Connecting the dots: the effects of macromolecular crowding on cell physiology

Abstract

The physicochemical properties of cellular environments with a high macromolecular content have been systematically characterized to explain differences observed in the diffusion coefficients, kinetics parameters, and thermodynamic properties of proteins inside and outside of cells. However, much less attention has been given to the effects of macromolecular crowding on cell physiology. Here, we review recent findings that shed some light on the role of crowding in various cellular processes, such as reduction of biochemical activities, structural reorganization of the cytoplasm, cytoplasm fluidity, and cellular dormancy. We conclude by presenting some unresolved problems that require the attention of biophysicists, biochemists, and cell physiologists. Although it is still underappreciated, macromolecular crowding plays a critical role in life as we know it.

Figure 1

Macromolecular crowding affects diffusion and the rates of enzyme-catalyzed reactions. In low macromolecular crowding conditions (top), diffusion is classical and differs from the anomalous diffusion observed in more crowded environments (bottom). Under high crowding and diffusion-limited conditions, the forward rate k₁ is believed to follow fractal-like kinetics. Association rate coefficients, such as k₁, decrease with increasing levels of crowding, but are also observed to increase under certain conditions. The formation of complexes is usually favored by high crowding. In the figure, S, E, C, and P represent the substrate, enzyme, enzyme-substrate complex, and product, respectively. The black squares represent the macromolecular crowding agents.

Figure 2

Modulation of cellular volume to control physiological processes via macromolecular crowding. The active cell and the dormant cell interchange states by undergoing RVD or RVI, respectively. In the dormant cells, the higher concentration of crowding agents (black dots in cytoplasm) leads to the formation of protein complexes. Proteins are indicated by light blue dots, and complexes represent filaments and clusters of proteins. In addition, the chromatin is compressed by higher crowding. Note that the quantity of crowding agents does not necessarily change, but a reduction of volume leads to a higher overall concentration of crowding agents. Upon formation of protein filaments and clusters in response to volume contraction, metabolic activity is slowed, which may correspond to a depletion of nutrients stopping active transport and inhibiting RVI, thus making the cell dormant.