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

Mutations on the periphery of the central pocket have differential effects on the binding of seven RNAs. (A) The location of substitutions on the AlphaFold model of ProQ^NTD (Varadi et al. 2022). (B) The raw gel data for 1 nM ³²P-labeled malM-3′ binding to the five proteins. (C) The plots of fraction bound versus protein concentration for the binding of cspE-3′, cspE81-3′, gapA-3′, malM-3′, RybB, SibA, and SibB RNAs to WT ProQ^NTD, and R32A, D41A, K35A, and R69A mutants measured using the gel shift assay. The data sets in which the maximum fraction bound was above 40% were analyzed by fitting to the quadratic equation. Raw gel data for all RNAs are presented in Supplemental Figures S7–S13. The obtained K_d values are shown in Table 1.