Potential influence of Asp in the Ca2+ coordination position 5 of parvalbumin on the calcium-binding affinity: A computational study

Journal of Inorganic Biochemistry

Volumn 100, Issue 11, 2006, Pages 1879-1887

  Zhao, Jingyan ^a   Nelson, Donald J ^a   Huo, Shuanghong ^a  

^a CLARK UNIVERSITY   (United States)

Author keywords

Calcium binding; Conformational changes; MD simulation; Parvalbumin

Indexed keywords

ASPARTIC ACID; CALCIUM; PARVALBUMIN;

ARTICLE; BINDING AFFINITY; BINDING SITE; CALCIUM BINDING; CALCIUM TRANSPORT; ENERGY TRANSFER; MOLECULAR DYNAMICS; PREDICTION;

AMINO ACID SEQUENCE; ASPARTIC ACID; BINDING SITES; BINDING, COMPETITIVE; CALCIUM; COMPUTER SIMULATION; EF HAND MOTIFS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PARVALBUMINS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; THERMODYNAMICS;

MERLUCCIUS BILINEARIS;

EID: 33749571012     PISSN: 01620134     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jinorgbio.2006.07.016     Document Type: Article

References (49)

1. R.H.A.N. Kretsinger, D.J., Coord. Chem. Rev. 18 (1976) 29-124.
2. Kretsinger R.H. In: Carafoli E., Clementi F., Drabikowski W., and Margeth A. (Eds). Calcium Transport in Contraction and Secretion (1975), North Holland Publishing Co., Amsterdam 469-478
3. Chard P.S., Bleakman D., Christakos S., Fullmer C.S., and Miller R.J. J. Physiol. 472 (1993) 341-357
4. Pauls T.L., Cox J.A., and Berchtold M.W. Biochim. Biophys. Acta 1306 (1996) 39-54
5. Jiang Y., Johnson J.D., and Rall J.A. Am. J. Physiol. 270 (1996) C411-C417
6. Rasmussen C.D., and Means A.R. Mol. Endocrinol. 3 (1989) 588-596
7. Andressen C., Gotzos V., Berchtold M.W., Pauls T.L., Schwaller B., Fellay B., and Celio M.R. Exp. Cell Res. 219 (1995) 420-426
8. Brewer J.M., Wunderlich J.K., Kim D.H., Carr M.Y., Beach G.G., and Ragland W.L. Biochem. Biophys. Res. Commun. 160 (1989) 1155-1161
9. Cox J.A., Milos M., and Macmanus J.P. J. Biol. Chem. 265 (1990) 6633-6637
10. Kawasaki H., Nakayama S., and Kretsinger R.H. Biometals 11 (1998) 277-295
11. Drake S.K., and Falke J.J. Biochemistry 35 (1996) 1753-1760
12. Fahie K., Pitts R., Elkins K., and Nelson D.J. J. Biomol. Struct. Dyn. 19 (2002) 821-837
13. Elkins K.M., Gatzeva-Topalova P.Z., and Nelson D.J. Protein Eng. 14 (2001) 115-126
14. M. Nelson,W. Chazin, The CaBP Data Library, 1992.
15. Marsden B.J., Shaw G.S., and Sykes B.D. Biochem. Cell Biol. 68 (1990) 587-601
16. Reid R.E., and Hodges R.S. J. Theor. Biol. 84 (1980) 401-444
17. Reid R.E. J. Biol. Chem. 265 (1990) 5971-5976
18. Marsden B.J., Hodges R.S., and Sykes B.D. Biochemistry 27 (1988) 4198-4206
19. Henzl M.T., Wycoff W.G., Larson J.D., and Likos J.J. Protein Sci. 11 (2002) 158-173
20. Henzl M.T., Hapak R.C., and Goodpasture E.A. Biochemistry 35 (1996) 5856-5869
21. Lee Y.H., Tanner J.J., Larson J.D., and Henzl M.T. Biochemistry 43 (2004) 10008-10017
22. Henzl M.T., Larson J.D., and Agah S. Anal. Biochem. 319 (2003) 216-233
23. Richardson R.C., King N.M., Harrington D.J., Sun H., Royer W.E., and Nelson D.J. Protein Sci. 9 (2000) 73-82
24. Pearlman D., Case D.A., Caldwell J.W., Ross W.S., Cheatham T.E., Debolt S., Ferguson D., Seibel G., and Kollman P.A. Comp. Phys. Commun. 91 (1995) 1-41
25. Wang J.M., Cieplak P., and Kollman P.A. J. Comp. Chem. 21 (2000) 1049-1074
26. Jorgensen W.L. J. Chem. Phys. 77 (1982) 4156-4163
27. Berendsen H.J.C., Postma J.P.M., Van Gunsteren W.F., Dinola A., and Haak J.R. J. Chem. Phys. 81 (1984) 3684-3690
28. Darden T., York D., and Pedersen L. J. Chem. Phys. 98 (1993) 10089-10092
29. Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. J. Comp. Phys. 23 (1977) 327-341
30. Kabsch W., and Sander C. Biopolymers 22 (1983) 2577-2637
31. Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W., Donini O., Cieplak P., Srinivasan J., Case D.A., and Cheatham I.T.E. Acc. Chem. Res. 33 (2000) 889-897
32. Sitkoff D., Sharp K.A., and Honig B. J. Phys. Chem. 98 (1994) 1978-1988
33. Mcphalen C.A., Sielecki A.R., Santarsiero B.D., and James M.N. J. Mol. Biol. 235 (1994) 718-732
34. Ahmed F.R., Przybylska M., Rose D.R., Birnbaum G.I., Pippy M.E., and Macmanus J.P. J. Mol. Biol. 216 (1990) 127-140
35. Shaw G.S., Hodges R.S., and Sykes B.D. Science 249 (1990) 280-283
36. Franchini P.L., and Reid R.E. J. Theor. Biol. 199 (1999) 199-211
37. Thepaut M., Strub M.P., Cave A., Baneres J.L., Berchtold M.W., Dumas C., and Padilla A. Proteins 45 (2001) 117-128
38. Wang W., Lim W.A., Jakalian A., Wang J., Wang J., Luo R., Bayly C.I., and Kollman P.A. J. Am. Chem. Soc. 123 (2001) 3986-3994
39. Wang W., and Kollman P.A. J. Mol. Biol. 303 (2000) 567-582
40. Schapira M., Totrov M., and Abagyan R. J. Mol. Recognit. 12 (1999) 177-190
41. Revett S.P., King G., Shabanowitz J., Hunt D.F., Hartman K.L., Laue T.M., and Nelson D.J. Protein Sci. 6 (1997) 2397-2408
42. Tsui V., and Case D.A. J. Phys. Chem. B 105 (2001) 11314-11325
43. Ahmed F.R., Rose D.R., Evans S.V., Pippy M.E., and To R. J. Mol. Biol. 230 (1993) 1216-1224
44. Fahie K. Molecular Dynamics Studies of Calcium Binding in Site Directed Mutants of Silver Hake Parvalbumin-isoform B and Rat Oncomodulin (2002), M.A. Clark University, Worcester
45. Declercq J., Tinant B., Parello J., and Rambaud J. J. Mol. Biol. 220 (1991) 1017-1039
46. Cates M.S., Teodoro M.L., and Phillips Jr. G.N. Biophys. J. 82 (2002) 1133-1146
47. Blancuzzi Y., Padilla A., Parello J., and Cave A. Biochemistry 32 (1993) 1302-1309
48. Allouche D., Parello J., and Sanejouand Y. J. Mol. Biol. 285 (1999) 857-873
49. Thompson J.D., Higgins D.G., and Gibson T.J. Nucleic Acids Res. 22 (1994) 4673-4680