Computational Bioluminescence

Bioluminescence (BL) is an amazing natural phenomenon whose visible light is produced by living organisms. Due to its high sensitivity, high selectivity and high signal‐to‐noise ratio, BL has been applied broadly in biotechnology and biomedical fields. However, for centuries, we can only receive some sporadic and static information from experimental observations, the mechanism of most BL is unknown. In the past 14 years, we have been performing theoretical study on all kinds of bioluminescent systems, and have uncovered the mechanism and details of several BLs. Here as an example, we qualitatively introduce our theoretical study of firefly BL in this account.     

基于生物发光的高灵敏度三磷酸腺苷检测研究

在微生物检测和食品安全控制中需要对低浓度的三磷酸腺苷(ATP)做出快速准确的测定,基于ATP光学反应原理,设计了一种微量光学反应池,结合萤火虫素-萤火虫素酶发光技术,构建了一种用于现场检测的高灵敏度ATP光学传感器系统.传感器响应波长为550 nm,ATP生物发光反应适宜pH为7.8,在优化实验条件下,发光强度和ATP浓度在对数坐标下呈线性相关,检出限可达1×10-16 mol/L ATP,检测样品仅需30 μL,测量时间60 s.这种检测方法具有响应范围宽,测试简便,快速可靠等特点,适用于ATP现场快速检测,具有很好的应用前景.     

生物超微弱发光现象及其应用

生物超微弱发光是普遍存在于有机体内的一种由生长代谢产生的自发化学发光现象。介绍了超微弱发光的可能作用机制及其检测方法,综述了其在生物医学、中医学、环境及农业领域的应用。     

Theoretical Study of Dinoflagellate Bioluminescence

Dinoflagellates are the most ubiquitous luminescent protists in the marine environment and have drawn much attention for their crucial roles in marine ecosystems. Dinoflagellate bioluminescence has been applied in underwater target detection. The luminescent system of dinoflagellates is a typical luciferin–luciferase one. However, the excited‐state oxyluciferin is not the light emitter of dinoflagellate bioluminescence as in most luciferin–luciferase bioluminescent organisms. The oxyluciferin of bioluminescent dinoflagellates is not fluorescent, whereas its luciferin emits bright fluorescence with similar wavelength of the bioluminescence. What is the light emitter of dinoflagellate bioluminescence and what is the chemical process of the light emission like? These questions have not been answered by the limited experimental evidence so far. In this study, for the first time, the density functional calculation is employed to investigate the geometries and properties of luciferin and oxyluciferin of bioluminescent dinoflagellate. The calculated results agree with the experimental observations and indicate the luciferin or its analogue, rather than oxyluciferin, is the bioluminophore of dinoflagellate bioluminescence. A rough mechanism involving energy transfer is proposed for dinoflagellate bioluminescence.     

超氧负离子在生物发光中的作用

活性氧物种和超氧负离子是生物体内的重要物质,本文通过超氧负离子在生物发光反应中的作用,针对几种不同的典型生物发光体系,综述了超氧负离子参与发光反应的相关理论和实验研究进展.     

光纤化学发光和生物发光传感器

本文综述国内外有关光纤华东安光和生物发光传感器的研究成果，涉及传感器的种类传感层的制作方法及传感器的设计等。     

Bioluminescence of monolayers of firefly luciferase immobilized on graphite

We report on the immobilization of the firefly protein luciferase on the hydrophobic surface of graphite. Observation by liquid-phase atomic force microscopy of islands with a height consistent with the size of a single molecule confirmed that the protein was contained within a monomolecular layer. The enzyme activity was assayed by single-photon counting of the bioluminescence, which is the catalytic product of luciferase. Attachment to the surface modified the efficiency of the enzyme, but the introduction of the substrates luciferin and ATP resulted in the reactivation of the enzyme. The functionalized graphite surface was employed as a cathode in a bioelectrochemical cell. This demonstrated that the electric field caused a substantial loss of enzyme catalytic activity.     

Mechanically Assisted Bioluminescence with Natural Luciferase

Mechanochemical analogues have recently been established for several enzymatic reactions, but they require periodic interruption of the reaction for sampling, dissolution, and (bio)chemical analysis to monitor their progress. By applying a mechanochemical procedure to induce bioluminescence analogous to that used by the marine ostracod Cypridina (Vargula) hilgendorfii, here we demonstrate that the light emitted by a bioluminescent reaction can be used to directly monitor the progress of a mechanoenzymatic reaction without sampling. Mechanical treatment of Cypridina luciferase with luciferin generates bright blue light which can be readily detected and analyzed spectroscopically. This mechanically assisted bioluminescence proceeds through a mechanism identical to that of bioluminescence in solution, but has higher activation energy due to being diffusion‐controlled in the viscous matrix. The results suggest that luciferases could be used as light‐emissive reporters of mechanoenzymatic reactions.     

Bioluminescence and chemiluminescence in drug screening

Drug screening, that is, the evaluation of the biological activity of candidate drug molecules, is a key step in the drug discovery and development process. In recent years, high-throughput screening assays have become indispensable for early stage drug discovery because of the developments in synthesis technologies, such as combinatorial chemistry and automated synthesis, and the discovery of an increasing number of new pharmacological targets.Bioluminescence and chemiluminescence represent suitable detection techniques for high-throughput screening because they allow rapid and sensitive detection of the analytes and can be applied to small-volume samples. In this paper we report on recent applications of bioluminescence and chemiluminescence in drug screening, both for in vitro and in vivo assays. Particular attention is devoted to the latest and most innovative bioluminescence and chemiluminescence-based technologies for drug screening, such as assays based on genetically modified cells, bioluminescence resonance energy transfer (BRET)-based assays, and in vivo imaging assays using transgenic animals or bioluminescent markers. The possible relevance of bioluminescence and chemiluminescence techniques in the future developments of high-throughput screening technologies is also discussed.     

Bioluminescence in Dinoflagellates: Evidence that the Adaptive Value of Bioluminescence in Dinoflagellates is Concentration Dependent

Three major hypotheses have been proposed to explain why dinoflagellate bioluminescence deters copepod grazing: startle response, aposematic warning, and burglar alarm. These hypotheses propose dinoflagellate bioluminescence (A) startles predatory copepods, (B) warns potential predators of toxicity, and (C) draws the attention of higher order visual predators to the copepod's location. While the burglar alarm is the most commonly accepted hypothesis, it requires a high concentration of bioluminescent dinoflagellates to be effective, meaning the bioluminescence selective advantage at lower, more commonly observed, dinoflagellate concentrations may result from another function (e.g. startle response or aposematic warning). Therefore, a series of experiments was conducted to evaluate copepod grazing (Acartia tonsa) on bioluminescent dinoflagellates (during bioluminescent and nonbioluminescent phases, corresponding to night and day, respectively) at different concentrations (10, 1000, and 3000 cells mL^?1), on toxic (Pyrodinium bahamense var. bahamense) and nontoxic (Lingulodinium polyedrum) bioluminescent dinoflagellates, and in the presence of nonluminescent diatoms (Thalassiosira eccentrica). Changes in copepod ingestion rates, clearance rates, and feeding preferences as a result of these experimental factors, particularly during the mixed trails with nonluminescent diatoms, indicate there is a concentration threshold at which the burglar alarm becomes effective and below which dinoflagellate bioluminescence functions as an aposematic warning.     

The Chemical Basis of Fungal Bioluminescence

Many species of fungi naturally produce light, a phenomenon known as bioluminescence, however, the fungal substrates used in the chemical reactions that produce light have not been reported. We identified the fungal compound luciferin 3‐hydroxyhispidin, which is biosynthesized by oxidation of the precursor hispidin, a known fungal and plant secondary metabolite. The fungal luciferin does not share structural similarity with the other eight known luciferins. Furthermore, it was shown that 3‐hydroxyhispidin leads to bioluminescence in extracts from four diverse genera of luminous fungi, thus suggesting a common biochemical mechanism for fungal bioluminescence.     

利用生物发光技术检测微量焦磷酸

利用生物发光技术建立了一种高灵敏度的检测微量焦磷酸 ( PPi)的新方法。其原理是首先利用 ATP硫酰化酶 ( ATP sulfurylase)将焦磷酸 ( PPi)定量转化成ATP,然后利用虫荧光素酶 ( Luciferase)系统发光检测 ATP的量 ,从而确定样品中PPi的含量。本法快速、灵敏 ,线性范围为 1× 1 0 - 9～ 5× 1 0 - 7mol/ L。方法用于 PCR扩增样品中 PPi的检测 ,获得满意结果     

The Sensitized Bioluminescence Mechanism of Bacterial Luciferase

After more than one‐half century of investigations, the mechanism of bioluminescence from the FMNH₂ assisted oxygen oxidation of an aliphatic aldehyde on bacterial luciferase continues to resist elucidation. There are many types of luciferase from species of bioluminescent bacteria originating from both marine and terrestrial habitats. The luciferases all have close sequence homology, and in vitro, a highly efficient light generation is obtained from these natural metabolites as substrates. Sufficient exothermicity equivalent to the energy of a blue photon is available in the chemical oxidation of the aldehyde to the corresponding carboxylic acid, and a luciferase‐bound FMNH‐OOH is a key player. A high energy species, the source of the exothermicity, is unknown except that it is not a luciferin cyclic peroxide, a dioxetanone, as identified in the pathway of the firefly and the marine bioluminescence systems. Besides these natural substrates, variable bioluminescence properties are found using other reactants such as flavin analogs or aldehydes, but results also depend on the luciferase type. Some rationalization of the mechanism has resulted from spatial structure determination, NMR of intermediates and dynamic optical spectroscopy. The overall light path appears to fall into the sensitized class of chemiluminescence mechanism, distinct from the dioxetanone types.     

New Perspectives on Turbulence

Russian Journal of Electrochemistry - Recent work on the dissipation theorem of turbulent flow is reviewed, with examples in rotating cylinders, pipe flow, and flow past a flat plate at zero...     

A Photodynamic System based on Endogenous Bioluminescence for in vitro Anticancer Studies

Photodynamic therapy (PDT) is becoming an important cancer treatment in recent years. However, at present, the therapeutic effect of PDT is limited due to insufficient penetration depth of light. In this study, a new photodynamic system (d ‐Lu)PCN‐224 is constructed by porphyrin‐based metal‐organic framework (MOF) PCN‐224 and bioluminescent molecule d ‐fluorescein (d ‐Lu). The bioluminescence (BL) spectrum of the reaction overlaps with the absorption spectrum of PCN‐224, so it is speculated that bioluminescence resonance energy transfer (BRET) between the MOF and d ‐Lu which indicates inner light can be gained and used for PDT. Confocal imaging analysis and cytotoxicity assays have demonstrated that (d ‐Lu)PCN‐224 can produce singlet oxygen and decrease the cell viability of SKOV‐3. This system provides a possibility of PDT for deep‐level organization without an external light source.     

萤火虫生物发光中加氧反应机理的理论研究

萤火虫生物发光是最常见的生物发光,在生物和医药等领域已得到重要应用.发光过程涉及到其活体内的一系列复杂的化学反应.引起发光的起始反应是单重态荧光素分子与三重态氧气的加成反应.这是一个自旋禁阻的酶催化反应,通常效率很低,但萤火虫是目前将化学能转化为光能最高效的系统.这个自旋禁阻的反应为什么能高效率发生?实验研究认为该反应由单电子转移(SET)诱发而发生,但对反应的详细过程和机理并没有完整的描述.本工作通过理论计算,描述了该反应的完整过程,解释了这个自旋禁阻反应高效发生的原因.     

QM/MM Study on the Light Emitters of Aequorin Chemiluminescence,Bioluminescence, and Fluorescence: A General Understanding of the Bioluminescence of Several Marine Organisms

Aequorea victoria is a type of jellyfish that is known by its famous protein, green fluorescent protein (GFP), which has been widely used as a probe in many fields. Aequorea has another important protein, aequorin, which is one of the members of the EF‐hand calcium‐binding protein family. Aequorin has been used for intracellular calcium measurements for three decades, but its bioluminescence mechanism remains largely unknown. One of the important reasons is the lack of clear and reliable knowledge about the light emitters, which are complex. Several neutral and anionic forms exist in chemiexcited, bioluminescent, and fluorescent states and are connected with the H‐bond network of the binding cavity in the protein. We first theoretically investigated aequorin chemiluminescence, bioluminescence, and fluorescence in real proteins by performing hybrid quantum mechanics and molecular mechanics methods combined with a molecular dynamics method. For the first time, this study reported the origin and clear differences in the chemiluminescence, bioluminescence and fluorescence of aequorin, which is important for understanding the bioluminescence not only of jellyfish, but also of many other marine organisms (that have the same coelenterazine caved in different coelenterazine‐type luciferases).