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13 results for “allostery”
Raw MS data for "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor"
<p>These are the raw HDX/MS data for our paper: "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor."</p>
Data for manuscript: The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops is Determined by Ligand Binding and Interprotomer Allostery
<div>The data is provided as a part of the manuscript "<strong>The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops is Determined by Ligand Binding and Interprotomer Allostery</strong>". This repository includes an archive with folders:</div> <div> </div> <div><strong>md_data </strong></div> <div> <ul> <li>a directory with MD data for all simulation systems considered in the manuscript. Initial and final conformations are provided.</li> </ul> </div> <div> </div> <div><strong>fig_data</strong></div> <div> <ul> <li>a directory with the data underlying all the main text in the manuscript. </li> </ul> </div> <div> </div> <div>Videos S1-S3 are also included.</div>
Supporting Data for "Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics"
<p>Molecular dynamics topologies (.prmtop), initial coordinates (.inpcrd), and trajectories (.nc) associated with the preprint: https://doi.org/10.1101/2023.07.23.550226. Tarballs are included for each of the six systems, named by the PDB ID for the starting structure and state (ligand/apo). The four replicates of 155ns are included in each tarball in AMBER's netcdf format (.nc). All trajectories have been stripped of solvent and ions and are autoimaged. Input files and an example script for running simulations in AMBER20 are provided (infiles.tar.gz) as well as the topologies and coordinates for the solvated systems (solvated_topologies.tar.gz).</p>
Allostery through DNA drives phenotype switching
<p>Allostery is a pervasive principle to regulate protein function. Here, we show that DNA also transmits allosteric signals over long distances to boost the binding cooperativity of transcription factors. Phenotype switching in <em>Bacillus subtilis</em> requires an all-or-none promoter binding of multiple ComK proteins. Using single-molecule FRET, we find that ComK-binding at one promoter site increases affinity at a distant site. Cryo-EM structures of the complex between ComK and its promoter demonstrate that this coupling is due to mechanical forces that alter DNA curvature. Modifications of the spacer between sites tune cooperativity and show how to control allostery, which paves new ways to design the dynamic properties of genetic circuits.</p>
Data from: Protein Conformational Space at the Edge of Allostery: Turning a Non-allosteric Malate Dehydrogenase into an "Allosterized" Enzyme using Evolution Guided Punctual Mutations
<p>This data accompanies the paper entitled <em>Protein Conformational Space at the Edge of Allostery: Turning a Non-allosteric Malate Dehydrogenase into an “Allosterized” Enzyme using Evolution Guided Punctual Mutations</em></p> <p>The zip archive contains the results of molecular dynamics simulations of the 4 systems investigated in the paper: wt of A. ful MalDH and three mutants. Each system has been simulated at two temperatures, 300 K and 340 K. Starting configurations of the proteins after equilibration are provided for all the systems in GRO Gromos87 format. Trajectories with the positions of the proteins every 100 ps are provided for all the systems in XTC gromacs format.</p>
Data from "Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family."
<p>This data accompanies the paper entitled Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family.</p> <p>The zip archive contains: </p> <p>1- Starting configurations of the proteins after equilibration in PDB format and trajectories of unrestrained molecular dynamics simulations with the positions of the proteins every 100 ps in XTC gromacs format are provided for all systems. </p> <p>2- The free energy profiles and histograms are provided for all umbrella sampling simulations and the scripts used to run it with gromacs.</p>
Data from " Allostery can convert binding free energies into concerted domain motions in enzymes"
<p>Data from " Allostery can convert binding free energies into concerted domain motions in enzymes"</p> <p> </p> <p>Electrophysiology data corresponding to the main text figures and supporting information figures. One representative set was chosen for each triplicate and included in this data set. For details are found in the ‘read me explanation.txt’</p> <p>PDB used for this paper can be found at; 4ake [http://doi.org/10.2210/pdb4AKE/pdb] and 1ake [http://doi.org/10.2210/pdb1AKE/pdb]</p> <p>Full uncropped scans of any cropped gel/blot images are provided.</p> <p>The zip folder contains the MATLAB code package HMM inference, specifically tailored to nanopore ionic current flow data, as analyzed in the publication and can also be found at: https://github.com/yulanvanoppen/nanopore-HMM</p> <pre><br> </pre>
Defining neutralization and allostery by antibodies against COVID-19 variants
<p>The changing landscape of mutations in the SARS-CoV-2 Spike protein is linked to the emergence of variants, immune-escape and reduced efficacy of the existing repertoire of anti-viral antibodies. A major factor that contributes to the functional activity of neutralizing antibodies are the intrinsic quaternary changes that occur as a result of antibody-Spike trimer interactions. In this study, we reveal the conformational dynamics and allosteric perturbations linked to binding of human monoclonal antibodies and the viral Spike protein. We identify epitope hotspots of known and novel antibodies, and associated changes in Spike dynamics that distinguish weak, moderate and strong neutralizing antibodies. We show the impact of mutations in Wuhan-Hu-1, Delta, and Omicron variants of concern (VoCs) on differences in the antibody-induced conformational changes in Spike and illustrate how these render certain antibodies ineffective. Our comparative analyses of the antibody-footprints on Spike variants reveal how antibodies with similar binding affinities may induce destabilizing or stabilizing allosteric effects. These differences have important implications for neutralization efficacy and for developing new antibodies targeting emerging variants. Our results provide mechanistic insights into the functional modes and synergistic behavior of human antibodies against COVID-19, and provide a foundation for the design of effective antiviral strategies.</p>
Files and code to replicate the analyses and figures in the manuscript "Genetics, energetics, and allostery in proteins with randomized cores and surfaces"
<p>Welcome to the Zenodo repository for the following publication: Genetics, energetics, and allostery in proteins with randomized cores and surfaces by Escobedo, Voigt, Faure and Lehner, Science 2025.</p> <p>This repository contains all files and code to replicate the analyses and figures associated with the publication. Code is also available at <a href="https://github.com/lehner-lab/combinatorialcores" target="_new" rel="noopener">GitHub</a>. Raw NGS fastq files are available at Gene Expression Omnibus [GEO: GSE266299] (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE266299" rel="nofollow">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE266299</a>)</p>
Receptor Allostery Promotes Sonic Hedgehog Signaling During Embryonic Development
GEO Series GSE283994. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
A Study of Allostery Within Liganded RARα:RXR Heterodimers at the Genome Scale [RNA-seq]
GEO Series GSE290329. Mus musculus. 15 samples. Type: Expression profiling by high throughput sequencing.
Genetics, energetics, and allostery in proteins with randomized cores and surfaces
GEO Series GSE266299. Saccharomyces cerevisiae. 22 samples. Type: Other.
A Study of Allostery Within Liganded RARα:RXR Heterodimers at the Genome Scale [CUT&Run]
GEO Series GSE290328. Mus musculus. 14 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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