蛋白质表面模块划分及其在结合位点预测中的应用

引用本文: 王攀文, 龚新奇, 李春华, 陈慰祖, 王存新. 蛋白质表面模块划分及其在结合位点预测中的应用[J]. 物理化学学报, doi: 10.3866/PKU.WHXB201208162 shu

Citation: WANG Pan-Wen, NG Xin-Qi, LI Chun-Hua, CHEN Wei-Zu, WANG Cun-Xin. Division of Protein Surface Patches and Its Application in Protein Binding Site Prediction[J]. Acta Physico-Chimica Sinica, doi: 10.3866/PKU.WHXB201208162 shu

蛋白质表面模块划分及其在结合位点预测中的应用

基金项目:
国家自然科学基金(31171267, 10974008) (31171267, 10974008)

北京市自然科学基金(4102006) (4102006)

科技部国际合作项目(2010DFA31710) (2010DFA31710)

北京市教委科技创新平台-自然基础研究项目资助

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:

English

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

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 Date: 25 May 2012
Available Online: 17 October 2012
Fund Project:
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)

北京市教委科技创新平台-自然基础研究项目资助

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 od 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:

1. [1]
  
  (1) Teichmann, S. A.; Murzin, A. G.; Chothia, C. Curr. Opin. Struct. Biol. 2001, 11 (3), 354. doi: 10.1016/S0959-440X(00)00215-3
  (1) Teichmann, S. A.; Murzin, A. G.; Chothia, C. Curr. Opin. Struct. Biol. 2001, 11 (3), 354. doi: 10.1016/S0959-440X(00)00215-3
2. [2]
  (2) Baker, D.; Sali, A. Science 2001, 294 (5540), 93. doi: 10.1126/science.1065659(2) Baker, D.; Sali, A. Science 2001, 294 (5540), 93. doi: 10.1126/science.1065659
3. [3]
  (3) Stark, A.; Shkumatov, A.; Russell, R. B. Structure 2004, 12 (8),1405. doi: 10.1016/j.str.2004.05.012(3) Stark, A.; Shkumatov, A.; Russell, R. B. Structure 2004, 12 (8),1405. doi: 10.1016/j.str.2004.05.012
4. [4]
  (4) Jones, S.; Thornton, J. M. Curr. Opin. Chem. Biol. 2004, 8 (1),3. doi: 10.1016/j.cbpa.2003.11.001(4) Jones, S.; Thornton, J. M. Curr. Opin. Chem. Biol. 2004, 8 (1),3. doi: 10.1016/j.cbpa.2003.11.001
5. [5]
  (5) Kinoshita, K.; Nakamura, H. Curr. Opin. Struct. Biol. 2003, 13 (3), 396. doi: 10.1016/S0959-440X(03)00074-5(5) Kinoshita, K.; Nakamura, H. Curr. Opin. Struct. Biol. 2003, 13 (3), 396. doi: 10.1016/S0959-440X(03)00074-5
6. [6]
  (6) Tseng, Y. Y.; Li,W. H. Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (13), 5313. doi: 10.1073/pnas.1102210108(6) Tseng, Y. Y.; Li,W. H. Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (13), 5313. doi: 10.1073/pnas.1102210108
7. [7]
  (7) Amos-Binks, A.; Patulea, C.; Pitre, S.; Schoenrock, A.; Gui, Y.;Green, J. R.; lshani, A.; Dehne, F. BMC Bioinformatics 2011,12, 225. doi: 10.1186/1471-2105-12-225(7) Amos-Binks, A.; Patulea, C.; Pitre, S.; Schoenrock, A.; Gui, Y.;Green, J. R.; lshani, A.; Dehne, F. BMC Bioinformatics 2011,12, 225. doi: 10.1186/1471-2105-12-225
8. [8]
  (8) Xiong, Y.; Liu, J.;Wei, D. Q. Proteins 2011, 79 (2), 509. doi: 10.1002/prot.v79.2(8) Xiong, Y.; Liu, J.;Wei, D. Q. Proteins 2011, 79 (2), 509. doi: 10.1002/prot.v79.2
9. [9]
  (9) He, X.; Chen, C. C.; Hong, F.; Fang, F.; Sinha, S.; Ng, H. H.;Zhong, S. PLoS One 2009, 4 (12), e8155.(9) He, X.; Chen, C. C.; Hong, F.; Fang, F.; Sinha, S.; Ng, H. H.;Zhong, S. PLoS One 2009, 4 (12), e8155.
10. [10]
  (10) Lensink, M. F.; Mendez, R.;Wodak, S. J. Proteins 2007, 69 (4),704. doi: 10.1002/prot.21804(10) Lensink, M. F.; Mendez, R.;Wodak, S. J. Proteins 2007, 69 (4),704. doi: 10.1002/prot.21804
11. [11]
  (11) Lichtarge, O.; Bourne, H. R.; Cohen, F. E. J. Mol. Biol. 1996,257 (2), 342. doi: 10.1006/jmbi.1996.0167(11) Lichtarge, O.; Bourne, H. R.; Cohen, F. E. J. Mol. Biol. 1996,257 (2), 342. doi: 10.1006/jmbi.1996.0167
12. [12]
  (12) Ofran, Y.; Rost, B. FEBS Lett. 2003, 544 (1-3), 236. doi: 10.1016/S0014-5793(03)00456-3(12) Ofran, Y.; Rost, B. FEBS Lett. 2003, 544 (1-3), 236. doi: 10.1016/S0014-5793(03)00456-3
13. [13]
  (13) Laskowski, R. A.; Luscombe, N. M.; Swindells, M. B.;Thornton, J. M. Protein Sci. 1996, 5 (12), 2438.(13) Laskowski, R. A.; Luscombe, N. M.; Swindells, M. B.;Thornton, J. M. Protein Sci. 1996, 5 (12), 2438.
14. [14]
  (14) Torrance, J.W.; Bartlett, G. J.; Porter, C. T.; Thornton, J. M. J. Mol. Biol. 2005, 347 (3), 565. doi: 10.1016/j.jmb.2005.01.044(14) Torrance, J.W.; Bartlett, G. J.; Porter, C. T.; Thornton, J. M. J. Mol. Biol. 2005, 347 (3), 565. doi: 10.1016/j.jmb.2005.01.044
15. [15]
  (15) Gao, Y.;Wang, R.; Lai, L. J. Mol. Model. 2004, 10 (1), 44. doi: 10.1007/s00894-003-0168-3(15) Gao, Y.;Wang, R.; Lai, L. J. Mol. Model. 2004, 10 (1), 44. doi: 10.1007/s00894-003-0168-3
16. [16]
  (16) Innis, C. A.; Anand, A. P.; Sowdhamini, R. J. Mol. Biol. 2004,337 (4), 1053. doi: 10.1016/j.jmb.2004.01.053(16) Innis, C. A.; Anand, A. P.; Sowdhamini, R. J. Mol. Biol. 2004,337 (4), 1053. doi: 10.1016/j.jmb.2004.01.053
17. [17]
  (17) de Vries, S. J.; Bonvin, A. M. Bioinformatics 2006, 22 (17),2094. doi: 10.1093/bioinformatics/btl275(17) de Vries, S. J.; Bonvin, A. M. Bioinformatics 2006, 22 (17),2094. doi: 10.1093/bioinformatics/btl275
18. [18]
  (18) Madabushi, S.; Yao, H.; Marsh, M.; Kristensen, D. M.; Philippi,A.; Sowa, M. E.; Lichtarge, O. J. Mol. Biol. 2002, 316 (1), 139.doi: 10.1006/jmbi.2001.5327(18) Madabushi, S.; Yao, H.; Marsh, M.; Kristensen, D. M.; Philippi,A.; Sowa, M. E.; Lichtarge, O. J. Mol. Biol. 2002, 316 (1), 139.doi: 10.1006/jmbi.2001.5327
19. [19]
  (19) Guharoy, M.; Chakrabarti, P. Proc. Natl Acad. Sci. U. S. A.2005, 102 (43), 15447. doi: 10.1073/pnas.0505425102(19) Guharoy, M.; Chakrabarti, P. Proc. Natl Acad. Sci. U. S. A.2005, 102 (43), 15447. doi: 10.1073/pnas.0505425102
20. [20]
  (20) Li, X.; Keskin, O.; Ma, B.; Nussinov, R.; Liang, J. J. Mol. Biol.2004, 344 (3), 781. doi: 10.1016/j.jmb.2004.09.051(20) Li, X.; Keskin, O.; Ma, B.; Nussinov, R.; Liang, J. J. Mol. Biol.2004, 344 (3), 781. doi: 10.1016/j.jmb.2004.09.051
21. [21]
  (21) Hintze, A.; Adami, C. Plos Comput. Biol. 2008, 4 (2), e23.(21) Hintze, A.; Adami, C. Plos Comput. Biol. 2008, 4 (2), e23.
22. [22]
  (22) Hwang, H.; Pierce, B.; Mintseris, J.; Janin, J.;Weng, Z. Proteins2008, 73 (3), 705. doi: 10.1002/prot.22106(22) Hwang, H.; Pierce, B.; Mintseris, J.; Janin, J.;Weng, Z. Proteins2008, 73 (3), 705. doi: 10.1002/prot.22106
23. [23]
  (23) Bai, H. J.; Lai, L. H. Acta Phys. -Chim. Sin. 2010, 26, 1988.[白红军, 来鲁华. 物理化学学报, 2010, 26, 1988.] doi: 10.3866/PKU.WHXB20100725(23) Bai, H. J.; Lai, L. H. Acta Phys. -Chim. Sin. 2010, 26, 1988.[白红军, 来鲁华. 物理化学学报, 2010, 26, 1988.] doi: 10.3866/PKU.WHXB20100725
24. [24]
  (24) ng, X. Q.; Liu, B.; Chang, S.; Li, C. H.; Chen,W. Z.;Wang,C. X. Sci. China Life Sci. 2010, 53 (9), 1152. doi: 10.1007/s11427-010-4050-0(24) ng, X. Q.; Liu, B.; Chang, S.; Li, C. H.; Chen,W. Z.;Wang,C. X. Sci. China Life Sci. 2010, 53 (9), 1152. doi: 10.1007/s11427-010-4050-0
25. [25]
  (25) ng, X. Q.;Wang, P.W.; Yang, F.; Chang, S.; Liu, B.; He, H.Q.; Cao, L. B.; Xu, X. J.; Li, C. H.; Chen,W. Z.;Wang, C. X.Proteins 2010, 78 (15), 3150. doi: 10.1002/prot.v78:15(25) ng, X. Q.;Wang, P.W.; Yang, F.; Chang, S.; Liu, B.; He, H.Q.; Cao, L. B.; Xu, X. J.; Li, C. H.; Chen,W. Z.;Wang, C. X.Proteins 2010, 78 (15), 3150. doi: 10.1002/prot.v78:15
26. [26]
  (26) Janin, J.; Henrick, K.; Moult, J.; Eyck, L. T.; Sternberg, M. J.;Vajda, S.; Vakser, I.;Wodak, S. J. Proteins 2003, 52 (1), 2.doi: 10.1002/(ISSN)1097-0134
  (26) Janin, J.; Henrick, K.; Moult, J.; Eyck, L. T.; Sternberg, M. J.;Vajda, S.; Vakser, I.;Wodak, S. J. Proteins 2003, 52 (1), 2.doi: 10.1002/(ISSN)1097-0134

扫一扫看文章

计量

PDF下载量: 700
文章访问数: 2641
HTML全文浏览量: 64

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

蛋白质表面模块划分及其在结合位点预测中的应用

English

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

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

蛋白质表面模块划分及其在结合位点预测中的应用

English

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

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

文章相关

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs