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418 results for “Dimerization”
Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase
<ul> <li><strong>Data type</strong>: spectroscopic measurements (UV-visible, ECD, EPR), DSC measurements, X-ray crystallography datasets, kinetic measurements, Molecular Dynamics simulations and data analysis.</li> <li>Files are in <strong>spc, par, DTA, DSC, dsx, csv, mtz </strong>formats</li> <li>Information on <strong>origin of the data</strong>: <ul> <li>EPR spectroscopic measurements in <strong>spc</strong>,<strong> par</strong>,<strong> DTA </strong>and<strong> DSC</strong> formats</li> <li>EPR spectroscopic simulation and analyses in <strong>m </strong>and<strong> mat</strong> format</li> <li>UV-vis spectroscopic measurements in <strong>csv</strong> format</li> <li>ECD measurements in <strong>dsx</strong> format</li> <li>Enzyme activity data in <strong>csv</strong> format</li> <li>DSC measurements in <strong>csv </strong>format</li> <li>X-ray data in <strong>mtz</strong> format</li> <li>MD simulations data are in<strong> xlsx</strong> format</li> </ul> </li> <li>The data are <strong>generated</strong> by: <ul> <li>UV−vis spectra were recorded using a Cary 60 UV−vis spectrophotometer (Agilent).</li> <li>Electronic circular dichroism spectroscopy was performed using Chirascan (Applied Photophysics, Leatherhead, U.K.).</li> <li>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.</li> <li>Enzyme activity was measured polarographically following the release of O2 by using a Clark-type oxygen electrode (Oxygraph Plus; Hansatech Instruments, Norfolk, U.K.).</li> <li>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.</li> <li>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.</li> <li>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.</li> <li> <ul> <li>Files in <strong>PARACAT_WP3_20211216_01_EPR </strong>folder includes EPR spectroscopic measurements and computer simulations/analyses, original data are in <strong>spc</strong>/<strong>par </strong>or<strong> DTA/DSC</strong> formats; files in <strong>m</strong> format were used to process the data.</li> <li>Files in <strong>PARACAT_WP3_20211216_02_UV-vis </strong>folder includes UV-Vis spectroscopic measurements of pH-titration in <strong>csv</strong> format.</li> <li>Files in <strong>PARACAT_WP3_20211216_03_ECD </strong>folder includes ECD measurements of the far UV (180–260 nm) and visible (260–500 nm) area, as well as unfolding curves in <strong>dsx</strong> format.</li> <li>Files in <strong>PARACAT_WP3_20211216_04_activity </strong>folder includes Clark electrode/activity measurements in<strong> csv</strong> format.</li> <li>Files in <strong>PARACAT_WP3_20211216_05_DSC </strong>folder includes DSC measurements in <strong>csv </strong>format.</li> <li>Files in <strong>PARACAT_WP3_20211216_06_Xray </strong>folder includes pre-processed (from the beamline pipeline) data sets in <strong>mtz</strong> format.</li> <li>Files in <strong>PARACAT_WP3_20211216_MD-Simulations </strong>folder includes pre-processed molecular dynamics data in<strong> xlsx</strong> format.</li> </ul> </li> </ul> </li> </ul> <p>NB. See the “READ ME” text file in each subfolder for more detailed information on files organization.</p> <ul> <li><strong>Information on</strong>: <ul> <li>Abbreviations:<strong> Cld</strong>, chlorite dismutase; <strong><em>C</em>Cld</strong>, chlorite dismutase from Cyanothece sp. PCC7425; <strong>CW</strong>, continuous wave; <strong><em>D</em></strong>, tetragonal zero-field splitting; <strong>DSC</strong>, differential circular calorimetry; <strong><em>E</em></strong>, rhombic zero-field splitting; <strong>ECD</strong>, electronic circular dichroism; <strong>EPR</strong>, electron paramagnetic resonance; <strong>HS</strong>, high-spin; <strong>LS</strong>, lowspin; <strong><em>Nd</em>Cld</strong>, chlorite dismutase from “Candidatus Nitrospira defluvii”; <strong>WT</strong>, wild type; <strong>ZFS</strong>, zero-field splitting.</li> </ul> </li> </ul> <p> </p> <ul> <li>Units of measurement: <ul> <li>Concentration: <strong>mM</strong> (millimolar), <strong>µM</strong> (micromolar), <strong>mg/mL</strong> (milligrams per milliliter), <strong>w/v %</strong> (weigth/volume) <strong>v/v %</strong> (volume/volume)</li> <li>Absorptivity: <strong>M<sup>-1</sup></strong> <strong>cm<sup>-1</sup></strong></li> <li>Volume: <strong>mL</strong> (milliliters), <strong>µL </strong>(microliters), <strong>nL</strong> (nanoliters)</li> <li>Wavelength:<strong> nm</strong> (nanometers)</li> <li>Temperature:<strong> °C</strong> (Celsius degrees), <strong>K</strong> (Kelvin degrees)</li> <li>Time:<strong> min</strong> (minutes), <strong>h</strong> (hours), <strong>ns</strong> (nanoseconds)</li> <li>Ellipticity: millidegrees</li> <li>Frequency: <strong>GHz</strong> (gigahertz), <strong>kHz</strong> (kilohertz)</li> <li>Power: <strong>mW</strong> (milliwatt)</li> <li>Pressure: <strong>atm</strong> (atmosphere)</li> </ul> </li> </ul>
Compound I Formation and Reactivity in Dimeric Chlorite Dismutase: Impact of pH and the Dynamics of the Catalytic Arginine
<ul> <li><strong>Data type</strong>: spectroscopic measurements (UV-visible, ECD, EPR), enzyme activity measurements, mass spectrometry, spectroelectrochemistry and data analysis.</li> <li>Files are in<strong> .DTA, .DSC, .xlsx, .m, .mat, .BSW, .csv, .txt, .dsx, .pdf, .uds </strong>formats</li> <li>Information on <strong>origin of the data</strong>: <ul> <li>EPR spectroscopic measurements in <strong>DTA </strong>and<strong> DSC</strong> formats</li> <li>EPR spectroscopic simulation and analyses in <strong>m </strong>and<strong> mat</strong> format</li> <li>Analysis of Rapid Freeze-Quench calibration curve is in <strong>xlsx</strong> format</li> <li>UV-vis spectroscopic measurements in <strong>csv, xlsx, txt, uds and dsx</strong> format</li> <li>ECD measurements in <strong>csv, xlsx and dsx</strong> format</li> <li>Enzyme activity data in <strong>csv and xlsx</strong> format</li> <li>Mass spectrometry data in <strong>pdf and xlsx</strong> format</li> <li>Spectroelectrochemistry data in <strong>BSW</strong> and <strong>xlsx</strong> format</li> </ul> </li> <li>The data are <strong>generated</strong> by: <ul> <li>UV−vis spectra were recorded using a Cary 60 UV–vis spectrophotometer (Agilent) and a U-3900 spectrophotometer (Hitachi, Mannheim, Germany).</li> <li>Electronic circular dichroism spectroscopy was performed using Chirascan (Applied Photophysics, Leatherhead, UK).</li> <li>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.</li> <li>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.)</li> <li>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).</li> <li>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.</li> <li>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).</li> <li>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.</li> </ul> </li> </ul> <p> </p> <p> </p> <ul> <li>If the dataset includes multiple files that relate to each other: <ul> <li>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.</li> <li>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</li> <li>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</li> <li>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</li> <li>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</li> <li>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.</li> </ul> </li> </ul> <p> </p> <p>NB. See the “READ ME” text file in each subfolder for more detailed information on files organization.</p> <p> </p> <ul> <li>Information on: <ul> <li><strong>Abbreviations:</strong> <ul> <li>, 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.</li> </ul> </li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Units of measurement</strong>: <ul> <li>Concentration: <strong>mM</strong> (millimolar), <strong>µM</strong> (micromolar), <strong>nM</strong> (nanomolar), <strong>mg/mL</strong> (milligrams per milliliter)</li> <li>Molecular mass: <strong>Da</strong> (Dalton)</li> <li>Absorptivity: <strong>M<sup>-1</sup></strong> <strong>cm<sup>-1</sup></strong></li> <li>Volume: <strong>mL</strong> (milliliters), <strong>µL </strong>(microliters), <strong>nL</strong> (nanoliters)</li> <li>Wavelength:<strong> nm</strong> (nanometers)</li> <li>Temperature:<strong> °C</strong> (Celsius degrees), <strong>K</strong> (Kelvin degrees)</li> <li>Time:<strong> ms</strong> (milliseconds), <strong>s</strong> (seconds), <strong>min</strong> (minutes), <strong>h</strong> (hours),</li> <li>Ellipticity: millidegrees</li> <li>Frequency: <strong>GHz</strong> (gigahertz), <strong>kHz</strong> (kilohertz)</li> <li>Power: <strong>mW</strong> (milliwatt)</li> <li>Magnetic field: <strong>mT</strong> (milliTesla)</li> <li>Reduction potential: <strong>mV </strong>(milliVolts)</li> </ul> </li> </ul>
A dissymmetric [Gd2] coordination molecular dimer hosting six addressable spin qubits. Open data sets
<p>Includes data relevant for publication with DOI <a href="https://doi.org/10.1038/s42004-020-00422-w">10.1038/s42004-020-00422-w</a> plus a table with information about how the data were obtained and processed.</p>
Controlled Formation of Dimers and Spatially Isolated Atoms in Bimetallic Au-Ru Catalysts via Carbon-Host Functionalization
<p>Enclosed we report the data in the article: "Controlled Formation of Dimers and Spatially Isolated Atoms in Bimetallic Au-Ru Catalysts via Carbon-Host Functionalization" by Pérez-Ramírez et al.</p>
In-depth Tissue-Level Dimerization Analysis of AtLEA proteins from Arabidopsis thaliana - Replicate 2
<p>Post 48-hour infiltration, leaves were examined utilizing a 3I Mariana Spinning Disc Confocal microscope equipped with a Zeiss Observer Z.1 Inverted base and a fluorescence spinning disk. In each experimental run, four plants were analyzed, each expressing one of three specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein: pYFN-4-/5pYFC-4-5 (representing the complete AtLEA4-5 protein), pYFN-4-51-77/pYFC-4-51-77 (encompassing the N-terminal region of AtLEA4-5), pYFN-4-578-158/pYFC-4-578-158 (comprising the C-terminal region of AtLEA4-5),pYFN-4-2/pYFC-4-2 (full length AtLEA4-2 protein), or pYFN-pYFC (serving as the control condition). Observations were conducted using a 20X—/0.8 NA air lens from Zeiss, under illumination provided by a pre-centered fiber illuminator from Intelligent Imaging Innovations, Inc. The detection of YFP fluorescence was facilitated by a 515 nm excitation laser and a 542/27 nm emission filter. Images were captured using an Andor Ixon 3 EMCCD camera (Model: DU-897E-CS0-#BV), adhering to protocols defined in SlideBook software version 6. Images were captured at specified intervals with exposure times ranging from 400 to 700 milliseconds. Each image consisted of a plane with a pixel size of 0.8 microns, spaced at 2 micrometer intervals. A total of 16 planes, correlating to an estimated depth of 32 micrometers per z-plane, were scrutinized. From each plant, up to three leaves were examined. The analysis included over 50 volumetric scenes per plant, with each scene encompassing a volume of 100 x 100 x 25 mm³. Image stacks were exported as *.tif </p> <p>Notation:</p> <p><strong> </strong></p> <p>Exp2_PYF: Replicate2 expressing one of four specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein.</p> <p>45: Fused to the full length AtLEA4-5 protein (pYFN-4-/5pYFC-4-5).</p> <p>4H: Fused to the N-terminal region of AtLEA4-5 (pYFN-4-51-77/pYFC-4-51-77).</p> <p>RC: Fused to the C-terminal region of AtLEA4-5 (pYFN-4-578-158/pYFC-4-578-158).</p> <p>control: The control condition (pYFN-pYFC).</p> <p>42: Fused to the full length AtLEA4-2 protein (pYFN-4-2/pYFC-4-2).</p> <p> </p>
In-depth Tissue-Level Dimerization Analysis of AtLEA proteins from Arabidopsis thaliana - Replicate 1
<p>Post 48-hour infiltration, leaves were examined utilizing a 3I Mariana Spinning Disc Confocal microscope equipped with a Zeiss Observer Z.1 Inverted base and a fluorescence spinning disk. In each experimental run, four plants were analyzed, each expressing one of three specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein: pYFN-4-/5pYFC-4-5 (representing the complete AtLEA4-5 protein), pYFN-4-51-77/pYFC-4-51-77 (encompassing the N-terminal region of AtLEA4-5), pYFN-4-578-158/pYFC-4-578-158 (comprising the C-terminal region of AtLEA4-5),pYFN-4-2/pYFC-4-2 (full length AtLEA4-2 protein), or pYFN-pYFC (serving as the control condition). Observations were conducted using a 20X—/0.8 NA air lens from Zeiss, under illumination provided by a pre-centered fiber illuminator from Intelligent Imaging Innovations, Inc. The detection of YFP fluorescence was facilitated by a 515 nm excitation laser and a 542/27 nm emission filter. Images were captured using an Andor Ixon 3 EMCCD camera (Model: DU-897E-CS0-#BV), adhering to protocols defined in SlideBook software version 6. Images were captured at specified intervals with exposure times ranging from 400 to 700 milliseconds. Each image consisted of a plane with a pixel size of 0.8 microns, spaced at 2 micrometer intervals. A total of 16 planes, correlating to an estimated depth of 32 micrometers per z-plane, were scrutinized. From each plant, up to three leaves were examined. The analysis included over 50 volumetric scenes per plant, with each scene encompassing a volume of 100 x 100 x 25 mm³. Image stacks were exported as *.tif </p> <p><strong> </strong>Notation:</p> <p>Exp1_PYF: Replicate1 expressing one of four specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein.</p> <p>45: Fused to the full length AtLEA4-5 protein (pYFN-4-/5pYFC-4-5).</p> <p>4H: Fused to the N-terminal region of AtLEA4-5 (pYFN-4-51-77/pYFC-4-51-77).</p> <p>RC: Fused to the C-terminal region of AtLEA4-5 (pYFN-4-578-158/pYFC-4-578-158).</p> <p>control: The control condition (pYFN-pYFC).</p> <p>42: Fused to the full length AtLEA4-2 protein (pYFN-4-2/pYFC-4-2).</p> <p> </p>
In-depth Tissue-Level Dimerization Analysis of AtLEA proteins from Arabidopsis thaliana - Replicate 4
<p> Post 48-hour infiltration, leaves were examined utilizing a 3I Mariana Spinning Disc Confocal microscope equipped with a Zeiss Observer Z.1 Inverted base and a fluorescence spinning disk. In each experimental run, four plants were analyzed, each expressing one of three specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein: pYFN-4-/5pYFC-4-5 (representing the complete AtLEA4-5 protein), pYFN-4-51-77/pYFC-4-51-77 (encompassing the N-terminal region of AtLEA4-5), pYFN-4-578-158/pYFC-4-578-158 (comprising the C-terminal region of AtLEA4-5),pYFN-4-2/pYFC-4-2 (full length AtLEA4-2 protein), or pYFN-pYFC (serving as the control condition). Observations were conducted using a 20X/0.8 NA air lens from Zeiss, under illumination provided by a pre-centered fiber illuminator from Intelligent Imaging Innovations, Inc. The detection of YFP fluorescence was facilitated by a 515 nm excitation laser and a 542/27 nm emission filter. Images were captured using an Andor Ixon 3 EMCCD camera (Model: DU-897E-CS0-#BV), adhering to protocols defined in SlideBook software version 6. Images were captured at specified intervals with exposure times ranging from 400 to 700 milliseconds. Each image consisted of a plane with a pixel size of 0.8 microns, spaced at 2 micrometer intervals. A total of 16 planes, correlating to an estimated depth of 32 micrometers per z-plane, were scrutinized. From each plant, up to three leaves were examined. The analysis included over 50 volumetric scenes per plant, with each scene encompassing a volume of 100 x 100 x 25 mm³. Image stacks were exported as *.tif </p> <p>Notation:</p> <p>Exp1_PYF: Replicate 4 expressing one of four specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein.</p> <p>45: Fused to the full length AtLEA4-5 protein (pYFN-4-/5pYFC-4-5).</p> <p>4H: Fused to the N-terminal region of AtLEA4-5 (pYFN-4-51-77/pYFC-4-51-77).</p> <p>RC: Fused to the C-terminal region of AtLEA4-5 (pYFN-4-578-158/pYFC-4-578-158).</p> <p>control: The control condition (pYFN-pYFC).</p> <p>42: Fused to the full length AtLEA4-2 protein (pYFN-4-2/pYFC-4-2).</p>
In-depth Tissue-Level Dimerization Analysis of AtLEA proteins from Arabidopsis thaliana - Replicate 3
<p>Post 48-hour infiltration, leaves were examined utilizing a 3I Mariana Spinning Disc Confocal microscope equipped with a Zeiss Observer Z.1 Inverted base and a fluorescence spinning disk. In each experimental run, four plants were analyzed, each expressing one of three specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein: pYFN-4-/5pYFC-4-5 (representing the complete AtLEA4-5 protein), pYFN-4-51-77/pYFC-4-51-77 (encompassing the N-terminal region of AtLEA4-5), pYFN-4-578-158/pYFC-4-578-158 (comprising the C-terminal region of AtLEA4-5),pYFN-4-2/pYFC-4-2 (full length AtLEA4-2 protein), or pYFN-pYFC (serving as the control condition). Observations were conducted using a 20X—/0.8 NA air lens from Zeiss, under illumination provided by a pre-centered fiber illuminator from Intelligent Imaging Innovations, Inc. The detection of YFP fluorescence was facilitated by a 515 nm excitation laser and a 542/27 nm emission filter. Images were captured using an Andor Ixon 3 EMCCD camera (Model: DU-897E-CS0-#BV), adhering to protocols defined in SlideBook software version 6. Images were captured at specified intervals with exposure times ranging from 400 to 700 milliseconds. Each image consisted of a plane with a pixel size of 0.8 microns, spaced at 2 micrometer intervals. A total of 16 planes, correlating to an estimated depth of 32 micrometers per z-plane, were scrutinized. From each plant, up to three leaves were examined. The analysis included over 50 volumetric scenes per plant, with each scene encompassing a volume of 100 x 100 x 25 mm³. Image stacks were exported as *.tif </p> <p> </p> <p>Notation:</p> <p> </p> <p>Exp3_PYF: Replicate 3 expressing one of four specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein.</p> <p>45: Fused to the full length AtLEA4-5 protein (pYFN-4-/5pYFC-4-5).</p> <p>4H: Fused to the N-terminal region of AtLEA4-5 (pYFN-4-51-77/pYFC-4-51-77).</p> <p>RC: Fused to the C-terminal region of AtLEA4-5 (pYFN-4-578-158/pYFC-4-578-158).</p> <p>control: The control condition (pYFN-pYFC).</p> <p>42: Fused to the full length AtLEA4-2 protein (pYFN-4-2/pYFC-4-2).</p> <p> </p> <p> </p>
Alphafold2 models of 47G4 (Hu19) scFv dimers and of VLVL dimers
<p><strong>Alphafold2 models of 47G4 (Hu19) scFv dimers show a variety of swapped VH-VL structures.</strong></p> <p>Alphafold2 dimers models of scFvs formed from VH and VL domains tend to swap to form diabodies with long linkers as for short linkers. The 47G4 scFv used in this study uses a VL-to-VH scFv construct with a long linker (see sequence in Figure 1)</p> <p>See Supplement files for:</p> <ul> <li>The 5 best Alphafold2 models of a predicted 47G4 (Hu19) scFv dimer, using the sequence in Figure 1. <ul> <li>In PDB format. The 5 models are ranked by AF2 in files: <ul> <li><strong>ranked_0...4.pdb </strong></li> </ul> </li> <li>The 5 models can be compared by superimposition of the VL domain of chain A: in iCn3D using an iCn3D PNG image file. To see the models and analyze them in 3D, invoke iCn3D with the link: <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html">https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html</a> ; open “iCn3D PNG image file” using the<strong> file:</strong> <ul> <li><strong>5models_Hu19_scFv_AF2_icn3d_loadable.png</strong></li> </ul> </li> </ul> </li> </ul> <p><strong>Alphafold2 models for 47G4 (Hu19) VL-VL dimers</strong></p> <ul> <li>In PDB format. The 25 models are ranked by AF2 in files: <ul> <li><strong>Hu19-VLVL-AF2-ranked_0…24.pdb </strong></li> <li>Only one out of 25 models offers an inverted interface but offers lower confidence. All other present the canonical interface.</li> </ul> </li> </ul> <p><strong>List of PDB structures containing VL-VL quaternary interfaces (PDB accessed on 10/11/2021)</strong></p> <ul> <li>See file: <strong>PDB-</strong><strong>Igs-VLVL-asu+bu-with-over-10contacts.xls</strong> <ul> <li>The file represents PDB structures that contain contacting VL domains with more than 10 arbitrary contacts in either the first biological Unit (BU) or asymmetric unit (ASU). Both BU and ASU are used as both may contain valid dimers, as in the the inverted VLVL dimer structure (7JO8)</li> <li>Some <strong>iCn3D links</strong> are provided in the excel file to look and analyze a number of structures. Some links compare 7JO8 to 1REI, or other VLVL parallel vs antiparallel dimer such as 1LVE vs 5LVE.</li> </ul> </li> </ul> <p><strong>VLVL based diabody models: canonical and inverted</strong></p> <ul> <li>A model predicted by Alphafold2 version 2.0 for the 47G4 (Hu19) scFv dimer, using the sequence in Figure 1. Supplement file in PDB format: <ul> <li><strong>Hu19-VLVL-diabody-model.pdb</strong></li> </ul> </li> <li>Model building of a scFv dimer using the observed VLVL dimer (7JO8) <ul> <li><strong>Hu19-inverted VLVL-diabody-model.pdb</strong></li> </ul> </li> <li>Both models compared:<strong> VLVLDIAB_VLINVDIAB_icn3d_loadable.png </strong></li> </ul> <p><em>Where no link is specified, PDBids can be directly loaded in iCn3D using the link</em> <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html">https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html</a></p> <p> </p>
Concentration-, Temperature- and Solvent-Dependent Self-Assembly: Merocyanine Dimerization as a Showcase Example for Obtaining Reliable Thermodynamic Data
<p><strong>Abstract:</strong> Mathematical models for the concentration-, temperature- and solvent-dependent analysis of self-assembly equilibria are derived for the most simple case of dimer formation, to highlight the assumptions these models and the thus determined thermodynamic parameters are based on. The three models were applied to UV/Vis absorption data for the dimerization of a highly dipolar merocyanine dye in 1,4-dioxane. Isothermal titration calorimetry (ITC) dilution experiments were performed as an independent reference technique. While the concentration-dependent analysis is according to our studies the most reliable method, also the less time-consuming temperature-dependent evaluation can give accurate results in the present example, despite small thermochromic effects. In contrast, the strong negative solvatochromism of the merocyanine tampers with the results from the solvent-dependent evaluation. Even though the studies presented in this work are limited to the monomer-dimer equilibrium of a dipolar dye, the basic principles can be transferred to other chromophores and different self-assembly models, including those for supramolecular polymerization.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer.</p> <p><strong>binding.zip</strong>: simulation starting from 21 dimer conformations with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation starting from dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation starting from 21 dimer conformations simulation</p> <p>Simulation setup files are also included in each folder.</p> <p>Details can be found in this paper:</p> <p><strong>Yunhui Ge</strong>, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Protein codes for tetrameric and dimeric 6-phosphogluconate dehydrogenases and their signature sequence relevant to the cofactor specificity in the 6PGDH family.
<p>Here we present the Uniprot or Genbank code for tetrameric and dimeric 6-phosphogluconate dehydrogenases collected from different organisms. Besides, we include the sequence of the <span class="math-tex">\(\beta2-\alpha2\)</span> motif regarding the cofactor specificity in the 6PGDH family. </p> <p>The sequence data allows generating a phylogenetic tree of the 6PGDH family. The enzymes cluster first by their oligomerization state and then by their sequence in the <span class="math-tex">\(\beta2-\alpha2\)</span> motif, as is shown in the annexed figure. </p>
Dataset of structural and energetic descriptors for optimized geometries of the pyrene dimer in the S1 state and Jupyter Notebbok used for the unsupervised clustering, analysis and visualization
<p>Geometrical and energy data extracted from a set of 188 optimized geometries for the pyrene dimer in the first excited singlet state at the TD-CAMB3LYP + D3BJ / 6-31G* / C-CPCM(Cyclohexane) level. </p> <p>Coordinates (in xyz format) of the 188 optimized geometries considered.</p> <p>Jupyter notebook used to perform unsupervised clustering and analysis of the available structures.</p>
Raw microscopy data from: Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers
<p>Protein folding homeostasis in the endoplasmic reticulum (ER) is regulated by a signaling network, termed the unfolded protein response (UPR). Inositol-requiring enzyme 1 (IRE1) is an ER membrane-resident kinase/RNase that mediates signal transmission in the most evolutionarily conserved branch of the UPR. Dimerization and/or higher-order oligomerization of IRE1 are thought to be important for its activation mechanism, yet the actual oligomeric states of inactive, active, and attenuated mammalian IRE1 complexes remained unknown. We developed an automated two-color single-molecule tracking approach to dissect the oligomerization of tagged endogenous human IRE1 in live cells. In contrast to previous models, our data indicate that IRE1 exists as a constitutive homodimer at baseline and assembles into small oligomers upon ER stress. We demonstrate that the formation of inactive dimers and stress-dependent oligomers is fully governed by IRE1's lumenal domain. Phosphorylation of IRE1's kinase domain occurs more slowly than oligomerization and is retained after oligomers disassemble back into dimers. Our findings suggest that assembly of IRE1 dimers into larger oligomers specifically enables trans- autophosphorylation, which in turn drives IRE1's RNase activity.</p> <p> </p>
(Cot)Lu(BF4)(thf)_dimer
<p>This contains the dataset for (Cot)Lu(BF4)(thf)_dimer</p>
leighfletcher/hydrogendimers: Hydrogen dimers in giant-planet infrared spectra
<p>Repository for hydrogen-hydrogen absorption spectra, including free-to-free, free-to-bound, bound-to-free and bound-to-bound components as published in Fletcher, Gustafsson and Orton (2017), ApJ Supplement.</p>
Supporting Data for: The V30 Benchmark Set for Anharmonic Vibrational Frequencies of Molecular Dimers
<p>Intermolecular vibrations are extremely challenging to describe but are the most crucial part for determining entropy and hence free energies, and enable for instance the distinction between different crystal-packing arrangements of the same molecule via THz spectroscopy. Herein, we introduce a benchmark data set - V30 - containing 30 small molecular dimers with intermolecular interactions ranging from exclusively van-der-Waals dispersion to systems with hydrogen bonds. All calculations are performed with the gold standard of Quantum Chemistry CCSD(T). We discuss vibrational frequencies obtained via different models starting with the harmonic approximation over independent Morse oscillators up to second-order vibrational perturbation theory (VPT2), which allows a proper anharmonic treatment including coupling of vibrational modes. However, large amplitude motions present in many low-frequency intermolecular modes are problematic for VPT2. In analogy to the often used treatment for internal rotations, we replace such problematic modes by a simple one-dimensional hindered rotor model. We compare selected dimers with available experimental data or high-level calculations of potential energy surfaces and show that VPT2 in combination with hindered rotors can yield a very good description of fundamental frequencies for the discussed subset of dimers involving small and semi-rigid molecules.<br><br>This supporting dataset includes the calculated force constants, harmonic frequencies, Morse frequencies, VPT2 frequencies, and the optimized structures for the V30 dataset. See the included README.md file for more details. The related preprint can be found at <a href="https://doi.org/10.48550/arXiv.2209.04392">https://doi.org/10.48550/arXiv.2209.04392</a>.</p>
Gaussian16 data for "Dynamic electronic structure fluctuations in the de novo peptide ACC-dimer revealed by first-principles theory and machine learning"
<p>This is the Gaussian 16 input and corresponding output, which was used as input into the machine learning presented in the paper titled "Dynamic electronic structure fluctuations in the de novo peptide ACC-dimer revealed by first-principles theory and machine learning". This upload is required before submission of the paper.<br><br>The 1001 and 100 snapshots from different extractions are preserved in separated directories. Each snapshot directory <code>*_snapshot</code> has the initial GROMACS snapshot <code>test_*.pdb</code> , the geometry after truncating the solvation shell in various formats, the Gaussian16 input, qsub input and the output directory <code>*.1</code> with a JobID number assigned by qsub. The output directory has the standard output from Gaussian in a <code>.log</code> file and <code>grep</code>ed output from the <code>.fchk</code> file in <code>*.out</code> .</p>
Exploring the interaction of a curcumin azobioisostere with Abeta42 dimers using replica exchange molecular dynamics simulations
<p>Structural data and parameters relative to the evaluation of the interaction of an anti aggregating azobioisostere compound with the full-length Aβ42 peptide by replica-exchange molecular dynamics (REMD) simulations. Two different force fields (Amber and CHARMM) were used to simulate the azobioisostere-Abeta42 (AZ-Ab42) complex in a monomeric and dimeric assembly.</p> <p>A brief description of the shared output data is reported below:</p> <p><strong>1. Amber and CHARMM-adapted parameters for the simulated azobioisostere (AZ) compound.</strong></p> <p><strong>2. Modified version of the CHARMM36m FF - (CHARMM36mW)</strong></p> <p><strong>3. Starting (equilibrated) structures (first 5 T-replicas) for REMD on each of the following three systems (PDB): </strong></p> <ul> <li>Amber: AZ-Ab42 (monomeric ensemble): <strong>Repl.0 </strong>(315.0 K), <strong>Repl.1</strong> (316.7 K), <strong>Repl.2</strong> (318.4 K), <strong>Repl.3</strong> (320.1 K), <strong>Repl.4</strong> (321.8 K) </li> <li>Amber: AZ-Ab42 (dimeric ensemble): <strong>Repl.0</strong> (315.0 K), <strong>Repl.1</strong> (316.0 K), <strong>Repl.2</strong> (317.0 K), <strong>Repl.3</strong> (318.0 K), <strong>Repl.4</strong> (319.1 K) </li> <li>CHARMM: AZ-Ab42 (dimeric ensemble): <strong>Repl.0</strong> (315.0 K), <strong>Repl.1</strong> (316.0 K), <strong>Repl.2</strong> (317.0 K), <strong>Repl.3 </strong>(318.0 K), <strong>Repl.4</strong> (319.1 K)</li> </ul> <p><strong>4. Most populated clusters for the three simulated systems (PDB):</strong></p> <ul> <li>Amber AZ-Ab42 (monomeric ensemble): <strong>7</strong> clusters (<strong>Cl.0</strong>: 12.4%, <strong>Cl.1</strong>: 10.1%, <strong>Cl.2</strong>: 9.8%, <strong>Cl.3</strong>: 5.4%, <strong>Cl.4</strong>: 3.7%,<strong> Cl.5</strong>: 3.6%, <strong>Cl.6</strong>: 2.0%) </li> <li>Amber AZ-Ab42 (dimeric ensemble): <strong>5</strong> clusters (<strong>Cl.0</strong>: 7.1%, <strong>Cl.1</strong>: 4.3%, <strong>Cl.2</strong>: 3.5%,<strong> Cl.3</strong>: 3.2%, <strong>Cl.4</strong>: 2.4%) </li> <li>CHARMM: AZ-Ab42 (dimeric ensemble): <strong>3</strong> clusters (<strong>Cl.0</strong>: 4.7%, <strong>Cl.1</strong>: 4.6%, <strong>Cl.2</strong>: 2.5%) </li> </ul>
Dimerization of melanocortin 4 receptor controls puberty onset and body size polymorphism
<p>Example dataset and scripts used in the analysis of PIE-based FRET-FLIM data of the Mc4r receptor. </p>
ScienceDex guides
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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.