Thermodynamic analysis of ionizable groups involved in the catalytic mechanism of human matrix metalloproteinase 7 (MMP-7).

Human matrix metalloproteinase 7 (MMP-7) exhibits a broad bell-shaped pH-dependence with the acidic and alkaline pK(e) (pK(e1) and pK(e2)) values of about 4 and 10. In this study, we estimated the ionizable groups involved in its catalytic mechanism by thermodynamic analysis. pK(a) of side chains of L-Asp, L-Glu, L-His, L-Cys, L-Tyr, L-Lys, and L-Arg at 25-45°C were determined by the pH titration of amino-acid solutions, from which their enthalpy changes, ∆H°, of deprotonation were calculated. pK(e1) and pK(e2) of MMP-7 at 15-45°C were determined in the hydrolysis of (7-methoxycoumarin-4-yl)acetyl-L-Pro-L-Leu-Gly-L-Leu-[N(3)-(2,4-dinitrophenyl)-L-2,3-diaminopropionyl]-L-Ala-L-Arg-NH(2), from which ∆H(o) for pK(e1) and pK(e2) was calculated. The ∆H(o) for pK(e1) (-20.6±6.1kJmol(-1)) was similar to that for L-Glu (-23.6±5.8kJmol(-1)), and the ∆H(o) for pK(e2) (89.9±4.0kJmol(-1)) was similar to those for L-Arg (87.6±5.5kJmol(-1)) and L-Lys (70.4±4.4kJmol(-1)). The mutation of the active-site residue Glu198 into Ala completely abolished the activity, suggesting that Glu198 is the ionizable group for pK(e1). On the other hand, no arginine or lysine residues are found in the active site of MMP-7. We proposed a possibility that a protein-bound water is the ionizable group for pK(e2).

Development of a multiple detection technique for fungi by DNA microarray with the simultaneous use of internal transcribed spacer region of ribosomal RNA gene and ß-tubulin gene probes.

We offer the first description of the development of a multiple detection technique for fungi by DNA microarray with the simultaneous use of internal transcribed spacer region (ITS) of ribosomal RNA gene and ß-tubulin gene probes. The assay uses 12 oligonucleotide probes and multiplex amplification to detect fungal species belonging to various sections of Aspergillus, the Eurotium genus, and the Penicillium genus. The specificity of each probe was tested using 231 reference fungal strains, including 79 target and 152 non-target strains in 102 species of 24 genera. We determined the optimum concentration of the primer pairs for multiplex PCR to be 0.5 µM for the ß-tubulin gene and 0.125 µM for the ITS region. In the field trial using 76 specimens containing 323 fungi (up to five fungal strains were included in one specimen), the concordance rate between the DNA microarray and the DNA sequencing results was 97.4％ at the species or genus levels.