Related papers: Enzyme kinetics at the molecular level
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
The equilibration of enzyme and complex concentrations in deterministic Michaelis-Menten reaction networks underlies the hyperbolic dependence between the input (substrates) and output (products). This relationship was first obtained by…
We develop an general formalism of single enzyme kinetics in two dimension where substrates diffuse stochastically on a square lattice in presence of disorder. The dynamics of the model could be decoupled effectively to two stochastic…
Michaelis-Menten equation is a basic equation of enzyme kinetics and gives an acceptable approximation of real chemical reaction processes. Analyzing the derivation of this equation yields the fact that its good performance of approximating…
The driving force for active physical and biological systems is determined by both the underlying landscape and the non-equilibrium curl flux. While landscape can be quantified in the experiments by the histograms of the collecting…
We consider a stochastic model of the Michaelis-Menten (MM) enzyme kinetic reactions in terms of Stochastic Differential Equations (SDEs) driven by Poisson Random Measures (PRMs). It has been argued that among various Quasi-Steady State…
A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon,…
Despite linear regression being the most popular statistical modelling technique, in real-life we often need to deal with situations where the true relationship between the response and the covariates is nonlinear in parameters. In such…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
Genetically identical cells under the same environmental conditions can show strong variations in protein copy numbers due to inherently stochastic events in individual cells. We here develop a theoretical framework to address how…
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis-Menten mechanism, which exemplifies an…
In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years,…
We analyze the standard model of enzyme-catalyzed reactions at various substrate-enzyme ratios to identify the regions of validity of the quasi-steady-state approximation. Certain prevalent conditions are checked and compared against the…
There is a vast amount of literature concerning the appropriateness of various perturbation parameters for the standard quasi-steady state approximation in the Michaelis-Menten reaction mechanism, and also concerning the relevance of these…
The Michaelis-Menten equation has played a central role in our understanding of biochemical processes. It has long been understood how this equation approximates the dynamics of irreversible enzymatic reactions. However, a similar…
Quasi-steady state reductions for the irreversible Michaelis--Menten reaction mechanism are of interest both from a theoretical and an experimental design perspective. A number of publications have been devoted to extending the parameter…
To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves…
The century-long Michaelis-Menten rate law and its modifications in the modeling of biochemical rate processes stand on the assumption that the concentration of the complex of interacting molecules, at each moment, rapidly approaches an…
We demonstrate that the Michaelis-Menten reaction mechanism can be accurately approximated by a linear system when the initial substrate concentration is low. This leads to pseudo-first-order kinetics, simplifying mathematical calculations…
The Michaelis-Menten enzymatic reaction is sufficient to perceive many subtleties of network modeling, including the concentration and time scales separations, the formal equivalence between bulk phase and single-molecule approaches, or the…