This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011
Characterization of the emergent properties of a synthetic quasi-cellular system
1 Dipartimento di Informatica, Università di Pisa, L.go B. Pontecorvo 3, 56127 Pisa, Italy
2 Dipartimento di Biologia, Università di Roma III, Via G. Marconi 446, 00146 Roma, Italy
3 Istituto di Biofisica del CNR, Via G. Moruzzi 1, 56124 Pisa, Italy
BMC Bioinformatics 2012, 13(Suppl 4):S9 doi:10.1186/1471-2105-13-S4-S9Published: 28 March 2012
The process of solutes entrapment during liposomes formation is interesting for the investigation of the relationship between the formation of compartments and the distribution of molecules inside them; a relevant issue in the studies of the origin of life. Theoretically, when no interactions are supposed among the chemical species to be entrapped, the entrapment is described by a standard Poisson process. But very recent experimental findings show that, for small liposomes (100 nm diameter), the distribution of entrapped molecules is best described by a power-law function. This is of a great importance, as the two random processes give rise to two completely different scenarios. Here we present an in silico stochastic simulation of the encapsulation of a cell-free molecular translation system (the PURE system), obtained following two different entrapment models: a pure Poisson process, and a power-law. The protein synthesis inside the liposomes has been studied in both cases, with the aim to highlight experimental observables that could be measured to assess which model gives a better representation of the real process.
Firstly, a minimal model for in vitro protein synthesis, based on the PURE system molecular composition, has been formalized. Then, we have designed a reliable experimental simulation where stochastic factors affect the reaction course inside the compartment. To this end, 24 solutes, which represent the PURE system components, have been stochastically distributed among vesicles by following either a Poisson or a power-law distribution. The course of the protein synthesis within each vesicle has been consequently calculated, as a function of vesicle size. Our study can predict translation yield in a population of small liposomes down to the attoliter (10-18 L) range. Our results show that the efficiency of protein synthesis peaks at approximately 3·10-16 L (840 nm diam.) with a Poisson distribution of solutes, while a relative optimum is found at around 10-17 L (275 nm diam.) for the power-law statistics.
Our simulation clearly shows that the wet-lab measurement of an effective protein synthesis at smaller volumes than 10-17 L would rule out, according to our models, a Poisson distribution of solutes.