Biological molecular energy machines as measuring devices

Abstract

A qualitative picture of operation modes of McClare's biological molecular energy machines is presented. On refuting published criticisms of McClare's idea, the present discussion suggests that the molecular energy stored locally in a biological molecular energy machine is conveyed to a sequence of non-equilibrium conformational states in some of which the machine does work. If the structure of the conformational space is favorable, the set of trajectories in this space decomposes into two families each of which terminates in another set of states. Whether the machine moves along one or the other family of trajectories depends on initial differences in interaction between the machine and a molecular object, so that the machine performs a measurement on the molecular object and processes it accordingly. Although a single dissipative step might suffice in principle, practical reasons require that all logically irreversible steps be also physically irreversible.