The Kinetic and Energetic Pull of Chemical Entropy On Small Ensembles of Proteins

Abstract

Biological systems are fundamentally containers of thermally fluctuating atoms that through unknown mechanisms are structurally layered across many thermal scales from atoms to amino acids to primary, secondary, and tertiary structures to functional proteins to functional macromolecular assemblies and up. Understanding how the irreversible kinetics (i.e., the arrow of time) of biological systems emerge from the equilibrium kinetics of constituent structures defined on smaller thermal scales is central to describing biological function. Muscles irreversible power stroke - with its mechanochemistry defined on both the thermal scale of muscle and the thermal scale of myosin motors - provides a clear solution to this problem. Individual myosin motors function as reversible force-generating switches induced by actin binding and gated by the release of inorganic phosphate, Pi. As shown in a companion article, when N individual switches thermally scale up to an ensemble of N switches in muscle, the entropy of a binary system of switches is created. We have shown in muscle that a change in state of this binary system of switches entropically drives actin-myosin binding (the switch) and muscles irreversible power stroke, and that this simple two-state model accurately accounts for most key aspects of muscle contraction. Extending this observation beyond muscle, here I show that the chemical kinetics of an ensemble of N molecules differs fundamentally from a conventional chemical analysis of N individual molecules, describing irreversible chemical reactions as being pulled into the future by the a priori defined entropy of a binary system rather than being pushed forward by the physical occupancy of chemical states (e.g., mass action).