Electrostatic Analysis of the Midpoints of the Cofactors in the Reaction Center Protein of Rp.viridis

  • M. R. Gunner
  • Barry Honig
Chapter

Abstract

The relative midpoints of the cofactors in the reaction center protein (RC) from Rp. viridis were calculated by solving the Poisson-Boltzmann equation with a finite difference algorithm. This yields the electrostatic potential throughout the RC which can provide the energetic cost of oxidizing or reducing each site. For the 4 hemes of the bound cytochrome subunit the calculations are in quite good agreement with the experimentally determined relative heme midpoints. The success of the method allows the factors that generate the differences in their in situ electrochemistry to be identified. In order of importance these appear to be: (1) the distribution of charged residues throughout the protein; (2) the perturbation of the midpoint of the high potential hemes by the oxidized lower potential sites; (3) the nature of the axial ligands; (4) differences in the stabilization of the charged heme by solvent. Preliminary calculations were also carried out on the cofactors within the RC.

Keywords

Solvation Energy Partial Charge Axial Ligand Electron Transfer Rate Reaction Center Protein 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in to check access.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Jortner, J., (1980) Biochim. biophys. Acta. 594, 193–230.PubMedCrossRefGoogle Scholar
  2. 2.
    Marcus, R. A., Sutin, N., (1985) Biochim. biophys. Acta. 811, 265–322.CrossRefGoogle Scholar
  3. 3.
    Closs, G. L, Miller, J. M., (1988) Science 240, 440–447.PubMedCrossRefGoogle Scholar
  4. 4.
    Gunner, M. R., Robertson, D. E., Dutton, P. L, (1986) J. Phys. Chem. 90, 3783–3795.CrossRefGoogle Scholar
  5. 5.
    Gunner, M. R., Dutton, P. L., (1989) J. Am. Chem. Soc. 111, 3400–3412.CrossRefGoogle Scholar
  6. 6.
    Deisenhofer, J., Epp, O., Miki, R., Michel, H., (1985) Nature 318, 618–624.PubMedCrossRefGoogle Scholar
  7. 7.
    Michel, H., Epp, O., Deisenhofer, J., (1986) The EMBO Journal 5, 2445–2451.PubMedGoogle Scholar
  8. 8.
    Allen, J. P., Feher, G., Yeates, T. O., Komiya, H., Rees, D. C, (1987) Proc. Natl. Acad. Sci. USA 84, 5730–5734.PubMedCrossRefGoogle Scholar
  9. 9.
    Chang, C. H., Tiede, D., Tang, J., Smith, U., Norris, J., Schiffer, M., (1986) FEBS Lett. 205, 82–86.PubMedCrossRefGoogle Scholar
  10. 10.
    Plato, M., Mobius, K., Michel-Beyerle, M. E., Bixon, M., Jortner, J., (1988) J. Am. Chem. Soc. 110, 7279–7285.CrossRefGoogle Scholar
  11. 11.
    Won, Y., Friesner, R. A., (1988) Biochim. Biophys. Acta 935, 9–18.CrossRefGoogle Scholar
  12. 12.
    Creighton, S., Hwang, J.-K., Warshel, A., Parson, W. W., Norris, J., (1988) Biochem. 27, 774–781.CrossRefGoogle Scholar
  13. 13.
    Warwicker, J., Watson, H. C, (1982) J. Mol. Biol. 157, 671–679.PubMedCrossRefGoogle Scholar
  14. 14.
    Gilson, M. K., Rashin, A., Fine, R., Honig, B., (1985) J. Mol. Biol. 183, 503–516.CrossRefGoogle Scholar
  15. 15.
    Gilson, M. K., Honig, B., (1988) Proteins 3, 32–52.PubMedCrossRefGoogle Scholar
  16. 16.
    Gilson, M. K., Honig, B., (1988) Proteins 4, 7–18.PubMedCrossRefGoogle Scholar
  17. 17.
    Warshel, A., Russell, S. T., (1984) Q. Rev. Biophys. 17, 283–422.PubMedCrossRefGoogle Scholar
  18. 18.
    Klapper, I., Hagstrom, R., Fine, R., Sharp, K., Honig, B., (1986) Proteins 1, 47–59.PubMedCrossRefGoogle Scholar
  19. 19.
    Gilson, M. K., Sharp, K. A., Honig, B. H., (1987) J. Comp. Chem. 9, 327–335.CrossRefGoogle Scholar
  20. 20.
    Nicholls, A., B., H., (1989) manuscript in preperationGoogle Scholar
  21. 21.
    Brunger, A. T., Kuriyan, J., Karplus, M., (1987) Science 235, 458–460.PubMedCrossRefGoogle Scholar
  22. 22.
    Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D.J., Swaminathan, S., Karplus, M., (1983) J.Comput. Chem 4, 187.CrossRefGoogle Scholar
  23. 23.
    Gilson, M. K., Honig, B., (1986) Biopolymers 25, 2097–2199.PubMedCrossRefGoogle Scholar
  24. 24.
    Kassner, R. J., (1972) Proc. Natl. Acad. Sci. USA 69, 2263–2267.PubMedCrossRefGoogle Scholar
  25. 25.
    Kassner, R. J., (1973) J. Am. Chem. Soc. 95, 2674–2676.PubMedCrossRefGoogle Scholar
  26. 26.
    Churg, A. K., Warshel, A., (1986) Biochemistry 25, 1675–1681.PubMedCrossRefGoogle Scholar
  27. 27.
    Dracheva, S. M., Drachev, L. A., Konstantinov, A. A., Semenov, A. Y. S., V.P.,Google Scholar
  28. Arutjunjan, A. M., Shulavlov, V. A., Zaberezhnaya, S. M., (1988) Eur. J. Biochem. 171, 253–264.PubMedCrossRefGoogle Scholar
  29. 28.
    Alegria, G., Dutton, P. L., (1988) Biophys. J. 53, 615a.Google Scholar
  30. 29.
    Nitschke, W., Rutherford, A. W., (1989) Biochemistry 28, 3161–3168.CrossRefGoogle Scholar
  31. 30.
    Bylina, E., Kirmaier, C, McDowell, L, Holten, D., Youvan, D. C, (1988) Nature 336, 182–184.CrossRefGoogle Scholar
  32. 31.
    Schonfeld, M., Montai, M., Feher, G., (1980) Biochem. 19, 1535–1542.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1990

Authors and Affiliations

  • M. R. Gunner
    • 1
  • Barry Honig
    • 1
  1. 1.Dept. of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUSA

Personalised recommendations