Changes in side-chain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein

The ribonucleoprotein (RNP) domain is one of the most common eukaryotic pro tein domains, and is found in many proteins involved in recognition of a wi de variety of RNAs. Two structures of RNA complexes of human U1A protein ha ve revealed important aspects of RNP-RNA recognition, but have also raised intriguing questions concerning how RNP domains discriminate between differ ent RNAs. Ln this work, we extend the investigation of U1A-RNA recognition by comparing the dynamics of U1A protein both free and in complex with RNA. We have also investigated the trimolecular complex between two U1A protein s and the complete polyadenylation inhibition element to study the effect o f RNA-dependent protein-protein interactions on protein conformational flex ibility. We report that changes in backbone dynamics upon complex formation identify regions of the protein where conformational exchange processes ar e quenched in the RNA-bound conformation. Furthermore, amino acids whose si de-chains experience significant changes in conformational flexibility coin cide with residues particularly important for the specificity of the U1A pr otein/RNA interaction. This study adds a new dimension to the description o f the coordinated changes in structure and dynamics that are critical to de fine the biological specificity of U1A and other RNP proteins. (C) 1999 Aca demic Press.