1,1,1-Trichloroethane-bound cytochrome P450cam dynamics. Does active site water make a difference?

Abstract

Abstract Cytochrome P450cam is capable of reductively dehalogenating several chlorinated alkanes at slow, but measurable, rates. To gain insight into the dynamic properties of the enzyme having an influence over its reactivity, molecular dynamics (MD) simulations are performed on the complex of wild-type P450cam and 1,1,1-trichloroethane (TCA), a long-lived pollutant. Previous simulations on this complex indicated that, unlike the enzyme complexed with camphor and camphor analogs, the behavior of TCA is sensitive to electrostatic interactions with the heme-Fe cofactor. Using recently developed partial charges for the heme, we conducted two 300 ps MD simulations on TCA-bound P450cam. Since water bound in the enzyme active site is thought to be an important mediator of catalysis, in one simulation three additional water molecules are docked into space left void when the native substrate, camphor, is replaced with TCA. For the majority of configurations sampled, TCA in close proximity to the heme-Fe, suggesting that, if a high degree of spin conversion were achieved, degradation of TCA might proceed at a measurable rate. In the simulation without active site water, TCA samples an alternate binding pocket that opens due to rearrangement of active site residues, leaving room for water to presumably coordinate Fe. This result is consistent with the experimental observation that TCA causes only a minor degree of heme spin conversion. The presence of active site water inhibits these significant dynamic fluctuations in the active site, indicating that including extra water molecules in this binding pocket does not provide information crucial to understanding dynamic properties of the enzymes that influence the behavior of TCA.