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Results for “structure-function”

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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS1999

Proteolytic dissection of Zab, the Z-DNA-binding domain of human ADAR1

Zalpha is a peptide motif that binds to Z-DNA with high affinity. This motif binds to alternating dC-dG sequences stabilized in the Z-conformation by means of bromination or supercoiling, but not to B-DNA. Zalpha is part of the N-terminal region of double-stranded RNA adenosine deaminase (ADAR1), a candidate enzyme for nuclear pre-mRNA editing in mammals. Zalpha is conserved in ADAR1 from many species; in each case, there is a second similar motif, Zbeta, separated from Zalpha by a more divergent linker. To investigate the structure-function relationship of Zalpha, its domain structure was studied by limited proteolysis. Proteolytic profiles indicated that Zalpha is part of a domain, Zab, of 229 amino acids (residues 133-361 in human ADAR1). This domain contains both Zalpha and Zbeta as well as a tandem repeat of a 49-amino acid linker module. Prolonged proteolysis revealed a minimal core domain of 77 amino acids (positions 133-209), containing only Zalpha, which is sufficient to bind left-handed Z-DNA; however, the substrate binding is strikingly different from that of Zab. The second motif, Zbeta, retains its structural integrity only in the context of Zab and does not bind Z-DNA as a separate entity. These results suggest that Zalpha and Zbeta act as a single bipartite domain. In the presence of substrate DNA, Zab becomes more resistant to proteases, suggesting that it adopts a more rigid structure when bound to its substrate, possibly with conformational changes in parts of the protein.

Non-NASA Center↗
NASA NTRS1998

Role of the flocculus of the cerebellum in motor learning of the vestibulo-ocular reflex

Structure-function studies at the systems level are an effective method for understanding the relationship of the central nervous system to behavior. Motor learning or adaptation of the vestibulo-ocular reflex is a clear example wherein this approach has been productive. During a vestibulo-ocular reflex the brain converts a head velocity signal, transduced through the vestibular semicircular canals, into an eye movement command delivered to the extraocular muscles. If the viewed target remains on the fovea of the retina, the reflex is compensatory, and its gain, eye velocity/head velocity, is one. When the image of the viewed object slips across the retina, visual acuity decreases, and the gain of the reflex, which is no longer one, is plastically adapted or adjusted until retinal stability is restored. The anatomic substrate for this plasticity thus involves brain structures in which visual-vestibular interaction can potentially occur, as well as vestibular and visual sensory and oculomotor motor structures. Further, it has been known for many years that removal of the flocculus of the cerebellum permanently precludes further vestibulo-ocular reflex adaptation, demonstrating the involvement of the cerebellum in this behavior. Maekawa and Simpson (J Neurophysiol 1973;36: 649-66) discovered that one visual input to the flocculus involved the accessory optic system and the inferior olive. Ensuing work has demonstrated that the visual signals used to adapt the vestibulo-ocular reflex are transmitted by this accessory optic system to the flocculus and subsequently to brain stem structures involved in vestibulo-ocular reflex plasticity. Presently the inclusive list of anatomic sites involved in vestibulo-ocular reflex circuitry and its adaptive plasticity is small. Our laboratory continues to believe that this behavior should be caused by interactions within this small class of neurons. By studying each class of identified neuron and its interactions with others within the list, we hope to ultimately understand the mechanisms used by the brain in the expression of this behavior.

Non-NASA Center↗
NASA NTRS2003

Modelling protein functional domains in signal transduction using Maude

Modelling of protein-protein interactions in signal transduction is receiving increased attention in computational biology. This paper describes recent research in the application of Maude, a symbolic language founded on rewriting logic, to the modelling of functional domains within signalling proteins. Protein functional domains (PFDs) are a critical focus of modern signal transduction research. In general, Maude models can simulate biological signalling networks and produce specific testable hypotheses at various levels of abstraction. Developing symbolic models of signalling proteins containing functional domains is important because of the potential to generate analyses of complex signalling networks based on structure-function relationships.

Signal Transduction↗
NASA NTRS2004

NASA Classroom Bioreactor

Exploration of space provides a compelling need for cell-based research into the basic mechanisms that underlie the profound changes that occur in terrestrial life that is transitioned to low gravity environments. Toward that end, NASA developed a rotating bioreactor in which cells are cultured while continuously suspended in a cylinder in which the culture medium rotates with the cylinder. The randomization of the gravity vector accomplished by the continuous rotation, in a low shear environment, provides an analog of microgravity. Because cultures grown in bioreactors develop structures and functions that are much closer to those exhibited by native tissue than can be achieved with traditional culture methods, bioreactors have contributed substantially to advancing research in the fields of cancer, diabetes, infectious disease modeling for vaccine production, drug efficacy, and tissue engineering. NASA has developed a Classroom Bioreactor (CB) that is built from parts that are easily obtained and assembled, user-friendly and versatile. It can be easily used in simple school settings to examine the effect cultures of seeds or cells. An educational brief provides assembly instructions and lesson plans that describes activities in science, math and technology that explore free fall, microgravity, orbits, bioreactors, structure-function relationships and the scientific method.

Scully, Robert↗
DOE OSTI2022

Determining the Role of Synthesis and Reaction Conditions on the Exposed Surface and Shape of ..beta..-Mo2C Catalysts

The production of drop-in quality biofuels typically can be achieved through catalytic fast pyrolysis (CFP) of biomass, followed by hydrodeoxygenation (HDO) of the vapor-phase product to reduce the oxygen content and stabilize the bio-oil product. To favor selectivity toward desired deoxygenation products, bifunctional catalysts with both acidic and hydrogenation sites are often employed. Due to both its oxophilicity and its ability to promote hydrogenation reactions, molybdenum carbide catalysts have shown promise for promoting the HDO of CFP vapors. However, the surface structure and composition of carbide catalyst particles are not well understood, precluding the establishment of fundamental structure-function relationships needed for the rational development of molybdedum carbide for HDO, as well as other reactions. For orthorhombic ..beta..-Mo2C, the (100) facet is largely studied for computational surface-reaction analyses, possibly due to its similarities with the close-packed (111) facet of noble-metal catalysts. However, it has previously been postulated through ab initio thermodynamic studies that the (111), (110), and (011) facets are most stable, though there is no consensus. Furthermore, while a majority of previous surface stability analyses of ..beta..-Mo2C focus on bulk terminations, the highly carburizing synthesis conditions and the use of ..beta..-Mo2C in carbon-containing reaction applications could introduce non-stoichiometric coverages of surface carbon. As such, this study uses ab initio thermodynamics calculations to assess the relative surface stability of the low-index facets of ..beta..-Mo2C, including consideration of varying the coverage of surface carbon. From this information, Wulff constructions are utilized to predict the synthesis and reaction condition-dependent shape and surface carbon composition of ..beta..-Mo2C catalyst particles.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗
DOE OSTI2023

Toward More Efficient Organic Solar Cells: A Detailed Study of Loss Pathway and Its Impact on Overall Device Performance in Low‐Offset Organic Solar Cells

Abstract Low‐offset organic solar cell systems have attracted great interest since nonfullerene acceptors came into the picture. While numerous studies have focused on the charge generation process in these low‐offset systems, only a few studies have focused on the details of each loss channel in the charge generation process and their impact on the overall device performance. Here, several nonfullerene acceptors are blended with the same polymer donor to form a series of low‐offset organic solar cell systems where significant variation in device performance is observed. Through detailed analyses of loss pathways, it is found that: i) the donor:acceptor interfaces of PM6:Y6 and PM6:TPT10 are close to the optimum energetic condition, ii) energetics at the donor:acceptor interface are the most important factor to the overall device performance, iii) exciton dissociation yield can be field‐dependent owing to the sufficiently small energetic offset at the donor:acceptor interface, and iv) the change in substituents in the terminal group of Y‐series acceptors in this work mainly affects energetics at the donor:acceptor interface instead of the interface density in the active layer. In general, this work presents a path toward more efficient organic solar cells.

14 SOLAR ENERGY↗
DOE OSTI2023

From Inside Out: How the Buried Interface, Shell Defects, and Surface Chemistry Conspire to Determine Optical Performance in Nonblinking Giant Quantum Dots

“Giant” or core/thick‐shell quantum dots (gQDs) are an important class of solid‐state quantum emitter characterized by strongly suppressed blinking and photobleaching under ambient conditions, and reduced nonradiative Auger processes. Together, these qualities provide distinguishing and useful functionality as single‐ and ensemble‐photon sources. For many applications, operation at elevated temperatures and under intense photon flux is desired, but performance is strongly dependent on the synthetic method employed for thick‐shell growth. Here, a comprehensive analysis of gQD structural properties “from the inside out” as a function of shell‐growth method is reported: successive ionic layer adsorption and reaction (SILAR) and high‐temperature continuous injection (HT‐CI), or sequential combinations of the two. Key correlations across synthesis methods, structural features (interfacial alloying, stacking‐fault density and surface‐ligand identity), and performance metrics (quantum yield, single‐gQD photoluminescence under thermal/photo stress, charging behavior and quantum‐optical properties) are identified. Surprisingly, it is found that interfacial alloying is the strongest indicator of gQD stability under stress, but this parameter is not the determining factor for Auger suppression. Furthermore, quantum yield is strongly influenced by surface chemistry and can approach unity even in the case of high shell‐defect density, while introduction of zinc‐blende stacking faults increases the likelihood that a gQD exhibits charged‐state emission.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Current understanding of Oxidative Coupling of Methane (OCM) reaction over supported Mn-Na 2 WO 4 catalysts

This perspective reviews the current understanding of the Oxidative Coupling of Methane (OCM) reaction over the supported Mn-Na 2 WO 4 /SiO 2 catalyst, with a focus on recent insights gained from state-of-the-art in-situ and operando spectroscopic characterization and chemical probe experiments under controlled environments. The supported Mn-Na 2 WO 4 /SiO 2 catalyst exhibits dynamic structural changes during the OCM reaction, involving multiple reactive lattice and adsorbed oxygen species, each associated with different oxide phases. These oxygen species play distinct roles in various steps of the OCM mechanism. The catalytic active sites for activation of CH 4 are associated with isolated surface Na-WO x sites on the SiO 2 support and the role of surface MnO x sites on SiO 2 is to oxidatively dehydrogenate C 2 H 6 to C 2 H 4 . Furthermore, this paper provides a detailed discussion of these roles and also introduces new experimental data from Temporal Analysis of Products (TAP) studies to clarify the ongoing debate in the literature regarding the contributions of lattice versus adsorbed oxygen species in OCM reaction product formation. Additionally, recommendations are offered for optimizing the performance of supported Mn-Na 2 WO 4 /SiO 2 catalysts to enhance CH 4 activation and C 2 product selectivity.

03 - NATURAL GAS↗
DOE OSTI2023

Chitosan as a Canvas for Studies of Macromolecular Controls on CaCO 3 Biological Crystallization

A mechanistic understanding of how macromolecules, typically as an organic matrix, nucleate and grow crystals to produce functional biomineral structures remains elusive. Advances in structural biology indicate that polysaccharides (e.g., chitin) and negatively charged proteoglycans (due to carboxyl, sulfate, and phosphate groups) are ubiquitous in biocrystallization settings and play greater roles than currently recognized. This review highlights studies of CaCO 3 crystallization onto chitinous materials and demonstrates that a broader understanding of macromolecular controls on mineralization has not emerged. With recent advances in biopolymer chemistry, it is now possible to prepare chitosan-based hydrogels with tailored functional group compositions. By deploying these characterized compounds in hypothesis-based studies of nucleation rate, quantitative relationships between energy barrier to crystallization, macromolecule composition, and solvent structuring can be determined. Finally, this foundational knowledge will help researchers understand composition-structure-function controls on mineralization in living systems and tune the designs of new materials for advanced applications.

15 GEOTHERMAL ENERGY↗
DOE OSTI2026

Thermally Stable Co@C3N4 Single-Atom Catalysts for CO Oxidation: Atomic-Level Insights into Structure and Activity

Single Co atoms supported on C3N4 (Co@C3N4) have demonstrated high activity and selectivity in photocatalysis. However, the investigation of structure–function relationships and reaction mechanisms under photocatalytic conditions is very challenging due to the complex conditions of light absorption, charge transfer, and catalysis. In this study, we employed thermal CO oxidation as a prototypical probe reaction to benchmark the intrinsic catalytic performance and track the active-site evolution of Co@C3N4. Single Co atoms were identified and shown to be the catalytically active sites for CO oxidation based on control experiments and isotope-labeling experiments. The Co sites remained atomically dispersed before, during, and after the reaction with temperatures up to 400 °C, as established by in situ X-ray absorption fine structure (XAFS) combined with density functional theory (DFT), FDMNES simulations, and dynamic-time-warping (DTW)-assisted X-ray absorption near edge structure (XANES) matching. Together with theoretical calculations, the integrated analysis reveals a stable coordination environment under reaction conditions, which correlates with sustained activity, establishing Co@C3N4 single-atom catalysts as thermally stable CO oxidation catalysts. Beyond these findings, the current study provides a workflow for unambiguously assigning active sites in Co@C3N4 for thermal CO oxidation. This workflow will aid the understanding of their behavior in photocatalysis in the future, where light-driven dynamics obscure direct structure–function links. Notably, this study provides fundamental insights for the rational design of robust single-atom catalysts and a foundation for the broader application of Co@C3N4 catalysts in oxidation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Structure–Function Relationships in Sequence-Controlled Copolymers for Rare Earth Element Chelation

The ability to tune material function through primary sequence is a defining feature of biological macromolecules, allowing precise control over structure and target interactions in complex aqueous environments. However, translating sequence–structure–function relationships to synthetic macromolecules is challenging due to their dispersity in sequence, conformation, and composition. Here, we report systematic studies of amphiphilic polymer chelators designed to probe how composition and patterning influence binding affinity and selectivity for rare earth elements (REEs), a series of technologically relevant metals with challenging separation profiles. A library of copolymers varying hydrophobic monomer composition and patterning was synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization, spanning statistical, gradient, and block architectures. REE binding was quantified using a high-throughput colorimetric assay, and reconstruction of polymer ensembles using kinetic stochastic simulations enabled quantitative comparisons of sequence heterogeneity, linking local monomer colocalization to emergent REE binding. Further, we investigated the role of different hydrophobic comonomers in tuning metal coordination, with binding trends linked to structural features that influence binding site desolvation. Complementary dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) measurements showed that both polymer and monomer architecture modulate metal-induced conformational changes, and that multichain assembly behavior emerges beyond critical hydrophobic thresholds. Sequence control also altered REE selectivity, with nonmonotonic differences observed across compositionally identical polymers with different sequence architectures. Together, these findings establish design principles that connect polymer sequence and structure to binding performance, guiding the design of macromolecular chelators with enhanced affinity and selectivity for applications in separations, sensing, and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Rubisco kinetic acclimation at the holoenzyme level

Kinetic acclimation enables proteins to adjust their activity in response to environmental perturbations. For the CO 2 -fixing enzyme Rubisco, kinetic acclimation may be conferred by its small subunits. Plants express multiple small subunits and vary their expression with temperature. Here, we demonstrate that different small subunits can bind to the same Rubisco to form a heterogeneous holoenzyme. These small subunits had distinct kinetic effects which aligned with changes in holoenzyme structure and stability. Our findings indicate that small subunits enable Rubisco kinetic acclimation via manipulation of flexibility. By assembling a more rigid active site in higher temperatures and a more flexible one in lower temperatures, plants maximize the efficiency of their Rubisco, and thus photosynthesis, over a wide range of temperatures.

CO2 fixation↗
DOE OSTI2022

Structural insights into the assembly and the function of the plant oxidative phosphorylation system

One of the key functions of mitochondria is the production of ATP to support cellular metabolism and growth. The last step of mitochondrial ATP synthesis is performed by the oxidative phosphorylation (OXPHOS) system, an ensemble of protein complexes embedded in the inner mitochondrial membrane. In the last 25 yr, many structures of OXPHOS complexes and supercomplexes have been resolved in yeast, mammals, and bacteria. However, structures of plant OXPHOS enzymes only became available very recently. In this review, we highlight the plant-specific features revealed by the recent structures and discuss how they advance our understanding of the function and assembly of plant OXPHOS complexes. Here we also propose new hypotheses to be tested and discuss older findings to be re-evaluated. Further biochemical and structural work on the plant OXPHOS system will lead to a deeper understanding of plant respiration and its regulation, with significant agricultural, environmental, and societal implications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

High-Resolution Structure of the Nuclease Domain of the Human Parvovirus B19 Main Replication Protein NS1

Two new structures of the N-terminal domain of the main replication protein, NS1, of human parvovirus B19 (B19V) are presented here. This domain (NS1-nuc) plays an important role in the “rolling hairpin” replication of the single-stranded B19V DNA genome, recognizing origin of replication sequences in double-stranded DNA, and cleaving (i.e., nicking) single-stranded DNA at a nearby site known as the terminal resolution site (trs). The three-dimensional structure of NS1-nuc is well conserved between the two forms, as well as with a previously solved structure of a sequence variant of the same domain; however, it is shown here at a significantly higher resolution (2.4 Å). Using structures of NS1-nuc homologues bound to single- and double-stranded DNA, models for DNA recognition and nicking by B19V NS1-nuc are presented that predict residues important for DNA cleavage and for sequence-specific recognition at the viral origin of replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile

ABSTRACT Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

In anaerobic reactors the microbial community structure depends on feed type, with no “keystone” species tied to COD removal

Two-stage anaerobic digestion (AD) systems provide treatment for high strength wastewater with high stability and performance. Encapsulation technology can intensify AD to facilitate the separation of the solids retention time from the hydraulic retention time (HRT), offering lower HRTs, smaller reactors, and high effluent quality. To support successful deployment, however, the encapsulated community must contain all the needed microorganisms for successful treatment and be flexible enough to treat a variety of wastewaters. Here, a two-stage system was investigated in which microbial cultures were enriched on various high-strength wastewaters in suspended flow-through systems to determine how feed type influenced performance and microbial community structure. The hypothesis was that specific genera, or so-called “keystone species” would positively correlate to organic carbon degradation for a given feed, enabling construction of a well-functioning community for encapsulation. Results showed that the number of total bacteria (as 16S rRNA gene copies) did not correlate to soluble chemical oxygen demand (sCOD) removal, indicating that the community structure and/or members were important for good performance. Results also showed that feed type strongly influenced carbon removal and microbial community structure for 1st-stage fermenting communities, but not 2nd-stage methanogenic communities. In this study, the “core” community members were defined as organisms common to all of either the 1st- or 2nd-stage reactors irrespective of the feed they received and were present in at least 50% of the samples throughout the entire experiment. “Unique” community members were specific to a single feed, and hence, only present in either the 1st- or 2nd-stage reactors receiving that feed. In both 1st- and 2nd-stage communities, only one core genera and no unique genera were positively and significantly correlated to sCOD removal. Verification experiments performed with encapsulated communities showed that organisms identified in flow-through system and correlated with carbon degradation, though not significantly, seemed to be important for performance. Our results suggest that one cannot construct a community containing specific populations in lieu of enrichment. Nevertheless, a single diverse encapsulated anaerobic community should provide good (>80%) carbon removal when fed a variety of influents, if time is provided for enrichment after deployment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Structural insights into binding of polyglutamylated tetrahydrofolate by serine hydroxymethyltransferase 8 from soybean

Tetrahydrofolate and its derivatives participate in one-carbon transfer reactions in all organisms. The cellular form of tetrahydrofolate (THF) is modified by multiple glutamate residues and polyglutamylation plays a key role in organellar and cellular folate homeostasis. In addition, polyglutamylation of THF is known to increase the binding affinity to enzymes in the folate cycle, many of which can utilize polyglutamylated THF as a substrate. Here, we use X-ray crystallography to provide a high-resolution view of interactions between the enzyme serine hydroxymethyltransferase (SHMT), which provides one carbon precursors for the folate cycle, and a polyglutamylated form of THF. Our 1.7 Å crystal structure of soybean SHMT8 in complex with diglutamylated 5-formyl-THF reveals, for the first time, a structural rearrangement of a loop at the entrance to the folate binding site accompanied by the formation of novel specific interactions between the enzyme and the diglutamyl tail of the ligand. Biochemical assays show that additional glutamate moieties on the folate ligand increase both enzyme stability and binding affinity. Together these studies provide new information on SHMT structure and function and inform the design of anti-folate agents.

59 BASIC BIOLOGICAL SCIENCES↗