The solvent structure and behavior around a protein were examined by analyzing a trajectory of molecular dynamics simulation of the trp-holorepressor in a periodic box of water. The calculated self diffusion coefficient indicated that the solvent within 10 A of the protein had lower mobility. Examination of the solvent diffusion around different atoms of different kinds of residues showed no general tendency. This fact suggested that the solvent mobility is not influenced significantly by the kind of the atom or residue they solvated. Distribution analysis around the protein revealed two peaks of water oxygen: a sharp one at 2.8 A around polar and charged atoms and a broad one at approximately 3.4 A around apolar atoms. The former was stabilized by water-protein hydrogen bonds, and the latter was stabilized by water-water hydrogen bonds, suggesting the existence of a hydrophobic shell. An analysis of protein atom-water radial distribution functions confirmed these shell structures around polar or charged atoms and apolar ones.

The nucleotide sequences of rbcL genes encoding the large subunit of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) were determined from six species of Prymnesiophyta to clarify their phylogenetic relationships. Molecular phylogenetic trees were constructed using PAUP (Phylogenetic Analysis Using Parsimony). These analyses suggest that the Prymnesiophyta, except for the Pavlovales, area relatively stable monophyletic group. Pleurochrysis carterae, included in the Isochrysidales, is a sister species of a monophyletic group consisting of other members of the Isochrysidales, Gephyrocapsa oceanica and Emiliania huxleyi, members of the Coccosphaerales, Calyptrosphaera sphaeroidea and Umbilicosphaera sibogae var. foliosa, and a member of the Prymnesiales, Chrysochromulina hirta. The nucleotide sequence of rbcL from G. oceanica was identical to that from E. huxleyi within the region examined. Our trees show that G. oceanica and E. huxleyi are more closely related to C. hirta than to U. sibogae, C. sphaeroidea, and P. carterae. These results suggest that orders in the Prymnesiophyceae, including the above‐mentioned genera, should be redefined.

Genes for the large (rbcL) and small (rbcS) subunits of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) from the prymnesiophyte Pleurochrysis carterae (Braarud and Fagerl.) Christensen were isolated and characterized. The genes are located close to each other, separated by an intergenic region of 87 nucleotide base pairs. Southern and Northern blot analyses indicate that these genes are encoded by plastid DNA and cotranscribed, as in the Cryptophyta, Chromophyta, and Rhodophyta studied so far. The genes of Pleurochrysis show higher identities with those of the Cryptophyta, Chromophyta, Rhodophyta, and the α (Type I)‐ and β‐purple bacteria than with those of the Chlorophyta or Cyanophyta. The molecular Phylogenetic tree of rbcL genes suggests that the plastids of the Prymnesiophyta, Cryptophyta, and Chromophyta originated from those of the Rhodophyta, which agrees with the secondary endosymbiotic theory. Northern analysis of Pleurochrysis demonstrated that a certain amount of the transcript is possibly processed around the 3′ end rbcL. When cells were transferred from light to dark for 6 h, the amount of Rubisco messenger RNA (mRNA) was almost the same as in continuous light. This suggests that Rubisco mRNA is synthesized and/or stable even in the dark.

Molecular dynamics simulations of Escherichia coli trp-aporepressor were carried out in the absence and presence of explicit water molecules. The vacuum simulations resulted in significant deformation of the initial X-ray structure. A solvated simulation with a nonbonded cut-off radius of 9 A gave a better result, and the most satisfactory result was obtained when electrostatic interactions within a cut-off radius of 18 A were considered by a twin-range method. The trajectory from the last simulation was used to analyze the dynamical properties of the aporepressor. The root-mean-square fluctuations of the residues showed the rigidity of the central core and the flexibility of the DNA-binding sites, consistent with the X-ray temperature factors. The dynamical cross-correlation map indicated a significant negative correlation between the central core and the two DNA-binding sites, and thus reproduced the three-domain format (a central core and two DNA-binding heads) from a dynamical point of view. The core region showed weak, but many, intra- and inter-molecular correlations, while the helix-turn-helix DNA-binding motifs were free from correlations with other regions.

Rhamnolipids, multifunctional glycolipid biosurfactants, and pyocyanine, a phenazine dye, were coproduced by Pseudomonas BOP100 from ethanol as the sole carbon source. Bacterial growth was dependent on the ethanol concentration in the medium. Pyocyanine was produced only during the exponential phase, while rhamnolipids production continued during the stationary phase, indicating two different ways of production for each of the products. Maximum coproduction capacity was observed at a concentration of 3% ethanol; yield of rhamnolipids was 3 g/L, and of pyocyanine 0.2 g/L. The products were characterized to confirm their chemical structures. JAOCS 73, 851-856 (1996).