In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory of automata to model the latter dynamics. In our model protein's behavior is modeled with the aid of two dynamical systems, ontic and epistemic, which describe evolution of conformational and functional states of proteins, respectively. The epistemic automaton is constructed from the ontic automaton on the basis of functional (observational) equivalence relation on the space of ontic states. This reminds a few approaches to emergent quantum mechanics in which a quantum (epistemic) state is treated as representing a class of prequantum (ontic) states. This approach does not match to the standard {\it protein structure-function paradigm.} However, it is perfect for modeling of behavior of intrinsically disordered proteins. Mathematically space of protein's ontic states (conformational states) is modeled with the aid of $p$-adic numbers or more general ultrametric spaces encoding the internal hierarchical structure of proteins. Connection with theory of $p$-adic dynamical systems is briefly discussed.