Molecular dynamics simulations of the unfolding of the starch binding domain from aspergillus niger glucoamylase

Journal of Biomolecular Structure and Dynamics

Volumn 20, Issue 5, 2003, Pages 615-621

  Liu, Hsuan Liang ^a   Wang, Wen Chi ^a  

^a NATIONAL TAIPEI UNIVERSITY OF TECHNOLOGY   (Taiwan)

Author keywords

Dielectric constant; Disulfide bond; Electrostatic interactions; Melting temperature; Temperature jump; strand

Indexed keywords

GLUCAN 1,4 ALPHA GLUCOSIDASE;

ARTICLE; ASPERGILLUS NIGER; BETA SHEET; BINDING SITE; CONFORMATIONAL TRANSITION; DIELECTRIC CONSTANT; DISULFIDE BOND; ELECTRICITY; ENZYME CONFORMATION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; TEMPERATURE DEPENDENCE;

ANIMALS; ASPERGILLUS NIGER; BINDING SITES; CATALYTIC DOMAIN; COMPUTER SIMULATION; CYCLODEXTRINS; GLUCAN 1,4-ALPHA-GLUCOSIDASE; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; STARCH;

ASPERGILLUS; ASPERGILLUS NIGER;

EID: 0037387089     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2003.10506878     Document Type: Article

References (48)

1. Sowdhamini, R., and Blundell, T. L., 1995. Protein Sci., 4:506–520.
2. Xu, D., Lin, S. L., and Nussinov, R., 1997. J. Mol. Biol., 265:68–84.
3. Nölting, B., and Andert, K., 2000. Proteins, 41:288–298.
4. Englander, S. W., and Mayne, L., 1992. Annu. Rev. Biophys. Biomol. Struct., 21:243–265.
5. Baldwin, P. W., 1993. Curr. Opin. Struct. Biol., 3:84–91.
6. Jennings, P. A., and Wright, P. E., 1993. Science, 262:892–896.
7. Dobson, C. M., Evans, P. A., and Radford, S. E., 1994. Trends Biochem. Sci., 19:31–37.
8. Ferst, A. R., 1993. FEBS Lett., 325:5–16.
9. Ferst, A. R., 1994. Biochem. Sco. Trans., 22:267–273.
10. Miranker, A., Robinson, C. V., Radford, S. E., Aplin, R. T., and Dobson, C. M., 1993. Science, 262:896–900.
11. Kuwajima, K., Semisotnov, G. V., Finkelstein, A. V., Sugai, S., and Ptitsyn, O. B., 1993. FEBS Lett., 334:265–268.
12. Blanco, F. J., Rivas, G., and Serrano, L., 1994. Nature Struct. Biol., 1:584–590.
13. Searle, M. S., Williams, D. H., and Packman, L. C., 1995. Nature Struct. Biol., 2:999–1006.
14. Searle, M. S., Zerella, R., Williams, D. H., and Packman, L. C., 1996. Protein Eng., 9:559–565.
15. Searle, M. S., and Jourdan, M., 2000. Bioorganic Medicinal Chem. Lett., 10:1139–1142.
16. Williams, S., Causgrove, T. P., Gilmanshin, R., Fang, K. S., Callender, R. H., Woodruff, W. H., and Dyer, R. B., 1996. Biochemistry, 35:691–697.
17. Mark, A. E., and van Gunsteren, W. F., 1992. Biochemistry, 31:7745–7748.
18. Hummer, G., Garde, S., Garcia, A. E., Paulaitis, M. E., and Pratt, L. R., 1998. Proc. Natl. Acad. Sci. USA, 95:1552–1555.
19. Karplus, M., and _ali, A., 1995. Curr. Opin. Struct. Biol., 5:58–73.
20. Daggett, V., and Levitt, M., 1994. Curr. Opin. Struct. Biol., 4:291–295.
21. Pace, C. N., Laurentz, D. V., and Erickson, R. E., 1992. Biochemistry, 31:1351–1361.
22. Daura, X., van Gunsteren, W. F., and Mark, A. E., 1999. Proteins:Struct. Funct. Genet., 34:269–280.
23. Lau, K. F., and Dill, K. A., 1989. K. A. Macromolecules, 22:3986–3997.
24. Fraternali, F., and van Gunsteren, W. F., 1996. J. Mol. Biol., 256:939–948.
25. Daura, X., Jaun, B., Seebach, D., van Gunsteren, W. F., and Mark, A. E., 1998. J. Mol. Biol., 280:925932
26. Daura, X., Mark, A. E., and van Gunsteren, W. F., 1999. Computer Phys. Commun., 123:97–102.
27. Caflisch, A., and Karplus, M., 1994. Proc. Natl. Acad. Sci. USA, 91:1746–1750.
28. Sugihara, M., and Segawa, S.-I., 1984. Biopolymers, 23:2473–2488.
29. Liu, H.-L., 2001. Recent Res. Devel. Protein Eng., 1:75–106.
30. Coutinho, P. M., and Reilly, P. J., 1997. Proteins, 29:334–347.
31. Jacks, A. J., Sorimachi, K., Gal-Coèffet, M. F.L., Williamson, G., Archer, D. B., and Williamson, M. P., 1995. Eur. J. Biochem., 233:568–578.
32. Sorimachi, K., Jacks, A. J., Gal-coèffet, M. F.L., Williamson, G., Archer, D. B., and Williamson, M. P., 1996. J. Mol. Biol., 259:970–987.
33. Sorimachi, K., Gal-coèffet, M. F.L., Williamson, G., Archer, D. B., and Williamson, M. P., 1997. Structure, 5:647–661.
34. Kabsch, W., and Sander, C., 1983. Biopolymers, 22:2577–2637.
35. Svensson, B., Pedersen, T. G., Svendsen, I., Sakai, T., and Ottesen, M., 1982. Carlsberg Res. Commun., 47:55–69.
36. Neustroev, K. N., Valter, S. N., Timchenko, N. V., Firsov, L. M., Golubev, A. M., and Khokhlov, S. E., 1993. Biochem. Mol. Biol. Int., 30:115–20.
37. Apparu, C., Diiguez, H., Williamson, G., and Svensson, B., 1995. Carbohydr Res., 277:313–320.
38. Takahashi, T., Kato, K., Ikegami, Y., and Irie, M., 1985. J. Biochem. (Tokyo), 98:663–671.
39. Coutinho, P. M., and Reilly, P. J., 1994. Protein Eng., 7:393–400.
40. Liu, H.-L., Coutinho, P. M., Ford, C., and Reilly, P. J., 1998. P. J. Protein Eng., 11:389–398.
41. Liu, H.-L., Ford, C., and Reilly, P. J., 1999. P. J. Protein Eng., 12:163–172.
42. Liu, H.-L., Doleyres, Y., Coutinho, P. M., Ford, C., and Reilly, P. J., 2000. Protein Eng., 13:655–659.
43. Li, Y., Coutinho, P. M., and Ford, C., 1998. Protein Eng., 11:661–667.
44. Richardson, J. S., 1981. Adv. Protein Chem., 34:167–339.
45. Hwang, M.-J., Ni, X., Waldman, M., Ewig, C. S., and Hagler, A. T., 1998. Biopolymers, 45:435–468.
46. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, K., and Haak, J. R., 1984. J. Comp. Phys., 81:3684–3690.
47. KoehI, P., 2001. Curr. Opin. Struct. Biol., 11:348–353.
48. Kabsch, W., 1976. Acta Cryst. A, 32:922–923.