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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain: Periplasmic Ligand Binding Protein Dret_0059

We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from the Salt Lake Retba in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously and their best known function is in solute transport across membranes. PAS-like sensor domains are commonly found in signal transduction proteins. These domains are widely observed as parts of many protein architectures and complexes but have not been observed previously within the same polypeptide chain. In the structure of Dret_0059, a ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS-like domain of the tandem PAS-like domain. Differential scanning flourimetry support the binding of ligands observed in the crystal structure. There is significant interaction between the SBP and tandem PAS-like domains, and it is possible that the binding of one ligand could have an effect on the binding of the other. We uncovered three other proteins with this structural architecture in the non-redundant sequence data base, and predict that they too bind the same substrates. The genomic context of this protein did not offer any clues for its function. We did not find any biological process in which the two observed ligands are coupled. The protein Dret_0059 could be involved in either signal transduction or solute transport.

Wu, R.↗
DOE OSTI2016

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

Plants and fungi use light and other signals to regulate development, growth, and metabolism. The fruiting bodies of the fungus Phycomyces blakesleeanus are single cells that react to environmental cues, including light, but the mechanisms are largely unknown [1]. The related fungus Mucor circinelloides is an opportunistic human pathogen that changes its mode of growth upon receipt of signals from the environment to facilitate pathogenesis [2]. Understanding how these organisms respond to environmental cues should provide insights into the mechanisms of sensory perception and signal transduction by a single eukaryotic cell, and their role in pathogenesis. We sequenced the genomes of P. blakesleeanus and M. circinelloides and show that they have been shaped by an extensive genome duplication or, most likely, a whole-genome duplication (WGD), which is rarely observed in fungi [3–6]. We show that the genome duplication has expanded gene families, including those involved in signal transduction, and that duplicated genes have specialized, as evidenced by differences in their regulation by light. The transcriptional response to light varies with the developmental stage and is still observed in a photoreceptor mutant of P. blakesleea-nus. A phototropic mutant of P. blakesleeanus with a heterozygous mutation in the photoreceptor gene madA demonstrates that photosensor dosage is important for the magnitude of signal transduction. We conclude that the genome duplication provided the means to improve signal transduction for enhanced perception of environmental signals. Our results will help to understand the role of genome dynamics in the evolution of sensory perception in eukaryotes.

Genome, Fungi↗
DOE OSTI2020

Cavity electro-optics in thin-film lithium niobate for efficient microwave-to-optical transduction

Linking superconducting quantum devices to optical fibers via microwave-optical quantum transducers may enable large-scale quantum networks. For this application, transducers based on the Pockels electro-optic (EO) effect are promising for their direct conversion mechanism, high bandwidth, and potential for low-noise operation. However, previously demonstrated EO transducers require large optical pump power to overcome weak EO coupling and reach high efficiency. Here, we create an EO transducer in thin-film lithium niobate, a platform that provides low optical loss and strong EO coupling. We demonstrate on-chip transduction efficiencies of up to and of optical pump power. The transduction efficiency can be improved by further reducing the microwave resonator’s piezoelectric coupling to acoustic modes, increasing the optical resonator quality factor to previously demonstrated levels, and changing the electrode geometry for enhanced EO coupling. We expect that with further development, EO transducers in thin-film lithium niobate can achieve near-unity efficiency with low optical pump power.

Holzgrafe, Jeffrey (ORCID:0000000160121451)↗
DOE OSTI2018

Energy Transduction in Nitrogenase

Nitrogenase is a complicated two-component enzyme system that uses ATP binding and hydrolysis energy to achieve one of the most difficult chemical reactions in nature, the reduction of N2 to NH3. One component of the Mo-based nitrogenase system, Fe protein, delivers electrons one at a time to the second component, the catalytic MoFe protein. This process occurs through a series of synchronized events collectively called the “Fe protein cycle”. Elucidating details of the events associated with this cycle has constituted an important challenge in understanding the nitrogenase mechanism. Electron delivery is a multistep process involving three metal clusters with intra- and interprotein events. It is proposed that the first electron transfer event is a gated intraprotein transfer of one electron from the MoFe protein P-cluster to the FeMo cofactor. Measurement of the effect of osmotic pressure on the rate of this electron transfer process revealed that it is gated by protein conformational changes. This first electron transfer is activated by binding of the Fe protein containing two bound ATP molecules. The mechanism of how this protein-protein association triggers electron transfer remains unknown. The second electron transfer event is proposed to be a rapid interprotein “backfill” with transfer of one electron from the reduced Fe protein 4Fe-4S cluster to the oxidized P-cluster. In this way, electron delivery can be viewed as a case of “deficit spending”. Such a deficit-spending electron transfer process can be envisioned as a way to achieve one-direction electron flow, limiting the potential for back electron flow. Hydrolysis of two ATP molecules associated with the Fe protein occurs after the electron transfer and therefore is not used to directly drive the electron transfer. Rather, ATP hydrolysis is proposed to contribute to relaxation of the “activated” conformational state associated with the ATP form of the complex, with the free energy from ATP hydrolysis being used to pay back energy associated with component protein association and electron transfer. Release of inorganic phosphate (Pi) and protein-protein dissociation follow electron transfer and ATP hydrolysis. The ratelimiting step for the Fe protein cycle is not dissociation of the two proteins, as previously believed, but rather is release of Pi after ATP hydrolysis, which is then followed by rapid protein-protein complex dissociation. Nitrogenase is composed of two catalytic halves that do not function independently but rather exhibit anticooperative nuclear motion in which electron transfer in one-half of the complex partially inhibits electron transfer and ATP hydrolysis in the other half. Calculations indicated the existence of anticooperative interactions across the entire nitrogenase complex, suggesting a mechanism for the control of events on opposite ends of this large complex. The mechanistic necessity for this anticooperative process remains unknown. This Account presents a working model for how all of these processes work together in the nitrogenase “machine” to transduce the energy from ATP binding and hydrolysis to drive N2 reduction.

Seefeldt, Lance C.↗
DOE OSTI2016

Unveiling the Structural Basis That Regulates the Energy Transduction Properties within a Family of Triheme Cytochromes from Geobacter sulfurreducens

A family of triheme cytochromes from Geobacter sulfurreducens plays an important role in extracellular electron transfer. In addition to their role in electron transfer pathways, two members of this family (PpcA and PpcD) were also found to be able to couple e(-)/H+ transfer through the redox Bohr effect observed in the physiological pH range, a feature not observed for cytochromes PpcB and PpcE. In attempting to understand the molecular control of the redox Bohr effect in this family of cytochromes, which is highly homologous both in amino acid sequence and structures, it was observed that residue 6 is a conserved leucine in PpcA and PpcD, whereas in the other two characterized members (PpcB and PpcE) the equivalent residue is a phenylalanine. To determine the role of this residue located close to the redox Bohr center, we replaced Leu(6) in PpcA with Phe and determined the redox properties of the mutant, as well as its solution structure in the fully reduced state. In contrast with the native form, the mutant PpcAL6F is not able to couple the e(-)/H+ pathway. We carried out the reverse mutation in PpcB and PpcE (i.e., replacing Phe(6) in these two proteins by leucine) and the mutated proteins showed an increased redox Bohr effect. The results clearly establish the role of residue 6 in the control of the redox Bohr effect in this family of cytochromes, a feature that could enable the rational design of G. sulfurreducens strains that carry mutant cytochromes with an optimal redox Bohr effect that would be suitable for various biotechnological applications.

Dantas, Joana M.↗
DOE OSTI2023

Channel capacity: limitation of entropy rate during cell signal transduction

Cellular signal transduction is mediated through chain activation reactions involving signalling molecules. Information thermodynamics may be a promising approach for quantifying signal transduction. A cell signal is transduced through the signal molecule activation as a step of a signal transduction cascade. In each step, two types of entropy can be defined. First, the signal transduction was defined using thermodynamic entropy production during the chemical activation of signal molecules. Second, the chronology was described as a code string, and the logarithm of the number of signal code strings corresponded to the information entropy. Finally, the total entropy during signal transduction was determined by summing the two entropies. When maximising the total entropy, the total entropy rate per signalling molecule concentration was found to be consistent independently of each transduction step (i.e., signal molecule types). Consequently, the speed limit of the entropy rate can be calculated, providing the capacity, which is an essential property of the signal transduction cascade. The theory introduced here is expected to provide a basic framework for understanding new methods of discovering signal cascades and intracellular signal transduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structures of the TMC-1 complex illuminate mechanosensory transduction

The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel1. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid–protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microwave and Optical Entanglement for Quantum Transduction with Electro-Optomechanics

Quantum transduction refers to the coherent conversion between microwave and optical states, which can be achieved by quantum teleportation if given high-fidelity microwave-optical entanglement, namely entanglement-based quantum transduction. Reliable microwave-optical entanglement can be generated using various platforms. Here, in this paper we base the discussion on a piezo-optomechanical system and make the teleportation induced conversion scheme more concrete in the framework of quantum channel theory. By comparing the quantum capacity between the entanglement-based conversion channel and the traditional direct quantum transduction channel, we show that the entanglement-based scheme indeed admits a positive transduction rate when the direct quantum transduction has zero quantum capacity. Given two piezo-optomechanical systems, we also investigate the generation of microwave-microwave entanglement from entanglement swapping within continuous-variable and discrete-variable settings, showing the potentials of directly connecting microwave quantum processors by microwave-microwave quantum teleportation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Kullback–Leibler Divergence of an Open-Queuing Network of a Cell-Signal-Transduction Cascade

Queuing networks (QNs) are essential models in operations research, with applications in cloud computing and healthcare systems. However, few studies have analyzed the cell’s biological signal transduction using QN theory. This study entailed the modeling of signal transduction as an open Jackson’s QN (JQN) to theoretically determine cell signal transduction, under the assumption that the signal mediator queues in the cytoplasm, and the mediator is exchanged from one signaling molecule to another through interactions between the signaling molecules. Each signaling molecule was regarded as a network node in the JQN. The JQN Kullback–Leibler divergence (KLD) was defined using the ratio of the queuing time (λ) to the exchange time (μ), λ/μ. The mitogen-activated protein kinase (MAPK) signal-cascade model was applied, and the KLD rate per signal-transduction-period was shown to be conserved when the KLD was maximized. Our experimental study on MAPK cascade supported this conclusion. This result is similar to the entropy-rate conservation of chemical kinetics and entropy coding reported in our previous studies. Thus, JQN can be used as a novel framework to analyze signal transduction.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Overcoming the fundamental limit of quantum transduction via intraband entanglement

A quantum transducer converts an input signal to an output probe at a distant frequency band while maintaining the quantum information with high fidelity, which is crucial for quantum networking and distributed quantum sensing and computing. In terms of microwave–optical quantum transduction, the state-of-the-art quantum transducers suffer low transduction efficiency from weak nonlinear coupling, wherein increasing pump power to enhance efficiency inevitably leads to thermal noise from heating. Moreover, we reveal that the efficiency-bandwidth product of a cavity electro-optical or electro-optomechanical transducer is fundamentally limited by pump power and nonlinear coupling coefficient, irrespective of cavity engineering efforts. To overcome this fundamental limit, we propose to noiselessly boost the transduction efficiency by consuming intraband entanglement (e.g., microwave–microwave or optical–optical entanglement in the case of microwave–optical transduction). Via a squeezer–coupler–antisqueezer sandwich structure, the protocol enhances the transduction efficiency to unity in the ideal lossless case, given an arbitrarily weak pump and nonlinear coupling. In practical cavity systems, our entanglement-assisted protocol surpasses the non-assisted fundamental limit of the efficiency-bandwidth product and reduces the threshold cooperativity for positive quantum capacity by a factor proportional to two-mode squeezing gain. Given a fixed cooperativity, our approach increases the broadband quantum capacity by orders of magnitude. The entanglement-assisted advantage is robust to ancilla loss and cavity detuning.

Shi, Haowei [Southern California U.] (ORCID:000000↗
DOE OSTI2018

Energy transduction ferroic materials

Ferroic materials and multiferroics, characterized by their ferroic orders, provide an efficient route for the coupling control of magnetic, mechanical, and electrical subsystems in energy transduction, which aims at converting one form of energy into another. A surge of interest in the ferroic coupling effect has stemmed from its potential use as a new versatile route for energy transduction. Here, the recent progress on the use of (multi)ferroic materials is reviewed, with special emphasis on the fundamental mechanisms that dictate the energy transduction process, including piezoelectricity, pyroelectricity, electrocaloric, magnetostriction, magnetocaloric, elastocaloric, magnetoelectricity, and emerging spin-charge conversion. Research on energy transduction ferroic materials paves the way for ubiquitous energy harvesting through magneto-mechano-electric-thermal coupling mechanisms. Lastly, a summary and the future prospective directions of this field are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Self-complementary and tyrosine-mutant rAAV vectors enhance transduction in cystic fibrosis bronchial epithelial cells

Recombinant adeno-associated virus (rAAV) vector platforms have shown considerable therapeutic success in gene therapy for inherited disorders. In cystic fibrosis (CF), administration of first-generation rAAV2 was safe, but clinical benefits were not clearly demonstrated. Therefore, next-generation vectors that overcome rate-limiting steps in rAAV transduction are needed to obtain successful gene therapy for this devastating disease. In this study, we evaluated the effects of single-strand or self-complementary (sc) rAAV vectors containing single or multiple tyrosine-to-phenylalanine (Y-F) mutations in capsid surface-exposed residues on serotypes 2, 8 or 9. For this purpose, CF bronchial epithelial (CFBE) cells were transduced with rAAV vectors, and the transgene expression of enhanced green fluorescence protein (eGFP) was analyzed at different time points. The effects of vectors on the cell viability, host cell cycle and in association with co-adjuvant drugs that modulate intracellular vector trafficking were also investigated. Six rAAV vectors demonstrated greater percentage of eGFP{sup +} cells compared to their counterparts at days 4, 7 and 10 post-transduction: rAAV2 Y(272,444,500,730)F, with 1.95-, 3.5- and 3.06-fold increases; rAAV2 Y(252,272,444,500,704,730)F, with 1.65-, 2.12-, and 2-fold increases; scrAAV2 WT, with 1.69-, 2.68-, and 2.32-fold increases; scrAAV8 Y773F, with 57-, 6.06-, and 7-fold increases; scrAAV9 WT, with 7.47-, 4.64-, and 3.66-fold increases; and scrAAV9 Y446F, with 8.39-, 4.62-, and 4.4-fold increases. At days 15, 20, and 30 post-transduction, these vectors still demonstrated higher transgene expression than transfected cells. Although the percentage of eGFP{sup +} cells reduced during the time-course analysis, the delta mean fluorescence intensity increased. These vectors also led to increased percentage of cells in G{sub 1}-phase without eliciting any cytotoxicity. Prior administration of bortezomib or genistein did not increase eGFP expression in cells transduced with either rAAV2 Y(272,444,500,730)F or rAAV2 Y(252,272,444,500,704,730)F. In conclusion, self-complementary and tyrosine capsid mutations on rAAV serotypes 2, 8, and 9 led to more efficient transduction than their counterparts in CFBE cells by overcoming the intracellular trafficking and second-strand DNA synthesis limitations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction

ABSTRACT Bacteriophytochrome photoreceptors (BphPs) and their cognate response regulators make up two-component signal transduction systems which direct bacteria to mount phenotypic responses to changes in environmental light quality. Most of these systems utilize single-domain response regulators to transduce signals through unknown pathways and mechanisms. Here we describe the photocycle and autophosphorylation kinetics of RtBphP1, a red light-regulated histidine kinase from the desert bacterium Ramlibacter tataouinensis . RtBphP1 undergoes red to far-red photoconversion with rapid thermal reversion to the dark state. RtBphP1 is autophosphorylated in the dark; this activity is inhibited under red light. The RtBphP1 cognate response regulator, the R. tataouinensis bacteriophytochrome response regulator (RtBRR), and a homolog, AtBRR from Agrobacterium tumefaciens , crystallize unexpectedly as arm-in-arm dimers, reliant on a conserved hydrophobic motif, hFWAhL (where h is a hydrophobic M, V, L, or I residue). RtBRR and AtBRR dimerize distinctly from four structurally characterized phytochrome response regulators found in photosynthetic organisms and from all other receiver domain homodimers in the Protein Data Bank. A unique cacodylate-zinc-histidine tag metal organic framework yielded single-wavelength anomalous diffraction phases and may be of general interest. Examination of the effect of the BRR stoichiometry on signal transduction showed that phosphorylated RtBRR is accumulated more efficiently than the engineered monomeric RtBRR (RtBRR mon ) in phosphotransfer reactions. Thus, we conclude that arm-in-arm dimers are a relevant signaling intermediate in this class of two-component regulatory systems. IMPORTANCE BphP histidine kinases and their cognate response regulators comprise widespread red light-sensing two-component systems. Much work on BphPs has focused on structural understanding of light sensing and on enhancing the natural infrared fluorescence of these proteins, rather than on signal transduction or the resultant phenotypes. To begin to address this knowledge gap, we solved the crystal structures of two single-domain response regulators encoded by a region immediately downstream of that encoding BphPs. We observed a previously unknown arm-in-arm dimer linkage. Monomerization via deletion of the C-terminal dimerization motif had an inhibitory effect on net response regulator phosphorylation, underlining the importance of these unusual dimers for signal transduction.

Baker, Anna W.↗
DOE OSTI2023

Thermodynamics of signal transduction systems and fluctuation theorem in a signal cascade

Biochemical chain reactions are signal transduction cascades that can transmit biological information about the intracellular environment. In this study, we modelled a chain reaction as a code string for applying information theory. Herein, we assumed that cell signal transduction selects a strategy to maximize the transduced signal per signal event duration. To investigate the same, we calculated the information transmission capacity of the reaction chain by maximizing the average entropy production rate per reaction time, indicating the idea of the entropy coding method. Moreover, we defined a signal cascade trajectory. Subsequently, we found that the logarithm of the forward and reverse transition ratio per reaction time is equal to the entropy production rate, which derives the form of the fluctuation theorem in signal transduction. Our findings suggest the application of information entropy theory for analysing signal transduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enhancement of microwave to optical spin-based quantum transduction via a magnon mode

We propose a method for converting single microwave photons to single optical sideband photons based on spinful impurities in magnetic materials. This hybrid system is advantageous over previous proposals because (i) the implementation allows much higher transduction rates (10 3 times faster at the same optical pump Rabi frequency) than state-of-the-art devices, (ii) high-efficiency transduction is found to happen in a significantly larger space of device parameters (in particular, over 1 GHz microwave detuning), and (iii) it does not require mode volume matching between optical and microwave resonators. We identify the needed magnetic interactions as well as potential materials systems to enable this speed up using erbium dopants for telecom compatibility. This is an important step towards realizing high-fidelity entangling operations between remote qubits and will provide additional control of the transduction through perturbation of the magnet.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Epidermal growth factor receptor cascade prioritizes the maximization of signal transduction

Many studies have been performed to quantify cell signaling. Cell signaling molecules are phosphorylated in response to extracellular stimuli, with the phosphorylation sequence forming a signal cascade. The information gain during a signal event is given by the logarithm of the phosphorylation molecule ratio. The average information gain can be regarded as the signal transduction quantity (ST), which is identical to the Kullback–Leibler divergence (KLD), a relative entropy. We previously reported that if the total ST value in a given signal cascade is maximized, the ST rate (STR) of each signaling molecule per signal duration (min) approaches a constant value. To experimentally verify this theoretical conclusion, we measured the STR of the epidermal growth factor (EGF)-related cascade in A431 skin cancer cells following stimulation with EGF using antibody microarrays against phosphorylated signal molecules. The results were consistent with those from the theoretical analysis. Thus, signaling transduction systems may adopt a strategy that prioritizes the maximization of ST. Furthermore, signal molecules with similar STRs may form a signal cascade. In conclusion, ST and STR are promising properties for quantitative analysis of signal transduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Aluminum scandium nitride films for piezoelectric transduction into silicon at gigahertz frequencies

Recent advances in the growth of aluminum scandium nitride films on silicon suggest that this material platform could be applied for quantum electromechanical applications. Here, we model, fabricate, and characterize microwave frequency silicon phononic delay lines with transducers formed in an adjacent aluminum scandium nitride layer to evaluate aluminum scandium nitride films, at 32% scandium, on silicon interdigital transducers for piezoelectric transduction into suspended silicon membranes. We achieve an electromechanical coupling coefficient of 2.7% for the extensional symmetric-like Lamb mode supported in the suspended material stack and show how this coupling coefficient could be increased to at least 8.5%, which would further boost transduction efficiency and reduce the device footprint. The one-sided transduction efficiency, which quantifies the efficiency at which the source of microwave photons is converted to microwave phonons in the silicon membrane, is 10% at 5 GHz at room temperature and, as we discuss, there is a path to increase this toward near-unity efficiency based on a combination of modified device design and operation at cryogenic temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A study of mechanoelectrical transduction behavior in polyvinyl chloride (PVC) gel as smart sensors

Abstract Polyvinyl chloride (PVC) gels are soft electroactive polymers (EAPs) being researched for soft robotic applications. Sensing properties of these EAPs have not been investigated in detail in regard to fundamental mechanoelectrical transduction behavior, but this smart material has been shown to exhibit a detectable response to external stimuli. This study shows PVC gels to be an extremely sensitive material when undergoing mechanoelectrical transduction and explores some response dependencies and proposes a theoretical framework for mechanoelectrical transduction within the gel. The work presented here also uncovers a very interesting phenomena under extremely low compressive loads during the initial contact with the gel. This phenomenon is attributed to a surface tension creeping motion onto the loading surface with an accompanying polarity inversion in the sensing signal relative to fully loaded gels in compression. Experimental work on hysteresis was also completed showing very little memory in steady state mechanoelectrical response to repeated stepped loading cycles. This study demonstrates the mechanoelectric ability of PVC gels to perform in sensing experiments and acts as a fundamental framework to further broaden the applications of PVC gel sensors.

Instruments & Instrumentation↗