DOI: 10.5281/zenodo.7707714
title: Compound I Formation and Reactivity in Dimeric Chlorite Dismutase: Impact of pH and the Dynamics of the Catalytic Arginine

description: <strong>Data type</strong>: spectroscopic measurements (UV-visible, ECD, EPR), enzyme activity measurements, mass spectrometry, spectroelectrochemistry and data analysis. Files are in<strong> .DTA, .DSC, .xlsx, .m, .mat, .BSW, .csv, .txt, .dsx, .pdf, .uds </strong>formats Information on <strong>origin of the data</strong>: EPR spectroscopic measurements in <strong>DTA </strong>and<strong> DSC</strong> formats EPR spectroscopic simulation and analyses in <strong>m </strong>and<strong> mat</strong> format Analysis of Rapid Freeze-Quench calibration curve is in <strong>xlsx</strong> format UV-vis spectroscopic measurements in <strong>csv, xlsx, txt, uds and dsx</strong> format ECD measurements in <strong>csv, xlsx and dsx</strong> format Enzyme activity data in <strong>csv and xlsx</strong> format Mass spectrometry data in <strong>pdf and xlsx</strong> format Spectroelectrochemistry data in <strong>BSW</strong> and <strong>xlsx</strong> format The data are <strong>generated</strong> by: UV−vis spectra were recorded using a Cary 60 UV–vis spectrophotometer (Agilent) and a U-3900 spectrophotometer (Hitachi, Mannheim, Germany). Electronic circular dichroism spectroscopy was performed using Chirascan (Applied Photophysics, Leatherhead, UK). Rapid Freeze-Quench of EPR sample was performed with the use of a device from BioLogic (Grenoble, France), consisting of an SFM-2000 stopped-flow unit and an MPS-70 controller unit, combined with a freeze-quench sample collector adapted for EPR tubes. The ejected volumes and flow rate were controlled by the BioLogic BIOKINE software, v. 4.72. X-Band CW-EPR experiments were performed on X-band ELEXSYS E580 spectrometer (Bruker BioSpin GmbH) operating at a microwave frequency of ∼9.4 GHz and equipped with a standard TE102 cavity and a liquid He cryostat (Oxford Inc.) Enzyme activity was measured polarographically following the release of O<sub>2</sub> by using a Clark-type oxygen electrode (Oxygraph Plus; Hansatech Instruments, Norfolk, UK). Stopped-flow spectroscopy measurements were performed with a SX-18MV or Pi-star from Applied Photophysics using either a diode array detector or a monochromator and photomultiplier detector. Mass spectrometry analysis was performed with an ion-trap mass spectrometer (amaZon speed ETD, Bruker) equipped with the standard ESI source in positive ion, DDA mode (i.e., switching to MSMS mode for eluting peaks). All spectroelectrochemistry experiments were conducted in a homemade OTTLE (optical transparent thin-layer spectroelectrochemical) cell. In detail, the three-electrode configuration consisted of a gold minigrid working electrode (Buckbee-Mears, Chicago, IL), a homemade Ag/AgCl/KCl<sub>sat</sub> microreference electrode separated from the working solution by a Vycor set, and a platinum wire as the counter electrode. UV−vis spectra were recorded using a Varian Cary C50 spectrophotometer. If the dataset includes multiple files that relate to each other: Files in <strong>PARACAT_WP3_20230302_01_EPR </strong>folder includes EPR spectroscopic measurements and computer simulations/analyses, original data are in <strong>DTA/DSC</strong> formats; files in <strong>m</strong> format were used to process the data. Files in <strong>PARACAT_WP3_20230302_02_UVVIS </strong>folder includes sequential and non-sequential stopped flow data, measured with detection by photodiode array or monochromator (time traces): original data is in <strong>dsx and csv </strong>format<strong>, xlsx </strong>format contains processed data; conventional photometric data is originally in <strong>txt and uds </strong>format, <strong>xlsx </strong>format contains processed data Files in <strong>PARACAT_WP3_20230302_03_ECD</strong> folder contain ECD spectra: original data is in <strong>dsx and csv </strong>format<strong>, xlsx </strong>format contains processed data Files in <strong>PARACAT_WP3_20230302_04_Enzyme activity </strong>folder contain polarographically detected changes in dioxygen concentration, due to enzyme activity: original data is in <strong>csv </strong>format<strong>, xlsx </strong>format contains processed data Files in <strong>PARACAT_WP3_20230302_05_MassSpec </strong>folder contain mass spectrometry data for the MNP assay: original data is in <strong>pdf </strong>format<strong>, xlsx </strong>format contains processed data Files in <strong>PARACAT_WP3_20230302_06_Spectroelectrochemistry </strong>folder includes spectroelectrochemistry measurements and computer analyses, original data are in <strong>BSW</strong> formats; files in <strong>xlsx</strong> format were used to process the data. NB. See the “READ ME” text file in each subfolder for more detailed information on files organization. Information on: <strong>Abbreviations:</strong> , chlorite dismutase; <strong><em>C</em>Cld</strong>, chlorite dismutase from Cyanothece sp. PCC7425; <strong>CcP</strong>, cytochrome c peroxidase;<strong> DaCld</strong>, chlorite dismutase from <em>Dechloromonas aromatica</em>; <strong>E°′</strong>, standard reduction potential; <strong>ECD</strong>, electronic circular dichroism; <strong>EPR</strong>, electron paramagnetic resonance; <strong>HRP</strong>, horseradish peroxidase; <strong>LPO</strong>, lactoperoxidase; <strong>MNP</strong>, 2-methyl-2-nitrosopropane; <strong>MPO</strong>, myeloperoxidase; <strong>PAA</strong>, peracetic acid; <strong>RFQ</strong>, rapid freeze-quench. <strong>Units of measurement</strong>: Concentration: <strong>mM</strong> (millimolar), <strong>µM</strong> (micromolar), <strong>nM</strong> (nanomolar), <strong>mg/mL</strong> (milligrams per milliliter) Molecular mass: <strong>Da</strong> (Dalton) Absorptivity: <strong>M<sup>-1</sup></strong> <strong>cm<sup>-1</sup></strong> Volume: <strong>mL</strong> (milliliters), <strong>µL </strong>(microliters), <strong>nL</strong> (nanoliters) Wavelength:<strong> nm</strong> (nanometers) Temperature:<strong> °C</strong> (Celsius degrees), <strong>K</strong> (Kelvin degrees) Time:<strong> ms</strong> (milliseconds), <strong>s</strong> (seconds), <strong>min</strong> (minutes), <strong>h</strong> (hours), Ellipticity: millidegrees Frequency: <strong>GHz</strong> (gigahertz), <strong>kHz</strong> (kilohertz) Power: <strong>mW</strong> (milliwatt) Magnetic field: <strong>mT</strong> (milliTesla) Reduction potential: <strong>mV </strong>(milliVolts)
description:  EPR data: The DTA and DSC files can be opened on proprietary EPR softwares from Bruker or MatLab (version R2022a, used by the authors) with EasySpin toolbox (v. 6.0.0-dev.41, used by the authors). The simulation scripts of EPR measurements can be opened and run on MatLab (version R2022a, used by the authors) with EasySpin toolbox (v. 6.0.0-dev.41, used by the authors). MatLab can be purchased/downloaded from: https://www.mathworks.com/products/matlab.html; EasySpin toolbox can be downloaded free of charge from: https://easyspin.org/ ; The xlsx data for the calibration of the Freeze-Quench device can be open with MS Excel or alternative open access software.  (Stopped-flow) UV-vis data: The dsx files can be opened with Pro Data Viewer SX (by Applied Photophysics Ltd, https://www.photophysics.com/) The xlsx and csv data for the calibration of the Freeze-Quench device can be open with MS Excel or alternative open access software. The txt files can be opened by the Windows Editor Tool and the uds files can be opened with UV Solutions 3.0 for U-3900 (by Hitachi, 2008, https://www.hitachi-hightech.com/global/en/products/analytical-systems/ ).  ECD data: The dsx files can be opened with Pro Data Viewer SX (by Applied Photophysics Ltd, https://www.photophysics.com/). The xlsx and csv data for the calibration of the Freeze-Quench device can be open with MS Excel or alternative open access software.  Enzyme activity data: The xlsx and csv data for the calibration of the Freeze-Quench device can be open with MS Excel or alternative open access software. csv data can be opened also with OxygraphPlus (2007 by Hansatech Instruments, https://www.hansatech-instruments.com/)  Mass spectrometry data: The pdf files can be opened by Adobe Acrobat Reader DC, Adobe PDF Reader (by Adobe) or alternative open access software. The xlsx data for the calibration of the Freeze-Quench device can be open with MS Excel or alternative open access software.  Spectroelectrochemistry data: the BSW files can be open with Cary WinUV Version 3.0 software; the xlsx data can be open with MS Excel or alternative open access software.