Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userMaster curve of boosted diffusion for ten catalytic enzymes
65
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Molecular agitation more rapid than thermal Brownian motion is reported for cellular environments, motor proteins, synthetic molecular motors, enzymes, and common chemical reactions, yet that chemical activity couples to molecular motion contrasts with generations of accumulated knowledge about diffusion at equilibrium. To test the limits of this idea, a critical testbed is mobility of catalytically active enzymes. Sentiment is divided about reality of enhanced enzyme diffusion with evidence for and against. Here a master curve shows that enzyme diffusion coefficient increases in proportion to the energy release rate, the product of Michaelis-Menten reaction rate and Gibbs free energy change with the highly satisfactory correlation coefficient of 0.97. For ten catalytic enzymes (urease, acetylcholinesterase, seven enzymes from the glucose cascade cycle, and another), our measurements span from roughly 40% enhanced diffusion coefficient at high turnover rate and negative Gibbs free energy to no enhancement at slow turnover rate and positive Gibbs free energy. Moreover, two independent measures of mobility show consistency, provided that one avoids undesirable fluorescence photophysics. The master curve presented here quantifies the limits of both ideas, that enzymes display enhanced diffusion and that they do not within instrumental resolution, and has possible implications for understanding enzyme mobility in cellular environments. The striking linear dependence for the exergonic enzymes (negative Gibbs free energy) together with the vanishing effect for endergonic enzyme (positive Gibbs free energy) are consistent with a physical picture where the mechanism boosting the diffusion is an active one, utilizing the available work from the chemical reaction.
rate research
Read More
Many experiments in recent years have reported that, when exposed to their corresponding substrate, catalytic enzymes undergo enhanced diffusion as well as chemotaxis (biased motion in the direction of a substrate gradient). Among other possible mechanisms, in a number of recent works we have explored several passive mechanisms for enhanced diffusion and chemotaxis, in the sense that they require only binding and unbinding of the enzyme to the substrate rather than the catalytic reaction itself. These mechanisms rely on conformational changes of the enzyme due to binding, as well as on phoresis due to non-contact interactions between enzyme and substrate. Here, after reviewing and generalizing our previous findings, we extend them in two different ways. In the case of enhanced diffusion, we show that an exact result for the long-time diffusion coefficient of the enzyme can be obtained using generalized Taylor dispersion theory, which results in much simpler and transparent analytical expressions for the diffusion enhancement. In the case of chemotaxis, we show that the competition between phoresis and binding-induced changes in diffusion results in non-trivial steady state distributions for the enzyme, which can either accumulate in or be depleted from regions with a specific substrate concentration.
In this note we establish exponentially fast smooth convergence for global curve diffusion flows, and discuss open problems relating embeddedness to global existence (Gigas conjecture) and the shape of Type I singularities (Chous conjecture).
Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion model. The optimal arrangement transitions from a cluster to a distributed profile as a single parameter, which controls the probability of reaction versus diffusive loss of pathway intermediates, is varied. We introduce the concept of enzyme exposure to explain how this transition arises from the stochastic nature of molecular reactions and diffusion.
We describe a technique for particle-based simulations of heterogeneous catalysis in open-cell foam structures, which is based on isotropic Stochastic Rotation Dynamics (iSRD) together with Constructive Solid Geometry (CSG). The approach is validated by means of experimental results for the low temperature water-gas shift reaction in an open-cell foam structure modeled as inverse sphere packing. Considering the relation between Sherwood and Reynolds number, we find two distinct regimes meeting approximately at the strut size Reynolds number 10. For typical parameters from the literature, we find that the catalyst density in the washcoat can be reduced considerably without a notable loss of conversion efficiency. We vary the porosity to determine optimum open-cell foam structures, which combine low flow resistance with high conversion efficiency and find large porosity values to be favorable not only in the mass transfer limited regime but also in the intermediate regime.
We show that any initial closed curve suitably close to a circle flows under length-constrained curve diffusion to a round circle in infinite time with exponential convergence. We provide an estimate on the total length of time for which such curves are not strictly convex. We further show that there are no closed translating solutions to the flow and that the only closed rotators are circles.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
