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.

Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome

“…This is a very well characterized system, for which binding free energies have been previously calculated using the linear interaction energy method (LIE) (Aqvist et al 1994;Almlöf et al 2007) and obtained experimentally (Ogle et al 2002). The largest deviation from experiment in our test calculations was only 0.3 kcal/mol (Table 2), and the rank order of the relative free energy differences agrees with the existing experimental values.…”

“…Furthermore, the hydration pattern around the RNA and antibiotic binding affinities were evaluated. The recent availability of high quality ribosome structures has resulted in a small number of atomistic simulation studies of the peptidyl transfer reaction (Trobro and Aqvist 2005) and of some aspects of codon:anticodon interactions in the decoding center (Sanbonmatsu and Joseph 2003;Sanbonmatsu 2006b;Almlöf et al 2007;Vaiana and Sanbonmatsu 2009), which has also been studied free in solution (Lahiri and Nilsson 2000). Despite the wealth of structural and biochemical/biophysical information available for ribosomes in many states (Ogle and Ramakrishnan 2005;Noller 2006;Agris et al 2007), there are still a number of unresolved issues.…”

“…We use the most exact computational method, free energy perturbation, to achieve this to the accuracy of the interaction model (i.e., the force field). Linear interaction energy calculations on tRNA Phe binding to different codons in the ribosomal decoding center (Almlöf et al 2007) and free energy calculations on the formation (Scheunemann et al 2010) of modified base pairs in RNA double helices in solution (Scheunemann et al 2010) have shown that current force fields and simulation protocols are capable of providing accurate results for this kind of system.…”

“…The system includes the mRNA, tRNA, and the surrounding ribosomal helices and proteins. This size of the system has been shown to model the ribosomal A-site well (Almlöf et al 2007), but we also simulated a larger system in a 34-Å -radius sphere using the 29OH updated CHARMM27d parameters for testing purposes. The spherical systems were solvated with TIP3P water (Jorgensen et al 1983).…”

Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons

“…3a, as they only yield binding free energies relative to UAA. However, by calculating the average MD interaction energies of the UAA codon for the four ribosome complexes with RF1, mtRF1a, mtRF1 and RF2 as done in earlier work on codonanticodon recognition 22 , the absolute binding affinities of the four factors for UAA can be compared. This shows that the affinities in the decoding site are expected to be similar for all four release factors (Fig.…”