Dynamics of the firefly luciferase–oxyluciferin complex in its electronic ground and excited states are studied using various theoretical approaches. By mimicking the physiological conditions with realistic models of the chromophore oxyluciferin, the enzyme luciferase, and solvating water molecules and by performing real time simulations with a molecular dynamics technique on the model surfaces, we reveal that the local chromophore-surrounding interaction patterns differ rather severely in the two states. Because of the presence of protein, the solvation dynamics of water around the chromophore is also peculiar and shows widely different time scales on the two terminal oxygen atoms. In addition, simulations of the emission with the quantum-mechanics/molecular-mechanics approach show a close relationship between the emission color variation and the environmental dynamics, mostly through electrostatic effects from the chromophore-surrounding interaction. We also discuss the importance of considering the tim...

Dynamics on the Electronically Excited State Surface of the Bioluminescent Firefly Luciferase–Oxyluciferin System

The paper investigates an application of luminescent bioassays to monitor the toxicity of organic halides. Effects of xanthene dyes (fluorescein, eosin Y, and erythrosin B), used as model compounds, on bioluminescent reactions of firefly Luciola mingrelica, marine bacteria Photobacterium leiognathi, and hydroid polyp Obelia longissima were studied. Dependence of bioluminescence quenching constants on the atomic weight of halogen substituents in dye molecules was demonstrated. Bacterial bioluminescence was shown to be most sensitive to heavy halogen atoms involved in molecular structure; hence, it is suitable for construction of sensors to monitor toxicity of halogenated compounds. Mechanisms of bioluminescence quenching—energy transfer processes, collisional interactions, and enzyme–dye binding—were considered. Changes of bioluminescence (BL) spectra in the presence of the dyes were analyzed. Interactions of the dyes with enzymes were studied using fluorescence characteristics of the dyes in steady-state and time-resolved experiments. The dependences of fluorescence anisotropy of enzyme-bound dyes, the average fluorescence lifetime, and the number of exponential components in fluorescence decay on the atomic weight of halogen substituents were demonstrated. The results are discussed in terms of “dark effect of heavy halogen atom” in the process of enzyme–dye binding; hydrophobic interactions were assumed to be responsible for the effect.

Effect of halogenated fluorescent compounds on bioluminescent reactions

The technique variously known as Electron Spin Resonance (ESR) or Electron Paramagnetic Resonance (EPR) continues to find important applications mainly in the Biomedical, Materials and Environmental Sciences. Among the advances which feature information gleaned through its agency, are studies of enzymes and membranes, conductive polymers and novel materials, fuel cells, antioxidants, environmental samples, catalysts and photocatalysts, spin-trapping agents, spin-probes and spin-labels. High-field methods are particularly useful in obtaining improved resolution of overlapping signals and the interpretation of many systems had benefited from the use of Density Functional Theory (DFT) calculations.

Electron spin resonance

The paper reports the experimental results of bioluminescence quenching in the coupled enzyme system NADH:FMN-oxidoreductase-luciferase in the presence of xanthene dyes (fluorescein, eosin Y, erythrosin B) featured by the rate constants of intersystem crossing. From the spectral data and with the help of kinetic model the rate constants of energy transfer from emitter to dye were determined (2.9 × 1012–6.5 × 1013 M−1 s−1) and the emitter lifetime was estimated (1.2–2.7 ns). The calculated rate constants of energy transfer in a series of xanthene molecules are higher than the diffusion-controlled constants. The rate constants of energy transfer correlate with the probability of intersystem crossing of a dye. The combined analysis of emitter fluorescence quenching and acceptor fluorescence enhancement indicates that the significant bioluminescence intensity decrease in the presence of xanthene dyes is determined by both the quenching processes via the energy transfer and the inhibition of bioluminescent reaction.

The role of energy transfer in bioluminescence quenching by xanthene dyes

Dark blue [CTC]2·(TCNE)·6THF and dark green [CTC]2·(TCNQ)·4THF are both exclusion complexes, with the cyanoalkene acceptor being sandwiched between the catechol rings of two cyclotricatechylene (CTC) host molecules. There is also extensive hydrogen bonding between the CTC and tetracyanoethene (TCNE) or tetracyanoquinodimethane (TCNQ) molecules, which is unusual for crystals containing these cyanoalkenes. Crystallographic, IR and UV–vis data show that these are typical donor–acceptor complexes, with strong charge–transfer interactions between the CTC and cyanoalkene acceptors. These are the first donor–acceptor complexes of a cyclotriveratrylene (CTV)-derived host, and the first crystallographically characterised adducts between TCNE or TCNQ and an organic cavitand. The solvate CTC·3.5THF·0.5H2O adopts a novel nanoporous crystal lattice, composed of undulating hydrogen-bonded sheets of CTC molecules. In contrast, the clathrates CTC·2EtOH, CTC·3DMA and CTC·5DMSO all adopt structures that are related to prev...

/pdf/six-new-crystalline-clathrates-of-cyclotricatechylene-ctc-4rxpo2kwhf.pdf

N.V. KrishnaMurthy

Papers

Molecular adducts between a few phenolic donors and π-acceptors in solid-state

Dye induced quenching of firefly luciferase-luciferin bioluminescence.