Microscopic diffusion-reaction coupling in steady-state enzyme kinetics.
TL;DR: The theory of diffusion-controlled processes is applied to describe the steady state of a reversible enzymatic reaction with special emphasis on the effects of enzyme saturation to justify the simpler macroscopic coupling scheme.
About: This article is published in Biophysical Chemistry.The article was published on 1983-01-01. It has received 7 citations till now.
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218 citations
TL;DR: This paper enables a seamless and physically consistent transition from the microscopic to the macroscopic frameworks of reaction-diffusion kinetics, and exemplifies the use of the methods by showing that a phosphorylation-dephosphorylation motif is predicted to display fluctuations that depend on the geometry of the system.
Abstract: Quantitative analysis of biochemical networks often requires consideration of both spatial and stochastic aspects of chemical processes. Despite significant progress in the field, it is still computationally prohibitive to simulate systems involving many reactants or complex geometries using a microscopic framework that includes the finest length and time scales of diffusion-limited molecular interactions. For this reason, spatially or temporally discretized simulations schemes are commonly used when modeling intracellular reaction networks. The challenge in defining such coarse-grained models is to calculate the correct probabilities of reaction given the microscopic parameters and the uncertainty in the molecular positions introduced by the spatial or temporal discretization. In this paper we have solved this problem for the spatially discretized Reaction-Diffusion Master Equation; this enables a seamless and physically consistent transition from the microscopic to the macroscopic frameworks of reaction-diffusion kinetics. We exemplify the use of the methods by showing that a phosphorylation-dephosphorylation motif, commonly observed in eukaryotic signaling pathways, is predicted to display fluctuations that depend on the geometry of the system.
134 citations
TL;DR: The physical and biochemical mechanisms that may be relevant in the regulation of translation are explored and the initiation, or initial ribosome adsorption binding required for maximal throughput, can vary dramatically depending on certain values of the bulk ribosomes concentration and diffusion constant.
99 citations
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...[Berg & Ehrenberg 1983] Berg, O. G. and M. Ehrenberg....
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TL;DR: Steady-state kinetic studies of the bovine carbonic anhydrase B-catalyzed hydration of CO2, dehydration of HCO3-, and hydrolysis of p-nitrophenylacetate were made in glycerol/water solvents of increased viscosity in order to determine the effect of diffusion-control on the substrate association reactions.
17 citations
03 Oct 2019
TL;DR: In the presence of the plane, spheroids experience an additional anisotropic drag, and consequently, their mobilities depend on their positions and orientations, and anomalies in the short-time dynamics observed under confinement can be explained in terms of the so-called diffusing-diffusivity mechanism.
Abstract: We investigated diffusion of spheroidal molecules near a planar surface, accounting for spatially dependent translational and rotational mobilities of molecules resulting from their hydrodynamic interactions with the plane. Rigid-body Brownian dynamics simulations of prolate ellipsoids of revolution of an axial ratio in the range of 1.5 to 3.0, suspended in a viscous fluid, with a no-slip flat boundary confining the suspension were employed. Mobility tensor matrices of molecules were evaluated as functions of spheroids' distance and orientation with respect to the plane. Hydrodynamic interactions with the surface lead to substantial changes of spheroids' translational diffusion coefficients both in the direction perpendicular and parallel to the plane when compared with the values characterizing the bulk diffusion. Moreover, the short-time translational diffusion of molecules, measured in the laboratory frame, both in an unbounded fluid and under the confinement, is non-Gaussian, with much larger deviations from Gaussianity observed in the latter case. In an unbounded fluid, distributions of translational displacements of molecules deviate from those expected for a simple Brownian motion as a result of shape anisotropy. In the presence of the plane, spheroids experience an additional anisotropic drag, and consequently, their mobilities depend on their positions and orientations. Therefore, anomalies in the short-time dynamics observed under confinement can be explained in terms of the so-called diffusing-diffusivity mechanism. Our findings have implications for understanding of a wide range of biological and technological processes that involve diffusion of anisotropic molecules near surfaces of natural and model cell membranes, biosensors and nanosensors, and electrodes.
13 citations
References
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328 citations
TL;DR: The theory of diffusion-controlled association is used to determine the time development of the corresponding dissociation process as discussed by the authors, and the departure from a pure exponential decay will influence the entire time course, and not just the initial transient as in the case of an association process.
119 citations
TL;DR: The ultimate accuracy of error correcting selective pathways is set by the displacement from equilibrium of the nucleoside triphosphates, which could explain antinomies in the amino acylation reaction as well as in mRNA translation, where small structural differences lead to large differences in flow rates between right and wrong substrates.
111 citations
TL;DR: The reversible enzymatic fast reaction system with multi-substrate and multi-product has been discussed, and a general equation for calculating the degree of reaction flow derived as well is given.
47 citations
TL;DR: With these criteria it is possible to conclude that a number of enzymes will exhibit no appreciable dependence of over-all rate on the medium viscosity, quite irrespective of the as yet unmeasured rate constants for association and dissociation of enzyme and substrate.
43 citations