Four resonance structures elucidate double-bond isomerisation of a biological chromophore

Gromov, Evgeniy V.; Domratcheva, Tatiana

doi:10.1039/d0cp00814a

Cited by 6 publications

(6 citation statements)

References 71 publications

(129 reference statements)

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“…The PYP S photocycle kinetics are in agreement with earlier spectroscopic reports 19,[23][24][25]27,28,35,[38][39][40][41][42][43][44][45] , while the PYP C results closely follow those observed in TRC by Schotte 2 , Jung 3 and Ten Boer et al 11 (Note that these latter three studies mutually agree on the data, but differ in the bond-order of the double bond that can isomerize in the chromophore, due the use of DFT optimized structure vs non-DFT optimized structures 46 . In a recent ab initio computational study, the former structure was favored 47 ). The agreement between the current data and those of TRC includes the dynamics on the 18 ns timescale associated with formation of pR 2 , 100% yield of pR 2 from pR 0 2 and the 22% overall pR yield 11 , though the former reported the pR 2 to pB transition to take place in 410 ms.…”

Section: Resultsmentioning

confidence: 99%

Confinement in crystal lattice alters entire photocycle pathway of the Photoactive Yellow Protein

et al. 2020

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Femtosecond time-resolved crystallography (TRC) on proteins enables resolving the spatial structure of short-lived photocycle intermediates. An open question is whether confinement and lower hydration of the proteins in the crystalline state affect the light-induced structural transformations. Here, we measured the full photocycle dynamics of a signal transduction protein often used as model system in TRC, Photoactive Yellow Protein (PYP), in the crystalline state and compared those to the dynamics in solution, utilizing electronic and vibrational transient absorption measurements from 100 fs over 12 decades in time. We find that the photocycle kinetics and structural dynamics of PYP in the crystalline form deviate from those in solution from the very first steps following photon absorption. This illustrates that ultrafast TRC results cannot be uncritically extrapolated to in vivo function, and that comparative spectroscopic experiments on proteins in crystalline and solution states can help identify structural intermediates under native conditions.

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Section: Resultsmentioning

confidence: 99%

Confinement in crystal lattice alters entire photocycle pathway of the Photoactive Yellow Protein

et al. 2020

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“…The LE form has been proposed as a diradicaloid structure at the methine bridge according to Olsen’s computational study . It has likewise been introduced in the context of retinal and other polyene chromophores as the 2A g state (as opposed to the 1B u state with a dominant charge-transfer character). − While for the neutral all- trans polyene, the diradicaloid state is indeed lower in energy than the charge-separated state, the former tends to have a small oscillator strength when excited from the ground state (1A g for all- trans polyenes) due to the unfavorable parity . The assignment of the diradicaloid behavior seems to be in contradiction to the large extinction coefficients for the protonated GFP chromophore observed from experiments and calculations, ,,− where the S 0 –S 1 transition is consistently designated to be of π–π* character.…”

Section: Resultsmentioning

confidence: 99%

Mechanism of Color and Photoacidity Tuning for the Protonated Green Fluorescent Protein Chromophore

Lin

Boxer

2020

J. Am. Chem. Soc.

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The neutral or A state of the green fluorescent protein (GFP) chromophore is a remarkable example of a photoacid naturally embedded in the protein environment and accounts for the large Stokes shift of GFP in response to near UV excitation. Its color tuning mechanism has been largely overlooked, as it is less preferable for imaging applications than the redder anionic or B state. Past studies, based on site-directed mutagenesis or solvatochromism of the isolated chromophore, have concluded that its color tuning range is much narrower than its anionic counterpart. However, as we performed extensive investigation on more GFP mutants, we found the color of the neutral chromophore to be much more sensitive to protein electrostatics. Electronic Stark spectroscopy reveals a fundamentally different electrostatic color tuning mechanism for the neutral state of the chromophore that demands a three-form model compared with that of the anionic state, which requires only two forms [1]. Specifically, an underlying zwitterionic charge transfer state is required to explain its sensitivity to electrostatics. As the Stokes shift is tightly linked to the protonated chromophore's photoacidity and excitedstate proton transfer (ESPT), we infer design principles of the GFP chromophore as a photoacid through the color tuning mechanisms of both protonation states. The threeform model could also be applied to similar biological and nonbiological dyes and complements the failure of two-form model for donor-acceptor systems with localized electronic distributions.

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“…All electronic configurations were generated from five reference configurations [the closed-shell, two single (HOMO-1 to LUMO and HOMO to LUMO) and two double (HOMO-1 to LUMO and HOMO to LUMO) excitations]. The active space (16,12) was employed which distributes 16 electrons in 12 orbitals: six π orbitals, two n orbitals and four π* orbitals. The state minima (S0_min and S1_min) and minimum-energy S0/S1 conical intersection (CI) geometries were optimized.…”

Section: Electronic Structure Calculationmentioning

confidence: 99%

“…[6][7][8][9][10] Owing to their importance, phytochromes have been extensively studied over decades. 9,[11][12][13][14][15][16][17][18] The biological functions of phytochrome are controlled by the switching between two forms (Pr and Pfr). 19 The physiologically inactive Pr form can absorb red light, and converts to the active Pfr form.…”

Section: Introductionmentioning

confidence: 99%

The Impact of the Different Geometrical Restrictions on the Nonadiabatic Photoisomerization of Biliverdin Chromophore

Fang

Huang

Lin

et al. 2022

Preprint

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The photoisomerization mechanism of the chromophore of bacterial biliverdin (BV) phytochromes is explored with the nonadiabatic dynamics simulation by using the on-the-fly trajectory surface-hopping method at the semi-empirical OM2/MRCI level. Particularly, the current study focuses on the influence of the geometrical constrains on the nonadiabatic photoisomerization dynamics of the BV chromophore. Here a rather simplified approach is employed in the nonadiabatic dynamics to capture the features of geometrical constrains, which adds the mechanical restriction on the specific moieties of the BV chromophore. This simplified method provides a rather quick approach to examine the influence of the geometrical restrictions on the photoisomerization. As expected, different constrains bring the distinctive influences on the photoisomerization mechanism of the BV chromophore, giving either strong or minor modification of both involved reaction channels and excited-state lifetimes after the constrains are added in different ring moieties. These observations not only contribute to the primary understanding of the role of the spatial restriction caused by biological environments in photoinduced dynamics of the BV chromophore, but also provide useful ideas for the artificial regulation of the photoisomerization reaction channels of phytochrome proteins.

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Four resonance structures elucidate double-bond isomerisation of a biological chromophore

Abstract: Four resonance structures determining the electronic structure of the chromophore’s ground and first excited states. Changing the relative energies of the structures by hydrogen-bonding interactions tunes all chromophore’s photochemical properties.

Cited by 6 publications

References 71 publications

Confinement in crystal lattice alters entire photocycle pathway of the Photoactive Yellow Protein

Confinement in crystal lattice alters entire photocycle pathway of the Photoactive Yellow Protein

Mechanism of Color and Photoacidity Tuning for the Protonated Green Fluorescent Protein Chromophore

The Impact of the Different Geometrical Restrictions on the Nonadiabatic Photoisomerization of Biliverdin Chromophore

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