Related papers: Dynamic control of catalysis within biological cel…
The celebrated Michaelis-Menten (MM) expression provides a fundamental relation between the rate of enzyme catalysis and substrate concentration. The validity of this classical expression is, however, restricted to macroscopic amounts of…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
The classic Michaelis-Menten equation describes the catalytic activities for ensembles of enzyme molecules very well. But recent single-molecule experiment showed that the waiting time distribution and other properties of single enzyme…
We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
It is well known in enzyme kinetics that the Michaelis-Menten (MM) equation is applicable only to enzymes in the steady state. We show that the result obtained in the previous work [Phys. Rev. Lett. 107, 218301 (2011)] is inconsistent with…
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…
All biological processes are controlled by complex systems of enzymatic chemical reactions. Although the majority of enzymatic networks have very elaborate structures, there are many experimental observations indicating that some turnover…
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…
Recent fluorescence spectroscopy measurements of single-enzyme kinetics have shown that enzymatic turnovers form a renewal stochastic process in which the inverse of the mean waiting time between turnovers follows the Michaelis-Menten…
Catalysis lies at the heart of chemical reactivity, yet its foundational principles remain fragmented across the distinct domains of homogeneous, heterogeneous, and enzymatic systems Here, we propose a unifying theoretical model that…
The progress of the successive rounds of catalytic conversion of substrates into product(s) by a single enzyme is characterized by the distribution of turnover times. Establishing the most general form of dependence of this distribution on…
Enzyme catalysis in reactors for industrial applications usually require an external intervention of the species involved in the chemical reactions. We analyze the most elementary open enzyme catalysis with competitive inhibition where a…
We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies…
Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions,…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
Conformational changes are observed in many enzymes, but their role in catalysis is highly controversial. Here we present a theoretical model that illustrates how rigid catalysts can be fundamentally limited and how a conformational change…
In the paper the kinetic model of the biochemical process of cellulose hydrolysis with cell application is presented. The model includes enzyme biosynthesis control and is open conditions it represents the dynamical system in the…
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…