Dynamic Characterization of the Human Heme Nitric Oxide/Oxygen (HNOX) Domain under the Influence of Diatomic Gaseous Ligands.

Rana Khalid,Abdul Siddiqi,Arooma Maryam,Efstratios Mylonas,Michael Kokkinidis

doi:10.3390/ijms20030698

Abstract

Soluble guanylate cyclase (sGC) regulates numerous physiological processes. The β subunit Heme Nitric Oxide/Oxygen (HNOX) domain makes this protein sensitive to small gaseous ligands. The structural basis of the activation mechanism of sGC under the influence of ligands (NO, O2, CO) is poorly understood. We examine the effect of different ligands on the human sGC HNOX domain. HNOX systems with gaseous ligands were generated and explored using Molecular Dynamics (MD). The distance between heme Fe2+ and histidine in the NO-ligated HNOX (NO-HNOX) system is larger compared to the O2, CO systems. NO-HNOX rapidly adopts the conformation of the five-group metal coordination system. Loops α, β, γ and helix-f exhibit increased mobility and different hydrogen bond networks in NO-HNOX compared to the other systems. The removal of His from the Fe coordination sphere in NO-HNOX is assisted by interaction of the imidazole ring with the surrounding residues which in turn leads to the release of signaling helix-f and activation of the sGC enzyme. Insights into the conformational dynamics of a human sGC HNOX domain, especially for regions which are functionally critical for signal transduction, are valuable in the understanding of cardiovascular diseases.

Highlights

There are two types of enzymes with guanylyl cyclase activity; membrane-bound particulate guanylate cyclase and cytosolic soluble guanylate cyclase [1]
The results indicate that O2 binding to the Heme Nitric Oxide/Oxygen (HNOX) domain has minor effects on the residual fluctuations, similar to apo-HNOX
Soluble guanylate cyclase is a regulatory protein involved in a multitude of physiological processes in humans such as platelet aggregation, vasodilation, and neurotransmission

Summary

Introduction

There are two types of enzymes with guanylyl cyclase activity; membrane-bound particulate guanylate cyclase (pGC) and cytosolic soluble guanylate cyclase (sGC) [1]. The crystal structure of the bacterial HNOX domain has been resolved, but essential heme binding pocket residues (Y135, S137, and R139, Y-S-R motif) are conserved in the human HNOX [7]. In this domain diatomic gaseous molecules such as NO, CO, and O2 bind with the heme group on the so-called distal site, while on the proximal side a coordinate bond forms between heme and histidine 105 (H105) (6c) [8]. The Fe2+ coordination state of the HNOX heme favors the binding of small gaseous ligands, such as NO, O2, and CO [14].

Homology Modeling

MD Simulations

Hydrogen Bond Occupancy

Conclusions