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Results for “Proton Pumps”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Changes within the central stalk of E. coli F 1 F o ATP synthase observed after addition of ATP

F 1 F o ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F o motor that is transferred to the F 1 motor to catalyze ATP production, with flexible F 1 /F o coupling required for efficient catalysis. F 1 F o ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli F 1 F o ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the F ο motor. This highlights the importance of the central rotor for flexible coupling of the F 1 and F o motors and provides further insight into the regulatory mechanism mediated by subunit ε.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Monomer and dimer structures of cytochrome bo 3 ubiquinol oxidase from Escherichia coli

Abstract The Escherichia coli cytochrome bo 3 ubiquinol oxidase is a four‐subunit heme‐copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts—the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo 3 ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo‐EM SPR) to a resolution of 3.15 and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67–74).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metabolic Fluxes of Nitrogen and Pyrophosphate in Chemostat Cultures of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum

This study discusses the fate of pyrophosphate in the metabolism of two thermophilic anaerobes that lack a soluble irreversible pyrophosphatase as present in Escherichia coli but instead use a reversible membrane-bound proton-pumping enzyme. In such organisms, the charging of tRNA with amino acids may become more reversible. This may contribute to the observed excretion of amino acids during sugar fermentation by Clostridium thermocellum and Thermoanaerobacterium saccharolyticum . Calculation of the energetic advantage of reversible pyrophosphate-dependent glycolysis, as occurs in Clostridium thermocellum , could not be properly evaluated, as currently available genome-scale models neglect the anabolic generation of pyrophosphate in, for example, polymerization of amino acids to protein. This anabolic pyrophosphate replaces ATP and thus saves energy. Its amount is, however, too small to cover the pyrophosphate requirement of sugar catabolism in glycolysis. Consequently, pyrophosphate for catabolism is generated according to ATP + P i → ADP + PP i .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage

Abstract Background Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean’s interior. SAR324 is a ubiquitous but poorly understood uncultivated clade of Deltaproteobacteria that inhabits the entire water column, from ocean surface waters to its deep interior. Although some progress has been made in elucidating potential metabolic traits of SAR324 in the dark ocean, very little is known about the ecology and the metabolic capabilities of this group in the euphotic and twilight zones. To investigate the comparative genomics, ecology, and physiological potential of the SAR324 clade, we examined the distribution and variability of key genomic features and metabolic pathways in this group from surface waters to the abyss in the North Pacific Subtropical Gyre, one of the largest biomes on Earth. Results We leveraged a pangenomic ecological approach, combining spatio-temporally resolved single-amplified genome, metagenomic, and metatranscriptomic datasets. The data revealed substantial genomic diversity throughout the SAR324 clade, with distinct depth and temporal distributions that clearly differentiated ecotypes. Phylogenomic subclade delineation, environmental distributions, genomic feature similarities, and metabolic capacities revealed strong congruence. The four SAR324 ecotypes delineated in this study revealed striking divergence from one another with respect to their habitat-specific metabolic potentials. The ecotypes living in the dark or twilight oceans shared genomic features and metabolic capabilities consistent with a sulfur-based chemolithoautotrophic lifestyle. In contrast, those inhabiting the sunlit ocean displayed higher plasticity energy-related metabolic pathways, supporting a presumptive photoheterotrophic lifestyle. In epipelagic SAR324 ecotypes, we observed the presence of two types of proton-pumping rhodopsins, as well as genomic, transcriptomic, and ecological evidence for active photoheterotrophy, based on xanthorhodopsin-like light-harvesting proteins. Conclusions Combining pangenomic and both metagenomic and metatranscriptomic profiling revealed a striking divergence in the vertical distribution, genomic composition, metabolic potential, and predicted lifestyle strategies of geographically co-located members of the SAR324 bacterial clade. The results highlight the utility of metapangenomic approaches employed across environmental gradients, to decipher the properties and variation in function and ecological traits of specific phylogenetic clades within complex microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54

Since the discovery of Mimivirus, viruses with large genomes encoding components of the translation machinery and other cellular processes have been described as belonging to the nucleocytoplasmic large DNA viruses. Recently, genome-resolved metagenomics led to the discovery of more than 40 viruses that have been grouped together in a proposed viral subfamily named Klosneuvirinae. Members of this group had genomes of up to 2.4Mb in size and featured an expanded array of translation system genes. Yet, despite the large diversity of the Klosneuvirinae in metagenomic data, there are currently only two isolates available. Here, we report the isolation of a novel giant virus known as Fadolivirus from an Algerian sewage site and provide morphological data throughout its replication cycle in amoeba and a detailed genomic characterization. The Fadolivirus genome, which is more than 1.5Mb in size, encodes 1,452 predicted proteins and phylogenetic analyses place this viral isolate as a near relative of the metagenome assembled Klosneuvirus and Indivirus. The genome encodes for 66 tRNAs, 23 aminoacyl-tRNA synthetases and a wide range of transcription factors, surpassing Klosneuvirus and other giant viruses. The Fadolivirus genome also encodes putative vacuolar-type proton pumps with the domains D and A, potentially constituting a virus-derived system for energy generation. The successful isolation of Fadolivirus will enable future hypothesis-driven experimental studies providing deeper insights into the biology of the Klosneuvirinae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress

Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with ≥5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Carbon fixation systems in plants and algae

Provided are methods for elevating cyclic electron transfer activity, improving carbon concentration, and enhancing carbon fixation in C3 and C4 plants, and algae, and producing biomass or other products from C3 or C4 plants, and algae, selected from among, for example, starches, oils, fatty acids, lipids, cellulose or other carbohydrates, alcohols, sugars, nutraceuticals, pharmaceuticals, fragrance and flavoring compounds, and organic acids, as well as transgenic plants produced thereby. These methods and transgenic plants and algae encompass the expression, or overexpression, of various combinations of genes that improve carbon concentrating systems in plants and algae, such as bicarbonate transport proteins, carbonic anhydrase, light driven proton pump, cyclic electron flow regulators, etc.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Carbon fixation systems in plants and algae

Provided are heterologous nucleic acid constructs, vectors and methods for elevating cyclic electron transfer activity, improving carbon concentration, and enhancing carbon fixation in C3 and C4 plants, and algae, and producing biomass or other products from C3 or C4 plants, and algae, selected from among, for example, starches, oils, fatty acids, lipids, cellulose or other carbohydrates, alcohols, sugars, nutraceuticals, pharmaceuticals, fragrance and flavoring compounds, and organic acids, as well as transgenic plants produced thereby. These methods and transgenic plants and algae encompass the expression, or overexpression, of various combinations of genes that improve carbon concentrating systems in plants and algae, such as bicarbonate transport proteins, carbonic anhydrase, light driven proton pump, cyclic electron flow regulators, etc.

Sayre, Richard Thomas↗
DOE OSTI2022

Carbon fixation systems in plants and algae

Provided are heterologous nucleic acid constructs, vectors and methods for elevating cyclic electron transfer activity, improving carbon concentration, and enhancing carbon fixation in C3 and C4 plants, and algae, and producing biomass or other products from C3 or C4 plants, and algae, selected from among, for example, starches, oils, fatty acids, lipids, cellulose or other carbohydrates, alcohols, sugars, nutraceuticals, pharmaceuticals, fragrance and flavoring compounds, and organic acids, as well as transgenic plants produced thereby. These methods and transgenic plants and algae encompass the expression, or overexpression, of various combinations of genes that improve carbon concentrating systems in plants and algae, such as bicarbonate transport proteins, carbonic anhydrase, light driven proton pump, cyclic electron flow regulators, etc.

Sayre, Richard Thomas↗
DOE OSTI2025

Specificity and tunability of efflux pumps: A new role for the proton gradient?

Efflux pumps that transport antibacterial drugs out of bacterial cells have broad specificity, commonly leading to broad spectrum resistance and limiting treatment strategies for infections. It remains unclear how efflux pumps can maintain this broad spectrum specificity to diverse drug molecules while limiting the efflux of other cytoplasmic content. We have investigated the origins of this broad specificity using theoretical models informed by the experimentally determined structural and kinetic properties of efflux pumps. We developed a set of mathematical models describing operation of efflux pumps as a discrete cyclic stochastic process across a network of states characterizing pump conformations and the presence/absence of bound ligands and protons. These include a minimal three-state model that lends itself to clear analytic calculations as well as a five-state model that relaxes some of the simpler model’s most strict assumptions. We found that the pump specificity is determined not solely by the drug affinity to the pump–as is commonly assumed–but it is also directly affected by the periplasmic pH and the transmembrane potential. Therefore, changes to the proton concentration gradient and voltage drop across the membrane can influence how effective the pump is at extruding a particular drug molecule. Furthermore, we found that while both the proton concentration gradient across the membrane and the transmembrane potential contribute to the thermodynamic force driving the pump, their effects on the efflux enter not strictly in a combined proton motive force. Rather, they have two distinguishable effects on the overall throughput. These results highlight the unexpected effects of thermodynamic driving forces out of equilibrium and illustrate how efflux pump structure and function are conducive to the emergence of multidrug resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Physical model and experimental validation of a high temperature proton exchange membrane electrochemical hydrogen pump cell for efficient single-stage extraction of low concentration hydrogen gas

There is interest in valorization of existing natural gas infrastructure to facilitate the co-transportation of hydrogen via blending of hydrogen gas initially at limited concentrations of 1–20 vol% H2 and to subsequently extract hydrogen at fuel cell quality standards (SAE J2719/ISO14687-2). High temperature proton exchange membrane electrochemical hydrogen pump (HT-PEM EHP) based on phosphoric acid doped polybenzimidazole (PA-PBI) exhibits good performance at elevated temperatures (>120 °C), which provides desirable tolerance to non-methane natural gas constituents that are problematic for lower temperature based EHP. To better understand the suitability of the HT-PEM EHP for such gas separation processes, a two-dimensional model of EHP based on PA-PBI was developed. The model is validated for several relevant operating conditions and across cells with differing amounts of phosphoric acid content in the electrodes. Operando micro x-ray computed tomography (CT) imaging of an HT-PEM EHP was used to further validate physical parameters and assumptions of the model. The impacts of pressure, relative humidity of the anode feed, and concentration of feed gases on separation performance are investigated. This study shows that a specific energy of separation of 5.1 kWh/kg H2 at a hydrogen recovery factor (HRF) of 50 vol% can be achieved in a single stage with the EHP, producing fuel cell quality hydrogen purity of 99.99 vol% H2 from a 2 vol% H2/CH4 feed blend, while pressurizing the product H2 at a pressure ratio of 1.3 relative to feed pressure.

Stansberry, John M↗
DOE OSTI2025

Hydrogen isotope fractionation – Fundamental insights leaving to process scaleup

This final report summarizes the PhD research of Dr. Mayura Silva who was supported on the project from inception in August 2021 to his graduation in December 2023. Dr. Silva undertook a detailed examination of the eGicacy of graphene interlayers on H/D selectivity in electrochemical proton / deuteron pump cells. His work focused on the role of impurity cations (especially NH 4 * and Cu 2+ which are resident in membranes as a residual from the ammonium persulfate treatment used to remove copper backing from the graphene during membrane preparation), and on the composition of evolved gases from hydrogen / deuterium pump cells that were fed a 50:50 mixture of H 2 and D 2 gas. The key finding is that previous reports of very high H/D selectivity in hydrogen pump cells having Nafion | graphene | Nafion membranes installed were not reproduced.

08 HYDROGEN↗
DOE OSTI2025

Technology for Electrically Enhanced Thermochemical Hydrogen (TEETH)

This is the Final Technical Report for the TEETH project. The TEETH concept couples high-temperature solar-thermochemical water splitting (TCWS) with electrochemical H 2 pumping through a proton conducting membrane (PCM) and capitalizes on the benefits of the individual technologies to synergistically providing new benefits. That is, TEETH is a coupled thermochemical/electrochemical process to produce H 2 from steam using solar energy. This approach is thermodynamically equivalent to other hybrid electrolytic processes but is unique in that the equilibrium of the reaction is driven forward by close coupling an electrically driven proton-conducting-membrane to the H 2 -producing reoxidation step. The process uniquely provides and benefits from the necessary H 2 /steam separation and, also unlike other hybrid processes, benefits thermodynamically from the use of readily generated high pressure steam. The concept also satisfies the objectives of previous concepts: 1) decreasing the reduction enthalpy (the reduction temperature), of the working metal-oxide (MO); 2) eliminating the need for a windowed receiver; and 3) widening the scope of material candidates, while also obviating the need for electrical connections to the working MO and avoiding the use of aqueous electrolytes and hydrated redox species (there is no liquid phase), without increasing mechanical complexity.

08 HYDROGEN↗
DOE OSTI2020

Determining Proton Transport in Pseudo Catalyst Layers Using Hydrogen Pump DC and AC Techniques

Optimizing electrode morphology with a more uniform ionomer distribution is key to reducing ohmic losses and increasing electrocatalyst utilization in polymer electrolyte fuel cells (PEFCs). Inherent ionomer conductivity, volume fraction and tortuosity determine effective ionic conductivity. We use hydrogen pump (HP) method to measure effective ionic conductivity of a pseudo catalyst layer (PCL) comprised of Vulcan XC-72 carbon black and 3M 825 EW ionomer with ionomer to carbon (I/C) ratios of 0.6, 1 and 1.4 and relative humidity (RH) range of 50 to 120%. These direct current (DC) experiments are then compared with electrochemical impedance spectroscopy (EIS). Both DC and EIS methods show good agreement, indicating that EIS can be used as an alternative to DC method in HP experiment. Ionic conductivity for PCL with I/C of 1 and 1.4 was found to be about one order of magnitude higher than I/C of 0.6 for most of the RH range. At 90% RH tortuosities for I/C = 1 and 1.4 were close to 1, whereas tortuosity for I/C = 0.6 was 3. With decrease in relative humidity tortuosities increased linearly and at 50% relative humidity a PCL with I/C = 0.6 had the highest tortuosity of 6.1.

25 ENERGY STORAGE↗
DOE OSTI2023

Improving Proton Conductivity by Navigating Proton Trapping in High Scandium-Doped Barium Zirconate Electrolytes

Proton-conducting oxides are used in intermediate-temperature (300 °C < T < 700 °C) applications of fuel cells, electrolyzers, membrane reactors, hydrogen pumps, and sensors. The proton conductivity of doped ABO 3 perovskites is partly dependent on the proton concentration and hence on the level of material hydration. However, how the material hydration ability is affected by differences in doping is not fully understood. Here, we show the prospect of proton trapping and detrapping that influences material hydration and dehydration. The proton-trapping influence is significant for Sc-doped BaZrO 3 compared to Y-doped BaZrO 3 . Here, our work offers a perspective to understand how defect interaction/associations influence the hydration ability of proton-conducting oxides. Furthermore, positron annihilation lifetime spectroscopy was revealed to be a valuable technique for studying the proton-trapping phenomena and the defect chemistry of dense proton conductors. Density functional theory calculations also showed that a high hydration level in Sc-doped BaZrO 3 boosts proton migration. In contrast, the effect of boosting the proton migration due to increased hydration is limited for Y-doped BaZrO 3 . This effect, in turn, might explain the trend of conductivity with dopant concentration in doped BaZrO 3 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Preface: special issues on photosystem II

Here, the appearance of oxygenic photosynthesis 3–4 billion years ago is arguably one of the most important evolutionary developments which radically transformed both the biotic and abiotic landscapes of Earth. The presence of molecular oxygen enabled the evolution of complex lifeforms requiring large amounts of chemical energy which could only be produced by aerobic respiration. Additionally, molecular oxygen remodeled the geochemistry of the planet during its transition from a reducing to an oxidizing atmosphere during the Great Oxidation Event. Central to these processes is Photosystem II (PS II), the light energy-driven, water-plastoquinone oxidoreductase which initially evolved in cyanobacteria and subsequently was incorporated, along with Photosystem I (PS I), the cytochrome b 6 f complex and the Ndh complex, into all algae and higher plants by the process of endosymbiosis. This membrane protein complex releases molecular oxygen and protons as the byproducts of water splitting and produces plastoquinol, which provides reducing equivalents that are used sequentially by the cytochrome b 6 /f complex, PS I, and ultimately, as NADPH + H + , by the Calvin–Benson–Bassham cycle. Additionally, the protons released by PS II (and those pumped by the cytochrome b 6 /f complex and the NDH complex (during cyclic electron transfer)) form the proton motive force that drives ATP synthesis via the ATP Synthase, thus providing the chemical energy source for carbon fixation.

59 BASIC BIOLOGICAL SCIENCES↗