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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 OSTI2011

Specificity and cooperativity at [beta]-lactamase position 104 in TEM-1/BLIP and SHV-1/BLIP interactions

Establishing a quantitative understanding of the determinants of affinity in protein-protein interactions remains challenging. For example, TEM-1/{beta}-lactamase inhibitor protein (BLIP) and SHV-1/BLIP are homologous {beta}-lactamase/{beta}-lactamase inhibitor protein complexes with disparate K{sub d} values (3 nM and 2 {mu}M, respectively), and a single substitution, D104E in SHV-1, results in a 1000-fold enhancement in binding affinity. In TEM-1, E104 participates in a salt bridge with BLIP K74, whereas the corresponding SHV-1 D104 does not in the wild type SHV-1/BLIP co-structure. Here, we present a 1.6 {angstrom} crystal structure of the SHV-1 D104E/BLIP complex that demonstrates that this point mutation restores this salt bridge. Additionally, mutation of a neighboring residue, BLIP E73M, results in salt bridge formation between SHV-1 D104 and BLIP K74 and a 400-fold increase in binding affinity. To understand how this salt bridge contributes to complex affinity, the cooperativity between the E/K or D/K salt bridge pair and a neighboring hot spot residue (BLIP F142) was investigated using double mutant cycle analyses in the background of the E73M mutation. We find that BLIP F142 cooperatively stabilizes both interactions, illustrating how a single mutation at a hot spot position can drive large perturbations in interface stability and specificity through a cooperative interaction network.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Manganese effects on plant residue decomposition and carbon distribution in soil fractions depend on soil nitrogen availability

Recent studies have highlighted the critical role of manganese (Mn) in plant litter decomposition and soil organic carbon (C) cycling in forest ecosystems. Long term nitrogen (N) deposition and N fertilization can increase soil acidity and mobilize bioavailable Mn (Mn 2+ ) in soil. However, no studies have examined the interactive effect of N and Mn fertilization on litter decomposition and carbon distribution in agricultural soils, despite agroecosystems being subject to both N and Mn management. We hypothesized that increased soil N and Mn availability would accelerate plant residue decomposition and transfer of its C to mineral-associated organic matter (MAOM), and that the combined effect of Mn and N enrichment would be greater than the individual effect. Here, we conducted a laboratory incubation experiment by adding 13 C-labeled residue of perennial grass Glyceria striata (Lam.) to agricultural soils that had received 225 kg N ha –1 yr –1 for 27 years (N 1 ) and comparable soils that received no N (N 0 ). Before the experiment, these soils also received three levels of dissolved Mn 2+ , designated M 0 (no additional Mn), M 1 (50 mg kg –1 ), or M 2 (250 mg kg –1 ). We measured total CO 2 production as well as distribution of 13 C from the residue into CO 2 , particulate organic matter (POM), MAOM, and dissolved organic carbon (DOC) over a 1-year period. Manganese amendments significantly increased CO 2 production from residue decomposition in the N 1 soil, but no such effect was observed in the N 0 soil. Manganese also accelerated the loss of residue-derived C from POM and DOC, but increased its recovery in MAOM. However, the positive effect of added Mn in decomposition and recovery in MAOM in the presence of N fertilization occurred only during the initial 30-day decomposition period, where M 2 showed a 12% increase in cumulative CO 2 production from residue, 8% increase in POM loss, and 43% increase in recovery of residue C in MAOM compared to M 0 . For M 1 , only CO 2 emission from residue was significantly higher than Mo during this period. At 365 days M 2 showed 8% increase in CO 2 production, 1% increase in POM loss, and 16% increase in recovery of residue C in MAOM compared to M 0 , but none of these were statistically significant (p < 0.05). This study adds to the growing evidence that increasing Mn availability enhances plant litter decomposition. However, the occurrence and magnitude of Mn-induced stimulation of decomposition is context specific. Further investigation with greater temporal resolution, involving a multitude of litter and soil types and including microbial compositional and functional characterization, is recommended to fully elucidate the interactive role of Mn and N on C cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Deformation response of AgCu interfaces investigated by in situ and ex situ TEM straining and MD simulations

The mechanisms of strain transfer across Ag/Cu interfaces were determined by a combination of in situ and ex situ TEM straining experiments and molecular dynamics simulations. Minimizing the magnitude of the Burgers vector of the residual dislocation generated in the interface was the dominant factor for determining the outcome of dislocation and deformation twin interactions with both non-coherent twin and cube-on-cube interfaces. This included the unexpected finding, due to the loading condition, of deformation twin activation in the Cu layer due to the intersection of deformation twins in Ag with the interface. As a result, deformation twin nucleation in Ag from the non-coherent twin interfaces was also explained by a Burgers vector minimization argument.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Proposed docking interface between peptidoglycan and the target recognition domain of zoocin A

Highlights: •Peptidoglycan added to zoocin rTRD perturbs NMR resonances around W115. •Simulations predict docking to a shallow surface groove near W115. •The docking interface is similar to mammalian antibody–antigen sites. •EDTA binds to a distinct surface site. -- Abstract: A docking model is proposed for the target recognition domain of the lytic exoenzyme zoocin A with the peptidoglycan on the outer cell surface of sensitive bacterial strains. Solubilized fragments from such peptidoglycans perturb specific backbone and side chain amide resonances in the recombinant form of the domain designated rTRD as detected in two-dimensional {sup 1}H–{sup 15}N correlation NMR spectra. The affected residues comprise a shallow surface cleft on the protein surface near W115, N53, N117, and Q105 among others, which interacts with the peptide portion of the peptidoglycan. Calculations with AutoDock Vina provide models of the docking interface. There is approximate homology between the rTDR-peptidoglycan docking site and the antigen binding site of Fab antibodies with the immunoglobin fold. EDTA was also found to bind to rTRD, but at a site distinct from the proposed peptidoglycan docking site.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

The folding of single domain proteins—have we reached a consensus?

Rather than stressing the most recent advances in the field, this review highlights the fundamental topics where disagreement remains and where adequate experimental data are lacking. These topics include properties of the denatured state and the role of residual structure, the nature of the fundamental steps and barriers, the extent of pathway heterogeneity and non-native interactions, recent comparisons between theory and experiment, and finally, dynamical properties of the folding reaction.

Sosnick, Tobin R.↗
DOE OSTI2019

HYSCORE Insights into the Distribution of the Unpaired Spin Density in an Engineered Cu A Site in Azurin and Its His120Gly Variant

A comparative study of the 1 H and 14 N hyperfine interactions between the Cu A site in an engineered Cu A center in azurin (WT-Cu A Az) and its His120Gly variant (H120G-Cu A Az) using the two-dimensional ESEEM technique, HYSCORE, is reported. HYSCORE spectroscopy has clarified conflicting results in previous electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) studies and found clear differences between the two Cu A azurins. Specifically, a hyperfine coupling A N⊥ of 15.3 MHz was determined for the first time from the frequencies of double-quantum transitions of 14 N histidine nitrogens coordinated to Cu A in WT-Cu A Az. In contrast, such coupling was not observed in the spectra of H120G-Cu A Az, indicating at least a several megahertz increase in A N⊥ for the coordinated nitrogen in this variant. In addition, 14 N HYSCORE spectra of WT-Cu A Az show interaction with only one type of weakly coupled nitrogen assigned to the remote N ε atom of coordinated imidazole residues based on the quadrupole coupling constant (e 2 Qq/4h) of ~0.4 MHz. The spectrum of H120G-Cu A Az resolves additional features typical for backbone peptide nitrogens with larger e 2 Qq/4h values of ~0.7 MHz. Hyperfine couplings with these nitrogens vary between ~0.4 and 0.7 MHz. In addition, the two resolved cross-peaks from C β protons in H120G-Cu A Az display only ~1 MHz shifts relative to the corresponding peaks in WT-Cu A Az. Finally, these new findings have provided the first experimental evidence of the previous density functional theory analysis that predicted changes in the delocalized electron spin population of ~0.02–0.03 (i.e., ~10%) on copper and sulfur atoms of the Cu A center in H120 variants relative to WT-Cu A Az and resolved contradicting results between EPR and ENDOR studies of the valence distribution in Cu A Az and its variants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A Thioether-Ligated Cupric Superoxide Model with Hydrogen Atom Abstraction Reactivity

The central role of cupric superoxide intermediates proposed in hormone and neurotransmitter biosynthesis by noncoupled binuclear copper monooxygenases like dopamine-β-monooxygenase has drawn significant attention to the unusual methionine ligation of the Cu M (“Cu B ”) active site characteristic of this class of enzymes. The copper–sulfur interaction has proven critical for turnover, raising still-unresolved questions concerning Nature’s selection of an oxidizable Met residue to facilitate C–H oxygenation. We describe herein a model for Cu M , [( TMG N 3 S)Cu I ] + ([1] + ), and its O 2 -bound analog [( TMG N 3 S)Cu II (O 2 •– )] + ([1·O 2 ] + ). The latter is the first reported cupric superoxide with an experimentally proven Cu–S bond which also possesses demonstrated hydrogen atom abstraction (HAA) reactivity. Introduction of O2 to a precooled solution of the cuprous precursor [1]B(C 6 F 5 ) 4 (-135 °C, 2-methyltetrahydrofuran (2-MeTHF)) reversibly forms [1·O 2 ]B(C 6 F 5 ) 4 (UV/vis spectroscopy: λ max 442, 642, 742 nm). Resonance Raman studies (413 nm) using 16 O 2 [ 18 O 2 ] corroborated the identity of [1·O 2 ] + by revealing Cu–O (446 [425] cm –1 ) and O–O (1105 [1042] cm –1 ) stretches, and extended X-ray absorption fine structure (EXAFS) spectroscopy showed a Cu–S interatomic distance of 2.55 Å. HAA reactivity between [1·O 2 ] + and TEMPO–H proceeds rapidly (1.28 × 10 –1 M –1 s –1 , -135 °C, 2-MeTHF) with a primary kinetic isotope effect of kH/kD = 5.4. Comparisons of the O 2 -binding behavior and redox activity of [1] + vs [2] + , the latter a close analog of [1]+ but with all N atom ligation (i.e., N 3 S vs N 4 ), are presented.

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

Inositol phosphates are assembly co-factors for HIV-1

A short, 14-amino-acid segment called SP1, located in the Gag structural protein, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP 6 ) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP 6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP 6 interaction promotes the assembly of the mature capsid lattice. Furthermore, these studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Invariant-mass spectroscopy in projectile fragmentation reactions

The fragmentation of a projectile into a number of pieces can lead to the creation of many resonances in different nuclei. We discuss application of the invariant-mass method to the products from such reactions to find some of the most exotic resonances located furthest beyond the proton drip line. We show examples from fragmentation of a fast 13 O beam including the production of the newly identified 9 N resonance. In extracting resonance parameters from invariant-mass spectra, accurate estimates of the background from nonresonant prompt protons are needed. These prompt protons are correlated with the resonances due to long-range Coulomb interactions and will suppress events when resonance decay products and the prompt protons have small invariant masses. The shape of this background is especially important in determining the widths of wide resonances typically found at the edge of the chart of nuclides. An event-mixing recipe is proposed to describe this background, where the mixed events have reduced weighting for the smaller invariant masses to account for the effect of the Coulomb final-state interactions. The weighting is based on the measured correlations of heavier hydrogen isotopes with the resonances or the projectile residues. We also show that the relative magnitude of the background can be reduced in some cases by selecting events where the resonance decay products are accompanied by a deuteron or triton cluster. Here, the deuteron and triton clusters are largely not products of resonant decay and thus events with an accompanying cluster are associated with fewer background protons than events without them. The width of the 5/2¯ state in 9 C with the new background prescription was found to be consistent with the value obtained using proton elastic scattering on 8 B. Improved values for the widths of 10 C, 10,11 N, and 12 O resonances were also obtained using the new background prescription.

6 ≤ A ≤ 19↗
DOE OSTI2019

Sudan Ebolavirus VP35-NP Crystal Structure Reveals a Potential Target for Pan-Filovirus Treatment

The filoviruses are etiological agents of life-threatening hemorrhagic fever with high mortality rate and risk of potential outbreak. Among members of this family, the Ebola (EBOV), Sudan (SUDV), and Marburg (MARV) viruses are considered the most pathogenic for humans. The ebolavirus nucleoprotein (NP) is the most abundant protein in infected cells and is essential for viral transcription and replication; thus, it represents an attractive target for therapeutic intervention. Here, we present the structure of SUDV NP in complex with the amino-terminal portion of the phosphoprotein VP35 at 2.3 Å. This structure captures VP35 chaperoning SUDV NP in a monomeric and RNA-free state. This transient state has been proposed to be key to maintaining a pool of monomeric and RNA-free NPs prior to NP-NP polymerization and encapsidation of the viral RNA genome. This structure also reveals a newly visualized interaction between NP and VP35, a well-defined beta sheet that is not present in previous structures. Affinity binding assays demonstrate that this beta sheet is essential for maintaining the high-affinity interaction between VP35 and a hydrophobic pocket on SUDV NP, and electron microscopy indicates the importance of this binding interaction to the oligomeric state and assembly of NP in human cells. Complementary structure-directed mutagenesis identifies critical residues conserved across the filovirus family that could be targeted by broadly effective antivirals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Photoionization of helium-like ions accompanied by the excitation of p-wave states of the residual atom

The single-photon ionization of the ground state of a helium-like multicharged ion, which is accompanied by a simultaneous excitation of the residual ion to the np states, is studied using nonrelativistic pertubation theory with respect to the electron-electron interaction. Formulas describing the cross section for the process being studied are obtained. These formulas exhibit a scaling behavior in the target-nucleus charge number Z and in the principal quantum number n. Numerical calculations are performed for nonrelativistic energies including the near-threshold region.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Towards the understanding of the genuine three-body interaction for p–p–p and p–p–Λ

Three-body nuclear forces play an important role in the structure of nuclei and hypernuclei and are also incorporated in models to describe the dynamics of dense baryonic matter, such as in neutron stars. So far, only indirect measurements anchored to the binding energies of nuclei can be used to constrain the three-nucleon force, and if hyperons are considered, the scarce data on hypernuclei impose only weak constraints on the three-body forces. In this work, we present the first direct measurement of the p–p–p and p–p–Λ systems in terms of three-particle correlation functions carried out for pp collisions at $\sqrt{s}$=13 TeV. Three-particle cumulants are extracted from the correlation functions by applying the Kubo formalism, where the three-particle interaction contribution to these correlations can be isolated after subtracting the known two-body interaction terms. A negative cumulant is found for the p–p–p system, hinting to the presence of a residual three-body effect while for p–p–Λ the cumulant is consistent with zero. This measurement demonstrates the accessibility of three-baryon correlations at the LHC.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1983

Solar concentrator degradation in Low Earth Orbit (LEO)

The use of parabolically or spherically-shaped mirrors is being considered in order to increase the solar energy intensity on solar cells. Their use will significantly decrease the size and number of the cells needed for a particular application, hence the total array cost. Questions arise, however, regarding the long-term (five to ten years) efficiency of these devices. Performance degradation of the mirror surfaces might result from known hostile elements in the low earth orbit (LEO) environment (150-350 nautical miles). The degradation issue is addressed in light of present knowledge of this environment. The following characteristics of the LEO environment are identified for study: (1) the vacuum of space; (2) sputtering by the residual atoms and particles in space; (3) solar electromagnetic radiation; (4) contamination of the mirror surface; (5) atomic oxygen interactions with the surface; (6) bombardment of the surface by meteoroids; and (7) irradiation of the surface by ionizing particles (protons). Using the best available information for the magnitudes of the necessary quantities, a mathematical analysis was carried out, where possible, to determine the degradation in reflectance or other loss caused by each characteristic. Otherwise, reasonable estimates are made of corresponding losses, based on already published data.

Thomas, R. G.↗
NASA NTRS1985

Simulation of the temperature distribution in crystals grown by Czochralski method

Production of perfect crystals, free of residual strain and dislocations and with prescribed dopant concentration, by the Czochralski method is possible only if the complex, interacting phenomena that affect crystal growth in a Cz-puller are fully understood and quantified. Natural and forced convection in the melt, thermocapillary effect and heat transfer in and around the crystal affect its growth rate, the shape of the crystal-melt interface and the temperature gradients in the crystal. The heat transfer problem in the crystal and between the crystal and all other surfaces present in the crystal pulling apparatus are discussed at length. A simulation and computer algorithm are used, based on the following assumptions: (1) only conduction occurs in the crystal (experimentally determined conductivity as a function of temperature is used), (2) melt temperature and the melt-crystal heat transfer coefficient are available (either as constant values or functions of radial position), (3) pseudo-steady state is achieved with respect to temperature gradients, (4) crystal radius is fixed, and (5) both direct and reflected radiation exchange occurs among all surfaces at various temperatures in the crystal puller enclosure.

Dudokovic, M. P.↗
NASA NTRS1989

Computational simulation of transition to turbulence through inverse modeling

The present investigation has focused on a computational methodology for the fundamental case of transition in channel flow, in which recently published experimental data are utilized both as a stimulus and as a measure of merit of the method. The research has proceeded along three avenues in parallel. The first task has consisted of the development and verification of a computer code which calculates the mean evolution of flow in a channel similar to the one employed experimentally by Blair and Anderson. An analytical test case was created for the dual purposes of code verification and of highlighting the interactions between the Reynolds stress and the mean velocity profile. This test case generated a Reynolds stress by the residue in the momentum equation which is produced by a typical analytical velocity profile. By a substitution of this Reynolds stress into the appropriate code module, the correctness of the code may be verified, along with the accuracy of the computational method. The second task pursued has involved the development of a triple layer model for the Reynolds stress profile, which was suggested and derived from experimental velocity profiles. It is demonstrated that the innermost length scale is based on the local friction velocity, the intermediate layer corresponds to the usual logarithmic law of the wall region in which the normalized Reynolds stress is approximately unity, and the outermost layer is represented by a closed mathematical form depending explicitly on the velocity profile in the wake region. The third task was comprised of scrutiny of the excellent databases developed by Blair and others, and the planning of its incorporation into the transition analysis. These extensive measurements indicate that turbulent statistics in the transition regime may be considered to alternate between laminar and fully turbulent types, the proportions of which are quantified by a measured intermittency function.

Sepri, Paavo↗
NASA NTRS2007

The Formation and Chronology of the PAT 91501 Impact-Melt L-Chondrite with Vesicle-Metal-Sulfide Assemblages

The L chondrite Patuxent Range (PAT) 41 91501 is an 8.5-kg unshocked, homogeneous, igneous-textured impact melt that cooled slowly compared to other meteoritic impact melts in a crater floor melt sheet or sub-crater dike. We conducted mineralogical and tomographic studies of previously unstudied mm- to cm-sized metal-sulfide-vesicle assemblages and chronologic studies of the silicate host. Metal-sulfide clasts constitute about 1 vol.%, comprise zoned taenite, troilite and pentlandite, and exhibit a consistent orientation between metal and sulfide and of metal-sulfide contacts. Vesicles make up approximately 2 vol.% and exhibit a similar orientation of long axes. Ar-39-Ar-40 measurements date the time of impact at 4.461 +/- 0.008 Gyr B.P. Cosmogenic noble gases and Be-10 and Al-2l activities suggest a pre-atmospheric radius of 40-60 cm and a cosmic ray exposure age of 25-29 Myr, similar to ages of a cluster of L chondrites. PAT 91501 dates the oldest known impact on the L chondrite parent body. The dominant vesicle-forming gas was S2 (approximately 15-20 ppm), which formed in equilibrium with impact-melted sulfides. The meteorite formed in an impact melt dike beneath a crater, as did other impact melted L chondrites, such as Chico. Cooling and solidification occurred over approximately 2 hours. During this time, approximately 90% of metal and sulfide segregated from the local melt. Remaining metal and sulfide grains oriented themselves in the local gravitational field, a feature nearly unique among meteorites. Many of these metal sulfide grains adhered to vesicles to form aggregates that may have been close to neutrally buoyant. These aggregates would have been carried upward with the residual melt, inhibiting further buoyancy-driven segregation. Although similar processes operated individually in other chondritic impact melts, their interaction produced the unique assemblage observed in PAT 91501.

Benedix, G. K.↗