Manipulating the Steady State of Metabolic Pathways

Abstract

Metabolic pathways show the complex interactions among enzymes that transform chemical compounds. The state of a metabolic pathway can be expressed as a vector, which denotes the yield of the compounds or the flux in that pathway at a given time. The steady state is a state that remains unchanged over time. Altering the state of the metabolism is very important for many applications such as biomedicine, biofuels, food industry, and cosmetics. The goal of the enzymatic target identification problem is to identify the set of enzymes whose knockouts lead the metabolism to a state that is close to a given goal state. Given that the size of the search space is exponential in the number of enzymes, the target identification problem is very computationally intensive. We develop efficient algorithms to solve the enzymatic target identification problem in this paper. Unlike existing algorithms, our method works for a broad set of metabolic network models. We measure the effect of the knockouts of a set of enzymes as a function of the deviation of the steady state of the pathway after their knockouts from the goal state. We develop two algorithms to find the enzyme set with minimal deviation from the goal state. The first one is a traversal approach that explores possible solutions in a systematic way using a branch and bound method. The second one uses genetic algorithms to derive good solutions from a set of alternative solutions iteratively. Unlike the former one, this one can run for very large pathways. Our experiments show that our algorithms' results follow those obtained in vitro in the literature from a number of applications. They also show that the traversal method is a good approximation of the exhaustive search algorithm and it is up to 11 times faster than the exhaustive one. This algorithm runs efficiently for pathways with up to 30 enzymes. For large pathways, our genetic algorithm can find good solutions in less than 10 minutes.