Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “AlAs”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Amino acids react with carbon dioxide (CO2) and form nanofibers and nanoflowers

A method for capturing CO2 comprising dissolving at least one pure amino acid (AA) in water without the use of a catalyst for establishing protonation of an amino group of the amino acid, adding at least one base solution to the amino acid and water solution to deprotonate the protonated amino group of the amino acid and forming an amino acid-XOH—H2O wherein X is sodium or potassium, and subjecting CO2 to the amino acid-XOH—H2O to form new nanomaterials is provided. A regenerable nanofiber is disclosed comprising a NaHCO3 nanofiber, a KHCO3 nanofiber, or an amino acid nanofiber made from subjecting a CO2 gas to an amino acid aqueous solvent. Preferably, the amino acid aqueous solvent is one or more of a Gly-NaOH—H2O, an Ala-NaOH—H2O, a Phe-NaOH—H2O, a Gly-KOH—H2O, an Ala-KOH—H2O, and a Phe-KOH—H2O.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A mutagenic analysis of NahE, a hydratase-aldolase in the naphthalene degradative pathway

NahE is a hydratase-aldolase that converts o-substituted trans-benzylidenepyruvates (H, OH, or CO 2 - ) to benzaldehyde, salicylaldehyde, or 2-carboxybenzaldehyde, respectively, and pyruvate. The enzyme is in a bacterial degradative pathway for naphthalene, which is a toxic and persistent environmental contaminant. Sequence, crystallographic, and mutagenic analysis identified the enzyme as a member of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. As such, it has a conserved lysine (Lys183) and tyrosine (Tyr155), for Schiff base formation, as well as a GXXGE motif for binding of the pyruvoyl carboxylate group. A crystal structure of the selenomethionine derivative of NahE shows these active site elements along with nearby residues that might be involved in the mechanism and/or specificity. Mutations of five active site amino acids (Thr65, Trp128, Tyr155, Asn157, and Asn281) were constructed and kinetic parameters measured in order to assess the effect(s) on catalysis. Here, the results show that the two Trp128 mutants (Phe and Tyr) have the least effect on catalysis, whereas amino acids with bulky side chains at Thr65 (Val) and Asn281 (Leu) have the greatest effect. Changing Tyr155 to Phe and Asn157 to Ala also hinders catalysis, and the effects fall in between these extremes. These observations are put into a structural context using a crystal structure of the Schiff base of the reaction intermediate. Trapping experiments with substrate, Na(CN)BH 3 , and wild type enzyme and selected mutants mostly paralleled the kinetic analysis, and identified two salicylaldehyde-modified lysines: the active site lysine (Lys183) and one outside the active site (Lys279). The latter could be responsible for the observed inhibition of NahE by salicylaldehyde. Together, the results provide new insights into the NahE-catalyzed reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Thermal power plant upgrade via a rotating detonation combustor and retrofitted turbine with optimized endwalls

Over the past decade, pressure gain combustion research has promised over 10 percentage-points of increase in power plant thermal efficiency. Alas, to realize such potential gain, one must effectively couple the turbine with the detonation combustor, whose exhaust conditions differ substantially from current state of the art gas turbines. This paper presents a modeling approach that enables a superior thermodynamic cycle with a rotating detonation combustor and a retrofitted gas turbine by including a diffuser downstream of the combustor and by contouring the turbine endwall, while preserving the airfoil geometry. We propose a multi-step optimization strategy, parametrizing the endwall geometry with a few control points, without altering the airfoil geometry, and with the stage turbine efficiency as objective function. In a first step the turbine performance is assessed with steady inlet conditions by solving the steady three-dimensional Reynolds-Averaged Navier-Stokes equations. In a second step, the inlet conditions are unsteady, as predicted from a detonation combustor and a diffuser, and three-dimensional full unsteady simulations are performed with an unsteady Reynolds-Averaged Navier-Stokes solver. By altering the vane endwall, the steady optimization yielded an efficiency increase of 12% relative to the baseline, while the unsteady optimization resulted in 21% increase compared to the datum turbine. Finally, a full engine analysis demonstrated the superiority of pressure gain combustion which included a realistic thermodynamic cycle of the combustor, the diffuser and the optimized turbine components.

42 ENGINEERING↗
DOE OSTI2024

Comparison of methods for the NMR measurement of motionally averaged dipolar couplings

Motionally averaged dipolar couplings are an important tool for understanding the complex dynamics of catalysts, polymers, and biomolecules. While there is a plethora of solid-state NMR pulse sequences available for their measurement, in can be difficult to gauge the methods’ strengths and weaknesses. In particular, there has not been a comprehensive comparison of their performance in natural abundance samples, where 1H homonuclear dipolar couplings are important and the use of large MAS rotors may be required for sensitivity reasons. In this work, we directly compared some of the more common methods for measuring C–H dipolar couplings in natural abundance samples using L-alanine (L-Ala) and the N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLF) tripeptide as model systems. Here, we evaluated their performance in terms of accuracy, resolution, sensitivity, and ease of implementation. We found that, despite the presence of 1H homonuclear dipolar interactions, all methods, with the exception of REDOR, were able to yield the reasonable dipolar coupling strengths for both mobile and static moieties. Of these methods, PDLF provides the most convenient workflow and precision at the expense of low sensitivity. In low-sensitivity cases, MAS-PISEMA and DIPSHIFT appear to be the better options.

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

Loss of biological control of enamel mineralization in amelogenin-phosphorylation-deficient mice

Amelogenin, the most abundant enamel matrix protein, plays several critical roles in enamel formation. Importantly, we previously found that the singular phosphorylation site at Ser16 in amelogenin plays an essential role in amelogenesis. Studies of genetically knock-in (KI) modified mice in which Ser16 in amelogenin is substituted with Ala that prevents amelogenin phosphorylation, and in vitro mineralization experiments, have shown that phosphorylated amelogenin transiently stabilizes amorphous calcium phosphate (ACP), the initial mineral phase in forming enamel. Furthermore, KI mice exhibit dramatic differences in the enamel structure compared with wild type (WT) mice, including thinner enamel lacking enamel rods and ectopic surface calcifications. Here, we now demonstrate that amelogenin phosphorylation also affects the organization and composition of mature enamel mineral. In this work, we compared WT, KI, and heterozygous (HET) enamel and found that in the WT elongated crystals are co-oriented within each rod, however, their c-axes are not aligned with the rods' axes. In contrast, in rod-less KI enamel, crystalline c-axes are less co-oriented, with misorientation progressively increasing toward the enamel surface, which contains spherulites, with a morphology consistent with abiotic formation. Furthermore, we found significant differences in enamel hardness and carbonate content between the genotypes. ACP was also observed in the interrod of WT and HET enamel, and throughout aprismatic KI enamel. In conclusion, amelogenin phosphorylation plays crucial roles in controlling structural, crystallographic, mechanical, and compositional characteristics of dental enamel. Thus, loss of amelogenin phosphorylation leads to a reduction in the biological control over the enamel mineralization process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Development and biodistribution studies of 77 As-labeled trithiol RM2 bioconjugates for prostate cancer: Comparison of [ 77 As]As-trithiol-Ser-Ser-RM2 vs. [ 77 As]As-trithiol-Glu-Ser-RM2

Recent progress with the production of 72 As (2.49 Mev β + max (64%), 3.33 Mev β + max (16%), 834 keV (81%), t 1/2 : 26 h) and 77 As (0.683 Mev β- max (97%), 239 keV (1.59%), t 1/2 : 38.8 h) has facilitated their evaluation as a potential “theranostic pair” for PET imaging and radiotherapy. Our 3 rd generation trithiol chelate with two carboxylic acid groups was further developed as a bifunctional chelate for radioarsenic. The As complex with the trithiol chelate was synthesized and characterized. No carrier added (nca) [ 77 As][H 2 AsO 4 - ] was used for radiolabeling studies. Here, the trithiol chelate was conjugated to the RM2 peptide (DPhe-Gln-Trp-Ala-VaI-Gly-His-Sta-Leu-NH 2 ) via solid phase peptide synthesis with two different linkers, Ser-Ser and Glu-Ser. The trithiol chelate and its RM2 bioconjugates were radiolabeled with nca 77 As, and the RM2 bioconjugates were compared in initial biodistribution studies. The As diacid trithiol complex was characterized by 1 H NMR, 13 C NMR and HR-ESI-MS. The trithiol-RM2 precursor and As trithiol bioconjugates were characterized by HR-ESI-MS and/or LC-ESI-MS. Radiolabeling of the RM2 bioconjugates with 77 As resulted in over 85% radiochemical yield for [ 77 As]As-trithiol-Ser-Ser-RM2 ([ 77 As]8) and 90% for [ 77 As]As-trithiol-Glu-Ser-RM2 ([ 77 As]9). Both radiotracers demonstrated excellent in vitro stability (≥ 90% remaining intact through 24 h in PBS buffer) and were more hydrophilic than previous analogues based on log D 7.4 values. Biodistribution results of the two radiotracers in healthy CF-1 male mice demonstrated blockable pancreatic uptake at 1 h (82% for ([ 77 As]8 and 78% for [ 77 As]9) indicating specific gastrin-releasing peptide receptor (GRPR) uptake. The primary route of excretion was through the gastrointestinal system for both radiotracers. A new trithiol chelate with improved hydrophilicity was successfully conjugated to the RM2 peptide via two linkers, and high radiolabeling yield with nca 77 As was achieved. In vivo biodistribution studies with both radiotracers demonstrated blockable pancreatic uptake suggestive of specific receptor uptake.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2020

Observation of an Unexpected n -Type Semiconducting Behavior in the New Ternary Zintl Phase Eu 3 InAs 3

The ternary arsenides Eu 3 InAs 3 and Sr 3 InAs 3 have been obtained by reactions of the elements in In flux at 1373 K. Structure elucidation by single-crystal X-ray diffraction reveals that Eu 3 InAs 3 and Sr 3 InAs 3 adopt the same orthorhombic structure (space group Pnma, Z = 4, Ca 3 AlAs 3 structure type) with unit cell parameters a = 12.9179(9) Å, b = 4.3990(3) Å, c = 13.9337(10) Å and a = 13.0218(11) Å, b = 4.4364(4) Å, c = 14.1339(12) Å, respectively. The structure consists of linear chains of corner-sharing InAs4 tetrahedra, [InAs 2 As 2/2 ] 6– , and Eu 2+ /Sr 2+ cations. Therefore, both Eu 3 InAs 3 and Sr 3 InAs 3 are valence-precise Zintl phases. As expected from the closed-shell electronic configurations, semiconducting behavior is confirmed by resistivity measurements on single crystals for both and by electronic band structure calculations for Sr 3 InAs 3 . The temperature dependence of resistivity and the computational work are in agreement that Eu 3 InAs 3 and Sr 3 InAs 3 are intrinsic semiconductors with narrow band gaps. Thermopower measurement on single-crystalline samples of Eu 3 InAs 3 shows that in the whole measured temperature range, from 300 to 700 K, the values for the Seebeck coefficient are negative. The observation of a negative Seebeck coefficient with very large absolute value (>400–500 μV K –1 at 700 K) is unexpected among the Zintl phases and suggestive that electrons are the majority charge carriers. Such a rare, n-type charge transport in an undoped compound such as Eu 3 InAs 3 , a material that has not been purposely optimized, could indicate native “defect” chemistry, and not extrinsic doping, as a reason for the unusual behavior. Here, a possible explanation involves a mixed-valent Eu 2+ /Eu 3+ state, which might be inferred from the measured effective paramagnetic moment of 7.2 μB per Eu atom, which is lower than the theoretically predicted value for free-ion moment of 7.9 μ B /Eu.

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

Yb Substitution and Ultralow Thermal Conductivity of the Ca 3– x Yb x AlSb 3 (0 ≤ x ≤ 0.81(1)) System

Here, a series of Yb-substituted Zintl phases in the Ca 3–x Yb x AlSb 3 (0 ≤ x ≤ 0.81(1)) system has been synthesized by initial arc melting and post-heat treatment, and their isotypic crystal structures were characterized by both powder and single crystal X-ray diffraction analysis. All four title compounds adopted the Ca 3 AlAs 3 -type structure (space group Pnma, Pearson code oP28, Z = 4). The overall structure can be described as a combination of the 1-dimensional (1D) infinite chain of ∞ 1 [Al(Sb 2 Sb 2/2 )] formed by two vertices sharing [AlSb 4 ] tetrahedral moieties and three Ca 2+ /Yb 2+ mixed sites located in between these 1D chains. The charge balance and the resultant independency of the 1D chains in the title system were explained by the Zintl-Klemm formalism [Ca 2+ /Yb 2+ ] 3 [(4b-Al 1– )(1b-Sb 2– ) 2 (2b-Sb 1– ) 2/2 ]. A series of DFT calculations proved that (1) the band overlap between the d-orbital states from two types of cations and the p-orbital states from Sb at the high symmetry Γ point implied a heavily doped degenerate semiconducting behavior of the quaternary Ca 2 YbAlSb 3 model and (2) the site preference of Yb for the M1 site was due to the electronic-factor criterion based on the Q values of each atomic site. The electron localization function calculations also proved that the two different shapes of lone pairs of the Sb atoms—the “umbrella-shape” and the “C-shape”—are determined by local geometry and the coordination environment on the anionic frameworks. Thermoelectric measurements of the quaternary title compound Ca 2.19(1) Yb 0.81 AlSb 3 showed an approximately two times larger ZT value than that of ternary Ca 3 AlSb 3 at 623 K due to increased electrical conductivity and ultralow thermal conductivity originated from Yb substitution for Ca.

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

An In Situ , Automated High-Explosives Aging Method Utilizing Two-Dimensional Gas Chromatography–Mass Spectrometry

Understanding chemical changes that occur in high explosives as they age is of great importance to the safe employment and storage of these compounds. Traditional methods of aging high explosives even under accelerated aging conditions are time intensive with durations on the order of months to years. The nature of traditional aging analyses reduces each sample to a snapshot data point often separated widely in time, requiring many assumptions as to how the degradation products develop. Further complicating matters, several analytical techniques are typically employed for each sample analysis in order to ascertain an entire picture of the decomposition pathways. To address these shortcomings with existing methods, a new method of accelerated aging of high explosives utilizing comprehensive two-dimensional gas chromatography coupled to high-resolution mass spectrometry (GC × GC-HRMS) was developed using 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) as a model compound for method development. This in situ automated method reduces the time scale of aging to a matter of hours using the inlet of the GC × GC as the aging vessel. GC × GC in combination with HRMS allowed for the collection of both evolved gases and other decomposition products produced during the entire aging process in real time with HRMS providing far greater certainty in identification of explosives aging products. Additionally, this method allowed for a higher throughput of samples with greatly simplified sample preparation. Chemometric analysis of the GC × GC-HRMS data set via the alteration analysis (ALA) enabled discovery of statistically significant chemical changes providing insight into the variation of decomposition pathways with varying aging temperatures.

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

13 C ENDOR Characterization of the Central Carbon within the Nitrogenase Catalytic Cofactor Indicates That the CFe 6 Core Is a Stabilizing “Heart of Steel”

Substrates and inhibitors of Mo-dependent nitrogenase bind and react at Fe ions of the active-site FeMo-cofactor [7Fe–9S–C–Mo–homocitrate] contained within the MoFe protein α-subunit. The cofactor contains a CFe 6 core, a carbon centered within a trigonal prism of six Fe, whose role in catalysis is unknown. Targeted 13 C labeling of the carbon enables electron-nuclear double resonance (ENDOR) spectroscopy to sensitively monitor the electronic properties of the Fe–C bonds and the spin-coupling scheme adopted by the FeMo-cofactor metal ions. Here this report compares 13 CFe 6 ENDOR measurements for (i) the wild-type protein resting state (E 0 ; α-Val 70 ) to those of (ii) α-Ile 70 , (iii) α-Ala 70 -substituted proteins; (iv) crystallographically characterized CO-inhibited “hi-CO” state; (v) E 4 (4H) Janus intermediate, activated for N 2 binding/reduction by accumulation of 4[ e– /H + ]; (vi) E 4 (2H)* state containing a doubly reduced FeMo-cofactor without Fe-bound substrates; and (vii) propargyl alcohol reduction intermediate having allyl alcohol bound as a ferracycle to FeMo-cofactor Fe6. All states examined, both S = 1/2 and 3/2 exhibited near-zero 13 C isotropic hyperfine coupling constants, $^Ca$ = [-1.3 ↔ +2.7] MHz. Density functional theory computations and natural bond orbital analysis of the Fe-C bonds show that this occurs because a (3 spin-up/3 spin-down) spin-exchange configuration of CFe 6 Fe-ion spins produces cancellation of large spin-transfers to carbon in each Fe–C bond. Previous X-ray diffraction and DFT both indicate that trigonal-prismatic geometry around carbon is maintained with high precision in all these states. The persistent structure and Fe–C bonding of the CFe 6 core indicate that it does not provide a functionally dynamic (hemilabile) “beating heart”-instead it acts as “a heart of steel”, stabilizing the structure of the FeMo-cofactor-active site during nitrogenase catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

X-ray structure of LeuT in an inward-facing occluded conformation reveals mechanism of substrate release

Neurotransmitter:sodium symporters (NSS) are conserved from bacteria to man and serve as targets for drugs, including antidepressants and psychostimulants. Here we report the X-ray structure of the prokaryotic NSS member, LeuT, in a Na+/substrate-bound, inward-facing occluded conformation. To obtain this structure, we were guided by findings from single-molecule fluorescence spectroscopy and molecular dynamics simulations indicating that L-Phe binding and mutation of the conserved N-terminal Trp8 to Ala both promote an inward-facing state. Compared to the outward-facing occluded conformation, our structure reveals a major tilting of the cytoplasmic end of transmembrane segment (TM) 5, which, together with release of the N-terminus but without coupled movement of TM1, opens a wide cavity towards the second Na + binding site. The structure of this key intermediate in the LeuT transport cycle, in the context of other NSS structures, leads to the proposal of an intracellular release mechanism of substrate and ions in NSS proteins.

Science & Technology - Other Topics↗
DOE OSTI2023

Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection

The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3–33 antibodies and highlight key features underlying the potent protection of this antibody family.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids

In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 through histone H2B mono-ubiquitin interaction, while the kinetoplastid Trypanosoma brucei di-methyltransferase DOT1A and tri-methyltransferase DOT1B efficiently methylate the homologous H3K76 without H2B mono-ubiquitination. Based on structural and biochemical analyses of DOT1A, we identify key residues in the methyltransferase motifs VI and X for efficient ubiquitin-independent H3K76 methylation in kinetoplastids. Substitution of a basic to an acidic residue within motif VI (Gx 6 K ) is essential to stabilize the DOT1A enzyme-substrate complex, while substitution of the motif X sequence VYGE by CAKS renders a rigid active-site loop flexible, implying a distinct mechanism of substrate recognition. We further reveal distinct methylation kinetics and substrate preferences of DOT1A (H3K76me0) and DOT1B (DOT1A products H3K76me1/me2) in vitro, determined by a Ser and Ala residue within motif IV, respectively, enabling DOT1A and DOT1B to mediate efficient H3K76 tri-methylation non-processively but cooperatively, and suggesting why kinetoplastids have evolved two DOT1 enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

High Carrier Lifetimes in Epitaxial Germanium-Tin/Al(In)As Heterostructures with Variable Tin Compositions

Group IV-based germanium-tin (Ge1-ySny) compositional materials have recently shown great promise for infrared detection, light emission and ultra-low power transistors. High carrier lifetimes are desirable for enhancing the detection limit and efficiency of photodetectors, low threshold current density in lasers, and low tunneling barrier height by lowering defects and dislocations at the heterointerface of a source and a channel. Here, carrier lifetimes in epitaxial germanium (Ge) and variable tin (Sn) compositional Ge1-ySny materials were experimentally determined on GaAs substrates using the contactless microwave photoconductive decay (u-PCD) technique at an excitation wavelength of 1500 nm. Sharp (2 x 2) reflection high energy electron diffraction patterns and low surface roughness were observed from the surface of the Ge0.97Sn0.03 epilayer. X-ray rocking curves from Ge0.97Sn0.03 and Ge0.94Sn0.06 layers demonstrated the pseudomorphic and lattice-matched growth on AlAs and In0.12Al0.88As buffers, respectively, further substantiated by reciprocal space maps and abrupt heterointerfaces evident from the presence of Pendellosung oscillations. High effective carrier lifetimes of 150 ns to 450 ns were measured for Ge1-ySny epilayers as a function of Sn composition, surface roughness, growth temperature, and layer thickness. The observed increase in the carrier lifetime with an increasing Ge layer thickness and a reducing surface roughness, by incorporating Sn, were explained. The enhancement of the carrier lifetime with an increasing Sn concentration was achieved by controlling the defects with lattice-matched Ge0.94Sn0.06/In0.12Al0.88As heterointerfaces or the pseudomorphic growth of Ge0.94Sn0.06 on GaAs. Therefore, our monolithic integration of variable Sn alloy compositional Ge1-ySny materials with high carrier lifetimes opens avenues to realize electronic and optoelectronic devices.

carrier lifetimes↗
DOE OSTI2024

Miniature fluorescence sensor for quantitative detection of brain tumour

Fluorescence-guided surgery has emerged as a vital tool for tumour resection procedures. As well as intraoperative tumour visualisation, 5-ALA-induced PpIX provides an avenue for quantitative tumour identification based on ratiometric fluorescence measurement. To this end, fluorescence imaging and fibre-based probes have enabled more precise demarcation between the cancerous and healthy tissues. These sensing approaches, which rely on collecting the fluorescence light from the tumour resection site and its “remote” spectral sensing, introduce challenges associated with optical losses. In this work, we demonstrate the viability of tumour detection at the resection site using a miniature fluorescence measurement system. Unlike the current bulky systems, which necessitate remote measurement, we have adopted a millimetre-sized spectral sensor chip for quantitative fluorescence measurements. A reliable measurement at the resection site requires a stable optical window between the tissue and the optoelectronic system. This is achieved using an antifouling diamond window, which provides stable optical transparency. The system achieved a sensitivity of 92.3% and specificity of 98.3% in detecting a surrogate tumour at a resolution of 1 × 1 mm 2 . In conclusion, as well as addressing losses associated with collecting and coupling fluorescence light in the current ‘remote’ sensing approaches, the small size of the system introduced in this work paves the way for its direct integration with the tumour resection tools with the aim of more accurate interoperative tumour identification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation

Naegleria gruberi RNA ligase (NgrRnl) exemplifies the Rnl5 family of adenosine triphosphate (ATP)-dependent polynucleotide ligases that seal 3'-OH RNA strands in the context of 3'-OH/5'-PO 4 nicked duplexes. Like all classic ligases, NgrRnl forms a covalent lysyl–AMP intermediate. A two-metal mechanism of lysine adenylylation was established via a crystal structure of the NgrRnl•ATP•(Mn 2+ ) 2 Michaelis complex. Here we conducted an alanine scan of active site constituents that engage the ATP phosphates and the metal cofactors. We then determined crystal structures of ligase-defective NgrRnl-Ala mutants in complexes with ATP/Mn 2+ . The unexpected findings were that mutations K170A, E227A, K326A and R149A (none of which impacted overall enzyme structure) triggered adverse secondary changes in the active site entailing dislocations of the ATP phosphates, altered contacts to ATP, and variations in the numbers and positions of the metal ions that perverted the active sites into off-pathway states incompatible with lysine adenylylation. Each alanine mutation elicited a distinctive off-pathway distortion of the ligase active site. Our results illuminate a surprising plasticity of the ligase active site in its interactions with ATP and metals. More broadly, they underscore a valuable caveat when interpreting mutational data in the course of enzyme structure-function studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Crystal structure of MutYX: a novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-oxoguanine recognition sphere

Abstract The [4Fe–4S] cluster is an important cofactor of the base excision repair (BER) adenine DNA glycosylase MutY to prevent mutations associated with 8-oxoguanine (OG). Several MutYs lacking the [4Fe–4S] cofactor have been identified. Phylogenetic analysis shows that clusterless MutYs are distributed in two clades suggesting cofactor loss has occurred in multiple independent evolutionary events. Herein, we determined the first crystal structure of a clusterless MutY complexed with DNA. On the basis of the dramatic structural divergence from canonical MutYs, we refer to this as representative of a clusterless MutY subgroup “MutYX.” Interestingly, MutYX compensates for the missing [4Fe–4S] cofactor to maintain positioning of catalytic residues by expanding a pre-existing α-helix and acquisition of a new α-helix. Surprisingly, MutYX also acquired a new C-terminal domain that uniquely recognizes OG using residues Gln201 and Arg209. Adenine glycosylase assays and binding affinity measurements indicate that Arg209 is the primary residue responsible for OG:A lesion specificity, while Gln201 assists by bridging OG and Arg209. Surprisingly, replacement of Arg209 and Gln201 with Ala increased activity toward G:A mismatches. The MutYX structure serves as an example of devolution, capturing structural features required to retain function in the absence of a metal cofactor considered indispensable.

Trasviña-Arenas, Carlos H [University of Californi↗