title: Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex.
abstract: The solution structure of a human immunodeficiency virus type-1 (HIV-1) Rev peptide bound to stem-loop IIB of the Rev response element (RRE) RNA was solved by nuclear magnetic resonance spectroscopy. The Rev peptide has an alpha-helical conformation and binds in the major groove of the RNA near a purine-rich internal loop. Several arginine side chains make base-specific contacts, and an asparagine residue contacts a G.A base pair. The phosphate backbone adjacent to a G.G base pair adopts an unusual structure that allows the peptide to access a widened major groove. The structure formed by the two purine-purine base pairs of the RRE creates a distinctive binding pocket that the peptide can use for specific recognition.
authors.affiliation: Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: J L
authors.initials: JL
authors.lastname: Battiste
authors.forename: H
authors.initials: H
authors.lastname: Mao
authors.forename: N S
authors.initials: NS
authors.lastname: Rao
authors.forename: R
authors.initials: R
authors.lastname: Tan
authors.forename: D R
authors.initials: DR
authors.lastname: Muhandiram
authors.forename: L E
authors.initials: LE
authors.lastname: Kay
authors.forename: A D
authors.initials: AD
authors.lastname: Frankel
authors.forename: J R
authors.initials: JR
authors.lastname: Williamson
mesh_terms: D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry; D001216:Asparagine / Q000737:chemistry; D001482:Base Composition; D001483:Base Sequence; D004268:DNA-Binding Proteins; D005656:Fungal Proteins / Q000737:chemistry; D015694:Gene Products, rev / Q000737:chemistry* / Q000378:metabolism*; D015752:Genes, env; D015497:HIV-1 / Q000737:chemistry*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011494:Protein Kinases / Q000737:chemistry; D017433:Protein Structure, Secondary; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins; D013912:Threonine / Q000737:chemistry; D054321:rev Gene Products, Human Immunodeficiency Virus
chemical_list: D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D015694:Gene Products, rev; D012367:RNA, Viral; D029701:Saccharomyces cerevisiae Proteins; D054321:rev Gene Products, Human Immunodeficiency Virus; D013912:Threonine; D001216:Asparagine; D001120:Arginine; D011494:Protein Kinases