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24 results for “myoglobin”
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>
Data from: Maximum cardiac performance of Antarctic fishes that lack haemoglobin and myoglobin: exploring the effect of warming on nature's natural knockouts
Comparisons among related species provide valuable insight into the functional consequences of natural genetic mutations. We assessed cardiac function at ambient and elevated temperatures in Antarctic notothenioids with contrasting levels of the oxygen binding proteins, haemoglobin (Hb) and myoglobin (Mb), to elucidate changes in cardiac performance that may compensate for impaired O2 transport. Notothenia coriiceps (Hb+Mb+) at 1oC had the highest maximum cardiac work rate (WC) and pressure generating capacity, but lowest relative ventricular mass and maximum cardiac output (Q̇) when compared with two icefish species, Chionodraco rastrospinosus (Hb-Mb+) and Chaenocephalus aceratus (Hb-Mb-). Cardiomegaly associated with absence of Hb generated an exceptionally large maximum stroke volume (VS) and Q̇, but a lower WC. However, C. rastrospinosus had a larger ventricle, a higher intrinsic heart rate (fH), and greater maximum VS and Q̇ than C. aceratus, suggesting that cardiac Mb has functional relevance. Warming to 4oC increased fH, but only increased maximum Q̇ in icefishes, while maximum WC and pressure development increased in N. coriiceps (both ~2.5x that of C. aceratus). The Hb+Mb+ myocardium generated considerable Q̇ against raised afterload, unlike icefish hearts. The presence of Hb and Mb enhances cardiac performance, and likely resilience to near-future ocean warming.
QENS spectra of myoglobin in solution to be used with the analysis codes deposited under 10.5281/zenodo.7058345
<p>Quasielastic Neutron Scattering spectra of myoglobin in solution recorded on the IN5 spectrometer at the Institut Laue-Langevin in Grenoble, France. The data sets are to be used with the analysis codes deposited under DOI:10.5281/zenodo.7058345, which are in turn related to the publication A. Hassani, A. M. Stadler, and G.R. Kneller, Quasi-analytical resolution-correction of elastic neutron scattering from proteins, to appear in the Journal of Chemical Physics (DOI:10.1063/5.0103960). </p> <p>The data can be freely used, citing properly the reference concerning the original data, A. M. Stadler, F. Demmel, J. Ollivier, and T. Seydel, Picosecond to Nanosecond Dynamics Provide a Source of Conformational Entropy for Protein Folding. Phys. Chem. Chem. Phys., 18(31):21527–21538, 2016 (DOI: 10.1039/c6cp04146a).</p> <p> </p>
Fast kinetics data of binding of azide to myoglobin, training data -- MetBio practicals
<p>These data files were acquired during the course of the 3rd <a href="http://frenchbic.cnrs.fr/">FrenchBIC</a> <a href="http://frenchbic.cnrs.fr/2021/01/25/3rd-frenchbic-summer-school-on-methods-for-studying-metals-in-biology/">MetBio summer school</a> taking place in and around Marseille. The data were acquired during the “stopped flow” practicals.</p> <p>The data correspond to the reaction of Myoglobin with various concentrations of azide, triggered using a stopped-flow apparatus and followed by UV/Visible spectroscopy.</p> <p>The concentrations of azide can be deduced from the names of the files and are expressed in millimolar. The concentrations of myoglobin are variable but always much lower than that of azide.</p> <p>The purpose of this dataset is to be used as training data for analysing multiwavelength kinetic data. It will be the subject of a data analysis tutorial using the free software <a href="https://bip.cnrs.fr/groups/bip06/software/">QSoas</a>, to be published <a href="https://vince-debian.blogspot.com/">there</a>.</p> <p>With the exception of the <code>WTV-Azide-0.5mm_3.txt</code>, all the files are in a “matrix” format, in which the first column gives the time and each column after the first corresponds to the absorbances over time of a single wavelength.</p> <p>The <code>WTV-Azide-0.5mm_3.txt</code> uses a different format, in which each line corresponds to a <em>wavelength</em> <em>time</em> <em>absorbance</em> triplet.</p> <p>Useful background reading:</p> <ul> <li> <p>Coletta <em>et al</em>, <strong>1996</strong>, DOI: 10.1111/j.1432-1033.1996.00049.x</p> </li> <li> <p>De Sanctis <em>et al</em>, <strong>2007</strong>, DOI: 10.1529/biophysj.106.098764</p> </li> </ul>
Data from: Maximum cardiac performance of Antarctic fishes that lack haemoglobin and myoglobin: exploring the effect of warming on nature’s natural knockouts
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VTR case studies datasets: myoglobin against hemoglobin, RBDs of SARS-CoV-1 vs. SARS-CoV-2, and glucose-tolerant vs. non-tolerant β-glucosidases
<p>Description of the four files:</p> <ol> <li><strong>contacts.xlsx</strong> <ul> <li>List of detected contacts for the three case studies</li> </ul> </li> <li><strong>pymol_files_case_study_1.zip</strong> <ul> <li>Contains files in PDB format of the analyzed structures, and files in PML format used to display visualizations in the PyMOL tool for the case study 1: comparison between contacts of myoglobin against hemoglobin</li> </ul> </li> <li><strong>pymol_files_case_study_2.zip</strong> <ul> <li>Contains files in PDB format of the analyzed structures, and files in PML format used to display visualizations in the PyMOL tool for the case study 2: comparison between contacts of RBDs of SARS-CoV-1 vs. SARS-CoV-2 both complexed with the cell receptor ACE2</li> </ul> </li> <li><strong>pymol_files_case_study_3.zip</strong> <ul> <li>Contains files in PDB format of the analyzed structures, and files in PML format used to display visualizations in the PyMOL tool for the case study 3: comparison between contacts of glucose-tolerant vs. non-tolerant β-glucosidases </li> </ul> </li> </ol>
Data from: The loss of hemoglobin and myoglobin does not minimize oxidative stress in Antarctic icefishes
The unusual pattern of expression of hemoglobin (Hb) and myoglobin (Mb) among Antarctic notothenioid fishes provides an exceptional model system for assessing the impact of these proteins on oxidative stress. We tested the hypothesis that the lack of oxygen-binding proteins may reduce oxidative stress. Levels and activity of pro-oxidants, small-molecule and enzymatic antioxidants, and levels of oxidized lipids and proteins in liver, oxidative skeletal muscle, and heart ventricle were quantified in five species of notothenioid fishes differing in the expression of Hb and Mb. Levels of ubiquitinated proteins and rates of protein degradation by the 20S proteasome were also quantified. Although levels of oxidized proteins and lipids, ubiquitinated proteins, and antioxidants are higher in red-blooded fishes than in Hb-less icefishes in some tissues, this pattern does not persist across all tissues. Expression of Mb is not associated with oxidative damage in heart ventricle, whereas the activity of citrate synthase and contents of heme are positively correlated with oxidative damage in most tissues. Despite some tissue differences in levels of protein carbonyls among species, rates of degradation by the 20S proteasome are not markedly different, suggesting either alternative pathways for eliminating oxidized proteins or redox tone varies among species. Together, our data indicate that the loss of Hb and Mb does not correspond with a clear pattern of either reduced oxidative defense or oxidative damage.
Repurposing myoglobin into an abiological asymmetric ketoreductase
<p>Data underlying the figures/tables of the publication "Repurposing myoglobin into an abiological asymmetric ketoreductase" Chem <span><span>Volume 10, Issue 8</span></span>, 8 August 2024, Pages 2577-2589. (<a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.chempr.2024.06.010" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.chempr.2024.06.010</span></span></a>)</p>
Data from: The loss of hemoglobin and myoglobin does not minimize oxidative stress in Antarctic icefishes
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Influence of pump laser fluence on ultrafast myoglobin structural changes
<p>DESCRIPTION OF TAR ARCHIVE CONTENTS</p><p>the folder SCRIPTS contains two subfolders: ANALYZE and REFINE</p><p>ANALYZE contains python3 scripts for analysis.<br>There are three files:<br>-analyze_pdb.py which contains functions, and<br>-make_figures.py which calls these functions.</p><p>In make_figures.py one needs to change the directories at the<br>beginning of the script so the script can find the files it needs.<br>Moreover, one needs to have numpy, scipy, and matplotlib installed.</p><p>As the functions in analyze_pdb cannot handle altlocs, there is a third file: extract_Bloc.py which takes the B altloc atoms out of a pdb file and makes a new file containing only these. In this way, the photolyzed structures, which are stored als altloc B by the refinement script (see below), can be analyzed.</p><p> </p><p>REFINE contains the files needed for multi-copy refinement.</p><p>There are several files:</p><p>-multicopy_refine performs the multicopy refinement (duh...); it needs to be edited to conform to your file names/directory structure. Instructions are at the top of the file. The script requires python2.7 and phenix. This version will use the automatically determined occupancy for final refinement. The file needs to be adapted when another, preset occupancy is required.</p><p>-refine_par.in contains parameters for phenix.refine that are called by multicopy_refine, and needs to be in the same directory.</p><p>-the pdb files are the starting structures for multicopy refinement. The "4 and 18 uJ" starting structures are for the 23- and 101 mJ/cm2 case (and the power titration), for the low-fluence data the other dark structures ("1 uJ") need to be substituted. Details of the multicopy refinement scheme are in the publication.</p><p> </p><p>Back in the top folder, the subfolder GEOMETRY contains the .cif file which describes the heme geometry used<br>for all refinements. In it, the prior ESDs for the planarity of the heme have been increased<br>from 0.02 to 0.2</p><p><br>The STREAMS folder contains the CrystFEL stream files used for Monte Carlo integration. There are four subdirectories, one for each time series, and a separate one for the power titration.</p><p>DARKS contains the refined dark structures as well as the MTZ files with the dark data. </p><p><br>POWERTITRATION contains the power titration multicopy refinement results, as well as the MTZ files with the integrated data.<br> </p><p>TIMESERIES contains the time series multicopy refinement results.</p>
Myoglobin as a conservation-relevant predictor of short-distance flight capacity in Neotropical forest birds
<p>Some forest-dwelling tropical bird species are unable or unwilling to fly even a few hundred meters across habitat discontinuities, restricting connectivity of isolated populations in fragmented landscapes. Experimental evidence for flight limitation has reliably predicted occurrence across archipelagoes of habitat fragments varying in their distance from potential source populations. Mechanistic explanations for large differences in flight capacity of tropical birds, even over remarkably short distances, have not been tested. We evaluated myoglobin concentration in pectoralis muscles and hearts of eight Neotropical species for which experimental evidence revealing a wide range of flight abilities exists. We found a strong positive relationship between myoglobin concentration in the pectoralis muscles, but not hearts, and average over-water flight distance during dispersal-challenge experiments. The approximately 2.5-fold difference in pectoralis myoglobin concentration is directly associated with flight capacity and allows predictions of species or species groups most likely to be impeded by habitat discontinuities and therefore at conservation risk in fragmented landscapes.</p>
Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers
<p>Identifying the phylogenomic underpinnings of specialized phenotypes that fueled evolutionary transitions into new adaptive zones is central to evolutionary biology. The order Eulipotyphla (e.g., moles, shrews, and hedgehogs) is ideally suited to address this question as semi-fossorial, fossorial, and semi-aquatic forms have repeatedly arisen from terrestrial forbearers. However, our understanding of the ecomorphological pathways leading to these diverse lifestyles has been confounded by a fragmentary fossil record and potential morphological convergence. The net surface charge of myoglobin (<i>Z</i><sub>Mb</sub>) is readily determined from its primary structure and provides an objective target to map ancient evolutionary transitions due to mechanistic linkages of <i>Z</i><sub>Mb</sub> with myoglobin concentration. Myoglobin facilitates O<sub>2</sub> storage and transport in muscle and its concentration is sharply elevated in breath-hold divers relative to terrestrial mammals, with fossorial and high-elevation species only showing minor increases. Here we trace the evolution of <i>Z</i><sub>Mb</sub> to unravel the history of lifestyle transitions in the clade containing the world's smallest endothermic divers. We first constructed a comprehensive phylogeny that resolved previously intractable intra-family relationships, and confirmed that <i>Z</i><sub>Mb</sub> accurately predicts aquatic habits within Eulipotyphla. Ancestral reconstructions of <i>Z</i><sub>Mb</sub>, which included representatives from all seven recognized semi-aquatic genera, provide key insights into the timing and mode of adaptations that underpin the evolution of the diverse ecomorphotypes within Eulipotyphla, and unambiguously revealed that semi-aquatic lifestyles evolved twice in moles, and three times in shrews. Our phylogenetically informed analysis supports <i>Z</i><sub>Mb</sub> as an effective tool to trace ancient secondary aquatic transitions of mammals based on protein sequence alone.</p>
Dataset for "Myoglobin-derived iron causes wound enlargement and impaired regeneration in pressure injuries of muscle"
<p>Primary images, data and quantification spreadsheets for "Myoglobin-derived iron causes wound enlargement and impaired regeneration in pressure injuries of muscle"</p>
Myoglobin Removal With CytoSorb in Rhabdomyolysis
ClinicalTrials.gov study NCT06503289. IPD Sharing: NO. Countries: 1. Publications: 3.
Myoglobin as a conservation-relevant predictor of short-distance flight capacity in Neotropical forest birds
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Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers
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Thermal profiles reveal stark contrasts in properties of biological membranes from heart among Antarctic notothenioid fishes which vary in expression of hemoglobin and myoglobin
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myoglobin
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Data from: Molecular dynamic simulations reveal the structural determinants of fatty acid binding to oxy-myoglobin
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Data from: Spectroscopic analysis of myoglobin and cytochrome c dynamics in isolated cardiomyocytes during hypoxia and reoxygenation
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