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47 results for “membrane dynamics”
Harnessing Pore Size in COF Membranes: A Concentration Gradient-Driven Molecular Dynamics (CGD-MD) Study on Enhanced H₂/CH₄ Separation
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Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations
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Molecular Probes for Tracking Lipid Droplet Membrane Dynamics
<p><strong><span>Abstract</span></strong></p> <p><span>Lipid droplets (LDs) and their membrane proteins play crucial roles in lipid metabolism, signaling, and information transport within cells. LDs feature a unique monolayer lipid membrane that has not been extensively studied due to the lack of suitable molecular probes that are able to distinguish this membrane from the LD lipid core. In this work, we present a three-pronged molecular probe design strategy that combines lipophilicity-based organelle targeting with microenvironment-dependent activation. As a proof-of-concept, we designed an <u>LD</u> <u>m</u>embrane labeling pro-probe called<strong> LDM</strong>, which selectively localizes around LD membranes. Upon activation by the HClO/ClO</span><sup><span>−</span></sup><span> microenvironment that surrounds LDs, <strong>LDM</strong> pro-probe undergoes a color change and releases<strong> LDM-OH</strong> probe that binds to LD membrane proteins. This localizes the probe to the LD-as</span><span>sociated protein space which is restricted to the membrane thus enabling visualization of the ring-like LD membrane. By utilizing<strong> LDM</strong>, we identified the dynamic mechanism of LD membrane contacts and their protein accumulation parameters. Furthermore, using <strong>LDM</strong> in liver cancer cells allowed us to examine the changes in LD/mitochondrial protein accumulation caused by the state of starvation these cells encounter. This led to the discovery that liver cancer cells respond to energy stress during hunger by enhancing LD-mitochondria interactions. Taken together, <strong>LDM</strong> represents the first molecular probe for imaging LD membranes in live cells, and represents an attractive tool for further investigations into the specific regulatory mechanisms and drug discovery associa</span><span>ted with LD related metabolism diseases.</span></p> <p><span> </span></p> <p><em><span>Keywords:</span></em><span> Molecular Imaging, Cancer, Lipid droplets, Super-resolution Imaging</span></p>
Molecular Dynamics Trajectories of Membrane-bound Influenza Hemagglutinin (A/duck/Alberta/35/76) in Complex with 0-3 Copies of FISW84 Fab Fragments
<p>MD simulation trajectories of influenza hemagglutinin (A/duck/Alberta/35/76) in a bilayer mimicking the viral membrane, with 0-3 copies of FISW84 antibody's Fab domains bound.</p> <p>Files are named as (copy number of Fab).(simulation replica ID).(file type extension). The systems were constructed in CHARMM format PSF files and the trajectories were recorded in DCD format.</p> <p>Simulations were performed with NAMD3. The trajectories were re-centered and re-wrapped about the periodic boundary from the raw trajectories, in order to keep the HA-Fab complex and the lipid bilayer appearing as a single continuous entity instead of isolated molecules at the opposite side of the periodic boundary. Water molecules in the simulation were removed in these trajectories due to file size limitations.</p>
Inflammatory Markers Dynamics in Response to Extra-corporeal Membrane Oxygenator Decannulation
ClinicalTrials.gov study NCT04678518. IPD Sharing: NO. Countries: 1. Publications: 14.
Complementary data to "Molecular dynamics trajectories for 630 drug-membrane potentials of mean force"
<p>Missing data from "Molecular dynamics trajectories for 630 drug-membrane potentials of mean force"</p> <p>Hoffmann, Christian; Centi, Alessia; Menichetti, Roberto; Bereau, Tristan (2020): Molecular dynamics trajectories for 630 drug-membrane potentials of mean force. figshare. Collection.</p> <p>https://doi.org/10.6084/m9.figshare.c.4641551.v1</p> <p>Includes:</p> <ul> <li>'bsResult.xvg' of DIM_P2-P3 in DLPC</li> </ul>
Data from: Membrane potential dynamics of spontaneous and visually evoked gamma activity in V1 of awake mice
Cortical gamma activity (30–80 Hz) is believed to play important functions in neural computation and arises from the interplay of parvalbumin-expressing interneurons (PV) and pyramidal cells (PYRs). However, the subthreshold dynamics underlying its emergence in the cortex of awake animals remain unclear. Here, we characterized the intracellular dynamics of PVs and PYRs during spontaneous and visually evoked gamma activity in layers 2/3 of V1 of awake mice using targeted patch-clamp recordings and synchronous local field potentials (LFPs). Strong gamma activity patterned in short bouts (one to three cycles), occurred when PVs and PYRs were depolarizing and entrained their membrane potential dynamics regardless of the presence of visual stimulation. PV firing phase locked unconditionally to gamma activity. However, PYRs only phase locked to visually evoked gamma bouts. Taken together, our results indicate that gamma activity corresponds to short pulses of correlated background synaptic activity synchronizing the output of cortical neurons depending on external sensory drive.
Data from: Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding
The ESCRT machinery mediates reverse membrane scission. By quantitative fluorescence lattice light-sheet microscopy, we have shown that ESCRT-III subunits polymerize rapidly on yeast endosomes, together with the recruitment of at least two Vps4 hexamers. During their 3-45 second lifetimes, the ESCRT-III assemblies accumulated 75-200 Snf7 and 15-50 Vps24 molecules. Productive budding events required at least two additional Vps4 hexamers. Membrane budding was associated with continuous, stochastic exchange of Vps4 and ESCRT-III components, rather than steady growth of fixed assemblies, and depended on Vps4 ATPase activity. An all-or-none step led to final release of ESCRT-III and Vps4. Tomographic electron microscopy demonstrated that acute disruption of Vps4 recruitment stalled membrane budding. We propose a model in which multiple Vps4 hexamers (four or more) draw together several ESCRT-III filaments. This process induces cargo crowding and inward membrane buckling, followed by constriction of the nascent bud neck and ultimately ILV generation by vesicle fission.
Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome 2B4
<p>This dataset contains coordinate files, scripts and input parameters to run and analyse molecular dynamics simulations of membrane bound CYP 2B4.</p> <p> </p> <p>The associated study is described in: </p> <p>data - containes input data & last simulation frames for all of the described MD simulations and analyses described in the manuscript</p> <p>Structures_used_for_figures - contains .pdb and .pse files of all protein structures depicted in the manuscript</p>
Cooperation of membrane-translocated syntaxin4 and basement membrane for dynamic mammary epithelial morphogenesis
<p>Mammary epithelia undergo dramatic morphogenesis after puberty. During pregnancy, luminal epithelial cells in ductal trees are arranged to form well-polarized cystic structures surrounded by a myoepithelial cell layer, an active supplier of the basement membrane (BM). Here, we identified a novel regulatory mechanism involved in this process by using a reconstituted BM-based three-dimensional culture and aggregates of a model mouse cell line, EpH4, that had either been manipulated for inducible expression of the t-SNARE protein syntaxin4 in an intact or signal peptide-connected form, or that were genetically deficient in syntaxin4. We found that cells extruded syntaxin4 upon stimulation with the lactogenic hormone, prolactin, which in turn accelerated the turnover of E-cadherin. In response to extracellular expression of syntaxin4, cell populations that were less affected by the BM actively migrated and integrated into the cell layer facing the BM. Concurrently, the BM-facing cells, which were simultaneously stimulated with syntaxin4 and BM, acquired unique epithelial characteristics to undergo dramatic cellular arrangement for cyst formation. These results highlight the importance of the concerted action of extracellular syntaxin4 extruded in response to the lactogenic hormone and BM components in epithelial morphogenesis.</p>
The inner membrane ring component SctD: An unexpected dynamic element governing assembly and secretion in the Type III Secretion System
<p>780- 6PEM_sctCDJ_big_ph7.4 (slice of the IM portion used as template for the Yersinia project)</p> <p>786- Yersinia_sctCDJ_v1_ph7.4 em<br>787a- Yersinia_sctCDJ_v1_ph4.0 em</p> <p>797- 6PEM_sctCDJ_big_ph4.0 (slice of the IM portion used as template for the Yersinia project)</p>
Cooperation of membrane-translocated syntaxin4 and basement membrane for dynamic mammary epithelial morphogenesis
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Data from: Membrane potential dynamics of spontaneous and visually evoked gamma activity in V1 of awake mice
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Data from: Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding
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Active nematic order and dynamic lane formation of microtubules driven by membrane-bound diffusing motors
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The dynamic recruitment of TRBP to neuronal membranes mediates dendritogenesis during development
GEO Series GSE106518. Rattus norvegicus. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening - Sample files
<p><strong>Initial and final snapshots of atomistic simulations of curved lipid bilayers</strong></p> <p>Each PDB file is named according to lipid composition and number of lipid molecules per leaflet.</p> <p>To reduce file size, solvent molecules were excluded and multiple snapshots of the same system zipped together.</p> <p>Reference: <a href="https://doi.org/10.1101/2023.02.02.525347">https://doi.org/10.1101/2023.02.02.525347</a></p>
Data from: Three-dimensional visualization of the internal plastid membrane network during runner bean chloroplast biogenesis: dynamic model of the tubular-lamellar transformation
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Dynamics of membrane potential variation and gene expression induced by Spodoptera littoralis, Myzus persicae, and Pseudomonas syringae in Arabidopsis
GEO Series GSE40926. Arabidopsis thaliana. 12 samples. Type: Expression profiling by array.
Inhibition of HIV infection by structural proteins of the inner nuclear membrane is associated with reduced chromatin dynamics
GEO Series GSE162019. Homo sapiens. 9 samples. Type: Expression profiling by array.
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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.