Prediction of water and metal binding sites and their affinities by using the Fold-X force field

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 29, 2005, Pages 10147-10152

  Schymkowitz, Joost W H ^b   Rousseau, Frederic ^b   Martins, Ivo C ^b   Ferkinghoff Borg, Jesper ^c   Stricher, Francois ^a   Serrano, Luis ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Ion; Structural water; Water bridge calcium; Zinc

Indexed keywords

CALCIUM ION; COPPER ION; LIGAND; MAGNESIUM ION; MANGANESE; METAL ION; PROTEIN; WATER; ZINC ION;

ARTICLE; BINDING AFFINITY; BINDING SITE; CALCULATION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DISSOCIATION CONSTANT; ENERGY; IONIC STRENGTH; PREDICTION; PRIORITY JOURNAL;

BIOPHYSICS; CHEMISTRY, ANALYTICAL; METALS, HEAVY; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN FOLDING; WATER;

EID: 22544450150     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0501980102     Document Type: Article

References (40)

1. Mendes, J., Guerois, R. & Serrano, L. (2002) Curr. Opin. Struct. Biol. 12, 441-446.
2. Lazaridis, T. & Karplus, M. (2000) Curr. Opin. Struct. Biol. 10, 139-145.
3. Guerois, R., Nielsen, J. E. & Serrano, L. (2002) J. Mol. Biol. 320, 369-387.
4. Reumers, J., Schymkowitz, J., Ferrkinghoff-Borg, J., Stricher, F., Serrano, L. & Rousseau, F. (2005) Nucleic Acids Res. 33, D527-D532.
5. Fernandez-Ballester, G., Blanes-Mira, C. & Serrano, L. (2004) J. Mol. Biol. 335, 619-629.
6. Guerois, R. & Serrano, L. (2000) J. Mol. Biol. 304, 967-982.
7. Lindorff-Larsen, K., Paci, E., Serrano, L., Dobson, C. M. & Vendruscolo, M. (2003) Biophys. J. 85, 1207-1214.
8. Guerois, R. & Serrano, L. (2001) Curr. Opin. Struct. Biol. 11, 101-106.
9. Selzer, T. & Schreiber, G. (1999) J. Mol. Biol. 287, 409-419.
10. Schymkowitz, J. W. H., Ferrkinghoff-Borg, J., Stricher, F., Rousseau, F., Nys, R. & Serrano, L. (2005) Nucleic Acids Res., in press.
11. Jones, S., van Heyningen, P., Berman, H. M. & Thornton, J. M. (1999) J. Mol. Biol. 287, 877-896.
12. Baker, N. A. (2005) Curr. Opin. Struct. Biol. 15, 137-143.
13. Mehta, R., Keawwattana, W. & Kyu, T. (2004) J. Chem. Phys. 120, 4024-4031.
14. Lee, M. S., Salsbury, F. R., Jr., & Olson, M. A. (2004) J. Comput. Chem. 25, 1967-1978.
15. Feig, M., Im, W. & Brooks, C. L., III (2004) J. Chem. Phys. 120, 903-911.
16. Feig, M. & Brooks, C. L., III (2004) Curr. Opin. Struct. Biol. 14, 217-224.
17. Petukhov, M., Cregut, D., Soares, C. M. & Serrano, L. (1999) Protein Sci. 8, 1982-1989.
18. Jiang, L., Kuhlman, B., Kortemme, T. & Baker, D. (2005) Proteins 58, 893-904.
19. Pitt, W. R. & Goodfellow, J. M. (1991) Protein Eng. 4, 531-537.
20. Chattopadhyaya, R., Meador, W. E., Means, A. R. & Quiocho, F. A. (1992) J. Mol. Biol. 228, 1177-1192.
21. Ogawa, Y. & Tanokura, M. (1984) J. Biochem. (Tokyo) 95, 19-28.
22. Kohse, K. P. & Heilmeyer, L. M., Jr. (1981) Eur. J. Biochem. 117, 507-513.
23. Clugston, S. L. & Honek, J. F. (2000) J. Mol. Evol. 50, 491-495.
24. Hakansson, K., Carlsson, M., Svensson, L. A. & Liljas, A. (1992) J. Mol. Biol. 227, 1192-1204.
25. Linse, S. & Forsen, S. (1995) Adv. Second Messenger Phosphoprotein Res. 30, 89-151.
26. Xu, J., Baase, W. A., Quillin, M. L., Baldwin, E. P. & Matthews, B. W. (2001) Protein Sci. 10, 1067-1078.
27. Kiel, C., Serrano, L. & Herrmann, C. (2004) J. Mol. Biol. 340, 1039-1058.
28. Askwith, C. & Kaplan, J. (1998) Trends Biochem. Sci. 23, 135-138.
29. Riordan, J. F. (1977) Ann. Clin. Lab. Sci. 7, 119-129.
30. Hellinga, H. W. (1996) Curr. Opin. Biotechnol. 7, 437-441.
31. Finney, L. A. & O'Halloran, T. V. (2003) Science 300, 931-936.
32. Gregory, D. S., Martin, A. C., Cheetham, J. C. & Rees, A. R. (1993) Protein Eng. 6, 29-35.
33. Naval, M. & Di Cera, E. (1994) Proc. Natl. Acad. Sci. 91, 817-821.
34. Yamashita, M. M., Wesson, L., Eisenman, G. & Eisenberg, D. (1990) Proc. Natl. Acad. Sci. USA 87, 5648-5652.
35. Yang, W., Wilkins, A. L., Ye, Y., Liu, Z. R., Li, S. Y., Urbauer, J. L., Hellinga, H. W., Kearney, A., van der Merwe, P. A. & Yang, J. J. (2005) J. Am. Chem. Soc. 127, 2085-2093.
36. Yang, W., Jones, L. M., Isley, L., Ye, Y., Lee, H. W., Wilkins, A., Liu, Z. R., Hellinga, H. W., Malchow, R., Ghazi, M. & Yang, J. J. (2003) J. Am. Chem. Soc. 125, 6165-6171.
37. Klemba, M., Gardner, K. H., Marino, S., Clarke, N. D. & Regan, L. (1995) Nat. Struct. Biol. 2, 368-373.
38. Lu, Y., Berry, S. M. & Pfister, T. D. (2001) Chem. Rev. 101, 3047-3080.
39. Wei, L. & Altman, R. B. (1998) Pacific Symp. Biocomput, 497-508.
40. Glusker, J. P. (1991) Adv. Protein Chem. 42, 1-76.