Conservation of lipid functions in cytochrome bc complexes

Journal of Molecular Biology

Volumn 414, Issue 1, 2011, Pages 145-162

  Hasan, S Saif ^a   Yamashita, Eiki ^b   Ryan, Christopher M ^c   Whitelegge, Julian P ^c   Cramer, William A ^a  

^a PURDUE UNIVERSITY   (United States)

^b OSAKA UNIVERSITY   (Japan)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

lipids; membrane proteins; structure

Indexed keywords

ALPHA CAROTENE; BETA CAROTENE; CARDIOLIPIN; CYTOCHROME; CYTOCHROME B6F; DIACYLGLYCEROL; DIGALACTOSYLDIGLYCERIDE; GALACTOSYLDIACYLGLYCEROL; PHOSPHATIDIC ACID; PHOSPHATIDYLCHOLINE; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PROTEIN CYTOCHROME BC1; SULFOQUINOVOSYLDIGLYCERIDE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; ENERGY TRANSFER; MEMBRANE STABILIZATION; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

ALGAE; CHLAMYDOMONAS REINHARDTII; CYANOBACTERIA;

EID: 81055157626     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.09.023     Document Type: Article

References (84)

1. 6f complex of oxygenic photosynthesis: tuning the cavity Science 302 2003 1009 1014 (Pubitemid 37386186)
2. 6f complex: binding site and intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone Proc. Natl Acad. Sci. USA 103 2006 67 74
3. n J. Mol. Biol. 370 2007 39 52 (Pubitemid 46817566)
4. 6f complex from Nostoc sp. PCC 7120 J. Biol. Chem. 284 2009 9861 9869
5. 6f complex Nature 426 2003 413 418 (Pubitemid 37490123)
6. 6f complex from spinach and the cyanobacterium, Mastigocladus laminosus Mol. Cell. Proteomics 1 2002 816 827
7. 6f complex: EPR spectroscopy and correlation with structure J. Am. Chem. Soc. 128 2006 14246 14247 (Pubitemid 44707720)
8. 6 in an algal mutant lacking photosystem I centers Biochim. Biophys. Acta 725 1983 25 33
9. Joliot P., and Joliot A. The low-potential electron-transfer chain in the cytochrome bf complex Biochim. Biophys. Acta 933 1988 319 333
10. 6f complex studied by EPR: a pair of strongly interacting hemes Proc. Natl. Acad. Sci. USA 104 2007 519 524 (Pubitemid 46123057)
11. 6f complex J. Am. Chem. Soc. 131 2009 12536 12537
12. 1 complex from bovine heart mitochondria Science 277 1997 60 66 (Pubitemid 27450644)
13. 1 complex Science 281 1998 64 71 (Pubitemid 28354043)
14. 1 Nature 392 1998 677 684 (Pubitemid 28207780)
15. 1 complex J. Bioenerg. Biomembr. 31 1999 177 190
16. 1 complex from the yeast Saccharomyces cerevisiae with an antibody Fv fragment Structure 8 2000 669 684 (Pubitemid 30409318)
17. 1 in complex with famoxadone: the role of aromatic-aromatic interaction in inhibition Biochemistry 41 2002 11692 11702
18. i site Biochemistry 42 2003 9067 9080 (Pubitemid 36935415)
19. o site inhibitor bound J. Biol. Chem. 278 2003 31303 31311 (Pubitemid 36994649)
20. 1 complex J. Mol. Biol. 341 2004 281 302 (Pubitemid 39090651)
21. Solmaz S.R., and Hunte C. Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer J. Biol. Chem. 283 2008 17542 17549
22. Soriano G.M., Smith J.L., and Cramer W.A. Cytochrome f A. Messerschmidt, R. Huber, K. Wieghardt, T. Poulos, Handbook of Metalloproteins 2001 Wiley London, UK 172 181
23. Carrell C.J., Zhang H., Cramer W.A., and Smith J.L. Biological identity and diversity in photosynthesis and respiration: structure of the lumen-side domain of the chloroplast Rieske protein Structure 5 1997 1613 1625 (Pubitemid 28051975)
24. 6f complex Ann. Rev. Biochem. 75 2006 769 790 (Pubitemid 44118052)
25. A. Azzi, U. Brodbeck, and P. Zahler Membrane Proteins: A Laboratory Manual 1981 Springer-Verlag Berlin, Germany
26. Nussberger S., Dorr K., Wang D.N., and Kuhlbrandt W. Lipid-protein interactions in crystals of the plant light-harvesting complex J. Mol. Biol. 234 1993 347 356 (Pubitemid 23361206)
27. Cartailler J.P., and Luecke H. X-ray crystallographic analysis of lipid-protein interactions in the bacteriorhodopsin purple membrane Annu. Rev. Biophys. Biomol. Struct. 32 2003 285 310 (Pubitemid 37056231)
28. Gantar M., Berry J.P., Thomas S., Wang M., Perez R., and Rein K.S. Allelopathic activity among Cyanobacteria and microalgae isolated from Florida freshwater habitats FEMS Microbiol. Ecol. 64 2008 55 64 (Pubitemid 351365093)
29. Hite R.K., Li Z.L., and Walz T. Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals EMBO J. 29 2010 1652 1658
30. Escriba P.V., Wedegaertner P.B., Goni F.M., and Vogler O. Lipid-protein interactions in GPCR-associated signaling Biochim. Biophys. Acta 1768 2007 836 852 (Pubitemid 46452537)
31. 2-adrenergic receptor Structure 16 2008 897 905 (Pubitemid 351778384)
32. + channel and its dependence on the lipid membrane Proc. Natl Acad. Sci. USA 102 2005 15441 15446 (Pubitemid 41528076)
33. + channel KvAP in DPhPC and POPE:POPG decane lipid bilayers J. Mol. Biol. 390 2009 902 912
34. Butterwick J.A., and MacKinnon R. Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP J. Mol. Biol. 403 2010 591 606
35. McAuley K.E., Fyfe P.K., Ridge J.P., Isaacs N.W., Cogdell R.J., and Jones M.R. Structural details of an interaction between cardiolipin and an integral membrane protein Proc. Natl Acad. Sci. USA 96 1999 14706 14711 (Pubitemid 30019704)
36. Camara-Artigas A., Brune D., and Allen J.P. Interaction between lipids and bacterial reaction centers determined by protein crystallography Proc. Natl Acad. Sci. USA 99 2002 11055 11060 (Pubitemid 34920878)
37. Fyfe P.K., Hughes A.V., Heathcote P., and Jones M.R. Proteins, chlorophylls and lipids: X-ray analysis of a three-way relationship Trends Plant Sci. 10 2005 275 282 (Pubitemid 40793513)
38. Jones M.R. Lipids in photosynthetic reaction centres: structural roles and functional holes Prog. Lipid Res. 46 2007 56 87
39. Wohri A.B., Wahlgren W.Y., Malmerberg E., Johansson L.C., Neutze R., and Katona G. Lipidic sponge phase crystal structure of a photosynthetic reaction center reveals lipids on the protein surface Biochemistry 48 2009 9831 9838
40. Guskov A., Kern J., Gabdulkhakov A., Broser M., Zouni A., and Saenger W. Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride Nat. Struct. Mol. Biol. 16 2009 334 342
41. 6f complex H. Wada, N. Murata, Lipids in Photosynthesis: Essential and Regulatory Functions 2009 Springer Dordrecht, The Netherlands 203 242
42. Umena Y., Kawakami K., Shen J.R., and Kamiya N. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å Nature 473 2011 55 60
43. Jordan P., Fromme P., Witt H.T., Klukas O., Saenger W., and Krauss N. Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution Nature 411 2001 909 917 (Pubitemid 32601481)
44. Shinzawa-Itoh K., Aoyama H., Muramoto K., Terada H., Kurauchi T., and Tadehara Y. Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase EMBO J. 26 2007 1713 1725 (Pubitemid 46480942)
45. Qin L., Hiser C., Mulichak A., Garavito R.M., and Ferguson-Miller S. Identification of conseved lipid/detergent binding site in a high resolution structure of the memebrane protein, cytochrome c oxidase Proc. Natl Acad. Sci. USA 103 2006 16117 16122
46. Qin L., Sharpe M.A., Garavito R.M., and Ferguson-Miller S. Conserved lipid-binding sites in membrane proteins: A focus on cytochrome c oxidase Curr. Opin. Struct. Biol. 17 2007 444 450 (Pubitemid 47451764)
47. Palsdottir H., and Hunte C. Lipids in membrane protein structures Biochim. Biophys. Acta 1666 2004 2 18 (Pubitemid 39425195)
48. Cramer W.A., Hasan S.S., and Yamashita E. The Q cycle of cytochrome bc complexes: a structure perspective Biochim. Biophys. Acta/Bioenergetics 1807 2011 788 802
49. Schutz M., Brugna M., Lebrun E., Baymann F., Huber R., and Stetter K.O. Early evolution of cytochrome bc complexes J. Mol. Biol. 300 2000 663 675
50. Saraste M. Location of haem-binding sites in the mitochondrial cytochrome b FEBS Lett. 166 1984 367 372
51. 6f complex: position of the cytochrome b hemes in the membrane Proc. Natl Acad. Sci. USA 81 1984 674 678 (Pubitemid 14199008)
52. 1 complex structure EMBO J 20 2001 6591 6600 (Pubitemid 33134190)
53. 1 complex FEBS Lett. 545 2003 39 46 (Pubitemid 36629634)
54. 1 complex Eur. J. Biochem. 190 1990 123 130 (Pubitemid 20183973)
55. Wenz T., Covian R., Hellwig P., Macmillan F., Meunier B., Trumpower B.L., and Hunte C. Mutational analysis of cytochrome b at the ubiquinol oxidation site of yeast complex III J. Biol. Chem. 282 2007 3977 3988 (Pubitemid 47084452)
56. 1 complex catalysis and supercomplex formation Biochim. Biophys. Acta 1787 2009 609 616
57. 6f complex of oxygenic photosynthesis Proc. Natl Acad. Sci. USA 100 2003 5160 5163 (Pubitemid 36542675)
58. 6f- Associated chlorophyll: structural and dynamic contribution to the different cytochrome functions Biochemistry 47 2008 5259 5265 (Pubitemid 351656969)
59. 6f turnover Biochemistry 37 1998 10395 10403 (Pubitemid 28357561)
60. 6f, as evidenced by the pH dependence of electron transfer in whole cells of Chlamydomonas reinhardtii Biochemistry 41 2002 7475 7482 (Pubitemid 34602466)
61. 1 complex account for the function of a dimeric complex? Biochim. Biophys. Acta 1777 2008 1001 1019
62. Fyfe P.K., Potter J.A., Cheng J., Williams C.M., Watson A.J., and Jones M.R. Structural responses to cavity-creating mutations in an integral membrane protein Biochemistry 46 2007 10461 10472 (Pubitemid 47417242)
63. 6f complex in tobacco Plant Physiol. 144 2007 1924 1935 (Pubitemid 47258095)
64. Hunte C., and Richers S. Lipids and membrane protein structures Curr. Opin. Struct. Biol. 18 2008 406 411
65. de Vitry C., Ouyang Y., Finazzi G., Wollman F.A., and Kallas T. The chloroplast Rieske iron-sulfur protein. At the crossroad of electron transport and signal transduction J. Biol. Chem. 279 2004 44621 44627 (Pubitemid 39430870)
66. Choquet Y., Zito F., Wostrikoff K., and Wollman F.A. Cytochrome f translation in Chlamydomonas chloroplast is autoregulated by its carboxyl-terminal domain Plant Cell 15 2003 1443 1454 (Pubitemid 36715184)
67. Iwai M., Takizawa K., Tokutsu R., Okamuro A., Takahashi Y., and MInagawa J. Isolation of the supercomplex that drives cyclic electron flow in photosynthesis Nature 464 2010 1210 1213
68. 1 from bovine heart mitochondria Biochemistry 46 2007 12579 12585 (Pubitemid 350060084)
69. n and n-side electron and proton transfer reactions P. Fromme, Photosynthetic Protein Complexes: A Structural Approach 2008 Wiley-VCH Weinheim, Germany 155 179
70. 2 treatment of spinach thylakoids Biochim. Biophys. Acta 635 1981 348 358
71. Unitt M.D., and Harwood J.L. Sidedness studies of thylakoid phosphatidylglycerol in higher plants Biochem. J. 228 1985 707 711
72. Gounaris K., Barber J., and Harwood J.L. The thylakoid membranes of higher plant chloroplasts Biochem. J. 237 1986 313 326
73. Hunte C. Specific protein-lipid interactions in membrane proteins Biochem. Soc. Trans. 33 2005 938 942 (Pubitemid 41659083)
74. 6f complex from Synechocystis PCC 6803 Res. Microbiol. 158 2007 45 50 (Pubitemid 46216776)
75. 1 complex from bovine heart Proc. Natl Acad. Sci. USA 95 1998 8026 8033 (Pubitemid 28326060)
76. 6f complex: unusual optical properties protect the complex against singlet oxygen Biophys. J. 88 2005 4178 4187 (Pubitemid 40991129)
77. 6f complex: new prosthetic groups, Q-space, and the "hors d'oeuvres hypothesis" for assembly of the complex Photosynth. Res. 85 2005 133 143
78. 6f complex R. Carpentier, Methods in Molecular Biology, Photosynthesis Research Protocols 2011 Humana Press Inc. Totowa, NJ
79. 6f complex J. Biol. Chem. 276 2001 38159 38165
80. Bernstein F.C., Koetzle T.F., Williams G.J., Meyer E.F. Jr., Brice M.D., and Rodgers J.R. The Protein Data Bank: a computer-based archival file for macromolecular structures J. Mol. Biol. 112 1977 535 542 (Pubitemid 8109216)
81. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680 (Pubitemid 24354800)
82. Emsley P., Lohkamp B., Scott W.G., and Cowtan K. Features and development of Coot Acta Crystallogr., Sect. D: Biol. Crystallogr. 66 2010 486 501
83. Sobolev V., Sorokine A., Prilusky J., Abola E.E., and Edelman M. Automated analysis of interatomic contacts in proteins Bioinformatics 15 1999 327 332 (Pubitemid 29213759)
84. Wessel D., and Fluegge U. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids Anal. Biochem. 138 1984 141 143 (Pubitemid 14146660)