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20 results for “Dynein”
Python code for Monte Carlo Simulation of dynein stepping
<p>This project is described in: Three-color single-molecule imaging reveals conformational dynamics of dynein undergoing motility (2020) and can be found on BioRxiv: (link to follow)</p> <p>Here, we provide the custom python code that is used simulate the stepping of dynein based on experimental data. Details on how the code works are given in the script itself. Moreover, we provided a pdf, which shows plots of all the input data.</p> <p>There are three different python scripts:</p> <ul> <li>Monte-Carlo-simulation_Dynein-stepping.py</li> <li>Monte-Carlo-simulation_Dynein-stepping_flexible-ring-position.py</li> <li>Monte-Carlo-simulation_Dynein-stepping_fixed-ring-angle.py</li> </ul> <p>And six folders with different experimental input data:</p> <ol> <li>Experimental-data-to-run-simulation_MT</li> <li>Experimental-data-to-run-simulation_MT_MTBD-distance-independent-angle</li> <li>Experimental-data-to-run-simulation_MT_no-forward-bias</li> <li>Experimental-data-to-run-simulation_MT_no-leading-trailing</li> <li>Experimental-data-to-run-simulation_MT_no-left-right</li> <li>Experimental-data-to-run-simulation_MT_no-stepping-bias</li> </ol> <p>The first python script can be used to generate the stepping movies (Supplementary Movies 3-10). The second python script is used to generate stepping traces and all other plots. The last python script is a special version of number one and two as it simulates the stepping of dynein for a fixed stalk-microtubule angle. It can generate stepping movies as well as stepping traces and all other plots.</p> <p>In order to simulate stepping of dynein for a wild-type condition, the first experimental dataset should be used as input (this dataset is also used for the fixed angle simulation). The other five datasets are used to simulate stepping of dynein when specific rules are ignored:</p> <ul> <li>for an on-axis distance-dependent bias to take more forward than backward steps (dataset #3),</li> <li>a distance-dependent bias to close the gap between the motor domains along the on- and off-axis when taking a step (dataset #4 and 5, respectively), </li> <li>a higher probability for the trailing domain instead of the leading domain to take the next step (dataset #6), and </li> <li>the relative movement between AAA ring and MTBD (for fixed angle see comments above and for MTBD on-axis distance independent angle changes dataset #2)</li> </ul>
Doublecortin and JIP3 are neural-specific counteracting regulators of dynein-mediated retrograde trafficking
Mutations in the microtubule (MT)-binding protein doublecortin (DCX) or in the MT-based molecular motor dynein result in lissencephaly. However, a functional link between DCX and dynein has not been defined. Here, we demonstrate that DCX negatively regulates dynein-mediated retrograde transport by reducing dynein's association with MTs and by disrupting the composition of the dynein motor complex. Previous work showed an increased binding of the adaptor protein C-Jun-amino-terminal kinase-interacting protein 3 (JIP3) to dynein in the absence of DCX. Using purified components, we demonstrate that JIP3 forms an active motor complex with dynein and its cofactor dynactin with two dyneins per complex. DCX competes with the binding of the second dynein, resulting in a velocity reduction of the complex. We conclude that DCX negatively regulates dynein-mediated retrograde transport through two critical interactions by regulating dynein binding to MTs and by regulating the association of JIP3 to the dynein motor complex.
Single molecule motility data of DYNEIN-DYNACTIN-HOOK3-KIF1C (DDHK) complexes plus various controls
<p>Single molecule motility data of DYNEIN-DYNACTIN-HOOK3-KIF1C (DDHK) complexes plus various controls leaving out components or using truncated motors without motor domains (KS - KIF1C stalk; Dt - Dynein tail).</p>
Data files for Axonal transport of autophagosomes is regulated by dynein activators JIP3/JIP4 and ARF/RAB GTPases
<p>Supporting data files for <strong>Axonal transport of autophagosomes is regulated by dynein activators JIP3/JIP4 and ARF/RAB GTPases</strong></p>
Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia
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Doublecortin and JIP3 are neural-specific counteracting regulators of dynein-mediated retrograde trafficking
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Kinesin and dynein use distinct mechanisms to bypass obstacles
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Active fluctuations of axoneme oscillations scale with number of dynein motors
<p> </p> <p>The dataset published here was used to measure the<strong> phase fluctuations</strong> <strong>(frequency jitter) </strong>of isolated and <strong>reactivated axonemes from <em>Chlamydomonas reinhardtii </em></strong>as a function of the dynein motor density in these axonemes. <br>The corresponding article is published in PNAS: https://doi.org/10.1073/pnas.2406244121</p> <p>Axonemes were isolated from wt(cc-125) and oda1(cc-2228) cells.</p> <p>Reactivation was performed:<br>(1) after dynein extraction with different amounts of salt (KCL) or<br>(2) in the presence of different concentrations of ATP .</p> <p>For all experimental conditions we provide the following data files:<br><br></p> <p><strong>Movies of reactivated axonemes:</strong></p> <p>Reactivated axonemes were imaged with phase-contrast microscopy. Recorded movies are organized in folders (.zip) which are labeled according to the respective reactivation condition (KCL and ATP concentration as well as the <em>Chlamydomonas</em> strain, from which the axonemes were purified, e.g. <strong>50mM_KCl_750uM_ATP_ODA_Extracted.zip</strong>).</p> <p>Those folders contain (1) movie files (multilayer .tif) of single axonemes and (.txt) files with a corresponding number-label (with microscope, camera settings and experimental condition (<em>Chlamydomonas</em> strain, [ATP], [KCL]).</p> <p>Using the number-label, the corresponding data file can be identified. <br><br></p> <p><strong>Data files (for the corresponding movies):</strong></p> <p>The experimental data is organized in MATLAB (.mat) files. Those files contain shape and waveform information (see below) for the respective reactivation condition (axoneme type, [ATP], [KCL] detailed below the file name).</p> <p><strong>WT_KCL_master.mat</strong> - WT axonemes, KCL extracted and reactivated with 750uM ATP</p> <p><strong>0mM_KCl_750uM_ATP_WT_Extracted<br>50mM_KCl_750uM_ATP_WT_Extracted<br>100mM_KCl_750uM_ATP_WT_Extracted<br>200mM_KCl_750uM_ATP_WT_Extracted<br>300mM_KCl_750uM_ATP_WT_Extracted<br>400mM_KCl_750uM_ATP_WT_Extracted<br></strong></p> <p><strong>WT_ATP_master.mat </strong> - WT axonemes reactivated with different ATP concentraions</p> <p><strong>0mM_KCl_50uM_ATP_WT<br>0mM_KCl_100uM_ATP_WT<br>0mM_KCl_370uM_ATP_WT<br>0mM_KCl_500uM_ATP_WT<br>0mM_KCl_750uM_ATP_WT<br></strong></p> <p><strong>ODA_KCL_master.mat </strong>- ODA axonemes, KCL extracted and reactivated with 750uM ATP</p> <p><strong>0mM_KCl_750uM_ATP_ODA_Extracted<br>50mM_KCl_750uM_ATP_ODA_Extracted<br>100mM_KCl_750uM_ATP_ODA_Extracted<br>200mM_KCl_750uM_ATP_ODA_Extracted<br>300mM_KCl_750uM_ATP_ODA_Extracted<br></strong></p> <p><strong>ODA_ATP_master.mat</strong> - ODA axonemes reactivated with different ATP concentraions</p> <p><strong>0mM_KCl_70uM_ATP_ODA<br>0mM_KCl_100uM_ATP_ODA<br>0mM_KCl_370uM_ATP_ODA<br>0mM_KCl_500uM_ATP_ODA<br>0mM_KCl_750uM_ATP_ODA</strong></p> <p>Each file includes a data-cell ‘Master’ with a columns for the different experimental conditions (e.g. concentrations of ATP or KCL). Data-cells contain one structure for each axoneme. </p> <p> </p> <p>These structures have the following fields:</p> <p>nframe… number of frames of the dataset</p> <p>phi_in_rad… phase angle (beat-cycle-phase) (rad)</p> <p>tangent_angle_psi_in_rad… the tangent angle for 24 positions along arc-length (rad)</p> <p>xy_in_micron… the x,y positions (µm)</p> <p>dt_in_second… time between adjacent frames (second)</p> <p>ds_in_micron… spacing between adjacent arc-length positions (µm)</p> <p>f0_in_Hz… beat frequency (Hz)</p> <p>A… beat amplitude (arc-length average) (rad)</p> <p>Q… quality factor</p> <p>sexp… string with experiment label</p> <p>KCL_in_mM… KCL concentration (mM) used for dynein extraction</p> <p>ATP_in_uM… ATP concentration (mM) used for reactivation</p> <p>File… filename, includes a number-label that corresponds to the imaging data provided</p>
Raw data related to KIF1C activates and extends dynein movement through the FHF cargo adaptor
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Evaluation of the Axonemal Dynein Heavy Chain 5 and Creatine Kinase Concentration in Cervical Fluid for Early Detection of the Ectopic Pregnancy
ClinicalTrials.gov study NCT02995356. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Python code and experimental data of three-color dynein stepping
<p>This project is described in: Three-color single-molecule imaging reveals conformational dynamics of dynein undergoing motility (2020) and can be found on BioRxiv: (link to follow)</p> <p>Here, we provide the experimental data of the three-color dynein stepping experiments together with the custom python code used for data analysis. Details on how the code works are given in the script itself.</p>
Data from: Cholesterol and ORP1L dependent clustering of dynein on endolysosmes in cells 2 revealed by super resolution microscopy
<p>The sub-cellular positioning of endolysosomes is crucial for regulating their function. Particularly, the positioning of endolysosomes between the cell periphery versus the peri-nuclear region impacts autophagy, mTOR (mechanistic target of rapamycin) signaling and other processes. The mechanisms that regulate the positioning of endolysosomes at these two locations are still being uncovered. Here, using quantitative super-resolution microscopy in intact cells, we show that the retrograde motor dynein forms nano-clusters on endolysosomal membranes containing 1-2 dyneins, with an average of ~3 nanoclusters per endolysosome. These data suggest that a very small number of dynein motors (1-6) drive endolysosome motility inside cells. Surprisingly, dynein nano-clusters are slightly larger on peripheral endolysosomes having higher cholesterol levels compared to peri-nuclear ones. By perturbing endolysosomal membrane cholesterol levels, we show that dynein copy number within nano-clusters is influenced by the amount of endolysosomal cholesterol while the total number of nano-clusters per endolysosome is independent of cholesterol. Finally, we show that the dynein adapter protein ORP1L (Oxysterol Binding Protein Homologue) regulates the number of dynein motors within nano-clusters in response to cholesterol levels. We propose a new model by which endolysosomal transport and positioning is influenced by the cholesterol sensing adapter protein ORP1L, which influences dynein's copy number within nano-clusters.</p>
Data from: A mathematical understanding of how cytoplasmic dynein walks on microtubules
Cytoplasmic dynein 1 is a dimeric motor protein that walks and transports intracellular cargos towards the minus end of microtubules. In this article we formulate, based on physical principles, a mechanical model to describe the stepping behaviour of cytoplasmic dynein walking on microtubules from the cell membrane towards the nucleus. Unlike previous studies on physical models of this nature, we base our formulation on the whole structure of cytoplasmic dynein 1 to include the temporal dynamics of the individual subunits such as the cargo (for example an endosome, vesicle or bead), two rings of six ATPase domains associated with diverse cellular activities (AAA+ rings) and the microtubule binding domains which allow dynein to bind to microtubules. This mathematical framework allows us to examine experimental observations on dynein across a wide range of different species, as well as being able to make predictions on the temporal behaviour of the individual components of dynein not currently experimentally measured. Furthermore, we extend the model framework to include backward stepping, variable step size and dwelling. The power of our model is in its predictive nature; first it reflects recent experimental observations that dynein walks on microtubules using a weakly coordinated stepping pattern with predominantly not passing steps. Second, the model predicts that interhead coordination in the ATP cycle of cytoplasmic dynein is important in order to obtain the alternating stepping patterns and long run lengths seen in experiments.
Data from: A mathematical understanding of how cytoplasmic dynein walks on microtubules
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Data from: Cholesterol and ORP1L dependent clustering of dynein on endolysosmes in cells 2 revealed by super resolution microscopy
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Antiviral function and viral antagonism of the rapidly evolving dynein activating adapter NINL
GEO Series GSE206784. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Dynlrb1 is Essential for Dynein Mediated Transport and Neuronal Survival
GEO Series GSE131455. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
A high-content arrayed CRISPR screen reveals genetic requirements for dynein-based trafficking
GEO Series GSE218249. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Biallelic deleterious variants in SNAPIN, a retrograde dynein adaptor, cause a prenatal-onset neurodevelopmental disorder [2]
GEO Series GSE298994. Danio rerio. 6 samples. Type: Expression profiling by high throughput sequencing.
Biallelic deleterious variants in SNAPIN, a retrograde dynein adaptor, cause a prenatal-onset neurodevelopmental disorder [1]
GEO Series GSE298991. Danio rerio. 4 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.
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