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3 results for “Metalloprotein”
Pitfalls in Sample Preparation of Metalloproteins for Low-Temperature EPR: The Example of Alkaline Myoglobin
<p><strong>Description of the dataset: </strong></p> <ul> <li><strong>Data type</strong>: Experimental spectroscopic measurements (EPR and UV-vis), computer simulations and data analysis</li> <li>Files are with filename extensions: <strong>DSC</strong>, <strong>DTA</strong>, <strong>m</strong>, <strong>mat</strong>, <strong>ods</strong>,<strong> tif</strong></li> <li>Information on <strong>origin of the data</strong>: <ul> <li>EPR spectroscopic measurements have filename extensions <strong>DSC</strong> and <strong>DTA</strong></li> <li>EPR spectroscopic simulation and analyses with filename extension <strong>m</strong></li> <li>UV-vis spectroscopic measurements have filename extensions <strong>ods</strong></li> <li>Processed data ready for simulation/figure preparation have filename extension <strong>mat </strong>(both for EPR and UV-vis)</li> <li>High-quality figures published in main text and supplementary are provided as <strong>tif</strong> files</li> </ul> </li> <li>CW-EPR measurements were generated with a Bruker ELEXSYS E580 X-band spectrometer equipped either with an Oxford CF935 continuous flow cryostat and a Bruker ER4118 SPT-N1 resonator or with an Oxford ESR 900 continuous-flow cryostat and a Bruker ER 4122 SHQ resonator.</li> <li>Pulse EPR experiments were performed with an Oxford CF935 continuous flow cryostat and a Bruker ER4118 SPT-N1 resonator.</li> <li>Simulations of EPR spectra and fitting were performed with the Easyspin software (v. 6.0.0-dev.26) implemented in Matlab (MathWorks, R2020b)</li> <li><strong>The dataset</strong>Files with extension <strong>m</strong> normally recall files with extension <strong>mat</strong> which should be stored in the same working folder <ul> <li>Files in <strong>PARACAT_WP3_20210929_01_CW</strong> folder include subfolders organised by topic: <ul> <li>“Alternative cryoprotectants” contains: ready-to-plot / ready-to-simulate data in <strong>mat</strong> format; simulation scripts in <strong>m</strong> format.</li> <li>“Glycerol effects - different buffers” contains: ready-to-plot / ready-to-simulate data in <strong>mat</strong> format; simulation scripts in <strong>m</strong> format.</li> </ul> </li> <li>Files in <strong>PARACAT_WP3_20210929_02_PULSE</strong> folder include pulse EPR spectroscopic measurements; original data are in <strong>DSC</strong> and <strong>DTA</strong> formats; processed data and fitting are in <strong>m</strong> format. Files in <strong>m</strong> format recall original data files, therefore they should be stored in the same working folder.</li> <li>Files in <strong>PARACAT_WP3_20210929_03_UV-VIS</strong> folder include UV-vis spectroscopic measurements; original and basic processed data are in <strong>ods</strong> format; ready-to-plot data are in <strong>mat</strong> format; scripts for figure preparation are in <strong>m</strong> format.</li> <li>Files in <strong>PARACAT_WP3_20210929_04_FIGURES</strong> folder include high-quality figures published in main text and supplementary, provided as <strong>tif</strong> files</li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Information on</strong>: <ul> <li><strong>Specialized abbreviations:</strong> <strong>EPR</strong> – Electron Paramagnetic Resonance, <strong>CW</strong> – Continuous Wave EPR, <strong><em>T<sub>m</sub></em></strong> or <strong><em>T<sub>2</sub></em></strong>– phase memory time, <strong>CAPS</strong> - N-cyclohexyl-3-aminopropanesulfonic acid, <strong>CHES</strong> - N-Cyclohexyl-2-aminoethanesulfonic acid</li> <li><strong>Definitions of variables:</strong> magnetic field (<strong>mT</strong> - milliTesla), pH (pH units), UV-vis absorbance intensity (<strong>A.U.</strong> – arbitrary units), EPR intensity (<strong>A.U.</strong> – arbitrary units), Hahn Echo Intensity (<strong>A.U.</strong> – arbitrary units), <em>g</em>-values (adimensional)</li> <li><strong>Units of measurements:</strong> <ul> <li>Concentration: <strong>mM</strong> (millimolar), <strong>µM</strong> (micromolar), <strong>% v/v</strong> (percentage volume/volume)</li> <li>Volume: <strong>mL</strong> (milliliters), <strong>µL</strong> (microliters)</li> <li>Wavelength: <strong>nm</strong> (nanometers)</li> <li>Temperature: <strong>°C</strong> (Celsius degrees), <strong>K</strong> (Kelvin degrees)</li> <li>Time: <strong>ns</strong> (nanoseconds)</li> <li>Frequency: <strong>GHz</strong> (gigahertz)</li> <li>Power: <strong>mW</strong> (milliwatt)</li> </ul> </li> </ul> </li> </ul>
Metalloprotein AlphaFold set with enzyme/non-enzyme labeled sites
<pre>The AlphaFold set contains computationally generated structures for metalloproteins that were used to test MAHOMES II's enzyme/non-enzyme predictive performance (Feehan et al. 2023). README.md - Detailed description of AlphaFold set generation. AF-...-model_v2.pdb - Files with the 3D atomic coordinates of a metalloprotein. MAHOMES-II_AlphaFold_set_site_data.csv - Contains the data used during the generation of the AlphaFold set for the final sites. Columns are - Entry: The UniProt accession number of the protein with the bound metal site. - struc_id: The structures AlphaFold DB name (Febuary 2022) and the name of the file in this directory with added metal site. - metal_resName: The two letter PDB residue abbreviation for the site's metal - metal_seqID: The residue index number for the added metal ion. - Enzyme: The enzyme (True) or non-enzyme (False) label. - Entry name: UniProt entry name. - Protein names: The UniProt provided metalloprotein name(s). - Number of homologs with solved structures (PDB): Number of protein sequences in the PDB (May 21, 2020) with an E-value < 1. - Number of homologs in MAHOMES II dataset and T-metal-sites10: Number of protein sequences used to train and evaluate MAHOMES II with an E-value < 1 (0 for all entries). - Metal binding note: UniProt metal binding note that includes information covering the metal’s identity and catalytic flag. - Metal coordinating residue seqIDs: The sequence indices for the metal coordinating residues included in the UniProt’s metal binding section.</pre>
Pico-meter resolution structure of the coordination sphere in the metal-binding site in a metalloprotein by NMR
<p>NMR datasets and pulse sequences used in the paper</p>
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