RNA Binding Domains and hnRNPs

RNA Binding Domains

The RNA binding domains are present on population of proteins which associate with RNA during different processes. They were discovered through HnRNPs, heterogeneous ribonucleoprotein particles, which associate with pre-mRNAs by examining their conservative features. Like DNA binding domains, the proteins' RNA binding domains have several structural motifs. 

RNA Recognition Motif (RRM) 

The most common RNA binding domain. 80 amino acids fold into a 4-stranded B sheet flanked by 2 a-helices, which contain RNP1 and RNP2 motifs that contact the phosphates of RNA. This is a charged interaction as the negative phosphate backbone attracts a positively charged binding motif. 

RRG Box

The motif contains 5 Arg-Gly-Gly repeats interspersed with aromatic amino acids, such as Phe, Tyr, and Trp. The structure is unknown. It is a charged interaction.

KH Motif

This has 35 residues, with a similar structure to the RRM domain, but the RNA binds by interacting with a hydrophobic surface formed by the alpha helices and one beta strand. 

A Note about hnRNPs

hnRNPs are a set of proteins that contain hnRNAs, which are pre-mRNAs and RNA processing intermediates with introns still present in their sequences. They prevent undue interaction from occurring between the pre-mRNA with other components of the cell as well as prevent it from interacting with itself to form a secondary structure, which would muck things up. Also, they are involved with different steps of RNA processing, sometimes associating with the splicing apparatus for instance, and transporting the mRNA from the nucleus to the cytoplasm.