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57 results for “oligomerization”
A2aR Oligomeric assemblies identified from MD simulations using in-vivo mimetic biomembranes
<p>GPCR oligomerisation is known to play an important role in the receptor signalling. However, due to the technical challenges, the structural information of GPCR oligomerisation is still very limited, which hinders our understanding of GPCR signalling in a fuller picture. In this deposit, we provide the structural coordinates of various oligomeric assemblies of Adenosine A2a receptor that were sampled from unbiased MD simulations.</p> <p>For more information regarding the MD simulation setup and definitions of the various calculated values, please check out our paper on <a href="https://www.biorxiv.org/content/10.1101/2020.06.24.168260v2">BioRxiv</a> (doi: https://doi.org/10.1101/2020.06.24.168260)</p> <p>** Simulation setup **<br> 9 copies of A2aR were randomly inserted into an <em>in-vivo </em>mimetic biomembrane (of size of 45nm x 45nm) to build the initial configuration of the simulations. 10 such systems were set up for A2aR in the inactive state, 10 for the active state and 10 for the active in complex with the mini Gs state. These systems were represented by MARTINI 2 coarse-grained models and were simulated for 50 micro-seconds. The use of MARTINI coarse-grained force field would freeze the receptor conformation in the initial configuration, thus decoupled the oligomerization from such process as ligand-induced conformational change. The more efficient sampling of coarse-grained force field therefore allowed us to explore fully the protein-protein associations in the oligomerisation process. Protein-protein associations were identified when any atoms from two protomers were getting closer than 0.75 nm. The oligomerisation process was monitored and the sampled various oligomeric assemblies were identified for calculation of oligomer residence time. </p> <p><br> ** Coordinate file explained **<br> These pdb files contain the A2aR oligomer structures in atomistic models. The coarse-grained oligomeric structures were converted back to atomistic models using CHARMM 36 force field. The identified oligomeric structures from each oligomeric order were clustered. 10 structures were randomly taken from each cluster and stored as individual models in the pdb files with a naming format <strong><em>{Conf. State}_OS{Oligomeric Order}_cl{Cluster id}.pdb</em></strong>. The pdb files can be viewed by such visualization tools as PyMol, Chimera or JMol etc.</p> <p><br> ** Spreadsheet file explained **<br> The calculated properties, including residence time and geometry, of each identified oligomer were stored in the Excel shreadsheet (Oligomeric_Assembly_Distribution.xlsx). Each oligomeric order, i.e. oligomer order = 2,3,4,5, opens an individual spreadsheet page where the calculated data were grouped by oligomers' conformational states (i.e. Inactive, Active and Act + mini Gs) and then ranked by oligomers' residence time. The measurements for describing the oligomer geometry were shown in columns after "Cluster ID" and before "Count". For definitions of these measurements, please refer to our paper. Pictures of the oligomers viewed from the extracellular side and intracellular side were also provided in the the spreadsheet to assist visualisation.</p>
Effect of older age and/or ACL injury on the dose–response relationship between ambulatory load magnitude and immediate load-induced change in serum cartilage oligomeric matrix protein
<p>The data presented here was used in the models in the pulication doi <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jshs.2024.100993" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.jshs.2024.100993</span></span></a>.</p> <p>The purpose of this study was to assess the influence of age, anterior cruciate ligament (ACL) injury, and sex on resting sCOMP concentration, on the immediate load-induced sCOMP kinetics after a 30-minute treadmill walking stress, and on the dose-response relationship between ambulatory load magnitude and the load-induced sCOMP change.</p> <p>Overall, data of 85 participants in four groups (20–30 years healthy, HEA<sub>20–30</sub>, n=24; 20–30 years ACL-injured, ACL<sub>20–30</sub>, n=23; 40–60 years healthy, HEA<sub>40–60</sub>, n=23; 40–60 years ACL-injured, ACL<sub>40–60</sub>, n=15) were included in this dataset. ACL injured participants suffered from an ACL injury 2-10 years prior to inclusion. The dateaset includes, patient data and serum cartilage oligomeric matrix protein (sCOMP) concentration measured on three testdays (m1, m2, m3) immediately before (t0) and immediately after 30 minutes of treadmill walking (t1) where the ambulatory loads were 80% bodyweight (BW), 100% BW or 120% BW (block randomized order). This dateset represents a subset of data collected in the parent study.</p> <p>The detailed experimental protocol of the parent study has been described in Herger, S., Vach, W., Nüesch, C., Liphardt, A. M., Egloff, C., & Mündermann, A. (2022). Dose-response relationship of in vivo ambulatory load and mechanosensitive cartilage biomarkers—The role of age, tissue health and inflammation: A study protocol. <em>PLoS One, 17</em>(8), e0272694. <a href="https://doi.org/10.1371/journal.pone.0272694">https://doi.org/10.1371/journal.pone.0272694</a></p>
Measurement of solubility product reveals the interplay of oligomerization and self-association for defining condensate formation
<p>This data set includes the raw confocal microscopy images, DLS, and SEC-MALS data used for Chattaraj, Baltaci, et al. <em>Mol. Biol. Cell.</em> 2024. </p>
Synaptic oligomeric tau in Alzheimer's disease – a potential culprit in the spread of tau pathology through the brain
<p>In Alzheimer’s disease (AD), fibrillar tau pathology accumulates and spreads through the brain and synapses are lost. Evidence from mouse models indicates that tau spreads trans-synaptically from pre- to postsynapses and that oligomeric tau is synaptotoxic, but data on synaptic tau in human brain is scarce. Here we used sub-diffraction-limit microscopy to study synaptic tau accumulation in post-mortem temporal and occipital cortices of human AD and control donors. Oligomeric tau is present in both pre- and postsynaptic terminals even in areas without abundant fibrillar tau deposition. Further, there is a higher proportion of oligomeric tau compared to phosphorylated or misfolded tau found at synaptic terminals. These data suggest that accumulation of oligomeric tau in synapses is an early event in disease pathogenesis, and that tau pathology may progress through the brain via trans-synaptic spread in human disease. Thus, specifically reducing oligomeric tau at synapses may be a promising therapeutic strategy for AD.</p>
Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (wtChR2-mEos3.2)
<p>This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555)</p> <p>Zip file contains PALM measurements of HEK293 cells expressing ChR2<sub>WT</sub> fused with mEos3.2.<br>Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames.</p> <p>Detailed protocols for sample preparation and data acquisition are described in the article.<br>Some details are listed below.</p> <p><strong>SAMPLE PREPARATION</strong></p> <p>cell line: Flp-In™ T-REx™ 293<br>transfection method: modified calcium-phosphate transient transfection [1]<br>fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperature<br>imaging buffer: PBS</p> <p><strong>PALM ACQUISITION</strong></p> <p>A custom-built setup for single-molecule localization microscopy is described in [2].<br>mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample).<br>PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera:<br>exposure time = 100 ms<br>frame size = 512x512 pixels<br>pixel size = 80 nm</p> <p> </p> <p>[1] Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.<br>[2] Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073</p>
Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (ChR2(C34A/C36A)-mEos3.2)
<p>This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555)</p> <p>Zip file contains PALM measurements of HEK293 cells expressing ChR2<sub>C34A/C36A</sub> fused with mEos3.2.<br>Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames.</p> <p>Detailed protocols for sample preparation and data acquisition are described in the article.<br>Some details are listed below.</p> <p><strong>SAMPLE PREPARATION</strong></p> <p>cell line: Flp-In™ T-REx™ 293<br>transfection method: modified calcium-phosphate transient transfection [1]<br>fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperature<br>imaging buffer: PBS</p> <p><strong>PALM ACQUISITION</strong></p> <p>A custom-built setup for single-molecule localization microscopy is described in [2].<br>mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample).<br>PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera:<br>exposure time = 100 ms<br>frame size = 512x512 pixels<br>pixel size = 80 nm</p> <p> </p> <p>[1] Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.<br>[2] Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073</p>
Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (b1AR-mEos3.2)
<p>This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555)</p> <p>Zip file contains PALM measurements of HEK293 cells expressing ß<sub>1</sub>AR fused with mEos3.2.<br>Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames.</p> <p>Detailed protocols for sample preparation and data acquisition are described in the article.<br>Some details are listed below.</p> <p><strong>SAMPLE PREPARATION</strong></p> <p>cell line: Flp-In™ T-REx™ 293<br>transfection method: modified calcium-phosphate transient transfection [1]<br>fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperature<br>imaging buffer: PBS</p> <p><strong>PALM ACQUISITION</strong></p> <p>A custom-built setup for single-molecule localization microscopy is described in [2].<br>mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample).<br>PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera:<br>exposure time = 100 ms<br>frame size = 512x512 pixels<br>pixel size = 80 nm</p> <p> </p> <ol> <li>Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.</li> <li>Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073</li> </ol>
Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (CD28-mEos3.2)
<p>This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555)</p> <p>Zip file contains PALM measurements of HEK293 cells expressing CD28 fused with mEos3.2.<br>Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames.</p> <p>Detailed protocols for sample preparation and data acquisition are described in the article.<br>Some details are listed below.</p> <p><strong>SAMPLE PREPARATION</strong></p> <p>cell line: Flp-In™ T-REx™ 293<br>transfection method: modified calcium-phosphate transient transfection [1]<br>fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperature<br>imaging buffer: PBS</p> <p><strong>PALM ACQUISITION</strong></p> <p>A custom-built setup for single-molecule localization microscopy is described in [2].<br>mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample).<br>PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera:<br>exposure time = 100 ms<br>frame size = 512x512 pixels<br>pixel size = 80 nm</p> <p> </p> <ol> <li>Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.</li> <li>Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073</li> </ol>
Data from: A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein
<p>Here we present NMR and MS data used in article A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein. NMR data contain full set of assignment experiments used to partially assign signals of non-myristoylated wt M-PMV MAPPHis, H-N HSQC spectra or myristoylated M-PMV MAPPHis wt, A79V and I51A mutants and results from TALOS+ program used to calculate the secondary structure of C-terminal part of both mristoylated and non-myristoylated wt MAPPHis. The MS data contain MS data measured both for non-labeled samples of myristoylated M-PMV MAPPHis wt, A79V and I51A mutants and non-myristoylated MAPPHis, as well as data measured on these proteins after deuterium exchange.</p>
MxiN Differentially Regulates Monomeric and Oligomeric Species of the Shigella Type Three Secretion System ATPase Spa47
<p>Enzyme kinetics data from "MxiN Differentially Regulates Monomeric and Oligomeric Species of the Shigella Type Three Secretion System ATPase Spa47".</p>
Dataset for: A marine cryptochrome with an inverse photo-oligomerization mechanism
<p>Raw data for all sequence analysis, SEC runs, MD simulations, and UV/Vis absorbance readings supporting the findings of the study 'A marine cryptochrome with an inverse photo-oligomerization mechanism'</p>
Serum Cartilage Oligomeric Matrix Protein Levels After 12 Weeks of Different Exercises
ClinicalTrials.gov study NCT01576159. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein
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Oligomeric state and ATP binding to <em>E. coli</em> Rho measured by native MS
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Data from: Oligomerization enables the selective targeting of an intrinsically disordered region by a small molecule
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Data from: Elovanoids counteract oligomeric β-Amyloid-induced gene expression and protect photoreceptors
<p><span>The onset of neurodegenerative diseases activates inflammation that leads to progressive neuronal cell death and impairments in cognition (Alzheimer's disease, AD) and sight (age-related macular degeneration, AMD). How neuroinflammation can be counteracted is not known. In AMD, amyloid β-peptide (Aβ) accumulates in subretinal drusen. In the 5xFAD retina, we found early functional deficiencies (ERG) without photoreceptor cell (PRC) death and identified early insufficiency in biosynthetic pathways of pro-homeostatic/neuroprotective mediators, neuroprotectin D1 (NPD1) and elovanoids (ELVs). To mimic an inflammatory milieu in wild-type (WT) mouse, we triggered retinal pigment epithelium (RPE) damage/PRC death by subretinally injected oligomeric β-Amyloid (OAβ) and observed that ELVs administration counteracted their effects, protecting these cells. In addition, ELVs prevented OAβ-induced changes in gene expression engaged in senescence, inflammation, autophagy, extracellular matrix remodeling and AMD. Moreover, since OAβ target the RPE, we used primary human RPE cell cultures and demonstrated that OAβ caused cell damage, while ELVs protected and restored gene expression as in mouse. Our data show OAβ activates senescence as reflected by enhanced expression of p16INK4a, MMP1, p53, p21, p27 and Il-6 and of <span>senescence-associated secretory phenotype</span> (SASP) secretome, followed by RPE and PRC demise and that elovanoids 32 and 34 blunt these events and elicits protection. In addition, ELVs counteracted OAβ-induced expression of genes engaged in AMD, autophagy and extracellular matrix (ECM) remodeling. Overall, our data uncovered that ELVs downplay OAβ-senescence program induction and inflammatory transcriptional events and protect RPE cells and PRC, and therefore have potential as a possible therapeutic avenue for AMD.</span></p>
Data for Observational Evidence for Criegee Intermediate Oligomerization Reactions Relevant to Aerosol Formation in the Troposphere
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Dataset for Ligand-independent oligomerization of TACI is controlled by the transmembrane domain and regulates proliferation of activated B cells.
<p>This data set provides:</p> <p>a) Details about plasmids used in this study. It is a pdf file, describing expressed sequences and other features of plasmids listed in Supplementary Table 2.</p> <p>b) An Excel file with data used to make graphs of the publication</p>
Molecular dynamics simulation data of the manuscript "KnowVolution of an efficient polyamidase through molecular dynamics simulations of incrementally docked oligomeric substrates"
<p>This repository provides the simulation data as well as the input and parameters files to reproduce our findings.</p> <p><strong>Acknowledgments</strong></p> <p>The authors gratefully acknowledge the computing time provided by RWTH Aachen University. Computations were performed with computing resources granted by RWTH Aachen University under project rwth1584.</p>
Cardiovascular Effects of Oligomeric Procyanidins (OPCs) in Smokers
ClinicalTrials.gov study NCT00742287. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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Allen Brain Atlas
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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.