物理化学学报 >> 2012, Vol. 28 >> Issue (11): 2729-2734.doi: 10.3866/PKU.WHXB201208162

生物物理化学 上一篇    下一篇

蛋白质表面模块划分及其在结合位点预测中的应用

王攀文1, 龚新奇2, 李春华1, 陈慰祖1, 王存新1   

  1. 1 北京工业大学生命科学与生物工程学院, 北京 100124;
    2 清华大学生命科学学院, 北京 100084
  • 收稿日期:2012-05-25 修回日期:2012-08-16 发布日期:2012-10-17
  • 通讯作者: 李春华, 王存新 E-mail:chunhuali@bjut.edu.cn; cxwang@bjut.edu.cn
  • 基金资助:

    国家自然科学基金(31171267, 10974008), 北京市自然科学基金(4102006), 科技部国际合作项目(2010DFA31710)和北京市教委科技创新平台-自然基础研究项目资助

Division of Protein Surface Patches and Its Application in Protein Binding Site Prediction

WANG Pan-Wen1, GONG Xin-Qi2, LI Chun-Hua1, CHEN Wei-Zu1, WANG Cun-Xin1   

  1. 1 College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China;
    2 School of Life Sciences, Tsinghua University, Beijing 100084, P. R. China
  • Received:2012-05-25 Revised:2012-08-16 Published:2012-10-17
  • Contact: LI Chun-Hua, WANG Cun-Xin E-mail:chunhuali@bjut.edu.cn; cxwang@bjut.edu.cn
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (31171267, 10974008), Beijing Natural Science Foundation, China (4102006), International Science & Technology Cooperation Program of China (2010DFA31710), and Fundamental Research Fund for the Beijing Municipal Education Commission Science and Technology Innovation Platform, China.

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摘要：

蛋白质-蛋白质复合物的结合位点预测是计算分子生物学的一个难题. 本文对蛋白质-蛋白质复合物数据集Benchmark 3.0 中的双链蛋白质复合物进行了研究, 计算了单体的残基溶剂可接近表面积和残基间的接触面积, 并据此提出了蛋白质表面模块划分方法. 发现模块的溶剂可接近表面积与其内部接触面积的乘积(PSAIA)值能够提供结合位点的信息. 在78 个双链蛋白质复合物中, 有74 个体系其受体或配体上具有最大或次大PSAIA值的模块是界面模块. 将该方法获得的结合位点信息应用在CAPRI竞赛Target 39 的复合物结构预测中取得了较好的结果. 本文提出的基于模块的蛋白质结合位点预测方法不同于以残基为基础且仅考虑表面残基的传统预测方法, 为蛋白质-蛋白质复合物结合位点预测提供了新思路.

关键词: 蛋白质结合位点预测, 模块划分, 溶剂可接近表面积, 内部接触面积

Abstract:

Binding site prediction for protein-protein complexes is a challenging problem in the area of computational molecular biology. Using a set of double-chain complexes in Benchmark 3.0, we calculated the solvent accessible surface areas and inter-residue contact areas for each monomer and propose a division method of protein surface patches. We found that the products of the solvent accessible surface areas and internal contact areas of patches, the PSAIA values, could provide protein binding site information. In a dataset of 78 complexes, either receptors or ligands of 74 complexes had interface patches with the first or second greatest PSAIA values among all surface patches. A good docking result was achieved when the binding site information obtained with this method was applied in Target 39 of the CAPRI experiment. This patch-based protein binding site prediction method differs from traditional methods, which are based on single residue and consider only surface residues. This provides a new method for binding site prediction in protein-protein interactions.

Key words: Protein binding site prediction, Patch division, Solvent accessible surface area, Interior contact area

MSC2000: 

  • O641