Interaction of anti-aggregation agent dimethylethylammonium propane sulfonate with acidic fibroblast growth factor

Prevention of aggregation is critical for analyzing protein structure. Non-detergent sulfobetaines (NDSBs) are known to prevent protein aggregation, but the molecular mechanisms of their anti-aggregation effect are poorly understood. To elucidate the underlying mechanisms, we analyzed the effects of dimethylethylammonium propane sulfonate (NDSB-195) on acidic fibroblast growth factor (aFGF). NDSB-195 (0.5M) increased both aggregation and denaturation temperatures of aFGF by 4 degrees C. Chemical shift perturbation analyses indicated that many affected residues were located at the junction between a beta-strand (or 3(10)-helix) and a loop, irrespective of the chemical properties of the residue. The apparent dissociation constants of the interaction ranged from 0.04 to 3M, indicating weak interactions between NDSB and protein molecules.     

Shimalactone Biosynthesis Involves Spontaneous Double Bicyclo-Ring Formation with 8π-6π Electrocyclization

Shimalactones A and B are neuritogenic polyketides possessing characteristic oxabicyclo[2.2.1]heptane and bicyclo[4.2.0]octadiene ring systems that are produced by the marine fungus Emericella variecolor GF10. We identified a candidate biosynthetic gene cluster and conducted heterologous expression analysis. Expression of ShmA polyketide synthase in Aspergillus oryzae resulted in the production of preshimalactone. Aspergillus oryzae and Saccharomyces cerevisiae transformants expressing ShmA and ShmB produced shimalactones A and B, thus suggesting that the double bicyclo-ring formation reactions proceed non-enzymatically from preshimalactone epoxide. DFT calculations strongly support the idea that oxabicyclo-ring formation and 8π-6π electrocyclization proceed spontaneously after opening of the preshimalactone epoxide ring through protonation. We confirmed the formation of preshimalactone epoxide in vitro, followed by its non-enzymatic conversion to shimalactones in the dark.     

Direct Estimation of the Surface Location of Immobilized Functional Groups for Concerted Catalysis Using a Probe Molecule

The location of active sites during concerted catalysis by a metal complex and tertiary amine on a SiO₂ surface is discussed based on the interaction between the functionalized SiO₂ surface and a probe molecule, p‐formyl phenylboronic acid. The interactions of the probe molecule with the surface functionalities, diamine ligand, and tertiary amine, were analyzed by FT‐IR and solid‐state ¹³C and ¹¹B MAS NMR. For the catalyst exhibiting high 1,4‐addition activity, the diamine ligand and tertiary amine base exist in closer proximity than in the catalyst with low activity.     

Tetrahedral Oligothiophenes; Synthesis,X‐ray Analysis,and Optoelectronic Properties of Highly Symmetrical, 3D‐Branched Oligothiophenes

Tetrakis(bithienyl)methane and tetrakis(terthienyl)methane have been synthesized from tetrakis(2‐thienyl)methane by use of Suzuki–Miyaura coupling as a key reaction. Their trimethylsilyl (TMS) derivatives are also synthesized. X‐ray analysis reveals that each oligothiophene moiety tends to adopt anti‐conformations and show relatively small torsion angles between the adjacent thiophene rings. While the longest absorption maxima of these tetrakis(oligothienyl)methanes exhibit only a slight bathochromic shift compared to the corresponding linear oligothiophene derivative, tetrakis(bithienyl)methane and its TMS derivative exhibit an appreciable red‐shift in their fluorescence spectra. The intramolecular interaction between thienyl groups of tetrakis(2‐thienyl)methane is supported by DFT calculation.     

Design of a doubly-curved crystal to improve X-ray fluorescence analysis of aerosol particles

Doubly-curved crystals (DCCs) can be very useful devices to focus and monochromatize radiation from an X-ray tube or a synchrotron, especially for X-ray fluorescence analysis. However, production of a DCC is somewhat difficult. In this paper we will present some basic theory about DCC geometries, different ways of DCC production and methods to test the quality of the DCCs.     

Distribution and Dynamic Pathway of Selenium Species in Selenium-deficient Mice Injected with (82)Se-enriched Selenite

In order to elucidate Se metabolism in a living body, (82)Se-enriched selenite was injected intravenously into mice fed Se-adequate and -deficient diets. We studied the time-dependent changes in the distribution of the labeled Se in organs, red blood cells, and plasma. The total Se was determined by flow-injection ICPMS, and Se speciation analysis was conducted by micro-affinity chromatography coupled with low-flow ICPMS. Total Se in almost all organs, including liver, showed the maximum at 1 h after injection. From speciation analysis, exogenous (82)Se as Se-containing proteins other than selenoprotein P (Sel-P) (selenium containing albumin (SeAlb) and extra cellular glutathione peroxidase (eGPx)), peaked at 1 h and quickly decreased from 1 to 6 h after injection, whereas that as Sel-P, peaked at 6 h, and gradually decreased from 6 to 72 h after injection. We found that there were two pathways for the transfer of Se in mice; one was as SeAlb until 1 h after injection, and the other was as Sel-P from 6 to 72 h after injection.     

Imaging of Oxygen Diffusion in Individual Platinum/Ce2Zr2Ox Catalyst Particles During Oxygen Storage and Release

The spatial distribution of Ce³⁺ and Ce⁴⁺ in each particle of Ce₂Zr₂O_x in a three‐way conversion catalyst system was successfully imaged during an oxygen storage/release cycle by scanning X‐ray absorption fine structure (XAFS) using hard X‐ray nanobeams. For the first time, nano‐XAFS imaging visualized and identified the modes of non‐uniform oxygen diffusion from the interface of Pt catalyst and Ce₂Zr₂O_x support and the active parts in individual catalyst particles.     

DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations

Molecular orbital calculations of the complex between DNA-ERE (estrogen response element) and ER (estrogen receptor)-DBD (DNA-binding domain) were performed using the fragment molecular orbital (FMO) method, which enables large-scale MO (molecular orbital) calculations by reducing the computational cost and by significantly increasing efficiency for parallel computation. Such a large system, which contains 3354 atoms, is impractical via conventional MO methods due to the immense computational cost. Details of the interaction between DNA-ERE and ER-DBD were revealed in this study as follows by using the FMO calculations to analyze the interfragment interaction energies (IFIEs) and the electrostatic potentials (ESPs). An area with a high positive ESP is identified on the DNA-binding side of ER-DBD and is the main driving force behind access to the DNA. The position of the ER-DBD monomer can be fixed on a phosphate group of DNA-ERE by the strong electrostatic interactions, whereas the rotation cannot be fixed. In contrast, both the position and rotation of the ER-DBD dimer can be fixed and can therefore form the stable (ER-DBD)2...DNA-ERE complex. Dimerization of the ER-DBD monomers, each of which have a charge of +5 , is mainly due to large attractive interaction energies of the second Zn fragments. The base pairs in the consensus sequence of DNA-ERE interact only with the recognition helix located in the major groove due to the large shielding effect of the phosphate groups of DNA. The recognition helix has weaker interactions with the base pairs than the electrostatic interactions with the phosphate groups. Thus, the DNA-binding machinery of the ER-DBD dimer, which can secure the recognition helix in the major groove of DNA, is crucial for interactions between the recognition helix and base pairs.     

Fano 3-folds with divisible anticanonical class

We show the nonvanishing of H ⁰(X,−K _X ) for any a Fano 3-fold X for which −K _X is a multiple of another Weil divisor in Cl(X). The main case we study is Fano 3-folds with Fano index 2: that is, 3-folds X with rank Pic(X)=1, -factorial terminal singularities and −K _X  = 2A for an ample Weil divisor A. We give a first classification of all possible Hilbert series of such polarised varieties (X,A) and deduce both the nonvanishing of H ⁰(X,−K _X ) and the sharp bound (−K _X )³≥ 8/165. We find the families that can be realised in codimension up to 4.     

Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask technique

A method for the determination of nucleotides based on pressure-assisted capillary electrophoresis-electrospray ionization mass spectrometry (PACE-MS) is described. To prevent multi-phosphorylated species from adsorbing onto the fused-silica capillary, silanol groups were masked with phosphate ions by preconditioning the capillary with the background electrolyte containing phosphate. During preconditioning, nebulizer gas was turned off to avoid contamination of MS detector with phosphate ions. To detect nucleotides using the CE positive mode at a pH 7.5, it was necessary to apply air pressure to the inlet capillary during electrophoresis to supplement the electroosmotic flow (EOF) toward the cathode. Moreover, we exchanged the running electrolyte every analysis using the buffer replenishment system to obtain the required reproducibility. Under the optimized conditions, 14 phosphorylated species such as nucleotides, nicotinamide-adenine dinucleotides and coenzyme A (CoA) compounds were well determined in less than 20 min. The relative standard deviations (n=6) of the method were better than 0.9% for migration times and between 1.7% and 8.1% for peak areas. The detection limits for these species were between 0.5 and 1.7 micromol/L with pressure injection of 50 mbar for 30 s (30 nL) at a signal-to-noise ratio of 3. This approach is robust and quantitative compared to the previous method, and its utility is demonstrated by the analysis of intracellular nucleotides and CoA compounds extracted from Escherichia coli wild type, pfkA and pfkB knockout mutants. The methodology was used to suggest that pfkA is the main functional enzyme.