Green/red light-sensing mechanism in the chromatic acclimation photosensor.

Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is regulated by a cyanobacteriochrome-class photosensor that reversibly photoconverts between green-absorbing (Pg) and red-absorbing (Pr) states. Here, we elucidated the structural basis of the green/red photocycle. In the Pg state, the bilin chromophore adopted the extended C15-Z,anti structure within a hydrophobic pocket. Upon photoconversion to the Pr state, the bilin is isomerized to the cyclic C15-E,syn structure, forming a water channel in the pocket. The solvation/desolvation of the bilin causes changes in the protonation state and the stability of π-conjugation at the B ring, leading to a large absorption shift. These results advance our understanding of the enormous spectral diversity of the phytochrome superfamily.

A Steric-Repulsion-Driven Clutch Stack of Triaryltriazines: Correlated Molecular Rotations and a Thermoresponsive Gearshift in the Crystalline Solid.

We report that a newly developed type of triaryltriazine rotor, which bears bulky silyl moieties on the para position of its peripheral phenylene groups, forms a columnar stacked clutch structure in the crystalline phase. The phenylene units of the crystalline rotors display two different and interconvertible correlated molecular motions. It is possible to switch between these intermolecular geared rotational motions via a thermally induced crystal-to-crystal phase transition. Variable-temperature solid-state 2H NMR measurements and X-ray diffraction studies revealed that the crystalline rotor is characterized by a vertically stacked columnar structure upon introducing a bulky Si moiety with bent geometry as the stator. The structure exhibits correlated flapping motions via a combination of 85° and ca. 95° rotations between 295 and 348 K, concurrent with a negative entropy change (ΔS‡ = -23 ± 0.3 cal mol-1 K-1). Interestingly, heating the crystal beyond 348 K induces an anisotropic expansion of the column and lowers the steric congestion between the adjacent rotators, thus altering the correlated motions from a flapping motion to a correlated 2-fold 180° rotation with a lower entropic penalty (ΔS‡ = -14 ± 0.5 cal mol-1 K-1). The obtained results of our study suggest that the intermolecular stacking of the C3-symmetric rotator driven by the steric repulsion of the bulky stator represents a promising strategy for producing various correlated molecular motions in the crystalline phase. Moreover, direct and reversible modulation of the intermolecularly correlated rotation is achieved via a thermally induced crystal-to-crystal phase transition, which operates as a gearshift function at the molecular level.

Vapor-Induced Assembly of a Platinum(II) Complex Loaded on Layered Double Hydroxide Nanoparticles.

Invited for the cover of this issue is the group of Masaki Yoshida and Masako Kato at Hokkaido University/Kwansei Gakuin University. The image depicts the changes in the assembly of PtII complexes with humidity on layered double hydroxide (LDH) nanoparticles, resulting in a drastic emission color change from green to orange. Read the full text of the article at 10.1002/chem.202301993.

Vapor-Induced Assembly of a Platinum(II) Complex Loaded on Layered Double Hydroxide Nanoparticles.

Controlled self-assembly of PtII complexes is key to the development of optical and stimuli-responsive materials, but designing and precisely controlling them is still difficult owing to weak intermolecular interactions. Herein, we report the successful water-vapor-induced assembly of an anionic PtII complex [Pt(CN)2 (ppy)]- (Hppy=2-phenylpyridine) electrostatically loaded onto cationically charged layered double hydroxide (LDH) nanoparticles consisting of Mg2+ and Al3+ ions. When the PtII complexes were densely loaded onto the LDH nanoparticles, the assembly was maintained, even in dilute aqueous media. In the case of sparse loading, the PtII complexes were loaded discretely in the dry state; however, when water vapor was adsorbed, the increased mobility of the PtII complexes led to their assembly on the LDH nanoparticles. The presence of water vapor led to a drastic change in luminescence from green to orange.

Giant Crystalline Molecular Rotors that Operate in the Solid State.

Molecular motion in the solid state is typically precluded by the highly dense environment, and only molecules with a limited range of sizes show such dynamics. Here, we demonstrate the solid-state rotational motion of two giant molecules, i.e., triptycene and pentiptycene, by encapsulating a bulky N-heterocyclic carbene (NHC) Au(I) complex in the crystalline media. To date, triptycene is the largest molecule (surface area: 245 Å2 ; volume: 219 Å3 ) for which rotation has been reported in the solid state, with the largest rotational diameter among reported solid-state molecular rotors (9.5 Å). However, the pentiptycene rotator that is the subject of this study (surface area: 392 Å2 ; volume: 361 Å3 ; rotational diameter: 13.0 Å) surpasses this record. Single-crystal X-ray diffraction analyses of both the developed rotors revealed that these possess sufficient free volume around the rotator. The molecular motion in the solid state was confirmed using variable-temperature solid-state 2 H spin-echo NMR studies. The triptycene rotor exhibited three-fold rotation, while temperature-dependent changes of the rotational angle were observed for the pentiptycene rotor.

Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals.

X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal clusters in large protein crystals, the experiment has proven difficult to perform, especially on radiation-sensitive proteins. Here, the development of serial X-ray fluorescence holography to allow the direct recording of hologram patterns before the onset of radiation damage is reported. By combining a 2D hybrid detector and the serial data collection used in serial protein crystallography, the X-ray fluorescence hologram can be directly recorded in a fraction of the measurement time needed for conventional XFH measurements. This approach was demonstrated by obtaining the Mn Kα hologram pattern from the protein crystal Photosystem II without any X-ray-induced reduction of the Mn clusters. Furthermore, a method to interpret the fluorescence patterns as real-space projections of the atoms surrounding the Mn emitters has been developed, where the surrounding atoms produce large dark dips along the emitter-scatterer bond directions. This new technique paves the way for future experiments on protein crystals that aim to clarify the local atomic structures of their functional metal clusters, and for other related XFH experiments such as valence-selective XFH or time-resolved XFH.

X-ray fluorescence holography of biological metal sites: Application to myoglobin.

X-ray fluorescence holography (XFH) is a relatively new technique capable of providing unique three-dimensional structural information around specific atoms that act as a light source in crystalline samples. So far, XFH has typically been applied to inorganic materials such as dopants in metals and semiconductors. Here, we investigate the possibility of using XFH to visualize the metal active site in sperm whale myoglobin (Mb), a monomeric oxygen storage heme protein. We demonstrate that the atomic images reconstructed from the hologram data of crystals of carbonmonoxy myoglobin (MbCO) are moderately consistent with the crystal structure, which is also determined in this study by X-ray crystallography in the near-atomic resolution, as well as simulation results. These results open up a new avenue for the application of XFH to local atomic and electronic structure imaging of metal-sites in biomolecules.

Laboratory diffracted x-ray blinking to monitor picometer motions of protein molecules and application to crystalline materials.

In recent years, real-time observations of molecules have been required to understand their behavior and function. To date, we have reported two different time-resolved observation methods: diffracted x-ray tracking and diffracted x-ray blinking (DXB). The former monitors the motion of diffracted spots derived from nanocrystals labeled onto target molecules, and the latter measures the fluctuation of the diffraction intensity that is highly correlated with the target molecular motion. However, these reports use a synchrotron x-ray source because of its high average flux, resulting in a high time resolution. Here, we used a laboratory x-ray source and DXB to measure the internal molecular dynamics of three different systems. The samples studied were bovine serum albumin (BSA) pinned onto a substrate, antifreeze protein (AFP) crystallized as a single crystal, and poly{2-(perfluorooctyl)ethyl acrylate} (PC8FA) polymer between polyimide sheets. It was found that not only BSA but also AFP and PC8FA molecules move in the systems. In addition, the molecular motion of AFP molecules was observed to increase with decreasing temperature. The rotational diffusion coefficients (DR) of BSA, AFP, and PC8FA were estimated to be 0.73 pm2/s, 0.65 pm2/s, and 3.29 pm2/s, respectively. Surprisingly, the DR of the PC8FA polymer was found to be the highest among the three samples. This is the first report that measures the molecular motion of a single protein crystal and polymer by using DXB with a laboratory x-ray source. This technique can be applied to any kind of crystal and crystalline polymer and provides atomic-order molecular information.

Vapochromic behaviour of a nickel(II)-quinonoid complex with dimensional changes between 1D and higher.

The nickel(ii)-chloranilato complex {Ni(ca)(VM)2}n (H2ca = chloranilic acid, VM = coordinated vapour molecules, such as water) shows reversible vapochromism upon exposure to various vapours and subsequent drying by heating. In contrast to the Ni(ii)-quinonoid complex, [Ni(HLMe)2] (H2LMe = 4-methylamino-6-methyliminio-3-oxocyclohexa-1,4-dien-1-olate), which was reported to exhibit vapochromic spin-state switching between high and low spin states, the chloranilato complex does not change its spin state even after the removal of coordinated vapour molecules. X-ray absorption fine structure (XAFS) analysis revealed that the six-coordinate geometry of {Ni(ca)(VM)2}n was maintained even after the removal of vapour molecules, in contrast to the [Ni(HLMe)2] complex. The unique vapochromism that follows the dimensional change between 1D and higher is influenced by the relatively weaker ligand field of the chloranilate ligand.

Isomeric difference in the crystalline-state chemiluminescence property of an adamantylideneadamantane 1,2-dioxetane with a phthalimide chromophore.

Syn- and anti-isomers of an adamantylideneadamantane 1,2-dioxetane having a phthalimide side chain were prepared and investigated their crystalline-state chemiluminescence (CL) properties. The isomers showed contrastive CL properties depending on their crystal-structural characteristics, indicating that CL provides an attractive target for real-time monitoring of a chemical reaction in the crystal.

Direct observation of ligand migration within human hemoglobin at work.

Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photodissociated CO molecules migrate along distinct pathways in the α and ß subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as α14Trp(A12), α105Leu(G12), ß15Trp(A12), and ß71Phe(E15). We also observe electron density evidence for the distal histidine [α58/ß63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in α subunits than in ß subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the α or ß subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.

Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family.

A newly identified microbial rhodopsin, NM-R3, from the marine flavobacterium Nonlabens marinus, was recently shown to drive chloride ion uptake, extending our understanding of the diversity of mechanisms for biological energy conversion. To clarify the mechanism underlying its function, we characterized the crystal structures of NM-R3 in both the dark state and early intermediate photoexcited states produced by laser pulses of different intensities and temperatures. The displacement of chloride ions at five different locations in the model reflected the detailed anion-conduction pathway, and the activity-related key residues-Cys105, Ser60, Gln224, and Phe90-were identified by mutation assays and spectroscopy. Comparisons with other proteins, including a closely related outward sodium ion pump, revealed key motifs and provided structural insights into light-driven ion transport across membranes by the NQ subfamily of rhodopsins. Unexpectedly, the response of the retinal in NM-R3 to photostimulation appears to be substantially different from that seen in bacteriorhodopsin.

Fast and stable vapochromic response induced through nanocrystal formation of a luminescent platinum(II) complex on periodic mesoporous organosilica.

A hybrid vapoluminescent system exhibiting fast and repeatable response was constructed using periodic mesoporous organosilica with bipyridine moieties (BPy-PMO) and a Pt(II) complex bearing a potentially luminescent 2-phenylpyridinato (ppy) ligand. An intense red luminescence appeared when the Pt(II)-complex immobilised BPy-PMO was exposed to methanol vapour and disappeared on exposure to pyridine vapour. The ON-OFF vapochromic behaviour occurred repeatedly in a methanol/pyridine/heating cycle. Interestingly, a rapid response was achieved in the second cycle and cycles thereafter. Scanning and transmission electron microscopies (SEM/TEM), absorption and emission, and nuclear magnetic resonance spectroscopies, mass spectrometry, and powder X-ray diffraction indicated that methanol vapour induced Si-C cleavage and thus liberated [Pt(ppy)(bpy)]Cl (bpy = 2,2'-bipyridine) from the BPy-PMO framework. Furthermore, the self-assembling properties of the Pt(II) complex resulted in the formation of highly luminescent micro/nanocrystals that were homogeneously dispersed on the porous support. The unique vapoluminescence triggered by the unprecedented protodesilylation on exposure to protic solvent vapour at room temperature is attributable to BPy-PMO being a giant ligand and an effective vapour condenser. Consequently, this hybrid system presents a new strategy for developing sensors using bulk powdery materials.

Shape Rememorization of an Organosuperelastic Crystal through Superelasticity-Ferroelasticity Interconversion.

As altering permanent shapes without loss of material function is of practical importance for material molding, especially for elastic materials, shape-rememorization ability would enhance the utility of elastic crystalline materials. Since diffusionless plastic deformability can preserve the crystallinity of materials, the interconversion of diffusionless mechanical deformability between superelasticity and ferroelasticity could enable shape rememorization of superelastic single crystals. This study demonstrates the shape rememorization of an organosuperelastic single crystal of 1,4-dicyanobenzene through time-reversible interconversion of superelasticity-ferroelasticity relaxation by holding the mechanically twinned crystal without heating. The shape-rememorization ability of the organosuperelastic crystal indicates the compatibility of superelasticity (antiferroelasticity) and ferroelasticity as well as the intrinsic workability of organic crystalline materials capable of recovering their crystal functions under mild conditions.

Saturated Fatty Acids Undergo Intracellular Crystallization and Activate the NLRP3 Inflammasome in Macrophages.

OBJECTIVE: Inflammation provoked by the imbalance of fatty acid composition, such as excess saturated fatty acids (SFAs), is implicated in the development of metabolic diseases. Recent investigations suggest the possible role of the NLRP3 (nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain containing 3) inflammasome, which regulates IL-1ß (interleukin 1ß) release and leads to inflammation, in this process. Therefore, we investigated the underlying mechanism by which SFAs trigger NLRP3 inflammasome activation. APPROACH AND RESULTS: The treatment with SFAs, such as palmitic acid and stearic acid, promoted IL-1ß release in murine primary macrophages while treatment with oleic acid inhibited SFA-induced IL-1ß release in a dose-dependent manner. Analyses using polarized light microscopy revealed that intracellular crystallization was provoked in SFA-treated macrophages. As well as IL-1ß release, the intracellular crystallization and lysosomal dysfunction were inhibited in the presence of oleic acid. These results suggest that SFAs activate NLRP3 inflammasome through intracellular crystallization. Indeed, SFA-derived crystals activated NLRP3 inflammasome and subsequent IL-1ß release via lysosomal dysfunction. Excess SFAs also induced crystallization and IL-1ß release in vivo. Furthermore, SFA-derived crystals provoked acute inflammation, which was impaired in IL-1ß-deficient mice. CONCLUSIONS: These findings demonstrate that excess SFAs cause intracellular crystallization and subsequent lysosomal dysfunction, leading to the activation of the NLRP3 inflammasome, and provide novel insights into the pathogenesis of metabolic diseases.

Ligation-Dependent Picosecond Dynamics in Human Hemoglobin As Revealed by Quasielastic Neutron Scattering.

Hemoglobin, the vital O2 carrier in red blood cells, has long served as a classic example of an allosteric protein. Although high-resolution X-ray structural models are currently available for both the deoxy tense (T) and fully liganded relaxed (R) states of hemoglobin, much less is known about their dynamics, especially on the picosecond to subnanosecond time scales. Here, we investigate the picosecond dynamics of the deoxy and CO forms of human hemoglobin using quasielastic neutron scattering under near physiological conditions in order to extract the dynamics changes upon ligation. From the analysis of the global motions, we found that whereas the apparent diffusion coefficients of the deoxy form can be described by assuming translational and rotational diffusion of a rigid body, those of the CO form need to involve an additional contribution of internal large-scale motions. We also found that the local dynamics in the deoxy and CO forms are very similar in amplitude but are slightly lower in frequency in the former than in the latter. Our results reveal the presence of rapid large-scale motions in hemoglobin and further demonstrate that this internal mobility is governed allosterically by the ligation state of the heme group.

Molecular mechanism of photoactivation of a light-regulated adenylate cyclase.

The photoactivated adenylate cyclase (PAC) from the photosynthetic cyanobacterium Oscillatoria acuminata (OaPAC) detects light through a flavin chromophore within the N-terminal BLUF domain. BLUF domains have been found in a number of different light-activated proteins, but with different relative orientations. The two BLUF domains of OaPAC are found in close contact with each other, forming a coiled coil at their interface. Crystallization does not impede the activity switching of the enzyme, but flash cooling the crystals to cryogenic temperatures prevents the signature spectral changes that occur on photoactivation/deactivation. High-resolution crystallographic analysis of OaPAC in the fully activated state has been achieved by cryocooling the crystals immediately after light exposure. Comparison of the isomorphous light- and dark-state structures shows that the active site undergoes minimal changes, yet enzyme activity may increase up to 50-fold, depending on conditions. The OaPAC models will assist the development of simple, direct means to raise the cyclic AMP levels of living cells by light, and other tools for optogenetics.

Protein crystallography beamline BL2S1 at the Aichi synchrotron.

The protein crystallography beamline BL2S1, constructed at one of the 5 T superconducting bending-magnet ports of the Aichi synchrotron, is available to users associated with academic and industrial organizations. The beamline is mainly intended for use in X-ray diffraction measurements of single-crystals of macromolecules such as proteins and nucleic acids. Diffraction measurements for crystals of other materials are also possible, such as inorganic and organic compounds. BL2S1 covers the energy range 7-17 keV (1.8-0.7 Å) with an asymmetric-cut curved single-crystal monochromator [Ge(111) or Ge(220)], and a platinum-coated Si mirror is used for vertical focusing and as a higher-order cutoff filter. The beamline is equipped with a single-axis goniometer, a CCD detector, and an open-flow cryogenic sample cooler. High-pressure protein crystallography with a diamond anvil cell can also be performed using this beamline.

Development of an X-ray fluorescence holographic measurement system for protein crystals.

Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α2ß2 tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm(3)) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

Cooling dynamics of self-assembled monolayer coating for integrated gold nanocrystals on a glass substrate.

Picosecond time-resolved X-ray diffraction has been used to study the nanoscale thermal transportation dynamics of bare gold nanocrystals and thiol-based self-assembled monolayer (SAM)-coated integrated gold nanocrystals on a SiO2 glass substrate. A temporal lattice expansion of 0.30-0.33% was observed in the bare and SAM-coated nanocrystals on the glass substrate; the thermal energy inside the gold nanocrystals was transported to the contacted substrate through the gold-SiO2 interface. The interfacial thermal conductivity between the single-layered gold nanocrystal film and the SiO2 substrate is estimated to be 45 MW m(-2) K(-1) from the decay of the Au 111 peak shift, which was linearly dependent on the transient temperature. For the SAM-coated gold nanocrystals, the thermal dissipation was faster than that of the bare gold nanocrystal film. The thermal flow from the nanocrystals to the SAM-coated molecules promotes heat dissipation from the laser-heated SAM-coated gold nanocrystals. The thermal transportation of the laser-heated SAM-coated gold nanocrystal film was analyzed using the bidirectional thermal dissipation model.