Fig. 4: Structure–activity relationships of ProSeDMA derivatives.
From: Structure and catalytic activity of the SAM-utilizing ribozyme SAMURI
a, Chemical structure of ProSeDMA. Color code representing the methionine amide unit (blue) and nucleoside unit (orange). b, Mutations of the methionine unit. c, Mutations of the nucleoside unit. d, Kinetics of transpropargylation with ProSeDMA derivatives. The kobs values were obtained under pseudo-first-order reaction conditions for 60 min. For ProSeDBA 7, ProSeDM 8a/b, ProSeNMA 11, ProSeGMA 12 and ProSeMA 13, incubation was extended to 4 h and a linear fit was applied for 8b and 11. Asterisks denote kobs values reported in a previous study43. e, Gel image showing product formation with ProSeDMA derivatives. Reaction conditions: 1 µM Cy5-labeled substrate R1 (Supplementary Table 1), 10 µM SAMURI wild type (R4), 10 µM ProSeDMA derivatives, 10 mM MgCl2, 37 °C, 0.5 h. Representative gel image of three individual experiments. f, Stability comparison of ProSeDMA 1a and ProSeDAB 5. Here, 1 mM cofactor was incubated in 50 mM HEPES (pH 7.0), 120 mM KCl, 5 mM NaCl and 10 mM MgCl2 at 37 °C for 15 h and analyzed by RP-HPLC. In d, individual data points and the mean ± s.d. of three independent experiments are shown.
