Spectral Tuning of Photoactive Yellow Protein. Theoretical and Experimental Analysis of Medium Effects on the Absorption Spectrum of the Chromophore

Yoda, Masaki; Houjou, Hirohiko; Inoue, Atsuyoshi; Sakurai, Minoru

doi:10.1021/jp011722v

Cited by 51 publications

(58 citation statements)

References 34 publications

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“…Also, hydrogen bonding by water to the proximal carbonyl oxygen, which is solventaccessible in Ppr-PYP (see above), could also contribute to a blue shift in absorption because of resonance stabilization between quinonic and phenolic forms of the chromophore (19). However, it is difficult to correlate the structural changes observed in this structure with the specific and nonspecific protein environmental effects that affect chromophore absorption in PYPs (45,46).…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of a photoactive yellow protein from a sensor histidine kinase: Conformational variability and signal transduction

Rajagopal

Moffat

2003

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

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Photoactive yellow protein (E-PYP) is a blue light photoreceptor, implicated in a negative phototactic response in Ectothiorhodospira halophila, that also serves as a model for the Per–Arnt–Sim superfamily of signaling molecules. Because no biological signaling partner for E-PYP has been identified, it has not been possible to correlate any of its photocycle intermediates with a relevant signaling state. However, the PYP domain (Ppr-PYP) from the sensor histidine kinase Ppr in Rhodospirillum centenum, which regulates the catalytic activity of Ppr by blue light absorption, may allow such issues to be addressed. Here we report the crystal structure of Ppr-PYP at 2 Å resolution. This domain has the same absorption spectrum and similar photocycle kinetics as full length Ppr, but a blue-shifted absorbance and considerably slower photocycle than E-PYP. Although the overall fold of Ppr-PYP resembles that of E-PYP, a novel conformation of the β4–β5 loop results in inaccessibility of Met-100, thought to catalyze chromophore reisomerization, to the chromophore. This conformation also exposes a highly conserved molecular surface that could interact with downstream signaling partners. Other structural differences in the α3–α4 and β4–β5 loops are consistent with these regions playing significant roles in the control of photocycle dynamics and, by comparison to other sensory Per–Arnt–Sim domains, in signal transduction. Because of its direct linkage to a measurable biological output, Ppr-PYP serves as an excellent system for understanding how changes in photocycle dynamics affect signaling by PYPs

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Section: Resultsmentioning

confidence: 99%

Crystal structure of a photoactive yellow protein from a sensor histidine kinase: Conformational variability and signal transduction

Rajagopal

Moffat

2003

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

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“…Substitution mutations at the residue under study in principle can affect three independent properties of the S 0 and S 1 energy surfaces: ΔE, R e , and W. The expected consequences of changes in these three properties can be formulated as described below. The electronic structure of PYP has been examined by a number of computational studies (24)(25)(26)(27), but the details of the shape of the S 0 and S 1 energy surfaces and Franck-Condon factors for the pCA in its active site are difficult to obtain with high accuracy. However, general trends in changes in the position and shape of the absorbance and emission fluorescence maxima as a result of changes in ΔE, R e , and W can be derived.…”

Section: Resultsmentioning

confidence: 99%

“…Experimental and computational work on PYP has confirmed that the chromophore absorbance band at 446 nm is a π-π Ã transition, has identified Glu46 and Tyr42 as the main contributors to the effect of the protein on the pCA absorbance spectrum, and has revealed that the hydrogen bonding interactions between these two side chains and the pCA are critical for spectral tuning in PYP (18)(19)(20)(21)(24)(25)(26)(27). These studies have all focused on the energy gap between the S 0 and S 1 states, i.e., ΔE-tuning.…”

Section: Correlating Fluorescence Quantum Yield and Excited State Lifmentioning

confidence: 99%

“…These interactions have been studied by both site-directed mutagenesis (18-21) and computational approaches (24-27) (SI Text). These studies have revealed Tyr42 and Glu46 as the two dominant side chains in the spectral tuning of PYP (18)(19)(20)(21)(24)(25)(26)(27)(28). Weakening of the Glu46-pCA hydrogen bond (29,30) in the E46Q mutant results in a red-shift to 460 nm, while complete disruption of the hydrogen bond in the E46V mutant results in a further red-shift to 478 nm (21).…”

mentioning

confidence: 99%

“…Weakening of the Glu46-pCA hydrogen bond (29,30) in the E46Q mutant results in a red-shift to 460 nm, while complete disruption of the hydrogen bond in the E46V mutant results in a further red-shift to 478 nm (21). Based on computational studies it has been proposed that hydrogen bonding, charge-charge interactions, and burial of the pCA in the hydrophobic protein interior are factors in the spectral tuning of PYP (24,25).…”

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confidence: 99%

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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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Photoactive Yellow Protein, the Xanthopsin

Horst

Hendriks

Vreede

et al. 2005

Handbook of Photosensory Receptors

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Spectral Tuning of Photoactive Yellow Protein. Theoretical and Experimental Analysis of Medium Effects on the Absorption Spectrum of the Chromophore

Cited by 51 publications

References 34 publications

Crystal structure of a photoactive yellow protein from a sensor histidine kinase: Conformational variability and signal transduction

Crystal structure of a photoactive yellow protein from a sensor histidine kinase: Conformational variability and signal transduction

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

Photoactive Yellow Protein, the Xanthopsin

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