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Using buried water molecules to explore the energy landscape of proteins

Nature Structural Biology volume 3, pages 505–509 (1996)Cite this article

Abstract

Buried water molecules constitute a highly conserved, integral part of nearly all known protein structures. Such water molecules exchange with external solvent as a result of protein conformational fluctuations. We report here the results of water 17O and 2H magnetic relaxation dispersion measurements on wild-type and mutant bovine pancreatic trypsin inhibitor in aqueous solution at 4–80 °C. These data lead to the first determination of the exchange rate of a water molecule buried in a protein. The strong temperature dependence of this rate is ascribed to large-scale conformational fluctuations in an energy landscape with a statistical ruggedness of ∼10 kJ mol−1.

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References

  1. Wagner, G. Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes. Q. Rev. Biophys. 16, 1–57 (1983).

    Article  CAS  Google Scholar 

  2. McCammon, J.A. & Harvey, S.C. Dynamics of Proteins and Nucleic Acids (Cambridge Univ. Press, Cambridge, 1987).

    Book  Google Scholar 

  3. Frauenfelder, H., Sligar, S.G. & Wolynes, P.G. The energy landscapes and motions of proteins. Science 254, 1598–1603 (1991).

    Article  CAS  Google Scholar 

  4. Frauenfelder, H. et al. Proteins and pressure. J. Phys. Chem. 94, 1024–1037 (1990).

    Article  CAS  Google Scholar 

  5. Steinbach, P.J. et al. Ligand binding to heme proteins: Connection between dynamics and function. Biochemistry 30, 3988–4001 (1991).

    Article  CAS  Google Scholar 

  6. Young, R.D. et al. Time and temperature dependence of large-scale conformational transitions in myoglobin. Chem. Phys. 158, 315–327 (1991).

    Article  CAS  Google Scholar 

  7. Zwanzig, R. Diffusion in a rough potential. Proc. Natl. Acad. Sci. USA 85, 2029–2030 (1988).

    Article  CAS  Google Scholar 

  8. Bryngelson, J.D. & Wolynes, P.G. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93, 6902–6915 (1989).

    Article  CAS  Google Scholar 

  9. Panchenko, A.R., Wang, J., Nienhaus, G.U. & Wolynes, P.G. Analysis of ligand binding to heme proteins using a fluctuating path description. J. Phys. Chem. 99, 9278–9282 (1995).

    Article  CAS  Google Scholar 

  10. Baker, E.N. Solvent interactions with proteins as revealed by X-ray crystallographic studies. In Protein-Solvent Interactions (R.B. Gregory, ed) 143–189 (M. Dekker, New York, 1995).

    Google Scholar 

  11. Wlodawer, A., Walter, J., Huber, R. & Sjölin, L. Structure of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 180, 301–329 (1984).

    Article  CAS  Google Scholar 

  12. Berndt, K.D., Güntert, P., Orbons, L.P.M. & Wüthrich, K. Determination of a high-quality nuclear magnetic resonance solution structure of the bovine pancreatic trypsin inhibitor and comparison with three crystal structures. J. Mol. Biol. 227, 757–775 (1992).

    Article  CAS  Google Scholar 

  13. Denisov, V.P. & Halle, B. Protein hydration dynamics in aqueous solution. J. Mol. Biol. 245, 682–697 (1995).

    Article  CAS  Google Scholar 

  14. Denisov, V.P. & Halle, B. Hydrogen exchange and protein hydration. J. Mol. Biol. 245, 698–709 (1995).

    Article  CAS  Google Scholar 

  15. Denisov, V.P. & Halle, B. Protein hydration dynamics in aqueous solution. Faraday Discuss., in the press.

  16. Otting, G., Liepinsh, E. & Wüthrich, K. Protein hydration in aqueous solution. Science 254, 974–980 (1991).

    Article  CAS  Google Scholar 

  17. Denisov, V.P., Halle, B., Peters, J. & Hörlein, H.D. Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its G36S mutant. Biochemistry 34, 9046–9051 (1995).

    Article  CAS  Google Scholar 

  18. Otting, G., Liepinsh, E. & Wüthrich, K. Disulfide bond isomerization in BPTI and BPTI(G36S): An NMR study of correlated mobility in proteins. Biochemistry 32, 3571–3582 (1993).

    Article  CAS  Google Scholar 

  19. Berndt, K.D., Beunink, J., Schröder, W. & Wüthrich, K. Designed replacement of an internal hydration water molecule in BPTI: Structural and functional implications of a glycine–to–serine mutation. Biochemistry 32, 4564–4570 (1993).

    Article  CAS  Google Scholar 

  20. Denisov, V.P. & Halle, B. Direct observation of calcium–coordinated water in calbindin D9k by nuclear magnetic relaxation dispersion. J. Am. Chem. Soc. 117, 8456–8465 (1995).

    Article  CAS  Google Scholar 

  21. Wagner, G., DeMarco, A. & Wüthrich, K. Dynamics of the aromatic amino acid residues in the globular conformation of the basic pancreatic trypsin inhibitor. Biophys. Struct Mech. 2, 139–158 (1976).

    Article  CAS  Google Scholar 

  22. Englander, S.W. & Kallenbach, N.R. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16, 521–655 (1984).

    Article  Google Scholar 

  23. Hänggi, P., Talkner, P. & Borkovec, M. Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62, 251–341 (1990).

    Article  Google Scholar 

  24. Iben, I.E.T. et al. Glassy behavior of a protein. Phys. Rev. Lett 62, 1916–1919 (1989).

    Article  CAS  Google Scholar 

  25. Ferry, J.D., Grandine, L.D. & Fitzgerald, E.R. Viscoelastic relaxation of polyisobutylene. J. Appl. Phys. 24, 911–921 (1953).

    Article  CAS  Google Scholar 

  26. de Gennes, P.G. Brownian motion of a classical particle through potential barriers. J. Stat. Phys. 12, 463–481 (1975).

    Article  Google Scholar 

  27. Bässler, H. Viscous flow in supercooled liquids analyzed in terms of transport theory for random media with energetic disorder. Phys. Rev. Lett. 58, 767–770 (1987).

    Article  Google Scholar 

  28. Northrup, S.H., Pear, M.R., Lee, C.Y., McCammon, J.A. & Karplus, M. Dynamical theory of activated processes in globular proteins. Proc. Natl. Acad. Sci. USA 79, 4035–4039 (1982).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Condensed Matter Magnetic Resonance Group, Department of Chemistry, Lund University, S–22100, Lund, Sweden

    Vladimir P. Denisov & Bertil Halle

  2. Bayer AG, PH–TO Biotechnologie, D-42096, Wuppertal, Germany

    Jörg Peters & Hans Dietrich Hörlein

Authors
  1. Vladimir P. Denisov
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  2. Jörg Peters
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  3. Hans Dietrich Hörlein
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  4. Bertil Halle
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Denisov, V., Peters, J., Hörlein, H. et al. Using buried water molecules to explore the energy landscape of proteins. Nat Struct Mol Biol 3, 505–509 (1996). https://doi.org/10.1038/nsb0696-505

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