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.

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.

An anisotropic hydrogel with electrostatic repulsion between cofacially aligned nanosheets.

Machine technology frequently puts magnetic or electrostatic repulsive forces to practical use, as in maglev trains, vehicle suspensions or non-contact bearings. In contrast, materials design overwhelmingly focuses on attractive interactions, such as in the many advanced polymer-based composites, where inorganic fillers interact with a polymer matrix to improve mechanical properties. However, articular cartilage strikingly illustrates how electrostatic repulsion can be harnessed to achieve unparalleled functional efficiency: it permits virtually frictionless mechanical motion within joints, even under high compression. Here we describe a composite hydrogel with anisotropic mechanical properties dominated by electrostatic repulsion between negatively charged unilamellar titanate nanosheets embedded within it. Crucial to the behaviour of this hydrogel is the serendipitous discovery of cofacial nanosheet alignment in aqueous colloidal dispersions subjected to a strong magnetic field, which maximizes electrostatic repulsion and thereby induces a quasi-crystalline structural ordering over macroscopic length scales and with uniformly large face-to-face nanosheet separation. We fix this transiently induced structural order by transforming the dispersion into a hydrogel using light-triggered in situ vinyl polymerization. The resultant hydrogel, containing charged inorganic structures that align cofacially in a magnetic flux, deforms easily under shear forces applied parallel to the embedded nanosheets yet resists compressive forces applied orthogonally. We anticipate that the concept of embedding anisotropic repulsive electrostatics within a composite material, inspired by articular cartilage, will open up new possibilities for developing soft materials with unusual functions.

Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers.

The existence of a 30-nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular structures formed by reversible Mg(2+)-dependent self-association of linear 12-mer nucleosomal arrays using microscopy and physicochemical approaches. These reconstituted chromatin structures, which we call "oligomers", are globular throughout all stages of cooperative assembly and range in size from ~50 nm to a maximum diameter of ~1,000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10-nm fibers, rather than folded 30-nm structures. Linker DNA was freely accessible to micrococcal nuclease, although the oligomers remained partially intact after linker DNA digestion. The organization of chromosomal fibers in human nuclei in situ was stabilized by 1 mM MgCl2, but became disrupted in the absence of MgCl2, conditions that also dissociated the oligomers in vitro These results indicate that a 10-nm array of nucleosomes has the intrinsic ability to self-assemble into large chromatin globules stabilized by nucleosome-nucleosome interactions, and suggest that the oligomers are a good in vitro model for investigating the structure and organization of interphase chromosomes.

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.

Blue light-excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis.

Phototropin2 (phot2) is a blue-light (BL) receptor that regulates BL-dependent activities for efficient photosynthesis in plants. phot2 comprises two BL-receiving light-oxygen-voltage-sensing domains (LOV1 and LOV2) and a kinase domain. BL-excited LOV2 is thought to be primarily responsible for the BL-dependent activation of the kinase. However, the molecular mechanisms by which small BL-induced conformational changes in the LOV2 domain are transmitted to the kinase remain unclear. Here, we used full-length wild-type and mutant phot2 proteins from Arabidopsis to study their molecular properties in the dark and under BL irradiation. Phosphorylation assays and absorption measurements indicated that the LOV1 domain assists the thermal relaxation of BL-excited LOV2 and vice versa. Using small-angle X-ray scattering and electron microscopy, we observed that phot2 forms a dimer and has a rod shape with a maximum length of 188 Å and a radius of gyration of 44 Å. Under BL, phot2 displayed large conformational changes that bent the rod shape. By superimposing the crystal structures of the LOV1 dimer, LOV2, and a homology model of the kinase to the observed changes, we inferred that the BL-dependent change consisted of positional shifts of both LOV2 and the kinase relative to LOV1. Furthermore, phot2 mutants lacking the photocycle in LOV1 or LOV2 still exhibited conformational changes under BL, suggesting that LOV1 and LOV2 cooperatively contribute to the conformational changes that activate the kinase. These results suggest that BL-activated LOV1 contributes to the kinase activity of phot2. We discuss the possible intramolecular interactions and signaling mechanisms in phot2.

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.

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.

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.

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.

Blue Light-excited Light-Oxygen-Voltage-sensing Domain 2 (LOV2) Triggers a Rearrangement of the Kinase Domain to Induce Phosphorylation Activity in Arabidopsis Phototropin1.

Phototropin1 is a blue light (BL) receptor in plants and shows BL-dependent kinase activation. The BL-excited light-oxygen-voltage-sensing domain 2 (LOV2) is primarily responsible for the activation of the kinase domain; however, the molecular mechanism by which conformational changes in LOV2 are transmitted to the kinase domain remains unclear. Here, we investigated BL-induced structural changes of a minimum functional fragment of Arabidopsis phototropin1 composed of LOV2, the kinase domain, and a linker connecting the two domains using small-angle x-ray scattering (SAXS). The fragment existed as a dimer and displayed photoreversible SAXS changes reflected in the radii of gyration of 42.9 Å in the dark and 48.8 Å under BL irradiation. In the dark, the molecular shape reconstructed from the SAXS profiles appeared as two bean-shaped lobes in a twisted arrangement that was 170 Å long, 80 Å wide, and 50 Å thick. The molecular shape under BL became slightly elongated from that in the dark. By fitting the crystal structure of the LOV2 dimer and a homology model of the kinase domain to their inferred shapes, the BL-dependent change could be interpreted as the positional shift in the kinase domain relative to that of the LOV2 dimer. In addition, we found that lysine 475, a functionally important residue, in the N-terminal region of LOV2 plays a critical role in transmitting the structural changes in LOV2 to the kinase domain. The interface between the domains is critical for signaling, suitably changing the structure to activate the kinase in response to conformational changes in the adjoining LOV2.

Human ER Oxidoreductin-1α (Ero1α) Undergoes Dual Regulation through Complementary Redox Interactions with Protein-Disulfide Isomerase.

In the mammalian endoplasmic reticulum, oxidoreductin-1α (Ero1α) generates protein disulfide bonds and transfers them specifically to canonical protein-disulfide isomerase (PDI) to sustain oxidative protein folding. This oxidative process is coupled to the reduction of O2 to H2O2 on the bound flavin adenine dinucleotide cofactor. Because excessive thiol oxidation and H2O2 generation cause cell death, Ero1α activity must be properly regulated. In addition to the four catalytic cysteines (Cys94, Cys99, Cys104, and Cys131) that are located in the flexible active site region, the Cys208-Cys241 pair located at the base of another flexible loop is necessary for Ero1α regulation, although the mechanistic basis is not fully understood. The present study revealed that the Cys208-Cys241 disulfide was reduced by PDI and other PDI family members during PDI oxidation. Differential scanning calorimetry and small angle X-ray scattering showed that mutation of Cys208 and Cys241 did not grossly affect the thermal stability or overall shape of Ero1α, suggesting that redox regulation of this cysteine pair serves a functional role. Moreover, the flexible loop flanked by Cys208 and Cys241 provides a platform for functional interaction with PDI, which in turn enhances the oxidative activity of Ero1α through reduction of the Cys208-Cys241 disulfide. We propose a mechanism of dual Ero1α regulation by dynamic redox interactions between PDI and the two Ero1α flexible loops that harbor the regulatory cysteines.

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

We report a method of femtosecond crystallography for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-Å radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.

An autonomous actuator driven by fluctuations in ambient humidity.

Devices that respond to negligibly small fluctuations in environmental conditions will be of great value for the realization of more sustainable, low-power-consumption actuators and electronic systems. Herein we report an unprecedented film actuator that seemingly operates autonomously, because it responds to the adsorption and desorption of a minute amount of water (several hundred nanograms per 10 mm(2)) possibly induced by fluctuations in the ambient humidity. The actuation is extremely rapid (50 ms for one curl) and can be repeated >10,000 times without deterioration. On heating or light irradiation, the film loses adsorbed water and bends quickly, so that it can jump vertically up to 10 mm from a surface or hit a glass bead. The film consists of a π-stacked carbon nitride polymer, formed by one-pot vapour-deposition polymerization of guanidinium carbonate, and is characterized by a tough, ultralightweight and highly anisotropic layered structure. An actuator partially protected against water adsorption is also shown to walk unidirectionally.

Silk Resin with Hydrated Dual Chemical-Physical Cross-Links Achieves High Strength and Toughness.

Native silk fibers are known to demonstrate excellent mechanical properties such as high strength and ductility. However, regenerated silk material has not yet been used as a tough structural material in our everyday life. To recreate the mechanical properties with regenerated silk material, the network structure and hydration state of silk materials are studied and optimized in this study. This is the first to demonstrate the effect of chemical and physical cross-links in hydrated and dehydrated silk materials, namely, silk hydrogels and resins. Mild hydration conditions (relative humidity 20-60%) realizes tough and strong silk materials with chemical and physical cross-links. In the case of relatively high concentrations of silk molecules, contributions to the high strength and toughness of silk-based materials are considered to come not only from ß-sheet cross-links and chemical dityrosine links but also from entanglements and assembly via the hydrophobic interactions of silk molecules. In addition, dehydration treatment does not disturb the biodegradability of the silk resins in natural environments. Based on the overall results, the silk resins with controlled network structures and hydration state have successfully achieved the highest toughness possible for a bulk silk material while maintaining favorable biodegradability.

Liquid Crystalline Granules Align in a Hierarchical Structure To Produce Spider Dragline Microfibrils.

The spider silk spinning process converts spidroins from an aqueous form to a tough fiber. This spinning process has been investigated by numerous researchers, and micelles or liquid crystals of spidroins have been reported to form silk fibers, which are bundles of silk microfibrils. However, the formation process of silk microfibrils has not been clarified previously. Here, we report that silk microfibrils are generated through the formation, homogenization, and linkage of liquid crystalline granules without micelle-like structures. Heterogeneous granules on the submicron to micron scale were observed in the storage sac, whereas homogeneous granules with diameters of approximately 100 nm were aligned along the tapering duct. In the spun fibers, the homogeneous granules were connected along the fiber axis. This is the first clear description of the formation of granule-based microfibrils in the spinning process, which is the key conversion process leading to the unique hierarchical structure of spider dragline.

Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair.

In all organisms, RecA-family recombinases catalyze homologous joint formation in homologous genetic recombination, which is essential for genome stability and diversification. In homologous joint formation, ATP-bound RecA/Rad51-recombinases first bind single-stranded DNA at its primary site and then interact with double-stranded DNA at another site. The underlying reason and the regulatory mechanism for this conserved binding order remain unknown. A comparison of the loop L1 structures in a DNA-free RecA crystal that we originally determined and in the reported DNA-bound active RecA crystals suggested that the aspartate at position 161 in loop L1 in DNA-free RecA prevented double-stranded, but not single-stranded, DNA-binding to the primary site. This was confirmed by the effects of the Ala-replacement of Asp-161 (D161A), analyzed directly by gel-mobility shift assays and indirectly by DNA-dependent ATPase activity and SOS repressor cleavage. When RecA/Rad51-recombinases interact with double-stranded DNA before single-stranded DNA, homologous joint-formation is suppressed, likely by forming a dead-end product. We found that the D161A-replacement reduced this suppression, probably by allowing double-stranded DNA to bind preferentially and reversibly to the primary site. Thus, Asp-161 in the flexible loop L1 of wild-type RecA determines the preference for single-stranded DNA-binding to the primary site and regulates the DNA-binding order in RecA-catalyzed recombinase reactions.

Effect of Cholesterol on the Interaction of Cytochrome P450 Substrate Drug Chlorzoxazone with the Phosphatidylcholine Bilayer.

Many drugs are oxidized by membrane protein cytochrome P450 (CYP) enzymes during their metabolism process. CYPs are located mainly in endoplasmic reticulum (ER) membranes. Recent studies have suggested that CYP substrate drugs first bind the lipid bilayers of ER membranes and then the drugs reach the active site of CYP by way of an access channel. The entrance of the channel is located in the hydrophobic regions of the lipid bilayers. One of the features of the ER membrane is a cholesterol content that is lower than those of other biomembranes. In this study, the cholesterol concentration dependence of the interaction of a CYP substrate drug, chlorzoxazone (CZX), with model membranes composed of phosphatidylcholine (PC) and cholesterol was examined via differential scanning calorimetry (DSC), UV-visible spectroscopy, and X-ray diffraction. Experimental results indicated that CZX can bind to pure PC bilayers in the absence of cholesterol and that, by contrast, a high cholesterol concentration (30-50 mol %) tends to prevent CZX from binding to PC bilayers. Interestingly, the effect of cholesterol on the binding and insertion of CZX was biphasic. In the case of palmitoyloleoylphosphatidylcholine (POPC) bilayers containing 5-10 mol % cholesterol, the CZX's binding and penetration into the bilayer were found to be greater than those with pure POPC bilayers. The concentration of 5-10 mol % nearly corresponds to the cholesterol concentration of ER membranes. The low cholesterol contents (12-20 mol %) of ER membranes might be the most suitable for the CYP drug metabolism process in ER membranes.

Ferritin Assembly Revisited: A Time-Resolved Small-Angle X-ray Scattering Study.

The assembly reaction of Escherichia coli ferritin A (EcFtnA) was studied using time-resolved small-angle X-ray scattering (TR-SAXS). EcFtnA forms a cagelike structure that consists of 24 identical subunits and dissociates into dimers at acidic pH. The dimer maintains nativelike secondary and tertiary structures and is able to reassemble into a 24-mer when the pH is increased. The reassembly reaction was induced by pH jump, and reassembly was followed by TR-SAXS. Time-dependent changes in the forward scattering intensity and in the gyration radius suggested the existence of a significant population of intermediate oligomers during the assembly reaction. The initial reaction was a mixture of second- and third-order reactions (formation of tetramers and hexamers) from the protein concentration dependence of the initial velocity. The time-dependent change in the SAXS profile was roughly explained by a simple model in which only tetramers, hexamers, and dodecamers were considered as intermediates.