The nature of the interaction of eukaryotic initiation factor 2 with double‐stranded RNA

In addition to binding messenger RNA molecules at specific sequences, eukaryotic initiation factor 2 (eIF‐2) also binds to double‐stranded RNA (dsRNA). The dsRNA is a powerful inhibitor of initiation of eukaryotik translation, causing the inactivation of eIF‐2, but in the presence of certain mRNA templates, dsRNA fails to establish inhibition. Such mRNA templates bind to eIF‐2 with higher affinty than does dsRNA, while globin mRNA, a template sensitive to inhibition, binds with lower affinity. Here, the nature of the interaction between dsRNA and eIF‐2 was studied by examining both the binding of eIF‐2 to Penicillium chrysogenum dsRNA molecules carrying ³²P label at their 5′ ends, and the ability of eIF‐2 to protect such label against pancreatic ribonuclease digestion. The results reveal binding sites for eIF‐2 at the 5′ ends, as well as throughout internal regions of the dsRNA molecule. At least 15 molecules of eIF‐2 can be accommodated on a 3000‐base molecule of P. chrysogenum dsRNA eIF‐2 protects a 105‐base‐pair 5′‐terminal fragment in dsRNA against digestion, but exhibits no noticeable preference for the 5′ ends. By contrast, eIF‐2 fails to protect label at the 5′ ends of denatured dsRNA molecules, even though it binds to them at internal sites more avidly than to native dsRNA. Binding of eIF‐2 to dsRNA is not restricted to specific sequences: eIF‐2 binds with equal affinity to the synthetic dsRNA sequence, poly(rI·rC). The data support the interpretation that eIF‐2 recoginzes the A conformation in dsRNA rather than sequence. Apparently binding of eIF‐2 at sites spaced 200 base pairs apart prevents relaxation of the intervening length of the double helix, thereby stabilizing the dsRNA molecule against ribonuclease attack. These results show that, even though dsRNA and mRNA compete in their binding to eIF‐2, the structural features recognized by eIF‐2 in these RNA species are distinct.