title: Dynamics of linker residues modulate the nucleic acid binding properties of the HIV-1 nucleocapsid protein zinc fingers.
abstract: The HIV-1 nucleocapsid protein (NC) is a small basic protein containing two zinc fingers (ZF) separated by a short linker. It is involved in several steps of the replication cycle and acts as a nucleic acid chaperone protein in facilitating nucleic acid strand transfers occurring during reverse transcription. Recent analysis of three-dimensional structures of NC-nucleic acids complexes established a new property: the unpaired guanines targeted by NC are more often inserted in the C-terminal zinc finger (ZF2) than in the N-terminal zinc finger (ZF1). Although previous NMR dynamic studies were performed with NC, the dynamic behavior of the linker residues connecting the two ZF domains remains unclear. This prompted us to investigate the dynamic behavior of the linker residues. Here, we collected 15N NMR relaxation data and used for the first time data at several fields to probe the protein dynamics. The analysis at two fields allows us to detect a slow motion occurring between the two domains around a hinge located in the linker at the G35 position. However, the amplitude of motion appears limited in our conditions. In addition, we showed that the neighboring linker residues R29, A30, P31, R32, K33 displayed restricted motion and numerous contacts with residues of ZF1. Our results are fully consistent with a model in which the ZF1-linker contacts prevent the ZF1 domain to interact with unpaired guanines, whereas the ZF2 domain is more accessible and competent to interact with unpaired guanines. In contrast, ZF1 with its large hydrophobic plateau is able to destabilize the double-stranded regions adjacent to the guanines bound by ZF2. The linker residues and the internal dynamics of NC regulate therefore the different functions of the two zinc fingers that are required for an optimal chaperone activity.
authors.affiliation: Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8113, Cachan, France.
authors.forename: Loussiné
authors.initials: L
authors.lastname: Zargarian
authors.affiliation: Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015, Paris, France.
authors.forename: Carine
authors.initials: C
authors.lastname: Tisné
authors.affiliation: Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Barraud
authors.affiliation: Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8113, Cachan, France; Department of Life Sciences, East China Normal University, Shanghai, People's Republic of China.
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Xu
authors.affiliation: Centre de Recherches de Gif, Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique, Gif sur Yvette, France.
authors.forename: Nelly
authors.initials: N
authors.lastname: Morellet
authors.affiliation: Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8113, Cachan, France.
authors.forename: Brigitte
authors.initials: B
authors.lastname: René
authors.affiliation: Laboratoire de Biophotonique et Pharmacologie, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7213, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Mély
authors.affiliation: Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8113, Cachan, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Fossé
authors.affiliation: Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8113, Cachan, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Mauffret
mesh_terms: D004247:DNA / Q000378:metabolism*; D015497:HIV-1; D008958:Models, Molecular; D019590:Nucleocapsid Proteins / Q000737:chemistry* / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*; D012399:Rotation; D016335:Zinc Fingers
chemical_list: D019590:Nucleocapsid Proteins; D012313:RNA; D004247:DNA