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51 results for “peroxidase”
Regulation of Dye-decolorizing Peroxidases Gene Expression in Pleurotus ostreatus Grown on Glycerol as the Carbon Source
<p>This dataset contains the raw data and code necessary to reproduce the results of: Regulation of dye peroxidas gene expression in Pleurotus ostreatus grown on glycerol as the carbon source.</p> <p> </p> <p>These data are also available at github: <a href="https://github.com/JLuisCuamatzi/Pleurotus_ostreatus_CarbonSources">JLuisCuamatzi/Pleurotus_ostreatus_CarbonSources: Data and scripts to reproduce the analysis performed at Regulation of dye peroxidas gene expression in Pleurotus ostreatus grown on glycerol as the carbon source (github.com)</a></p>
Hydrolase and Peroxidase Activity of Gold Nanocluster Composites with Lysozyme and Cross-Linked Lysozyme Crystals
<div> <div> <p>Lysozyme (Lyz) and cross-linked Lyz crystals (CLLC) are among the proteins and templates used in the bio-inspired synthesis of subnanometer-sized gold nanoclusters (AuNCs) utilized in various biological applications as biosensors or bioimaging agents and recyclable catalyst, respectively. While previous studies have explored the formation and stabilization of AuNCs in the presence of Lyz, little is known about the enzymatic activity of Lyz after stabilization of AuNCs with the protein (AuNC@Lyz) and in CLLC (AuNC@CLLC). In this study, we conducted a comprehensive analysis of AuNC@Lyz, including hydrodynamic characteristics using multiwavelength fluorescence analytical ultracentrifugation and enzymatic activity assays. AuNC@Lyz exhibited bactericidal performance as efficiently as Lyz at pH 4.0, with enzymatic activity assays indicating more efficient hydrolytic activity of AuNC@Lyz compared to Lyz under the same conditions. Additionally, AuNC@Lyz showed peroxidase-like performance due to the catalytically active surface of AuNCs in the presence of H<sub>2</sub>O<sub>2</sub> and a chromogenic substrate. The multifunctional catalytic capabilities of AuNC@Lyz, including lytic activity and mimic peroxidase function, were highlighted. Additionally, we conducted fluorescent-based hydrolytic activity assays of CLLC, revealing that morphological variations of CLLC influence the catalytic performance of the enzyme crystals depending on the size of solvent channels and Lyz conformation within the CLLC. Furthermore, the bio-inspired synthesis of AuNCs in CLLC resulted in size distributions of AuNCs correlated with pore sizes. As a consequence of the occluded solvent channels and limited breathing of CLLC, AuNC@CLLC displayed a diminishing hydrolytic performance.</p> </div> </div>
Peroxidase-induced C-N Bond Formation via Nitroso Ene and Diels-Alder Reactions
<p>We herein provide the raw data that form the basis of the manuscript "Peroxidase-induced C-N Bond Formation via Nitroso Ene and Diels-Alder Reactions". Please find the abstract below:</p> <p>The formation of new carbon-nitrogen bonds is indisputably one of the most important tasks in synthetic organic chemistry. Here, nitroso compounds offer a highly interesting reactivity that complements traditional amination strategies, allowing for the introduction of nitrogen functionalities via ene-type reactions or Diels-Alder cycloadditions. In this study, we highlight the potential of horseradish peroxidase as biological mediator for the generation of reactive nitroso species under environmentally benign conditions. Exploiting a non-natural peroxidase reactivity, in combination with glucose oxidase as oxygen-activating biocatalyst, aerobic activation of a broad range of <em>N</em>-hydroxycarbamates and hydroxamic acids is achieved. Thus both intra- and intermolecular nitroso-ene as well as nitroso-Diels-Alder reactions are performed with high efficiency. Relying on a commercial and robust enzyme system, the aqueous catalyst solution can be recycled over numerous reaction cycles without significant loss of activity. Overall, this green and scalable C-N bond-forming strategy enables the production of allylic amides and various <em>N</em>-heterocyclic building blocks utilizing only air and glucose as sacrificial reagents.</p>
Annotated genes harboring major effect markers (R2 ≥ 15%). Highlighted in green are genes annotated from Rhodes et al. 2014,2017, in orange genes annotated as similar to Peroxidase, in yellow new annotations from sorghum genome in Atlas. In the first three columns start and stop position on the sorghum genome and transcript name, followed by the nearest marker name and the distance of the gene from the nearest marker, then a column where are shown the GWAS methods and target traits for which the linked SNP was significant, the last column shows the category of the genes.
<p><strong>We conducted a comprehensive genomics study to map genomic loci determining the production of antioxidants in sorghum grains. Encouraging results were obtained and published in peer-reviewed article with impact factor (https://doi.org/10.1371/journal.pone.0225979). Annotated genes harboring major effect markers (R<sup>2</sup> ≥ 15%) were identified and will be of worldwide interest. </strong></p>
Dataset of the research article "Choline Oxidase and Choline Ionic Liquids in Biocatalytic Heme Peroxidase Cascades"
<p>The dataset contains primary data related to the article entitled "Choline Oxidase and Choline Ionic Liquids in Biocatalytic Heme Peroxidase Cascades", published in ChemCatChem. The dataset contains spreadsheet data detailing kinetic measurements and calculations.</p>
Interaction between cytochrome c and DNA: conformation, peroxidase activity and molecular dynamics simulation
A mixed system of cytochrome c (Cyt c, a typical hemoprotein) and DNA was constructed and the interaction between Cyt c and DNA were analyzed by experiment and molecular dynamics (MD) simulation methods, respectively. On the one hand, the experimental results showed: 1. The peroxidase activity of the mixed system was significantly enhanced relative to the Cyt c in 50 mM phosphate buffer solution at 25ºC. 2. UV-Vis spectra study found that, compared with the Cyt c solution, the absorbance of the Cyt c-DNA mixed system increased significantly at 280 nm, while the absorbance decreased at 405 nm, indicating that the overall structure of Cyt c in the mixed system became loose, and the structure around heme group became more compact. 3. Circular Dichroism (CD) studies showed that there was a weak interaction between DNA and Cyt c in the mixed system, which had little effects on the secondary structures of Cyt c. On the other hand, MD simulation results showed: 1. DNA and Cyt c were combined by hydrogen bonding and non-bonding interactions in the mixed system. 2. During the simulation process, N-Terminal α-Helix changed, and Lys13-Cys17 opened, exposing the active center (heme structure) of Cyt c, which may increase the binding of the mixed system to the substrate. 3. The bond length of Fe-N (N in His18 and Fe in heme group) became slightly shorter after equilibrium in the presence of DNA. 4. The Cyt c became loose after binding with DNA. 5. The total binding free energy between Cyt c and DNA was calculated to be -141.9 kJ/mol. The Cyt c-DNA system was in a relatively stable state from energy perspective. The results of the research on the structure and function of the Cyt c-DNA mixed system using experimental method and MD simulation method were consistent. The combination of experimental method and simulation method may provide useful research ideas and effective research methods for further studying the interaction mechanism between hemeprotein and DNA.
Data for: Engineering A-type Dye-decolorizing Peroxidases by Modification of a Conserved Glutamate Residue
<p><span>Dye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type DyPs. First, we did site saturation mutagenesis of this residue, replacing it with all possible amino acids in bacterial DyPs from Bacillus subtilis (BsDyP) and from Kitasatospora aureofaciens (KaDyP1), the latter being characterized here for the first time. We screened the resulting libraries of variants for activity towards ABTS and identified variants with increased catalytic efficiency. The selected variants were purified and characterized for activity and stability. We furthermore used Molecular Dynamics simulations to rationalize the increased catalytic efficiency and found that the main reason is the electron channeling becoming easier from surface-exposed tryptophans. Based on our findings, we also propose that this glutamate could work as a pH switch in the wild-type enzyme, preventing intracellular damage. </span></p>
Crosslinking of T6SS and T0SS for the secretion of unconventional peroxidase contributes to bacterial lignin utilization
<p>S<span>ecretion</span> of lignolytic enzymes is a competitive advantage for microbial survival in the heterogeneous environments. They are commonly by signal peptides to be transported to the extracellular milieu for lignin catabolism, as the highly complex polymer cannot be translocated through the cell membrane. However, some bacterial lignolytic enzymes lack signal peptides, yet, can still be secreted. It remains unclear how these leaderless proteins cross the inner and outer membranes. Here, we reveal a novel secretion mechanism for the unconventional B-type dye-decolorizing peroxidases (DypB) in<em> Pseudomonas putida</em>. Type VI secretion system (T6SS) mediates the inner membrane channel, where interaction of DypB with VgrG and Hcp accounts for periplasmic delivery. Once in the periplasm, DypB is allocated into outer membrane vesicles (OMVs), also called T0SS, and released to extracellular space. The crosslinked translocation model for DypB delivery represents a novel and ingenious mechanism by which bacteria harness extant systems to thrive in a dynamically changing environment. Moreover, we developed an OMV-surface display platform to improve DypB secretion and further enhance lignin utilization, exemplifying the applicability of OMVs as a lignin biocatalytic nanoreactor. Our study provides multiple new perspectives on unconventional protein secretion and its biotechnological applications.</p>
Fig. 7. Superimposed 3D in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 7. Superimposed 3D structure of HRP-C (in brown) on A) 1AP2 and B) POXalf. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 6. A) RMSD and B) RMSF plots obtained from the analysis of MD simulations (120 ns) of POXalf model.
Fig. 5. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 5. A) Approved 3D model of POXalf (residues 61–75 are 80% transparent). B) Topology of helices in 3D structures of POXalf and HRP (PDB:1HCH). C) Stereo environments of distal and proximal Ca ions in POXalf structure.
Fig. 3. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 3. A) The 2-D gel IEF of POXalf. B) Optimal pH of activity, C) optimal temperature of activity, and D) the thermal stability of POXalf in the presence of phenol (●) and guaiacol (▴). The average of triple assays of POXsolution (stored at 4 ◦ C) activity in the presence of phenol on E) day 1 and F) day 720. All the phenol (8.6 mM) alf and guaiacol (5 mM) reactions were carried out in PBS (10 mM) in the presence of constant amounts of POXalf (65.35 nM) and H2O2 (6.76 mM). Constant pH of 7 and 6 (for phenol and guaiacol, respectively) and constant temperature (20 ± 1 ◦ C) were applied when needed. POXwas maintained 10 min at the desired pH and alf temperature prior to the assays for the stability examinations.
Fig. 2. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 2. A) SDS-PAGE of purified POXalf [lane1: Ladder, lane2:HRP, lanes3,4&5: POXalf] stained by Coomassie blue (left) and silver nitrate (right). Chromatograms of POXalf purification on B) size exclusion column [Sephadex G50, pH 6] and C) ion-exchange column [S-Sepharose, pH 6, NaCl 0.2 M]. D) UV–Visible spectrum of purified POXalf. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 1. A) A. frigida callus at the end of a 31- day subculture and B) its corresponding growth profile. C) POX production in the calluses of A. frigida [A.f], Arnebia euchroma [A.e], Lithospermum officinale [L.o], Onosma dasytrichum [O.d], and Nonea caspica [N.c]. D) POX (filled columns) and CAT (dashed columns) activities in the extract of A. frigida callus during a 31-day subculture. The subcultures were carried out on solid MS medium containing kinetin (10 μM), 2,4-D (1 μM), and sucrose (5% w/v) in darkness at 25 ◦ C. See the experimental section for the enzymatic assays conditions.
Interaction between cytochrome c and DNA: conformation, peroxidase activity and molecular dynamics simulation
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Modulation of Aleurone Peroxidases in Insect-Resistant Maize Kernels (Zea mays L.; P84C3R) After Mechanical and Insect Damage
<p>MS/MS spectra of proteins from insect-resistant endosperms, which were purified using ion-exchange chromatogragy . The data set contains the raw data, the *.mzML and the *.mgf files. </p> <p>The acquisition of the data is described in: L. Margarita López-Castillo<strong>, </strong>Alán González-Leyzaola, M. Fernanda DíazFlores-Rivera, Robert Winkler, Natalie Wielsch and Silverio García-Lara. 2020. "Modulation of Aleurone Peroxidases in Kernels of Insect-Resistant Maize (<em>Zea mays</em> L.; Pob84-C3R) After Mechanical and Insect Damage". 2020. <em>Frontiers in Plant Science</em>. Publication pending.</p>
A novel colorimetric method for Salmonella spp. detection based on the peroxidase activity of Cu(II)-modified reduced graphene oxide nanoparticles and PCR
<p>Figure 1s. The zeta potential of nanomaterials in sodium acetate buffer (pH 4)</p>
Investigating the role of Pseudomonas dye-decolorizing peroxidases in quinone redox cycling for bio-design of a DypB-based lignin degrading enzyme cocktail
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Identification of B6T173 (ZmPrx35) as the prevailing peroxidase in highly insect-resistant maize (Zea mays, p84C3) kernels by activity-directed purification
<p>Dataset for publication https://doi.org/10.3389/fpls.2015.00670</p>
Polymer–Lipid Hybrid Membranes as a Model Platform to Drive Membrane–Cytochrome c Interaction and Peroxidase-like Activity
<p>Data underlying the figures in the publication “Polymer–Lipid Hybrid Membranes as a Model Platform to Drive Membrane–Cytochrome c Interaction and Peroxidase-like Activity”, published in <em>J. Phys. Chem. B.,</em> <strong>2020</strong>, 124, 22, 4454–4465. <a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.0c02727">https://pubs.acs.org/doi/10.1021/acs.jpcb.0c02727</a></p> <p>Table of contents:</p> <p><strong>1. Figure 1</strong>; Zip file containing the BAM images (<em>Figure 1b)</em> and excel files with the numerical data for the Langmuir isotherm graphs (<em>Figure 1a).</em></p> <p><strong>2. Figure 2, 5</strong>: Zip file containing the AFM images for the characterization of the solid-supported bilayers (<em>Figure 2</em>) and of the different membranes after protein insertion (<em>Figure</em> <em>5).</em> </p> <p><strong>3. Figure 4</strong>: Zip file containing the numerical data for <em>Figure 4,</em> showing the QCM-D plots of protein combination with supported membranes.</p> <p><strong>4. Figure 6</strong>: Zip file containing the numerical data for <em>Figure 6,</em> showing the qualitative comparison of protein activity by fluorimetric studies.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.