Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 67
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
European J Org Chem ; 2021(39): 5424-5429, 2021 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-34819798

RESUMO

Polycyclic aromatic hydrocarbons (PAHs) are widely used in organic electronic devices. The electronic, magnetic, and optical properties of PAHs can be tuned by structural modifications to the aromatic backbone to introduce an inherent distortion from planarity, such as bending or twisting. However, it remains difficult to isolate and control the effects of such distortions. Here, we sought to understand how backbone twisting and bending affect the electronic properties of acenes, as models for larger PAHs. We found that, even when highly distorted from planarity (30° per ring), acenes maintain their aromatic character and π orbital delocalization with minor mixing of the σ and π orbitals. In addition, the energy gap between the HOMO and LUMO decreases with increasing twist, while the gap is hardly affected by bending, since the energy of both orbitals increase to a similar extent. For bent acenes in the triplet state, the spin becomes more localized with increasing bend, whereas twisting produces an evenly distributed spin delocalization. These findings can guide the synthesis of PAHs with tailored properties.

2.
Comput Struct Biotechnol J ; 19: 4184-4191, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34336146

RESUMO

During the rapid worldwide spread of SARS-CoV-2, the viral genome has been undergoing numerous mutations, especially in the spike (S) glycoprotein gene that encode a type-I fusion protein, which plays an important role in the infectivity and transmissibility of the virus into the host cell. In this work, we studied the effect of S glycoprotein residue mutations on the binding affinity and mechanisms of SARS-CoV-2 using molecular dynamics simulations and sequence analysis. We quantitatively determined the degrees of binding affinity caused by different S glycoprotein mutations, and the result indicated that the 501Y.V1 variant yielded the highest enhancements in binding affinity (increased by 36.8%), followed by the N439K variant (increased by 29.5%) and the 501Y.V2 variant (increased by 19.6%). We further studied the structures, chemical bonds, binding free energies (enthalpy and entropy), and residue contribution decompositions of these variants to provide physical explanations for the changes in SARS-CoV-2 binding affinity caused by these residue mutations. This research identified the binding affinity differences of the SARS-CoV-2 variants and provides a basis for further surveillance, diagnosis, and evaluation of mutated viruses.

3.
J Chem Theory Comput ; 17(10): 6302-6313, 2021 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-34255519

RESUMO

Channelrhodopsins are photosensitive proteins that trigger flagella motion in single-cell algae and have been successfully utilized in optogenetic applications. In optogenetics, light is used to activate neural cells in living organisms, which can be achieved by exploiting the ion channel signaling of channelrhodopsins. Tailoring channelrhodopsins for such applications includes the tuning of the absorption maximum. In order to establish rational design and to obtain a desired spectral shift, a basic understanding of the absorption spectrum is required. We have studied the chimera C1C2 as a representative of this protein family and the first member with an available crystal structure. For this purpose, we sampled the conformations of C1C2 using quantum mechanical/molecular mechanical molecular dynamics and subjected the resulting snapshots of the trajectory to excitation energy calculations using ADC(2) and simplified time-dependent density functional theory. In contrast to previous reports, we found that different hydrogen-bonding networks-involving the retinal protonated Schiff base, the putative counterions E162 and D292, and water molecules-had only a small impact on the absorption spectrum. However, in the case of deprotonated E162, increasing the distance to the Schiff base hydrogen-bonding partner led to a systematic blue shift. The ß-ionone ring rotation was identified as another important contributor. Yet the most important factors were found to be the bond length alternation and bond order alternation that were linearly correlated to the absorption maximum by up to 62 and 82%, respectively. We ascribe this novel insight into the structural basis of the absorption spectrum to our enhanced protein setup that includes membrane embedding as well as long and extensive sampling.

4.
J Phys Chem Lett ; 12(27): 6284-6291, 2021 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-34213348

RESUMO

We report a transient signature in the near-UV absorption of Krokinobacter eikastus rhodopsin 2 (KR2), which spans from the femtosecond up to the millisecond time scale. The signature rises with the all-trans to 13-cis isomerization of retinal and decays with the reisomerization to all-trans in the late photocycle, making it a promising marker band for retinal configuration. Hybrid quantum mechanics/molecular mechanics simulations show that the near-UV absorption signal corresponds to an S0 → S3 and/or an S0 → S5 transition, which is present in all photointermediates. These transitions exhibit a negligible spectral shift by the altering protein environment, in contrast to the main absorption band. This is rationalized by the extension of the transition densities that omits the Schiff base nitrogen. Further characterization and first steps into possible optogenetic applications were performed with near-UV quenching experiments of an induced photostationary state, yielding an ultrafast regeneration of the parent state of KR2.


Assuntos
Absorção Fisico-Química , Flavobacteriaceae/metabolismo , Rodopsina/química , Rodopsina/metabolismo , ATPase Trocadora de Sódio-Potássio/metabolismo , Raios Ultravioleta , Membrana Celular/metabolismo , Flavobacteriaceae/citologia , Simulação de Dinâmica Molecular , Conformação Proteica , Análise Espectral
5.
Chem Asian J ; 16(16): 2307-2313, 2021 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-34155813

RESUMO

In this contribution, we report on a class of emitters based on bridged oxo- and/or thioethers revealing striking photoluminescence properties in fluid solution and in the solid state. In total, nine compounds were investigated concerning their photophysical properties, which were interpreted by quantum chemical calculations. To our delight, we discovered compounds possessing nearly identical photoluminescence quantum yields (ΦF ) in solution and in the solid state, which has been rarely reported so far. Besides these efforts, we shed light on the influence of polymorphism and solvent polarity on the emission properties. In addition, an in-depth X-ray diffractometric analysis was conducted to correlate molecular packing in the crystal with differences in the photophysical properties.

6.
Phys Chem Chem Phys ; 23(21): 12494, 2021 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-34014244

RESUMO

Correction for 'Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2' by Aditya G. Rao et al., Phys. Chem. Chem. Phys., 2021, DOI: 10.1039/d0cp05314g.

7.
Phys Chem Chem Phys ; 23(12): 7359-7367, 2021 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-33876095

RESUMO

Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. These photochemical properties make them an attractive target for biotechnological applications. However, their application is impeded by structural heterogeneity that reduces the yield of the photoconversion. The heterogeneity can originate either from the chromophore structure or the protein environment. Here, we study the origin of the heterogeneity in AnPixJg2, a representative member of the red/green cyanobacteriochrome family, that has a red absorbing parental state and a green absorbing photoproduct state. Using molecular dynamics simulations and umbrella sampling we have identified the protonation state of a conserved histidine residue as a trigger for structural heterogeneity. When the histidine is in a neutral form, the chromophore structure is homogenous, while in a positively charged form, the chromophore is heterogeneous with two different conformations. We have identified a correlation between the protonation of the histidine and the structural heterogeneity of the chromophore by detailed characterization of the interactions in the protein binding site. Our findings reconcile seemingly contradicting spectroscopic studies that attribute the heterogeneity to different sources. Furthermore, we predict that circular dichroism can be used as a diagnostic tool to distinguish different substates.


Assuntos
Proteínas de Bactérias/metabolismo , Cianobactérias/química , Histidina/metabolismo , Proteínas de Bactérias/química , Cianobactérias/metabolismo , Teoria da Densidade Funcional , Histidina/química , Modelos Moleculares , Estrutura Molecular , Prótons
8.
Phys Chem Chem Phys ; 23(11): 6544-6551, 2021 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-33690760

RESUMO

In photosynthetic complexes, tuning of chlorophyll light-absorption spectra by the protein environment is crucial to their efficiency and robustness. Recombinant type II water soluble chlorophyll-binding proteins from Brassicaceae (WSCPs) are useful for studying spectral tuning mechanisms due to their symmetric homotetramer structure, and the ability to rigorously modify the chlorophyll's protein surroundings. Our previous comparison of the crystal structures of two WSCP homologues suggested that protein-induced chlorophyll ring deformation is the predominant spectral tuning mechanism. Here, we implement a more rigorous analysis based on hybrid quantum mechanics and molecular mechanics calculations to quantify the relative contributions of geometrical and electrostatic factors to the absorption spectra of WSCP-chlorophyll complexes. We show that when considering conformational dynamics, geometry distortions such as chlorophyll ring deformation accounts for about one-third of the spectral shift, whereas the direct polarization of the electron density accounts for the remaining two-thirds. From a practical perspective, protein electrostatics is easier to manipulate than chlorophyll conformations, thus, it may be more readily implemented in designing artificial protein-chlorophyll complexes.


Assuntos
Proteínas de Ligação à Clorofila/química , Clorofila/química , Sítios de Ligação , Brassicaceae/metabolismo , Cristalografia por Raios X , Simulação de Dinâmica Molecular , Estrutura Terciária de Proteína , Teoria Quântica , Eletricidade Estática
9.
Biophys J ; 120(5): 964-974, 2021 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-33545103

RESUMO

In nature, sensory photoreceptors underlie diverse spatiotemporally precise and generally reversible biological responses to light. Photoreceptors also serve as genetically encoded agents in optogenetics to control by light organismal state and behavior. Phytochromes represent a superfamily of photoreceptors that transition between states absorbing red light (Pr) and far-red light (Pfr), thus expanding the spectral range of optogenetics to the near-infrared range. Although light of these colors exhibits superior penetration of soft tissue, the transmission through bone and skull is poor. To overcome this fundamental challenge, we explore the activation of a bacterial phytochrome by a femtosecond laser emitting in the 1 µm wavelength range. Quantum chemical calculations predict that bacterial phytochromes possess substantial two-photon absorption cross sections. In line with this notion, we demonstrate that the photoreversible Pr ↔ Pfr conversion is driven by two-photon absorption at wavelengths between 1170 and 1450 nm. The Pfr yield was highest for wavelengths between 1170 and 1280 nm and rapidly plummeted beyond 1300 nm. By combining two-photon activation with bacterial phytochromes, we lay the foundation for enhanced spatial resolution in optogenetics and unprecedented penetration through bone, skull, and soft tissue.


Assuntos
Fitocromo , Bactérias , Proteínas de Bactérias , Luz
10.
Nat Commun ; 12(1): 629, 2021 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-33504778

RESUMO

Many transmembrane receptors have a desensitized state, in which they are unable to respond to external stimuli. The family of microbial rhodopsin proteins includes one such group of receptors, whose inactive or dark-adapted (DA) state is established in the prolonged absence of light. Here, we present high-resolution crystal structures of the ground (light-adapted) and DA states of Archaerhodopsin-3 (AR3), solved to 1.1 Å and 1.3 Å resolution respectively. We observe significant differences between the two states in the dynamics of water molecules that are coupled via H-bonds to the retinal Schiff Base. Supporting QM/MM calculations reveal how the DA state permits a thermodynamic equilibrium between retinal isomers to be established, and how this same change is prevented in the ground state in the absence of light. We suggest that the different arrangement of internal water networks in AR3 is responsible for the faster photocycle kinetics compared to homologs.


Assuntos
Proteínas Arqueais/metabolismo , Proteínas de Membrana Transportadoras/química , Proteínas de Membrana Transportadoras/metabolismo , Água/química , Cristalografia por Raios X , Elétrons , Ligação de Hidrogênio , Isomerismo , Lipídeos/química , Conformação Molecular , Processamento de Proteína Pós-Traducional , Prótons , Retinaldeído/química , Retinaldeído/metabolismo
11.
Photochem Photobiol ; 97(2): 243-269, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33369749

RESUMO

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.


Assuntos
Proteínas de Bactérias/química , Proteínas de Fluorescência Verde/química , Modelos Moleculares , Fotorreceptores Microbianos/química , Fitocromo/química , Rodopsina/química , Distribuição de Poisson , Teoria Quântica , Eletricidade Estática
12.
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
13.
Chem Sci ; 11(21): 5511-5525, 2020 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-32874494

RESUMO

Two covalently linked donor-acceptor copper phenanthroline complexes (C-A dyads) of interest for solar energy conversion/storage schemes, [Cu(i)(Rphen(OMV)2 4+)2]9+ = RC+A4 8+ with RC+ = [Cu(i)Rphen2]+ involving 2,9-methyl (R = Me) or 2,9-phenyl (R = Ph)-phenanthroline ligands that are 5,6-disubstituted by 4-(n-butoxy) linked methylviologen electron acceptor groups (A2+ = OMV2+), have been synthesized and investigated via quantum chemical calculations and nanosecond laser flash spectroscopy in 1,2-difluorobenzene/methanol (dfb/MeOH) mixtures. Upon photoexcitation, charge transfer (CT) states RC2+A+A3 6+ are formed in less than one ns and decay by charge recombination on a time scale of 6-45 ns. The CT lifetime of RC2+A+A3 6+ has a strong dependence on MeOH solvent fraction when R = Me, but is unaffected if R = Ph. This solvent effect is due to coordination of MeOH solvent in MeC+A4 8+ (i.e. exciplex formation) allowed by conformational flattening of the ligand sphere, which cannot occur in PhC+A4 8+ having bulkier Phphen ligand framework. Interestingly, the decay time of the CT state increases for both species at low magnetic fields with a maximum increase of ca. 30% at ca. 150 mT, then decreases as the field is increased up to 1500 mT, the highest field investigated. This magnetic field effect (MFE) is due to magnetic modulation of the spin dynamics interconverting 3CT and 1CT states. A quantitative modeling according to the radical pair mechanism involving ab initio multireference calculations of the complexes revealed that the spin process is dominated by the effect of Cu hyperfine coupling. The external magnetic field suppresses the hyperfine coupling induced spin state mixing thereby lengthening the CT decay time. This effect is counteracted by the field dependent processes of T0-S mixing through the Δg-mechanism and by a local mode spin-orbit mechanism. Further, the maximum MFE is limited by a finite rate of direct recombination of 3CT states and the spin-rotational mechanism of spin relaxation. This study provides a first comprehensive characterization of Cu(ii)-complex spin chemistry and highlights how spin chemistry can be used to manipulate solar energy harvesting and storage materials.

14.
Biophys J ; 119(3): 705-716, 2020 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-32697975

RESUMO

The function of photoreceptors relies on efficient transfer of absorbed light energy from the chromophore to the protein to drive conformational changes that ultimately generate an output signal. In retinal-binding proteins, mainly two mechanisms exist to store the photon energy after photoisomerization: 1) conformational distortion of the prosthetic group retinal, and 2) charge separation between the protonated retinal Schiff base (RSBH+) and its counterion complex. Accordingly, energy transfer to the protein is achieved by chromophore relaxation and/or reduction of the charge separation in the RSBH+-counterion complex. Combining FTIR and UV-Vis spectroscopy along with molecular dynamics simulations, we show here for the widely used, red-activatable Volvox carteri channelrhodopsin-1 derivate ReaChR that energy storage and transfer into the protein depends on the protonation state of glutamic acid E163 (Ci1), one of the counterions of the RSBH+. Ci1 retains a pKa of 7.6 so that both its protonated and deprotonated forms equilibrate at physiological conditions. Protonation of Ci1 leads to a rigid hydrogen-bonding network in the active-site region. This stabilizes the distorted conformation of the retinal after photoactivation and decelerates energy transfer into the protein by impairing the release of the strain energy. In contrast, with deprotonated Ci1 or removal of the Ci1 glutamate side chain, the hydrogen-bonded system is less rigid, and energy transfer by chromophore relaxation is accelerated. Based on the hydrogen out-of-plane (HOOP) band decay kinetics, we determined the activation energy for these processes in dependence of the Ci1 protonation state.


Assuntos
Simulação de Dinâmica Molecular , Bases de Schiff , Channelrhodopsins , Transferência de Energia , Ligação de Hidrogênio
15.
Nature ; 583(7815): 314-318, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32499654

RESUMO

Light-driven sodium pumps actively transport small cations across cellular membranes1. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. Although the resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved2,3, it is unclear how structural alterations over time allow sodium to be translocated against a concentration gradient. Here, using the Swiss X-ray Free Electron Laser4, we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds. Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds. Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond. In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit. These results provide direct molecular insight into the dynamics of active cation transport across biological membranes.


Assuntos
Flavobacteriaceae/química , Rodopsinas Microbianas/química , Rodopsinas Microbianas/efeitos da radiação , ATPase Trocadora de Sódio-Potássio/química , ATPase Trocadora de Sódio-Potássio/efeitos da radiação , Sítios de Ligação , Cristalografia , Elétrons , Transporte de Íons , Isomerismo , Lasers , Prótons , Teoria Quântica , Retinaldeído/química , Retinaldeído/metabolismo , Bases de Schiff/química , Sódio/metabolismo , Análise Espectral , Eletricidade Estática , Fatores de Tempo
16.
J Chem Phys ; 152(21): 214117, 2020 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-32505150

RESUMO

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

17.
Proc Natl Acad Sci U S A ; 117(28): 16356-16362, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32591422

RESUMO

Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z ⇄ E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. We have studied a single-domain bilin-binding photoreceptor All2699g1 (Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (Pr) and far red-absorbing (Pfr) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the Pr form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ∼300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.


Assuntos
Fitocromo/química , Fitocromo/metabolismo , Pigmentos Biliares/química , Pigmentos Biliares/metabolismo , Cristalografia por Raios X , Isomerismo , Cinética , Modelos Moleculares , Nostoc/metabolismo , Processos Fotoquímicos , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/metabolismo , Conformação Proteica , Análise Espectral , Relação Estrutura-Atividade
18.
J Mol Biol ; 432(7): 2099-2120, 2020 03 27.
Artigo em Inglês | MEDLINE | ID: mdl-32067952

RESUMO

ABC importers are membrane proteins responsible for the transport of nutrients into the cells of prokaryotes. Although the structures of ABC importers vary, all contain four conserved domains: two nucleotide-binding domains (NBDs), which bind and hydrolyze ATP, and two transmembrane domains (TMDs), which help translocate the substrate. ABC importers are also dependent on an additional protein component, a high-affinity substrate-binding protein (SBP) that specifically binds the target ligand for delivery to the appropriate ABC transporter. AbnE is a SBP belonging to the ABC importer for arabino-oligosaccharides in the Gram-positive thermophilic bacterium Geobacillus stearothermophilus. Using isothermal titration calorimetry (ITC), purified AbnE was shown to bind medium-sized arabino-oligosaccharides, in the range of arabino-triose (A3) to arabino-octaose (A8), all with Kd values in the nanomolar range. We describe herein the 3D structure of AbnE in its closed conformation in complex with a wide range of arabino-oligosaccharide substrates (A2-A8). These structures provide the basis for the detailed structural analysis of the AbnE-sugar complexes, and together with complementary quantum chemical calculations, site-specific mutagenesis, and isothermal titration calorimetry (ITC) experiments, provide detailed insights into the AbnE-substrate interactions involved. Small-angle X-ray scattering (SAXS) experiments and normal mode analysis (NMA) are used to study the conformational changes of AbnE, and these data, taken together, suggest clues regarding its binding mode to the full ABC importer.


Assuntos
Arabinose/química , Arabinose/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Geobacillus stearothermophilus/enzimologia , Conformação Proteica , Proteínas de Bactérias/genética , Cristalografia por Raios X , Modelos Moleculares , Mutagênese Sítio-Dirigida , Mutação , Ligação Proteica
19.
Molecules ; 25(4)2020 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-32075128

RESUMO

Channelrhodopsins (ChR) are light-gated ion-channels heavily used in optogenetics. Upon light excitation an ultrafast all-trans to 13-cis isomerization of the retinal chromophore takes place. It is still uncertain by what means this reaction leads to further protein changes and channel conductivity. Channelrhodopsin-1 in Chlamydomonas augustae exhibits a 100 fs photoisomerization and a protonated counterion complex. By polarization resolved ultrafast spectroscopy in the mid-IR we show that the initial reaction of the retinal is accompanied by changes in the protein backbone and ultrafast protonation changes at the counterion complex comprising Asp299 and Glu169. In combination with homology modelling and quantum mechanics/molecular mechanics (QM/MM) geometry optimization we assign the protonation dynamics to ultrafast deprotonation of Glu169, and transient protonation of the Glu169 backbone, followed by a proton transfer from the backbone to the carboxylate group of Asp299 on a timescale of tens of picoseconds. The second proton transfer is not related to retinal dynamics and reflects pure protein changes in the first photoproduct. We assume these protein dynamics to be the first steps in a cascade of protein-wide changes resulting in channel conductivity.


Assuntos
Channelrhodopsins/química , Modelos Moleculares , Conformação Proteica , Rodopsina/química , Channelrhodopsins/ultraestrutura , Chlamydomonas/química , Isomerismo , Luz , Simulação de Dinâmica Molecular , Prótons , Teoria Quântica , Rodopsina/ultraestrutura , Análise Espectral
20.
Biochemistry ; 59(9): 1023-1037, 2020 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-32073262

RESUMO

Phytochromes are biological photoswitches that interconvert between two parent states (Pr and Pfr). The transformation is initiated by photoisomerization of the tetrapyrrole chromophore, followed by a sequence of chromophore and protein structural changes. In the last step, a phytochrome-specific peptide segment (tongue) undergoes a secondary structure change, which in prokaryotic phytochromes is associated with the (de)activation of the output module. The focus of this work is the Pfr-to-Pr photoconversion of the bathy bacteriophytochrome Agp2 in which Pfr is the thermodynamically stable state. Using spectroscopic techniques, we studied the structural and functional consequences of substituting Arg211, Tyr165, His278, and Phe192 close to the biliverdin (BV) chromophore. In Pfr, substitutions of these residues do not affect the BV structure. The characteristic Pfr properties of bathy phytochromes, including the protonated propionic side chain of ring C (propC) of BV, are preserved. However, replacing Arg211 or Tyr165 blocks the photoconversion in the Meta-F state, prior to the secondary structure transition of the tongue and without deprotonation of propC. The Meta-F state of these variants displays low photochemical activity, but electronic excitation causes ultrafast alterations of the hydrogen bond network surrounding the chromophore. In all variants studied here, thermal back conversion from the photoproducts to Pfr is decelerated but substitution of His278 or Phe192 is not critical for the Pfr-to-Pr photoconversion. These variants do not impair deprotonation of propC or the α-helix/ß-sheet transformation of the tongue during the Meta-F-to-Pr decay. Thus, we conclude that propC deprotonation is essential for restructuring of the tongue.


Assuntos
Biliverdina/metabolismo , Fitocromo/química , Fitocromo/ultraestrutura , Agrobacterium tumefaciens , Proteínas de Bactérias/química , Ligação de Hidrogênio , Luz , Fitocromo/fisiologia , Prótons , Análise Espectral Raman/métodos , Tetrapirróis/química , Tetrapirróis/metabolismo
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...