title: Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein.
abstract: The mature HIV-1 nucleocapsid protein NCp7 (NC) plays a key role in reverse transcription facilitating the two obligatory strand transfers. Several properties contribute to its efficient chaperon activity: preferential binding to single-stranded regions, nucleic acid aggregation, helix destabilization, and rapid dissociation from nucleic acids. However, little is known about the relationships between these different properties, which are complicated by the ability of the protein to recognize particular HIV-1 stem-loops, such as SL1, SL2, and SL3, with high affinity and without destabilizing them. These latter properties are important in the context of genome packaging, during which NC is part of the Gag precursor. We used NMR to investigate destabilization of the full-length TAR (trans activating response element) RNA by NC, which is involved in the first strand transfer step of reverse transcription. NC was used at a low protein:nucleotide (nt) ratio of 1:59 in these experiments. NMR data for the imino protons of TAR identified most of the base pairs destabilized by NC. These base pairs were adjacent to the loops in the upper part of the TAR hairpin rather than randomly distributed. Gel retardation assays showed that conversion from the initial TAR-cTAR complex to the fully annealed form occurred much more slowly at the 1:59 ratio than at the higher ratios classically used. Nevertheless, NC significantly accelerated the formation of the initial complex at a ratio of 1:59.
authors.affiliation: LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France.
authors.forename: Anissa
authors.initials: A
authors.lastname: Belfetmi
authors.affiliation: LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France.
authors.forename: Loussiné
authors.initials: L
authors.lastname: Zargarian
authors.affiliation: Laboratoire de Cristallographie et RMN biologiques, Université Paris Descartes, CNRS UMR 8015, 75006 Paris Cedex, France.
authors.forename: Carine
authors.initials: C
authors.lastname: Tisné
authors.affiliation: Laboratoire de Cristallographie et RMN biologiques, Université Paris Descartes, CNRS UMR 8015, 75006 Paris Cedex, France.
authors.forename: Dona
authors.initials: D
authors.lastname: Sleiman
authors.affiliation: Centre de Recherches de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 91190 Gif sur Yvette Cedex, France.
authors.forename: Nelly
authors.initials: N
authors.lastname: Morellet
authors.affiliation: Centre de Recherches de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 91190 Gif sur Yvette Cedex, France.
authors.forename: Ewen
authors.initials: E
authors.lastname: Lescop
authors.affiliation: LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France.
authors.forename: Ouerdia
authors.initials: O
authors.lastname: Maskri
authors.affiliation: LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France.
authors.forename: Brigitte
authors.initials: B
authors.lastname: René
authors.affiliation: Laboratoire de Biophotonique et Pharmacologie, CNRS UMR 7213, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch Cedex, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Mély
authors.affiliation: LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Fossé
authors.affiliation: LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Mauffret
mesh_terms: D001483:Base Sequence; D015497:HIV-1 / Q000235:genetics*; D055029:Inverted Repeat Sequences; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D020871:RNA Stability; D012367:RNA, Viral / Q000737:chemistry*; D020218:Response Elements; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000737:chemistry*
chemical_list: C071884:NCP7 protein, Human immunodeficiency virus 1; D012367:RNA, Viral; D054301:gag Gene Products, Human Immunodeficiency Virus
keywords: HIV-1 nucleocapsid protein; NMR spectroscopy; imino protons; kinetic model; nucleic acid dynamics
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