Variable elimination in post-translational modification reaction networks with mass-action kinetics

TL;DR

This paper introduces a mathematical framework using cuts to simplify the analysis of steady states in post-translational modification networks with mass-action kinetics, enabling variable elimination and parameterization.

Contribution

It develops a linear elimination method based on cuts for reducing variables in polynomial systems of biological reaction networks, providing a new approach to analyze steady states.

Findings

Provides a linear elimination procedure using cuts

Parameterizes steady states algebraically by core variables

Identifies conservation laws via connected components in the species graph

Abstract

We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well as theoretically. The steady states of such a system are solutions to a system of polynomial equations with as many variables as equations. Even for small systems the task of finding the solutions is daunting. We develop a mathematical framework based on the notion of a cut, which provides a linear elimination procedure to reduce the number of variables in the system. The steady states are parameterized algebraically by a set of "core" variables, and the non-negative steady states correspond to non-negative values of the core variables. Further, minimal cuts are the connected components in the species graph and provide conservation laws. A criterion for when a set of independent conservation laws can be derived from cuts is given.