Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples

Background: The Rex protein of the human T cell leukemia virus type 1 (HTLV -1) belongs to a family of proteins that use arginine-rich motifs (ARMs) to recognize their RNA targets. Previously, an in vitro selected RNA aptamer sequence was identified that mediates mRNA transport in vivo when placed in the primary binding site on stem-loop IID of the Rex response element, We present the solution structure of the HTLV-1 arginine-rich Rex peptide boun d to its RNA aptamer target determined by multidimensional heteronuclear NM R spectroscopy, Results: The Rex peptide in a predominantly extended conformation threads t hrough a channel formed by the shallow and widened RNA major groove and a l ooped out guanine, The RNA aptamer contains three stems separated by a pair of two-base bulges, and adopts an unanticipated fold in which both junctio nal sites are anchored through base triple formation, Binding specificity i s associated with intermolecular hydrogen bonding between guanidinium group s of three non-adjacent arginines and the guanine base edges of three adjac ent G.C pairs. Conclusions: The extended S-shaped conformation of the Rex peptide, togethe r with previous demonstrations of a beta-hairpin conformation for the bovin e immunodeficiency virus (BIV) Tat peptide and an alpha-helical conformatio n for the human immunodeficiency virus (HIV) Rev peptide in complex with th eir respective RNA targets, expands our understanding of the strategies emp loyed by ARMs for adaptive recognition and highlights the importance of RNA tertiary structure in accommodating minimalist elements of protein seconda ry structure.