Conformational plasticity modulates sequence specificity in non-canonical tandem RRM-RNA binding

The Dead End protein, a key regulator of germline cell fate, utilizes two RNA Recognition Motifs (RRM) in tandem to bind AU-rich RNA in a non-canonical manner. Only one RRM uses the known RNA binding interface, whereas the second motif has only minimal contacts with the RNA. To characterize the structural features and dynamics that contribute to RNA binding, we performed a series of atomistic molecular dynamics simulations and show that the complex is highly flexible, undergoing large conformational transitions and deviating significantly from the initial experimental structure. We found that RNA binding significantly restricts but does not abolish the inter-domain movement of the two motifs, whereas the cooperative action of both RRM domains restricts RNA dynamics. Despite the extensive comformational plasticity of the complex, the core of the RNA binding interface and the sequence specificity is maintained. In the absence of one RRM, the RNA binding interface of the first RRM is extended whereas that of the second RRM is diminished leading to destabilization of the RRM-RNA interaction and even unbinding. This is in agreement with previous findings suggesting that the second RRM does not bind RNA on its own. The cooperative binding of the two RRMs is required for maintaining the core sequence specificity. These findings provide a paradigm shift towards considering highly dynamic RNA binding interfaces as key in RNA binding and regulation.