Abstract
Confinement of molecules in specific small volumes and areas within a cell is likely to be a general strategy that is developed during evolution for regulating the interactions and functions of biomolecules. The cellular plasma membrane, which is the outermost membrane that surrounds the entire cell, was considered to be a continuous two-dimensional liquid, but it is becoming clear that it consists of numerous nano-meso-scale domains with various lifetimes, such as raft domains and cytoskeleton-induced compartments, and membrane molecules are dynamically trapped in these domains. In this article, we give a theoretical account on the effects of molecular confinement on reversible bimolecular reactions in a partitioned surface such as the plasma membrane. By performing simulations based on a lattice-based model of diffusion and reaction, we found that in the presence of membrane partitioning, bimolecular reactions that occur in each compartment proceed in bursts during which the reaction rate is sharply and briefly increased even though the asymptotic reaction rate remains the same. We characterized the time between reaction bursts and the burst amplitude as a function of the model parameters, and discussed the biological significance of the reaction bursts in the presence of strong inhibitor activity.
Highlights
Reaction kinetics is undoubtedly one of the most immensely studied subjects in chemistry and physics, both from theoretical and experimental aspects
Recent experimental and computational findings provided evidence for how molecular confinement in cytoskeleton induced domains can affect the dynamics of EGF [14,15,16] and B-cell receptor signaling [17], how lipid rafts can enhance the interaction between receptor proteins and their downstream signaling molecules [18,19], and how membrane molecules are brought closer to each other by active processes involving actin filaments [20,21]
Using kinetic Monte Carlo simulations, we study the dynamic equilibrium between monomers and dimers that perform a discrete time random walk in a two-dimensional lattice partitioned into compartments by periodically placed permeable barriers
Summary
Reaction kinetics is undoubtedly one of the most immensely studied subjects in chemistry and physics, both from theoretical and experimental aspects. The cellular plasma membrane is considered to be a twodimensional liquid [10], where many membrane molecules perform various vital functions for the cell, including signal processing and selective internalization of external molecules. Recent experimental and computational findings provided evidence for how molecular confinement in cytoskeleton induced domains can affect the dynamics of EGF (epidermal growth factor) [14,15,16] and B-cell receptor signaling [17], how lipid rafts can enhance the interaction between receptor proteins and their downstream signaling molecules [18,19], and how membrane molecules are brought closer to each other by active processes involving actin filaments [20,21]
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