In eukaryotic cells, a multitude of RNA-binding proteins play key roles in the posttranscriptional regulation of gene expression. Characterization of these proteins has led to the identification of several RNA-binding motifs, and recent experiments have begun to illustrate how several of them bind RNA. The significance of these interactions is reflected in the recent discoveries that several human and other vertebrate genetic disorders are caused by aberrant expression of RNA-binding proteins. The major RNA-binding motifs are described and examples of how they may function are given.

https://science.sciencemag.org/content/sci/265/5172/615.full.pdf

Conserved structures and diversity of functions of RNA-binding proteins.

The RNA recognition motif (RRM), also known as RNA-binding domain (RBD) or ribonucleoprotein domain (RNP) is one of the most abundant protein domains in eukaryotes. Based on the comparison of more than 40 structures including 15 complexes (RRM–RNA or RRM–protein), we reviewed the structure–function relationships of this domain. We identified and classified the different structural elements of the RRM that are important for binding a multitude of RNA sequences and proteins. Common structural aspects were extracted that allowed us to define a structural leitmotif of the RRM–nucleic acid interface with its variations. Outside of the two conserved RNP motifs that lie in the center of the RRM β-sheet, the two external β-strands, the loops, the C- and N-termini, or even a second RRM domain allow high RNA-binding affinity and specific recognition. Protein–RRM interactions that have been found in several structures reinforce the notion of an extreme structural versatility of this domain supporting the numerous biological functions of the RRM-containing proteins.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1742-4658.2005.04653.x

The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression

The crystal structure of the RNA-binding domain of the small nuclear ribonucleoprotein U1A bound to a 21-nucleotide RNA hairpin has been determined at 1.92 A resolution. The ten-nucleotide RNA loop binds to the surface of the β-sheet as an open structure, and the AUUGCAC sequence of the loop interacts extensively with the conserved RNP1 and RNP2 motifs and the C-terminal extension of the RNP domain. These interactions include stacking of RNA bases with aromatic side chains of proteins and many direct and water-mediated hydrogen bonds. The structure reveals the stereochemical basis for sequence-specific RNA recognition by the RNP domain.

Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin.

Publisher Summary The use of selenomethionyl proteins for phase determination is growing in popularity for isomorphous replacement or multiwavelength anomalous dispersion (MAD) experiments. In some cases, it provides crucial phasing information and the key to solve a crystal structure. With the increase in the availability of synchrotron facilities (ESRF, APS) with beam lines dedicated to crystallographic studies, and MAD data collection in particular, selenomethionyl proteins may find routine use in phase determination. The procedures for engineering and crystallizing selenomethionyl proteins are divided into four steps: expression, cell growth, purification, and crystallization. The storage and properties of selenomethionyl protein crystals are discussed in this chapter. Selenomethionyl protein crystals should be kept in a reducing medium containing dithiothreitol (DTT) and ethylenediaminetetraacetic acid (EDTA) and stored in an anaerobic chamber. Selenomethionyl protein crystals tend to be isomorphous with the native crystals, and selenomethionine incorporation does not usually alter diffraction limits. However, in some cases, selenomethionyl protein crystals are more radiation sensitive than their natural counterparts.

[29] Preparation of selenomethionyl proteins for phase determination.

Specific interactions between proteins implicated in splice site selection and regulated alternative splicing

The crystal structure of the RNA binding domain of the U1 small nuclear ribonucleoprotein A, which forms part of the ribonucleoprotein complex involved in the excision of introns, has been solved It contains a four-stranded beta sheet and two alpha helices The highly conserved segments designated RNP1 and RNP2 lie side by side on the middle two beta strands U1 RNA binding studies of mutant proteins suggest that the RNA binds to the four-stranded beta sheet and to the flexible loops on one end

Timm H. Jessen

Papers

Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A