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Kinetic model of a compartmentalized protometabolic network.

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posted on 2012-06-27, 02:13 authored by Gabriel Piedrafita, Kepa Ruiz-Mirazo, Pierre-Alain Monnard, Athel Cornish-Bowden, Francisco Montero

Two different domains are defined: an external environment, considered as an unlimited source of precursor molecules (S, T and U); and a system in which a set of protometabolic processes take place, encapsulated by a semipermeable membrane (represented as a sphere). Its boundaries allow for the passive diffusion of the precursors into the inner aqueous core. Three intertwined catalytic cycles, highlighted in different colors, define the core protometabolism (reactions depicted as black arrows), transforming the precursors into catalysts STU, ST and SU; whereas three accessory reactions, shown in light grey, correspond to the non-catalyzed formation of these catalysts, which are also irreversibly degraded through steps 4, 8 and 11 (dashed arrows). The concentrations of the distinct species inside the system are treated as variables, and all processes except the degradation reactions are reversible. Forward rate constants are denoted , adjacent to their corresponding processes (direction of the arrows), while reverse rate constants, when pertinent, appear as . The nutrients S, T and U can diffuse through the membrane in both directions: the same rate constants are assumed for their incorporation and efflux.


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