Modeling Biochemical Pathways - Mathematical Approaches to Polymer Sequence Analysis and Related Problems - page 111

Chapter 6
Modeling Biochemical Pathways

Ettore Mosca and Luciano Milanesi

Abstract Sequence analysis methods predict macromolecule properties and
intermolecular interactions. These data can be used to reconstruct molecular net-
works, which are complex systems that regulate cell functions. Systems biology
uses mathematical modeling and computer-based numerical simulations in order
to understand emergent properties of these systems. This chapter describes the
approaches to define kinetic models to simulate biochemical pathways dynamics. It
deals with three main steps: the definition of the system's structure, the mathemati-
cal formulation to reproduce the time evolution and the parameter estimation to find
the set of parameter values such that the model behavior fits the experimental data.

6.1 Introduction

Sequence analysis provides a series of information related both to macromolecules
and to their intermolecular interactions. In fact, the analysis of DNA, RNA and pro-
tein sequences allows us to infer some of the sequence's properties: for instance,
it is possible to identify coding and non-coding regions in a genome and to pre-
dict the secondary and the tridimensional structure assumed by RNAs and proteins.
Sequence analysis also plays an important role when inferring physical interactions
between these molecular components. Computational methods exist for the iden-
tification of RNA- and DNA-binding proteins: for instance, this is the case of the
transcription factors-DNA interactions, which provide knowledge about the genes
regulated by specific transcription factors. Another interesting domain of applica-
tion is the binding between non-coding RNAs (RNAs that are not translated into
proteins) and other types of RNAs: for instance, microRNAs (also referred to as
miRNAs or

RNAs) bind to mRNAs (messenger RNAs) preventing the translation.