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Structural water in oxidized and reduced horse heart cytochrome c

Nature Structural Biology volume 1, pages 378–382 (1994)Cite this article

Abstract

The existence of structural water in the interior of both oxidized and reduced horse-heart cytochrome c in solution is demonstrated using nuclear magnetic resonance spectroscopy. Six water molecules have been located in ferrocytochrome c and five in ferricytochrome c, with residence times greater than a few hundred picoseconds. Two water molecules are located in the haem crevice, one of which is found to undergo a large change in position with a change of oxidation state. Both of these observations indicate that buried structural waters in the haem crevice have, by microscopic dielectric effects, significant roles in the setting of the solvent reorganization energy associated with electron transfer.

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References

  1. Marcus, R.A. & Sutin, N. Electron transfers in chemistry and biology. Biochem. biophys. Acta 811, 265–322 (1985).

    CAS  Google Scholar 

  2. McLendon, G. Long-distance electron transfer in proteins and model systems. Acc. chem. Res. 21, 160–167 (1988).

    Article  CAS  Google Scholar 

  3. Wuttke, D.S., Bjerrum, M.J., Winkler, J.R. & Gray, H.B. Electron-tunnelling pathways in cytochrome c. Science 256, 1007–1009 (1992).

    Article  CAS  Google Scholar 

  4. Moser, C.C., Keske, J.M., Warncke, K., Farid, R.S. & Dutton, P.L. Nature of biological electron transfer. Nature 355, 796–802 (1992).

    Article  CAS  Google Scholar 

  5. Evenson, J.W. & Karplus, M. Effective coupling in biological electron transfer: Exponential or complex distance dependence? Science 262, 1247–1249 (1993).

    Article  CAS  Google Scholar 

  6. Mauk, M.R., Reid, L.S. & Mauk, A.G. Spectrophotometric analysis of the interaction between cytochrome B5 and cytochrome c. Biochemistry 21, 1843–1846 (1982).

    Article  CAS  Google Scholar 

  7. McLendon, G. & Miller, J.R. The dependence of biological electron transfer rates on exothermicity: The cytochrome c/cytochrome b5 couple. J. Am. chem. Soc. 107, 7811–7816 (1985).

    Article  CAS  Google Scholar 

  8. Mauk, M.R., Mauk, A.G., Weber, P.C. & Matthew, J.B. Electrostatic analysis of the interaction of cytochrome c with native and dimethyl ester heme substituted cytochrome b5 . Biochemistry 25, 7085–7091 (1986).

    Article  CAS  Google Scholar 

  9. Rodgers, K.K., Pochapsky, T.C. & Sligar, S.G. Probing the mechanisms of macromolecular recognition: The cytochrome b5-cytochrome c complex Science 240, 1657–1659 (1988).

    Article  CAS  Google Scholar 

  10. Rodgers, K.K. & Sligar, S.G. Mapping electrostatic interactions in macromolecular association. J. molec. Biol. 221, 1453–1460 (1991)

    Article  CAS  Google Scholar 

  11. Willie, A. et al. Intracomplex electron transfer between ruthenium-65-cytochrome b5 and position-82 variants of yeast iso-1-cytochrome c. Biochemistry 32. 7519–7525 (1993).

    Article  CAS  Google Scholar 

  12. Qi, P.X., Di Stefano, D.L. & Wand, A.J. The solution structure of horse heart ferrocytochrome c determined by high resolution NMR and restrained simulated annealing. Biochemistry, (in the press).

  13. Takano, T. & Dickerson, R.E. Conformation change of cytochrome c 1. Ferrocytochrome c structure refined at 1.5 Å resolution J. molec. Biol. 153, 79–94 (1981).

    Article  CAS  Google Scholar 

  14. Takano, T. & Dickerson, R.E. Conformation change of cytochrome c 2. Ferricytochrome c refinement at 1.8 Å and comparison with the ferrocytochrome structure. J. molec. Biol. 153, 95–114 (1981).

    Article  CAS  Google Scholar 

  15. Churg, A.K., Weiss, R.M., Warshel, A. & Takano, T. On the action of cytochrome c: Correlating geometry changes upon oxidation with activation energies of electron transfer. J. phys. Chem. 87, 1683–1694 (1983).

    Article  CAS  Google Scholar 

  16. Churg, A.K. & Warshel, A. Modeling the activation energy and dynamics of electron transfer reactions in proteins. in Structure & Motion: Membranes, Nucleic Acids & Proteins (eds E. Clementi, G. Corongiu, G., Sarma, M. H. & Sarma, R. H.) 361–374 (Adenine; 1985).

    Google Scholar 

  17. Churg, A.K. & Warshel, A. Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins. Biochemistry 25, 1675–1681 (1986).

    Article  CAS  Google Scholar 

  18. Feng, Y., Roder, H. & Englander, S.W. Redox-dependent structure change and hyperfine NMR shifts in cytochrome c. Biochemistry 29, 3494–3504 (1990).

    Article  CAS  Google Scholar 

  19. Dickerson, R.E. et al. Ferricytochrome c I. General features of the horse and bonito proteins at 2.8 Å resolution. J. biol. Chem. 246, 1511–1535 (1971).

    CAS  PubMed  Google Scholar 

  20. Swanson, R., Trus, B.L., Mandel, N., Mandel, G., Kallai, O.B. & Dickerson, R.E. Tuna cytochrome c at 2.0 Å resolution. J. biol. Chem. 252, 759–775 (1977).

    CAS  PubMed  Google Scholar 

  21. Louie, G.V., Hucheon, W. & Brayer, G.D. Yeast iso-1-cytochrome c. A 2.8 Å resolution three dimensional structure determination. J. molec. Biol. 199, 295–314 (1988).

    Article  CAS  Google Scholar 

  22. Bushnell, G.W., Louie, G.V. & Brayer, G.D. High-resolution three-dimensional structure of horse heart cytochrome c. J. molec. Biol. 214, 585–595 (1990).

    Article  CAS  Google Scholar 

  23. Louie, G.V. & Brayer, G.D. High-resolution refinement of yeast iso-1-cytochrome c and comparison with other eukaryotic cytochromes c. J. molec. Biol. 214, 527–555 (1990)

    Article  CAS  Google Scholar 

  24. Berghuis, A.M. & Brayer, G.D. Oxidation state-dependent conformational changes in cytochrome c. J. molec. Biol. 223, 959–976 (1992).

    Article  CAS  Google Scholar 

  25. Moore, G.R. & Williams, RJ.P. NMR studies of ferrocytochrome c. pH and temperature dependence. Eur. J. Biochem. 103, 513–522 (1980).

    Article  CAS  Google Scholar 

  26. Moore, G.R. & Williams, RJ.P. The stability of ferricytochrome c: Temperature dependence of its NMR spectrum. Eur. J. Biochem. 103, 523–532 (1980).

    Article  CAS  Google Scholar 

  27. Otting, G. & Wüthrich, K. Studies of protein hydration in acqueous solution by direct NMR observation of individual protein-bound water molecules. J. Am. chem. Soc. 111, 1871–1875 (1989)

    Article  CAS  Google Scholar 

  28. Otting, G., Liepinsh, E., Farmer, B.T. & Wüthrich, K. Protein hydration studied with homonuclear 3D 1H NMR experiments. J. biomolecular NMR 1, 209–215 (1991).

    Article  CAS  Google Scholar 

  29. Wüthrich, K., Otting, G. & Liepinsh, E. Protein hydration in acqueous solution. Faraday. Discuss. 93, 35–45 (1992).

    Article  Google Scholar 

  30. Clore, G.M., Bax, A., Wingfield, P.T. & Gronenborn, A.M. Identification and localization of bound internal water in the solution structure of interleukin 1b by heteronuclear three-dimensional 1H rotating-frame Overhauser 15N-1H multiple quantum coherence NMR spectroscopy. Biochemistry 29, 5671–5676 (1990).

    Article  CAS  Google Scholar 

  31. Forman-Kay, J.D., Gronenborn, A.M., Wingfield, P.T. & Clore, G.M. Determination of the positions of bound water molecules in the solution structure of reduced human thioredoxin by heteronuclear three-dimensional nuclear magnetic resonance spectroscopy. J. molec. Biol. 220, 209–216 (1991).

    Article  CAS  Google Scholar 

  32. Kriwacki, R.W., Hill, R.B., Flanagan, J.M., Caraonna, J.P. & Prestegard, J.H. New NMR methods for the characterization of bound waters in macromolecules. J. Am. chem. Soc. 115, 8907–8911 (1993).

    Article  CAS  Google Scholar 

  33. Bothner-By, A.A., Stephens, R.L., Lee, J., Waren, C.D. & Jeanloz, R.W. Structure determination of a tetrasaccharide: Transient nuclear Overhauser effects in the rotating frame. J. Am. chem. Soc. 106, 811–813 (1984).

    Article  CAS  Google Scholar 

  34. Wand, A.J. & Englander, S.W. Two-dimensional NMR studies of cytochrome C. Biochemistry 24, 5290–5294 (1985).

    Article  CAS  Google Scholar 

  35. Wand, A.J., Di Stefano, D.L., Feng, Y., Roder, H. & Englander, S.W. Proton resonance assignments of horse ferrocytochrome c. Biochemistry 28, 186–194 (1989).

    Article  CAS  Google Scholar 

  36. Feng, Y., Roder, H., Englander, S.W., Wand, A.J. & Di Stefano, D.L. Proton resonance assignments of horse ferricytochrome c. Biochemistry 28, 195–203 (1989).

    Article  CAS  Google Scholar 

  37. Brünger, A.T. X-PLOR version 3.0 A system for crystallography and NMR X-PLOR Manual (Yale University, New Haven, CT, USA; 1990).

    Google Scholar 

  38. Vuister, G.W., Boelens, R. & Kaptein, R. Nonselective three-dimensional NMR spectroscopy. The 3D NOE-HOHAHA experiment. J. magn. Reson. 80, 176–185 (1988).

    CAS  Google Scholar 

  39. Bax, A. & Davis, D.G. Practical aspects of two-dimensional transverse NOE spectroscopy. J. magn. Reson. 63, 207–213 (1985).

    CAS  Google Scholar 

  40. Nilges, M., Clore, G.M. & Gronenborn, A.M. Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229, 317–324 (1988).

    Article  CAS  Google Scholar 

  41. Carson, M. Ribbon models of macromolecules. J. molec. Graph. 5, 103–106 (1987).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA

    Phoebe Xiurong Qi, Jeffrey L. Urbauer, Ernesto J. Fuentes, Mary Frances Leopold & A. Joshua Wand

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  1. Phoebe Xiurong Qi
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  2. Jeffrey L. Urbauer
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  3. Ernesto J. Fuentes
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  4. Mary Frances Leopold
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  5. A. Joshua Wand
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Qi, P., Urbauer, J., Fuentes, E. et al. Structural water in oxidized and reduced horse heart cytochrome c. Nat Struct Mol Biol 1, 378–382 (1994). https://doi.org/10.1038/nsb0694-378

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