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175 results for “Membrane Protein”

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zenodo56/100

Homologous membrane protein structures (HOMEP) version 1

Table 1 = List of membrane protein structures in the HOMEP data set (version 1). From Forrest, Tang & Honig 2006 Biophysical Journal (Supplementary Table 1) <a href="https://www.ncbi.nlm.nih.gov/pubmed/16648166">https://www.ncbi.nlm.nih.gov/pubmed/16648166</a> Contains the following columns: PDB-Code Protein-Name    Source  Res-(Å) Length (Num-TM) Number-of-TM-domains    Family Table 2 = List of pairs of membrane protein structures in the HOMEP data set (version 1). From Forrest, Tang & Honig 2006 Biophysical Journal (Supplementary Table 2) Contains the following columns: Model   Family  Query   Template   ID(%)  RMS(Å) GDT_TS(%)  TM-ID(%)   TM-RMS(Å)  TM GDT_TS(%) Table 3 = Manually-defined transmembrane regions in the HOMEP data set (version 1), listed for each family by transmembrane segment number. From Forrest, Tang & Honig 2006 Biophysical Journal (Supplementary Table 3). Contains the columns defined as follows: Protein chain identifier, start (-s) and end (-e) residues for each PDB structure in the family

opencc-by-4.0Apr 2006View details →

zenodo48/100

Homologous membrane protein structures (HOMEP) dataset version v2

Protein structures from the dataset of Homologous MEmbrane Protein structures (HOMEP) version v2 created in 2010, published in 2013. A more automated version of HOMEP v1: <a href="https://doi.org/10.5281/zenodo.2646534">10.5281/zenodo.2646534</a>   Table 1 = List of protein databank structure entries From Stamm et al, PLOS One 2013, <a href="https://www.ncbi.nlm.nih.gov/pubmed/23469223">https://www.ncbi.nlm.nih.gov/pubmed/23469223</a>, Supplementary Table 1, with the following entries: Family grouping, Protein databank identifier, Name, Source organism, Resolution (Å)   Table 2 = List of pairs of structures From Stamm et al, PLOS One 2013, <a href="https://www.ncbi.nlm.nih.gov/pubmed/23469223">https://www.ncbi.nlm.nih.gov/pubmed/23469223</a>, Supplementary Table 2, with the following entries: Family grouping, PDB code for first structure, Chain ID from PDB1, PDB for second structure, Chain ID from PDB2, protein structural difference (PSD), % sequence identity   File S2 HOMEP2 Dataset.tar.gz = Protein databank format files (PDB) are attached in the Dataset tar zipped file, organized by family. From Stamm et al, PLOS One 2013, <a href="https://www.ncbi.nlm.nih.gov/pubmed/23469223">https://www.ncbi.nlm.nih.gov/pubmed/23469223</a>, Supplementary dataset.

openother-openMar 2013View details →

zenodo48/100

Data in: Aging power spectrum of membrane protein transport and other subordinated random walks

Datasets generated in the report "Aging power spectrum of membrane protein transport and other subordinated random walks". Included data are: Numerical simulations  RWdata1.mat: 10,000 realizations, subordinated random walk with Hurst exponent, H=0.3 and \(\alpha\)=0.4. RWdata3.mat: 10,000 realizations, subordinated random walk with Hurst exponent, H=0.7 and \(\alpha\)=0.4. RWdata8.mat: 5,000 realizations, subordinated random walk with Hurst exponent, H=0.75 and \(\alpha\)=0.8. RWdataCTRW.mat: 10,000 realizations, continuous time random walk (CTRW), \(\alpha\)=0.7. Spectra of simulations PSDdata1.mat: Power spectral density (PSD) of a subordinated random walk with Hurst exponent, H=0.3 and \(\alpha\)=0.4. Five different realization times are used to compute the PDS: 2^8, 2^10, 2^12, 2^14, and 2^16. PSDdata3.mat: PSD of a subordinated random walk with Hurst exponent, H=0.7 and \(\alpha\)=0.4. Five different realization times are used to compute the PDS: 2^8, 2^10, 2^12, 2^14, and 2^16. PSDdata8.mat: PSD of a subordinated random walk with Hurst exponent, H=0.75 and \(\alpha\)=0.8. Four different realization times are used to compute the PDS: 2^15, 2^16, 2^17, and 2^18. PSDs_CTRW.mat: PSD of a continuous-time random walk (CTRW), \(\alpha\)=0.7. Five different realization times are used to compute the PDS: 2^8, 2^10, 2^12, 2^14, and 2^16. Experimental data of Nav1.6 channels in the soma of hippocampal neurons NavMSDtimes.csv: ensemble-averaged (EA) MSD and time-averaged (TA) MSD. The TA-MSD is measured for three observation times, 64, 128, and 256 frames (3.2, 6.4, and 12.8 s). NavPSD.csv: Power spectral density (PSD) measured for three observation times, 64, 128, and 256 frames.

opencc-by-4.0Sep 2021View details →

zenodo44/100

Dataset for publication: "Photosystem II supercomplexes lacking light-harvesting antenna protein LHCB5 and their organization in the thylakoid membrane"

Data repository for "Photosystem II supercomplexes lacking light-harvesting antenna protein LHCB5 and their organization in the thylakoid membrane". FIGURE 1 Phenotype and photosynthetic characteristics of the lhcb5 mutant. (A) Phenotype of Arabidopsis thaliana wild type (WT) and lhcb5 mutant plants grown at controlled conditions for 6 weeks (8 h light/16 h dark cycle; 22/20°C; 110 µmol photons m-2 s-1; 60% humidity). (B) Immunoblot analysis of thylakoid membranes of WT and lhcb5 mutant plants with antibody directed against LHCB5. (C) Content of light-harvesting proteins LHCB1-6 evaluated relatively to the content of CP43 protein in the WT and the lhcb5 mutant. The protein content was determined in isolated thylakoid membranes by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The columns represent means ± SD, individual points show technical replicates. All data passed the normality and equal variance tests and according to Student t-test the datasets of WT and lhcb5 were not significantly different (α ≤ 0,05), except for the relative content of LHCB5/CP43. (D) Protein ratios of photosynthesis-related thylakoid membrane proteins of the WT and the lhcb5 mutant. The protein content was determined by LC-MS/MS in isolated thylakoid membranes. PSII represents the sum of relative PG intensities of D1, D2, CP43, and CP47 proteins, LHCII - LHCB1–3 proteins, PSI - PSAA and PSAB proteins, LHCI - LHCA1–4 proteins, ATPS - α and β subunits of ATP synthase, and cyt f represents cytochrome f component of cytochrome b6f complex. The columns represent means ± SD, individual points show technical replicates. All data passed the normality and equal variance tests and according to Student t-test the datasets of WT and lhcb5 are not significantly different (α ≤ 0,05). FIGURE 2 Separation and structural characterization of PSII supercomplexes from lhcb5 mutant plants. (A) Separation of pigment–protein complexes from thylakoid membranes from Arabidopsis&ensp;thaliana WT and lhcb5 mutant plants by clear native polyacrylamide gel electrophoresis. Thylakoid membranes were solubilized by n-dodecyl α-D-maltopyranoside (detergent/chlorophyll mass ratio of 10). (B) Electron density maps of characteristic PSII supercomplexes from the separated green gel bands of the lhcb5 mutant designated as C2S2M2, C2S2M and C2SM. Projection maps are fitted by corresponding structural high-resolution models of PSII supercomplexes (Van Bezouwen et al., 2017) without LHCB5. Individual PSII subunits are color-coded according to (E). (C), (D) Comparison of structural models of the PSII C2S2M2 supercomplexes from Arabidopsis thaliana WT and the lhcb5 mutant. (C) Projection map of the PSII C2S2M2 supercomplex from Arabidopsis thaliana wild type (Ilíková et al., 2021) fitted by the high-resolution structure from Van Bezouwen et al. (2017). (D) Overlay of structural models of the PSII C2S2M2 supercomplex from Arabidopsis thaliana wild type (surface representation, partially transparent) and the lhcb5 mutant shows a specific shift of the S and M LHCII trimers as well as the monomeric antenna LHCB6 (see arrows in the corresponding colors) due to the absence of LHCB5. Individual PSII subunits are color-coded according to (E). (E) Legend of individual PSII subunits, which are color-coded as follows: PSII core complex in green, S and M LHCII trimers in red and blue, respectively, and the monomeric antenna proteins, LHCB4, LHCB5, LHCB6, in yellow, cyan, and dark orange, respectively. FIGURE 3 Organization of photosystem II in thylakoid membranes of the lhcb5 mutant. (A, B) Examples of electron micrographs of negatively stained thylakoid membrane isolated from the lhcb5 mutant with densities corresponding to the PSII core complex. Representative picture of PSII supercomplexes “randomly” organized (A) and organized into 2D semi-crystalline array (B). (C, D, E) Projection maps of PSII megacomplexes obtained using image analysis of PSII particles in thylakoid membranes. Three specific associations of PSII supercomplexes are shown and fitted by the model of PSII supercomplex C2S2M2 without LHCB5 (see Figure 2B). Megacomplexes are averaged projections of 1 925 (C), 2 241 (D), and 2 305 (E) particles. (F) Isolated PSII particle from thylakoid membranes with “randomly” organized PSII as an average projection of 3 741 particles fitted by the model of PSII supercomplex C2S2M2 without LHCB5 (see Figure 2B). (G) PSII supercomplexes organized into 2D semi-crystalline array as an average projection of 418 sub-areas together with the fitted model of PSII C2S2M2 supercomplexes (see Figure 2B). Projection maps of PSII supercomplexes show core complexes in green, S trimers in red, M trimers in blue, LHCB4 in yellow, and LHCB6 in dark orange color. FIGURE 4 Distribution of mutual distances between neighboring photosystem II particles in thylakoid membranes of Arabidopsis thaliana WT and the lhcb5 mutant. The distances between two closest neighboring PSII supercomplexes were analyzed using EM. Histograms are normalized to the maximum. SUPPORTING FIGURE 1 Analysis of chosen photosystem I and II photosynthesis related parameters. (A) Quantum yield of photochemistry of PSI - Y(I). (B) Quantum yield of photochemistry of PSII - Y(II). (C) Non-photochemical quenching – NPQ. Parameters were measured during actinic light exposure (800 µmol photons m-2 s-1) and dark relaxation using saturating light pulses (300 ms, 10 000 µmol photons m-2 s-1) in WT and lhcb5 mutant plants. Results represent mean values ± SD from 4 measurements. Plants were dark-adapted for 30 min before the measurement. SUPPORTING FIGURE 2 Single-particle image analysis and classification of protein complexes from CN−PAGE C2S2M2 band from the Arabidopsis lhcb5 mutant (Figure 2A). Number of averaged projections in given classes are indicated. SUPPORTING FIGURE 3 Single-particle image analysis and classification of protein complexes from CN−PAGE C2S2M band from the Arabidopsis lhcb5 mutant (Figure 2A). Number of averaged projections in given classes are indicated. SUPPORTING FIGURE 4 Single-particle image analysis and classification of protein complexes from CN−PAGE C2SM band from the Arabidopsis lhcb5 mutant (Figure 2A). Number of averaged projections in given classes are indicated. SUPPORTING FIGURE 5 A histogram of the relative abundance of PSII semi-crystalline arrays in thylakoid membranes of Arabidopsis lhcb5 mutant. The bars represent the number of electron micrographs where the 2D arrays cover the indicated percentage of the membrane. The histogram was obtained by evaluation of 50 randomly selected images. SUPPORTING TABLE 1 Physiological parameters of Arabidopsis WT and lhcb5 mutant plants. SUPPORTING TABLE 2 Density of bands corresponding to LHCB5-less PSII supercomplexes evaluated relatively to WT. Figure 1 C-D - source data for Figure 1. (panels C-D) Documentation of similar physiology of Arabidopsis thaliana wild type (WT), and its mutant with loss of LHCB5 protein subunit (lhcb5): (C) relative content of photosysthesis related proteins in thylakoid membranes of Arabidopsis thaliana lhcb5 genotype normalised to WT determined by LC-MS/MS; (D) relative protein ratios normalised to WT of photosynthesis related thylakoid membrane proteins of Arabidopsis thaliana lhcb5 genotype determined in isolated thylakoid membranes by LC-MS/MS. Figure 4 - source data for Figure 4. Relative distribution of photosystem II (PSII) distances in thylakoid grana membranes of Arabidopsis thaliana wild type (WT) and mutant with missing LHCB5 protein (lhcb5). Supporting figure 1 Source data for supporting figure 1 Photosynthesis related parametres describing PSI and PSII function. (A) quantum yield of photochemistry of PSI (Y(I)) in Arabidopsis thaliana WT and lhcb5 genotype leaves during red acitinic light exposure and dark relaxation; (B) quantum yield of photochemistry of PSII (Y(II)) in Arabidopsis thaliana WT and lhcb5 genotype leaves during red acitinic light exposure and dark relaxation; (C) non-photochemical quenching of Arabidopsis thaliana genotypes: The level of NPQ estimated during red acitinic light exposure and dark relaxation of WT and lhcb5 leaves. Supporting figure 5 Source data for Supplement figure 4. Relative abundance of 2D PSII arrays in the thylakoid membranes of Arabidopsis thaliana lhcb5 mutant from 50 randomly selected images. Supporting table 1 - source data Source data for supporting table 1. Physiological parameters of witl type (WT) Arabidopsis thaliana and its mutant lacking LHCB5 protein (lhcb5): Repetitions of data measured for each genotypes. Supporting table 2 - source data Source data for supporting table 2. Density of bands corresponding to LHCB5-less PSII supercomplexes evaluated relatively to WT: Repetitions of data measured for each genotypes. Figure 1B source WB Source WB picture for FIGURE 1B. Figure 1B source WB, marker Source WB picture with molecular marker for FIGURE 1B.

opencc-by-4.0Sep 2024View details →

zenodo44/100

Intermolecular interactions in G protein-coupled receptor allosteric sites at the membrane interface from molecular dynamics simulations and quantum chemical calculations

Allosteric modulators are called to be promising candidates in G protein-coupled receptor (GPCR) drug development by displaying target selectivity and fewer side effects. Among the allosteric sites known to date, extrahelical cavities represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability; the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze the dynamics and interactions in the PAR2, C5aR1, and GCGR receptors unbound and bound to allosteric modulators at the receptor-lipid interface using molecular dynamics simulations in three lipid compositions. In addition, we performed quantum chemical calculations to further explore electrostatic interactions and the strength of atom pairwise contacts in the stabilization of the ligand-receptor complexes. We show that besides classical hydrogen bonds weak polar interactions such as O-HC, O-Br, and S-HC contacts and aromatic interactions contribute to the binding of allosteric modulators at the extrahelical sites in the middle of the membrane. The allosteric cavities are open and detectable in various membrane compositions but not always predicted as druggable.  The availability of polar atoms for interactions in such cavities can be assessed by water molecules from the simulations. Although ligand-lipid interactions are weak, the lipid tails play a role in sizing and shaping the large part of the allosteric cavity.  You will find the following files: <ul> <li>Input files of the equilibration and production protocols of MD simulations (MD_simulations_inputs.zip)</li> <li>Input files and coordinate files of F-SAPT and NCIPLOT calculations (quantum_chemical_coordiates_inputs.zip)</li> </ul>

opencc-by-4.0Jun 2022View details →

zenodo44/100

Data for UV Plasmon-Enhanced Chiroptical Spectroscopy of Membrane-Binding Proteins, June 2024

Extinction spectra of arrays of aluminum nanoparticles with diameters between 40 - 100 nm. Circular dichroism spectra of Tol-BINAP films on Al nanoparticle arrays before and after annealing of the films. Electromagnetic simulations of phase, electric (Eenh) field and magnetic (Henh) field enhancements as well as optical chirality density (Cenh) enhancement around flat aluminum hexagonal pyramid at specified wavelength. The simulations were performed with FDTD using Ansys Lumerical.

opencc-by-4.0Jun 2024View details →

zenodo44/100

X-Ray Diffraction data from Membrane transport protein AcrB, V612F mutant with bound minocycline, source of 9FHC structure

Crystals were grown of the membrane transport protein AcrB, V612F mutant, with bound minocycline.  X-ray diffraction data of this upload: 400 frames of 0.5° width were collected on 2007-04-30 at the X06SA beamline of Swiss Light Source at Paul-Scherrer-Institute (Switzerland). The data can be processed with XDS; XDS.INP is provided as part of the upload. The data are the basis of the PDB 9FHC structure.

opencc-by-4.0Jun 2024View details →

zenodo44/100

Homologous membrane protein structures (HOMEP) version 3

Homologous membrane protein structures (HOMEP) version 3 (created 2013) An updated version of v2 <a href="https://doi.org/10.5281/zenodo.2646539">10.5281/zenodo.2646539</a> and v1: <a href="https://doi.org/10.5281/zenodo.2646534">10.5281/zenodo.2646534</a> Table 1 = Alpha-helical membrane protein structures in the HOMEP3 data set (2013), listed by family From Stamm M, Forrest LR, Proteins 2015 (Supplementary Table 1):<a href="http://https://www.ncbi.nlm.nih.gov/pubmed/26178143"> https://www.ncbi.nlm.nih.gov/pubmed/26178143</a>  Contains the following columns: Protein family, Protein databank identifier, Chain identifier, Name, Source organism, Resolution (Å)   Table 2 = Beta-barrel membrane protein structures in the HOMEP3 data set (2013), listed by family From Stamm M, Forrest LR, Proteins 2015 (Supplementary Table 2) Contains the following columns: Protein family, Protein databank identifier, Chain identifier, Name, Source organism, Resolution (Å)   HOMEP3_pairs_alpha.txt List of all pairs of protein structure chains of alpha-helical proteins   HOMEP3_pairs_beta.txt List of all pairs of protein structure chains of beta-barrel proteins   HOMEP3_pdbs.tar.gz All pdb files for individual chains in both alpha-helical and beta-barrel subsets

openother-atJul 2015View details →

zenodo44/100

A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs

EM Quantitation: Raw data gathered from EM images taken to determine nanodisc population size distribution.   NNB TGN46 analysis: Data analysis of the Native Nanobleach experiments of TGN46 in native nanodiscs to determine population distribution of oligomeric organizations.   Polymer conditions: Physiochemical characteristic and extraction conditions for all polymers in the library both commercially available and in-house.   Protein groups polymer screen original file: Original output of MaxQuant data processing of polymer screen data.   Organelle matching: Code used for mathcing proteins identified in the proteomics output to organelle or residence for all organellar annotations.   Polymer code: Code used to process and normalize the MaxQuant output and calulate extraction efficiency across all detected proteins.   MAP Library Details: Graphic and table explaining chemical details of all polymer used in the screen, both commerically available and in-house synthesized.   NNB TGN46: Raw scope files for the TIRF microscopy single molecule step photobleaching experiment with TGN46.   Organellar Breakdown Database: Proteins detected in the polymer screen through proteomics experiments stratified into organelle of residence.   Human Proteome FASTA: The FASTA file used for proteome searching in processing the proteomics data to build the screening database.   Hand Curated Organellar Proteomes: Organellar proteomes used for organellar sorting and identification of proteins detected in the screen.   Polymer SEC Superdex75: Size exculsion chromatography traces for chloroSMA series of polymers. Was used to characterize length and population polydispersity.   Negative Stain Raw: RAW TEM scope images of purified synaptophysin-vamp2 containing nanodiscs. Populatoin size distribution was determined.   FSEC Polymer CS80: Fluoresence size exclusion chromatogram for purified synaptophysin-vamp2 containing nanodiscs to ensure population homogeneity and purity. NMR Raw data: NMR raw files for characterizing the in-house synthesized Chloro-SMA series and AASTY series.

opencc-by-4.0May 2024View details →

zenodo40/100

A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane

This upload contains files documented in a preprint and a publication. Preprint: https://doi.org/10.1101/2022.03.30.486314 Publication: <a href="https://doi.org/10.1073/pnas.2205425119">https://doi.org/10.1073/pnas.2205425119</a> The files uploaded here are: - Alphafold predictions for VPS13A N-term (a.a. 1-2100) and C-term (a.a. 1021-3174). The .pse file is the pymol structure alignment of the two predicted VPS13A portions, join at aminoacid position D14 with the different representations presented throughout the paper stored as pymol "scenes".  - AlphaFold-Multimer prediction for the interaction between XK and the C-term region of VPS13A is also included. - An excel file containing the tabular data for the graphs in Figures 1G, S2E and 4D.

opencc-by-4.0Jun 2022View details →

zenodo40/100

Dataset 2 for UV Plasmon-Enhanced Chiroptical Spectroscopy of Membrane-Binding Proteins, June 2024

Scanning electron microscopy images of Al nanostructures

opencc-by-4.0May 2024View details →

zenodo40/100

"Palmitoylation Mediates Membrane Association of Hepatitis E Virus ORF3 Protein and is Required for Infectious Particle Secretion"

Hepatitis E virus (HEV) is a positive-strand RNA virus encoding 3 open reading frames (ORF). HEV ORF3 protein is a small, hitherto poorly characterized protein involved in viral particle secretion and possibly other functions. Here, we show that HEV ORF3 protein forms membrane-associated oligomers. Immunoblot analyses of ORF3 protein expressed in cell-free vs. cellular systems suggested a posttranslational modification. Further analyses revealed that HEV ORF3 protein is palmitoylated at cysteine residues in its N-terminal region, as corroborated by 3H-palmitate labeling, the investigation of cysteine-to-alanine substitution mutants and treatment with the palmitoylation inhibitor 2-bromopalmitate (2-BP). Abrogation of palmitoylation by site-directed mutagenesis or 2-BP treatment altered the subcellular localization of ORF3 protein, reduced the stability of the protein and strongly impaired the secretion of infectious particles. Moreover, selective membrane permeabilization coupled with immunofluorescence microscopy revealed that HEV ORF3 protein is entirely exposed to the cytosolic side of the membrane, allowing to propose a model for its membrane topology and interactions required in the viral life cycle. In conclusion, palmitoylation determines the subcellular localization, membrane topology and function of HEV ORF3 protein in the HEV life cycle.

opencc-by-4.0Dec 2017View details →

dryad36/100

Data from: A multiscale biophysical model for the recruitment of actin nucleating proteins at the membrane interface

The dynamics and organization of the actin cytoskeleton are crucial to many cellular events such as motility, polarization, cell shaping, and cell division. The intracellular and extracellular signaling associated with this cytoskeletal network is communicated through cell membranes. Hence the organization of membrane macromolecules and actin filament assembly are highly interdependent. Although the actin-membrane linkage is known to happen through many routes, the major class of interactions is through the direct interaction of actin-binding proteins with the lipid class containing poly-phosphatidylinositols (PPIs). Among the PPIs, phosphatidylinositol bisphosphate (PI(4,5)P2) acts as a significant factor controlling actin polymerization in the proximity of the membrane by binding to actin-associated proteins. The molecular interactions between these actin-binding proteins and the membrane lipids remain elusive. Here, using molecular modeling, analytical theory, and experimental methods, we investigate the binding of three different actin-binding proteins, mDia2, NWASP, and gelsolin, to membranes containing PI(4,5)P2 lipids. We perform molecular dynamics simulations on the protein-bilayer system and analyze the membrane binding in the form of hydrogen bonds and salt bridges at various PI(4,5)P2 and cholesterol concentrations. Our experimental study with PI(4,5)P2-containing large unilamellar vesicles mimics the computational experiments. Using the multivalencies of the proteins obtained in molecular simulations and the cooperative binding mechanisms of the proteins, we also propose a multivalent binding model that predicts the actin filament distributions at various PI(4,5)P2 and protein concentrations.

opencc-zeroMay 2020View details →

zenodo36/100

pLMMoRF: A web server that accurately predicts membrane-interacting molecular recognition features by employing a protein language model

pLMMMoRF predictor scrips and MemMoRF prediction of the human proteome.

opencc-by-4.0Nov 2024View details →

zenodo36/100

Coordinate files from LipIDens: Simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.

Coordinate files from the first and last frame of coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulations used throughout the LipIDens pipeline.CG simulations were run for HHAT, OTOP1, ELIC, MscS, TRPV6, ChRmine, Ste2, Connexin-50, NPC1 and the PAT complex. All CG simulations were run for 10 x 15 μs with the exception of NPC1 which was simulated for 10 x 30 μs.AT simulations were run for HHAT (5 x 200 ns) and ELIC (3 x 200 ns) in apo configurations.File description:Directories for each protein are listed with the suffix CG or AT used to indicate the simulation resolution. md_fit_firstframe_X.gro - GROMACS structure file for the first frame of replicate X. md_fit_lastframe_X.gro - GROMACS structure file for the last frame of replicate X.

opencc-by-4.0Oct 2023View details →

dryad36/100

Data from: A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein

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.

opencc-zeroDec 2023View details →

dryad36/100

Conserved structural elements specialize ATAD1 as a membrane protein extraction machine

The mitochondrial AAA protein ATAD1 (in humans; Msp1 in yeast) removes mislocalized membrane proteins, as well as stuck import substrates from the mitochondrial outer membrane, facilitating their re-insertion into their cognate organelles and maintaining mitochondria's protein import capacity. In doing so, it helps to maintain proteostasis in mitochondria. How ATAD1 tackles the energetic challenge to extract hydrophobic membrane proteins from the lipid bilayer and what structural features adapt ATAD1 for its particular function has remained a mystery. Previously, we determined the structure of Msp1 in complex with a peptide substrate (Wang et al., 2020). The structure showed that Msp1's mechanism follows the general principle established for AAA proteins while adopting several structural features that specialize it for its function. Among these features in Msp1 was the utilization of multiple aromatic amino acids to firmly grip the substrate in the central pore. However, it was not clear whether the aromatic nature of these amino acids were required, or if they could be functionally replaced by aliphatic amino acids. In this work, we determined the cryo-EM structures of the human ATAD1 in complex with a peptide substrate at near atomic resolution. The structures show that phylogenetically conserved structural elements adapt ATAD1 for its function while generally adopting a conserved mechanism shared by many AAA proteins. We developed a microscopy-based assay reporting on protein mislocalization, with which we directly assessed ATAD1's activity in live cells and showed that both aromatic amino acids in pore-loop 1 are required for ATAD1's function and cannot be substituted by aliphatic amino acids. A short α-helix at the C-terminus strongly facilitates ATAD1's oligomerization, a structural feature that distinguishes ATAD1 from its closely related proteins.

opencc-zeroMay 2022View details →

zenodo36/100

Hyperactive antifreeze protein from the beetle Rhagium mordax stabilizes model lipid membranes during temperature dependent phase transition

Data from the study submitted in the paper Hyperactive antifreeze protein from the beetle Rhagium mordax stabilises model lipid membranes during temperature-dependent phase transition Data Includes; 1. DSC results of RmAFPs interactions with liposomes showing Tm, ΔHcal and Full width at half maximum (FWHM) as well as Phase transitions thermographs by DSC on 1.5mg/ml SUV liposomes either with 60μM (or 0.75mg/ml) RmAFPs or without RmAFPs as control. 2. fluorescence spectroscopy data, a complete compilation

opencc-by-4.0Jul 2022View details →

zenodo36/100

Nanoscale dipole dynamics of protein membranes studied by broadband dielectric microscopy

Original data in support of our publication: Nanoscale dipole dynamics of protein membranes studied by broadband dielectric microscopy

opencc-by-4.0Apr 2019View details →

zenodo36/100

Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts"

Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts" by Julia R Rogers and Phillip L Geissler (<a href="https://doi.org/10.1371/journal.pcbi.1010992">Rogers, J. R.; Geissler, P. L. PLoS Comput. Biol. 2023, 19, e1010992</a>; bioRxiv DOI: https://doi.org/10.1101/2022.09.10.507427). All input coordinates, topologies, and parameter files in addition to equilibrium simulation trajectories and analysis results are provided.

opencc-by-4.0Sep 2022View details →

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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.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

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.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

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.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

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.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record