MOLECULAR RECOGNITION IN THE BOVINE IMMUNODEFICIENCY VIRUS TAT PEPTIDE TAR RNA COMPLEX

Background: In lentiviruses such as human immunodeficiency virus (HIV) and bovine immunodeficiency virus (BIV), the Tat (trans-activating) p rotein enhances transcription of the viral RNA by complexing to the 5' -end of the transcribed mRNA, at a region known as TAR (the trans-acti vation response element). Identification of the determinants that acco unt for specific molecular recognition requires a high resolution stru cture of the Tat peptide-TAR RNA complex. Results: We report here on t he structural characterization of a complex of the recognition domains of BIV Tat and TAR in aqueous solution using a combination of NMR and molecular dynamics. The 17-mer Tat peptide recognition domain folds i nto a beta-hairpin and penetrates in an edge-on orientation deep into a widened major groove of the 28-mer TAR RNA recognition domain in the complex. The RNA fold is defined, in part, by two uracil bulged bases ; U12 has a looped-out conformation that widens the major groove and U 10 forms a U . AU base triple that buttresses the RNA helix. Together, these bulged bases induce a similar to 40 degrees bend between the tw o helical stems of the TAR RNA in the complex. A set of specific inter molecular hydrogen bonds between arginine side chains and the major-gr oove edge of guanine residues contributes to sequence specificity. The se peptide-RNA contacts are complemented by other intermolecular hydro gen bonds and intermolecular hydrophobic packing contacts involving gl ycine and isoleucine side chains. Conclusions: We have identified a ne w structural motif for protein-RNA recognition, a beta-hairpin peptide that interacts :vith the RNA major groove. Specificity is associated with formation of a novel RNA structural motif, a U . AU base triple, which facilitates hydrogen bonding of an arginine residue to a guanine and to a backbone phosphate. These results should facilitate the desi gn of inhibitors that can disrupt HIV Tar-TAR association.