title: Decoding the decoding region: analysis of eukaryotic release factor (eRF1) stop codon-binding residues.
abstract: Peptide synthesis in eukaryotes terminates when eukaryotic release factor 1 (eRF1) binds to an mRNA stop codon and occupies the ribosomal A site. Domain 1 of the eRF1 protein has been implicated in stop codon recognition in a number of experimental studies. In order to further pinpoint the residues of this protein involved in stop codon recognition, we sequenced and compared eRF1 genes from a variety of ciliated protozoan species. We then performed a series of computational analyses to evaluate the conservation, accessibility, and structural environment of each amino acid located in domain 1. With this new dataset and methodology, we were able to identify eight specific amino acid sites important for stop codon recognition and also to propose a set of cooperative paired substitutions that may underlie stop codon reassignment. Our results are more consistent with current experimental data than previously described models.
authors.affiliation: Department of Chemistry, Princeton University, NJ 08544, USA. lfl@princeton.edu
authors.forename: Han
authors.initials: H
authors.lastname: Liang
authors.forename: Jonathan Y
authors.initials: JY
authors.lastname: Wong
authors.forename: Qing
authors.initials: Q
authors.lastname: Bao
authors.forename: Andre R O
authors.initials: AR
authors.lastname: Cavalcanti
authors.forename: Laura F
authors.initials: LF
authors.lastname: Landweber
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016798:Ciliophora / Q000235:genetics*; D016000:Cluster Analysis; D018388:Codon, Terminator / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence / Q000235:genetics; D017931:DNA Primers; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010454:Peptide Termination Factors / Q000235:genetics* / Q000378:metabolism; D017434:Protein Structure, Tertiary / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018388:Codon, Terminator; D017931:DNA Primers; D010454:Peptide Termination Factors