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? 2000 Nature America Inc. ? review Induced fit in RNA–protein recognition James R. Williamson Two generalizations can be drawn from the recent rapid progress in understanding RNA–protein interactions. First, there is a great diversity of observed protein and RNA structural motifs. Second, formation of almost every RNA–protein complex that has been characterized involves conformational changes in the protein, the RNA, or both. The role of these conformational changes in the biological function of RNA–protein complexes is not at all clear. Whether or not conformational changes are a critical feature of ribonucleoprotein complex assembly or are an unimportant mechanistic detail, the ubiquity of these changes warrants careful consideration of their implications. There are many terms in popular usage to describe conforma- and the RNA undergoes little conformational change, while the tional changes that accompany binding: induced fit, cofolding, protein undergoes a significant change (Fig. 1b). Finally, there is mutually induced fit, ligand-induced conformational change, mutually induced fit, or cofolding, where both the RNA and pro- and tertiary structure capture. These terms are used to describe tein components change conformation (Fig. 1c). Each of these various aspects of local macromolecular folding in the formation different cases results in formation of a stable RNA–protein .com of intermolecular complexes. Typically, there is only information complex that has properties that are different from the free forms available about the structure and relative energy of the free and of the RNA and protein, and this complex results in a particular bound states of the RNA and protein. That is, there is no specific biological function. information about the binding pathway, which might include a In the following discussion, I will focus on induced fit se