title: Comparative analysis of RNA/protein dynamics for the arginine-rich-binding motif and zinc-finger-binding motif proteins encoded by HIV-1.
abstract: We report a comparative study in which a single-molecule fluorescence resonance energy transfer approach was used to examine how the binding of two families of HIV-1 viral proteins to viral RNA hairpins locally changes the RNA secondary structures. The single-molecule fluorescence resonance energy transfer results indicate that the zinc finger protein (nucleocapsid) locally melts the TAR RNA and RRE-IIB RNA hairpins, whereas arginine-rich motif proteins (Tat and Rev) may strengthen the hairpin structures through specific binding interactions. Competition experiments show that Tat and Rev can effectively inhibit the nucleocapsid-chaperoned annealing of complementary DNA oligonucleotides to the TAR and RRE-IIB RNA hairpins, respectively. The competition binding data presented here suggest that the specific nucleic acid binding interactions of Tat and Rev can effectively compete with the general nucleic acid binding/chaperone functions of the nucleocapsid protein, and thus may in principle help regulate critical events during the HIV life cycle.
authors.affiliation: Department of Chemistry and Biochemistry, University of Texas, Austin, TX, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Ma
authors.forename: Yu-Shan
authors.initials: YS
authors.lastname: Yeh
authors.forename: Yongjin
authors.initials: Y
authors.lastname: Zhu
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Daugherty
authors.forename: Alan D
authors.initials: AD
authors.lastname: Frankel
authors.forename: Karin
authors.initials: K
authors.lastname: Musier-Forsyth
authors.forename: Paul F
authors.initials: PF
authors.lastname: Barbara
mesh_terms: D000595:Amino Acid Sequence; D001120:Arginine / Q000378:metabolism*; D001483:Base Sequence; D024202:Electrophoretic Mobility Shift Assay; D031541:Fluorescence Resonance Energy Transfer; D016325:HIV Long Terminal Repeat / Q000235:genetics; D015497:HIV-1 / Q000378:metabolism*; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D019590:Nucleocapsid Proteins / Q000378:metabolism*; D011485:Protein Binding; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020218:Response Elements / Q000235:genetics; D016335:Zinc Fingers; D054321:rev Gene Products, Human Immunodeficiency Virus / Q000737:chemistry / Q000378:metabolism*; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000737:chemistry / Q000378:metabolism*
chemical_list: D019590:Nucleocapsid Proteins; D012367:RNA, Viral; D054321:rev Gene Products, Human Immunodeficiency Virus; D054322:tat Gene Products, Human Immunodeficiency Virus; D001120:Arginine