Energetics of Codon−Anticodon Recognition on the Small Ribosomal Subunit
- 1 January 2007
- journal article
- research article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 46 (1) , 200-209
- https://doi.org/10.1021/bi061713i
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.Keywords
This publication has 14 references indexed in Scilit:
- Binding affinity prediction with different force fields: Examination of the linear interaction energy methodJournal of Computational Chemistry, 2004
- Correlated ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment and in Aqueous Solution. Guanine: Surprising Stabilization of Rare Tautomers in Aqueous SolutionJournal of the American Chemical Society, 2003
- Fidelity of Aminoacyl-tRNA Selection on the Ribosome: Kinetic and Structural MechanismsAnnual Review of Biochemistry, 2001
- Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureJournal of Molecular Biology, 1999
- Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systemsJournal of Molecular Graphics and Modelling, 1998
- Tautomerism and Protonation of Guanine and Cytosine. Implications in the Formation of Hydrogen-Bonded ComplexesJournal of the American Chemical Society, 1996
- An all-atom empirical energy function for the simulation of nucleic acidsJournal of the American Chemical Society, 1995
- A stereospecific mechanism for the aminoacyl‐tRNA selection at the ribosomeFEBS Letters, 1982
- Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanesJournal of Computational Physics, 1977
- The origin of the genetic codeJournal of Molecular Biology, 1968