Spectral Tuning of Photoactive Yellow Protein†

Yamato, Takahisa; Ishikura, Takakazu; Kakitani, Toshiaki; Kawaguchi, Kazutomo; Watanabe, Hiroshi

doi:10.1562/2006-06-16-ra-930

Cited by 9 publications

(18 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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).…”

mentioning

confidence: 99%

See 3 more Smart Citations

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.

View full text Add to dashboard Cite

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...

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Correlating Fluorescence Quantum Yield and Excited State Lifmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

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.

View full text Add to dashboard Cite

show abstract

“…Calculations of the absorption maxima of various PYP mutants have been presented in refs. [251,252]. These studies employed a partitioning scheme similar to ONIOM, in which the fragment molecular orbital method was employed as a lowlevel QM approach in combination with CASPT2 as a high-level approach.…”

Section: Pypmentioning

confidence: 99%

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

Neugebauer

2009

ChemPhysChem

123

View full text Add to dashboard Cite

The absorption properties of chromophores in biomolecular systems are subject to several fine-tuning mechanisms. Specific interactions with the surrounding protein environment often lead to significant changes in the excitation energies, but bulk dielectric effects can also play an important role. Moreover, strong excitonic interactions can occur in systems with several chromophores at close distances. For interpretation purposes, it is often desirable to distinguish different types of environmental effects, such as geometrical, electrostatic, polarization, and response (or differential polarization) effects. Methods that can be applied for theoretical analyses of such effects are reviewed herein, ranging from continuum and point-charge models to explicit quantum chemical subsystem methods for environmental effects. Connections to physical model theories are also outlined. Prototypical applications to optical spectra and excited states of fluorescent proteins, biomolecular photoreceptors, and photosynthetic protein complexes are discussed.

show abstract

A Conserved Helical Capping Hydrogen Bond in PAS Domains Controls Signaling Kinetics in the Superfamily Prototype Photoactive Yellow Protein

et al. 2010

View full text Add to dashboard Cite

PAS domains form a divergent protein superfamily with more than 20,000 members that perform a wide array of sensing and regulatory functions in all three domains of life. Only 9 residues are well-conserved in PAS domains, with an Asn residue at the start of α-helix 3 showing the strongest conservation. The molecular functions of these 9 conserved residues are unknown. We use static and time-resolved visible and FTIR spectroscopy to investigate receptor activation in the photosensor photoactive yellow protein (PYP), a PAS domain prototype. The N43A and N43S mutants allow an investigation of the role of side chain hydrogen bonding at this conserved position. The mutants exhibit a blue-shifted visible absorbance maximum and up-shifted chromophore pKa. Disruption of the hydrogen bonds in N43A PYP causes both a reduction in protein stability and a 3,400-fold increase in the lifetime of the signaling state of this photoreceptor. A significant part of this increase in lifetime can be attributed to the helical capping interaction of Asn43. This extends the known importance of helical capping for protein structure to regulating functional protein kinetics. A model for PYP activation has been proposed in which side chain hydrogen bonding of Asn43 is critical for relaying light-induced conformational changes. However, FTIR spectroscopy shows that both Asn43 mutants retain full allosteric transmission of structural changes. Analysis of 30 available high resolution structures of PAS domains reveals that the side chain hydrogen bonding of residue 43 but not residue identity is highly conserved, and suggests that its helical cap affects signaling kinetics in other PAS domains.

show abstract

Spectral Tuning of Photoactive Yellow Protein†

Cited by 9 publications

References 27 publications

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

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

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

A Conserved Helical Capping Hydrogen Bond in PAS Domains Controls Signaling Kinetics in the Superfamily Prototype Photoactive Yellow Protein

Contact Info

Product

Resources

About