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. 1998 Aug;75(2):683–694. doi: 10.1016/S0006-3495(98)77558-7

Model for the light-harvesting complex I (B875) of Rhodobacter sphaeroides.

X Hu 1, K Schulten 1
PMCID: PMC1299743  PMID: 9675170

Abstract

The light-harvesting complex I (LH-I) of Rhodobacter sphaeroides has been modeled computationally as a hexadecamer of alphabeta-heterodimers, based on a close homology of the heterodimer to that of light-harvesting complex II (LH-II) of Rhodospirillum molischianum. The resulting LH-I structure yields an electron density projection map that is in agreement with an 8.5-A resolution electron microscopic projection map for the highly homologous LH-I of Rs. rubrum. A complex of the modeled LH-I with the photosynthetic reaction center of the same species has been obtained by a constrained conformational search. This complex and the available structures of LH-II from Rs. molischianum and Rhodopseudomonas acidophila furnish a complete model of the pigment organization in the photosynthetic membrane of purple bacteria.

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Selected References

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

  1. Aagaard J., Sistrom W. R. Control of synthesis of reaction center bacteriochlorophyll in photosynthetic bacteria. Photochem Photobiol. 1972 Feb;15(2):209–225. doi: 10.1111/j.1751-1097.1972.tb06240.x. [DOI] [PubMed] [Google Scholar]
  2. Allen J. P., Feher G., Yeates T. O., Komiya H., Rees D. C. Structure of the reaction center from Rhodobacter sphaeroides R-26: the protein subunits. Proc Natl Acad Sci U S A. 1987 Sep;84(17):6162–6166. doi: 10.1073/pnas.84.17.6162. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  4. Barz W. P., Verméglio A., Francia F., Venturoli G., Melandri B. A., Oesterhelt D. Role of the PufX protein in photosynthetic growth of Rhodobacter sphaeroides. 2. PufX is required for efficient ubiquinone/ubiquinol exchange between the reaction center QB site and the cytochrome bc1 complex. Biochemistry. 1995 Nov 21;34(46):15248–15258. doi: 10.1021/bi00046a033. [DOI] [PubMed] [Google Scholar]
  5. Brunisholz R. A., Jay F., Suter F., Zuber H. The light-harvesting polypeptides of Rhodopseudomonas viridis. The complete amino-acid sequences of B1015-alpha, B1015-beta and B1015-gamma. Biol Chem Hoppe Seyler. 1985 Jan;366(1):87–98. doi: 10.1515/bchm3.1985.366.1.87. [DOI] [PubMed] [Google Scholar]
  6. Cowan S. W., Schirmer T., Rummel G., Steiert M., Ghosh R., Pauptit R. A., Jansonius J. N., Rosenbusch J. P. Crystal structures explain functional properties of two E. coli porins. Nature. 1992 Aug 27;358(6389):727–733. doi: 10.1038/358727a0. [DOI] [PubMed] [Google Scholar]
  7. Dracheva T. V., Novoderezhkin V. I., Razjivin A. P. Exciton delocalization in the antenna of purple bacteria: exciton spectrum calculations using Z-ray data and experimental site inhomogeneity. FEBS Lett. 1996 May 27;387(1):81–84. doi: 10.1016/0014-5793(96)00456-5. [DOI] [PubMed] [Google Scholar]
  8. Engelhardt H., Engel A., Baumeister W. Stoichiometric model of the photosynthetic unit of Ectothiorhodospira halochloris. Proc Natl Acad Sci U S A. 1986 Dec;83(23):8972–8976. doi: 10.1073/pnas.83.23.8972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Engelman D. M., Steitz T. A., Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem. 1986;15:321–353. doi: 10.1146/annurev.bb.15.060186.001541. [DOI] [PubMed] [Google Scholar]
  10. Ermler U., Fritzsch G., Buchanan S. K., Michel H. Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 A resolution: cofactors and protein-cofactor interactions. Structure. 1994 Oct 15;2(10):925–936. doi: 10.1016/s0969-2126(94)00094-8. [DOI] [PubMed] [Google Scholar]
  11. Farchaus J. W., Gruenberg H., Oesterhelt D. Complementation of a reaction center-deficient Rhodobacter sphaeroides pufLMX deletion strain in trans with pufBALM does not restore the photosynthesis-positive phenotype. J Bacteriol. 1990 Feb;172(2):977–985. doi: 10.1128/jb.172.2.977-985.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Farchaus J. W., Oesterhelt D. A Rhodobacter sphaeroides puf L, M and X deletion mutant and its complementation in trans with a 5.3 kb puf operon shuttle fragment. EMBO J. 1989 Jan;8(1):47–54. doi: 10.1002/j.1460-2075.1989.tb03347.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Flores T. P., Orengo C. A., Moss D. S., Thornton J. M. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci. 1993 Nov;2(11):1811–1826. doi: 10.1002/pro.5560021104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Geourjon C., Deléage G. SOPM: a self-optimized method for protein secondary structure prediction. Protein Eng. 1994 Feb;7(2):157–164. doi: 10.1093/protein/7.2.157. [DOI] [PubMed] [Google Scholar]
  15. Germeroth L., Lottspeich F., Robert B., Michel H. Unexpected similarities of the B800-850 light-harvesting complex from Rhodospirillum molischianum to the B870 light-harvesting complexes from other purple photosynthetic bacteria. Biochemistry. 1993 Jun 1;32(21):5615–5621. doi: 10.1021/bi00072a017. [DOI] [PubMed] [Google Scholar]
  16. Holley L. H., Karplus M. Neural networks for protein structure prediction. Methods Enzymol. 1991;202:204–224. doi: 10.1016/0076-6879(91)02012-x. [DOI] [PubMed] [Google Scholar]
  17. Hu X., Damjanović A., Ritz T., Schulten K. Architecture and mechanism of the light-harvesting apparatus of purple bacteria. Proc Natl Acad Sci U S A. 1998 May 26;95(11):5935–5941. doi: 10.1073/pnas.95.11.5935. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hu X., Xu D., Hamer K., Schulten K., Koepke J., Michel H. Predicting the structure of the light-harvesting complex II of Rhodospirillum molischianum. Protein Sci. 1995 Sep;4(9):1670–1682. doi: 10.1002/pro.5560040903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996 Feb;14(1):33-8, 27-8. doi: 10.1016/0263-7855(96)00018-5. [DOI] [PubMed] [Google Scholar]
  20. Jay F., Lambillotte M., Stark W., Mühlethaler K. The preparation and characterisation of native photoreceptor units from the thylakoids of Rhodopseudomonas viridis. EMBO J. 1984 Apr;3(4):773–776. doi: 10.1002/j.1460-2075.1984.tb01883.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. doi: 10.1002/bip.360221211. [DOI] [PubMed] [Google Scholar]
  22. Karrasch S., Bullough P. A., Ghosh R. The 8.5 A projection map of the light-harvesting complex I from Rhodospirillum rubrum reveals a ring composed of 16 subunits. EMBO J. 1995 Feb 15;14(4):631–638. doi: 10.1002/j.1460-2075.1995.tb07041.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kiley P. J., Donohue T. J., Havelka W. A., Kaplan S. DNA sequence and in vitro expression of the B875 light-harvesting polypeptides of Rhodobacter sphaeroides. J Bacteriol. 1987 Feb;169(2):742–750. doi: 10.1128/jb.169.2.742-750.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Koepke J., Hu X., Muenke C., Schulten K., Michel H. The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum. Structure. 1996 May 15;4(5):581–597. doi: 10.1016/s0969-2126(96)00063-9. [DOI] [PubMed] [Google Scholar]
  25. Krauss N., Schubert W. D., Klukas O., Fromme P., Witt H. T., Saenger W. Photosystem I at 4 A resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system. Nat Struct Biol. 1996 Nov;3(11):965–973. doi: 10.1038/nsb1196-965. [DOI] [PubMed] [Google Scholar]
  26. Kühlbrandt W., Wang D. N., Fujiyoshi Y. Atomic model of plant light-harvesting complex by electron crystallography. Nature. 1994 Feb 17;367(6464):614–621. doi: 10.1038/367614a0. [DOI] [PubMed] [Google Scholar]
  27. Landolt-Marticorena C., Williams K. A., Deber C. M., Reithmeier R. A. Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins. J Mol Biol. 1993 Feb 5;229(3):602–608. doi: 10.1006/jmbi.1993.1066. [DOI] [PubMed] [Google Scholar]
  28. Lee J. K., DeHoff B. S., Donohue T. J., Gumport R. I., Kaplan S. Transcriptional analysis of puf operon expression in Rhodobacter sphaeroides 2.4.1 and an intercistronic transcription terminator mutant. J Biol Chem. 1989 Nov 15;264(32):19354–19365. [PubMed] [Google Scholar]
  29. McGlynn P., Hunter C. N., Jones M. R. The Rhodobacter sphaeroides PufX protein is not required for photosynthetic competence in the absence of a light harvesting system. FEBS Lett. 1994 Aug 8;349(3):349–353. doi: 10.1016/0014-5793(94)00701-2. [DOI] [PubMed] [Google Scholar]
  30. Meckenstock R. U., Krusche K., Brunisholz R. A., Zuber H. The light-harvesting core-complex and the B820-subunit from Rhodopseudomonas marina. Part II. Electron microscopic characterisation. FEBS Lett. 1992 Oct 19;311(2):135–138. doi: 10.1016/0014-5793(92)81384-x. [DOI] [PubMed] [Google Scholar]
  31. Monger T. G., Parson W. W. Singlet-triplet fusion in Rhodopseudomonas sphaeroides chromatophores. A probe of the organization of the photosynthetic apparatus. Biochim Biophys Acta. 1977 Jun 9;460(3):393–407. doi: 10.1016/0005-2728(77)90080-9. [DOI] [PubMed] [Google Scholar]
  32. Olsen J. D., Hunter C. N. Protein structure modelling of the bacterial light-harvesting complex. Photochem Photobiol. 1994 Dec;60(6):521–535. doi: 10.1111/j.1751-1097.1994.tb05144.x. [DOI] [PubMed] [Google Scholar]
  33. Olsen J. D., Sockalingum G. D., Robert B., Hunter C. N. Modification of a hydrogen bond to a bacteriochlorophyll a molecule in the light-harvesting 1 antenna of Rhodobacter sphaeroides. Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):7124–7128. doi: 10.1073/pnas.91.15.7124. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Olsen J. D., Sturgis J. N., Westerhuis W. H., Fowler G. J., Hunter C. N., Robert B. Site-directed modification of the ligands to the bacteriochlorophylls of the light-harvesting LH1 and LH2 complexes of Rhodobacter sphaeroides. Biochemistry. 1997 Oct 14;36(41):12625–12632. doi: 10.1021/bi9710481. [DOI] [PubMed] [Google Scholar]
  35. Persson B., Argos P. Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J Mol Biol. 1994 Mar 25;237(2):182–192. doi: 10.1006/jmbi.1994.1220. [DOI] [PubMed] [Google Scholar]
  36. Savage H., Cyrklaff M., Montoya G., Kühlbrandt W., Sinning I. Two-dimensional structure of light harvesting complex II (LHII) from the purple bacterium Rhodovulum sulfidophilum and comparison with LHII from Rhodopseudomonas acidophila. Structure. 1996 Mar 15;4(3):243–252. doi: 10.1016/s0969-2126(96)00029-9. [DOI] [PubMed] [Google Scholar]
  37. Schiffer M., Chang C. H., Stevens F. J. The functions of tryptophan residues in membrane proteins. Protein Eng. 1992 Apr;5(3):213–214. doi: 10.1093/protein/5.3.213. [DOI] [PubMed] [Google Scholar]
  38. Schuler G. D., Altschul S. F., Lipman D. J. A workbench for multiple alignment construction and analysis. Proteins. 1991;9(3):180–190. doi: 10.1002/prot.340090304. [DOI] [PubMed] [Google Scholar]
  39. Shreve A. P., Trautman J. K., Frank H. A., Owens T. G., Albrecht A. C. Femtosecond energy-transfer processes in the B800-850 light-harvesting complex of Rhodobacter sphaeroides 2.4.1. Biochim Biophys Acta. 1991 Jun 17;1058(2):280–288. doi: 10.1016/s0005-2728(05)80248-8. [DOI] [PubMed] [Google Scholar]
  40. Stark W., Kühlbrandt W., Wildhaber I., Wehrli E., Mühlethaler K. The structure of the photoreceptor unit of Rhodopseudomonas viridis. EMBO J. 1984 Apr;3(4):777–783. doi: 10.1002/j.1460-2075.1984.tb01884.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Sturgis J. N., Olsen J. D., Robert B., Hunter C. N. Functions of conserved tryptophan residues of the core light-harvesting complex of Rhodobacter sphaeroides. Biochemistry. 1997 Mar 11;36(10):2772–2778. doi: 10.1021/bi962524a. [DOI] [PubMed] [Google Scholar]
  42. Theiler R., Suter F., Wiemken V., Zuber H. The light-harvesting polypeptides of Rhodopseudomonas sphaeroides R-26.1. I. Isolation, purification and sequence analyses. Hoppe Seylers Z Physiol Chem. 1984 Jul;365(7):703–719. doi: 10.1515/bchm2.1984.365.2.703. [DOI] [PubMed] [Google Scholar]
  43. Walz T., Ghosh R. Two-dimensional crystallization of the light-harvesting I-reaction centre photounit from Rhodospirillum rubrum. J Mol Biol. 1997 Jan 17;265(2):107–111. doi: 10.1006/jmbi.1996.0714. [DOI] [PubMed] [Google Scholar]
  44. Weiss M. S., Schulz G. E. Structure of porin refined at 1.8 A resolution. J Mol Biol. 1992 Sep 20;227(2):493–509. doi: 10.1016/0022-2836(92)90903-w. [DOI] [PubMed] [Google Scholar]

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