Coherent oscillations in ultrafast fluorescence of photoactive yellow protein

Nakamura, Ryosuke; Hamada, Norio; Ichida, Hideki; Tokunaga, Fumio; Kanematsu, Yasuo

doi:10.1063/1.2802297

Cited by 32 publications

(47 citation statements)

References 54 publications

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“…After photoexcitation, the hydrogen bond of the phenolate oxygen of the chromophore suddenly reforms into the similar structure to that of E46Q within our time resolution of 150 fs. This ultrafast reformation is consistent with ultrafast relaxation process from the Franck-Condon state observed with time-resolved fluorescence spectroscopy [10]. According to the previous reports [2,3], this reformation presumably corresponds to weakening of the hydrogen bond between Glu46 and the phenolate oxygen.…”

Section: 1supporting

confidence: 69%

Structural Evolution in Photoactive Yellow Protein Studied by Femtosecond Stimulated Raman Spectroscopy

Nakamura

Hamada

Abe

et al. 2013

EPJ Web of Conferences

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Section: 1supporting

confidence: 69%

Structural Evolution in Photoactive Yellow Protein Studied by Femtosecond Stimulated Raman Spectroscopy

Nakamura

Hamada

Abe

et al. 2013

EPJ Web of Conferences

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“…We make the approximation that electronic transitions are initiated from the vibrational ground state of S 0 and that fluorescence emission occurs from the vibrational ground state of S 1 . This assumption is supported by the relatively small contribution of vibrational cooling during the lifetime of the S 1 state in PYP as experimentally detected by ultrafast changes in the chromophore fluorescence emission spectrum of PYP (31). For the sake of simplicity we first describe the spectra based on harmonic energy potentials for the S 0 and S 1 states and consider the changes in Franck-Condon factors for absorption and fluorescence emission expected for changes in ΔE, R e , and W of these two energy surfaces.…”

Section: Resultsmentioning

confidence: 51%

Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface

Philip

Nome

Papadantonakis

et al. 2010

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

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Protein-chromophore interactions in photoreceptors often shift the chromophore absorbance maximum to a biologically relevant spectral region. A fundamental question regarding such spectral tuning effects is how the electronic ground state S 0 and excited state S 1 are modified by the protein. It is widely assumed that changes in energy gap between S 0 and S 1 are the main factor in biological spectral tuning. We report a generally applicable approach to determine if a specific residue modulates the energy gap, or if it alters the equilibrium nuclear geometry or width of the energy surfaces. This approach uses the effects that changes in these three parameters have on the absorbance and fluorescence emission spectra of mutants. We apply this strategy to a set of mutants of photoactive yellow protein (PYP) containing all 20 side chains at active site residue 46. While the mutants exhibit significant variation in both the position and width of their absorbance spectra, the fluorescence emission spectra are largely unchanged. This provides strong evidence against a major role for changes in energy gap in the spectral tuning of these mutants and reveals a change in the width of the S 1 energy surface. We determined the excited state lifetime of selected mutants and the observed correlation between the fluorescence quantum yield and lifetime shows that the fluorescence spectra are representative of the energy surfaces of the mutants. These results reveal that residue 46 tunes the absorbance spectrum of PYP largely by modulating the width of the S 1 energy surface.photoreceptor | protein-chromophore interactions | wavelength regulation L ight-driven proteins, consisting of a protein-chromophore complex, employ two general strategies to optimize the biological effectiveness of the position of their absorbance spectra. First, covalent modifications of a chromophore can shift its absorbance maximum λ abs max . An important example is the strong red-shift in the absorbance spectrum of bacteriochlorophyll compared to plant chlorophyll (1). Second, specific protein-chromophore interactions can shift the absorbance spectrum of the protein-bound chromophore. A classic example of this spectral tuning phenomenon is color vision in vertebrates (2, 3): the same retinal chromophore can absorb in the blue, green, and red, depending on the amino acid sequence of the rhodopsin to which it is bound. Spectral tuning provides an example of protein-ligand interactions that tune the properties of the cofactor to biologically relevant values.Two main approaches have been used to unravel the factors involved in spectral tuning: determining (i) which amino acids in the protein contribute to spectral tuning, and (ii) what type of protein-chromophore interactions cause spectral tuning. Interactions that alter the degree of charge delocalization over the chromophore are of particular importance. These two issues have been explored extensively in animal visual rhodopsins and the archaeal rhodopsins (4-7). Here we study spectral tuning in a more r...

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“…Notably, excited state decay has been shown to be multi-phasic from femtosecond fluorescence and transient absorption spectroscopy [8,20]. It is also well established that excited state population that persists for picoseconds is unproductive in the formation of the cis-like photoproduct I0, and photoisomerisation proceeds with a dominant time constant of ~600 fs [8,22,23].…”

Section: Primary Photochemical Reactions and Coherence Of Pypmentioning

confidence: 99%

“…The time-constant for photoisomerisation of the PYP chromophore has been reported with values ranging from ~400 fs to 1.4 ps, depending on the details of optical conditions and spectroscopic probe, and also sample conditions [19][20][21][22]. Notably, excited state decay has been shown to be multi-phasic from femtosecond fluorescence and transient absorption spectroscopy [8,20].…”

Section: Primary Photochemical Reactions and Coherence Of Pypmentioning

confidence: 99%

Populations and coherence in femtosecond time resolved X-ray crystallography of the photoactive yellow protein

Hutchison

Thor

2017

International Reviews in Physical Chemistry

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Ultrafast X-ray crystallography of the Photoactive Yellow Protein with femtosecond delays using an X-ray Free Electron Laser has successfully probed the dynamics of an early FranckCondon species. The femtosecond pump-probe application of protein crystallography represents a new experimental regime that provides an X-ray structural probe for coherent processes that were previously accessible primarily using ultrafast spectroscopy. We address how the optical regime of the visible pump, that is necessary to successfully resolve ultrafast structural differences, affects the motions that are measured using the technique. The subpicosecond photochemical dynamics in PYP involves evolution of a mixture of electronic ground and excited state populations. Additionally, within the dephasing time structural motion include vibrational coherence arising from excited states, the ground state and a ground state intermediate under experimental conditions used for ultrafast crystallography. Intense optical pulses are required to convert population levels in PYP crystals that allow detection by X-ray crystallography, but the compromise currently needed for the optical bandwidth and power has consequences with regard to the contributions to the motions that are experimentally measured with femtosecond delays. We briefly review the ultrafast spectroscopy literature of the primary photoreactions of PYP and discuss relevant physical models taken from coherent control and femtosecond coherence spectroscopy literature that address both the population transfer as well 2 as the vibrational coherences. We apply linear response theory, with the additional use of a high power approximation, of on-resonance impulsive vibrational coherence in the ground state and the non-impulsive coherence in the excited state and discuss experimental approaches to manipulate the coherence contributions. The results are generalised and extended to discuss the future capabilities of high repetition rate XFEL instruments providing enhanced sensitivity to perform the crystallographic equivalent of an impulsive Raman measurement of vibrational coherence.

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Coherent oscillations in ultrafast fluorescence of photoactive yellow protein

Cited by 32 publications

References 54 publications

Structural Evolution in Photoactive Yellow Protein Studied by Femtosecond Stimulated Raman Spectroscopy

Structural Evolution in Photoactive Yellow Protein Studied by Femtosecond Stimulated Raman Spectroscopy

Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface

Populations and coherence in femtosecond time resolved X-ray crystallography of the photoactive yellow protein

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