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1.
Phys Chem Chem Phys ; 23(25): 13934-13950, 2021 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-34142688

RESUMO

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.


Assuntos
Glutamina/química , Sequência de Aminoácidos , Avena/química , Cisteína/química , Mononucleotídeo de Flavina/química , Ligação de Hidrogênio , Isomerismo , Modelos Moleculares , Distribuição Normal , Processos Fotoquímicos , Fototropinas/química , Ligação Proteica , Conformação Proteica , Espectrofotometria Infravermelho , Sphingomonadaceae/química , Relação Estrutura-Atividade , Termodinâmica
2.
Nat Commun ; 12(1): 2291, 2021 04 16.
Artigo em Inglês | MEDLINE | ID: mdl-33863895

RESUMO

Plants need to protect themselves from excess light, which causes photo-oxidative damage and lowers the efficiency of photosynthesis. Photosystem II subunit S (PsbS) is a pH sensor protein that plays a crucial role in plant photoprotection by detecting thylakoid lumen acidification in excess light conditions via two lumen-faced glutamates. However, how PsbS is activated under low-pH conditions is unknown. To reveal the molecular response of PsbS to low pH, here we perform an NMR, FTIR and 2DIR spectroscopic analysis of Physcomitrella patens PsbS and of the E176Q mutant in which an active glutamate has been replaced. The PsbS response mechanism at low pH involves the concerted action of repositioning of a short amphipathic helix containing E176 facing the lumen and folding of the luminal loop fragment adjacent to E71 to a 310-helix, providing clear evidence of a conformational pH switch. We propose that this concerted mechanism is a shared motif of proteins of the light-harvesting family that may control thylakoid inter-protein interactions driving photoregulatory responses.


Assuntos
Adaptação Fisiológica , Bryopsida/fisiologia , Luz/efeitos adversos , Complexo de Proteína do Fotossistema II/metabolismo , Estresse Fisiológico , Bryopsida/efeitos da radiação , Ácido Glutâmico/genética , Concentração de Íons de Hidrogênio/efeitos da radiação , Mutagênese Sítio-Dirigida , Ressonância Magnética Nuclear Biomolecular , Fotossíntese/fisiologia , Complexo de Proteína do Fotossistema II/genética , Complexo de Proteína do Fotossistema II/isolamento & purificação , Complexo de Proteína do Fotossistema II/ultraestrutura , Conformação Proteica em alfa-Hélice , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/ultraestrutura , Tilacoides/efeitos da radiação
3.
Nat Commun ; 11(1): 5682, 2020 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-33173168

RESUMO

The Rhizoclosmatium globosum genome encodes three rhodopsin-guanylyl cyclases (RGCs), which are predicted to facilitate visual orientation of the fungal zoospores. Here, we show that RGC1 and RGC2 function as light-activated cyclases only upon heterodimerization with RGC3 (NeoR). RGC1/2 utilize conventional green or blue-light-sensitive rhodopsins (λmax = 550 and 480 nm, respectively), with short-lived signaling states, responsible for light-activation of the enzyme. The bistable NeoR is photoswitchable between a near-infrared-sensitive (NIR, λmax = 690 nm) highly fluorescent state (QF = 0.2) and a UV-sensitive non-fluorescent state, thereby modulating the activity by NIR pre-illumination. No other rhodopsin has been reported so far to be functional as a heterooligomer, or as having such a long wavelength absorption or high fluorescence yield. Site-specific mutagenesis and hybrid quantum mechanics/molecular mechanics simulations support the idea that the unusual photochemical properties result from the rigidity of the retinal chromophore and a unique counterion triad composed of two glutamic and one aspartic acids. These findings substantially expand our understanding of the natural potential and limitations of spectral tuning in rhodopsin photoreceptors.


Assuntos
Quitridiomicetos/genética , Rodopsina , Biologia Computacional , Fluorescência , Corantes Fluorescentes/química , Corantes Fluorescentes/isolamento & purificação , Genes Fúngicos , Genoma Fúngico , Mutagênese Sítio-Dirigida , Processos Fotoquímicos , Células Fotorreceptoras/fisiologia , Rodopsina/biossíntese , Rodopsina/química , Rodopsina/genética
4.
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
5.
J Am Chem Soc ; 141(1): 520-530, 2019 01 09.
Artigo em Inglês | MEDLINE | ID: mdl-30511841

RESUMO

The orange carotenoid protein (OCP) is a two-domain photoactive protein that noncovalently binds an echinenone (ECN) carotenoid and mediates photoprotection in cyanobacteria. In the dark, OCP assumes an orange, inactive state known as OCPO; blue light illumination results in the red active state, known as OCPR. The OCPR state is characterized by large-scale structural changes that involve dissociation and separation of C-terminal and N-terminal domains accompanied by carotenoid translocation into the N-terminal domain. The mechanistic and dynamic-structural relations between photon absorption and formation of the OCPR state have remained largely unknown. Here, we employ a combination of time-resolved UV-visible and (polarized) mid-infrared spectroscopy to assess the electronic and structural dynamics of the carotenoid and the protein secondary structure, from femtoseconds to 0.5 ms. We identify a hereto unidentified carotenoid excited state in OCP, the so-called S* state, which we propose to play a key role in breaking conserved hydrogen-bond interactions between carotenoid and aromatic amino acids in the binding pocket. We arrive at a comprehensive reaction model where the hydrogen-bond rupture with conserved aromatic side chains at the carotenoid ß1-ring in picoseconds occurs at a low yield of <1%, whereby the ß1-ring retains a trans configuration with respect to the conjugated π-electron chain. This event initiates structural changes at the N-terminal domain in 1 µs, which allow the carotenoid to translocate into the N-terminal domain in 10 µs. We identified infrared signatures of helical elements that dock on the C-terminal domain ß-sheet in the dark and unfold in the light to allow domain separation. These helical elements do not move within the experimental range of 0.5 ms, indicating that domain separation occurs on longer time scales, lagging carotenoid translocation by at least 2 decades of time.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Carotenoides/metabolismo , Luz , Modelos Moleculares , Domínios Proteicos , Estrutura Secundária de Proteína
6.
J Phys Chem Lett ; 7(17): 3472-6, 2016 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-27537211

RESUMO

Light-triggered reactions of biological photoreceptors have gained immense attention for their role as molecular switches in their native organisms and for optogenetic application. The light, oxygen, and voltage 2 (LOV2) sensing domain of plant phototropin binds a C-terminal Jα helix that is docked on a ß-sheet and unfolds upon light absorption by the flavin mononucleotide (FMN) chromophore. In this work, the signal transduction pathway of LOV2 from Avena sativa was investigated using time-resolved infrared spectroscopy from picoseconds to microseconds. In D2O buffer, FMN singlet-to-triplet conversion occurs in 2 ns and formation of the covalent cysteinyl-FMN adduct in 10 µs. We observe a two-step unfolding of the Jα helix: The first phase occurs concomitantly with Cys-FMN covalent adduct formation in 10 µs, along with hydrogen-bond rupture of the FMN C4═O with Gln-513, motion of the ß-sheet, and an additional helical element. The second phase occurs in approximately 240 µs. The final spectrum at 500 µs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.


Assuntos
Proteínas de Arabidopsis/química , Proteínas de Ligação a DNA/química , Fotorreceptores Microbianos/química , Análise Espectral/métodos , Ligação de Hidrogênio , Modelos Moleculares , Desdobramento de Proteína , Vibração
7.
J Phys Chem Lett ; 7(15): 3046-51, 2016 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-27447848

RESUMO

Far-red fluorescent proteins are critical for in vivo imaging applications, but the relative importance of structure versus dynamics in generating large Stokes-shifted emission is unclear. The unusually red-shifted emission of TagRFP675, a derivative of mKate, has been attributed to the multiple hydrogen bonds with the chromophore N-acylimine carbonyl. We characterized TagRFP675 and point mutants designed to perturb these hydrogen bonds with spectrally resolved transient grating and time-resolved fluorescence (TRF) spectroscopies supported by molecular dynamics simulations. TRF results for TagRFP675 and the mKate/M41Q variant show picosecond time scale red-shifts followed by nanosecond time blue-shifts. Global analysis of the TRF spectra reveals spectrally distinct emitting states that do not interconvert during the S1 lifetime. These dynamics originate from photoexcitation of a mixed ground-state population of acylimine hydrogen bond conformers. Strategically tuning the chromophore environment in TagRFP675 might stabilize the most red-shifted conformation and result in a variant with a larger Stokes shift.


Assuntos
Proteínas Luminescentes/química , Fluorescência , Ligação de Hidrogênio , Conformação Molecular , Simulação de Dinâmica Molecular
8.
J Phys Chem Lett ; 7(12): 2170-4, 2016 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-27214167

RESUMO

Fluorescent proteins with large Stokes shifted emission beyond 600 nm are actively sought for live-cell imaging applications. The mechanism of excited-state relaxation leading to the Stokes shift in the mPlum fluorescent protein, which emits at a peak wavelength of 650 nm, has been previously investigated by both ultrafast spectroscopy and theoretical methods. Here, we report that femtosecond time-resolved area-normalized emission spectra of mPlum show a clear isoemissive point. This feature can only result from a system with two emitting states, rather than a system that undergoes a continuous spectral red shift, for example, as expected from typical solvation. Global analysis of the femtosecond time-resolved fluorescence spectra reveals time constants associated with chromophore relaxation, excited-state population transfer, and an excited-state lifetime of the final state. The observations confirm the findings of recent quantum chemical calculations on mPlum.


Assuntos
Proteínas de Fluorescência Verde/química , Espectrometria de Fluorescência/métodos , Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Teoria Quântica
9.
J Phys Chem B ; 119(8): 3414-22, 2015 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-25635507

RESUMO

Red fluorescent proteins (RFPs) are widely used probes for monitoring subcellular processes with extremely high spatial and temporal precision. In this work, we employed spectrally resolved transient absorption (SRTA) and two-dimensional double quantum coherence (2D2Q) spectroscopy to investigate the excited state electronic structure of mPlum, a well-known RFP. The SRTA spectra reveal the presence of excited state absorption features at both the low- and high-energy sides of the dominant ground state bleach contribution. The 2D2Q spectra measured at several excitation wavelengths reveal a peak pattern consistent with the presence of more than three electronic states (i.e., ground, excited, and doubly excited). Numerical modeling of this response suggests that the features are consistent with a 1-1-2 electronic structure. The two closely spaced (∼1500 cm(-1)) levels in the double quantum manifold appear at opposite anharmonicities relative to twice the energy of the lowest energy transition. These observations explain the excited state absorption contributions observed in spectrally resolved transient grating and transient absorption measurements and demonstrate the utility of multidimensional spectroscopy in unraveling congested spectra relative to conventional one-dimensional methods.


Assuntos
Proteínas Luminescentes/química , Análise Espectral/métodos , Simulação por Computador , Escherichia coli , Modelos Químicos , Teoria Quântica
10.
J Phys Chem B ; 113(44): 14549-54, 2009 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-19817498

RESUMO

Phase segregation of 2,3,7,8,12,13,17,18-octaethyl-21H,23H-porphine ruthenium(II)carbonyl (RuOEP) and regioregular poly(3-hexylthiophene-2,5-diyl) (P3HT) in thin films is investigated with infrared and UV-visible spectroscopies as well as transmission electron microscopy (TEM). The Fourier transform infrared (FTIR) spectrum of the ruthenium-bound CO symmetric stretching mode exhibits significant changes as these films are annealed in solvent vapors. The development of multiple inhomogeneously broadened microenvironments is observed, and UV-visible spectra and TEM support a model of homogeneous porphyrin distribution throughout the P3HT films that gradually becomes more heterogeneous as the P3HT and RuOEP molecules phase segregate. A complete model for the phase segregation process experienced by the embedded RuOEP is proposed to explain the collective experimental observations.

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