Peptide-triggered conformational switch in HIV-1 RRE RNA complexes

We have used NMR spectroscopy to determine the solution structure of a comp lex between an oligonncleotide derived from stem IIB of the Rev responsive element (RRE-IIB) of HIV-I mRNA and an in vivo selected, high affinity bind ing Arg-rich peptide. The peptide binds in a partially alpha -helical confo rmation into a pocket within the RNA deep groove. Comparison with the struc ture of a complex between an alpha -helical Rev peptide and RRE-IIB reveals that the sequence of the bound peptide determines the local conformation o f the RRE peptide binding site. A conformational switch of an unpaired urid ine base was revealed; this points out into the solvent in the Rev peptide complex, but it is stabilized inside the RNA deep groove by stacking with a n Arg side chain in the selected peptide complex. The conformational switch has been visualized by NMR chemical shift mapping of the uridine H5/H6 ato ms during a competition experiment in which Rev peptide was displaced from RRE-IIB by the higher affinity binding selected peptide.