Prompted by the recent growing evidence of oscillatory behavior involving MAPK cascades we present a systematic approach of analyzing models and elucidating the nature of biochemical oscillations based on reaction network theory. In particular, we formulate a minimal biochemically consistent mass action subnetwork of the Huang-Ferrell model of the MAPK signalling that provides an oscillatory response when a parameter controlling the activation of the top-tier kinase is varied. Such dynamics are either intertwined with or separated from the earlier found bistable/hysteretic behavior in this model. Using the theory of stability of stoichiometric networks, we reduce the original MAPK model, convert kinetic to convex parameters and examine those properties of the minimal subnetwork that underlie the oscillatory dynamics. We also use the methods of classification of chemical oscillatory networks to explain the rhythmic behavior in physicochemical terms, i.e., we identify of the role of individual biochemical species in positive and negative feedback loops and describe their coordinated action leading to oscillations. Our approach provides an insight into dynamics without the necessity of knowing rate coefficients and thus is useful prior the statistical evaluation of parameters.
A bistable switch from a low pH (unreacted "off") state to a high pH (reacted "on") state was obtained in enzyme-loaded gel beads in response to supra-threshold substrate concentrations.
We study a model system of three diffusively coupled reaction cells arranged in a linear array that display Turing patterns with special focus on the case of equal coupling strength for all components. As a suitable model reaction we consider a two-variable core model of glycolysis. Using numerical continuation and bifurcation techniques we analyze the dependence of the system's steady states on varying rate coefficient of the recycling step while the coupling coefficients of the inhibitor and activator are fixed and set at the ratios 100:1, 1:1, and 4:5. We show that stable Turing patterns occur at all three ratios but, as expected, spontaneous transition from the spatially uniform steady state to the spatially nonuniform Turing patterns occurs only in the first case. The other two cases possess multiple Turing patterns, which are stabilized by secondary bifurcations and coexist with stable uniform periodic oscillations. For the 1:1 ratio we examine modular spatiotemporal perturbations, which allow for controllable switching between the uniform oscillations and various Turing patterns. Such modular perturbations are then used to construct chemical computing devices utilizing the multiple Turing patterns. By classifying various responses we propose: (a) a single-input resettable sensor capable of reading certain value of concentration, (b) two-input and three-input memory arrays capable of storing logic information, (c) three-input, three-output logic gates performing combinations of logical functions OR, XOR, AND, and NAND.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.