Dynamic activation of an allosteric regulatory protein (original) (raw)

References

  1. Kuriyan, J. & Eisenberg, D. The origin of protein interactions and allostery in colocalization. Nature 450, 983–990 (2007)
    CAS Google Scholar
  2. Goodey, N. M. & Benkovic, S. J. Allosteric regulation and catalysis emerge via a common route. Nature Chem. Biol. 4, 474–482 (2008)
    CAS Google Scholar
  3. Smock, R. G. & Gierasch, L. M. Sending signals dynamically. Science 324, 198–203 (2009)
    CAS Google Scholar
  4. del Sol, A., Tsai, C. J., Ma, B. & Nussinov, R. The origin of allosteric functional modulation: multiple pre-existing pathways. Structure 17, 1042–1050 (2009)
    CAS Google Scholar
  5. Lee, J. et al. Surface sites for engineering allosteric control in proteins. Science 322, 438–442 (2008)
    CAS Google Scholar
  6. Changeux, J. P. & Edelstein, S. J. Allosteric mechanisms of signal transduction. Science 308, 1424–1428 (2005)
    CAS Google Scholar
  7. Won, H. S., Lee, Y. S., Lee, S. H. & Lee, B. J. Structural overview on the allosteric activation of cyclic AMP receptor protein. Biochim. Biophys. Acta 1794, 1299–1308 (2009)
    CAS Google Scholar
  8. Schultz, S. C., Shields, G. C. & Steitz, T. A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253, 1001–1007 (1991)
    CAS Google Scholar
  9. Popovych, N., Tzeng, S. R., Tonelli, M., Ebright, R. H. & Kalodimos, C. G. Structural basis for cAMP-mediated allosteric control of the catabolite activator protein. Proc. Natl Acad. Sci. USA 106, 6927–6932 (2009)
    CAS Google Scholar
  10. Passner, J. M., Schultz, S. C. & Steitz, T. A. Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 Å resolution. J. Mol. Biol. 304, 847–859 (2000)
    CAS Google Scholar
  11. Berg, J. M., Tymoczko, J. L. & Stryer, L. Biochemistry 6th edn (Freeman, 2006)
    Google Scholar
  12. Dai, J., Lin, S. H., Kemmis, C., Chin, A. J. & Lee, J. C. Interplay between site-specific mutations and cyclic nucleotides in modulating DNA recognition by Escherichia coli cyclic AMP receptor protein. Biochemistry 43, 8901–8910 (2004)
    CAS Google Scholar
  13. Baichoo, N. & Heyduk, T. Mapping conformational changes in a protein: application of a protein footprinting technique to cAMP-induced conformational changes in cAMP receptor protein. Biochemistry 36, 10830–10836 (1997)
    CAS Google Scholar
  14. Aiba, H., Nakamura, T., Mitani, H. & Mori, H. Mutations that alter the allosteric nature of cAMP receptor protein of Escherichia coli . EMBO J. 4, 3329–3332 (1985)
    CAS Google Scholar
  15. Mittermaier, A. & Kay, L. E. New tools provide new insights in NMR studies of protein dynamics. Science 312, 224–228 (2006)
    CAS Google Scholar
  16. Palmer, A. G. NMR characterization of the dynamics of biomacromolecules. Chem. Rev. 104, 3623–3640 (2004)
    CAS Google Scholar
  17. Kern, D. & Zuiderweg, E. R. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13, 748–757 (2003)
    CAS Google Scholar
  18. Akke, M., Bruschweiler, R. & Palmer, 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)
    CAS Google Scholar
  19. 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)
    CAS Google Scholar
  20. Cavanagh, J. & Akke, M. May the driving force be with you — whatever it is. Nature Struct. Biol. 7, 11–13 (2000)
    CAS Google Scholar
  21. Zhang, F. & Bruschweiler, R. Contact model for the prediction of NMR N-H order parameters in globular proteins. J. Am. Chem. Soc. 124, 12654–12655 (2002)
    CAS Google Scholar
  22. 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)
    CAS Google Scholar
  23. 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)
    CAS Google Scholar
  24. Mauldin, R. V., Carroll, M. J. & Lee, A. L. Dynamic dysfunction in dihydrofolate reductase results from antifolate drug binding: modulation of dynamics within a structural state. Structure 17, 386–394 (2009)
    CAS Google Scholar
  25. Frederick, K. K., Marlow, M. S., Valentine, K. G. & Wand, A. J. Conformational entropy in molecular recognition by proteins. Nature 448, 325–329 (2007)
    CAS Google Scholar
  26. Popovych, N., Sun, S., Ebright, R. H. & Kalodimos, C. G. Dynamically driven protein allostery. Nature Struct. Mol. Biol. 13, 831–838 (2006)
    CAS Google Scholar
  27. MacRaild, C. A., Daranas, A. H., Bronowska, A. & Homans, S. W. Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein. J. Mol. Biol. 368, 822–832 (2007)
    CAS Google Scholar
  28. Kim, J., Adhya, S. & Garges, S. Allosteric changes in the cAMP receptor protein of Escherichia coli: hinge reorientation. Proc. Natl Acad. Sci. USA 89, 9700–9704 (1992)
    CAS Google Scholar
  29. Wand, A. J. Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nature Struct. Biol. 8, 926–931 (2001)
    CAS Google Scholar
  30. Henzler-Wildman, K. & Kern, D. Dynamic personalities of proteins. Nature 450, 964–972 (2007)
    CAS Google Scholar
  31. Parkinson, G. et al. Structure of the CAP-DNA complex at 2.5 Å resolution: a complete picture of the protein-DNA interface. J. Mol. Biol. 260, 395–408 (1996)
    CAS Google Scholar
  32. Takeuchi, K., Ng, E., Malia, T. J. & Wagner, G. 1-13C amino acid selective labeling in a 2H15N background for NMR studies of large proteins. J. Biomol. NMR 38, 89–98 (2007)
    CAS Google Scholar
  33. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995)
    CAS Google Scholar
  34. Johnson, B. A. Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol. Biol. 278, 313–352 (2004)
    CAS Google Scholar
  35. Evenäs, J. et al. Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. J. Mol. Biol. 309, 961–974 (2001)
    Google Scholar
  36. Palmer, A. G. III. ModelFree. 〈http://www.palmer.hs.columbia.edu/software/modelfree.html
  37. Cole, R. & Loria, J. P. FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data. J. Biomol. NMR 26, 203–213 (2003)
    CAS Google Scholar
  38. d'Auvergne, E. J. & Gooley, P. R. Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR 40, 107–119 (2008)
    CAS Google Scholar
  39. 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)
    CAS Google Scholar
  40. 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)
    CAS Google Scholar
  41. Hwang, P. M., Skrynnikov, N. R. & Kay, L. E. Domain orientation in beta-cyclodextrin-loaded maltose binding protein: diffusion anisotropy measurements confirm the results of a dipolar coupling study. J. Biomol. NMR 20, 83–88 (2001)
    CAS Google Scholar
  42. Palmer, A. G. III. quadric_diffusion. 〈http://www.palmer.hs.columbia.edu/software/quadric.html
  43. Dosset, P., Hus, J. C., Blackledge, M. & Marion, D. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J. Biomol. NMR 16, 23–28 (2000)
    CAS Google Scholar
  44. Mandel, A. M., Akke, M. & Palmer, A. G. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J. Mol. Biol. 246, 144–163 (1995)
    CAS Google Scholar
  45. Loria, J. P., Rance, M. & Palmer, A. G. A TROSY CPMG sequence for characterizing chemical exchange in large proteins. J. Biomol. NMR 15, 151–155 (1999)
    CAS Google Scholar
  46. Mulder, F. A., Mittermaier, A., Hon, B., Dahlquist, F. W. & Kay, L. E. Studying excited states of proteins by NMR spectroscopy. Nature Struct. Biol. 8, 932–935 (2001)
    CAS Google Scholar
  47. Carver, J. P. & Richards, R. E. A general two-site solution for the chemical exchange produced dependence of T2 upon the Carr-Purcell pulse separation. J. Magn. Reson. 6, 89–105 (1972)
    CAS Google Scholar
  48. Watt, E. D., Shimada, H., Kovrigin, E. L. & Loria, J. P. The mechanism of rate-limiting motions in enzyme function. Proc. Natl Acad. Sci. USA 104, 11981–11986 (2007)
    CAS Google Scholar
  49. Henzler-Wildman, K. A. et al. Intrinsic motions along an enzymatic reaction trajectory. Nature 450, 838–844 (2007)
    CAS Google Scholar
  50. Boehr, D. D., McElheny, D., Dyson, H. J. & Wright, P. E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313, 1638–1642 (2006)
    CAS Google Scholar
  51. Korzhnev, D. M. et al. Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature 430, 586–590 (2004)
    CAS Google Scholar
  52. Palmer, A. G. III. CPMGFit. 〈http://www.cumc.columbia.edu/dept/gsas/biochem/labs/palmer/software/cpmgfit.html
  53. Millet, O., Loria, J. P., Kroenke, C. D., Pons, M. & Palmer, A. G. The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale. J. Am. Chem. Soc. 122, 2867–2877 (2000)
    CAS Google Scholar

Download references