Team:Oxford/why do we need microcompartments
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- | + | <h1>Modelling the effect of introducing a microcompartment on reaction rate</h1> | |
+ | Our main approach to reducing the accumulation of toxic intermediates in the DCM degradation pathway is the expression of Pdu microcompartments in our bacteria that will contain high concentrations of both the DcmA enzyme and FdhA enzyme. In doing so, this increases the likelihood of a formaldehyde molecule produced by the action of DcmA encountering an FdhA enzyme before it leaves the microcompartment thus reducing the accumulation of formaldehyde. | ||
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+ | To model the increased likelihood of reaction, we started with the Smoluchowski diffusion model above but discretized the system such that molecules could only occupy a fixed set of co-ordinates. This was done in order to define a reaction as occurring whenever two molecules occupied the same co-ordinate at the same time. While this does not necessarily ensure a reaction in the real system, we are assuming that collision rate is proportional to reaction rate and can therefore be used as an analogy. | ||
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+ | Plotted here are two systems- one with complete freedom of molecular movement and one in which spatial constraints have been placed such that molecules which encounter the boundaries are reflected back into the system to represent the presence of the microcompartment: | ||
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+ | In the models above, collisions are indicated through red marks. As suspected, the likelihood of a collision in a spatially constrained environment are far higher than in one where the molecules have complete freedom of movement. This is particularly true not only because of the region of movement allowed by the microcompartment but also the initial distance between the enzyme and substrate at the point of substrate formation. Note also that the rate of diffusion of the enzyme, in green, has been made substantially lower than that of the formaldehyde- the far lighter and therefore more diffusive compound. | ||
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+ | <h1>3D collision model</h1> | ||
+ | The 1-D collision model described above was quite easily expanded into a 3-D collision model that is more representative of the actual system. This results in simulations which appear far more realistic. | ||
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+ | Illustrated above are the molecular trajectories of two different species- enzyme and substrate. The enzymes (red) are constrained to move within the micro-compartment and are reflected at the micro-compartment boundaries while the substrates (in blue) can freely diffuse anywhere in the system. While these simulations are very similar to the 1-D simulations previously described, they are far more computationally laborious. | ||
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+ | Although the original plan was to run the simulation for several hundred enzymes and substrates and study the total number of collisions achieved, collisions are used as an analogy for reaction, it was quickly apparent that using this simulation to provide analytic results on the scales we wanted required far too much computation. | ||
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+ | Given more time, access to more powerful computers and economization of our Matlab scripts, it would be possible to run this simulation for greater numbers of molecules than have been done thus far. This would then yield more data on the proportional increase in rate that results from introducing the micro-compartment into the system. | ||
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