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29 results for “protein crystal”
Data From: Exploring Gelatin-A and Mouse Proline-Rich Protein 5 as Probes for Wine Polyphenols analysis by Quartz Crystal Microbalance with Dissipation Monitoring
<p>Polyphenols are essential in winemaking, affecting the wine's quality, color, astringency, bitterness, and chemical stability. Conventional methods for assessing polyphenolic content are both expensive and time-intensive, underscoring the need for new, efficient techniques.</p> <p>The Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D) sensor is recognized for its speed and reliability as a label-free detection tool. This study applies QCM-D to evaluate Gelatin Type A (Gel-A) from porcine skin and Mouse Proline-Rich Protein 5 (MP5) for polyphenol analysis in red wines without pre-treatment. MP5 notably exhibited a linear dissipation signal response with both total polyphenol and hydroxybenzoic acid concentrations. These findings highlight the potential for creating a stand-alone sensor platform for real-time polyphenol monitoring in winemaking.</p>
Data for manuscript: Functional Protein Dynamics in a Crystal
<p>The data is provided as a part of the manuscript "<strong>Functional Protein Dynamics in a Crystal</strong>". This repository includes an archive with folders:<br> <br> <strong>md_data</strong></p> <ul> <li>contains various simulation systems (crystal supercell, apo and ligand-bound solution) built from the crystal structure of the PDZ domain (PDB ID: 5E11) and carried out using three force fields: Amber ff14SB, CHARMM36m, Amber ff94. <em>The details of the simulations are provided in the Methods and Supplementary methods sections of the manuscript. </em></li> </ul> <p><strong>fig_data</strong></p> <ul> <li>contains the data sets underlying Figures 1-5 of the manuscript's main text. </li> </ul> <p> </p>
Dataset for Diamond-coated quartz crystal microbalance sensors: Challenges in high yield production and enhanced detection of ethanol and sars-cov-2 proteins
<p>The data set to paper: </p> <p>Name: Diamond-coated quartz crystal microbalance challenges in mass production and enhanced detection of ethanol and sars-cov-2 proteins</p> <p>Authors: Tibor Izsák1*, Marian Varga1, Michal Kočí2,3, Ondrej Szabó2, Katarína Aubrechtová Dragounová2, Gabriel Vanko2, Miroslav Gál4, Jana Korčeková5, Michaela Hornychová 4, Alexandra Poturnayová5, Alexander Kromka2*</p> <p>Affiliations: 1 Department of Microelectronics and Sensors, Institute of Electrical Engineering, Slovak Academy of Sciences, Dúbravská Cesta 9, Bratislava, 841 04, Slovak Republic<br> 2 Department of Semiconductors, Institute of Physics of the Czech Academy of Sciences, Cukrovarnicka 10/112, Prague 6 162 00, Czech Republic<br> 3 Department of Microelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, Prague 6, 166 27, Czech Republic<br> 4 Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovak Republic<br> 5 Center of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovak Republic<br> *corresponding author: tibor.izsak@savba.sk</p> <p>Data manager: Kristýna Dostálová: dostalovak@fzu.cz</p> <p>Date of collection: 1. 5. 2023 - 31. 7. 2024</p> <p>Description: Figure 1: Photos of QCM substrates oriented horizontally or vertically on the substrate holder in the deposition chamber (left) and during the diamond CVD process with ignited plasma (right).<br> Figure 2: a) 3D model of the measurement setup and b) photograph of the open gas chamber with embedded QCM sample.<br> Figure 3: Photo of the a) measurement setup and b) disassembled flow cell with V-Dia-QCM. c) Side view photo of the assembled flow cell in the measurement setup.<br> Figure 4: a) SEM images revealing surface morphology and b) corresponding Raman spectra of Dia-QCM and Dia-Si substrates horizontally or vertically oriented on the substrate holder and corresponding optical photos. There is also the Raman spectrum of the bare QCM (Au-QCM) sample before the diamond deposition.<br> Figure 5: a) Raman spectra and b) SEM images depicting surface morphology of porous diamond film grown on Si (H-PorDia-Si) and QCM (H-PorDia-QCM) substrate. The inset in Fig. 5a represents the optical photo of diamond-coated QCM. Note: ‘H-’ in sample names means horizontally loaded samples.<br> Figure 6: The response delta fR of diamond-coated QCM sensors horizontally and vertically oriented, i.e., single-sided and double-sided diamond-coated QCMs, when applying periodic switching (at 3-minute intervals) of ethanol vapour (E) with various concentrations (from 10 ppm to 100 ppm) and synthetic air (Air).<br> Figure 7: a) First resonant frequency shift (delta fR) of individual QCM sensors and b) mean values of delta fR with corresponding error bars for each QCM sensor group dependent on ethanol concentration.<br> Figure 8: a) The changes of the resonant frequency, delta fR, after the addition of neutravidin (NA) dissolved in water, biotinylated 1C aptamers (1C APT) dissolved in PBS with MgCl2, and 50 pg/mL S-RBD protein in PBS. The addition of neutravidin, aptamers, proteins, and surface washings by water (H2O) or buffer (PBS) are highlighted by arrows. b) Zoom in on the highlighted area in Fig. 8a.<br> Figure 9: Decrease of the resonant frequency, fR, at various S-RBD protein concentrations. The comparison of the sensitivity of diamond and gold QCM surfaces on which S-RBD was determined is indicated in the graph legend.</p>
Diffraction images of a crystal of the F-BAR domain of PSTPIP1 (Proline-serine-threonine phosphatase-interacting protein 1) mutant G258A (PDB entry 7AAL)
<p>Diffraction images of a crystal of the F-BAR domain of PSTPIP1 (residues 1-289), mutant G258A.</p> <p>Data were collected on a single crystal at the beamline i03 of the Diamond Light Source synchrotron (Didcot, UK) using radiation of 0.9999 Å wavelength and a PILATUS3 6M detector. The dataset consists of 2400 images (0.15 degree oscillation per image). Crystals belong to the space group P2(1)2(1)2(1) with unit cell dimensions a=48.19 Å, b=73.02 Å, c=205.25 Å. The asymmetric unit contains an homodimer of the F-BAR domain (~53% solvent content), which is the biological unit.</p> <p>Diffraction data was notably anisotropic. The lowest resolution limit was 2.92 Å in the direction b* and the highest limits were 1.97 Å and 2.09 in the directions a* and c*, respectively.</p> <p> </p> <p>The structure derived form these data is published in:</p> <p>Manso, J.A., Marcos, T., Ruiz-Martín, V. Casas J, Alcón P, Sánchez Crespo M, Bayón Y, de Pereda JM, Alonso A <em>PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders</em>. <strong>Cell. Mol. Life Sci</strong>. 79, 131 (2022). <a href="https://doi.org/10.1007/s00018-022-04173-w">https://doi.org/10.1007/s00018-022-04173-w</a></p> <p>The structure is available at the PDB under the code 7AAL:</p> <p><a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7aal">https://www.ebi.ac.uk/pdbe/entry/pdb/7aal</a></p>
Diffraction images of a crystal of the F-BAR domain of PSTPIP1 (Proline-serine-threonine phosphatase-interacting protein 1) bound to the C-terminal homology (CTH) segment of the phosphatase LYP (PTPN22) (PDB entry 7AAM)
<p>Diffraction images of a crystal of the F-BAR domain of human PSTPIP1 (residues 1-289, Uniprot reference O43586-1) in complex with the CTH of LYP (residues 787-807, Uniprot Q9Y2R2-1).</p> <p>Data were collected on a single crystal at the beamline i03 of the Diamond Light Source synchrotron (Didcot, UK) using radiation of 0.99987 Å wavelength and a PILATUS3 6M detector. The dataset consists of 3 groups, each containing of 1800 images (0.1 degree oscillation per image), collected at three different positions of the same crystal. Crystal belongs to the space group P2(1)2(1)2(1) with unit cell dimensions a=48.0 Å, b=72.0 Å, c=205.0 Å. The asymmetric unit contains an homodimer of the F-BAR domain bound to a LYP-CTH (~53% solvent content), which is the biological complex.</p> <p>Diffraction data was notably anisotropic. The lowest resolution limit was 4.05 Å in the direction b* and the highest limits were 2.11 Å and 2.10 in the directions a* and c*, respectively.</p> <p> </p> <p>The structure derived form these data is published in:</p> <p>Manso, J.A., Marcos, T., Ruiz-Martín, V. Casas J, Alcón P, Sánchez Crespo M, Bayón Y, de Pereda JM, Alonso A <em>PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders</em>. <strong>Cell. Mol. Life Sci</strong>. 79, 131 (2022). <a href="https://doi.org/10.1007/s00018-022-04173-w">https://doi.org/10.1007/s00018-022-04173-w</a></p> <p>The structure is available at the PDB under the code <strong>7AAM</strong>:</p> <p><a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7aam">https://www.ebi.ac.uk/pdbe/entry/pdb/7aam</a></p>
Diffraction images of a crystal of the F-BAR domain of PSTPIP1 (Proline-serine-threonine phosphatase-interacting protein 1) (PDB entry 7AAN)
<p>Diffraction images of a crystal of the F-BAR domain of PSTPIP1 (residues 1-289).</p> <p>Data were collected on a single crystal at the beamline i03 of the Diamond Light Source synchrotron (Didcot, UK) using radiation of 0.99987 Å wavelength and a PILATUS3 6M detector. The dataset consists of 3600 images (0.15 degree oscillation per image) that were collected: 2400 at one position and the other 1200 at a second site in the same crystal. Crystal belongs to the space group P2(1)2(1)2(1) with unit cell dimensions a=48.3 Å, b=71.9 Å, c=204.6 Å. The asymmetric unit contains an homodimer of the F-BAR domain (~53% solvent content), which is the biological unit.</p> <p>Diffraction data was notably anisotropic. The lowest resolution limit was 4.32 Å in the direction b* and the highest limits were 2.12 Å and 2.17 in the directions a* and c*, respectively.</p> <p>The structure derived form these data is published in:</p> <p>Manso, J.A., Marcos, T., Ruiz-Martín, V. Casas J, Alcón P, Sánchez Crespo M, Bayón Y, de Pereda JM, Alonso A <em>PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders</em>. <strong>Cell. Mol. Life Sci</strong>. 79, 131 (2022). <a href="https://doi.org/10.1007/s00018-022-04173-w">https://doi.org/10.1007/s00018-022-04173-w</a></p> <p>The structure is available at the PDB under the code <strong>7AAN</strong>:</p> <p><a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7aan">https://www.ebi.ac.uk/pdbe/entry/pdb/7aan</a></p>
MD simulation of the crystal unit cell of the second PDZ domain of LNX2 protein
<p>This molecular dynamics simulation data is provided as part of the manuscript "<strong>LAWS: Local Alignment for Water Sites - a method to analyze crystallographic water in simulations</strong>". The code for the algorithm is provided: <a href="https://github.com/rauscher-lab/LAWS">on github</a><br> <br> The system contains one unit cell of the crystal (PDB ID: 5E11) with 4 symmetrically related protein chains. The total simulation length is 1 microsecond. </p> <p><strong>Force field + water model</strong>: CHARMM36m + CHARMM-modified TIP3P<br> <strong>Number of atoms</strong>: 9650<br> <strong>Number of time frames:</strong> 100,000 with 10-ps stride<br> <em>The details of the simulations are provided in the manuscript.</em></p>
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid - 3lambda SeMAD dataset
<p>bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) for 3 wavelength Se MAD experiment (infl, inflection point, peak, peak, rem, high energy remote) and the associated data processing files (xds_inf, xds_peak, xds_rem) </p>
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with an adenosine nucleotide analog.
<p>bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) and the associated data processing files (xds) </p>
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid - native dataset
<p>bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) and the associated data processing files (xds) </p>
Statistical analyses of the impact of X-ray damage effects on conformational heterogeneity in room temperature (277 K) and cryo-cooled (100 K) protein crystals
<p>These data are published in support of the manuscript "Evaluating the impact of X-ray damage on conformational heterogeneity in room temperature and cryo-cooled protein crystals" submitted to Acta Crystallographica section D, authors:</p> <p>Filip Yabukarski<sup>1,</sup><sup>#,</sup>*, Tzanko Doukov<sup>5</sup>, Daniel A Mokhtari<sup>1</sup>, Siyuan Du<sup>1</sup>, Daniel Herschlag<sup>1,2,3,4</sup><sup>,</sup>*</p> <p><sup>1</sup>Department of Biochemistry, <sup>2</sup>Department of Chemistry, <sup>3</sup>Department of Chemical Engineering, <sup>4</sup>Stanford ChEM-H, Stanford University, Stanford, California 94305, United States, <sup>5</sup>Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States.</p> <p># Current address: Bristol Myers Squibb, San Diego, California 92121, United States.</p> <p>* Correspondence: fyabukar@stanford.edu, herschla@stanford.edu</p>
CHiMP Detector Datasets: Images of Sitting Drop Protein Crystallisation Experiments with Associated Image Masks of Drops and Crystals
<p>The CHiMP Detector Datasets consist of images of protein crystallisation experiments along with corresponding zipped NumPy archive files (.npz). All images have had their histograms adjusted using the Contrast Limited Adaptive Histogram Equalization ((CLAHE) algorithm using the OpenCV library with grid size of 12 and are in JPEG format. The .npz files contain class labels and instance segmentation masks for both the experimental droplets and any crystals that an expert annotator has deemed to be interesting/mountable. To class labels and masks can be loaded in the following way:</p> <pre><code>import numpy as np # load in the mask and class label list from .npz file located at mask_path mask_file = np.load(mask_path) masks = list(mask_file["masks"].astype(int)) class_labels = list(mask_file["class_labels"])</code></pre> <p>There are two datasets within this archive:</p> <ol> <li><strong>The VMXi CHiMP Detector Dataset</strong>. This consists of 237 images of resolution 1688 × 1352 pixels with corresponding masks. These images were collected on a Rock Imager 1000 (Formulatrix, USA) automated microplate imager at the VMXi experimental facility at Diamond Light Source, UK. These images and masks were used to train the VMXi CHiMP (Crystal Hits in My Plate) Detector network that performs object detection and instance segmentation of crystals in experimental micrographs using a Mask-R-CNN architecture. The files "vmxi_detector_training.csv" and "vmxi_detector_validation.csv" provide the filenames of the members of the training and validation sets respectively.</li> <li><strong>The XChem CHiMP Detector Dataset.</strong> This consists of 350 images of resolution 1024 × 1224 pixels with corresponding masks. These images were collected on a Rock Imager 1000 (Formulatrix, USA) automated microplate imager at the Crystallisation Facility@Harwell, located in the Research Complex at Harwell (RCaH). In addition to the images in the VMXi CHiMP Detector, these images were used to train the XChem CHiMP (Crystal Hits in My Plate) Detector network that performs object detection and instance segmentation of masks and crystals in experimental micrographs using a Mask-R-CNN architecture. The files "xchem_detector_training.csv" and "xchem_detector_validation.csv" provide the filenames of the members of the training and validation sets respectively.</li> </ol>
Protonation state of proteins in crystals (CpHMD simulations)
<p>Input files to run simulations for:</p> <p>"What is the protonation state of proteins in crystals: insights from constant pH molecular dynamics simulations"</p> <p>by Noora Aho*<strong>†</strong><em>, </em>Gerrit Groenhof*<em>, </em>and Pavel Buslaev* (manuscript submitted in August 2024)</p> <p>*Nanoscience Center and Department of Chemistry, University of Jyväskylä, Finland</p> <p><strong>†</strong>Theoretical Physics and Center for Biophysics, Saarland University, Germany</p> <p> </p>
Eiger HDF5 protein crystal diffraction images of TTR-Pt
<p>These data will be used during the Pasteur Course 3rd Integrative Structural Biology 2018 MX tutorials.</p> <p>The sequence of the protein is (127 amino acids, MW 13.76 kDa):</p> <p>> TTR<br> GPTGTGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLT<br> TEEEFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYST<br> TAVVTNPKE</p> <p> </p> <p>There are 5 main platinum sites.</p>
Single Crystal X-ray Diffraction Data for PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein
<p>Single Crystal X-ray Diffraction Data for PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein collected at Diamond Light Source, Beamline I03 2018-07-21</p>
Raw Diffraction Images: Formation of a highly dense tetra rhenium cluster in a protein crystal and its implications in medical imaging.
<p>Exploration of a “time on shelf” protein structure containing the radiopharmaceutical synthon <em>fac</em>-[Re(CO)<sub>3</sub>(H<sub>2</sub>O)<sub>3</sub>]<sup>+ </sup>as an <em>in vivo</em> reaction vessel to form tetranuclear rhenium clusters appropriate for theranostic applications.That a protein crystal can serve as a chemical reaction vessel is intrinsically fascinating. That it can produce an electron dense tetranuclear rhenium cluster compound from a rhenium tricarbonyl tribromo starting compound adds to the fascination. The cluster has been synthesised before in vitro when it formed under basic conditions. Therefore its synthesis in a protein crystal grown at pH4.5 is even more unexpected. The X-ray crystal structures presented here are for the protein hen egg white lysozyme incubated with the rhenium tricarbonyl tribromo compound for periods of 1 year and 2 years. These reveal a completed, very well resolved, tetra rhenium cluster after two years and an intermediate state after 1 year where the carbonyl ligands to the rhenium cluster are not yet clearly resolved. A dense tetra-nuclear rhenium cluster, and its technetium form, offers enhanced medical imaging contrast. The raw diffraction images for the one year and two year protein structure, described in the manuscript, is made avaliable on the Zenodo repository.</p>
Data from crystal of Leucine-Rich Repeat Protein from Leptospira interrogans recorded during routine commissioning on Diamond Light Source beamline I04
<p>Samples as part of ongoing research / collaboration; for more details see https://www.ncbi.nlm.nih.gov/pubmed/26057675</p>
Single Crystal X-ray Diffraction Data for mixed PMP/PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein
<p>Single Crystal X-ray Diffraction Data for mixed PMP/PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein collected at Diamond Light Source, Beamline I04, 2017-09-09</p>
Synchrotron diffraction images for the 0.86-Å crystal structure of hydrogenated human myelin protein P2
<p>1000 X-ray diffraction images collected from a crystal of hydrogenated human myelin protein P2. Key processing files for the XDS package are included. The data were collected on the EMBL/DESY synchrotron beamline P13. </p>
Case studies from: Sequence assignment validation in protein crystal structure models with checkMySequence
<p>Case studies from "Sequence assignment validation in protein crystal structure models with checkMySequence"</p>
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