Effect of buffer conditions on CYP2C8-mediated paclitaxel 6α-hydroxylation and CYP3A4-mediated triazolam α- and 4-hydroxylation by human liver microsomes.

1. Buffer conditions in in vitro metabolism studies using human liver microsomes (HLM) have been reported to affect the metabolic activities of several cytochrome P450 (CYP) isozymes in different ways, although there are no reports about the dependence of CYP2C8 activity on buffer conditions. 2. The present study investigated the effect of buffer components (phosphate or Tris-HCl) and their concentration (10-200 mM) on the CYP2C8 and CYP3A4 activities of HLM, using paclitaxel and triazolam, respectively, as marker substrates. 3. The Km (or S50) and Vmax values for both paclitaxel 6α-hydroxylation and triazolam α- and 4-hydroxylation, estimated by fitting analyses based on the Michaelis-Menten or Hill equation, greatly depended on the buffer components and their concentration. 4. The CLint values in phosphate buffer were 1.2-3.0-fold (paclitaxel) or 3.1-6.4-fold (triazolam) higher than in Tris-HCl buffer at 50-100 mM. These values also depended on the buffer concentration, with a maximum 2.3-fold difference observed between 50 and 100 mM which are both commonly used in drug metabolism studies. 5. These findings suggest the necessity for optimization of the buffer conditions in the quantitative evaluation of metabolic clearances, such as in vitro-in vivo extrapolation and also estimating the contribution of a particular enzyme in drug metabolism.

A color-determining amino acid residue of proteorhodopsin.

Proteorhodopsin (PR) is a light-driven proton pump found in marine bacteria. More than 1000 PRs are classified as blue-absorbing (λmax ∼ 490 nm) and green-absorbing (λmax ∼ 525 nm) PRs. The color determinant is known to be at position 105, where blue-absorbing and green-absorbing PRs possess Gln and Leu, respectively. This suggests hydrophobicity at position 105 plays a key role in color tuning. Here we successfully introduced 19 amino acid residues into position 105 of green-absorbing PR in the membrane environment and investigated the absorption properties. High-performance liquid chromatography analysis shows that the isomeric composition of the all-trans form is >70% for all mutants, indicating little influence of different isomers on color tuning. Absorption spectra of the wild-type and 19 mutant proteins were well-characterized by the pH-dependent equilibria of the protonated and deprotonated counterion (Asp97) of the Schiff base, whereas the λmax values of these two states and the pKa value differed significantly among mutants. Although Gln and Leu are hydrophilic and hydrophobic residues, respectively, the λmax values of the two states and the pKa value did not correlate with the hydropathy index of residues. In contrast, the λmax and pKa were correlated with the volume of residues, though Gln and Leu possess similar volumes. This observation concludes that the λmax and pKa of Asp97 are determined by local and specific interactions in the Schiff base moiety, in which the volume of the residue at position 105 is more influential than its hydrophobicity. We suggest that the hydrogen-bonding network in the Schiff base moiety plays a key role in the λmax and pKa of Asp97, and the hydrogen-bonding network is significantly perturbed by large amino acid residues but may be preserved by additional water molecule(s) for small amino acid residues at position 105.

Analysis of relationship between microbial and methanogenic biomass in methane fermentation.

To analyze the relationship between biomass of microorganisms and methane production, the total biomass of bacteria and archaea (BA) during methane fermentation was analyzed by the environmental DNA analysis method. In the case of using methanogenic sludge as a seed which is generally used for methane fermentation, the total BA biomass reached to 1.5 x 10(8) to 3.6 x 10(8) cells/ml when methane was produced. On the other hand, soil suspension was used as a seed; methane was not produced for 14-day cultivation. However, the total BA biomass reached to above 1.5 x 10(8) cells/ml. The methanogen biomass was counted by using a fluorescence microscope (coenzyme F420), and the methanogen biomass and the ratio of methanogens in the total of BA were analyzed during methane fermentation. At the methane-producing phase, the methanogen biomass reached to 1.3 x 10(8) cells/ml, and the ratio of methanogens was above 70% of the total BA. When the ratio of methanogens in a seed was changed, the methane-producing phase was moved. However, the relationship between methanogens and other microorganisms at the methane-producing phase was almost similar.