Acta Phys. -Chim. Sin. ›› 2012, Vol. 28 ›› Issue (10): 2390-2400.doi: 10.3866/PKU.WHXB201209111

• BIOPHYSICAL CHEMISTRY • Previous Articles     Next Articles

Protein-RNA Interaction Interface Prediction and Design

HUANG Yang-Yu, YANG Xiu-Feng, LI Hao-Tian, JI Xiao-Feng, CHENG Hong-Li, ZHAO Yun-Jie, GUO Da-Chuan, LI Lin, LIU Shi-Yong   

  1. Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
  • Received:2012-08-23 Revised:2012-09-11 Published:2012-09-26
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (31100522); and the National High Technology Research and Development Program of China (2012AA020402); and Specialized Research Fund for the Doctoral Program of Higher Education, China (20110142120038).


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.

Key words: Protein-RNA interaction, Molecular docking, Interface design, Complex structure prediction