Site–site communication in the EF-hand Ca2+-binding protein calbindin D9k (original) (raw)

References

  1. Forsén, S., Kördel, J., Grundström, T. & Chazin, W.J. The molecular anatomy of a calcium-binding protein. Acc. Chem. Res. 26, 7–14 ( 1993).
    Article Google Scholar
  2. Linse, S. et al. Electrostatic contributions to the binding of Ca2+ in calbindin D9k . Biochemistry 30, 154–162 (1991).
    Article CAS Google Scholar
  3. Linse, S., Jonsson, B. & Chazin, W.J. The effect of protein concentration on ion binding . Proc. Natl. Acad. Sci. USA 92, 4748– 4752 (1995).
    Article CAS Google Scholar
  4. Akke, M., Forsén, S. & Chazin, W.J. Molecular basis for co-operativity in Ca2+ binding to calbindin D9k. 1H nuclear magnetic resonance studies of (Cd2+)1-bovine calbindin D 9k . J. Mol. Biol. 220, 173– 189 (1991).
    Article CAS Google Scholar
  5. Akke, M., Forsén, S. & Chazin, W.J. Solution structure of (Cd2+)1-calbindin D9k reveals details of the stepwise structural changes along the Apo → (Ca2+)II 1 → (Ca2+)I,II 2 binding pathway. J. Mol. Biol. 252, 102– 121 (1995).
    Article CAS Google Scholar
  6. Carlström, G. & Chazin, W.J. Two-dimensional 1H nuclear magnetic resonance studies of the half-saturated (Ca2+)1 state of calbindin D9k. Further implications for the molecular basis of cooperative Ca2+ binding. J. Mol. Biol. 231, 415–430 (1993).
  7. Wimberly, B., Thulin, E. & Chazin, W.J. Characterization of the N-terminal half-saturated state of calbindin D9k: NMR studies of the N56A mutant. Protein Sci. 4, 1045–1055 (1995).
    Article CAS Google Scholar
  8. Skelton, N.J., Kördel, J., Akke, M. & Chazin, W.J. Nuclear magnetic resonance studies of the internal dynamics in Apo (Cd2+)1 and (Ca2+)2 calbindin D 9k. The rates of amide proton exchange with solvent. J. Mol. Biol. 227, 1100–1117 ( 1992).
    Article CAS Google Scholar
  9. Akke, M., Skelton, N.J., Kordel, J., Palmer, A.G. III, & Chazin, W.J. Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation. Biochemistry 32, 9832–9844 (1993).
    Article CAS Google Scholar
  10. Akke, M., Brüschweiler, R., Palmer, A.G. III. NMR order parameters and free energy: an analytical approach and its application to cooperative Ca2+ binding by calbindin D9k . J. Am. Chem. Soc. 115, 9832–9833 (1993).
    Article CAS Google Scholar
  11. Spassov, V. & Bashford, D. Electrostatic coupling to pH-titrating sites as a source of cooperativity in protein–ligand binding. Protein Sci. 7, 2012–2025 (1998).
    Article CAS Google Scholar
  12. Linse, S. & Chazin, W.J. Quantitative measurements of the cooperativity in an EF-hand protein with sequential calcium binding. Protein Sci. 4, 1038–1044 (1995).
    Article CAS Google Scholar
  13. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures . J. Appl. Crystallogr. 26, 283– 291 (1993).
    Article CAS Google Scholar
  14. Kördel, J., Skelton, N.J., Akke, M. & Chazin, W.J. High-resolution structure of calcium-loaded calbindin D9k . J. Mol. Biol. 231, 711–734 ( 1993).
    Article Google Scholar
  15. Skelton, N.J., Kördel, J. & Chazin, W.J. Determination of the solution structure of Apo calbindin D9k by NMR spectroscopy. J. Mol. Biol. 249 , 441–462 (1995).
    Article CAS Google Scholar
  16. Kroenke, C.D., Loria, J.P., Lee, L.K., Rance, M., & Palmer, A.G. III., Longitudinal and transverse 1H-15N dipolar/15N chemical shift anisotropy relaxation interference: unambiguous determination of rotational diffusion tensors and chemical exchange effects in biological macromolecules. J. Am. Chem. Soc. 120, 7905–7915 (1998).
    Article CAS Google Scholar
  17. Spyracopoulos, L., Gagne, S.M., Li, M.X. & Sykes, B.D. Dynamics and thermodynamics of the regulatory domain of human cardiac troponin C in the apo- and calcium-saturated states. Biochemistry 37, 18032– 18044 (1998).
    Article CAS Google Scholar
  18. Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546–4559 (1982).
    Article CAS Google Scholar
  19. Clore, G.M. et al. Deviations from simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins . J. Am. Chem. Soc. 112, 4989– 4991 (1990).
    Article CAS Google Scholar
  20. Yang, D. & Kay, L.E. Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J. Mol. Biol. 263, 369–382 (1996).
    Article CAS Google Scholar
  21. Li, Z., Raychaudhuri, S. & Wand, A.J. Insights into the local residual entropy of proteins provided by NMR relaxation. Protein Sci. 5, 2647–2650 (1996).
    Article CAS Google Scholar
  22. Bracken, C., Carr, P.A., Cavanagh, J., & Palmer, A.G., III . Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA. J. Mol. Biol. 285, 2133–2146 (1999).
    Article CAS Google Scholar
  23. Gagne, S.M., Tsuda, S., Spyracopoulos, L., Kay, L.E. & Sykes, B.D. Backbone and methyl dynamics of the regulatory domain of troponin C: anisotropic rotational diffusion and contribution of conformational entropy to calcium affinity. J. Mol. Biol. 278, 667–686 (1998).
    Article CAS Google Scholar
  24. Kay, L.E., Muhandiram, D.R., Wolf, G., Shoelson, S.E. & Forman-Kay, J.D. Correlation between binding and dynamics at SH2 domain interfaces. Nature Struct. Biol. 5, 156–163 (1998).
    Article CAS Google Scholar
  25. Fisher, M.W.F., Majumdar, A. & Zuiderweg, E.R.P. Protein NMR relaxation: theory, applications and outlook. Prog. NMR Spectrosc. 33, 207– 272 (1998).
    Article Google Scholar
  26. Cavanagh, J., Palmer, III,A.G., Fairbrother, W. & Skelton, N.J. Protein NMR spectroscopy. Principles and practice. (Academic Press, San Diego, California; 1996).
    Google Scholar
  27. Skelton, N.J. et al. Practical aspects of two-dimensional proton-detected 15N spin relaxation measurements. J. Magn. Reson. 102, 253–264 (1993).
    Article CAS Google Scholar
  28. Gippert, G. New Computational Methods for 3D NMR Data Analysis and Protein Structure Determination in High-Dimensional Internal Coordinate Space. Ph.D. thesis, The Scripps Research Institute (1995).
    Google Scholar
  29. Mäler, L., Potts, B.C. & Chazin, W.J. High resolution solution structure of apo calcyclin and structural variations in the S100 family of calcium-binding proteins. J. Biomol. NMR 13, 233–247 (1999).
    Article Google Scholar
  30. Güntert, P., Braun, W. & Wüthrich, K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517–530 ( 1991).
    Article Google Scholar
  31. Güntert, P. & Wüthrich, K. Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J. Biomol. NMR 1, 447–456 ( 1991).
    Article Google Scholar
  32. Pearlman, D.A. et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Commun. 91, 1–41 (1995).
    Article CAS Google Scholar
  33. Smith, J.A., Gomez-Paloma, L., Case, D.A. & Chazin, W.J. Molecular dynamics docking driven by NMR-derived restraints to determine the structure of the calicheamicin gamma(I) oligosaccharide domain complexed to duplex DNA. Magn. Reson. Chem. 34, 147– 155 (1996).
    Article Google Scholar
  34. Mandel, A.M., Akke, M., & Palmer, A.G., III. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J. Mol. Biol. 246, 144– 163 (1995).
    Article CAS Google Scholar

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