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

2019 ◽  
Vol 20 (3) ◽  
pp. 698 ◽  
Author(s):  
Rana Khalid ◽  
Abdul Siddiqi ◽  
Efstratios Mylonas ◽  
Arooma Maryam ◽  
Michael Kokkinidis
Keyword(s):  
Nitric Oxide ◽  
Soluble Guanylate Cyclase ◽  
Conformational Dynamics ◽  
Imidazole Ring ◽  
Activation Mechanism ◽  
Structural Basis ◽  
Physiological Processes ◽  
Hydrogen Bond Networks ◽  
Coordination System

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.

scholarly journals Butyl Isocyanide as a Probe of the Activation Mechanism of Soluble Guanylate Cyclase

2007 ◽  
Vol 282 (49) ◽  
pp. 35741-35748 ◽  
Author(s):  
Emily R. Derbyshire ◽  
Michael A. Marletta
Keyword(s):  
Nitric Oxide ◽  
Binding Site ◽  
Guanylate Cyclase ◽  
Electronic Absorption ◽  
Soluble Guanylate Cyclase ◽  
Activation Mechanism ◽  
Activation Process ◽  
Absorbance Maximum ◽  
No Activation ◽  
Allosteric Activator

Nitric oxide (NO) is a physiologically relevant activator of the hemoprotein soluble guanylate cyclase (sGC). In the presence of NO, sGC is activated several hundredfold above the basal level by a mechanism that remains to be elucidated. The heme ligand n-butyl isocyanide (BIC) was used to probe the mechanism of NO activation of sGC. Electronic absorption spectroscopy was used to show that BIC binds to the sGC heme, forming a 6-coordinate complex with an absorbance maximum at 429 nm. BIC activates sGC 2-5-fold, and synergizes with the allosteric activator YC-1, to activate the enzyme 15-25-fold. YC-1 activates the sGC-BIC complex, and leads to an increase in both the Vmax and Km. BIC was also used to probe the mechanism of NO activation. The activity of the sGC-BIC complex increases 15-fold in the presence of NO, without displacing BIC at the heme, which is consistent with previous reports that proposed the involvement of a non-heme NO binding site in the activation process.

Structural characterization of nitric oxide-bound soluble Guanylate Cyclase using resonance Raman spectroscopy

2013 ◽  
Vol 17 (03) ◽  
pp. 240-246
Author(s):  
Biswajit Pal ◽  
Katsuhiro Tanaka ◽  
Shigeo Takenaka ◽  
Tajith B. Shaik ◽  
Teizo Kitagawa
Keyword(s):  
Nitric Oxide ◽  
Raman Spectroscopy ◽  
Guanylate Cyclase ◽  
Protein Interactions ◽  
Bound States ◽  
Soluble Guanylate Cyclase ◽  
Resonance Raman Spectroscopy ◽  
Resonance Raman ◽  
Bending Modes

Mammalian soluble Guanylate Cyclase (sGC), working as a physiological NO receptor, is investigated using resonance Raman spectroscopy for NO bound states with different saturation levels in the presence and absence of effectors. The Fe–NO (νFe–NO) and N–O (νN-O) stretching bands appeared at 521 and 1681 cm-1, respectively, without effectors, but νN-O was split into 1681 and 1699 cm-1 in the presence of GTP and shifted to 1687 cm-1 in the presence of YC-1 or BAY 41-2272, while νFe-NO remained unaltered. The split two νN-O bands were independent of NO saturation levels. GTP or YC-1/BAY 41-2272 altered the vinyl and propionate bending modes from 423 to 399 cm-1 and 376 to 367 cm-1, respectively. Based on these observations, allosteric effects on NO …protein interactions are discussed.

scholarly journals Comparative Studies of the Dynamics Effects of BAY60-2770 and BAY58-2667 Binding with Human and Bacterial H-NOX Domains

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2141 ◽  
Author(s):  
Rana Rehan Khalid ◽  
Muhammad Tahir ul Qamar ◽  
Arooma Maryam ◽  
Ayesha Ashique ◽  
Farooq Anwar ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Soluble Guanylate Cyclase ◽  
Physiological Processes ◽  
Conformational Transformations ◽  
Key Enzyme ◽  
Key Residues ◽  
Critical Regions ◽  
Novel Drug

Soluble guanylate cyclase (sGC) is a key enzyme implicated in various physiological processes such as vasodilation, thrombosis and platelet aggregation. The enzyme’s Heme-Nitric oxide/Oxygen (H-NOX) binding domain is the only sensor of nitric oxide (NO) in humans, which on binding with NO activates sGC to produce the second messenger cGMP. H-NOX is thus a hot target for drug design programs. BAY60-2770 and BAY58-2667 are two widely studied activators of sGC. Here we present comparative molecular dynamics studies to understand the molecular details characterizing the binding of BAY60-2770 and BAY58-2667 with the human H-NOX (hH-NOX) and bacterial H-NOX (bH-NOX) domains. HartreeFock method was used for parametrization of both the activators. A 50 ns molecular dynamics (MD) simulation was run to identify the functionally critical regions of the H-NOX domains. The CPPTRAJ module was used for analysis. BAY60-2770 on binding with bH-NOX, triggered rotational movement in signaling helix F and significant dynamicity in loops α and β, but in hH-NOX domain the compound showed relatively lesser aforementioned structural fluctuations. Conversely, hH-NOX ligated BAY58-2667 experienced highest transitions in its helix F due to electrostatic interactions with D84, T85 and R88 residues which are not conserved in bH-NOX. These conformational transformations might be essential to communicate with downstream PAS, CC and cyclase domains of sGC. Comparative MD studies revealed that BAY bound bHNOX dynamics varied from that of hH-NOX, plausibly due to some key residues such as R40, F74 and Y112 which are not conserved in bacteria. These findings will help to the design of novel drug leads to cure diseases associated to human sGC.

scholarly journals Conformational Characterization of the Co-Activator Binding Site Revealed the Mechanism to Achieve the Bioactive State of FXR

2021 ◽  
Vol 8 ◽  
Author(s):  
Anita Kumari ◽  
Lovika Mittal ◽  
Mitul Srivastava ◽  
Dharam Pal Pathak ◽  
Shailendra Asthana
Keyword(s):  
Conformational Changes ◽  
Rational Design ◽  
Conformational Dynamics ◽  
Activation Mechanism ◽  
Activation Process ◽  
Bioactive Conformation ◽  
Structural Determinants ◽  
Critical Residue ◽  
Molecular Bonding

FXR bioactive states are responsible for the regulation of metabolic pathways, which are modulated by agonists and co-activators. The synergy between agonist binding and ‘co-activator’ recruitment is highly conformationally driven. The characterization of conformational dynamics is essential for mechanistic and therapeutic understanding. To shed light on the conformational ensembles, dynamics, and structural determinants that govern the activation process of FXR, molecular dynamic (MD) simulation is employed. Atomic insights into the ligand binding domain (LBD) of FXR revealed significant differences in inter/intra molecular bonding patterns, leading to structural anomalies in different systems of FXR. The sole presence of an agonist or ‘co-activator’ fails to achieve the essential bioactive conformation of FXR. However, the presence of both establishes the bioactive conformation of FXR as they modulate the internal wiring of key residues that coordinate allosteric structural transitions and their activity. We provide a precise description of critical residue positioning during conformational changes that elucidate the synergy between its binding partners to achieve an FXR activation state. Our study offers insights into the associated modulation occurring in FXR at bound and unbound forms. Thereafter, we also identified hot-spots that are critical to arrest the activation mechanism of FXR that would be helpful for the rational design of its agonists.

scholarly journals Characterization of a novel monoclonal antibody that senses nitric oxide-dependent activation of soluble guanylate cyclase

FEBS Letters ◽  
1999 ◽  
Vol 455 (3) ◽  
pp. 291-294 ◽  
Author(s):  
Shingo Tsuyama ◽  
Eri Yamazaki ◽  
Takeshi Tomita ◽  
Hideshi Ihara ◽  
Shigeo Takenaka ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Monoclonal Antibody ◽  
Guanylate Cyclase ◽  
Soluble Guanylate Cyclase

Soluble Guanylate Cyclase Stimulators and Activators: Where are We and Where to Go?

2019 ◽  
Vol 19 (18) ◽  
pp. 1544-1557 ◽  
Author(s):  
Sijia Xiao ◽  
Qianbin Li ◽  
Liqing Hu ◽  
Zutao Yu ◽  
Jie Yang ◽  
...  
Keyword(s):  
Guanylate Cyclase ◽  
Soluble Guanylate Cyclase ◽  
Muscle Relaxation ◽  
Cyclic Guanosine Monophosphate ◽  
Guanosine Monophosphate ◽  
Smooth Muscle Relaxation ◽  
Secondary Messenger ◽  
Physiological Processes ◽  
Cgmp Pathway ◽  
Preclinical And Clinical Studies

Soluble Guanylate Cyclase (sGC) is the intracellular receptor of Nitric Oxide (NO). The activation of sGC results in the conversion of Guanosine Triphosphate (GTP) to the secondary messenger cyclic Guanosine Monophosphate (cGMP). cGMP modulates a series of downstream cascades through activating a variety of effectors, such as Phosphodiesterase (PDE), Protein Kinase G (PKG) and Cyclic Nucleotide-Gated Ion Channels (CNG). NO-sGC-cGMP pathway plays significant roles in various physiological processes, including platelet aggregation, smooth muscle relaxation and neurotransmitter delivery. With the approval of an sGC stimulator Riociguat for the treatment of Pulmonary Arterial Hypertension (PAH), the enthusiasm in the discovery of sGC modulators continues for broad clinical applications. Notably, through activating the NO-sGC-cGMP pathway, sGC stimulator and activator potentiate for the treatment of various diseases, such as PAH, Heart Failure (HF), Diabetic Nephropathy (DN), Systemic Sclerosis (SS), fibrosis as well as other diseases including Sickle Cell Disease (SCD) and Central Nervous System (CNS) disease. Here, we review the preclinical and clinical studies of sGC stimulator and activator in recent years and prospect for the development of sGC modulators in the near future.

scholarly journals Glucocorticoid resistance conferring mutation in the C-terminus of GR alters the receptor conformational dynamics

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anna Kaziales ◽  
Florian Rührnößl ◽  
Klaus Richter
Keyword(s):  
Glucocorticoid Receptor ◽  
Steroid Hormones ◽  
In Silico ◽  
Conformational Dynamics ◽  
Glucocorticoid Resistance ◽  
Physiological Processes ◽  
C Terminus ◽  
Hsp90 Chaperone ◽  
In Silico Methods

AbstractThe glucocorticoid receptor is a key regulator of essential physiological processes, which under the control of the Hsp90 chaperone machinery, binds to steroid hormones and steroid-like molecules and in a rather complicated and elusive response, regulates a set of glucocorticoid responsive genes. We here examine a human glucocorticoid receptor variant, harboring a point mutation in the last C-terminal residues, L773P, that was associated to Primary Generalized Glucocorticoid Resistance, a condition originating from decreased affinity to hormone, impairing one or multiple aspects of GR action. Using in vitro and in silico methods, we assign the conformational consequences of this mutation to particular GR elements and report on the altered receptor properties regarding its binding to dexamethasone, a NCOA-2 coactivator-derived peptide, DNA, and importantly, its interaction with the chaperone machinery of Hsp90.

Nitric oxide preconditioning regulates endothelial monolayer integrity via the heat shock protein 90-soluble guanylate cyclase pathway

2007 ◽  
Vol 292 (2) ◽  
pp. H893-H903 ◽  
Author(s):  
Galina N. Antonova ◽  
Connie M. Snead ◽  
Alexander S. Antonov ◽  
Christiana Dimitropoulou ◽  
Richard C. Venema ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Endothelial Cells ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Cell Injury ◽  
Soluble Guanylate Cyclase ◽  
Heat Shock Protein 90 ◽  
Protective Effects ◽  
No Donor ◽  
Spermine Nonoate

Large (pathological) amounts of nitric oxide (NO) induce cell injury, whereas low (physiological) NO concentrations often ameliorate cell injury. We tested the hypotheses that pretreatment of endothelial cells with low concentrations of NO (preconditioning) would prevent injury induced by high NO concentrations. Apoptosis, induced in bovine aortic endothelial cells (BAECs) by exposing them to either 4 mM sodium nitroprusside (SNP) or 0.5 mM N-(2-aminoethyl)- N-(2-hydroxy-2-nitrosohydrazino)-1,2-ethylenediamine (spermine NONOate) for 8 h, was abolished by 24-h pretreatment with either 100 μM SNP, 10 μM spermine NONOate, or 100 μM 8-bromo-cGMP (8-Br-cGMP). Repair of BAECs following wounding, measured as the recovery rate of transendothelial electrical resistance, was delayed by 8-h exposure to 4 mM SNP, and this delay was significantly attenuated by 24-h pretreatment with 100 μM SNP. NO preconditioning produced increased association and expression of soluble guanyl cyclase (sGC) and heat shock protein 90 (HSP90). The protective effect of NO preconditioning, but not the injurious effect of 4 mM SNP, was abolished by either a sGC activity inhibitor 1H-[1,2,4]oxadiazolo-[4,3- a]quinoxalin-1-one (ODQ) or a HSP90 binding inhibitor (radicicol) and was mimicked by 8-Br-cGMP. We conclude that preconditioning with a low dose of NO donor accelerates repair and maintains endothelial integrity via a mechanism that includes the HSP90/sGC pathway. HSP90/sGC may thus play a role in the protective effects of NO-generating drugs from injurious stimuli.

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