The idea of this project is to develop the method of predictions of stationary genes expression levels in bacterial systems. In the end of the project we are planning to develop software, which is available to give in the exit the value of stationary expression in case of entering primary gene (or mRNA) sequence and necessary metabolites in it. At first sight, based on the name and problem statement difficulty, is seems that our research have fundamental meaning only. However, in is not completely such case, because it is connected with one very important applied problem. The matter concerns foreign proteins expression in bacterial cells. The importance of this problem confirms the fact that at present time there are no alternative to bacterial cells as factories for protein from other organisms production. At that, researches in this field confront often with the fact that difficulties arise during some protein expression, i.e. the process is not going or its rate is no enough. For these problem removal scientists have to carry out additional researches, which irreversible reflects on time. Software presented in this work would help to the researchers to remove such obstacles.

Molecular biology have clearly demonstrated lately, that gene sequence contains not only qualitative but also quantitative information about protein structure. In DNA code contains the information not only about amino acid sequence in the protein but also about its rate of expression and degradation, and consequently, about final concentration. Several various types of gene expression regulation are known. In the first place is mRNA transcription regulation. It is the key step because exactly here the question – is it necessary or not to synthesis this protein in such conditions are solved. In contrast, in case of regulation on the stage of translation such questions are not solving, but the rate of expression was defined. It happens at the expense of special information, containing in gene consequence, which could be divided into four main categories:

1. Shine-Dalgarno sequence (the region of connection mRNA with ribosome) when at the expense of different set of nucleotides in the mRNA region the affinity of transcript to the ribosome varies, and consequently – the rate of translation initiation.
2. mRNA secondary structure, when on the RNA molecule the elements of secondary structure (stem-loops, etc) forms that prevent ribosome transference along matrix and block peptide chain synthesis. Some proteins and mRNA signal molecules sometimes act analogously to secondary structure elements formation. In both cases the process is very similar to the transcription attenuation, marked for tryptophan regulon of Escherichia coli.
3. Rare codons using, when because of genome degeneracy (possibility of one amino acid coding by a number of codons) the rate of transcription elongation decreases. This category can be divided in two subsections – presence of rare codons (with deficient concentration of corresponding aminoacyl-tRNA) and weak codons (with little life time of complex codon/anticodon). In both cases during such codons passing the movement of ribosome along mRNA is delayed right up to polypeptide synthesis prohibition.
4. The presence of sites of ribonuclease and protease action in the gene sequence, which conditions the higher level of degradation of transcripts and proteins coding by them.

At present time we just start kinetic model development, which describes all the aspects mentioned above. However already at the first step we have to face with serious problem because of deficiency of experimental data. Therefore we are actively looking for researchers-experimentalists for productive collaboration in the frameworks of this project.