Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size

Abstract

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Reaction-diffusion kinetics on lattice at the microscopic scale

“…Apart from the RDME lattice models, there is another class of schemes, which we refer as microscopic lattice method (MLM) that represents molecules at single particle resolution [39][40][41][42][43][44][45][46][47][48][49][50]. In most of these schemes [39, 41-45, 47, 50], the size of the voxel follows the molecule size, whereas in the small-voxel tracking algorithm (SVTA) [48], a particle can occupy multiple voxels, providing greater spatial resolution at the cost of higher computational complexity.…”

Effects of Macromolecular Crowding on Alcohol Dehydrogenase Activity Are Substrate-Dependent

“…At first glance, our observation that the effect of dextran on YADH kinetics is independent of polymer size contradicts previous trends with enzymes of similar dimensions. 15,24,31 An extensive study by the Mas group reported larger decreases in both V max and K m values with larger dextran polymers, revealing that obstacle size plays a major role in the magnitude of crowding effects for >100 kDa enzymes. 32 The authors explain that large crowders reduce the frequency of enzyme−substrate encounters, but this decrease is partially counterbalanced by caging effects with smaller crowders.…”

Macromolecular Crowding Effect upon in Vitro Enzyme Kinetics: Mixed Activation–Diffusion Control of the Oxidation of NADH by Pyruvate Catalyzed by Lactate Dehydrogenase

“…This behavior suggests that the possible substrate inhibition reported in the earlier literature does not explain the obtained values. Recent simulation and experimental studies reported on diffusion processes of enzymes in crowded media 47,[52][53][54][55] show that the effective diffusion coefficient is higher in dilute samples than in crowding situations. A decrease in the diffusion coefficient may imply a decrease in the bimolecular constant (݇ ଵ ) with crowding [45][46] .…”

“…In a situation of diffusion control, an increase in ‫ܭ‬ ୫ value can be expected since the bimolecular constant (݇ ଵ ) will decrease with the crowding [45][46][47] . In the literature, there are few works that report this situation 21,37,[45][46][47] . In these reported cases, a high diffusion resistance in the sample is responsible of a ‫ܭ‬ ୫ increase with Dextran concentration.…”