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.     

Adenosine-1,3-diazaphenoxazine derivative for selective base pair formation with 8-oxo-2'-deoxyguanosine in DNA

The selective detection of 8-oxo-2'-deoxyguanosine (8-oxo-dG) in DNA without chemical or enzymatic treatment is an attractive tool for genomic research. We designed and synthesized the non-natural nucleoside analogue, the adenosine-1,3-diazaphenoxazine (Adap) derivative, for selective recognition of 8-oxo-dG in DNA. This study clearly showed that Adap has a highly selective stabilizing effect on the duplex containing the Adap-8-oxo-dG base pair. Furthermore, the fluorescent property of Adap was shown to be useful for the selective detection of 8-oxo-dG in the duplex DNA. To the best of our knowledge, this is the first successful demonstration of a non-natural nucleoside with a high selectivity for 8-oxo-dG in DNA.     

Effects of heme on the thermal stability of mesophilic and thermophilic cytochromes c: comparison between experimental and theoretical results

We have recently proposed a measure of the thermal stability of a protein: the water-entropy gain at 25?°C upon folding normalized by the number of residues, which is calculated using a hybrid of the angle-dependent integral equation theory combined with the multipolar water model and the morphometric approach. A protein with a larger value of the measure is thermally more stable. Here we extend the study to analyses on the effects of heme on the thermal stability of four cytochromes c (PA c(551), PH c(552), HT c(552), and AA c(555)) whose denaturation temperatures are considerably different from one another despite that they share significantly high sequence homology and similar three-dimensional folds. The major conclusions are as follows. For all the four cytochromes c, the thermal stability is largely enhanced by the heme binding in terms of the water entropy. For the holo states, the measure is the largest for AA c(555). However, AA c(555) has the lowest packing efficiency of heme and the apo polypeptide with hololike structure, which is unfavorable for the water entropy. The highest stability of AA c(555) is ascribed primarily to the highest efficiency of side-chain packing of the apo polypeptide itself. We argue for all the four cytochromes c that due to covalent heme linkages, the number of accessible conformations of the denatured state is decreased by the steric hindrance of heme, and the conformational-entropy loss upon folding becomes smaller, leading to an enhancement of the thermal stability. As for the apo state modeled as the native structure whose heme is removed, AA c(555) has a much larger value of the measure than the other three. Overall, the theoretical results are quite consistent with the experimental observations (e.g., at 25?°C the α-helix content of the apo state of AA c(555) is almost equal to that of the holo state while almost all helices are collapsed in the apo states of PA c(551), PH c(552), and HT c(552)).     

Terminal Redox‐Site Effect on the Long‐Range Electron Conduction of Fe(tpy)2 Oligomer Wires on a Gold Electrode

This article completes our comprehensive understanding of the electron transport properties of our original π‐conjugated redox‐active molecular wires comprising Fe bridged by p‐phenylene linkers (tpy=2,2′:6′,2′′‐terpyridine). The Fe(tpy)₂ oligomer wires comprise three types of tpy ligands: the anchor tpy ligand ( A series) makes a junction between the wire and electrode, the bridging bis‐tpy ligand ( L series) connects the Fe(tpy)₂ units, and the terminal tpy ligand ( T series) possesses a redox site as a probe for the long‐range electron transport ability. Taking advantage of the precise tunability of the composition of the Fe(tpy)₂ oligomer wires, thus far we investigated how A and L impacted on the electron‐transport ability. The excellent long‐range electron transport ability with ultrasmall attenuation constants (β^d, 0.002 Å^?1 as the minimum) depends on L significantly [Chem. Asian J. 2009 , 4, 1361], whereas A is unrelated to the β^d value, but influences the zero‐distance electron‐transfer rate constant, k_et⁰ [J. Am. Chem. Soc. 2010 , 132, 4524]. Herein we study the influence of terminal ligand T ^x (x=1–3). β^d is independent of T , however, T³ , with a cyclometallated Ru complex as the redox site, gives rise to a k_et⁰ value greater than T¹ and T² with ferrocene. This series of simple but definitive conclusions indicates that we have reached the stage of being able to precisely design molecular wires to attain desirable single‐molecule electron conduction.     

One-step production of nanofibrillated bacterial cellulose (NFBC) from waste glycerol using Gluconacetobacter intermedius NEDO-01

A major by-product of biodiesel production is waste glycerol, which has numerous potential applications. In this study, we isolated a novel bacterium capable of producing cellulose from waste glycerol, and identified it as a novel strain (named NEDO-01) of Gluconacetobacter intermedius. Scanning electron microscopy revealed that the morphology of the pellicle produced by NEDO-01 was similar to that of cellulose produced by Gluconacetobacter hansenii ATCC23769. Furthermore, X-ray diffraction and solid-state nuclear magnetic resonance spectroscopic analyses suggested that cellulose produced by NEDO-01 had molecular and crystalline structures similar to those of cellulose produced by ATCC23769. After the optimization of cultivation conditions, NEDO-01 mediated the one-step production of nanofibrillated bacterial cellulose (NFBC) from waste glycerol in a medium supplemented with carboxymethyl cellulose. Transmission electron microscopic analysis revealed that the NFBC was composed of relatively uniform fibers with diameters of approximately 20 nm. NFBC was produced as uniform water suspensions, the yield of which was 3.4 g/L from cultivation in 7.5 L medium in a 10-L jar fermenter. The bioconversion of waste glycerol to NFBC, which has superior fluidity, moldability, and miscibility, has a wide variety of applications, including potential uses in the medical and materials engineering fields.     

Decomposition and Detection of Hydrogen Peroxide Using δ‐MnO2 Thin Film Electrode with Self‐Healing Property

A thin film of δ‐type MnO₂ grown cathodically has been investigated with respect to the ability toward anodic decomposition of H₂O₂ and durability. With polarization at less positive potentials than +0.4 V vs. Ag/AgCl, the film was dissolved exclusively as a result of reduction of Mn⁴⁺ sites in the oxide by H₂O₂ to soluble Mn²⁺. At +0.9 V, MnO₂ remained unchanged and decomposed H₂O₂ in solution. At +0.8 V, the film was once dissolved in the initial stage; however, it was self‐healed via reoxidation of the liberated Mn²⁺ ions. Amperometric flow‐injection analysis of H₂O₂ was carried out with the δ‐MnO₂ film.     

Characteristics of train noise in above-ground and underground stations with side and island platforms

Railway stations can be principally classified by their locations, i.e., above-ground or underground stations, and by their platform styles, i.e., side or island platforms. However, the effect of the architectural elements on the train noise in stations is not well understood. The aim of the present study is to determine the different acoustical characteristics of the train noise for each station style. The train noise was evaluated by (1) the A-weighted equivalent continuous sound pressure level (L_Aeq), (2) the amplitude of the maximum peak of the interaural cross-correlation function (IACC), (3) the delay time (τ₁) and amplitude (?₁) of the first maximum peak of the autocorrelation function. The IACC, τ₁ and ?₁ are related to the subjective diffuseness, pitch and pitch strength, respectively. Regarding the locations, the L_Aeq in the underground stations was 6.4 dB higher than that in the above-ground stations, and the pitch in the underground stations was higher and stronger. Regarding the platform styles, the L_Aeq on the side platforms was 3.3 dB higher than on the island platforms of the above-ground stations. For the underground stations, the L_Aeq on the island platforms was 3.3 dB higher than that on the side platforms when a train entered the station. The IACC on the island platforms of the above-ground stations was higher than that in the other stations.     

Motion Capture and Manipulation of a Single Synthetic Molecular Rotor by Optical Microscopy

Single‐molecule imaging and manipulation with optical microscopy have become essential methods for studying biomolecular machines; however, only few efforts have been directed towards synthetic molecular machines. Single‐molecule optical microscopy was now applied to a synthetic molecular rotor, a double‐decker porphyrin (DD). By attaching a magnetic bead (ca. 200 nm) to the DD, its rotational dynamics were captured with a time resolution of 0.5 ms. DD showed rotational diffusion with 90° steps, which is consistent with its four‐fold structural symmetry. Kinetic analysis revealed the first‐order kinetics of the 90° step with a rate constant of 2.8 s^?1. The barrier height of the rotational potential was estimated to be greater than 7.4 kJ mol^?1 at 298 K. The DD was also forcibly rotated with magnetic tweezers, and again, four stable pausing angles that are separated by 90° were observed. These results demonstrate the potency of single‐molecule optical microscopy for the elucidation of elementary properties of synthetic molecular machines.     

Chemoselective and Direct Functionalization of Methyl Benzyl Ethers and Unsymmetrical Dibenzyl Ethers by Using Iron Trichloride

Methyl and benzyl ethers are widely utilized as protected alcohols due to their chemical stability, such as the low reactivity of the methoxy and benzyloxy groups as leaving groups under nucleophilic conditions. We have established the direct azidation of chemically stable methyl and benzyl ethers derived from secondary and tertiary benzyl alcohols. The present azidation chemoselectively proceeds at the secondary or tertiary benzylic positions of methyl benzyl ethers or unsymmetrical dibenzyl ethers and is also applicable to direct allylation, alkynylation, and cyanation reactions, as well as the azidation. The present methodologies provide not only a novel chemoselectivity but also the advantage of shortened synthetic steps, due to the direct process without the deprotection of the methyl and benzyl ethers.