Structural variety of arginine-rich RNA-binding peptides.

Abstract

Arginine-rich domains are used by a variety of RNA-binding proteins to recognize specific RNA hairpins. It has been shown previously that a 17-aa arginine-rich peptide from the human immunodeficiency virus Rev protein binds specifically to its RNA site when the peptide is in an a-helical conformation. Here (2), and in the third primarily to the phosphate backbone (3). Important contacts also are made to anticodon loop nucleotides (1, 2). The cocrystal structure of an R17 phage coat protein-RNA complex shows important contacts to bulge and loop nucleotides of an RNA hairpin (4). These studies provide detailed views of RNA-protein interactions and include rather different types of protein structures. In other RNA-binding proteins, conserved sequence motifs are found that suggest similar structures (5, 6). One motif, the arginine-rich motif, consists of a short region of basic amino acids (-8-20 residues in length) particularly rich in arginine. This motif is found in bacterial antiterminators, ribosomal proteins, coat proteins from RNA viruses, the human immunodeficiency virus (HIV) Tat and Rev proteins (7), and the bovine immunodeficiency virus (BIV) Tat protein (8).Studies with model peptides from HIV Rev, HIV Tat, and BIV Tat have shown that isolated arginine-rich domains can bind RNA with high affinity and recognize features of the RNA similar to the intact proteins (8-13). In HIV Rev, a 17-aa peptide binds specifically to RRE RNA when the peptide is in an a-helical conformation and requires six amino acids (four arginines, one threonine, and one asparagine) for binding (9).NMR studies indicate that Rev peptide binding stabilizes the structure of an internal RNA loop, forming G-G and G-A base pairs and two looped-out bases (14, 15). In HIV Tat, a single arginine residue in the arginine-rich domain is largely responsible for recognition of a bulge region in TAR RNA (12), and arginine, even as the free amino acid, binds to TAR in the sameThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. manner as in the Tat peptide (16), suggesting that a defined peptide conformation may not be needed for recognition. An NMR model of the TAR-arginine complex suggests that the arginine guanidinium group hydrogen bonds to a guanine base in the major groove and to two phosphates and that the complex is stabilized by a base triple interaction between a U in the bulge and an AU base pair above the bulge (17). Recent NMR studies of the equine infectious anemia virus (EIAV) Tat protein (18) and of a peptide containing the HIV Tat arginine-rich domain fused to the core regulatory domain of EIAV Tat (19) have suggested that these arginine-rich domains have a tendency to form a-helices, but it is not known whether they are helical when bound to RNA.To better define the structural repertoire of the argininerich RNA-binding motif, we have examined the RNA-binding and confo...

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