Title :
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
fDate :
Aug. 30 2006-Sept. 3 2006
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;
Conference_Titel :
Engineering in Medicine and Biology Society, 2006. EMBS '06. 28th Annual International Conference of the IEEE
Conference_Location :
New York, NY
Print_ISBN :
1-4244-0032-5
Electronic_ISBN :
1557-170X
DOI :
10.1109/IEMBS.2006.259717
