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16 results for “proton transport”
Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter
<p>Input and structure files for the All Atom Molecular Dynamics simulations and Umbrella Sampling simulations performed to determine the transport mechanism of the CLC<sup>F</sup> F<sup>-</sup>/H<sup>+ </sup>antiporter protein.</p> <p>The tar file contains two directories:</p> <p>1. AA-MD: 4 sets of prmtop and inpcrd files representing each combination of protonation states for Glu<sub>ext</sub> and Glu<sub>int</sub>. Also contains the input files used to run the simulations in Amber20</p> <p>2. Umbrella Sampling: Similar to AA-MD, there are 4 sets of files for the differing protonation states, but each set contains 47 separate prmtop and inpcrd files, one for each window used in the umbrella sampling simulations. Also contains the input files used to run the simulations in Amber20</p> <p> </p> <p> </p>
Lattice Boltzmann simulation of liquid water transport in gas diffusion layers of proton exchange membrane fuel cells: Impact of gas diffusion layer and microporous layer degradation on effective transport properties
<p><span>Underlying data to publication Sarkezi-Selsky et al., <em>J. Pow. Sour.</em> 556 (2023) 232415,<span> https://doi.org/10.1016/j.jpowsour.2022.232415</span> <br><br>Polymer Electrolyte Membrane Fuel Cells (PEMFCs) represent a promising technology for clean drivetrain solutions, in particular for heavy-duty applications. However, lifetime requirements demand high durability of each cell component.<br></span><span>In this work, transport of liquid water through pristine and degraded gas diffusion layers (GDL) was simulated with a 3D Color-Gradient Lattice Boltzmann model. The GDL microstructure was reconstructed </span><span>from high-resolution X-ray micro-computed tomography (</span><span>μ</span><span>-CT) of an impregnated Freudenberg H14. The </span><span>effect of a microporous layer (MPL) was considered by reconstruction of an impregnated and MPL-coated H14. Aged microstructures were generated artificially, assuming loss of polytetrafluoroethylene (PTFE) within the GDL and increase of MPL macroporosity as main degradation mechanisms. Liquid water transport within aged microstructures was simulated by imposing a liquid phase flow rate until breakthrough was reached. Subsequently, the GDL microstructures were analyzed for their breakthrough characteristics by means of saturation and effective gas transport properties. When the MPL was pristine, no distinct GDL degradation effect was observable, this was attributed to the MPL dominating capillary transport. MPL aging, however, led to increased saturations and thus to a deterioration of the effective gas transport. With a partially degraded MPL, aging of the GDL then appeared to affect the breakthrough characteristics.</span></p>
Neural-network-based molecular dynamics simulations reveal that proton transport in water is doubly gated by sequential hydrogen-bond exchange: Neural network potentials training data
<h1>Neural network potentials of an excess proton in bulk water, training data</h1> <p>This dataset contains 2188 configurations labeled at two hybrid DFT levels (revPBE0-D3 and B3LYP-D3).</p> <p>The configurations are given as a single XYZ file: configurations.xyz</p> <p>The box dimensions are written in box.txt</p> <p>The energies for all configurations at a given level of theory are written in energies_LEVEL.txt (one configuration per line)</p> <p>The atomic forces for each configuration at a given level of theory are gathered in a XYZ file: forces_LEVEL.xyz</p> <p>The relative displacements of the Wannier centroids, with respect to the closest oxygen atom, for each configuration at a given level of theory, are in the following XYZ file: wannier-centroids-displacements_LEVEL.xyz</p>
Replication Data for: Proton transport through nanoscale corrugations in two-dimensional crystals
<p>This dataset contains source data for Main Figures from "Proton transport through nanoscale corrugations in two-dimensional crystals, <i>Nature,</i> volume 620, pages 782–786" Data plotted as curves and histograms are provided in .xlsx files. AFM data are provided in both .txt and SPIP-compatible .asc file types. Filenames correspond to the figure labels and plot information as in the publication.</p>
Data for: Energetics of substrate transport in proton-dependent oligopeptide transporters
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Cellular bicarbonate accumulation and vesicular proton transport promote calcification in the sea urchin larva
The sea urchin embryo develops a calcitic endoskeleton through intracellular formation of amorphous calcium carbonate (ACC). Intracellular precipitation of ACC, requires HCO3-/CO32- concentrating as well as proton export mechanisms to promote calcification. These processes are of fundamental importance in biological mineralization, but remain largely unexplored. Here we demonstrate that the calcifying primary mesenchyme cells (PMCs) utilize Na+/H+- exchange (NHE) mechanisms to control cellular pH homeostasis during maintenance of the skeleton. During skeleton re-calcification, pHi of PMCs is increased accompanied by substantial elevations in intracellular [HCO3-] mediated by the Na+/HCO3-cotransporter Sp-Slc4a10. However, PMCs lower their pHi regulatory capacities associated with a reduction in NHE activity. Live-cell imaging using GFP reporter constructs in combination with intra-vesicular pH measurements demonstrated alkaline and acidic populations of vesicles in PMCs and extensive trafficking of large V-type H+-ATPase (VHA)-rich acidic vesicles in blastocoelar filopodial cells (BFCs). Pharmacological and gene expression analyses underline a central role of the VHA isoforms Sp-ATP6V0a1, Sp-ATP6V01_1 and Sp-ATPa1-4 for the process of skeleton re-calcification. These results highlight novel pH regulatory strategies in calcifying cells of a marine species with important implications for our understanding of the mineralization process in times of rapid changes in oceanic pH.
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>
Detection of proton-dependent peptide uptake into liposomes by bacterial peptide transporter DtpB using pyranine assay
<p>For more details please see:</p> <p><strong>Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition</strong></p> <p>https://dx.doi.org/10.1016/j.celrep.2023.112831</p>
Proton-transporting heliorhodopsins from marine giant viruses
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Cellular bicarbonate accumulation and vesicular proton transport promote calcification in the sea urchin larva
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Single-chain heteropolymers transport protons selectively and rapidly
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Effect of Inhibitors of the Proton Pump on Intestinal Transporters
ClinicalTrials.gov study NCT02524210. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Naphthoquinone preferentially pairs with non-proton-pumping NADH dehydrogenase for respiratory electron transport
GEO Series GSE303520. Escherichia coli. 10 samples. Type: Expression profiling by high throughput sequencing.
Computational data for Covalent benzenesulfonic functionalization of a graphene nanopore for enhanced and selective proton transport
<p>Computational data for publication: Covalent benzenesulfonic functionalization of a graphene nanopore for enhanced and selective proton transport</p> <p>1) ReaxFF_MD_trajectories_and_data:</p> <ul> <li>NPT, NVT, metadynamics trajectories;</li> <li>Metadynamics COLVAR and HILLS files;</li> <li>Metadyncamics_Gibbs_free_energiy_estimations.ods</li> </ul> <p>2) Areal_proton_conductivity_script.py: for estimation of areal proton conductivity using the Gibbs free energies extracted from the ReaxFF MD metadynamics.</p> <p> </p>
Fatty acid-activated proton transporter SR4 prevents hepatic steatosis and metabolic alterations in diabetic mice by improving mitochondria function, energy balance and oxidative stress
GEO Series GSE308701. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
Wind Energetic Particle Acceleration, Composition and Transport (EPACT) APE-B Telescope Proton Fluxes 18.90 to 21.90 MeV, Level 2, 1 hr Data
The Energetic Particles: Acceleration, Composition and Transport, EPACT, on Wind. The APE-B Telescope measures Proton Fluxes at Particle Energies of 18.90 MeV to 21.90 MeV.
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