title: Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics.
abstract: The stereospecificity of aminoacyl-tRNA synthetases helps exclude d-amino acids from protein synthesis and could perhaps be engineered to allow controlled d-amino acylation of tRNA. We use molecular dynamics simulations to probe the stereospecificity of the class I tyrosyl- and glutaminyl-tRNA synthetases (TyrRS, GlnRS), including wildtype enzymes and three point mutants suggested by three different protein design methods. l/d binding free energy differences are obtained by alchemically and reversibly transforming the ligand from L to D in simulations of the protein-ligand complex. The D81Q mutation in Escherichia coli TyrRS is homologous to the D81R mutant shown earlier to have inverted stereospecificity. D81Q is predicted to lead to a rotated ligand backbone and an increased, not a decreased l-Tyr preference. The E36Q mutation in Methanococcus jannaschii TyrRS has a predicted l/d binding free energy difference ΔΔG of just 0.5±0.9kcal/mol, compared to 3.1±0.8kcal/mol for the wildtype enzyme (favoring l-Tyr). The ligand ammonium position is preserved in the d-Tyr complex, while the carboxylate is shifted. Wildtype GlnRS has a similar preference for l-glutaminyl adenylate; the R260Q mutant has an increased preference, even though Arg260 makes a large contribution to the wildtype ΔΔG value.
authors.affiliation: Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91128 Palaiseau, France.
authors.forename: Karen
authors.initials: K
authors.lastname: Druart
authors.affiliation: Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91128 Palaiseau, France.
authors.forename: Maeva Le
authors.initials: ML
authors.lastname: Guennec
authors.affiliation: Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91128 Palaiseau, France.
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Palmai
authors.affiliation: Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91128 Palaiseau, France. Electronic address: thomas.simonson@polytechnique.fr.
authors.forename: Thomas
authors.initials: T
authors.lastname: Simonson
mesh_terms: D000249:Adenosine Monophosphate / Q000737:chemistry; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry* / Q000235:genetics; D004926:Escherichia coli / Q000201:enzymology; D063747:Methanocaldococcus / Q000201:enzymology; D056004:Molecular Dynamics Simulation; D017354:Point Mutation; D014176:Protein Biosynthesis / Q000235:genetics*; D015202:Protein Engineering; D014448:Tyrosine-tRNA Ligase / Q000737:chemistry* / Q000235:genetics
chemical_list: D000596:Amino Acids; D000249:Adenosine Monophosphate; D000604:Amino Acyl-tRNA Synthetases; D014448:Tyrosine-tRNA Ligase; C020659:glutaminyl-tRNA synthetase
keywords: Computer simulations; Free energy; Genetic code; Ligand binding; Protein design