Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: An index of cooperativity

Abstract

Here we have systematically studied the cooperative binding of substrate molecules on the active sites of a single oligomeric enzyme in a chemiostatic condition. The average number of bound substrate and the net velocity of the enzyme catalyzed reaction are studied by the formulation of stochastic master equation for the cooperative binding classified here as spatial and temporal. We have estimated the entropy production for the cooperative binding schemes based on single trajectory analysis using a kinetic Monte Carlo technique. It is found that the total as well as the medium entropy production show the same generic diagnostic signature for detecting the cooperativity, usually characterized in terms of the net velocity of the reaction. This feature is also found to be valid for the total entropy production rate at the nonequilibrium steady state. We have introduced an index of cooperativity, C, defined in terms of the ratio of the surprisals or equivalently, the stochastic system entropy associated with the fully bound state of the cooperative and non-cooperative cases. The criteria of cooperativity in terms of C is compared with that of the Hill coefficient and gives a microscopic insight on the cooperative binding of substrate on a single oligomeric enzyme which is usually characterized by macroscopic reaction rate.

References in corpus (19)

• A nonequilibrium equality for free energy differences
• The Entropy Production Fluctuation Theorem and the Nonequilibrium Work Relation for Free Energy Differences
• Dynamical Ensembles in Nonequilibrium Statistical Mechanics
• Entropy production along a stochastic trajectory and an integral fluctuation theorem
• A Gallavotti-Cohen Type Symmetry in the Large Deviation Functional for Stochastic Dynamics
• Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
• Steady State Thermodynamics of Langevin Systems
• The Nonequilibrium Thermodynamics of Small Systems
• Diamondoid Molecules
• The Three Faces of the Second Law: I. Master Equation Formulation
• Thermodynamics of a Colloidal Particle in a Time-Dependent Non-Harmonic Potential
• Fluctuation Theorems
• Chaotic hypothesis: Extension of Onsager reciprocity to large fields and the chaotic hypothesis
• Stochastic thermodynamics of chemical reaction networks
• Measurement of Stochastic Entropy Production
• A two-state kinetic model for the unfolding of single molecules by mechanical force
• Entropy production for mechanically or chemically driven biomolecules
• Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation
• Measurement of work in single-molecule experiments