Solution structures of the Shewanella woodyiH‐NOX protein in the presence and absence of soluble guanylyl cyclase stimulator IWP‐051

Abstract

Heme-nitric oxide/oxygen binding (H-NOX) domains bind gaseous ligands for signal transduction in organisms spanning prokaryotic and eukaryotic kingdoms. In the bioluminescent marine bacterium Shewanella woodyi (Sw), H-NOX proteins regulate quorum sensing and biofilm formation. In higher animals, soluble guanylyl cyclase (sGC) binds nitric oxide with an H-NOX domain to induce cyclase activity and regulate vascular tone, wound healing and memory formation. sGC also binds stimulator compounds targeting cardiovascular disease. The molecular details of stimulator binding to sGC remain obscure but involve a binding pocket near an interface between H-NOX and coiled-coil domains. Here, we report the full NMR structure for CO-ligated Sw H-NOX in the presence and absence of stimulator compound IWP-051, and its backbone dynamics. Nonplanar heme geometry was retained using a semiempirical quantum potential energy approach. Although IWP-051 binding is weak, a single binding conformation was found at the interface of the two H-NOX subdomains, near but not overlapping with sites identified in sGC. Binding leads to rotation of the subdomains and closure of the binding pocket. Backbone dynamics are similar across both domains except for two helixconnecting loops, which display increased dynamics that are further enhanced

Backbone and side chain NMR assignment of the heme-nitric oxide/oxygen binding (H-NOX) domain from Nostoc punctiforme

“…As a consequence, the high flexibility of the heme and the Fe(II)-H-NOX coordination state (5-coordination complex), which is also noted to other related bacterial H-NOX domains, may have an effect on peak broadening (beyond detection) due to conformational exchange among the multiple poses adopted by the 5-coordinated heme into its cavity. All the above corroborate with the phenomenon of the large number of missing peaks (Erbil et al, 2009;Alexandropoulos et al, 2016;Makrynitsa et al, 2021;Chen et al, 2021).…”

Revisiting Nitric Oxide Signaling: Where Was It, and Where Is It Going?

“…Montfort and colleagues have studied the binding of a stimulator to bacterial H-NOX domains and related those findings to the YC-1 binding site observed in full length sGC. 42 Bayer continues to develop sGC stimulators with new and diverse structures. Astellas, Cyclerion (spun out of Ironwood), and Merck are also developing sGC stimulators.…”

“…It is reasonable to assume so, but it will have to be proved. Montfort and colleagues have studied the binding of a stimulator to bacterial H-NOX domains and related those findings to the YC-1 binding site observed in full length sGC . Bayer continues to develop sGC stimulators with new and diverse structures.…”