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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Meeting report: The first soil viral workshop 2022

Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15 and 17th of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarized in this report.

09 BIOMASS FUELS↗
DOE OSTI2014

Thermodynamics and solvent linkage of macromolecule–ligand interactions

Binding involves two steps, desolvation and association. While water is ubiquitous and occurs at high concentration, it is typically ignored. In vitro experiments typically use infinite dilution conditions, while in vivo, the concentration of water is decreased due to the presence of high concentrations of molecules in the cellular milieu. Our paper discusses isothermal titration calorimetry approaches that address the role of water in binding. For example, use of D2O allows the contribution of solvent reorganization to the enthalpy component to be assessed. Furthermore, the addition of osmolytes will decrease the water activity of a solution and allow effects on Ka to be determined. In most cases, binding becomes tighter in the presence of osmolytes as the desolvation penalty associated with binding is minimized. In other cases, the osmolytes prefer to interact with the ligand or protein, and if their removal is more difficult than shedding water, then binding can be weakened. Lastly, these complicating layers can be discerned by different slopes in ln(Ka) vs osmolality plots and by differential scanning calorimetry in the presence of the osmolyte.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH results in an ATP binding site that is undisturbed by crystal contacts and adopts a conformation consistent with nucleotide binding and hydrolysis. Strikingly, this new FRH structure adopts an arch domain conformation that is dramatically altered from previous structures. Comparison of the existing FRH structures reveals conserved hinge points that appear to facilitate arch motion. Regions in the arch have been previously shown to mediate a variety of protein-protein interactions critical for RNA surveillance and circadian clock functions. The conformational changes highlighted in the FRH structures provide a platform for investigating the relationship between arch dynamics and Mtr4/FRH function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Empirical evidence that glucan-interacting amino acid side chains within the transmembrane channel collectively facilitate cellulose synthase function

The fundamental mechanism of cellulose synthesis is widely conserved across Kingdoms and depends on cellulose synthases, which are processive, dual-function, family 2 glycosyltransferases (GT-2). These enzymes polymerize glucose on the cytoplasmic side of the plasma membrane and export the glucan chain to the cell surface through an integral transmembrane (TM) channel. Structural studies of active plant cellulose synthases (CESAs) have revealed interactions between the nascent glucan chain and the side chains of polar, charged, and aromatic amino acid residues that line the TM channel. However, the functional consequences of modifying these side chains have not been tested in vivo in CESAs or other processive GT-2s. To test this, we used an established in vivo assay based on genetic complementation of CESA5 in the moss, Physcomitrium patens. For accurate prediction of glucan-interacting amino acid residues, we generated a complete homotrimeric molecular model of PpCESA5 using a combination of homology and de novo modeling. All-atom molecular dynamics-based analyses of contact metrics and interaction energy identified 23 amino acid residues with high propensity to interact with the nascent glucan chain within the TM channel or on the apoplastic surface of PpCESA5. Mutating any one of 18 of these amino acid residues to alanine, thereby removing their side chains, abolished or impaired CESA function, with the strongest effects observed upon the loss of charged amino acid side chains. This provides direct evidence to support the hypothesis that multiple amino acid residues collectively maintain a smooth energy landscape within the TM channel to facilitate glucan translocation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Mechanism of RecO recruitment to DNA by single-stranded DNA binding protein

RecO is a recombination mediator protein (RMP) important for homologous recombination, replication repair and DNA annealing in bacteria. In all pathways, the single-stranded (ss) DNA binding protein, SSB, plays an inhibitory role by protecting ssDNA from annealing and recombinase binding. Conversely, SSB may stimulate each reaction through direct interaction with RecO. We present a crystal structure of Escherichia coli RecO bound to the conserved SSB C-terminus (SSB-Ct). SSB-Ct binds the hydrophobic pocket of RecO in a conformation similar to that observed in the ExoI/SSB-Ct complex. Hydrophobic interactions facilitate binding of SSB-Ct to RecO and RecO/RecR complex in both low and moderate ionic strength solutions. In contrast, RecO interaction with DNA is inhibited by an elevated salt concentration. The SSB mutant lacking SSB-Ct also inhibits RecO-mediated DNA annealing activity in a salt-dependent manner. Neither RecO nor RecOR dissociates SSB from ssDNA. Therefore, in E. coli, SSB recruits RMPs to ssDNA through SSB-Ct, and RMPs are likely to alter the conformation of SSB-bound ssDNA without SSB dissociation to initiate annealing or recombination. Intriguingly, Deinococcus radiodurans RecO does not bind SSB-Ct and weakly interacts with the peptide in the presence of RecR, suggesting the diverse mechanisms of DNA repair pathways mediated by RecO in different organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex

Multi-aminoacyl-tRNA synthetase complex (MSC) is the second largest machinery for protein synthesis in human cells and also regulates multiple nontranslational functions through its components. Prior studies have shown that the MSC can respond to external signals by releasing its components to function outside it. The internal assembly is fundamental to MSC regulation. Here, using crystal structural analyses (at 1.88 Å resolution) along with molecular modeling, gel-filtration chromatography, and co-immunoprecipitation, we report that human lysyl-tRNA synthetase (LysRS) forms a tighter assembly with the scaffold protein aminoacyl-tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2) than previously observed. Wefound that two AIMP2 N-terminal peptides form an antiparallel scaffold and hold two LysRS dimers through four binding motifs and additional interactions. Of note, the four catalytic subunits of LysRS in the tightly assembled complex were all accessible for tRNA recognition. We further noted that two recently reported human disease-associated mutations conflict with this tighter assembly, cause LysRS release from the MSC, and inactivate the enzyme. These findings reveal a previously unknown dimension of MSC subcomplex assembly and suggest that the retractility of this complex may be critical for its physiological functions.

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

From Protein Design to the Energy Landscape of a Cold Unfolding Protein

Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein–water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ~0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Synthesis, crystal structure, and magnetic properties of bis(aqua)[μ-(terepthalato-κo,κo´)]copper(II)monohydrate [Cu(C₈O₄)(OH₂)₂]·H₂O

A novel one dimensional Cu(II) coordination polymer [Cu(C₈O₄)(OH₂)₂] ·H₂O 1 has been synthesized and characterized by elemental analysis, IR spectroscopy, X-ray crystal diffraction and magnetic measurements. Single-crystal structural analysis shows that complex 1 consist of 1D Cu(II) chain containing threefold bridging ligands, one (syn–syn) carboxylate and two water molecules. The magnetic study of 1 has been investigated, indicating an overall antiferromagnetic interaction in the complex. - Graphical abstract: The complex [Cu(C₈O₄)(OH₂)₂] ·H₂O was prepared by the reaction of solid copper(II)basic carbonate with an aqueous solution of sodium terephthalate under heating at 50–60 {sup o}C after which it was allowed to crystallize at room temperature. The structure of the complex is distorted octahedral. Magnetic study of the complex reveals antiferromagnetic behaviour. Highlights: • A novel copper(II) coordination polymer with terepthalate dianion was grown in an aqueous solution. • The single crystal growth temperature was 25 °C for period of two weeks. • The magnetic property of the complex was studied using SQUID. • The complex showed antiferromagnetic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Climate change alters slug abundance but not herbivory in a temperate grassland

Climate change will significantly impact the world’s ecosystems, in part by altering species interactions and ecological processes, such as herbivory and plant community dynamics, which may impact forage quality and ecosystem production. Yet relatively few field experimental manipulations assessing all of these parameters have been performed to date. To help fill this knowledge gap, we evaluated the effects of increased temperature (+3°C day and night, year-round) and precipitation (+30% of mean annual rainfall) on slug herbivory and abundance and plant community dynamics biweekly in a pasture located in central Kentucky, U.S.A. Warming increased slug abundance once during the winter, likely due to improving conditions for foraging, whereas warming reduced slug abundance at times in late spring, mid-summer, and early fall (from 62–95% reduction depending on month). We found that warming and increased precipitation did not significantly modify slug herbivory at our site, despite altering slug abundance and affecting plant community composition and forage quality. Climate change will alter seasonal patterns of slug abundance through both direct effects on slug biology and indirect effects mediated by changes in the plant community, suggesting that pasture management practices may have to adapt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Status of Lattice QCD Calculations of One and Two-Nucleon Matrix Elements

Lattice QCD calculations of basic hadronic quantities are now often performed with systematic control over the physical pion mass, continuum and infinite volume limits. This progress signals a new era in which lattice QCD will be used to compute basic properties of hadrons, nucleons and light nuclei directly from the Standard Model (SM). In particular, we will be able to use lattice QCD, combined with Effective Field Theory, to make quantitative statements about the interaction of SM matter and potential beyond the SM physics ranging from direct dark matter detection to permanent electric dipole moments. I will briefly review the status and challenges of lattice QCD calculations of select one- and two-nucleon matrix elements. These calculations are significantly more challenging than the basic quantities computed with all systematics controlled, but substantial progress is being made.

Walker-Loud, Andre↗
DOE OSTI2016

Probing Lipophilic Adamantyl Group as the P1-Ligand for HIV-1 Protease Inhibitors: Design, Synthesis, Protein X-ray Structural Studies, and Biological Evaluation

A series of potent HIV-1 protease inhibitors with a lipophilic adamantyl P1 ligand have been designed, synthesized, and evaluated. We have developed an enantioselective synthesis of adamantane-derived hydroxyethylamine isosteres utilizing Sharpless asymmetric epoxidation as the key step. Various inhibitors incorporating P1-adamantylmethyl in combination with P2 ligands such as 3-(R)-THF, 3-(S)-THF, bis-THF, and THF-THP were examined. The S1' pocket was also probed with phenyl and phenylmethyl ligands. Inhibitor 15d, with an isobutyl P1' ligand and a bis-THF P2 ligand, proved to be the most potent of the series. Lastly, the cLogP value of inhibitor 15d is improved compared to inhibitor 2 with a phenylmethyl P1-ligand. X-ray structural studies of 15d, 15h, and 15i with HIV-1 protease complexes revealed molecular insight into the inhibitor–protein interaction.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1988

Fluctuations and massive separation in three-dimensional shock-wave/boundary-layer interactions

Shock-wave unsteadiness was observed in rapidly compressed supersonic turbulent boundary layer flows with significant separation. A Mach 2.85 shock-wave/turbulent boundary layer flow was set up over a series of cylinder-flare bodies in the High Reynolds Number Channel 1. The transition from fully attached to fully separated flow was studied using axisymmetric flares with increasing compression angles. In the second phase, the 30 deg flare was inclined relative to the cylinder axis, so that the effect on a separated flow of increasing 3 dimensionality could be observed. Two 3-D separated cases are examined. A simple conditional sampling technique is applied to the data to group them according to an associated shock position. Mean velocities and turbulent kinetic energies, computed from the conditionally samples data, are compared to those from the unsorted data and to computed values. Three basic questions were addressed: can conditional sampling be used to provide snapshots of the flow; are averaged turbulence quantities dominated by the bimodal nature of the interaction; and is the shock unsteadiness really important to computational accuracy.

Kussoy, M. I.↗
DOE OSTI2013

Isolation of Two Agostic Isomers of an Organometallic Cation: Different Structures and Colors

Two isomers of [CpMo(CO)2(PiPr3)]+ were isolated, and both were characterized by x-ray crystallography and spectroscopic data. The two differ in the location of the agostic interaction with the metal, from either the CH (methine) or CH3 (methyl) group of the ligand. We thank the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences for support of this work. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The computational studies were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL.

agostic interactions↗
NASA NTRS1988

Fluctuations and massive separation in three-dimensional shock-wave/boundary-layer interactions

Shock-wave unsteadiness was observed in rapidly compressed supersonic turbulent boundary layer flows with significant separation. A Mach 2.85 shock-wave/turbulent boundary layer flow was set up over a series of cylinder-flare bodies in the High Reynolds Number Channel 1. The transition from fully attached to fully separated flow was studied using axisymmetric flares with increasing compression angles. In the second phase, the 30-deg flare was inclined relative to the cylinder axis, so that the effect on a separated flow of increasing three-dimensionality could be observed. Two 3-D separated cases are examined. A simple conditional sampling technique is applied to the data to group them according to an associated shock position. Mean velocities and turbulent kinetic energies, computed from the conditionally sampled data, are compared to those from the unsorted data and to computed values. Three basic questions were addressed: can conditional sampling be used to provide snapshots of the flow; are averaged turbulence quantities dominated by the bimodal nature of the interaction; and is the shock unsteadiness really important to computational accuracy.

Kussoy, M. I.↗
NASA NTRS2001

ISS Microgravity Research Payload Training Methodology

The NASA Microgravity Research Discipline has multiple categories of science payloads that are being planned and currently under development to operate on various ISS on-orbit increments. The current program includes six subdisciplines; Materials Science, Fluids Physics, Combustion Science, Fundamental Physics, Cellular Biology and Macromolecular Biotechnology. All of these experiment payloads will require the astronaut various degrees of crew interaction and science observation. With the current programs planning to build various facility class science racks, the crew will need to be trained on basic core operations as well as science background. In addition, many disciplines will use the Express Rack and the Microgravity Science Glovebox (MSG) to utilize the accommodations provided by these facilities for smaller and less complex type hardware. The Microgravity disciplines will be responsible to have a training program designed to maximize the experiment and hardware throughput as well as being prepared for various contingencies both with anomalies as well as unexpected experiment observations. The crewmembers will need various levels of training from simple tasks as power on and activate to extensive training on hardware mode change out to observing the cell growth of various types of tissue cultures. Sample replacement will be required for furnaces and combustion type modules. The Fundamental Physics program will need crew EVA support to provide module change out of experiment. Training will take place various research centers and hardware development locations. It is expected that onboard training through various methods and video/digital technology as well as limited telecommunication interaction. Since hardware will be designed to operate from a few weeks to multiple research increments, flexibility must be planned in the training approach and procedure skills to optimize the output as well as the equipment maintainability. Early increment lessons learned will be addressed.

Schlagheck, Ronald↗
DOE OSTI2018

Modeling Host-Pathogen Interactions in the Context of the Microenvironment: Three-Dimensional Cell Culture Comes of Age

Tissues and organs provide the structural and biochemical landscapes upon which microbial pathogens and commensals function to regulate health and disease. While flat two-dimensional (2-D) monolayers composed of a single cell type have provided important insight into understanding host-pathogen interactions and infectious disease mechanisms, these reductionist models lack many essential features present in the native host microenvironment that are known to regulate infection, including three-dimensional (3-D) architecture, multicellular complexity, commensal microbiota, gas exchange and nutrient gradients, and physiologically relevant biomechanical forces (e.g., fluid shear, stretch, compression). Here, a major challenge in tissue engineering for infectious disease research is recreating this dynamic 3-D microenvironment (biological, chemical, and physical/mechanical) to more accurately model the initiation and progression of host-pathogen interactions in the laboratory. Here we review selected 3-D models of human intestinal mucosa, which represent a major portal of entry for infectious pathogens and an important niche for commensal microbiota. We highlight seminal studies that have used these models to interrogate host-pathogen interactions and infectious disease mechanisms, and we present this literature in the appropriate historical context. Models discussed include 3-D organotypic cultures engineered in the rotating wall vessel (RWV) bioreactor, extracellular matrix (ECM)-embedded/organoid models, and organ-on-a-chip (OAC) models. Collectively, these technologies provide a more physiologically relevant and predictive framework for investigating infectious disease mechanisms and antimicrobial therapies at the intersection of the host, microbe, and their local microenvironments.

3-D↗
DOE OSTI2021

Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts

Abstract Predicting the quaternary structure of protein complex is an important problem. Inter‐chain residue‐residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter‐chain contacts. Here, we develop the first method based on gradient descent optimization (GD) to build quaternary structures of protein dimers utilizing inter‐chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true/predicted contacts and monomer structures as input. GD consistently performs better than both simulated annealing and Markov Chain Monte Carlo simulation. Starting from an arbitrarily quaternary structure randomly initialized from the tertiary structures of protein chains and using true inter‐chain contacts as input, GD can reconstruct high‐quality structural models for homodimers and heterodimers with average TM‐score ranging from 0.92 to 0.99 and average interface root mean square distance from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter‐chain contacts as restraints, the average TM‐score of the structural models built by GD is 0.76. For 46% of the homodimers, high‐quality structural models with TM‐score ≥ 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. Only a moderate precision or recall of inter‐chain contact prediction is needed to build good structural models for most homodimers. Moreover, GD improves the quality of quaternary structures predicted by AlphaFold2 on a Critical Assessment of Techniques for Protein Structure Prediction–Critical Assessments of Predictions of Interactions dataset.

59 BASIC BIOLOGICAL SCIENCES↗