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

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Abstract
Temperature-jump kinetic studies of the early melting transition of E. coli 5S rRNA are reported. A single measurable relaxation time .tau., independent of concentration, was found at 266 nm. The transition temperature tm for this process (in the range from 0-40.degree. C) as a function of Mg2+, Na+, K+, spermidine and H+ concentrations was monitored. Contrary to the usual effect of salts on nucleic acid stability, addition of mono- and multivalent counterions decreases tm for the early melting transition. A strong dependence of tm on pH in the physiological range of 7-8 was found. Quantitative analysis of the data indicates that about 0.7 protons are released 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. The enthalpy of the transition was estimated to be 15-20 kcal/mol (63-84 kJ/mol); the forward and reverse rate constant and activation energies for the transition, along with the influence of ions on the transition dynamics are reported. 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. Possible physiological roles for the transition are discussed.