Molecular dynamics simulation of temperature-dependent flexibility of thermophilic xylose isomerase

Chinese Journal of Chemical Physics

Volumn 22, Issue 5, 2009, Pages 467-472

  Xu, Wei ^a   Cai, Ping ^b   Yan, Ming ^b   Xu, Lin ^b   Ouyang, Ping Kai ^b  

^a YANCHENG INSTITUTE OF TECHNOLOGY   (China)

^b NANJING TECH UNIVERSITY   (China)

Author keywords

Flexibility; Molecule dynamics; Structure; Xylose isomerase

Indexed keywords

EID: 70450238007     PISSN: 16740068     EISSN: None     Source Type: Journal    
DOI: 10.1088/1674-0068/22/05/467-472     Document Type: Article

References (39)

1. Bhosale S H, M B Rao and V V Deshpande 1996 Microbiol. Rev. 60 280
2. Hahn H B, C F Wahlbom, M Grdonyi, W H van Zyl, R R C Otero and L J Jönsson 2001 Adv. Biochem. Eng. Biotechnol. 73 53
3. Wang Y, W L Shi, X Y Liu, Y Shen, X M Bao, F W Bai and Y B Qu 2004 Biotechnol. Lett. 26 885
4. Walfridsson M, X Bao, M Anderlund, G Lilius, L Bulow and B H Hagerdal 1996 Environ. Microbiol. 62 4648
5. Liu X L, N Jiang, P He, D J Lu and A Shen 2005 Chin. Sci. Bull. 50 653
6. Kuyper M, M J Toirkens, J A Diderich, A A Winkler, J P van Dijken and J T Pronk 2005 FEMS Yeast Res. 5 925
7. Dekker K, H Yamagata, K Sakaguchi and S Udaka 1991 J. Bacteriol. 173 3078
8. Mrk G and H H Bärbel 2003 Enzyme Microb. Tech. 32 252
9. Shen Y, Y Wang, X M Bao and Y B Qu 2003 Chin. J. Biotechnol. 19 636
10. D'Amico S, P Claverie, T Collins, D Georlette, E Gratia, A Hoyoux, M A Meuwis, G Feller and C Gerday 2002 Phil. Trans. R. Soc. Lond. B. 357 1423
11. Igor N B and I S Eugene 2005 PNAS 102 12742
12. Lönn A, M Grdonyi, W van Zyl, B H Hagerdal and R C Otero 2002 Eur. J. Biochem. 269 157
13. Zeikus J G 1996 Enzymes for Carbohydrate Eng. 12 145
14. Farber G K, A Glasfeld, G Tiraby, D Ringe and G A Petsko 1989 Biochemistry 28 7289
15. Chang C, B C Park, D S Lee and S W Suh 1999 J. Mol. Biol. 288 623
16. Elan Z E, M Oscar, L Wladimir, M K Dmitry, W W Magnus, A B Daryl, S J Jack, E K Lewis and K Dorothee 2005 Nature 438 7064
17. Daniel R M, R V Dunn, J L Finney and J C Smith 2003 Annu. Rev. Bioph. Biom. 32 69
18. Martin K and J M Andrew 2002 Nat. Struct. Biol. 9 646
19. Beck D A and V Daggett 2004 Methods 34 112
20. Snow C D, E J Sorin, Y M Rhee and V S Pande 2005 Annu. Rev. Bioph. Biom. 34 43
21. Wintrode P L, D Q Zhang, N Vaidehi, F H Arnold and W A Goddard 2003 J. Mol. Biol. 327 745
22. Kumar S and R Nussinov 2001 Cell. Mol. Life Sci. 58 1216
23. Sotirios K, V O John and N Willem 2005 Proteins 61 377
24. Johanna K, P Tarja and H Santa 2004 Protein Eng. Des. Sel. 17 861
25. Santa H, J Kammonen, I Lehtonen, J Karimaki, O Pastinen, M Leisola and O Turunen 2005 Biochim. Biophys. Acta 65 1749
26. Garcia V M, T D Poulsen, D G Truhlar and J Gao 2004 Protein Sci. 13 2341
27. Xu W, P Cai, M Yan, L Xu and P K Ouyang 2007 Chem. J. Chin. Univ. 28 971
28. Guex N, A Diemand and M C Peitsch 1999 Trends Biochem. Sci. 24 364
29. Xu W, M Yan, L Ding and L Xu 2006 Comp. Appl. Chem. 23 531
30. Phillips J C, R Braun, W Wang, J Gumbart, E Tajkhorshid, E Villa, C Chipot, R D Skeel, L Kalé and K Schulten 2005 J. Comput. Chem. 26 1781
31. Kale L, R Skeel, M Bhandarkar, R Brunner, A Gursoy, N Krawetz, J Phillips, A Shinozaki, K Varadarajan and K Schulten 1999 J. Comput. Phys. 151 283
32. Jorgensen W L, J Chandrasekhar, J D Madura, R W Impey and M L Klein 1983 J. Chem. Phys. 79 926
33. Cao Z X 2008 PhD Dissertation (Hefei: University of Science and Technology of China)
34. Humphrey W, A Dalke and K Schulten 1996 J. Mol. Graph. 14 33
35. Feller S E, Y Zhang, R W Pastor and B R Brooks 1995 J. Chem. Phys. 103 4613
36. Darden T, D York and L Pedersen 1993 J. Chem. Phys. 98 10089
37. Liskin S K and C S Brown 2005 Bioinformatics 21 3327
38. Liskin S K 2004 Biochemistry-US. 43 10886
39. Xu W, M Yan, L Xu, L Ding and P K Ouyang 2009 Enzyme Microb. Tech. 44 77