Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase
| Main Authors: | Ilenia Serra, Daniel Schmidt, Vera Pfanzagl, Georg Mlynek, Stefan Hofbauer, Kristina Djinović-Carugo, Paul G. Furtmüller, Inés García-Rubio, Sabine Van Doorslaer, Christian Obinger |
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| Format: | info dataset Journal |
| Bahasa: | eng |
| Terbitan: |
, 2022
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/5878430 |
Daftar Isi:
- Data type: spectroscopic measurements (UV-visible, ECD, EPR), DSC measurements, X-ray crystallography datasets, kinetic measurements, Molecular Dynamics simulations and data analysis. Files are in spc, par, DTA, DSC, dsx, csv, mtz formats Information on origin of the data: EPR spectroscopic measurements in spc, par, DTA and DSC formats EPR spectroscopic simulation and analyses in m and mat format UV-vis spectroscopic measurements in csv format ECD measurements in dsx format Enzyme activity data in csv format DSC measurements in csv format X-ray data in mtz format MD simulations data are in xlsx format The data are generated by: UV−vis spectra were recorded using a Cary 60 UV−vis spectrophotometer (Agilent). Electronic circular dichroism spectroscopy was performed using Chirascan (Applied Photophysics, Leatherhead, U.K.). X-Band CW-EPR experiments were performed on A) a Bruker ESP300E spectrometer equipped with a liquid helium cryostat (Oxford Inc.); B) a Bruker ELEXSYS E580 X-band spectrometer equipped with an Oxford ESR 900 continuous-flow helium cryostat and a Bruker ER 4122 SHQ resonator. Enzyme activity was measured polarographically following the release of O2 by using a Clark-type oxygen electrode (Oxygraph Plus; Hansatech Instruments, Norfolk, U.K.). Differential scanning calorimetry experiments were performed on a Micro-Cal PEAQ-DSC Automated instrument (Malvern Panalytical Ltd., Malvern, U.K.) equipped with an autosampler for 96-well plates and controlled by the MicroCal PEAQ-DSC software. Crystallization experiments were performed using the sitting drop vapor diffusion method in SWISSCI MRC three-well crystallization plates (Molecular Dimensions, Newmarket, U.K.). Crystallization drops were set up using a mosquito crystallization robot (TTP Labtech). Commercially available crystallization screens were used for further screening. Crystallization plates were stored in a Formulatrix RI-1000 imaging device at 22 °C. Data were collected at 100 K using an Eiger2 XE 16 M detector at the beamline i04 at the Diamond Light Source (DLS, Didcot, United Kingdom). Further data was collected at 100 K at beamline ID30A-3 using a Eiger X 4 M detector, at beamline ID-23-1 using a Pilatus 6 M detector and at beamline ID23-2 using a PILATUS3 X 2 M detector at the of European Synchrotron Radiation Facility (ESRF, Grenoble, France). Data sets were processed with XDS, and symmetry equivalent reflections merged with XDSCONV. Molecular dynamics simulations were performed using the GROMOS11 molecular simulation package and GROMOS force field 54A8. Analyses of the coordinate trajectories was done with Gromos++ programs hbond, rdf and mdf. Coordinates at specific time point were generated using Gromos++ program frameout and analysed using PyMOL Molecular Graphics System. Files in PARACAT_WP3_20211216_01_EPR folder includes EPR spectroscopic measurements and computer simulations/analyses, original data are in spc/par or DTA/DSC formats; files in m format were used to process the data. Files in PARACAT_WP3_20211216_02_UV-vis folder includes UV-Vis spectroscopic measurements of pH-titration in csv format. Files in PARACAT_WP3_20211216_03_ECD folder includes ECD measurements of the far UV (180–260 nm) and visible (260–500 nm) area, as well as unfolding curves in dsx format. Files in PARACAT_WP3_20211216_04_activity folder includes Clark electrode/activity measurements in csv format. Files in PARACAT_WP3_20211216_05_DSC folder includes DSC measurements in csv format. Files in PARACAT_WP3_20211216_06_Xray folder includes pre-processed (from the beamline pipeline) data sets in mtz format. Files in PARACAT_WP3_20211216_MD-Simulations folder includes pre-processed molecular dynamics data in xlsx format. NB. See the “READ ME” text file in each subfolder for more detailed information on files organization. Information on: Abbreviations: Cld, chlorite dismutase; CCld, chlorite dismutase from Cyanothece sp. PCC7425; CW, continuous wave; D, tetragonal zero-field splitting; DSC, differential circular calorimetry; E, rhombic zero-field splitting; ECD, electronic circular dichroism; EPR, electron paramagnetic resonance; HS, high-spin; LS, lowspin; NdCld, chlorite dismutase from “Candidatus Nitrospira defluvii”; WT, wild type; ZFS, zero-field splitting. Units of measurement: Concentration: mM (millimolar), μM (micromolar), mg/mL (milligrams per milliliter), w/v % (weigth/volume) v/v % (volume/volume) Absorptivity: M-1 cm-1 Volume: mL (milliliters), μL (microliters), nL (nanoliters) Wavelength: nm (nanometers) Temperature: °C (Celsius degrees), K (Kelvin degrees) Time: min (minutes), h (hours), ns (nanoseconds) Ellipticity: millidegrees Frequency: GHz (gigahertz), kHz (kilohertz) Power: mW (milliwatt) Pressure: atm (atmosphere)
- EPR data: The spc, par, DTA and DSC files can be opened on proprietary EPR softwares from Bruker or MatLab (version R2020b, used by the authors) with EasySpin toolbox (version 6.0.0-dev.26, used by the authors). The simulation scripts of EPR measurements can be opened and run on MatLab (version R2021a, used by the authors) with EasySpin toolbox (version 6.0.0-dev.26, used by the authors). MatLab can be purchased/downloaded from: https://www.mathworks.com/products/matlab.html; EasySpin toolbox can be downloaded from: https://easyspin.org/ UV-vis data: The csv files can be opened with programs like Microsoft Excel/Open Office Calc. ECD data: The dsx files can be opened with Pro-Data Viewer from Applied Photophysics. Activity data: The csv files can be opened with programs like Microsoft Excel/Open Office Calc. DSC data: The csv files can be opened with programs like Microsoft Excel/Open Office Calc. X-ray data: The mtz files can be opened with software suites for the automated determination and refinement of macromolecular structures like PHENIX or CCP4i2. MD-simulations data: The xlsx files can be opened with programs like Microsoft Excel/Open Office Calc.