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Dataset results
715 results for “folding”
Folded wave guide TWT for 92 – 95 GHz band outdoor wireless frontend
<p>Underlying data from the conference paper: C. Paoloni, F. André, V. Krozer, R. Zimmermann, Q.T. Le, R. Letizia, S. Kohler, A. Sabaawi, G. Ulisse, “Folded wave guide TWT for 92 – 95 GHz band outdoor wireless frontend”, Workshop on Microwave Technology and Techniques (MTT), ESA/ESTEC, The Netherlands, April 2017.</p>
Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong></p> <p> </p> <p><strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Akira Kitamura<sup>2,*</sup>, Johan Tornmalm<sup>1,*</sup>, Baris Demirbay<sup>1</sup>, Joachim Piguet<sup>1</sup>, Masataka Kinjo<sup>2</sup>, Jerker Widengren<sup>1+</sup></p> <p> </p> <p><sup>1</sup> Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden</p> <p><sup>2</sup> Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan</p> <p><sup>* </sup>Contributed equally</p> <p><sup>+</sup> To whom correspondence should be addressed. Email: jwideng@kth.se. Tel: +46-8-7907813</p> <p> </p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.</p>
West Spitsbergen Fold and Thrust Belt: a digital educational data package for teaching structural geology
<p>The following digital educational data package is provided as part of the submission of the publication Horota et al. (2022) <em>West Spitsbergen Fold and Thrust Belt: a digital educational data package for teaching structural geology</em>, considered for publication in the Journal of Structural Geology. The dataset contains a QGIS, ArcGIS Pro and a Petrel projects with all the associated data.</p>
MS2Query results 20-fold cross validation
<p>The zip file contains the raw results of the 20-fold cross validation, the raw data downloaded from GNPS on 01-11-2022 and all the test data splits made. </p> <p>The raw results are stored in JSON format. The results of MS2Query and the benchmarking methods (cosine, modified cosine and MS2Deepscore) are stored. For each test spectrum three values are stored. The first value is the predicted score, the second value the tanimoto score between the correct annotation and the prediction and the last value is a boolean showing if the predicted spectrum was an exact 2D structure match. </p> <p>The figures in the MS2Query paper can be reproduced using the functions in https://github.com/iomega/ms2query/blob/main/ms2query/benchmarking/create_accuracy_vs_recall_plot.py </p>
To fold or not to fold: diastereomeric optimization of an α-helical antimicrobial peptide
<p>The upload contains additional primary data associated with the publication <a href="https://doi.org/10.1021/acs.jmedchem.3c00460">https://doi.org/10.1021/acs.jmedchem.3c00460</a>, including raw data in the original file format whenever possible.</p> <p>Data content: HPLC-MS for characterization and serum stability, HRMS, CD, Vesicle leakage, Cytotoxicity, Molecular Dynamics, Crystallography (primary electron density maps), pictures for microbiological and hemolysis assays and Supporting Information.</p>
Folding pathway of a discontinuous two-domain protein_1
<p>This data set contains all the raw data collected for the preparation of the manuscript "Folding pathway of a discontinuous two-domain protein".</p> <p>Raw data for the main figures Figure 1B-C, Figure 2A, C-D, Figure 4B-C, Figure 5B, C-D and for the supplementary figures Figure S1A-B, Figure S3C, E, G, Figure S5, Figure S7A-B, Figure S8A, D, Figure S9, and Figure S15A-C are deposited. Data is given figure-wise in folders and figure panels in sub-folders. The recurrent raw data used for multiple figures is mentioned for respective figures. Document explaining in detail about the figures and respective data set is also provided.</p> <p>Data is given as measured single-molecule TCSPC data as well as the background measurements as buffer and IRF as dpbs measurements in each respective folder.</p> <p>Due to size, the repository is uploaded in two parts. This part I has all the data for above figures except Figure S3, Figure S8, Figure S9 and Figure S15 for which associated data are deposited in part II repository with Zenodo DOI https://doi.org/10.5281/zenodo.8136592.</p>
The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini
<p>The deposited data set contains data for the main figure 3 of the manuscript "The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini" by Blaimschein et al. published in Structure (2023).</p>
The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini
<p>The deposited data set contains data for the main figure 2 of the manuscript "The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini" by Blaimschein et al. published in Structure (2023).</p>
The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini
<p>The deposited data set contains data for the main figure 6 of the manuscript "The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini" by Blaimschein et al. published in Structure (2023).</p>
Computing free energies of fold-switching proteins using MELD x MD
<p>In this Zenodo repository, we provide the MELD script and data for a few representative systems in the DP-MELD.zip, GA_GB-MELD.zip, and RfaH-MELD.zip files. The contents of the repository are described below:</p> <ol> <li> <p>MELD Simulation:</p> <ul> <li>Filename: DP-MELD.zip, GA_GB-MELD.zip, and RfaH-MELD.zip</li> <li>Description: These archives contain the necessary files and scripts for the MELD simulation.</li> </ul> </li> <li> <p>Setup Script:</p> <ul> <li>Filename: setup.py</li> <li>Description: This script is used to set up the MELD simulation.</li> </ul> </li> <li> <p>Trajectory Analysis Script:</p> <ul> <li>Filename: Clustering.sh</li> <li>Description: This script analyzes the trajectories obtained from the MELD simulation.</li> </ul> </li> <li> <p>Protein Information:</p> <ul> <li>Location: TEMPLATES folder</li> <li>Files: <ul> <li>Protein topology file: .top</li> <li>Coordinate file: .crd</li> <li>PDB file: .PDB</li> </ul> </li> <li>Description: These files provide input information for a few representative proteins.</li> </ul> </li> <li> <p>Residue-Residue Contact Information:</p> <ul> <li>Files: <ul> <li>contact_model1.dat</li> <li>contact_model2.dat</li> </ul> </li> <li>Description: These files contain information about the contacts between residues.</li> </ul> </li> <li> <p>Replica Trajectory Files:</p> <ul> <li>Filename: trajectory.00.dcd</li> <li>Description: These files contain the trajectories obtained from the simulation for the corresponding bottom replica.</li> </ul> </li> <li>Clustering Output: <ul> <li>Folders: Cluster_6 or Cluster_3.5</li> <li>Description: These folders contain the results of the clustering analysis, including the computed population and the average conformers for each cluster.</li> </ul> </li> </ol> <p>Furthermore, we provide an additional archive called unfold.zip:</p> <ol> <li>Unfolded Ensemble: <ul> <li>Filename: unfold.zip</li> <li>Description: This archive contains the unfolded ensemble, which is used to determine the force required for rebalancing two group springs for the MELD run between two conformers (A and B) before executing the MELD simulation.</li> </ul> </li> </ol>
Fig. 6 in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 6. (A) Three-dimensional (3D) structural model of the ICChI- NAG complex illustrating by Docking. (B) DIMPLOT result revels the interacting amino acid residue during formation of complex.
Fig. 2 in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 2. The three dimensional crystal structure of ICChI where outer ball and stick (green-red) are glycan ligands, Alpha helices (red coil); parallel beta sheets (yellow arrow); random coils or loop (green); (A) topview of ICChI structure, (B) side view of ICChI structure.
Fig. 1 in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 1. (A) Silver stained 12.5% SDS-PAGE gel of purified ICChI. Lane 1 contains molecular weight markers (Pageruler prestained protein ladder, Fermentas SM0671) and lane 2 represents pure and homogeneous ICChI protein shown by arrow. (B) Crystals of ICChI grown in 4–5 days in a hanging drop at 291 K equilibrated against 750 μl reservoir solution containing 0.005 M Cobalt chloride, 0.005 M Cadmium chloride, 0.005 M Magnesium chloride, 0.005 M Nickel chloride and 11% (w/v) PEG 3350 in 0.1 M HEPES buffer, pH 7.0. The tetragonal bipyramide-shaped crystals had a typical size of 300 × 200 × 200 μm. (C) X-ray diffraction from the crystal of ICChI protein produced interference pattern.
Fig. 5. The electron density and N in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 5. The electron density and N-linked glycosylation sites. (A) Asparagine residue 45. (B) Asparagine residue 172. (C) Asparagine residue 194.
Fig. 4 in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 4. The catalytic residues of the ICChI structure are: aspartate 125; glutamate 127 and tyrosine 184. The grey mesh is electron density whereas the amino acid residues are green.
Effect of a New HA Filler in Correcting Nasolabial Fold
ClinicalTrials.gov study NCT06574750. IPD Sharing: NO. Countries: 1. Publications: 1.
DL6049 Versus Cosmoplast in the Treatment of Nasolabial Fold Wrinkles, Long Term Follow-up
ClinicalTrials.gov study NCT00444353. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Total Versus Partial Arytenoidectomy in Bilateral Vocal Fold Paralysis
ClinicalTrials.gov study NCT01824849. IPD Sharing: Not stated. Countries: 1. Publications: 13.
Evaluation of Nail Fold Microcirculation in CKD
ClinicalTrials.gov study NCT03682952. IPD Sharing: NO. Countries: 1. Publications: 7.
Vocal Folds Irregular Mucosal Changes: A Clinical, Pathological and Genetic Study
ClinicalTrials.gov study NCT04006197. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
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OpenNeuro
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