Computational Photobiology and Beyond

Schapiro, Igor; Ryazantsev, Mikhail N.; Ding, Wan Jian; Huntress, Mark; Melaccio, Federico; Andruniów, Tadeusz; Olivucci, Massimo

doi:10.1071/ch09563

Cited by 38 publications

(38 citation statements)

References 95 publications

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“…First, the observed 347 nm (3.57 eV) l max for the S 0 !S 1 excitation is relatively well-reproduced by the computed 3.67 eV vertical excitation energy, and within the typical error of the employed method. [38,39] The computed deactivation path is consistent with the observed ultrafast (ca. 500 fs) S 1 lifetime in EtFlOH, [11] and with the low (3 10 À3 ) fluorescence quantum yield, since fluorescence must compete with the internal conversion taking place at the CI.…”

Section: Methodssupporting

confidence: 87%

“…The employed CASPT2//CASSCF/6-31G* protocol has been shown to be accurate for a number of organic biochromophores. [39,53,54] This protocol benefits from a cancellation of errors, [55] as discussed in the SI. The CASPT2 MEP profile of the chromophore in the gas-phase, without the effect of the solvent, is shown in Figure S6 in the SI.…”

Section: Ab Initio Calculationsmentioning

confidence: 98%

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A Conical Intersection Controls the Deactivation of the Bacterial Luciferase Fluorophore

et al. 2014

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The photophysics of flavins is highly dependent on their environment. For example, 4a-hydroxy flavins display weak fluorescence in solution, but exhibit strong fluorescence when bound to a protein. To understand this behavior, we performed temperature-dependent fluorescent studies on an N(5)-alkylated 4a-hydroxy flavin: the putative bacterial luciferase fluorophore. We find an increase in fluorescence quantum yield upon reaching the glass transition temperature of the solvent. We then employ multiconfigurational quantum chemical methods to map the excited-state deactivation path of the system. The result reveals a shallow but barrierless excited state deactivation path that leads to a conical intersection displaying an orthogonal out-of-plane distortion of the terminal pyrimidine ring. The intersection structure readily explains the observed spectroscopic behavior in terms of an excitedstate barrier imposed by the rigid glass cavity.Oxidized flavin cofactors like flavin mononucleotide (FMN) contain a planar, stiff flavin moiety that displays intense fluorescence in solutions (with a lifetime of ca. 5 ns).[1] Such a fluorescence is quenched when the cofactor is proteinbound due to fast excited-state electron transfer from the flavin to neighboring aromatic amino acid residues (such as tyrosine or tryptophan). This behavior of oxidized flavins has been exploited to follow the conformational changes of flavoproteins over the course of enzymatic reactions. [2][3][4][5] In contrast, the 1,5 and 4a,5 flavin adducts (see Scheme 1 a) such as those found in reduced (FMNH 2 ) [6] and 4a-hydroxylated (FMNHOH) cofactors, respectively, [7] display a weak fluorescence in solution. [8,9] However, when the same cofactors are protein-bound, the confinement [6,7] leads to an enhanced fluorescence emission. [10][11][12][13][14][15] The exact geometry and electronic structure of the emitting conformer and the mechanism preventing the efficient internal conversion occurring in solution are presently unknown.A spectacular manifestation of the effects of protein confinement on flavin cofactors is seen in bacterial luciferases where a 4a,5 flavin adduct is held responsible for the bioluminescence of a vast group of marine eubacteria. In organisms such as Vibrio harveyi, the emission of the fluorophore may be strong enough to cause a blue luminescence of the microbial population that is so intense as to be observable from satellites.[16] Moreover, such flavin adducts are frequent intermediates in enzymatic catalysis by flavinbased monooxygenases, which activate molecular oxygen and catalyze the insertion of atomic oxygen into a number of substrates (e.g. in hydroxylations, sulfoxidations, epoxidations and Baeyer-Villiger oxidations).[17] A specific type of such monooxygenase activity is responsible for the bacterial luciferase fluorescence, [18][19][20][21][22] where the oxidation of aldehydes to acids via molecular oxygen would generate the 4a-hydroxy flavin byproduct as the putative light-emitting intermediate (FMNHOH in Sche...

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Section: Methodssupporting

confidence: 87%

Section: Ab Initio Calculationsmentioning

confidence: 98%

A Conical Intersection Controls the Deactivation of the Bacterial Luciferase Fluorophore

et al. 2014

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“…16 The coordinates (X 1 X 2 ) corresponding to the branching plane and reaction path. The black and red arrows indicate the opposite phase if one were to treat the branching-space vectors as vibrations.…”

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confidence: 99%

In This Molecule There Must Be a Conical Intersection

Robb¹

2014

Advances in Physical Organic Chemistry

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“…To calculate absorption maxima, we used the methodology that has been proven as efficient in a number of our previous studies for different kind of rhodopsins and rhodopsin mimics [21][22][23][24][25][26][27] . The structures of the archaerhodopsin-3 obtained at the previous step were optimized using two-layer ONIOM (QM:MM-EE) scheme.…”

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confidence: 99%

A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

et al. 2017

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It was demonstrated in recent studies that some rhodopsins can be used in optogenetics as fluorescent indicators of membrane voltage. One of the promising candidates for these applications is archaerhodopsin-3. However, the fluorescent signal for wild-type achaerhodopsin-3 is not strong enough for real applications. Rational design of mutants with an improved signal is an important task, which requires both experimental and theoretical studies. Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level multireference ab initio methodology (SORCI+Q/AMBER) to model optical properties of this protein. We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3. The results of this study can be utilized for computational molecular design of efficient fluorescent indicators of membrane voltage for modern optogenetics on the basis of archaerhodopsin-3.

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Computational Photobiology and Beyond

Cited by 38 publications

References 95 publications

A Conical Intersection Controls the Deactivation of the Bacterial Luciferase Fluorophore

A Conical Intersection Controls the Deactivation of the Bacterial Luciferase Fluorophore

In This Molecule There Must Be a Conical Intersection

A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

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