Journal ArticleDOI
Propensity approach to nonequilibrium thermodynamics of a chemical reaction network: controlling single E-coli β-galactosidase enzyme catalysis through the elementary reaction steps.
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This work develops an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the elementary reaction propensities, and thoroughly analyzes the temporal as well as the steady state behavior of various thermodynamic quantities for each elementary reaction.Abstract:
In this work, we develop an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the elementary reaction propensities. The method is akin to the microscopic formulation of the dissipation function in terms of the Kullback-Leibler distance of phase space trajectories in Hamiltonian system. The formalism is applied to a single oligomeric enzyme kinetics at chemiostatic condition that leads the reaction system to a nonequilibrium steady state, characterized by a positive total entropy production rate. Analytical expressions are derived, relating the individual reaction contributions towards the total entropy production rate with experimentally measurable reaction velocity. Taking a real case of Escherichia coli β-galactosidase enzyme obeying Michaelis-Menten kinetics, we thoroughly analyze the temporal as well as the steady state behavior of various thermodynamic quantities for each elementary reaction. This gives a useful insight in the relative magnitudes of various energy terms and the dissipated heat to sustain a steady state of the reaction system operating far-from-equilibrium. It is also observed that, the reaction is entropy-driven at low substrate concentration and becomes energy-driven as the substrate concentration rises.read more
Citations
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Journal Article
Single Enzyme Pathways and Substrate Fluctuations
TL;DR: A simple theory is developed which predicts that certain classes of enzyme pathways can be distinguished by studying the turnover rate, V, as a function of substrate concentration, [S], and it is found to depend sensitively on the manner in which substrate molecules in the bath are replenished.
Journal ArticleDOI
The guiding role of dissipation in kinetic proofreading networks: Implications for protein synthesis
TL;DR: Dissipation plays a guiding role in the optimization of the catalytic rate in the tRNA selection network of protein synthesis, and the network tends to maximize both the EPR and catalytic rates, but not the accuracy.
Journal ArticleDOI
Large deviation theory for the kinetics and energetics of turnover of enzyme catalysis in a chemiostatic flow
Biswajit Das,Gautam Gangopadhyay +1 more
TL;DR: Using some special properties of the Legendre transformation, here, a relation between the fluctuations of fluxes and dissipation rates is provided, and among them, the fluctuation of the turnover rate is routinely estimated but the fluctuations in the dissipation rate is yet to be characterized for small systems.
Journal ArticleDOI
Nonequilibrium thermodynamics and a fluctuation theorem for individual reaction steps in a chemical reaction network
TL;DR: In this paper, an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the propensities of individual elementary reactions and corresponding reverse reactions is introduced.
Journal ArticleDOI
Entropy production for mechanically or chemically driven biomolecules
TL;DR: In this article, entropy change along a single stochastic trajectory of a biomolecule is discussed for two different sources of non-equilibrium entropy, and the total entropy change obeys an integral fluctuation theorem and a class of further exact relations.
References
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Journal ArticleDOI
Exact Stochastic Simulation of Coupled Chemical Reactions
TL;DR: In this article, a simulation algorithm for the stochastic formulation of chemical kinetics is proposed, which uses a rigorously derived Monte Carlo procedure to numerically simulate the time evolution of a given chemical system.
Journal ArticleDOI
A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions
TL;DR: In this paper, an exact method is presented for numerically calculating, within the framework of the stochastic formulation of chemical kinetics, the time evolution of any spatially homogeneous mixture of molecular species which interreact through a specified set of coupled chemical reaction channels.
Journal ArticleDOI
Regulation of noise in the expression of a single gene
TL;DR: The results provide the first direct experimental evidence of the biochemical origin of phenotypesic noise, demonstrating that the level of phenotypic variation in an isogenic population can be regulated by genetic parameters.
Journal ArticleDOI
Single-Molecule Enzymatic Dynamics
TL;DR: A molecular memory phenomenon, in which an enzymatic turnover was not independent of its previous turnovers because of a slow fluctuated of protein conformation, was evidenced by spontaneous spectral fluctuation of FAD.
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