Abstract
The successful use of process calculi to specify behavioural models allows us to compare RNA and protein folding processes from a new perspective. We model the folding processes as behaviours resulting from the interactions that nucleotides and amino acids (the elementary units that compose RNAs and proteins respectively) perform on their linear sequences. This approach is intended to provide new knowledge about the studied systems without strictly relying on empirical data. By applying Milner’s CCS process algebra to highlight the distinguishing features of the two folding processes, we discovered an abstraction level at which they show behavioural equivalences. We believe that this result could be interpreted as a clue in favour of the highly-debated RNA World theory, according to which, in the early stages of cell evolution, RNA molecules played most of the functional and structural roles carried out today by proteins.
Highlights
The successful use of process calculi to specify behavioural models allows us to compare RNA and protein folding processes from a new perspective
We focus our study on the interactions carried out by the elementary units that compose RNAs and proteins, describing the whole folding process as the resulting behaviour of such interactions
As we show with our models, the cells cope with this necessity by the formation of molecules whose elementary units are able to perform more complex interactions than nucleotides
Summary
The successful use of process calculi to specify behavioural models allows us to compare RNA and protein folding processes from a new perspective. By applying Milner’s CCS process algebra to highlight the distinguishing features of the two folding processes, we discovered an abstraction level at which they show behavioural equivalences We believe that this result could be interpreted as a clue in favour of the highly-debated RNA World theory, according to which, in the early stages of cell evolution, RNA molecules played most of the functional and structural roles carried out today by proteins. The definition of the models we propose in this paper is based on the idea that all the components involved in a system, and the communication media themselves, can be formally modelled as processes This approach has been applied to study biological systems by modelling entire molecules[3,4], and can be extended to analyse their substructures or even their elementary units, since it allows describing every kind of interaction they perform; it is possible to identify similarities among different classes of molecules and in the functions they carry out
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