Poly(A) tail affects equilibrium and thermodynamic behavior of tobacco etch virus mRNA with translation initiation factors eIF4F, eIF4B and PABP

We have investigated the effects of poly(A)-tail on binding of eIF4F, eIF4B and PABP with tobacco etch virus (TEV) IRES RNA. The fluorescence anisotropy data showed that the addition of poly(A)20 increases the binding affinity of eIF4F·4B and eIF4F·PABP complexes to IRES RNA ~ 2- and 4-fold, respectively. However, the binding affinity of eIF4F with PK1 was enhanced ~ 11-fold with the addition of PABP, eIF4B, and poly(A)20 together. Whereas, poly(A)20 alone increases the binding affinity of eIF4F·4B·PABP with PK1 RNA about 3-fold, showing an additive effect rather than the large increase in affinity as shown for cap binding. Thermodynamic data showed that PK1 RNA binding to protein complexes in the presence of poly(A)20 was enthalpy-driven and entropy-favorable. Poly(A)20 decreased the entropic contribution 75% for binding of PK1 RNA to eIF4F·4B·PABP as compared to eIF4F alone, suggesting reduced hydrophobic interactions for complex formation and an overall conformational change. Overall, these results demonstrate the first direct effect of poly(A) on the equilibrium and thermodynamics of eIF4F and eIF4F·4B·PABP with IRES-RNA.

Research Highlights
► The binding affinity of eIF4F with TEV PK1 RNA was enhanced 11-fold with eIF4B, PABP and Poly(A)20.
► Poly(A)20 alone enhanced binding of the protein complex 3-fold, an additive rather than synergistic effect.
► PK1 binding to protein complexes in the presence of Poly(A)20 was enthalpy driven and entropy favorable.
► Poly(A)20 decreased the entropy of binding by 75%, suggesting an overall conformational change in the protein complex.