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Tethered hydroxyl-radical probing has been used to determine the orientation of binding of polypyrimidine tract-binding protein (PTB) to the poliovirus type 1 (Mahoney) (PV-1(M)) internal ribosome entry site/segment (IRES)-the question of which RNA-binding domain (RBD) binds to which sites on the IRES. The results show that under conditions in which PTB strongly stimulates IRES activity, a single PTB is binding to the IRES, a finding which was confirmed by mass spectrometry of PTB/IRES complexes. RBDs1 and 2 interact with the basal part of the Domain V irregular stem loop, very close to the binding site of eIF4G, and RBDs3 and 4 interact with the single-stranded regions flanking Domain V. The binding of PTB is subtly altered in the presence of the central domain (p50) of eIF4G, and p50 binding is likewise modified if PTB is present. This suggests that PTB stimulates PV-1(M) IRES activity by inducing eIF4G to bind in the optimal position and orientation to promote internal ribosome entry, which, in PV-1(M), is at an AUG triplet 30 nt downstream of the base of Domain V.

Original publication




Journal article



Publication Date





3710 - 3722


Base Pairing, Base Sequence, Binding Sites, Codon, Initiator, Encephalomyocarditis virus, Eukaryotic Initiation Factor-4G, Molecular Sequence Data, Nucleic Acid Conformation, Poliovirus, Polypyrimidine Tract-Binding Protein, Protein Biosynthesis, Protein Structure, Tertiary, RNA, Viral, Ribosomes, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization