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

Abstract

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...

Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs)

“…Color tuning has been studied with fluorescent proteins (71), PYP (72), and retinal proteins ("opsin shift") (73), which all adjust the energy gaps between the excited and ground states. These energy gaps correlate well with electrostatic interactions experienced by the chromophores (74)(75)(76).…”

“…Furthermore, the overall structure, folding efficiency, and chromophore maturation efficiency have to be preserved on mutations, complicating the protein design problem. Second, structure-energetics knowledge is necessary and can be obtained either from computational predictions using X-ray structures (44,49) or by characterizing exhaustive mutations on important residues of model systems for specific photochemistry (64,72).…”

Dynamics and mechanisms of DNA repair by photolyase

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Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein

“…Since the photoresponse of the PYP chromophore is a model for other photoactive and signal transduction proteins, such as those in the rhodopsin family, it is important to understand how the computational treatment of the dynamics of the chromophore in the protein and solution environment tune the spectral response. 41 This work is also the first application of the T era C hem / A mber QM/MM interface for robust computation of QM/MM dynamics of large QM regions. The interface is used to compute the spectra of the PYP chromophore in successively more complicated dynamic environments: vacuum, aqueous solution, and in the protein.…”