Simple SummaryTraditionally, enzymes have been studied in standardized buffers, but in real life, inside cells, they have to function under conditions far from “ideal”. The intracellular milieu is crowded by numerous molecules with various physical and chemical properties. What consequences does it have for enzymatic reactions? How do enzymes deal with disturbing neighbors? To examine this issue, we studied the mechanisms of influence of seven model substances with different molecular sizes on the reaction catalyzed by bacterial luciferase. This reaction passes through several stages and ends with light emission. We analyzed the responses rate in different stages to the addition of alcohols, saccharides, and biopolymers and found the counteraction of two effects. On the one hand, increased viscosity slows down many of the stages, both associative and dissociative. On the other hand, it is accompanied by an increase in the catalytic constant of luciferase, which compensates for kinetic disadvantages. We assumed that both effects could be caused by the same property of the added substances—their ability to interact with water. Our findings serve not only to shed light on the organization of the cellular metabolism, but also to improve enzyme-based biotechnologies using the recipes of nature.AbstractA complex heterogeneous intracellular environment seems to affect enzymatic catalysis by changing the mobility of biomolecules, their stability, and their conformational states, as well as by facilitating or hindering continuously occurring interactions. The evaluation and description of the influence of the cytoplasmic matrix components on enzymatic activity are problems that remain unsolved. In this work, we aimed to determine the mechanisms of action of two-component media with cosolvents of various molecular sizes on the complex multi-stage bioluminescent reaction catalyzed by bacterial luciferase. Kinetic and structural effects of ethylene glycol, glycerol, sorbitol, glucose, sucrose, dextran, and polyethylene glycol on bacterial luciferase were studied using stopped-flow and fluorescence spectroscopy techniques and molecular dynamics simulations. We have found that diffusion limitations in the presence of cosolvents promote the stabilization of flavin substrate and peroxyflavin intermediate of the reaction, but do not provide any advantages in bioluminescence quantum yield, because substrate binding is slowed down as well. The catalytic constant of bacterial luciferase has been found to be viscosity-independent and correlated with parameters of water–cosolvent interactions (Norrish constant, van der Waals interaction energies). Crowding agents, in contrast to low-molecular-weight cosolvents, had little effect on peroxyflavin intermediate decay and enzyme catalytic constant. We attributed specific kinetic effects to the preferential interaction of the cosolvents with enzyme surface and their penetration into the active site.