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Principles of stop-codon reading on the ribosome
TLDR
Molecular dynamics free-energy calculations on different cognate and non-cognate termination complexes quantitatively explain the basic principles of decoding in all three codon positions and reveal the key elements responsible for specificity of the release factors. Expand
Structure-based energetics of mRNA decoding on the ribosome.
TLDR
It is shown that the tRNA-mRNA interaction energetics varies drastically along the path from initial selection to peptide bond formation, and the distinctly unequal population of the high-selectivity states for cognate and noncognates that is the key discriminatory factor. Expand
Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons.
TLDR
Three-dimensional structural models of humanmtRF1a and mtRF1 based on their homology to bacterial RF1 in the codon recognition domain, and the strong conservation between mitochondrial and bacterial ribosomal RNA in the decoding region are presented. Expand
Binding site preorganization and ligand discrimination in the purine riboswitch.
TLDR
It is found that these receptors have an unusually high degree of electrostatic preorganization for their cognate ligands, and this effect is further quantified by explicit free-energy calculations, which show that the standard electrostatic linear interaction energy parametrization is suboptimal in this case. Expand
Bridging the gap between ribosome structure and biochemistry by mechanistic computations.
TLDR
A range of methodologies including molecular dynamics simulations, free energy calculations, molecular docking and quantum chemical approaches have already been put to work with promising results and can lead towards a quantitative structure-based description of translation. Expand
Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models
TLDR
A new variant of the LIE model, where ligand–metal ion interactions are scaled separately, predicts the saccharide binding preference of PA‐IIL on mutation of the receptor, which may be useful for protein engineering of lectins. Expand
The Use of Low Protein Diets for Turkeys on Range
TLDR
The value of poultry pasture for decreasing feed costs has been reviewed by Heuser, Norris and Bruckner, Kennard (1951) and Payne and Gish (1943), and recent field reports have questioned the value of range in poultry rearing. Expand
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