The Mechanism of Biochemical NO‐Sensing: Insights from Computational Chemistry

Abstract

The binding of small gas molecules such as NO and CO plays a major role in the signaling routes of the human body. The sole NO-receptor in humans is soluble guanylyl cyclase (sGC) -a histidine-ligated heme protein, which, upon NO binding, activates a downstream signaling cascade. Impairment of NO-signaling is linked, among others, to cardiovascular and inflammatory diseases. In the present work, we use a combination of theoretical tools such as MD simulations, high-level quantum chemical calculations and hybrid QM/MM methods to address various aspects of NO binding and to elucidate the most likely reaction paths and the potential intermediates of the reaction. As a model system, the H-NOX protein from Shewanella oneidensis (So H-NOX) homologous to the NO-binding domain of sGC is used. The signaling route is predicted to involve NO binding to form a six-coordinate intermediate heme-NO complex, followed by relatively facile His decoordination yielding a fivecoordinate adduct with NO on the distal side with possible isomerization to the proximal side through binding of a second NO and release of the first one. MD simulations show that the His sidechain can quite easily rotate outward into solvent, with this motion being accompanied in our simulations by shifts in helix positions that are consistent with this decoordination leading to significant conformational change in the protein.

Gaseous inhibition of the transsulfuration pathway by cystathionine β-synthase

“…There is also some evidence that the NO-bound form involves a proximal NO ligand, i.e., bound on the same side as the departing histidine sidechain. We have previously suggested 33 that this proximal NO state could be formed by reaction of a second NO equivalent with the initially formed penta-coordinate Fe(II)-NO system with a distal NO, to form a transient hexacoordinate NO-Fe(II)-NO system (C ‡ ) that would then lose the first NO to yield the isomeric penta-coordinate NO-Fe(II) (C*) (see Fig. 2).…”