A proton-coupled conformational switch of Escherichia coli 5S ribosomal RNA.

We report temperature-jump kinetic studies of the early melting transition of Escherichia coli 5S rRNA. A single measurable relaxation time tau, independent of concentration, was found at 266 nm. We monitored the transition temperature tm for this process (in the range from 0 to 40 degrees C) as a function of Mg2+, Na+, K+, spermidine, and H+ concentrations. Contrary to the usual effect of salts on nucleic acid stability, addition of mono- and multivalent counterions decreases tm for the early melting transition. Also unexpectedly, we found a strong dependence of tm on pH in the physiological range of 7--8. Quantitative analysis of the data indicates that about 0.7 protons are release when the ordered (low-temperature) form melts, whereas about 2 NA+ (or K+) and 0.5 Mg2+ are taken up by the melted (high-temperature) form. We estimate the enthalpy of the transition to be 15--20 kcal/mol (63--84 kJ/mol) and also report the forward and reverse rate constants and activation energies for the transition, along with the influence of ions on the transition dynamics. Diffusion constant measurements reveal that the low-temperature form has a frictional coefficient about 10% larger than that of the high-temperature form. The data imply a low-temperature tertiary structure capable of binding a proton. Increase of pH, temperature, or counterion concentration (all at near-physiological values) causes a tertiary conformational switch to a more compact form that has greater counterion binding but less proton binding. We discuss possible physiological roles for the transition.