Talk abstracts
Talk on Thursday 11:15-11:30am submitted by Elan Shatoff
Integrating double stranded RNA binding proteins into RNA secondary structure prediction
Elan Shatoff (Department of Physics), Ralf Bundschuh (Department of Physics)
Abstract:
RNA binding proteins are fundamental to many cellular processes. Double stranded RNA binding proteins (dsRBPs) in particular are crucial for RNA interference, mRNA elongation, A-to-I editing, host defense, splicing, and a multitude of other important mechanisms. Since dsRBPs require double stranded RNA to bind, their binding affinity depends on the possible secondary structures of the target RNA molecule. Here, we introduce a quantitative model that allows calculation of the effective affinity of dsRBPs to any RNA given a base affinity and the sequence of the RNA, while fully taking into account the entire secondary structure ensemble of the RNA. We implement this within the Vienna RNA folding package while maintaining its O(n3) time complexity. We find that proteins will bind to random sequences with a ~10,000-fold change in effective binding affinity, simply based on the structural interactions between their double stranded footprint and the rest of the molecule. We also validate our quantitative model by comparing with experimentally determined binding affinities for transactivation response element RNA-binding protein (TRBP).
Keywords: RNA, dsRBP, RNA-binding proteins