RNA-binding proteins: modular design for efficient function

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Abstract
Many RNA-binding proteins have a modular structure and are composed of multiple repeats of a few small domains. By arranging the domains in various ways, these proteins can satisfy the diverse biological roles they play. The modular nature of RNA-binding proteins allows them to satisfy their functional roles in various ways. Multiple domains allow the recognition of long sequence stretches, sequences that are separated from each other or even sequences on different RNAs. The domains can pre-organize themselves to arrange the RNA in a particular topology or, conversely, the proteins can be arranged to interact with a particular RNA structure. Last, enzymatic domains can be combined with RNA-binding domains to regulate catalytic activity. One of the most common arrangements is to have two domains separated by a short linker. This allows the protein to create a larger interaction surface that can interact with many more nucleotides than the isolated domains. Interdomain linkers often have key functional roles in organizing the domains to facilitate the recognition of a particular substrate. Many of the RNA-binding modules can participate in protein–protein interactions, which can facilitate assembly of higher-order complexes. RNA-binding modules can be combined with enzymatic domains to properly position the catalytic domain on the RNA or to regulate the activity of the enzyme.