Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Incorporation of Pseudo‐complementary Bases 2,6‐Diaminopurine and 2‐Thiouracil into Serinol Nucleic Acid (SNA) to Promote SNA/RNA Hybridization

Serinol nucleic acid (SNA) is a promising candidate for nucleic acid‐based molecular probes and drugs due to its high affinity for RNA. Our previous work revealed that incorporation of 2,6‐diaminpurine (D), which can form three hydrogen bonds with uracil, into SNA increases the melting temperature of SNA‐RNA duplexes. However, D incorporation into short self‐complementary regions of SNA promoted self‐dimerization and hindered hybridization with RNA. Here we synthesized a SNA monomer of 2‐thiouracil (sU), which was expected to inhibit base pairing with D by steric hindrance between sulfur and the amino group. To prepare the SNA containing D and sU in high yield, we customized the protecting groups on D and sU monomers that can be readily deprotected under acidic conditions. Incorporation of D and sU into SNA facilitated stable duplex formation with target RNA by suppressing the self‐hybridization of SNA and increasing the stability of the heteroduplex of SNA and its complementary RNA. Our results have important implications for the development of SNA‐based probes and nucleic acid drugs.     

Sorption and partial molar volumes of C2 and C3 hydrocarbons in polypropylene copolymers

The sorption of C₂ and C₃ hydrocarbons in two ethylene–propylene copolymers and a propylene homopolymer and the simultaneous dilation of the polymers were measured at temperatures of 287–363 K and pressures up to 4 MPa. The sorption isotherms were well described by the Flory–Huggins theory of dissolution. Dilation isotherms in the form of elongation versus pressure were similar in shape to the corresponding sorption isotherms. Solubility coefficients, partial molar volumes, and Flory–Huggins interaction parameters were determined from these isotherms. The thermal expansivities of the hydrocarbons dissolved in the polymers were 0.002–0.005 K^?1, and the Flory–Huggins interaction parameters depended not only on temperature but also on concentration. At 323 K, the calculated solubilities of propylene in the ethylene–propylene‐rubber regions of the copolymers were 1.8 times higher than in the amorphous regions of the propylene homopolymer. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1255–1262, 2001     

New approach of semiconductor laser related technologies for ultrafast photonics

Ultrashort laser pulses offer new jump in information and communication technology. Especially semiconductor laser based ultrafast photonic devices and systems are promising. We review our new approaches for femtosecond pulse generation, and thin film technology for broad band semiconductor optical amplifiers.     

Role of Arg123 in Light‐driven Anion Pump Mechanisms of pharaonis Halorhodopsin†

Halorhodopsin (HR) acts as a light‐driven chloride pump which transports a chloride ion from the extracellular (EC) to the cytoplasmic space during a photocycle reaction that includes some photointermediates initiated by illumination. To understand the chloride uptake mechanisms, we focused on a basic residue Arg123 of HR from Natronomonas pharaonis (NpHR), which is the only basic residue located in the EC half ion channel. By the measurements of the visible absorption spectra in the dark and the light‐induced inward current through the membrane, it was shown that the chloride binding and transport ability of NpHR completely disappeared by the change of arginine to glutamine. From flashphotolysis analysis, the photocycle of R123Q differed from that of wildtype NpHR completely. The response of the R123H mutant depended on pH. These facts imply that the positive charge at position 123 is essential for chloride binding in the ground state and for the chloride uptake under illumination. On the basis of the molecular structures of HR and the anion‐transportable mutants of bacteriorhodopsin, the effects of the positive charge and the conformational change of the Arg123 side chain as well as the chloride‐pumping mechanism are discussed.     

Sorption and partial molar volume of gases in poly (dimethyl siloxane)

Sorption of N₂, O₂, Ar, CH₄, CO₂, C₂H₄, and C₂H₆ in poly (dimethyl siloxane) liquid and rubber and the dilation of the polymers due to sorption of the gases are studied at 25°C under pressures up to 50 atm. In the liquid, the sorption isotherms for low-solubility and high-solubility gases are described by Henry's law and the Flory–Huggins equation, respectively. Gas sorption in the rubber, which contains a 29 wt % silica filler, follows the dual-mode sorption model, though marked hysteresis is observed in the sorption of O₂ and CH₄. The dilation isotherms increase linearly or exponentially in both polymers with increasing pressure. Considering that gas molecules adsorbed into micropores of the filler particles do not participate in the dilation, partial molar volumes of the dissolved gases in the rubber are determined from data of sorption and dilation. The values are nearly equal to the partial molar volumes in the liquid (48–60 cm³/mol).     

Gas sorption in poly(vinyl benzoate)

High-pressure sorption (up to 50 atm) for CO₂, N₂, and Ar in poly(vinyl benzoate) (PVB) was studied at temperatures from 25 to 70°C by a gravimetric method utilizing an electromicrobalance. The results are described by Henry's law above the glass transition temperature T_g for all gases. The dual-mode sorption model, Henry's law plus a Langmuir isotherm, applies to the sorption isotherms of N₂ and Ar in the glassy state, and the dual-mode parameters are given. For CO₂, a new type of sorption isotherm is observed below T_g. The isotherm is concave to the pressure axis in the low-pressure region and turns into a straight line with increasing CO₂ pressure which can be extrapolated back to the coordinate origin. The linear part of the isotherm is characteristic of the rubbery state, while the nonlinear part stems from glassystate behavior. The “glass transition solubility” of CO₂, at which PVB film changes from the glassy to the rubbery state, decrease as the temperature increases. The disappearance of microvoids, that is, the decrease of the Langmuir capacity, may be due to a large plasticizing effect of sorbed CO₂. The difference between the N₂ and Ar isotherms and the CO₂ isotherm is discussed from this standpoint.