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The spatial organization of enzymes often plays a crucial role in the functionality and efficiency of enzymatic pathways. To fully understand the design and operation of enzymatic pathways, it is therefore crucial to understand how the relative arrangement of enzymes affects pathway function. Here we investigate the effect of enzyme localization on the flux of a minimal two-enzyme pathway within a reaction-diffusion model. We consider different reaction kinetics, spatial dimensions, and loss mechanisms for intermediate substrate molecules. Our systematic analysis of the different regimes of this model reveals both universal features and distinct characteristics in the phenomenology of these different systems. In particular, the distribution of the second pathway enzyme that maximizes the reaction flux undergoes a generic transition from co-localization with the first enzyme when the catalytic efficiency of the second enzyme is low, to an extended profile when the catalytic efficiency is high. However, the critical transition point and the shape of the extended optimal profile is significantly affected by specific features of the model. We explain the behavior of these different systems in terms of the underlying stochastic reaction and diffusion processes of single substrate molecules.
Transcription regulation typically involves the binding of proteins over long distances on multiple DNA sites that are brought close to each other by the formation of DNA loops. The inherent complexity of the assembly of regulatory complexes on loope
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic parameters of the m
In the present study, we show that ascorbic acid dose-dependently inhibited interleukin-1beta (IL-1beta)-mediated PGE2 synthesis in the human neuronal cell line, SK-N-SH. Furthermore, in combination with aspirin, ascorbic acid augmented the inhibitor
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into account the
The interaction between actin filaments and microtubules is crucial for many eukaryotic cellular processes, such as, among others, cell polarization, cell motility and cellular wound healing. The importance of this interaction has long been recognise