Porphyrins and porphines strongly inhibit the action of the RNA subunit of the Escherichia coli ribonuclease P (M1 RNA). Meso-tetrakis(N-methyl-pyridyl) porphine followed linear competitive kinetics with pre-tRNAGly1 from E. coli as variable substrate (Ki 0.960 μM). Protoporphyrin IX showed linear competitive inhibition versus pre-tRNAGly1 from E. coli (Ki 1.90 μM). Inhibition by meso-tetrakis[4-(trimethylammonio) phenyl]porphine versus pre-tRNAGly1 from E. coli followed non-competitive kinetics (Ki 4.1 μM). The porphyrins bound directly to E. coli tRNAVal, E. coli pre-tRNAGly1 and M1 RNA and dissociation constants for the 1:1 complexes were determined using fluorescence spectroscopy. Dissociation constants (μM) against E. coli tRNAVal and E. coli pre-tRNAGly were: meso-tetrakis(N- methyl-pyridyl)porphine 1.21 and 0.170; meso-tetrakis[4-(trimethylammonio) phenyl]porphine, 0.107 and 0.293; protoporphyrin IX, 0.138 and 0.0819. For M1 RNA, dissociation constants were 32.8 nM for meso-tetrakis(N-methyl-pyridyl) porphine and 59.8 nM for meso-tetrakis[4-(trimethylammonio)phenyl]porphine and excitation and emission spectra indicate a binding mode with strong π-stacking of the porphine nucleus and base pairs in a rigid low-polarity environment. Part of the inhibition of ribonuclease P is from interaction with the pre-tRNA substrate, resulting from porphyrin binding to the D-loop/T-loop region which interfaces with M1 RNA during catalysis, and part from the porphyrin binding to the M1 RNA component.
|ジャーナル||Biochimica et Biophysica Acta - Gene Structure and Expression|
|出版物ステータス||Published - 2005 7 25|
ASJC Scopus subject areas
- Structural Biology