  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.
