Document Detail

RNAmodel web server: modeling classic attenuation in bacteria.
MedLine Citation:
PMID:  18415978     Owner:  NLM     Status:  MEDLINE    
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.
Lev Rubanov; Vassily Lyubetsky
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  In silico biology     Volume:  7     ISSN:  1386-6338     ISO Abbreviation:  In Silico Biol. (Gedrukt)     Publication Date:  2007  
Date Detail:
Created Date:  2008-04-16     Completed Date:  2008-05-21     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9815902     Medline TA:  In Silico Biol     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  285-308     Citation Subset:  IM    
Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Russia.
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MeSH Terms
Bacteria / genetics*
Base Sequence
Computer Simulation
Models, Genetic*
Models, Molecular
Molecular Sequence Data
Nucleic Acid Conformation
RNA, Bacterial / genetics*
RNA, Messenger / chemistry,  genetics
Reg. No./Substance:
0/RNA, Bacterial; 0/RNA, Messenger

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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