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. case of the emergence of tertiary structure, which is then biologically relevant, we know that, if the general mechanism is correct, it must be the case that the equilibrium of the primary structure is disturbed. This scenario thus predicts that, in some way, the protein under study has a property of structural disorder, such as a long disorder-to-order transition (see [Figure 5](#fig5){ref-type="fig"}).
{#fig5}
This property, in turn, could be the property to which the evolutionary origin of the protein is traceable. In other words, the transition from a non--ordered to a structured state might be the primary event responsible for the origin of the protein as a new function. Such a hypothesis, if correct, would mean that the emergence of the tertiary structure would not necessarily be coincidental, because an ancestral protein could have evolved with this property in mind. In fact, both computational and experimental results have already provided a hint in this sense. In particular, studies of the emergence of a functionally active form of proteins have led to the conclusion that, if the protein is capable of folding into some relevant conformation, the equilibrium among various unfolded conformations can play a significant role for the emergence of the tertiary structure ([@bib13]; [@bib3]).
The hypothesis of a long transition from disordered to structured forms would thus provide a more accurate interpretation of how the function of proteins evolved than the current, widely adopted, scenario in which the tertiary structure is considered the new form.
To summarize, we have presented a simple but general theoretical model of the evolution of proteins. The model, simple as it is, can lead to nontrivial conclusions, and its predictions are consistent with the observation of the equilibrium properties of protein sequences. More work is obviously needed to extend the model to include the wide variety of biological phenomena that have been observed in proteins. However, our preliminary results have also led us to the conclusion that the emergence of the function of proteins might be traced back to a transition of disordered conformations into a structured state that is relevant for the new function. These results are interesting, because they represent an example of the plausibility of considering that the origin of a function in proteins could be traced back to a deep change of the organization of the conformational space.
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