Ribosome-inactivating proteins (RIPs) are naturally occurring cytotoxic N-glycosidase agents and are found in numerous plant, fungi, and bacterial species. They inhibit protein synthesis by depurinating A4324 on the conserved sarcin/ricin loop (SRL) of the 28S rRNA. Pokeweed Antiviral Protein (PAP) is a type I RIP that has also long been recognized as an important antiviral agent. It is also able to inhibit infection without loss of host cell translation.

We report in vitro fluorescence spectroscopic studies of PAP-eIFiso4G binding revealing a binary interaction with a Kd of approximately 100 nM. This interaction enhances PAP's binding to the cap analog m⁷GTP 3.6-fold. Our measurements place PAP's affinity for cap between that of the wheat germ cap binding proteins eIFiso4E and eIFiso4F. ATP and GTP compete with cap for PAP binding; both nucleotides and the cap analog show little salt dependence in binding, suggesting that the interactions are specific for these nucleotides. The biological significance of the cap binding remains unclear, however this may serve as a means to target RNA or, since ATP binds to the same site, this may be a protective mechanism for host cell capped RNA. The interaction with eIFiso4G suggests that additional proteins may aid PAP in accessing particular RNA and distinguish structural elements of the RNA. These results support a model where PAP's interaction with initiation factors may play a regulatory role in its enzymatic activity. PAP's binding to the SRL oligonucleotide sequence was measured; it is weaker than for cap analog and is described.