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641 results for “Protein interaction”
Lateral interactions govern self-assembly of the bacterial biofilm matrix protein BslA (experimental and simulation data)
<p>The soil bacterium Bacillus subtilis is a model organism to investigate the formation of biofilms, the predominant form of microbial life. The secreted protein BslA self-assembles at the surface of the biofilm to give the B. subtilis biofilm its characteristic hydrophobicity. To understand the mechanism of BslA self-assembly at interfaces, here we built a molecular model based on the previous BslA crystal structure and the newly determined crystal structure of the BslA paralogue YweA. Our analysis revealed two conserved protein-protein interaction interfaces supporting BslA self-assembly into an infinite 2d lattice that fits previously determined transmission microscopy images. Molecular dynamics simulations and in vitro protein assays further support our model of BslA elastic film formation, while mutagenesis experiments highlight the importance of the identified interactions for biofilm structure. Based on this knowledge, YweA was engineered to form more stable elastic films and rescue biofilm structure in bslA deficient strains. These findings shed new light on protein film assembly and will inform the development of BslA technologies which range from surface coatings to emulsions in fast-moving consumer goods.</p>
Mass spectroscopy analysis of Nuclear YAP1 interacting proteins
<p>YAP1 regulates the expression of several genes involved in diverse cell biology, including cell growth, cell survival, cell differentiation, cell transformation, carcinogenesis, and metastasis. In the present study, we employed co-immunoprecipitations combined with mass spectroscopy to identify nuclear YAP1 interacting proteins in the well-established human prostate tumor cell models steroid. Our proteomics analysis demonstrated that androgen hormone signaling regulates the YAP1 interacting proteins. Our functional annotation clustering showed that YAP1-associated proteins were enriched for diverse cellular pathways, including RNA transport, RNA processing, RNA translation, posttranscriptional regulation, protein folding, metabolism, etc. Furthermore, we characterized the molecular and functional interaction between multifunctional, polycomb group protein SCML2 and YAP1 in cultures. Our results demonstrate that YAP1 cooperates with the epigenetic regulatory protein SCML2 to module cell growth, cell survival, and oncogenesis downstream of steroid hormone androgen signaling.</p>
Simulation trajectories for CLas BamA protein interacting with high-affinity short peptides
<p>Trajectories of molecular dynamics simulations done using Schrodinger Desmond for interaction of BamA protein of <em>Candidatus </em>Liberibacter asiaticus with three short peptides with a high affinity towards BamA. Simulations were conducted for 100 ns. </p>
Data from: Protein-Chromophore interactions controlling photoisomerization in red/green cyanobacteriochromes
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Data from: BioID2-based tau interactome reveals novel and known protein interactions associated with multiple cellular pathways
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Data from: Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants
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Structural ontogeny of protein-protein interactions
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Data from: Mechanisms of antibiofilm compounds JG-1 and M4 across multiple species: Alterations of protein interactions essential to biofilm formation
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Data for: Walnut PR10/Bet v1-like proteins interact with chitinase in response to anthracnose stress
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Data from: β-aminobutyric acid-induced resistance in postharvest peach fruit involves interaction between the MAPK cascade and SNARE13 protein in salicylic acid-dependent pathway
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NGS data from: Deploying synthetic coevolution and machine learning to engineer protein-protein interactions
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Lemon zinc finger protein ClSUP induces the accumulation of reactive oxygen species and inhibits citrus yellow vein-clearing virus infection via interactions with ClDOF3.4
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Quantitative Multiplex Immunoprecipitation (QMI) analysis of protein interaction network rearrangements during homeostatic plasticity
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Exploring voltage-gated sodium channel conformations and protein-protein interactions using AlphaFold2
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Supplementary data from: Assessing the structural boundaries of broadly reactive antibody interactions with diverse H3 influenza hemagglutinin proteins
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Data from: Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein
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A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
<p>The Krogan Laboratory used affinity-purification mass spectrometry to identify 332 high confidence SARS-CoV-2-human protein-protein interactions, including 67 druggable human proteins or host factors targeted by 69 known drugs. Results may be relevant to antiviral drug production.</p>
A human IgSF cell-surface interactome reveals a complex network of protein-protein interactions
<p>Cell-surface protein-protein interactions (PPIs) mediate cell-cell communication, recognition and responses. We executed an interactome screen of 564 human cell-surface and secreted proteins, most of which are immunoglobulin superfamily (IgSF) proteins, using a high-throughput, automated ELISA-based screening platform employing a pooled-protein strategy to test all 318,096 PPI combinations. Screen results, augmented by phylogenetic homology analysis, revealed ~380 previously unreported PPIs. We validated a subset using surface plasmon resonance and cell binding assays. Observed PPIs reveal a large and complex network of interactions both within and across biological systems. We identified new PPIs for receptors with well-characterized ligands, and binding partners for 'orphan' receptors. New PPIs include proteins expressed on multiple cell types, and involved in diverse processes including immune and nervous system development and function, differentiation/proliferation, metabolism, vascularization, and reproduction. These PPIs provide a resource for further biological investigation into their functional relevance, and may offer new therapeutic drug targets.</p>
Data set for validation of a Python script for computation of Protein-Ligand Interaction Fingerprints
<p><strong>1. Data set for for validation of the Protein-Ligand Interaction Fingerprints, which includes examples of protein structures (original PDB and equilibrated) and molecular dynamics trajectories (equilibration and ligand dissociation generated using Random Acceleration MD simulations, RAMD)</strong></p> <p><strong>mdifp_validation_data.tar.gz - </strong>archive that contains benchmark dataset for evaluation of the protein-ligand IFP protocol (PDB structures of protonated complexes, ligands, and MOL2 files of ligands) published in D. B. Kokha, B. Doser, S. Richter, F. Ormersbach, X. Cheng, R. C. Wade "A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories" J. Chem. Phys. <strong>153</strong>, 125102 (2020); <a href="https://doi.org/10.1063/5.0019088">https://doi.org/10.1063/5.0019088</a></p> <p>(2020) <a href="https://arxiv.org/abs/2006.11066">arXiv:2006.11066</a> </p> <p><strong>2YKI </strong>- protein-ligand complex , PDB ID 2YKI<br> - 2yki_MOE.pdb complex with hydrogen added and energy minimized using MOE software (https://www.chemcomp.com/)<br> - ligand_2yki_MOE.mol2 and ligand_2yki_MOE.pdb - ligand structure with hydrogens prepered by MOE software (https://www.chemcomp.com/)</p> <p><strong>6EI5</strong> - MD trajectory of the protein-ligand complex generated from PDB ID 6EI5<br> - ref-min.pdb minimized structure<br> - ref.prmtop topology file<br> - moe.mol2 - ligand structure in mol2 format<br> - amber2namd2.dcd generated MD trajectory </p> <p><strong>SAD_3-RAMD-03-2020.pkl </strong>- a pkl dataset with IFPs generated from RAMD dissociation trajectory of the complex PDB ID: 5LQ9 (trajectories from the paper Front. Mol. Biosci., 2019 DOI:10.3389/fmolb.2019.00036)</p> <p><strong>HSP90_Gromacs.zip </strong>- an archive that contains three pkl data sets of protein-ligand IFPs (for three HSP90 complexes; PDB ID: 5J64, 5J86, 5LQ9) generated from RAMD dissociation trajectories simulated using new Gromacs-RAMD engine (https://github.com/HITS-MCM/gromacs-ramd)</p> <p>The rest of the files contains data obtained from simulation of the complex of <strong>GPCR muscarinic receptor M2 (PDB ID:4MQT);</strong> immersed in a mixed membrane: 50% CHL, 30% POPC, 20% POPE) with a small molecule agonist iperoxo. <br> - <strong>IXO.pdb and moe.mol2 </strong>- PDBand MOL2 structure of iperoxo<br> - <strong>AMBER_eq.tar.gz</strong> - structure of the equilibrated complex generated using AMBER software<br> -<strong> NAMD_eq.tar.gz </strong>- two equilibration trajectories in dcd format generated using NAMD software <br> - <strong>RAMD_eq.tar.gz </strong>- dissociation tarjectoris of iprtoxo from the M2 protein generated from the last snapshot of two NAMD equilibration trajectories (for each case 2 RAMD dissociaiton trajectories are available) </p> <p>( *csv files were added erroneously and do not belong to the project)</p>
Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group C2)
<p>Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group C2). The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7AV9">7AV9</a>.</p> <p> </p> <p>Additional information:</p> <p>dataset: PHIPA-x1724<br> beamline: Diamond Light Source I04-1<br> visit: nt11175-63<br> date: 16-04-2015<br> Ω Start: 144.0°<br> Ω Osc: 0.12°<br> Ω Overlap: 0°<br> No. Images: 1500<br> Resolution: 1.50Å<br> Wavelength: 0.9173Å<br> Exposure: 0.040s<br> Transmission: 100.00%<br> Beamsize: 60x50μm</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.