An insight into the thermostability of a pair of xylanases: The role of hydrogen bonds

Molecular Physics

Volumn 107, Issue 1, 2009, Pages 59-69

  Vieira, Davi Serradella ^a   Degrève, Léo ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Hydrogen bonds and structural stability; Molecular dynamics; Structure activity relationship; Thermostability; Xylanases

Indexed keywords

BACTERIOLOGY; BINDING SITES; CATALYSTS; DYNAMICS; ENZYMES; HYDROGEN; MOLECULAR DYNAMICS; STABILITY;

ACTIVE SITES; ANIMAL FOODS; BACILLUS CIRCULANS; BIOTECHNOLOGICAL APPLICATIONS; FAMILY 11; HIGH TEMPERATURES; INTRA-MOLECULAR INTERACTIONS; INTRAMOLECULAR HYDROGEN BONDS; MESOPHILIC; MOLECULAR DYNAMICS SIMULATIONS; PULP BLEACHING; SALT BRIDGES; SITE-DIRECTED MUTAGENESIS; STRUCTURE/ACTIVITY RELATIONSHIP; TEMPERATURE TOLERANCES; THERMOMYCES LANUGINOSUS; THERMOSTABILITY; XYLANASE; XYLANASES;

HYDROGEN BONDS;

EID: 61349159248     PISSN: 00268976     EISSN: 13623028     Source Type: Journal    
DOI: 10.1080/00268970902717959     Document Type: Article

References (40)

1. R. Predag, Z. Obradovic, D.K. Smith, G. Zhu, S. Vucetic, C. J, Brown, and J.D. Lawson, Protein Sci. 13, 71 (2004).
2. A. Szilágyi and P. Závodszky, Structure 8, 493 (2000).
3. N. Kulkarni, A. Shendy, and M. Rao, FEMS Microbiol. Rev. 23, 411 (1999).
4. S. Kumar, C. Tsai, and R. Nussinov, Protein Eng. 113, 179 (2000).
5. W. Harris, R.W. Pickersgill, I. Connerton, P. Debeire, J. Touzel, C. Breton, and S. Pérez, Proteins 29, 77 (1997).
6. M.W.W.W. Adams and R.M. Kelly, Chem. Eng. News. 73, 32 (1995).
7. P.L. Wintrode, D. Zhang, V. Nagarajan, F.H. Arnold, and W.A. Goddard, J. Mol. Biol. 327, 745 (2003).
8. Q.K. Beg, M. Kapoor, L. Mahajan, and G.S. Hoondal, Appl. Microbiol. Biotechnol. 56, 326 (2001).
9. W.W. Wakarchuk, W.L. Sung, R.L. Campbell, A. Cunningham, D.C. Watson, and M. Yaguchi, Protein Eng. 7, 1379 (1994).
10. W.W. Wakarchuk, R.L. Campbell, W.L., Sung, J. Voodi, and M. Yaguchi, Protein Sci. 3, 467 (1994).
11. J. Georis, F.L. Esteves, J. Lamotte-Brasseur, V. Bougnet, B. Devreese, F. Giannotta, and B. Granier, Protein Sci. 9, 466 (2000).
12. M. Torrez, M. Schultehenrich, and D.R. Livesay, Biophys. J. 85, 2845 (2003).
13. T.E. Creighton, Current Biol. 1, 5 (1991).
14. A.J. Doig and D.H. Williams, J. Am. Chem. Soc. 114, 338 (1992).
15. B. Honig and A.S. Yang, Adv. Protein. Chem. 46, 27 (1995).
16. K.P. Murphy and S.J. Gill, J. Mol. Biol. 222, 699 (1991).
17. C. Pace, B. Shirley, M. McNutt, and K. Gajiwala, FASEB J. 10, 75 (1996).
18. K.A. Dill, Biochemistry. 29, 7133 (1990).
19. T.E. Wales and M.C. Fitzgerald, J. Am. Chem. Soc. 1232, 7709 (2001).
20. G. Vogt, S. Woell, and P. Argos, J. Mol. Biol. 269, 631 (1997).
21. G. Brancaleoni, M.R. Lourenzoni, and L. Degrève, Genet. Mol. Res. 5, 350 (2006).
22. M. Purmonen, J. Valjakka, K. Takkinen, T. Laitinen, and J. Rouvinen, Protein Eng. 30, 1 (2007).
23. M. Karplus and G.A. Petsko, Nature 347, 631 (1990).
24. M.T. Murakami, R.K. Arni, D.S. Vieira, L., Degrève, R. Ruller, and R.J. Ward, FEBS Lett. 579, 6505 (2005).
25. H.J.C. Berendsen, J.P.M. Postma, A. DiNola, and J.R. Haak, J. Chem. Phys. 81, 3684 (1984).
26. B. Hess, H. Becker, H.J. Berendsen, and J.G.E.M. Fraaije, J. Comput. Chem. 18, 1463 (1997).
27. S. Miyamoto and P.A. Kollman, J. Comp. Chem. 13, 952 (1992).
28. R.W. Hockney and S.P. Goel, J. Comput. Phys. 14, 148 (1974).
29. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
30. Protein Data Bank. http://www.rcsb.org/pdb
31. G. Arfken, The Method of Steepest Descents in Mathematical Methods for Physicists, 3rd ed (Academic Press, Orlando, 1985).
32. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans, in Interactions models for water in relation to protein hydration, Intermolecular Forces, edited by B. Pullman (Reidel Publishing Company, Dordrecht, 1981).
33. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Model. 7, 306 (2001).
34. W.F. van Gunsteren, S.R. Billeter, A.A. Eising, P.H. Hünenberger, P. Krüger, A.E. Mark, W.R.P. Scott, and I.G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide (Biomos, Groningen, 1996).
35. S. Toba and K.M. Merz Jr, J. Am. Chem. Soc. 119, 9939 (1997).
36. F.H. Stillinger and A.A. Rahman, J. Chem. Phys. 60, 1545(1974).
37. L.B. Silva and L. Degrève, Mol. Phys. 100, 3111 (2002).
38. K. Gruber, G. Klinstschar, M. Hayn, A. Schlacher, W. Steiner, and C. Kratky, Biochemistry 37, 13475(1998).
39. A. Törrönen, A. Harkki, and J. Rouvinen, The EMBO J. 13, 2493 (1994).
40. J. Muilu, A. Törronen, M. Peräkyä, and J. Rouvinen, Proteins 31, 434 (1998).