Designer nucleic-acid-binding proteins show potential in their ability to be reprogrammed in both binding target and overall protein function. The family of pentatricopeptide repeat (PPR) proteins is found widely in land plants with over 400 members, but only seven currently known in human cells (1,2). PPR proteins are characterised by degenerate 35 amino acid repeats that form repetitive helix-turn-helix motifs that are involved in binding individual RNA bases. Amino acids at specific residues are known to confer binding specificity of each repeat for target RNA bases (3). These proteins are found to be involved in inhibition of nuclease activity, altering the secondary structure of mRNA, and participation in RNA editing and maturation (2).
Designer PPR proteins have already successfully been targeted to novel RNA sequences (in vitro) thereby highlighting their potential use as biotechnological tools. Following our previously-published structure of a designer PPR protein (3), we have now solved the structure of a complex with RNA. Comparison of the structures of these designer proteins in their bound and unbound states reveals insight into the RNA-binding mechanisms of the PPR family of proteins. Interestingly, while the width and cylindrical gap inside remain almost unchanged between bound and unbound forms, a change of the pitch between alpha-helices of each repeat results in a significant change to the overall conformation, analogous to the compression of a spring. With this additional structural and mechanistic information, we draw closer to fully understanding the PPR binding code and how to effectively target them to new RNA sequences and for new purposes.