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1,028 results for “proton”
Optimised geometries of a number of protonation models.
<p>Optimised geometries in pdb format presented in Fig.S12 of "A novel subgroup of light-driven sodium pumps with an additional Schiff base counterion" paper (https://doi.org/10.1101/2023.10.11.561842).</p>
Response of protonated, adduct, and fragmented ions in Vocus proton-transfer-reaction time-of-flight mass (PTR-ToF-MS) spectrometer
<p>Here, we provide the time series and processed results of two sets of experiments: RH experimental results and instrument setting results:</p> <p><a href="../api/records/10947779/draft/files/202305015_E_N_BSQ_RF.pxp/content" target="_blank" rel="noopener noreferrer">202305015_E_N_BSQ_RF.pxp</a>: instrument setting results.</p> <p><a href="../api/records/10947779/draft/files/VOC_PTR_RH_20230427.pxp/content" target="_blank" rel="noopener noreferrer">VOC_PTR_RH_20230427.pxp</a>: RH experimental results.</p> <p><a href="../api/records/10947779/draft/files/VOC_PTR_S_k_20230501.pxp/content" target="_blank" rel="noopener noreferrer">VOC_PTR_S_k_20230501.pxp</a>: k value result analysis</p>
[Dataset] Intensity and Dimensionality-Dependent Dynamics of Laser-Proton Acceleration in 1D, 2D, and 3D Particle-in-Cell Simulations
<p>The included Jupyter Notebooks (.ipynb) were used to generate figures and make calculations for the work. The resulting image files are saved in Figure_Outputs.tar.gz. The other archives (1D.tar.gz, 2DS.tar.gz, 2DP.tar.gz, 3D.tar.gz, laser_focus.tar.gz, and EField.tar.gz) are compressed directories containing EPOCH PIC simulation outputs for the paper (relevant directories should be extracted to replicate analysis with provided files). </p> <p>Since the last version, a new figure (Figure 6, an ion phase space) has been added. Notebooks for later figures have been renumbered and the figure outputs have been updated. </p>
Mimicry of the Proton Wire Mechanism of Enzymes Inside a Supramolecular Capsule Enables β-Selective O-Glycosylations
<p>Data underlying the figures in the publication “Mimicry of the proton wire mechanism of enzymes inside a supramolecular capsule enables β-selective O-glycosylations”, published in <em>Nature Chemistry</em>.</p> <p>Table of contents:</p> <p><strong>1. Figure 1</strong>: An editable chemdraw graphic of <em>Figure 1</em>.</p> <p><strong>2. Figure 2</strong>: .zip archive containing an editable chemdraw graphic of <em>Figure 2</em>, and NMR spectra of compounds 7 and 9.</p> <p><strong>3. Figure 3</strong>: .zip archive containing an editable chemdraw graphic of <em>Figure 3</em>, and source data underlying <em>Figures 3a</em>, <em>3c</em> and <em>3d</em>.</p> <p><strong>4. Figure 4</strong>: .zip archive containing an editable chemdraw graphic of <em>Figure 4</em>, NMR spectra of <em>Figure 4c</em> and source data underlying <em>Figures 4d</em> and <em>4e</em>.</p> <p><strong>5. Figure 5</strong>: .zip archive containing an editable chemdraw graphic of <em>Figure 5</em>, and NMR spectra of compounds 26-31, S8 and S9.</p> <p><strong>6. Table 1</strong>: .zip archive containing an editable chemdraw graphic of <em>Table 1</em>, and NMR spectra of all compounds shown in <em>Table 1</em>.</p>
Structural dynamics determine voltage and pH gating in human voltage-gated proton channel
<p>Voltage-gated ion channels are key players of electrical signaling in cells. As a unique subfamily, voltage-gated proton (Hv) channels are standalone voltage sensors without separate ion conductive pores. Hv channels are gated by both voltage and transmembrane proton gradient (i.e ∆pH), serving as acid extruders in most cells. Amongst their many functions, Hv channels are known for regulating the intracellular pH of human spermatozoa and compensating for the charge and pH imbalances caused by NADPH oxidases in phagocytes. Like the canonical voltage sensors, Hv channels are a bundle of 4 helices (named S1 through S4), with the S4 segment carrying 3 positively charged Arg residues. Extensive structural and electrophysiological studies on voltage-gated ion channels, in general, agree on an outwards movement of the S4 segment upon activating voltage, but the real-time conformational transitions are still unattainable. With purified human voltage-gated proton (hHv1) channels reconstituted in liposomes, we have examined its conformational dynamics, including the S4 segment at different voltage and pHs using single-molecule fluorescence resonance energy transfer (smFRET). Here, we provide the first glimpse of real-time conformational trajectories of the hHv1 voltage sensor and show that both voltage and pH gradient shift the conformational dynamics of the S4 segment to control channel gating. Our results indicate that the S4 segment transits among 3 major conformational states and kinetic analysis suggest that only the transitions between the inward and outward conformations are highly dependent on voltage and pH changes. Our smFRET studies uncover the stochastic conformational dynamics of S4 and demonstrate how voltage and pH shift its conformational distributions to regulate channel gating. Altogether, we propose a kinetic model that explains the mechanisms underlying voltage and pH gating in Hv channels, which may also serve as a general framework for understanding the voltage sensing and gating in other voltage-gated ion channels.</p>
Proton-transporting heliorhodopsins from marine giant viruses
<p><span>Rhodopsins convert light into signals and energy in animals and microbes. Heliorhodopsins (HeRs), a recently discovered new rhodopsin family, are widely present in archaea, bacteria, unicellular eukaryotes, and giant viruses, but their function remains unknown. Here we report that a viral HeR from <em>Emiliania huxleyi</em> virus 202 (V2HeR3) is a light-activated proton transporter. V2HeR3 absorbs blue-green light, and the active intermediate contains the deprotonated retinal Schiff base. Site-directed mutagenesis study revealed that E191 in TM6 constitutes the gate together with the retinal Schiff base. E205 and E215 form a proton accepting group of the Schiff base, whose mutations converted the protein into an outward proton pump. Three environmental viral HeRs from the same group, as well as a more distantly related HeR exhibited similar proton-transport activity, indicating that HeR functions might be diverse similarly to type-1 microbial rhodopsins. Some strains of <em>E. huxleyi</em> contain one HeR that is related to the viral HeRs, while its viruses <em>Eh</em>V-201 and <em>Eh</em>V-202 contain two and three HeRs, respectively. Except for V2HeR3 from <em>Eh</em>V-202, none of these proteins exhibit ion-transport activity. Thus, when expressed in the <em>E. huxleyi</em> cell membranes, only V2HeR3 has the potential to depolarize the host cells by light, possibly to overcome the host defense mechanisms or to prevent superinfection. The neuronal activity generated by V2HeR3 suggests that it can potentially be used as an optogenetic tools, like type-1 microbial rhodopsins.</span></p>
Input files and structures for article "Carbon dioxide fixation in RuBisCO is protonation state dependent and irreversible"
<p>Pdb file and amber topology of the initial RuBisCO model together with parameter files for the MD simulations with AMBER to equilibrate the system.</p> <p>Structures of reactant, transition state and products in the enzyme RuBisCo used to correct the activation and reaction free energies. Molpro input files used in the projector-based embedding calculations are provided. The same holds for the calculations involving the Zn cation. </p> <p>Optimized structures used to calculate descriptors with conceptual DFT. </p>
Source data for "Membrane curvature sensing and symmetry breaking of the M2 proton channel from Influenza A"
<p>Data files for Figures 2 and 3. </p>
Asymmetry in Uranus' high energy proton radiation belts
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STEM and XRD files of Water and Hydroxide Trapping in Cobalt Tungstate for Proton Exchange Membrane Water Electrolysis
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All-optical steering on the proton emission in laser-induced nanoplasmas - This is a new version. The data name of Figures 2 and 3 in version 2 is wrong, the data in Figure 2 correspods to Figure 3, and the data in Figure 3 correspods to Figure 2 in manuscript.
<p>all the raw data for the main figures of our literature "All-optical steering on the proton emission in laser-induced nanoplasmas"</p>
Proton Cyclotron Waves and Pickup Ion Ring Distribution Instabilities Upstream of Mars
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Data Set of Playing with Protons
<p>Data Set of Playing with Protons</p>
Proton temperature anisotropy constraint associated with alpha beam instability in the solar wind
<p>Simulation data and code repository for the paper "Proton temperature anisotropy constraint associated with alpha beam instability in the solar wind". This repository contains the particle-in-cell hybrid simulation code based on CAM-CL scheme and the simulation results. The parameter files are also included in the archived tar file. Another package contains the files for the data used in the paper.</p> <p> </p>
Dissected Antiporter Modules Establish Minimal Proton-Conduction Elements in the Respiratory Complex I
<ul> <li>Snapshots from MD simulations (see SI table 4 for reference)</li> </ul>
Supporting Material: Proof-of-principle of 3D-printed track-end detectors for dosimetry in proton therapy
<p><strong>Project description and contents of the submitted manuscript:</strong></p> <p><strong>Background: </strong>Dosimetric equipment in particle therapy (PT) is associated with high costs. There is a lack of versatile, tissue-equivalent detectors suitable for in-vivo dosimetry. Faraday-cup (FC) type detectors are sensitive to stopped protons, i.e. to trackends. They experience a renaissance in PT as they can cope with high dose rates. Owing to their simple functional principle, production of FC could benefit from the dynamic technological developments in additive manufacturing of sensors.</p> <p><strong>Purpose: </strong>To build FC-type detectors for PT by standard 3D-printing. This study seeks to build an integrating, single-channel FC for replacement of a traditional FC and a 2×2 array of FC elements indicating the feasibility of a spatially resolving detector.</p> <p><strong>Methods: </strong>Samples of FCs were produced with a dual-extruder 3D-printer with polylactic-acid filaments, which contained graphite in the conductive parts of the detector. Production was optimizied in terms of materials and printing temperature. Samples were characterized by electrical tests and non-destructive 3D x-ray imaging. Beam tests were conducted at a clinical PT machine.</p> <p><strong>Results: </strong>Operational FC-type detectors for proton fields were printed. The detected charge of the single-channel FC corresponded qualitatively to the one of a traditional FC. A 2 × 2 FC array was fabricated in a single run. There was a linear relationship between the response of the individual FC elements and the machine output.</p> <p><strong>Conclusions: </strong>3D-printing is a viable method for producing low-cost, tissue-equivalent, FC-type detectors for PT. They could potentially be used as track-end detectors in anthropomorphic phantoms.</p> <h3>Shared files:</h3> <p>2x2_FC_matrix: design CAD files of FC array</p> <p>Single_channel_FC: design CAD files of simplified, single-channel FC</p> <p>CT_matrix: high-resolution x-ray CT image set of the 2x2 FC array</p> <p>Measured_values_for_MedPhys_technical_note: Excel sheet of the data presented in the paper</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Processed data of "Observations of Ring Current Proton Fast Local Loss Associated with Deepening Local Minimum in Phase Space Density in Earth's Inner Magnetosphere"
<p>The dataset includs the processed observation data of "Observations of Ring Current Proton Fast Local Loss Associated with Deepening Local Minimum in Phase Space Density in Earth’s Inner Magnetosphere". *.sav files are the phase space densities of protons and the corresponding adiabatic invariants (μ, K, and L*) which are calculated under the T89D magnetic field model (using the observation data measured by the RBSPICE on the Van Allen Probes from 24th to 26th Jun 2017), which are used to plot Figure 1. The data in Processed data for Figures 2-5.zip are the processed data for Figures 2-5. </p>
Cryo-electron microscopic and X-ray crystallographic analysis of the light- driven proton pump proteorhodopsin reveals a pentameric assembly
<p>Data files to Hirschi et al. (2020), J. Struct. Biol.</p>
Engineering and Production of the Light-Driven Proton Pump Bacteriorhodopsin in 2D Crystals for Basic Research and Applied Technologies
<p>Data to Stauffer et al. (2020), Methods Protoc.</p>
Increasing the sensitivity of hyperpolarized [15N2]urea detection by serial transfer of polarization to spin-coupled protons
<p>This upload contains the raw data, MATLAB scripts and Mathematica notebooks used for the publication.</p> <p>Figure 2, 3, 7 and 8 where generated with the Mathematica notebooks in the folder Mathematica_Notebooks.</p> <p>Figure 4 was generated with the raw data in NOE_data/20190821 and processed with the script NOE_data/20190821/H1to15NNOEin15N2urea.m</p> <p>Figure 5a is based on data in Polarization_Transfer_Data/spectral/timecourse/_fk_BHINDER_flipback_15Nto1H_hyp_20180609_01.fid processed with Polarization_Transfer_Data/spectral/timecourse/_fk_BHINDER_flipback_15Nto1H_hyp_20180609_01.fid/timecourse.m</p> <p>Figure 5b is based on Polarization_Transfer_Data/imaging/_fk_BHINDER_flipback_EPIP_hyp_10perc_20180531_01.img . From this raw data image2 - image60 are acquired after polarisation transfer. Image1 is a direct acquisition of the water resonance .</p> <p>The brightness and contrast of the images was adjusted and a montage of images 2 to 9 was created with (Fiji <a href="https://imagej.net/software/fiji/">https://imagej.net/software/fiji/</a>) .</p> <p>Figure 6 is based on data in Polarization_Transfer_Data/spectral/interleaved processed with Polarization_Transfer_Data/spectral/interleaved/comparision.m</p> <p>The script Pulse_Generation/createIRRUPT.m was used to generate the adiabatic pulses.</p>
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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.