RNA recognition by arginine-rich peptide motifs.

A ubiquitious class of RNA-binding proteins is distinguished by an arginine-rich motif. Such proteins function in transcription, translation, RNA trafficking, and packaging. Peptide models are derived from viral regulatory proteins, including the virulence factors Tat and Rev of mammalian immunodeficiency viruses. Structures of model peptide-RNA complexes exhibit diverse strategies of recognition based in each case on structural transitions. Induced RNA structures contain noncanonical elements such as purine-purine mismatches, base triples, and flipped bases. Such elements enlarge and extend the RNA major groove to create specific peptide-binding pockets and surfaces. The repertoire of bound peptide structures--beta-hairpin, alpha-helix, and helix-bend-helix-reflects the diversity of induced RNA architectures. This repertoire, reminiscent of primordial exon-encoded peptides, may recapitulate early events in the transition between RNA and protein worlds. Peptide-directed changes in modern RNA structures can provide a mechanism of signaling in higher-order RNA-protein assemblies.