Related papers: Enzyme kinetics at the molecular level
We present a new kinetic equation for cell migration driven by mechanical interactions with the substrate, an effect not previously captured in kinetic models, and essential for explaining observed collective behaviors such as those in…
We investigate theoretically the violations of Einstein and Onsager relations, and the efficiency for a single processive motor operating far from equilibrium using an extension of the two-state model introduced by Kafri {\em et al.}…
The cellular milieu is teeming with biochemical nano-machines whose activity is a strong source of correlated non-thermal fluctuations termed active noise. Essential elements of this circuitry are enzymes, catalysts that speed up the rate…
We demonstrate asymmetric enzyme kinetics of a biomolecular motor F1-ATPase between synthesis and hydrolysis of adenosine triphosphate (ATP). Our experiments show that ATP hydrolysis follows Michaelis-Menten kinetics, but ATP synthesis,…
We present a quantitative analysis of recent data on the kinetics of ATP hydrolysis, which has presented a puzzle regarding the load dependence of the Michaelis constant. Within the framework of coarse grained two-state ratchet models, our…
The conditions for the validity of the standard quasi-steady-state approximation in the Michaelis--Menten mechanism in a closed reaction vessel have been well studied, but much less so the conditions for the validity of this approximation…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
Michaelis--Menten analysis is often conducted by nonlinear least squares under a constant-variance assumption, even though enzyme-kinetic data frequently display concentration-dependent heteroscedasticity and often include repeated or…
Different graphical plots involving the catalytic rate with the (initial) substrate concentration exist in the enzyme kinetics literature to estimate the reaction constants. But, none of these standard plots can unambiguously distinguish…
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis and its consequences can be studied by computational models…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
Single enzyme chemotaxis is a phenomenon by which a non-equilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We contrast the dynamics after excitation of a quantum mechanical system with that of a classical system. We demonstrate…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
Enzyme kinetics are cyclic. A more realistic reversible three-step mechanism of the Michaelis-Menten kinetics is investigated in detail, and three kinds of waiting cycle times $T$, $T_{+}$, $T_{-}$ are defined. It is shown that the mean…
Chemotaxis is the physical phenomenon that bacteria adjust their motions according to chemical stimulus. A classical model for this phenomenon is a kinetic equation that describes the velocity jump process whose tumbling/transition kernel…
To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the…
A minimal design for a molecular swimmer is proposed that is a based on a mechanochemical propulsion mechanism. Conformational changes are induced by electrostatic actuation when specific parts of the molecule temporarily acquire net…
We study the role of active coupling on the transport properties of homogeneously charged macromolecules in an infinitely dilute solution. An enzyme becomes actively bound to a segment of the macromolecule, exerting an electrostatic force…