物理化学学报 >> 2012, Vol. 28 >> Issue (10): 2390-2400.doi: 10.3866/PKU.WHXB201209111

生物物理化学 上一篇    下一篇

蛋白质-RNA相互作用界面预测与设计

黄阳玉, 阳秀凤, 李昊田, 纪晓峰, 程洪礼, 赵蕴杰, 郭大川, 李林, 刘士勇   

  1. 华中科技大学物理学院生物分子物理与模建小组, 武汉 430074
  • 收稿日期:2012-08-23 修回日期:2012-09-11 发布日期:2012-09-26
  • 通讯作者: 刘士勇 E-mail:liushiyong@gmail.com
  • 基金资助:

    国家自然科学基金(31100522), 国家高技术研究发展计划(2012AA020402), 高等学校博士学科点专项科研基金(20110142120038)资助.

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).

摘要:

蛋白质-RNA之间的相互作用是蛋白质在细胞里面行使功能的重要方式之一. 结构生物学家利用实验手段可以得到蛋白质-RNA复合物的三维结构, 通过原子水平的晶体结构来解释蛋白质与RNA的识别过程. 但实验取得蛋白质-RNA的复合物结构非常困难, 耗钱、耗时, 同时受限于其相互作用强度. 因而利用理论的方法对蛋白质-RNA相互作用界面进行预测与设计在生物医学研究中十分重要. 本文主要综述了近期蛋白质-RNA相互作用界面预测与设计方面的进展, 包括以下几个方面: (1) 蛋白质-RNA分子对接算法以及对接前后存在的构象变化的处理; (2) 蛋白质-RNA 识别机制的研究; (3) 基于蛋白质-RNA 相互作用界面的分子设计. 蛋白质-RNA分子对接算法逐步完善将有助于我们对大量未知功能的蛋白质与RNA进行功能注释, 而基于生物大分子相互作用界面的分子设计将在药物设计领域中有广阔的应用前景.

关键词: 蛋白质-RNA相互作用, 分子对接, 界面设计, 复合物结构预测

Abstract:

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

MSC2000: 

  • O641