Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Crystal structures”

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 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Lattice Dynamics and Optoelectronic Properties of Vacancy-Ordered Double Perovskite Cs 2 TeX 6 (X = Cl – , Br – , I – ) Single Crystals

The soft, dynamic lattice of inorganic lead halide perovskite CsPbX 3 (X = Cl ⁻ , Br ⁻ , I ⁻ ) leads to the emergence of many interesting photophysical and optoelectronic phenomena. However, probing their lattice dynamics with vibrational spectroscopy remains challenging. The influence of the fundamental octahedral building block in the perovskite lattice can be better resolved in zero-dimensional (0D) vacancy-ordered double perovskites of form A 2 BX 6 . Here we study Cs 2 TeX 6 (X = Cl ⁻ , Br ⁻ , I ⁻ ) single crystals to yield detailed insight into the fundamental octahedral building block and to explore the effect that its isolation in the crystal structure has on structural and electronic properties. The isolated [TeX 6 ] 2- octahedral units serve as the vibrational, absorbing, and emitting centers within the crystal. Serving as the vibrational centers, the isolated octahedra inform the likelihood of a random distribution of 10 octahedral symmetries within the mixed-halide spaces, as well as the presence of strong exciton-phonon coupling and anharmonic lattice dynamics. Serving as the absorbing and emitting centers, the isolated octahedra exhibit compositionally tunable absorption (1.50-3.15 eV) and emission (1.31-2.11 eV) energies. Due to greater molecular orbital overlap between neighboring octahedra with increasing halide anion size, there is a transition from a more molecule-like electronic structure in Cs 2 TeCl 6 and Cs 2 TeBr 6 -as expected from the effective 0D nature of these single crystals-to a dispersive electronic structure in Cs 2 TeI 6 , typical of three-dimensional (3D) bulk single crystals.

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

Quasi-One-Dimensional Structure and Possible Helical Antiferromagnetism of RbMn 6 Bi 5

Quasi-one-dimensional materials exhibit not only unique crystal structure but also abundant physical properties such as charge density wave, Luttinger liquid, and superconductivity. In this study, we report the discovery, structure, and physical properties of a new manganese-based quasi-one-dimensional material RbMn 6 Bi 5 , which crystallizes in a monoclinic space group C 2/ m (No. 12) with lattice parameters a = 23.286(5) Å, b = 4.6215(9) Å, c = 13.631(3) Å, and β = 125.00(3)°. The structure features [Mn 6 Bi 5 ] –1 double-walled column extending along the [010] direction, together with Bi–Bi homoatomic bonds linking the columns and the countercation Rb + . The temperature-dependent resistivity clearly indicates a significant resistivity anisotropy for RbMn 6 Bi 5 , whereas the magnetic susceptibility and specific heat measurements show that RbMn 6 Bi 5 is antiferromagnetic below 82 K. The density functional theory calculations indicate that RbMn 6 Bi 5 is a quasi-one-dimensional metal with possible helical antiferromagnetic configuration. The discovery of RbMn 6 Bi 5 confirms the viability of discovering new quasi-one-dimensional materials in manganese-based compounds.

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

Structural, Vibrational, and Electronic Properties of 1D-TlInTe 2 under High Pressure: A Combined Experimental and Theoretical Study

Analogous to 2D layered transition-metal dichalcogenides, the TlSe family of quasi-one dimensional chain materials with the Zintl-type structure exhibits novel phenomena under high pressure. In the present work, we have systematically investigated the high-pressure behavior of TlInTe 2 using Raman spectroscopy, synchrotron X-ray diffraction (XRD), and transport measurements, in combination with first principles crystal structure prediction (CSP) based on evolutionary approach. We found that TlInTe2 undergoes a pressure-induced semiconductor-to-semimetal transition at 4 GPa, followed by a superconducting transition at 5.7 GPa (with T c = 3.8 K). An unusual giant phonon mode (A g ) softening appears at ~10–12 GPa as a result of the interaction of optical phonons with the conduction electrons. The high-pressure XRD and Raman spectroscopy studies reveal that there is no structural phase transitions observed up to the maximum pressure achieved (33.5 GPa), which is in agreement with our CSP calculations. In addition, our calculations predict two high-pressure phases above 35 GPa following the phase transition sequence as I4/mcm (B37) → Pbcm → Pm$\bar{3}$m (B2). Electronic structure calculations suggest Lifshitz (L1 & L2-type) transitions near the superconducting transition pressure. Furthermore, our findings on TlInTe 2 open up a new avenue to study unexplored high-pressure novel phenomena in TlSe family induced by Lifshitz transition (electronic driven), giant phonon softening, and electron–phonon coupling.

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

Critical structural parameter determining magnetic phases in the F⁡e 2 ⁢M⁢o 3 ⁢O 8 altermagnet system

A systematic structural investigation of F⁡e 2 ⁢M⁢o 3⁢ O 8 as a function of pressure, temperature, and magnetic field reveals that the 𝑃⁢6 3 ⁢𝑚⁢𝑐 space group remains robust over a wide range of conditions. No changes in the long-range crystal structure are observed for pressures up to 10 GPa, temperatures between 11 K and 300 K, and magnetic fields up to 9 T. The magnetostructural response, quantified by Δ⁢𝑐/𝑐, is determined for magnetic fields applied transverse to the crystallographic 𝑐 axis, demonstrating strong magnetoelastic coupling. The well-known magnetic-field-induced transition is confirmed to be first order and isostructural, occurring between two distinct altermagnetic states. Importantly, this transition can also be accessed using magnetic fields applied within the 𝑎𝑏 plane. When expressed in terms of the 𝑐/𝑎 ratio, the structural evolution under pressure (0–10 GPa) maps continuously onto that observed across the full Zn substitution range in (F⁡e 1−𝑦⁢ Z⁢n 𝑦 )2 M⁢o 3 ⁢O 8 ⁢(0 ≤ 𝑦 ≤ 1), indicating a common underlying structural control parameter. Furthermore, these results demonstrate that the 𝑐-axis lattice parameter is the primary structural degree of freedom governing magnetic behavior under external tuning parameters. More broadly, they indicate that magnetic order in this family of complex oxides (𝐴 2 ⁢M⁢o 3 ⁢O 8 , 𝐴 = Co,Mn,Ni) can be systematically tuned via pressure. This tunability highlights these materials as promising platforms for controllable magnetic switching, particularly in thin films integrated with piezoelectric substrates.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Multiscale structural analysis of polymorphic phase boundaries in doped antiferroelectric sodium niobate

In the current work, we have performed multiscale structural analysis of a Pb-free sodium niobate-based smart system, i.e., 0.9⁢NaNbO 3 –0.1⁢Ba 0.9 ⁢Ca 0.1 ⁢TiO 3 (NN-10BCT) reported earlier for its high ferroelectric response. We have investigated the temperature-dependent evolution of crystal structure at long, medium, and short ranges using synchrotron x-ray diffraction (SXRD), Raman scattering, and pair distribution function(PDF) techniques in conjunction with dielectric studies. Temperature-dependent synchrotron x-ray diffraction data combined with dielectric analysis suggest two unique polymorphic phase boundaries (PPB) with two coexisting ferroelectric phases stable in the wide temperature ranges. These PPBs are stable in different regions viz. (i) cryogenic temperatures with coexisting R3c and Pmc⁢2 1 phases (ii) vicinity of room temperatures with coexisting Pmc⁢2 1 and Amm2 phases. In contrast to the conclusions drawn from SXRD, PDF reveals structures having lower symmetry (with coexisting Cc+ Pmc2 1 phases at 1.7 ≤r≤ 20 Å) at short ranges for these PPBs. In conclusion, the presence of different long- and short-range symmetries (accommodating tilt-oriented ferroelectric phases) in the unique polymorphic phase boundaries makes them thermally stable and advantageous for technological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Synthesis and Structural Characterization of 2′‐Deoxy‐2′‐Methoxy‐ L ‐Cytidine Nucleic Acids

Abstract We report here for the first time the synthesis of a novel 2′‐methoxy‐modified L‐cytidine analog and its phosphoramidite, as well as its incorporation into oligonucleotides via solid‐phase synthesis. Our measure the thermostability of the modified L‐nucleic acids by UV‐melting studies, and find out the 2′‐methoxy‐derivatization enhances the thermostability of the L‐duplexes. Consistent with the thermostability result, our X‐ray crystal structure study reveals that the 2′‐methoxy‐L‐deoxycytidine forms the Watson‐Crick base pair with L‐guanosine virtually as the mirror‐image fashion of native pair. This novel chemically modified L‐cytidine provides a useful biochemical and structural strategy to create mirror‐image nucleic acid molecules with expanded functionalities.

2′-Methoxy↗
DOE OSTI2021

Spin and Orbital Effects on Asymmetric Exchange Interaction in Polar Magnets: M(IO 3 ) 2 (M = Cu and Mn)

We report magnetic polar materials feature an astonishing range of physical properties, such as magnetoelectric coupling, chiral spin textures, and related new spin topology physics. This is primarily attributable to their lack of space inversion symmetry in conjunction with unpaired electrons, potentially facilitating an asymmetric Dzyaloshinskii–Moriya (DM) exchange interaction supported by spin–orbital and electron–lattice coupling. However, engineering the appropriate ensemble of coupled degrees of freedom necessary for enhanced DM exchange has remained elusive for polar magnets. Here, we study how spin and orbital components influence the capability of promoting the magnetic interaction by studying two magnetic polar materials, α-Cu(IO 3 ) 2 ( 2 D) and Mn(IO 3 ) 2 ( 6 S), and connecting their electronic and magnetic properties with their structures. The chemically controlled low-temperature synthesis of these complexes resulted in pure polycrystalline samples, providing a viable pathway to prepare bulk forms of transition-metal iodates. Rietveld refinements of the powder synchrotron X-ray diffraction data reveal that these materials exhibit different crystal structures but crystallize in the same polar and chiral P2 1 space group, giving rise to an electric polarization along the b-axis direction. The presence and absence of an evident phase transition to a possible topologically distinct state observed in α-Cu(IO 3 ) 2 and Mn(IO 3 ) 2 , respectively, imply the important role of spin–orbit coupling. Neutron diffraction experiments reveal helpful insights into the magnetic ground state of these materials. While the long-wavelength incommensurability of α-Cu(IO 3 ) 2 is in harmony with sizable asymmetric DM interaction and low dimensionality of the electronic structure, the commensurate stripe AFM ground state of Mn(IO 3 ) 2 is attributed to negligible DM exchange and isotropic orbital overlapping. The work demonstrates connections between combined spin and orbital effects, magnetic coupling dimensionality, and DM exchange, providing a worthwhile approach for tuning asymmetric interaction, which promotes evolution of topologically distinct spin phases.

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

The Zintl phases A In 2 As 2 (A = Ca, Sr, Ba): new topological insulators and thermoelectric material candidates

Recently, there has been a lot of interest in topological insulators (TIs), being electronic materials, which are insulating in their bulk but with the gapless exotic metallic state on their surface. The surface states observed in such materials behave as a perfect conductor thereby making them more suited for several cutting-edge technological applications such as spintronic devices. Here, we report the synthesis and structural characterization of the Zintl phases AIn 2 As 2 (A = Ca, Sr, Ba), which could become a new class of TIs. Crystal structure elucidation by single-crystal X-ray diffraction reveals that CaIn 2 As 2 and SrIn 2 As 2 are isostructural and crystallize in the EuIn 2 P 2 structure type (space group P6 3 /mmc, no. 194, Z = 2) with unit cell parameters a = 4.1482(6) Å, c = 17.726(4) Å; and a = 4.2222(6) Å, c = 18.110(3) Å, respectively. Their hexagonal structure is made up of alternating [In 2 As 2 ] 2– layers separated by slabs of A 2+ cations. BaIn 2 As 2 on the other hand crystallizes in the monoclinic EuGa 2 P 2 structure type (space group P2/m, no. 10, Z = 4) with unit cell parameters a = 10.2746(11) Å, b = 4.3005(5) Å, c = 13.3317(14) Å and β = 95.569(2)°. This structure is also layered, and it is made up of different type of polyanionic [In 2 As 2 ] 2– units and Ba 2+ cations. The valence electron count for all three compounds adheres to the Zintl-Klemm formalism, and all elements achieve closed-shell electronic configurations. Bulk electronic structure calculations indicate the opening of a bandgap E g ~ 0.03 eV (CaIn 2 As 2 and Sr 2 In 2 As 2 ), and E g ~0.21 eV (BaIn 2 As 2 ) in the absence of strain and spin–orbit coupling (SOC). Furthermore, these results argue in favor of the realization of a nontrivial topological insulator state under the influence of tensile strain and SOC. Preliminary transport properties on BaIn 2 As 2 are suggestive of a degenerate p-type semiconductor—a behavior which is sought after in thermoelectric (TE) materials. Since both TIs and excellent TE materials are known to favor the same material properties such as narrow bandgap, heavy elements, and strong SOC, these three Zintl phases are also projected as candidates TE materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

In Situ X-ray Diffraction of High Density Polyethylene During Dynamic Compression: Polymer Chain Compression and Phase Transformations

Polymers are widely implemented materials often used for safety and security in our daily lives. However, we do not have a thorough understanding of the phase transformations of these materials when exposed to extreme condition, high strain rate, events. To study polymers in these severe environments, we performed plate impact experiments that impart a one-dimensional shock wave, at high pressures and temperatures, to observe the materials response. Generally, velocimetry is the experimental diagnostic used to capture the movement of high velocity interfaces to then calculate the mechanical variables associated with shock compression. However, when a material undergoes a phase transition, such as between two crystalline phases or melting to decomposition during shock compression, velocimetry does not explicitly indicate what structural change occurred. At the Dynamic Compression Sector at the Advanced Photon Source gas gun driven compression has been paired with x-ray diffraction, providing the ability to study both the shock parameters and structural changes concurrently. We explored high density polyethylene (HDPE) both on its reactants Hugoniot (<10.12 GPa) and within its transition region (24.3 GPa) where HDPE is hypothesized to decompose from reactants to products. With x-ray diffraction we observed both polymer chain compression and crystal structure reorientation from orthorhombic to monoclinic above 6 GPa, as well as either a possible phase change or chemical decomposition at 24.3 GPa. With these experiments we were able to determine the crystalline and amorphous Hugoniot loci at pressures below the polymer transition region.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis

Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α) 8 -barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with k cat = 6.0 ± 0.6 s –1 and K m = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Derivatization of Mirror-Image L -Nucleic Acids with 2'-OMe Modification for Thermal and Structural Stabilization

To further expand the functionality and enhance the stability of mirror-image nucleic acids as advanced agents for basic research and therapeutic design, we have synthesized 2'-deoxy-2'-methoxy- L -uridine phosphoramidite and incorporated it into L -DNA and L -RNA by solid-phase synthesis quantitatively. We found that the thermostability of L -nucleic acids is dramatically improved after introducing the modifications. Moreover, we successfully crystallized both L -DNA and L -RNA duplexes containing the 2'-OMe modifications and sharing identical sequences. Crystal structure determination and analysis revealed the overall structures of the mirror-image nucleic acids, and for the first time it was possible to interpret the structural deviations caused by 2'-OMe and 2'-OH groups in the oligonucleotides, which are very similar. In conclusion, this novel chemical nucleic acid modification has the potential to be used to design nucleic acid-based therapeutics and materials in the future.

2'-OMe-modifications↗
DOE OSTI2025

An alternative pocket for binding the N‐degrons by the UBR1 and UBR2 ubiquitin E3 ligases

The UBR family of ubiquitin ligases binds to N-termini of their targets (known as N-degron) to induce their ubiquitination and degradation via a conserved domain known as UBR-box. UBR1 and UBR2 share the highest sequence homology among the family, and substantial structural studies were previously performed for substrate binding by the UBR-boxes of UBR1 and UBR2. Here, we describe a new pocket in the UBR-boxes of UBR1 and UBR2 for binding the second residues of N-degrons through determining five co-crystal structures of the UBR-boxes with various N-degron peptides. Together with binding affinities measured by fluorescence polarization, we show that the two highly homologous UBR-boxes can interact with the second residue of an N-degron differently. In addition, the UBR-boxes undergo different conformational changes when binding N-degrons. Furthermore, we demonstrate that the sidechain of the third amino acid of an N-degron has no contribution to binding the UBR-boxes. These findings represent a new conceptual advancement for the UBR E3 ligases and the new insights described here can be leveraged for developing their selective ligands for research and potential therapies.

N-end rule↗
DOE OSTI2025

Interstitial Atoms and the Frustrated and Allowed Structural Transitions Principle: Tunability in the Electronic Structure of AuCu 3 ‐type Frameworks in Dy 4 T 1− x Ga 12 (T = Ag, Ir)

In this Article, we explore how the chemical pressure (CP) features of an intermetallic phase may provide opportunities to couple perturbations in electron count with the stabilization of the underlying geometrical structure. AuCu 3 ‐type LnGa 3 (Ln = lanthanide or group 3 metal) phases contain octahedral cavities of negative CP held open by overly compressed Ln–Ga interactions, leading to a series of transition metal‐stuffed derivatives. We present new additions to this family with the synthesis and crystal structures of Dy 4 T 1−x Ga 12 with (T, x) = (Ag, 0.29) and (Ir, 0.15), adopting Y 4 PdGa 12 ‐type superstructures of the AuCu 3 ‐type. density functional Ttheory (DFT)‐CP calculations, when adjusted to avoid dipolar CP features, affirm that T atom incorporation provides a mechanism for the relief of packing tensions, while electronic density of states distributions illustrate that the T atoms serve largely as electron or hole donors to the band structure, as needed for them to attain d 10 configurations. The maximum obtainable value for x may be limited by a mismatch between the Fermi energy and pseudogap, in line with the balance of factors envisioned by the frustrated and allowed structural transitions principle. Furthermore, trends in resistivity measurements on T = Ir, Pd, and Ag compounds are interpretable in terms of the varying degrees of disorder arising from x < 1.0.

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

Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1

In humans, a single enzyme 2-aminoadipic semialdehyde synthase (AASS) catalyses the initial two critical reactions in the lysine degradation pathway. This enzyme evolved to be a bifunctional enzyme with both lysine-2-oxoglutarate reductase (LOR) and saccharopine dehydrogenase domains (SDH). Moreover, AASS is a unique drug target for inborn errors of metabolism such as glutaric aciduria type 1 that arise from deficiencies downstream in the lysine degradation pathway. While work has been done to elucidate the SDH domain structurally and to develop inhibitors, neither has been done for the LOR domain. Here, we purify and characterize LOR and show that it is activated by alkylation of cysteine 414 by N-ethylmaleimide. We also provide evidence that AASS is rate-limiting upon high lysine exposure of mice. Finally, we present the crystal structure of the human LOR domain. Our combined work should enable future efforts to identify inhibitors of this novel drug target.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Anisotropic Ferromagnetism in CrAu 3 Sb 6

The crystal structure and properties of CrAu 3 Sb 6 are presented, determined by measurements on single crystal and polycrystalline samples and first-principles calculations. The trigonal structure (space group P$\overline{3}$1m) comprises a CdI 2 -like sublattice of AuSb 2 with Cr occupying octahedral holes in a fully ordered triangular array. It can be viewed as a variation of the interesting and well-known families of partially intercalated transition metal dichalcogenides, but with stronger interactions along the stacking direction evidenced by short Cr–Au distances. The compound is metallic and ferromagnetic with a Curie temperature of 164 K. A strong anomalous contribution to the Hall effect is seen in the ferromagnetic state, and quantum oscillations are observed in magnetization at 2 K. Magnetization measurements show that the ordered moments of 1.5 μ B per Cr are oriented along the c-axis with relatively strong magnetocrystalline anisotropy. Electronic structure calculations confirm this uniaxial anisotropy and the important role of spin–orbit coupling in CrAu 3 Sb 6 and reveal strongly favored ferromagnetic ground state consistent with the measured Curie temperature. Through combined experiment and theory, this work provides a detailed picture of the basic properties and behaviors of this uniquely structured, Cr-based, anisotropic ferromagnet.

Crystal structure↗
DOE OSTI2023

Structure of Rhizobium sp. 4-9 histamine dehydrogenase and analysis of the electron transfer pathway to an abiological electron acceptor

Histamine dehydrogenase from the gram-negative bacterium Rhizobium sp. 4-9 (HaDHR) is a member of a small family of dehydrogenases containing a covalently attached FMN, and the only member so far identified to date that does not exhibit substrate inhibition. Here, in this study, we present the 2.1 Å resolution crystal structure of HaDHR. This new structure allowed for the identification of the internal electron transfer pathway to abiological ferrocene-based mediators. Alanine 437 was identified as the exit point of electrons from the Fe 4 S 4 cluster. The enzyme was modified with a Ser436Cys mutation to facilitate covalent attachment of a ferrocene moiety. When modified with Fc-maleimide, this new construct demonstrated direct electron transfer from the enzyme to a gold electrode in a histamine concentration-dependent manner without the need for any additional electron mediators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN

High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3'-to-5' exoribonuclease (ExoN) in nonstructural protein 14 (nsp14), which excises nucleotides including antiviral drugs misincorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here, we determined a 1.6-Å resolution crystal structure of severe acute respiratory syndrome CoV 2 (SARS-CoV-2) ExoN in complex with its essential cofactor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3' end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. We also show that the ExoN activity can rescue a stalled RNA primer poisoned with sofosbuvir and allow RdRp to continue its extension in the presence of the chain-terminating drug, biochemically recapitulating proofreading in SARS-CoV-2 replication. Molecular dynamics simulations further show remarkable flexibility of multidomain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA binding to support its exonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN–nsp10 complex serves as a platform for future development of anticoronaviral drugs or strategies to attenuate the viral virulence.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structure, dynamics, and redox reactivity of an all-purpose flavodoxin

The flavodoxin of Rhodopseudomonas palustris CGA009 (Rp9Fld) supplies highly reducing equivalents to crucial en- zymes such as hydrogenase, especially when the organism is iron-restricted. By acquiring those electrons from photodriven electron flow via the bifurcating electron transfer flavoprotein, Rp9Fld provides solar power to vital metabolic processes. To understand Rp9Fld’s ability to work with diverse partners, we solved its crystal structure. We observed the canonical fla- vodoxin (Fld) fold and features common to other long-chain Flds but not all the surface loops thought to recognize part- ner proteins. Moreover, some of the loops display alternative structures and dynamics. To advance studies of protein– protein associations and conformational consequences, we assigned the 19F NMR signals of all five tyrosines (Tyrs). Our electrochemical measurements show that incorporation of 3- 19 F-Tyr in place of Tyr has only a modest effect on Rp9Fld’s redox properties even though Tyrs flank the flavin on both sides. Meanwhile, the 19 F probes demonstrate the expected paramagnetic effect, with signals from nearby Tyrs becoming broadened beyond detection when the flavin semiquinone is formed. However, the temperature dependencies of chemical shifts and linewidths reveal dynamics affecting loops close to the flavin and regions that bind to partners in a variety of systems. These coincide with patterns of amino acid type conservation but not retention of specific residues, arguing against detailed specificity with respect to partners. We pro- pose that the loops surrounding the flavin adopt altered con- formations upon binding to partners and may even participate actively in electron transfer.

19F NMR↗