIR spectra whereas SNV (standard normal variate transformation) was sufficient for the evaluation of fluorescence spectra. When combining NIR and fluorescence spectra, the fluorescence spectra were also multiplied with a factor to adjust the intensity levels. The best prediction results for the evaluation of the combined spectra were obtained for Kenyan samples with prediction errors below 0.2 g/100 g. For all other samples the absolute prediction error was 0.51 g/100 g for fat and 0.62 g/100 g for protein. It is possible to determine the amount of protein and fat of chia seeds by fluorescence and NIR spectroscopy. The combination of both methods is beneficial for the predictions. Chia seeds from Kenya had similar protein and lipid contents as South American seeds.
| S-EPMC8085002 | biostudies-literature
Project description:The ability of the cellular prion protein (PrP(C)) to bind copper in vivo points to a physiological role for PrP(C) in copper transport. Six copper binding sites have been identified in the nonstructured N-terminal region of human PrP(C). Among these sites, the His111 site is unique in that it contains a MKHM motif that would confer interesting Cu(I) and Cu(II) binding properties. We have evaluated Cu(I) coordination to the PrP(106-115) fragment of the human PrP protein, using NMR and X-ray absorption spectroscopies and electronic structure calculations. We find that Met109 and Met112 play an important role in anchoring this metal ion. Cu(I) coordination to His111 is pH-dependent: at pH >8, 2N1O1S species are formed with one Met ligand; in the range of pH 5-8, both methionine (Met) residues bind to Cu(I), forming a 1N1O2S species, where N is from His111 and O is from a backbone carbonyl or a water molecule; at pH <5, only the two Met residues remain coordinated. Thus, even upon drastic changes in the chemical environment, such as those occurring during endocytosis of PrP(C) (decreased pH and a reducing potential), the two Met residues in the MKHM motif enable PrP(C) to maintain the bound Cu(I) ions, consistent with a copper transport function for this protein. We also find that the physiologically relevant Cu(I)-1N1O2S species activates dioxygen via an inner-sphere mechanism, likely involving the formation of a copper(II) superoxide complex. In this process, the Met residues are partially oxidized to sulfoxide; this ability to scavenge superoxide may play a role in the proposed antioxidant properties of PrP(C). This study provides further insight into the Cu(I) coordination properties of His111 in human PrP(C) and the molecular mechanism of oxygen activation by this site.
| S-EPMC4804749 | biostudies-literature
Project description:Protein S-nitrosation has been argued to be the most important signaling pathway mediating the bioactivity of NO. This post-translational modification of protein thiols is the result of chemical nitrosation of cysteine residues. The term NO-donors covers very different chemical classes, from clinical therapeutics to probes of routine use in chemical biology; their different chemistry is predicted to result in distinctive biology regulated by protein S-nitrosation. To measure the extent of protein S-nitrosation by NO-donors, a proteomic mass spectrometry method was developed, which quantitates free thiol versus nitrosothiol for each modified cysteine residue, coined d-Switch. This method is adapted from the biotin switch (BST) method, used extensively to identify S-nitrosated proteins in complex biological mixtures; however, BST does not quantitate free thiol. Since glutathione-S-transferase P1-1 (GST-P1) has been proposed to be a biological "NO-carrier", GST-P1 was used as a reporter protein. The 5 different chemical classes of NO-donors compared by d-Switch demonstrated very different profiles of protein S-nitrosation and response to O(2) and cysteine, although all NO-donors were oxidants toward GST-P1. The low limits of detection and the ability to use established MS database searching allowed facile generalization of the d-Switch method. Therefore after incubation of neuronal cell cultures with nitrosothiol, it was possible to quantitate not only S-nitrosation of GST-P1 but also many other proteins, including novel targets such as ubiquitin carboxyl-terminal esterase L1 (UCHL1). Moreover, d-Switch also allowed identification of non-nitrosated proteins and quantitation of degree of nitrosation for individual protein thiols.
| S-EPMC2941763 | biostudies-literature