Nanomachines in living matters: the soft-robot cytochrome P450

This story emerges from molecular dynamics simulations of cytochrome P450 (CYP450s) enzymes, which are nanomachines of ‘living matters’. The simulations project CYP450s as 3D materials that possess a fourth dimension: the ability to sense and respond to stimuli. The stimulus is the binding of a substrate molecule that eventually undergoes oxidation in a catalytic cycle. Due to the tight space within the protein, the enzyme senses the substrate and functions as a soft-robot that interacts with the substrate using soft-impact modes of weak interactions. These modes transfer kinetic energy that elicits movements of protein parts and of molecules it contains (water, O₂, etc.). These molecules enter/leave the enzymes’ cavity and finally generate the oxoiron species that oxidize a great variety of substrates.