title: A computational model for reading frame maintenance.
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.
authors.affiliation: Dept. of Electr. & Comput. Eng., North Carolina State Univ., Raleigh, NC 27695, USA.
authors.forename: L
authors.initials: L
authors.lastname: Ponnala
authors.forename: D L
authors.initials: DL
authors.lastname: Bitzer
authors.forename: A
authors.initials: A
authors.lastname: Stomp
authors.forename: M A
authors.initials: MA
authors.lastname: Vouk
mesh_terms: D000465:Algorithms; D003062:Codon; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism / Q000502:physiology*; D016368:Frameshift Mutation; D008957:Models, Genetic; D015233:Models, Statistical; D008962:Models, Theoretical; D009693:Nucleic Acid Hybridization; D016366:Open Reading Frames; D010454:Peptide Termination Factors / Q000378:metabolism / Q000502:physiology*; D012333:RNA, Messenger / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000737:chemistry*; D012270:Ribosomes / Q000235:genetics / Q000502:physiology*; D012815:Signal Processing, Computer-Assisted; D012984:Software
chemical_list: D003062:Codon; D029968:Escherichia coli Proteins; D010454:Peptide Termination Factors; D012333:RNA, Messenger; D012336:RNA, Ribosomal, 16S; C489006:prfB protein, E coli