Coarse‐grained molecular dynamics simulations of protein–ligand binding

Coarse‐grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein–ligand binding processes. We chose two protein–ligand systems, the levansucrase–sugar (glucose or sucrose), and LinB–1,2‐dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand‐binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse‐grained (CG) ligand molecules revealed potential ligand‐binding sites on the protein surfaces other than the real ligand‐binding sites. The ligands bound most strongly to the real ligand‐binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase–sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand‐binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein–ligand binding processes. © 2014 Wiley Periodicals, Inc.     

Lactate biosensors: current status and outlook

Many research efforts over the last few decades have been devoted to sensing lactate as an important analytical target in clinical care, sport medicine, and food processing. Therefore, research in designing lactate sensors is no longer in its infancy and now is more directed toward viable sensors for direct applications. In this review, we provide an overview of the most immediate and relevant developments toward this end, and we discuss and assess common transduction approaches. Further, we critically describe the pros and cons of current commercial lactate sensors and envision how future sensing design may benefit from emerging new technologies.     

Gate control characteristics in GaAs nanometer-scale Schottky wrap gate structures

Gate control characteristics of GaAs-based quantum wire transistors (QWRTrs) controlled by a nanometer-scale Schottky wrap gate (WPG) are investigated theoretically and experimentally. Gate bias dependence of the effective wire width of fabricated WPG QWRTrs determined theoretically as well as experimentally from Landau plots showed that the nanometer-scale WPG controls the potential very tightly near channel pinch-off and that the pinch-off threshold voltage is strongly dependent on the gate length, L_G, when L_G is shorter than 400 nm. The theory based on the three-dimensional (3D) potential simulation pointed out that Fermi level pinning on the semiconductor surface around the WPGs strongly affects the gate controllability in the nanometer-scale Schottky WPG structure.     

Strategy for Molecular Design of Photochromic Diarylethenes Having Thermal Functionality

Thermal reactivities of photochromic diarylethene closed‐ring isomers can be controlled by the introduction of substituents at the reactive positions. Diarylethenes having bulky alkyl groups undergo thermal cycloreversion reactions. When bulky alkoxy groups are introduced, the diarylethenes have both thermal cycloreversion reactivities and low photocycloreversion quantum yields. Such photochromic compounds can be applied to thermally reusable photoresponsive‐image recordings. The thermal cycloreversion reactivity of the closed‐ring isomers can be evaluated using specific steric substituent constants and be correlated with the parameters. By introduction of trimethylsilyl or methoxymethyl groups at the reactive positions, the diarylethene closed‐ring isomers undergo thermal irreversible reactions to produce by‐products at high temperatures. These diarylethenes may be useful for secret‐image recordings. Furthermore, thiophene‐S,S‐dioxidized diarylethenes having secondary alkyl groups at the reactive positions undergo thermal by‐product formation reactions, in addition to the photostability of the colored closed‐ring isomers. Such materials may be used for light‐starting thermosensors. The thermal by‐product formation reactivity can be evaluated by the specific substituent constants and theoretical calculations of quantum chemistry. These results supply the strategy for the molecular design of the photochromic diarylethenes having thermal functionality.

     

Pair Distribution Function from Liquid Jet Nanoparticle Suspension using Femtosecond X-ray Pulses

X-ray scattering data measured on femtosecond timescales at the SACLA X-ray Free Electron Laser (XFEL) facility on a suspension of HfO₂ nanoparticles in a liquid jet were used for pair distribution function (PDF) analysis. Despite a non-optimal experimental setup resulting in a modest Q_max of ~8 Å⁻¹, a promising PDF was obtained. The main features were reproduced when comparing the XFEL PDF to a PDF obtained from data measured at the PETRA III synchrotron light source. Refining structural parameters such as unit cell dimension and particle size from the XFEL PDF provided reliable values. Although the reachable Q_max limited the obtainable information, the present results indicate that good quality PDFs can be obtained on femtosecond timescales if the experimental conditions are further optimized. The study therefore encourages a new direction in ultrafast structural science where structural features of amorphous and disordered systems can be studied.     

Improved method for immunostaining of mucin separated by supported molecular matrix electrophoresis by optimizing the matrix composition and fixation procedure

Mucins are a family of heavily glycosylated high molecular mass proteins that have great potential as novel clinical biomarkers for the diagnosis of various malignant tumors. Supported molecular matrix electrophoresis (SMME) is a new type of membrane electrophoresis that can be used to characterize mucins. In SMME, mucins migrate in a molecular matrix supported by membrane materials. Here, we have developed an immunostaining method for the identification of SMME-separated mucins. The novel method involves stably fixing the mucins onto the SMME membrane and optimizing the molecular matrix for the fixation process. We applied this technique for the detection of MUC1 produced from three cancer cell lines (T47D, HPAF-II and BxPC3) and also analyzed their O-linked glycans by mass spectrometry. Our results revealed that properties of the MUC1 molecules from the three cell lines are different in terms of migrating position in SMME and glycan profile. The present method allows simple and rapid characterization of mucins in terms of both glycans and core proteins. The method will be a useful tool for the exploration of mucin alterations associated with various diseases such as cancer.     

Plasmonic enhancement of gold nanoparticles on photocycloreversion reaction of diarylethene derivatives depending on particle size, distance from the particle surface, and irradiation wavelength

We newly synthesized various sized gold nanoparticles covered with photochromic polymers consisting of diarylethenes with various structures to investigate an effect of the gold nanoparticles on the photocycloreversion reaction of the diarylethene chromophores upon irradiation with visible light. The gold nanoparticles covered with the photochromic polymers exhibited reversible changes in localized surface plasmon resonance (LSPR) absorption along with the photochromic reaction depending on the diameter of the particle, the distance between the gold surface and the chromophore, and the structure of the diarylethene chromophore. The rate of the photocycloreversion reaction of the chromophores around the particle was enhanced by the gold nanoparticles and the degree of the enhancement was affected by the diameter of the particle and the distance from the gold surface, while a structural difference in the diarylethene chromophore had no effect on the degree of the enhancement. The larger enhancement of the photocycloreversion reaction was observed by irradiation at longer wavelength side than visible light corresponding to the LSPR frequency.     

Toward Ultralow-Bandgap Liquid Crystalline Semiconductors: Use of Triply Fused Metalloporphyrin Trimer-Pentamer as Extra-large π-Extended Mesogenic Motifs

In contrast with their dimeric homologue, triply fused zinc porphyrin trimer-pentamer, as extra-large π-extended mesogens, assemble into columnar liquid crystals (LCs) when combined with 3,4,5-tri(dodecyloxy)phenyl side groups (3?P(Zn) -5?P(Zn) , Figure?1). Their LC mesophases develop over a wide temperature range, namely, 41-280?°C (on heating) for 5?P(Zn) , and all adopt an oblique columnar geometry, typically seen in columnar LC materials involving strong mesogenic interactions. These LC materials are characterized by their wide light-absorption windows from the entire visible region up to a near infrared (NIR) region. Such ultralow-bandgap LC materials are chemically stable and serve as hole transporters, in which 5?P(Zn) gives the largest charge carrier mobility (2.4×10(-2) cm?V(-1) s(-1) ) among the series. Despite a big dimensional difference, they coassemble without phase separation, in which the resultant LC materials display essentially no deterioration of the intrinsic conducting properties.