Structural basis for recognition of 5;#8242;-phosphotyrosine adducts by Tdp2
Abstract not provided
Shi, Ke↗
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The DDB1–DCAF1–Vpr–UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction
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Wu, Ying↗
Structural characterization of the ICOS/ICOS-L immune complex reveals high molecular mimicry by therapeutic antibodies
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99 GENERAL AND MISCELLANEOUS↗
High-temperature superconductivity on the verge of a structural instability in lanthanum superhydride
Abstract The possibility of high, room-temperature superconductivity was predicted for metallic hydrogen in the 1960s. However, metallization and superconductivity of hydrogen are yet to be unambiguously demonstrated and may require pressures as high as 5 million atmospheres. Rare earth based “superhydrides”, such as LaH 10 , can be considered as a close approximation of metallic hydrogen even though they form at moderately lower pressures. In superhydrides the predominance of H-H metallic bonds and high superconducting transition temperatures bear the hallmarks of metallic hydrogen. Still, experimental studies revealing the key factors controlling their superconductivity are scarce. Here, we report the pressure and magnetic field dependence of the superconducting order observed in LaH 10 . We determine that the high-symmetry high-temperature superconducting Fm-3m phase of LaH 10 can be stabilized at substantially lower pressures than previously thought. We find a remarkable correlation between superconductivity and a structural instability indicating that lattice vibrations, responsible for the monoclinic structural distortions in LaH 10 , strongly affect the superconducting coupling.
36 MATERIALS SCIENCE↗
Decoding reactive structures in dilute alloy catalysts
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99 GENERAL AND MISCELLANEOUS↗
Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids
Abstract Poleroviruses, enamoviruses, and luteoviruses are icosahedral, positive sense RNA viruses that cause economically important diseases in food and fiber crops. They are transmitted by phloem-feeding aphids in a circulative manner that involves the movement across and within insect tissues. The N-terminal portion of the viral readthrough domain ( N RTD) has been implicated as a key determinant of aphid transmission in each of these genera. Here, we report crystal structures of the N RTDs from the poleroviruses turnip yellow virus (TuYV) and potato leafroll virus (PLRV) at 1.53-Å and 2.22-Å resolution, respectively. These adopt a two-domain arrangement with a unique interdigitated topology and form highly conserved dimers that are stabilized by a C-terminal peptide that is critical for proper folding. We demonstrate that the PLRV N RTD can act as an inhibitor of virus transmission and identify N RTD mutant variants that are lethal to aphids. Sequence conservation argues that enamovirus and luteovirus N RTDs will follow the same structural blueprint, which affords a biological approach to block the spread of these agricultural pathogens in a generalizable manner.
Schiltz, Carl J. (ORCID:0000000332030784)↗
Design of protein-binding proteins from the target structure alone
The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder–target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein–protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
59 BASIC BIOLOGICAL SCIENCES↗
Cryo-EM structure of the human neutral amino acid transporter ASCT2
Human ASCT2 belongs to the SLC1 family of secondary transporters and is specific for the transport of small neutral amino acids. ASCT2 is upregulated in cancer cells and serves as the receptor for many retroviruses; hence, it has importance as a potential drug target. Here we used single-particle cryo-EM to determine a structure of the functional and unmodified human ASCT2 at 3.85-Å resolution. ASCT2 forms a homotrimeric complex in which each subunit contains a transport and a scaffold domain. Prominent extracellular extensions on the scaffold domain form the predicted docking site for retroviruses. Relative to structures of other SLC1 members, ASCT2 is in the most extreme inward-oriented state, with the transport domain largely detached from the central scaffold domain on the cytoplasmic side. In conclusion, this domain detachment may be required for substrate binding and release on the intracellular side of the membrane.
59 BASIC BIOLOGICAL SCIENCES↗
Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions
Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here in this paper, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box–tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate ‘discriminator’ structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.
59 BASIC BIOLOGICAL SCIENCES↗
Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA
NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identifed as a 3'→5' exonuclease, but we show here that NrnA is bidirectional, degrading 2–5 nucleotide long RNA oligomers from the 3' end, and longer RNA substrates from the 5' end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5'→3' DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3'→5' activity.
59 BASIC BIOLOGICAL SCIENCES↗
Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT
Abstract Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H 2 O 2 and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H 2 O 2 -treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H 2 O 2 . The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H 2 O 2 -consumption assays. Furthermore, an entrance channel for H 2 O 2 was identified and key residues implicated in H 2 O 2 activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation.
54 ENVIRONMENTAL SCIENCES↗
Structural Effects of Lanthanide Dopants on Alumina
Lanthanide (Ln 3+ ) doping in alumina has shown great promise for stabilizing and promoting desirable phase formation to achieve optimized physical and chemical properties. However, doping alumina with Ln elements is generally accompanied by formation of new phases (i.e. LnAlO3, Ln2O3), and therefore inclusion of Ln-doping mechanisms for phase stabilization of the alumina lattice is indispensable. In this study, Ln-doping (400 ppm) of the alumina lattice crucially delays the onset of phase transformation and enables phase population control, which is achieved without the formation of new phases. The delay in phase transition (θ → α), and alteration of powder morphology, particle dimensions, and composition ratios between α- and θ-alumina phases are studied using a combination of solid state nuclear magnetic resonance, electron microscopy, digital scanning calorimetry, and high resolution X-ray diffraction with refinement fitting. Loading alumina with a sparse concentration of Ln-dopants suggests that the dopants reside in the vacant octahedral locations within the alumina lattice, where complete conversion into the thermodynamically stable α-domain is shown in dysprosium (Dy)- and lutetium (Lu)-doped alumina. This study opens up the potential to control the structure and phase composition of Ln-doped alumina for emerging applications.
36 MATERIALS SCIENCE↗
Dynamic recovery in silicate-apatite structures under irradiation and implications for long-term immobilization of actinides
The irradiation responses of Ca2La8(SiO4)6O2 and Sr2Nd8(SiO4)6O2 with the apatite structure are investigated to predict their long-term behaviour as host phases for immobilization of actinide elements from the nuclear fuel cycle. Different ions and energies are used to study the effects of dose, temperature, atomic displacement rate and ionization rate on irradiation-induced amorphization and recrystallization. The dose for amorphization increases with temperature in two stages, below and above 150 K. In the high temperature stage relevant to actinide immobilization, the increase of amorphization dose with temperature exhibits a strong dependence on the ratio of ionization rate to displacement rate for the different ions. Data analysis using a dynamic model for amorphization reveals that ionization-induced processes, with activation energy of 0.15 0.02 eV, dominate dynamic recovery for ions from Ne through Xe. For heavier Au ions or for alpha-recoil nuclei emitted in alpha decay of actinides, ionization becomes less dominant and dynamic recovery is controlled primarily by thermally-driven processes. In post-irradiation annealing studies of amorphous samples, epitaxial thermal recrystallization is observed at 1123 K, and irradiation-enhanced nucleation of nanocrystallites is observed under irradiation with heavier ions. The recrystallization temperature under irradiation decreases with increasing ion mass to a value of ~ 823 K, which also defines the thermally-driven critical temperature for amorphization under irradiation with heavy ions. Some partial recovery due to alpha particle irradiation at 300 K is observed that suggests a self-healing mechanism in apatite phases containing actinides. Based on the results and dynamic model, the temperature and time dependences of amorphization in silicate-apatite host phases for actinide immobilization are predicted.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Silicon-on-glass pore network micromodels with oxygen-sensing fluorophore films for chemical imaging and defined spatial structure
Pore network microfluidic models were fabricated by a silicon-on-glass technique that provides the precision advantage of dry etched silicon while creating a structure that is transparent across all microfluidic channels and pores, and can be imaged from either side. A silicon layer is bonded to an underlying borosilicate glass substrate and thinned to the desired height of the microfluidic channels and pores. The silicon is then patterned and through-etched by deep reactive ion etching (DRIE), with the underlying glass serving as an etch stop. After bonding on a transparent glass cover plate, one obtains a micromodel in oxygen impermeable materials with water wet surfaces where the microfluidic channels are transparent and structural elements such as the pillars creating the pore network are opaque. The micromodel can be imaged from either side. The advantageous features of this approach in a chemical imaging application are demonstrated by incorporating a Pt porphyrin fluorophore in a PDMS film serving as the oxygen sensing layer and a bonding surface, or in a polystyrene film coated with a PDMS layer for bonding. The sensing of a dissolved oxygen gradient was demonstrated using fluorescence lifetime imaging, and it is shown that different matrix polymers lead to optimal use in different ranges dissolved oxygen concentration. Imaging with the opaque pillars in between the observation direction and the continuous fluorophore film yields images that retain spatial information in the sensor image.
chemical imaging↗
Molecular Structures of Polymer/Sulfur Composites for Lithium-Sulfur Batteries with Long Cycle Life
Vulcanizedpolyaniline/sulfur (SPANI/S) nanostructures were investigated for Li-S battery applications, but the detailed molecular structures of such composites have not been fully illustrated. In this paper, we synthesize SPANI/S composites with different S content in a nanorod configuration. FTIR, Raman, XPS, XRD, SEM and elemental analysis methods are used to characterize the molecular structure of the materials. We provide clear evidence that a portion of S was grafted on PANI during heating and connected the PANI chains with disulfide bonds to form a crosslinked network and the rest of S was encapsulated within it.. Polysulfides and elementary sulfur nanoparticles are physically trapped inside the polymer network and are not chemically bound to the polymer. The performance of the composites is further improved by reducing the particle size. Even after 500 cycles a capacity retention rate of 68.8% is observed in the SPANI/S composite with 55% S content.
Environmental Molecular Sciences Laboratory↗
Structural phase transformation and Fe valence evolution in FeOxF2-x/C nanocomposite electrodes during lithiation and de-lithiation processes
In this study, the structural changes of FeOxF2-x/C during the first discharge and recharge cycles were studied by ex situ electron microscopy techniques including annular dark field scanning transmission electron microscopy (DF-STEM) imaging, selected area electron diffraction (SAED) and electron energy loss spectroscopy (EELS) as well as by in situ X-ray absorption spectroscopy (XAS). The evolution of the valence state of Fe was determined by combined EELS using the Fe-L edge and XAS using the Fe-K edge. The results of this investigation show that the conversion reaction path during 1st lithiation is very different from the re-conversion path during 1st delithiation. During lithiation, intercalation is first observed followed by conversion into a lithiated rocksalt (Li–Fe–O–F) structure, and metallic Fe and LiF phases. During delithiation, the rocksalt phase does not disappear, but co-exists with an amorphous (rutile type) phase formed initially by the reaction of LiF and Fe. However, a de-intercalation stage is still observed at the end of reconversion similar to a single phase process despite the coexistence of these two (rocksalt and amorphous) phases.
36 MATERIALS SCIENCE↗