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36 results for “hydrolysis”
Data of uranyl-, Nd-, Ce-hydrolysis and their mixtures induced by thermal decomposition of urea
<p>The hydrolysis of UO<sub>2</sub><sup>2+</sup>, Nd<sup>III</sup> , Ce<sup>III</sup> and Ce<sup>IV</sup> cations, induced by thermal decomposition of urea, was studied. Moreover, we investigated binary mixtures of uranyl and the lanthanides, as well as ternary mixtures of uranyl and both lanthanides using Ce<sup>III</sup> or Ce<sup>IV</sup>. The impact of the urea content and the temperature on the reaction kinetics and the formed precipitate was evaluated and the results are in depth discussed in <a href="https://doi.org/10.1002/ejic.202100453">our article</a>, some results are also summarised in <a href="https://doi.org/10.5281/zenodo.5034714">this presentation</a>.</p> <p>Uranyl ions precipitated as ammonium diuranate (ADU) with different stoichiometry under the applied conditions. Nd<sup>III</sup> and Ce<sup>III</sup> cations showed a comparable pH evolution during hydrolysis and <em>Ln</em>CO<sub>3</sub>OH products were identified, whereas Ce<sup>IV</sup> hydrolysed at a lower pH and formed nanocrystalline CeO<sub>2</sub>. Depending on the urea content, a partial co-precipitation was observed for mixtures of UO<sub>2</sub><sup>2+</sup> and Nd<sup>III</sup>. The products of Ce<sup>III</sup> and Ce<sup>IV</sup> hydrolysis were also identified in the precipitates of binary uranyl and cerium mixtures. For ternary U/Nd/Ce mixtures, a simultaneous precipitation of Nd<sup>III</sup> and Ce<sup>III</sup> and a partial incorporation of the <em>Ln</em> phase into the ADU phase was observed, whereas the presence of Ce<sup>IV</sup>/CeO<sub>2</sub> resulted in three individual phases. The precipitation reaction was followed by monitoring the pH evolution and the metal concentration in the supernatant, applying UV/Vis and ICP-MS. The formed precipitates were characterised by XRD and SEM.</p> <p>The data accrued during the study are part of this data set. Please note that the provision of this dataset is based on a voluntary basis. You are welcome to use the data from this set in your work. If you do so and publish resulting findings, please cite our work as required by the license.</p>
Additional Data of O.Buß and S.Jager: "Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of ß-Keto Esters")
<p>The additional data set includes:</p> <ul> <li>Pdb structure files, which were used for calculations/pictures.</li> <li>R-scripts for calculation of statistical measures like Z-factor, SSMD and others.</li> <li>Data of different activity assays, which were used for R-script calculations.</li> <li>a SDS-PAGE (gel with all used enzymes)</li> </ul> <p>View our publication under: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0146104</p>
Imipenem hydrolysis by the L1 and the NDM-1 metallo-beta-lactamases: QM/MM structures of the stationary points
<p>Stationary points (transition states and minima) for the hydrolysis reactions of the imipenem in the active sites of the L1 and NDM-1 metallo-beta-lactamases. The reactions occure in three elementary steps each. For the NDM-1 there are two compeeting pathways leading to the different products. Enamine and imine forms of the hydrolyzed imipenem may form and those are marked with "N" and "C", respectively, according to the atom being protonated at the last step. Structures are calculated at the QM(PBE0-D3/6-31G**)/MM(AMBER) level.</p>
Dataset for article: Nanostructure Formation in Glycerolipid Films during Enzymatic Hydrolysis: A GISAXS Study
<p><strong>Dataset for publication:</strong></p> <p>Nanostructure Formation in Glycerolipid Films during Enzymatic Hydrolysis: A GISAXS Study<br>Rafael V. M. Freire, Bettina Tran, Meron Debas, Mahsa Zabara, Heinz Amenitsch, and Stefan Salentinig<br>ACS Appl. Mater. Interfaces 2024, 16, 44, 61262–61271 (DOI 10.1021/acsami.4c12125)</p> <p>Setup and conditions for the experiments are described in the experimental section of the published manuscript.</p> <p>Data description in README.txt file.</p>
3D structures along the reaction pathways of GTP hydrolysis by Arl3-RP2
<p>PDB files of 3D structures along the reaction pathways of GTP hydrolysis by Arl3-RP2 with the reaction coordinate values close to those obtained for minima and transitions states during the umbrella integration analysis of the reaction coordinate distributions.</p> <p>The filename includes the name of the minimum / transition state along the reaction path and the theory level.</p>
Data for thesis titled: The impact of processing conditions on enzymatic protein hydrolysis performance from sardine (Sardina pilchardus) by-products using Alcalase 2.4L, and the influence on final spray dried hydrolysate powder properties
<p>The data answer the objectives that focused on:</p> <ol> <li>determining the substrate-specific optimum hydrolysis temperature and pH for the particular enzyme-substrate (Alcalase-sardine by-product) combination,</li> <li>investigating the effect of mixing speed, solids concentration and enzyme dosage on dry solids yield and protein recovery during enzymatic hydrolysis of sardine processing by-products,</li> <li>evaluating the influence of solids concentration on emulsion formation during enzymatic hydrolysis,</li> <li>determining the effect of solids concentration and emulsion formation on molecular weight distribution of protein hydrolysates,</li> <li>investigating the effect of mixing speed and solids concentration on the viscosity and mixing regime of material during enzymatic hydrolysis,</li> <li>establishing the role played by processing conditions (degree of hydrolysis (DH), maltodextrin addition and inlet air temperature) on powder recovery during spray drying, and</li> <li>investigating the role of DH, maltodextrin concentration and spray drying temperature on handling and storage properties of spray dried protein hydrolysates.</li> </ol> <p>This data also appears in journal papers with the following titles:</p> <p>Chiodza, K. & Goosen, N.J. 2023a. Evaluation of handling and storage stability of spray dried protein hydrolysates from sardine (Sardina pilchardus) processing by-products: Effect of enzymatic hydrolysis time, spray drying temperature and maltodextrin concentration. <em>Food and Bioproducts Processing</em>. (June, 30). DOI: <a href="https://www.sciencedirect.com/science/article/pii/S0960308523000743?via%3Dihub">https://doi.org/10.1016/j.fbp.2023.06.009</a>.</p> <p>Chiodza, K. & Goosen, N.J. 2023b. Influence of mixing speed, solids concentration and enzyme dosage on dry solids yield and protein recovery during enzymatic hydrolysis of sardine (Sardina pilchardus) processing by-products using Alcalase 2.4L: a multivariable optimisation approach. <em>Biomass Conversion and Biorefinery</em>. 1:1–23. DOI: <a href="https://link.springer.com/article/10.1007/s13399-023-03829-2">https://doi.org/10.1007/s13399-023-03829-2</a>. </p> <p>Chiodza, K. & Goosen, N.J. 2023c. Emulsion formation during enzymatic protein hydrolysis and its effect on protein recovery and molecular weight distribution of protein hydrolysates from sardine (Sardina pilchardus) by-products. <em>Biomass Conversion and Biorefinery</em>. 1:1–12. DOI: <a href="https://link.springer.com/article/10.1007/s13399-023-04438-9">https://doi.org/10.1007/s13399-023-04438-9</a>.</p>
Important contribution of N2O5 hydrolysis to the daytime nitrate in Xi'an, China during haze periods: isotopic analysis and WRF-Chem model simulation
<p>To quantify the contributions of major formation pathways to nitrate, a field observation, coupling with a WRF-Chem model simulation, was conducted in Xi’an, an inland megacity of China. Here is the dataset of ions, stable isotope compositions of nitrogen and oxygen of nitrate, T, RH and the results simulated by WRF-Chem model.</p>
Influence of variable conditions of microwave-assisted hydrotropic pretreatment on the composition of biomass and its susceptibility to enzymatic hydrolysis.
<p>The results of the first stage of research concerning the influence of variable process conditions of microwave-assisted hydrotropic pretreatment with the use of NaCS on the composition of biomass of various origins, the level of extractivity and susceptibility to hydrolysis. The work was supported by the National Science Centre, Poland, grant No. 2020/37/B/NZ9/00372.</p>
Hydrolysis of SeCN and SCN in the active site of TcDH: QM/MM stationary points
<p>Equilibrium geometry configurations of the enzyme-substrate complexes (ES), transition states (TS) and reaction products (EP) for the SeCN and SCN hydrolysis in the active site of the TcDH enzyme calculated at the QM(uPBE0-D3/6-31G**)/MM(AMBER99 level) using NWChem software. The "qm" in the file name denotes that only QM part is included.</p>
Structures of reaction intermediates of the NAAG hydrolysis by glutamate carboxypeptidase II
<p>Representative frames from the molecular dynamics simulations in the regions of minima along the reaction path calculated at the QM(PBE0-D3/6-31G**)/MM(AMBER) level.</p>
Ultrasonication followed by enzymatic hydrolysis as a sample pre-treatment for the determination of Ag nanoparticles in edible seaweed by SP-ICP-MS
<p>Seaweed can bioaccumulate <a href="https://www.sciencedirect.com/topics/chemistry/nanomaterial">nanomaterials</a> that would be transferred to the trophic chain. This work describes the optimization of a method for the separation of <a href="https://www.sciencedirect.com/topics/chemistry/silver-nanoparticle">silver nanoparticles</a> (AgNPs) from seaweed using an ultrasound-assisted <a href="https://www.sciencedirect.com/topics/chemistry/enzymatic-hydrolysis">enzymatic hydrolysis</a> method and ulterior determination by single particle <a href="https://www.sciencedirect.com/topics/chemistry/inductively-coupled-plasm-mass-spectrometry-icpms">inductively coupled plasma mass spectrometry</a> (SP-ICP-MS).</p> <p>The following parameters affecting the isolation of AgNPs were optimized using a <em>Palmaria palmata</em> (red seaweed) sample previously exposed to AgNPs: type of <a href="https://www.sciencedirect.com/topics/chemistry/sonication">sonication</a> (bath vs. ultrasonic probe), ultrasound amplitude, sonication time, sonication mode (pulsed vs. continuous sonication), concentration of the enzymes mixture (Macerozyme R-10®), and enzymatic hydrolysis time. The stability of AgNPs during extraction was tested by <a href="https://www.sciencedirect.com/topics/chemistry/transmission-electron-microscopy">transmission electron microscopy</a> (TEM) and using a standard of 15 nm of polyvinylpyrrolidone (PVP)-coated AgNPs analyzed by SP-ICP-MS. The analytical performance was evaluated with good results. For total Ag determination, the limits of detection and quantification were 2.2 and 7.7 ng g<sup>−1</sup>, respectively; and for AgNPs determination, the limits of detection in size and number were 14 nm and 4.34 × 10<sup>7</sup> part g<sup>−1</sup>, respectively. Besides, the matrix effect, the repeatability and the analytical recovery were also studied. Finally, the method was applied to the analysis of several red (<em>Palmaria palmata</em>) and green (<em>Ulva</em> sp.) seaweed samples.</p>
D-Glu hydrolysis in the active site of the AmicoTA, a transaminase from the Gram-negative mesophilic bacterium Aminobacterium colombiense
<p>500 frames from the QM(PBE0-D3/6-31G**)/MM molecular dynamic trajectory in the transition state region. The external potential is centered at 3.9 Å of the collective variable (a sum of the distances between the hydrogen atom of the protonated amino group and an oxygen atom the α-carboxylate group of the substrate and between the nitrogen atom of the substrate and a C4´ atom of PLP).</p> <p>In the PDB file the QM atoms have beta=1 and MM beta=0.</p>
Data for New cold-adapted bacteria for efficient hydrolysis of feather waste at low temperature paper
<p>A novel cold-adapted bacteria <em>Arthrobacter oryzae</em> BIM B-1663 isolated from Antarctic green snow showed keratinase activity and efficient poultry feather degradation. <em>A. oryzae</em> strain degraded more than 80% of chicken feathers within 7 days of cultivation at 25°C. The optimal keratinase activity for <em>A. oryzae</em> BIM B-1663 was observed at 50°C, both for α-keratin (44.86 U/mL) and for β-keratin (94 mU/mL). The obtained results from sulfite and thiol groups tests and Fourier transform infrared spectroscopy (FTIR) showed that <em>A. oryzae</em> strain has a different keratin degradation mechanism than the reference strain <em>Bacillus</em> <em>licheniformis</em> CCM 2145<sup>T</sup>. FTIR fingerprinting can be used for monitoring of feather hydrolysis as it showed distinct chemical differences in feather meal hydrolysates, retentate and permeate from <em>A. oryzae</em> and <em>B.</em> <em>licheniformis</em> strains. </p>
MM and QMMM trayectories from "Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations"
<p>Here are provided two trayectories from the results of "Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations".</p> <p><em>ZikaNS3h-MMtrajectory.nc</em> contains a Molecular Mechanics MD simulation of the system with ATP bound to the active site.</p> <p><em>TS1-mech1-QMMMtrajectory.nc</em> contains a QMMM MD simulation of the system with TS1 of the base-assisted mechanism bound to the active site.</p> <p><em>ZikaNS3h.prmtop</em> is the parameter file.</p> <p> </p>
Computational Data Archive in Support of the Ping-Pong Mechanism for Peptide Bond Formation and Hydrolysis
<p>In search for the goldilocks zone in the chemical space for amino acid oligomerization that is relevant to the emergence of protein-based metabolism, we identified a significant gap in our understanding about how peptide bond is formed and hydrolyzed under ambient aqueous conditions. We identified a six-step mechanism that reproduces the experimentally known experimental barriers. By careful evaluation of a comprehensive set of levels of theory, modelling of solvation effect, and calculation of thermochemical parameters, we established a robust computational model to expand the bulk water focus to interfacial phenomena of atmospheric/hydrospheric and litospheric/hydrospheric boundaries. </p> <p>While we cannot travel back in time billions of years to witness the "birth" of the first macromolecule with pre-biotic relevance, we present the dataset and the corresponding publication in RSC Organic and Biomolecular Chemistry (July 26, 2023 issue) our attempt to establish an unbiased computational platform where we can evaluate experiments and generate experimentally testable ideas.</p>
Supplementary Material for "Kinetic Analysis of the Hydrolysis of Pentose-1-phosphates through Apparent Nucleoside Phosphorolysis Equilibrium Shifts"
<p>This is the external Supplementary Information for our publication "Kinetic Analysis of the Hydrolysis of Pentose-1-phosphates through Apparent Nucleoside Phosphorolysis Equilibrium Shifts".</p> <p>The .pdf file contains the Supplementary Information: author contributions, experimental procedures, derivation of equations and supplementary items.</p> <p>The .zip file contains the raw data and metadata for all items (supplementary and main text) and the calculations.</p> <p>Like most publications, this one builds on previous work. The Python code used for spectral unmixing is available on this platform (10.5281/zenodo.3243376) and has been described in our previous publications (10.3390/mps2030060, 10.5281/zenodo.3333469, 10.1002/cbic.202000204, 10.5281/zenodo.3723806 ). Further applications of this method can be found in our recent article in <em>Adv. Synth. Catal.</em> (10.1002/adsc.201901230) and its supporting material (10.5281/zenodo.3568858), as well as a preprint (10.26434/chemrxiv.12993416.v1) and its supporting material (10.5281/zenodo.4043929).</p>
Computational output dataset for monoterpene glycoside hydrolysis: Supplement to 10.5281/zenodo.5346588
<p>Computational data resulting from optimisation and vibrational analysis of monoterpenes, geraniol and linalool, resulting from acid-catalysed hydrolysis of geraniol glucoside. Supplementary dataset for the computation described in:</p> <p>Hixson, Josh, Pisaniello, Lisa, Parker, Mango, Grebneva, Yevgeniya, Bilogrevic, Eleanor, Stegmann, Robin, & Francis, Leigh. (2021, August 31). Methods for predicting and assessing flavour evolution during white wine ageing. https://doi.org/10.5281/zenodo.5346589</p> <p>Structures were drawn in Avogadro (version 1.2.0), then optimised (UFF) and systematic rotor conformer search performed, with the resulting geometry used to create initial input files for GAMESS (Linux distribution, version 2019 R2, University of Iowa, USA) running on the University of South Australia’s High Performance Compute Cluster. Calculations were first performed for molecules in the gas phase (RHF/3-21G) to provide starting geometries which were then used as the input for density functional theory (B3LYP/6-311G(d)) equilibrium geometry calculations in water (SMD solvent model). Local minima were confirmed by vibrational analysis and the presence of all real frequencies. Each calculation was performed in parallel across eight cores.</p> <p>The chemical structures input into Avagadro and the naming used in computational files can be found in 'starting_structures_naming.png' and the scheme of glucoside hydrolysis and rearrangement from the original manuscript has been re-published here as 'glycoside_hydrolysis_scheme.png'. Two computational output files (.log) are present for each structure: an output of the geometry optimisation ending in '_B3LYP_6311G_aq.log', and; the optimised geometry analysed by vibrational analysis, including thermochemistry, denoted with '_vibrational.log'. </p> <p>The compounds, compound file naming (starting_structures_naming.png) and structure numbering in the original work (glycoside_hydrolysis_scheme.png) are as follows: geraniol glucoside, geraniol_gluc, compound 1; protonated geraniol glucoside, geraniol_gluc_protonated, compound 2; linalyl or geranyl cation (identical structures found after geometry optimisation), linalyl_cation or geranyl cation, compound 3, protonated geraniol, geraniol_protonated, compound 4; geraniol, geraniol, compound 5; protonated linalool, linalool_protonated, compound 6; linalool, linalool, compound 7.</p> <p> </p> <p> </p>
Data Supporting "Effects of Microhydration on the Mechanisms of Hydrolysis and Cl- Substitution in Reactions of N2O5 and Seawater"
<p>All structures used in paper "Effects of Microhydration on the Mechanisms of Hydrolysis and Cl- Substitution in Reactions of N2O5 and Seawater". See README for more information.</p>
Understanding Titan's Prebiotic Chemistry: Synthesizing Amino Acids through Aminonitrile Alkaline Hydrolysis
<p>This folder accompanies the study titled, “Understanding Titan’s Prebiotic Chemistry: Synthesizing Amino Acids through Aminonitrile Alkaline Hydrolysis” by Farnsworth et al. Here, you will find an excel file with two tabs that provides the raw data used to create the two LCMS figures in the paper. Thanks, and enjoy!</p>
Supplementary Material for "Engineering of a β-galactosidase from Bacillus coagulans to relieve product inhibition and improve hydrolysis performance""
<p><a href="https://zenodo.org/record/5109535">Suppl. Information</a> Tab. S1<a href="https://zenodo.org/record/5109535">:</a> Primers of alanine scanning</p> <p><a href="https://zenodo.org/record/5109535">Suppl. Information</a> Tab. S2<a href="https://zenodo.org/record/5109535">:</a> Primers of N148 saturation mutation</p> <p><a href="https://zenodo.org/record/5109535">Suppl. Information</a> Fig. S1<a href="https://zenodo.org/record/5109535">:</a> Reaction mechanism of β-galactosidase.</p> <p> </p>
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