Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR
Publication date: Available online 24 February 2017
Source:Journal of Inorganic Biochemistry
Author(s): Leah M. Seebald, Christopher M. DeMott, Srivathsan Ranganathan, Papa Nii Asare Okai, Anastasia Glazunova, Alan Chen, Alexander Shekhtman, Maksim Royzen
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 constructing the protein's contact surface map. This new paradigm has been applied to study binding of HIV-1 nucleocapsid protein, NCp7, to a model RNA pentanucleotide.
Graphical abstract
More...