Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 1998 Aug;75(2):777–784. doi: 10.1016/S0006-3495(98)77567-8

Experimental and theoretical characterization of the high-affinity cation-binding site of the purple membrane.

L Pardo 1, F Sepulcre 1, J Cladera 1, M Duñach 1, A Labarta 1, J Tejada 1, E Padrós 1
PMCID: PMC1299752  PMID: 9675179

Abstract

Binding of Mn2+ or Mg2+ to the high-affinity site of the purple membrane from Halobacterium salinarium has been studied by superconducting quantum interference device magnetometry or by ab initio quantum mechanical calculations, respectively. The binding of Mn2+ cation, in a low-spin state, to the high-affinity site occurs through a major octahedral local symmetry character with a minor rhombic distortion and a coordination number of six. A molecular model of this binding site in the Schiff base vicinity is proposed. In this model, a Mg2+ cation interacts with one oxygen atom of the side chain of Asp85, with both oxygen atoms of Asp212 and with three water molecules. One of these water molecules is hydrogen bonded to both the nitrogen of the protonated Schiff base and the Asp85 oxygen. It could serve as a shuttle for the Schiff base proton to move to Asp85 in the L-M transition.

Full Text

The Full Text of this article is available as a PDF (150.5 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ariki M., Lanyi J. K. Characterization of metal ion-binding sites in bacteriorhodopsin. J Biol Chem. 1986 Jun 25;261(18):8167–8174. [PubMed] [Google Scholar]
  2. Chang C. H., Chen J. G., Govindjee R., Ebrey T. Cation binding by bacteriorhodopsin. Proc Natl Acad Sci U S A. 1985 Jan;82(2):396–400. doi: 10.1073/pnas.82.2.396. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chang C. H., Jonas R., Melchiore S., Govindjee R., Ebrey T. G. Mechanism and role of divalent cation binding of bacteriorhodopsin. Biophys J. 1986 Mar;49(3):731–739. doi: 10.1016/S0006-3495(86)83699-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cladera J., Galisteo M. L., Sabés M., Mateo P. L., Padrós E. The role of retinal in the thermal stability of the purple membrane. Eur J Biochem. 1992 Jul 15;207(2):581–585. doi: 10.1111/j.1432-1033.1992.tb17084.x. [DOI] [PubMed] [Google Scholar]
  5. Cladera J., Sabés M., Padrós E. Fourier transform infrared analysis of bacteriorhodopsin secondary structure. Biochemistry. 1992 Dec 15;31(49):12363–12368. doi: 10.1021/bi00164a010. [DOI] [PubMed] [Google Scholar]
  6. Duñach M., Padrós E., Muga A., Arrondo J. L. Fourier-transform infrared studies on cation binding to native and modified purple membranes. Biochemistry. 1989 Oct 31;28(22):8940–8945. doi: 10.1021/bi00448a038. [DOI] [PubMed] [Google Scholar]
  7. Duñach M., Padrós E., Seigneuret M., Rigaud J. L. On the molecular mechanism of the blue to purple transition of bacteriorhodopsin. UV-difference spectroscopy and electron spin resonance studies. J Biol Chem. 1988 Jun 5;263(16):7555–7559. [PubMed] [Google Scholar]
  8. Duñach M., Seigneuret M., Rigaud J. L., Padrós E. Influence of cations on the blue to purple transition of bacteriorhodopsin. Comparison of Ca2+ and Hg2+ binding and their effect on the surface potential. J Biol Chem. 1988 Nov 25;263(33):17378–17384. [PubMed] [Google Scholar]
  9. Duñach M., Seigneuret M., Rigaud J. L., Padrós E. The relationship between the chromophore moiety and the cation binding sites in bacteriorhodopsin. Biosci Rep. 1986 Nov;6(11):961–966. doi: 10.1007/BF01114972. [DOI] [PubMed] [Google Scholar]
  10. Eicher H., Trautwein A. Electronic structure and quadrupole splittings of ferrous iron in hemoglobin. J Chem Phys. 1969 Mar 15;50(6):2540–2551. doi: 10.1063/1.1671413. [DOI] [PubMed] [Google Scholar]
  11. Fischer W. B., Sonar S., Marti T., Khorana H. G., Rothschild K. J. Detection of a water molecule in the active-site of bacteriorhodopsin: hydrogen bonding changes during the primary photoreaction. Biochemistry. 1994 Nov 1;33(43):12757–12762. doi: 10.1021/bi00209a005. [DOI] [PubMed] [Google Scholar]
  12. Friedman N., Rousso I., Sheves M., Fu X., Bressler S., Druckmann S., Ottolenghi M. Time-resolved titrations of ASP-85 in bacteriorhodopsin: the multicomponent kinetic mechanism. Biochemistry. 1997 Sep 23;36(38):11369–11380. doi: 10.1021/bi970646c. [DOI] [PubMed] [Google Scholar]
  13. Fu X., Bressler S., Ottolenghi M., Eliash T., Friedman N., Sheves M. Titration kinetics of Asp-85 in bacteriorhodopsin: exclusion of the retinal pocket as the color-controlling cation binding site. FEBS Lett. 1997 Oct 20;416(2):167–170. doi: 10.1016/s0014-5793(97)01194-0. [DOI] [PubMed] [Google Scholar]
  14. Grigorieff N., Ceska T. A., Downing K. H., Baldwin J. M., Henderson R. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J Mol Biol. 1996 Jun 14;259(3):393–421. doi: 10.1006/jmbi.1996.0328. [DOI] [PubMed] [Google Scholar]
  15. Henderson R., Baldwin J. M., Ceska T. A., Zemlin F., Beckmann E., Downing K. H. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol. 1990 Jun 20;213(4):899–929. doi: 10.1016/S0022-2836(05)80271-2. [DOI] [PubMed] [Google Scholar]
  16. Jonas R., Ebrey T. G. Binding of a single divalent cation directly correlates with the blue-to-purple transition in bacteriorhodopsin. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):149–153. doi: 10.1073/pnas.88.1.149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kamikubo H., Kataoka M., Váró G., Oka T., Tokunaga F., Needleman R., Lanyi J. K. Structure of the N intermediate of bacteriorhodopsin revealed by x-ray diffraction. Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1386–1390. doi: 10.1073/pnas.93.4.1386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kimura Y., Ikegami A., Stoeckenius W. Salt and pH-dependent changes of the purple membrane absorption spectrum. Photochem Photobiol. 1984 Nov;40(5):641–646. doi: 10.1111/j.1751-1097.1984.tb05353.x. [DOI] [PubMed] [Google Scholar]
  19. Kimura Y., Vassylyev D. G., Miyazawa A., Kidera A., Matsushima M., Mitsuoka K., Murata K., Hirai T., Fujiyoshi Y. Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Nature. 1997 Sep 11;389(6647):206–211. doi: 10.1038/38323. [DOI] [PubMed] [Google Scholar]
  20. Lanyi J. K. Proton translocation mechanism and energetics in the light-driven pump bacteriorhodopsin. Biochim Biophys Acta. 1993 Dec 7;1183(2):241–261. doi: 10.1016/0005-2728(93)90226-6. [DOI] [PubMed] [Google Scholar]
  21. Logunov I., Humphrey W., Schulten K., Sheves M. Molecular dynamics study of the 13-cis form (bR548) of bacteriorhodopsin and its photocycle. Biophys J. 1995 Apr;68(4):1270–1282. doi: 10.1016/S0006-3495(95)80301-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Metz G., Siebert F., Engelhard M. Asp85 is the only internal aspartic acid that gets protonated in the M intermediate and the purple-to-blue transition of bacteriorhodopsin. A solid-state 13C CP-MAS NMR investigation. FEBS Lett. 1992 Jun 1;303(2-3):237–241. doi: 10.1016/0014-5793(92)80528-o. [DOI] [PubMed] [Google Scholar]
  23. Mowery P. C., Lozier R. H., Chae Q., Tseng Y. W., Taylor M., Stoeckenius W. Effect of acid pH on the absorption spectra and photoreactions of bacteriorhodopsin. Biochemistry. 1979 Sep 18;18(19):4100–4107. doi: 10.1021/bi00586a007. [DOI] [PubMed] [Google Scholar]
  24. Oesterhelt D., Stoeckenius W. Functions of a new photoreceptor membrane. Proc Natl Acad Sci U S A. 1973 Oct;70(10):2853–2857. doi: 10.1073/pnas.70.10.2853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Oesterhelt D., Stoeckenius W. Isolation of the cell membrane of Halobacterium halobium and its fractionation into red and purple membrane. Methods Enzymol. 1974;31:667–678. doi: 10.1016/0076-6879(74)31072-5. [DOI] [PubMed] [Google Scholar]
  26. Oesterhelt D., Stoeckenius W. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol. 1971 Sep 29;233(39):149–152. doi: 10.1038/newbio233149a0. [DOI] [PubMed] [Google Scholar]
  27. Pebay-Peyroula E., Rummel G., Rosenbusch J. P., Landau E. M. X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science. 1997 Sep 12;277(5332):1676–1681. doi: 10.1126/science.277.5332.1676. [DOI] [PubMed] [Google Scholar]
  28. Roselli C., Boussac A., Mattioli T. A., Griffiths J. A., el-Sayed M. A. Detection of a Yb3+ binding site in regenerated bacteriorhodopsin that is coordinated with the protein and phospholipid head groups. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14333–14337. doi: 10.1073/pnas.93.25.14333. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Sepulcre F., Cladera J., García J., Proietti M. G., Torres J., Padrós E. An extended x-ray absorption fine structure study of the high-affinity cation-binding site in the purple membrane. Biophys J. 1996 Feb;70(2):852–856. doi: 10.1016/S0006-3495(96)79627-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Subramaniam S., Gerstein M., Oesterhelt D., Henderson R. Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin. EMBO J. 1993 Jan;12(1):1–8. doi: 10.1002/j.1460-2075.1993.tb05625.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Subramaniam S., Marti T., Khorana H. G. Protonation state of Asp (Glu)-85 regulates the purple-to-blue transition in bacteriorhodopsin mutants Arg-82----Ala and Asp-85----Glu: the blue form is inactive in proton translocation. Proc Natl Acad Sci U S A. 1990 Feb;87(3):1013–1017. doi: 10.1073/pnas.87.3.1013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Thomanek U. F., Parak F., Formanek S., Kalvius G. M. Mössbauer and susceptibility experiments on different compounds of Fe3+-myoglobin. Biophys Struct Mech. 1977 Sep 28;3(3-4):207–227. doi: 10.1007/BF00535697. [DOI] [PubMed] [Google Scholar]
  33. Zhang Y. N., Sweetman L. L., Awad E. S., El-Sayed M. A. Nature of the individual Ca binding sites in Ca-regenerated bacteriorhodopsin. Biophys J. 1992 May;61(5):1201–1206. doi: 10.1016/S0006-3495(92)81929-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Zhang Y. N., el-Sayed M. A., Bonet M. L., Lanyi J. K., Chang M., Ni B., Needleman R. Effects of genetic replacements of charged and H-bonding residues in the retinal pocket on Ca2+ binding to deionized bacteriorhodopsin. Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1445–1449. doi: 10.1073/pnas.90.4.1445. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES