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

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: 16 August 2012
Fund Project: 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)

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.
- Protein binding site prediction,
- Patch division,
- Solvent accessible surface area,
- Interior contact area
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
2. [2]
  (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
4. [4]
  (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
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
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
8. [8]
  (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.
10. [10]
  (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
12. [12]
  (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.
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
15. [15]
  (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
17. [17]
  (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
19. [19]
  (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
21. [21]
  (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
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
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
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
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
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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

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

南开大学师唯/华北电力大学（保定）刘景维：二维配位聚合物中有序的亲锂冠醚位点用于无枝晶锂沉积

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通讯作者: 陈斌, bchen63@163.com