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101 results for “Binding motif”
Double-stranded RNA structural elements holding the key to translational regulation in cancer: the case of editing in RNA Binding Motif Protein 8A
<p>Raw data supporting the manuscript</p> <p>Abukar, A.;Wipplinger, M.;<br> Hariharan, A.; Sun, S.; Ronner, M.;<br> Sculco, M.; Okonska, A.;<br> Kresoja-Rakic, J.; Rehrauer, H.; Qi, W.;<br> et al. Double-Stranded RNA<br> Structural Elements Holding the Key<br> to Translational Regulation in Cancer:<br> The Case of Editing in RNA-Binding<br> Motif Protein 8A. Cells 2021, 10, 3543.<br> https://doi.org/10.3390/<br> cells10123543</p>
Data from: Residues neighboring an SH3-binding motif participate in determining affinity and specificity in vivo
<p>In signaling networks, many protein-protein interactions are mediated by modular domains that bind short linear motifs. The motifs' sequences modulate many factors, among them affinity and specificity, or the ability to bind strongly and to bind the appropriate partners. Previous studies have proposed a trade-off between affinity and specificity, suggesting that motifs with high affinity are less capable of differentiating between domains with similar sequences and structures. Using Deep Mutational Scanning to create a mutant library of a well characterized binding motif, and protein complementation assays to measure protein-protein interactions, we tested this trade-off in vivo for the first time. We measured the binding strength and specificity of a library of mutants of a binding motif on the MAP kinase kinase Pbs2, which binds the SH3 domain of the osmosensor protein Sho1 in Saccharomyces cerevisiae. We find that many mutations in the region surrounding the binding motif modify binding strength, but that few mutations have a strong impact on specificity. Moreover, we find no systematic relationship between affinity and specificity as measured in vivo. Interestingly, all Pbs2 mutations which increase affinity or specificity are situated outside of the Pbs2 residues that interact with the canonical SH3-binding pocket, suggesting that other surfaces on Sho1 contribute to binding. We use predicted structures to propose a model of binding which involves residues neighboring the core Pbs2 motif binding outside of the canonical SH3-binding pocket, allowing affinity and specificity to be determined by a broader range of sequences than what has previously been considered.</p>
Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly - Molecular Dynamics Simulation Dataset
<p>The molecular dynamics (MD) simulation dataset. The contents:</p> <ul> <li><strong>5ire_BIOMT_expanded.pdb</strong>: The complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE) </li> <li><strong>5ire_Mprotein_BIOMT_expanded.pdb</strong>: The M proteins extracted from the complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE). The biological assembly shows the dimeric organization of M proteins.</li> <li><strong>0chol.zip, 10chol.zip, 20chol.zip, and 30chol.zip</strong> contain simulation input and output files for the simulated membrane compositions: 0:100, 10:90, 20:80, 30:70 (mol%:mol%) Cholesterol:POPC, respectively. <ul> <li>In each zip file, there are 5 directories: <strong>wt, R253L+F257A, R253L+F257S, K275L+Y278A, K275L+Y278S</strong> corresponding to each simulated M protein dimer variant: wild type, CARC 2-A, CARC 2-S, CARC 3-A, and CARC 3-S. In each directory, there are the following files: <ul> <li><strong>toppar</strong>: This directory contains all force field topologies and parameters</li> <li><strong>topol.top</strong>: GROMACS topology (top) file</li> <li><strong>index.ndx</strong>: GROMACS index (ndx) file</li> <li><strong>prod.mdp</strong>: GROMACS MD parameters (mdp) file</li> <li><strong>0, 1, 2, 3, 4, 5, 6, 7, 8, 9</strong>: These directories contain the simulation inputs and outputs for each simulation repeat. In each of these directories, there are the following files: <ul> <li><strong>t0.pdb</strong>: The pdb file of the starting coordinates</li> <li><strong>prod0.tpr</strong>: GROMACS binary run input (tpr) file </li> <li><strong>prod0.edr</strong>: GROMACS energy (edr) file</li> <li><strong>prod0.gro</strong>: GROMACS output coordinates and velocities after 1 microsecond of simulation</li> <li><strong>prod0.cpt</strong>: GROMACS checkpoint file after 1 microsecond of simulation</li> <li><strong>noW.pdb</strong>: The pdb file of the starting coordinates with all water molecules removed</li> <li><strong>noW.xtc</strong>: GROMACS compressed trajectory (xtc) file with all water molecules removed</li> </ul> </li> </ul> </li> </ul> </li> </ul>
Supplementary data accompanying HOCOMOCO v12 collection of transcription factor binding motifs
<p><strong>*** SUMMARY ***</strong></p><p>This dataset contains supplementary data accompanying HOCOMOCO v12 collection</p><p>of DNA binding motifs for human and mouse transcription factors, https://hocomoco.autosome.org</p><p> </p><p>The contents include:</p><p>- the complete initial set of motifs discovered from ChIP-Seq and HT-SELEX data;</p><p>- the curated subset of motifs associated with distinct motif subtypes that were used in benchmarking;</p><p>- the benchmarking results and the resulting final motif collections, including motif logos;</p><p>- accompanying metadata.</p><p> </p><p>Please refer to the README and the HOCOMOCO website for further details.</p><p> </p>
Data from: Residues neighboring an SH3-binding motif participate in the interaction in vivo
Open the record for dataset details and reuse information.
Data for the paper "Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study".
<p>Data for the paper "Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study".</p>
FASST Structure Database files for "Tertiary motifs as building blocks for the design of protein-binding peptides"
<p>FASST Database files for use in the <a href="https://github.com/swanss/peptide_design">peptide design</a> pipeline.</p> <p>A complete list of structures provided in the databases is provided in the supplementary information of the Protein Science article.</p> <p>Singlechain structures: <a href="https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fpro.4322&file=pro4322-sup-0004-TableS6.txt">pro4322-sup-0004-TableS6.txt</a> (format: PDBID_CHAINID)</p> <p>Multichain structures: <a href="https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fpro.4322&file=pro4322-sup-0005-TableS7.txt">pro4322-sup-0005-TableS7.txt</a> (format: PDBID)</p>
Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase
<p>We have provided all the necessary files, outputs, as well as the ReadMe file for this work to be redone.</p>
Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C
<p>Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.</p>
[PART 3] A twist of fate: the helix-turn-helix motif in Pseudomonas aeruginosa ExsA can allosterically stabilize the ligand-binding domain
<p>1273- ExsA - Dimer1 without DNA - alphaFold compact - 230ns/day 10x500ns<br>*1274- ExsA - Dimer2 without DNA - xtal extended (like 1026) - 10x1µs (not everything is 1 µs)<br>1275- ExsA - Dimer3 without DNA - made by hand / 150ns/day (reps 1-5 broken, reps 6-10 correct)<br>*1276- ExsA- monomer - Site1-PexoT - 240 ns/day - 10x1µs (some replicas have pieces missing)<br>*1277- ExsA- monomer - Site2-PexoT - 10x1µs<br>*1278- ExsA - Dimer2 with broken DNA - xtal extended (like 1026) - 5x200ns?</p>
[PART 2] A twist of fate: the helix-turn-helix motif in Pseudomonas aeruginosa ExsA can allosterically stabilize the ligand-binding domain
<p>1273- ExsA - Dimer1 without DNA - alphaFold compact <br>1274- ExsA - Dimer2 without DNA - xtal extended <br>1275- ExsA - Dimer3 without DNA - made by hand (reps 1-5 broken, reps 6-10 correct)<br>1276- ExsA- monomer - Site1-PexoT <br>1277- ExsA- monomer - Site2-PexoT<br>1278- ExsA - Dimer2 with broken DNA</p>
Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97
<p>Biosensor techniques have become increasingly important for fragment-based drug discovery during the last years. The AAA+ ATPase p97 is an essential protein with key roles in protein homeostasis and a possible target for cancer chemotherapy. Currently available p97 inhibitors address its ATPase activity and globally impair p97-mediated processes. In contrast, inhibition of cofactor binding to the N-domain by a protein-protein-interaction inhibitor would enable the selective targeting of specific p97 functions. Here, we describe a biolayer interferometry-based fragment screen targeting the N-domain of p97 and demonstrate that a region known as SHP-motif binding site can be targeted with small molecules. Guided by molecular dynamics simulations, the binding sites of selected screening hits were postulated and experimentally validated using protein- and ligand-based NMR techniques, as well as X-ray crystallography, ultimately resulting in the first structure of a small molecule in complex with the N-domain of p97. The identified fragments provide insights into how this region could be targeted and present first chemical starting points for the development of a protein-protein interaction inhibitor preventing the binding of selected cofactors to p97.</p> <p><br> Here we publish the primary data of the biolayer-interferometry (BLI), STD-NMR, HSQC-NMR and mixed-solvent MD simulation results.<br> For BLI, the sensorgrams of 10 binding fragments identified in the screening are given. Measurements were conducted with the N-domain and the ND1-construct of p97. Additionaly, the measurements with ADP as positive control (n=6) are provided.<br> Four of the 10 fragments were selected as most promising hits for further investigation: TROLL2, TROLL7, TROLL8 and TROLL12. For these fragemnts, the STD-NMR build-up data, the HSQC-NMR spectra and the representative poses from the mixed solvent MD simulations used for CORCEMA predictions are provided. For TROLL2 the anomalous map of the bromine atom of the crystal structure (PDB entry: 7PUX) is given.</p>
Dataset associated with the study titled "Systematic discovery of regulatory motifs associated with human insulator sites" It includes data used for predicting insulator-associated DNA-binding proteins.
<p><strong>This dataset was used in the study on the prediction of insulator-associated DNA-binding proteins.</strong></p> <p>The three files included here are intended for use with the code available in the following GitHub repository:<br><a href="https://github.com/reposit2/insulator" target="_new" rel="noopener">https://github.com/reposit2/insulator</a></p> <p>To use the data, extract all three files and place them in the same directory as the code files.</p>
Assessment of the Humoral Immune Response to the SARS-CoV-2 Spike Protein Receptor Binding Motif
<p><strong>Figure S1.</strong> Purification of human antibodies against the RBM region of the SARS-CoV-2 spike protein using a recombinant RBM Sepharose 4B affinity column (3 x 1 cm, inner diameter) (A) and SDS-PAGE (10%) analysis of the eluate (1) alongside a standard low molecular weight marker (Sigma Chemical Co, Saint Louis, Mo, U.S.A.) stained with Coomassie Blue. <strong>Table S1</strong>: Microscale thermophoresis (MST) traces of anti-RBM antibodies binding to different concentrations of S1WT (red) and S2WT (green) peptides by MST. Relative fluorescence (RF) between the bound and unbound state was determined over a time of 21s with 20s MST-on time for evaluation. The blue bar indicates the ΔRF before the temperature gradient was applied, whereas the red bar shows the ΔRF during the thermophoresis. For interaction experi ments, the amount of NT.647-labeled antibodies was kept constant, while the concentration of unlabeled peptides varied from 0.5 µg/mL–0.12 ng/mL. The assay was performed in PBS containing 0.05% Tween 20 and after a short incubation period, the samples were analyzed in standard glass MST NT.115 capillaries. <strong>Table S2:</strong> One-dose regime AstraZeneca-Oxford vaccinated serum information. <strong>Table S3</strong>: Heterologous booster dose vaccinated serum information.</p>
Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT
<p>Underlying data of the<em> in silico</em> work performed in this study. </p> <p>1. i-Tasser predictions for HTTExon1Q<sub>48 </sub></p> <p>2. HDOCK results of DNAJB1-HTTExon1Q<sub>48 </sub>docking</p> <p>3. TIGER2h structures and trajectories. The original data and filtered trajectories for the individual clusters</p> <p>4. MD Simulation structures and trajectories for DNAJB1 protein variants alone and as complexes with HTTExon1Q<sub>48.</sub></p>
The PDZ-binding motif of SARS-CoV envelope protein is a determinant of viral pathogenesis
GEO Series GSE52920. Mus musculus. 9 samples. Type: Expression profiling by array.
PCBP1 binding to single-stranded poly-cytosine motifs enhances cGAS sensing and impairs breast cancer development
GEO Series GSE307616. Mus musculus. 11 samples. Type: Expression profiling by high throughput sequencing.
Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes
GEO Series GSE48857. Arabidopsis thaliana. 9 samples. Type: Expression profiling by array.
PCBP1 binding to single-stranded poly-cytosine motifs enhances cGAS sensing and impairs breast cancer development [snRNA-Seq]
GEO Series GSE307750. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Transcription Factor Binding Sites by Motifs Scan
GEO Series GSE53962. Homo sapiens. 0 samples. Type: Third-party reanalysis; Genome binding/occupancy profiling by high throughput sequencing.
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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.