SUNY at Albany
June 19-23, 2001
Determinants For Specificity in U1A-RNA Interaction
Involved in the recognition of RNA sequences, U1A acts as part of the U1 snRNP complex that carries out pre-mRNA splicing in eukaryotes. Although the interactions between U1A and RNA targets have been described at high resolution (Oubridge et al., Nature 372:432, 1994; Avis et al., J. Mol. Biol. 257:398, 1996), the mechanisms for molecular recognition and the energetic contributions to binding are not yet fully understood. Computational methods were used to identify the determinants for specificity in binding U1A to stem loop II RNA, a hairpin fragment from U1 snRNA. Physical properties of the free and complexed states of the protein and RNA were sampled with molecular dynamics protocols which model the conditions used experimentally in biochemical assays. The energetics of binding was characterized from a thermocycle scheme in which the total free energy was decomposed into adaptation, solvation, and ionic contributions, with explicit incorporation of entropic effects (Jayaram et al., J. Comp. Phys. 151:333, 1999). The adaptation free energy component will be discussed in relationship to structural and dynamic properties of the free molecules that favor the association process. Results will be compared with experimental data that support a modulatory action of the C-terminal helix of U1A in exposing hydrophobic residues for interaction with RNA (Mittermaier et al., J. Mol. Biol. 294:967, 1999).
Felicia Pitici and David L. Beveridge
Department of Chemistry, Wesleyan University, Middletown, CT 06457