Figure 1

Pictorial representation of the steps employed to enforce a competition for amino acid availability between protein \(\bar{G}\) and a protein \(\Gamma \), and to test its effect on the folding ability of protein \(\bar{G}\) in presence and absence of the artificial partner. (I) Create a Caterpillar version of the experimentally determined crystal structure of protein G (II) Shape four competing partner proteins \(\Gamma \) modelled as moulds of increasing portions of the protein G. The size of the mould will influence the competition for resources, as further explained in the following sections. The larger the surface, the higher the competition. (III) Design each of the four systems considering simultaneously the proteins \(\bar{G}\) and \(\Gamma \). The procedure consists in searching for the ensemble of sequences that minimise the energy of both protein \(\bar{G}\) and \(\Gamma \) while keeping the system conformation frozen in space. The competition for the amino acids is created at this stage of our simulations. (IV) After selecting the best designed sequence (see the Design subsection for details about the criterion) for each system, isolate the portion relative to the protein \(\bar{G}\) and test its folding ability in a single-protein folding simulation. (V) Check how the folding of the latter sequences is influenced by the presence of protein \(\Gamma \) frozen in the simulation box (bearing the sequence designed concurrently to protein \(\bar{G}\)).