Crystal structure of Staphylococcus aureus lipase complex with unsaturated petroselinic acid.

Staphylococcus aureus produces large amounts of toxins and virulence factors. In patients with underlying diseases or compromised immune systems, this bacterium can lead to severe infections and potentially death. In this study, the crystal structure of the complex of S. aureus lipase (SAL), which is involved in the growth of this bacterium, with petroselinic acid (PSA), an inhibitor of unsaturated fatty acids, was determined by X-ray crystallography. Recently, PSA was shown to inhibit S. aureus biofilm formation and the enzymatic activity of SAL. To further characterize the inhibitory mechanism, we determined the half-inhibitory concentration of SAL by PSA and the crystal structure of the complex. The IC50 of the inhibitory effect of PSA on SAL was 3.4 µm. SAL and PSA inhibitors were co-crystallized, and diffraction data sets were collected to 2.19 Å resolution at SPring-8 to determine the crystal structure and elucidate the detailed structural interactions. The results show that the fatty acid moiety of PSA is tightly bound to a hydrophobic pocket extending in two directions around the catalytic residue Ser116. Ser116 was also covalently bonded to the carbon of the unsaturated fatty acid moiety, and an oxyanion hole in SAL stabilized the electrons of the double bond. The difference in inhibitory activity between PSA and ester compounds revealed a structure-activity relationship between SAL and PSA. Additional research is required to further characterize the clinical potential of PSA.

Time-Resolved Small-Angle X-Ray Scattering of Protein Cage Assembly.

Recent improvements in X-ray detectors and synchrotron light sources have made it possible to measure time-resolved small-angle X-ray scattering (TR-SAXS) at millisecond time resolution. As an example, in this chapter we describe the beamline setup, experimental scheme, and the points that should be noted in stopped-flow TR-SAXS experiments for investigating the ferritin assembly reaction.

Enabling metallic behaviour in two-dimensional superlattice of semiconductor colloidal quantum dots.

Semiconducting colloidal quantum dots and their assemblies exhibit superior optical properties owing to the quantum confinement effect. Thus, they are attracting tremendous interest from fundamental research to commercial applications. However, the electrical conducting properties remain detrimental predominantly due to the orientational disorder of quantum dots in the assembly. Here we report high conductivity and the consequent metallic behaviour of semiconducting colloidal quantum dots of lead sulphide. Precise facet orientation control to forming highly-ordered quasi-2-dimensional epitaxially-connected quantum dot superlattices is vital for high conductivity. The intrinsically high mobility over 10 cm2 V-1 s-1 and temperature-independent behaviour proved the high potential of semiconductor quantum dots for electrical conducting properties. Furthermore, the continuously tunable subband filling will enable quantum dot superlattices to be a future platform for emerging physical properties investigations, such as strongly correlated and topological states, as demonstrated in the moiré superlattices of twisted bilayer graphene.

Reconstitution of microtubule into GTP-responsive nanocapsules.

Nanocapsules that collapse in response to guanosine triphosphate (GTP) have the potential as drug carriers for efficiently curing diseases caused by cancer and RNA viruses because GTP is present at high levels in such diseased cells and tissues. However, known GTP-responsive carriers also respond to adenosine triphosphate (ATP), which is abundant in normal cells as well. Here, we report the elaborate reconstitution of microtubule into a nanocapsule that selectively responds to GTP. When the tubulin monomer from microtubule is incubated at 37 °C with a mixture of GTP (17 mol%) and nonhydrolysable GTP* (83 mol%), a tubulin nanosheet forms. Upon addition of photoreactive molecular glue to the resulting dispersion, the nanosheet is transformed into a nanocapsule. Cell death results when a doxorubicin-containing nanocapsule, after photochemically crosslinked for properly stabilizing its shell, is taken up into cancer cells that overexpress GTP.

Mechanism of Elastic Properties of Biodegradable Poly[(R)-3-Hydroxybutyrate-co-4-hydroxybutyrate] Films Revealed by Synchrotron Radiation.

Reversible elastic films of biobased and biodegradable poly[(R)-3-hydroxybutyrate-co-4-hydroxybutyrate] [P(3HB-co-4HB)] were prepared by uniaxial drawing procedures. Mechanical properties and highly ordered film structures were investigated by tensile testing and both static-state and in situ wide-angle X-ray diffraction and small-angle X-ray scattering with synchrotron radiation during stretching and relaxing. Despite the crystalline nature of the polymers, the elongation at break of these films was greater than 1500%. Reversible elasticity was achieved after the first 10 times of uniaxial stretching. X-ray measurement results indicated that on stretching, ß-form molecular chains with a planar zigzag conformation were introduced from molecular chains with random coils in the amorphous regions between α-form lamellar crystals. Notably, the orientation of the α-form lamellar crystals increased after relaxation of the molecular chains with a planar zigzag conformation (ß-form) between the lamellar crystals (α-form). Reversible elastic properties were regenerated by a planar zigzag conformation between the lamellar crystals, the extension of molecular chains in lamellar crystals by the rotation of molecular conformation, and changes in the degree of orientation of the lamellar crystals.

Structural flexibility of the tetanus neurotoxin revealed by crystallographic and solution scattering analyses.

Although the tetanus neurotoxin (TeNT) delivers its protease domain (LC) across the synaptic vesicle lumen into the cytosol via its receptor binding domain (HC) and translocation domain (HN), the molecular mechanism coordinating this membrane translocation remains unresolved. Here, we report the high-resolution crystal structures of full-length reduced TeNT (rTeNT, 2.3 Å), TeNT isolated HN (TeNT/iHN, 2.3 Å), TeNT isolated HC (TeNT/iHC, 1.5 Å), together with the solution structures of TeNT/iHN and beltless TeNT/iHN (TeNT/blHN). TeNT undergoes significant domains rotation of the HN and LC were demonstrated by structural comparison of rTeNT and non-reduced-TeNT (nrTeNT). A linker loop connects the HN and HC is essential for the self-domain rotation of TeNT. The TeNT-specific C869-C1093 disulfide bond is sensitive to the redox environment and its disruption provides linker loop flexibility, which enables domain arrangement of rTeNT distinct from that of nrTeNT. Furthermore, the mobility of C869 in the linker loop and the sensitivity to redox condition of C1093 were confirmed by crystal structure analysis of TeNT/iHC. On the other hand, the structural flexibility of HN was investigated by crystallographic and solution scattering analyses. It was found that the region (residues 698-769), which follows the translocation region had remarkable change in TeNT/iHN. Besides, the so-called belt region has a high propensity to swing around the upper half of TeNT/iHN at acidic pH. It provides the first overview of the dynamics of the Belt in solution. These newly obtained structural information that shed light on the transmembrane mechanism of TeNT.

Vibrio cholerae biofilm scaffolding protein RbmA shows an intrinsic, phosphate-dependent autoproteolysis activity.

Vibrio cholerae is the causative agent of the diarrheal disease cholera, for which biofilm communities are considered to be environmental reservoirs. In endemic regions, and after algal blooms, which may result from phosphate enrichment following agricultural runoff, the bacterium is released from biofilms resulting in seasonal disease outbreaks. However, the molecular mechanism by which V. cholerae senses its environment and switches lifestyles from the biofilm-bound state to the planktonic state is largely unknown. Here, we report that the major biofilm scaffolding protein RbmA undergoes autocatalytic proteolysis via a phosphate-dependent induced proximity activation mechanism. Furthermore, we show that RbmA mutants that are defective in autoproteolysis cause V. cholerae biofilms to grow larger and mechanically stronger, correlating well with the observation that RbmA stability directly affects microbial community homeostasis and rheological properties. In conclusion, our biophysical study characterizes a novel phosphate-dependent breakdown pathway of RbmA, while microbiological data suggest a new, sensory role of this biofilm scaffolding element.

A mechanically adaptive hydrogel with a reconfigurable network consisting entirely of inorganic nanosheets and water.

Although various biomimetic soft materials that display structural hierarchies and stimuli responsiveness have been developed from organic materials, the creation of their counterparts consisting entirely of inorganic materials presents an attractive challenge, as the properties of such materials generally differ from those of living organisms. Here, we have developed a hydrogel consisting of inorganic nanosheets (14 wt%) and water (86 wt%) that undergoes thermally induced reversible and abrupt changes in its internal structure and mechanical elasticity (23-fold). At room temperature, the nanosheets in water electrostatically repel one another and self-assemble into a long-periodic lamellar architecture with mutually restricted mobility, forming a physical hydrogel. Upon heating above 55 °C, the electrostatic repulsion is overcome by competing van der Waals attraction, and the nanosheets rearrange into an interconnected 3D network of another hydrogel. By doping the gel with a photothermal-conversion agent, the gel-to-gel transition becomes operable spatiotemporally on photoirradiation.

Modification of decellularized vascular xenografts with 8-arm polyethylene glycol suppresses macrophage infiltration but maintains graft degradability.

Because acellular vascular xenografts induce an immunological reaction through macrophage infiltration, they are conventionally crosslinked with glutaraldehyde (GA). However, the GA crosslinking reaction inhibits not only the host immune reaction around the graft but also the graft's enzymatic degradability, which is one of the key characteristics of acellular grafts that allow them to be replaced by host tissue. In this study, we used an 8-arm polyethylene glycol (PEG) to successfully suppress macrophage infiltration, without eliminating graft degradation. Decellularized ostrich carotid arteries were modified with GA or N-hydroxysuccinimide-activated 8-arm PEG (8-arm PEG-NHS), which has a molecular weight of 17 kDa. To evaluate the enzymatic degradation in vitro, the graft was immersed in a collagenase solution for 12 hr. The 8-arm PEG-modified graft was degraded to the same extent as the unmodified graft, but the GA-modified graft was not degraded. The graft was transplanted into rat subcutaneous tissue for up to 8 weeks. Although CD68-positive cells accumulated in the unmodified graft, they did not infiltrate into either modified graft. However, the GA-modified grafts calcified, but the 8-arm PEG-modified graft did not calcify after transplantation. These data suggested that 8-arm PEG-NHS is a promising modification agent for biodegradable vascular xenografts, to suppress acute macrophage infiltration only.

Crystal structure of pathogenic Staphylococcus aureus lipase complex with the anti-obesity drug orlistat.

Staphylococcus aureus lipase (SAL), a triacylglycerol esterase, is an important virulence factor and may be a therapeutic target for infectious diseases. Herein, we determined the 3D structure of native SAL, the mutated S116A inactive form, and the inhibitor complex using the anti-obesity drug orlistat to aid in drug development. The determined crystal structures showed a typical α/ß hydrolase motif with a dimeric form. Fatty acids bound near the active site in native SAL and inactive S116A mutant structures. We found that orlistat potently inhibits SAL activity, and it covalently bound to the catalytic Ser116 residue. This is the first report detailing orlistat-lipase binding. It provides structure-based information on the production of potent anti-SAL drugs and lipase inhibitors. These results also indicated that orlistat can be repositioned to treat bacterial diseases.

Molecular shape under far-red light and red light-induced association of Arabidopsis phytochrome B.

Phytochrome B (phyB) is a plant photoreceptor protein that regulates various photomorphogenic responses to optimize plant growth and development. PhyB exists in two photoconvertible forms: a red light-absorbing (Pr) and a far-red light-absorbing (Pfr) form. Therefore, to understand the mechanism of phototransformation, the structural characterization of full-length phyB in these two forms is necessary. Here, we report the molecular structure of Arabidopsis thaliana phyB in Pr form and the molecular properties of the Pfr form determined by small-angle X-ray scattering coupled with size-exclusion chromatography. In solution, the Pr form associated as a dimer with a radius of gyration of 50 Å. The molecular shape was a crossed shape, in which the orientation of the photosensory modules differed from that in the crystal structure of dimeric photosensory module. PhyB exhibited structural reversibility in the Pfr-to-Pr phototransformation and thermal reversion from Pfr to Pr in the dark. In addition, Pfr only exhibited nonspecific association, which distinguished molecular properties of Pfr form from those of the inactive Pr form.

Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding.

Time-resolved direct observations of proteins in action provide essential mechanistic insights into biological processes. Here, we present mechanisms of action of protein disulfide isomerase (PDI)-the most versatile disulfide-introducing enzyme in the endoplasmic reticulum-during the catalysis of oxidative protein folding. Single-molecule analysis by high-speed atomic force microscopy revealed that oxidized PDI is in rapid equilibrium between open and closed conformations, whereas reduced PDI is maintained in the closed state. In the presence of unfolded substrates, oxidized PDI, but not reduced PDI, assembles to form a face-to-face dimer, creating a central hydrophobic cavity with multiple redox-active sites, where substrates are likely accommodated to undergo accelerated oxidative folding. Such PDI dimers are diverse in shape and have different lifetimes depending on substrates. To effectively guide proper oxidative protein folding, PDI regulates conformational dynamics and oligomeric states in accordance with its own redox state and the configurations or folding states of substrates.

Perfluorophenyl-Directed Giant Porphyrin J-Aggregates.

Quadrupolar interactions of porphyrin bearing two pentafluorophenylethynyl terminals (1) drove the formation of a successive one-dimensional staircase structure, i.e., J-aggregates, to yield millimeter-length needles with a single-crystalline character in methylcyclohexane solution. In contrast, π-stacked interactions of porphyrin bearing two nonfluorinated phenyl terminals (2) formed no aggregates in solution. A spin-cast film of 1 also showed bathochromic shift of the Soret and Q bands, indicating the formation of J-aggregates. The molecular arrangement of the J-aggregates was revealed by microbeam glazing-incidence wide-angle X-ray diffraction (GIWAXD), and was in good agreement with the optimized structure generated by density functional theory (DFT) calculations.

Chiral crystal-like droplets displaying unidirectional rotational sliding.

The self-assembly of organic molecules into supramolecular materials with structural ordering beyond the nanometre scale is challenging. Here, we report the spontaneous self-assembly of a chiral discotic triphenylene derivative into millimetre-sized droplets. The structure of the droplets is characterized by high positional and orientational ordering and a three-dimensional integrity similar to that of single crystals. Notwithstanding, these assemblies slide when placed on a vertical substrate demonstrating their fluid nature. X-ray imaging shows that during the sliding process the internal crystal-like structure is maintained and that the droplets undergo clockwise or counterclockwise unidirectional rotation, depending on the chirality of their molecular components. Rheological measurements suggest that this rotational behaviour might result from the distinct yield stress between the (R)- and (S)-enantiomers. Overall, our findings demonstrate that molecular chirality can determine the movement direction of a supramolecular structure, thus expanding the fundamental understanding of the structure and dynamics of soft materials.

Nematic-to-columnar mesophase transition by in situ supramolecular polymerization.

Disk- and rod-shaped molecules are incompatible in coassembly, as the former tend to stack one-dimensionally whereas the latter tend to align in parallel. Because this type of incompatibility can be more pronounced in condensed phases, different-shaped molecules generally exclude one another. We report that supramolecular polymerization of a disk-shaped chiral monomer in nematic liquid crystals comprising rod-shaped molecules results in order-increasing mesophase transition into a single mesophase with a core-shell columnar geometry. This liquid crystalline material responds quickly to an applied electric field, resulting in unidirectional columnar ordering. Moreover, it can be modularly customized to be optoelectrically responsive simply by using a photoisomerizable rod-shaped module. The modular strategy allows for cooperative integration of different functions into elaborate dynamic architectures.

An Anisotropic Hydrogel Actuator Enabling Earthworm-Like Directed Peristaltic Crawling.

Peristaltic crawling, which is the moving mechanism of earthworm-like limbless creatures in narrow spaces, is a challenging target to mimic by using soft materials. Here we report an unprecedented hydrogel actuator that enables not only a peristaltic crawling motion but also reversing its direction. Our cylindrically processed hydrogel contains gold nanoparticles for photothermal conversion, a thermoresponsive polymer network for switching the electrical permittivity of the gel interior, and cofacially oriented 2D electrolytes (titanate nanosheets; TiNSs) to synchronously change their anisotropic electrostatic repulsion. When a hydrogel, which was designed to include cofacially oriented TiNSs along the cylindrical gel axis, is pointwisely photoirradiated with a visible-light laser, it spatiotemporally expands immediately (<0.5 s) and largely (80 % of its original length) in an isovolumetric manner. When the irradiation spot is moved along the cylindrical gel axis, the hydrogel undergoes peristaltic crawling due to quick and sequential elongation/contraction events and moves oppositely toward the laser scanning direction. Thus, when the scanning direction is switched, the crawling direction is reversed. When gold nanorods are used in place of gold nanoparticles, the hydrogel becomes responsive to a near-infrared light, which can deeply penetrate into bio tissues.

Extra-Large Mechanical Anisotropy of a Hydrogel with Maximized Electrostatic Repulsion between Cofacially Aligned 2D Electrolytes.

In our previous work, we have shown that "electrostatic forces", when generated anisotropically in aqueous media by 2D electrolytes upon cofacial orientation, enable the formation of a hydrogel with an anisotropic parameter, as defined by the ratio of elastic moduli E⊥ /E∥ , of 3.0. Herein, we successfully developed the design strategy for a hydrogel with an anisotropic parameter of no less than 85. This value is not only 28 times greater than that of our previous anisotropic hydrogel but also 6 times larger than the current champion record in synthetic hydrogels (E⊥ /E∥ ∼15). Firstly, we simply lowered ionic contaminants in the hydrogel and were able to enhance the anisotropic parameter from 3.0 to 18. Then, we chose a supporting polymer network allowing the hydrogel to carry a higher interior permittivity. Consequently, the anisotropic parameter was further enhanced from 18 to 85. Owing to the enhanced mechanical anisotropy, our new hydrogel displayed a superb ability of seismic isolation.

Fully Conjugated Porphyrin Glass: Collective Light-Harvesting Antenna for Near-Infrared Fluorescence beyond 1 µm.

Expanded π-systems with a narrow highest occupied molecular orbital-lowest unoccupied molecular orbital band gap encounter deactivation of excitons due to the "energy gap law" and undesired aggregation. This dilemma generally thwarts the near-infrared (NIR) luminescence of organic π-systems. A sophisticated cofacially stacked π-system is known to involve exponentially tailed disorder, which displays exceptionally red-shifted fluorescence even as only a marginal emission component. Enhancement of the tail-state fluorescence might be advantageous to achieve NIR photoluminescence with an expected collective light-harvesting antenna effect as follows: (i) efficient light-harvesting capacity due to intense electronic absorption, (ii) a long-distance exciton migration into the tail state based on a high spatial density of the chromophore site, and (iii) substantial transmission of NIR emission to circumvent the inner filter effect. Suppression of aggregation-induced quenching of fluorescence could realize collective light-harvesting antenna for NIR-luminescence materials. This study discloses an enhanced tail-state NIR fluorescence of a self-standing porphyrin film at 1138 nm with a moderate quantum efficiency based on a fully π-conjugated porphyrin that adopts an amorphous form, called "porphyrin glass".

Kinetically Stable Bicelles with Dilution Tolerance, Size Tunability, and Thermoresponsiveness for Drug Delivery Applications.

Mixtures of a phospholipid (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine, DPPC) and a sodium-cholate-derived surfactant (SC-C5 ) at room temperature formed phospholipid bilayer fragments that were edge-stabilized by SC-C5 : so-called "bicelles". Because the bilayer melting point of DPPC (41 °C) is above room temperature and because SC-C5 has an exceptionally low critical micelle concentration (<0.5 mm), the bicelles are kinetically frozen at room temperature. Consequently, they exist even when the mixture is diluted to a concentration of 0.04 wt %. In addition, the lateral size of the bicelles can be fine-tuned by altering the molar ratio of DPPC to SC-C5 . On heating to ≈37 °C, the bicelles transformed into micelles composed of DPPC and SC-C5 . By taking advantage of the dilution tolerance, size tunability, and thermoresponsiveness, we demonstrated in vitro drug delivery based on use of the bicelles as carriers, which suggests their potential utility in transdermal drug delivery.

Combination of Amorphous Silk Fiber Spinning and Postspinning Crystallization for Tough Regenerated Silk Fibers.

An artificial spinning system using regenerated silk fibroin solutions is adopted to produce high-performance silk fibers. In previous studies, alcohol-based agents, such as methanol or ethanol, were used to coagulate silk dope solutions, producing silk fiber with poor mechanical properties compared with those of native silk fibers. The alcohol-based coagulation agents induce rapid ß-sheet crystallization of the silk molecules, which inhibits subsequent alignment of the ß-sheet crystals. Here, we induce gradual ß-sheet formation to afford adequate ß-sheet alignment similar to that of native silk fiber. To this aim, we developed an amorphous silk fiber spinning process that prevents fast ß-sheet formation in silk molecules by using tetrahydrofuran (THF) as a coagulation solvent. In addition, we apply postdrawing to the predominantly amorphous silk fibers to induce ß-sheet formation and orientation. The resultant silk fibers showed a 2.5-fold higher extensibility, resulting in 1.5-fold tougher silk fibers compared with native Bombyx mori silk fiber. The amorphous silk fiber spinning process developed here will pave the way to the production of silk fibers with desired mechanical properties.