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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 OSTI2021

Proline hydroxylase domain-containing enzymes regulate calcium levels in cardiomyocytes by TRPA1 ion channel

Highlights: • PHD induces calcium release from cardiomyocytes through ryanodine channel. • PHD activates TRPA1 to induce extracellular calcium ions into the cell and further activate the ryanodine channel. • TRPA1 is involved in the regulation of PHD-Ca2+-AMPK signaling pathway. The proline hydroxylase domain-containing enzymes (PHDs) acts as cellular oxygen sensors, inducing a series of responses to hypoxia, especially during the regulation of metabolism and energy homeostasis. The increase of Ca{sup 2+} in cardiomyocytes, induced by the opening of PHD signaling pathway, is the key initiation signal necessary for the PHD-mediated regulation of the energy metabolism pathway, but the underlying molecular mechanism remains incompletely understood. This study used PHD inhibitors (PHIs) and PHD2-specific RNA interference (PHD2shRNA) to inhibit PHD signals in cardiomyocytes to explore whether transient receptor potential ankyrin 1 (TRPA1) is involved in the regulation of calcium ion influx in the PHD activation pathway associated with to AMP-activated protein kinase (AMPK). The Fluo-3AM probe was used to measure changes in free intracellular calcium ion concentrations, and Western blot analysis was used to detect the levels of phosphorylated (P)-AMPK, TRPA1, and P–Ca{sup 2+}/calmodulin-dependent protein kinase Ⅱ (CaMKⅡ) levels. The PHI-mediated inhibition of PHD resulted in an increase in free Ca{sup 2+} fluorescence in cardiomyocytes, which activated AMPK, TRPA1, and CaMKⅡ. The TRPA1 inhibitor HC030031, the CaMKII inhibitor KN93, and a ryanodine inhibitor (Ryanodine) were all able to inhibit the PHI-induced increase in intracellular Ca{sup 2+} and AMPK activation. Both PHIs and PHD2shRNA were able to effectively activate CaMKII and TRPA1. However, an inositol 1,4,5-triphosphate receptor (IP3R) inhibitor and the protein kinase A (PKA) inhibitor H89 did not significantly inhibit the PHI-induced increase in intracellular Ca{sup 2+} and AMPK activation. These results indicated that PHD might activate the CaMKⅡ pathway through the TRPA1 ion channel, inducing the release of calcium from the sarcoplasmic reticulum through ryanodine receptor 2 (RyR2), activating AMPK to initiate the protective effects of hypoxia in cardiomyocytes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel–Ligand Docking

The identification of promising lead compounds showing pharmacological activities toward a biological target is essential in early stage drug discovery. With the recent increase in available small-molecule databases, virtual high-throughput screening using physics-based molecular docking has emerged as an essential tool in assisting fast and cost-efficient lead discovery and optimization. However, the best scored docking poses are often suboptimal, resulting in incorrect screening and chemical property calculation. We address the pose classification problem by leveraging data-driven machine learning approaches to identify correct docking poses from AutoDock Vina and Glide screens. To enable effective classification of docking poses, we present two convolutional neural network approaches: a three-dimensional convolutional neural network (3D-CNN) and an attention-based point cloud network (PCN) trained on the PDBbind refined set. We demonstrate the effectiveness of our proposed classifiers on multiple evaluation data sets including the standard PDBbind CASF-2016 benchmark data set and various compound libraries with structurally different protein targets including an ion channel data set extracted from Protein Data Bank (PDB) and an in-house KCa3.1 inhibitor data set. Our experiments show that excluding false positive docking poses using the proposed classifiers improves virtual high-throughput screening to identify novel molecules against each target protein compared to the initial screen based on the docking scores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Water, Protons, and the Gating of Voltage-Gated Potassium Channels

Ion channels are ubiquitous throughout all forms of life. Potassium channels are even found in viruses. Every cell must communicate with its surroundings, so all cells have them, and excitable cells, in particular, especially nerve cells, depend on the behavior of these channels. Every channel must be open at the appropriate time, and only then, so that each channel opens in response to the stimulus that tells that channel to open. One set of channels, including those in nerve cells, responds to voltage. There is a standard model for the gating of these channels that has a section of the protein moving in response to the voltage. However, there is evidence that protons are moving, rather than protein. Water is critical as part of the gating process, although it is hard to see how this works in the standard model. Here, we review the extensive evidence of the importance of the role of water and protons in gating these channels. Our principal example, but by no means the only example, will be the Kv1.2 channel. Evidence comes from the effects of D2O, from mutations in the voltage sensing domain, as well as in the linker between that domain and the gate, and at the gate itself. There is additional evidence from computations, especially quantum calculations. Structural evidence comes from X-ray studies. The hydration of ions is critical in the transfer of ions in constricted spaces, such as the gate region and the pore of a channel; we will see how the structure of the hydrated ion fits with the structure of the channel. In addition, there is macroscopic evidence from osmotic experiments and streaming current measurements. The combined evidence is discussed in the context of a model that emphasizes the role of protons and water in gating these channels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Ion Channel Laser Based on Direct Laser Acceleration of a Shaped Beam Driver (Final Technical Report)

The main focus of our research was to understand the synergies between an electron bunch and a laser pulse when the two co-propagate through the plasma. We have clearly demonstrated using theoretical and computational modeling that the propagation distance of both the bunch and the laser pulse could be extended. The ability of the combined bunch/pulse system to extend the propagation distance and the size of the plasma bubble enables highly-efficient sources of relativistic electrons. As pointed out by the Plasma Decadal Study, such electron sources can be used for generating extremely bright x-rays for a variety of applications can serve as probes and diagnostics for other plasma experiments: high energy density (HED) sciences, inertial confinement fusion (ICF), and potentially Fusion Materials and Technology (FM&T). Development of advanced diagnostics of plasma-based accelerators is yet another key area identified by recent reports. Even broader security and medical applications of compact accelerator-based radiation sources, such as very high energy electron (VHEE) sources for FLASH radiobiology, have been identified by a recent multi-agency panel. A number of key technical issues were considered and successfully resolved during the course of the grant. Those include: beam loading effect of both the driver and witness bunches on the wake, laser channeling by the bunch, and the direct laser acceleration (DLA) of the driver bunch by the laser pulse. To demonstrate clear synergy, we were able to ascertain that the total energy gain of a witness bunch in the wake of the combined bunch/laser complex is large than the sum of the energy gains in the wake of the laser pulse alone, and the driver bunch alone. We have also demonstrated that not only the energy gain is improved, but the energy spread is not sacrificed. To carry out these simulations, we have to develop a range of in-house computational tools, including a fully-3D code WAND-PIC.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Electrosome assembly: Structural insights from high voltage-activated calcium channel (CaV)–chaperone interactions

Ion channels are multicomponent complexes (termed here as“electrosomes”) that conduct the bioelectrical signals required for life. It has been appreciated for decades that assembly is critical for proper channel function, but knowledge of the factors that undergird this important process has been lacking. Although there are now exemplar structures of representatives of most major ion channel classes, there has been no direct structural information to inform how these complicated, multipart complexes are put together or whether they interact with chaperone proteins that aid in their assembly. Recent structural characterization of a complex of the endoplasmic membrane protein complex (EMC) chaperone and a voltage-gated calcium channel (CaV) assembly intermediate comprising the pore-forming CaVα1 and cytoplasmic CaVβ subunits offers the first structural view into the assembly of a member of the largest ion channel class, the voltagegated ion channel (VGIC) superfamily. The structure shows how the EMC remodels the CaVα1/CaVβ complex through a set of rigid body movements for handoff to the extracellular CaVα2δ subunit to complete channel assembly in a process that involves intersubunit coordination of a divalent cation and ordering of CaVα1 elements. These findings set a new framework for deciphering the structural underpinnings of ion channel biogenesis that has implications for understanding channel function, how drugs and disease mutations act, and for investigating how other membrane proteins may engage the ubiquitous EMC chaperone.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Structural interplay of anesthetics and paralytics on muscle nicotinic receptors

General anesthetics and neuromuscular blockers are used together during surgery to stabilize patients in an unconscious state. Anesthetics act mainly by potentiating inhibitory ion channels and inhibiting excitatory ion channels, with the net effect of dampening nervous system excitability. Neuromuscular blockers act by antagonizing nicotinic acetylcholine receptors at the motor endplate; these excitatory ligand-gated ion channels are also inhibited by general anesthetics. The mechanisms by which anesthetics and neuromuscular blockers inhibit nicotinic receptors are poorly understood but underlie safe and effective surgeries. Here we took a direct structural approach to define how a commonly used anesthetic and two neuromuscular blockers act on a muscle-type nicotinic receptor. We discover that the intravenous anesthetic etomidate binds at an intrasubunit site in the transmembrane domain and stabilizes a non-conducting, desensitized-like state of the channel. The depolarizing neuromuscular blocker succinylcholine also stabilizes a desensitized channel but does so through binding to the classical neurotransmitter site. Rocuronium binds in this same neurotransmitter site but locks the receptor in a resting, non-conducting state. Together, this study reveals a structural mechanism for how general anesthetics work on excitatory nicotinic receptors and further rationalizes clinical observations in how general anesthetics and neuromuscular blockers interact.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels

Abstract Kainate receptors (KARs) are a subtype of ionotropic glutamate receptor (iGluR) channels, a superfamily of ligand-gated ion channels which mediate the majority of excitatory neurotransmission in the central nervous system. KARs modulate neuronal circuits and plasticity during development and are implicated in neurological disorders, including epilepsy, depression, schizophrenia, anxiety, and autism. Calcium-permeable KARs undergo ion channel block, but the therapeutic potential of channel blockers remains underdeveloped, mainly due to limited structural knowledge. Here, we present closed-state structures of GluK2 KAR homotetramers in complex with ion channel blockers NpTx-8, PhTx-74, Kukoamine A, and spermine. We find that blockers reside inside the GluK2 ion channel pore, intracellular to the closed M3 helix bundle-crossing gate, with their hydrophobic heads filling the central cavity and positively charged polyamine tails spanning the selectivity filter. Molecular dynamics (MD) simulations of our structures illuminate interactions responsible for different affinity and binding poses of the blockers. Our structures elucidate the trapping mechanism of KAR channel block and provide a template for designing new blockers that can selectively target calcium-permeable KARs in neuropathologies.

Science & Technology - Other Topics↗
DOE OSTI2022

In Vitro and In Vivo Inhibition of the Mycobacterium tuberculosis Phosphopantetheinyl Transferase PptT by Amidinoureas

A newly validated target for tuberculosis treatment is phosphopantetheinyl transferase, an essential enzyme that plays a critical role in the biosynthesis of cellular lipids and virulence factors in Mycobacterium tuberculosis. The structure–activity relationships of a recently disclosed inhibitor, amidinourea (AU) 8918 (1), were explored, focusing on the biochemical potency, determination of whole-cell on-target activity for active compounds, and profiling of selective active congeners. These studies show that the AU moiety in AU 8918 is largely optimized and that potency enhancements are obtained in analogues containing a para-substituted aromatic ring. Preliminary data reveal that while some analogues, including 1, have demonstrated cardiotoxicity (e.g., changes in cardiomyocyte beat rate, amplitude, and peak width) and inhibit Ca v 1.2 and Na v 1.5 ion channels (although not hERG channels), inhibition of the ion channels is largely diminished for some of the para-substituted analogues, such as 5k (p-benzamide) and 5n (p-phenylsulfonamide).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Mechanically activated and deactivated ion transport across nanopores with heterogeneous surface charge distributions

To mimic the intricate and adaptive functionalities of biological ion channels, electrohydrodynamic ion transport has been studied extensively, albeit mostly, across uniformly charged nanochannels. Here, we analyze the ion transport under coupled electric field and pressure across heterogeneously charged nanopores with oppositely charged sections on their lateral surface. We only consider such pores with symmetric hourglass-like and cylindrical shapes to focus on the effects of the non-uniform surface charge distribution. Finite-element simulations of a continuum model demonstrate that a pressure applied in either direction of the pore-axis equally suppresses or amplifies the ionic conductance, depending on the electric field polarity, by distorting the quasi-static distribution of ions in the pore. The resulting anomalous mechanical deactivation and activation of ionic current under opposite voltage biases exhibit the functional modularity of our setup, while their intensities are highly tunable, substantially greater than those of analogous behaviors in other nanochannels, and fundamentally correlated to ionic current rectification (ICR) in our pores. A detailed study of ICR subsequently reveals its counterintuitive non-monotonous variations, in the pores, with the magnitude of applied voltage and the pore length, that can help optimize their diode-like behavior. We further illustrate that while the hourglass-shaped nanopores yield the more efficient mechanical suppressors of ion transport, their cylindrical analogs are the superior rectifiers and mechanical amplifiers of ion conduction. Therefore, this article provides a blueprint for the strategic design of nanofluidic circuits to attain a robust, modular, and tunable control of ion transport under external electrical and mechanical stimuli.

Physics↗
DOE OSTI2022

Heterosynaptic plasticity in biomembrane memristors controlled by pH

Abstract In biology, heterosynaptic plasticity maintains homeostasis in synaptic inputs during associative learning and memory, and initiates long-term changes in synaptic strengths that nonspecifically modulate different synapse types. In bioinspired neuromorphic circuits, heterosynaptic plasticity may be used to extend the functionality of two-terminal, biomimetic memristors. In this article, we explore how changes in the pH of droplet interface bilayer aqueous solutions modulate the memristive responses of a lipid bilayer membrane in the pH range 4.97–7.40. Surprisingly, we did not find conclusive evidence for pH-dependent shifts in the voltage thresholds ( V* ) needed for alamethicin ion channel formation in the membrane. However, we did observe a clear modulation in the dynamics of pore formation with pH in time-dependent, pulsed voltage experiments. Moreover, at the same voltage, lowering the pH resulted in higher steady-state currents because of increased numbers of conductive peptide ion channels in the membrane. This was due to increased partitioning of alamethicin monomers into the membrane at pH 4.97, which is below the pKa (~5.3–5.7) of carboxylate groups on the glutamate residues of the peptide, making the monomers more hydrophobic. Neutralization of the negative charges on these residues, under acidic conditions, increased the concentration of peptide monomers in the membrane, shifting the equilibrium concentrations of peptide aggregate assemblies in the membrane to favor greater numbers of larger, increasingly more conductive pores. It also increased the relaxation time constants for pore formation and decay, and enhanced short-term facilitation and depression of the switching characteristics of the device. Modulating these thresholds globally and independently of alamethicin concentration and applied voltage will enable the assembly of neuromorphic computational circuitry with enhanced functionality. Impact statement We describe how to use pH as a modulatory “interneuron” that changes the voltage-dependent memristance of alamethicin ion channels in lipid bilayers by changing the structure and dynamical properties of the bilayer. Having the ability to independently control the threshold levels for pore conduction from voltage or ion channel concentration enables additional levels of programmability in a neuromorphic system. In this article, we note that barriers to conduction from membrane-bound ion channels can be lowered by reducing solution pH, resulting in higher currents, and enhanced short-term learning behavior in the form of paired-pulse facilitation. Tuning threshold values with environmental variables, such as pH, provide additional training and learning algorithms that can be used to elicit complex functionality within spiking neural networks. Graphical abstract

36 MATERIALS SCIENCE↗
DOE OSTI2020

Quantitative investigation of surface structure and interatomic potential with impact-collision ion scattering spectroscopy

Helium ion beam interactions with materials have important implications for magnetic confinement fusion, material modification, and helium ion microscopy. These interactions depend on the precise physics of how helium ions channel into the materials, which can vary greatly based on the local crystalline orientation. Here, we performed a dedicated experiment to investigate helium ion channeling in a well-characterized tungsten single crystal. Time-of-flight impact-collision ion scattering spectroscopy was used to obtain multi-angle maps of the backscattering intensity for 3 keV He + → W(111). We found that the backscattering intensity profile arising from helium ion channeling could be well described by a shadow cone analysis. This analysis revealed that subsurface W atoms as deep as the ninth monolayer contributed to the backscattering intensity profile. Binary collision approximation simulations were performed with MARLOWE to model the experimental maps with sufficient accuracy to allow for quantitative comparisons using reliability factors. These quantitative comparisons were applied to investigate how the W lattice structure and He–W interatomic potential affect the multi-angle maps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗