Effect of macromolecular crowding on the rate of diffusion-limited enzymatic reaction

Abstract

The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with increase in macromolecular crowding. Moreover, many cellular processes are dependent on molecular diffusion in the cell cytosol. The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some of the experimental observations.

New insights into diffusion in 3D crowded media by Monte Carlo simulations: effect of size, mobility and spatial distribution of obstacles

“…The high concentration of macromolecules in intracellular environments results into non-specific interactions (macromolecular crowding), which have a great influence on the kinetics and thermodynamics of possible reactions that occur in these systems, e.g. diffusion processes and reaction kinetics [3][4][5][6][7][8][9][10][11][12][13][14][15] .…”

Diffusion in macromolecular crowded media: Monte Carlo simulation of obstructed diffusion vs. FRAP experiments

“…However, the high concentration of macromolecules in intracellular environments (in vivo) results in non-specific interactions (macromolecular crowding), which have a great influence on the kinetics and thermodynamics of possible reactions that occur in these systems [1][2][3][4][5][6][7][8]. In fact, macromolecular crowding has been shown to alter molecular diffusion both quantitatively and qualitatively [1,5,7,[9][10].…”

Macroscopic Transport Equations in Many-Body Systems from Microscopic Exclusion Processes in Disordered Media: A Review

“…Another related issue is that of diffusion-limited reactions [35], which are ubiquitous in many domains in biology and chemistry, touching upon problems such as association, folding and stability of proteins [13,36] and bimolecular reactions in solution [37][38][39][40][41], including enzyme kinetics [42], but also the dynamics of active agents [43,44]. Many theoretical studies have tackled these and related problems under different angles [13,39,42,[44][45][46][47].…”

“…Many theoretical studies have tackled these and related problems under different angles [13,39,42,[44][45][46][47]. Nevertheless, a full theoretical comprehension of transport in non-ideal media remains an elusive task, Fick's law itself and the very notion of effective diffusion coefficient being questionable in a disordered medium [31].…”