Protein-RNA Interaction Interface Prediction and Design

RNA-protein interactions play key roles in many biological processes. The three dimensional (3D) structure of protein-RNA complexes can be determined experimentally by structural biologists. The recognition between protein and RNA can be understood from the 3D atomic structure. However, the structure determination of protein-RNA complexes by experimental methods is often difficult and costly, and limited to the binding strength. Thus, the prediction and design of protein-RNA complex structures is important in biological medical research. In this review, we will discuss the recent progress in protein-RNA interface prediction and design, which includes the following aspects: (1) protein-RNA docking and the conformational change on binding; (2) the recognition mechanism of protein-RNA binding; (3) the molecular design based on the protein-RNA interface. Improvement of the protein-RNA docking algorithm will help us annotate a large number of proteins and RNA with unknown function, and molecular design based on macromolecular interactions will be useful in drug design.