RNA binding mediates the local cooperativity between the β-sheet and the C-terminal tail of the human U1A RBD1 protein

Pairwise coupling theory is applied here to determine the energetic interactions between two elements of the N-terminal RNA binding domain (RBD) of the human U1A protein. The novel application of the theory to this system incorporates both measurements of protein stability and RNA binding to define thermodynamic cycles. In this first example of the application, two regions of the protein are selected for study: tyrosine 13, one of the conserved aromatic residues on the surface of the β-sheet, and the C-terminal tail of the RBD. The six initial pairwise coupling free energies derived from this system describe the communication between these positions, both in the free and RNA-bound states of the protein. The results show that in the absence of RNA, these two elements of the protein act independently. However, when RNA is bound, there is indirect coupling between Tyr13 and the tail, mediated through the RNA. Subsequent thermodynamic cycles involving additional perturbations to the C-terminal tail further define the communication between the C terminus and the β-sheet. This work demonstrates the general applicability of the pairwise coupling theory to protein:nucleic acid interactions, and illustrates the necessity of such analyses to describe the network of energetic interactions that comprise RNA recognition by this RBD.