QM/MM Investigations on the Bioluminescent Decomposition of Coelenterazine Dioxetanone in Obelin

Mechanistic Investigation of Green Fluorescent Protein Acquiring Energy for Emitting Light: A Theoretical Study

Green fluorescent protein (GFP) is famous for noninvasively observing the internal biological processes of cells and organisms, revolutionizing the field of cell biology. GFP was first discovered in jellyfish Aequorea victoria (AV). The GFP bioluminescence (BL) in AV can be divided into three stages: the first singlet excited state coelenteramide (S1-CTD) is formed in aequorin; GFP acquires energy from S1-CTD via an energy transfer (ET) process; and GFP emits green light. The first and final stages have been well studied, whereas the detailed mechanism of the second stage remains unclear, with only sporadic experimental evidence. The purpose of this study is to clarify how GFP acquires energy before emitting green light in AV. Through protein-protein docking, molecular dynamics simulations, and combined quantum mechanics and molecular mechanics calculations, we demonstrate that the ET process occurs via the Förster resonance energy transfer (FRET) mechanism. The calculated FRET rate is faster than the radiative and nonradiative decay ones of S1-CTD, which means the ET process can occur efficiently. Additionally, the calculated fluorescence quantum yield explains the experimentally observed BL enhancement after the ET. This is the first theoretical report on the ET mechanism in BL. This study not only clearly interprets how GFP acquires energy for emitting light but also helps to understand the ET mechanism in other bioluminescent systems and sheds new light on bioluminescence resonance energy transfer.

A Structural Model of Truncated Gaussia princeps Luciferase Elucidating the Crucial Catalytic Function of No.76 Arginine towards Coelenterazine Oxidation

Gaussia Luciferase (GLuc) is a renowned reporter protein that can catalyze the oxidation of coelenterazine (CTZ) and emit a bright light signal. GLuc comprises two consecutive repeats that form the enzyme body and a central putative catalytic cavity. However, deleting the C-terminal repeat only limited reduces the activity (over 30% residual luminescence intensity detectable), despite being a key part of the cavity. How does the remaining GLuc (tGLuc) catalyze CTZ? To address this question, we built a structural model of tGLuc by removing the C-terminal repeat from the resolved structure of intact GLuc, and verified that the cavity-forming component in GLuc remains stable and provides an open-mouth cavity in tGLuc during 500 ns MD simulations in water. Docking simulation and a followed umbrella sampling analysis further revealed that the cavity on tGLuc has a high affinity for CTZ, with a binding energy of up to -114 kJ/mol. Moreover, R76, a validated activity-critical amino acid residue, resides in the cavity and forms a stable hydrogen bond with CTZ. Then, we constructed a cluster model to examine the CTZ oxidation pathway in the cavity using Density Functional Theory (DFT) calculations. The result showed that the pathway consists of four elementary reactions, with the highest Gibbs energy barrier being 65.4 kJ/mol. Both intramolecular electron transfer and the convergence of S1/S0 potential energy surfaces occurred in the last elementary reaction, which was regarded as the reported Chemically-Initiated-Electron-Exchange-Luminescence (CIEEL) reaction. Geometry and wavefunction analysis on the pathway indicated that R76 plays a vital role in CTZ oxidation, which first anchors the environmental oxygen molecule and induces it to form a singlet biradical state, facilitating its attack on CTZ. Subsequently, R76 and the adjacent Q88, positioned near R76 through the tGLuc refolding process, stabilize the transition states and facilitate the emergence of radical electrons on CTZ at the onset of the CIEEL reaction, which contributes to the subsequent intramolecular electron transfer and the production of excited amide product. This study provides a comprehensive explanation of tGLuc's catalytic mechanism. However, it is important to note that these findings are specific to tGLuc and may not extend to other CTZ-based luciferases, particularly those lacking arginine in their catalytic cavities, which likely operate via distinct mechanisms.

The crucial role of Y109 and R162 as catalytic residues of nanoKAZ: insights from molecular docking, molecular dynamics simulation, and quantum chemical investigations

CONTEXT

nanoKAZ is a compact luciferase that exhibits intense blue light emission when it catalyzes the substrate Furimazine (FMZ) as a luciferin, making it an excellent candidate as a reporter protein. However, the specific catalytic residues and mechanism of nanoKAZ have not been revealed. Recently, the structure of nanoKAZ was determined, and it was observed that the luminescent properties changed when FMZ analogs with naphthalene replacing benzene were used. It is speculated that the substituted naphthalene may influence the interaction between the catalytic residues and luciferins, thereby affecting the energy of the emitted light signal.

METHOD

Therefore, the primary objective of this study is to analyze and compare the molecular recognition between nanoKAZ and FMZ along with its four activity-altered naphthalene analogs, with aiming to identify the catalytic residues. Molecular docking was employed to construct all nanoKAZ-luciferin models, followed by a 500 ns molecular dynamics simulation. The simulation trajectory was subjected to MM/PBSA analysis to identify crucial residues that contribute significantly to luciferin binding. In the result, two polar residues Y109, and R162 were identified as active residues as their notable contributions to the binding energy. Subsequently, an oxygen molecule was introduced into the local region of the nanoKAZ-FMZ complex and followed with quantum chemical calculations (semiempirical and DFT methods were used) to investigate the catalysis details. The results illustrated the involvement of Y109 and R162 in the oxygenation of FMZ, leading to the formation of dioxetanone, which has been suggested as an important intermediate in the oxidation process among various luciferins sharing the same functional group as FMZ.

Theoretical Study on the Formation and Decomposition Mechanisms of Coelenterazine Dioxetanone

Bioluminescence has been drawing broad attention due to its high signal-to-noise ratio and high bioluminescence quantum yields, which has been widely applied in the fields of biomedicine, bioanalysis, and so on. Among numerous bioluminescent substrates, coelenterazine is famous for its wide distribution. However, the oxygenation reaction mechanism of coelenterazine is far from being completely understood. In this paper, the formation and decomposition mechanisms of coelenterazine dioxetanone were investigated via density functional theory (DFT) and time-dependent (TD) DFT approaches. The results showed that the oxygenation reaction first occurred along the triplet-state potential energy surface (PES), after the intersystem crossing (ISC), second jumped to the diradical-state PES, and ultimately formed coelenterazine dioxetanone. For the decomposition mechanism of dioxetanone, the computational results showed that the chemiexcitation of neutral dioxetanone was more efficient than that of other dioxetanone species. Moreover, the diradical properties and the degree of ionic character are modified by the counter ions.

The Role of Tyr-His-Trp Triad and Water Molecule Near the N1-Atom of 2-Hydroperoxycoelenterazine in Bioluminescence of Hydromedusan Photoproteins: Structural and Mutagenesis Study

Hydromedusan photoproteins responsible for the bioluminescence of a variety of marine jellyfish and hydroids are a unique biochemical system recognized as a stable enzyme-substrate complex consisting of apoprotein and preoxygenated coelenterazine, which is tightly bound in the protein inner cavity. The binding of calcium ions to the photoprotein molecule is only required to initiate the light emission reaction. Although numerous experimental and theoretical studies on the bioluminescence of these photoproteins were performed, many features of their functioning are yet unclear. In particular, which ionic state of dioxetanone intermediate decomposes to yield a coelenteramide in an excited state and the role of the water molecule residing in a proximity to the N1 atom of 2-hydroperoxycoelenterazine in the bioluminescence reaction are still under discussion. With the aim to elucidate the function of this water molecule as well as to pinpoint the amino acid residues presumably involved in the protonation of the primarily formed dioxetanone anion, we constructed a set of single and double obelin and aequorin mutants with substitutions of His, Trp, Tyr, and Ser to residues with different properties of side chains and investigated their bioluminescence properties (specific activity, bioluminescence spectra, stopped-flow kinetics, and fluorescence spectra of Ca²⁺-discharged photoproteins). Moreover, we determined the spatial structure of the obelin mutant with a substitution of His64, the key residue of the presumable proton transfer, to Phe. On the ground of the bioluminescence properties of the obelin and aequorin mutants as well as the spatial structures of the obelin mutants with the replacements of His64 and Tyr138, the conclusion was made that, in fact, His residue of the Tyr-His-Trp triad and the water molecule perform the "catalytic function" by transferring the proton from solvent to the dioxetanone anion to generate its neutral ionic state in complex with water, as only the decomposition of this form of dioxetanone can provide the highest light output in the light-emitting reaction of the hydromedusan photoproteins.

Conical Intersection in Chemiluminescence of Cyclic Peroxides

Chemiluminescence (CL) utilizing chemiexcitation for energy transformation is one of the most highly sensitive and useful analytical techniques. The chemiexcitation is a chemical process of a ground-state reactant producing an excited-state product, in which a nonadiabatic event is facilitated by conical intersections (CIs), the specific molecular geometries where electronic states are degenerated. Cyclic peroxides, especially 1,2-dioxetane/dioxetanone derivatives, are the iconic chemiluminescent substances. In this Perspective, we concentrated on the CIs in the CL of cyclic peroxides. We first present a computational overview on the role of CIs between the ground (S₀) state and the lowest singlet excited (S₁) state in the thermolysis of cyclic peroxides. Subsequently, we discuss the role of the S₀/S₁ CI in the CL efficiency and point out misunderstandings in some theoretical studies on the singlet chemiexcitations of cyclic peroxides. Finally, we address the challenges and future prospects in theoretically calculating S₀/S₁ CIs and simulating the dynamics and chemiexcitation efficiency in the CL of cyclic peroxides.

H2O-Bridged Proton-Transfer Channel in Emitter Species Formation in Obelin Bioluminescence

Bioluminescence of a number of marine organisms is conditioned by Ca²⁺-regulated photoprotein (CaRP) with coelenterazine as the reaction substrate. The reaction product, coelenteramide, at the first singlet excited state (S₁) is the emitter of CaRP. The S₁-state coelenteramide is produced via the decomposition of coelenterazine dioxetanone. Experiments suggested that the neutral S₁-coelenteramide is the primary emitter species. This supposition contradicts with theoretical calculations showing that the anionic S₁-coelenteramide is a primary product of the decomposition of coelenterazine dioxetanone. In this study, applying molecular dynamic (MD) simulations and the hybrid quantum mechanics/molecular mechanics (QM/MM) method, we investigated a proton-transfer (PT) process taking place in CaRP obelin from Obelia longissima for emitter formation. Our calculations demonstrate a concerted PT process with a water molecule as a bridge between anionic S₁-coelenteramide and the nearest histidine residue. The low activation barrier as well as the strong hydrogen-bond network between the proton donor and the proton acceptor suggests a fast PT process comparable with that of the lifetime of excited anionic S₁-coelenteramide. The existence of the PT process eliminates the discrepancy between experimental and theoretical studies. The fast PT process at emitter formation can also take place in other CaRPs.

Three S0/S1 Conical Intersections Control Electron-Transfer-Catalyzed Chemiluminescence of 1,2-Dioxetanedione

Chemiluminescence (CL) utilizing four-membered cyclic peroxides is one of the most useful analytical techniques. Up to now, the CL mechanisms for nonketone (1,2-dioxetanes) and monoketone (1,2-dioxetanones) derivatives of four-membered cyclic peroxides have been intensively studied experimentally and theoretically in the past several decades, but no general mechanism has been concluded to rationalize the origin of high-efficiency singlet chemiexcitation. In contrast, as the only diketone derivative of four-membered cyclic peroxide, the electron-transfer (ET)-catalyzed CL of 1,2-dioxetanedione (DDO), which is most suggested as a critical step in the well-known peroxyoxalate CL (POCL), has never been theoretically investigated and uncovered yet. In this work, we theoretically investigated the rubrene-catalyzed decomposition of DDO for the first time, with a hybrid quantum mechanical/molecular mechanical model and nonadiabatic molecular dynamics simulation. The computation shows a stepwise ET-catalyzed decomposition and three S₀/S₁ conical intersection (CI)-controlled singlet chemiexcitation. The three universal S₀/S₁ CIs play different roles in the high-efficiency singlet chemiexcitation in ET-catalyzed CL of DDO and should be the true origin of the high-efficiency singlet CL. We believe that the current work could not only provide a further understanding for high-efficiency singlet CL but also provide some general clues to designed new high-efficient CL systems.

Luminescence Activity Decreases When v-coelenterazine Replaces Coelenterazine in Calcium-Regulated Photoprotein-A Theoretical and Experimental Study

Calcium-regulated photoproteins are found in at least five phyla of organisms. The light emitted by those photoproteins can be tuned by mutating the photoprotein and/or by modifying the substrate coelenterazine (CTZ). Thirty years ago, Shimomura observed that the luminescence activity of aequorin was dramatically reduced when the substrate CTZ was replaced by its analog v-CTZ. The latter is formed by adding a phenyl ring to the π-conjugated moiety of CTZ. The decrease in luminescence activity has not been understood until now. In this paper, through combined quantum mechanics and molecular mechanics calculations as well as molecular dynamics simulations, we discovered the reason for this observation. Modification of the substrate changes the conformation of nearby aromatic residues and enhances the π-π stacking interactions between the conjugated moiety of v-CTZ and the residues, which weakens the charge transfer to form light emitter and leads to a lower luminescence activity. The microenvironments of CTZ in obelin and in aequorin are very similar, so we predicted that the luminescence activity of obelin will also dramatically decrease when CTZ is replaced by v-CTZ. This prediction has received strong evidence from currently theoretical calculations and has been verified by experiments.

Tuning the fluorescence of calcium-discharged photoprotein obelin via mutating at the His22-Phe88-Trp92 triad - a QM/MM study

The fluorescence (FL) of calcium-discharged photoprotein (CaDP) can be altered by easily mutating CaDP without modifying coelenteramide (CLM), which is the decarboxylation product of coelenterazine in calcium-regulated photoprotein. The His22-Phe88-Trp92 triad (the ordering numbers of three amino acids are sorted by a crystal structure (PDB: 2F8P) of calcium-discharged obelin, i.e., CaDP-obelin) is closely related to CaDP-obelin FL, since it exists in close proximity to the 5-p-hydroxyphenyl of CLM. Therefore, it is important to thoroughly investigate how the mutations of this triad affect the emission color of CaDP-obelin FL. In this study, by mutating wild-type CaDP-obelin (WT) at the His22-Phe88-Trp92 triad, we theoretically constructed its nine mutants of separable FL colors. Through combined quantum mechanics and molecular mechanics (QM/MM) calculations and molecular dynamics (MD) simulations, the influence of the mutations of this triad on the CaDP-obelin FL was analyzed considering the H-bond effect and the charge effect. This study demonstrated that the mutations at the His22-Phe88-Trp92 triad redistribute the charges on the D-π-A molecule, CLM, change the charge transfer from the D to the (π + A) moiety, and thereby alter the FL emission. Appending more negative charges on the phenolate moiety of CLM benefits the FL redshift.