Structural characterization of the complex of the Rev response element RNAwith a selected peptide

Introduction: The RSG-1.2 peptide was selected for specific binding to the Rev response element RNA, as the natural Rev peptide does. The RSG-1.2 sequ ence has features incompatible with the helical structure of the bound Rev peptide, indicating that it must bind in a different conformation. Results: The binding of the RSG-1,2 peptide to the Rev response element RNA was characterized using multinuclear, multidimensional NMR. The RSG-1.2 pe ptide is shown to bind with the N-terminal segment of the peptide along the major groove in an extended conformation and turn preceding a C-terminal h elical segment, which crosses the RNA groove in the region widened by the p resence of purine-purine base pairs. These features make the details of the bound state rather different than that of the Rev peptide which targets th e same RNA sequence binding as a single helix along the groove axis. Conclusions: These studies further demonstrate the versatility of arginine- rich peptides in recognition of specific RNA elements and the lack of conse rved structural features in the bound state. (C) 2001 Elsevier Science Ltd. All rights reserved.