Redistribution and loss of side chain entropy upon formation of a calmodulin–peptide complex (original) (raw)

References

  1. Wintrode, P.L. & Privalov, P.L. Energetics of target peptide recognition by calmodulin: a calorimetric study. J. Mol. Biol. 266, 1050–1062 ( 1997).
    Article CAS Google Scholar
  2. Murphy, K.P., Xie, D., Garcia, K.C., Amzel, L.M. & Freire, E. Structural energetics of peptide recognition: angiotensin II/antibody binding. Proteins 15, 113– 120 (1993).
    Article CAS Google Scholar
  3. Lee, K.H., Xie, D., Freire, E. & Amzel, L.M. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins 20, 68–84 (1994).
    Article CAS Google Scholar
  4. Makhatadze, G.I. & Privalov, P.L. Energetics of protein structure. Adv. Prot. Chem. 47, 307–425 (1995).
    CAS Google Scholar
  5. Weber, G. Thermodynamics of the association and the pressure dependence of oligomeric proteins. J. Phys. Chem. 97, 7108– 7115 (1993).
    Article CAS Google Scholar
  6. Karplus, M. & Kushick, J.N. Method for estimating the configurational entropy of macromolecules. Macromolecules 14, 325–332 (1981).
    Article CAS Google Scholar
  7. Doig, A.J. & Sternberg, J.E. Side-chain conformational entropy in protein folding. Protein Sci. 4, 2247 –2251 (1995).
    Article CAS Google Scholar
  8. Rasmussen, B.F., Stock, A.M., Ringe, D. & Petsko, G.A. Crystalline ribonuclease A loses function below the dynamical transition at 220 K. Nature 357, 423–424 ( 1992).
    Article CAS Google Scholar
  9. Feher, V.A. & Cavanagh, J. Millisecond-timescale motions contribute to the function of the bacterial response regulator protein SpoOF. Nature 400, 289–293 ( 1999).
    Article CAS Google Scholar
  10. Stock, A. Relating dynamics to function. Nature 400, 221–222 (1999).
    Article CAS Google Scholar
  11. Akke, M., Brüschweiler, R. & Palmer III, A.G. 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
  12. Li, Z., Raychaudhuri, S. & Wand, A.J. Insights into the local entropy of proteins provided by NMR relaxation. Protein Sci. 5, 2647– 2650 (1996).
    Article CAS Google Scholar
  13. 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
  14. Vogel, H.J. Calmodulin: a versatile calcium mediator protein. Biochem. Cell Biol. 72, 357–375 ( 1994).
    Article CAS Google Scholar
  15. Babu, Y.S. et al. Three-dimensional structure of calmodulin. Nature 315, 37–40 ( 1985).
    Article CAS Google Scholar
  16. Barbato, G., Ikura, M., Kay, L.E., Pastor, R.W. & Bax, A. Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. Biochemistry 31, 5269 –5278 (1992).
    Article CAS Google Scholar
  17. Zhang, M., Tanaka, T. & Ikura, M. Calcium-induced conformational transition revealed by the solution structure of apocalmodulin. Nature Struct. Biol. 2, 758–767 (1995).
    Article CAS Google Scholar
  18. Kuboniwa, H. et al. Solution structure of calcium-free calmodulin. Nature Struct. Biol. 2, 768–776 (1995).
    Article CAS Google Scholar
  19. Ikura, M. et al. Solution structure of a calmodulin–target peptide complex by multidimensional NMR. Science 256, 632 –638 (1992).
    Article CAS Google Scholar
  20. Meador, W.E., Means, A.R. & Quiocho, F.A. Target enzyme recognition by calmodulin: 2.4 Å structure of a calmodulin–peptide complex. Science 257, 1251–1256 (1992).
    Article CAS Google Scholar
  21. Meador, W.E., Means, A.R. & Quiocho, F.A. Modulation of calmodulin plasticity in molecular recognition on the basis of x-ray structures. Science 262, 1718–1721 (1993).
    Article CAS Google Scholar
  22. Osawa, M. et al. A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase. Nature Struct. Biol. 6, 819–824 (1999).
    Article CAS Google Scholar
  23. Muhandiram, D.R., Yamazaki, T., Sykes, B.D. & Kay, L.E. Measurement of 2H _T_1 and _T_1ρ relaxation times in uniformly 13C-labeled and fractionally 2H-labeled proteins in solution. J. Am. Chem. Soc. 117, 11536–11544 (1995).
    Article CAS Google Scholar
  24. 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
  25. Lee, A.L., Flynn, P.F. & Wand, A.J. Comparison of 2H and 13C NMR relaxation techniques for the study of protein methyl group dynamics in solution. J. Am. Chem. Soc. 121, 2891– 2902 (1999).
    Article CAS Google Scholar
  26. Lukas, T.J., Burgess, W.H., Prendergast, F.G., Lau, W. & Watterson, D.M. Calmodulin binding domains: characterization of a phosphorylation and calmodulin binding site from myosin light chain kinase. Biochemistry 25, 1458 –1464 (1987).
    Article Google Scholar
  27. Kemp, B.E., Pearson, R.B., Guerriero, V., Bagchi, I.C. & Means, A.R. The calmodulin binding domain of chicken smooth muscle myosin light chain kinase contains a pseudosubstrate sequence. J. Biol. Chem. 262, 2542– 2548 (1987).
    CAS PubMed Google Scholar
  28. Seeholzer, S.H. & Wand, A.J. Structural characterization of the interactions between calmodulin and skeletal muscle myosin light chain kinase: effect of peptide (576–594)G binding on the Ca2+-binding domains. Biochemistry 28, 4011– 4019 (1989).
    Article CAS Google Scholar
  29. Roth, S.M. et al. Structure of the smooth muscle myosin light-chain kinase calmodulin-binding domain peptide bound to calmodulin. Biochemistry 30, 10078–10084 ( 1991).
    Article CAS Google Scholar
  30. Roth, S.M. et al. Characterization of the secondary structure of calmodulin in complex with a calmodulin-binding domain peptide. Biochemistry 31, 1443–1451 ( 1992).
    Article CAS Google Scholar
  31. Mittermaier, A., Kay, L.E. & Forman-Kay, J.D. Analysis of deuterium relaxation-derived methyl axis order parameters and correlation with local structure. J. Biol. NMR 13, 181–185 ( 1999).
    Article CAS Google Scholar
  32. O'Neil, K.T. & DeGrado, W.F. How calmodulin binds its targets: sequence independent recognition of amphiphilic α-helices. Trends Biochem. Sci. 15, 59–64 (1990).
    Article CAS Google Scholar
  33. Gellman, S.H. On the role of methionine residues in the sequence -independent recognition of nonpolar protein surfaces. Biochemistry 30, 6633–6636 (1991).
    Article CAS Google Scholar
  34. Siivari, K., Zhang, M., Palmer, A.G. & Vogel, H.J. NMR studies of the methionine methyl groups in calmodulin. FEBS Lett. 366, 104–108 (1995).
    Article CAS Google Scholar
  35. Chin, D. & Means, A.R. Methionine to glutamine substitutions in the C-terminal domain of calmodulin impair the activation of three protein kinases. J. Biol. Chem. 271, 30465– 30471 (1996).
    Article CAS Google Scholar
  36. Edwards, R.A., Walsh, M.P., Sutherland, C. & Vogel, H.J. Activation of calcineurin and smooth muscle myosin light chain kinase by Met-to-Leu mutants of calmodulin. Biochem. J. 331, 149–152 (1998).
    Article CAS Google Scholar
  37. Kay, L.E., Muhandiram, D.R., Farrow, N.A., Aubin, Y. & Forman-Kay, J.D. Correlation between dynamics and high affinity binding in an SH2 domain interaction. Biochemistry 35, 361–368 ( 1996).
    Article CAS Google Scholar
  38. Constantine, K.L. et al. Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins. Biochemistry 37, 7965–7980 ( 1998).
    Article CAS Google Scholar
  39. Gerstein, M., Tsai, J. & Levitt, M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J. Mol. Biol. 249, 955–966 (1995).
    Article CAS Google Scholar
  40. Jacrot, B., Cusack, S., Dianoux, A.J. & Engelman, D.M. Inelastic neutron scattering analysis of hexokinase dynamics and its modifacation on binding of glucose. Nature 300, 84– 86 (1982).
    Article CAS Google Scholar
  41. Bracken, C., Carr, P.A., Cavanagh, J. & Palmer, A.G. 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
  42. Clackson, T. & Wells, J.A. A hot spot of binding energy in a hormone–receptor interface. Science 267, 383–386 (1995).
    Article CAS Google Scholar
  43. Urbauer, J.L., Short, J.H., Dow, L.K. & Wand, A.J. Structural analysis of a novel interaction by calmodulin: high-affinity binding of a peptide in the absence of calcium. Biochemistry 34, 8099–8109 (1995).
    Article CAS Google Scholar
  44. Bax, A., Delaglio, F., Grzesiek, S. & Vuister, G.W. Resonance assignment of methionine methyl groups and χ3 angular information from long-range proton-carbon and carbon-carbon J correlation in a calmodulin–peptide complex. J. Biol. NMR 4, 787–797 (1994).
    Article CAS Google Scholar
  45. Brüschweiler, R., Liao, X. & Wright, P.E. Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling. Science 268, 886–889 (1995).
    Article Google Scholar
  46. Tjandra, N., Feller, S.E., Pastor, R.W. & Bax, A. Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation. J. Am. Chem. Soc. 117, 12562–12566 (1995).
    Article CAS Google Scholar
  47. Lee, L.K., Rance, M., Chazin, W.J. & Palmer, A.G. Rotational anisotropy of proteins from simultaneous analysis of 15N and 13CΣϒβα/Σϒβ nuclear spin relaxation. J. Biol. NMR 9, 287–298 (1997).
    Article CAS Google Scholar
  48. Lee, A.L. & Wand, A.J. Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation. J. Biol. NMR 13, 101–112 (1999).
    Article CAS Google Scholar
  49. Brüschweiler, R. & Wright, P.E. NMR order parameters of biomolecules: a new analytical representation and application to the Gaussian axial fluctuation model. J. Am. Chem. Soc. 116, 8426–8427 (1994).
    Article Google Scholar
  50. Koradi, R., Billeter, M. & Wüthrich, K. A program for display and analysis of macromolecular structures. J. Mol. Graphics 14, 51– 55 (1996).
    Article CAS Google Scholar

Download references