Visualizing induced fit in early assembly of the human signal recognition particle

Assembly of almost all ribonucleoprotein complexes involves induced fit in the RNA and, thus, formation of one or more intermediate states. In assembl y of the human signal recognition particle (SRP), we show that SRP19 bindin g to SRP RNA involves obligatory intermediates. An apparent discrepancy exi sts between the ratio of dissociation and association rate constants, deter mined in a partitioning experiment, and the equilibrium binding constant; t his kinetic signature reflects formation of a stable intermediate in assemb ly of the ribonucleoprotein complex. Assembly intermediates were observed d irectly by time-resolved footprinting. SRP19 binds rapidly to SRP RNA to fo rm an initial labile, but structurally specific, encounter complex involvin g both helices III and IV. Two subsequent steps of structural consolidation yield the native RNA-protein interface. SRP19 binding stabilizes helix IV in the region recognized by SRP54, consistent with protein-protein cooperat ivity mediated in part by mutual recognition of similar RNA structures. Thi s mechanism illustrates principles general to ribonucleoprotein assembly re actions that rely on recruitment of architectural RNA binding proteins.