Quantum Molecular Modeling of Glycyl-Adenylate

Abstract

Glycyl-adenylate is the simplest model for understanding the central role played by amino- acyl-adenylates in the protein synthesis, and may be also in the prebiotic evolution. Optimized conformation of glycyl-adenylate (GlyAMP), in vacuum, was determined using ab initio RHF/6–31Gdp computations. GlyAMP in vacuum (form corresponding to neutral pH conditions) possesses a specific conformation of the glycyl-phosphate stem with a double seven membered ring that results from the electrostatic interaction between the anionic phosphate and the cationic ammonium. This structure is explained on the basis of the theoretical infrared vibrational spectrum and discussed with regard to those of glycyl-adenylate (GAP1550 and GAP2550 forms) in the active pockets of glycyl-tRNA synthetase. The electrostatic properties of these different conformations are presented, and the influence of the charged residues (anionic GLU188, GLU239, GLU359, and cationic ARG220) and Mg⁺⁺, in interaction with GAP1550 are discussed, taking into account the computation of the electronic chemical potential, the electron affinity and the electrophilic index.