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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

The Enzyme Activity and Substrate Specificity of Two Major Cinnamyl Alcohol Dehydrogenases in Sorghum ( Sorghum bicolor ), SbCAD2 and SbCAD4

Cinnamyl alcohol dehydrogenase (CAD) catalyzes the final step in monolignol biosynthesis, reducing sinapaldehyde, coniferaldehyde, and p-coumaraldehyde to their corresponding alcohols in an NADPHdependent manner. Because of its terminal location in monolignol biosynthesis, the variation in substrate specificity and activity of CAD can result in significant changes in overall composition and amount of lignin. Our in-depth characterization of two major CAD isoforms, SbCAD2 (Brown midrib 6 [bmr6]) and SbCAD4, in lignifying tissues of sorghum (Sorghum bicolor), a strategic plant for generating renewable chemicals and fuels, indicates their similarity in both structure and activity to Arabidopsis (Arabidopsis thaliana) CAD5 and Populus tremuloides sinapyl alcohol dehydrogenase, respectively. This first crystal structure of a monocot CAD combined with enzyme kinetic data and a catalytic model supported by site-directed mutagenesis allows full comparison with dicot CADs andelucidates the potential signature sequence for their substrate specificity and activity. Here, the L119W/G301F-SbCAD4 double mutant displayed its substrate preference in the order coniferaldehyde > p-coumaraldehyde > sinapaldehyde, with higher catalytic efficiency than that of both wild-type SbCAD4 and SbCAD2. As SbCAD4 is the only major CAD isoform in bmr6 mutants, replacing SbCAD4 with L119W/G301F-SbCAD4 in bmr6 plants could produce a phenotype that is more amenable to biomass processing.

09 BIOMASS FUELS↗
DOE OSTI2025

Design Basis Document / Owner’s Technical Specification for Nitrate Salt Systems in CSP Projects: Volume 1 Specifications for Parabolic Trough Projects, Volume 2 - Specifications for Central Receiver Projects, Volume 3 - Narrative

Design Basis Documents / Owner’s Technical Specifications are developed for parabolic trough and central receiver power plants using nitrate salt as the heat transport fluid and the thermal storage medium. The goals were to 1) distill the successful experience with nitrate salt systems from as many commercial projects as possible, 2) provide technical bases for equipment design/selection that an owner can impose on an EPC contractor, 3) compile this information in one location to provide guidance on salt systems that is as broadly applicable to as many projects as possible, and 4) work toward an industry consensus on a Design Basis Document that reflects the lessons learned from earlier commercial projects. The document allows an owner to provide design guidance, and to impose a minimum set of requirements, above and beyond those in the normal Codes and Standards, on an EPC contractor in an effort to avoid a repeat of past mistakes. If successful, this would allow salt systems to achieve the same levels of reliability and availability as commercial parabolic trough plants using diphenyl oxide / biphenyl (i.e., Dowtherm A, Therminol VP-1) as the heat transfer fluid. The report consists of 3 volumes: • Volume 1 - Specifications for Parabolic Trough Projects • Volume 2 - Specifications for Central Receiver Projects • Volume 3 - Narrative Volumes 1 and 2 include discussions of the following topics: • Plant functional requirements for the salt systems • Plant operating states, and transitions between states, for the salt systems • Risk analysis of the principal salt components • Plant requirements for the salt systems to meet the functional and the operating requirements • Type of specification for the principal salt components: functional; or prescriptive • Current state of the art for salt systems. Volume 3 discusses a number of cases in which the salt equipment at commercial parabolic trough and central receiver projects has not met the projected levels of reliability and availability. Possible reasons for the sources of the problems are discussed, as is a range of possible alternate designs that could avoid the known problems.

14 SOLAR ENERGY↗
DOE OSTI2018

Potential-specific structure at the hematite-electrolyte interface

The atomic-scale structure of interfaces between metal oxides and aqueous electrolytes controls their catalytic, geochemical, and corrosion behavior. Measurements that probe these interfaces in situ provide important details of ion and solvent arrangements, but atomically precise structural models do not exist for common oxide-electrolyte interfaces far from equilibrium. Using a novel cell, we measured the structure of the hematite (a-Fe 2 O 3 ) (110$\bar{2}$)-electrolyte interface under controlled electrochemical bias using synchrotron crystal truncation rod X ray scattering. At increasingly cathodic potentials, charge-compensating protonation of surface oxygen groups increases the coverage of specifically bound water while adjacent water layers displace outwardly and became disordered. Returning to open circuit potential leaves the surface in a persistent metastable protonation state. The flux of current and ions at applied potential is thus regulated by a unique interfacial electrolyte environment, suggesting that electrical double layer models should be adapted to the dynamically changing interfacial structure far from equilibrium.

electrochemistry↗
DOE OSTI2015

Degradation in PV Encapsulation Transmittance: An Interlaboratory Study Towards a Climate-Specific Test: Preprint

Reduced optical transmittance of encapsulants resulting from ultraviolet (UV) degradation has frequently been identified as a cause of decreased PV module performance through the life of service in the field. The present module safety and qualification standards, however, apply short UV doses only capable of examining design robustness or 'infant mortality' failures. Essential information that might be used to screen encapsulation through product lifetime remains unknown. For example, the relative efficacy of xenon-arc and UVA-340 fluorescent sources or the typical range of activation energy for degradation is not quantified. We have conducted an interlaboratory experiment to provide the understanding that will be used towards developing a climate- and configuration-specific (UV) weathering test. Five representative, known formulations of EVA were studied in addition to one TPU material. Replicate laminated silica/polymer/silica specimens are being examined at 14 institutions using a variety of indoor chambers (including Xenon, UVA-340, and metal-halide light sources) or field aging. The solar-weighted transmittance, yellowness index, and the UV cut-off wavelength, determined from the measured hemispherical transmittance, are examined to provide understanding and guidance for the UV light source (lamp type) and temperature used in accelerated UV aging tests.

14 SOLAR ENERGY↗
DOE OSTI2014

Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-Monophosphate

Cyclic nucleotide phosphodiesterases (PDEs) decompose second messengers cAMP and cGMP that play critical roles in many physiological processes. PDE1 of Saccharomyces cerevisiae has been subcloned and expressed in Escherichia coli . Recombinant yPDE1 has a K M of 110 μM and a k cat of 16.9 s⁻¹ for cAMP and a K M of 105 μM and a k cat of 11.8 s₅⁻¹ for cGMP. Thus, the specificity constant (k cat /K M cAMP )/(k cat /K M cGMP ) of 1.4 indicates a dual specificity of yPDE1 for hydrolysis of both cAMP and cGMP. The crystal structures of unliganded yPDE1 and its complex with GMP at 1.31 Å resolution reveal a new structural folding that is different from those of human PDEs but is partially similar to that of some other metalloenzymes such as metallo-β-lactamase. In spite of their different structures and divalent metals, yPDE1 and human PDEs may share a common mechanism for hydrolysis of cAMP and cGMP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A Real-Time Vehicle-Specific Eco-Routing Model for On-Board Navigation Applications Capturing Transient Vehicle Behavior

The paper develops a real-time vehicle-specific eco-routing model for use in on-board navigation systems for both conventional fuel- and battery-powered electric vehicles. The model uses a novel link cost function that retains all microscopic transient behavior along a link by capturing within-link speed, acceleration, and road grade variations. Specifically, eight vehicle-agnostic link-specific variables are transmitted to the cloud and fused with information received from other connected vehicles. The fused data are then sent back to the connected vehicles and used to compute vehicle-specific eco-routes (edge computing). The solution produces an energy-efficient dynamic user-equilibrium traffic assignment that is solved incrementally. A numerical experiment is first designed to test the model, demonstrating the benefits associated with vehicle-specific eco-routes compared to those produced by traditional models. The model is then implemented in a micro-simulation framework to evaluate the network-wide impacts of the proposed energy-efficient user-optimum incremental traffic assignment for different traffic demand levels. Results demonstrate that the proposed model produces lower network-wide energy consumption levels compared to traditional energy-efficient and travel time user-optimum traffic assignment methods for both conventional fuel and electric vehicles. Conventional fuel savings relative to travel time routing decrease with increasing traffic demand levels, while electric power savings do not vary monotonically with congestion levels. Energy savings relative to traditional eco-routing are also demonstrated to not vary monotonically with demand levels. Results of the study also demonstrate that the transportation network layout significantly affects the eco-routing system performance. Finally, the feasibility of the proposed model in real-world applications is discussed and presented.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
NASA NTRS1992

Specification Reformulation During Specification Validation

The goal of the ARIES Simulation Component (ASC) is to uncover behavioral errors by 'running' a specification at the earliest possible points during the specification development process. The problems to be overcome are the obvious ones the specification may be large, incomplete, underconstrained, and/or uncompilable. This paper describes how specification reformulation is used to mitigate these problems. ASC begins by decomposing validation into specific validation questions. Next, the specification is reformulated to abstract out all those features unrelated to the identified validation question thus creating a new specialized specification. ASC relies on a precise statement of the validation question and a careful application of transformations so as to preserve the essential specification semantics in the resulting specialized specification. This technique is a win if the resulting specialized specification is small enough so the user my easily handle any remaining obstacles to execution. This paper will: (1) describe what a validation question is; (2) outline analysis techniques for identifying what concepts are and are not relevant to a validation question; and (3) identify and apply transformations which remove these less relevant concepts while preserving those which are relevant.

Benner, Kevin M.↗
DOE OSTI2015

Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

ABSTRACT Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ- d -Glu-A 2 pm (A 2 pm is diaminopimelic acid) cysteine amidase (or dl -endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l -Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation. IMPORTANCE Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.

Xu, Qingping↗
DOE OSTI2012

Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase

Purine nucleoside phosphorylases catalyze the phosphorolytic cleavage of the glycosidic bond of purine (2{prime}-deoxy)nucleosides, generating the corresponding free base and (2{prime}-deoxy)ribose 1-phosphate. Two classes of PNPs have been identified: homotrimers specific for 6-oxopurines and homohexamers that accept both 6-oxopurines and 6-aminopurines. Bacillus cereus adenosine phosphorylase (AdoP) is a hexameric PNP; however, it is highly specific for 6-aminopurines. To investigate the structural basis for the unique substrate specificity of AdoP, the active-site mutant D204N was prepared and kinetically characterized and the structures of the wild-type protein and the D204N mutant complexed with adenosine and sulfate or with inosine and sulfate were determined at high resolution (1.2-1.4 {angstrom}). AdoP interacts directly with the preferred substrate through a hydrogen-bond donation from the catalytically important residue Asp204 to N7 of the purine base. Comparison with Escherichia coli PNP revealed a more optimal orientation of Asp204 towards N7 of adenosine and a more closed active site. When inosine is bound, two water molecules are interposed between Asp204 and the N7 and O6 atoms of the nucleoside, thus allowing the enzyme to find alternative but less efficient ways to stabilize the transition state. The mutation of Asp204 to asparagine led to a significant decrease in catalytic efficiency for adenosine without affecting the efficiency of inosine cleavage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

SoyCSN: Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data

The Soybean Gene Atlas project provides a comprehensive map for understanding gene expression patterns in major soybean tissues from flower, root, leaf, nodule, seed, and shoot and stem. The RNA-Seq data generated in the project serve as a valuable resource for discovering tissue-specific transcriptome behavior of soybean genes in different tissues. We developed a computational pipeline for Soybean context-specific network (SoyCSN) inference with a suite of prediction tools to analyze, annotate, retrieve, and visualize soybean context-specific networks at both transcriptome and interactome levels. BicMix and Cross-Conditions Cluster Detection algorithms were applied to detect modules based on co-expression relationships across all the tissues. Soybean context-specific interactomes were predicted by combining soybean tissue gene expression and protein–protein interaction data. Functional analyses of these predicted networks provide insights into soybean tissue specificities. For example, under symbiotic, nitrogen-fixing conditions, the constructed soybean leaf network highlights the connection between the photosynthesis function and rhizobium–legume symbiosis. SoyCSN data and all its results are publicly available via an interactive web service within the Soybean Knowledge Base (SoyKB) at http://soykb.org/SoyCSN. SoyCSN provides a useful web-based access for exploring context specificities systematically in gene regulatory mechanisms and gene relationships for soybean researchers and molecular breeders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease

HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Position-specific isotope effects during alkaline hydrolysis of 2,4-dinitroanisole resolved by compound-specific isotope analysis, 13 C NMR, and density-functional theory

Compound-specific isotope analysis (CSIA), position-specific isotope analysis (PSIA), and computational modeling (e.g., quantum mechanical models; reactive-transport models) are increasingly being used to monitor and predict biotic and abiotic transformations of organic contaminants in the field. However, identifying the isotope effect(s) associated with a specific transformation remains challenging in many cases. We describe and interpret the position-specific isotope effects of C and N associated with a SN 2 Ar reaction mechanism by a combination of CSIA and PSIA using quantitative 13 C nuclear magnetic resonance spectrometry, and density-functional theory, using 2,4-dinitroanisole (DNAN) as a model compound. The position-specific 13 C enrichment factor of O–C 1 bond at the methoxy group attachment site (ε C1 ) was found to be approximately -41‰, a diagnostic value for transformation of DNAN to its reaction products 2,4-dinitrophenol and methanol. Theoretical kinetic isotope effects calculated for DNAN isotopologues agreed well with the position-specific isotope effects measured by CSIA and PSIA. This combination of measurements and theoretical predictions demonstrates a useful tool for evaluating degradation efficiencies and/or mechanisms of organic contaminants and may promote new and improved applications of isotope analysis in laboratory and field investigations.

13C NMR↗