Citation: XU Hai-Song, LI Xiao-Qin, ZENG Yi. Statistical Coupling Analysis of a SH3 Domain Sequence Set[J]. Acta Physico-Chimica Sinica, ;2011, 27(10): 2447-2456. doi: 10.3866/PKU.WHXB20111009 shu

Statistical Coupling Analysis of a SH3 Domain Sequence Set

1.
School of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China

Received Date: 19 April 2011
Available Online: 17 August 2011
Fund Project: 北京市自然科学基金(4092008, 4112010)资助项目 (4092008, 4112010)

Given the long range correlation characteristics of information about protein foldability and thermostability the multiple sequence alignment of a SH3 domain was analyzed using the modified statistical coupling analysis (SCA) method. Results show that the statistically conserved energy from the SCA method could be used to evaluate the site conservation of the SH3 sequence set properly. Sites with a high average coupling energy correspond to structurally and functionally important positions. Perturbing analysis on several sites revealed local and nonlocal perturbing modes in the SH3 domain. By combining the SCA and the clustering reorder method the structural core and the non-structural core sites of the SH3 domain, and detailed differences between several functional sites could be distinguished. Different perturbing modes that involve different sites exist in the SH3 domain. By sharing the common perturbing sites and the responding sites, different perturbing modes can interact. The coupling responding mode of all the sites in the structure was thus determined. Coupling information about the SH3 domain can improve our understanding about the relationship between the protein sequence and its structure as well as its function. It is also valuable in new protein design.
- Protein function,
- Protein stability,
- Perturbing mode,
- Coupling responding mode,
- Residue coevolution
1. [1]
  (1) Kauzmann,W. Some Factors in the Interpretation of Protein Denaturation. In Adv. Protein Chem.; Academic Press: London, 1959; Vol. 14; p 1.
2. [2]
  (2) Anfinsen, C. B.; Haber, E.; Sela, M.; White, J. F.W. Proc. Natl. Acad. Sci. U. S. A. 1961, 47, 1309.
3. [3]
  (3) Levinthal, C. J. Chim. Phys. Phys.-Chim. Biol. 1968, 65, 44.
4. [4]
  (4) Onuchic, J. N.;Wolynes, P. G. Curr. Opin. Struct. Biol. 2004, 14, 70.
5. [5]
  (5) Hao, M. H.; Scheraga, H. A. J. Mol. Biol. 1998, 277, 973.
6. [6]
  (6) Bryngelson, J. D.;Wolynes, P. G. Proc. Natl. Acad. Sci. U. S. A. 1987, 84, 7524.
7. [7]
  (7) Malakauskas, S. M.; Mayo, S. L. Nat. Struct. Biol. 1998, 5, 470.
8. [8]
  (8) Eijsink, V. G.; Gaseidnes, S.; Borchert, T. V.; van den Burg, B. Biomol. Eng. 2005, 22, 21.
9. [9]
  (9) Daniel, R. M.; Dines, M.; Petach, H. H. Biochem. J. 1996, 317, 1.
10. [10]
  (10) Unsworth, L. D.; van der Oost, J.; Koutsopoulos, S. FEBS J. 2007, 274, 4044.
11. [11]
  (11) Korkegian, A.; Black, M. E.; Baker, D.; Stoddard, B. L. Science 2005, 308, 857.
12. [12]
  (12) Mirny, L. A.; Shakhnovich, E. I. J. Mol. Biol. 1999, 291, 177.
13. [13]
  (13) Mirny, L.; Shakhnovich, E. J. Mol. Biol. 2001, 308, 123.
14. [14]
  (14) Di Nardo, A. A.; Larson, S. M.; Davidson, A. R. J. Mol. Biol. 2003, 333, 641.
15. [15]
  (15) Doolittle, R. F. Science 1981, 214, 149.
16. [16]
  (16) Doolittle, R. F. Trends Biochem. Sci. 1989, 14, 244.
17. [17]
  (17) Larson, S. M.; Ruczinski, I.; Davidson, A. R.; Baker, D.; Plaxco, K.W. J. Mol. Biol. 2002, 316, 225.
18. [18]
  (18) Tseng, Y. Y.; Liang, J. J. Mol. Biol. 2004, 335, 869.
19. [19]
  (19) Crooks, G. E.;Wolfe, J.; Brenner, S. E. Proteins 2004, 57, 804.
20. [20]
  (20) Afonnikov, D. A.; Kolchanov, N. A. Nucleic Acids Res. 2004, 32, 64.
21. [21]
  (21) Blades, M. J.; Ison, J. C.; Ranasinghe, R.; Findlay, J. B. C. Protein Sci. 2005, 14, 13.
22. [22]
  (22) Lockless, S.W.; Ranganathan, R. Science 1999, 286, 295.
23. [23]
  (23) Suel, G. M.; Lockless, S.W.;Wall, M. A.; Ranganathan, R. Nat. Struct. Biol. 2003, 10, 59.
24. [24]
  (24) Socolich, M.; Lockless, S.W.; Russ,W. P.; Lee, H.; Gardner, K. H.; Ranganathan, R. Nature 2005, 437, 512.
25. [25]
  (25) Russ,W. P.; Lowery, D. M.; Mishra, P.; Yaffe, M. B.; Ranganathan, R. Nature 2005, 437, 579.
26. [26]
  (26) Fodor, A. A.; Aldrich, R.W. Proteins 2004, 56, 211.
27. [27]
  (27) Dekker, J. P.; Fodor, A.; Aldrich, R.W.; Yellen, G. Bioinformatics 2004, 20, 1565.
28. [28]
  (28) Chi, C. N.; Elfstrom, L.; Shi, Y.; Snall, T.; Engstrom, A.; Jemth, P. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 4679.
29. [29]
  (29) Estabrook, R. A.; Luo, J.; Purdy, M. M.; Sharma, V.;Weakliem, P.; Bruice, T. C.; Reich, N. O. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 994.
30. [30]
  (30) Shen, H.; Xu, F.; Hu, H.;Wang, F.;Wu, Q.; Huang, Q.;Wang, H. J. Struct. Biol. 2008, 164, 281.
31. [31]
  (31) Riddle, D. S.; Grantcharova, V. P.; Santia , J. V.; Alm, E.; Ruczinski, I.; Baker, D. Nat. Struct. Mol. Biol. 1999, 6, 1016.
32. [32]
  (32) Larson, S. M.; Davidson, A. R. Protein Sci. 2000, 9, 2170.
33. [33]
  (33) Sigrist, C. J. A.; Cerutti, L.; de Castro, E.; Langendijk- Genevaux, P. S.; Bulliard, V.; Bairoch, A.; Hulo, N. Nucleic Acids Res. 2010, 38, D161.
34. [34]
  (34) Rivoire, O.; Leibler, S.; Ranganathan, R. A Summary of SCA Calculations. http://www.hhmi.swmed.edu/Labs/rr/Note103_files/Note103_v4.html (2008-08-18).
35. [35]
  (35) Brown, C. A.; Brown, K. S. PLoS ONE 2010, 5, e10779.
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]
  Shitao Fu , Jianming Zhang , Cancan Cao , Zhihui Wang , Chaoran Qin , Jian Zhang , Hui Xiong . Study on the Stability of Purple Cabbage Pigment. University Chemistry, 2024, 39(4): 367-372. doi: 10.3866/PKU.DXHX202401059
3. [3]
  Xuyang Wang , Jiapei Zhang , Lirui Zhao , Xiaowen Xu , Guizheng Zou , Bin Zhang . Theoretical Study on the Structure and Stability of Copper-Ammonia Coordination Ions. University Chemistry, 2024, 39(3): 384-389. doi: 10.3866/PKU.DXHX202309065
4. [4]
  Xiaoning TANG , Junnan LIU , Xingfu YANG , Jie LEI , Qiuyang LUO , Shu XIA , An XUE . Effect of sodium alginate-sodium carboxymethylcellulose gel layer on the stability of Zn anodes. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1452-1460. doi: 10.11862/CJIC.20240191
5. [5]
  Jiaxi Xu , Yuan Ma . Influence of Hyperconjugation on the Stability and Stable Conformation of Ethane, Hydrazine, and Hydrogen Peroxide. University Chemistry, 2024, 39(11): 374-377. doi: 10.3866/PKU.DXHX202402049
6. [6]
  Jing SU , Bingrong LI , Yiyan BAI , Wenjuan JI , Haiying YANG , Zhefeng Fan . Highly sensitive electrochemical dopamine sensor based on a highly stable In-based metal-organic framework with amino-enriched pores. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1337-1346. doi: 10.11862/CJIC.20230414
7. [7]
  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
8. [8]
  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
9. [9]
  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
10. [10]
  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
11. [11]
  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
12. [12]
  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
13. [13]
  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
14. [14]
  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
15. [15]
  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
16. [16]
  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
17. [17]
  Xinyue Zhang , Yifeng Ding , Ning Ma . Research on the “Project-based” Master’s Degree Model for Graduate Students in Materials and Chemical Engineering. University Chemistry, 2024, 39(6): 98-102. doi: 10.3866/PKU.DXHX202312093
18. [18]
  Jing Li , Lin Tian , Zhao Li , Yan Chen , Zongfei Yang , Huanhuan Shi . Exploration and Practice of the “134” Ideological and Political Teaching Model in the Introduction to Applied Chemistry. University Chemistry, 2024, 39(8): 7-15. doi: 10.3866/PKU.DXHX202311047
19. [19]
  Zeyu XU , Anlei DANG , Bihua DENG , Xiaoxin ZUO , Yu LU , Ping YANG , Wenzhu YIN . Evaluation of the efficacy of graphene oxide quantum dots as an ovalbumin delivery platform and adjuvant for immune enhancement. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1065-1078. doi: 10.11862/CJIC.20240099
20. [20]
  Weihua Jiang , Yongsheng Zhou , Qiaoqiao Teng . Progressive Teaching Model in the Practice and Exploration of Ideological and Political Education in Laboratory Courses: Taking the Organic Chemistry Experiment “Synthesis of Aspirin” as an Example. University Chemistry, 2024, 39(2): 99-104. doi: 10.3866/PKU.DXHX202306028

Get Citation

PDF

XML

Metrics

PDF Downloads(808)
Abstract views(2019)
HTML views(5)

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