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1.
J Comput Chem ; 45(17): 1493-1504, 2024 Jun 30.
Article in English | MEDLINE | ID: mdl-38476039

ABSTRACT

Avena sativa phototropin 1 light-oxygen-voltage 2 domain (AsLOV2) is a model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N-terminal A'α helix in the dark state followed by the unfolding of the C-terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, ß-sheets are identified as crucial components for mediating allosteric signal transmission between the two termini. Through combined experimental and computational investigations, the Hß and Iß strands are recognized as the most critical and influential ß-sheets in AsLOV2's allosteric mechanism. To elucidate the role of these ß-sheets, we introduced 13 distinct mutations (F490L, N492A, L493A, F494L, H495L, L496F, Q497A, R500A, F509L, Q513A, L514A, D515V, and T517V) and conducted comprehensive molecular dynamics simulations. In-depth hydrogen bond analyses emphasized the role of two hydrogen bonds, Asn482-Leu453 and Gln479-Val520, in the observed distinct behaviors of L493A, L496F, Q497A, and D515V mutants. This illustrates the role of ß-sheets in the transmission of the allosteric signal upon the photoactivation of the light state.


Subject(s)
Molecular Dynamics Simulation , Allosteric Regulation , Protein Conformation, beta-Strand , Phototropins/chemistry , Phototropins/metabolism , Hydrogen Bonding , Protein Conformation
2.
J Mol Biol ; 436(5): 168356, 2024 Mar 01.
Article in English | MEDLINE | ID: mdl-37944792

ABSTRACT

The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.


Subject(s)
Optogenetics , Phototropins , Oxygen , Protein Domains/radiation effects , Phototropins/chemistry , Phototropins/radiation effects , Light
3.
J Photochem Photobiol B ; 224: 112305, 2021 Nov.
Article in English | MEDLINE | ID: mdl-34562831

ABSTRACT

Phototropin (phot) is a blue light photoreceptor in plants and possesses two photosensory light­oxygen-voltage (LOV1 and LOV2) domains with different photo-thermochemical properties. While liverworts contain a single copy of PHOT (e.g., MpPHOT in Marchantia polymorpha), many land plant species contain multicopy PHOT genes (e.g., AtPHOT1 and 2 in Arabidopsis thaliana) due to evolutionary gene duplication. The LOV domains of duplicated phot proteins have been studied in detail, but those of single-copy phot proteins remain to be characterized. As phot has not been duplicated in liverworts, we hypothesized that Mpphot may retain the ancestral function and photo-thermochemical properties. To learn more about the unduplicated phot proteins, we analyzed chloroplast relocation movement and the photo-thermochemical properties of LOV1 and LOV2 in Mpphot (Mpphot-LOV1 and Mpphot-LOV2, respectively). The function of Mpphot-LOV1, which induced a response to move chloroplasts to weak light (the accumulation response) in the absence of photoactive LOV2, differed from that of LOV1 of the duplicated phot proteins of A. thaliana (e.g., Atphot1-LOV1 preventing the accumulation response). On the other hand, the function of Mpphot-LOV2 was similar to that of LOV2 of the duplicated phots. The photo-thermochemical properties of Mpphot were a hybrid of those of the duplicated phots; the photochemical and thermochemical reactions of Mpphot were similar to those of the phot2- and phot1-type proteins, respectively. Our findings reveal conservation and diversification among LOV domains during phot duplication events in land plant evolution.


Subject(s)
Biological Evolution , Genes, Plant , Marchantia/metabolism , Phototropins/physiology , Chloroplasts/metabolism , Phototropins/chemistry , Phototropins/genetics
4.
Phys Chem Chem Phys ; 23(25): 13934-13950, 2021 Jun 30.
Article in English | MEDLINE | ID: mdl-34142688

ABSTRACT

Photosensory receptors containing the flavin-binding light-oxygen-voltage (LOV) domain are modular proteins that fulfil a variety of biological functions ranging from gene expression to phototropism. The LOV photocycle is initiated by blue-light and involves a cascade of intermediate species, including an electronically excited triplet state, that leads to covalent bond formation between the flavin mononucleotide (FMN) chromophore and a nearby cysteine residue. Subsequent conformational changes in the polypeptide chain arise due to the remodelling of the hydrogen bond network in the cofactor binding pocket, whereby a conserved glutamine residue plays a key role in coupling FMN photochemistry with LOV photobiology. Although the dark-to-light transition of LOV photosensors has been previously addressed by spectroscopy and computational approaches, the mechanistic basis of the underlying reactions is still not well understood. Here we present a detailed computational study of three distinct LOV domains: EL222 from Erythrobacter litoralis, AsLOV2 from the second LOV domain of Avena sativa phototropin 1, and RsLOV from Rhodobacter sphaeroides LOV protein. Extended protein-chromophore models containing all known crucial residues involved in the initial steps (femtosecond-to-microsecond) of the photocycle were employed. Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path. In turn, for each evolving species, infrared difference spectra were constructed and compared to experimental EL222 and AsLOV2 transient infrared spectra, the former from original work presented here and the latter from the literature. The good agreement between theory and experiment permitted the assignment of the majority of observed bands, notably the ∼1635 cm-1 transient of the adduct state to the carbonyl of the glutamine side chain after rotation. Moreover, both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration. Additionally, the computed infrared shifts of the glutamine and interacting residues could guide experimental research addressing early events of signal transduction in LOV proteins.


Subject(s)
Glutamine/chemistry , Amino Acid Sequence , Avena/chemistry , Cysteine/chemistry , Flavin Mononucleotide/chemistry , Hydrogen Bonding , Isomerism , Models, Molecular , Normal Distribution , Photochemical Processes , Phototropins/chemistry , Protein Binding , Protein Conformation , Spectrophotometry, Infrared , Sphingomonadaceae/chemistry , Structure-Activity Relationship , Thermodynamics
5.
J Biol Chem ; 296: 100594, 2021.
Article in English | MEDLINE | ID: mdl-33781746

ABSTRACT

The phototropins (phots) are light-activated kinases that are critical for plant physiology and the many diverse optogenetic tools that they have inspired. Phototropins combine two blue-light-sensing Light-Oxygen-Voltage (LOV) domains (LOV1 and LOV2) and a C-terminal serine/threonine kinase domain, using the LOV domains to control the catalytic activity of the kinase. While much is known about the structure and photochemistry of the light-perceiving LOV domains, particularly in how activation of the LOV2 domain triggers the unfolding of alpha helices that communicate the light signal to the kinase domain, many questions about phot structure and mechanism remain. Recent studies have made progress addressing these questions by utilizing small-angle X-ray scattering (SAXS) and other biophysical approaches to study multidomain phots from Chlamydomonas and Arabidopsis, leading to models where the domains have an extended linear arrangement, with the regulatory LOV2 domain contacting the kinase domain N-lobe. We discuss this and other advances that have improved structural and mechanistic understanding of phot regulation in this review, along with the challenges that will have to be overcome to obtain high-resolution structural information on these exciting photoreceptors. Such information will be essential to advancing fundamental understanding of plant physiology while enabling engineering efforts at both the whole plant and molecular levels.


Subject(s)
Light , Phototropins/chemistry , Phototropins/metabolism , Arabidopsis/chemistry , Arabidopsis/metabolism , Chlamydomonas reinhardtii/chemistry , Chlamydomonas reinhardtii/metabolism , Crystallography, X-Ray , Models, Molecular , Plant Proteins/chemistry , Plant Proteins/metabolism , Protein Conformation
6.
Biochemistry ; 59(35): 3206-3215, 2020 09 08.
Article in English | MEDLINE | ID: mdl-32786255

ABSTRACT

Phototropins are photoreceptor proteins that regulate blue light-dependent biological processes for efficient photosynthesis in plants and algae. The proteins consist of a photosensory domain that responds to the ambient light and an output module that triggers cellular responses. The photosensory domain of phototropin from Chlamydomonas reinhardtii contains two conserved LOV (light-oxygen-voltage) domains with flavin chromophores. Blue light triggers the formation of a covalent cysteine-flavin adduct and upregulates the phototropin kinase activity. Little is known about the structural mechanism that leads to kinase activation and how the two LOV domains contribute to this. Here, we investigate the role of the LOV1 domain from C. reinhardtii phototropin by characterizing the structural changes occurring after blue light illumination with nano- to millisecond time-resolved X-ray solution scattering. By structurally fitting the data with atomic models generated by molecular dynamics simulations, we find that adduct formation induces a rearrangement of the hydrogen bond network from the buried chromophore to the protein surface. In particular, the change in conformation and the associated hydrogen bonding of the conserved glutamine 120 induce a global movement of the ß-sheet, ultimately driving a change in the electrostatic potential on the protein surface. On the basis of the change in the electrostatics, we propose a structural model of how LOV1 and LOV2 domains interact and regulate the full-length phototropin from C. reinhardtii. This provides a rationale for how LOV photosensor proteins function and contributes to the optimal design of optogenetic tools based on LOV domains.


Subject(s)
Light Signal Transduction/physiology , Phototropins/chemistry , Phototropins/metabolism , Binding Sites , Chlamydomonas reinhardtii , Light , Models, Molecular , Molecular Dynamics Simulation , Photochemistry , Protein Conformation , Protein Domains , Scattering, Radiation , X-Ray Diffraction
7.
J Biol Chem ; 295(33): 11729-11741, 2020 08 14.
Article in English | MEDLINE | ID: mdl-32580943

ABSTRACT

Proteins are usually studied in well-defined buffer conditions, which differ substantially from those within a host cell. In some cases, the intracellular environment has an impact on the mechanism, which might be missed by in vitro experiments. IR difference spectroscopy previously has been applied to study the light-induced response of photoreceptors and photoenzymes in vitro Here, we established the in-cell IR difference (ICIRD) spectroscopy in the transmission and attenuated total reflection configuration to investigate the light-induced response of soluble proteins in living bacterial cells. ICIRD spectroscopy on the light, oxygen, or voltage (LOV) domains of the blue light receptors aureochrome and phototropin revealed a suppression of the response of specific secondary structure elements, indicating that the intracellular environment affects LOV photoreceptor mechanisms in general. Moreover, in-cell fluorescence spectroscopy disclosed that the intracellular environment slows down the recovery of the light-induced flavin adduct. Segment-resolved ICIRD spectroscopy on basic-region leucine zipper (bZIP)-LOV of aureochrome 1a from the diatom Phaeodactylum tricornutum indicated a signal progression from the LOV sensor to the bZIP effector independent of unfolding of the connecting A'α-helix, an observation that stood in contrast to in vitro results. This deviation was recapitulated in vitro by emulating the intracellular environment through the addition of the crowding agent BSA, but not by sucrose polymers. We conclude that ICIRD spectroscopy is a noninvasive, label-free approach for assessing conformational changes in receptors in living cells at ambient conditions. As demonstrated, these near-native responses may deviate from the mechanisms established under in vitro conditions.


Subject(s)
Spectrophotometry, Infrared/methods , Chlamydomonas reinhardtii/chemistry , Diatoms/chemistry , Light , Models, Molecular , Phototropins/chemistry , Protein Domains , Protein Structure, Secondary
8.
Biophys Chem ; 259: 106337, 2020 04.
Article in English | MEDLINE | ID: mdl-32126442

ABSTRACT

LOV2 (Light-Oxygen-Voltage) domain from Avena sativa phototropin 1 (AsLOV2) belongs to the superfamily of PAS (Per-Arnt-Sim) domains, members of which function as signaling sensors. AsLOV2 undergoes a conformational change upon blue-light absorption by its FMN cofactor. AsLOV2 wild type (wt) is intensively studied as a photo-switchable element in conjugation with various proteins. On the other hand, its variant AsLOV2 with replaced cysteinyl residue C450, which is critical for the forming a covalent adduct with FMN upon irradiation, forms a precursor for some recently developed genetically encoded photosensitizers. In the presented work, we investigated conformational properties of AsLOV2 wt and its variant C450A by circular dichroism, tryptophan and FMN fluorescence, and differential scanning calorimetry in dependence on pH and temperature. We show that both variants are similarly sensitive towards pH of solvent. On the other hand, the mutation C450A leads to a more stable AsLOV2 variant in comparison with the wild type. Thermal transitions of the AsLOV2 proteins monitored by circular dichroism indicate the presence of significant residual structure in thermally-denatured states of both proteins in the pH range from 4 to 9. Both pH- and thermal- transitions of AsLOV2 are accompanied by FMN leaching to solvent. Higher stability, reversibility of thermal transitions, and efficiency of FMN rebinding in the case of C450A variant suggest that the cofactor release may be modulated by suitable mutations in combination with a suitable physicochemical perturbation. These findings can have implications for a design of genetically encoded photosensitizers.


Subject(s)
Phototropins/chemistry , Plant Proteins/chemistry , Amino Acid Substitution , Avena/chemistry , Avena/metabolism , Calorimetry, Differential Scanning , Circular Dichroism , Flavin Mononucleotide/chemistry , Hydrogen-Ion Concentration , Models, Molecular , Protein Conformation, alpha-Helical , Protein Domains , Spectrometry, Fluorescence , Structure-Activity Relationship , Tryptophan/chemistry
9.
J Phys Chem B ; 123(51): 10939-10950, 2019 12 26.
Article in English | MEDLINE | ID: mdl-31790257

ABSTRACT

Phototropin (phot) is a blue light sensor involved in the light responses of several species from green algae to higher plants. Phot consists of two photoreceptive domains (LOV1 and LOV2) and a Ser/Thr kinase domain. These domains are connected by a hinge and a linker domain. So far, studies on the photochemical reaction dynamics of phot have been limited to short fragments, and the reactions of intact phot have not been well elucidated. Here, the photoreactions of full-length phot and of several mutants from Chlamydomonas reinhardtii (Cr) were investigated by the transient grating and circular dichroism (CD) methods. Full-length Cr phot is in monomeric form in both dark and light states and shows conformational changes upon photoexcitation. When LOV1 is excited, the hinge helix unfolds with a time constant of 77 ms. Upon excitation of LOV2, the linker helix unfolds initially followed by a tertiary structural change of the kinase domain with a time constant of 91 ms. The quantum yield of conformational change after adduct formation of LOV2 is much smaller than that of LOV1, indicating that reactive and nonreactive forms exist. The conformational changes associated with the excitations of LOV1 and LOV2 occur independently and additively, even when they are excited simultaneously. Hence, the role of LOV1 is not to enhance the kinase activity in addition to LOV2 function; we suggest LOV1 has different functions such as regulation of intermolecular interactions.


Subject(s)
Algal Proteins/chemistry , Chlamydomonas reinhardtii/chemistry , Phototropins/chemistry , Algal Proteins/genetics , Catalytic Domain , Chlamydomonas reinhardtii/genetics , Chlamydomonas reinhardtii/radiation effects , Chromatography, Gel , Circular Dichroism , Cryptochromes/chemistry , Cryptochromes/genetics , Flavin Mononucleotide/chemistry , Flavin Mononucleotide/genetics , Light , Models, Molecular , Mutation , Photochemical Processes , Phototropins/genetics , Protein Conformation , Protein Serine-Threonine Kinases/chemistry , Protein Serine-Threonine Kinases/genetics
10.
Plant Signal Behav ; 14(10): e1652521, 2019.
Article in English | MEDLINE | ID: mdl-31434535

ABSTRACT

The American biologist Winslow Russel Briggs (1928-2019) was a global leader in plant physiology, genetics and photobiology. In this contribution, we try to share our knowledge of the remarkable career of this outstanding scientist. After earning his PhD at Harvard (Cambridge, Massachusetts), he started his independent research program at Stanford University (California). Among many major contributions was his elegant experiment that conclusively demonstrated the role of auxin transport in the phototropic bending response of grass coleoptiles. During subsequent years as Professor of biology at Harvard University, Briggs focused on phytochrome and photomorphogenesis. In 1973, he re-located to Stanford to become Director of the Department of Plant Biology, Carnegie Institution for Science, and faculty member in the Biology Department at Stanford University. After his retirement (1993), he continued his research on "light and plant development" as an emeritus at Carnegie until the day of his death on February 11, 2019. Through his long research career, Briggs stayed at the cutting edge by re-inventing himself from a plant physiologist, to biochemist, geneticist, and molecular biologist. He made numerous discoveries, including the LOV-domain photoreceptor phototropin. Winslow Briggs, who was also a naturalist and gifted pianist, inspired and promoted the work of generations of young scientists - as mentor, colleague and friend.


Subject(s)
Light , Phototropins/metabolism , Plant Development/radiation effects , History, 20th Century , History, 21st Century , Morphogenesis/radiation effects , Phototropins/chemistry
11.
Nat Methods ; 15(11): 924-927, 2018 11.
Article in English | MEDLINE | ID: mdl-30377362

ABSTRACT

Anti-CRISPR proteins are powerful tools for CRISPR-Cas9 regulation; the ability to precisely modulate their activity could facilitate spatiotemporally confined genome perturbations and uncover fundamental aspects of CRISPR biology. We engineered optogenetic anti-CRISPR variants comprising hybrids of AcrIIA4, a potent Streptococcus pyogenes Cas9 inhibitor, and the LOV2 photosensor from Avena sativa. Coexpression of these proteins with CRISPR-Cas9 effectors enabled light-mediated genome and epigenome editing, and revealed rapid Cas9 genome targeting in human cells.


Subject(s)
Biosensing Techniques , CRISPR-Associated Proteins/antagonists & inhibitors , CRISPR-Cas Systems , Gene Editing , Optogenetics , Phototropins/chemistry , Protein Engineering , Epigenomics , Genome , HEK293 Cells , Humans , Light , Streptococcus pyogenes/enzymology
12.
ACS Synth Biol ; 7(12): 2898-2907, 2018 12 21.
Article in English | MEDLINE | ID: mdl-30441907

ABSTRACT

Optogenetic techniques use light-responsive proteins to study dynamic processes in living cells and organisms. These techniques typically rely on repurposed naturally occurring light-sensitive proteins to control subcellular localization and activity. We previously engineered two optogenetic systems, the light activated nuclear shuttle (LANS) and the light-inducible nuclear exporter (LINX), by embedding nuclear import or export sequence motifs into the C-terminal helix of the light-responsive LOV2 domain of Avena sativa phototropin 1, thus enabling light-dependent trafficking of a target protein into and out of the nucleus. While LANS and LINX are effective tools, we posited that mutations within the LOV2 hinge-loop, which connects the core PAS domain and the C-terminal helix, would further improve the functionality of these switches. Here, we identify hinge-loop mutations that favorably shift the dynamic range (the ratio of the on- to off-target subcellular accumulation) of the LANS and LINX photoswitches. We demonstrate the utility of these new optogenetic tools to control gene transcription and epigenetic modifications, thereby expanding the optogenetic "tool kit" for the research community.


Subject(s)
Avena/metabolism , Phototropins/metabolism , Plant Proteins/metabolism , Protein Engineering/methods , Amino Acid Sequence , Cell Nucleus/metabolism , Cytoplasm/metabolism , Fluorescence Polarization , HeLa Cells , Humans , Light , Mutagenesis , Phototropins/chemistry , Phototropins/genetics , Plant Proteins/chemistry , Plant Proteins/genetics
13.
Chembiochem ; 19(12): 1217-1231, 2018 06 18.
Article in English | MEDLINE | ID: mdl-29577530

ABSTRACT

Signal transductions are the basis for all cellular functions. Previous studies investigating signal transductions mainly relied on pharmacological inhibition, RNA interference, and constitutive active/dominant negative protein expression systems. However, such studies do not allow the modulation of protein activity with high spatial and temporal precision in cells, tissues, and organs in animals. Recently, non-channelrhodopsin-type optogenetic tools for regulating signal transduction have emerged. These photoswitches address several disadvantages of previous techniques, and allow us to control a variety of signal transductions such as cell membrane dynamics, calcium signaling, lipid signaling, and apoptosis. In this review we summarize recent advances in the development of such photoswitches and in how these optotools are applied to signaling processes.


Subject(s)
Optogenetics/methods , Proteins/genetics , Signal Transduction , Animals , Cell Membrane/genetics , Cell Membrane/metabolism , Cell Membrane/radiation effects , Gene Expression Regulation/radiation effects , Humans , Light , Luminescent Proteins/chemistry , Luminescent Proteins/genetics , Luminescent Proteins/metabolism , Phototropins/chemistry , Phototropins/genetics , Phototropins/metabolism , Phytochrome/chemistry , Phytochrome/genetics , Phytochrome/metabolism , Proteins/chemistry , Proteins/metabolism , Signal Transduction/radiation effects
14.
J Phys Chem B ; 122(6): 1801-1815, 2018 02 15.
Article in English | MEDLINE | ID: mdl-29355019

ABSTRACT

Phototropin is a blue light sensor protein found in higher plants and green algae. Photochemical reactions of a variety of differently truncated constructs of a phototropin from Chlamydomonas reinhardtii (Cr) (LOV1, LOV1-hinge, LOV2, LOV2-linker, and hinge-LOV2) are investigated. In the dark state, LOV1 is in dynamic equilibrium between the monomer and dimer, and the main photochemical reaction is dimerization of the monomer and dissociation of the dimer. On the other hand, LOV1-hinge exists as the monomer and the photochemical reaction is the dimerization reaction associated with the unfolding of the helix of the hinge domain. LOV2 in the dark state is monomeric. The conformation changes after the photoexcitation of LOV2 and LOV2-linker are minor, which differs notably from the reaction of LOV2-Jα and LOV2-linker from Arabidopsis thaliana (At). The linker region, including the Jα helix, is rather stable upon photoexcitation. The helix of the hinge domain of hinge-LOV2 is slightly unfolded in the dark state, and the major photoreaction is the dimerization event. The dark recovery rate of LOV2 was found to decrease significantly in the presence of the hinge domain. These photochemical properties of Cr phot are considerably different from those of At phot regarding conformational changes and their kinetics, although Cr phot has been reported to rescue the phot function in At. The differences and the diversity of phots are discussed.


Subject(s)
Chlamydomonas reinhardtii/chemistry , Phototropins/chemistry , Thermodynamics , Chlamydomonas reinhardtii/metabolism , Kinetics , Photochemical Processes , Phototropins/metabolism , Protein Conformation
15.
J Biol Chem ; 293(3): 963-972, 2018 01 19.
Article in English | MEDLINE | ID: mdl-29196607

ABSTRACT

Phototropin2 (phot2) is a blue-light (BL) receptor that regulates BL-dependent activities for efficient photosynthesis in plants. phot2 comprises two BL-receiving light-oxygen-voltage-sensing domains (LOV1 and LOV2) and a kinase domain. BL-excited LOV2 is thought to be primarily responsible for the BL-dependent activation of the kinase. However, the molecular mechanisms by which small BL-induced conformational changes in the LOV2 domain are transmitted to the kinase remain unclear. Here, we used full-length wild-type and mutant phot2 proteins from Arabidopsis to study their molecular properties in the dark and under BL irradiation. Phosphorylation assays and absorption measurements indicated that the LOV1 domain assists the thermal relaxation of BL-excited LOV2 and vice versa. Using small-angle X-ray scattering and electron microscopy, we observed that phot2 forms a dimer and has a rod shape with a maximum length of 188 Å and a radius of gyration of 44 Å. Under BL, phot2 displayed large conformational changes that bent the rod shape. By superimposing the crystal structures of the LOV1 dimer, LOV2, and a homology model of the kinase to the observed changes, we inferred that the BL-dependent change consisted of positional shifts of both LOV2 and the kinase relative to LOV1. Furthermore, phot2 mutants lacking the photocycle in LOV1 or LOV2 still exhibited conformational changes under BL, suggesting that LOV1 and LOV2 cooperatively contribute to the conformational changes that activate the kinase. These results suggest that BL-activated LOV1 contributes to the kinase activity of phot2. We discuss the possible intramolecular interactions and signaling mechanisms in phot2.


Subject(s)
Arabidopsis Proteins/metabolism , Light , Arabidopsis/metabolism , Arabidopsis/radiation effects , Arabidopsis Proteins/chemistry , Crystallography, X-Ray , Phototropins/chemistry , Phototropins/metabolism , Signal Transduction/radiation effects
16.
Biochemistry ; 57(5): 494-497, 2018 02 06.
Article in English | MEDLINE | ID: mdl-29261300

ABSTRACT

The light oxygen voltage-sensing (LOV) domain plays a crucial role in blue light (BL) sensing in plants and microorganisms. LOV domains are usually associated with the effector domains and regulate the activities of effector domains in a BL-dependent manner. Photozipper (PZ) is monomeric in the dark state. BL induces reversible dimerization of PZ and subsequently increases its affinity for the target DNA sequence. In this study, we report the analyses of PZ by pulsed electron-electron double resonance (PELDOR). The neutral flavin radical was formed by BL illumination in the presence of dithiothreitol in the LOV-C254S (without the bZIP domain) and PZ-C254S mutants, where the cysteine residue responsible for adduct formation was replaced with serine. The magnetic dipole interactions of 3 MHz between the neutral radicals were detected in both LOV-C254S and PZ-C254S, indicating that these mutants are dimeric in the radical state. The PELDOR simulation showed that the distance between the radical pair is close to that estimated from the dimeric crystal structure in the "light state" [Heintz, U., and Schlichting, I. (2016) eLife 5, e11860], suggesting that in the radical state, LOV domains in PZ-C254S form a dimer similar to that of LOV-C254S, which lacks the bZIP domain.


Subject(s)
Phototropins/chemistry , Stramenopiles/chemistry , Databases, Protein , Diatoms/chemistry , Diatoms/metabolism , Diatoms/radiation effects , Dithiothreitol/metabolism , Light , Models, Molecular , Phototropins/metabolism , Protein Conformation/radiation effects , Protein Domains/radiation effects , Protein Multimerization/radiation effects , Stramenopiles/metabolism , Stramenopiles/radiation effects
17.
Biochemistry ; 56(24): 3099-3108, 2017 06 20.
Article in English | MEDLINE | ID: mdl-28530801

ABSTRACT

The light oxygen voltage (LOV) domain is a flavin-binding blue-light receptor domain, originally found in a plant photoreceptor phototropin (phot). Recently, LOV domains have been used in optogenetics as the photosensory domain of fusion proteins. Therefore, it is important to understand how LOV domains exhibit light-induced structural changes for the kinase domain regulation, which enables the design of LOV-containing optogenetics tools with higher photoactivation efficiency. In this study, the hydrogen bonding environment of the N3-H group of flavin mononucleotide (FMN) of the LOV2 domain from Adiantum neochrome (neo) 1 was investigated by low-temperature Fourier transform infrared spectroscopy. Using specifically 15N-labeled FMN, [1,3-15N2]FMN, the N3-H stretch was identified at 2831 cm-1 for the unphotolyzed state at 150 K, indicating that the N3-H group forms a fairly strong hydrogen bond. The N3-H stretch showed temperature dependence, with a shift to lower frequencies at ≤200 K and to higher frequencies at ≥250 K from the unphotolyzed to the intermediate states. Similar trends were observed in the LOV2 domains from Arabidopsis phot1 and phot2. By contrast, the N3-H stretch of the Q1029L mutant of neo1-LOV2 and neo1-LOV1 was not temperature dependent in the intermediate state. These results seemed correlated with our previous finding that the LOV2 domains show the structural changes in the ß-sheet region and/or the adjacent Jα helix of LOV2 domain, but that such structural changes do not take place in the Q1029L mutant or neo1-LOV1 domain. The environment around the N3-H group was also investigated.


Subject(s)
Arabidopsis Proteins/metabolism , DNA-Binding Proteins/metabolism , Flavin Mononucleotide/chemistry , Flavin Mononucleotide/metabolism , Phototropins/chemistry , Phototropins/metabolism , Arabidopsis Proteins/chemistry , DNA-Binding Proteins/chemistry , Hydrogen Bonding
18.
Nat Commun ; 8: 15017, 2017 05 12.
Article in English | MEDLINE | ID: mdl-28497795

ABSTRACT

Engineering light-sensitive protein regulators has been a tremendous multidisciplinary challenge. Optogenetic regulators of MAPKs, central nodes of cellular regulation, have not previously been described. Here we present OptoJNKi, a light-regulated JNK inhibitor based on the AsLOV2 light-sensor domain using the ubiquitous FMN chromophore. OptoJNKi gene-transfer allows optogenetic applications, whereas protein delivery allows optopharmacology. Development of OptoJNKi suggests a design principle for other optically regulated inhibitors. From this, we generate Optop38i, which inhibits p38MAPK in intact illuminated cells. Neurons are known for interpreting temporally-encoded inputs via interplay between ion channels, membrane potential and intracellular calcium. However, the consequences of temporal variation of JNK-regulating trophic inputs, potentially resulting from synaptic activity and reversible cellular protrusions, on downstream targets are unknown. Using OptoJNKi, we reveal maximal regulation of c-Jun transactivation can occur at unexpectedly slow periodicities of inhibition depending on the inhibitor's subcellular location. This provides evidence for resonance in metazoan JNK-signalling circuits.


Subject(s)
Neurons/drug effects , Optogenetics/methods , Protein Kinase Inhibitors/pharmacology , p38 Mitogen-Activated Protein Kinases/antagonists & inhibitors , Animals , Avena/genetics , Avena/metabolism , COS Cells , Cells, Cultured , Chlorocebus aethiops , Drug Design , Female , HEK293 Cells , Humans , Light , MAP Kinase Signaling System/drug effects , MAP Kinase Signaling System/genetics , MAP Kinase Signaling System/radiation effects , Male , Neurons/metabolism , Neurons/radiation effects , Phototropins/chemistry , Phototropins/genetics , Phototropins/metabolism , Protein Kinase Inhibitors/chemistry , Rats , p38 Mitogen-Activated Protein Kinases/genetics , p38 Mitogen-Activated Protein Kinases/metabolism
19.
J Phys Chem B ; 121(17): 4414-4421, 2017 05 04.
Article in English | MEDLINE | ID: mdl-28387114

ABSTRACT

Phototropins (phots) are blue light sensors found in a variety of higher plants and algae. The photochemical reactions of this family of proteins have attracted much attention since their discovery. Phots have two light sensor domains called light-oxygen-voltage 1 (LOV1) and LOV2. After the formation of the characteristic adduct of the LOV domain, a conformational change of the C-terminal region of the LOV2 domain occurs, and characterizing this change is important for understanding biological function, that is, kinase activation. Here, the reaction dynamics of the Jα-helix and the extended region adjacent to the Jα-helix (connector) have been investigated. The conformation of the connector part and the Jα-helix were found to alter significantly in a two-state manner. Furthermore, the conformational change of the kinase domain was also successfully detected as a change in translational diffusion, although the CD intensity due to the kinase domain movement was almost silent. These observations indicate that the tertiary structure of the kinase domain changes. The rate of the kinase domain change is almost the same as that of the change for the LOV2-linker, suggesting that the conformational change of the linker is the rate-determining step for kinase activation.


Subject(s)
Arabidopsis Proteins/chemistry , DNA-Binding Proteins/chemistry , Light , Phosphotransferases/chemistry , Phototropins/chemistry , Phosphotransferases/metabolism , Protein Conformation
20.
Phys Chem Chem Phys ; 19(17): 10808-10819, 2017 May 03.
Article in English | MEDLINE | ID: mdl-28271102

ABSTRACT

LOV (light-, oxygen- or voltage-sensitive) domains act as photosensory units of many prokaryotic and eukaryotic proteins. Upon blue light excitation they undergo a photocycle via the excited triplet state of their flavin chromophore yielding the flavin-cysteinyl adduct. Adduct formation is highly conserved among all LOV domains and constitutes the primary step of LOV domain signaling. But recently, it has been shown that signal propagation can also be triggered by flavin photoreduction to the neutral semiquinone offering new prospects for protein engineering. This, however, requires mutation of the photo-active Cys. Here, we report on LOV1 mutants of C. reinhardtii phototropin in which adduct formation is suppressed although the photo-active Cys is present. Introduction of a Tyr into the LOV core induces a proton coupled electron transfer towards the flavin chromophore. Flavin radical species are formed via either the excited flavin singlet or triplet state depending on the geometry of donor and acceptor. This photoreductive pathway resembles the photoreaction observed in other blue light photoreceptors, e.g. blue-light sensors using flavin adenine dinucleotide (BLUF) domains or cryptochromes. The ability to tune the photoreactivity of the flavin chromophore inside the LOV core has implications for the mechanism of adduct formation in the wild type and may be of use for protein engineering.


Subject(s)
Cysteine/chemistry , Light , Oxygen/chemistry , Phototropins/chemistry , Phototropins/metabolism , Protein Domains , Chlamydomonas reinhardtii/genetics , Chlamydomonas reinhardtii/metabolism , Cysteine/metabolism , Dinitrocresols/chemistry , Electron Transport , Mutation , Phototropins/genetics
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