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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Mechanistic Insights Revealed by YbtPQ in the Occluded State

Recently, several ATP-binding cassette (ABC) importers have been found to adopt the typical fold of type IV ABC exporters. Presumably, these importers would function under the transport scheme of “alternating access” like those exporters, cycling through inward-open, occluded, and outward-open conformations. Understanding how the exporter-like importers move substrates in the opposite direction requires structural studies on all the major conformations. To shed light on this, here we report the structure of yersiniabactin importer YbtPQ from uropathogenic Escherichia coli in the occluded conformation trapped by ADP-vanadate (ADP-Vi) at a 3.1 Å resolution determined by cryo-electron microscopy. The structure shows unusual local rearrangements in multiple helices and loops in its transmembrane domains (TMDs). In addition, the dimerization of the nucleotide-binding domains (NBDs) promoted by the vanadate trapping is highlighted by the “screwdriver” action at one of the two hinge points. These structural observations are rare and thus provide valuable information to understand the structural plasticity of the exporter-like ABC importers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structures and Mechanisms of a Novel Bacterial Transport System for Fatty Acids

Abstract Bacterial acquisition of metabolites is largely facilitated by transporters with unique substrate scopes. The tripartite ATP‐independent periplasmic (TRAP) transporters comprise a large family of bacterial proteins that facilitate the uptake of a variety of small molecules. It has been reported that some TRAP systems encode a fourth protein, the T component. The T‐component, or TatT, is predicted to be a periplasmic‐facing lipoprotein that enables the uptake of metabolites from the outer membrane. However, no substrates were revealed for any TatT and their functional role(s) remained enigmatic. We recently identified a homolog in Methylococcus capsulatus that binds to sterols, and herein, we report two additional homologs that demonstrate a preference for long‐chain fatty acids. Our bioinformatics, quantitative analyses of protein‐ligand interactions, and high‐resolution crystal structures suggest that TatTs might facilitate the trafficking of hydrophobic or lipophilic substrates and represent a new class of bacterial lipid and fatty acid transporters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Carbon nanotube nanofluidics

Fluid flow under extreme spatial confinement exhibits unusual physical behaviors. This nanofluidic transport regime is relevant to a variety of mass transport, separation, and energy production processes in biological and industrial systems. Carbon nanotubes (CNTs) offer a nearly ideal platform for exploring nanofluidic transport because of their extremely narrow, smooth, hydrophobic inner pores, which enable very fast molecular flow while providing strong selectivity. In this review, we aim to provide a comprehensive understanding of nanofluidics in CNTs, focusing on the basic physics of mass transport in CNTs, various experimental platforms developed to investigate these phenomena, and key results on the permeation of water, protons, and ions. We focus on the critical factors that influence transport efficiency and selectivity, such as slip flow and charge regulation in CNTs, and the roles of entrance effects, dehydration processes and ion–charge interactions at the CNT entrances. We also explore the confinement effects, highlighting how the unique one-dimensional structure of CNTs imposes distinct constraints on fluid behavior and leads to novel single-file transport phenomena. Finally, we address current challenges and future directions of CNT nanofluidics.

Li, Zhongwu [Lawrence Livermore National Laborator↗
DOE OSTI2024

Building a framework to genetically characterize “feather spots” and understand demographic impacts of solar energy sites on migratory bird populations

The lack of data on the impact of utility-scale solar facilities on avian species and populations adds to the cost of siting and operation. As much as 32 percent of the avian biological material (feathers and carcasses) recovered from solar facilities remain unidentified, because they often take the form of “feather spots”. Feather spots are remains of impacted animals that can be separated into two broad categories: 1) those remains that may be visually identified to a species, or 2) those that cannot be visually identified to a species due to degradation from the environment and/or scavenger activity (listed as “unknown”). Even when feather spots can be identified to species, they cannot be visually assigned to particular breeding populations. In some cases, it is unknown whether multiple feather spots represent single or multiple individuals. This project’s objectives were to: 1. Use a developed, genetic-based technique to identify and determine the species, population of origin, and number of individuals found in feather spots recovered from solar facilities. 2. Implement collected data and resulting analyses to develop a publicly accessible web-based decision-making tool that can be used by the solar industry, regulators and other stakeholders to inform siting, mitigation, and conservation management efforts. 3. Establish a not-for-profit fee-for-service center at UCLA to ensure collection and identification of feather spots continue after the project period of performance. During the Project Period, we proposed to establish a pipeline for collecting, transporting, and storing of avian biological material collected at solar facilities and the collection and identification of feather spots to species and individual. We proposed the development of a genetic-based framework that would recover viable DNA from feather spots, amplify this DNA (i.e., make millions of copies of the original DNA), and use it to match the resulting sequences to a national database of known species of birds. The result would be the identification of feathers spots that were previously unidentified, and the incorporation of these samples into a larger database that included all samples recovered from solar facilities. The resulting report (below) details the result of this work and its alignment with proposed activities. We proposed the use of the data collected to assess the comparative risk to specific species or populations of species from solar facilities. For some species, we have already identified genomic markers of specific breeding populations and developed “genoscapes,” maps of unique genetic variation across the full breeding range of a species. We used these (previously and newly developed) genoscapes to probabilistically link a feather spot to the specific breeding populations from which it originated (assignment probabilities range from 75%-100% depending on species and population groups). For those species without genoscapes, we developed a vulnerability and susceptibility estimate that determines the relative local and regional risk to populations that are in geographic proximity to solar facilities, using citizen science data (Breeding Bird Survey (BBS) and eBird). These two feather spot processing pipelines (see Figure 1 below) provide quantitative estimates as to the numbers of individuals from a given population of origin that are affected by solar facilities, and ultimately can reduce costs to the consumer by reducing the industry costs associated with mitigation and siting strategies for future solar energy development.

14 SOLAR ENERGY↗
NASA NTRS1998

Ma'adim Vallis Estuarine Delta in Elysium Basin and Its Relevance as a Landing Site for Exobiology Exploration on Mars

The debouche of Ma'adim Vallis in the Elysium Basin generated a transitional transported sediment structure, which planimetric shape is controlled by the enclosing topography of a deep reentrant gulf of the Basin into the highland. We defined it as an estuarine delta. The location and the importance of this estuarine delta is supported by the theoretical model of graded profile constructed for Ma'adim Vallis, and by two approaches: (i) the reconstruction of Ma'adim Vallis downstream course from Gusev to Elysium Basin, and (ii) the survey of the sediment deposit in the alleged estuary. The longitudinal graded profile of Ma'adim Vallis finds its base-level in the Elysium Basin, at a about 1000 m elevation, which is in agreement with the observed Basin shoreline. This model is supported by observational evidence of flow between the northern rim of Gusev crater, and the Elysium Basin shoreline. This downstream course of Ma'adim Vallis can be divided into three hydrogeologic regions. into three hydrogeologic regions. (a) The first region is a flooded plain (Zephiria Mensae), consisting in chaotic terrain formed by highland rocks, and disintegrated lava of the western flank of Apollinaris. Morphologic indicators of the flood process are: (1) the sediment deposit over the Gusev crater northern rim that reflects the overspilling of the crater-lake water through a 40-km wide gap provided by an ancient impact crater, (2) the tear-drop shaped feature on the northeastern flank of Apollinaris Patera, and (3) the chaotic terrain that suggest the emergence of ground water generated by the seepage of the crater lake through high-permeable broken rampart material. This underground water circulation sustained by the hydrostatic pressure of the crater-lake has likely generated a hydrothermal system in the volcanic environment of Apollinaris Patera. The stratigraphy of the flooded area is identified as Hesperian age, with occurrences of Noachian hilly individual features, and as Amazonian flooded plain and chaotic material, (b) The second region is located on the western flank of Apollinaris Patera. It is surrounded by relics of deep valleys that suggest a former downstream course of Ma'adim Vallis. The geologic setting of this region (Lucus Planum) is interpreted to be an Amazonian formation composed by the middle and lower members of the Medusae Formation., c) The third region corresponds to the convergence of the west and east branches of Ma'adirn Vallis into a deep re-entrant wide gulf that penetrates about 100 km into the highland. This topographic depression is delineated by the 1000 in elevation contour. This gulf has formed an estuarine configuration centered at 3S/190W within the Elysium Basin. This configuration has favored the formation of a estuarine sedimentary delta, because of topographically controlled lateral migration. This estuarine structure is strongly dominated by the incoming supply of Ma'adim Vallis fluvial sediment extracted from Zephiria Mensae and Lucus Planum. The obtuse-angle geometry of the estuary increases the sedimentation rate, which is higher than in the course of the channel. The sediment deposition process is governed by the estuarine water circulation. The inflowing loaded fluvial water enters the estuary as a bottom current, and mixes with the relatively less-loaded water of the receiving basin. When they mixed. the inflowing fluvial material, and the landward basin circulating water generate an accumulation of highly-diversified estuarine deposit stratification. This accumulation of material is mostly centered in the transitional zone of the delta. The sediment trapping efficiency of the estuary is function of the energy balance between the inflowing fluvial water, and the ingoing basin current. The submergence of the delta by the rising of the water-level increases the estuary water-depth, and consequently the sediment entrapment is favored. The locus of sediment accumulation moves landward in the zone of inflowing fluvial water. This results in the rising of the channel base-level, thus in the increase of the length of the longitudinal graded-profile. The sediment deposit facies of the zone A shows a generally smooth surface. The longitudinal deposit is bordered by alluvial terraces that reflect the variations of the channel level. The waning of the Elysium Basin caused the erosion of the Basin estuarine zone by small channels, this episode being characterized by dissected tear-drop shaped mesa-like morphologies in the delta. Our estuarine delta model predicts a lithostratigraphic depositional sequence associated with the water submergence and the transgression of Elysium Basin. The thickness of the estuarine sediment corresponds to the Elysium Basin levels changes relatively to the bed floor of the estuary, The depositional sequence of Ma'adim Vallis are described: (1) a pro-current filled region (A), where fluvial are longitudinally accumulated by the inflowing water, (2) inverse current from Elysium Basin (B), where fluvial and lacustrine sediments are accumulated, and (3) zone of current equilibrium (C), where the sediments are distributed as a shoreline at the boundary of the estuarine delta. The estuary sedimentology dynamics collects and keeps the record of the geologic unit material crossed by Ma'adim Vallis, and those of the lakebed deposit of Elysium Basin. The predicted mixed stratigraphic sequence from fluvial and lacustrine sediment makes this site an exceptional environment to concentrate potential multi-origin biologic records. We envision four possible strategies to explore this sedimentologic record: (1) longitudinal surface and subsurface traverses in region A to investigate outcrop levees, (2) exploration of the mesa walls in region B, (3) deep drilling hole lodging of the sequential deposits in the zones A and B, and (4) surface and subsurface exploration of the shoreline delta. The expected results for each of these strategies are: (1) in the deepest layers of region A are predicted frequent and abundant coarse material, sandy lenses lamination grading downward from sand to cobbles. Volcanic debris from the Noachian crustal Plateau unit material, hydrothermal altered rocks, carbonates, Hesperian and possibly Amazonian volcanic material, from Apollinaris Patera, altered rocks and carbonates from Zephiria Mensae are expected. As a favorable environment for inception of life, possible biological records are expected in transported rock, (2) At the surface, and subsurface (<=100 m), large deposits sandy to silted material from Elysium paleolake basin mixed with fine-grained sediments from Ma'adim Vallis are expected mostly in the upstream part of region B, (3) on the shoreline of the estuarine delta, abundant fine material from Elysium paleolake basin (evaporites, carbonates), mostly Amazonian in age are expected. The Ma'adini estuary is a favorable landing site for all the above mentioned science aspects, and .for its location. The site lies near the equator, which is favorable for the rover solar power supply, and at 1000m elevation, which is a favorable configuration for the descent system braking. Another advantage is the extent of the area of high scientific interest (33,000 sq km), which provides a good ellipse, and potential long study traverses.

Grin, E. A.↗
DOE OSTI2021

Photoferrotrophy and phototrophic extracellular electron uptake is common in the marine anoxygenic phototroph Rhodovulum sulfidophilum

Photoferrotrophy allows anoxygenic phototrophs to use reduced iron as an electron donor for primary productivity. Recent work shows that freshwater photoferrotrophs can use electrons from solid-phase conductive substances via phototrophic extracellular electron uptake (pEEU), and the two processes share the underlying electron uptake mechanism. However, the ability of marine phototrophs to perform photoferrotrophy and pEEU, and the contribution of these processes to primary productivity is largely unknown. To fill this knowledge gap, we isolated 15 new strains of the marine anoxygenic phototroph Rhodovulum sulfidophilum on electron donors such as acetate and thiosulfate. We observed that all of the R. sulfidophilum strains isolated can perform photoferrotrophy. Furthermore, we chose strain AB26 as a representative strain to study further, and find that it can also perform pEEU from poised electrodes. We show that during pEEU, AB26 transfers electrons to the photosynthetic electron transport chain. Furthermore, systems biology-guided mutant analysis shows that R. sulfidophilum AB26 uses a previously unknown diheme cytochrome c protein, which we call EeuP, for pEEU but not photoferrotrophy. Homologs of EeuP occur in a range of widely distributed marine microbes. Overall, these results suggest that photoferrotrophy and pEEU contribute to the biogeochemical cycling of iron and carbon in marine ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Human exposure to large solar particle events in space

Whenever energetic solar protons produced by solar particle events traverse bulk matter, they undergo various nuclear and atomic collision processes which significantly alter the physical characteristics and biologically important properties of their transported radiation fields. These physical interactions and their effect on the resulting radiation field within matter are described within the context of a recently developed deterministic, coupled neutron-proton space radiation transport computer code (BRYNTRN). Using this computer code, estimates of human exposure in interplanetary space, behind nominal (2 g/sq cm) and storm shelter (20 g/sq cm) thicknesses of aluminum shielding, are made for the large solar proton event of August 1972. Included in these calculations are estimates of cumulative exposures to the skin, ocular lens, and bone marrow as a function of time during the event. Risk assessment in terms of absorbed dose and dose equivalent is discussed for these organs. Also presented are estimates of organ exposures for hypothetical, worst-case flare scenarios. The rate of dose equivalent accumulation places this situation in an interesting region of dose rate between the very low values of usual concern in terrestrial radiation environments and the high-dose-rate values prevalent in radiation therapy.

Townsend, L. W.↗
NASA NTRS1992

Space medicine research: Needs for the 21st century

Space medicine research in the 21st century will continue to focus on the four major areas including: (1) expansion of the current incomplete knowledge base of clinical and subclinical physiological changes due to microgravity; (2) development of countermeasures to extend the capabilities of the human performance envelope in extended duration flights; (3) development of novel methods for delivering all aspects of a comprehensive health care system in extreme remote conditions: and (4) further research and application of systems for biological materials processing. New space transportation vehicles will place unique physiologic and human factors demands on the human system, while providing better access to platforms for materials processing. Success in meeting the demands in each of the noted research areas will require an extensive, interactive team approach. Personnel from the medical research,operational, developmental, and basic science communities will be essential to success.

Pepper, L. J.↗
NASA NTRS2016

Transcriptomic Response of Drosophila Melanogaster Pupae Developed in Hypergravity

The metamorphosis of Drosophila is evolutionarily adapted to Earth's gravity, and is a tightly regulated process. Deviation from 1g to microgravity or hypergravity can influence metamorphosis, and alter associated gene expression. Understanding the relationship between an altered gravity environment and developmental processes is important for NASA's space travel goals. In the present study, 20 female and 20 male synchronized (Canton S, 2 to 3day old) flies were allowed to lay eggs while being maintained in a hypergravity environment (3g). Centrifugation was briefly stopped to discard the parent flies after 24hrs of egg laying, and then immediately continued until the eggs developed into P6-staged pupae (25 - 43 hours after pupation initiation). Post hypergravity exposure, P6-staged pupae were collected, total RNA was extracted using Qiagen RNeasy mini kits. We used RNA-Seq and qRT-PCR techniques to profile global transcriptomic changes in early pupae exposed to chronic hypergravity. During the pupal stage, Drosophila relies upon gravitational cues for proper development. Assessing gene expression changes in the pupa under altered gravity conditions helps highlight gravity dependent genetic pathways. A robust transcriptional response was observed in hypergravity-exposed pupae compared to controls, with 1,513 genes showing a significant (q < 0.05) difference in gene expression. Five major biological processes were affected: ion transport, redox homeostasis, immune response, proteolysis, and cuticle development. This outlines the underlying molecular changes occurring in Drosophila pupae in response to hypergravity.

RNASeq↗
NASA NTRSDate not supplied

Biomanufacturing in Space: BioNutrients and CO2-Based Manufacturing

Biomanufacturing can provide on-demand production of mission-critical compounds and materials to support long-duration space exploration while circumventing the challenges of transporting materials from Earth. Synthetic Biology Project is developing two biomanufacturing capabilities: BioNutrients and CO2-Based Manufacturing. BioNutrients is an ongoing mission aboard the International Space Station focused on the production of perishable nutrients in an on demand for direct for consumption. The first flight experiment of this project targeted the production of carotenoids: β-carotene and zeaxanthin, in recombinant yeast strains. Since then, the project has expanded to encompass the production of the fermented consumables like yogurt and kefir for use as a nutrient delivery mechanism. The CO2-Based Manufacturing system aims to use in situ resources to allow for biomanufacturing with minimal re-supply required. The manufacturing platform is combined with an electrochemical CO2 conversion system which can produce simple carbon substrates to support microbial based biomanufacturing. A comprehensive ground-based platform for recombinant protein purification is in development with the goal of producing a thermostable carbonic anhydrase enzyme from E. coli utilizing CO2-derived acetate. Our group hopes to propel advancements in space biomanufacturing for long duration space flight by harnessing the tools of synthetic biology.

Matthew Brian Paddock↗
NASA NTRS1992

Glucose transporters and maximal transport are increased in endurance-trained rat soleus

Voluntary wheel running induces an increase in the concentration of the regulatable glucose transporter (GLUT4) in rat plantaris muscle but not in soleus muscle (K. J. Rodnick, J. O. Holloszy, C. E. Mondon, and D. E. James. Diabetes 39: 1425-1429, 1990). Wheel running also causes hypertrophy of the soleus in rats. This study was undertaken to ascertain whether endurance training that induces enzymatic adaptations but no hypertrophy results in an increase in the concentration of GLUT4 protein in rat soleus (slow-twitch red) muscle and, if it does, to determine whether there is a concomitant increase in maximal glucose transport activity. Female rats were trained by treadmill running at 25 m/min up a 15% grade, 90 min/day, 6 days/wk for 3 wk. This training program induced increases of 52% in citrate synthase activity, 66% in hexokinase activity, and 47% in immunoreactive GLUT4 protein concentration in soleus muscles without causing hypertrophy. Glucose transport activity stimulated maximally with insulin plus contractile activity was increased to roughly the same extent (44%) as GLUT4 protein content in soleus muscle by the treadmill exercise training. In a second set of experiments, we examined whether a swim-training program increases glucose transport activity in the soleus in the presence of a maximally effective concentration of insulin. The swimming program induced a 44% increase in immunoreactive GLUT4 protein concentration. Glucose transport activity maximally stimulated with insulin was 62% greater in soleus muscle of the swimmers than in untrained controls. Training did not alter the basal rate of 2-deoxyglucose uptake.(ABSTRACT TRUNCATED AT 250 WORDS).

Non-NASA Center↗
NASA NTRS2001

Measurement of Charged Particle Interactions in Spacecraft and Planetary Habitat Shielding Materials

The Microgravity Materials Program, through its 98-HEDS-04 Research Announcement, has called for research to support 'enhanced human radiation protection through the development of light weight soft goods with high radiation protection characteristics.' Given the nature of the particle flux from the Galactic Cosmic Radiation (GCR), and the many constraints on the depth and type of shielding in spacecraft and planetary habitats, it is clear that the health risks these particles present to astronauts in deep space cannot be entirely eliminated. It is the objective of this project to develop a highly accurate model of GCR transport so that NASA can develop and validate the properties of protective shielding materials with the best available information. The validity of the GCR transport model depends in large part on having accurate and precise input data in the form of the charge-changing and fragment production cross sections for the heavy ions of greatest biological significance. The accuracy of the transport model can be evaluated and enhanced by employing the following a three-step strategy: (1) New cross section data will be made available to the NASA-Langley scientists responsible for the transport codes, and will be used as inputs to the codes; (2) The codes will be used to predict additional cross sections and/or details of the radiation field behind realistic shielding arrangements, where the materials and configurations may be quite complex. Mock-ups of the shielding configurations suitable for use in accelerator experiments will obtained by the NASA-Langley co-investigators; and (3) The transport model predictions will be tested in accelerator-based experiments. The time scale for one pass through these steps is well-suited to a four-year schedule. Over a longer term, these steps may be repeated, leading to still further refinements of the transport code, new predictions, and an additional round of measurements, until the desired predictive accuracy is achieved. The focus of this work is primarily on the first of these steps, the determination of fragmentation cross sections, which will be the main task in years one and two. The detailed strategy for carrying out the remainder of the program is more difficult to specify, as it depends on unpredictable factors such as the extent to which the transport model must be modified, schedules for accelerator time, target fabrication, etc.

Zeitlin, C.↗
DOE OSTI2022

Structure of the human cation–chloride cotransport KCC1 in an outward-open state

Cation–chloride cotransporters (CCCs) catalyze electroneutral symport of Cl - with Na + and/or K + across membranes. CCCs are fundamental in cell volume homeostasis, transepithelia ion movement, maintenance of intracellular Cl - concentration, and neuronal excitability. Here, we present a cryoelectron microscopy structure of human K + –Cl - cotransporter (KCC)1 bound with the VU0463271 inhibitor in an outward-open state. In contrast to many other amino acid–polyamine–organocation transporter cousins, our first outward-open CCC structure reveals that opening the KCC1 extracellular ion permeation path does not involve hinge-bending motions of the transmembrane (TM) 1 and TM6 half-helices. Instead, rocking of TM3 and TM8, together with displacements of TM4, TM9, and a conserved intracellular loop 1 helix, underlie alternate opening and closing of extracellular and cytoplasmic vestibules. We show that KCC1 intriguingly exists in one of two distinct dimeric states via different intersubunit interfaces. Our studies provide a blueprint for understanding the mechanisms of CCCs and their inhibition by small molecule compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media

We report that microbial biofilms are ubiquitous within porous media and the dynamics of their growth influence surface and subsurface flow patterns which impacts the physical properties of porous media and large-scale transport of solutes. Here, a two-dimensional pore-scale numerical model was used to evaluate the impact of biofilm-induced flow heterogeneities on conservative transport. Our study integrates experimental biofilm images of Paenibacillus 300A strain in a microfluidic device packed with cylindrical grains in a hexagonal distribution, with mathematical modeling. Biofilm is represented as a synthetic porous structure with locally varying physical properties that honors the impact of biofilm on the porous medium. We find that biofilm plays a major role in shaping the observed conservative transport dynamics by enhancing anomalous characteristics. More specifically, when biofilm is present, the pore structure in our geometry becomes more spatially correlated. We observe intermittent behavior in the Lagrangian velocities that switches between fast transport periods and long trapping events. Our results suggest that intermittency enhances solute spreading in breakthrough curves which exhibit extreme anomalous slope at intermediate times and very marked late solute arrival due to solute retention. The efficiency of solute retention by the biofilm is controlled by a transport regime which can extend the tailing in the concentration breakthrough curves. These results indicate that solute retention by the biofilm exerts a strong control on conservative solute transport at pore-scale, a role that to date has not received enough attention.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1999

Water transport by the bacterial channel alpha-hemolysin

This study is an investigation of the ability of the bacterial channel alpha-hemolysin to facilitate water permeation across biological membranes. alpha-Hemolysin channels were incorporated into rabbit erythrocyte ghosts at varying concentrations, and water permeation was induced by mixing the ghosts with hypertonic sucrose solutions. The resulting volume decrease of the ghosts was followed by time-resolved optical absorption at pH 5, 6, and 7. The average single-channel permeability coefficient of alpha-hemolysin for water ranged between 1.3x10-12 cm/s and 1.5x10-12 cm/s, depending on pH. The slightly increased single-channel permeability coefficient at lower pH-values was attributed to an increase in the effective pore size. The activation energy of water transport through the channel was low (Ea=5.4 kcal/mol), suggesting that the properties of water inside the alpha-hemolysin channel resemble those of bulk water. This conclusion was supported by calculations based on macroscopic hydrodynamic laws of laminar water flow. Using the known three-dimensional structure of the channel, the calculations accurately predicted the rate of water flow through the channel. The latter finding also indicated that water permeation data can provide a good estimate of the pore size for large channels.

Non-NASA Center↗
DOE OSTI2024

Perspective on Integrative Simulations of Bioenergetic Domains

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, in this work, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Arabidopsis ABCG14 forms a homodimeric transporter for multiple cytokinins and mediates long-distance transport of isopentenyladenine-type cytokinins

Phytohormone cytokinins (CKs), primarily including trans-zeatin (tZ) and isopentenyladenine (iP) types, play critical roles in plant growth, development, and stress response. Long-distance transport of trans-zeatin (tZ)-type CKs has been well elucidated. However, long-distance transport of isopentenyladenine (iP)-type CKs remains unknown. Here, we demonstrated that the physiologically characterized ABC transporter AtABCG14 is also involved in long-distance transport of iP-type CKs. Biochemical characterization of AtABCG14 revealed that it forms homodimers and exhibits transporter properties towards multiple CKs, including iP and tZ types. AtABCG14 expression was induced by iP-type CKs in wild type and cyp735a1/a2 (cypDM) double mutant. The triple mutant atabcg14 cypDM exhibited more severe developmental phenotypes than atabcg14 and cypDM. CK quantification and 2 H 6 -iP isotope tracer experiment showed that the root-to-shoot transport of iP-type CKs was suppressed in atabcg14 cypDM. The reciprocal grafting of atabcg14 cypDM and cypDM revealed that AtABCG14 is responsible for the root xylem-loading and shoot phloem-distribution in the shootward transport of iP-type cytokinoins. Additionally, 2 H 6 -iP tracer experiment showed that the rootward transport of iP-type CKs was dependent on AtABCG14 expression in the roots. Collectively, our results demonstrate the long-distance circular transport of iP-type CKs mediated by AtABCG14 and provide new insights into the transport of CKs and other phytohormones.

59 BASIC BIOLOGICAL SCIENCES↗