Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 108; no. 13; pp. 5215 - 5220
• Main Authors: Schrader, Jared M, Chapman, Stephen J, Uhlenbeck, Olke C
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 29.03.2011; National Acad Sciences
• Subjects: Amino acids; Bacteria; Bacterial proteins; Base Sequence; Binding sites; Biochemistry; Biological Sciences; Chimeras; codons; crystal structure; E coli; Escherichia coli; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; esterification; Hydrogen bonds; Hydrolysis; Models, Molecular; Molecular Sequence Data; mutants; Mutation; Nucleic Acid Conformation; Peptide Elongation Factor Tu - genetics; Peptide Elongation Factor Tu - metabolism; Peptide elongation factors; Peptides; Protein Binding; Protein Biosynthesis; Protein Conformation; Ribosomes; Ribosomes - metabolism; RNA, Transfer, Amino Acyl - genetics; RNA, Transfer, Amino Acyl - metabolism; Standard error; Thermodynamics; Transfer RNA
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1102128108

To better understand why aminoacyl-tRNAs (aa-tRNAs) have evolved to bind bacterial elongation factor Tu (EF-Tu) with uniform affinities, mutant tRNAs with differing affinities for EF-Tu were assayed for decoding on Escherichia coli ribosomes. At saturating EF-Tu concentrations, weaker-binding aa-tRNAs decode their cognate codons similarly to wild-type tRNAs. However, tighter-binding aa-tRNAs show reduced rates of peptide bond formation due to slow release from EF-Tu•GDP. Thus, the affinities of aa-tRNAs for EF-Tu are constrained to be uniform by their need to bind tightly enough to form the ternary complex but weakly enough to release from EF-Tu during decoding. Consistent with available crystal structures, the identity of the esterified amino acid and three base pairs in the T stem of tRNA combine to define the affinity of each aa-tRNA for EF-Tu, both off and on the ribosome.