Nanomachines in living matters: the soft-robot cytochrome P450

Abstract

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.