An enquiry into metabolite domains

¹ Centro de Estudios Científicos

^* To whom correspondence should be addressed. E-mail: fbarros{at}cecs.cl.

Submitted on December 1, 2006
Revised on January 19, 2007
Accepted on 7 February 2007

	Abstract

It is currently assumed that two or more pools of the same metabolite can co-exist in the cytosolic compartment of mammalian cells. These pools are thought to be generated by the differential subcellular location of enzymes and transporters, much in the way calcium microdomains arise by the combined workings of channels, buffers and pumps. With the aim of estimating the amplitude and spatial dimensions of these metabolite pools, we developed an analytical tool based on Brownian diffusion and the turnover numbers of the proteins involved. The outcome of the analysis is that ATP, glucose, pyruvate, lactate and glutamate can not be concentrated at their sources to an extent that would affect their downstream targets. For these metabolites, and others produced by slow enzymes or transporters and present at micromolar concentrations or higher, the cytosol behaves as well-mixed, homogenous compartment. In contrast, the analysis showed microdomains known to be generated by calcium channels and revealed that calcium and pH nanodomains are to be found in the vicinity of slow enzymes and transporters in the steady state. The analysis can be readily be applied to any other molecule provided knowledge is available about rate of production, average concentration and diffusion coefficient. Our main conclusion is that the notion of cytosolic compartmentation of metabolites needs re-evaluation, as it seems to be in conflict with the underlying physical chemistry.

Key Words: Brownian diffusion, Compartmentation, Metabolite pool, Microdomain, Steady-state flux

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