Biochemical and genetic dissection of the RNA-binding surface of the FinO domain of Escherichia coli ProQ

The substitutions of peripheral residues K35 and R69 have indirect effects on the RNA binding in the central pocket of the ProQ^NTD. The RNA secondary structures were predicted using RNAstructure software (Reuter and Mathews 2010). The data sets in which the maximum fraction bound was above 40% were analyzed by fitting to the quadratic equation. Data for cspE-3′ are the same as in Figures 3 and 4. The average equilibrium dissociation constant (K_d) values are shown in Table 3, and raw gel data are presented in Supplemental Figure S16.