Dynamics based recognition mechanism of dsrbd dsrna interaction

Abstract

The broad range of cellular activities 8211 ranging from cell growth development to death 8211 involves interaction between double stranded RNAs dsRNAs and dsRNA binding domains dsRBDs The dsRBDs are known to interact with A form helical dsRNAs via minor major minor grooves spanning a length of about 12 base pairs A handful of dsRBDs in the cell are exposed to a large number of dsRNAs with an assortment of topologies The variation in topologies is generated as a result of defects in the A form helical structure These defects result due to the frequent presence of mismatches and bulges in the RNA secondary structure dsRBDs are known to target such topologically different dsRNAs with similar binding affinities They are present as modular units in proteins like TRBP TAR RNA binding protein ADAR Adenosine deaminase acting on RNA and Staufen are involved in RNAi RNA editing RNA transport respectively Recent reports have shown that dsRBDs slides along the length of the dsRNAs having different secondary structures in an ATP independent manner These observations lead to the broader question that is 8220 how do dsRBDs target a versatile range of dsRNA topologies 8221 We hypothesized that conformational dynamics in the dsRBDs might play a role in the above mentioned dsRBD dsRNA interactions We have employed two dsRBDs from two different species 8211 Homo sapiens and Drosophila melanogaster as model systems TRBP2 dsRBD1 and dADAR dsRBD1 respectively that have similar secondary and tertiary fold but different primary sequence TRBP has three dsRBD domains which it uses to target dsRNA with dsRBD1 and dsRBD2 and bind to Dicer with dsRBD3 so that Dicer an endonuclease can act on target dsRNA sites On the other hand ADAR contains two N terminal dsRBDs that allows binding to dsRNAs and a deaminase domain at C terminus that targets dsRNAs to carry out A to I editing post transcriptionally We first performed a systematic study of dsRBD dynamics in absence and presence of substrate dsRNAs of multiple topologies using NMR