- Article -
| In Silico Biology 7, 0044 (2007); ©2007, Bioinformation Systems e.V. |
RNAmodel web server: Modeling classic attenuation in bacteria
Lev Rubanov* and Vassily Lyubetsky
Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences
* Corresponding author
Email: rubanov@iitp.ru
Edited by S. Rodin (guest editor) and N. Kolchanov; received January 30, 2007; revised and accepted May 04, 2007; published August 19, 2007
Abstract
RNAmodel web server was recently established at the IITP RAS to implement our previously proposed model of the classic attenuation regulation of gene expression in bacteria. This new model is based on the concept of resonant-like interaction between RNA polymerase and hairpins of RNA secondary structure formed during transcription. Our modeling relies on standard Monte Carlo procedures and covers all essential stages of the process, including initiation and elongation of transcription and translation; the deceleration of ribosome on regulatory codons, which depends on the concentration of charged amino acyl-tRNA; the polymerase shifting delay caused by secondary structure folded into the mRNA segment between ribosome and polymerase; and, ultimately, either transcription terminating prematurely or polymerase reaching a region of structural genes (antitermination). By means of Monte Carlo simulation we build a function p(c) which expresses the probability of termination (i. e., an enzyme activity) vs. the concentration of charged amino acyl-tRNA or of amino acid itself, measured in actual or relative units.
Keywords: classic attenuation, transcription regulation, mathematic modeling, web server implementation