Design of fMet-tRNA and Calculation of its Bonding Properties by Quantum Mechanics

Abstract

It is generally accepted that initiation of protein synthesis in Escherichia coli starts with formyl-methionine, directed by the codons of AUG or GUG. In one case, reinitiating on the mRNA of amber mutants of UUG is used as the initiation codon. Early studies indeed showed that the triplets AUG, GUG, and UUG are the most effective in stimulating fMet-tRNA binding to ribosomes in vitro. We study the bonding properties of fMet-tRNA. The structure was optimized at the Hartree-Fock (HF) level of theory. We performed nonempirical quantum mechanical calculations at the HF and BLYP and B3LYP/3-21G, 6-31G, and 6-31G* levels of theory in the gas phase and water solvent at temperature of 310 K. Finally, we employed the density functional theory (DFT) and HF to calculate nuclear magnetic resonance spectra and infrared spectra.

Keywords:

• Formyl methionine-tRNA (fMet-tRNA)
• Hartree-Fock (HF)
• density functional theory (DFT)