title: Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.
abstract: Paramagnetic resonance enhancement (PRE) is an NMR technique that allows studying three-dimensional structures of RNA-protein complexes in solution. RNA strands are typically spin labeled using nitroxide reagents, which provide minimal perturbation to the native structure. The current work describes an alternative approach, which is based on a Co2+-based probe that can be covalently attached to RNA in the vicinity of the protein's binding site using 'click' chemistry. Similar to nitroxide spin labels, the transition metal based probe is capable of attenuating NMR signal intensities from protein residues localized <40Å away. The extent of attenuation is related to the probe's distance, thus allowing for construction of the protein's contact surface map. This new paradigm has been applied to study binding of HIV-1 nucleocapsid protein 7, NCp7, to a model RNA pentanucleotide.
authors.affiliation: Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States.
authors.forename: Leah M
authors.initials: LM
authors.lastname: Seebald
authors.affiliation: Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: DeMott
authors.affiliation: Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States.
authors.forename: Srivathsan
authors.initials: S
authors.lastname: Ranganathan
authors.affiliation: Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States.
authors.forename: Papa Nii
authors.initials: PN
authors.lastname: Asare-Okai
authors.affiliation: Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States.
authors.forename: Anastasia
authors.initials: A
authors.lastname: Glazunova
authors.affiliation: Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States.
authors.forename: Alan
authors.initials: A
authors.lastname: Chen
authors.affiliation: Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States.
authors.forename: Alexander
authors.initials: A
authors.lastname: Shekhtman
authors.affiliation: Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States. Electronic address: mroyzen@albany.edu.
authors.forename: Maksim
authors.initials: M
authors.lastname: Royzen
mesh_terms: D057930:Click Chemistry; D003035:Cobalt / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy; D015497:HIV-1 / Q000737:chemistry*; D015335:Molecular Probes / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D012367:RNA, Viral / Q000737:chemistry*; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000737:chemistry*
chemical_list: D015335:Molecular Probes; C071884:NCP7 protein, Human immunodeficiency virus 1; D012367:RNA, Viral; D054301:gag Gene Products, Human Immunodeficiency Virus; D003035:Cobalt
keywords: Cobalt; HIV-1; HSQC; NCp7; Paramagnetic NMR; RNA-protein interactions