Mechanistic Insights into the Bacterial Luciferase-based Bioluminescence Resonance Energy Transfer Luminescence: The Role of Protein Complex Dimer.

Bacterial bioluminescence holds significant potential in the realm of optical imaging due to the inherent advantages of bioluminescence and ease of operation. However, its practical utility is hindered by its low light intensity. The fusion of bacterial luciferase with a highly fluorescent protein has been demonstrated to significantly enhance autonomous luminescence. Nevertheless, the underlying mechanism behind this enhancement remains unclear, and there is a dearth of research investigating the mechanistic aspects of bioluminescence resonance energy transfer (BRET) luminescence, whether it occurs naturally or can be achieved through experimental means. In this study, we investigated the phenomenon of bacterial luciferase-based BRET luminescence employing a range of computational techniques, including structural modeling, molecular docking, molecular dynamics simulations, as well as combined quantum mechanics and molecular mechanics calculations. The theoretical findings suggest that the BRET luminescence occurs through resonance energy transfer between the excited bioluminophore and the ground chromophore within the protein complex dimer. The proposed mechanism of the protein complex dimer offers a microscopic understanding of the intriguing BRET phenomenon and has the potential to inspire further practical applications in the field of optical imaging.

Thorough Understanding of Bioluminophore Production in Bacterial Bioluminescence.

Bioluminophore of bioluminescence (BL) comes from the decomposition of peroxide, which is an intermediate produced in the complicated chemical reactions of BL. The peroxide is a dioxetanone in most BL cases and an endoperoxide in fungal BL. The decomposition mechanisms of these two types of peroxides have been exclusively studied. However, the peroxide is a linear organic peroxide in bacterial BL, whose decomposition explanations are quite controversial, and seven mechanisms have been proposed. To thoroughly understand the mechanism of bioluminophore production in bacterial BL, this paper systematically discusses the seven proposed mechanisms via the present computational results and previous experimental and theoretical results. Our research results indicate that the bioluminophore in bacterial BL is produced through the charge-transfer initiated luminescence (CTIL) mechanism. The decomposition mechanism of linear organic peroxide was compared with the decomposition mechanisms of the other two types of peroxides, dioxetanone and endoperoxide. This study is also helpful in understanding the bioluminophore production in other BLs via the decomposition of an organic peroxide, such as dinoflagellate BL.

Mechanistic Investigation on Chemiluminescent Formaldehyde Probes.

A first-generation pair of chemiluminescent formaldehyde (FA) probes (CFAP540 and CFAP700) was reported recently. CFAP540 and CFAP700, with high selectivity and sensitivity to FA, are, respectively, suitable in cell and in vivo. Experimentalists have confirmed that both probes utilize a general 2-aza-Cope FA-reactive trigger and a chemiluminogenic phenoxydioxetane scaffold. The mechanism and detailed process of CFAP chemiluminescence (CL) remain largely unknown. In the present paper, (time-dependent) density functional theory calculations are performed on the entire reaction process of CFAP540 with FA to produce CL. The calculations elucidated the CL-producing process: FA initiates the decomposition of CFAP540 by dehydration condensation, and a phenoxy 1,2-dioxetane is formed through a series of reactions of aza-Cope rearrangement, hydrolysis of imine, and ß-elimination of alkoxyl group. Afterwards, the produced phenoxy 1,2-dioxetane decomposes to produce the m-oxybenzoate derivative in the first singlet state (S1 ) via two crossings between potential energy surfaces of the ground state (S0 ) and S1 state. This m-oxybenzoate derivative was assigned as the light emitter of the CFAP540 CL. The CL-producing process and assignment of the light emitter of CFAP700 CL are similar with the corresponding ones of CFAP540. By analyzing the D-π-A architecture of the light emitters of CFAP540 and CFAP700, a series of CFAPs is theoretically designed and a scheme to modulate their CL from visible to near-infrared region is proposed by adjusting the length and structure of the π-bridge.

Gas phase transformation from organic acid to organic sulfuric anhydride: Possibility and atmospheric fate in the initial new particle formation.

New particle formation (NPF) process has been observed frequently in various environments and produces a large fraction of atmospheric aerosols. However, the chemical species participating in the nucleation as well as the corresponding nucleation mechanism in the atmosphere still remain ambiguous. Recent research by Leopold et al. shows that cycloaddition reaction of SO3 to carboxylic acids could contribute to the formation of organic sulfuric anhydride which would have lower vapor pressure compared with the corresponding carboxylic acid and hence kick-start new particle formation in the gas phase. In the present study, energy profile for the formation of 3-methyl-1,2,3-butanetricarboxylic sulfuric anhydride (MBTCSA) through the cycloaddition of SO3 to 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA) has been investigated using computational methods. As a result, such a process would be effectively barrierless for one of the terminal carboxy group and has very low energy barriers for the other two carboxy groups (0.6 and 2.8 kcal/mol, respectively), indicating the whole process is a plausible gas phase pathway to MBTCSA formation. Furthermore, by evaluating the stability of the generated atmospheric clusters through topological and kinetic analysis, interaction between atmospheric nucleation precursor with MBTCSA is found to be more thermodynamically favourable and stronger than those with sulfuric acid and MBTCA which is identified from further-generation oxidation of a-pinene. Hence MBTCSA is speculated to be a potential participator in the initial new particle formation and the further particles growth.