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Volumn 92, Issue 10, 2007, Pages 3633-3642

Characterization of the solution structure of the M intermediate of photoactive yellow protein using high-angle solution x-ray scattering

Author keywords

[No Author keywords available]

Indexed keywords

PHOTOACTIVE YELLOW PROTEIN;

EID: 34247844505     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.097287     Document Type: Article
Times cited : (18)

References (50)
  • 1
    • 0022430790 scopus 로고
    • Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila
    • Meyer, T. E. 1985. Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila. Biochim. Biophys. Acta. 806:175-183.
    • (1985) Biochim. Biophys. Acta , vol.806 , pp. 175-183
    • Meyer, T.E.1
  • 2
    • 0027324441 scopus 로고
    • The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein
    • Sprenger, W. W., W. D. Hoff, J. P. Armitage, and K. J. Hellingwerf. 1993. The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein. J. Bacteriol. 175:3096-3104.
    • (1993) J. Bacteriol , vol.175 , pp. 3096-3104
    • Sprenger, W.W.1    Hoff, W.D.2    Armitage, J.P.3    Hellingwerf, K.J.4
  • 3
    • 0029110488 scopus 로고
    • 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: Unusual fold, active site, and chromophore
    • Borgstahl, G. E., D. R. Williams, and E. D. Getzoff. 1995. 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Biochemistry. 34:6278-6287.
    • (1995) Biochemistry , vol.34 , pp. 6278-6287
    • Borgstahl, G.E.1    Williams, D.R.2    Getzoff, E.D.3
  • 4
    • 0032568630 scopus 로고    scopus 로고
    • Photoactive yellow protein: A structural prototype for the three-dimensional fold of the PAS domain superfamily
    • Pellequer, J. L., K. A. Wager-Smith, S. A. Kay, and E. D. Getzoff. 1998. Photoactive yellow protein: a structural prototype for the three-dimensional fold of the PAS domain superfamily. Proc. Natl. Acad. Sci. USA. 95:5884-5890.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5884-5890
    • Pellequer, J.L.1    Wager-Smith, K.A.2    Kay, S.A.3    Getzoff, E.D.4
  • 5
  • 6
    • 0023152468 scopus 로고
    • Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin
    • Meyer, T. E., E. Yakali, M. A. Cusanovich, and G. Tollin. 1987. Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin. Biochemistry. 26:418-423.
    • (1987) Biochemistry , vol.26 , pp. 418-423
    • Meyer, T.E.1    Yakali, E.2    Cusanovich, M.A.3    Tollin, G.4
  • 8
    • 0029803844 scopus 로고    scopus 로고
    • Photoreaction cycle of photoactive yellow protein from Ectothiorhodospira halophila studied by low-temperature spectroscopy
    • Imamoto, Y., M. Kataoka, and F. Tokunaga. 1996. Photoreaction cycle of photoactive yellow protein from Ectothiorhodospira halophila studied by low-temperature spectroscopy. Biochemistry. 35:14047-14053.
    • (1996) Biochemistry , vol.35 , pp. 14047-14053
    • Imamoto, Y.1    Kataoka, M.2    Tokunaga, F.3
  • 9
    • 0031808072 scopus 로고    scopus 로고
    • New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: Picosecond transient absorption spectroscopy
    • Ujj, L., S. Devanathan, T. E. Meyer, M. A. Cusanovich, G. Tollin, and G. H. Atkinson. 1998. New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy. Biophys. J. 75:406-412.
    • (1998) Biophys. J , vol.75 , pp. 406-412
    • Ujj, L.1    Devanathan, S.2    Meyer, T.E.3    Cusanovich, M.A.4    Tollin, G.5    Atkinson, G.H.6
  • 10
    • 0035918547 scopus 로고    scopus 로고
    • Primary photoreaction of photoactive yellow protein studied by subpicosecond-nanosecond spectroscopy
    • Imamoto, Y., M. Kataoka, F. Tokunaga, T. Asahi, and H. Masuhara. 2001. Primary photoreaction of photoactive yellow protein studied by subpicosecond-nanosecond spectroscopy. Biochemistry. 40:6047-6052.
    • (2001) Biochemistry , vol.40 , pp. 6047-6052
    • Imamoto, Y.1    Kataoka, M.2    Tokunaga, F.3    Asahi, T.4    Masuhara, H.5
  • 13
    • 0034745934 scopus 로고    scopus 로고
    • Structure of the I1 early intermediate of photoactive yellow protein by FTIR spectroscopy
    • Brudler, R., R. Rammelsberg, T. T. Woo, E. D. Getzoff, and K. Gerwert. 2001. Structure of the I1 early intermediate of photoactive yellow protein by FTIR spectroscopy. Nat. Struct. Biol. 8:265-270.
    • (2001) Nat. Struct. Biol , vol.8 , pp. 265-270
    • Brudler, R.1    Rammelsberg, R.2    Woo, T.T.3    Getzoff, E.D.4    Gerwert, K.5
  • 14
    • 0035852878 scopus 로고    scopus 로고
    • Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation
    • Xie, A., L. Kelemen, J. Hendriks, B. J. White, K. J. Hellingwerf, and W. D. Hoff. 2001. Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation. Biochemistry. 40:1510-1517.
    • (2001) Biochemistry , vol.40 , pp. 1510-1517
    • Xie, A.1    Kelemen, L.2    Hendriks, J.3    White, B.J.4    Hellingwerf, K.J.5    Hoff, W.D.6
  • 15
    • 0029950952 scopus 로고    scopus 로고
    • Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein
    • Van Brederode, M. E., W. D. Hoff, I. H. van Stokkum, M. L. Groot, and K. J. Hellingwerf. 1996. Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein. Biophys. J. 71:365-380.
    • (1996) Biophys. J , vol.71 , pp. 365-380
    • Van Brederode, M.E.1    Hoff, W.D.2    van Stokkum, I.H.3    Groot, M.L.4    Hellingwerf, K.J.5
  • 16
    • 0035814881 scopus 로고    scopus 로고
    • Light induces destabilization of photoactive yellow protein
    • Ohishi, S., N. Shimizu, K. Mihara, Y. Imamoto, and M. Kataoka. 2001. Light induces destabilization of photoactive yellow protein. Biochemistry. 40:2854-2859.
    • (2001) Biochemistry , vol.40 , pp. 2854-2859
    • Ohishi, S.1    Shimizu, N.2    Mihara, K.3    Imamoto, Y.4    Kataoka, M.5
  • 17
    • 33646193715 scopus 로고    scopus 로고
    • Conformational changes of PYP monitored by diffusion coefficient: Effect of N-terminal alpha-helices
    • Khan, J. S., Y. Imamoto, M. Harigai, M. Kataoka, and M. Terazima. 2006. Conformational changes of PYP monitored by diffusion coefficient: effect of N-terminal alpha-helices. Biophys. J. 90:3686-3693.
    • (2006) Biophys. J , vol.90 , pp. 3686-3693
    • Khan, J.S.1    Imamoto, Y.2    Harigai, M.3    Kataoka, M.4    Terazima, M.5
  • 20
    • 0036685014 scopus 로고    scopus 로고
    • Effect of organic anions on the photoreaction of photoactive yellow protein
    • Shimizu, N., H. Kamikubo, K. Mihara, Y. Imamoto, and M. Kataoka. 2002. Effect of organic anions on the photoreaction of photoactive yellow protein. J. Biochem. (Tokyo). 132:257-263.
    • (2002) J. Biochem. (Tokyo) , vol.132 , pp. 257-263
    • Shimizu, N.1    Kamikubo, H.2    Mihara, K.3    Imamoto, Y.4    Kataoka, M.5
  • 21
  • 22
    • 0037137227 scopus 로고    scopus 로고
    • Light-induced global conformational change of photoactive yellow protein in solution
    • Imamoto, Y., H. Kamikubo, M. Harigai, N. Shimizu, and M. Kataoka. 2002. Light-induced global conformational change of photoactive yellow protein in solution. Biochemistry. 41:13595-13601.
    • (2002) Biochemistry , vol.41 , pp. 13595-13601
    • Imamoto, Y.1    Kamikubo, H.2    Harigai, M.3    Shimizu, N.4    Kataoka, M.5
  • 23
    • 0345707600 scopus 로고    scopus 로고
    • Role of an N-terminal loop in the secondary structural change of photoactive yellow protein
    • Harigai, M., Y. Imamoto, H. Kamikubo, Y. Yamazaki, and M. Kataoka. 2003. Role of an N-terminal loop in the secondary structural change of photoactive yellow protein. Biochemistry. 42:13893-13900.
    • (2003) Biochemistry , vol.42 , pp. 13893-13900
    • Harigai, M.1    Imamoto, Y.2    Kamikubo, H.3    Yamazaki, Y.4    Kataoka, M.5
  • 26
    • 0033001996 scopus 로고    scopus 로고
    • Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing
    • Svergun, D. I. 1999. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76:2879-2886.
    • (1999) Biophys. J , vol.76 , pp. 2879-2886
    • Svergun, D.I.1
  • 27
    • 0035010533 scopus 로고    scopus 로고
    • Determination of domain structure of proteins from X-ray solution scattering
    • Svergun, D. I., M. V. Petoukhov, and M. H. J. Koch. 2001. Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 80:2946-2953.
    • (2001) Biophys. J , vol.80 , pp. 2946-2953
    • Svergun, D.I.1    Petoukhov, M.V.2    Koch, M.H.J.3
  • 28
    • 0034613196 scopus 로고    scopus 로고
    • Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron x-ray solution scattering
    • Funari, S. S., G. Rapp, M. Perbandt, K. Dierks, M. Vallazza, C. Betzel, V. A. Erdmann, and D. I. Svergun. 2000. Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron x-ray solution scattering. J. Biol. Chem. 275:31283-31288.
    • (2000) J. Biol. Chem , vol.275 , pp. 31283-31288
    • Funari, S.S.1    Rapp, G.2    Perbandt, M.3    Dierks, K.4    Vallazza, M.5    Betzel, C.6    Erdmann, V.A.7    Svergun, D.I.8
  • 29
    • 0035946936 scopus 로고    scopus 로고
    • Direct observation of three conformations of MutS protein regulated by adenine nucleotides
    • Kato, R., M. Kataoka, H. Kamikubo, and S. Kuramitsu. 2001. Direct observation of three conformations of MutS protein regulated by adenine nucleotides. J. Mol. Biol. 309:227-238.
    • (2001) J. Mol. Biol , vol.309 , pp. 227-238
    • Kato, R.1    Kataoka, M.2    Kamikubo, H.3    Kuramitsu, S.4
  • 30
    • 0016818864 scopus 로고
    • A "block" approach to the study of highly helical proteins by x-ray scattering in solution
    • Fedorov, B. A. 1975. A "block" approach to the study of highly helical proteins by x-ray scattering in solution. J. Mol. Biol. 98:341-353.
    • (1975) J. Mol. Biol , vol.98 , pp. 341-353
    • Fedorov, B.A.1
  • 31
    • 0022703901 scopus 로고
    • X-ray scattering study on hemoglobin solution with synchrotron radiation: A simple analysis of scattering profile at moderate angles in terms of arrangement of subunits
    • Ueki, T., Y. Inoko, M. Kataoka, Y. Amemiya, and Y. Hiragi. 1986. X-ray scattering study on hemoglobin solution with synchrotron radiation: a simple analysis of scattering profile at moderate angles in terms of arrangement of subunits. J. Biochem. (Tokyo). 99:1127-1136.
    • (1986) J. Biochem. (Tokyo) , vol.99 , pp. 1127-1136
    • Ueki, T.1    Inoko, Y.2    Kataoka, M.3    Amemiya, Y.4    Hiragi, Y.5
  • 32
    • 0029032691 scopus 로고
    • Structural characterization of the molten globule and native states of apomyoglobin by solution x-ray scattering
    • Kataoka, M., I. Nishii, T. Fujisawa, T. Ueki, F. Tokunaga, and Y. Goto. 1995. Structural characterization of the molten globule and native states of apomyoglobin by solution x-ray scattering. J. Mol. Biol. 249:215-228.
    • (1995) J. Mol. Biol , vol.249 , pp. 215-228
    • Kataoka, M.1    Nishii, I.2    Fujisawa, T.3    Ueki, T.4    Tokunaga, F.5    Goto, Y.6
  • 33
    • 84985665860 scopus 로고
    • On the interpretation and prediction of x-ray scattering profiles from biomolecules in solution
    • Pickover, C. A., and D. M. Engelman. 1982. On the interpretation and prediction of x-ray scattering profiles from biomolecules in solution. Biopolymers. 21:817-831.
    • (1982) Biopolymers , vol.21 , pp. 817-831
    • Pickover, C.A.1    Engelman, D.M.2
  • 34
    • 0030914406 scopus 로고    scopus 로고
    • Functional expression and site-directed mutagenesis of photoactive yellow protein
    • Mihara, K., O. Hisatomi, Y. Imamoto, M. Kataoka, and F. Tokunaga. 1997. Functional expression and site-directed mutagenesis of photoactive yellow protein. J. Biochem. (Tokyo). 121:876-880.
    • (1997) J. Biochem. (Tokyo) , vol.121 , pp. 876-880
    • Mihara, K.1    Hisatomi, O.2    Imamoto, Y.3    Kataoka, M.4    Tokunaga, F.5
  • 36
    • 0029185933 scopus 로고
    • CRYSOL - a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinate
    • Svergun, D. I., C. Baberato, and M. H. J. Koch. 1995. CRYSOL - a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinate. J. Appl. Crystallogr. 28:768-773.
    • (1995) J. Appl. Crystallogr , vol.28 , pp. 768-773
    • Svergun, D.I.1    Baberato, C.2    Koch, M.H.J.3
  • 37
    • 0043125483 scopus 로고    scopus 로고
    • Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation
    • Getzoff, E. D., K. N. Gutwin, and U. K. Genick. 2003. Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation. Nat. Struct. Biol. 10:663-668.
    • (2003) Nat. Struct. Biol , vol.10 , pp. 663-668
    • Getzoff, E.D.1    Gutwin, K.N.2    Genick, U.K.3
  • 39
    • 27144534241 scopus 로고    scopus 로고
    • Effect of salt and pH on the activation of photoactive yellow protein and gateway mutants Y98Q and Y98F
    • Borucki, B., J. A. Kyndt, C. P. Joshi, H. Otto, T. E. Meyer, M. A. Cusanovich, and M. P. Heyn. 2005. Effect of salt and pH on the activation of photoactive yellow protein and gateway mutants Y98Q and Y98F. Biochemistry. 44:13650-13663.
    • (2005) Biochemistry , vol.44 , pp. 13650-13663
    • Borucki, B.1    Kyndt, J.A.2    Joshi, C.P.3    Otto, H.4    Meyer, T.E.5    Cusanovich, M.A.6    Heyn, M.P.7
  • 40
    • 33749346005 scopus 로고    scopus 로고
    • The transient accumulation of the signaling state of photoactive yellow protein is controlled by the external pH
    • Borucki, B., C. P. Joshi, H. Otto, M. A. Cusanovich, and M. P. Heyn. 2006. The transient accumulation of the signaling state of photoactive yellow protein is controlled by the external pH. Biophys. J. 91:2991-3001.
    • (2006) Biophys. J , vol.91 , pp. 2991-3001
    • Borucki, B.1    Joshi, C.P.2    Otto, H.3    Cusanovich, M.A.4    Heyn, M.P.5
  • 41
    • 33645224079 scopus 로고    scopus 로고
    • pH-dependent equilibrium between long lived near-UV intermediates of photoactive yellow protein
    • Shimizu, N., Y. Imamoto, M. Harigai, H. Kamikubo, Y. Yamazaki, and M. Kataoka. 2006. pH-dependent equilibrium between long lived near-UV intermediates of photoactive yellow protein. J. Biol. Chem. 281:4318-4325.
    • (2006) J. Biol. Chem , vol.281 , pp. 4318-4325
    • Shimizu, N.1    Imamoto, Y.2    Harigai, M.3    Kamikubo, H.4    Yamazaki, Y.5    Kataoka, M.6
  • 42
    • 0026244076 scopus 로고
    • Small-angle scattering studies of disordered, porous and fractal systems
    • Schmidt, P. W. 1991. Small-angle scattering studies of disordered, porous and fractal systems. J. Appl. Crystallogr. 24:414-435.
    • (1991) J. Appl. Crystallogr , vol.24 , pp. 414-435
    • Schmidt, P.W.1
  • 43
    • 0030324821 scopus 로고    scopus 로고
    • X-ray solution scattering studies of protein folding
    • Kataoka, M., and Y. Goto. 1996. X-ray solution scattering studies of protein folding. Fold. Des. 1:107-114.
    • (1996) Fold. Des , vol.1 , pp. 107-114
    • Kataoka, M.1    Goto, Y.2
  • 44
    • 0034505693 scopus 로고    scopus 로고
    • Probing protein fine structures by wide angle solution x-ray scattering
    • Zhang, R., P. Thiyagarajan, and D. M. Tiede. 2000. Probing protein fine structures by wide angle solution x-ray scattering. J. Appl. Crystallogr. 33:565-568.
    • (2000) J. Appl. Crystallogr , vol.33 , pp. 565-568
    • Zhang, R.1    Thiyagarajan, P.2    Tiede, D.M.3
  • 45
    • 0037188386 scopus 로고    scopus 로고
    • Protein conformations explored by difference high-angle solution x-ray scattering: Oxidation state and temperature dependent changes in cytochrome c
    • Tiede, D. M., R. Zhang, and S. Seifert. 2002. Protein conformations explored by difference high-angle solution x-ray scattering: oxidation state and temperature dependent changes in cytochrome c. Biochemistry. 41:6605-6614.
    • (2002) Biochemistry , vol.41 , pp. 6605-6614
    • Tiede, D.M.1    Zhang, R.2    Seifert, S.3
  • 46
    • 1342302339 scopus 로고    scopus 로고
    • Conformational changes associated with protein-protein interactions
    • Goh, C. S., D. Milburn, and M. Gerstein. 2004. Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol. 14:104-109.
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 104-109
    • Goh, C.S.1    Milburn, D.2    Gerstein, M.3
  • 47
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar, S., B. Ma, C. J. Tsai, N. Sinha, and R. Nussinov. 2000. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9:10-19.
    • (2000) Protein Sci , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 48
    • 0035432947 scopus 로고    scopus 로고
    • Molecular recognition by induced fit: How fit is the concept?
    • Bosshard, H. R. 2001. Molecular recognition by induced fit: how fit is the concept? News Physiol. Sci. 16:171-173.
    • (2001) News Physiol. Sci , vol.16 , pp. 171-173
    • Bosshard, H.R.1
  • 49
    • 18144418170 scopus 로고    scopus 로고
    • Protein structural change upon ligand binding. Linear response theory
    • 94: article 078102
    • Ikeguchi, M., J. Ueno, M. Sato, and A. Kidera. 2005. Protein structural change upon ligand binding. Linear response theory. Phys. Rev. Lett. 94: article 078102.
    • (2005) Phys. Rev. Lett
    • Ikeguchi, M.1    Ueno, J.2    Sato, M.3    Kidera, A.4
  • 50
    • 0034835787 scopus 로고    scopus 로고
    • Evidence for large structural fluctuations of the photobleached intermediate of photoactive yellow protein in solution
    • Shiozawa, M., M. Yoda, N. Kamiya, N. Asakawa, J. Higo, Y. Inoue, and M. Sakurai. 2001. Evidence for large structural fluctuations of the photobleached intermediate of photoactive yellow protein in solution. J. Am. Chem. Soc. 123:7445-7446.
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 7445-7446
    • Shiozawa, M.1    Yoda, M.2    Kamiya, N.3    Asakawa, N.4    Higo, J.5    Inoue, Y.6    Sakurai, M.7


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