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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.

SUBMITTER: Seebald LM

PROVIDER: S-EPMC5956527 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.

Seebald Leah M LM DeMott Christopher M CM Ranganathan Srivathsan S Asare-Okai Papa Nii PN Glazunova Anastasia A Chen Alan A Shekhtman Alexander A Royzen Maksim M

Journal of inorganic biochemistry 20170224

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 Co<sup>2+</sup>-based probe that can be covalently attached to RNA in the vicinity of the protein's binding site using 'click' chemistry. Similar to nitro ...[more]

PMID: 28260679

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