Citation: BAI Shu, CHANG Ying, LIU Xiao-Juan, LIU Fu-Feng. Interactions between Trehalose and Amino Acids by Molecular Dynamics Simulations[J]. Acta Physico-Chimica Sinica, ;2014, 30(7): 1239-1246. doi: 10.3866/PKU.WHXB201405151 shu

Interactions between Trehalose and Amino Acids by Molecular Dynamics Simulations

BAI Shu ^1,2 ,
CHANG Ying ¹ ,
LIU Xiao-Juan ¹ ,
LIU Fu-Feng ^1,2,

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

Received Date: 4 March 2014
Available Online: 15 May 2014
Fund Project:

Although trehalose is used as a protein stabilizer, the mechanism by which this stability is induced is not fully understood at present. In this study, we investigated the interactions between trehalose and all 20 common amino acids using all-atom molecular dynamics simulations. It is found that all the amino acids exhibit a preference for contact with water, especially the polar and charged amino acids. Conversely, only the hydrophobic amino acids were found to have a slight preference for contact with trehalose molecules. This tendency is most pronounced in the case of contact between trehalose and aromatic or hydrophobic side chains, whereas the backbones of each amino acids all show similar propensities for contact with water. Furthermore, hydrogen bonds between amino acids and trehalose were found to be significantly weaker than those between amino acids and water, although both trehalose and water can interact with the amino acids via hydrogen bonds. These findings are important with regard to the exploration of the molecular mechanism of protein stability induced by trehalose and the rational design of highly efficient protein stabilizers.
- Trehalose,
- Osmolyte,
- Molecular dynamics simulation,
- Protein stability,
- Hydrogen bond
1. [1]
  
  (1) Richards, A. B.; Krakowka, S.; Dexter, L. B.; Schmid, H.; Wolterbeek, A. P.;Waalkens-Berendsen, D. H.; Shi yuki, A.; Kurimoto, M. Food Chem. Toxicol. 2002, 40, 871. doi: 10.1016/S0278-6915(02)00011-X
2. [2]
  (2) Singer, M. A.; Lindquist, S. Trends Biotechnol. 1998, 16, 460. doi: 10.1016/S0167-7799(98)01251-7
3. [3]
  (3) Crowe, J. H.; Crowe, L. M.; Carpenter, J. F.;Wistrom, A. C. Biochem. J. 1987, 242, 1.
4. [4]
  (4) Ohtake, S.;Wang, Y. J. J. Pharm. Sci. 2011, 100, 2020. doi: 10.1002/jps.22458
5. [5]
  (5) Zhang, N.; Liu, F. F.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B 2012, 116, 7040. doi: 10.1021/jp300171h
6. [6]
  (6) Zhang, N.; Liu, F. F.; Dong, X. Y.; Sun, Y. Biochem. Eng. J. 2013, 70, 188. doi: 10.1016/j.bej.2012.11.004
7. [7]
  (7) Liu, F. F.; Ji, L.; Zhang, L.; Dong, X. Y.; Sun, Y. J. Chem. Phys. 2010, 132, 225103. doi: 10.1063/1.3453713
8. [8]
  (8) Liu, F. F.; Ji, L.; Dong, X. Y. Acta Phys. -Chim. Sin. 2010, 26, 2813. [刘夫锋, 纪络, 董晓燕. 物理化学学报, 2010, 26, 2813.]
9. [9]
  (9) Zhang, N.; Liu, F. F.; Dong, X. Y.; Sun, Y. Biochem. Eng. J. 2013, 79, 120. doi: 10.1016/j.bej.2013.07.007
10. [10]
  (10) Dong, X. Y.; Liu, J. H.; Liu, F. F.; Sun, Y. Biochem. Eng. J. 2009, 43, 321. doi: 10.1016/j.bej.2008.10.015
11. [11]
  (11) Liu, F. F.; Ji, L.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B 2009, 113, 11320. doi: 10.1021/jp905580j
12. [12]
  (12) Liu, F. F.; Dong, X. Y.; Sun, Y. Acta Phys. -Chim. Sin. 2010, 26, 1643. [刘夫锋, 董晓燕, 孙彦. 物理化学学报, 2010, 26, 1643.]
13. [13]
  (13) Bolen, D.W.; Rose, G. D. Annu. Rev. Biochem. 2008, 77, 339. doi: 10.1146/annurev.biochem.77.061306.131357
14. [14]
  (14) Lins, R. D.; Pereira, C. S.; Hunenberger, P. H. Proteins 2004, 55, 177. doi: 10.1002/prot.10632
15. [15]
  (15) Ansari, A.; Jones, C. M.; Henry, E. R.; Hofrichter, J.; Eaton,W. A. Science 1992, 256, 1796. doi: 10.1126/science.1615323
16. [16]
  (16) Allison, S. D.; Chang, B.; Randolph, T.W.; Carpenter, J. F. Arch. Biochem. Biophys. 1999, 365, 289. doi: 10.1006/abbi.1999.1175
17. [17]
  (17) Lins, R. D.; Hunenberger, P. H. J. Comput. Chem. 2005, 26, 1400. doi: 10.1002/jcc.20275
18. [18]
  (18) Liu, F. F.; Dong, X. Y.; Sun, Y. J. Mol. Graph. Model. 2008, 27, 421. doi: 10.1016/j.jmgm.2008.07.002
19. [19]
  (19) Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435. doi: 10.1021/ct700301q
20. [20]
  (20) Berendsen, H. J. C.; Postma, J. P. M.; van gunsteren,W. F.; Hermans, J. In Intermolecular Forces; Pullman, B. Ed.; Reidel: Dordecht, Holland, 1981; pp 331.
21. [21]
  (21) van gunsteren,W. F.; Billeter, S. R.; Eising, A. A.; Hunenberger, P. H.; Mark, A. E.; Scott,W. R. P.; Tironi, I. G. Biomolecular Simulation : The GROMOS96 Manual and User Guide; Zurich: Groninigen, 1996.
22. [22]
  (22) Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463. doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
23. [23]
  (23) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089. doi: 10.1063/1.464397
24. [24]
  (24) Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren,W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684. doi: 10.1063/1.448118
25. [25]
  (25) Liu, F. F.; Dong, X. Y.;Wang, T.; Sun, Y. J. Chromatogr. A 2007, 1175, 249. doi: 10.1016/j.chroma.2007.10.074
26. [26]
  (26) Stumpe, M. C.; Grubmuller, H. J. Am. Chem. Soc. 2007, 129, 16126. doi: 10.1021/ja076216j
27. [27]
  (27) Sheu, S. Y.; Yang, D. Y.; Selzle, H. L.; Schlag, E.W. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 12683. doi: 10.1073/ pnas.2133366100
28. [28]
  (28) Jenkins, S.; Morrison, I. Chem. Phys. Lett. 2000, 317, 97. doi: 10.1016/S0009-2614(99)01306-8
29. [29]
  (29) Li,W.; Qin, M.; Tie, Z.;Wang,W. Phys. Rev. E 2011, 84, 041933. doi: 10.1103/PhysRevE.84.041933
30. [30]
  (30) Li,W.; Zhang, J.;Wang, J.;Wang,W. J. Am. Chem. Soc. 2008, 130, 892. doi: 10.1021/ja075302g
31. [31]
  (31) Lei, H.; Duan, Y. Curr. Opin. Struct. Biol. 2007, 17, 187. doi: 10.1016/j.sbi.2007.03.003
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