SPring-8

In all kingdoms of life, the regulation of membrane-bound enzyme function via oligomerization is a fundamental aspect of cell physiology. Often, the mechanistic role of oligomerization is unclear, due to a lack of structure-function comparisons between constituent forms of the enzyme. Here, we elucidate the structural underpinnings of enzyme regulation and oligomerization in the quinol-dependent nitric oxide reductase (qNOR) from Neisseria meningitidis, by high-resolution structural analyses of the less active monomeric form (2.25 Å) and the highly active dimeric form (1.89 Å). The comparison revealed that broad helical flexibility near the dimer interface of the monomer causes a conformational change in a critical amino acid near the active site, located apart from the dimer interface. We demonstrate that the crosstalk between the dimer interface and catalytic site in qNOR allows enhanced activation of the enzyme via dimerization. Given Neisseria meningitidis' dependence on qNOR to detoxify the host's immune response of nitric oxide, our results pave a way for new strategies to combat bacterial infections, via the inactivation of qNOR by monomerization. More broadly, this provides new insights into the role of membrane protein oligomerization and its influence on regulating activity.

Coulomb explosion imaging (CEI) provides a direct means of imaging molecular geometry by correlating fragment ion momenta following the fragmentation of a molecular polycation. Here, we demonstrate the use of three-body covariance and four-body cumulant analysis to extract three-dimensional (3D) structural information from the X-ray-induced Coulomb explosion of tert-butyl iodide (C4H9I). Site-selective ionization at the iodine 4d edge with intense femtosecond soft X-ray pulses from an X-ray free-electron laser (XFEL) enables rapid charge buildup and molecular breakup. By correlating ionic fragments in the molecular frame, we isolate complete dissociation channels and reveal subtle structural changes, such as umbrella-type motion of the branched alkyl chain, during the ionization process. Comparison with point-charge simulations of the Coulomb explosion shows close agreement, validating the approach. These results establish covariance/cumulant mapping as a powerful strategy for imaging complex three-dimensional molecular structures and point the way toward time-resolved CEI using both XFEL and tabletop sources for capturing ultrafast structural dynamics.

Metalloproteins represent a major fraction of the protein kingdom and often exploit the redox chemistry of transition metals to drive key biological events involving proton and electron transfer. Copper is one of the most widely used transition metals whose redox properties are utilised in both electron transfer and catalysis of chemical substrates. Copper nitrite reductases (CuNiRs) utilise two types of copper centres and have become a model system for studying complex biological events that underpin the reaction mechanisms of redox enzymes, including proton-coupled electron transfer and substrate gating. We utilised the higher X-ray energy (13 keV) available at the SACLA X-ray Free Electron Laser (XFEL) and SHELXL refinement to obtain accurate atomic resolution structures of CuNiRs at ~1 Å from three organisms - in the oxidised (low and high pH), reduced and substrate-bound states. A consistent picture now emerges with the observation of a pentacoordinated oxidised catalytic type-2 Cu (T2Cu2+) centre in all cases. A tetracoordinated reduced T2Cu+ site with a single solvent ligand has also been captured, giving structural support to the random-sequential schemewith ordered pathway being dominant.

The S=2 Heisenberg antiferromagnet on the orthogonal dimer lattice is studied. The edges of the exact dimer and Neel-ordered phases in the ground state of the system are examined by the numerical diagonalization method. Our present results are discussed by combining them with previously obtained estimates for smaller-S cases. We find that an intermediate region between the exact dimer and Neel-ordered phases gradually widens as spin S is increased up to S=2.

Recently, the generation of ultrashort x-ray free-electron laser (XFEL) pulses of less than 1 fs has been reported using additional electron bunch compression in front of undulators. In this bunch compression, a self-modulated energy chirp provided by space charge force is used. In the present paper, we discuss an optimal bunch compression scheme using a two-Double Bend Achromat (DBA) dogleg and an electron bunch having the energy chirp which is reversed with respect to that used for a conventional magnetic chicane bunch compressor. After giving analytical expressions of <a:math xmlns:a="http://www.w3.org/1998/Math/MathML" display="inline"> <a:mrow> <a:msub> <a:mi>R</a:mi> <a:mn>56</a:mn> </a:msub> </a:mrow> </a:math> and <c:math xmlns:c="http://www.w3.org/1998/Math/MathML" display="inline"> <c:mrow> <c:msub> <c:mi>T</c:mi> <c:mn>566</c:mn> </c:msub> </c:mrow> </c:math> of an ordinary DBA section, a method for evaluating <e:math xmlns:e="http://www.w3.org/1998/Math/MathML" display="inline"> <e:mrow> <e:msub> <e:mi>R</e:mi> <e:mn>56</e:mn> </e:msub> </e:mrow> </e:math> and <g:math xmlns:g="http://www.w3.org/1998/Math/MathML" display="inline"> <g:mrow> <g:msub> <g:mi>T</g:mi> <g:mn>566</g:mn> </g:msub> </g:mrow> </g:math> is presented for varied bending angle cases to achieve additional bunch compression. When changing the bending angles for controlling <i:math xmlns:i="http://www.w3.org/1998/Math/MathML" display="inline"> <i:mrow> <i:msub> <i:mi>R</i:mi> <i:mn>56</i:mn> </i:msub> </i:mrow> </i:math> and <k:math xmlns:k="http://www.w3.org/1998/Math/MathML" display="inline"> <k:mrow> <k:msub> <k:mi>T</k:mi> <k:mn>566</k:mn> </k:msub> </k:mrow> </k:math> , the electron beam no longer passes the magnetic center of focusing quadrupole magnets of the DBA section, but the electron beam trajectory and transverse envelope remain the same downstream of the two-DBA dogleg, including the undulators. The analytical framework proposed in this paper would be useful to design and finely tune the bunch compression in front of the undulators to generate ultrashort XFEL pulses.

CRISPR-Cas3 represents a mechanistically distinct genome-editing system compared to Cas9 that generates long-range deletions rather than small indels, thereby reducing the risk of residual protein function from in-frame mutations. Here we evaluated CRISPR-Cas3 to correct mutations in the TTR gene causing transthyretin amyloidosis, a systemic proteinopathy where loss of mutant TTR in the liver offers therapeutic benefit. Through CRISPR RNA optimization we achieved 58.9% ± 0.5% editing at the TTR locus in vitro, inducing large deletions that abolished TTR expression. Cas3 generated mostly directional deletions up to 75 kb without reproducible off-target mutations, in contrast to Cas9, which induced indels at several off-target sites. In vivo, a single lipid-nanoparticle-based treatment achieved 48.7% ± 1.1% hepatic editing and reduced serum TTR levels by 80.1% ± 4.6%. Deletion size was limited to 21 kb. In TTR exon-humanized mice, Cas3 editing reduced serum TTR without in-frame mutations and attenuated macrophage-associated TTR deposition. These findings highlight Cas3 as an efficient and distinct sytem for in vivo genome editing.

A liquid-nitrogen-cooled silicon channel-cut monochromator was developed and experimentally evaluated under high-thermal-load conditions. Under the maximum load of 417 W, the first reflecting surface exhibited a concave deformation, resulting in only an 11% reduction in vertical beam size at 16 m downstream. The deformation radius was estimated at 510 m. Despite the deformation, no significant changes were observed in the angular profile or intensity of the monochromatic beam. Interference fringes caused by edge diffraction at an upstream slit confirmed excellent preservation of spatial coherence. For the stability test of the monochromator, intensity fluctuation of the monochromatic beam was monitored and linearly fitted with upstream beam-position monitor signals, which were synchronously acquired. A high correlation (R2 = 0.95) confirmed that the inherent stability of the channel-cut design remained under cryogenic cooling. Additionally, a double channel-cut monochromator configuration for fixed-exit beam operation was tested and produced the expected output beam intensity. These results confirm the feasibility of using channel-cut monochromators as high-stability high-heat-load-tolerant optical elements for next-generation synchrotron beamlines.

Chemical doping in transition metal oxides drives a complex interplay among lattice, charge, and spin degrees of freedom. Herein, we investigate the structural and magnetic evolution of Nd2-xSrxNiO4+δ (0 ≤ x ≤ 0.7), a layered nickelate system with mixed-valence Ni2+/Ni3+ ions and tunable oxygen nonstoichiometry (δ), using high-resolution synchrotron X-ray and neutron diffraction, complemented by macroscopic measurements over a broad temperature range. High-temperature solid-state synthesis in air promotes oxygen interstitial incorporation, yielding hyper-stoichiometric compounds (δ > 0). For Nd2NiO4.23 (x = 0), excess oxygen atoms exhibit long-range ordering, giving rise to incommensurate structural modulations and a sequence of order-order transitions persisting up to 800 K. Sr substitution disrupts this ordering via Coulombic effects and suppresses both oxygen uptake and NiO6 octahedral tilting. Stripe-like spin ordering emerges at x = 0.25, 0.33, and 0.5. The x = 0.5 sample exhibits magnetic incommensurability (ε ≈ 0.44) below 95 K, indicative of charge discommensuration in NiO2 planes. Unlike the oxygen-doped (x = 0) phase, Sr-doped samples show quasi-two-dimensional magnetism, with in-plane and out-of-plane magnetic correlation lengths of 114(2) Å and 16(3) Å, respectively. These results reveal strong coupling among chemical doping, crystal structure, oxygen ordering, and magnetism in layered nickelates.

Precisely tailoring the electronic structure of the single-atom center is significant to improve the intrinsic reactivity of single-atom catalysts and elucidate the underlying reaction mechanism, but this remains highly challenging. Herein, we construct covalently oxygen-bridged single-Fe-atom sites on carbon nanotubes, dominated by low-spin (LS) Fe(III) sites, as an efficient catalyst for boosting the intrinsic catalytic performance for the electrochemical CO2 reduction reaction (CO2RR). A maximal CO Faradaic efficiency of 99% with an extremely high turnover frequency of 5.3 × 104 h-1 at an applied cathodic potential of -0.7 V vs RHE is achieved, showing a more than 20-fold increase as compared to that of high-spin (HS) Fe(III) sites. Taking advantage of operando and rapid freeze-quenched 57Fe Mössbauer spectroscopy, together with operando X-ray absorption spectroscopy, a spin-driven CO2 electroreduction mechanism is identified, wherein the in-situ-generated HS Fe(II) and LS Fe(II) sites dominate the CO2RR at the low and high overpotentials, respectively. Furthermore, results from operando Raman and attenuated total reflectance surface-enhanced infrared absorption spectroscopy reveal that the one-electron reduction of phthalocyanine (Pc) coordinated to the central Fe leads to a weaker bonding strength of *CO on the LS O-Fe(II)Pc- sites. Density functional theory calculations further illustrate the increased Bader charge and d-band center of the in-situ-generated LS O-Fe(II)Pc-, facilitating the delocalization of electrons from the Fe 3d orbital to the 2pz orbital of CO2, thus reducing the formation free energy of the *COOH intermediate and boosting the CO2RR performance.