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Acta Chimica Sinica >

2012 , Vol. 0 >Issue 05: 606 - 610

DOI: https://doi.org/10.6023/A1107031

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Molecular Dynamics of an Extremely Thermophilic Ribose Binding Protein

  • Feng Xianli ,
  • Zhao Xi ,
  • Yu Hui ,
  • Wang Yibo ,
  • Sun Tiedong ,
  • Huang Xuri
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  • State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023

Received date: 2011-07-03

  Revised date: 2011-11-20

  Online published: 2011-12-06

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Abstract

Molecular dynamics simulations for extremely thermophilic protein thermoanaerobacter tengcongensis ribose binding protein (tteRBP) were performed to investigate the thermophilic mechanism of the protein. The comparative analysis of molecular trajectories of room temperature (300 K) and optimal activity temperature (375 K) shows that the protein conformations are stably maintained, but the concerted motions are different. The flexibility of the protein at 375 K significantly increases, so the protein can adjust the local conformation to adapt to extreme temperature. The analysis of the changes in protein structure confirmed that the local conformation adjustment at 375 K plays a key role on the extreme high temperature stability.

Key words： tteRBP (Thermoanaerobacter tengcongensis ribose binding protein); molecular dynamics; intramolecular concerted motions; flexibility; extremely hemophilic

Cite this article

Feng Xianli , Zhao Xi , Yu Hui , Wang Yibo , Sun Tiedong , Huang Xuri . Molecular Dynamics of an Extremely Thermophilic Ribose Binding Protein[J]. Acta Chimica Sinica, 2012 , 0(05) : 606 -610 . DOI: 10.6023/A1107031

References

1 Kumar, S.; Nussinov, R. Cell. Mol. Life Sci. 2001, 58, 1216.  

2 Berezovsky, N.; akhnovich, E. I. Proc. Natl. Acad. Sci. U. S. A. 2005, 102(36), 12742.  

3 Vieille, C.; Zeikus, G. J. Microbiol. Mol. Biol. Rev. 2001,65(1), 1.  

4 Jaenicke, R.; Bohm, G. Curr. Opin. Struct. Biol. 1998, 8(6),738.

5 Querol, E.; Perez-Pons, J. A.; Mozo-Villarias, A. Protein Eng. 1996, 9, 256.

6 Kumar, S.; Tsai, C. J.; Nussinov, R. Protein Eng. 2000, 13,179.  

7 Haney, P.; Konisky, J.; Koretke, K. K.; Luthey-Schulten, Z.; Wolynes, P. G. Proteins 1997, 28, 117.  

8 Xue, Y. F.; Xu, Y.; Liu, Y.; Ma, Y. H.; Zhou, P. Int. J. Syst. Evol. Microbiol. 2001, 51, 1335.

9 Boos, W.; Shuman, H. Microbiol. Mol. Biol. Rev. 1998,62(1), 204.  

10 Davidson, A. L.; Shuman, H. A.; Nikaido, H. Proc. Natl. Acad. Sci. U. S. A. 1992, 89(6), 2360.

11 Neiditch, M. B.; Federle, M. J.; Pompeani, A. J.; Kelly, R. C.; Swem, D. L.; Jeffrey, P. D.; Bassler, B. L.; Hughson, F. M. Cell 2006, 126(6), 1095.

12 Bjorkman, A. J.; Mowbray, S. L. J. Mol. Biol. 1998, 279(3),651.  

13 Magnusson, U.; Chaudhuri, B. N.; Ko, J.; Park, C.; Jones, T. A.; Mowbray, S. L. J. Biol. Chem. 2002, 277(16), 14077.

14 Sharff, A. J.; Rodseth, L. E.; Spurlino, J. C.; Quiocho, F. A. Biochemistry 1992, 31(44), 10657.

15 Matthew, J. C.; Yaji, T.; Malin, A.; Homme, W. H. BMC Struct. Biol. 2008, 8, 20.  

16 Berendsen, H. J. C.; Van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43.  

17 Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model.2001, 7, 6.

18 Spoel, D. V. D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 701.

19 Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A. J. Comput. Chem. 2003,24, 999.

20 Hess, B.; Bekker, H.; Berendsen, H.; Fraaije, J. J. Comput. Chem. 1997, 18, 1463.  

21 Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.

22 Schafer, H.; Mark, A. E.; van Gunsteren, W. J. Chem. Phys.2000, 113(18), 7809.  

23 Andricioaei, I.; Karplus, M. J. Chem. Phys. 2001, 115(14),6289.  

24 Amadei, A.; Linssen, A. B.; de Groot, B. L.; van Aalten, D. M.; Berendsen, H. J. J. Biomol. Struct. Dynm. 1996, 13,615.

25 Groot, B. L. d.; Amadei, A.; Scheek, R. M.; Nuland, N. A. J. V.; Berendsen, H. J. C. Struct. Funct. Genetics 1996, 26,314.  
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