An analysis of conformational changes upon RNA-protein binding

Abstract

RNA-binding proteins (RBPs) have myriad functions in transcription, translation, and post-transcriptional gene regulation, with central roles in normal development as well as in both genetic and infectious diseases. When a protein binds RNA, a conformational change often occurs. For RNA-protein complexes that have been characterized, conformational changes have been observed in the protein, the RNA, or both. These conformational changes have not been sufficiently characterized, however, in part due to the small number of structures of bound and unbound complexes of RNA-binding proteins available until recently. Here we systematically analyze a new dataset of 90 pairs of bound and unbound proteins to evaluate the conformational changes that occur upon RNA binding. Most of the conformational changes were observed in non-interfacial regions of the RNA-binding proteins. Detailed analyses of the modes of RNA binding and any associated conformational changes in proteins are critical for fully understanding the mechanisms of RNA-protein recognition, for developing better RNA-protein docking methods and methods for predicting interfacial residues, and for RNA-based drug design.