Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations

We investigate the structures of the Hras-GTP and the Hras-GDP complexes in water solvents in order to understand the mechanism of GTP hydrolysis in the Hras-GTP complex. We performed MD simulations of these complexes in order to study the positions and the orientations of water molecules around the guanosine nucleotides. Using trajectories we calculated the angular distribution of water molecules around the most distant phosphorus from guanosine in our previous work. It was shown that water molecules are distributed evenly in GTP, although unevenly in GDP. This suggests that the trigger of GTP hydrolysis is possibly the attack of water molecule to γ?phosphate from the appropriate direction. In this paper, in order to investigate the role of water molecules in GTP hydrolysis in detail, we calculate the orientation of water molecules. The distribution of the orientation is different between GTP and GDP. In order to investigate the cause of this difference, we examine the hydrogen bonds between water molecules and oxygen atom of the most distant phosphate from guanosine. We find that these hydrogen bonds are formed. We also find that the oxygen atom of hydrogen bond is determined by the position of the water molecule of hydrogen bond.     

Effect of glycerol and its analogs on polyhydroxyalkanoate biosynthesis by recombinant Ralstonia eutropha: A quantitative structure–activity relationship study of chain transfer agents

Triglycerides such as plant and vegetable oils are desirable feedstock for the fermentative production of polyhydroxyalkanoate (PHA) because the weight yield of PHA from triglycerides is higher than that obtained from sugars. However, glycerol, a multi-hydroxy component of triglyceride, is known to function as a chain transfer (CT) agent in PHA polymerization, resulting in the formation of low-molecular-weight PHA. In this study, we evaluated how glycerol alters the molecular weight of PHA using recombinant Ralstonia eutropha as a practical host for PHA production. We demonstrated that glycerol has the ability to reduce molecular weight of PHA, even as a component of triglyceride. Furthermore, various alcohols that are structurally related to glycerol were examined for their reducing abilities to perform a quantitative structure–activity relationship (QSAR) study. It was found that alcohols with higher hydrophobicity (log P) exhibited higher reducing ability for PHA molecular weight. Glycerol, a less hydrophobic alcohol, was able to reduce PHA molecular weight; however, the efficacy was relatively weak among the examined alcohols.     

Preparation of L-Alanine Crystals Containing Gold Nanoparticles

Amino acids provide useful foods, medicines, health foods, and nutritional supplements. We studied the morphology control of alanine, an amino acid. We also studied the effects of amino acid addition on the dispersion stability of gold nanoparticles. We then studied hybridization between alanine crystals and arginine-capped gold nanoparticles. Alanine crystal growth in a supersaturated alanine solution was found to increase linearly over time, and alanine crystal growth stopped as supersaturation decreased. Alanine crystals with arginine grew toward the c-axis because arginine was adsorbed onto the face (120) of alanine crystals. Absorption wavelengths of colloidal solutions changed for gold nanoparticles with arginine, suggesting that arginine was adsorbed onto gold nanoparticles. The change in alanine crystal morphology was the same for alanine crystals with arginine-capped gold nanoparticles in that it grew toward the c-axis. Alanine crystals contained arginine-capped gold nanoparticles toward the c-axis.     

Stereoselective Inclusion and Structure of Equatorial-trans-1,2-dichlorocyclohexane

Abstract

Optically active (R,R)-(-)-trans-1,2-dichlorocyclohexane (DCC) was isolated as an inclusion crystal with the optically active host, (R,R)-(-)-trans-2,3-(hydroxydiphenylmethyl)-1,4-dioxaspiro[4.4]-nonane, and the structure of the 2:1 inclusion crystal has been determined by X-ray analysis. Crystal data: C₇₂H₇₄O₈Cl₂, orthorhombic, P2₁2₁2 (No. 18), a = 17.465(6) Å, b = 20.095(6) Å, c = 8.664(5) Å, V = 3040(2) ų, Z = 2, D_c = 1.24g cm^?3, D_m = 1.23g cm^?3, T = 293 K and final R ₁ = 0.050 for 2766 observed data (I > 2σ(I)). The conformation of DCC in the inclusion crystal has been found to be equatorial and the absolute configuration was definitely determined to be (R,R) on the basis of the known configuration of the host.     

MALDI-Q-TOF mass spectrometric determination of gold and platinum in tissues using their diethyldithiocarbamate chelate complexes

A rapid determination method is presented for gold (Au³⁺) and platinum (Pt⁴⁺) in tissues using matrix-assisted laser desorption ionization quadrupole time-of-flight mass spectrometry (MALDI-Q-TOF-MS). Au and Pt ions in wet-ashed tissue solution were reacted with diethyldithiocarbamate (DDC), and the resulting chelate complex ions Au(DDC)₂ ⁺ and Pt(DDC)₃ ⁺ were detected by MALDI-Q-TOF-MS using α-cyano-4-hydroxycinnamic acid as a matrix. The limit of detection (LOD) was 0.8 ng/g tissue and the quantification range was 2–400 ng/g for Au, and the LOD was 6 ng/g tissue and the quantification range was 20–4,000 ng/g for Pt. The Pt levels detected by MALDI-Q-TOF-MS in several tissues of a patient overdosed with cisplatin were nearly the same as those detected by flow-injection electrospray ionization mass spectrometry. The LODs of Au and Pt were 0.04 pg per well (sample spot) and 0.3 pg per well, respectively. To our knowledge, this is the first attempt to quantify Au³⁺ and Pt⁴⁺ ions in tissues by MALDI-Q-TOF-MS.

Nitroxyl‐Radical‐Catalyzed Oxidative Coupling of Amides with Silylated Nucleophiles through N‐Halogenation

A nitroxyl‐radical‐catalyzed oxidative coupling reaction between amines with an N‐protecting electron‐withdrawing group (EWG) and silylated nucleophiles was developed to furnish coupling products in high yields, thus opening up new frontiers in organocatalyzed reactions. This reaction proceeded through the activation of N‐halogenated amides by a nitroxyl‐radical catalyst, followed by carbon–carbon coupling with silylated nucleophiles. Studies of the reaction mechanism indicated that the nitroxyl radical activates N‐halogenated amides, which are generated from N‐EWG‐protected amides and a halogenation reagent, to give the corresponding imines.     

Photomodulation of ionic interaction and reactivity: reversible photoconversion between imidazolium and imidazolinium

An interconversion system between imidazolium and imidazolinium has been proposed for the first time. Imidazolium and imidazolinium cations exhibit different reactivity due to the difference in the aromaticity and charge localization structure, which is successfully controlled by means of photoirradiation in the present system. A 4,5-dithiazolylimidazolium salt was prepared and studied as a new class of photochromic materials modulating electrostatic interactions and chemical reactivities. The photochromic 4,5-dithiazolylimidazolium showed reversible photoconversions between imidazolium open-form and imidazolinium closed-form upon successive irradiation with UV and visible light. The imidazolinium closed-form exhibited characteristic solvato- and ionochromisms in which the absorption maximum shifted by more than 80 nm depending on the solvent polarity and counteranions, whereas the imidazolium open-form showed no such solvent-dependent property. Because the corresponding nonionic 4,5-dithiazolylimidazole also did not exhibit the solvent-dependent absorption profile both in open- and closed-forms, the appearance of these chromisms in imidazolinium closed-form was attributed to the change in the extent of ionic interaction, which was brought about by the photoconversion of imidazolium to imidazolinium. The photoderived strong ionic interaction of imidazolinium with counteranion was further applied to the photocontrolled nucleophilic reaction system. Whereas the imidazolium open-form was inert to nucleophiles such as sodium methoxide, the imidazolinium closed-form was reactive to the nucleophilic reaction, demonstrating a photogated reaction system.     

Highly sensitive and rapid tandem bioluminescent immunoassay using aequorin labeled Fab fragment and biotinylated firefly luciferase

We established a simultaneous bioluminescent assay utilizing aequorin (Aq) and biotinylated firefly luciferase (b-Luc); furthermore, we developed a highly sensitive and rapid tandem bioluminescent immunoassay (BLIA) involving the Aq-labeled Fab fragment and b-Luc-streptavidin complex. Minimum detection limits of Aq and b-Luc were 9.4 × 10⁻²¹ mol assay⁻¹ (blank + 3S.D.) and 3.6 × 10⁻¹⁹ mol assay⁻¹ (blank + 3S.D.), respectively. Measurements of two luminescent proteins were completed in 4 s with a single assay medium. In this study, prostatic acid phosphatase (PAP) and prostate specific antigen (PSA), which served as analytes, were measured in the tandem BLIA. PAP and PSA were detected by the Aq-labeled anti-Dig Fab fragment and b-Luc-streptavidin complex, respectively. The measurable ranges of PAP and PSA were 0.04-100 and 0.2-200 ng mL⁻¹, respectively. This technique was also applied to the simultaneous measurement of PSA and α-fetoprotein (AFP). Measurable ranges of PSA and AFP were 0.2-200 and 1.95-1000 ng mL⁻¹, respectively. Levels of PAP and PSA or PSA and AFP in human serum could be accurately determined with the proposed BLIA. Satisfactory correlations were observed between results obtained from the proposed BLIA and those derived from commercial kits.     

Synchrotron x-ray studies of molecular liquid SnI4

Synchrotron x-ray diffraction measurements were performed on liquid SnI4 up to a scattering vector of 25 A(-1), utilizing a horizontal two-axis diffractometer installed at the SPring-8 bending magnet beam line BL04B2 in Japan. An effective method based on the maximum entropy method was devised to transform the measured total structure factor to the reduced radial distribution function. The reliability of the density estimation is discussed.