Scaffold-independent analysis of RNA-protein interactions: the Nova-1 KH3-RNA complex.
We describe a method to analyze the sequence specificity of an RNA-binding domain. The method, which we have named scaffold-independent analysis, reports on the specificity for each nucleotide position within an RNA target, uncoupled from the surrounding structural and sequence context. We expect this information to improve our understanding of protein-RNA interfaces in ssRNA binding domains (e.g., KH or RRM domains) and to be useful to the design of novel protein-RNA recognition surfaces. Our NMR binding assays using the third KH domain of the Nova-1 protein provide a proof-of-principle for the method and novel information on the specificity of this domain for its RNA targets.
Beuth
Barbara
B
Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, U.K.
García-Mayoral
María Flor
MF
Taylor
Ian A
IA
Ramos
Andres
A
D000951:Antigens, Neoplasm / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000378:metabolism; D000090682:Neuro-Oncological Ventral Antigen; D019906:Nuclear Magnetic Resonance, Biomolecular; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism
D000951:Antigens, Neoplasm; D009419:Nerve Tissue Proteins; D000090682:Neuro-Oncological Ventral Antigen; D016601:RNA-Binding Proteins; D012313:RNA