What nucleic acids cannot do: a model for information processing in protein molecules

Biological functions of proteins that are not realizable by nucleic acids as a genetic material are investigated. Based on the essential differences of the information processing mechanism between proteins and nucleic acids, i.e. the possibility of error propagation in a molecule, a simple model of proteins is proposed. The Monte Carlo simulation for two-dimensional binary dodecamers shows that the sequence-specific conformation selectivity for isolated and some associated states can be reproduced. Moreover, the allostery-like cooperative conformational change in a dimeric state, orientation-controlled polymerization and one-directional sliding along a fibrous structure can be induced by a site-specific substitution, which mimics a post-translational modification within a chain. These results suggest that such a class of dynamic behaviors represent the information processing proper to proteins and that they are the elementary processes of intermolecular communication.