The Ab initio Study and NBO Analysis of the Solvent Dielectric Constant Effects on the Structural Stability of the fMet-tRNA
By M. Noei, H.Mossalayi, H.Aghaee, F.Naderi, F.Mollaamin
Formyl-methionine is always the first amino acid of polypeptide chain in prokaryote systems, although frequently it is removed after translation .In this case we studied about amino acid linkage to the proper tRNA which this process is controlled by the amino-acyl-tRNA synthesis. Theoretical study of binding the amino acid (formyl-methionine) to tRNA has been performed using quantum computational Ab initio HF and density functional B3LYP method using 3-21G(d,p) basis set in the different solvents to calculate structural optimization and the major stabilizing orbital for the bond (fMet-tRNA ) were calculated by natural bond orbital(NBO) methodology. By NBO analysis we observed an effective interaction between the O32 lone pair(LP)and sigma anti bonding orbital (σ *)of O29-C30.This suggests an electronic transference from oxygen LP to anti bonding orbital(hyper conjugation effect) . Finally, we employed the density functional theory (DFT) and Hartree-Fock (HF) to calculated NMR parameters.
Keyword: Natural bond orbital(NBO), fMet-tRNA ,Hartree-fock(HF),Density functional theory(DFT), amino-acyl-tRNA