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Biology subjects

Tostevin, F.

Publications and source records attributed to Tostevin, F..

3 recordsLinked to original sources

Optimal spatial allocation of enzymes as an investment problem

Given a limited number of molecular components, cells face various allocation problems demanding decisions on how to distribute their resources. For instance, cells decide which enzymes to produce at what quantity, but also where to position them. Here we focus on the spatial allocation problem of how to distribute enzymes such as to maximize the total reaction flux produced by them in a system with given geometry and boundary conditions. So far, such distributions have been studied by computational optimization, but a deeper theoretical understanding was lacking. We derive an optimal allocation principle, which demands that the available enzymes are distributed such that the marginal flux returns at each occupied position are equal. This homogeneous marginal returns criterion (HMR criterion) corresponds to a portfolio optimization criterion in a scenario where each investment globally feeds back onto all payoffs. The HMR criterion allows us to analytically understand and characterize a localization-delocalization transition in the optimal enzyme distribution that was previously observed numerically. In particular, our analysis reveals the generality of the transition, and produces a practical test for the optimality of enzyme localization by comparing the reaction flux to the influx of substrate. Based on these results, we devise an additive construction algorithm, which builds up optimal enzyme arrangements systematically rather than by trial and error. Taken together, our results reveal a common principle in allocation problems from biology and economics, which can also serve as a design principle for synthetic biomolecular systems.

bioengineering↗

Four different mechanisms for switching cell polarity

The mechanisms and design principles of regulatory systems establishing stable polarized protein patterns within cells are well studied. However, cells can also dynamically control their cell polarity. Here, we ask how an upstream signaling system can switch the orientation of a polarized pattern. We use a mathematical model of a core polarity system based on three proteins as the basis to study different mechanisms of signal-induced polarity switching. The analysis of this model reveals four general classes of switching mechanisms with qualitatively distinct behaviors: the transient oscillator switch, the reset switch, the prime-release switch, and the push switch. Each of these regulatory mechanisms effectively implements the function of a spatial toggle switch, however with different characteristics in their nonlinear and stochastic dynamics. We identify these characteristics and also discuss experimental signatures of each type of switching mechanism.

biophysics↗

Trade-offs and design principles in the spatial organization of catalytic particles

Spatial organization of catalytic particles is ubiquitous in biological systems across different length scales, from enzyme complexes to metabolically coupled cells. Despite the different scales, these systems share common features of localized reactions with partially hindered diffusive transport, determined by the collective arrangement of the catalysts. Yet it remains largely unexplored how different arrangements affect the interplay between the reaction and transport dynamics, which ultimately determines the flux through the reaction pathway. Here we show that two fundamental trade-offs arise, the first between efficient inter-catalyst transport and depletion of substrate, and the second between steric confinement of intermediate products and accessibility of catalysts to substrate. We use a model reaction pathway to characterize the general design principles for the arrangement of catalysts that emerge from the interplay of these trade-offs. We find that the question of optimal catalyst arrangements generalizes the famous Thomson problem of electrostatics.

biophysics↗