In Silico Dynamics of Carbon Monoxide in the Active Site Pocket of Nitrogenase

Abstract

The Nitrogenase enzyme system catalyzes the reduction of dinitrogen (N2) to, the more biologically utilizable, ammonia at the site of an unusual [Fe7S9MoC] cofactor named FeMo-co. The mechanism of enzymatic nitrogen fixation remains a mystery due to the transient nature of the reaction intermediates, and many investigators have sought to look at the reversible inhibitor carbon monoxide (CO) as an analogue to the dynamics and kinetics of the natural substrate. Previous work has proposed that a μ2-CO can bind to the Fe-2 and Fe-6 of a 4Fe-4S (Fe-[2,3,6,7]) face of FeMo-co, and dependent on binding conditions, as a terminal ligand. We investigated the ligand-active site dynamics around FeMo-co for CO using the molecular dynamics package GROMACS, for both wild type and key residue mutants. The purpose of investigation was to determine: if the Fe-2 or Fe-6 served as a more sterically accessible binding site for terminal CO, the location of any active site pockets to trap CO near FeMo-co, and to probe the dynamics of the proximal gas channel entrance to the active site. The results of this research can be used to improve the existing model for reversible CO inhibition dynamics of Nitrogenase. Furthermore, these data will lead to new kinetics experiments involving CO and in vitro active site mutagenesis. Finally, our conclusions can be abstracted to provide clues about the short-lived active site behavior of the substrate N2.