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208 results for “unfolding”
Data from: FEATHER: automated analysis of force spectroscopy unbinding and unfolding data via a Bayesian algorithm
Single-molecule force spectroscopy (SMFS) provides a powerful tool to explore the dynamics and energetics of individual proteins, protein-ligand interactions, and nucleic acid structures. In the canonical assay, a force probe is retracted at constant velocity to induce a mechanical unfolding/unbinding event. Next, two energy landscape parameters, the zero-force dissociation rate constant (ko) and the distance to the transition state (Δx‡), are deduced by analyzing the most probable rupture force as a function of the loading rate, the rate of change in force. Analyzing the shape of the rupture force distribution reveals additional biophysical information, such as the height of the energy barrier (ΔG‡). Accurately quantifying such distributions requires high-precision characterization of the unfolding events and significantly larger data sets. Yet, identifying events in SMFS data is often done in a manual or semiautomated manner and is obscured by the presence of noise. Here, we introduce, to our knowledge, a new algorithm, FEATHER (force extension analysis using a testable hypothesis for event recognition), to automatically identify the locations of unfolding/unbinding events in SMFS records and thereby deduce the corresponding rupture force and loading rate. FEATHER requires no knowledge of the system under study, does not bias data interpretation toward the dominant behavior of the data, and has two easy-to-interpret, user-defined parameters. Moreover, it is a linear algorithm, so it scales well for large data sets. When analyzing a data set from a polyprotein containing both mechanically labile and robust domains, FEATHER featured a 30-fold improvement in event location precision, an eightfold improvement in a measure of the accuracy of the loading rate and rupture force distributions, and a threefold reduction of false positives in comparison to two representative reference algorithms. We anticipate FEATHER being leveraged in more complex analysis schemes, such as the segmentation of complex force-extension curves for fitting to worm-like chain models and extended in future work to data sets containing both unfolding and refolding transitions.
IMAGE SSP2 RCP 26 unfold datapackage
<p>Unfold datapackage for ScenarioLink</p>
Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation
<p>These are the files needed to carry out the temperature induced infolding of crambin using Gromacs.</p>
Unraveling the Unfolding Mechanism of Pseudoazurin: Insights into Stabilizing Cupredoxin Fold as a Common Domain of Cu-Containing Proteins
<p>This dataset includes molecular dynamics (MD) simulation trajectories and experimental data used in the title named study. The MD trajectories cover simulations of pseudoazurin under various conditions: apo (pH 2, pH 3, pH 7), holo (pH 2, pH 3, pH 7), and explicit water simulations of holo at pH 7. Additionally, the dataset contains raw experimental data, including small-angle neutron scattering (SANS) curves, visible (Vis) absorption spectra, and circular dichroism (CD) spectra. This comprehensive dataset supports the investigation of unfolding mechanism of Pseudoazurin.</p>
Data from: Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins
Protein folding occurs as a set of transitions between structural states within an energy landscape. An oversimplified view of the folding process emerges when transiently populated states are undetected because of limited instrumental resolution. Using force spectroscopy optimized for 1-microsecond resolution, we reexamined the unfolding of individual bacteriorhodopsin molecules in native lipid bilayers. The experimental data reveal the unfolding pathway in unprecedented detail. Numerous newly detected intermediates—many separated by as few as two or three amino acids—exhibited complex dynamics, including frequent refolding and state occupancies of <10 μs. Equilibrium measurements between such states enabled the folding free-energy landscape to be deduced. These results sharpen the picture of the mechanical unfolding of membrane proteins and, more broadly, enable experimental access to previously obscured protein dynamics.
Scrolls unfold skeleton animation
Scrolls unfold skeleton animation Source: Objaverse 1.0 / Sketchfab
MD simulations associated to the paper "A PDZ tandem repeat folds and unfolds via different pathways"
<p>These are the MD simulation data generated for this study. The files are:</p> <p>x11_plain_simulation: training data, charmm22*+tip3p simulation of X11 PD1-PDZ2</p> <p>x11_random_coil: reference random coil data for X11 PDZ1-PDZ2</p> <p>x11_e0.21_0.335_folding_t310: 200 folding simulations</p> <p>x11_e0.21_0.335_melting_t380: 200 unfolding simulations</p> <p>x11d2_e0.21_0.33_folding_t310: 200 folding simulations for the isolated PDZ2</p> <p>x11_e0.21_0.33_folding_t310_d2open: 200 folding simulations for X11 PDZ1-PDZ2 starting with PDZ1 folded and the C-ter tail bound</p>
IMAGE SSP2-RCP19 unfold datapackage
<p>Datapackage for unfold.</p>
IMAGE SSP2-Base unfold datapackage
<p>Datapackage for unfold.</p>
IMAGE SSP1-Base unfold datapackage
<p>Datapackage for unfold.</p>
Artifact for 'Unfolding State Variables Improves Model Checking'
<p>This is a reproduction package for the experiments that were performed as part of the work 'Unfolding State Variables Improves Model Checking'.</p>
PYTHIA Jet Datasets for cDDPM Unfolder
<p>Datasets of QCD jets used for studying unfolding in "Towards Universal Unfolding using Denoising Diffusion Probabilistic Models" consist of two different detector simulation frameworks:</p> <h3>Data-driven detector smearing:</h3> <ul> <li>Events were generated using PYTHIA 8.3 for proton-proton collisions at √s = 14 TeV</li> <li>Several physics processes were simulated: <ul> <li>ttbar production with various PDFs (CT14lo, NNPDF23, CTEQ6L1)</li> <li>Z+jets (Z → μμ) with CT14lo, NNPDF23, CTEQ6L1</li> <li>W+jets (W → μν) with CT14lo, NNPDF23, CTEQ6L1</li> <li>Dijet production</li> <li>Leptoquark production</li> </ul> </li> <li>Jets with radius parameter R = 0.4 were reconstructed using the anti-kT algorithm at particle-level ("gen_jets"), and then detector effects were applied ("reco_jets")</li> <li>Detector effects were simulated using ATLAS 8 TeV calibration data-derived jet resolution functions for pT, η, and φ</li> <li>Phase space bias was applied to some samples to enhance high-pT statistics: (pT_hat/pT_ref)^a with pT_ref = 100 GeV and a = 5</li> </ul> <h3> </h3> <h3>DELPHES CMS detector simulation:</h3> <ul> <li>Events were generated using PYTHIA 8.3 for proton-proton collisions at √s = 14 TeV</li> <li>Physics processes included: <ul> <li>ttbar production with CTEQ6L1</li> <li>Z+jets (Z → μμ) with CTEQ6L1</li> <li>W+jets (W → μν) with CTEQ6L1</li> <li>Dijet production with CTEQ6L1</li> <li>Leptoquark production with CTEQ6L1</li> </ul> </li> <li>Events were passed through DELPHES 3.4.2 fast detector simulation using the CMS detector configuration</li> <li>Jets with radius parameter R = 0.4 were reconstructed using the anti-kT algorithm at both particle level ("gen_jets") and detector level ("reco_jets")</li> <li>Phase space bias was applied to some samples using (pT_hat/pT_ref)^a with pT_ref = 100 GeV and a = 5</li> </ul> <p> </p> <p>For both frameworks, each dataset consists of several arrays containing jet kinematic information (pT, η, φ, E, px, py, pz) at both truth ("gen_jets") and detector ("reco_jets") level. Additional features such as event identifiers ("event_num") are included to enable reconstruction of event-level observables.</p>
Research data supporting: K. Tashiro, K. Katayama, K. Tamaki, L. Pesce, N. Shimizu, H. Takagi, R. Haruki, R. Heenan, M. J. Hollamby, G. M. Pavan, S. Yagai, "Non-uniform Photoinduced Unfolding of Supramolecular Polymers Leading to Topological Block Nanofibers"
<p>Raw research data supporting the article K. Tashiro, K. Katayama, K. Tamaki, L. Pesce, N. Shimizu, H. Takagi, R. Haruki, R. Heenan, M. J. Hollamby, G. M. Pavan, S. Yagai, "Non-uniform Photoinduced Unfolding of Supramolecular Polymers Leading to Topological Block Nanofibers".</p>
Folding and unfolding of the tryptophan zipper in the presence of two thioamide substitutions
<p>We studied the stability and folding and unfolding kinetics of the tryptophan zipper, containing dierent double thioamide subsitutions. Conformation change was triggered by photoisomerization of an integrated AMPP photoswitch in the turn region of the hairpin, and transient spectra were recorded in the deep UV and the mid-IR, covering the time window of the (un)folding transition from picoseconds to tens of microseconds. Thio-substitution of inward-pointing backbone carbonyls was found to strongly destabilize the β-hairpin structures, whereas molecules with two outward pointing thio-carbonyls showed similar or enhanced stability with respect to the unsubstituted sequence, which we attribute to stronger interstrand hydrogen bonding. Thiolation of the two Trp residues closest to the turn can even prevent the opening of the hairpin after cis-trans isomerization of the switch. The circular dichroism due to the two thioamide ππ∗ transitions is spectrally well-separated from the aromatic tryptophan signal. It changes upon photo-switching, reflecting a local change in coupling and geometry.</p>
Unfolding the Wisdom Within: CFT for Adolescents in Residential Care
ClinicalTrials.gov study NCT06219057. IPD Sharing: Not stated. Countries: 1. Publications: 17.
The Seven Trial: Exploiting the Unfolded Protein Response
ClinicalTrials.gov study NCT06076837. IPD Sharing: NO. Countries: 1. Publications: 2.
Semi-automatic Download of Prostate Biopsy Cores While Keeping the Orientation, Unfolding and Unity of the Sample
ClinicalTrials.gov study NCT01692405. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: FEATHER: automated analysis of force spectroscopy unbinding and unfolding data via a Bayesian algorithm
Open the record for dataset details and reuse information.
Data from: Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world
Open the record for dataset details and reuse information.
Folding and unfolding of the tryptophan zipper in the presence of two thioamide substitutions
Open the record for dataset details and reuse information.
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