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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 1,441 records · Page 80
All sourcesNASA NTRSDOE OSTI
NASA NTRS1985

In vivo inhibition of polyamine biosynthesis and growth in tobacco ovary tissues

Post fertilization growth of tobacco ovary tissues treated with inhibitors of polyamine (PA) biosynthesis was examined in relation to endogenous PA titers and the activities of arginine decarboxylase (ADC, EC 4.1.1.19) and ornithine decarboxylase (ODC, EC 4.1.1.17). DL-alpha-Difluoromethylornithine (DFMO) and DL-alpha-difluoromethylarginine (DFMA), specific, irreversible ("suicide") inhibitors of ODC and ADC in vitro, were used to modulate PA biosynthesis in excised flowers. ODC represented >99% of the total decarboxylase activity in tobacco ovaries. In vivo inhibition of ODC with DFMO resulted in a significant decrease in PA titers, ovary fresh weight and protein content. Simultaneous inhibition of both decarboxylases by DFMO and DFMA produced only a marginally greater depression in growth and PA titers, indicating that ODC activity is rate-limiting for PA biosynthesis in these tissues. Paradoxically, DFMA alone inhibited PA biosynthesis, not as a result of a specific inhibition of ADC, but primarily through the inactivation of ODC. In vivo inhibition of ODC by DFMA appears to result from arginase-mediated hydrolysis of this inhibitor to urea and DFMO, the suicide substrate for ODC. Putrescine conjugates in tobacco appear to function as a storage form of this amine which, upon hydrolysis, may contribute to Put homeostasis during growth.

NASA Program Space Biology↗
NASA NTRS2008

Final Report on NASA Portable Laser Coating Removal Systems Field Demonstrations and Testing

Processes currently used throughout the National Aeronautics and Space Administration (NASA) to remove corrosion and coatings from structures, ground service equipment, small parts and flight components result in waste streams consisting of toxic chemicals, spent media blast materials, and waste water. When chemicals are used in these processes they are typically high in volatile organic compounds (VOC) and are considered hazardous air pollutants (HAP). When blast media is used, the volume of hazardous waste generated is increased significantly. Many of the coatings historically used within NASA contain toxic metals such as hexavalent chromium, and lead. These materials are highly regulated and restrictions on worker exposure continue to increase. Most recently the Occupational Safety and Health Administration (OSHA) reduced the permissible exposure limit (PEL) for hexavalent chromium (CrVI) from 52 to 5 micrograms per cubic meter of air as an 8-hour time-weighted average. Hexavalent chromium is found in numerous pretreatment and primer coatings used within the Space Shuttle Program. In response to the need to continue to protect assets within the agency and the growing concern over these new regulations, NASA is researching different ways to continue the required maintenance of both facility and flight equipment in a safe, efficient, and environmentally preferable manner. The use of laser energy to prepare surfaces for a variety of processes, such as corrosion and coating removal, weld preparation, and non destructive evaluation (NDE) is a relatively new application of the technology that has been proven to be environmentally preferable and in many cases less labor intensive than currently used removal methods. The novel process eliminates VOCs and blast media and captures the removed coatings with an integrated vacuum system. This means that the only waste generated are the coatings that are removed, resulting in an overall cleaner process. The development of a Portable Laser Coating Removal System (PLCRS) started as the goal of a Joint Group on Pollution Prevention (JG-PP) project, led by the Air Force, where several types of lasers in several configurations were thoroughly evaluated. Following this project, NASA decided to evaluate the best performers on processes and coatings specific to the agency. Laser systems used during this project were all of a similar design, between 40 and 500 Watts, most of which had integrated vacuum systems in order to collect materials removed from substrate surfaces during operation.

Rothgeb, Matthew J↗
DOE OSTI2023

Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography

Pyridoxal 5’-phosphate (PLP)-dependent enzymes utilize a vitamin B 6 -derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-l-arabinofuranosidase activity

The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. A gene from the heterotrophic, halothermophilic marine bacterium Halothermothrix orenii has been cloned and overexpressed in Escherichia coli. This gene encodes the only glycoside hydrolase of family 43 (GH43) produced by H. orenii. The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. As for other GH43 members, the enzyme folds as a five-bladed β-propeller. The structure features a metal-binding site on the propeller axis, near the active site. Based on thermal denaturation data, the H. orenii glycosidase depends on divalent cations in combination with high salt for optimal thermal stability against unfolding. A maximum melting temperature of 76°C was observed in the presence of 4 M NaCl and Mn{sup 2+} at pH 6.5. The gene encoding the H. orenii GH43 enzyme has previously been annotated as a putative α-l-arabinofuranosidase. Activity was detected with p-nitrophenyl-α-l-arabinofuranoside as a substrate, and therefore the name HoAraf43 was suggested for the enzyme. In agreement with the conditions for optimal thermal stability against unfolding, the highest arabinofuranosidase activity was obtained in the presence of 4 M NaCl and Mn{sup 2+} at pH 6.5, giving a specific activity of 20–36 µmol min{sup −1} mg{sup −1}. The active site is structurally distinct from those of other GH43 members, including arabinanases, arabinofuranosidases and xylanases. This probably reflects the special requirements for degrading the unique biomass available in highly saline aqueous ecosystems, such as halophilic algae and halophytes. The amino-acid distribution of HoAraf43 has similarities to those of mesophiles, thermophiles and halophiles, but also has unique features, for example more hydrophobic amino acids on the surface and fewer buried charged residues.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Compressive strain turns 𝑠 ± - into 𝑑-wave pairing in a one-unit-cell La 3 ⁢Ni 2 ⁢O 7 thin film via substrate-induced hole doping

Motivated by recent reports of ambient-pressure superconductivity in La 3 ⁢Ni 2⁢ O 7 films grown on LaSrAlO 4 , we investigate the superconducting instability in a one-unit-cell (1UC) thin film using ab initio and random-phase approximation techniques. Compared to the high-pressure bulk system, the ratio of interlayer 𝑑 3⁢𝑧 2 −𝑟 2 hopping to intralayer 𝑑 𝑥 2 −𝑦 2 hopping is suppressed in the 1UC thin film, and the crystal-field splitting of the 𝑒 𝑔 orbitals is increased. Here, our calculation indicates that spin-fluctuation-driven pairing correlations are weak for the stoichiometric case at ambient pressure, but increase significantly under hole doping. The leading pairing symmetry is also found to change by hole doping. Specifically, we obtain a leading 𝑑 𝑥 2 −𝑦 2 pairing state at moderate hole doping, followed by a 𝑑 𝑥⁢𝑦 state at higher doping. These states are driven by intraband spin-fluctuation scattering within the 𝛾 hole pocket centered around the 𝑀 point, and arise primarily from states in the Ni layer farther from the substrate. These results strongly suggest that the thin-film superconducting samples are hole-doped and that pairing in this system predominantly arises in the layer, as opposed to the interlayer pairing in the pressurized bulk system.

Zhang, Yang [Oak Ridge National Laboratory (ORNL),↗
DOE OSTI2017

Preliminary Analysis of Damage to MPFDs Caused by Reactor Pulses

The need for next-generation, accident-tolerant fuels has generated significant interest in the restart of domestic fuels testing at the Transient Reactor Test (TREAT) facility. The TREAT reactor is designed to produce large, transient fluxes that replicate the effects of a wide variety of accident conditions on an irradiated fuel sample. Peak powers generated during short pulses approach 20 GW with a neutron flux of approximately 10{sup 17} n cm{sup -2} s{sup -1}. As part of the restart effort, new vehicle designs are being explored for sample irradiation, including the Static Environment Rodlet Transient Test Apparatus (SERTTA) and variants. As part of the SERTTA designs, micro-pocket fission detectors (MPFDs) are being explored for localized flux measurements before, during, and after transient operations. These detectors are also being considered as part of future, core-wide instrumentation for the TREAT reactor. However, the high fluxes associated with the pulses in the TREAT core present certain thermodynamic concerns given their intensity and the amount of energy they will release within the MPFDs within such a short amount of time. Assuming each fission that occurs in a MPFD results in a fission fragment depositing 85 MeV of energy in the substrate on average and each MPFD has 0.5 μg of natural uranium deposited on it, a 100 ms long pulse in the TREAT reactor at 1017 n cm{sup -2} s{sup -1} flux will produce approximately 4.6 x 10{sup 6} fissions in an MPFD. This pulse deposits 6.3 x 10{sup -5} J in the substrate over a 100 ms duration. That amount of energy is sufficient to melt roughly 33% of the Pt under the UO{sub 2} deposition or a circular spot with a diameter of approximately 860 μm. Of course, the above estimate makes a number of simplifying assumptions and ignores heat transfer, but does serve to illustrate the point that this rapid heating effect could be detrimental to the integrity and life of these in-core MPFDs. To study how these layers are affected by large transient neutron fluxes, five samples were prepared, pre-analyzed, and then subjected to a pulse in the central thimble of the Kansas State University TRIGA Mark II reactor to a peak power of 1.58 GW. After being allowed to decay to safer radiation levels, the sample substrates and coatings were inspected using scanning electron microscopy (SEM) to identify any changes to their surface morphology. Indeed, certain changes were found and are discussed in greater detail in this paper.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2015

A Micromegas-based low-background x-ray detector coupled to a slumped-glass telescope for axion research

Here, we report on the design, construction and operation of a low background x-ray detection line composed of a shielded Micromegas detector of the microbulk technology. The detector is made from radiopure materials and is placed at the focal point of a ~ 5 cm diameter, 1.5 m focal-length, cone-approximation Wolter I x-ray telescope (XRT) assembled from thermally-formed (or "slumped") glass substrates deposited with multilayer coatings. The system has been conceived as a technological pathfinder for the future International Axion Observatory (IAXO), as it combines two of the techniques (optic and detector) proposed in the conceptual design of the project. It is innovative for two reasons: it is the first time an x-ray optic has been designed and fabricated specifically for axion research, and the first time a Micromegas detector has been operated with an x-ray optic. The line has been installed at one end of the CERN Axion Solar Telescope (CAST) magnet and is currently looking for solar axions. Furthermore, the combination of the XRT and Micromegas detector provides the best signal-to-noise ratio obtained so far by any detection system of the CAST experiment with a background rate of 5.4×10 –3 counts per hour in the energy region-of-interest and signal spot area.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS2007

Toward a III-V Multijunction Space Cell Technology on Si

High efficiency compound semiconductor solar cells grown on Si substrates are of growing interest in the photovoltaics community for both terrestrial and space applications. As a potential substrate for III-V compound photovoltaics, Si has many advantages over traditional Ge and GaAs substrates that include higher thermal conductivity, lower weight, lower material costs, and the potential to leverage the extensive manufacturing base of the Si industry. Such a technology that would retain high solar conversion efficiency at reduced weight and cost would result in space solar cells that simultaneously possess high specific power (W/kg) and high power density (W/m2). For terrestrial solar cells this would result in high efficiency III-V concentrators with improved thermal conductivity, reduced cost, and via the use of SiGe graded interlayers as active component layers the possibility of integrating low bandgap sub-cells that could provide for extremely high conversion efficiency.1 In addition to photovoltaics, there has been an historical interest in III-V/Si integration to provide optical interconnects in Si electronics, which has become of even greater relevance recently due to impending bottlenecks in CMOS based circuitry. As a result, numerous strategies to integrate GaAs with Si have been explored with the primary issue being the approx.4% lattice mismatch between GaAs and Si. Among these efforts, relaxed, compositionally-graded SiGe buffer layers where the substrate lattice constant is effectively tuned from Si to that of Ge so that a close lattice match to subsequent GaAs overlayers have shown great promise. With this approach, threading dislocation densities (TDDs) of approx.1 x 10(exp 6)/sq cm have been uniformly achieved in relaxed Ge layers on Si,5 leading to GaAs on Si with minority carrier lifetimes greater than 10 ns,6 GaAs single junction solar cells on Si with efficiencies greater than 18%,7 InGaAs CW laser diodes on Si,8 and room temperature GaInP red laser diodes on Si.9 Here we report on the first high performance dual junction GaInP/GaAs solar cells grown on Si using this promising SiGe engineered substrate approach.

Ringel, S. A.↗
DOE OSTI2016

M3FT-16OR020202112 - Report on viability of hydrothermal corrosion resistant SiC/SiC Joint development

Hydrothermal corrosion of four types of the silicon carbide (SiC) to SiC plate joints were investigated under PWR and BWR relevant chemical conditions without irradiation. The joints were formed by metal diffusion bonding using molybdenum or titanium interlayer, reaction sintering using Ti-Si-C system, and SiC nanopowder sintering. Most of the formed joints withstood the corrosion tests for five weeks. The recession of the SiC substrates was limited. Based on the recession rate of the bonding layers, it was concluded that all the joints except for the molybdenum diffusion bond are promising under the reducing activity environments. The SiC nanopowder sintered joint was the most corrosion tolerant under the oxidizing activity environment among the four joints.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2015

Structural Basis of Clade-specific Engagement of SAMHD1 (Sterile α Motif and Histidine/Aspartate-containing Protein 1) Restriction Factors by Lentiviral Viral Protein X (Vpx) Virulence Factors

Sterile α motif (SAM) and histidine/aspartate (HD)-containing protein 1 (SAMHD1) restricts human/simian immunodeficiency virus infection in certain cell types and is counteracted by the virulence factor Vpx. Current evidence indicates that Vpx recruits SAMHD1 to the Cullin4-Ring Finger E3 ubiquitin ligase (CRL4) by facilitating an interaction between SAMHD1 and the substrate receptor DDB1- and Cullin4-associated factor 1 (DCAF1), thereby targeting SAMHD1 for proteasome-dependent down-regulation. Host-pathogen co-evolution and positive selection at the interfaces of host-pathogen complexes are associated with sequence divergence and varying functional consequences. Two alternative interaction interfaces are used by SAMHD1 and Vpx: the SAMHD1 N-terminal tail and the adjacent SAM domain or the C-terminal tail proceeding the HD domain are targeted by different Vpx variants in a unique fashion. In contrast, the C-terminal WD40 domain of DCAF1 interfaces similarly with the two above complexes. Comprehensive biochemical and structural biology approaches permitted us to delineate details of clade-specific recognition of SAMHD1 by lentiviral Vpx proteins. We show that not only the SAM domain but also the N-terminal tail engages in the DCAF1-Vpx interaction. Furthermore, we show that changing the single Ser-52 in human SAMHD1 to Phe, the residue found in SAMHD1 of Red-capped monkey and Mandrill, allows it to be recognized by Vpx proteins of simian viruses infecting those primate species, which normally does not target wild type human SAMHD1 for degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Activity–Based Protein Profiling of Bile Salt Hydrolysis in the Human Gut Microbiome with Beta–Lactam or Acrylamide–Based Probes

Microbial bile salt hydrolases (BSHs) found in the intestine catalyze the deconjugation of taurine– and glycine–linked bile salts produced in the liver. The resulting bile salts are biological detergents and are critical in aiding lipophilic nutrient digestion. Therefore, the activity of BSHs in the gut microbiome is directly linked to human metabolism and overall health. Bile salt metabolism has also been associated with disease phenotypes such as liver and colorectal cancer. In order to reshape the gut microbiome to optimize bile salt metabolism, tools to characterize and quantify these processes must exist to enable a much–improved understanding of how metabolism goes awry in the face of disease, and how it can be improved through an altered lifestyle and environment. Furthermore, it is necessary to attribute metabolic activity to specific members and BSHs within the microbiome. To this end, we have developed activity–based probes with two different reactive groups to target bile salt hydrolases. Finally, these probes bind similarly to the authentic bile salt substrates, and we demonstrate enzyme labeling of active bile salt hydrolases by using purified protein, cell lysates, and in human stool.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds

The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases removes methyl groups from methylated lysine 4 of histone H3. Accumulating evidence supports a role for KDM5 family members as oncogenic drivers. In this work, we compare the in vitro inhibitory properties and binding affinity of ten diverse compounds with all four family members, and present the crystal structures of the KDM5A-linked Jumonji domain in complex with eight of these inhibitors in the presence of Mn(II). All eight inhibitors structurally examined occupy the binding site of α-ketoglutarate, but differ in their specific binding interactions, including the number of ligands involved in metal coordination. We also observed inhibitor-induced conformational changes in KDM5A, particularly those residues involved in the binding of α-ketoglutarate, the anticipated peptide substrate, and intramolecular interactions. We discuss how particular chemical moieties contribute to inhibitor potency and suggest strategies that might be utilized in the successful design of selective and potent epigenetic inhibitors.

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

Architecture-Dependent Thin Film Self-Assembly of Star Polystyrene-poly(2-vinylpyridine) Block Copolymers

Controlling the orientation of nanostructured block copolymer (BCP) thin films is essential for their use in templating, transport, and pattern transfer. Conventional efforts mainly focus on adjusting enthalpic interactions between the blocks and interfaces, while entropic contributions are often overlooked. Here, we show that the morphology of BCP thin films can be precisely tuned by the architectural design of star BCPs. Specifically, we synthesized multiarm star BCPs with a polystyrene (PS) core and poly(2-vinylpyridine) (P2VP) corona, which exhibits a lamellar microdomain morphology. The entropic penalty associated with a parallel orientation of the microdomains to the substrate is controlled by varying the number of arms comprising the star BCPs, from 2-arms (triblock) to 3-arms and 4-arms. We systematically investigated the thin film morphology at different depths using grazing incidence small-angle X-ray and neutron scattering (GISAXS and GISANS), atomic force microscopy (AFM), water contact angle (WCA), and interference microscopy. The results show that 2-arm star BCPs show a parallel orientation, the 3-arm star BCPs form a uniform PS film at the air surface with a vertical orientation of the microdomains underneath, and the 4-arm star BCPs exhibit a parallel microdomain orientation at the air surface with mixed parallel and perpendicular microdomain orientation in the bulk. Additionally, we found that the inclination angle of microdomains at the edges of islands and holes, resulting from the incommensurability between film thickness and the characteristic period of the microdomain morphology, increases with a higher number of arms. This suggests a greater grain boundary tilt angle in the microdomains of star-shaped block copolymers (BCPs). When silicon substrates were modified with PS homopolymer, the selective interaction between substrate and core blocks promotes a parallel orientation for the 4-arm star BCPs. In conclusion, this work shows that control of arm number in star BCPs affords diverse BCP thin film morphologies, offering insights into the star BCP conformations in thin films across different depths.

36 MATERIALS SCIENCE↗
DOE OSTI2021

On the Development of Order and Interfaces during the Growth of Ultrathin La 2 CuO 4 Films by Molecular Beam Epitaxy

While the atomic structure of interfaces in complex oxide heterostructures created by epitaxial growth has been investigated extensively, few studies have been conducted on how interfaces form and restructure at the initial stage of film growth. The dynamic aspects of the growth behavior can strongly influence the final interfacial atomic structure, which may lead to the emergence of interface-specific properties, such as the rise of interfacial superconductivity between certain Ruddlesden-Popper oxide materials. In this report, the structural development of La2CuO 4 thin films grown by molecular beam epitaxy on a LaSrAlO 4 substrate is investigated by X-ray diffraction measurements with rapid scans over a volume of reciprocal space. This method provides far more detailed information on interface formation than traditional fixed-point measurements. The results show that the atomic structure of the interface becomes fully established after just a single unit cell of growth. Interestingly, restructuring continues to occur within the topmost half to one unit cell of the film during the deposition process. However, diffraction intensity oscillations from both reflection high-energy electron and X-ray measurements stabilize only after the growth of two unit cells, indicating that the growth front morphology continues to evolve until the start of the third unit cell. This multimodal investigation provides insights into the atomic processes taking place during layered oxide interface formation, including the dynamical rearrangement of LaO and CuO 2 layers. Such information is not only relevant to the engineering and optimization of functional layer structures but can also be critical for ultrathin films.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural basis for substrate recognition and chemical inhibition of oncogenic MAGE ubiquitin ligases

Testis-restricted melanoma antigen (MAGE) proteins are frequently hijacked in cancer and play a critical role in tumorigenesis. MAGEs assemble with E3 ubiquitin ligases and function as substrate adaptors that direct the ubiquitination of novel targets, including key tumor suppressors. However, how MAGEs recognize their targets is unknown and has impeded the development of MAGE-directed therapeutics. Here, we report the structural basis for substrate recognition by MAGE ubiquitin ligases. Biochemical analysis of the degron motif recognized by MAGE-A11 and the crystal structure of MAGE-A11 bound to the PCF11 substrate uncovered a conserved substrate binding cleft (SBC) in MAGEs. Mutation of the SBC disrupted substrate recognition by MAGEs and blocked MAGE-A11 oncogenic activity. A chemical screen for inhibitors of MAGE-A11:substrate interaction identified 4-Aminoquinolines as potent inhibitors of MAGE-A11 that show selective cytotoxicity. These findings provide important insights into the large family of MAGE ubiquitin ligases and identify approaches for developing cancer-specific therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Orbital configuration in CaTiO 3 films on NdGaO 3

Despite its use as a constituent layer for realization of a polar metal and interfacial conductivity, the microscopic study of electronic structure of CaTiO 3 is still very limited. Here, we epitaxially stabilized CaTiO 3 films on NdGaO 3 (110) substrates in a layer-by-layer way by pulsed laser deposition. The structural and electronic properties of the films were characterized by reflection-high-energy-electron-diffraction, X-ray diffraction, and element-specific resonant X-ray absorption spectroscopy. To reveal the orbital polarization and the crystal field splitting of the titanium 3d state, X-ray linear dichroism was carried out on CaTiO 3 films, demonstrating the orbital configuration of d xz /d yz < d xy < d 3z 2 -r 2 < d x 2 -y 2 . To further explore the origin of this configuration, we performed the first-principles density function theory calculations, which linked the orbital occupation to the on-site energy of Ti 3d orbitals. Finally, these findings can be important for understanding and designing exotic quantum states in heterostructures based on CaTiO 3 .

36 MATERIALS SCIENCE↗
DOE OSTI2017

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'–3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. Furthermore, the striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Regulation of FANCD2 and FANCI monoubiquitination by their interaction and by DNA

FANCD2 and FANCI function together in the Fanconi anemia network of deoxyribonucleic acid (DNA) crosslink repair. These proteins form the dimeric ID2 complex that binds DNA and becomes monoubiquitinated upon exposure of cells to DNA crosslinking agents. The monoubiquitinated ID2 complex is thought to facilitate DNA repair via recruitment of specific nucleases, translesion DNA polymerases and the homologous recombination machinery. Using the ubiquitin conjugating enzyme (E2) UBE2T and ubiquitin ligase (E3) FANCL, monoubiquitination of human FANCD2 and FANCI was examined. The ID2 complex is a poor substrate for monoubiquitination, consistent with the published crystal structure showing the solvent inaccessibility of the target lysines. Importantly, FANCD2 monoubiquitination within the ID2 complex is strongly stimulated by duplex or branched DNA, but unstructured singlestranded DNA or chromatinized DNA is ineffective. Interaction of FANCL with the ID2 complex is indispensable for its E3 ligase efficacy. Interestingly, mutations in FANCI that impair its DNA binding activity compromise DNA-stimulated FANCD2 monoubiquitination. Moreover, we demonstrate that in the absence of FANCD2, DNA also stimulates FANCI monoubiquitination, but in a FANCL-independent manner. These results implicate the role of a proper DNA ligand in FANCD2 and FANCI monoubiquitination, and reveal regulatory mechanisms that are dependent on protein–protein and protein–DNA interactions.

59 BASIC BIOLOGICAL SCIENCES↗