Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark‐ and Light‐Adapted States of a Blue‐Light YtvA LOV Photoreceptor

Chang, Xue-Ping; Gao, Yuan‐Jun; Fang, Wei‐Hai; Cui, Ganglong; Thiel, Walter

doi:10.1002/anie.201703487

Cited by 28 publications

(29 citation statements)

References 35 publications

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“…Moreover, two intermediates can be placed on the triplet manifold, before (T 1 ) and after H-transfer to N 5 (T 1-H ), while in the adduct, the ground state S 0 0 is the most valid electronic state since formation on that surface proceeds barrierless. 13 With respect to the conserved glutamine (Scheme 1), at each one of the intermediates described above, it can have the side chain amide group either towards the FMN or flipped, and can also be in amidic or imidic tautomeric form as was suggested for the BLUF proteins. 37 By combining Scheme 1 and Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The mechanism of H-transfer (simultaneous/concerted) will not be investigated here, only the resultant neutral biradical species. Subsequently, a covalent bond is formed between the cysteine sulfur and flavin C 4a atoms with a concomitant crossing to the electronic ground state at typical time scales of 0.2-20 ms, [13][14][15][16][17] which is indicated by an absorption signal at 390 nm. 18 Once the biradical (T 1-H ) or the adduct ðS 0 0 Þ intermediates have been formed in the LOV domain, large scale effects are initiated, 19,20 which ultimately enable the parental full-length protein to perform its assigned function.…”

Section: Introductionmentioning

confidence: 99%

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QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors

Andrikopoulos

Chaudhari

Liu

et al. 2021

Phys. Chem. Chem. Phys.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors

Andrikopoulos

Chaudhari

Liu

et al. 2021

Phys. Chem. Chem. Phys.

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“…Molecular dynamics (MD) simulations have previously guided hypotheses into the mechanism of formation, 21 and breakdown, 22 of the Cys-FMN adduct, and the accompanying structural dynamics, 13,23 in native LOV domains and mutants lacking the Cys residue. 24 Initial studies by Peter et al focused on the role of the Iβ and Hβ strands in signal propagation, 23 resulting in the proposal that stress on Iβ leads to rearrangement of the hydrogen bonding contacts between Hβ and the Jα helix and helix unfolding.…”

Section: Introductionmentioning

confidence: 99%

Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix

Iuliano

Collado

Gil

et al. 2020

Preprint

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22Light-activated protein domains provide a convenient, modular, and genetically encodable sensor 23 for optogenetics and optobiology. Although these domains have now been deployed in numerous 24 systems, the precise mechanism of photoactivation and the accompanying structural dynamics that 25 modulate output domain activity remain to be fully elucidated. In the C-terminal light, oxygen, 26 voltage (LOV) domain of plant phototropins (LOV2), blue light activation leads to formation of 27 an adduct between a conserved Cys residue and the embedded FMN chromophore, rotation of a 28 conserved Gln (Q513), and unfolding of a helix (Jα-helix) which is coupled to the output partner. 29 In the present work, we focus on the allosteric pathways leading to Jα helix unfolding in Avena 30 sativa LOV2 (AsLOV2) using an interdisciplinary approach involving molecular dynamics 31 simulations extending to 7 μs, time-resolved infrared spectroscopy, solution NMR spectroscopy, 32 and in-cell optogenetic experiments. In the dark state, the side chain of N414 is hydrogen bonded 33 to the backbone N-H of Q513. The simulations predict a lever-like motion of Q513 after Cys 34 adduct formation resulting in loss of the interaction between the side chain of N414 and the 35 backbone C=O of Q513, and formation of a transient hydrogen bond between the Q513 and N414 36 side chains. The central role of N414 in signal transduction was evaluated by site-directed 37 mutagenesis supporting a direct link between Jα helix unfolding dynamics and the cellular function 38 of the Zdk2-AsLOV2 optogenetic construct. Through this multifaceted approach, we show that 39 Q513 and N414 are critical mediators of protein structural dynamics, linking the ultrafast (sub-ps) 40 excitation of the FMN chromophore to the microsecond conformational changes that result in 41 photoreceptor activation and biological function.42 43 44 The C-terminal light, oxygen, voltage (LOV) domain from plant phototropins are versatile 45 protein domains that have been adapted for protein engineering and molecular imaging. 1,2 LOV 46 photoreceptors are members of the Per-ARNT-Sim (PAS) domain superfamily and use a non-47 covalently bound flavin mononucleotide (FMN) cofactor to sense 450 nm (blue) light (Figure 48 1A). 3 Light excitation initiates a photocycle in which a singlet excited state undergoes intersystem 49 crossing to a triplet excited state which subsequently forms a covalent Cys-FMN-C4a adduct on 50 the μs timescale that absorbs at 390 nm (A390). 4 Formation of the A390 Cys adduct and 51 accompanying protonation of the adjacent N5 position 5 are thought to be the driving force behind 52 the structural changes that accompany effector activation in the LOV domain family including 53 alterations in the structure and conformation of the C-terminal Jα helix. 6 54 4 55 Figure 1: The AsLOV2 domain. (A) The isoalloxazine ring of the FMN cofactor. (B) The FMN 56 cofactor (yellow) makes hydrogen bonding interactions with Q513, N492 and N482. Q513 in turn 57 is hydrogen bonded to N...

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“…376 Exploiting their intrinsic photochromicity (cf. section 3.2.2.), 157,377 wt LOV domains with intact cysteine residues can also function as LOV-based FPs. The photochromicity of Bs YtvA has been employed for localization-based super-resolution microscopy, where blue light completely switched off fluorescence and violet light recovered fluorescence at the single-molecule level, thus achieving ca.…”

Section: Off-label Use Of Photoreceptorsmentioning

confidence: 99%

Blue-Light Receptors for Optogenetics

2018

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Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.

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Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark‐ and Light‐Adapted States of a Blue‐Light YtvA LOV Photoreceptor

Cited by 28 publications

References 35 publications

QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors

QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors

Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix

Blue-Light Receptors for Optogenetics

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