pH-dependent and ligand induced conformational changes of eucaryotic protein synthesis initiation factor eIF-(iso)4F:...

The structural features of wheat germ protein synthesis initiation factor eIF-(iso)4F, which has a cap binding protein as one of its two subunits, are unknown. In this study, circular dichroism (CD) spectra and secondary structure prediction were obtained for eIF-(iso)4F and its two subunits, p28 and p86. The alpha-helix content of eIF-(iso)4F changed from 42% at pH 6.3 to 15% at pH 7.6, the optimum pH for cap binding. The beta-sheet content increased from 14% (pH 6.3) to 38% at pH 7.6. The CD spectra of the two subunits, p28 and p86 were also measured and analyzed. The separated subunits both had a higher alpha-helix content at pH 7.6 than the native protein, giving values of 60% and 34% alpha-helix for p28 and p86, respectively. Binding of the dinucleotide cap analog to p28 reduced the alpha-helix content to approximately 8% with an increase in the beta sheet content from 10% to 37%. The conformational changes in eIF-(iso)4F upon binding with mRNA are dependent on cap or oligonucleotide structure. A conformation consisting of approximately the same alpha-helix and beta-sheet content can be induced by ligands even at non-optimal pH values. This large conformational transition suggests eIF-(iso)4F binds nucleic acids by interaction of a beta-sheet motif and that this conformational transition may have a regulatory role.