Recognition of diverse RNAs by a single protein structural framework

The coat proteins of different single-strand RNA phages utilize a common structural framework to recognize different RNA targets, making them suitable models for studies of RNA–protein recognition generally, especially for the class of proteins that bind RNA on a β-sheet surface. Here we show that structurally distinct molecules are capable of satisfying the requirements for binding to Qβ coat protein. Although the predicted secondary structures of the RNAs differ markedly, we contend that they are approximately equivalent structurally in their complexes with coat protein. Based on our prior observations that the RNA-binding specificities of Qβ and MS2 coat proteins can be interconverted with as few as one amino acid substitution each, and taking into account details of the structures of complexes of MS2 coat protein with wild-type and aptamer RNAs, we propose a model for the Qβ coat protein–RNA complex.