Find research datasets worth reusing

Simulation POPC_512_WALP23_10_5up_5down_NaCl_150mM_310K membrane

Title publication: A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction Year publication: 2018 DOI publication: 10.1021/acscentsci.7b00582 Description: Simulation POPC membrane containing ten WALP23 peptides ausing charmm36 at 310K. MD engine: gromacs 5.0.4 Force field: charmm36 Temperature: 310 K Pressure: 1 bar Simulation time: 2000 ns Saving frequency: 100 ps Molecular content: WALP23       10 POPC         512 SOL        20480 NA               55 CL                55 Additional information:     * Membrane containing WALP23 peptides (Ac-GWWLALALALALALALALALWWA-NH2).

Simulation POPC_512_TM4_10_5up_5down_NaCl_150mM_310K membrane

Title publication: A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction Year publication: 2018 DOI publication: 10.1021/acscentsci.7b00582 Description: Simulation POPC membrane containing ten LAPTM4B-TM4 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K. MD engine: gromacs 5.1.2 Force field: charmm36 Temperature: 310 K Pressure: 1 bar Simulation time: 4190 ns Saving frequency: 100 ps Molecular content: TM4            10 POPC        512 SOL       20470 NA              55 CL               65 Additional information:     * Membrane containing LAPTM4B TM4 peptides (Ac-CLVLIILLFISIILTFKGYLISCVWNC-NH2).

Simulation CER160_128_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K_rep1 membrane

Title publication: A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction Year publication: 2018 DOI publication: 10.1021/acscentsci.7b00582 Description: Simulation of a membrane containing 512 POPC and 128 ceramide (CER160) together with ten LAPTM4B-TM3 peptides using charmm36 at 310K. MD engine: 2016.2-dev-20170105-4feb0be Force field: charmm36 Temperature: 310 K Pressure: 1 bar Simulation time: 3200 ns Saving frequency: 100 ps Molecular content: TM3            10 POPC        512 CER160     128 SOL       31990 NA              96 CL               86 Additional information:     * Membrane containing LAPTM4B TM3 peptides (Ac-AWIIPFFCYQIFDFALNMLVAITVLIY-NH2).

Simulation CER160_128_POPC_512_NaCl_150mM_310K_rep1 membrane

Title publication: A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction Year publication: 2018 DOI publication: 10.1021/acscentsci.7b00582 Description: Simulation 512 POPCs membrane containing 128 ceramides (CER160)  using charmm36 at 310K. MD engine: gromacs 2016.1 Force field: charmm36 Temperature: 310 K Pressure: 1 bar Simulation time: 3000 ns Saving frequency: 100 ps Molecular content: POPC        512 CER160    128 SOL      32000 NA             86 CL              86 Additional information:

opencc-by-4.0Nov 2018View details →

High performance cation exchange membranes synthesized via in-situ emulsion polymerization without organic solvents and corrosive acids

Dataset supporting journal publication: Abstract: The synthesis of cation exchange membranes (CEMs) usually involves using organic solvents and/or sulfonation process. In this study, green and scalable synthesis of high performance CEMs is achieved without organic solvents and sulfonation. The synthesis is carried out via in-situ polymerization of lithium styrene sulfonate in porous support. Different preparation procedures are developed and optimized. Functional sulfonate groups were successfully loaded onto and into the membrane support, as verified by FTIR. Besides, water plays an important role during membrane synthesis. By reducing the amount of water used, the ratio of functional polymers to membrane support in the synthesized CEMs is increased. Therefore, the synthesized CEMs show increased ion exchange capacity (IEC). This is significant because it means that high IEC can be achieved without introducing cation exchange resins to the membranes. Finally, the synthesized membranes demonstrate high desalination performance. This new methodology may shed new light on preparing CEMs in an efficient and eco-friendly way.

opencc-by-4.0Aug 2019View details →

A Review on Emerging Organic-containing Microporous Material Membranes for Carbon Capture and Separation

Published article: Prasetya, N., Himma, N. F., Doddy Sutrisna, P., Wenten, I. G. & Ladewig, B. P. Chem. Eng. J. 123575 (2019). <a href="https://doi.org/10.1016/j.cej.2019.123575">https://doi.org/10.1016/j.cej.2019.123575</a> Abstract Membrane technology has gained great attention as one of the promising strategies for carbon capture and separation. Intended for such application, membrane fabrication from various materials has been attempted. While gas separation membranes based on dense polymeric materials have been long developed, there is a growing interest to use porous materials as the membrane material. This review then focuses on emerging porous materials to be used for the fabrication of membranes that are designed for CO2separation. Criteria for selecting microporous material are first discussed, including physical and chemical properties, and parameters in membrane fabrication. Membranes based on emerging porous materials,such as metal-organic frameworks, porous organic frameworks, and microporous polymers,are then reviewed. Finally, special attention is given to recent advances, challenges, and perspectives in the development of such membranes for carbon capture and separation.

opencc-by-4.0Nov 2019View details →

Cdc42 couples T cell receptor endocytosis to GRAF1-mediated tubular invaginations of the plasma membrane

This Dataset contains primary data used for the publication "Cdc42 couples T cell receptor endocytosis to GRAF1-mediated tubular invaginations of the plasma membrane" published online on 04. November 2019 doi:10.3390/cells8111388 Abstract: T cell activation is immediately followed by internalization of the T cell receptor (TCR). TCR endocytosis is required for T cell activation, but the mechanisms supporting removal of TCR from the cell surface remain incompletely understood. Here we report that TCR endocytosis is linked to the clathrin-independent carrier (CLIC) and GPI-enriched endocytic compartments (GEEC) endocytic pathway. We show that unlike the canonical clathrin cargo transferrin or the adaptor protein Lat, internalized TCR accumulates in tubules shaped by the small GTPase Cdc42 and the Bin/amphiphysin/Rvs (BAR) domain containing protein GRAF1 in T cells. Preventing GRAF1-positive tubules to mature into endocytic vesicles by expressing a constitutively active Cdc42 impairs the endocytosis of TCR, while having no consequence on the uptake of transferrin. Together, our data reveal a link between TCR internalization and the CLIC/GEEC endocytic route supported by Cdc42 and GRAF1.   Data are organised in compressed (.zip) folders entitled as the corresponding Figures in the publication. Programs we recommend to view the files are: .fcs files:     FlowJo software v10 (Tree Star, Ashland, OR, USA) .lif files:       LAS X v3 (Leica Microsystems, Wetzlar, Germany) .pzfx files:   Prism v7 software (GraphPad, San Diego, CA, USA)   In case this Dataset is updated, new version will be available with doi:10.5281/zenodo.3545842

HPTLC Data of "Metal Ion Cofactors Modulate Integral Enzyme Activity By Varying Differential Membrane Curvature Stress"

Lipid hydrolysis by the integral membrane protein OmpLA (outer membrane phospholipase). The enzymatic degradation of the proteoliposomes was determined by TLC. After lipid extraction against organic solvent (2:1 vol/vol chloroform/methanol) based on the Folch extraction method, the samples were spotted on a silica plate (Sigma-Aldrich, Steinheim, Germany) with the automatic TLC sampler 4 (CAMAG, Muttenz, Switzerland). The mobile phase in the developing chamber was a solvent mixture composed of 32.5:12.5:2 vol/vol/vol CHCl_3/MeOH/H_2O. After drying, the plate was immersed in a developing bath (5.08 g MnCl_2 dissolved in 480 ml H_2O, 480 ml EtOH and 32 ml H_2SO_4), which is sensitive to double bonds, and dried for 15 min at 120°C. To quantify the lipid concentrations the plate was scanned with the TLC scanner 3 (CAMAG, Muttenz, Switzerland) and further analyzed with WinCats software. Lipids: <ul> <li>1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)</li> <li>1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE)</li> <li>1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG)</li> </ul>

Lipid-polymer nanoparticles to probe the native-like environment of intra-membrane rhomboid protease GlpG and its activity

Polymers can facilitate detergent-free extraction of membrane proteins into nanodiscs (e.g., SMALPs, DIBMALPs), incorporating both integral membrane proteins as well as co-extracted native membrane lipids. Lipid-only SMALPs and DIBMALPs have been shown to possess a unique property; the ability to exchange lipids through ‘collisional lipid mixing’. Here we expand upon this mixing to include protein-containing DIBMALPs, using the rhomboid protease GlpG. Through lipidomic analysis before and after incubation with DMPC or POPC DIBMALPs, we show that lipids are rapidly exchanged between protein and lipid-only DIBMALPs, and can be used to identify bound or associated lipids through ‘washing-in’ exogenous lipids. Additionally, through the requirement of rhomboid proteases to cleave intra-membrane substrates, we show that this mixing can be performed for two protein-containing DIBMALP populations, assessing the native function of intramembrane proteolysis and demonstrating that this mixing has no deleterious effects on protein stability or structure

Research data for the article "Membrane-Active Antibiotics Affect Domains in Bacterial Membranes as the First Step of Their Activity" by Adéla Melcrová, Christiaan Klein, and Wouter Roos, Nano Letters 2024.

Research data for the publication Membrane-Active Antibiotics Affect Domains in Bacterial Membranes as the First Step of Their Activity, Nano Letters, 2024. <a href="https://doi.org/10.1021/acs.nanolett.4c01873" target="_blank" rel="noopener">https://doi.org/10.1021/acs.nanolett.4c01873</a> The data set contains experimental data on the study of antimicrobial N-alkylamide 3d and its interaction with the membrane extracted from the bacteria Staphylococcus aureus. Experimental details can be found in the Methods section of the Supporting Information of the mentioned article.  The data set contains underlying data for each Figure in the publication including the figures in the Supporting Information.  <ul> <li>Figure 1, S2, S3, S6, S8 - Atomic Force Microscopy images in the raw format as collected on JPK Nano Wizard Ultra Speed AFM.</li> <li>Figure 2, 3, S1 - High-Speed Atomic Force Microscopy images in the raw format as collected on high-speed AFM RIBM machine. The data could be opened in Kodec software. The full trajectories recorded on the high-speed AFM machine are presented here. Only snapshots were used in the publication Figures.</li> <li>Figure S7, S9 - Snapshots from the High-Speed AFM measurements showing the cross-section lines (.bmp) together with the cross-section profiles (.csv) that were used to measure the height of supramolecular structures on top of the bacterial membrane.</li> <li>Data underlying Figure S5 and Supporting Video 1 overlap with the data presented in Figure 2a.</li> </ul>

N-glycosylation acts as a switch for FGFR1 trafficking between the plasma membrane and nuclear envelope - yet unpublished supplementary data regarding Fig. 1C

Fibroblast growth factor receptor 1 (FGFR1) is a heavily N-glycosylated cell surface receptor tyrosine kinase that transmits signals across the plasma membrane, in response to fibroblast growth factors (FGFs). Balanced FGF/FGFR1 signaling is crucial for the development and homeostasis of the human body, and aberrant FGFR1 is frequently observed in various cancers. In addition to its predominant localization to the plasma membrane, FGFR1 has also been detected inside cells, mainly in the nuclear lumen, where it modulates gene expression. However, the exact mechanism of FGFR1 nuclear transport is still unknown. In this study, we generated a glycosylation-free mutant of FGFR1, FGFR1.GF, and demonstrated that it is localized primarily to the nuclear envelope. We show that reintroducing N-glycans into the D3 domain cannot redirect FGFR1 to the plasma membrane or exclude the receptor from the nuclear envelope. Reestablishment of D2 domain N-glycans largely inhibits FGFR1 accumulation in the nuclear envelope, but the receptor continues to accumulate inside the cell, mainly in the ER. Only the simultaneous presence of N-glycans of the D2 and D3 domains of FGFR1 promotes efficient transport of FGFR1 to the plasma membrane. We demonstrate that while disturbed FGFR1 folding results in partial FGFR1 accumulation in the ER, impaired FGFR1 secretion drives FGFR1 trafficking to the nuclear envelope. Intracellular FGFR1.GF displays a high level of autoactivation, suggesting the presence of nuclear FGFR1 signaling, which is independent of FGF. Using mass spectrometry and proximity ligation assay, we identified novel binding partners of the nuclear envelope-localized FGFR1, providing insights into its cellular functions. Collectively, our data define N-glycosylation of FGFR1 as an important regulator of FGFR1 kinase activity and, most importantly, as a switchable signal for FGFR1 trafficking between the nuclear envelope and plasma membrane, which, due to spatial restrictions, shapes FGFR1 interactome and cellular function.   These data are raw data of Fig. 1C generated by Aleksandra Chorążewska. These data are not present in supplementary data od publication

opencc-by-4.0Jul 2024View details →

Dataset for article: Potent and reversible open-channel blocker of NMDA receptor derived from dizocilpine with enhanced membrane-to-channel inhibition

<div>This version shows the correct number of n for Figure 6.</div> <div> </div>

Role of Divalent Ions in Membrane Models of Polymyxin-Sensitive and Resistant Gram-Negative Bacteria - Dataset

The present dataset holds all the input files linked to the related work, concerning the effect of the removal and displacement of membrane-bound divalent ions in models of the outer membrane of Gram-negative bacteria. This dataset presents a comprehensive collection of input data for Molecular Dynamics (MD) simulations performed using the GROMACS simulation software concerning the effect of the removal and displacement of membrane-bound divalent ions in models of the outer membrane of Gram-negative bacteria. The dataset consists of the input files stored in five tarballs each related to a part of this work: <ol> <li>all_atom_global_stress.tar.gz: Set of simulations used to investigate the effect of divalent ions (calcium ions) removal on the properties of the outer membrane of Gram-negative bacteria. The simulations involve a set of four models of the outer membrane of Salmonella enterica, two of which are polymyxin-sensitive (P2 and P1), while the two other are polymyxin-resistant (PEtn and Ara-4N). Four replicas were made for each simulation of divalent ion removal.</li> <li>all_atom_local_stress.tar.gz: Set of simulations introducing a new collective variable (CV) used to study the effect of divalent ions displacement. Simulations are made for the four model membranes described in 1. For each system, a steered MD (SMD) simulation is present, where the system is pulled along the CV to create a defect in the membrane. This SMD simulation is used to calculate a free profile along the CV using an umbrella sampling (US) procedure. One simulation set is devoted to the case of the presence of a polymyxin molecule in the vicinity of the defect.</li> <li>coarse_grained_local_stress.tar.gz: Analog dataset as in 2. but ported for coarsed-grained MD simulations.</li> <li>polymyxin_e.tar.gz: Topology parameters for polymyxin E for CHARMM36 and Martini 2.2.</li> <li>force_fields.tar.gz: The versions of CHARMM36 and Martini 2.2 used for this work.</li> </ol> For each membrane type, the dataset provides three replicas. The dataset includes initial and final structures (.gro files), simulation parameter files (.mdp), index files (.ndx), and topology files (.itp and .top) applicable to all systems.  Refer to the manuscript and to the provided README for more information. In case of further questions, you can address them to: timothee.rivel@ceitec.muni.cz Version log: Version 1.0: initial release of the dataset Version 1.1: files in all_atom_global_stress updated for the global stress run

opencc-by-4.0Sep 2024View details →

Data for publication: Pixelated High-Q Metasurfaces for in Situ Biospectroscopy and Artificial Intelligence-Enabled Classification of Lipid Membrane Photoswitching Dynamics

Open the record for dataset details and reuse information.

opencc-by-4.0Sep 2024View details →

SupplementaryData_A_helper_NLR_targets_organellar_membranes_to_trigger_immunity

Supplementary data for "A_helper_NLR_targets_organellar_membranes_to_trigger_immunity" including: 1.Phylogenetics analysis - Data S1 to 6) - Fig. 1A and S1 2.AlphaFold3 Models - Data S7 - Fig. 1B and S2 3.NRG1_delta14(Nb)_delta16(At) alignment - Data S8 4.nrg1 KO plants genotyping (Data S9) - more details in Materials and Methods. 5.HR_index_data - Data S10 - raw HR data presented in manuscript. 6.Movie S1 - NRG1 puncta upon XopQ activation.

opencc-by-4.0Sep 2024View details →

Data for: In situ generation of (sub) nanometer pores in MoS2 membranes for ion-selective transport

Source data for Fig 1-3 includes data for ion transport measurements and pore size distributions. Source data for Fig. 4 includes trajectory data for molecular dynamics simulations, exclusively for ions within MoS2 nanopores, as well as full trajectory data for the calculation of water-diffusion in 1 nm, 2 nm pores and the bulk reservoir (without an applied electric field).

opencc-by-4.0Oct 2024View details →

Membrane staining and segmentation of a developing mouse embryo from 4 to 26 cells

<h1>Intent</h1> The role of this dataset is to provide an example of segmentable and trackable data using signal from cell membrane. This dataset contains one file with the pre-processed imaged embryo (imaging.zip -> imaging.tif) and one file with the outcome of a segmentation using Cellpose (segmentation.zip -> segmentation.tif). <blockquote> This embryo corresponds to the embryo "C1" in the <a href="https://doi.org/10.1126/science.adh1145" target="_blank" rel="noopener">original publication</a> </blockquote> <h1>Animal</h1> This set of data represents a mouse embryo developing from the 4-cell stage. The embryo at the last processed timepoint has 26 cells. The mother and the father were both mTmG animals (tdTomato anchored at the membrane of the cells). <blockquote> Details can be found in the <a href="https://doi.org/10.1126/science.adh1145" target="_blank" rel="noopener">original publication</a> </blockquote> <h1>Culture conditions</h1> The embryo was imaged in an inverted SPIM from Luxendo (now Bruker), laying at the bottom of a PFE imaging dish. The embryo developed in a small pocket made by deforming the PFE with a glass tip. We used approx. 150μL of KSOM-AA to cutlure the embryos at 37ºC ± 0.2ºC in 5% CO2 and 5% O2. The medium was covered with approx. 100μL of mineral oil. <blockquote> Details can be found in the <a href="https://doi.org/10.1126/science.adh1145" target="_blank" rel="noopener">original publication</a> </blockquote> <h1>Imaging conditions</h1> The tdTomato was excited with a 561nm laser using as little intensity as possible (0% in the settings + a small fraction leaking through the shutter). We used a 561 LP filter to acquire the signal. Imaging was set with a lateral resolution of 0.208μm and a axial resolution of 1μm. Because of technical issues with the stage of the microscope at the time, the resulting axial resolution was ultimately 1.338μm. In total, 181 slices were acquired per time point. Two consecutive timepoints start with 15 minutes of interval. Although this embryo was imaged for a longer period of time, this dataset shows only the first 117 timepoints. <blockquote> Details can be found in the <a href="https://doi.org/10.1126/science.adh1145" target="_blank" rel="noopener">original publication</a> </blockquote> <h1>Processing conditions</h1> <table> <tbody> <tr> <td>Operation</td> <td>Lateral resolution</td> <td>Axial resolution</td> <td>File</td> </tr> <tr> <td>Imaging</td> <td>0.208 μm</td> <td>1.338 μm</td> <td>-</td> </tr> <tr> <td>Cropping </td> <td>0.208 μm</td> <td>1.338 μm</td> <td>-</td> </tr> <tr> <td>Lateral binning (average)</td> <td>0.416 μm</td> <td>1.338 μm</td> <td>-</td> </tr> <tr> <td>Isotropic rescaling</td> <td>0.416 μm</td> <td>0.416 μm</td> <td>-</td> </tr> <tr> <td>Lateral binning (average)</td> <td>0.832 μm</td> <td>0.832 μm</td> <td>imaging.tif</td> </tr> <tr> <td>Segmentation (cellpose)</td> <td>0.832 μm</td> <td>0.832 μm</td> <td>segmentation.tif</td> </tr> </tbody> </table>

dryad36/100

Data from: Antibiotic uptake across gram-negative outer membranes: better predictions towards better antibiotics

Crossing the gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer-membrane uptake of drug-like molecules, which we combine with a new medium-throughput experimental assay of outer membrane vesicle swelling. Parallel molecular dynamics simulations of compound uptake through E. coli OmpF are used to successfully and quantitatively predict experimental permeabilities measured via either outer membrane swelling or via prior liposome swelling measurements. These simulations are analyzed using an inhomogeneous solubility-diffusion model to yield predictions of permeability. For most polar molecules we test, outer membrane permeability also correlates well with whole-cell uptake. The ability to accurately predict and measure outer-membrane uptake of a wide variety of small molecules will enable simpler determination of which molecular scaffolds and which derivatives are most promising prior to extensive chemical synthesis. It will also assist in formulating a more systematic understanding of the chemical determinants of outer-membrane permeability.

opencc-zeroOct 2019View details →