Screening protein – Single stranded RNA complexes by NMR spectroscopy for structure determination

• Published in: Methods (San Diego, Calif.) Vol. 65; no. 3; pp. 288 - 301
• Main Authors: Foot, Jaelle N., Feracci, Mikael, Dominguez, Cyril
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-02-2014; Academic Press
• Subjects: Adaptor Proteins, Signal Transducing - chemistry; Adaptor Proteins, Signal Transducing - genetics; Amino Acid Sequence; Aptamers, Nucleotide - chemical synthesis; Aptamers, Nucleotide - chemistry; Binding Sites; Crystallography, X-Ray; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; Escherichia coli - genetics; Escherichia coli - metabolism; Gene Expression; Humans; Magnetic Resonance Spectroscopy; Molecular Sequence Data; NMR spectroscopy; Protein Binding; Protein Structure, Tertiary; Protein–RNA complex; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; Sam68; Sequence Alignment; Sequence Homology, Amino Acid; STAR proteins; T-STAR; Protein–RNA complex; T-STAR; NMR spectroscopy; STAR proteins; Sam68
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1016/j.ymeth.2013.09.018

In the past few years, RNA molecules have been revealed to be at the center of numerous biological processes. Long considered as passive molecules transferring genetic information from DNA to proteins, it is now well established that RNA molecules play important regulatory roles. Associated with that, the number of identified RNA binding proteins (RBPs) has increased considerably and mutations in RNA molecules or RBP have been shown to cause various diseases, such as cancers. It is therefore crucial to understand at the molecular level how these proteins specifically recognise their RNA targets in order to design new generation drug therapies targeting protein–RNA complexes. Nuclear magnetic resonance (NMR) is a particularly well-suited technique to study such protein–RNA complexes at the atomic level and can provide valuable information for new drug discovery programs. In this article, we describe the NMR strategy that we and other laboratories use for screening optimal conditions necessary for structural studies of protein-single stranded RNA complexes, using two proteins, Sam68 and T-STAR, as examples.