Information processing in biological molecular machines

A BSTRACT Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics of conformational transitions which often manifests in fluctuating rates of the catalyzed processes and the presence of short-term memory resulting from the preference of certain conformations. For arbitrarily complex stochastic dynamics of protein machines, we proved the generalized fluctuation theorem predicting the possibility of reducing free energy dissipation at the expense of creating some information stored in memory. That this may be the case has been shown by interpreting results of computer simulations for a complex model network of stochastic transitions. The subject of the analysis was the time course of the catalyzed processes expressed by sequences of jumps at random moments of time. Since similar signals can be registered in the observation of real systems, all theses of the paper are open to experimental verification. STATEMENT OF SIGNIFICANCE The transient utilization of memory for storing information turns out to be crucial for the movement of protein motors and the reason for most protein machines to operate as dimers or higher organized assemblies. From a broader physical point of view, the division of free energy into the operation and organization energies is worth emphasizing. Information can be assigned a physical meaning of a change in the value of both these functions of state.