Molecular dynamics and thermodynamics of protein-RNA interactions: Mutation of a conserved aromatic residue modifies stacking interactions and structural adaptation in the U1A-stem loop 2 RNA complex

Molecular dynamics (MD) simulations and free energy component analysis have been performed to evaluate the molecular origins of the 5.5 kcal/mol desta bilization of the complex formed between the N-terminal RNP domain of U1A a nd stem loop 2 of U1 snRNA upon mutation of a conserved aromatic residue, P he56, to Ala. MD simulations, including counterions and water, have been ca rried out on the wild type and Phe56Ala peptide-stem loop 2 RNA complexes, the free wild type and Phe56Ala peptides, and the free stem loop 2 RNA. The MD structure of the Phe56Ala-stem loop 2 complex is similar to that of the wild type complex except the stacking interaction between Phe56 and A6 of stem loop 2 is absent and loop 3 of the peptide is more dynamic. However, t he MD simulations predict large changes in the structure and dynamics of he lix C and increased dynamic range of loop 3 for the free Phe56Ala peptide c ompared to the wild type peptide. Since helix C and loop 3 are highly varia ble regions of RNP domains, this indicates that a significant contribution to the reduced affinity of the Phe56Ala peptide for RNA results from cooper ation between highly conserved and highly variable regions of the RNP domai n of U1A. Surprisingly, these structural effects, which are manifested as c ooperative free energy changes, occur in the free peptide, rather than in t he complex, and are revealed only by study of both the initial and final st ates of the complexation process. Free energy component analysis correctly accounts for the destabilization of the Phe5BAla-stem loop 2 complex, and i ndicates that similar to 80% of the destabilization is due to the loss of t he stacking interaction and similar to 20% is due to differences in U1A ada ptation.