Dioxygen (O2) and other gas molecules have a fundamental role in a variety of enzymatic reactions. Yet, it is only poorly understood which diffusion mechanism enzymes employ to promote efficient catalysis and how general this is. We investigated O2 diffusion pathways into monooxygenase and oxidase flavoenzymes using an integrated computational and experimental approach. Enhanced-diffusion molecular dynamics simulations reveal O2 spontaneous diffusion from the bulk solvent to pre-organized protein cavities. The predicted protein-guided diffusion paths and the importance of key cavity residues for oxygen reactivity were verified by combining site-directed mutagenesis, rapid kinetics experiments, and high-resolution X-ray structures. Monooxygenase and oxidase flavoenzymes employ multiple funnel-shaped diffusion pathways to absorb O2 from the solvent and direct it to the reacting C4a atom of the flavin cofactor. The difference among dehydrogenases, monooxygenases, and oxidases ultimately resides in the fine chemical modulation of the local environment embedding the reactive locus of the flavin.
A combined computational and biochemical analysis of oxygen diffusion and reactivity in a flavoprotein monooxygenase and oxidase
Alfieri A.;FORNERIS, FEDERICO;MATTEVI, ANDREA;
2009-01-01
Abstract
Dioxygen (O2) and other gas molecules have a fundamental role in a variety of enzymatic reactions. Yet, it is only poorly understood which diffusion mechanism enzymes employ to promote efficient catalysis and how general this is. We investigated O2 diffusion pathways into monooxygenase and oxidase flavoenzymes using an integrated computational and experimental approach. Enhanced-diffusion molecular dynamics simulations reveal O2 spontaneous diffusion from the bulk solvent to pre-organized protein cavities. The predicted protein-guided diffusion paths and the importance of key cavity residues for oxygen reactivity were verified by combining site-directed mutagenesis, rapid kinetics experiments, and high-resolution X-ray structures. Monooxygenase and oxidase flavoenzymes employ multiple funnel-shaped diffusion pathways to absorb O2 from the solvent and direct it to the reacting C4a atom of the flavin cofactor. The difference among dehydrogenases, monooxygenases, and oxidases ultimately resides in the fine chemical modulation of the local environment embedding the reactive locus of the flavin.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
