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175 results for “Membrane Protein”
PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid
<p>Harvest yields depend on the plant's ability to fix carbon and deal with changing environmental conditions. Especially during seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals through metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from <em>Arabidopsis thaliana </em>is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, almost 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated. In the simulations, PLAFP does bind to the plasma membrane independent of the PA concentration, and it adopts a binding pose, where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequently, PA does insert into PLAFP's beta-sandwich and multiple amino acids besides W41 and R82 are identified that drive the insertion. Fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids could allow modulating the signaling sensitivity to the climate the plant is supposed to grow in.</p>
Subset of non-redundant, high resolution multi-pass membrane protein PDB structure files from OPM
<p>A subset of OPM PDB structure files with membrane predictions curated for the MSc thesis project '<strong>Structural characterization of triplets of transmembrane α-helical segments consecutive in sequence in integral membrane proteins: a fragment-based computational pipeline'. </strong>The dataset contains PDB files downloaded from OPM on 22/02/2023. The files are alpha-helical integral membrane proteins with at least three transmembrane regions at better than 2.7 Angtrom resolution. They are non-redundant, with a sequence identity of less than 40% based on clustering with the cd-hit algorithm. </p>
Data from: A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein
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Data from: Bioinspired design rules for flipping across the lipid bilayer from systematic simulations of membrane protein segments
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Conserved structural elements specialize ATAD1 as a membrane protein extraction machine
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Data from: A multiscale biophysical model for the recruitment of actin nucleating proteins at the membrane interface
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High-throughput discovery of transmembrane helix dimers from human single-pass membrane proteins with TOXGREEN sort-seq
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Simulations of single-protein membranes
<p>Nine simulations, each with a single copy of a single protein (1–7,A,B) and 400 DPPC lipids per protein per leaflet. The simulations are performed using the coarse-grained Martini model with scaled-down protein–protein interactions. These systems are described carefully in:</p> <p>M. Javanainen, H. Martinez-Seara, R. Metzler, and I. Vattulainen; Diffusion of Integral Membrane Proteins in Protein-Rich Membranes. J. Phys. Chem. Lett., 2017, 8 (17), pp 4308–4313, DOI: 10.1021/acs.jpclett.7b01758</p> <p>The topologies for proteins A&B are included in https://doi.org/10.5281/zenodo.3572241, whereas other ones can be obtained from: https://doi.org/10.5281/zenodo.846428</p> <p> </p>
Large membranes crowded with proteins at different temperatures
<p>Simulation data for crowded coarse-grained (Martini) membranes with 36 proteins per system. Nomenclature follows that in the paper (CITATION TO BE ADDED), where also all simulation details are found. Simulations are performed at 4 temperatures (300, 315, 330, and 345 K), and there are a total of 3600 lipids in the systems. The topology and index files are common for all simulations. The simulation parameters follow DOI:10.5281/zenodo.846428, and the required topologies can also be obtained from that upload. smaller simulations of the same system are uploaded to DOI:10.5281/zenodo.3604282 and DOI:10.5281/zenodo.3604289</p> <p>.</p>
Simulations of a membrane with a dilute concentration of proteins in different system sizes
<p>Simulations of a dilute (400 lipids per protein per leaflet) DPPC membranes with seven types of embedded proteins. The systems are a 50% smaller (S) and 4 times larger (L) versions of the lp400 simulation in the upload: DOI:10.5281/zenodo.846428. Topologies and simulation parameters are identical to those in that upload.</p>
Medium membranes crowded with proteins at different temperatures
<p>Simulation data for crowded coarse-grained (Martini) membranes with 9 proteins per system. Nomenclature follows that in the paper (CITATION TO BE ADDED), where also all simulation details are found. Simulations are performed at 4 temperatures (300, 315, 330, and 345 K), and there are a total of 900 lipids in the systems. The topology and index files are common for all simulations. The simulation parameters follow DOI:10.5281/zenodo.846428, and the required topologies can also be obtained from that upload. Smaller and larger simulations of the same system are uploaded to DOI:10.5281/zenodo.3604282 and DOI:10.5281/zenodo.3604293</p> <p>.</p>
Large membranes with a single protein at different temperatures
<p>Simulation data for coarse-grained (Martini) membranes containing a single protein. Nomenclature follows that in the paper (CITATION TO BE ADDED), where also all simulation details are found. Simulations are performed at 4 temperatures (300, 315, 330, and 345 K), and there are a total of 7200 lipids (3600 per leaflet) in the systems. The topology and index files are common for all simulations. The simulation parameters follow DOI:10.5281/zenodo.846428, and the required topologies can also be obtained from that upload. Smaller simulaions with a single protein and 800 lipids (400 per leaflet) are at 315 K are available at DOI:10.5281/zenodo.3572299 and at other temperatures at 10.5281/zenodo.3604448. Medium simulations with 3200 lipids (1600 per leaflet) are available at DOI:10.5281/zenodo.3604687</p>
Medium membranes with a single protein at different temperatures
<p>Simulation data for coarse-grained (Martini) membranes containing a single protein. Nomenclature follows that in the paper (CITATION TO BE ADDED), where also all simulation details are found. Simulations are performed at 4 temperatures (300, 315, 330, and 345 K), and there are a total of 3200 lipids (1600 per leaflet) in the systems. The topology and index files are common for all simulations. The simulation parameters follow DOI:10.5281/zenodo.846428, and the required topologies can also be obtained from that upload. Smaller simulaions with a single protein and 800 lipids (400 per leaflet) are at 315 K are available at DOI:10.5281/zenodo.3572299 and at other temperatures at 10.5281/zenodo.3604448. Larger simulations with 7200 lipids (3600 per leaflet) are available at DOI:10.5281/zenodo.3604731</p> <p> </p>
Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress
<p>The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM's unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin's LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.</p>
144 NaK channel proteins in a DPPC membrane
<p>144 NaK channels embedded in a DPPC membrane formed by 14400 lipid molecules simulated for 25 microseconds using the protein model by Sansom et al. [1,2] and the Martini lipid model [3]. The membrane is solvated by a total of 294163 water beads, counter ions, and a NaCl concentration of 154 mM. Files are compatible with Gromacs 4.6. and above.</p> <p>[1] Peter Bond and Mark Sansom, Insertion and assembly of membrane proteins via simulation, J. Am. Chem. Soc., 2006, 128 (8), pp 2697–2704</p> <p>[2] Kathryn A. Scott et al., Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly, Structure, 2008, 16 (4), pp 621–630</p> <p>[3] Siewert J. Marrink et al., Coarse Grained Model for Semiquantitative Lipid Simulations, J. Phys. Chem. B, 2004, 108 (2), pp 750–760</p>
Coarse-grained simulations of lipid membranes with various concentrations of embedded proteins
<p>Membranes with a polydisperse set of proteins with lipid/protein ratios of 50 (lp50), 75 (lp75), 100 (lp100), 200 (lp200), and 400 (lp400) are simulated for 100 µs. The protein–protein interactions are scaled down to prevent excessive aggregation. </p> <p>For all simulated lipid/protein ratio, a trajectory (.xtc) file is stored every 10 ns. Note that water beads and ions have been removed for a smaller file size. All beads, including solvent ones, are present in initial and final structures (.gro). Energy terms are stored every 1 ns (.edr). Simulation run input files (.tpr) and checkpoint files (.cpt) enable the rerunning or continuation of the simulations. Topology (.top) and index (.ndx) files for each system are also provided.</p> <p>The topology files for scaled protein–protein interactions work as follows: The bead types of the proteins in their topology files (.itp) are changed to those with a 'p', for example P4–>P4p. The interactions between normal beads are listed in martini_v2.2_standard.itp, while the interactions among 'p' beads as well as the cross terms between 'p' beads and normal beads are given in martini_v2.2_scaled_80.itp. The force constant of the elastic network was increased to enable an integration time step of 20 fs.</p> <p>The lipid head groups are gently restrained in the direction normal to the membrane to prevent excessive fluctuations and they hence simulate the presence of an actin cytoskeleton.</p> <p>The simulation parameters, common for all systems, are listed in the file md.mdp. </p> <p>All files are compatible with Gromacs 5.0.</p> <p>The results extracted from these simulations are presented in the paper</p> <p>M. Javanainen, H. Martinez-Seara, R. Metzler, and I. Vattulainen; Diffusion of Integral Membrane Proteins in Protein-Rich Membranes. J. Phys. Chem. Lett., 2017, 8 (17), pp 4308–4313, DOI: 10.1021/acs.jpclett.7b01758</p> <p>The Martini topologies are obtained form http://cgmartini.nl</p>
Molecular Dynamics Simulation Dataset for "Hydrophobic Mismatch Drives Self-Organization of Designer Proteins into Synthetic Membranes"
<p>This repository contains molecular dynamics (MD) simulation data from the study on the self-organization of designer proteins in synthetic membranes. The data includes simulations for different single lipid compositions (DOPC, DPPC, DYPC) denoted as [lipid]-PL* where PL stands for the different TMD constructs. Multi component simulation are named accordingly. The repository provides initial (eqi.gro) and final (prod.gro) coordinates for each simulation. The 'cmd' file in each directory outlines the assembly process of each simulation, and the 'mdp' folder contains all input files for the simulations. </p>
Datasets generated for the manuscript: The basement membrane regulates the cellular localization and the cytoplasmic interactome of Yes-Associated Protein (YAP) in mammary epithelial cells
<p><strong>File proteinGroups-CoIP-Yap1:</strong> Dataset of co-Immunoprecipitation followed of Yes-associated protein (YAP) followed by proteomics to identify YAP interactants.</p> <p><strong>File Gene_set_file_YAP: </strong>Gene sets used for gene set enrichment analysis.</p> <p><strong>Files enrichr_x: </strong>output of the EnrichR tool</p>
Mitochondrial and ER membrane protein trafficking CRISPR screens
<p><span>The trafficking of specific protein cohorts to the correct subcellular location at the correct time is essential for every signaling and regulatory process in biology. Gene perturbation screens could provide a powerful approach to probe the molecular mechanisms of protein trafficking, but only if protein localization or mislocalization can be tied to a simple and robust phenotype for cell selection, such as cell proliferation or FACS. To broadly empower the study of protein trafficking processes with gene perturbation, we developed a genetically-encoded molecular tool named HiLITR. HiLITR converts protein colocalization into proteolytic release of a membrane-anchored transcription factor, which drives the expression of a chosen reporter gene. Using HiLITR in combination with FACS-based CRISPRi screening in human cell lines, we identify genes that influence the trafficking of mitochondrial and ER tail-anchored proteins. </span>We show that loss of the SUMO E1 component SAE1 results in the mislocalization and destabilization of mitochondrial tail-anchored proteins. We also demonstrate a distinct regulatory role for EMC10 in the ER membrane complex, opposing the transmembrane-domain insertion activity of the complex. Through transcriptional integration of complex cellular functions, HiLITR expands the scope of biological processes that can be studied by genetic perturbation screening technologies.</p>
Spectroscopy study of albumin interaction with negatively charged liposome membranes: Mutual structural effects of the protein and the bilayers
<p>Deconvolution of the signals of carbonyl groups in the ATR-FTIR spectra of lipids in the region 1700–1760 cm<sup>−1</sup> obtained during liposome incubation with albumin.</p>
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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.