Selectivity in substrate–enzyme complexation studied by surface forces measurement

The selectivity of substrate in substrate–enzyme complexation of heptaprenyl diphosphate synthase was directly investigated using colloidal probe atomic force microscopy (AFM). This enzyme is composed of two dissociable subunits, which exhibits a catalytic activity only when they are associated together in the presence of a cofactor, Mg²⁺, and a substrate, farnesyl diphosphate (FPP). We have recently succeeded to directly demonstrate a specific interaction involved in this enzyme reaction and obtain new insights into the molecular mechanism of the reaction using the approach based on the colloidal probe AFM. The AFM measurement showed the adhesive force between the subunits only in the presence of both Mg²⁺ and FPP. In this study, we studied the substrate selectivity in the complexation by monitoring the adhesive force. The substrates studied are pyrophosphate (PPi), isopentenyl diphosphate (IPP), geranyl diphosphate (GPP), farnesyl monophosphate (FP), and farnesyl geranyl diphosphate (FGPP). No adhesion was observed in the case of PPi, IPP, and GPP. On the other hand, the significant adhesion was observed for phosphate derivatives, which bear prenyl units longer than three. This is in good agreement with the selectivity of the substrates by this enzyme, which catalyzes the condensation reaction of four IPP molecules with FPP to give heptaprenyl (C₃₅) diphosphates. Our study showed a useful methodology for examining the elemental processes of biological reactions.     

Relative stereochemistries of the ether rings and sugar moieties in durinskiol A

Durinskiol A (1) is a long carbon-chain polyol compound with a molecular weight of 2128 mu isolated from the symbiotic dinoflagellate Durinskia sp. The relative stereochemistries of ether rings and sugar moieties in 1 were established based on 2D-NMR analysis and molecular modeling studies. Conformational analysis of the 6,5,6-bis-spiroacetal ring in 1 was also examined by using ab initio methods.     

Odd-even effect and metal induced structural convergence in self-assembled monolayers of bipyridine derivatives

Scanning tunneling microscopy (STM) observations reveal that bipyridine derivatives which exhibit various two-dimensional structures due to the odd-even chain length effect are converged into a lamellar structure upon metal coordination.     

Synthesis of the entire carbon framework of the kedarcidin chromophore aglycon

In advanced studies directed toward the total synthesis of the kedarcidin chromophore, we have successfully achieved the late-stage installation of the nine-membered diyne ring in the presence of the highly functionalised ansamacrocyclic bridge.     

Vibrational relaxation on the mixed vibronic levels of the and states in all-trans-neurosporene as revealed by subpicosecond time-resolved, stimulated emission and transient absorption spectroscopy

In all-trans-neurosporene, whose level is lower than the level by one vibrational quantum, the following two steps of vibrational relaxation from the mixed vibronic states were identified, in the order, stimulated emission stimulated emission transient absorption. The stimulated emission patterns were simulated by the use of Franck–Condon factors in the transitions from the pair of mixed vibronic levels down to the ground vibronic levels. The vibronic levels of the mixed and state were characterized theoretically based on the diabatic approximation.     

Multiple nuclear Bragg scattering

Multiple nuclear resonant scattering from an ⁵⁷FeBO₃ single crystal has been observed in the three-beam case. A change of the lifetime and a modulation of the quantum beat were observed in our study. The high brilliance of synchrotron radiation and the high perfection of the synthetic ⁵⁷FeBO₃ single crystal enabled us to observe such an effect. This revised version was published online in August 2006 with corrections to the Cover Date.     

Polycondensations of dicarboxylic acids and diols derived from optically active amino alcohols

Polycondensations of dicarboxylic acids with diols having amide moieties derived from optically active amino alcohols were carried out. Polymers with M _ns 8,700–17,400 were obtained by the polycondensations using 1.2 eq. of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC·HCl) in DMF at room temperature for 8 h in satisfactory yields. The T_g of the polymer rose with decrease of the methylene chain length of the dicarboxylic acid. In the T_gs of the polymers from L-leucinol, even-odd effect was observed with increase of the methylene chain length of the dicarboxylic acid. The molecular rotation values of the polymers were constant except for the polymer from succinic acid, which showed the negatively largest one. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 2925–2934, 1997     

Luminescence imaging of biological subjects during X-ray irradiations lower energy than Cerenkov-light threshold

It is commonly thought that UV or visible-light luminescence imaging of biological subjects during X-ray irradiation at the energy below 120 keV is impossible because the secondary electrons produced in this energy range do not emit Cerenkov light. Contrary to this consensus, we found UV or visible-light luminescence imaging of the subjects were possible with X-ray irradiations of this energy range. We placed one of the biological subjects in a black box; visible-light luminescence images were measured with a high-sensitivity, cooled charge coupled device (CCD) camera during X-ray irradiation at energy below 120 keV. We also conducted the imaging of air without subjects during irradiation of the same X-ray. The biological subjects emitted visible-light luminescence, and the imaging was possible with the irradiation of the X-ray below 120 keV. The luminescence images were observed in only the X-ray irradiated areas. Also air luminescence images could be obtained and the intensity of the luminescence measured from the images was proportionally increased with the exposure dose. UV or visible-light luminescence imaging of biological subjects was possible during X-ray irradiations lower energy than the Cerenkov-light threshold. The phenomenon was different from general X-ray fluorescence because wavelength of the luminescence is UV or visible-light. The luminescence imaging method is promising for estimating the irradiated area with X-ray, which could be used for interventional radiology (IVR). Also air luminescence imaging would be applied to the exposure dose distribution measurements for X-ray of diagnostic X-ray systems.     

Influence of nanometer scale film structure of ZDDP tribofilm on Its mechanical properties: A computational chemistry study

We investigated the influence of a nanometer scale film structure of a tribofilm generated from zinc dialkyldithiophosphate (ZDDP) anti-wear additive on its mechanical properties using a combined molecular dynamics (MD) and finite element (FE) method. The frictional behavior of an interface between a native iron oxide layer on steel surface and zinc metaphosphate - regarded as a model material of ZDDP tribofilm - was firstly studied using the MD method. The results showed that the iron atoms in the oxide layer diffused into the phosphate layer during the friction process. The zinc atoms in the phosphate layer also diffused into the oxide layer. Significant interdiffusion of iron and zinc atoms was observed with increasing simulation time. Thus, metallic phosphate with a gradient composition of iron and zinc atoms was formed on the phosphate/oxide interface. We then constructed an axisymmetric nanoindentation simulation model from the MD-derived structures at a certain simulation time and carried out a FE calculation. As a result, we found that the rubbed ZDDP tribofilm, including the phosphate with the gradient composition of metallic atoms, showed larger contact stiffness and hardness. The combined MD/FE simulation indicates that the tribofilm becomes stiffer and harder due to the interdiffusion of iron and zinc atoms on the tribofilm/oxide interface. We have found that the gradient composition formation in ZDDP tribofilm during friction process influences on its mechanical properties.