The widely distributed phytochrome photoreceptors carry a bilin chromophore, which is covalently attached to the protein during a lyase reaction. In plant phytochromes, the natural chromophore is coupled by a thioether bond between its ring A ethylidene side chain and a conserved cysteine residue within the so-called GAF domain of the protein. Many bacterial phytochromes carry biliverdin as natural chromophore, which is coupled in a different manner to the protein. In phytochrome Agp1 of Agrobacterium tumefaciens, biliverdin is covalently attached to a cysteine residue close to the N terminus (position 20). By testing different natural and synthetic biliverdin derivatives, it was found that the ring A vinyl side chain is used for chromophore attachment. Only those bilins that have ring A vinyl side chain were covalently attached, whereas bilins with an ethylidene or ethyl side chain were bound in a noncovalent manner. Phycocyanobilin, which belongs to the latter group, was however covalently attached to a mutant in which a cysteine was introduced into the GAF domain of Agp1 (position 249). It is proposed that the regions around positions 20 and 249 are in close contact and contribute both to the chromophore pocket. In competition experiments it was found that phycocyanobilin and biliverdin bind with similar strength to the wild type protein. However, in the V249C mutant, phycocyanobilin bound much more strongly than biliverdin. This finding could explain why during phytochrome evolution in cyanobacteria, the chromophore-binding site swapped from the N terminus into the GAF domain.Phytochromes are biliprotein photoreceptors that were discovered in plants (1) but were recently also found in bacteria (2-4), fungi (5), and slime molds (6). The photocycle of phytochromes has two long-lived forms, the red-absorbing form (Pr), 1

We have developed an algorithm for sampling the conformational space of large flexible molecules in solution, which combines the molecular dynamics (MD) method and the three-dimensional reference interaction site model (3D-RISM) theory. The solvent-induced force acting on solute atoms was evaluated as the gradient of the solvation free energy with respect to the solute-atom coordinates. To enhance the computation speed, we have applied a multiple timestep algorithm based on the RESPA (Reversible System Propagator Algorithm) to the combined MD/3D-RISM method. By virtue of the algorithm, one can choose a longer timestep for renewing the solvent-induced force compared with that of the conformational update. To illustrate the present MD/3D-RISM simulation, we applied the method to a model of acetylacetone in aqueous solution. The multiple timestep algorithm succeeded in enhancing the computation speed by 3.4 times for this model case. Acetylacetone possesses an intramolecular hydrogen-bonding capability between the hydroxyl group and the carbonyl oxygen atom, and the molecule is significantly stabilized due to this hydrogen bond, especially in gas phase. The intramolecular hydrogen bond was kept intact during almost entire course of the MD simulation in gas phase, while in the aqueous solutions the bond is disrupted in a significant number of conformations. This result qualitatively agrees with the behavior on a free energy barrier lying upon the process for rotating a torsional degree of freedom of the hydroxyl group, where it is significantly reduced in aqueous solution by a cancellation between the electrostatic interaction and the solvation free energy.

Although it has been suggested that the tacticity affects the hydrophilicity of poly(N-isopropylacrylamide) (PNiPA), little is known about the physical background of this phenomenon. In this study, we investigated the solubility of the dimer model compounds (DNiPA). The partition coefficient of DNiPA in the two phases of a water/chloroform mixture has indicated that DNiPA with the racemo configuration (r-DNiPA) is more soluble in water than DNiPA with the meso configuration (m-DNiPA). The difference of the hydration free energy between m- and r-DNiPA is estimated to be 1.2 kJ mol(-1). The molecular mechanics (MM) calculations with the GB/SA model have revealed that r-DNiPA in water is more stable by ca. 1 kJ mol(-1) than m-DNiPA, which is in excellent agreement with the experimental result. The MM calculations have also indicated that the intramolecular interaction of m-DNiPA is stronger than that of r-DNiPA, while r-DNiPA is advantageous in terms of the hydration free energy and conformational entropy.

Effects of Ru addition on the activity and the sustainability of Ni/Mg(Al)O catalysts were investigated in the daily start-up and shutdown (DSS) operation of the steam reforming of CH 4. Mg 2.5 (Ni 0.5)-Al hydrotalcite was prepared by coprecipitation and calcined to form Mg 2.5 (Al,Ni 0.5)O periclase. When the powders of the periclase were dipped in an aqueous solution of Ru(III) nitrate, the hydrotaclite was reconstituted on the surface of Mg 2.5 (Al,Ni 0.5)O particles, resulting in the formation of highly dispersed Ru/Ni bimetal supported catalysts after the calcination, followed by the reduction. The addition of Ru on Ni caused a decrease in the reduction temperature of Ni and an increase in the amount of H 2 uptake on the Ni over the catalyst. Formation of Ru-Ni alloy or strong interaction between Ru and Ni was also suggested. When Ru-Ni 0.5 /Mg 2.5 (Al)O catalysts were tested in the DSS-like operation under steam purging, the deactivation due to the oxidation of Ni metal by steam was effectively suppressed by hydrogen spillover. Moreover, only 0.05 wt% of Ru loading was enough to effectively suppress the deactivation during the DSS-like operation.