Significant anisotropic deformation and optical shifts in stretched cholesteric liquid crystal elastomers.

This study explores the opto-mechanical response of cholesteric liquid crystal elastomers (CLCEs) subjected to uniaxial stretching along the x-axis, perpendicular to their helical z-axis. A definitive crossover is observed in the strain (εx) dependencies of various optical and mechanical properties, such as the transmission spectra, degree of mesogen orientation, Poisson's ratios, and tensile stress. At low strains, CLCEs exhibit a blue shift in the selective reflection band due to a reduction in the helical pitch, accompanied by a decrease in reflection selectivity for circularly polarized light. Beyond a certain critical strain further pitch alterations halt. This strain regime is marked by substantial anisotropic lateral contractions without any z-axis contraction, as indicated by a Poisson's ratio (µxz) of zero. Within this intermediate strain regime, local directors predominantly reorient towards the x-direction within the xy-plane, resulting in a quasi-plateau of tensile stress. Approaching a higher critical strain a complete loss of reflective selectivity occurs. Past this threshold, while the mechanical responses resemble those of isotropic conventional rubber, they retain a periodic structure albeit without phase chirality. These observed features are accounted for by the Mao-Terentjev-Warner model, especially when the network anisotropy parameter is adjusted to match the critical strain magnitude associated with the cessation of selective reflection.

X-ray zooming optics for analyzer-based multi-contrast computed tomography.

An X-ray analyzer-based optics with a zoom function is proposed for observing various samples with apparent-absorption contrast, phase contrast and scattering contrast. The proposed X-ray optics consists of a collimator crystal and an analyzer crystal arranged in a nondispersive (+, -) geometry with a sample placed between them. For the implementation of the zoom function, an asymmetrically cut crystal in the rotated-inclined geometry was used for the analyzer. Proof-of-principle experiments were performed at the vertical wiggler beamline BL-14B of the Photon Factory. First, the magnification was set to 1×, and then it was zoomed into the optimal magnification (10×). At these magnifications, tri-modal contrast cross-sectional images of a sample were obtained by computed tomography. It was confirmed that the image quality at 10× was superior to that at 1×. This achievement opens up new possibilities for observing an entire sample or regions of interest within a sample at optimal magnification, and is expected to be useful for materials science, condensed matter physics, archeology and biomedical science.

Conceptual design of the Hybrid Ring with superconducting linac.

The Hybrid Ring with a superconducting-linac injector as a highly flexible synchrotron radiation source to enable new experimental techniques and enhance many existing ones is proposed. It is designed to be operated with the coexistence of the storage (SR) bunches characterized by the performance of the storage ring, and the single-pass (SP) bunches characterized by the performance of the superconducting linac. Unique experiments can be performed by simultaneous use of the SR and SP beams, in addition to research with various experimental techniques utilizing the versatile SR beam and research in the field of ultrafast dynamics utilizing the ultrashort pulse of the SP beam. The extendability of the Hybrid Ring will allow it to be developed into a synchrotron radiation complex.

Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition.

The mechanisms of protein stabilization by uncharged solutes, such as polyols and sugars, have been intensively studied with respect to the chemical thermodynamics of molecular crowding. In particular, many experimental and theoretical studies have been conducted to explain the mechanism of the protective action on protein structures by glycerol through the relationship between hydration and glycerol solvation on protein surfaces. We used wide-angle x-ray scattering (WAXS), small-angle neutron scattering, and theoretical scattering function simulation to quantitatively characterize the hydration and/or solvation shell of myoglobin in aqueous solutions of up to 75% v/v glycerol. At glycerol concentrations below ∼40% v/v, the preservation of the hydration shell was dominant, which was reasonably explained by the preferential exclusion of glycerol from the protein surface (preferential hydration). In contrast, at concentrations above 50% v/v, the partial penetration or replacement of glycerol into or with hydration-shell water (neutral solvation by glycerol) was gradually promoted. WAXS results quantitatively demonstrated the neutral solvation, in which the replacement of hydrated water by glycerol was proportional to the volume fraction of glycerol in the solvent multiplied by an exchange rate (ß ≤ 1). These phenomena were confirmed by small-angle neutron scattering measurements. The observed WAXS data covered the entire hierarchical structure of myoglobin, ranging from tertiary to secondary structures. We separately analyzed the effect of glycerol on the thermal stability of myoglobin at each hierarchical structural level. The thermal transition midpoint temperature at each hierarchical structural level was raised depending on the glycerol concentration, with enhanced transition cooperativeness between different hierarchical structural levels. The onset temperature of the helix-to-cross ß-sheet transition (the initial process of amyloid formation) was evidently elevated. However, oligomerization connected to fibril formation was suppressed, even at a low glycerol concentration.

Structure of liposome encapsulating proteins characterized by X-ray scattering and shell-modeling.

Lipid liposomes are promising drug delivery systems because they have superior curative effects owing to their high adaptability to a living body. Lipid liposomes encapsulating proteins were constructed and the structures examined using synchrotron radiation small- and wide-angle X-ray scattering (SR-SWAXS). The liposomes were prepared by a sequential combination of natural swelling, ultrasonic dispersion, freeze-throw, extrusion and spin-filtration. The liposomes were composed of acidic glycosphingolipid (ganglioside), cholesterol and phospholipids. By using shell-modeling methods, the asymmetric bilayer structure of the liposome and the encapsulation efficiency of proteins were determined. As well as other analytical techniques, SR-SWAXS and shell-modeling methods are shown to be a powerful tool for characterizing in situ structures of lipid liposomes as an important candidate of drug delivery systems.

Improvements toward highly accurate diffraction experiments at the macromolecular micro-crystallography beamline BL-17A.

BL-17A is a macromolecular crystallography beamline dedicated to diffraction experiments conducted using micro-crystals and structure determination studies using a lower energy X-ray beam. In these experiments, highly accurate diffraction intensity measurements are definitively important. Since this beamline was constructed, the beamline apparatus has been improved in several ways to enable the collection of accurate diffraction data. The stability of the beam intensities at the sample position was recently improved by modifying the monochromator. The diffractometer has also been improved. A new detector table was installed to prevent distortions in the diffractometer's base during the repositioning of the diffractometer detector. A new pinhole system and an on-axis viewing system were installed to improve the X-ray beam profile at the sample position and the centering of tiny crystal samples.

Significantly High Melting Temperature of Homopolymer Crystals Obtained in a Poly(l-Lactic Acid)/Poly(d-Lactic Acid) (50/50) Blend.

The isothermal crystallization of a poly(l-lactic acid) (PLLA)/poly(d-lactic acid) (PDLA) (50/50) blend, neat PLLA, and neat PDLA, was studied at different crystallization temperatures (110 °C, 150 °C, 170 and 180 °C) for different durations (1-300 min) by means of differential scanning calorimetry (DSC), polarized optical microscope (POM) observations, and time-resolved wide-angle X-ray diffraction (WAXD). The effects of both the isothermal crystallization temperature and the duration of the isothermal crystallization were investigated for the blend specimens fully crystallized at these crystallization temperatures. The formation of homopolymer crystallites (HC) was confirmed at the isothermal crystallization temperature of 170 °C, which was previously considered too high for its formation, after 70 min had elapsed from the temperature stabilization. Moreover, the melting temperature of the formed HC was found to be significantly high (Tm = 187.5 °C) compared to the one obtained during the nonisothermal DSC measurement of the same specimen of the PLLA/PDLA (50/50) blend, as well as the neat PLLA and PDLA specimens. To the best of our knowledge, this extremely high Tm (=187.5 °C) for HC has never been reported before.

Alignment and use of microbeam with full-field x-ray microscopes.

Demonstration tests of the alignment of Fresnel zone plate focusing optics using a full-field x-ray microscope and microbeam x-ray diffraction measurements combined with the full-field x-ray microscope were performed. It was confirmed that the full-field x-ray microscope enables direct two-dimensional observation of a microbeam with sub-micrometer spatial resolution. This allowed visualization of the misalignment of the focusing optics, resulting in accurate alignment of the optics within a short time. In addition, the microscope could be used to observe the sample as well as the microbeam, which enabled clarification of the position and two-dimensional shape of the microbeam on the sample. This realized a measurement procedure that a 100-µm-size sample was imaged with sub-micrometer spatial resolution, and then, microbeam-use measurements were performed for only the region of interest determined by the microscope, which has been difficult with conventional microbeam applications. The combination of observations by a full-field x-ray microscope and measurements using a microbeam is expected to open a new style of measurement.

X-ray zooming microscopy with two Fresnel zone plates.

We propose a variable-magnification full-field x-ray microscope using two Fresnel zone plates (FZPs). By moving the positions of the two FZPs, the magnification can be continuously changed even if the sample and camera positions are fixed. It was demonstrated that the magnification can be changed in the range of 25-150× using a hard x-ray beam at 14.4 keV. Using the first FZP as a convex lens and the second FZP as a concave lens, high magnification can be achieved at a short camera length. Even under the condition of a camera length of about 7 m, a magnification higher than 300× was achieved, and a line and space pattern with a pitch of 40 nm was observed at 10 keV. By inserting a knife edge at an appropriate position in the optical system, a phase-contrast image can be easily obtained, which is useful for soft-tissue observation of biological samples.

UV LED lighting for automated crystal centring.

A direct outcome of the exponential growth of macromolecular crystallography is the continuously increasing demand for synchrotron beam time, both from academic and industrial users. As more and more projects entail screening a profusion of sample crystals, fully automated procedures at every level of the experiments are being implemented at all synchrotron facilities. One of the major obstacles to achieving such automation lies in the sample recognition and centring in the X-ray beam. The capacity of UV light to specifically react with aromatic residues present in proteins or with DNA base pairs is at the basis of UV-assisted crystal centring. Although very efficient, a well known side effect of illuminating biological samples with strong UV sources is the damage induced on the irradiated samples. In the present study the effectiveness of a softer UV light for crystal centring by taking advantage of low-power light-emitting diode (LED) sources has been investigated. The use of UV LEDs represents a low-cost solution for crystal centring with high specificity.

Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T.

Head-to-tail polymerization of tropomyosin is crucial for its actin binding, function in actin filament assembly, and the regulation of actin-myosin contraction. Here, we describe the 2.1 A resolution structure of crystals containing overlapping tropomyosin N and C termini (TM-N and TM-C) and the 2.9 A resolution structure of crystals containing TM-N and TM-C together with a fragment of troponin-T (TnT). At each junction, the N-terminal helices of TM-N were splayed, with only one of them packing against TM-C. In the C-terminal region of TM-C, a crucial water in the coiled-coil core broke the local 2-fold symmetry and helps generate a kink on one helix. In the presence of a TnT fragment, the asymmetry in TM-C facilitates formation of a 4-helix bundle containing two TM-C chains and one chain each of TM-N and TnT. Mutating the residues that generate the asymmetry in TM-C caused a marked decrease in the affinity of troponin for actin-tropomyosin filaments. The highly conserved region of TnT, in which most cardiomyopathy mutations reside, is crucial for interacting with tropomyosin. The structure of the ternary complex also explains why the skeletal- and cardiac-muscle specific C-terminal region is required to bind TnT and why tropomyosin homodimers bind only a single TnT. On actin filaments, the head-to-tail junction can function as a molecular swivel to accommodate irregularities in the coiled-coil path between successive tropomyosins enabling each to interact equivalently with the actin helix.

Stress-Strain and Stress-Relaxation Behaviors of Solution-Coated Layers Composed of Block Copolymers Mixed with Tackifiers.

The relationship between the mechanical properties and the structure of block copolymers mixed with tackifiers whose relative solubility to the respective components of block copolymers differs was examined. Coated layers were prepared by solution coating using a block copolymer composed of polystyrene (PS) and polyisoprene (PI), which forms spherical microdomains of PS in the PI matrix, mixed with three types of tackifiers: aliphatic (C5) resin, aliphatic-aromatic (C5-C9) resin, and rosin ester (RE) resin. Furthermore, the correlation between the changes in the nanostructure and mechanical properties including the stress-relaxation behaviors was clarified by two-dimensional small-angle X-ray scattering measurement. The amount of the PI-bridge conformation in the case of C5 resin is the lowest, resulting in the lowest stress. On the contrary, the largest amount of RE resin was solubilized in the PS phase so that it can be considered that pulling out of the PS chains took place easily. We were able to explain the stress-relaxation behavior by fitting with the three-component exponent functions. The triple exponential decay functions indicate the hierarchy of the structures that are the origins of the ″fast mode″ relating to the local relaxation due to the rotation of the repeating unit of polymer chains; the ″intermediate mode″ of the disentanglement of the mid-PI chains; and the ″slow mode″ relating to, in this particular case, pulling out of the PS chains from the PS sphere.

Crystallization of small proteins assisted by green fluorescent protein.

The generation of crystal lattice contacts by proteinaceous tags fused to target proteins is an attractive approach to aid in the crystallization of otherwise intractable proteins. Here, the use of green fluorescent protein (GFP) fusions for this purpose is demonstrated, using ubiquitin and the ubiquitin-binding motif (UBM) of Y-family polymerase ι as examples. The structure of the GFP-ubiquitin fusion protein revealed that the crystal lattice was formed by GFP moieties. Ubiquitin was accommodated in the lattice through interactions with the peripheral loops of GFP. However, in the GFP-UBM fusion crystal UBM formed extensive interactions with GFP and these interactions, together with UBM dimerization, mediated the crystal packing. Interestingly, the tyrosine residues that are involved in mediating crystal contacts in both GFP-ubiquitin and GFP-UBM crystals are arranged in a belt on the surface of the ß-barrel structure of GFP. Therefore, it is likely that GFP can assist in the crystallization of small proteins and of protein domains in general.

Structural basis for transcription inhibition by tagetitoxin.

Tagetitoxin (Tgt) inhibits transcription by an unknown mechanism. A structure at a resolution of 2.4 A of the Thermus thermophilus RNA polymerase (RNAP)-Tgt complex revealed that the Tgt-binding site within the RNAP secondary channel overlaps that of the stringent control effector ppGpp, which partially protects RNAP from Tgt inhibition. Tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to Tgt in vitro. Importantly, a Tgt phosphate, together with two active site acidic residues, coordinates the third Mg(2+) ion, which is distinct from the two catalytic metal ions. We show that Tgt inhibits all RNAP catalytic reactions and propose a mechanism in which the Tgt-bound Mg(2+) ion has a key role in stabilization of an inactive transcription intermediate. Remodeling of the active site by metal ions could be a common theme in the regulation of catalysis by nucleic acid enzymes.

[Advancement of synchrotron radiation protein crystallography in the targeted protein research program: beamline developments at the photon factory].

The Targeted Protein Research Program (TPRP) started in 2007 as a sequel of the Protein 3000 Project which lasted from 2002 to 2007. In the new project, four cores, Protein Production, Structure Analysis, Control of Protein Functions with Compounds, and Informatics, have been established as focus of methodology developments critical for functional and structural studies by the target protein research teams. Within the "Analysis Core" synchrotron radiation plays a pivotal role providing X-ray beams for structural analyses of the target proteins. The two large Japanese synchrotron radiation facilities, SPring-8 and Photon Factory (PF), along with three protein crystallography groups from Hokkaido, Kyoto and Osaka Universities have teamed up to develop two complementary micro-beam beamlines, one on each synchrotron site, and associated technologies for cutting edge structural biology research. At the PF, there are 5 operational beamlines which are equipped with state-of-the-art instrumentation for high-throughput protein crystallography experiments. Within the TPRP framework, the PF is developing a micro-focus beamline optimized for a lower energy single anomalous diffraction (SAD) experiment. This will be particularly useful for structure determination of difficult protein targets for which heavy atom derivatives or selenomethionine substitution does not work and other standard phasing methods fail to give structure solutions. This will augment the capabilities of the PF structural biology beamlines with similar look-and-feel experimental environments.

Short-Distance Intermolecular Correlations of Mono- and Disaccharides in Condensed Solutions: Bulky Character of Trehalose.

Organisms with tolerance to extreme environmental conditions (cryptobiosis) such as desiccation and freezing are known to accumulate stress proteins and/or sugars. Trehalose, a disaccharide, has received considerable attention in the context of cryptobiosis. It has already been shown to have the highest glass-transition temperature and different hydration properties from other mono- and disaccharides. In spite of the importance of understanding cryptobiosis by experimentally clarifying sugar-sugar interactions such as the clustering in concentrated sugar solutions, there is little direct experimental evidence of sugar solution structures formed by intermolecular interactions and/or correlation. Using a wide-angle X-ray scattering method with the real-space resolution from ∼3 to 120 Å, we clarified the characteristics of the structures of sugar solutions (glucose, fructose, mannose, sucrose, and trehalose), over a wide concentration range of 0.05-0.65 g/mL. At low concentrations, the second virial coefficients obtained indicated the repulsive intermolecular interactions for all sugars and also the differences among them depending on the type of sugar. In spite of the presence of such repulsive force, a short-range intermolecular correlation was found to appear at high concentrations for every sugar. The concentration dependence of the observed scattering data and p(r) functions clearly showed that trehalose prefers a more disordered arrangement in solution compared to other sugars, that is, bulky arrangement. The present findings will afford a new insight into the molecular mechanism of the protective functions of the sugars relevant to cryptobiosis, particularly that of trehalose.

Structural Evolution in Isothermal Crystallization Process of Poly(L-lactic acid) Enhanced by Silk Fibroin Nano-Disc.

The nucleating effect of silk fibroin nano-disc (SFN) on the crystallization behavior of poly(L-lactic acid) (PLLA) was investigated by simultaneous synchrotron small- and wide-angle X-ray scattering measurements. For the isothermal crystallization at 110 °C from the melt, the induction period of the PLLA specimens containing 1% SFN was reduced compared to that of the neat specimens, indicating the acceleration of the nucleation of PLLA. The final degree of crystallinity was also increased, and the crystallization half-time was decreased, which indicates that the overall crystallization process was accelerated. Furthermore, the final value of the crystallite size (the lateral size of the crystalline lamella) was slightly lower for the specimens containing 1% SFN than that for the PLLA neat specimen, although the crystallites started growing much earlier. However, it was found that there was no effect of SFN on the growth rate of the crystallite size. The lamellar thickening process was also accelerated with a clear overshooting phenomenon with the inclusion of 1% SFN. As for the polymorphism, the α' phase is dominant with about 96%, but a small amount of the α phase (4%) is found to exist. It was found that the SFN can also accelerate the formation of the minor α phase as well as the major α' phase.

Structure of Ultrafine Bubbles and Their Effects on Protein and Lipid Membrane Structures Studied by Small- and Wide-Angle X-ray Scattering.

Ultrafine bubbles (UFBs) are defined as small gas-filled bubbles with a diameter smaller than 1 µm. UFBs are stable for several weeks in aqueous solutions due to their small size. Although the mechanism of the stability of UFBs remains under intensive investigation, industrial applications of UFBs have recently arisen in various fields such as agricultural and fishery industries and medical therapy. The relevance of ions (protons and hydroxide anions) in UFB solutions has been discussed; however, the mechanism underlying the behavior of UFBs is still ambiguous and there is little direct evidence of the effect of UFBs on biological materials. This study deals with gaseous UFBs in aqueous solutions. Using small- and wide-angle X-ray scattering, we have investigated the structures of UFBs (air-UFBs, O2-UFBs, and N2-UFBs) and their effect on protein and lipid membrane structures. X-ray scattering and modeling data suggest that UFBs present a dynamic diffusive boundary (interface) due to the continuous release and absorption of gas. UFBs were found to not affect the structures of proteins at all hierarchal structure levels (from quaternary to tertiary, to internal, to secondary), whereas they did influence the packing and fluctuation of the hydrocarbon chains in the liposomes but not their shapes.

Preferential Intercalation of Human Amyloid-ß Peptide into Interbilayer Region of Lipid-Raft Membrane in Macromolecular Crowding Environment.

This study focuses on the interaction of human amyloid ß-peptide (Aß) with a lipid-raft model membrane under macromolecular crowding conditions that mimic the intracellular environment. Aß is central to the development of Alzheimer's disease (AD) and has been studied extensively to determine the molecular mechanisms of Aß-induced cellular dysfunctions underlying the pathogenesis of AD. According to evidence from spectroscopic studies, ganglioside clusters are key to the fibrillization process of Aß. Gangliosides are a major component of glycosphingolipids and are acidic lipids of the central nervous system known to form so-called lipid rafts. In this study, the small unilamellar vesicle (SUV) membrane, composed of monosialogangliosides, cholesterol, and 1,2-dipalmitoyl- sn-glycero-3-phosphocholine, did not show any structural changes after the addition of Aß under noncrowding conditions. However, the addition of Aß under crowding conditions induced shape deformation and aggregation to SUV resulting in multilamellar stacking. The time evolution of the lamellar peak suggested the preferential cohesion or intercalation of the Aß peptide into the interbilayer region. This phenomenon was only observed at the gel (Lß) phase. These results suggest that an intracellular crowding environment promotes Aß-membrane interaction and a selective accumulation of Aß peptides into the interbilayer regions.