RESUMEN
Several years ago the discovery of a conical intersection offered an explanation for the ultafast photodissociation of pyrrole. Subsequently, the photodissociation of pyrrole ammonia complexes PyH*(NH3)n with n ≥ 3 was studied in the gas phase as a model for a hydrogen-bond forming solvent. Two alternative mechanisms, electron coupled proton transfer (ECPT) and hydrogen atom transfer (HAT, also called the impulsive model, IM), have been proposed. The parent 1 : 1 complex was never studied, due to the short lifetime of the NH4 radical fragment. Here we report experiments on the deuterated species PyD*(ND3)n, including the 1 : 1 complex (n = 1). The velocity distribution of the ND4 radical is well approximated by a Maxwell-Boltzmann distribution of T ≈ 530 K, with a negative anisotropy parameter of ß = -0.3. The impulsive model predicts a much narrower velocity distribution with larger negative anisotropy. The ECPT model predicts a long lived intermediate that should allow thermal equilibration of the vibrational energy but should also destroy the rotational memory of the initially excited state. The average kinetic energy agrees with the prediction of the impulsive model, whereas the wide range of kinetic energies is more in line with ECPT. Hence the mechanism seems to be more complex and requires further theoretical modelling.
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The electronic structure and photophysical properties of a series of N-methyl and N-acetyl substituted alloxazines (AZs) were investigated with extensive density functional theory (DFT) and time-dependent density functional theory (TD-DFT) based calculations. We showed that non-radiative decays from the lowest singlet and triplet excited states of these AZs are dominant over their radiative counterparts. The fast non-radiative decays of the excited AZs can be attributed to the energy consumption (Ereorg) through structural reorganization facilitated by the intrinsic normal modes of the alloxazine framework, as well as their coupling with those of the functional groups. Substitution with functional groups may lead to further perturbation of the electronic structure of the AZ chromophore, which may enhance intersystem crossing with the ππ* states of the AZs. Due to the different bonding of N1 and N3 within the alloxazine framework, substitution may result in AZs with different photophysical properties. Specifically, functionalization at N1 may help in maintaining or even reducing Ereorg and would promote the absorption and radiative decay from the excited AZs. However, the strong coupling of the vibrational modes of acetyl at N3 with the intrinsic normal modes of the alloxazine framework would contribute significantly to Ereorg, and benefit the non-radiative decay of the excited AZs. We expect that the findings would pave the way for rational design of novel AZs with extraordinary photophysical properties.
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The dye rhodamineâ 6G can act as a photocatalyst through photoinduced electron transfer. After electronic excitation with green light, rhodamineâ 6G takes an electron from an electron donor, such as N,N-diisopropylethylamine, and forms the rhodamineâ 6G radical. This radical has a reduction potential of around -0.90â V and can split phenyl iodide into iodine anions and phenyl radicals. Recently, it has been reported that photoexcitation of the radical at 420â nm splits aryl bromides into bromide anions and aryl radicals. This requires an increase in reduction potential, hence the electronically excited rhodamineâ 6G radical was proposed as the reducing agent. Here, we present a study of the mechanism of the formation and photoreactions of the rhodamineâ 6G radical by transient absorption spectroscopy in the time range from femtoseconds to minutes in combination with quantum chemical calculations. We conclude that one photon of 540â nm light produces two rhodamineâ 6G radicals. The lifetime of the photoexcited radicals of around 350â fs is too short to allow diffusion-controlled interaction with a substrate. A fraction of the excited radicals ionize spontaneously, presumably producing solvated electrons. This decay produces hot rhodamineâ 6G and hot rhodamineâ 6G radicals, which cool with a time constant of around 10â ps. In the absence of a substrate, the ejected electrons recombine with rhodamineâ 6G and recover the radical on a timescale of nanoseconds. Photocatalytic reactions occur only upon excitation of the rhodamineâ 6G radical, and due to its short excited-state lifetime, the electron transfer to the substrate probably takes place through the generation of solvated electrons as an additional step in the proposed photochemical mechanism.
RESUMEN
Spin-orbit charge-transfer intersystem crossing (SOCT-ISC) is useful for the preparation of heavy atom-free triplet photosensitisers (PSs). Herein, a series of perylene-Bodipy compact electron donor/acceptor dyads showing efficient SOCT-ISC is prepared. The photophysical properties of the dyads were studied with steady-state and time-resolved spectroscopies. Efficient triplet state formation (quantum yield ΦT =60 %) was observed, with a triplet state lifetime (τT =436â µs) much longer than that accessed with the conventional heavy atom effect (τT =62â µs). The SOCT-ISC mechanism was unambiguously confirmed by direct excitation of the charge transfer (CT) absorption band by using nanosecond transient absorption spectroscopy and time-resolved electron paramagnetic resonance (TREPR) spectroscopy. The factors affecting the SOCT-ISC efficiency include the geometry, the potential energy surface of the torsion, the spin density for the atoms of the linker, solvent polarity, and the energy matching of the 1 CT/3 LE states. Remarkably, these heavy atom-free triplet PSs were demonstrated as a new type of efficient photodynamic therapy (PDT) reagents (phototoxicity, EC50 =75â nm), with a negligible dark toxicity (EC50 =78.1â µm) compared with the conventional heavy atom PSs (dark toxicity, EC50 =6.0â µm, light toxicity, EC50 =4.0â nm). This study provides in-depth understanding of the SOCT-ISC, unveils the design principles of triplet PSs based on SOCT-ISC, and underlines their application as a new generation of potent PDT reagents.
Asunto(s)
Materiales Biocompatibles/química , Fármacos Fotosensibilizantes/química , Materiales Biocompatibles/síntesis química , Materiales Biocompatibles/farmacología , Supervivencia Celular/efectos de los fármacos , Diseño de Fármacos , Espectroscopía de Resonancia por Spin del Electrón , Electrones , Células HeLa , Humanos , Fármacos Fotosensibilizantes/síntesis química , Fármacos Fotosensibilizantes/farmacología , Teoría Cuántica , Oxígeno Singlete/química , Oxígeno Singlete/metabolismo , Solventes/química , Marcadores de SpinRESUMEN
Orthogonal phenoxazine-styryl BODIPY compact electron donor/acceptor dyads were prepared as heavy atom-free triplet photosensitizers (PSs) with strong red light absorption (ϵ=1.33×105 â M-1 cm-1 at 630â nm), whereas the previously reported triplet photosensitizers based on the spin-orbit charge transfer intersystem crossing (SOCT-ISC) mechanism show absorption in a shorter wavelength range (<500â nm). More importantly, a long-lived triplet state (τT =333â µs) was observed for the new dyads. In comparison, the triplet state lifetime of the same chromophore accessed with the conventional heavy atom effect (HAE) is much shorter (τT =1.8â µs). Long triplet state lifetime is beneficial to enhance electron or energy transfer, the primary photophysical processes in the application of triplet PSs. Our approach is based on SOCT-ISC, without invoking of the HAE, which may shorten the triplet state lifetime. We used bisstyrylBodipy both as the electron acceptor and the visible light-harvesting chromophore, which shows red-light absorption. Femtosecond transient absorption spectra indicated the charge separation (109â ps) and SOCT-ISC (charge recombination, CR; 2.3â ns) for BDP-1. ISC efficiency of BDP-1 was determined as ΦT =25 % (in toluene). The dyad BDP-3 was used as triplet PS for triplet-triplet annihilation upconversion (upconversion quantum yield ΦUC =1.5 %; anti-Stokes shift is 5900â cm-1 ).
RESUMEN
The bacterium Rhodobacter sphaeroides has a short LOV (light-oxygen-voltage) domain, which is not connected to an effector domain but has an α-helix extension at the N-terminus as well as a helix-turn-helix (HTH) motiv at the C-terminus. These extensions offer possibilities for interactions with effector enzymes or DNA. Whereas many LOV domains show a tendency to form dimers in the light state, RsLOV is unique in that it is a dimer in the dark state but dissociates into monomers after blue-light excitation. We studied the kinetics of this dimerization process by a combination of FRET spectroscopy and stopped-flow experiments with a time resolution of ≈10 ms. Although excitation of the flavin chromophore in dye-labeled LOV domains leads to considerable FRET from flavin to the dye, the typical adduct formation between flavin and a nearby cysteine still occurs with considerable yield. We obtain a rate constant for LOV-LOV dimerization in the range (0.8-1.8) × 105 M-1 s-1, and an equilibrium constant of the dark-state dimer in the range (3.0-7.0) × 10-6 M. Dissociation of the dimers in the light state and reforming of dimers after return to the dark state was monitored using an anti-FRET effect caused by excitonic interaction between dye labels on different monomers. Reforming of the dark state dimers is slower than recovery of the flavin-cysteinyl adduct, indicating that light-induced conformational changes in the LOV domain persist for much longer time than the adduct lifetime.
Asunto(s)
Transferencia Resonante de Energía de Fluorescencia , Rhodobacter sphaeroides/química , Colorantes/química , Dimerización , Flavinas/química , Cinética , Luz , Conformación Proteica en Hélice alfa , Dominios Proteicos , Rhodobacter sphaeroides/metabolismoRESUMEN
Intersystem crossing (ISC) of triplet photosensitizers is a vital process for fundamental photochemistry and photodynamic therapy (PDT). Herein, we report the co-existence of efficient ISC and long triplet excited lifetime in a heavy atom-free bodipy helicene molecule. Via theoretical computation and time-resolved EPR spectroscopy, we confirmed that the ISC of the bodipy results from its twisted molecular structure and reduced symmetry. The twisted bodipy shows intense long wavelength absorption (ϵ=1.76×105 m-1 cm-1 at 630â nm), satisfactory triplet quantum yield (ΦT =52 %), and long-lived triplet state (τT =492â µs), leading to unprecedented performance as a triplet photosensitizer for PDT. Moreover, nanoparticles constructed with such helical bodipy show efficient PDT-mediated antitumor immunity amplification with an ultra-low dose (0.25â µg kg-1 ), which is several hundred times lower than that of the existing PDT reagents.
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Compuestos de Boro/química , Fotoquimioterapia , Fármacos Fotosensibilizantes/química , Relación Dosis-Respuesta a Droga , Espectroscopía de Resonancia por Spin del Electrón , Estructura Molecular , Teoría CuánticaRESUMEN
The first example for the photocatalytic generation of a highly electrophilic intermediate that is not based on radical reactivity is reported. The single-electron reduction of bench-stable and commercially available 4-(trifluoromethoxy)benzonitrile by an organic photosensitizer leads to its fragmentation into fluorophosgene and benzonitrile. The in situ generated fluorophosgene was used for the preparation of carbonates, carbamates, and urea derivatives in moderate to excellent yields via an intramolecular cyclization reaction. Transient spectroscopic investigations suggest the formation of a catalyst charge-transfer complex-dimer as the catalytic active species. Fluorophosgene as a highly reactive intermediate, was indirectly detected via its next downstream carbonyl fluoride intermediate by NMR. Furthermore, detailed NMR analyses provided a comprehensive reaction mechanism including a water dependent off-cycle equilibrium.
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Luz , Fosgeno/química , Carbamatos/síntesis química , Carbamatos/química , Catálisis , Ciclización , Espectroscopía de Resonancia MagnéticaRESUMEN
The emission properties of a series of flavin (FL) decorated Ru (II) polyimine complexes were investigated by extensive time-dependent (TD) density functional theory (DFT) and DFT based calculations. We attributed the moderate emission properties of FL decorated Ru(II) polyimine complex (Ru-1), such as triplet lifetime and luminescence quantum yield, to the dominant fast nonradiative decay due to the small adiabatic energy gap between the ground state and the lowest lying triplet state (Δ Ead) and the slow radiative decay owing to the ligand localized triplet (3IL) nature of the emissive state. Electron withdrawing groups such as F and Cl were attached to the FL moiety of Ru-1 to alter Δ Ead. Both the radiative and nonradiative decay rates were found to be sensitive to Δ Ead and may result in a drastic change of the photophysical properties of the Ru(II) complexes. Specifically, substitution with F leads to an increase in the Δ Ead from 1.85 to 1.93 eV, resulting in a nearly doubled phosphorescent quantum yield and triplet lifetime with respect to Ru-1. These findings are vital for the rational design of phosphorescent transition metal complexes.
RESUMEN
A fast and efficient method is presented that recovers a three-dimensional cylindrically symmetric probability distribution from its two-dimensional projection onto a plane parallel to the cylinder axis. This problem arises regularly in the analysis of data from velocity map imaging or photoelectron imaging experiments. The data can be considered the (numerically stable) Abel transform of the unknown probability distribution. The inverse Abel transform belongs to the class of ill-posed problems. In 2014 I presented two methods which solve this problem, termed maximum entropy velocity image reconstruction (MEVIR) and maximum entropy velocity Legendre reconstruction (MEVELER) (Phys. Chem. Chem. Phys., 2014, 16, 570). The maximum entropy concept finds the most probable solution that agrees with the data for a Gaussian or Poissonian particle statistics. The new method presented here also uses the maximum entropy concept and finds a solution in terms of an expansion in Legendre polynomials like MEVELER. The new method dramatically reduces the size of the numerical problem by using an expansion in terms of Legendre polynomials also for the image data. The new method performs at least as well as MEVELER (i.e. down to intensities of ca. 0.01 counts per pixel), but requires only a small fraction of the CPU time and core memory. It should hence be applicable for on-the-fly data analysis during measurements. It can analyze distributions containing higher-order and odd-order Legendre polynomials, whereas MEVELER performed well only for Legendre polynomials of order l = 0 and l = 2. Higher-order and odd-order Legendre polynomials are required in the analysis of multiphoton dissociation reactions, photoelectrons from higher harmonics experiments, or involving circular dichroism.
RESUMEN
A bipyridine ruthenium(ii) complex (Ru-1) with a flavin moiety connected to one of the bipyridine ligands via an acetylene bond was designed and synthesized, and its photophysical properties were investigated. Compared with the tris(bipyridine) Ru(ii) complex (Ru-0), which has an extinction coefficient ε = 1.36 × 104 M-1 cm-1 at 453 nm, the introduction of the flavin moiety endows Ru-1 with strong absorption in the visible range (ε = 2.34 × 104 M-1 cm-1 at 456 nm). Furthermore, Ru-1 exhibits phosphorescence (λem = 643 nm, ΦP = 1%, τP = 1.32 µs at 293 K and 4.53 µs at 77 K). We propose that the emission of Ru-1 originates from the low lying triplet excited state of 3IL according to the time-resolved transient difference absorption spectra, the calculated T1 spin density and the T1 thermo-vibration modes localized on the flavin-decorated bipyridine ligand. This is the first time that the phosphorescence of flavin was observed within Ru(ii) complexes. Consequently, Ru-1 was used for triplet-triplet annihilation upconversion, showing a reasonable quantum yield of 0.7% with respect to the phosphorescence quantum yield of 1%. These findings pave the way for the rational design of phosphorescence transition metal complexes. Also, further approaches that may improve the performance of flavin-decorated Ru(ii) bipyridine complexes are proposed.
RESUMEN
Hydrogen bonding in cyclic complexes of water with tautomeric pairs of molecules M0 and M1 is calculated to be stronger by more than 25% for the less stable tautomer M1 in all cases where the energy gap between the two tautomers is large (ΔE(M0 - M1) > 10 kcal mol-1). This is accompanied by a large red-shift (>200 cm-1) of the N-H/O-H stretch frequency in the complexes involving M1. Large barriers for double proton transfer in both directions should permit an experimental verification. Exceptions to this rule were found in heterocycles with an N-C[double bond, length as m-dash]O fragment incorporated into a conjugated cycle resulting in two nearly degenerate tautomers - keto and enol forms. The wavefunction of the keto form has a large contribution from a zwitterionic VB structure which is also aromatic. This increases the polarity of the keto group, making the oxygen atom a strong H-bond acceptor. It can also stabilize the keto form below the aromatic enol form. In this case the extra-HB stabilization is observed for the most stable tautomer (i.e. for the keto form). H-bonding enhances the aromatic character of less aromatic molecules, but the more aromatic tautomers partially loose aromaticity.
RESUMEN
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.
Asunto(s)
Cisteína/química , Luz , Oxígeno/química , Fototropinas/química , Fototropinas/metabolismo , Dominios Proteicos , Chlamydomonas reinhardtii/genética , Chlamydomonas reinhardtii/metabolismo , Cisteína/metabolismo , Dinitrocresoles/química , Transporte de Electrón , Mutación , Fototropinas/genéticaRESUMEN
The orteronel, abiraterone and galeterone, which were developed to treat castration resistant prostate cancer, inhibit 17,20 lyase activity but little is known about their effects on adrenal androgen biosynthesis. We studied the effect of several inhibitors and found that orteronel was selective towards 17,20 lyase activity than abiraterone and galeterone. Gene expression analysis showed that galeterone altered the expression of HSD3B2 but orteronel did not change the expression of HSD3B2, CYP17A1 and AKR1C3. The CYP19A1 activity was not inhibited except by compound IV which lowered activity by 23%. Surprisingly abiraterone caused complete blockade of CYP21A2 activity. Analysis of steroid metabolome by gas chromatography - mass spectrometry revealed changes in steroid levels caused by different inhibitors. We can conclude that orteronel is a highly specific inhibitor of 17,20 lyase activity. The discovery of these specific drug actions on steroidogenic enzyme activities would be valuable for understanding the regulation of androgens.
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Glándulas Suprarrenales/metabolismo , Andrógenos/biosíntesis , Antineoplásicos/administración & dosificación , Neoplasias de la Próstata/tratamiento farmacológico , Esteroide 17-alfa-Hidroxilasa/antagonistas & inhibidores , Glándulas Suprarrenales/citología , Glándulas Suprarrenales/efectos de los fármacos , Androstadienos/administración & dosificación , Androstenos/administración & dosificación , Bencimidazoles/administración & dosificación , Línea Celular , Relación Dosis-Respuesta a Droga , Humanos , Imidazoles/administración & dosificación , Masculino , Naftalenos/administración & dosificaciónRESUMEN
The activation of aryl-Br bonds was achieved by sequential combination of a triplet-triplet annihilation process of the organic dyes, butane-2,3-dione and 2,5-diphenyloxazole, with a single-electron-transfer activation of aryl bromides. The photophysical and chemical steps were studied by time-resolved transient fluorescence and absorption spectroscopy with a pulsed laser, quenching experiments, and DFT calculations.
RESUMEN
The chromophores ethynyl pyrene as blue, ethynyl perylene as green and ethynyl Nile red as red emitter were conjugated to the 5-position of 2'-deoxyuridine via an acetylene bridge. Using phosphoramidite chemistry on solid phase labelled DNA duplexes were prepared that bear single chromophore modifications, and binary and ternary combinations of these chromophore modifications. The steady-state and time-resolved fluorescence spectra of all three chromophores were studied in these modified DNA duplexes. An energy-transfer cascade occurs from ethynyl pyrene over ethynyl perylene to ethynyl Nile red and subsequently an electron-transfer cascade in the opposite direction (from ethynyl Nile red to ethynyl perylene or ethynyl pyrene, but not from ethynyl perylene to ethynyl pyrene). The electron-transfer processes finally provide charge separation. The efficiencies by these energy and electron-transfer processes can be tuned by the distances between the chromophores and the sequences. Most importantly, excitation at any wavelength between 350 and 700â nm finally leads to charge separated states which make these DNA samples promising candidates for light-harvesting systems.
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ADN/química , Oligonucleótidos/química , Secuencia de Bases , Transporte de Electrón , Transferencia de Energía , Fluorescencia , Luz , Perileno/química , Pirenos/química , Espectrofotometría UltravioletaRESUMEN
BACKGROUND: Normal pregnancy depends on pronounced adaptations in steroid hormone concentrations. Although in recent years, the understanding of these hormones in pregnancy has improved, the interpretation is hampered by insufficient reference values. Our aim was to establish gestation-specific reference intervals for spot urinary steroid hormone levels in normal singleton pregnancies and 6 weeks postpartum. METHODS: Cross-sectional multicentre observational study. Women recruited between 2008 and 2013 at 3 University Hospitals in Switzerland (Bern), Scotland (Glasgow) and Austria (Graz). Spot urine was collected from healthy women undergoing a normal pregnancy (age, 16-45 years; mean, 31 years) attending routine antenatal clinics at gestation weeks 11, 20, and 28 and approximately 6 weeks postpartum. Urine steroid hormone levels were analysed using gas-chromatography mass spectrometry. Creatinine was also measured by routine analysis and used for normalisation. RESULTS: From the results, a reference interval was calculated for each hormone metabolite at each trimester and 6 weeks postpartum. Changes in these concentrations between trimesters and postpartum were also observed for several steroid hormones and followed changes proposed for index steroid hormones. CONCLUSIONS: Normal gestation-specific reference values for spot urinary steroid hormones throughout pregnancy and early postpartum are now available to facilitate clinical management and research approaches to steroid hormone metabolism in pregnancy and the early postpartum period.
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Edad Gestacional , Hormonas Esteroides Gonadales/orina , Periodo Posparto/orina , Embarazo/orina , Adolescente , Adulto , Estudios de Cohortes , Estudios Transversales , Femenino , Hormonas Esteroides Gonadales/metabolismo , Humanos , Persona de Mediana Edad , Periodo Posparto/metabolismo , Embarazo/metabolismo , Valores de Referencia , Urinálisis/normas , Adulto JovenRESUMEN
LOV domains are the light sensitive parts of phototropins and many other light-activated enzymes that regulate the response to blue light in plants and algae as well as some fungi and bacteria. Unlike all other biological photoreceptors known so far, the photocycle of LOV domains involves the excited triplet state of the chromophore. This chromophore is flavin mononucleotide (FMN) which forms a covalent adduct with a cysteine residue in the signaling state. Since the formation of this adduct from the triplet state involves breaking and forming of two bonds as well as a change from the triplet to the singlet spin state, various intermediates have been proposed, e.g. a protonated triplet state (3)FMNH(+), the radical anion (2)FMNË(-), or the neutral semiquinone radical (2)FMNHË. We performed an extensive search for these intermediates by two-dimensional transient absorption (2D-TA) with a streak camera. However, no transient with a rate constant between the decay of fluorescence and the decay of the triplet state could be detected. Analysis of the decay associated difference spectra results in quantum yields for the formation of the adduct from the triplet of ΦA(LOV1) ≈ 0.75 and ΦA(LOV2) ≈ 0.80. This is lower than the values ΦA(LOV1) ≈ 0.95 and ΦA(LOV2) ≈ 0.99 calculated from the rate constants, giving indirect evidence of an intermediate that reacts either to form the adduct or to decay back to the ground state. Since there is no measurable delay between the decay of the triplet and the formation of the adduct, we conclude that this intermediate reacts much faster than it is formed. The LOV1-C57S mutant shows a weak and slowly decaying (τ > 100 µs) transient whose decay associated spectrum has bands at 375 and 500 nm, with a shoulder at 400 nm. This transient is insensitive to the pH change in the range 6.5-10.0 but increases on addition of ß-mercaptoethanol as the reducing agent. We assign this intermediate to the radical anion which is protected from protonation by the protein. We propose that the adduct is formed via the same intermediate by combination of the radical ion pair.
Asunto(s)
Chlamydomonas reinhardtii/química , Fotorreceptores de Plantas/química , Proteínas de Plantas/química , Aniones/química , Escherichia coli , Concentración de Iones de Hidrógeno , Cinética , Mercaptoetanol/química , Mutación , Fotoblanqueo , Proteínas de Plantas/genética , Estructura Terciaria de Proteína , Sustancias Reductoras/química , Análisis EspectralRESUMEN
Devising analysis tools for elucidating the regulatory mechanism of complex enzymes has been a challenging task for many decades. It generally requires the determination of the structural-dynamical information of protein solvent systems far from equilibrium over multiple length and time scales, which is still difficult both theoretically and experimentally. To cope with the problem, we introduce a full-residue space multiscale simulation method based on a combination of the kinetic Monte Carlo and molecular dynamics techniques, in which the rates of the rate-determining processes are evaluated from a biomolecular forcefield on the fly during the simulation run by taking into account the full space of residues. To demonstrate its reliability and efficiency, we explore the light-induced functional behavior of the full-length phototropin1 from Chlamydomonas reinhardtii (Cr-phot1) and its various subdomains. Our results demonstrate that in the dark state the light oxygen voltage-2-Jα (LOV2-Jα) photoswitch inhibits the enzymatic activity of the kinase, whereas the LOV1-Jα photoswitch controls the dimerization with the LOV2 domain. This leads to the repulsion of the LOV1-LOV2 linker out of the interface region between both LOV domains, which results in a positively charged surface suitable for cell-membrane interaction. By contrast, in the light state, we observe that the distance between both LOV domains is increased and the LOV1-LOV2 linker forms a helix-turn-helix (HTH) motif, which enables gene control through nucleotide binding. Finally, we find that the kinase is activated through the disruption of the Jα-helix from the LOV2 domain, which is followed by a stretching of the activation loop (A-loop) and broadening of the catalytic cleft of the kinase.
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Adenosina Trifosfato/metabolismo , Chlamydomonas reinhardtii/enzimología , Fototropinas/metabolismo , Sitios de Unión , Luz , Simulación de Dinámica Molecular , Método de Montecarlo , Unión Proteica , Pliegue de Proteína , Estructura Terciaria de Proteína , Transducción de SeñalRESUMEN
A new method for the reconstruction of velocity maps from ion images is presented, which is based on the maximum entropy concept. In contrast to other methods used for Abel inversion the new method never applies an inversion or smoothing to the data. Instead, it iteratively finds the map which is the most likely cause for the observed data, using the correct likelihood criterion for data sampled from a Poissonian distribution. The entropy criterion minimizes the information content in this map, which hence contains no information for which there is no evidence in the data. Two implementations are proposed, and their performance is demonstrated with simulated and experimental data: Maximum Entropy Velocity Image Reconstruction (MEVIR) obtains a two-dimensional slice through the velocity distribution and can be compared directly to Abel inversion. Maximum Entropy Velocity Legendre Reconstruction (MEVELER) finds one-dimensional distribution functions Q(l)(v) in an expansion of the velocity distribution in Legendre polynomials P((cos θ) for the angular dependence. Both MEVIR and MEVELER can be used for the analysis of ion images with intensities as low as 0.01 counts per pixel, with MEVELER performing significantly better than MEVIR for images with low intensity. Both methods perform better than pBASEX, in particular for images with less than one average count per pixel.