메뉴 건너뛰기




Volumn 80, Issue 10, 2012, Pages 2384-2396

Crystal structure of the O intermediate of the Leu93→Ala mutant of bacteriorhodopsin

Author keywords

O intermediate; Proton pump; Retinal isomerization; Retinal protein; X ray crystallography

Indexed keywords

ALANINE; ARGININE; BACTERIORHODOPSIN; CARBON; GLUTAMIC ACID; LEUCINE; LYSINE; OXYGEN; PROTON PUMP; RETINAL; WATER;

EID: 84865981364     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24124     Document Type: Article
Times cited : (22)

References (55)
  • 1
    • 0025292355 scopus 로고
    • Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy
    • Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, Downing KH.Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy.J Mol Biol 1990;213:899-929.
    • (1990) J Mol Biol , vol.213 , pp. 899-929
    • Henderson, R.1    Baldwin, J.M.2    Ceska, T.A.3    Zemlin, F.4    Beckmann, E.5    Downing, K.H.6
  • 2
    • 58149376459 scopus 로고    scopus 로고
    • Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin
    • Phatak P, Ghosh N, Yu H, Cui Q, Elstner M.Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin.Proc Natl Acad Sci USA 2008;105:19672-19677.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 19672-19677
    • Phatak, P.1    Ghosh, N.2    Yu, H.3    Cui, Q.4    Elstner, M.5
  • 3
    • 65249113392 scopus 로고    scopus 로고
    • Theoretical modeling of the O-intermediate structure of bacteriorhodopsin
    • Watanabe HC, Ishikura T, Yamato T.Theoretical modeling of the O-intermediate structure of bacteriorhodopsin.Proteins 2009;75:53-61.
    • (2009) Proteins , vol.75 , pp. 53-61
    • Watanabe, H.C.1    Ishikura, T.2    Yamato, T.3
  • 4
    • 79955667818 scopus 로고    scopus 로고
    • Water pathways in the bacteriorhodopsin proton pump
    • Bondar AN, Fischer S, Smith JC.Water pathways in the bacteriorhodopsin proton pump.J Membr Biol 2011;239:73-84.
    • (2011) J Membr Biol , vol.239 , pp. 73-84
    • Bondar, A.N.1    Fischer, S.2    Smith, J.C.3
  • 5
    • 0025299602 scopus 로고
    • The role of back-reactions and proton uptake during the N----O transition in bacteriorhodopsin's photocycle: a kinetic resonance Raman study
    • Ames JB, Mathies RA.The role of back-reactions and proton uptake during the N----O transition in bacteriorhodopsin's photocycle: a kinetic resonance Raman study.Biochemistry 1990;29:7181-7190.
    • (1990) Biochemistry , vol.29 , pp. 7181-7190
    • Ames, J.B.1    Mathies, R.A.2
  • 6
    • 0035498345 scopus 로고    scopus 로고
    • Charge motion during the photocycle of bacteriorhodopsin
    • Der A, Keszthelyi L.Charge motion during the photocycle of bacteriorhodopsin.Biochemistry (Mosc) 2001;66:1234-1248.
    • (2001) Biochemistry (Mosc) , vol.66 , pp. 1234-1248
    • Der, A.1    Keszthelyi, L.2
  • 7
    • 34250796827 scopus 로고    scopus 로고
    • Studies of the bacteriorhodopsin photocycle without the use of light: clues to proton transfer coupled reactions
    • Lanyi JK.Studies of the bacteriorhodopsin photocycle without the use of light: clues to proton transfer coupled reactions.J Mol Microbiol Biotechnol 2007;12:210-217.
    • (2007) J Mol Microbiol Biotechnol , vol.12 , pp. 210-217
    • Lanyi, J.K.1
  • 9
    • 0036971196 scopus 로고    scopus 로고
    • Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal
    • Schobert B, Cupp-Vickery J, Hornak V, Smith S, Lanyi J.Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal.JMol Biol 2002;321:715-726.
    • (2002) JMol Biol , vol.321 , pp. 715-726
    • Schobert, B.1    Cupp-Vickery, J.2    Hornak, V.3    Smith, S.4    Lanyi, J.5
  • 10
    • 0036452022 scopus 로고    scopus 로고
    • Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin
    • Matsui Y, Sakai K, Murakami M, Shiro Y, Adachi S, Okumura H, Kouyama T.Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin.JMol Biol 2002;324:469-481.
    • (2002) JMol Biol , vol.324 , pp. 469-481
    • Matsui, Y.1    Sakai, K.2    Murakami, M.3    Shiro, Y.4    Adachi, S.5    Okumura, H.6    Kouyama, T.7
  • 11
    • 0034632821 scopus 로고    scopus 로고
    • Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin
    • Royant A, Edman K, Ursby T, Pebay-Peyroula E, Landau EM, Neutze R.Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin.Nature 2000;406:645-648.
    • (2000) Nature , vol.406 , pp. 645-648
    • Royant, A.1    Edman, K.2    Ursby, T.3    Pebay-Peyroula, E.4    Landau, E.M.5    Neutze, R.6
  • 12
    • 0346366810 scopus 로고    scopus 로고
    • Crystal structure of the L intermediate of bacteriorhodopsin: evidence for vertical translocation of a water molecule during the proton pumping cycle
    • Kouyama T, Nishikawa T, Tokuhisa T, Okumura H.Crystal structure of the L intermediate of bacteriorhodopsin: evidence for vertical translocation of a water molecule during the proton pumping cycle.J Mol Biol 2004;335:531-546.
    • (2004) J Mol Biol , vol.335 , pp. 531-546
    • Kouyama, T.1    Nishikawa, T.2    Tokuhisa, T.3    Okumura, H.4
  • 13
    • 33845971819 scopus 로고    scopus 로고
    • Structural changes in the L photointermediate of bacteriorhodopsin
    • Lanyi JK, Schobert B.Structural changes in the L photointermediate of bacteriorhodopsin.J Mol Biol 2007;365:1379-1392.
    • (2007) J Mol Biol , vol.365 , pp. 1379-1392
    • Lanyi, J.K.1    Schobert, B.2
  • 14
    • 0033536594 scopus 로고    scopus 로고
    • Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution
    • Luecke H, Schobert B, Richter HT, Cartailler JP, Lanyi JK.Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution.Science 1999;286:255-261.
    • (1999) Science , vol.286 , pp. 255-261
    • Luecke, H.1    Schobert, B.2    Richter, H.T.3    Cartailler, J.P.4    Lanyi, J.K.5
  • 18
    • 0037466289 scopus 로고    scopus 로고
    • 2' intermediates of the photocycle
    • 2' intermediates of the photocycle.J Mol Biol 2003;328:439-450.
    • (2003) J Mol Biol , vol.328 , pp. 439-450
    • Lanyi, J.K.1    Schobert, B.2
  • 19
    • 3843096037 scopus 로고    scopus 로고
    • Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix
    • Takeda K, Matsui Y, Kamiya N, Adachi S, Okumura H, Kouyama T.Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix.J Mol Biol 2004;341:1023-1037.
    • (2004) J Mol Biol , vol.341 , pp. 1023-1037
    • Takeda, K.1    Matsui, Y.2    Kamiya, N.3    Adachi, S.4    Okumura, H.5    Kouyama, T.6
  • 20
    • 70349783811 scopus 로고    scopus 로고
    • Crystal structures of different substrates of bacteriorhodopsin's M intermediate at various pH levels
    • Yamamoto M, Hayakawa N, Murakami M, Kouyama T.Crystal structures of different substrates of bacteriorhodopsin's M intermediate at various pH levels.J Mol Biol 2009;393:559-573.
    • (2009) J Mol Biol , vol.393 , pp. 559-573
    • Yamamoto, M.1    Hayakawa, N.2    Murakami, M.3    Kouyama, T.4
  • 21
    • 0034658269 scopus 로고    scopus 로고
    • Structure of the bacteriorhodopsin mutant F219L N intermediate revealed by electron crystallography
    • Vonck J.Structure of the bacteriorhodopsin mutant F219L N intermediate revealed by electron crystallography.EMBO J 2000;19:2152-2160.
    • (2000) EMBO J , vol.19 , pp. 2152-2160
    • Vonck, J.1
  • 22
    • 0038649076 scopus 로고    scopus 로고
    • Crystallographic structures of the M and N intermediates of bacteriorhodopsin: Assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff BASE
    • Schobert B, Brown LS, Lanyi JK.Crystallographic structures of the M and N intermediates of bacteriorhodopsin: Assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff BASE.J Mol Biol 2003;330:553-570.
    • (2003) J Mol Biol , vol.330 , pp. 553-570
    • Schobert, B.1    Brown, L.S.2    Lanyi, J.K.3
  • 24
    • 22544465841 scopus 로고    scopus 로고
    • Crystal structures of acid blue and alkaline purple forms of bacteriorhodopsin
    • Okumura H, Murakami M, Kouyama T.Crystal structures of acid blue and alkaline purple forms of bacteriorhodopsin.J Mol Biol 2005;351:481-495.
    • (2005) J Mol Biol , vol.351 , pp. 481-495
    • Okumura, H.1    Murakami, M.2    Kouyama, T.3
  • 25
    • 0025991585 scopus 로고
    • Replacement of leucine-93 by alanine or threonine slows down the decay of the N and O intermediates in the photocycle of bacteriorhodopsin: implications for proton uptake and 13-cis-retinal----all-trans-retinal reisomerization
    • Subramaniam S, Greenhalgh DA, Rath P, Rothschild KJ, Khorana HG.Replacement of leucine-93 by alanine or threonine slows down the decay of the N and O intermediates in the photocycle of bacteriorhodopsin: implications for proton uptake and 13-cis-retinal----all-trans-retinal reisomerization.Proc Natl Acad Sci USA 1991;88:6873-6877.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 6873-6877
    • Subramaniam, S.1    Greenhalgh, D.A.2    Rath, P.3    Rothschild, K.J.4    Khorana, H.G.5
  • 26
    • 0031042723 scopus 로고    scopus 로고
    • Electron diffraction studies of light-induced conformational changes in the Leu-93-->Ala bacteriorhodopsin mutant
    • Subramaniam S, Faruqi AR, Oesterhelt D, Henderson R.Electron diffraction studies of light-induced conformational changes in the Leu-93-->Ala bacteriorhodopsin mutant.Proc Natl Acad Sci USA 1997;94:1767-1772.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 1767-1772
    • Subramaniam, S.1    Faruqi, A.R.2    Oesterhelt, D.3    Henderson, R.4
  • 28
    • 17444435414 scopus 로고    scopus 로고
    • Late events in the photocycle of bacteriorhodopsin mutant L93A
    • Toth-Boconadi R, Keszthelyi L, Stoeckenius W.Late events in the photocycle of bacteriorhodopsin mutant L93A.Biophys J 2003;84:3848-3856.
    • (2003) Biophys J , vol.84 , pp. 3848-3856
    • Toth-Boconadi, R.1    Keszthelyi, L.2    Stoeckenius, W.3
  • 29
    • 0024730742 scopus 로고
    • Transformation of the archaebacterium Halobacterium volcanii with genomic DNA
    • Cline SW, Schalkwyk LC, Doolittle WF.Transformation of the archaebacterium Halobacterium volcanii with genomic DNA.J Bacteriol 1989;171:4987-4991.
    • (1989) J Bacteriol , vol.171 , pp. 4987-4991
    • Cline, S.W.1    Schalkwyk, L.C.2    Doolittle, W.F.3
  • 30
    • 0021668558 scopus 로고
    • A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance
    • Boeke JD, LaCroute F, Fink GR.A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance.Mol Gen Genet 1984;197:345-346.
    • (1984) Mol Gen Genet , vol.197 , pp. 345-346
    • Boeke, J.D.1    LaCroute, F.2    Fink, G.R.3
  • 31
    • 0015244581 scopus 로고
    • Rhodopsin-like protein from the purple membrane of Halobacterium halobium
    • Oesterhelt D, Stoeckenius W.Rhodopsin-like protein from the purple membrane of Halobacterium halobium.Nat New Biol 1971;233:149-152.
    • (1971) Nat New Biol , vol.233 , pp. 149-152
    • Oesterhelt, D.1    Stoeckenius, W.2
  • 32
    • 0032561127 scopus 로고    scopus 로고
    • A novel three-dimensional crystal of bacteriorhodopsin obtained by successive fusion of the vesicular assemblies
    • Takeda K, Sato H, Hino T, Kono M, Fukuda K, Sakurai I, Okada T, Kouyama T.A novel three-dimensional crystal of bacteriorhodopsin obtained by successive fusion of the vesicular assemblies.J Mol Biol 1998;283:463-474.
    • (1998) J Mol Biol , vol.283 , pp. 463-474
    • Takeda, K.1    Sato, H.2    Hino, T.3    Kono, M.4    Fukuda, K.5    Sakurai, I.6    Okada, T.7    Kouyama, T.8
  • 33
    • 0036215576 scopus 로고    scopus 로고
    • Optical monitoring of freeze-trapped reaction intermediates in protein crystals: a microspectrophotometer for cryogenic protein crystallography
    • Sakai K, Matsui Y, Kouyama T, Shiro Y, Adachi S-I.Optical monitoring of freeze-trapped reaction intermediates in protein crystals: a microspectrophotometer for cryogenic protein crystallography.J Appl Crystallogr 2002;35:270-273.
    • (2002) J Appl Crystallogr , vol.35 , pp. 270-273
    • Sakai, K.1    Matsui, Y.2    Kouyama, T.3    Shiro, Y.4    Adachi, S.-I.5
  • 34
    • 0024282741 scopus 로고
    • Bacteriorhodopsin photoreaction: identification of a long-lived intermediate N (P,R350) at high pH and its M-like photoproduct
    • Kouyama T, Nasuda-Kouyama A, Ikegami A, Mathew MK, Stoeckenius W.Bacteriorhodopsin photoreaction: identification of a long-lived intermediate N (P, R350) at high pH and its M-like photoproduct.Biochemistry 1988;27:5855-5863.
    • (1988) Biochemistry , vol.27 , pp. 5855-5863
    • Kouyama, T.1    Nasuda-Kouyama, A.2    Ikegami, A.3    Mathew, M.K.4    Stoeckenius, W.5
  • 35
    • 56249149226 scopus 로고    scopus 로고
    • Effect of xenon binding to a hydrophobic cavity on the proton pumping cycle in bacteriorhodopsin
    • Hayakawa N, Kasahara T, Hasegawa D, Yoshimura K, Murakami M, Kouyama T.Effect of xenon binding to a hydrophobic cavity on the proton pumping cycle in bacteriorhodopsin.J Mol Biol 2008;384:812-823.
    • (2008) J Mol Biol , vol.384 , pp. 812-823
    • Hayakawa, N.1    Kasahara, T.2    Hasegawa, D.3    Yoshimura, K.4    Murakami, M.5    Kouyama, T.6
  • 37
    • 84946063031 scopus 로고
    • An improved algorithm for computing the singular value decomposition
    • Chan TF.An improved algorithm for computing the singular value decomposition.ACM Trans Math Softw 1982;8:72-83.
    • (1982) ACM Trans Math Softw , vol.8 , pp. 72-83
    • Chan, T.F.1
  • 38
    • 0000614826 scopus 로고    scopus 로고
    • An algorithm for automatic indexing of oscillation images using Fourier analysis
    • Steller I, Bolotovsky R, Rossmann MG.An algorithm for automatic indexing of oscillation images using Fourier analysis.J Appl Crystallogr 1997;30:1036-1040.
    • (1997) J Appl Crystallogr , vol.30 , pp. 1036-1040
    • Steller, I.1    Bolotovsky, R.2    Rossmann, M.G.3
  • 39
    • 0030841590 scopus 로고    scopus 로고
    • Collaborative computational project, number 4: providing programs for protein crystallography
    • Dodson EJ, Winn M, Ralph A.Collaborative computational project, number 4: providing programs for protein crystallography.Methods Enzymol 1997;277:620-633.
    • (1997) Methods Enzymol , vol.277 , pp. 620-633
    • Dodson, E.J.1    Winn, M.2    Ralph, A.3
  • 42
    • 0037432333 scopus 로고    scopus 로고
    • Water molecule rearrangements around Leu93 and Trp182 in the formation of the L intermediate in bacteriorhodopsin's photocycle
    • Maeda A, Tomson FL, Gennis RB, Balashov SP, Ebrey TG.Water molecule rearrangements around Leu93 and Trp182 in the formation of the L intermediate in bacteriorhodopsin's photocycle.Biochemistry 2003;42:2535-2541.
    • (2003) Biochemistry , vol.42 , pp. 2535-2541
    • Maeda, A.1    Tomson, F.L.2    Gennis, R.B.3    Balashov, S.P.4    Ebrey, T.G.5
  • 43
    • 0030069626 scopus 로고    scopus 로고
    • Titration of aspartate-85 in bacteriorhodopsin: what it says about chromophore isomerization and proton release
    • Balashov SP, Imasheva ES, Govindjee R, Ebrey TG.Titration of aspartate-85 in bacteriorhodopsin: what it says about chromophore isomerization and proton release.Biophys J 1996;70:473-481
    • (1996) Biophys J , vol.70 , pp. 473-481
    • Balashov, S.P.1    Imasheva, E.S.2    Govindjee, R.3    Ebrey, T.G.4
  • 44
    • 23944444834 scopus 로고    scopus 로고
    • Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state
    • Nishikawa T, Murakami M, Kouyama T.Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state.J Mol Biol 2005;352:319-328.
    • (2005) J Mol Biol , vol.352 , pp. 319-328
    • Nishikawa, T.1    Murakami, M.2    Kouyama, T.3
  • 46
    • 0030069626 scopus 로고    scopus 로고
    • Titration of aspartate-85 in bacteriorhodopsin: what it says about chromophore isomerization and proton release
    • Balashov SP, Imasheva ES, Govindjee R, Ebrey TG.Titration of aspartate-85 in bacteriorhodopsin: what it says about chromophore isomerization and proton release.Biophys J 1996;70:473-481.
    • (1996) Biophys J , vol.70 , pp. 473-481
    • Balashov, S.P.1    Imasheva, E.S.2    Govindjee, R.3    Ebrey, T.G.4
  • 47
    • 0031007935 scopus 로고    scopus 로고
    • Reducing the flexibility of retinal restores a wild-type-like photocycle in bacteriorhodopsin mutants defective in protein-retinal coupling
    • Delaney JK, Yahalom G, Sheves M, Subramaniam S.Reducing the flexibility of retinal restores a wild-type-like photocycle in bacteriorhodopsin mutants defective in protein-retinal coupling.Proc Natl Acad Sci USA 1997;94:5028-5033.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 5028-5033
    • Delaney, J.K.1    Yahalom, G.2    Sheves, M.3    Subramaniam, S.4
  • 48
    • 0021934245 scopus 로고
    • Photoconversion from the light-adapted to the dark-adapted state of bacteriorhodopsin
    • Kouyama T, Bogomolni RA, Stoeckenius W.Photoconversion from the light-adapted to the dark-adapted state of bacteriorhodopsin.Biophys J 1985;48:201-208.
    • (1985) Biophys J , vol.48 , pp. 201-208
    • Kouyama, T.1    Bogomolni, R.A.2    Stoeckenius, W.3
  • 50
    • 0026577708 scopus 로고
    • Temperature and pH sensitivity of the O(640) intermediate of the bacteriorhodopsin photocycle
    • Chizhov I, Engelhard M, Chernavskii DS, Zubov B, Hess B.Temperature and pH sensitivity of the O(640) intermediate of the bacteriorhodopsin photocycle.Biophys J 1992;61:1001-1006.
    • (1992) Biophys J , vol.61 , pp. 1001-1006
    • Chizhov, I.1    Engelhard, M.2    Chernavskii, D.S.3    Zubov, B.4    Hess, B.5
  • 52
    • 80053324109 scopus 로고    scopus 로고
    • Crystal structures of an O-like blue form and an anion-free yellow form of pharaonis halorhodopsin
    • Kanada S, Takeguchi Y, Murakami M, Ihara K, Kouyama T.Crystal structures of an O-like blue form and an anion-free yellow form of pharaonis halorhodopsin.J Mol Biol 2011;413:162-176.
    • (2011) J Mol Biol , vol.413 , pp. 162-176
    • Kanada, S.1    Takeguchi, Y.2    Murakami, M.3    Ihara, K.4    Kouyama, T.5
  • 53
    • 0033534585 scopus 로고    scopus 로고
    • Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation
    • Ihara K, Umemura T, Katagiri I, Kitajima-Ihara T, Sugiyama Y, Kimura Y, Mukohata Y.Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation.J Mol Biol 1999;285:163-174.
    • (1999) J Mol Biol , vol.285 , pp. 163-174
    • Ihara, K.1    Umemura, T.2    Katagiri, I.3    Kitajima-Ihara, T.4    Sugiyama, Y.5    Kimura, Y.6    Mukohata, Y.7
  • 54
    • 77949330298 scopus 로고    scopus 로고
    • Crystal structure of the light-driven chloride pump halorhodopsin from Natronomonas pharaonis
    • Kouyama T, Kanada S, Takeguchi Y, Narusawa A, Murakami M, Ihara K.Crystal structure of the light-driven chloride pump halorhodopsin from Natronomonas pharaonis.J Mol Biol 2010;396:564-579.
    • (2010) J Mol Biol , vol.396 , pp. 564-579
    • Kouyama, T.1    Kanada, S.2    Takeguchi, Y.3    Narusawa, A.4    Murakami, M.5    Ihara, K.6
  • 55
    • 0034687788 scopus 로고    scopus 로고
    • Time-resolved x-ray diffraction reveals multiple conformations in the M-N transition of the bacteriorhodopsin photocycle
    • Oka T, Yagi N, Fujisawa T, Kamikubo H, Tokunaga F, Kataoka M.Time-resolved x-ray diffraction reveals multiple conformations in the M-N transition of the bacteriorhodopsin photocycle.Proc Natl Acad Sci USA 2000;97:14278-14282.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 14278-14282
    • Oka, T.1    Yagi, N.2    Fujisawa, T.3    Kamikubo, H.4    Tokunaga, F.5    Kataoka, M.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.