title: Energetics of codon-anticodon recognition on the small ribosomal subunit.
abstract: Recent crystal structures of the small ribosomal subunit have made it possible to examine the detailed energetics of codon recognition on the ribosome by computational methods. The binding of cognate and near-cognate anticodon stem loops to the ribosome decoding center, with mRNA containing the Phe UUU and UUC codons, are analyzed here using explicit solvent molecular dynamics simulations together with the linear interaction energy (LIE) method. The calculated binding free energies are in excellent agreement with experimental binding constants and reproduce the relative effects of mismatches in the first and second codon position versus a mismatch at the wobble position. The simulations further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with the Phe UUU codon. It is also found that the ribosome significantly enhances the intrinsic stability differences of codon-anticodon complexes in aqueous solution. Structural analysis of the simulations confirms the previously suggested importance of the universally conserved nucleotides A1492, A1493, and G530 in the decoding process.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
authors.forename: Martin
authors.initials: M
authors.lastname: Almlöf
authors.forename: Martin
authors.initials: M
authors.lastname: Andér
authors.forename: Johan
authors.initials: J
authors.lastname: Aqvist
mesh_terms: D000926:Anticodon / Q000737:chemistry* / Q000378:metabolism; D001483:Base Sequence; D003062:Codon / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012270:Ribosomes / Q000378:metabolism*; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D000926:Anticodon; D003062:Codon