A thermodynamic model for water activity and redox potential in evolution and development

Abstract

As gene sequences change through evolution, and as the abundances of different proteins change through development, the distinct elemental composition of the proteins at different times can be represented as an overall chemical reaction. Compositional and thermodynamic analysis of these reactions leads to novel insight on biochemical changes and enables predictions of intensive variables including redox potential. The stoichiometric hydration state refers to the number of H2O in theoretical reactions to form the proteins from a set of thermodynamic components. By analyzing published phylostratigraphy and transcriptomic and proteomic datasets, I found that of proteins decreases on evolutionary timescales (from single-celled organisms to metazoans) and on developmental timescales in Bacillus subtilis biofilms. Moreover, values of computed for a developmental proteome of fruit flies are aligned with organismal water content from larva to adult stages. I present a thermodyamic model for the equilibrium chemical activity of target proteins in a genomic background. Conditions that maximize the activity of the target proteins are found by optimizing the values of water activity and oxygen fugacity, which are then combined to calculate effective values of redox potential (Eh). The effective Eh values during evolution range between values reported for mitochondria, the cytosol, and extracellular compartments. These results suggest a central role for water, and water activity, in the biochemistry of evolution and development.