MULTIPLE RNA-BINDING DOMAINS (RBDS) JUST DONT ADD UP

One of the most common motifs for binding RNA in eukaryotes is the RNA binding domain (RBD) or RNA Recognition Motif (RRM). One of the more intriguing aspects of these proteins is their modular nature. Proteins have been found containing from one to four RRMs, in most instances, these domains have some basal level of non-sequence specific RNA bindi ng affinity. In addition, many also have a higher affinity for a speci fic structure or sequence of RNA. In the cases of heterogenous nuclear ribonucleoprotein Al (hnRNP Al), yeast poly-A binding protein and spl icing factor U2AF(65), the individual free energy of binding of the RB Ds for RNA are not strictly additive. By invoking a model in which the amino acids connecting adjoining RBDs are considered to be flexible l inkers with an interresidue spacing of about 3.5 Angstrom, it is possi ble to predict the apparent association constants for at least some mu lti-RBD proteins to single-stranded RNA. We have surveyed the literatu re and found that individual RBDs are separated by 'linker' sequences of highly variable length. These linkers provide a critical determinan t of binding affinity and may modulate cis versus trans binding. A cle arer understanding of multi-RBD binding is essential to critically eva luating the role of these proteins in RNA splicing, packaging and tran sport.