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

Biophysical Journal

Volumn 75, Issue 2, 1998, Pages 683-694

  Hu, Xiche ^a   Schulten, Klaus ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER MODEL; ELECTRON MICROSCOPY; NONHUMAN; PHOTOSYNTHESIS; RHODOBACTER SPHAEROIDES; STRUCTURE ANALYSIS;

BACTERIA (MICROORGANISMS); PHAEOSPIRILLUM MOLISCHIANUM; PROTEOBACTERIA; RHODOBACTER SPHAEROIDES; RHODOBLASTUS ACIDOPHILUS; RHODOPSEUDOMONAS; RHODOSPIRILLUM; RHODOSPIRILLUM MOLISCHIANUM;

EID: 0031824352     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77558-7     Document Type: Article

References (81)

1. Aagaard, J., and W. Sistrom. 1972. Control of synthesis of reaction center bacteriochlorophyll in photosynthetic bacteria. Photochem. Photobiol. 15:209-225.
2. Allen, J. P., T. O. Yeates, H. Komiya, and D. C. Rees. 1987. Structure of the reaction center from Rhodobacter sphaeroides R-26: the protein subunits. Proc. Natl. Acad. Sci. U.S.A. 84:6162-6166.
3. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
4. B site and the cytochrome bc1 complex. Biochemistry. 34:15248-15258.
5. Boonstra, A. F., L. Germeroth, and E. J. Boekema. 1994. Structure of the light harvesting antenna from Rhodospirillum molischianum studied by electron microscopy. Biochim. Biophys. Acta. 1184:227-234.
6. Boonstra, A. F., R. W. Visschers, F. Calkoen, R. van Grondelle, E. F. van Bruggen, and E. J. Boekema. 1993. Structural characterization of the B800-850 and B875 light-harvesting antenna complexes from Rhodobacter-sphaeroides by electron microscopy. Biochim. Biophys. Acta. 1142:181-188.
7. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMm: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217.
8. Brünger, A. T. 1996. X-PLOR, Version 3.8: A System for X-ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
9. Brunisholz, R., F. Jay, F. Suter, and H. Zuber. 1985. The light-harvesting polypeptides of Rhodopseudomonas viridis: the complete amino-acid sequences of B1015-α, B1015-α and B1015-γ. Biol. Chem. Hoppe-Seyler. 366:87-98.
10. CCP4. 1994. Collaborative computer project number 4, the CCP4 suite: programs for protein crystallography. Acta Crystallogr. D. 50:760-763.
11. Cowan, S. W., T. Schirmer, G. Rummel, M. Steiert, R. Ghosh, R. A. Pauptit, J. N. Jansonius, and J. P. Rosenbusch. 1992. Crystal structures explain functional properties of 2 E. coli porins. Nature. 358:727-733.
12. Damjanović, A., T. Ritz, and K. Schulten. 1998. Energy transfer between carotenoids and bacteriochlorophylls in a light harvesting protein. Phys. Rev. E. In press.
13. Deisenhofer, J., O. Epp, K. Miki, R. Huber, and H. Michel. 1985. Structure of the protein subunits in the photosynthetic reaction center of Rhodopseudomonas viridis at 3 Å resolution. Nature. 318:618-624.
14. Dracheva, T. V., V. I. Novoderezhkin, and A. Razjivin. 1996. Exciton delocalization in the antenna of purple bacteria: exciton spectrum calculations using x-ray data and experimental site inhomogeneity. FEBS Lett. 387:81-84.
15. Drews, G., and J. R. Golecki. 1995. Structure, molecular organization, and biosynthesis of membranes of purple bacteria. In Anoxygenic Photosynthetic Bacteria. R. E. Blankenship, M. T. Madigan, and C. E. Bauer, editors. Kluwer Academic Publishers, Dordrecht, The Netherlands. 231-257.
16. Engelhardt, H., A. Engel, and W. Baumeister. 1986. Stoichiometric model of the photosynthetic unit of Ectothiorhodospira halochloris. Proc. Natl. Acad. Sci. U.S.A. 83:8972-8976.
17. Engelman, D. M., T. A. Steitz, and A. Goldman. 1986. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Ann. Rev. Biophys. Biophys. Chem. 15:321-353.
18. Engh, R. A., and R. Huber. 1991. Accurate bond and angle parameters for x-ray protein structure refinement. Acta Crystallogr. A. 47:392-400.
19. Ermler, U., G. Fritzsch, S. K. Buchanan, and H. Michel. 1994. Structure of the photosynthetic reaction center from Rhodobacter sphaeroides at 2.65 Å resolution: cofactors and protein-cofactor interactions. Structure. 2:925-936.
20. Farchaus, J., H. Gruenberg, and D. Oesterhelt. 1990. Complementation of a reaction center-deficient Rhodobacter sphaeroides pufLMX deletion strain in trans with pufBALM does not restore the photosynthesis-positive phenotype. J. Bacteriol. 172:977-985.
21. Farchaus, J., and D. Oesterhelt. 1989. 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. 8:47-54.
22. Fleming, G. R., and R. van Grondelle. 1994. The primary steps of photosynthesis. Phys. Today 47:48-55.
23. Flores, T. P., C. A. Orengo, D. S. Moss, and J. M. Thornton. 1993. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci. 2:1811-1826.
24. Franck, J., and E. Teller. 1938. Migration and photochemical action of excitation energy in crystals. J. Chem. Phys. 6:861-872.
25. Frenkel, J. 1931. On the transformation of light into heat in solids. I. Phys. Rev. 37:17-44.
26. Geourjon, C., and G. Deleage. 1994. SOPM: a self optimised prediction method for protein secondary structure prediction. Protein Eng. 7:157-164.
27. Germeroth, L., F. Lottspeich, B. Robert, and H. Michel. 1993. Unexpected similarities of the B800-850 light-harvesting complex from Rhodospirillum molischianum to the B870 light-harvesting complexes from other purple photosynthetic bacteria. Biochemistry. 32:5615-5621.
28. Ghosh, R., H. Hauser, and R. Bachofen. 1988. Reversible dissociation of the B873 light-harvesting complex from Rhodospirillum rubrum G9+. Biochemistry. 27:1004-1014.
29. Gouterman, M. 1961. Spectra of porphyrins. J. Mol. Spectrosc. 6:138-163.
30. Holley, L. H., and M. Karplus. 1991. Neural networks for protein structure prediction. Methods Enzymol. 202:204-224.
31. Hu, X., A. Damjanovic, T. Ritz, and K. Schulten. 1998. Architecture and function of the light harvesting apparatus of purple bacteria. Proc. Natl. Acad. Sci. U.S.A. 95:5935-5941.
32. Hu, X., T. Ritz, A. Damjanovic, and K. Schulten. 1997. Pigment organization and transfer of electronic excitation in the purple bacteria. J. Phys. Chem. B. 101:3854-3871.
33. Hu, X., and K. Schulten. 1997a. How nature harvests sunlight. Phys. Today. 50:28-34.
34. Hu, X., and K. Schulten. 1997b. Pigment organization of bacterial photosynthetic membrane and dynamics of energy transfer. Biophys. J. 72: A125.
35. Hu, X., D. Xu, K. Hamer, K. Schulten, J. Koepke, and H. Michel. 1995. Predicting the structure of the light-harvesting complex II of Rhodospirillum molischianum. Protein Sci. 4:1670-1682.
36. Hu, X., D. Xu, K. Hamer, K. Schulten, J. Koepke, and H. Michel. 1996. Knowledge-based structure prediction of the light-harvesting complex II of Rhodospirillum molischianum. In Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding. P. M. Pardalos, D. Shalloway, and G. Xue, editors. American Mathematical Society, Providence, RI. 97-122.
37. Humphrey, W. F., A. Dalke, and K. Schulten. 1996. VMD: Visual Molecular Dynamics. J. Mol. Graphics. 14:33-38.
38. Hunter, C. N., J. D. Pennoyer, J. N. Sturgis, D. Farrelley, and R. A. Niederman. 1988. Oligomerization states and associations of light-harvesting pigment-protein complexes of Rhodopseudomonas sphaeroides as analysed by lithium dodecyl sulphate-polyacrylamide gel electrophoresis. Biochemistry. 27:3459-3467.
39. Jay, F., M. Lambillotte, W. Stark, and K. Mühlethaler. 1984. The preparation and characterization of native photoreceptor units from the thylakoids of Rhodopseudomonas viridis. EMBO J. 3:773-776.
40. Joo, T., Y. Jia, J.-Y. Yu, D. Jonas, and G. Fleming. 1996. Dynamics in isolated bacterial light harvesting antenna LH2 of Rhodobacter sphaeroides at room temperature. J. Phys. Chem. 100:2399-2409.
41. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
42. Karrasch, S., P. A. Bullough, and R. Ghosh. 1995. 8.5 Å projection map of the light-harvesting complex I from Rhodospirillum rubrum reveals a ring composed of 16 subunits. EMBO J. 14:631-638.
43. Kiley, P.S., T. J. Donohue, W. A. Havelka, and S. Kaplan. 1987. DNA sequence and in vitro expression of the B875 light-harvesting polypeptides of Rhodobacter sphaeroides. J. Bacteriol. 169:742-750.
44. Koepke, J., X. Hu, C. Münke, K. Schulten, and H. Michel. 1996. The crystal structure of the light harvesting complex II (B800-850) from Rhodospirillum molischianum. Structure. 4:581-597.
45. Krauss, N., W.-D. Schubert, O. Klukas, P. Fromme, H. T. Witt, and W. Saenger. 1996. Photosystem 1 at 4 Å resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system. Nature Struct. Biol. 3:965-973.
46. Kühlbrandt, W., D.-N. Wang, and Y. Fujiyoshi. 1994. Atomic model of plant light-harvesting complex by electron crystallography. Nature. 367: 614-621.
47. Lancaster, C. R. D., U. Ermler, and H. Michel. 1995. The structure of photosynthetic reaction centers from purple bacteria as revealed by x-ray crystallography. In Anoxygenic Photosynthetic Bacteria. R. E. Blankenship, M. T. Madigan, and C. E. Bauer, editors. Kluwer Academic Publishers, Dordrecht, The Netherlands. 503-526.
48. Landolt-Marticorena, C., K. Williams, C. Deber, and R. Reithmeier. 1993. Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins. J. Mol. Biol. 229: 602-608.
49. Lee, J., B. DeHoff, T. Donohue, R. Gumport, and S. Kaplan. 1989. Transcriptional analysis of puf operon expression in Rhodobacter sphaeroides 2.4.1 and an intercistronic transcription terminator mutant. J. Biol. Chem. 264:19354-19365.
50. Loach, P. A., and P. S. Parkes-Loach. 1995. Structure-function relationships in core light-harvesting complexes (LHI) as determined by characterization of the structural subunits and by reconstitution experiments. In Anoxygenic Photosynthetic Bacteria. R. E. Blankenship, M. T. Madigan, and C. E. Bauer, editors. Kluwer Academic Publishers. Dordrecht, The Netherlands. 437-471.
51. McDermott, G., S. Prince, A. Freer, A. Hawthornthwaite-Lawless, M. Papiz, R. Cogdell, and N. Isaacs. 1995. Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria. Nature. 374:517-521.
52. McGlynn, P., C. Hunter, and M. Jones. 1994. The Rhodobacter sphaeroides PufX protein is not required for photosynthetic competence in the absence of a light harvesting system. FEBS Lett. 349:349-353.
53. Meckenstock, R. U., K. Krusche, R. A. Brunisholz, and H. Zuber. 1992. The light-harvesting core-complex and the B820-subunit from Rhodopseudomonas marina. II. Electron microscopic characterisation. FEBS Lett. 311:135-138.
54. Miller, K. 1982. Three-dimensional structure of a photosynthetic membrane. Nature. 300:53-55.
55. Monger, T., and W. Parson. 1977. Singlet-triplet fusion in Rhodopseudomonas sphaeroides chromatophores: a probe of the organization of the photosynthetic apparatus. Biochim. Biophys. Acta. 460:393-407.
56. MSI. 1994. QUANTA 4.0. Molecular Simulations Inc., Burlington, Mass.
57. Olsen, J. D., and C. N. Hunter. 1994. Protein structure modelling of the bacterial light-harvesting complex. Photochem. Photobiol. 60:521.
58. Olsen, J. D., G. D. Sockalingum, B. Robert, and C. N. Hunter. 1994. 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. 91:7124-7128.
59. Olsen, J., J. Sturgis, W. Westerhuis, G. Fowler, C. Hunter, and B. Robert. 1997. Site-directed modification of the ligands to the bacteriochlorophylls of the light-harvesting LH1 and LH2 complexes of Rhodobacter sphaeroides. Biochemistry. 36:12625-12632.
60. Papiz, M. Z., S. M. Prince, A. M. Hawthornthwaite-Lawless, G. McDermott, A. A. Freer, N. W. Isaacs, and R. J. Cogdell. 1996. A model for the photosynthetic apparatus of purple bacteria. Trends Plant Sci. 1:198-206.
61. Parson, W. W., and A. Warshel. 1995. Theoretical analysis of electron-transfer reaction. In Anoxygenic Photosynthetic Bacteria. R. E. Blankenship, M. T. Madigan, and C. E. Bauer, editors. Kluwer Academic Publishers, Dordrecht, The Netherlands. 559-575.
62. Persson, B., and P. Argos. 1994. Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J. Mol. Biol. 237: 182-192.
63. Pullerits, T., and V. Sundstrom. 1996. Photosynthetic light-harvesting pigment-protein complexes: toward understanding how and why. Acc. Chem. Res. 29:381-389.
64. Ritz, T., X. Hu, A. Damjanović, and K. Schulten. 1998. Excitons and excitation transfer in the photosynthetic unit of purple bacteria. J. Luminesc. 76-77:310-321.
65. Robert, B., and M. Lutz. 1985. Structure of antenna complexes of several Rhodospirillales from their resonance raman spectra. Biochim. Biophys. Acta. 807:10-23.
66. Sauer, K., R. J. Cogdell, S. M. Prince, A. Freer, N. W. Isaacs, and H. Scheer. 1996. Structure-based calculations of the optical spectra of the LH2 bacteriochlorophyll-protein complex from Rhodopseudomonas acidophila. Photochem. Photobiol. 64:564-576.
67. Savage, H., M. Cyrklaff, G. Montoya, W. Kuhlbrandt, and I. Sinning. 1996. Two-dimensional structure of light harvesting complex II (LHII) from the purple bacterium Rhodovulum sulfidophilum and comparison with LHII from Rhodopseudomonas acidophila. Structure. 4:243-252.
68. Schiffer, M., C. Chang, and F. J. Stevens. 1992. The functions of tryptophan residues in membrane proteins. Protein Eng. 5:213-214.
69. Schuler, G. D., S. F. Altschul, and D. J. Lipman. 1991. A workbench for multiple alignment construction and analysis. Proteins Struct. Funct. Genet. 9:180.
70. Shreve, A. P., J. K. Trautman, H. A. Frank, T. G. Owens, and A. C. Albrecht. 1991. Femtosecond energy-transfer processes in the B800-850 light-harvesting complex of Rhodobacter sphaeroides 2.4.1. Biochim. Biophys. Acta. 1058:280-288.
71. Stark, W., W. Kühlbrandt, I. Wildhaber, E. Wehrli, and K. Mühlethaler. 1984. The structure of the photoreceptor unit of Rhodopseudomonas viridis. EMBO J. 3:777-783.
72. Sturgis, J. N., J. D. Olsen, B. Robert, and C. N. Hunter. 1997. Functions of conserved tryptophan residues of the core light harvesting complex of Rhodobacter sphaeroides. Biochemistry. 36:2772-2778.
73. Theiler, R., F. Suter, V. Wiemken, and H. Zuber. 1984. The light-harvesting polypeptides of Rhodopseudomonas sphaeroides R-26.1. I. isolation, purification and sequence analyses. Hoppe Seylers Z. Physiol. Chem. 365:703-719.
74. van Grondelle, R., J. Dekker, T. Gillbro, and V. Sundstrom. 1994. Energy transfer and trapping in photosynthesis. Biochim. Biophys. Acta. 1187: 1-65.
75. Walz, T., and R. Ghosh. 1997. Two-dimensional crystallization of the light-harvesting I reaction centre photounit from Rhodospirillum rubrum. J. Mol. Biol. 265:107-111.
76. Weiss, M. S., and G. E. Schulz. 1992. Structure of porin refined at 1.8 angstrom resolution. J. Mol. Biol. 227:493-509.
77. Woodbury, N. W., and J. Allen. 1995. The pathway, kinetics and thermodynamics of electron transfer in wild type and mutant reaction center of purple nonsulfur bacteria. In Anoxygenic Photosynthetic Bacteria. R. E. Blankenship, M. T. Madigan, and C. E. Bauer, editors. Kluwer Academic Publishers, Dordrecht, The Netherlands. 527-557.
78. Wu, H.-M., N. R. S. Reddy, and G. J. Small. 1997. Direct observation and hole burning of the lowest exciton level (B870) of the LH2 antenna complex of Rhodopseudomonas acidophila (strain 10050). J. Phys. Chem. B. 101:651.
79. Zerner, M. C., M. G. Cory, X. Hu, and K. Schulten. 1998. Electronic excitations in aggregate of bacteriochlorophylls. J. Phys. Chem. B. In press.
80. Zuber, H. 1985. Structure and function of light-harvesting complexes and their polypeptides. Photochem. Photobiol. 42:821-825.
81. Zuber, H., and R. A. Brunisholz. 1991. Structure and function of antenna polypeptides and chlorophyll-protein complexes: principles and variability. In Chlorophylls. H. Scheer, editor. CRC Press, Boca Raton, FL. 627-692.