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68 results for “conformational dynamics”
Example dataset for openPMD-conform molecular dynamics data (MD domain extension)
<p>This dataset results from the molecular dynamics (MD) simulation of the photon-sample interaction. The photons are propagated through the SASE1 beamline and the SPB-SFX instrument at European XFEL, with an initial energy of 5 keV. The sample is the two-nitrogenase iron protein (2nip) with 4348 atoms. The simulation is performed with a demo version of XMDYN. The datasets were rewritten from the original XMDYN output into an hdf5 format that complies with the openPMD metadata standard for particle and mesh data and the proposed domain extension of this standard for MD data. The dataset "pure_2nip_pmi_out.opmd.h5" conforms the openPMD metadata MD domain extension strictly, while the dataset "pure_2nip_pmi_out.opmd.ff.h5" stores form factor results additionally for SingFEL diffraction simulation.</p> <p>This dataset is part of the Deliverable D5.1 in Workpackage 5 (Virtual Neutron and X-ray Laboratory) of the Photon and Neutron Open Science Cloud (PaNOSC).</p> <p>This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 823852.<br> </p>
'Invisible' Molecular Dynamics Revealed for a Conformationally Chiral π-Stacked Perylene Bisimide Foldamer
<p>Additional data to report <a href="https://doi.org/10.1002/anie.202414069">https://doi.org/10.1002/anie.202414069</a>:</p> <p><a name="_Hlk172654864"></a>Whilst energetic and kinetic aspects of folding processes are meanwhile well understood for natural biomacromolecules, the folding dynamics in so far studied artificial foldamer counterparts remain largely unexplored. This is due to the low energy barriers between their conformational isomers that make the dynamic processes undetectable with conventional methods such as UV/vis absorption, fluorescence, and NMR spectroscopy, making such processes ‘invisible’. Here we present an asymmetric perylene bisimide dimer (bis-PBI <strong>1</strong>) that possesses conformational chirality in its folded state. Owing to the large interconversion barrier (≥ 116 kJ mol<sup>–1</sup>), four stereoisomers could be separated and isolated. Since the interconversion between these stereoisomers requires the foldamer to first open and then to re-fold, the transformation of one stereoisomer into others allowed us to ‘visualize’ the dynamics of folding with time and determine its lifetimes and the energetic barriers associated with the folding process. Supported by quantum chemical calculations, we identified the open structure to be only a fleeting metastable state of higher energy. Our experimental observation of the kinetics associated with the molecular dynamics in the PBI foldamer advances the fundamental understanding of folding in synthetic foldamers and paves the way for the design of smart functional materials.</p>
Molecular dynamics trajectories for "Reservoir-REMD facilitates kinetic rescue from metastable peptide conformations
<p>The molecular dynamics-generated ensemble dataset for cyclo-(cGHHQKLV), used in the manuscript "Reservoir-REMD facilitates kinetic rescue from metastable peptide conformations". The dataset consists of 14 + 6 =20 .dcd files, and one .pdb file for rendering.</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 80 wt% C12E5, T=298K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin
<p><a name="_Hlk145518059"></a><span>Human calcitonin (hCT) regulates calcium-phosphorus metabolism, but its amyloid aggregation disrupts physiological activity, increases thyroid carcinoma risk, and hampers its clinical use for bone-related diseases like osteoporosis and Paget’s disease. Improving hCT with targeted modifications to mitigate amyloid formation while maintaining function holds promise as a strategy. Understanding how each residue in hCT's amyloidogenic core affects its structure and aggregation dynamics is crucial for designing effective analogs. Mutants F16L-hCT and F19L-hCT, where Phe residues in the core are replaced with Leu as in non-amyloidogenic salmon calcitonin, showed different aggregation kinetics. However, the molecular effects of these substitutions in hCT are still unclear. Here, </span><a name="OLE_LINK4"></a><span><span>we systematically investigated the folding and self-assembly conformational dynamics of hCT, F16L-hCT, and F19L-hCT through multiple long-timescale independent atomistic discrete molecular dynamics (DMD) simulations. </span></span><span><span>Our results indicated that the hCT monomer primarily assumed unstructured conformations with dynamic helices around residues 4-12 and 14-21. During self-assembly, the amyloidogenic core of hCT<sub>14-21</sub> converted from dynamic helices to β-sheets. However, substituting F16L did not induce significant conformational changes, as F16L-hCT exhibited similar characteristics to wild-type hCT in both monomeric and oligomeric states. In contrast, F19L-hCT exhibited substantially more helices and fewer β-sheets than hCT, irrespective of their monomers or oligomers. The substitution of F19L significantly enhanced the stability of the helical conformation for hCT<sub>14-21</sub>, thereby suppressing the helix-to-β-sheet conformational conversion. Overall, our findings elucidate the molecular mechanisms underlying hCT aggregation and the effects of F16L and F19L substitutions on the conformational dynamics of hCT, highlighting the critical role of F19 as an important target in the design of amyloid-resistant hCT analogs for future clinical applications.</span></span></p>
Phosphorylation regulated conformational diversity and topological dynamics of an intrinsically disordered nuclear receptor
<p>Molecular dynamics simulations of AF1c region of human glucocorticoid receptor and its phosphovariants as described in the below paper: </p> <p>Phosphorylation regulated conformational diversity and topological dynamics of an intrinsically disordered nuclear receptor</p> <p>Vasily Akulov, Alba Jiménez Panizo, Eva Estébanez-Perpiñá, John van Noort, Alireza Mashaghi</p> <p> </p> <p>The data related to this project has been deposited in two repositories. This repository contains the second part of the data; the first part can be found at DOI: 10.5281/zenodo.13820169</p>
AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes
<p>Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2 that combines<span> randomized</span> <span><span> </span>alanine<span> </span>sequence masking<span> </span>with shallow multiple sequence alignment<span> </span>subsampling to expand the conformational diversity of the predicted structural<span> </span>ensembles and<span> </span>capture conformational changes between apo and holo protein forms. Using several well-established datasets of<span> </span>structurally diverse apo-holo protein pairs, the proposed approach </span><span>enables<span> </span>robust predictions of apo and holo structures and conformational ensembles, while also displaying notably similar dynamics distributions. These observations are consistent with<span> </span>the view </span><span> </span>that the intrinsic dynamics of allosteric proteins is defined by the structural topology of the fold and favors conserved conformational motions driven by soft modes among orthologs. We also found<span> </span>a significant <span>correlation </span>between conformational flexibility and <span> </span>AlphaFold2 metric of statistical significance pLDDT for the apo-holo pairs in which ligand binding induced local moderate conformational changes. For apo-holo pairs exhibiting larger structural changes, this relationship<span> </span>becomes nonlinear, reflecting inability of AlphaFold2 confidence metrics to identify high energy functional conformations. Our findings support the notion that AlphaFold2 approaches can yield reasonable accuracy in predicting minor conformational adjustments between apo and holo states, especially for proteins with <span> </span>moderate localized changes upon ligand binding. However, for large, hinge-like domain movements, AF2 tends to predict the most stable domain orientation which is typically the apo form rather than the full range of functional conformations characteristic of the holo ensemble. These results indicate that modeling of multiple functional states of proteins may require more accurate detection of flexible region conformations and cannot solely rely on the pLDDT metric as the major determinant of the prediction accuracy in reproducing functional conformational ensembles.<span> </span></p>
The GET insertase exhibits conformational plasticity and induces membrane thinning - The Molecular Dynamics Dataset
<p>The molecular dynamics simulation systems.</p> <p>List of files: </p> <ol> <li><strong>SimulationSystems.pdf</strong>: List of all simulation systems reported and their compositions</li> <li><strong>ProteinComplex.pdb</strong>: The initial model for the hsGet2ΔN-Get1/Get3 complex used in simulations was constructed based on the cryo-EM structure (PDB accession 6SO5). Missing residues (except the terminal ones) were modeled using Modeller.</li> <li><strong>prod.mdp</strong>: The GROMACS molecular dynamics parameters (mdp) file used for all simulations</li> <li><strong>toppar.zip</strong>: The Charmm36(m) force field parameter and topology set used for all simulations generated by CHARMM-GUI.</li> <li>Compressed (zip) files containing simulations inputs and trajectories</li> </ol> <p><strong>1-PC.zip<br> 2-1:4_PI:PC.zip<br> 3-1:4_PE:PC.zip<br> 4-1:4_PS:PC.zip<br> 5-1:4_CL:PC.zip<br> 6-1:4_chol:PC.zip<br> 7-1:1:1:1_PC:PI:PS:PE.zip<br> 8-1:1:1:1:1:1_PC:PDPC:PS:PI:PE:chol.zip</strong></p> <p>Each zip file contains the following files:</p> <ol> <li><strong>System_0ns.pdb</strong>: The initial configuration used for the simulations generated using CHARMM-GUI and equilibrated following the CHARMM-GUI equilibration protocol</li> <li><strong>index.ndx</strong>: GROMACS index file</li> <li><strong>topol.top</strong>: GROMACS topology file</li> <li><strong>prod0.tpr, prod1.tpr, prod2.tpr</strong>: GROMACS run topology files (tpr) for each repeat</li> <li><strong>prod0.gro, prod1.gro, prod2.gro</strong>: The final configuration after 3 μs production runs for each repeat</li> <li><strong>noW_0ns.pdb</strong>: The initial configuration without the water molecules.</li> <li><strong>noW_0.xtc, noW_1.xtc, noW_2.xtc</strong>: The 3 μs processed production trajectories. The water molecules were removed, and the trajectories were subsampled at 1 ns intervals.</li> </ol> <p> </p> <p> </p>
Data from: Conformational dynamics in TRPV1 channels reported by an encoded coumarin amino acid
TRPV1 channels support the detection of noxious and nociceptive input. Currently available functional and structural data suggest that TRPV1 channels have two gates within their permeation pathway: one formed by a ′bundle-crossing′ at the intracellular entrance and a second constriction at the selectivity filter. To describe conformational changes associated with channel gating, the fluorescent non-canonical amino acid coumarin-tyrosine was genetically encoded at Y671, a residue proximal to the selectivity filter. Total internal reflection fluorescence microscopy was performed to image the conformational dynamics of the channels in live cells. Photon counts and optical fluctuations from coumarin encoded within TRPV1 tetramers correlates with channel activation by capsaicin, providing an optical marker of conformational dynamics at the selectivity filter. In agreement with the fluorescence data, molecular dynamics simulations display alternating solvent exposure of Y671 in the closed and open states. Overall, the data point to a dynamic selectivity filter that may serve as a gate for permeation.
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 70 wt% C12E5, T=298K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 70 wt% C12E5, T=320K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 70 wt% C12E5, T=333K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 60 wt% C12E5, T=333K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 60 wt% C12E5, T=320K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 60 wt% C12E5, T=298K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Dataset (II) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
<p>MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</p> <p>dataset I: systems SRL+Co, C-100 and BAY-1797</p> <p>dataset I: each file contains all branched replicas and the main replica.</p> <p>dataset1: C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).</p> <p>dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches.</p> <p>dataset I: system SRL+Co ;each file contains one main replica</p> <p>dataset I: system BAY-1797; each file contains one main replica</p> <p>dataset II:system SRL ; each file contains one main replica.</p>
Dataset (I) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
<p>MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</p> <p>dataset I: systems SRL+Co, C-100 and BAY-1797</p> <p>dataset I: each file contains all branched replicas and the main replica.</p> <p>dataset1: C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).</p> <p>dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches.</p> <p>dataset I: system SRL+Co ;each file contains one main replica</p> <p>dataset I: system BAY-1797; each file contains one main replica</p> <p>dataset II:system SRL ; each file contains one main replica.</p>
Dataset (III) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
<p>MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</p> <p>dataset I: systems SRL+Co, C-100 and BAY-1797</p> <p>dataset I: each file contains all branched replicas and the main replica.</p> <p>dataset1: C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).</p> <p>dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches.</p> <p>dataset I: system SRL+Co ;each file contains one main replica</p> <p>dataset I: system BAY-1797; each file contains one main replica</p> <p>dataset II:system SRL ; each file contains one main replica.</p> <p>dataset III:system C-100+Co (compound 100 in presence of SRC-1 coactivator) ; each file contains one main replica.</p>
Extended conformational states dominate the Hsp90 chaperone dynamics
<p>aMD and cgMD simulation trajectories for publication "Extended conformational states dominate the Hsp90 chaperone dynamics"<br> Jussupow et al. doi: 10.1016/j.jbc.2022.102101</p>
Dataset for Conformational dynamics of loop L3 in OmpF: Implications towards antibiotic translocation and voltage gating
<p>Dataset supporting the work in the publication titled, "Conformational dynamics of loop L3 in OmpF: Implications towards antibiotic translocation and voltage gating".</p>
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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.