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641 results for “Protein interaction”
Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P212121)
<p>Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P212121). The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7BBO">7BBO</a>.</p> <p> </p> <p>Additional information:</p> <p>dataset: PHIPA-x1738<br> beamline: Diamond Light Source I04-1<br> visit: nt11175-63<br> date: 16-04-2015<br> Ω Start: 90.0°<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>
Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac
<p>Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac. The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7BBP">7BBP</a>.</p> <p> </p> <p>Additional information:</p> <p>dataset: PHIPA-x2179<br> beamline: Diamond Light Source I04-1<br> visit: mx10619-76<br> date: 20-06-2016<br> Ω Start: 216.3°<br> Ω Osc: 0.15°<br> Ω Overlap: 0°<br> No. Images: 1200<br> Resolution: 2.00Å<br> Wavelength: 0.9282Å<br> Exposure: 0.050s<br> Transmission: 100.00%</p>
Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group p21212)
<p>Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group p21212). The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7AV8">7AV8</a>.</p> <p>Additional information:</p> <p>dataset: PHIPA-x152<br> beamline: Diamond Light Source I04-1<br> visit: mx8421-63<br> date: 02-03-2014<br> Ω Start: 90.0°<br> Ω Osc: 0.10°<br> Ω Overlap: 0°<br> No. Images: 1800<br> Resolution: 1.50Å<br> Wavelength: 0.9200Å<br> Exposure: 0.050s<br> Transmission: 100.00%<br> Beamsize: 60x50μm</p>
Supplemental data: Interfering Peptides Targeting Protein-Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence
<p>This dataset supplements the chapter "Interfering Peptides Targeting Protein-Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence" published in Methods in Molecular Biology. It includes sample files that illustrate data collection and processing outlined in the article.</p>
Data from: Proteomic analysis of barley mapping population subjected to drought identifies proteins with genotype×environment interaction and pQTLs
Drought is one of the major abiotic stresses negatively influencing crop yield and is a serious issue in modern agriculture. To achieve further substantial crop improvements in terms of drought resistance it is necessary to incorporate scientific results into breeding strategies. However, most of the data on plant drought responses arises mostly from small-scale studies and, therefore, its use in breeding programs is very limited. Here, we present the results of the large-scale proteomic analysis performed on barley recombinant inbred lines (RILs) and their parental genotypes subjected to drought, applied shortly before tillering. The conducted proteomic analyses enabled us to monitor drought-induced proteome changes in leaf and root tissue, and to identify proteins that responded to drought in a genotype-specific manner, for instance Rubisco activase, luminal binding protein, phosphoglycerate mutase, glutathione S-transferase, heat shock proteins as well as enzymes involved in phenylpropanoid biosynthesis. We also demonstrated feasibility of incorporating proteomic data resulting from large-scale study into genetic linkage analysis, which constitutes a fundament in biotechnology-driven breeding strategies.
Data from: Epistatic interaction of the melanocortin 1 receptor and agouti signaling protein genes modulates wool color in the Brazilian Creole sheep
Different pigmentation genes have been associated with color diversity in domestic animal species. The melanocortin 1 receptor (MC1R), agouti signaling protein (ASIP), tyrosinase related protein-1 (TYRP1) and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) genes are candidate genes responsible for variation in wool color among breeds of sheep. Although the influence of these genes has been described in some breeds, in many others the effect of interactions among genes underlying wool color has not been investigated. The Brazilian Creole sheep is a local breed with a wide variety of wool color, ranging from black to white with several intermediate hues. We analyzed in this study the influence of the genes MC1R, ASIP, TYRP1 and KIT on the control of wool color in this breed. A total of 410 samples were analyzed, including 148 white and 262 colored individuals. The MC1R and ASIP polymorphisms were significantly associated with the segregation of either white or colored wool. The dominant MC1R allele (ED p.M73K and p.D121N) was present only in colored animals. All white individuals were homozygous for the MC1R recessive allele (E+) and carriers of the duplicated copy of ASIP. A gene expression essay showed that only the carrier of the duplicated copy of ASIP produces increased levels in skin, not detectable in the single homozygous copy. These results demonstrate that the epistatic interaction of the genotypes in the MC1R and ASIP gene is responsible for the striking color variation in the Creole breed.
Expression and purification of huntingtin interacting protein HMGB1 2017/07/07
<p>Huntingtin structure-function open lab notebook</p>
Expression and purification of huntingtin interacting protein HMGB1 - 2nd attempt (2017/07/20)
<p>Huntingtin structure-function open lab notebook project</p>
Expression and purification of huntingtin interaction protein High mobility group protein B1 (HMGB1) – 2017/08/14
<p>Huntingtin structure-function open lab notebook project</p>
Targeting host-virus interactions: In silico analysis of the binding of human milk oligosaccharides to viral proteins involved in respiratory infections
<p><span>Respiratory viral infections, a major public health concern, necessitate the continuous development of novel antiviral strategies, particularly in the face of emerging and re-emerging pathogens. In this study, we </span><span>explored</span><span> the potential of human milk oligosaccharides (HMOs) as broad-spectrum antiviral agents against key respiratory viruses. </span><span>By examining the</span><span> structural mimicry of host cell receptors and </span><span>their </span><span>known biological functions, including antiviral activities, we assessed the </span><span>ability</span><span> of HMOs to bind and potentially inhibit viral proteins crucial for host</span><span> </span><span>cell entry. Our <em>in silico</em> analysis </span><span>focused</span><span> on viral proteins integral to host-virus interactions</span><span>, namely,</span><span> the hemagglutinin protein of influenza, fusion proteins of respiratory syncytial and human metapneumovirus, and the spike protein of SARS-CoV-2. Using molecular docking and simulation studies, we </span><span>demonstrated</span><span> that HMOs exhibit varying binding affinities to these viral proteins, suggesting their potential as viral entry inhibitors. </span><span>This</span><span> study </span><span>identified</span><span> several HMOs with promising binding profiles, highlighting their potential in antiviral drug development. This research provides a foundation for utilizing HMOs as a natural source for designing new therapeutics, offering a novel approach in the fight against respiratory viral infections.</span></p>
Datasets for "Physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data"
<div> <p>Datasets used for implementing the <a href="https://github.com/huankoh/PSICHIC">PSICHIC</a> experiments shown in the <a href="https://doi.org/10.1101/2023.09.17.558145">manuscript</a>.</p> <p> </p> </div>
Supporting data for transmembrane domain self association simulations in "Recalibration of protein interactions in Martini 3"
<p>This repository contains the data of transmembrane helix self-association simulation from "Recalibration of protein interactions in Martini 3". Simulations were run with the Martini 3.0 force field, along with two modified versions of Martini 3.0 in which the well-depth, ε, in the Lennard-Jones potential between all protein and water beads was rescaled by a factor <em>λ</em><sub>PW</sub>, ε in the Lennard-Jones potential between all protein beads was rescaled by a factor <em>λ</em><sub>PP</sub>. The simulation files are kept in one single zip file, which contains trajectories for two protein EphA1 and ErbB1 systems with three versions of force fields. The trajectory files are in xtc format, and are accompanied by a structure in pdb format for system topology and a tpr file to start the simulation. In each version of force field for each protein, name of the files corresponds to that specific umbrella sampling window. Umbrella sampling windows ranges from 0.6 nm to 3.4 nm with a spacing of 0.2 nm. </p>
Molecular docking analysis was performed to assess the affinity of onalespib for their targets LOX, elucidating binding poses, protein interactions, and associated binding energies.
<p>To analyze the binding affinities and interaction modes between the drug candidates and their targets, we employed the Autodock Vina software [21]. Molecular structures of the candidate drugs and targets of hub genes were retrieved from Pubchem (https://pubchem.ncbi.nlm.nih.gov/) and Protein Data Bank database (http://www.rcsb.org/), respectively. <span>In the analysis of docking, the files for all proteins and molecules were converted to PDBQT format. Water molecules were removed and polar hydrogen atoms were added. The grid box was positioned at the center to encompass the protein domain, allowing for unrestricted movement of molecules.</span></p>
HerpesFolds: All-versus-all protein interaction network - VZV
<p>For VZV, all possible protein-protein combinations within the species were structurally predicted with AlphaFold 2.3. A user interface and network visualization can be found at: https://herpesfolds.org/</p>
PoxFolds: All-versus-all protein interaction network - MPOX
<p>For MPOX, all possible protein-protein combinations within the species were structurally predicted with AlphaFold 2.3. A user interface and network visualization can be found at: https://www.poxfolds.org/</p>
Electrostatic interactions contribute to the control of intramolecular thiol–disulfide isomerization in a protein
<p>The role of structural factors and of electrostatic interactions with the environment on the outcome of thiol–disulfide exchange reactions were investigated in a mutated immunoglobulin domain (I27*) under mechanical stress. An extensive ensemble of molecular dynamics trajectories was generated by means of QM/MM simulations for a total sampling of 5.7 μs. A significant number of thiol–disulfide exchanges were observed, and the Cys32 thiolate preferred to attack Cys55 over Cys24, in agreement with previous experimental and computational studies. The structural features as well as electronic structures of the thiol–disulfide system along the reaction were analyzed, as were the electrostatic interactions with the environment. The previous findings of better accessibility of Cys55 were confirmed. Additionally, the reaction is found to be directed by the electrostatic interactions of the involved sulfur atoms with the molecular environment. The relationships of atomic charges, which stem from the electrostatic interactions, lead to the kinetic preference of the attack on Cys55. Further, QM/MM metadynamics simulations of thiol–disulfide exchange in a small model system with varied artificial external electric potentials revealed changes in reaction kinetics of the same magnitude as in I27*. Therefore, the electrostatic interactions are confirmed to play a role in the regioselectivity of the thiol–disulfide exchange reactions in the protein.</p>
Impact of New Variants on SARS-CoV-2 Infectivity and Neutralization: A Molecular Assessment of the Alterations in the Spike-Host Protein Interactions
<p>MD simulation trajectories and structural models from the work which first appeared on bioRxiv (https://doi.org/10.1101/2021.01.10.426143), later ssrn (<a href="https://dx.doi.org/10.2139/ssrn.3907841">http://dx.doi.org/10.2139/ssrn.3907841</a>), and finally accepted for publication by Iscience.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run1_WT_RBD_ACE2.zip">Run1_WT_RBD_ACE2.zip</a></p> <p>Description: A compressed (zipped) folder contains three independent MD trajectories of WT RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run2_N501Y_RBD_ACE2.zip">Run2_N501Y_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Alpha RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run3_Beta_RBD_ACE2.zip">Run3_Beta_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Beta RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run4_Delta_RBD_ACE2.zip">Run4_Delta_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Delta RBD-ACE2 complex</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run5_UK2_E484K_N501Y_ACE2.zip">Run5_UK2_E484K_N501Y_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of UK2 RBD-ACE2 complex</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Structural_model_PDBs.zip">Structural_model_PDBs.zip</a></p> <p>Description: A compressed folder contains eight pdb files of those structural models plotted in Figs 1, 3, 5, 6, 7 and S1.</p>
i-Tasser 3D Strucutres of Blood Plasma Proteins for United Atom Multiscale Modelling Of Bio-Nano Interactions
<p>3D Structures of blood plasma proteins as per proteomic data on protein corona for AgNPs presented in this publication:</p> <blockquote> <p>Gorshkov V, Bubis JA, Solovyeva EM, Gorshkov M, KjeldsenF. Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution. Environ. Sci.: Nano, 2019,6, 1089-1098. doi: 10.1039/C8EN01054D</p> </blockquote> <p>Note, that the dataset is different from the one used in this publication:</p> <blockquote> <p>Alsharif SA, Power D, Rouse I, Lobaskin V. In Silico Prediction of Protein Adsorption Energy on Titanium Dioxide and Gold Nanoparticles. Nanomaterials (Basel). 2020 Oct 4;10(10):1967. doi: 10.3390/nano10101967.</p> </blockquote> <p>Files were prepared with I-TASSER utility:</p> <blockquote> <p>J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8 (2015).</p> </blockquote> <p> </p>
i-Tasser 3D Strucutres of Milk Proteins for United Atom Multiscale Modelling Of Bio-Nano Interactions
<p>The list of milk proteins was obtained from this work:</p> <blockquote> <p>Tacoma R, Fields J, Ebenstein DB, Lam YW, Greenwood SL. Characterization of the bovine milk proteome in early-lactation Holstein and Jersey breeds of dairy cows. Journal of Proteomics, 2016 (130), 200-210.</p> </blockquote> <p>Files were prepared with I-TASSER utility:</p> <blockquote> <p>J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8 (2015).</p> </blockquote>
Chr21 protein–protein interactions: enrichment in proteins involved in intellectual disability, autism, and late-onset Alzheimer's disease
<p>Description of the Bait and the full protein/protein interaction dataset obtained in saturated yeast 2-Hybrid screens. Interaction will be later release in Intact under IMEX=IM-27626.</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.