Electronic effects on the reaction mechanism of the metalloenzyme peptide deformylase

Abstract

The metalloenzyme peptide deformylase (PDF) plays a crucial role in the biosynthesis of proteins by eubacteria, making the enzyme a promising target for antibacterial agents. In a reaction catalyzed by an Fe(II) coordination complex in the enzyme active site, PDF cleaves a formyl group from the N-terminus of nascent eubacterial proteins. Computational chemistry methods are combined with the use of in silico models of the enzyme chemistry to examine specific effects on the enzymatic catalysis. In particular, density functional theory calculations have been carried out on a biomimetic model system based on a heteroscorpionate N2Sthiolate biomimetic ligand system bearing a range of electron-donating and electron-withdrawing substituents. In this way, the effects of electronic changes to the metal coordination environment on the thermodynamics and kinetics of the deformylation reaction are determined. The reaction was found to be more thermodynamically favorable as the added substituents shifted from electron-withdrawing to electron-donating [or, equivalently, with decreasing Hammett parameters (σp) for the substituents]. As the substituents change from electron-withdrawing to electron-donating, the hydroxide ligand responsible for initiating nucleophilic attack on the carbonyl group of the formyl-terminated peptide substrate is shown to become decreasingly strongly bound to the metal, making the reaction less endergonic. The rate of reaction was found to be fastest for substituents with σp ≈ 0, and progressively slower as the substituents became increasingly electron-donating or electron-withdrawing. At σp ≈ 0, a balance is found between the reactivity of the hydroxide ligand involved in the nucleophilic attack and activation of the carbonyl group by the iron center toward that nucleophilic attack.