uva-dare (digital academic repository) structure/function ... · protein:: protonation equilibrium...

UvA-DARE is a service provided by the library of the University of Amsterdam (http://dare.uva.nl)

UvA-DARE (Digital Academic Repository)

Structure/function relations in Photoactive Yellow Protein

van der Horst, M.A.

Link to publication

Citation for published version (APA):van der Horst, M. A. (2004). Structure/function relations in Photoactive Yellow Protein. Enschede: Print partnersIpskamp.

General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s),other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons).

Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, statingyour reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Askthe Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam,The Netherlands. You will be contacted as soon as possible.

Download date: 26 Jun 2020

https://dare.uva.nl/personal/pure/en/publications/structurefunction-relations-in-photoactive-yellow-protein(70864579-0a4f-4fc7-a65f-1f7e882b101a).html

References s

References s

Ahmad,, M. and A. R. Cashmore (1993). HY4 gene of A. thaliana encodes a protein with characteristics of a

blue-lightt photoreceptor. Nature 366(6451): 162-6.

Ahmad,, M., N. Grancher, M. Heil, R. C. Black, B. Giovani, P. Galland and D. Lardemer (2002). Action

spectrumm for cryptochrome-dependent hypocotyl growth inhibition in Arabidopsis. Plant Physiol

129(2):: 774-85.

Albert,, A. D„ A. Watts, P. Spooner, G. Groebner, J. Young and P. L. Yeagle (1997). A distance

measurementt between specific sites on the cytoplasmic surface of bovine rhodopsin in rod outer

segmentt disk membranes. Biochim Biophys Acta 1328(1): 74-82.

Amezcua,, C. A., S. M. Harper, J. Rutter and K. H. Gardner (2002). Structure and interactions of PAS kinase

N-terminall PAS domain: model for intramolecular kinase regulation. Structure (Camb) 10(10):

1349-61. .

Armitage,, J. P. and K. J. Hellingwerf (2003). Light-induced behavioral responses ('phototaxis') in

prokaryotes.. Photosynthesis Research 76(1-3): 145-155.

Aubert,, C, M. H. Vos, P. Mathis, A. P. Eker and K. Brettel (2000). Intraprotein radical transfer during

photoactivationn of DNA photolyase. Nature 405(6786): 586-90.

Aulin-Erdtman,, G. and R. Sandn (1968). Contributions to lignin chemistry IX. Acta Chem Scand22: 1187-

1209. .

Baca,, M., G. E. Borgstahl, M. Boissinot, P. M. Burke, D. R. Williams, K. A. Slater and E. D. Getzoff

(1994),, Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-

hydroxycinnamyll chromophore and photocycle chemistry. Biochemistry 33(48): 14369-77.

Balashov,, S. P. and T. G. Ebrey (2001). Trapping and spectroscopic identification of the photointermediates

off bacteriorhodopsin at low temperatures. Photochem Photohiol 73(5): 453-62.

Balashov,, S. P., M. Sumi and N. Kamo (2000). The M intermediate of Pharaonis phoborhodopsin is

photoactive.. Biophys J78(6): 3150-9.

Ballario,, P., C. Talora, D. Galli, H. Linden and G. Macino (1998). Roles in dimerization and blue light

photoresponsee of the PAS and LOV domains of Neurospora crassa white collar proteins. Mol

MicrobiolMicrobiol 29(3): 719-29.

Barns,, S. M., C. F. Delwiche, J. D. Palmer and N. R, Pace (1996). Perspectives on archaeal diversity,

thermophilyy and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA

93(17):: 9188-93.

Beja,, O., L. Aravind, E. V. Koonin, M. T. Suzuki, A. Hadd, L. P. Nguyen, S. B. Jovanovich, C. M. Gates,

R,, A. Feldman, J. L. Spudich, E. N. Spudich and E. F. DeLong (2000). Bacterial rhodopsin:

evidencee for a new type of phototrophy in the sea. Science 289(5486): 1902-6.

Bieszke,, J. A., E. N. Spudich, K. L. Scott, K. A. Borkovich and J. L. Spudich (1999). A eukaryotic protein,

NOP-1,, binds retinal to form an archaeal rhodopsin-like photochemically reactive pigment.

BiochemistryBiochemistry 38(43): 14138-45.

118 8

References s

Borgstahl,, G. E., D. R. Williams and E. D. Getzoff (1995). 1.4 A structure of photoactive yellow protein, a

cytosolicc photoreceptor: unusual fold, active site, and chromophore. Biochemistry 34(19): 6278-

87. .

Borthwick,, H. A., Hendricks, S.B., Parker, M.W., Toole, E.H., Toole, V.K. (1952). A reversible

photoreactionn controlling seed germination. Proc Natl Acad Sci USA 38: 662-666.

Borucki,, B., H. Otto, C. P. Joshi, C. Gasperi, M. A. Cusanovich, S. Devanathan, G. Toilin and M. P. Heyn

(2003).. pH dependence of the photocycle kinetics of the E46Q mutant of photoactive yellow

protein:: Protonation equilibrium between 1-1 and 1-2 intermediates, chromophore deprotonation

byy hydroxyl uptake, and protonation relaxation of the dark state. Biochemistry 42(29): 8780-8790.

Braatsch,, S., M. Gomelsky, S. Kuphal and G. Klug (2002). A single flavoprotein, AppA, integrates both

redoxx and light signals in Rhodobacter sphaeroides. Mol Microbiol 45(3): 827-36.

Brasier,, M. D., O. R. Green, A. P. Jephcoat, A. K. Kleppe, M J. Van Kranendonk, J. F. Lindsay, A. Steele

andd N. V. Grassineau (2002). Questioning the evidence for Earth's oldest fossils. Nature

416(6876):: 76-81.

Briggs,, W. R. and E. Huala (1999). Blue-light photoreceptors in higher plants. Annu Rev Cell Dev Biol 15:

33-62. .

Briggs,, W. R. and M. A. Olney (2001). Photoreceptors in plant photomorphogenesis to date, five

phytochromes,, two cryptochromes, one phototropin, and one superchrome. Plant Physiol 125(1):

85-8. .

Brudler,, R., K. Hitomi, H. Daiyasu, H. Toh, K. Kucho, M. Ishiura, M. Kanehisa, V. A. Roberts, T. Todo, J.

A.. Tainer and E. D. Getzoff (2003). Identification of a new cryptochrome class. Structure,

function,, and evolution. Mol Cell 11(1): 59-67.

Brudler,, R„ R. Rammelsberg, T. T. Woo, E. D. Getzoff and K. Gerwert (2001). Structure of the II early

intermediatee of photoactive yellow protein by FTIR spectroscopy. Nat Struct Biol 8(3): 265-70.

Cashmore,, A. R., J. A. Jarillo, Y. J. Wu and D. Liu (1999). Cryptochromes: blue light receptors for plants

andd animals. Science 284(5415): 760-5.

Cervantes,, M. and F. J. Murill o (2002). Role for vitamin B(12) in light induction of gene expression in the

bacteriumm Myxococcus xanthus. J Bacteriol 184(8): 2215-24.

Changenet-Barret,, P., P. Plaza and M. M. Martin (2001). Primary events in the photoactive yellow protein

chromophoree in solution. Chemical Physics Letters 336(5-6): 439-444.

Chen,, E., T. Gensch, A. B. Gross, J. Hendriks, K. J. Hellingwerf and D. S. Kliger (2003a). Dynamics of

proteinn and chromophore structural changes in the photocycle of photoactive yellow protein

monitoredd by time-resolved optical rotatory dispersion. Biochemistry 42(7): 2062-71.

Chen,, E. F„ T. Gensch, A. B. Gross, J. Hendriks, K. J. Hellingwerf and D. S. Kliger (2003b). Dynamics of

proteinn and chromophore structural changes in the photocycle of photoactive yellow protein

monitoredd by time- resolved optical rotatory dispersion. Biochemistry 42(7): 2062-2071.

Christie,, J. M. and W. R. Briggs (2001). Blue light sensing in higher plants. J Biol Chem 276(15): 11457-

60. .

119 9

References s

Christie,, J. M., T. E. Swartz, R. A. Bogomolni and W. R. Briggs (2002). Phototropin LOV domains exhibit

distinctt roles in regulating photoreceptor function. Plant J 32(2): 205-19.

Clayton,, R. K. (1953). Studies in the phototaxis of Rhodospirillum rubrum. II. The relation between

phototaxiss and photosynthesis. Arch Mikrohiol 19(2): 125-40.

Cordfunke,, R., R. Kort, A. Pierik, B. Gobets, G. J. Koomen, J. W. Verhoeven and K. J. Hellingwerf (1998).

Trans/ciss (Z/E) photoisomerization of the chromophore of photoactive yellow protein is not a

prerequisitee for the initiation of the photocycle of this photoreceptor protein. Proc Natl Acad Sci

USAUSA 95(13): 7396-401.

Craven,, C. J., N. M. Derix, J. Hendriks, R. Boelens, K. J. Hellingwerf and R. KLaptein (2000). Probing the

naturee of the blue-shifted intermediate of photoactive yellow protein in solution by NMR:

Hydrogen-- deuterium exchange data and pH studies. Biochemistry 39(47): 14392-14399.

Crosson,, S. and K. Moffat (2001). Structure of a flavin-binding plant photoreceptor domain: insights into

light-mediatedd signal transduction. Proc Natl Acad Sci USA 98(6): 2995-3000.

Crosson.. S. and K. Moffat (2002). Photoexcited structure of a plant photoreceptor domain reveals a light-

drivenn molecular switch. Plant Cell 14(5): 1067-75.

Crosson,, S., S. Rajagopal and K. Moffat (2003). The LOV Domain Family: Photoresponsive Signaling

Moduless Coupled to Diverse Output Domains. Biochemistry 42(3): 2-10.

Cusanovich,, M. A. and T. E. Meyer (2003). Photoactive Yellow Protein: A Prototypic PAS Domain

Sensoryy Protein and Development of a Common Signaling Mechanism. Biochemistry 42(17):

4759-70. .

Davis,, S. J., A. V. Vener and R. D. Vierstra (1999). Bacteriophytochromes: phytochrome-like

photoreceptorss from nonphotosynthetic eubacteria. Science 286(5449): 2517-20.

Delaney,, J. K.., T. L. Brack, G. H. Atkinson, M. Ottolenghi, G. Steinberg and M. Sheves (1995). Primary

picosecondd molecular events in the photoreaction of the BR5.12 artificial bacteriorhodopsin

pigment.. Proc Natl Acad Sci USA 92(6): 2101-5.

Dencher,, N. A,, H. J. Sass and G. Büldt (2000). Water and bacteriorhodopsin: structure, dynamics, and

function.. Biochim Biophys Acta 1460(1): 192-203.

Derix,, N. M. (2004). PhD thesis, Utrecht University, Utrecht, The Netherlands.

Derix,, N. M., R. W. Wechselberger, M. A. Van Der Horst, K. J. Hellingwerf, R. Boelens, R. Kaptein and N.

A.. Van Nuland (2003). Lack of Negative Charge in the E46Q Mutant of Photoactive Yellow

Proteinn Prevents Partial Unfolding of the Blue-Shifted Intermediate. Biochemistry 42(49): 14501-

14506. .

Devanathan,, S., U. K. Genick, I. L. Canestrelli, T. E. Meyer, M. A. Cusanovich, E. D. Getzoff and G. Tollin

(1998).. New insights into the photocycle of Ectothiorhodospira halophila photoactive yellow

protein:: photorecovery of the long-lived photobleached intermediate in the MetlOOAla mutant.


Douglas,, R. H., J. C. Partridge, K. S. Dulai, D. M. Hunt, C. W. Mullineaux and P. H. Hynninen (1999).

Enhancedd retinal longwave sensitivity using a chlorophyll-derived photosensitiser in Malacosteus

niger,, a deep-sea dragon fish with far red bioluminescence. Vision Res 39(17): 2817-32.

120 0

References s

Dutta,, A. K., K. Kamada and K. Ohta (1996). Spectroscopic studies of nile red in organic solvents and

polymers.. Journal of Photochemistry and Photobiology a-Chemistry 93(!): 57-64.

Düx,, P., G. Rubinstenn, G. W. Vuister, R. Boelens, F. A. Mulder, K. Hard, W. D. Hoff, A. R. Kroon, W.

Crietaard,, K. J. Hellingwerf and R. Kaptein (1998). Solution structure and backbone dynamics of

thee photoactive yellow protein. Biochemistry 37(37): 12689-99.

Edman,, K.., P. Nollert, A. Royant, H. Belrhali, E. Pebay-Peyroula, J. Hajdu, R. Neutze and E. M. Landau

(1999).. High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin

photocycle.. Nature 401(6755): 822-6.

Engelmann,, T. W. (1 883). Bacterium photometricum. Ein Beitrag zur vergleichenden Physiologie des

Licht-undd Farbensinnes. Arch. PhysioI.(3Q): 95-124.

Fankhauser,, C. (2001). The phytochromes, a family of red/far-red absorbing photoreceptors. J Bio! Chem

276(15):: 11453-6.

Franklin,, K. A. and G. C. Whitelam (2004). Light signals, phytochromes and cross-talk with other

environmentall cues. J Exp Bot 55(395): 271-6.

Friedman,, N., S. Druckmann, J. Lanyi. R. Needleman, A. Lewis, M. Ottolenghi and M. Sheves (1994). A

covalentt link between the chromophore and the protein backbone of bacteriorhodopsin is not

requiredd for forming a photochemically active pigment analogous to the wild type. Biochemistry

33(8):: 1971-6.

Friedrich,, T., S. Geibel, R. Kalmbach, 1. Chizhov, K. Ataka, J. Heberle, M, Engelhard and E. Bamberg

(2002).. Proteorhodopsin is a light-driven proton pump with variable vectoriality. J Mol Biol

321(5):: 821-38.

Fuhrmann,, M., A. Stahlberg, E. Govorunova, S. Rank and P. Hegemann (2001). The abundant retinal

proteinn of the Chlamydomonas eye is not the photoreceptor for phototaxis and photophobic

responses.. J Cell Set 114(Pt 21): 3857-63.

Galland.. P. and N. Tolle (2003). Light-induced fluorescence changes in Phycomyces: evidence for blue

light-receptorr associated flavo-semiquinones. Planta 217(6): 971-82.

Galperin,, M. Y., A. N. Nikolskaya and E. V. (Coonin (2001). Novel domains of the prokaryotic two-

componentt signal transduction systems. FEMS Microbiol Lett 203(1): 11-21.

Ganter,, U. M., C. Longstaff, M. A. Pajares, R. R. Rando and F. Siebert (1991). Fourier transform infrared

studiess of active-site-methylated rhodopsin. Implications for chromophore-protein interaction,

transducinn activation, and the reaction pathway. Biophys J 59(3): 640-4.

Genick,, U. K., G. E. Borgstahl, K. Ng, Z. Ren, C. Pradervand, P. M. Burke, V. Srajer, T. Y. Teng, W.

Schildkamp,, D. E. McRee, K. Moffat and E. D. Getzoff (1997a). Structure of a protein photocycle

intermediatee by millisecond time- resolved crystallography. Science 275(5305): 1471-5.

Genick,, U. K., S. Devanathan, T. E. Meyer, I. L. Canestrelli, E. Williams, M. A. Cusanovich, G. Tollin and

E.. D. Getzoff (1997b). Active site mutants implicate key residues for control of color and light

cyclee kinetics of photoactive yellow protein. Biochemistry 36(1): 8-14.

Genick,, U. K., S. M. Soltis, P. Kuhn, I. L. Canestrelli and E. D. Getzoff (1998). Structure at 0.85 A

resolutionn of an early protein photocycle intermediate. Nature 392(6672): 206-9.

121 1

References s

Getzoff,, E. D., K. N. Gutwin and U. K. Genick (2003). Anticipatory active-site motions and chromophore

distortionn prime photoreceptor PYP for light activation. Nature Structural Biology 10(8): 663-668.

Giovani,, B., M. Byrdin, M. Ahmad and K. Brettel (2003). Light-induced electron transfer in a cryptochrome

blue-lightt photoreceptor. Nat Struct Biol 10(6): 489-90.

Giraud,, E., J. Fardoux, N. Fourrier, L. Hannibal, B. Genty, P. Bouyer, B. Dreyfus and A. Vermeglio (2002).

Bacteriophytochromee controls photosystem synthesis in anoxygenic bacteria. Nature 417(6885):

202-5. .

Gomelsky,, M. and S. Kaplan (1995). appA, a novel gene encoding a trans-acting factor involved in the

regulationn of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J Bacterial

177(16):: 4609-18.

Gomelsky,, M. and G. Klug (2002). BLUF: a novel FAD-binding domain involved in sensory transduction

inn microorganisms. Trends Biochem Sci 27(10): 497-500.

Gordeliy,, V. I., J. Labahn, R. Moukhametzianov, R. Efremov, J. Granzin, R. Schlesinger, G. Büldt, T.

Savopol,, A. J. Scheidig, J. P. Klare and M. Engelhard (2002). Molecular basis of transmembrane

signallingg by sensory rhodopsin II- transducer complex. Nature 419(6906): 484-7.

Gorham,, H. C., S. J. McGowan, P. R. Robson and D. A. Hodgson (1996). Light-induced carotenogenesis in

Myxococcuss xanthus: light-dependent membrane sequestration of ECF sigma factor CarQ by anti-

sigmaa factor CarR. Mol Microbiol 19(1): 171-86.

Groenhof,, G., M. F. Lensink, H. J. Berendsen, J. G. Snijders and A. E. Mark (2002). Signal transduction in

thee photoactive yellow protein. 1. Photon absorption and the isomerization of the chromophore.

ProteinsProteins 48(2): 202-11.

Groot,, M. L., L. J. van Wilderen, D, S. Larsen, M. A. van der Horst, I. H. van Stokkum, K. J. Hellingwerf

andd R. van Grondelle (2003). Initial steps of signal generation in photoactive yellow protein

revealedd with femtosecond mid-infrared spectroscopy. Biochemistry 42(34): 10054-9.

Haker,, A. (2002). The Photoactive Yellow Protein of Rhodobacter sphaeroides. Ph.D. Thesis, University of

Amsterdam,Amsterdam, Amsterdam, The Netherlands.

Haker,, A., J. Hendriks, T. Gensch, K. Hellingwerf and W. Crielaard (2000). Isolation, reconstitution and

functionall characterisation of the Rhodobacter sphaeroides photoactive yellow protein. FEBS Lett

486(1):: 52-6.

Haker,, A., J. Hendriks, I. H. van Stokkum, J. Heberle, K. J. Hellingwerf, W. Crielaard and T. Gensch

(2003).. The two photocycles of photoactive yellow protein from Rhodobacter sphaeroides. J Biol

ChemChem 278(10): 8442-51.

Hamada,, N., K. Mihara, Y. Imamoto, M. Kataoka, K. Yoshihara and F. Tokunaga (1998). 1998 Asian-

Pacificc Forum on Science and Technology - Optical Probing and Creation of Advance Photoactive

Materialss (abstract), Ishikawa.

Harper,, S. M., L. C. Neil and K. H. Gardner (2003). Structural basis of a phototropin light switch. Science

301(5639):: 1541-4.

122 2

References s

Hayashi,, S., E. Tajkhorshid, E. Pebay-Peyroula, A. Royant, E. M. Landau, J. Navarro and K. Schuiten

(2001).. Structural determinants of spectral tuning in retinal proteins- bacteriorhodopsin vs sensory

rhodopsinn II. Journal of Physical Chemistry B 105(41): 10124-10131.

Hellingwerf,, K., J. Hendriks and T. Gensch (2003). Photoactive Yellow Protein, A New Type of

Photoreceptorr Protein: Will This "Yellow Lab" Bring Us Where We Want to Go? J Phys Chem A

107(8):: 1082-1094.

Hellingwerf,, K. J. (2000), Key issues in the photochemistry and signalling-state formation of photosensor

proteins.. J Photochem Photobiol B 54(2-3): 94-102.

Hellingwerf,, K. J. (2002). The molecular basis of sensing and responding to light in microorganisms.

AntonieAntonie Van Leeuwenhoek SI(\-4): 51-9.

Hellingwerf,, K, J., Hendriks, J., van der Horst, M.A., Haker, A., Crielaard, W. and Gensch, Th. (2003). The

familyy of Photoactive Yellow Proteins, the Xanthopsins: From structure and mechanism of

photoactivationn to biological function.

Hellingwerf,, K. J., W. D. Hoff and W. Crielaard (1996). Photobiology of microorganisms: how

photosensorss catch a photon to initialize signalling. Mol Microbiol 21(4): 683-93.

Henderson,, R. and P. N. Unwin (1975). Three-dimensional model of purple membrane obtained by electron

microscopy.. Nature 257(5521): 28-32,

Hendriks,, J., T. Gensch, L. Hviid, M. A. van der Horst, K. J. Hellingwerf and J. J. van Thor (2002).

Transientt exposure of hydrophobic surface in the photoactive yellow protein monitored with Nile

Red.. Biophys J 82(3): 1632-43.

Hendriks,, J., W. D. Hoff, W. Crielaard and K. J. Hellingwerf (1999a). Protonation/deprotonation reactions

triggeredd by photoactivation of photoactive yellow protein from Ectothiorhodospira halophila. J

BiolBiol Chem 274(25): 17655-60.

Hendriks,, J., I. H, M. van Stokkum, W. Crielaard and K. J. Hellingwerf (1999b). Kinetics of and

intermediatess in a photocycle branching reaction of the photoactive yellow protein from

Ectothiorhodospiraa halophila. FEBS Lett 458(2): 252-6.

Hendriks,, J., I. H. M. van Stokkum and K. J. Hellingwerf (2003). Deuterium isotope effects in the

photocyclee transitions of the photoactive yellow protein. Biophys J84(2 Pt 1): 1180-91.

Herbst,, J., K. Heyne and R. Diller (2002). Femtosecond infrared spectroscopy of bacteriorhodopsin

chromophoree isomerization. Science 297(5582): 822-5.

Hitomi,, K., K. Okamoto, H. Daiyasu, H. Miyashita, S. Iwai, H. Toh, M. Ishiura and T. Todo (2000).

Bacteriall cryptochrome and photolyase: characterization of two photolyase-like genes of

Synechocystiss sp. PCC6803. Nucleic Acids Res 28(12): 2353-62.

Hoff,, W. D., B. Devreese, R. Fokkens, I. M. Nugteren-Roodzant, J. Van Beeumen, N. Nibbering and K. J.

Hellingwerff (1996). Chemical reactivity and spectroscopy of the thiol ester-linked p- coumaric

acidd chromophore in the photoactive yellow protein from Ectothiorhodospira halophila.


Hoff,, W. D., P. Düx, K. Hard, B. Devreese, I. M. Nugteren-Roodzant, W. Crielaard, R. Boelens, R. Kaptein,

J.. van Beeumen and K. J. Hellingwerf (1994a). Thiol ester-linked p-coumaric acid as a new

123 3

References s

photoactivee prosthetic group in a protein with rhodopsin-like photochemistry. Biochemistry

33(47):: 13959-62.

Hoff,, W. D., K. H. Jung and J. L. Spudich (1997a). Molecular mechanism of photosignaling by archaeal

sensoryy rhodopsins. Annu Rev Biophys Biomol Struct 26: 223-58.

Hoff,, W. D., S. L. S. Kwa, R. Van Grondelle and K. J. Hellingwerf (1992). Low-Temperature Absorbency

andd Fluorescence Spectroscopy of the Photoactive Yellow Protein from Ectothiorhodospira-

Halophila.. Photochemistry and Photobiology 56{4): 529-539.

Hoff,, W. D.. H. C. P. Matthijs, H. Schubert, W. Crielaard and K. J. Hellingwerf (1995). Rhodopsin(s) in

eubacteria.. Biophysical Chemistry 56(1-2): 193-199.

Hoff,, W. D., 1. H. M. Van Stokkum, J. Gural and K. J. Hellingwerf (1997b). Comparison of acid

denaturationn and light activation in the eubacterial blue-light receptor photoactive yellow protein.

BiochimicaBiochimica Et Biophysica Acta-Bioenirgetics 1322(2-3): 151 -162.

Hoff,, W. D., I. H. M van Stokkum, H. J. van Ramesdonk, M. E. van Brederode, A. M. Brouwer, J. C. Fitch,

T.. E. Meyer, R. van Grondelle and K. J. Hellingwerf (1994b). Measurement and global analysis of

thee absorbance changes in the photocycle of the photoactive yellow protein from

Ectothiorhodospiraa halophila. Biophys J 67'(4): 1691-705.

Hoff,, W. D., A. Xie, 1. H. M. Van Stokkum, X. J. Tang, J. Gural, A. R. Kroon and K. J. Hellingwerf (1999).

Globall conformational changes upon receptor stimulation in photoactive yellow protein.


Hou,, Y. W., A. M. Bardo, C. Martinez and D. A. Higgins (2000). Characterization of molecular scale

environmentss in polymer films by single molecule spectroscopy. Journal of Physical Chemistry B

104(2):: 212-219.

Huala,, E., P. W. Oeller, E. Liscum, I. S. Han, E. Larsen and W. R. Briggs (1997). Arabidopsis NPH1: a

proteinn kinase with a putative redox-sensing domain. Science 278(5346): 2120-3.

Hubschmann,, T., T. Borner, E. Hartmann and T. Lamparter (2001). Characterization of the Cphl holo-

phytochromee from Synechocystis sp. PCC 6803. Eur J Biochem 268(7): 2055-63.

Hughes,, J., T. Lamparter, F. Mittmann, E. Hartmann, W. Gartner, A. Wilde and T. Borner (1997). A

prokaryoticc phytochrome. Nature 386(6626): 663.

Hustede,, E., M. Liebergesell and H. G. Schlegel (1989). The Photophobic Response of Various Sulfur and

Nonsulfurr Purple Bacteria. Photochemistry and Photobiology 50(6): 809-815.

Im,, Y. J., S. H. Rho, C. M. Park, S. S. Yang, J. G. Kang, J. Y. Lee, P. S. Song and S. H. Eom (2002).

Crystall structure of a cyanobacterial phytochrome response regulator. Protein Sci 11(3): 614-24.

Imamoto,, Y., M. Kataoka and F. Tokunaga (1996). Photoreaction cycle of photoactive yellow protein from

Ectothiorhodospiraa halophila studied by low-temperature spectroscopy. Biochemistry 35(45):

14047-53. .

Imhoff,, J. F., J. Suling and R. Petri (1998). Phylogenetic relationships among the Chromatiaceae, their

taxonomiee reclassification and description of the new genera Allochromatium, Halochromatium,

Isochromatium,, Marichromatium, Thiococcus, Thiohalocapsa and Thermochromatium. Int J Syst

BacteriolBacteriol 48 Pt 4: 1129-43.

124 4

References s

Iseki,, M„ S. Matsunaga, A. Murakami, K. Ohno, K. Shiga, K. Yoshida, ML Sugai, T. Takahashi, T. Hori and

MLL Watanabe (2002). A blue-light-activated adenylyl cyclase mediates photoavoidance in Euglena

gracilis.. Nature 415(6875): 1047-51.

Iwata,, T., D. Nozaki, S. Tokutomi, T. Kagawa, M. Wada and H. Kandori (2003). Light-induced structural

changess in the LOV2 domain of Adiantum phytochrome3 studied by low-temperature FTIR and

UV-visiblee spectroscopy. Biochemistry 42(27): 8183-8191.

Jetten,, M. S., O. Sliekers, M. Kuypers, T. Dalsgaard, L. Van Niftrik , I. Cirpus, K. Van De Pas-Schoonen, G.

Lavik,, B. Thamdrup, D. Le Paslier, H. J. Op Den Camp, S. Hulth, L. P. Nielsen, W. Abma, K.

Third,, P. Engstrom, J. G. Kuenen, B. B. Jorgensen, D. E. Canfteld, J. S. Sinninghe Damste, N. P.

Revsbech,, J. Fuerst, J. Weissenbach, M. Wagner, I. Schmidt, M. Schmid and M. Strous (2003).

Anaerobicc ammonium oxidation by marine and freshwater planctomycete-like bacteria. Appl

MicrobiolMicrobiol Biotechnol 63(2): 107-14.

Jiang,, Z., L. R. Swem, B. G. Rushing, S. Devanathan, G. Tollin and C. E. Bauer (1999). Bacterial

photoreceptorphotoreceptor with similarity to photoactive yellow protein and plant phytochromes. Science

285(5426):: 406-9.

Jorissen,, H. J., B. Quest, I. Lindner, N. Tandeau de Marsac and W. Gartner (2002a). Phytochromes with

noncovalentlyy bound chromophores: the ability of apophytochromes to direct tetrapyrrole

photoisomerization.. Photochem Photobiol 75(5): 554-9.

Jorissen,, H. J., B. Quest, A. Remberg, T. Coursin, S. E. Braslavsky, K. Schaffner, N. T. de Marsac and W.

Gartnerr (2002b). Two independent, light-sensing two-component systems in a filamentous

cyanobacterium.cyanobacterium. Eur J Biochem 269(11): 2662-71.

Jung,, K. H., E. N. Spudich, V. D. Trivedi and J. L. Spudich (2001). An archaeal photosignal-transducing

modulee mediates phototaxis in Escherichia coli. J Bacterial 183(21): 6365-71.

Jung,, K. H., V. D. Trivedi and J. L. Spudich (2003). Demonstration of a sensory rhodopsin in eubacteria.

MolMol Microbiol 47(6): 1513-22.

Kandori,, H.. T. Iwata, J. Hendriks, A. Maeda and K. J. Hellingwerf (2000). Water structural changes

involvedd in the activation process of photoactive yellow protein. Biochemistry 39(27): 7902-9.

Kirschfeld,, K. and N. Franceschini (1977). Evidence for a sensitising pigment in fly photoreceptors. Nature

269(5627):: 386-90.

Kondou,, Y., N. Mogami, F. Hoshi, S. Kutsuna, M. Nakazawa, T. Sakurai, M. Matsui, T. Kaneko, S. Tabata,

I.. Tanaka and K. Manabe (2002). Bipolar localization of putative photoreceptor protein for

phototaxiss in thermophilic cyanobacterium Synechococcus elongatus. Plant Cell Physiol 43(12):

1585-8. .

Korenstein,, R. and B. Hess (1977). Hydration effects on the photocycle of bacteriorhodopsin in thin layers

off purple membrane. Nature 270(5633): 184-6.

Kort,, R. (1999). Studies on a bacterial photosensor. Ph.D. Thesis, University of Amsterdam, Amsterdam,

TheThe Netherlands.

Kort,, R., W. Crielaard, J. L. Spudich and K. J. Hellingwerf (2000). Color-sensitive motility and methanol

releasee responses in Rhodobacter sphaeroides. Journal of Bacteriology 182(11): 3017-3021.

125 5

References s

Kort,, R., W. D. HofF, M. Van West, A. R. Kroon, S. M. Hoffer, K. H. Vlieg, W. Crielaand, J. J. Van

Beeumenn and K. J. Hellingwerf (!996a). The xanthopsins: a new family of eubacterial blue-light

photoreceptors.. Embo J 15(13): 3209-18.

Kort,, R., R. B. Ravelli, F. Schone, D. Bourgeois, W. Crielaard, K. J. Hellingwerf and M. Wulff (2003).

Characterizationn of photocycle intermediates in crystalline photoactive yellow protein. Photochem

PhotobiolPhotobiol 78(2): 131-7.

Kort,, R., H. Vonk, X. Xu, W. D. Hoff, W. Crielaard and K. J. Hellingwerf (1996b). Evidence for trans-cis

isomerizationn of the p-coumaric acid chromophore as the photochemical basis of the photocycle

off photoactive yellow protein. FEBS Lett 382(1-2): 73-8.

Kraft,, B. J., S. Masuda, J. Kikuchi, V. Dragnea, G. Tollin, J. M. Zaleski and C. E. Bauer (2003).

Spectroscopicc and mutational analysis of the blue-light photoreceptor AppA: A novel photocycle

involvingg flavin stacking with an aromatic amino acid. Biochemistry 42(22): 6726-6734.

Kroon,, A. R., W. D. Hoff, H. P. Fennema, J. Gijzen, G. J. Koomen, J. W. Verhoeven, W. Crielaard and K.

J.. Hellingwerf (1996). Spectral tuning, fluorescence, and photoactivity in hybrids of photoactive

yelloww protein, reconstituted with native or modified chromophores. J Biol Chem 271(50): 31949-

56. .

Kumauchi,, M., N. Hamada, J. Sasaki and F. Tokunaga (2002). A role of methionine 100 in facilitating

PYP(M)-decayy process in the photocycle of photoactive yellow protein. J Biochem (Tokyo)

132(2):: 205-10.

Kyndt,, J. A., F. Vanrobaeys, J. C. Fitch, B. V. Devreese, T. E. Meyer, M. A. Cusanovich and J. J. Van

Beeumenn (2003). Heterologous Production of Halorhodospira halophila Holo-Photoactive Yellow

Proteinn through Tandem Expression of the Postulated Biosynthetic Genes. Biochemistry 42(4):

965-70. .

Laan,, W., M. A. van der Horst, 1. H. van Stokkum and K. J. Hellingwerf (2003). Initial characterization of

thee primary photochemistry of AppA, a blue-light-using flavin adenine dinucleotide-domain

containingg transcriptional antirepressor protein from Rhodobacter sphaeroides: a key role for

reversiblee intramolecular proton transfer from the flavin adenine dinucleotide chromophore to a

conservedd tyrosine? Photochem Photobiol 78(3): 290-7.

Lagarias,, J. C, Rapoport, H. (1980). Chromopeptides from phytochrome. The structure and linkage of the

PRR form of the phytochrome chromophore. J Am Chem Soc: 4821-4828.

Lamparter,, T., N. Michael, F. Mittmann and B. Esteban (2002). Phytochrome from Agrobacterium

tumefacienss has unusual spectral properties and reveals an N-terminal chromophore attachment

site.. Proc Natl Acad Sci U S A 99(18): 11628-33.

Lanyi,, J. and B. Schobert (2002). Crystallographic structure of the retinal and the protein after deprotonation

off the Schiff base: the switch in the bacteriorhodopsin photocycle. J Mol Biol 321(4): 727-37.

Larsen,, D. S., M. Vengris, I. H. M. van Stokkum, M. A. van der Horst, R. A. Cordfunke, K. J. Hellingwerf

andd R. van Grondelle (2003). Initial photo-induced dynamics of the photoactive yellow protein

chromophoree in solution. Chemical Physics Letters 369(5-6): 563-569.

126 6

References s

Li,, J. M., C. S. Russell and S. D. Cosloy (1989). The structure of the Escherichia coli hemB gene. Gene

75(1):: 177-84.

Lin,, C. (2002a). Blue light receptors and signal transduction. Plant Cell 14(Suppl): S207-25.

Lin,, C. (2002b). Phototropin blue light receptors and light-induced movement responses in plants. Sci STKE

2002(118):: E5.

Long,, J. C. and G. I. Jenkins (1998). Involvement of plasma membrane redox activity and calcium

homeostasiss in the UV-B and UV-A/blue light induction of gene expression in Arabidopsis. Plant

CellCell 10(12): 2077-86.

Losi,, A., E. Polverini, B. Quest and W. Gartner (2002). First evidence for phototropin-related blue-light

receptorss in prokaryotes. Biophys J 82(5): 2627-34.

Losi,, A., B. Quest and W. Gartner (2003). Listening to the blue: the time-resolved thermodynamics of the

bacteriall blue-light receptor YtvA and its isolated LOV domain. Photochemical &

PhotobiologicalPhotobiological Sciences 2(7): 759-766.

Luecke,, H., B. Schobert, J. K. Lanyi, E. N. Spudich and J. L. Spudich (2001). Crystal structure of sensory

rhodopsinn II at 2.4 angstroms: insights into color tuning and transducer interaction. Science

293(5534):: 1499-503.

Luecke,, H., B. Schobert, H. T. Richter, J. P. Cartailler and J. K. Lanyi (1999a). Structural changes in

bacteriorhodopsinn during ion transport at 2 angstrom resolution. Science 286(5438): 255-61.

Luecke,, H., B. Schobert, H. T. Richter, J. P. Cartailler and J. K. Lanyi (1999b). Structure of

bacteriorhodopsinn at 1.55 A resolution. J Mol Biol 291(4): 899-911.

Man,, D. L., W. W. Wang, G. Sabehi, L. Aravind, A. F. Post, R. Massana, E. N. Spudich, J. L. Spudich and

O.. Beja (2003). Diversification and spectral tuning in marine proteorhodopsins. Embo Journal

22(8):: 1725-1731.

Mano,, E., H. Kamikubo, Y. Imamoto and M. Kataoka (2003). Comparison of the photochemical reaction of

photoactivee yellow protein in crystal with reaction in solution. Spectroscopy-an International

JournalJournal 17(2-3): 345-353.

Masuda,, S. and C. E. Bauer (2002). AppA is a blue light photoreceptor that antirepresses photosynthesis

genee expression in Rhodobacter sphaeroides. Cell 110(5): 613-23.

Matsushita,, T., N. Mochizuki and A. Nagatani (2003). Dimers of the N-terminal domain of phytochrome B

aree functional in the nucleus. Nature 424(6948): 571-574.

McRee,, D. E., J. A. Tainer, T. E. Meyer, J. Van Beeumen, M. A. Cusanovich and E. D. Getzoff (1989).

Crystallographicc structure of a photoreceptor protein at 2.4 A resolution. Proc Natl Acad Sci US

AA 86(17): 6533-7.

Meyer,, T. E. (1985). Isolation and characterization of soluble cytochromes, ferredoxins and other

chromophoricc proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila.

BiochimBiochim Biophys Acta 806( 1): 175-83.

Meyer,, T. E., S. Devanathan, T. Woo, E. D.. Getzoff, G. Tollin and M. A. Cusanovich (2003). Site-specific

mutationss provide new insights into the origin of pH effects and alternative spectral forms in the

photoactivee yellow protein from Halorhodospira halophila. Biochemistry 42(11): 3319-25.

127 7

References s

Meyer,, T. E., G. Tollin, J. H. Hazzard and M. A. Cusanovich (1989). Photoactive yellow protein from the

purplee phototrophic bacterium, Ectothiorhodospira halophila. Quantum yield of photobleaching

andd effects of temperature, alcohols, glycerol, and sucrose on kinetics of photobleaching and

recovery.. Biophys J 56(3): 559-64.

Meyer,, T. E., E. Yakali, M. A. Cusanovich andG. Tollin (1987). Properties of a water-soluble, yellow

proteinn isolated from a halophilic phototrophic bacterium that has photochemical activity

analogouss to sensory rhodopsin. Biochemistry- 26(2): 418-23.

Mihara,, K., O. Hisatomi, Y. Imamoto, M. Kataoka and F. Tokunaga (1997). Functional expression and site-

directedd mutagenesis of photoactive yellow protein. J Biochem (Tokyo) 121(5): 876-80.

Miller ,, A., H. Leigeber, W. D. Hoff and K. J. Hellingwerf (1993). A Light-Dependent Branching-Reaction

inn the Photocycle of the Yellow Protein from Ectothiorhodospira-Halophila. Biochimica Et

BiophysicaBiophysica Acta 1141(2-3): 190-196.

Moffat,, K. (2003). The frontiers of time-resolved macromolecular crystallography: movies and chirped X-

rayy pulses. Faraday Discuss 122: 65-77; discussion 79-88.

Molina,, V. and M Merchan (2001). On the absorbance changes in the photocycle of the photoactive yellow

protein:: a quantum-chemical analysts. Proc Natl Acad Sci USA 98(8): 4299-304.

Neiss,, C. a. S., P (2003). Ab initio Quantum Chemical Investigation of the First Steps of the Photocycle of

Phototropin:: A Model Study. Photochemistry and Photobiohgy 77(1): 101-109.

Ng,, W. O., A. R. Grossman and D. Bhaya (2003). Multiple light inputs control phototaxis in Synechocystis

spp strain PCC6803. Journal of Bacteriology 185(5): 1599-1607.

Ni,, M., J. M. Tepperman and P. H. Quail (1999). Binding of phytochrome B to its nuclear signalling partner

PIF33 is reversibly induced by light. Nature 400(6746): 781-4.

Oesterhelt,, D. (1998). The structure and mechanism of the family of retinal proteins from halophilic

archaea.. Curr Opin Struct Biol 8(4): 489-500.

Oka,, T., N, Yagi, T. Fujisawa, H. Kamikubo, F. Tokunaga and M. Kataoka (2000). Time-resolved x-ray

diffractionn reveals multiple conformations in the M- N transition of the bacteriorhodopsin

photocycle.. Proc Natl Acad Sci U S A 91(26): 14278-82.

Okada,, T., O. P. Ernst, K. Palczewski and K. P. Hofmann (2001). Activation of rhodopsin: new insights

fromfrom structural and biochemical studies. Trends Biochem Sci 26(5): 318-24.

Okada,, T., Y. Fujiyoshi, M. Silow, J. Navarro, E. M. Landau and Y. Shichida (2002). Functional role of

internall water molecules in rhodopsin revealed by X- ray crystallography. Proc Natl Acad Sci US

AA 99(9): 5982-7.

Parker,, M. W., Hendricks, S.B., Borthwick, H. A., Went, F.W. (1949). Spectral sensitivities for leaf and

stemm growth of etiolated pea seedlings and their similarity to action spectra for photoperiodism.

AmAm J Bot 36: 194-204.

Pebay-Peyroula,, E., A. Royant, E. M. Landau and J. Navarro (2002). Structural basis for sensory rhodopsin

function.. Biochim Biophys Acta 1565(2): 196-205.

128 8

References s

Pebay-Peyroula,, E., G. Rummel, J. P. Rosenbusch and E. M. Landau (1997). X-ray structure of

bacteriorhodopsinn at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science

277(5332):: 1676-81.

Pellequer,, J. L., K. A. Wager-Smith, S. A. Kay and E. D. Getzoff (1998). Photoactive yellow protein: a

structurall prototype for the three- dimensional fold of the PAS domain superfamily. Proc Natl

AcadSciAcadSci USA 95(11): 5884-90.

Pepe,, I. M. (1999). Rhodopsin and phototransduction. J Photochem Photobiol B 48( 1): 1-10.

Perman,, B., S. Anderson, M. Schmidt and K. Moffat (2000). New techniques in fast time-resolved structure

determination.. Cell Mol Biol (Noisy-le-grand) 46(5): 895-913.

Perman,, B., V. Srajer, Z. Ren, T. Teng, C. Pradervand, T. Ursby, D. Bourgeois, F. Schotte, M. Wulff, R.

Kort,, K. Hellingwerf and K. Moffat (1998). Energy transduction on the nanosecond time scale:

earlyy structural events in a xanthopsin photocycle. Science 279(5358): 1946-50.

Premvardhan,, L. L., M. A. Van Der Horst, K. J. Hellingwerf and R. Van Grondelle (2003). Stark

Spectroscopyy on Photoactive Yellow Protein, E46Q, and a Nonisomerizing Derivative, Probes

Photo-Inducedd Charge Motion. Biophys 784(5): 3226-39.

Provencio,, I., G. Jiang, W. J. De Grip, W. P. Hayes and M. D. Rollag (1998). Melanopsin: An opsin in

melanophores,, brain, and eye. Proc Nad Acad Sci USA 95(1): 340-5.

Quail,, P. H. (1998). The phytochrome family: dissection of functional roles and signalling pathways among

familyy members. Philos Tram R Soc LondB Bio! Sci 353( 1374): 1399-403.

Quail,, P. H. (2002). Photosensory perception and signalling in plant cells: new paradigms? Cinr Opin Cell

BiolBiol 14(2): 180-8.

Quail,, P. H., M. T. Boylan, B. M. Parks, T. W. Short, Y. Xu and D. Wagner (1995). Phytochromes:

photosensoryy perception and signal transduction. Science 268(5211): 675-80.

Radding,, W., T. Romo and G. N. Phillips, Jr. (1999). Protein-assisted pericyclic reactions: an alternate

hypothesiss for the action of quantal receptors. Biophys J 77(6): 2920-9.

Ragatz,, L., Z. Y. Jiang, C. E. Bauer and H. Gest (1995). Macroscopic phototactic behavior of the purple

photosyntheticc bacterium Rhodospirillum centenum. Arch Microbiol 163(1): 1-6.

Rajagopal,, S. and K. Moffat (2003a). Crystal structure of a photoactive yellow protein from a sensor

histidinee kinase: Conformational variability and signal transduction. Proc Nad Acad Sci USA 31:

31. .

Rajagopal,, S. and K. Moffat (2003b). Crystal structure of a photoactive yellow protein from a sensor

histidinee kinase: Conformational variability and signal transduction (vol 100, pg 1649, 2003).

ProceedingsProceedings of the National Academy of Sciences of the United States of America 100(13): 8037-

8037. .

Raymond,, J. C. and W. R. Sistrom (1969). Ectothiorhodospira halophila: a new species of the genus

Ectothiorhodospira.Ectothiorhodospira. Arch. Microbiol. 69: 121-126.

Ren,, L.. C. H. Martin, K. J. Wise, N. B. Gillespie, H. Luecke, J. K. Lanyi, J. L. Spudich and R. R. Birge

(2001a).. Molecular mechanism of spectral tuning in sensory rhodopsin II. Biochemistry 40(46):

13906-14. .

129 9

References s

Ren,, Z., B. Perman, V. Srajer, T. Y. Teng, C. Pradervand, D. Bourgeois, F. Schotte, T. Ursby, R. Kort, M.

Wulfff and K. Moffat (2001b). A molecular movie at 1.8 A resolution displays the photocycle of

photoactivee yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds.


Rubinstenn,, G., G. W. Vuister, F. A. Mulder, P. E. Düx, R. Boelens, K. J. Hellingwerf and R. Kaptein

(1998).. Structural and dynamic changes of photoactive yellow protein during its photocycle in

solution.. Nat Struct Biol 5(7): 568-70.

Sakai,, T., T. Kagawa, M. Kasahara, T. E. Swartz, J. M. Christie, W. R. Briggs, M. Wada and K. Okada

(2001).. Arabidopsis npht and npll: blue light receptors that mediate both phototropism and

chloroplastt relocation. Proc Natl Acad Sci USA 98(12): 6969-74.

Sakamoto,, K. and A. Nagatani (1996). Nuclear localization activity of phytochrome B. Plant J 10(5): 859-

68. .

Salomon,, M., J. M. Christie, E. Knieb, U. Lempert and W. R. Briggs (2000). Photochemical and mutational

analysiss of the FMN-binding domains of the plant blue light receptor, phototropin. Biochemistry

39(31):: 9401-10.

Salomon,, M., W. Eisenreich, H. Durr, E. Schleicher, E. Knieb, V. Massey, W. Rudiger, F. Muller, A.

Bacherr and G. Richter (2001). An optomechanical transducer in the blue light receptor

phototropinn from Avena sativa. Proc Natl Acad Sci USA 98(22): 12357-61.

Sambrook,, J., E. F. Fritsch and T. Maniatis (1989). Molecular Cloning: A Laboratory Manual, 2nd edn.,

Coldd Spring Harbor Laboratory Press, Plainview, NY.

Sancar,, A. (1994). Structure and function of DNA photolyase. Biochemistry 33( 1): 2-9.

Sass,, H. J., I. W. Schachowa, G. Rapp, M. H. Koch, D. Oesterhelt, N. A. Dencher and G. Büldt (1997). The

tertiaryy structural changes in bacteriorhodopsin occur between M states: X-ray diffraction and

Fourierr transform infrared spectroscopy. Embo J 16(7): 1484-91.

Schlichting,, I., J. Berendzen, K. Chu, A. M. Stock, S. A. Maves, D. E. Benson, R. M. Sweet, D. Ringe, G.

A.. Petsko and S. G. Sligar (2000). The catalytic pathway of cytochrome p450cam at atomic

resolution.. Science 287(5458): 1615-22.

Schmidt,, M., S. Rajagopal, Z. Ren and K. Moffat (2003). Application of singular value decomposition to

thee analysis of time-resolved macromolecular X-ray data. Biophysical Journal84(3): 2112-2129.

Schmitz,, O., M. Katayama, S. B. Williams, T. Kondo and S. S. Golden (2000). CikA, a

bacteriophytochromee that resets the cyanobacterial circadian clock. Science 289(5480): 765-8.

Schobert,, B., J. Cupp-Vickery, V. Hornak, S. Smith and J. Lanyi (2002). Crystallographic structure of the K

intermediatee of bacteriorhodopsin: conservation of free energy after photoisomerization of the

retinal.. J Mol Biol 321(4): 715-26.

Schoenlein,, R. W., L. A. Peteanu, R. A. Mathies and C. V. Shank (1991). The first step in vision:

femtosecondd isomerization of rhodopsin. Science 254(5030): 412-5.

Schopf,, J. W. and B. M. Packer (1987). Early Archean (3.3-billion to 3.5-billion-year-old) microfossils from

Warrawoonaa Group, Australia. Science 237: 70-3.

130 0

References s

Schweiger,, U., J. Tittor and D. Oesterhelt (1994). Bacteriorhodopsin can function without a covalent

linkagee between retinal and protein. Biochemistry 33(2): 535-41.

Sergi,, A., M. Gaining, M. Ferrario and F. Buda (2001). Density Functional study of the photoactive yellow

protein'ss chromophore. Journal of Physical Chemistry B 105(19): 4386-4391.

Shalitin,, D., H. Yang, T. C. Mockler, M. Maymon, H. Guo, G. C. Whitelam and C. Lin (2002). Regulation

off Arabidopsis cryptochrome 2 by blue-light-dependent phosphorylation. Nature 417(6890): 763-

7. .

Shalitin,, D., X. Yu, M. Maymon, T. Mockler and C. Lin (2003). Blue Light-Dependent in Vivo and in Vitro

Phosphorylationn of Arabidopsis Cryptochrome 1. Plant Cell.

Shimizu-Sato,, S„ E. Huq, J. M. Tepperman and P. H. Quail (2002). A light-switchable gene promoter

system.. Nat Biotechnol 20( 10): 1041 -4.

Short,, T. W., M. Porst, J. Palmer, E. Fernbach and W. R. Briggs (1994). Blue Light Induces

Phosphorylationn at Seryl Residues on a Pea (Pisum sativum L.) Plasma Membrane Protein. Plant

PhysiolPhysiol 104(4): 1317-1324,

Sineshchekov,, O. A., K. H. Jung and J. L. Spudich (2002). Two rhodopsins mediate phototaxis to low- and

high-intensityy light in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 99(13): 8689-94.

Small,, G. D., B. Min and P. A. Lefebvre (1995). Characterization of a Chlamydomonas reinhardtii gene

encodingg a protein of the DNA photolyase/blue light photoreceptor family. Plant Mol Biol 28(3):

443-54. .

Sprenger,, W. W., W. D. Hoff, J. P. Armitage and K. J. Hellingwerf (1993). The eubacterium

Ectothiorhodospiraa halophila is negatively phototactic, with a wavelength dependence that fits the

absorptionn spectrum of the photoactive yellow protein. J Bacteriol 175(10): 3096-104.

Spudich,, J. L. and R. A. Bogomolni (1984). Mechanism of colour discrimination by a bacterial sensory

rhodopsin.. Nature 312(5994): 509-13.

Spudich,, J. L. and H. Luecke (2002). Sensory rhodopsin II: functional insights from structure. Curr Opin

StructStruct flib/12(4): 540-6.

Spudich,, J. L., C. S. Yang, K. H. Jung and E. N. Spudich (2000). Retinylidene proteins: structures and

functionss from archaea to humans. Anmt Rev Cell Dev Bio! 16: 365-92.

Srajer,, V., T. Teng, T. Ursby, C. Pradervand, Z. Ren, S. Adachi, W. Schildkamp, D. Bourgeois, M. Wulff

andd K. Moffat (1996). Photolysis of the carbon monoxide complex of myoglobin: nanosecond

time-resolvedd crystallography. 5cience 274(5293): 1726-9.

Stock,, A. M., V. L. Robinson and P. N. Goudreau (2000). Two-component signal transduction. Annual

ReviewReview of Biochemistry 69: 183-215.

Stockhaus,, J., A. Nagatani, U. Halfter, S. Kay, M. Furuya and N. H. Chua (1992). Serine-to-alanine

substitutionss at the amino-terminal region of phytochrome A result in an increase in biological

activity.. Genes Dev 6(\2A): 2364-72.

Stoeckenius,, W. and R. H. Lozier (1974). Light energy conversion in Halobacterium halobium. J Supra mol

StructStruct 2(5-6): 769-74.

131 1

References s

Subramaniam,, S., M. Lindahl, P. Bullough, A. R. Faruqi, J. Tittor, D. Oesterhelt, L. Brown, J. Lanyi and R.

Hendersonn (1999). Protein conformational changes in the bacteriorhodopsin photocycle. J Mol

BiolBiol 287(1): 145-61.

Swartz,, T. E., S. B. Corchnoy, J. M. Christie, J. W. Lewis, 1. Szundi, W. R. Briggs and R. A. Bogomolni

(2001).. The photocycle of a flavin-binding domain of the blue light photoreceptor phototropin. J

BiolBiol Chem 276(39): 36493-500.

Tittor,, J., S. Paula, S. Subramaniam, J. Heberle. R. Henderson and D. Oesterhelt (2002). Proton

translocationn by bacteriorhodopsin in the absence of substantial conformational changes. J Mol

BiolBiol 319(2): 555-65.

Todo,, T., H. Ryo, K. Yamamoto, H. Ton, T. Inui, H. Ayaki, T. Nomura and M. Ikenaga (1996). Similarity

amongg the Drosophila (6-4)photolyase, a human photolyase homolog, and the DNA photolyase-

blue-lightt photoreceptor family. Science 272(5258): 109-12.

Tokutomi,, S., K. T. Yamamoto and M. Furuya (1988). Photoreversible Proton Dissociation and Association

inn Pea Phytochrome and Its Chromopeptides. Photochemistry andPhotohiology 47(3): 439-445.

Ujj ,, L., S. Dcvanathan, T. E. Meyer, M, A. Cusanovich, G. Tollin andG. H. Atkinson (1998). New

photocyclee intermediates in the photoactive yellow protein from Ectothiorhodospira halophila:

picosecondd transient absorption spectroscopy. Biophys J 75( 1): 406-12.

Vann Aalten, D. M., W. Crielaard, K. J. Hellingwerf and L. Joshua-Tor (2002a). Structure of the photoactive

yelloww protein reconstituted with caffcic acid at 1.16 A resolution. Acta Crystallogr D Biol

Crysta/hgrCrysta/hgr 58(Pt 4): 585-90.

Vann Aalten, D. M., A. Haker, J. Hendriks, K. J. Hellingwerf, L. Joshua-Tor and W. Crielaard (2002b).

Engineeringg photocycle dynamics. Crystal structures and kinetics of three photoactive yellow

proteinn hinge-bending mutants. J Biol Chem 277(8): 6463-8.

Vann Aalten, D. M., W. D. Hoff, J. B. Findlay, W. Crielaard and K. J. Hellingwerf (1998). Concerted

motionss in the photoactive yellow protein. Protein Eng 11(10): 873-9.

Vann Aalten, D. M. F., W. Crielaard, K. J. Hellingwerf and L. Joshua-Tor (2000). Conformational substates

inn different crystal forms of the photoactive yellow protein - Correlation with theoretical and

experimentall flexibility . Protein Science 9(1): 64-72.

Vann Aalten, D. M. F., A. Haker, J. Hendriks, K. J. Hellingwerf, L. Joshua-Tor and W. Crielaard (2002c).

Engineeringg photocycle dynamics - Crystal structures and kinetics of three photoactive yellow

proteinn hinge-bending mutants. The Journal of Biological Chemistry 277(8): 6463-6468.

Vann Beeumen, J. J., B. V. Devreese, S. M. Van Bun, W. D. Hoff, K. J. Hellingwerf, T. E. Meyer, D. E.

McReee and M. A. Cusanovich (1993). Primary structure of a photoactive yellow protein from the

phototrophicc bacterium Ectothiorhodospira halophila, with evidence for the mass and the binding

sitesite of the chromophore. Protein Sci 2(7): 1114-25.

Vann Brederode, M. E., W. D. Hoff, I. H. Van Stokkum, M. L. Groot and K. J. Hellingwerf (1996). Protein

foldingg thermodynamics applied to the photocycle of the photoactive yellow protein. Biophys J

71(1):: 365-80.

132 2

References s

Vann der Horst, M. A., I. H. M. Van Stokkum, W. Crielaard and K. J. Hellingwerf (2001). The role of the N-

terminall domain of photoactive yellow protein in the transient partial unfolding during signalling

statee formation. FEBS Lett 497( 1): 26-30.

Vann Thor, J. J., B. Borucki, W. Crielaard, H. Otto, T. Lamparter, J. Hughes, K. J. Hellingwerf and M. P.

Heynn (2001). Light-induced proton release and proton uptake reactions in the cyanobacterial

phytochromee Cphl. Biochemistry* 40(38): 11460-71.

Varo,, G. and J. K. Lanyi (1991). Distortions in the photocycle of bacteriorhodopsin at moderate

dehydration.. Biophys J 59(2): 313-22.

Verdegem,, P. J., P. H. Bovee-Geurts, W. J. de Grip, J. Lugtenburg and H. J. de Groot (1999). Retinylidene

ligandd structure in bovine rhodopsin, metarhodopsin-1, and 10-methylrhodopsin from internuclear

distancee measurements using 13C- labeling and 1-D rotational resonance MAS NMR.


Verschueren,, K. H., F. Seljee, H. J. Rozeboom, K. H. Kalk and B. W. Dijkstra (1993). Crystallographic

analysiss of the catalytic mechanism of haloalkane dehalogenase. Nature 363(6431): 693-8.

Vreede,, J., M. A. van der Horst, K. J. Hellingwerf, W. Crielaard and D. M. F. van Aalten (2003). PAS

domainss - Common structure and common flexibility . Journal of Biological Chemistry 278(20):

18434-18439. .

Wall,, M. E., S. C. Gallagher and J. Trewhella (2000). Large-scale shape changes in proteins and

macromolecularr complexes. Annu Rev Phys Chem 51: 355-80.

Warshel,, A. and Z. T. Chu (2001). Nature of the surface crossing process in bacteriorhodopsin: Computer

simulationss of the quantum dynamics of the primary photochemical event. Journal of Physical

ChemistryChemistry B 105(40): 9857-9871.

Wilde,, A., B. Fiedler and T. Borner (2002). The cyanobacterial phytochrome Cph2 inhibits phototaxis

towardss blue light. Mol Microbiol 44(4): 981-8.

Woese,, C. R., O. Kandler and M. L. Wheelis (1990). Towards a natural system of organisms: proposal for

thee domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87(12): 4576-9.

Wolff,, E. K., R. A. Bogomolni, P. Scherrer, B. Hess and W. Stoeckenius (1986). Color discrimination in

halobacteria:: spectroscopic characterization of a second sensory receptor covering the blue-green

regionn of the spectrum. Proc Natl Acad Sci USA 83: 7272-7276.

Xiao,, W., L. S. Brown, R. Needleman, J. K. Lanyi and Y. K. Shin (2000). Light-induced rotation of a

transmembranee alpha-helix in bacteriorhodopsin. J Mol Biol 304(5): 715-21.

Xie,, A., W. D. Hoff, A. R. Kroon and K. J. Hellingwerf (1996). Glu46 donates a proton to the 4-

hydroxycinnamatee anion chromophore during the photocycle of photoactive yellow protein.


Xie,, A., L. Kelemen, J. Hendriks, B. J. White, K. J. Hellingwerf and W. D. Hoff (2001). Formation of a new

buriedd charge drives a large-amplitude protein quake in photoreceptor activation. Biochemistry

40(6):: 1510-7.

Xiong,, J. and C. E. Bauer (2002). Complex evolution of photosynthesis. Annu Rev Plant Biol 53: 503-21.

133 3

References s

Yan,, B., T. Takahashi, R. Johnson and J. L. Spudich (1991). Identification of signaling states of a sensory

receptorr by modulation of lifetimes of stimulus-induced conformations: the case of sensory

rhodopsinn II. Biochemistry 30(44): 10686-92.

Yang,, H. Q., Y. J. Wu, R. H. Tang, D. Liu, Y. Liu and A. R. Cashmore (2000). The C termini of

Arabidopsiss cryptochromes mediate a constitutive light response. Cell 103(5): 815-27.

Yeh,, K. C. and J. C. Lagarias (1998). Eukaryotic phytochromes: light-regulated serine/threonine protein

kinasess with histidine kinase ancestry. Proc Natl Acad Sci USA 95(23): 13976-81.

Zadok,, U., A. Khatchatouriants, A. Lewis, M. Ottolenghi and M. Sheves (2002). Light-induced charge

redistributionn in the retinal chromophore is required for initiating the bacteriorhodopsin

photocycle.. J Am Chem Soc 124(40): 11844-5.

Zhukovsky,, E. A., P. R. Robinson and D. D. Oprian (1991). Transducin activation by rhodopsin without a

covalentt bond to the 11-cis-retinal chromophore. Science 251(4993): 558-60.

Zhulin,, I. B., B. L. Taylor and R. Dixon (1997). PAS domain S-boxes in Archaea, Bacteria and sensors for

oxygenn and redox. Trends Biochem Sci 22(9): 331-3.

134 4

uva-dare (digital academic repository) structure/function ... · protein:: protonation equilibrium...

Documents