A quantum chemical study of the formation of 2-hydroperoxy-coelenterazine in the Ca<Superscript>2+</Superscript>-regulated photoprotein obelin

The Ca²⁺-regulated photoprotein obelin determines the luminescence of the marine hydroid Obelia longissima. Bioluminescence is initiated by calcium and appears as a result of the oxidative decarboxylation related to the coelenterazine substrate. The luciferase of the luminescent marine coral Renilla muelleri (RM) also uses coelenterazine as a substrate. However, three proteins are involved in the in vivo bioluminescence of these animals: luciferase, green fluorescent protein, and Ca²⁺-regulated coelenterazine-binding protein (CBP). In fact, CBP that contains one strongly bound coelenterazine molecule is the RM luciferase substrate in the in vivo bioluminescent reaction. Coelenterazine becomes available for oxygen and the reaction with luciferase only after binding CBP with calcium ions. Unlike Ca²⁺-regulated photoproteins, the coelenterazine molecule is not activated by oxygen in the CBP molecule. In this work, by means of quantum chemical methods the behavior of substrates in these proteins is analyzed. It is shown that coelenterazine can form different tautomers: CLZ(2H) and CLZ(7H). The formation of 2-hydroperoxy-coelenterazine is studied. According to the obtained data, these proteins use different forms of the substrates for the reaction. In obelin, the substrate is in the CLZ(2H) form that affords hydrogen peroxide. In RM, coelenterazine is in the CLZ(7H) form, and therefore, CBP is not activated by oxygen.     

Bioluminescent properties of obelin and aequorin with novel coelenterazine analogues

The main analytical use of Ca²⁺-regulated photoproteins from luminous coelenterates is for real-time non-invasive visualization of intracellular calcium concentration ([Ca²⁺]_i) dynamics in cells and whole organisms. A limitation of this approach for in vivo deep tissue imaging is the fact that blue light emitted by the photoprotein is highly absorbed by tissue. Seven novel coelenterazine analogues were synthesized and their effects on the bioluminescent properties of recombinant obelin from Obelia longissima and aequorin from Aequorea victoria were evaluated. Only analogues having electron-donating groups (m-OCH₃ and m-OH) on the C6 phenol moiety or an extended resonance system at the C8 position (1-naphthyl and α-styryl analogues) showed a significant red shift of light emission. Of these, only the α-styryl analogue displayed a sufficiently high light intensity to allow eventual tissue penetration. The possible suitability of this compound for in vivo assays was corroborated by studies with aequorin which allowed the monitoring of [Ca²⁺]_i dynamics in cultured CHO cells and in hippocampal brain slices. Thus, the α-styryl coelenterazine analogue might be potentially useful for non-invasive, in vivo bioluminescence imaging in deep tissues of small animals.     

Hybrid Minimal Core Streptavidin–Obelin as a Versatile Reporter for Bioluminescence‐based Bioassay

Ca²⁺‐regulated photoprotein obelin was genetically fused with a minimum‐sized core streptavidin. Hybrid protein (SAV–OL) was produced by bacterial expression and applied as a specific bioluminescent probe in diverse solid‐phase assays. The obtained results clearly demonstrate specific activity of each domain indicating its proper folding with favorable space orientation. SAV–OL has been shown to be a much more sensitive label than the chemical conjugate of a full‐length streptavidin with obelin.     

The Ca2+-Regulated Photoprotein Obelin as a Tool for SELEX Monitoring and DNA Aptamer Affinity Evaluation

Bioluminescent solid-phase analysis was proposed to monitor the selection process and to determine binding characteristics of the aptamer–target complexes during design and development of the specific aptamers. The assay involves Ca²⁺-regulated photoprotein obelin as a simple, sensitive and fast reporter. Applicability and the prospects of the approach were exemplified by identification of DNA aptamers to cardiac troponin I, a highly specific early biomarker for acute myocardial infarction. Two structurally different aptamers specific to various epitopes of troponin I were obtained and then tested in a model bioluminescent assay.     

Mutants of Ca2+‐regulated Photoprotein Obelin for Site‐specific Conjugation

Color variants of Ca²⁺‐regulated photoprotein obelin were shown to be an important tool for dual‐analyte binding assay. To provide site‐directed conjugation with biospecific molecules, several obelin color mutants carrying unique cysteine residues were obtained and characterized for their novel properties. A pair of obelins Y138F,A5C and W92F,H22E,D12C was found to be most suitable (in terms of high bioluminescent activity and stability) as reporters in simultaneous assay of two targets in a sample. Availability of SH‐groups, accessible for chemical modification, essentially simplifies the synthesis of biospecific conjugates, increases their yield and conserves obelins' bioluminescence activity. Conjugates with immunoglobulin and oligonucleotide were produced and successfully applied in single nucleotide polymorphism genotyping.     

Three Efficient Methods for Preparation of Coelenterazine Analogues

The growing popularity of bioluminescent assays has highlighted the need for coelenterazine analogues possessing properties tuned for specific applications. However, the structural diversity of known coelenterazine analogues has been limited by current syntheses. Known routes for the preparation of coelenterazine analogues employ harsh reaction conditions that limit access to many substituents and functional groups. Novel synthetic routes reported here establish simple and robust methods for synthesis and investigation of structurally diverse marine luciferase substrates. Specifically, these new routes allow synthesis of coelenterazine analogues containing various heterocyclic motifs and substituted aromatic groups with diverse electronic substituents at the R² position. Interesting analogues described herein were characterized by their physicochemical properties, bioluminescent half‐life, light output, polarity and cytotoxicity. Some of the analogues represent leads that can be utilized in the development of improved bioluminescent systems.     

Effects of alcohols on fluorescence intensity and color of a discharged-obelin-based biomarker

Photoproteins are responsible for bioluminescence of marine coelenterates; bioluminescent and fluorescent biomarkers based on photoproteins are useful for monitoring of calcium-dependent processes in medical investigations. Here, we present the analysis of intensity and color of light-induced fluorescence of Ca²⁺-discharged photoprotein obelin in the presence of alcohols (ethanol and glycerol). Complex obelin spectra obtained at different concentrations of the alcohols at 350- and 280-nm excitation (corresponding to polypeptide-bound coelenteramide and tryptophan absorption regions) were deconvoluted into Gaussian components; fluorescent intensity and contributions of the components to experimental spectra were analyzed. Five Gaussian components were found in different spectral regions—ultraviolet (tryptophan emission), blue-green (coelenteramide emission), and red (hypothetical indole-coelenteramide exciplex emission). Inhibition coefficients and contributions of the components to experimental fluorescent spectra showed that presence of alcohols increased contributions of ultraviolet, violet, and red components, but decreased contributions of components in the blue-green region. The effects were related to (1) changes of proton transfer efficiency in fluorescent S*₁ state of coelenteramide in the obelin active center and (2) formation of indole-coelenteramide exciplex at 280-nm photoexcitation. The data show that variation of fluorescence color and intensity in the presence of alcohols and dependence of emission spectra on excitation wavelength should be considered while applying the discharged obelin as a fluorescence biomarker.     

Trapped interfacial redox introduces reversibility in the oxygen reduction reaction in a non-aqueous Ca2+ electrolyte

Electrochemical investigations of the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) have been conducted in a Ca²⁺-containing dimethyl sulfoxide electrolyte. While the ORR appears irreversible, the introduction of a tetrabutylammonium perchlorate (TBAClO₄) co-salt in excess concentrations results in the gradual appearance of a quasi-reversible OER process. Combining the results of systematic cyclic voltammetry investigations, the degree of reversibility depends on the ion pair competition between Ca²⁺ and TBA⁺ cations to interact with generated superoxide (O₂⁻). When TBA⁺ is in larger concentrations, and large reductive overpotentials are applied, a quasi-reversible OER peak emerges with repeated cycling (characteristic of formulations without Ca²⁺ cations). In situ Raman microscopy and rotating ring-disc electrode (RRDE) experiments revealed more about the nature of species formed at the electrode surface and indicated the progressive evolution of a charge storage mechanism based upon trapped interfacial redox. The first electrochemical step involves generation of O₂⁻, followed primarily by partial passivation of the surface by Ca_xO_y product formation (the dominant initial reaction). Once this product matrix develops, the subsequent formation of TBA⁺--O₂⁻ is contained within the Ca_xO_y product interlayer at the electrode surface and, consequently, undergoes a facile oxidation reaction to regenerate O₂.

An interlayer product of oxygen reduction with Ca²⁺/TBA⁺ yields a quasi-reversible oxygen evolution reaction by inducing a trapped interfacial redox process.     

Revised mechanism of carboxylation of ribulose‐1,5‐biphosphate by rubisco from large scale quantum chemical calculations

Here, we describe a computational approach for studying enzymes that catalyze complex multi‐step reactions and apply it to Ribulose 1,5‐bisphosphate carboxylase–oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5‐step carboxylase reaction, the substrate Ribulose‐1,5‐bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO₂. Hydration of the RuBP.CO₂ complex is followed by C C bond scission and stereospecific protonation. However, details of the roles and protonation states of active‐site residues, and sources of protons and water, remain highly speculative. Large‐scale computations on active‐site models provide a means to better understand this complex chemical mechanism. The computational protocol comprises a combination of hybrid semi‐empirical quantum mechanics and molecular mechanics within constrained molecular dynamics simulations, together with constrained gradient minimization calculations using density functional theory. Alternative pathways for hydration of the RuBP.CO₂ complex and associated active‐site protonation networks and proton and water sources were investigated. The main findings from analysis of the resulting energetics advocate major revision to existing mechanisms such that: hydration takes place anti to the CO₂; both hydration and C C bond scission require early protonation of CO₂ in the RuBP.CO₂ complex; C C bond scission and stereospecific protonation reactions are concerted and, effectively, there is only one stable intermediate, the C3‐gemdiolate complex. Our main conclusions for interpreting enzyme kinetic results are that the gemdiolate may represent the elusive Michaelis–Menten‐like complex corresponding to the empirical K_m (=K_c) with turnover to product via bond scission concerted with stereospecific protonation consistent with the observed catalytic rate. © 2018 Wiley Periodicals, Inc.     

Fluorescence properties of Ca2+-independent discharged obelin and its application prospects

Discharged obelin, a complex of coelenteramide and polypeptide, is a fluorescent protein produced from the photoprotein obelin, which is responsible for bioluminescence of the marine hydroid Obelia longissima. Discharged obelin is stable and nontoxic and its spectra are variable, and this is why it can be used as a fluorescent biomarker of variable color in vivo and in vitro. Here we examined light-induced fluorescence of Ca²⁺-independent discharged obelin (obtained without addition of Ca²⁺). Its emission and excitation spectra were analyzed under variation of the excitation wavelength (260–390 nm) and the emission wavelength (400–700 nm), as well as the 40 °C exposure time. The emission spectra obtained with excitation at 260–300 nm (tryptophan absorption region) included three peaks with maxima at 355, 498, and 660 nm, corresponding to fluorescence of tryptophan, polypeptide-bound coelenteramide, and a hypothetical indole–coelenteramide exciplex, respectively. The emission spectra obtained with excitation at 310–380 nm (coelenteramide absorption region) did not include the 660-nm maximum. The peak in the red spectral region (λ _max?=?660 nm) has not been previously reported. Exposure to 40 °C under excitation at 310–380 nm shifted the obelin fluorescence spectra to the blue, whereas excitation at 260–300 nm shifted them to the red. Hence, red emission and variation of the excitation wavelength form a basis for development of new medical techniques involving obelin as a colored biomarker. The addition of red color to the battery of known (violet to yellow) colors increases the potential of application of obelin.     

Structure of the Michaelis Complex and Function of the Catalytic Center in the Reductive Half‐Reaction of Computational and Synthetic Models of Sulfite Oxidase

By using frontier‐molecular‐orbital and electrostatic (nucleophilic) interactions as well as relaxed potential‐energy surface scans, it is shown that the initial step in the oxygen‐atom transfer (OAT) reaction of [Mo^VIO₂‐(S₂C₂Me₂)SMe]^?1 ( 1 ) and [Mo^VIO₂‐{(S₂C₂(CN)₂}₂]^2? ( 2 ) with HSO₃^? takes place by oxoanionic binding of the substrate to the Mo^VI center with the formation of a stable Michaelis complex. The gas‐phase and solvent‐corrected enthalpy profile with fully optimized minima and transition states for the OAT reaction of 1 and 2 with HSO₃^? showed the release of reaction energy for both complexes. The optimized geometries of 1 and 2 in the respective enzyme–substrate complexes showed a common feature with the participation of hydrogen bonding of the substrate with the axial (spectator) oxo group in the subsequent formation of the six‐membered MoO₂HOS transition state. The enzyme–substrate complex of 2 shows heptacoordination as proposed earlier, although the trans (to axial oxo)‐Mo? S(dithiolene) bond is elongated to 2.948 Å.     

Sulfone-Modified Covalent Organic Frameworks Enabling Efficient Photocatalytic Hydrogen Peroxide Generation via One-Step Two-Electron O2 Reduction

Photocatalytic oxygen reduction reaction (ORR) offers a promising hydrogen peroxide (H₂O₂) synthetic strategy, especially the one-step two-electron (2e⁻) ORR route holds great potential in achieving highly efficient and selectivity. However, efficient one-step 2e⁻ ORR is rarely harvested and the underlying mechanism for regulating the ORR pathways remains greatly obscure. Here, by loading sulfone units into covalent organic frameworks (FS-COFs), we present an efficient photocatalyst for H₂O₂ generation via one-step 2e⁻ ORR from pure water and air. Under visible light irradiation, FS-COFs exert a superb H₂O₂ yield of 3904.2 μmol h⁻¹ g⁻¹, outperforming most reported metal-free catalysts under similar conditions. Experimental and theoretical investigation reveals that the sulfone units accelerate the separation of photoinduced electron-hole (e⁻-h⁺) pairs, enhance the protonation of COFs, and promote O₂ adsorption in the Yeager-type, which jointly alters the reaction process from two-step 2e⁻ ORR to the one-step one, thereby achieving efficient H₂O₂ generation with high selectivity.     

On the formation and stability of O− and O−2 radicals in type a zeolites and demonstration of cation interactions

Electron spin resonance studies show tha O^? is formed as the major paramagnetic oxygen species in γ-irradiated Ca₆-A zeolite followed by oxygen adsorption. This is a new method to generate this highly reactive catalytic intermediate. O^?₂ is formed in addition to O^? if oxygen is adsorbed prior to irradiation. In Na₁₂-A zeolite O^? is also seen but it transforms to O^?₂ in several hours. Thus O^? appears to be more stable in divalent exchanged zeolites. By electron spin echo modulation spectrometry interactions fo O^?₂ with Li⁺ have been detected which suggests that oxygen species locations in zeolites can be delineated.     

Characterization of hydromedusan Ca2+-regulated photoproteins as a tool for measurement of Ca2+concentration

Calcium ion is a ubiquitous intracellular messenger, performing this function in many eukaryotic cells. To understand calcium regulation mechanisms and how disturbances of these mechanisms are associated with disease states, it is necessary to measure calcium inside cells. Ca²⁺-regulated photoproteins have been successfully used for this purpose for many years. Here we report the results of comparative studies on the properties of recombinant aequorin from Aequorea victoria, recombinant obelins from Obelia geniculata and Obelia longissima, recombinant mitrocomin from Mitrocoma cellularia, and recombinant clytin from Clytia gregaria as intracellular calcium indicators in a set of identical in vitro and in vivo experiments. Although photoproteins reveal a high degree of identity of amino acid sequences and spatial structures, and, apparently, have a common mechanism for the bioluminescence reaction, they were found to differ in the Ca²⁺ concentration detection limit, the sensitivity of bioluminescence to Mg²⁺, and the rates of the rise of the luminescence signal with a sudden change of Ca²⁺ concentration. In addition, the bioluminescence activities of Chinese hamster ovary cells expressing wild-type photoproteins also differed. The light signals of cells expressing mitrocomin, for example, slightly exceeded the background, suggesting that mitrocomin may be hardly used to detect intracellular Ca²⁺ without modifications improving its properties. On the basis of experiments on the activation of endogenous P2Y₂ receptor in Chinese hamster ovary cells by ATP, we suggest that wild-type aequorin and obelin from O. longissima are more suitable for calcium detection in cytoplasm, whereas clytin and obelin from O. geniculata can be used for calcium measurement in cell compartments with high Ca²⁺ concentration. Figure

Hydromedusan photoproteins differ in Ca²⁺ concentration detection limit, sensitivity of bioluminescence to Mg²⁺, and rates of rise of luminescence signal with a sudden change of [Ca²⁺] despite a high degree of identity of their amino acid sequences and spatial structures, and, apparently, a common mechanism for the bioluminescence reaction.     

双帽Keggin型杂多阴离子[H4As3Mo12O40]-和Keggin型杂多酸H3PM12O40 (M＝Mo, W)质子化的DFT研究

选用B3LYP方法在LanL2MB水平下, 对双帽α-Keggin型杂多阴离子[H₄As₃Mo₁₂O₄₀]^-的电子结构和质子的定位进行了密度泛函理论(DFT)研究. 结果表明, 双帽的形成大大影响了杂多阴离子[As₃Mo₁₂O₄₀]^5－的电子结构和性质, NBO分析显示参与成帽的三桥氧上的电子密度比双桥氧上的要大, 简单地从电荷密度来看, 质子将首先在三桥氧上定域成键, 但通过比较质子定域在几种桥氧上质子化稳定化能的大小, 发现[H₄As₃Mo₁₂O₄₀]^-中的四个质子将在八个双桥氧中的其中四个氧原子上定位, 而不是如文献中报道的在四个三桥氧上定域成键. 对杂多酸H₃PM₁₂O₄₀ (M＝Mo, W)中质子的定位也进行了理论计算并与文献进行了比较, 结果显示, H₃PMo₁₂O₄₀中质子是定位在双桥氧上; 而H₃PW₁₂O₄₀中质子将优先在双桥氧上定位, 但也可在端氧上定位; 这一结果与文献报道的相一致.     

Oxygen permeation and phase structure properties of partially A-site substituted BaCo0.7Fe0.225Ta0.075O3-δ perovskites

Ba_0.9R_0.1Co_0.7Fe_0.225Ta_0.075O_3-δ (BRCFT, R = Ca, La or Sr) membranes were synthesized by a solid-state reaction. Metal cation Ca²⁺, La³⁺ or Sr²⁺ doping on A-site partially substituted Ba²⁺ in BaCo_0.7Fe_0.225Ta_0.075O_3-δ oxides, and its subsequent effects on phase structure stability, oxygen permeability and oxygen desorption were systematically investigated by XRD, TG-DSC, H₂-TPR, O₂-TPD techniques and oxygen permeation experiments. The partial substitution with Ca²⁺, La³⁺ or Sr²⁺, whose ionic radii are smaller than that of Ba²⁺, succeeded in stabilizing the cubic perovskite structure without formation of impurity phases, as revealed by XRD analysis. Oxygen-involving experiments showed that BRCFT with A-site fully occupied by Ba²⁺ exhibited good oxygen permeation flux under He flow, reaching about 2.3 mL·min⁻¹ ·cm⁻² at 900 °C with 1 mm thickness. Of all the membranes, BLCFT membrane showed better chemical stability in CO₂, owing to the reduction in alkalinity of the mixed conductor oxide by La doping. In addition, we also found the stability of the perovskite structure under reducing atmospheres was strengthened by increasing the size of A-site cation (Ba²⁺>La³⁺>Sr²⁺>Ca²⁺).     

A QM/MM Study on the Initiation Reaction of Firefly Bioluminescence—Enzymatic Oxidation of Luciferin

Among all bioluminescent organisms, the firefly is the most famous, with a high luminescent efficiency of 41%, which is widely used in the fields of biotechnology, biomedicine and so on. The entire bioluminescence (BL) process involves a series of complicated in-vivo chemical reactions. The BL is initiated by the enzymatic oxidation of luciferin (LH₂). However, the mechanism of the efficient spin-forbidden oxygenation is far from being totally understood. Via MD simulation and QM/MM calculations, this article describes the complete process of oxygenation in real protein. The oxygenation of luciferin is initiated by a single electron transfer from the trivalent anionic LH₂ (L³⁻) to O₂ to form ¹[L^•2−…O₂^•−]; the entire reaction is carried out along the ground-state potential energy surface to produce the dioxetanone (FDO⁻) via three transition states and two intermediates. The low energy barriers of the oxygenation reaction and biradical annihilation involved in the reaction explain this spin-forbidden reaction with high efficiency. This study is helpful for understanding the BL initiation of fireflies and the other oxygen-dependent bioluminescent organisms.     

Vitamin C: an experimental and theoretical study on the gas‐phase structure and ion energetics of protonated ascorbic acid

In order to investigate the gas‐phase mechanisms of the acid catalyzed degradation of ascorbic acid (AA) to furan, we undertook a mass spectrometric (ESI/TQ/MS) and theoretical investigation at the B3LYP/6‐31 + G(d,p) level of theory. The gaseous reactant species, the protonated AA, [C₆H₈O₆]H⁺, were generated by electrospray ionization of a 10^?3 M H₂O/CH₃OH (1 : 1) AA solution. In order to structurally characterize the gaseous [C₆H₈O₆]H⁺ ionic reactants, we estimated the proton affinity and the gas‐phase basicity of AA by the extended Cooks's kinetic method and by computational methods at the B3LYP/6‐31 + G(d,p) level of theory. As expected, computational results identify the carbonyl oxygen atom (O2) of AA as the preferred protonation site. From the experimental proton affinity of 875.0 ± 12 kJ mol^?1 and protonation entropy ΔS_p 108.9 ± 2 J mol^?1 K^?1, a gas‐phase basicity value of AA of 842.5 ± 12 kJ mol^?1 at 298 K was obtained, which is in agreement with the value issuing from quantum mechanical computations. Copyright © 2016 John Wiley & Sons, Ltd.     

An Optochemical Oxygen Scavenger Enabling Spatiotemporal Control of Hypoxia

We present an optochemical O₂ scavenging system that enables precise spatiotemporal control of the level of hypoxia in living cells simply by adjusting the light intensity in the illuminated region. The system employs rhodamine containing a selenium or tellurium atom as an optochemical oxygen scavenger that rapidly consumes O₂ by photochemical reaction with glutathione as a coreductant upon visible light irradiation (560–590 nm) and has a rapid response time, within a few minutes. The glutathione-consuming quantum yields of the system were calculated as about 5 %. The spatiotemporal O₂ consuming in cultured cells was visualized with a hypoxia-responsive fluorescence probe, MAR. Phosphorescence lifetime imaging was applied to confirmed that different light intensities could generate different levels of hypoxia. To illustrate the potential utility of this system for hypoxia research, we show that it can spatiotemporally control calcium ion (Ca²⁺) influx into HEK293T cells expressing the hypoxia-responsive Ca²⁺ channel TRPA1.     

A High‐Valent Non‐Heme μ‐Oxo Manganese(IV) Dimer Generated from a Thiolate‐Bound Manganese(II) Complex and Dioxygen

This study deals with the unprecedented reactivity of dinuclear non‐heme Mn^II–thiolate complexes with O₂, which dependent on the protonation state of the initial Mn^II dimer selectively generates either a di‐μ‐oxo or μ‐oxo‐μ‐hydroxo Mn^IV complex. Both dimers have been characterized by different techniques including single‐crystal X‐ray diffraction and mass spectrometry. Oxygenation reactions carried out with labeled ¹⁸O₂ unambiguously show that the oxygen atoms present in the Mn^IV dimers originate from O₂. Based on experimental observations and DFT calculations, evidence is provided that these Mn^IV species comproportionate with a Mn^II precursor to yield μ‐oxo and/or μ‐hydroxo Mn^III dimers. Our work highlights the delicate balance of reaction conditions to control the synthesis of non‐heme high‐valent μ‐oxo and μ‐hydroxo Mn species from Mn^II precursors and O₂.