Photoinduced volume change and energy storage associated with the early transformations of the photoactive yellow protein from Ectothiorhodospira halophila

Brederode, Marion E. van; Gensch, Thomas; Hoff, Wouter D.; Hellingwerf, Klaas J.; Braslavsky, Silvia E.

doi:10.1016/s0006-3495(95)80284-5

Cited by 102 publications

(117 citation statements)

References 44 publications

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“…4 (perpendicular plane). The momentum carried by the twisted state along the reaction coordinate is conserved better in the protein than in the isolated system because of the ultrashort interaction time in the CI region, and therefore more cis isomers can be formed with high reaction quantum yield (0.24-0.64) (8,11,28,29). That is a critical design by the protein environment to enhance trans-to-cis isomerization in the PYP photocycle.…”

Section: Resultsmentioning

confidence: 99%

Primary steps of the photoactive yellow protein: Isolated chromophore dynamics and protein directed function

Lee

Zewail

2006

Proc. Natl. Acad. Sci. U.S.A.

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The cycle of the photoactive yellow protein (PYP) has been extensively studied, but the dynamics of the isolated chromophore responsible for transduction is unknown. Here, we present realtime observation of the dynamics of the negatively charged chromophore and detection of intermediates along the path of transto-cis isomerization using femtosecond mass selection͞electron detachment techniques. The results show that the role of the protein environment is not in the first step of double-bond twisting (barrier crossing) but in directing efficient conversion to the cisstructure and in impeding radical formation within the protein.femtobiology ͉ transduction ͉ molecular dynamics ͉ photoelectron spectroscopy P hotoactive yellow protein (PYP) is a water-soluble photoreceptor found in Halorhodospira halophila and related halophilic bacterial species (1). The chromophore responsible for perception of light and phototactic response is a deprotonated trans-4-hydroxycinnamic acid (also known as p-coumaric acid) covalently linked to a cysteine residue of the protein via a thioester bond (Fig. 1). Light absorption of the PYP chromophore leads to the initiation of a complex photocycle involving several intermediates. With a variety of biophysical techniques (2-5), it is concluded that the first intermediate (I 0 ) in the photocycle is formed within a few picoseconds, with the chromophore changing to the cis configuration, in a trans-to-cis isomerization process (7-11). The intermediates at longer times have been trapped and identified by x-ray crystallography (12, 13).The critical change of the chromophore in the primary process of isomerization is accompanied or followed by several other processes: proton transfer, protein conformational change, solvation, and disruption of hydrogen-bonding. This complexity can be reduced if the chromophore in its true anionic, not neutral, structure can be studied free of perturbations. With model compounds, the solvent effect can be assessed by studying them in the solution phase (14-18). However, the nature of intramolecular change and the timescales involved are still unknown. It is, therefore, desirable to study the primary isomerization dynamics of the PYP chromophore in isolation, especially in view of the fact that the mechanism for forming the first intermediate (I 0 ) is debatable (2). A gas-phase spectroscopic study has already been reported (19), but it was for the neutral molecule, not the anion structure in the protein.In this work, we report direct observation of the dynamics of the isolated PYP anionic chromophore. To disentangle the role of protein binding and distant torsions, we preserved the central structure involved in the isomerization about the double bond but use the CH 3 group for termination (see Fig. 1). The chromophore, hereafter called P, is excited with a femtosecond pulse from its ground state, the dark state in the protein, to the trans configuration using the mass-selected ions. For probing we use another femtosecond pulse to photodetach and resolve the phot...

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Section: Resultsmentioning

confidence: 99%

Primary steps of the photoactive yellow protein: Isolated chromophore dynamics and protein directed function

Lee

Zewail

2006

Proc. Natl. Acad. Sci. U.S.A.

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“…Photoactivity was first reported by Meyer et al (1987), and continuing kinetics analysis has shown that the photocycle is remarkably similar to the bacterial rhodopsins from Halobacterium halobium and related species (Meyer et al, , 1991Hoff et al, 1992;Miller et al, 1993;Ng et al, 1995;Van Brederode et al, 1995). PYP is partially bleached and redshifted from 446 to 465 nm in less than 1 ns, and then it is completely bleached and blue-shifted to 356 nm in 100 µs and finally returns to ground state in 260 ms.…”

mentioning

confidence: 85%

Sequence Evidence for Strong Conservation of the Photoactive Yellow Proteins from the Halophilic Phototrophic Bacteria Chromatium salexigens and Rhodospirillum salexigens

et al. 1996

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Sequence evidence for strong conservation of the photoactive yellow proteins from the halophilic phototrophic bacteria Chromatium salexigens and Rhodospirillum salexigens Koh, M.; van Driessche, G.; Samyn, B.; Hoff, W.D.; Meyer, T.E.; Cusanovich, M.A.; van Beeumen, J.J. Published in: Biochemistry DOI:10.1021/bi951494tLink to publication Citation for published version (APA):Koh, M., van Driessche, G., Samyn, B., Hoff, W. D., Meyer, T. E., Cusanovich, M. A., & van Beeumen, J. J. (1996). Sequence evidence for strong conservation of the photoactive yellow proteins from the halophilic phototrophic bacteria Chromatium salexigens and Rhodospirillum salexigens. Biochemistry, 35, 2526-2543. DOI: 10.1021/bi951494t 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, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://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. ABSTRACT: The photoactive yellow proteins (PYP) have been found to date only in three species of halophilic purple phototrophic bacteria. They have photochemical activity remarkably similar to that of the bacterial rhodopsins. In contrast to rhodopsins, however, the PYPs are small water-soluble proteins. We now report the complete amino acid sequences of Rhodospirillum salexigens and Chromatium salexigens PYP which allow comparison with the known sequence and three-dimensional structure of the prototypic protein from Ectothiorhodospira halophila. Although isolated from three different families of bacteria, the PYP sequences are 70-76% identical. All three contain 125 amino acid residues, and no insertions or deletions are necessary for alignment. This is a remarkable result when it is considered that electron transfer proteins from these purple bacterial species are only 25-40% identical and that insertions and deletions are needed for their proper alignment. It thus appears that PYP has the same important function in each of the purple bacteria and that most of the amino acid residues are necessary to maintain structure and function. By most standards, PYP would be called a "slowly evolving protein". R. salexigens PYP is uniquely degraded by proteolysis at low ionic strength, probably as a consequence of unfolding due to electrostatic repulsion of the excess negative charge. Therefore it may also be classified as a "halophilic protein".

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“…The factor 2.303 results from the conversion of the naperian to the decadie absorption coefficient. O4,m equals 0.35 [25], 8446 is 4550 m 2 mo1-1 [26] and 144~, as determined with a quantum sensor, is ,,~3.0× 10 -4 mol photons m -2 s -t. Consequently, kl equals 1.1 s -1. The rate constant k2, referring to the rate of pG recovery, was determined to be 0.05 s -1 at pH 4 [16].…”

Section: The Isomeric State Of L-coumaric Acid In the Blue-shifted Pmentioning

confidence: 99%

Evidence for trans‐cis isomerization of the p‐coumaric acid chromophore as the photochemical basis of the photocycle of photoactive yellow protein

et al. 1996

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Analysis of the chromophore p-coumaric acid, extracted from the ground state and the long-lived blue-shifted photocycle intermediate of photoactive yellow protein, shows that the chromophore is reversibly converted from the trans to the cis configuration, while progressing through the photocycle. The detection of the trans and ¢is isomers was carried out by high performance capillary zone electrophoresis and further substantiated by tH NMR spectroscopy. The data presented here establish the photo.isomerization of the vinyl double bond in the chromophore as the photochemical basis for the photocycle of photoactive yellow protein, a euhacterlal photosensory protein. A similar isomerization process occurs in the structurally very different sensory rhodopsins, offering an explanatimJ for the strong spectroscopic similarities between photoactive yellow protein and the sensory rhodopsins. This is the first demonstration of light-induced isomerization of a chromophore double bond as the photochemical basis for photosensing in the domain of Bacteria.

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Photoinduced volume change and energy storage associated with the early transformations of the photoactive yellow protein from Ectothiorhodospira halophila

Cited by 102 publications

References 44 publications

Primary steps of the photoactive yellow protein: Isolated chromophore dynamics and protein directed function

Primary steps of the photoactive yellow protein: Isolated chromophore dynamics and protein directed function

Sequence Evidence for Strong Conservation of the Photoactive Yellow Proteins from the Halophilic Phototrophic Bacteria Chromatium salexigens and Rhodospirillum salexigens

Evidence for trans‐cis isomerization of the p‐coumaric acid chromophore as the photochemical basis of the photocycle of photoactive yellow protein

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