title: Confinement and diffusion modulate bistability and stochastic switching in a reaction network with positive feedback.
abstract: Positive feedback is a common feature in signal transduction networks and can lead to phenomena such as bistability and signal propagation by domain growth. Physical features of the cellular environment, such as spatial confinement and the mobility of proteins, play important but inadequately understood roles in shaping the behavior of signaling networks. Here, we use stochastic, spatially resolved kinetic Monte Carlo simulations to explore a positive feedback network as a function of system size, system shape, and mobility of molecules. We show that these physical properties can markedly alter characteristics of bistability and stochastic switching when compared with well-mixed simulations. Notably, systems of equal volume but different shapes can exhibit qualitatively different behaviors under otherwise identical conditions. We show that stochastic switching to a state maintained by positive feedback occurs by cluster formation and growth. Additionally, the frequency at which switching occurs depends nontrivially on the diffusion coefficient, which can promote or suppress switching relative to the well-mixed limit. Taken together, the results provide a framework for understanding how confinement and protein mobility influence emergent features of the positive feedback network by modulating molecular concentrations, diffusion-influenced rate parameters, and spatiotemporal correlations between molecules.
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Mlynarczyk
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA.
authors.forename: Robert H
authors.initials: RH
authors.lastname: Pullen
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Abel
mesh_terms: D004058:Diffusion; D025461:Feedback, Physiological; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D011506:Proteins / Q000737:chemistry*; D013269:Stochastic Processes
chemical_list: D011506:Proteins