Citation: FAN Di, LIU Zhen-Ming, JIN Hong-Wei, ZHANG Liang-Ren. Classification of Coenzyme-A Binding Proteins Based on Co-Factor Binding Modes[J]. Acta Physico-Chimica Sinica, ;2011, 27(05): 1223-1231. doi: 10.3866/PKU.WHXB20110439 shu

Classification of Coenzyme-A Binding Proteins Based on Co-Factor Binding Modes

1.
State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China

Received Date: 17 December 2010
Available Online: 18 March 2011
Fund Project: 重大新药创制国家科技重大专项(2009ZX09501-002) (2009ZX09501-002)国家自然科学基金(20802006)资助项目 (20802006)

This study developed a mutual recognition of the proteins based on molecular classification, data mining strategies and the statistical clustering method, which was applied to study and classify clusters of coenzyme-A (CoA) binding proteins with their binding patterns extracted by using Pocket1.0 program. Several strategies have been evaluated for the accuracy of the system analysis and the two-step clustering method has been shown to be the best. The results revealed that the known CoA binding proteins can be clustered into three groups by using this approach. The designed classification coefficient was used effectively to identify the critical features for classification. The results show that both hydrogen bonds and hydrophobic interactions are important in all three clusters and that quite a few important residues related to biological activities are involved in the formation of hydrogen bonds. The classification of these interactions and the discovery of the characteristics and differences between the three clusters will have some utility for the design of specific a nists and anta nists.
- Coenzyme-A,
- Protein classification,
- Binding mode,
- Cluster analysis,
- Pantetheine
1. [1]
  
  (1) Andersson, C. D.; Chen, B. Y.; Linusson, A. Proteins 2010, 78, 1408.
2. [2]
  (2) ld, N. D.; Jackson, R. M. J. Chem. Inf. Model. 2006, 46, 736.
3. [3]
  (3) Arnold, J. R.; Burdick, K. W.; Pegg, S. C. H. J. Chem. Inf. Comp. Sci. 2004, 44, 2190.
4. [4]
  (4) Hoppe, C.; Steinbeck, C.; Wohfahrt, G. J. Mol. Graph. Model. 2006, 24, 328.
5. [5]
  (5) ld, N. D.; Jackson, R. M. J. Mol. Biol. 2006, 355, 1112.
6. [6]
  (6) Izrailev, S.; Farnum, M. A. Proteins 2004, 57, 711.
7. [7]
  (7) Liu, Z. M.; Li, B.; Lai, L. H. Acta Phys. -Chim. Sin. 2005, 21, 1143.
8. [8]
  [刘振明, 李博, 来鲁华. 物理化学学报, 2005, 21,1143.]
9. [9]
  (8) Cappello, V.; Tramontano, A.; Koch, U. Proteins 2002, 47, 106.
10. [10]
  (9) Kinnings, S. L.; Jackson, R. M. J. Chem. Inf. Model. 2009, 49, 318.
11. [11]
  (10) Doppelt-Azeroual, O.; Delfaud, F.?; Moriaud, F.?Protein Sci. 2010, 19, 847.
12. [12]
  (11) Li, B.; Liu, Z. M.; Zhang, L. G.; Lai, L. H. J. Chem. Inf. Model. 2009, 49, 1725.
13. [13]
  (12) Balakin, K. V.; Tkachenko, S. E.; Lang, S. A.?J. Chem. Inf. Comp. Sci. 2002, 43, 1332.
14. [14]
  (13) Patel, R. Y.; Doerksen, R. J. J. Proteome Res. 2010, 9, 4433.
15. [15]
  (14) Cai, C. Z.; Han, L. Y.; Ji, Z. L. Nucl. Acids Res. 2003, 31, 3692.
16. [16]
  (15) Cai, C. Z.; Wang, W. L.; Sun, L. Z. Math. Biosci. 2003, 185, 111.
17. [17]
  (16) Shamim, M. T. A.; Anwaruddin, M.; Nagarajaram, H. A. Bioinformatics 2007, 23, 3320.
18. [18]
  (17) Vapnik,V. N. The Nature of Statistical Learning Theory, 1st ed.; Springer-Verlag: New York, 1999; pp 30-39.
19. [19]
  (18) Markowetz, F.; Edler, L.; Vingron, M. Biometrical J. 2003, 45, 377.
20. [20]
  (19) Shen, H. B.; Yang, J.; Liu, X. J. Biophys. Res. Commun. 2005, 334, 577.
21. [21]
  (20) Kong, J. H.; Fish, D. R.; Rockhill, R. L. J. Comp. Neurol. 2005, 489, 293.
22. [22]
  (21) Liu, Y.; Li, X. Q.; Xu, H. S.; Qiao, H. Acta Phys. -Chim. Sin. 2009, 25, 2558.
23. [23]
  [刘岳, 李晓琴, 徐海松, 乔辉. 物理化学学报, 2009, 25, 2558.]
24. [24]
  (22) Kertész-Farkas, A.; Dhir, S.; Sone , P.; Pacurar, M.; Netoteia, S.; Nijveen, H.; Kuzniar, A.; Leunissen, J. A. M.; Kocsor, A.; Pon r, S. J. Biochem. Biophys. Methods 2008, 70, 1215.
25. [25]
  (23) Welcome to Brookhaven Protein Data Bank. http://www.rcsb.org (accessed, 2010).
26. [26]
  (24) Leonardi, R.; Zhang, Y. M.; Rock, C. O. Prog. Lipid Res. 2005, 44, 125.
27. [27]
  (25) Rudel, L. L.; Lee, R. G.; Cockman, T. Curr. Opin. Lipidol. 2001, 12, 121.
28. [28]
  (26) Sybyl 6.91. http://www.tripos.com. Tripos; USA, 2001.
29. [29]
  (27) Discovery Studio 2.0. http://www.accelrys.com/.Accelrys; USA, 2008.
30. [30]
  (28) Chen, J.; Lai, L. H. J. Chem. Inf. Model. 2006, 46, 2684.
31. [31]
  (29) Chang, C.; Lin, C. LIBSVM, Version 2.3; Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm. 2001.
32. [32]
  (30) Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. J. Mol. Biol. 1995, 247, 536.
33. [33]
  (31) Andreeva, A.; Howorth, D.; Chandonia, J. M.; Brenner, S. E.; Hubbard, T. J. P.; Chothia, C.; Murzin, A. G. Nucleic Acids Res. 2008, 36, D419.
34. [34]
  (32) Gasteiger, E.; Gattiker, A.; Hoogland, C.; Ivanyi, I.; Appel, R.D.; Bairoch, A. Nucleic Acids. Res. 2003, 31, 3784.
1. [1]
  Xinyi Hong , Tailing Xue , Zhou Xu , Enrong Xie , Mingkai Wu , Qingqing Wang , Lina Wu . Non-Site-Specific Fluorescent Labeling of Proteins as a Chemical Biology Experiment. University Chemistry, 2024, 39(4): 351-360. doi: 10.3866/PKU.DXHX202310010
2. [2]
  Tianlong Zhang , Rongling Zhang , Hongsheng Tang , Yan Li , Hua Li . Exploration on the Integration Mode of Instrumental Analysis with Science and Education under the Background of Artificial Intelligence Era. University Chemistry, 2024, 39(8): 365-374. doi: 10.12461/PKU.DXHX202403014
3. [3]
  Yaqian Duan , Juan Su , Meiyu Lin , Yuxin Fang , Wenyi Liang . Exploration of the Implementation Path of Ideological and Political Education in the “Dual-Track Teaching” Model: a Case Study of Analytical Chemistry Experiment. University Chemistry, 2024, 39(2): 181-188. doi: 10.3866/PKU.DXHX202307024
4. [4]
  Jiaqi Chen , Shuwei Chen , Suocai Ren , Yue Sun , Chunhui Luan , Xu Wu . Exploring the People-Centered Safety Construction Model in Basic Chemistry Laboratories: A Case Study in Analytical Chemistry Laboratories. University Chemistry, 2024, 39(7): 264-271. doi: 10.3866/PKU.DXHX202311009
5. [5]
  Meiyu Lin , Yuxin Fang , Songzhang Shen , Yaqian Duan , Wenyi Liang , Chi Zhang , Juan Su . Exploration and Implementation of a Dual-Pathway Blended Teaching Model in General Chemistry Experiment Course: A Case Study of Copper Glycine Synthesis and Its Thermal Analysis. University Chemistry, 2024, 39(8): 48-53. doi: 10.3866/PKU.DXHX202312042
6. [6]
  Jin Yan , Chengxia Tong , Yajie Li , Yue Gu , Xuejian Qu , Shigang Wei , Wanchun Zhu , Yupeng Guo . Construction of a “Dual Support, Triple Integration” Chemical Safety Practical Education System. University Chemistry, 2024, 39(7): 69-75. doi: 10.12461/PKU.DXHX202405008
7. [7]
  Jibin Miao , Changjie Mao , Baokang Jin . Exploration and Practice of Virtual and Real Combination Practical Curriculum During the Construction of the National Demonstration Center for Experimental Education: A Case Study of the National Demonstration Center for Experimental Chemistry & Chemical Engineering Education (Anhui University). University Chemistry, 2024, 39(7): 106-109. doi: 10.12461/PKU.DXHX202405021
8. [8]
  Zhuomin Zhang , Hanbing Huang , Liangqiu Lin , Jingsong Liu , Gongke Li . Course Construction of Instrumental Analysis Experiment: Surface-Enhanced Raman Spectroscopy for Rapid Detection of Edible Pigments. University Chemistry, 2024, 39(2): 133-139. doi: 10.3866/PKU.DXHX202308034
9. [9]
  Zhenli Sun , Ning Wang , Kexin Lin , Qin Dai , Yufei Zhou , Dandan Cao , Yanfeng Dang . Visual Analysis of Hotspots and Development Trends in Analytical Chemistry Education Reform. University Chemistry, 2024, 39(11): 57-64. doi: 10.12461/PKU.DXHX202403095
10. [10]
  Chengxia Tong , Yajie Li , Jin Yan , Xuejian Qu , Shigang Wei , Yong Fan , Zhiguang Song , Yupeng Guo . The Construction and Practice of a Comprehensive and Three-Dimensional Practical Education Model. University Chemistry, 2024, 39(7): 49-55. doi: 10.12461/PKU.DXHX202404155
11. [11]
  Junlin Yan , Changhao Wang , Quanguo Zhai , Chenghui Liu , Dong Xue . A New Construction Model and Practice of Demonstration Center for Experimental Chemistry Education. University Chemistry, 2024, 39(7): 64-68. doi: 10.12461/PKU.DXHX202405005
12. [12]
  Weizhou Jiao , Zhiwei Liu , Chao Zhang , Zhiguo Yuan , Guisheng Qi , Jing Gao . Construction and Implementation of a Mode of Chemical Talent Training Driven by Practice and Innovation Ability. University Chemistry, 2024, 39(7): 76-81. doi: 10.12461/PKU.DXHX202405011
13. [13]
  Yecang Tang , Shan Ling , Zhen Fang . Exploration of a Hierarchical and Integration-Oriented Talent Training Model in the Demonstration Center for Experimental Chemistry Education. University Chemistry, 2024, 39(7): 188-192. doi: 10.12461/PKU.DXHX202405107
14. [14]
  Xu Liu , Chengfang Liu , Jie Huang , Xiangchun Li , Wenyong Lai . Research on the Application of Diversified Teaching Models in the Teaching of Physical Chemistry. University Chemistry, 2024, 39(8): 112-118. doi: 10.3866/PKU.DXHX202402021
15. [15]
  Yan Liu , Xiaojun Han , Ping Xu , Guoxu Zhang , Yu Wang , Zhicheng Zhang , Dianpeng Qi . “Five Measures” Based Science and Education Integration Experimental Teaching Mode to Promote the Construction of “Specialized Experiment” Curriculum. University Chemistry, 2024, 39(10): 299-307. doi: 10.12461/PKU.DXHX202405002
16. [16]
  Zhening Lou , Quanxing Mao , Xiaogeng Feng , Lei Zhang , Xu Xu , Yuyang Zhang , Xueyan Liu , Hongling Kang , Dongyang Feng , Yongku Li . Practice of Implementing Blended Teaching in Shared Analytical Chemistry Course. University Chemistry, 2024, 39(2): 263-269. doi: 10.3866/PKU.DXHX202308089
17. [17]
  Yan Zhang , Ping Wang , Tiebo Xiao , Futing Zi , Yunlong Chen . Measures for Ideological and Political Construction in Analytical Chemistry Curriculum. University Chemistry, 2024, 39(4): 255-260. doi: 10.3866/PKU.DXHX202401017
18. [18]
  Xiaofei Zhou , Yu-Qing Cao , Feng Zhu , Li Qi , Linhai Liu , Ni Yan , Zhiqiang Zhu . Missions and Challenges of Instrumental Analysis Course in the New Era. University Chemistry, 2024, 39(6): 174-180. doi: 10.3866/PKU.DXHX202310058
19. [19]
  Liqiang Lu , Qin Shuai , Xike Tian , Chenggang Zhou , Guo'e Cheng , Bo han , Yulun Nie , Hongtao Zheng , Lei Ouyang . Exploration and Practice of Deep Integration of Production and Education in Applied Chemistry Major under the Background of Emerging Engineering Education. University Chemistry, 2024, 39(3): 138-142. doi: 10.3866/PKU.DXHX202309015
20. [20]
  Yaqing Zhou , Jialin Liu , Jili Wang , Xin Zhou , Yong Sun , Wenhai Wu . Reform and Exploration of Assessment Models for Elective Courses in Local Universities: A Case Study of Hanjiang Normal University. University Chemistry, 2024, 39(4): 244-250. doi: 10.3866/PKU.DXHX202309056

Get Citation

PDF

XML

Metrics

PDF Downloads(1162)
Abstract views(2407)
HTML views(20)

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