Citation: LIU Fu-Feng, JI Luo, DONG Xiao-Yan. Effects ofMolecular Volume and Fractional Polar Surface Area of Osmolytes on the Thermal Stability of Chymotrypsin Inhibitor 2[J]. Acta Physico-Chimica Sinica, ;2010, 26(10): 2813-2820. doi: 10.3866/PKU.WHXB20101011 shu

Effects ofMolecular Volume and Fractional Polar Surface Area of Osmolytes on the Thermal Stability of Chymotrypsin Inhibitor 2

1.
Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, P. R. China

Received Date: 28 June 2010
Available Online: 27 September 2010
Fund Project: 国家自然科学基金(20636040, 20876111, 20906068) (20636040, 20876111, 20906068) 国家重点基础研究发展规划项目(973) (2009CB724705) (973) (2009CB724705) 天津市科委自然科学重点基金(08JCZDJC17100) 和天津大学自主创新基金资助 (08JCZDJC17100)

We correlated the protective ability of osmolytes on proteins with their fractional polar surface area (f_pSA) and molecular volume (V). Thus, both parameters need to be considered when the protective ability of osmolytes is analyzed. We carried out molecular dynamics simulations of the chymotrypsin inhibitor 2 (CI2) in different osmolytes to probe the molecular basis of the stabilizing effect. Based on the simulation data, a one-dimensional structure parameter was first calculated. We then used a statistical bivariate fit model to obtain a theoretical model, which represents the stability capacity of the osmolytes. Finally, the model was used to analyze the correlation between the two parameters (f_pSA and V) and the protective ability of the osmolytes. We found that the one-dimensional structure parameter characterized the protective ability of the osmolytes well. Using this model, the protective stability of the osmolytes can be analyzed accurately. The inclusion of V and the two-order term of f_pSA greatly increases the accuracy of the model. The protective capacity of the osmolytes increases with V. In addition, we introduced the two-order term of f_pSA into the fit formula. We found that the f_pSA of the osmolytes is negatively correlated with its protective ability when it is less than 0.7. However, when the f_pSA of the osmolytes is larger than 0.7, it is positively correlated with its protective ability.
- Molecular dynamics simulation,
- Protein stability,
- Osmolyte,
- Fractional polar surface area,
- Molecular volume
1. [1]
  
  1. Yancey, P. H. American Zoologist, 2001, 41: 699
2. [2]
  2. Timasheff, S. N. Annu. Rev. Biophys. Biomol. Struct., 1993, 22: 67
3. [3]
  3. Ou,W. B.; Park, Y. D.; Zhou, H. M. Eur. J. Biochem., 2001, 268: 5901
4. [4]
  4. Arakawa, T.; Timasheff, S. N. Biophys. J., 1985, 47: 411
5. [5]
  5. Ma, L.; Wei, Z. Q.; Huang, A. M.; Yang, H.; He, W. R.; Lin, R. S. Acta Chim. Sin., 2009, 67: 1566 [马林,魏志强,黄爱民,杨华, 何维仁,林瑞森. 化学学报, 2009, 67: 1566]
6. [6]
  6. Auton, M.; Bolen, D. W. Methods Enzymol., 2007, 428: 397
7. [7]
  7. Bolen, D. W.; Rose, G. D. Annu. Rev. Biochem., 2008, 77: 339
8. [8]
  8. Bolen, D. W.; Baskakov, I. V. J. Mol. Biol., 2001, 310: 955
9. [9]
  9. Liu, Y.; Bolen, D. W. Biochemistry, 1995, 34: 12884
10. [10]
  10. Street, T. O.; Bolen, D. W.; Rose, G. D. Proc. Natl. Acad. Sci. U. S. A., 2006, 103: 13997
11. [11]
  11. Li, S. Q.; Lin, R. S. Acta Phys. -Chim. Sin., 2002, 18: 825 [李淑芹,林瑞森.物理化学学报, 2002, 18: 825]
12. [12]
  12. Zhang, Y.; Ji, B.; Ling, P.; Zhang, T. Eur. J. Pharm. Biopharm., 2007, 65: 18
13. [13]
  13. Li, S. Q.; Sang,W. Q.; Lin, R. S. Acta Phys. -Chim. Sin., 2002, 18: 1110 [李淑芹,桑文强,林瑞森. 物理化学学报, 2002, 18: 1110]
14. [14]
  14. Lerbret, A.; Bordat, P.; Affouard, F.; Hedoux, A.; Guinet, Y.; Descamps, M. J. Phys. Chem. B, 2007, 111: 9410
15. [15]
  15. Liu, F.; Ji, L.; Dong, X. Y.; Sun, Y. J. Chem. Phys., 2010, DOI: 10.1063/1.3453713
16. [16]
  16. Otzen, D. E.; Itzhaki, L. S.; elMasry, N. F.; Jackson, S. E.; Fersht, A. R. Proc. Natl. Acad. Sci. U. S. A., 1994, 91: 10422
17. [17]
  17. McPhalen, C. A.; Svendsen, I.; Jonassen, I.; James, M. N. Proc. Natl. Acad. Sci. U. S. A., 1985, 82: 7242
18. [18]
  18. Day, R.; Bennion, B. J.; Ham, S.; Daggett, V. J. Mol. Biol., 2002, 322: 189
19. [19]
  19. Day, R.; Daggett, V. Protein Sci., 2005, 14: 1242
20. [20]
  20. Bennion, B. J.; Daggett, V. Proc. Natl. Acad. Sci. U. S. A., 2003, 100: 5142
21. [21]
  21. Bennion, B. J.; Daggett, V. Proc. Natl. Acad. Sci. U. S. A., 2004, 101: 6433
22. [22]
  22. Jackson, S. E.; Fersht, A. R. Biochemistry, 1991, 30: 10428
23. [23]
  23. Kundu, S.; Roy, D. J. Mol. Graph. Model., 2008, 27: 88
24. [24]
  24. Duan, Y.; Kollman, P. A. Science, 1998, 282: 740
25. [25]
  25. Beck, D. A.; Daggett, V. Biophys. J., 2007, 93: 3382
26. [26]
  26. van Aalten, D. M.; Bywater, R.; Findlay, J. B.; Hendlich, M.; Hooft, R. W.; Vriend, G. J. Comput. Aided Mol. Des., 1996, 10: 255
27. [27]
  27. Melo, E. P.; Chen, L.; Cabral, J. M.; Fojan, P.; Petersen, S. B. Otzen, D. E. Biochemistry, 2003, 42: 7611
28. [28]
  28. Lins, R. D.; Pereira, C. S.; Hunenberger, P. H. Proteins, 2004, 55: 177
29. [29]
  29. Sun, H.; Jiang, Y. J.; Yu, Q. S.; Zou, J. W. Acta Phys. -Chim. Sin., 2009, 25: 635 [孙浩, 蒋勇军, 俞庆森,邹建卫.物理化学学报, 2009, 25: 635]
30. [30]
  30. Zhao, Y. S.; Zheng, Q. C.; Zhang, H. X.; Chu, H. Y.; Sun, C. C. Acta Phys. -Chim. Sin., 2009, 25: 417 [赵勇山,郑清川,张红星, 楚慧郢,孙家钟.物理化学学报, 2009, 25: 417]
31. [31]
  31. Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. J. Comput. Chem., 2005, 26: 1701
32. [32]
  32. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular simulation: the GROMOS96 manual and user guide. Vdf Hochschulverlag AGan der ETH Zürich: Zürich, 1996
33. [33]
  33. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys., 1993, 98: 10089
34. [34]
  34. van Gunsteren, W. F.; Berendsen, H. J. C. Mol. Phys., 1977, 34: 1311
35. [35]
  35. Beredsen, H. J. C.; Postma, J. P. M.; van Gunsteren,W. F.; Di Nola, A.; Haak, J. R. J. Chem. Phys., 1984, 81: 3684
36. [36]
  36. Humphrey,W.; Dalke, A.; Schulten, K. J. Mol. Graph., 1996, 14: 33
37. [37]
  37. Timasheff, S. N. Biochemistry, 1992, 31: 9857
38. [38]
  38. Shimizu, S.; Smith, D. J. J. Chem. Phys., 2004, 121: 1148
1. [1]
  Congying Lu , Fei Zhong , Zhenyu Yuan , Shuaibing Li , Jiayao Li , Jiewen Liu , Xianyang Hu , Liqun Sun , Rui Li , Meijuan Hu . Experimental Improvement of Surfactant Interface Chemistry: An Integrated Design for the Fusion of Experiment and Simulation. University Chemistry, 2024, 39(3): 283-293. doi: 10.3866/PKU.DXHX202308097
2. [2]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
3. [3]
  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
4. [4]
  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
5. [5]
  Pingping Zhu , Yongjun Xie , Yuanping Yi , Yu Huang , Qiang Zhou , Shiyan Xiao , Haiyang Yang , Pingsheng He . Excavation and Extraction of Ideological and Political Elements for the Virtual Simulation Experiments at Molecular Level: Taking the Project “the Simulation and Computation of Conformation, Morphology and Dimensions of Polymer Chains” as an Example. University Chemistry, 2024, 39(2): 83-88. doi: 10.3866/PKU.DXHX202309063
6. [6]
  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
7. [7]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
8. [8]
  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
9. [9]
  Jinfu Ma , Hui Lu , Jiandong Wu , Zhongli Zou . Teaching Design of Electrochemical Principles Course Based on “Cognitive Laws”: Kinetics of Electron Transfer Steps. University Chemistry, 2024, 39(3): 174-177. doi: 10.3866/PKU.DXHX202309052
10. [10]
  Yeyun Zhang , Ling Fan , Yanmei Wang , Zhenfeng Shang . Development and Application of Kinetic Reaction Flasks in Physical Chemistry Experimental Teaching. University Chemistry, 2024, 39(4): 100-106. doi: 10.3866/PKU.DXHX202308044
11. [11]
  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
12. [12]
  Zhaomei LIU , Wenshi ZHONG , Jiaxin LI , Gengshen HU . Preparation of nitrogen-doped porous carbons with ultra-high surface areas for high-performance supercapacitors. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 677-685. doi: 10.11862/CJIC.20230404
13. [13]
  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
14. [14]
  Xuzhen Wang , Xinkui Wang , Dongxu Tian , Wei Liu . Enhancing the Comprehensive Quality and Innovation Abilities of Graduate Students through a “Student-Centered, Dual Integration and Dual Drive” Teaching Model: A Case Study in the Course of Chemical Reaction Kinetics. University Chemistry, 2024, 39(6): 160-165. doi: 10.3866/PKU.DXHX202401074
15. [15]
  Dexin Tan , Limin Liang , Baoyi Lv , Huiwen Guan , Haicheng Chen , Yanli Wang . Exploring Reverse Teaching Practices in Physical Chemistry Experiment Courses: A Case Study on Chemical Reaction Kinetics. University Chemistry, 2024, 39(11): 79-86. doi: 10.12461/PKU.DXHX202403048
16. [16]
  Jin Tong , Shuyan Yu . Crystal Engineering for Supramolecular Chirality. University Chemistry, 2024, 39(3): 86-93. doi: 10.3866/PKU.DXHX202308113
17. [17]
  Yong Shu , Xing Chen , Sai Duan , Rongzhen Liao . How to Determine the Equilibrium Bond Distance of Homonuclear Diatomic Molecules: A Case Study of H₂. University Chemistry, 2024, 39(7): 386-393. doi: 10.3866/PKU.DXHX202310102
18. [18]
  Xinlong WANG , Zhenguo CHENG , Guo WANG , Xiaokuen ZHANG , Yong XIANG , Xinquan WANG . Enhancement of the fragile interface of high voltage LiCoO₂ by surface gradient permeation of trace amounts of Mg/F. Chinese Journal of Inorganic Chemistry, 2024, 40(3): 571-580. doi: 10.11862/CJIC.20230259
19. [19]
  Yiying Yang , Dongju Zhang . Elucidating the Concepts of Thermodynamic Control and Kinetic Control in Chemical Reactions through Theoretical Chemistry Calculations: A Computational Chemistry Experiment on the Diels-Alder Reaction. University Chemistry, 2024, 39(3): 327-335. doi: 10.3866/PKU.DXHX202309074
20. [20]
  Yue Wu , Jun Li , Bo Zhang , Yan Yang , Haibo Li , Xian-Xi Zhang . Research on Kinetic and Thermodynamic Transformations of Organic-Inorganic Hybrid Materials for Fluorescent Anti-Counterfeiting Application information: Introducing a Comprehensive Chemistry Experiment. University Chemistry, 2024, 39(6): 390-399. doi: 10.3866/PKU.DXHX202403028

Get Citation

PDF

XML

Metrics

PDF Downloads(1251)
Abstract views(3228)
HTML views(19)

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