title: Polyamines accelerate codon recognition by transfer RNAs on the ribosome.
abstract: The selection of aminoacyl-tRNAs by the ribosome is a fundamental step in the elongation cycle of protein synthesis. tRNA selection is a multistep process that ensures only correct aminoacyl-tRNAs are accepted while incorrect aminoacyl-tRNAs are rejected. A key step in tRNA selection is the formation of base pairs between the anticodon of the aminoacyl-tRNA and the mRNA codon in the A site, called "codon recognition". Here, we report the development of a new, fluorescence-based, kinetic assay for monitoring codon recognition by the ribosome. Using this assay, we show that codon recognition is a second-order binding step under optimal conditions. Additionally, we show that at low Mg(2+) concentrations, the polyamines spermine and spermidine stimulate codon recognition by the ribosome without a loss of fidelity. Polyamines may accelerate codon recognition by altering the structure and dynamics of the anticodon arm of the aminoacyl-tRNA.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314, USA.
authors.forename: Byron
authors.initials: B
authors.lastname: Hetrick
authors.forename: Prashant K
authors.initials: PK
authors.lastname: Khade
authors.forename: Kristin
authors.initials: K
authors.lastname: Lee
authors.forename: Jenise
authors.initials: J
authors.lastname: Stephen
authors.forename: Alex
authors.initials: A
authors.lastname: Thomas
authors.forename: Simpson
authors.initials: S
authors.lastname: Joseph
mesh_terms: D003062:Codon / Q000378:metabolism*; D004926:Escherichia coli / Q000378:metabolism*; D005470:Fluorometry / Q000379:methods*; D006160:Guanosine Triphosphate / Q000378:metabolism; D006868:Hydrolysis; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D011073:Polyamines / Q000378:metabolism*; D012329:RNA, Bacterial / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D003062:Codon; D011073:Polyamines; D012329:RNA, Bacterial; D006160:Guanosine Triphosphate; D012343:RNA, Transfer; D008274:Magnesium