Structure of the TRAF4 TRAF domain with a coiled-coil domain and its implications for the TRAF4 signalling pathway.

The TNF receptor-associated factor (TRAF) proteins are structurally similar scaffold proteins that mediate between members of the TNF receptor (TNFR) family and downstream effector molecules such as kinases in the immune signalling pathway. Seven TRAFs have been identified, including TRAF4, which is a unique member that participates in many ontogenic processes, including nerve-system development. TRAFs commonly contain the TRAF domain, which mediates interaction with target receptors and effectors. As a first step towards elucidating the molecular mechanisms of the TRAF4-mediated signalling pathway, the first crystal structure of the human TRAF4 TRAF domain with a coiled-coil domain is reported at 2.3 Šresolution.

A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily.

The Death Domain (DD) superfamily, which is one of the largest classes of protein interaction modules, plays a pivotal role in apoptosis, inflammation, necrosis and immune cell signaling pathways. Because aberrant or inappropriate DD superfamily-mediated signaling events are associated with various human diseases, such as cancers, neurodegenerative diseases and immunological disorders, the studies in these fields are of great biological and clinical importance. To facilitate the understanding of the molecular mechanisms by which the DD superfamily is associated with biological and disease processes, we have developed the DD database (http://www.deathdomain.org), a manually curated database that aims to offer comprehensive information on protein-protein interactions (PPIs) of the DD superfamily. The DD database was created by manually curating 295 peer-reviewed studies that were published in the literature; the current version documents 175 PPI pairs among the 99 DD superfamily proteins. The DD database provides a detailed summary of the DD superfamily proteins and their PPI data. Users can find in-depth information that is specified in the literature on relevant analytical methods, experimental resources and domain structures. Our database provides a definitive and valuable tool that assists researchers in understanding the signaling network that is mediated by the DD superfamily.

Preliminary X-ray crystallographic studies of the short form of the human TRAF4 TRAF domain.

TNF (tumour necrosis factor) receptor-associated factor 4 (TRAF4) is a unique TRAF protein that participates in morphogenetic and developmental function and cell migration. TRAF-family proteins contain a TRAF domain for target interaction. In this study, the short form of the human TRAF4 TRAF domain, corresponding to amino acids 290-462, was overexpressed in Escherichia coli using engineered C-terminal His tags. The short form of the TRAF4 TRAF domain was purified to homogeneity and crystallized at 293 K. Finally, X-ray diffraction data were collected to a resolution of 4.2 Å from a crystal belonging to the hexagonal space group P32, with unit-cell parameters a = b = 147.17, c = 202.69 Å.

Preliminary X-ray crystallographic studies of the TRAF domain of human TRAF4.

TNF receptor-associated factor (TRAF) proteins were initially identified as tumour necrosis factor receptor (TNFR)-interacting proteins that perform critical functions in the regulation of inflammation, antiviral responses and apoptosis. Although TRAF4 is a canonical TRAF protein, it contains a unique domain boundary and functions differently in the cell. In this study, the human TRAF4 TRAF domain, corresponding to amino acids 290-470, was overexpressed in Escherichia coli using engineered C-terminal His tags. The TRAF4 TRAF domain was then purified to homogeneity and crystallized at 293 K. Finally, X-ray diffraction data were collected to a resolution of 2.3 Šfrom a crystal belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 58.9, b = 87.9, c = 117.3 Å, α = ß = γ = 90°.

Fabrication of N-doped porous ZnO nanosheets by annealing Zn films at low temperatures.

In this work, the direct growth of nitrogen (N)-doped porous ZnO nanosheets at low temperatures via the conventional plasma-enhanced chemical vapor deposition (PECVD) method is presented. The growth was based on the thermal annealing of a Zn film composed of Zn nanosheets in oxygen and nitrogen vapors produced via PECVD, with N2O as a source gas. The ZnO nanosheets with well-defined crystallinity were found to have been grown at temperatures over 280 degrees C, and to have had N-doped porous structures. The ZnO nanosheets grown at 380 degrees C were shown to have had a mean thickness of about 5 nm, a mean pore diameter of about 13.3 nm, and 6.7% porosity, and exhibited Raman and photoluminescence peaks characteristic of N-doped ZnO. It is suggested that the ZnO nanosheets were likely formed through their direct oxidation.

Crystal structure of Rab6A'(Q72L) mutant reveals unexpected GDP/Mg²âº binding with opened GTP-binding domain.

The Ras small G protein-superfamily is a family of GTP hydrolases whose activity is regulated by GTP/GDP binding states. Rab6A, a member of the Ras superfamily, is involved in the regulation of vesicle trafficking, which is critical for endocytosis, biosynthesis, secretion, cell differentiation and cell growth. Rab6A exists in two isoforms, termed RabA and Rab6A'. Substitution of Gln72 to Leu72 (Q72L) at Rab6 family blocks GTP hydrolysis activity and this mutation usually causes the Rab6 protein to be constitutively in an active form. Here, we report the crystal structure of the human Rab6A'(Q72L) mutant form at 1.9Å resolution. Unexpectedly, we found that Rab6A'(Q72L) possesses GDP/Mg(2+) in the GTP binding pockets, which is formed by a flexible switch I and switch II. Large conformational changes were also detected in the switch I and switch II regions. Our structure revealed that the non-hydrolysable, constitutively active form of Rab6A' can accommodate GDP/Mg(2+) in the open conformation.

Crystallization and preliminary X-ray crystallographic studies of Rab6A'(Q72L): a GTP-locked form.

Rab6A, a member of the Ras superfamily of small G proteins, is involved in the regulation of vesicle trafficking, which is critical for endocytosis, cell differentiation and cell growth. Rab6A can exist in two isoforms termed Rab6A and Rab6A'. The substitution of Gln72 by Leu (Q72L) in the Rab6A family blocks GTP-hydrolysis activity, and this mutation usually causes the Rab6A protein to be in a constitutively active form. In this study, in order to understand the functional uniqueness of Rab6A' and the molecular mechanism of the control of activity by GTP and GDP from the crystal structure, a Rab6A'(Q72L) mutant form was overexpressed in Escherichia coli with an engineered N-terminal His tag. Rab6A'(Q72L) was then purified to homogeneity and crystallized at 293 K. X-ray diffraction data were collected to a resolution of 1.9 Å from a crystal belonging to space group P22(1)2(1) with unit-cell parameters a = 36.84, b = 96.78, c = 109.99 Å. The asymmetric unit was estimated to contain two molecules.

Crystallization and preliminary X-ray crystallographic studies of ß-transaminase from Mesorhizobium sp. strain LUK.

ß-Transaminase (ß-TA) catalyzes the transamination reaction between ß-aminocarboxylic acids and keto acids. This enzyme is a particularly suitable candidate for use as a biocatalyst for the asymmetric synthesis of enantiochemically pure ß-amino acids for pharmaceutical purposes. The ß-TA from Mesorhizobium sp. strain LUK (ß-TAMs) belongs to a novel class in that it shows ß-transaminase activity with a broad and unique substrate specificity. In this study, ß-TAMs was overexpressed in Escherichia coli with an engineered C-terminal His tag. ß-TAMs was then purified to homogeneity and crystallized at 293 K. X-ray diffraction data were collected to a resolution of 2.5 Šfrom a crystal that belonged to the orthorhombic space group C222(1), with unit-cell parameters a = 90.91, b = 192.17, c = 52.75 Å.

Synthesis of cobalt-based nanocrystal layer in silicon dioxide for nonvolatile memory applications.

Cobalt silicide (CoSi) nanocrystal (NC) layer distributed within narrow spatial region is synthesized by thermal annealing of a sandwich structure comprised of a thin cobalt (Co) film sandwiched between two silicon-rich oxide (SiO(x)) layers. It is shown that the size of the CoSi NCs can be controlled by varying the Co film thickness, an increase in the size with increasing thickness. Capacitance-voltage (C-V) measurements on a test metal/oxide/semiconductor (MOS) structure with floating gate based on CoSi NCs of 3.8 nm in diameter and 1.4 x 10(12) cm2 in density are shown to have C-V characteristics suitable for nonvolatile memory applications, including a C-V memory window of about 9.5 V for sweep voltages between -15 V and +8, a retention time >10(8) s, and an endurance > 10(6) program/erase cycles.

Fabrication of Sn@Al2O3 Core-shell Nanoparticles for Stable Nonvolatile Memory Applications.

Sn@Al2O3 core-shell nanoparticles (NPs) with narrow spatial distributions were synthesized in silicon dioxide (SiO2). These Sn@Al2O3 core-shell NPs were self-assembled by thermally annealing a stacked structure of SiOx/Al/Sn/Al/SiOx sandwiched between two SiO2 layers at low temperatures. The resultant structure provided a well-defined Sn NP floating gate with a SiO2/Al2O3 dielectric stacked tunneling barrier. Capacitance-voltage (C-V) measurements on a metal-oxide-semiconductor (MOS) capacitor with a Sn@Al2O3 core-shell NP floating gate confirmed an ultra-high charge storage stability, and the multiple trapping of electron at the NPs, as expected from low-k/high-k dielectric stacked tunneling layers and metallic NPs, respectively.

Molecular mechanism of constitutively active Rab11A was revealed by crystal structure of Rab11A S20V.

Rab11A is a small GTP-binding protein involved in the regulation of vesicle trafficking during recycling of endosomes. Substitution of S20 to V (S20V) at Rab11A inhibits the GTP hydrolysis activity of Rab11A. This mutation is known to be constitutively in an active form. Here, we report the crystal structure of the human Rab11A S20V mutant form complexed with GTP at a resolution of 2.4 Å. Without adding any substrate, Rab11A contained non-hydrolyzed natural substrate GTP in the nucleotide binding pocket with Mg(2+). In our observations, substituted V20 of Rab11A was found to interfere with proper localization of the water molecule, which mediated GTP hydrolysis, resulting in GTP being locked in an active form of Rab11A S20V.

A novel scheme for nanoparticle steering in blood vessels using a functionalized magnetic field.

Magnetic drug targeting is a drug delivery approach in which therapeutic magnetizable particles are injected, generally into blood vessels, and magnets are then used to guide and concentrate them in the diseased target organ. Although many analytical, simulation, and experimental studies on capturing schemes for drug targeting have been conducted, there are few studies on delivering the nanoparticles to the target region. Furthermore, the sticking phenomenon of particles to vessels walls near the injection point, and far from the target region, has not been addressed sufficiently. In this paper, the sticking issue and its relationship to nanoparticle steering are investigated in detail using numerical simulations. For wide ranges of blood vessel size, blood velocity, particle size, and applied magnetic field, three coefficient numbers are uniquely generalized: vessel elongation, normal exit time, and force rate. With respect these new parameters, we investigated particle distribution trends for a Y-shaped channel and computed ratios of correctly guided particles and particles remaining in the vessel. We found that the sticking of particles to vessels occurred because of low blood flow velocity near the vessel walls, which is the main reason for low targeting efficiency when using a constant magnetic gradient. To reduce the sticking ratio of nanoparticles, we propose a novel field function scheme that uses a simple time-varying function to separate the particles from the walls and guide them to the target point. The capabilities of the proposed scheme were examined by several simulations of both Y-shaped channels and realistic three-dimensional (3-D) model channels extracted from brain vessels. The results showed a significant decrease in particle adherence to walls during the delivery stage and confirmed the effectiveness of the proposed magnetic field function method for steering nanoparticles for targeted drug delivery.

Purification, crystallization and X-ray crystallographic analysis of human RAB11(S20V), a constitutively active GTP-binding form.

RAB11, a member of the Ras superfamily of small G proteins, is involved in the regulation of vesicle trafficking during endosome recycling. Substitution of Ser20 by Val20 in Rab11 [RAB11(S20V)] inhibits its GTP hydrolysis activity and produces a constitutively active GTP-binding form. In this study, the RAB11(S20V) mutant was overexpressed in Escherichia coli with an engineered C-terminal His tag. RAB11(S20V) was then purified to homogeneity and was crystallized at 293 K. X-ray diffraction data were collected to a resolution of 2.4 Šfrom a crystal belonging to space group I4, with unit-cell parameters a = 74.11, b = 74.11, c = 149.44 Å. The asymmetric unit was estimated to contain two molecules of RAB11(S20V).

The changes in particle charge distribution during rapid growth of particles in the plasma reactor.

The changes in particle charging were investigated during the rapid growth of particles in the plasma reactor by the discrete-sectional model and the Gaussian charge distribution function. The particle size distribution becomes bimodal in the plasma reactor and most of the large particles are charged negatively, but some fractions of small particles are in a neutral state or even charged positively. As the particles accumulate in the plasma reactor, the amount of electrons absorbed onto the particles increases, while the electron concentration in the plasma decreases. As the mass generation rate of small particles (monomers) decreases or as the initial electron concentration increases, the electron concentration in the plasmas increases and the particle charge distribution is shifted in the negative direction and the fraction of particles charged negatively and the average number of electrons per particle increase. With the decrease in monomer diameter, the electron concentration decreases in the beginning of plasma discharge, but, later, increases. For high mass generation rate of monomers or for low initial electron concentration or for small monomer diameter, the fraction of particles in a neutral state increases and the particle size distribution becomes broader.

Modeling of marine litter drift and beaching in the Japan Sea.

Characteristics of drift and beaching of floating marine litter in the Japan Sea are examined numerically using the reanalysis data of the Japan Sea Forecasting System of Kyushu University. The residence time of model marine litter deployed uniformly over the surface of the Japan Sea strongly depends on the buoyancy ratio. However, almost all litter beaches or flows out through straits within 3years. Experiments with inputs of litter imposed at large cities and the Tsushima Straits as well as river basins of the Japan Sea exhibit a good agreement with beach surveys with regard to country ratios of beached litter along the Japanese coast in cases of lighters. In a case of lighter, almost all lighters originating from Japan beach along the Japanese coast, while almost all lighters originating from a country surrounding the Japan Sea except Japan beach along the coast of that country and the Japanese coast.