A computational model for reading frame maintenance

Author

Ponnala, L. ; Bitzer, D.L. ; Stomp, A. ; Vouk, M.A.

Author_Institution

Dept. of Electr. & Comput. Eng., North Carolina State Univ., Raleigh, NC

fYear

2006

fDate

Aug. 30 2006-Sept. 3 2006

Firstpage

4540

Lastpage

4543

Abstract

The free energy released during the interaction of the 16S rRNA tail with the mRNA sequence during translation contains a weak sinusoidal pattern of frequency 1/3 cycles/nucleotide. We hypothesize that this signal encodes information related to the maintenance of reading frame during elongation. In the case of the well-studied +1 frameshifter, prfB in E. coli, we have observed a direct relationship between cumulative signal phase and reading frame. Based on this observation, we have developed a model that indicates how likely it is for the ribosome to stay in frame throughout the process of elongation. We validate this model by analyzing verified coding sequences in E. coli

Keywords

cellular biophysics; free energy; genetics; macromolecules; microorganisms; molecular biophysics; organic compounds; E. coli; coding sequences; computational model; cumulative signal phase; elongation process; free energy; mRNA sequence; prfB gene; rRNA tail; reading frame maintenance; ribosome; sinusoidal frequency pattern; translation process; Cities and towns; Computational modeling; Computer science; Peptides; Proteins; Sequences; Signal analysis; Signal synthesis; Tail; USA Councils;

fLanguage

English

Publisher

ieee

Conference_Titel

Engineering in Medicine and Biology Society, 2006. EMBS '06. 28th Annual International Conference of the IEEE

Conference_Location

New York, NY

ISSN

1557-170X

Print_ISBN

1-4244-0032-5

Electronic_ISBN

1557-170X

Type

conf

DOI

10.1109/IEMBS.2006.259717

Filename

4462812