QUATERNARY STRUCTURE OF PEA PHYTOCHROME I DIMER STUDIED WITH SMALL-ANGLE X-RAY SCATTERING and ROTARY-SHADOWING ELECTRON MICROSCOPY

Abstract— The quaternary structure of pea phytochrome type I (PI) dimer in the red-light-absorbing form was studied by small-angle X-ray scattering (SAXS) technique and rotary-shadowing electron microscopy. Structural parameters for PI 114 kDa chromopeptide dimer and its tryptically digested N-terminal 59 kDa chromopeptide monomer, such as average electron density, molecular volume and the second moment of electron density distribution, were determined in terms of SAXS using the contrast variation method. Furthermore, by means of model simulation for the scattering profiles of the chromopeptides, most plausible structural models for both peptides were constructed. The distance between the chromophoric domains was estimated to be about 70 A in the resultant model for 114 kDa chromopeptide dimer. Furthermore, the model was consistent with the electron-micrographic images of both the intact PI dimer and the PI 114 kDa chromopeptide dimer, so that the N-terminal 7 kDa fragment did not significantly contribute the low-resolution images of the dimer.     

Simple indole alkaloids and those with a non-rearranged monoterpenoid unit

This review covers newly isolated simple indole alkaloids, structure determinations, total syntheses and biological activities reported in the literature in 2003.     

Method to determine quadruple points of a two-component system containing a simple hydrate phase and behavior of the system near these points

A method for determining quadruple points of a two-component system containing a simple hydrate phase is proposed. This method utilizes the quasi-static change of the system along three-phase equilibrium lines and was proved to be able to determine the quadruple points as accurately as the conventional method. By using this method, even though some preparation is necessary, a quadruple point can be determined in just a single experimental run. The behavior of the system near the quadruple points was also examined experimentally, for both the quasi-static and the irreversible change cases. At the quadruple points, the temperature and pressure of the system were kept constant for a while, as at the triple point of water. In both cases, the representative point of the state of the system passed through the quadruple point on a p–T diagram.     

Synthesis and Crystal Structure of p-tert-Butylthiacalix[8]arene: A New Member of Thiacalixarenes

Even though it was obtained in poor yield, p-tert-butylthiacalix[8]arene (TC8A) has been synthesized as a new member of thiacalix[n]arenes by the terephthalate-induced cyclization of a mixture of acyclic oligomers, which was obtained by the reaction between p-tert-butylphenol and sulfur with CaO in ethylene glycol/diphenyl ether system. Slow evaporation of the chloroform solution of TC8A afforded guest-free crystals consisting of TC8A itself. The close-packed crystal structure of TC8A resembles that of p-tert-butylcalix[8]arene (C8A) closely, containing a plated loop molecular structure.This revised version was published online in July 2005 with a corrected issue number.     

Water molecules in a protein cavity detected by a statistical-mechanical theory

Four water molecules confined in a small cavity of hen egg-white lysozyme were detected by means of the three-dimensional (3D) RISM theory, a statistical-mechanical theory of molecular solutions. This is the first theoretical realization of confined molecules in a protein without making nonsense tricks, such as placing the molecules in the space a priori. Possible impacts which the result may have on biochemistry and biophysics, including the molecular recognition, enzymatic reactions, etc., are discussed.     

Partial molar volume of proteins studied by the three-dimensional reference interaction site model theory

The three-dimensional reference interaction site model (3D-RISM) theory is applied to the analysis of hydration effects on the partial molar volume of proteins. For the native structure of some proteins, the partial molar volume is decomposed into geometric and hydration contributions using the 3D-RISM theory combined with the geometric volume calculation. The hydration contributions are correlated with the surface properties of the protein. The thermal volume, which is the volume of voids around the protein induced by the thermal fluctuation of water molecules, is directly proportional to the accessible surface area of the protein. The interaction volume, which is the contribution of electrostatic interactions between the protein and water molecules, is apparently governed by the charged atomic groups on the protein surface. The polar atomic groups do not make any contribution to the interaction volume. The volume differences between low- and high-pressure structures of lysozyme are also analyzed by the present method.     

Unidirectional crystallization of charged colloidal silica due to the diffusion of a base

Dilute aqueous dispersions of charged colloidal silica (particle volume fraction = approximately 0.03-0.04, particle diameter = 110 nm) exhibit unidirectional crystal growth due to the diffusion of a weak base, pyridine (Py). Similar diffusion-crystallization is enabled by a salt of a weak acid and a strong base, sodium hydrogen carbonate (NaHCO3). The resulting crystals consist of columnar (or cubic) crystal grains with a maximum height of a few centimeters and a maximum width of 1 cm. The crystal growth process is attributed to a combination of (i) the diffusion of Py or NaHCO3 accompanied by a charging reaction of the silica particles and (ii) the charge-induced crystallization of the silica colloids. Theoretical growth curves based on the reaction-diffusion model for the case of Py were in good agreement with the observed curves. We also report the immobilization of the resulting large crystals by using a polymer hydrogel matrix.