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1.
J Mol Biol ; 436(5): 168463, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38307159

RESUMO

Adaptation to rapid environmental changes is crucial for maintaining optimal photosynthetic efficiency and is ultimately key to the survival of all photosynthetic organisms. Like most of them, cyanobacteria protect their photosynthetic apparatus against rapidly increasing light intensities by nonphotochemical quenching (NPQ). In cyanobacteria, NPQ is controlled by Orange Carotenoid Protein (OCP) photocycle. OCP is the only known photoreceptor that uses carotenoid for its light activation. How carotenoid drives and controls this unique photoactivation process is still unknown. However, understanding and potentially controlling the OCP photocycle may open up new possibilities for improving photosynthetic biomass. Here we investigate the effect of the carbonyl group in the ß2 ring of the carotenoid on the OCP photocycle. We report microsecond to minute OCP light activation kinetics and Arrhenius plots of the two OCP forms: Canthaxanthin-bound OCP (OCPCAN) and echinenone-bound OCP (OCPECH). The difference between the two carotenoids is the presence of a carbonyl group in the ß2-ring located in the N-terminal domain of the protein. A combination of temperature-dependent spectroscopy, flash photolysis, and pump-probe transient absorption allows us to report the previously unresolved OCP intermediate associated primarily with the absorption bleach (OCPB). OCPB dominates the photokinetics in the µs to subms time range for OCPCAN and in the µs to ms range for OCPECH. We show that in OCPCAN the OCP photocycle steps are always faster than in OCPECH: from 2 to almost 20 times depending on the step. These results suggest that the presence of the carbonyl group in the ß2-ring of the carotenoid accelerates the OCP photocycle.


Assuntos
Proteínas de Bactérias , Fotorreceptores Microbianos , Fotossíntese , Proteínas de Bactérias/química , Proteínas de Bactérias/efeitos da radiação , Luz , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/efeitos da radiação , Análise Espectral , Cinética
2.
J Mol Biol ; 436(5): 168439, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38185322

RESUMO

The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.


Assuntos
Adenilil Ciclases , Proteínas de Bactérias , Oscillatoria , Fotorreceptores Microbianos , Trifosfato de Adenosina/química , Adenilil Ciclases/química , Adenilil Ciclases/efeitos da radiação , Proteínas de Bactérias/química , Proteínas de Bactérias/efeitos da radiação , Flavina-Adenina Dinucleotídeo/química , Transdução de Sinais , Espectroscopia de Infravermelho com Transformada de Fourier , Oscillatoria/enzimologia , Domínio Catalítico , Triptofano/química , Metionina/química , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/efeitos da radiação , Ativação Enzimática
3.
Adv Biol (Weinh) ; 6(7): e2000337, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35481696

RESUMO

In the rapidly expanding field of molecular optogenetics, the performance of the engineered systems relies on the switching properties of the underlying genetically encoded photoreceptors. In this study, the bacterial phytochromes Cph1 and DrBphP are engineered, recombinantly produced in Escherichia coli, and characterized regarding their switching properties in order to synthesize biohybrid hydrogels with increased light-responsive stiffness modulations. The R472A mutant of the cyanobacterial phytochrome 1 (Cph1) is identified to confer the phytochrome-based hydrogels with an increased dynamic range for the storage modulus but a different light-response for the loss modulus compared to the original Cph1-based hydrogel. Stiffness measurements of human atrial fibroblasts grown on these hydrogels suggest that differences in the loss modulus at comparable changes in the storage modulus affect cell stiffness and thus underline the importance of matrix viscoelasticity on cellular mechanotransduction. The hydrogels presented here are of interest for analyzing how mammalian cells respond to dynamic viscoelastic cues. Moreover, the Cph1-R472A mutant, as well as the benchmarking of the other phytochrome variants, are expected to foster the development and performance of future optogenetic systems.


Assuntos
Proteínas de Bactérias , Hidrogéis , Mecanotransdução Celular , Optogenética , Fotorreceptores Microbianos , Fitocromo , Proteínas Quinases , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/efeitos da radiação , Benchmarking , Cianobactérias/genética , Escherichia coli/metabolismo , Fibroblastos , Engenharia Genética , Humanos , Hidrogéis/química , Mecanotransdução Celular/efeitos da radiação , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/genética , Fotorreceptores Microbianos/efeitos da radiação , Fitocromo/química , Fitocromo/genética , Fitocromo/efeitos da radiação , Proteínas Quinases/química , Proteínas Quinases/genética , Proteínas Quinases/efeitos da radiação , Viscosidade
4.
Biochemistry ; 59(50): 4703-4710, 2020 12 22.
Artigo em Inglês | MEDLINE | ID: mdl-33287544

RESUMO

YtvA from Bacillus subtilis is a sensor protein that responds to blue light stress and regulates the activity of transcription factor σB. It is composed of the N-terminal LOV (light-oxygen-voltage) domain, the C-terminal STAS (sulfate transporter and anti-sigma factor antagonist) domain, and a linker region connecting them. In this study, the photoreaction and kinetics of full-length YtvA and the intermolecular interaction with a downstream protein, RsbRA, were revealed by the transient grating method. Although N-YLOV-linker, which is composed of the LOV domain of YtvA with helices A'α and Jα, exhibits a diffusion change due to the rotational motion of the helices, the YtvA dimer does not show the diffusion change. This result suggests that the STAS domain inhibits the rotational movement of helices A'α and Jα. We found that the YtvA dimer formed a heterotetramer with the RsbRA dimer probably via the interaction between the STAS domains, and we showed the diffusion change upon blue light illumination with a time constant faster than 70 µs. This result suggests a conformational change of the STAS domains; i.e., the interface between the STAS domains of the proteins changes to enhance the friction with water by the rotation structural change of helices A'α and Jα of YtvA.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/efeitos da radiação , Fosfoproteínas/química , Fosfoproteínas/efeitos da radiação , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/efeitos da radiação , Bacillus subtilis/química , Bacillus subtilis/metabolismo , Bacillus subtilis/efeitos da radiação , Proteínas de Bactérias/metabolismo , Difusão Dinâmica da Luz , Luz , Modelos Moleculares , Fosfoproteínas/metabolismo , Processos Fotoquímicos , Fotorreceptores Microbianos/metabolismo , Domínios e Motivos de Interação entre Proteínas/efeitos da radiação , Estrutura Quaternária de Proteína/efeitos da radiação
5.
Biochemistry ; 59(51): 4810-4821, 2020 12 29.
Artigo em Inglês | MEDLINE | ID: mdl-33334095

RESUMO

PYPs (photoactive yellow proteins) are blue light sensor proteins found in more than 100 species. Compared with the extensive and intensive studies of the reactions of PYP from Halorhodospira halophila (Hh-PYP), studies of the reactions of other PYPs are scarce. Here, the photoreaction of PYP from Rhodobacter capsulatus (Rc-PYP) was studied in detail using ultraviolet-visible absorption and transient grating methods. Rc-PYP exhibits two absorption peaks at 375 and 438 nm. By using the transient absorption and the temperature-dependent absorption spectrum, the absorption spectra of two forms, pUV and pBL, were determined. Upon photoexcitation of pBL, two intermediates are observed before returning back to the dark state, with a time constant of 1.2 ms, which is 3 orders of magnitude faster than the dark recovery of Hh-PYP. Upon photoexcitation of pUV, two intermediates are observed to produce a long-lived final product, although one of the processes is spectrally silent. The diffusion coefficients decreased transiently for both pBL and pUV reactions, suggesting a relatively large conformational change during the reactions. It is particularly interesting to observe that the blue light irradiation of the long-lived product of pUV returns the product to the dark state. This result suggests different opposing responses of the biological function due to photoexcitation by ultraviolet and blue lights.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/efeitos da radiação , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/efeitos da radiação , Rhodobacter capsulatus/química , Conformação Proteica/efeitos da radiação , Raios Ultravioleta
6.
Nat Commun ; 11(1): 4248, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32843623

RESUMO

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.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Cristalografia por Raios X/métodos , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/metabolismo , Proteínas de Bactérias/efeitos da radiação , Cinética , Luz , Estrutura Molecular , Processos Fotoquímicos , Fotorreceptores Microbianos/efeitos da radiação , Conformação Proteica , Análise Espectral
7.
Proc Natl Acad Sci U S A ; 117(27): 15573-15580, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32571944

RESUMO

Cyanobacteriochromes (CBCRs) are small, bistable linear tetrapyrrole (bilin)-binding light sensors which are typically found as modular components in multidomain cyanobacterial signaling proteins. The CBCR family has been categorized into many lineages that roughly correlate with their spectral diversity, but CBCRs possessing a conserved DXCF motif are found in multiple lineages. DXCF CBCRs typically possess two conserved Cys residues: a first Cys that remains ligated to the bilin chromophore and a second Cys found in the DXCF motif. The second Cys often forms a second thioether linkage, providing a mechanism to sense blue and violet light. DXCF CBCRs have been described with blue/green, blue/orange, blue/teal, and green/teal photocycles, and the molecular basis for some of this spectral diversity has been well established. We here characterize AM1_1499g1, an atypical DXCF CBCR that lacks the second cysteine residue and exhibits an orange/green photocycle. Based on prior studies of CBCR spectral tuning, we have successfully engineered seven AM1_1499g1 variants that exhibit robust yellow/teal, green/teal, blue/teal, orange/yellow, yellow/green, green/green, and blue/green photocycles. The remarkable spectral diversity generated by modification of a single CBCR provides a good template for multiplexing synthetic photobiology systems within the same cellular context, thereby bypassing the time-consuming empirical optimization process needed for multiple probes with different protein scaffolds.


Assuntos
Proteínas de Bactérias/metabolismo , Evolução Molecular , Luz , Fotorreceptores Microbianos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/efeitos da radiação , Cor , Cianobactérias/genética , Cianobactérias/metabolismo , Cianobactérias/efeitos da radiação , Mutagênese Sítio-Dirigida , Nostoc/genética , Nostoc/metabolismo , Nostoc/efeitos da radiação , Fotobiologia/métodos , Fotorreceptores Microbianos/efeitos da radiação , Biologia Sintética/métodos , Tetrapirróis/metabolismo
8.
Phys Chem Chem Phys ; 22(16): 8535-8544, 2020 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-32301950

RESUMO

Photoinduced double-bond isomerisation of the chromophore of photoactive yellow protein (PYP) is highly sensitive to chromophore-protein interactions. On the basis of high-level ab initio calculations, we scrutinise the effect of hydrogen bonds on the photophysical and photochemical properties of the chromophore. We identify four resonance structures - two closed-shell and two biradicaloid - that elucidate the electronic structure of the ground and first excited states involved in the isomerisation process. Changing the relative energies of the resonance structures by hydrogen-bonding interactions tunes all photochemical properties of the chromophore in an interdependent manner. Our study sheds new light on the role of the chromophore electronic structure in tuning in photosensors and fluorescent proteins.


Assuntos
Proteínas de Bactérias/química , Fotoquímica , Fotorreceptores Microbianos/química , Proteínas de Bactérias/efeitos da radiação , Ligação de Hidrogênio , Isomerismo , Luz , Fotorreceptores Microbianos/efeitos da radiação , Estrutura Terciária de Proteína
9.
J Phys Chem Lett ; 11(7): 2470-2476, 2020 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-32150415

RESUMO

We have employed the QM(CASPT2//CASSCF)/MM method to explore the excited-state isomerization and decay mechanism of a single-bond-rotation locked photoactive yellow protein (PYP) chromophore in wild-type and mutant proteins. The S1 state is a spectroscopically bright state in the Franck-Condon region. In this state, there exist two excited-state isomerization pathways separately related to the clockwise and anticlockwise rotations of the C=C bond. The clockwise path is favorable because of a small barrier of 2 kcal/mol and uses a novel bicycle-pedal unidirectional photoisomerization mechanism in which the involved two dihedral angles rotate asynchronously because of the reinforced hydrogen-bonding interaction between the chromophore and Cys69. Near the twisted S1 minimum, the chromophore hops to the S0 state via the S1/S0 conical intersection. Finally, the R52A mutation has small effects on the excited-state properties and photoisomerization of the locked PYP chromophore. The present work provides new insights for understanding the photochemistry of PYP chromophores in protein surroundings.


Assuntos
Proteínas de Bactérias/química , Fotorreceptores Microbianos/química , Propionatos/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/efeitos da radiação , Ácidos Cumáricos , Ligação de Hidrogênio , Isomerismo , Modelos Químicos , Mutação , Processos Fotoquímicos , Fotorreceptores Microbianos/genética , Fotorreceptores Microbianos/efeitos da radiação , Propionatos/efeitos da radiação , Teoria Quântica , Estereoisomerismo , Termodinâmica
10.
Sci Rep ; 10(1): 2061, 2020 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-32029866

RESUMO

Blue Light Using Flavin (BLUF) domains are increasingly being adopted for use in optogenetic constructs. Despite this, much remains to be resolved on the mechanism of their activation. The advent of unnatural amino acid mutagenesis opens up a new toolbox for the study of protein structural dynamics. The tryptophan analogue, 7-aza-Trp (7AW) was incorporated in the BLUF domain of the Activation of Photopigment and pucA (AppA) photoreceptor in order to investigate the functional dynamics of the crucial W104 residue during photoactivation of the protein. The 7-aza modification to Trp makes selective excitation possible using 310 nm excitation and 380 nm emission, separating the signals of interest from other Trp and Tyr residues. We used Förster energy transfer (FRET) between 7AW and the flavin to estimate the distance between Trp and flavin in both the light- and dark-adapted states in solution. Nanosecond fluorescence anisotropy decay and picosecond fluorescence lifetime measurements for the flavin revealed a rather dynamic picture for the tryptophan residue. In the dark-adapted state, the major population of W104 is pointing away from the flavin and can move freely, in contrast to previous results reported in the literature. Upon blue-light excitation, the dominant tryptophan population is reorganized, moves closer to the flavin occupying a rigidly bound state participating in the hydrogen-bond network around the flavin molecule.


Assuntos
Proteínas de Bactérias/metabolismo , Flavinas/metabolismo , Flavoproteínas/metabolismo , Luz , Fotorreceptores Microbianos/metabolismo , Triptofano/análogos & derivados , Proteínas de Bactérias/química , Proteínas de Bactérias/efeitos da radiação , Flavinas/química , Flavinas/efeitos da radiação , Flavoproteínas/química , Flavoproteínas/efeitos da radiação , Transferência Ressonante de Energia de Fluorescência , Ligação de Hidrogênio/efeitos da radiação , Conformação Molecular , Simulação de Dinâmica Molecular , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/efeitos da radiação , Triptofano/química , Triptofano/metabolismo , Triptofano/efeitos da radiação
11.
Anal Chem ; 92(1): 1024-1032, 2020 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-31769286

RESUMO

The application of vibrational labels such as thiocyanate  (-S-C≡N) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the C≡N oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the C≡N stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interactions.


Assuntos
Proteínas de Bactérias/química , Óxido de Deutério/química , Fotorreceptores Microbianos/química , Tiocianatos/química , Proteínas de Bactérias/efeitos da radiação , Halorhodospira halophila/química , Luz , Simulação de Dinâmica Molecular , Fotorreceptores Microbianos/efeitos da radiação , Conformação Proteica , Espectrofotometria Infravermelho , Tiocianatos/efeitos da radiação , Vibração
12.
Biochemistry ; 58(24): 2720-2729, 2019 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-31120245

RESUMO

Phytochromes (Phys) are photoreceptor proteins that sense red/far-red light in plants, fungi, and bacteria. The proteins consist of a light-sensing photosensory module and a signaling output module, which is typically a histidine kinase (HK) domain in bacteriophytochromes. Although the time-resolved detection of the HK domain is essential for obtaining insights into the reaction mechanism of photoactivation, it has been very difficult to detect the change. Here, the reaction of Cph1, one of the Phys found in the cyanobacterium Synechocystis sp. PCC6803, was studied using time-resolved translational diffusion detection. It was found that the kinetics of the HK domain movement of the Cph1 dimer could be monitored successfully. The diffusion coefficient of the Cph1 dimer decreases significantly with a time constant similar to that of the final step of the reaction monitored by the transient absorption method (780 ms), whereas the monomer does not exhibit this change. We attribute this change to the closed-to-open type of conformational change in the HK domain of the Cph1 dimer without the secondary structure change. The fact that the rate is similar to that from the transient absorption method suggests that the proton uptake at His260 is the rate-determining step of the conformational change.


Assuntos
Proteínas de Bactérias/química , Fotorreceptores Microbianos/química , Proteínas Quinases/química , Synechocystis/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/efeitos da radiação , Difusão , Escherichia coli/genética , Cinética , Luz , Fotorreceptores Microbianos/genética , Fotorreceptores Microbianos/efeitos da radiação , Conformação Proteica , Domínios Proteicos , Proteínas Quinases/genética , Proteínas Quinases/efeitos da radiação , Estrutura Quaternária de Proteína
13.
Biochemistry ; 58(18): 2297-2306, 2019 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-30973006

RESUMO

Cyanobacteriochromes (CBCRs) make up a diverse family of cyanobacterial photoreceptors distantly related to the phytochrome photoreceptors of land plants. At least two lineages of CBCRs have reacquired red-absorbing dark states similar to the phytochrome Pr resting state but are coupled to green-absorbing light-adapted states rather than the canonical far-red-absorbing light-adapted state. One such lineage includes the canonical red/green (R/G) CBCRs that includes AnPixJg2 (UniProtKB Q8YXY7 ) and NpR6012g4 (UniProtKB B2IU14 ) that have been extensively characterized. Here we examine the forward Pr photodynamics of NpR3784 (UniProtKB B2J457 ), a representative member of the second R/G CBCR subfamily. Using broadband transient absorption pump-probe spectroscopy, we characterize both primary (100 fs to 10 ns) and secondary (10 ns to 1 ms) forward (Pr → Pg) photodynamics and compare the results to temperature-jump cryokinetics measurements. Our studies show that primary isomerization dynamics occur on an ∼10 ps timescale, yet remarkably, the red-shifted primary Lumi-Rf photoproduct found in all photoactive canonical R/G CBCRs examined to date is extremely short-lived in NpR3784. These results demonstrate that differences in reaction pathways reflect the evolutionary history of R/G CBCRs despite the convergent evolution of their photocycle end products.


Assuntos
Proteínas de Bactérias/metabolismo , Luz , Nostoc/metabolismo , Fotorreceptores Microbianos/metabolismo , Cinética , Nostoc/efeitos da radiação , Processos Fotoquímicos/efeitos da radiação , Fotorreceptores Microbianos/efeitos da radiação , Espectrofotometria
14.
Biochemistry ; 58(18): 2307-2317, 2019 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-30977638

RESUMO

In the companion paper (10.1021/acs.biochem.8b01274), we examined the forward Pr photodynamics of NpR3784 (UniProtKB B2J457 ), a representative member of a noncanonical red/green (R/G) cyanobacteriochrome (CBCR) subfamily. Here the reverse Pg → Pr photodynamics of NpR3784 was studied by broadband transient absorption pump-probe spectroscopy. Primary (100 fs to 10 ns) and secondary (10 ns to 1 ms) photodynamics were characterized over nine decades of time, which also were complemented with temperature-jump cryokinetics measurements. In contrast with canonical R/G CBCRs, the NpR3784 reverse photoconversion yielded two spectrally distinct primary photoproducts, Lumi-Go and Lumi-Gr, which decay on different time scales. The two primary photoproducts of NpR3784 equilibrate on the 40 ns time scale and subsequently propagate as a single intermediate population into Pr. Such heterogeneity could arise from differences in the direction of D-ring rotation, in chromophore protonation or hydrogen bonding, or in the mobility of protein residues or of solvent water nearby the chromophore or some combination therein. We conclude that the atypical photodynamics of NpR3784 reflects chromophore-protein interactions that differ from those present in the canonical R/G CBCR family.


Assuntos
Proteínas de Bactérias/metabolismo , Luz , Nostoc/metabolismo , Fotorreceptores Microbianos/metabolismo , Cinética , Nostoc/efeitos da radiação , Processos Fotoquímicos/efeitos da radiação , Fotorreceptores Microbianos/efeitos da radiação , Espectrofotometria
15.
Biochemistry ; 57(39): 5648-5653, 2018 10 02.
Artigo em Inglês | MEDLINE | ID: mdl-30204425

RESUMO

Inducible chemical-genetic fluorescent markers are promising tools for live cell imaging requiring high spatiotemporal resolution and low background fluorescence. The fluorescence-activating and absorption shifting tag (FAST) was recently developed to form fluorescent molecular complexes with a family of small, synthetic fluorogenic chromophores (so-called fluorogens). Here, we use rational design to modify the binding pocket of the protein and screen for improved fluorescence performances with four different fluorogens. The introduction of a single mutation results in improvements in both quantum yield and dissociation constant with nearly all fluorogens tested. Our improved FAST (iFAST) allowed the generation of a tandem iFAST (td-iFAST) that forms green and red fluorescent reporters 1.6-fold and 2-fold brighter than EGFP and mCherry, respectively, while having a comparable size.


Assuntos
Proteínas de Bactérias/química , Corantes Fluorescentes/química , Fotorreceptores Microbianos/química , Rodanina/análogos & derivados , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/efeitos da radiação , Sítios de Ligação , Escherichia coli/química , Fluorescência , Corantes Fluorescentes/metabolismo , Células HEK293 , Halorhodospira halophila/química , Humanos , Luz , Microscopia Confocal , Mutagênese Sítio-Dirigida , Mutação , Fotodegradação/efeitos da radiação , Fotorreceptores Microbianos/genética , Fotorreceptores Microbianos/metabolismo , Fotorreceptores Microbianos/efeitos da radiação , Ligação Proteica , Rodanina/metabolismo , Espectrometria de Fluorescência
16.
Chembiochem ; 19(17): 1887-1895, 2018 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-29939486

RESUMO

Cyanobacteriochromes (CBCRs) are photoreceptors in cyanobacteria that present a bilin chromophore-binding GAF domain as a photochromic element to control the activity of a downstream enzyme or regulator. CBCR Slr1393 from Synechocystis PCC 6803 carries three GAF domains, but only the third one binds phycocyanobilin covalently. Slr1393 shows photochromicity between red and green absorbing states and regulates a C-terminally located histidine kinase. In this work, we fused this third GAF domain to an adenylyl cyclase (AC) from Microcoleus chthonoplastes PCC7420 that in its genuine form is under blue-light control from a LOV domain. A series of RGS-AC variants were constructed with various lengths of the linkers between RGS and AC. Assays in vitro and in living Escherichia coli cells (AC-deletion mutant) demonstrated that the activity of AC was light regulated, namely, the red-light-converted form of RGSΔ14-Δ4AC (in vitro) was about three times more active than the green-light-converted form. Expression of the fusion protein RGSΔ14-Δ4AC in vivo again showed highest light regulation with at least threefold amplification of the AC function. In some experiments, even tenfold higher activity was observed, which indicated that the protein, if expressed under in vivo conditions, was part of the E. coli physiological conditions and thereby subjected to more complex and variable regulation through other E. coli inherent factors.


Assuntos
Adenilil Ciclases/metabolismo , Fotorreceptores Microbianos/metabolismo , Proteínas Recombinantes de Fusão/metabolismo , Synechocystis/química , Adenilil Ciclases/química , Adenilil Ciclases/efeitos da radiação , Sequência de Aminoácidos , Cianobactérias/enzimologia , Escherichia coli/enzimologia , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Proteínas de Escherichia coli/efeitos da radiação , Luz , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/efeitos da radiação , Domínios Proteicos , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/efeitos da radiação
17.
Chemphyschem ; 19(5): 566-570, 2018 03 05.
Artigo em Inglês | MEDLINE | ID: mdl-29327408

RESUMO

Phytochromes are modular bimodal photoswitches that control gene expression for morphogenetic processes in plants. These functions are triggered by photoinduced conversions between the inactive and active states of the photosensory module, denoted as Pr and Pfr, respectively. In the present time-resolved resonance Raman spectroscopic study of bacterial representatives of this photoreceptor family, we demonstrate that these phototransformations do not represent linear processes but include a branching reaction back to the initial state, prior to (de)activation of the output module. Thus, only a fraction of the photoreceptors undergoing the phototransformations can initiate the downstream signaling process, consistent with phytochrome's function as a sensor for more durable changes of light conditions.


Assuntos
Proteínas de Bactérias/efeitos da radiação , Fotorreceptores Microbianos/efeitos da radiação , Agrobacterium , Proteínas de Bactérias/química , Luz , Modelos Moleculares , Fotorreceptores Microbianos/química , Análise Espectral Raman
18.
Biochemistry ; 57(5): 620-630, 2018 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-29239168

RESUMO

The light, oxygen, voltage (LOV) domain proteins are blue light photoreceptors that utilize a noncovalently bound flavin mononucleotide (FMN) cofactor as the chromophore. The modular nature of these proteins has led to their wide adoption in the emerging fields of optogenetics and optobiology, where the LOV domain has been fused to a variety of output domains leading to novel light-controlled applications. In this work, we extend our studies of the subpicosecond to several hundred microsecond transient infrared spectroscopy of the isolated LOV domain AsLOV2 to three full-length photoreceptors in which the LOV domain is fused to an output domain: the LOV-STAS protein, YtvA, the LOV-HTH transcription factor, EL222, and the LOV-histidine kinase, LovK. Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate. However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain. While the rate of adduct formation varies by only 3.6-fold among the proteins, the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.


Assuntos
Fotorreceptores Microbianos/efeitos da radiação , Fotorreceptores de Plantas/efeitos da radiação , Espectroscopia de Infravermelho com Transformada de Fourier/métodos , Sítios de Ligação , Cristalografia por Raios X , Cisteína/química , Mononucleotídeo de Flavina/química , Ligação de Hidrogênio , Modelos Moleculares , Fotodegradação , Fotoquímica , Fotorreceptores Microbianos/química , Fotorreceptores de Plantas/química , Conformação Proteica , Domínios Proteicos , Estrutura Secundária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/efeitos da radiação , Técnica de Subtração
19.
J Am Chem Soc ; 139(41): 14638-14648, 2017 10 18.
Artigo em Inglês | MEDLINE | ID: mdl-28876066

RESUMO

The flavin chromophore in blue-light-using FAD (BLUF) photoreceptors is surrounded by a hydrogen bond network that senses and responds to changes in the electronic structure of the flavin on the ultrafast time scale. The hydrogen bond network includes a strictly conserved Tyr residue, and previously we explored the role of this residue, Y21, in the photoactivation mechanism of the BLUF protein AppABLUF by the introduction of fluorotyrosine (F-Tyr) analogues that modulated the pKa and reduction potential of Y21 by 3.5 pH units and 200 mV, respectively. Although little impact on the forward (dark- to light-adapted form) photoreaction was observed, the change in Y21 pKa led to a 4000-fold increase in the rate of dark-state recovery. In the present work we have extended these studies to the BLUF protein PixD, where, in contrast to AppABLUF, modulation in the Tyr (Y8) pKa has a profound impact on the forward photoreaction. In particular, a decrease in Y8 pKa by 2 or more pH units prevents formation of a stable light state, consistent with a photoactivation mechanism that involves proton transfer or proton-coupled electron transfer from Y8 to the electronically excited FAD. Conversely, the effect of pKa on the rate of dark recovery is markedly reduced in PixD. These observations highlight very significant differences between the photocycles of PixD and AppABLUF, despite their sharing highly conserved FAD binding architectures.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/efeitos da radiação , Flavoproteínas/metabolismo , Flavoproteínas/efeitos da radiação , Flúor/metabolismo , Luz , Fotorreceptores Microbianos/metabolismo , Fotorreceptores Microbianos/efeitos da radiação , Tirosina/metabolismo , Sítios de Ligação , Cor , Transporte de Elétrons , Flavina-Adenina Dinucleotídeo/metabolismo , Ligação de Hidrogênio , Concentração de Íons de Hidrogênio , Domínios Proteicos , Prótons , Synechocystis/química
20.
Proc Natl Acad Sci U S A ; 114(7): 1480-1485, 2017 02 14.
Artigo em Inglês | MEDLINE | ID: mdl-28137837

RESUMO

Blue light using flavin adenine dinucleotide (BLUF) proteins are essential for the light regulation of a variety of physiologically important processes and serve as a prototype for photoinduced proton-coupled electron transfer (PCET). Free-energy simulations elucidate the active site conformations in the AppA (activation of photopigment and puc expression) BLUF domain before and following photoexcitation. The free-energy profile for interconversion between conformations with either Trp104 or Met106 closer to the flavin, denoted Trpin/Metout and Trpout/Metin, reveals that both conformations are sampled on the ground state, with the former thermodynamically favorable by ∼3 kcal/mol. These results are consistent with the experimental observation of both conformations. To analyze the proton relay from Tyr21 to the flavin via Gln63, the free-energy profiles for Gln63 rotation were calculated on the ground state, the locally excited state of the flavin, and the charge-transfer state associated with electron transfer from Tyr21 to the flavin. For the Trpin/Metout conformation, the hydrogen-bonding pattern conducive to the proton relay is not thermodynamically favorable on the ground state but becomes more favorable, corresponding to approximately half of the configurations sampled, on the locally excited state. The calculated energy gaps between the locally excited and charge-transfer states suggest that electron transfer from Tyr21 to the flavin is more facile for configurations conducive to proton transfer. When the active site conformation is not conducive to PCET from Tyr21, Trp104 can directly compete with Tyr21 for electron transfer to the flavin through a nonproductive pathway, impeding the signaling efficiency.


Assuntos
Proteínas de Bactérias/química , Simulação por Computador , Flavoproteínas/química , Fotorreceptores Microbianos/química , Rhodobacter sphaeroides/metabolismo , Proteínas de Bactérias/efeitos da radiação , Domínio Catalítico , Transporte de Elétrons , Mononucleotídeo de Flavina/química , Flavoproteínas/efeitos da radiação , Glutamina/química , Ligação de Hidrogênio , Luz , Metionina/química , Modelos Moleculares , Fotorreceptores Microbianos/efeitos da radiação , Conformação Proteica/efeitos da radiação , Domínios Proteicos , Rhodobacter sphaeroides/efeitos da radiação , Triptofano/química , Tirosina/química , Tirosina/efeitos da radiação
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