John H. Byrne

CHAPTER 14 – Mathematical Modeling and Analysis of Intracellular Signaling Pathways

This chapter provides an overview of concepts and techniques necessary to describe and analyze the operation of intracellular signaling pathways with concise mathematical language. By use of these techniques, it is possible to model series (either unbranched or branched) of enzyme reactions. Such series are commonly termed “metabolic pathways,”“biochemical pathways,” or “signaling pathways.” Mathematical models are essential for synthesizing large amounts of data concerning the intracellular signaling pathway dynamics and the regulation of gene expression. Standard modeling techniques have been developed to represent common biochemical elements such as allosteric interactions, feedback interactions in biochemical pathways and gene networks, and intracellular transport of molecules. The chapter relies primarily on qualitative models. Such models illustrate the way typical biochemical elements can give rise to the specific types of pathway dynamics. For all models, it is essential to determine the sensitivity of model behavior to parameters and to assess the parameters that are not well-constrained by data. Experiments that estimate parameters that are the key control points of model behavior constitute the stringent tests of a model.