Modeling metabolic processes between molecular and systems biology

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

The present work is the first of a series of papers aiming at a coherent and unified development of the thermodynamics of metabolism and the rationalization of feasibility analysis of metabolic pathways. The focus in this part is on high-level quantum chemical calculations of the thermochemical quantities of relatively heavy metabolites such as amino acids/oligopeptides, nucleosides, saccharides and their derivatives in the ideal gas state. The results of this study will be combined with the corresponding hydration/solvation results in subsequent parts of this work in order to derive the desired thermochemical quantities in aqueous solutions. The above metabolites exist in a vast conformational/isomerization space including rotational conformers, tautomers or anomers exhibiting often multiple or cooperative intramolecular hydrogen bonding. We examine the challenges posed by these features for the reliable estimation of thermochemical quantities. We discuss conformer search, conformer distribution and averaging processes. We further consider neutral metabolites as well as protonated and deprotonated metabolites. In addition to the traditional presentation of gas-phase acidities, basicities and proton affinities, we also examine heats and free energies of ionic species. We obtain simple linear relations between the thermochemical quantities of ions and the formation quantities of their neutral counterparts. Furthermore, we compare our calculations with reliable experimental measurements and predictive calculations from the literature, when available. Finally, we discuss the next steps and perspectives for this work.

Cellular and molecular structure as a unifying framework for whole-cell modeling

Whole-cell modeling has the potential to play a major role in revolutionizing our understanding of cellular biology over the next few decades. A computational model of the entire cell would allow cellular biologists to integrate data from many disparate sources in a single consistent framework. Such a comprehensive model would be useful both for hypothesis testing and in the discovery of new behaviors that emerge from complex biological networks. Cellular and molecular structure can and should be a key organizing principle in a whole-cell model, connecting models across time and length scales in a multiscale approach. Here I present a summary of recent research centered around using molecular and cellular structure to model the behavior of cells.