Mechanisms of Viscous Media Effects on Elementary Steps of Bacterial Bioluminescent Reaction

• Published in: International journal of molecular sciences Vol. 22; no. 16; p. 8827
• Main Authors: Lisitsa, Albert E., Sukovatyi, Lev A., Bartsev, Sergey I., Deeva, Anna A., Kratasyuk, Valentina A., Nemtseva, Elena V.
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 17.08.2021; MDPI
• Subjects: Aldehydes; bacterial luciferase; Binding; Bioluminescence; Biophysics; Catalysis; diffusion limitation; Diffusion rate; Efficiency; Enzyme kinetics; Experiments; Flavin; Gene expression; Glycerol; Light; Mathematical models; Microenvironments; Molecular dynamics; non-steady-state reaction kinetics; Ordinary differential equations; Reaction kinetics; Software; Sucrose; Viscosity; Russia
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms22168827

Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial bioluminescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. Moreover, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important αGlu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis.