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418 results for “Dimerization”
Gamma-hemolysin components: computational strategies for LukF-Hlg2 dimer reconstruction on a model membrane
<p>Project files provided as supporting information to the manuscript “Gamma-Hemolysin Components: Computational Strategies for LukF-Hlg2 Dimer Reconstruction on a Model Membrane”. The data set contains the following folders:</p> <ul> <li>LukF_Hlg2_distance: files with the minimum distance between LukF and Hlg2 as a function of time for the simulated replica (Fig. S1); files with the minimum distance between each LukF residue and the Hlg2 monomer and vice versa, averaged over the last 600 ns of simulation in the replica where the spontaneous dimerization is observed (fig. S5).</li> <li>HADDOCK_dimer_crystal_pore_displacement: files with the displacement between Hlg2 residues in the HADDOCK model dimer and the same dimer in the crystal pore, after alignment on the LukF monomer (for both the HADDOCK model in presence and in absence of the LukF N-ter) (Fig. S13)</li> <li>interface_area: files with the interface area between the LukF and the Hlg2 monomers in the replica where the spontaneous dimerization on the membrane is observed, as a function of time (total interface and contribution of LukF and Hlg2 rim domains) (Fig. S4)</li> <li>angles: files with the histograms of the angle between LukF and the axis perpendicular to the membrane, for the simulation of the single LukF monomer and for that capturing the spontaneous dimerization on the membrane (Fig. 4); file with the angle between the LukF and the Hlg2 axis as a function of time in the replica where the spontaneous dimerization is observed (Fig. S6)</li> <li>HADDOCK_scores: files with the HADDOCK scores of the predicted LukF-Hlg2 dimers and their RMSD values computed with respect to the same dimer in the crystal pore. The data are reported for the four top-scored models of each cluster ( for both the HADDOCK models in the presence and in the absence of the LukF N-ter) (Fig. 5).</li> <li>RMSD: files with the RMSD as a function of time for the LukF and the Hlg2 monomers in the replica where the spontaneous dimerization on the membrane is observed (Fig. 2, Fig. S2, Fig. S3)</li> <li>RMSF: files with the RMSF of the LukF and the Hlg2 residues in the replica where the spontaneous dimerization on the membrane is observed and in the simulations of the single monomers (Fig. 2)</li> <li>interaction_persistences: files with H-bond (side chain + backbone and backbone only atoms) salt-bridge, and hydrophobic contact persistence matrices for the single LukF monomer simulated alone (299 x 299) and for the LukF-Hlg2 dimer (299+280 x 299+280) (Fig. 4, Fig. S7 + interactions reported in the manuscript)</li> <li>distance_protein_membrane: files with the minimum distance between each monomer and the membrane, in the last 200ns of the simulation of spontaneous dimerization on the membrane (Figure S9).</li> <li>distance_residues_interface: files with the distance between functionally relevant residues measured along the simulation of the HADDOCK dimer in the absence of LukF N-terminus (Figure S14).</li> </ul>
Data from: "Fragmentation and detachment of hot copper and silver dimer anions: a comparison"
<p>The files found here are text files with data related to the article: "Fragmentation and detachment of hot copper and silver dimer anions: a comparison" published in Phys Rev A (DOI: 10.1103/PhysRevA.107.062824). The files contain the information necessary to reproduce all figures containing data from the experiment or from the described calculations. Each file contains a header explaining the data sets which follow.</p>
Voltage-tunable optical parametric oscillator with an alternating dispersion dimer integrated on chip
<p>With this commit we present or theoretical and experimental data together with plotting codes for our manuscript entitled "Voltage-tunable optical parametric oscillator with an alternating dispersion dimer integrated on chip".</p> <p>Optical parametric oscillators enable the conversion of pump light to new frequency bands using nonlinear optical processes. Recent advances in integrated nonlinear photonics have led to the creation of compact, chip-scale sources via Kerr nonlinearity-induced parametric oscillations. While these sources have provided broadband wavelength tuning, the ability to tune the emission wavelength via dynamically altering the dispersion, has not been attained so far. Here we present a voltage-tunable, on-chip integrated optical parametric oscillator based on an alternating-dispersion dimer, allowing us to tune the emission over nearly 20 THz near 1550 nm. Unlike previous approaches, our device eliminates the need for a widely tunable pump laser source and provides efficient pump filtering at the drop port of the auxiliary ring. Integration of this scheme on a chip opens up the possibility of compact and low-cost voltage-tunable parametric oscillators with diverse application possibilities.</p>
Raw microscopy data from: Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers
Open the record for dataset details and reuse information.
Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH) (dimer only)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer. Simulation starts from the crystal pose (PDB: 5FII) and is motivated by this paper:</p> <p>Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Evolutionary variation in MADS-box dimerization affects floral development and protein abundance in maize
<p>Interactions between MADS-box transcription factors are critical in the regulation of floral development, and shifting MADS-box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation in protein-protein interactions affects MADS-box protein function remains unknown. To assess the impact of changing MADS-box protein-protein interactions on transcription factor function, we turned to the grasses, where interactions between B-class MADS-box proteins vary. We tested the functional consequences of this evolutionary variability using maize as an experimental system. We found that differential B-class dimerization was associated with subtle, quantitative differences in stamen shape. In contrast, differential dimerization resulted in large-scale changes to downstream gene expression. Differential dimerization also affected B-class complex composition and abundance, independent of transcript levels. This indicates that differential B-class dimerization affects protein degradation, revealing an important consequence for evolutionary variability in MADS-box interactions. Our results highlight complexity in the evolution of developmental gene networks - changing protein-protein interactions could affect not only the composition of transcription factor complexes, but also their degradation and persistence in developing flowers. Our results also show how coding change in a pleiotropic master regulator could have small, quantitative effects on development.</p>
Non-covalent Dimers and Trimers (NCDT) database
<p><strong>Non-Covalent Dimers and Trimers (NCDT) database</strong></p> <p>Database of equilibrium geometries of benchmark-quality, as well as accurate interaction energies at the specified geometries.</p> <p>NCDT.py is a Psi4 database module, executable with:</p> <pre><code class="language-python">db(method, "NCDT")</code></pre> <p>Optional arguments are subsets of the database:</p> <ul> <li>subset = "16": original NCDT16 from [1]</li> <li>subset = "17": first revised version including Xe-OCS, DMS-SO2, and excluding Ne-OCS</li> <li>subset = "HB": hydrogen-bonded complexes only</li> <li>subset = "DD": dispersion-dominated complexes only</li> <li>subset = "MX": mixed interaction complexes only</li> </ul> <p>Contents:</p> <ul> <li>Ne - C<sub>2</sub>H<sub>4</sub> <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>Ar - C<sub>2</sub>H<sub>4</sub> <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>Ne - OCS <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1], not suitable for geometry benchmarking [3]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> <li>experimental mass-dependent structure [3]</li> </ul> </li> <li>Ar - OCS <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>Kr - OCS <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>HCl - H<sub>2</sub>CO <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>HF - H<sub>2</sub>CO <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>HCN - H<sub>2</sub>CO <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>CS<sub>2</sub> - OCS <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>CH<sub>2</sub>ClF - HCCH <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>HCCH - HCCH <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>Ne - Ne - NNO <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>Ne - Ar - NNO <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>Ar - Ar - NNO <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>Ne - Ar - HCl <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>HF - HF - NH<sub>3</sub> <ul> <li>semi-experimental structure, based on B2PLYP-D3BJ anharmonic corrections [1]</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>DMS - SO<sub>2</sub> <ul> <li>semi-experimental structure, based on ChS corrections [2], xyz reconstructed from SI data</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pv[tq5]z</li> <li>MP2/cc-pv[q5]z</li> <li>CCSD(T)/cc-pv[tq]z</li> </ul> </li> </ul> </li> <li>Xe - OCS <ul> <li>experimental mass-dependent structure [3], note: O=C and hence Xe···O distance unreliable</li> <li>interaction energy from counterpoise-corrected recipe: <ul> <li>HF/cc-pwcv[tq5]z-pp</li> <li>MP2/cc-pwcv[q5]z-pp</li> <li>CCSD(T)/cc-pwcv[tq]z-pp</li> </ul> </li> </ul> </li> </ul> <p> </p> <p>References:</p> <p>[1] Kraus, Obenchain and Frank, <em>Benchmark-Quality Semiexperimental Structural Parameters of van der Waals Complexes</em>, J. Phys. Chem A 122 (2018) 1077, <a href="http://dx.doi.org/10.1021/acs.jpca.7b10797">DOI: 10.1021/acs.jpca.7b10797</a></p> <p>[2] Obenchain, Spada, Alessandrini, Rampino, Herbers, Tasinato, Mendolicchio, Kraus, Gauss, Puzzarini, Grabow, and Barone, <em>Unveiling the sulfur-sulfur bridge: Accurate structural and energetic characterization of a homochalcogen intermolecular bond</em>, Angew. Chem. Int. Ed. 57 (2018) 15822, <a href="http://dx.doi.org/10.1002/anie.201810637">DOI: 10.1002/anie.201810637</a></p> <p>[3] Kraus, Obenchain, Herbers, Wachsmuth, Frank, and Grabow, <em>Xe···OCS: Relatively straightforward?</em>, Phys. Chem. Chem. Phys. <em>accepted article</em> (2020), <a href="http://dx.doi.org/10.1039/D0CP00334D">DOI: 10.1039/D0CP00334D</a></p> <p> </p> <p>Changes since v2.0:</p> <ul> <li>added reference_lengths.xlsx file listing the current bond lengths for benchmarking</li> <li>added Ne - OCS r<sub>m</sub><sup>(2)</sup> structure and deprecated Ne - OCS r<sub>e</sub><sup>SE</sup> bond lengths.</li> </ul> <p>Changes since v1.0:</p> <ul> <li>added DMS - SO<sub>2</sub> and Xe - OCS</li> <li>added NCDT.py to facilitate interaction energy benchmarking in Psi4</li> </ul>
Dataset of confocal microscopy - Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants
<p>This contains additional data relative to version 1, corresponding to a new versio of the manuscript. </p> <p>This data set contains confocal images (3D stacks and 2D projections) from propidium iodide stained <em>Arabidopsis thaliana </em>dark grown hypocotyls of various wildtype and mutant plants reported in the study "Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants" (https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1). Data was acquired following method described in the publication.</p> <p> </p>
The steered discrete molecular dynamics simulation data of amyloids with EC1 and EC12 cadherin dimer
<p>The steered discrete molecular dynamics (sDMD) simulation parameters are provided.</p> <p>Binding frequency of amyloids with EC1 and EC1-2 cadherin dimer.</p> <p>Trajectories of sDMD simulations of EC1 cadherin dimer with Abeta species.</p>
Computational data for The odd-number cyclo[13]carbon and its dimer cyclo[26]carbon
<p>This dataset contains the computational data associated with "The odd-number cyclo[13]carbon and its dimer cyclo[26]carbon". </p>
Raw data to: Biochemical Analyses of Cystatin-C Dimers and Cathepsin-B reveals a Trypsin-Driven Feedback Mechanism in Acute Pancreatitis
<p>This repository contains the initial structures, full conformational ensembles sampled using the TIGER2hPE replica-exchange MD simulation technique, and clusters resulting from subsequent ccPCA analysis, to extract major complex structures between proteins. Also attached are the initial structures of mCTSB and mCST3 predicted by AlphaFold2.</p> <table> <tbody> <tr> <td> <p><strong>Simulation Nr.</strong></p> </td> <td> <p><strong>Components simulated<br></strong></p> </td> </tr> <tr> <td> <p><strong>1</strong></p> </td> <td> <p>CTSB</p> </td> </tr> <tr> <td> <p><strong>2</strong></p> </td> <td> <p>CTSB</p> </td> </tr> <tr> <td> <p><strong>3</strong></p> </td> <td> <p>CTSB + mCST3</p> </td> </tr> <tr> <td> <p><strong>4</strong></p> </td> <td> <p>CTSL + mCST3</p> </td> </tr> <tr> <td> <p><strong>5</strong></p> </td> <td> <p>CTSB + mCST3-R71</p> </td> </tr> <tr> <td> <p><strong>6</strong></p> </td> <td> <p>CTSB + mCST3-R45</p> </td> </tr> <tr> <td> <p><strong>7</strong></p> </td> <td> <p>CTSB + dCST3-R45</p> </td> </tr> <tr> <td> <p><strong>8</strong></p> </td> <td> <p>CTSB + dCST3-R28</p> </td> </tr> </tbody> </table>
Time-resolved smPIFE data - alpha-Synuclein dimer
<p>Photon-HDF5 files of time-resolved smPIFE measurements: four different sCy3-labeled aslpha-Synuclein positions, in the presence of varying concentrations of wt-alpha-Synuclein, including Jupyter notebooks summarizing the analysis pipeline of these results.</p>
Processed and additional data for our publication titled "Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers"
<p>This is an updated version of our original data archive (which can be found under the doi 10.5281/zenodo.5513025) that reflects changes we've made to the manuscript over the course of the review process and incorporates the new data we've collected since the time of the initial bioRxiv submission.</p> <p>This data archive contains all raw data EXCEPT for single-particle microscopy movies (which are deposited separately due to their size) for our paper titled "Endoplasmic reticulum stress activates human IRE1a through reversible assembly of inactive dimers into small oligomers". These raw data are stored in "non_SPT_data_final_v2.zip". Additionally, full plasmid sequences for all plasmids used in this paper are stored in GenBank format in the file "plasmid_sequences_v2.zip". Finally, this repository contains processed single-particle movies in the form of dual-color tracks from the TrackMate ImageJ plugin in XML format (file: "SPT_processed_data_and_settings_final_v2.zip").</p> <p>The processed XML tracks are organized in the same way as the raw data files in the separate repository. They are sorted into subfolders by date of acquisition first, followed by experimental conditions. To recreate the figures from the paper, follow instructions in the README.md file included with the source code repository and use the JSON settings files saved here under "analysis_settings".</p>
Key features of inhibitor binding to the human mitochondrial pyruvate carrier hetero-dimer
<p><span><span><span><span><strong><em>Objective</em></strong>: The mitochondrial pyruvate carrier (MPC) has emerged as a promising drug target for metabolic disorders, including non-alcoholic steatohepatitis and diabetes, metabolically dependent cancers and neurodegenerative diseases. A range of structurally diverse small molecule inhibitors have been proposed but the nature of their interaction with MPC is not understood. Moreover, the composition of the functional human MPC is still debated. The goal of this study was to characterize the human MPC protein <em>in vitro</em>, to understand the chemical features that determine binding of structurally diverse inhibitors and to develop novel higher affinity ones.</span></span></span></span></p> <p><span><span><span><span><strong><em>Results</em></strong>: We have determined that the functional unit of human MPC is a hetero-dimer. We have compared all different classes of MPC inhibitors to find that three closely arranged hydrogen bond acceptors followed by an aromatic ring are shared characteristics of all inhibitors and represent the minimal requirement for high potency. We also demonstrate that high affinity binding is not attributed to covalent bond formation with MPC cysteines, as previously proposed. Following the basic pharmacophore properties, we identify 14 new inhibitors of MPC, one outperforming compound UK5099 by tenfold. Two of them are the commonly prescribed drugs entacapone and nitrofurantoin, suggesting an off-target mechanism associated with their adverse effects. </span></span></span></span></p> <p><span><span><span><span><strong><em>Conclusion</em></strong>: This work defines the composition of human MPC and the essential MPC inhibitor characteristics. In combination with the functional assays we describe, this new understanding will accelerate the development of clinically relevant MPC modulators.</span></span></span></span></p>
Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 2)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the second out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p>
Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the third out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p>
Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 1)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the first out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p>
Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments
<p>This dataset contains molecular dynamics (MD) trajectories used for preparation of the following manuscript: <br> "Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments". </p>
Water Solvent Reorganization upon Ultrafast Resonant Stimulated X‑ray Raman Excitation of a Metalloporphyrin Dimer
<p><strong>Abstract</strong></p> <p>We propose an X-ray Raman pump - X-ray diffraction probe scheme to follow solvation dynamics upon charge migration in a solute molecule. The X-ray Raman pump selectively prepares a valence electronic wavepacket in the solute, while the probe provides information on the entire molecular ensemble. A combination of Molecular Dynamics (MD) and <em>ab initio</em> quantum chemistry simulations is applied to a Zn-Ni porphyrin dimer in water. Using time-resolved X-ray diffraction and pair distribution functions, solvation shell dynamics are extracted.</p> <p><strong>Datasets for the plots</strong></p> <p>data_rdf: Contains RDF data in netcdf4 (readable by xarray) and averaged CSV files.</p> <p>data_sfac: Contains scattering data in netcdf4 (readable by xarray) and averaged CSV files.</p> <p>data_ener: Contains CP2K energy file data for all reference and production runs.</p> <p>data_cdf: Contains csv data files for cumulative distribution function.</p> <p>data_sdf: Contains the cubes files for spatial distribution function.</p> <p>python_codes: Contains python code snippets for recreating figures from the above datasets.</p>
Simulations of PKA RIα Homodimer Reveal cAMP-coupled Conformational Dynamics of Each Protomer and the Dimer Interface with Functional Implications
<p>Protein kinase A (PKA) is a ubiquitous cAMP-dependent enzyme in mammalian tissues. The inactive PKA holoenzyme disassociates into a homodimer of regulatory (R) subunits and two active catalytic (C) subunits upon cAMP binding to two tandem domains (termed <span>CBD-A</span> <span>and</span> <span>CBD</span>-<span>B</span>) in R subunits. The release of cAMP facilitates reassociation of R and C subunits<span>,</span> resetting PKA to its basal state. The cAMP-mediated structural changes in the activation-termination cycle <span>remain</span> <span>partially</span> <span>understood</span>. The multimeric states of PKA complicate the issue and are particularly <span>less</span> <span>studied</span>. Therefore, we computationally investigate the conformational dynamics of PKA <span>RI</span>a homodimer in different cAMP-bound states. The absence of cAMP in two CBDs affect differently the <span>conformational</span> <span>dynamics</span> of protomers. Moreover, <span>such</span> disparate <span>responses</span> are extended to the dimer interface <span>constituted</span> <span>by</span> <span>the</span> <span>N</span>-<span>terminal</span> <span>helical</span> <span>sub-domains</span> termed N3A motifs. T<span>he removal of cAMP from CBD-A induces large-scale structure</span> changes <span>of individual </span>R subunits <span>towards the holoenzyme state,</span> consist with previous simulations of a single R subunit. <span>Meanwhile</span> <span>it</span> <span>keeps the structural heterogeneity of the </span>N3A-N3A' <span>dimer interface observed in the fully bound state.</span> By contrast, the removal of cAMP from CBD-B does not affect <span>individual </span>R subunits but alters the conformational space of the N3A-N3A' dimer interface. The cAMP-coupled s<span>tructural</span> <span>changes</span> <span>of</span> <span>each</span> <span>protomer</span> <span>and</span> conserved conformational space of <span>the</span> N3A-N3A' <span>dimer</span> <span>interface</span> are essential for t<span>he</span> <span>transition</span> <span>between</span> the fully cAMP-bound R<sub>2</sub> homodimer and the R<sub>2</sub>C<sub>2</sub> holoenzyme as suggested by their crystal structures. Our work provides structural insights into <span>the</span> regulatory mechanism of cAMP in PKA signaling. </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.