Mathematical models and computational methods for the analysis of genome-scale protein synthesis

Proteins are a ubiquitous and indispensable element for every living organism, from simple bacteria to mammals. Already in the simplest organisms, there exist some thousands of different protein species that take up a great variety of structures, and thus different roles, letting them precisely orchestrate the functioning of each cell. Despite this diversity of functions and shapes, all proteins are emerging from a same root: the DNA that encodes all proteins, in a same way as a dictionary contains the definition of each word. When a cell needs a specific protein, it will therefore "read" this "DNA dictionary" and translate it into another "language": from a nucleotide sequence of the DNA to an amino acids sequence, which is the basis of each protein. This process of "reading" the DNA to form a protein, or in better terms the protein synthesis, lies at the heart of every organism. Indeed 80% of the cellular energy is devoted to protein synthesis. The main mechanisms of this process are the same for all proteins and for all kingdoms of life. A good understanding of this process is therefore essential to biology; any malfunctioning could potentially lead to diseases and, on the other hand, any of the steps of protein synthesis could be a prospective drug target. This is already the case of various antibiotics. In addition to that, a good understanding of this system is also valuable in recombinant vaccine and recombinant drug production, in order to help improve the yield of these proteins. Recombinant proteins technology is used for example to synthesize the hepatitis B vaccine in yeast cells or to synthesize the recombinant human insulin in Escherichia coli cells. This is done by inserting into the organism a DNA plasmid that encodes the given protein so that the transfected organism will then synthesize this protein nearly as if it was from its own DNA. A further benefit from an in -depth knowledge of protein synthesis relates to circuit design in synthetic biology. There, the goal is to design cells that will respond to their environment in a predefined manner, and again, this is done by inserting specific genes into the cells. Understanding protein synthesis can help to estimate the sensibility of such a system as well as help to define characteristics of its response. Nowadays, the many facets of protein synthesis and its regulation are getting increasingly better understood. Nevertheless, it also becomes increasingly more evident that the classical approach of studying every component in isolation should be left aside and the system or cell should be studied as a whole, due to the interconnections of all of its elements: we have entered in the systems biology era. With the recent advances in genomics, transcriptomics, proteomics and other –omics technologies, we are able to measure the state of cells under different conditions in a high -throughput manner, enabling some global, genome -scale view as aimed at by systems biology. The huge amou