IRON REGULATORY ELEMENT AND INTERNAL LOOP BULGE STRUCTURE FOR FERRITIN MESSENGER-RNA STUDIED BY COBALT(III) HEXAMMINE BINDING, MOLECULAR MODELING, AND NMR-SPECTROSCOPY/

The ferritin IRE, a highly conserved (96-99% in vertebrates) mRNA tran slation regulatory element in animal mRNA, was studied by molecular mo deling (using MC-SYM and DOCKING) and by NMR spectroscopy. Cobalt(III) hexammine was used to model hydrated Mg2+ IRE isoforms in other mRNAs regulate mRNA translation or stability; all IREs bind IRPs (iron regu latory proteins). A G.C base pair, conserved in ferritin IREs, spans a n internal loop/bulge in the middle of an A-helix and, combined with a dynamic G.U base pair, formed a pocket suitable for Co(III) hexammine binding. On the basis of the effects of Co(III) hexammine on the H-1 NMR spectrum and results of automatic docking into the IRE model, the IRE bound Co(III) hexammine at the pocket in the major groove; Mg2+ ma y bind to the IRE at the same site on the basis of an analogy to Co(II I) hexammine and on the Mg2+ inhibition of Cu(phen)(2) cleavage at the site. Distortion of the IRE helix by the internal loop/bulge near a c onserved unpaired C required for IRP binding and adjacent to an IRP cr oss-linking site suggests a role for the pocket in ferritin IRE/IRP in teractions.