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1.
J Mol Biol ; 436(3): 168235, 2024 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-37572934

RESUMO

Nitric oxide (NO) regulates large swaths of animal physiology including wound healing, vasodilation, memory formation, odor detection, sexual function, and response to infectious disease. The primary NO receptor is soluble guanyly/guanylate cyclase (sGC), a dimeric protein of ∼150 kDa that detects NO through a ferrous heme, leading to a large change in conformation and enhanced production of cGMP from GTP. In humans, loss of sGC function contributes to multiple disease states, including cardiovascular disease and cancer, and is the target of a new class of drugs, sGC stimulators, now in clinical use. sGC evolved through the fusion of four ancient domains, a heme nitric oxide / oxygen (H-NOX) domain, a Per-ARNT-Sim (PAS) domain, a coiled coil, and a cyclase domain, with catalysis occurring at the interface of the two cyclase domains. In animals, the predominant dimer is the α1ß1 heterodimer, with the α1 subunit formed through gene duplication of the ß1 subunit. The PAS domain provides an extensive dimer interface that remains unchanged during sGC activation, acting as a core anchor. A large cleft formed at the PAS-PAS dimer interface tightly binds the N-terminal end of the coiled coil, keeping this region intact and unchanged while the rest of the coiled coil repacks, and the other domains reposition. This interface buries ∼3000 Å2 of monomer surface and includes highly conserved apolar and hydrogen bonding residues. Herein, we discuss the evolutionary history of sGC, describe the role of PAS domains in sGC function, and explore the regulatory factors affecting sGC function.


Assuntos
Translocador Nuclear Receptor Aril Hidrocarboneto , Óxido Nítrico , Guanilil Ciclase Solúvel , Animais , Humanos , Translocador Nuclear Receptor Aril Hidrocarboneto/química , Heme/metabolismo , Óxido Nítrico/metabolismo , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/genética , Transdução de Sinais , Domínios Proteicos
2.
Biomol NMR Assign ; 16(2): 379-384, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36066818

RESUMO

Soluble guanylate cyclase (sGC) is considered as the primary NO receptor across several known eukaryotes. The main interest regarding the biological role and its function, focuses on the H-NOX domain of the ß1 subunit. This domain in its active form bears a ferrous b type heme as prosthetic group, which facilitates the binding of NO and other diatomic gases. The key point that still needs to be answered is how the protein selectively binds the NO and how the redox state of heme and coordination determines H-NOX active state upon binding of diatomic gases. H-NOX domain is present in the genomes of both prokaryotes and eukaryotes, either as a stand-alone protein domain or as a partner of a larger polypeptide. The biological functions of these signaling modules for a wide range of genomes, diverge considerably along with their ligand binding properties. In this direction, we examine the prokaryotic H-NOX protein domain from Nostoc punctiforme (Npun H-NOX). Herein, we first report the almost complete NMR backbone and side-chain resonance assignment (1H, 13C, 15 N) of Npun H-NOX domain together with the NMR chemical shift-based prediction of the domain's secondary structure elements.


Assuntos
Nostoc , Guanilato Ciclase/química , Guanilato Ciclase/metabolismo , Heme/química , Ligantes , Óxido Nítrico/metabolismo , Ressonância Magnética Nuclear Biomolecular , Oxigênio/metabolismo , Receptores Citoplasmáticos e Nucleares , Guanilil Ciclase Solúvel/química
3.
Chemistry ; 28(49): e202200930, 2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-35670519

RESUMO

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 five-coordinate 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.


Assuntos
Química Computacional , Hemeproteínas , Heme/química , Hemeproteínas/química , Humanos , Óxido Nítrico/química , Ligação Proteica , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/metabolismo
4.
J Inorg Biochem ; 228: 111666, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-34923187

RESUMO

This study aimed to investigate the synthesis and potential vasodilator effect of a novel ruthenium complex, cis-[Ru(bpy)2(2-MIM)(NO2)]PF6 (bpy = 2,2'-bipyridine and 2-MIM = 2-methylimidazole) (FOR711A), containing an imidazole derivative via an in silico molecular docking model using ß1 H-NOX (Heme-nitric oxide/oxygen binding) domain proteins of reduced and oxidized soluble guanylate cyclase (sGC). In addition, pharmacokinetic properties in the human organism were predicted through computational simulations and the potential for acute irritation of FOR711A was also investigated in vitro using the hen's egg chorioallantoic membrane (HET-CAM). FOR711A interacted with sites of the ß1 H-NOX domain of reduced and oxidized sGC, demonstrating shorter bond distances to several residues and negative values of total energy. The predictive study revealed molar refractivity (RM): 127.65; Log Po/w = 1.29; topological polar surface area (TPSA): 86.26 Å2; molar mass (MM) = 541.55 g/mol; low solubility, high unsaturation index, high gastrointestinal absorption; toxicity class 4; failure to cross the blood-brain barrier and to react with cytochrome P450 (CYP) enzymes CYP1A2, CYP2C19, CYP2C9, CYP2D6 and CYP3A4. After the HET-CAM assay, the FOR711A complex was classified as non-irritant (N.I.) and its vasodilator effect was confirmed through greater evidence of blood vessels after the administration and ending of the observation period of 5 min. These results suggest that FOR711A presented a potential stimulator/activator effect of sGC via NO/sGC/cGMP. However, results indicate it needs a vehicle for oral administration.


Assuntos
Complexos de Coordenação/química , Óxido Nítrico/química , Rutênio/química , Vasodilatadores/química , Vasodilatadores/farmacologia , Animais , Galinhas , Membrana Corioalantoide/metabolismo , Heme/química , Humanos , Imidazóis/química , Simulação de Acoplamento Molecular/métodos , Óxido Nítrico/metabolismo , Oxigênio/química , Domínios Proteicos , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/metabolismo
5.
J Biomol Struct Dyn ; 40(13): 6128-6150, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-33522438

RESUMO

Modulating the activity of human soluble guanylate cyclase (hsGC) through allosteric regulation of the ßH-NOX domain has been considered as an immediate treatment for cardiovascular disorder (CVDs). Currently available ßH-NOX domain-specific agonists including cinaciguat are unable to deal with the conundrum raised due to oxidative stress in the case of CVDs and their associated comorbidities. Therefore, the idea of investigating novel compounds for allosteric regulation of hsGC activation has been rekindled to circumvent CVDs. Current study aims to identify novel ßH-NOX domain-specific compounds that can selectively turn on sGC functions by modulating the conformational dynamics of the target protein. Through a comprehensive computational drug-discovery approach, we first executed a target-based performance assessment of multiple docking (PLANTS, QVina, LeDock, Vinardo, Smina) scoring functions based on multiple performance metrices. QVina showed the highest capability of selecting true-positive ligands over false positives thus, used to screen 4.8 million ZINC15 compounds against ßH-NOX domain. The docked ligands were further probed in terms of contact footprint and pose reassessment through clustering analysis and PLANTS docking, respectively. Subsequently, energy-based AMBER rescoring of top 100 low-energy complexes, per-residue energy decomposition analysis, and ADME-Tox analysis yielded the top three compounds i.e. ZINC000098973660, ZINC001354120371, and ZINC000096022607. The impact of three selected ligands on the internal structural dynamics of the ßH-NOX domain was also investigated through molecular dynamics simulations. The study revealed potential electrostatic interactions for better conformational dialogue between ßH-NOX domain and allosteric ligands that are critical for the activation of hsGC as compared to the reference compound.


Assuntos
Doenças Cardiovasculares , Simulação de Dinâmica Molecular , NADPH Oxidases , Guanilil Ciclase Solúvel , Doenças Cardiovasculares/tratamento farmacológico , Humanos , Ligantes , Simulação de Acoplamento Molecular , NADPH Oxidases/química , Ligação Proteica , Guanilil Ciclase Solúvel/química
6.
Nat Commun ; 12(1): 5492, 2021 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-34535643

RESUMO

Soluble guanylate cyclase (sGC) is the receptor for nitric oxide (NO) in human. It is an important validated drug target for cardiovascular diseases. sGC can be pharmacologically activated by stimulators and activators. However, the detailed structural mechanisms, through which sGC is recognized and positively modulated by these drugs at high spacial resolution, are poorly understood. Here, we present cryo-electron microscopy structures of human sGC in complex with NO and sGC stimulators, YC-1 and riociguat, and also in complex with the activator cinaciguat. These structures uncover the molecular details of how stimulators interact with residues from both ß H-NOX and CC domains, to stabilize sGC in the extended active conformation. In contrast, cinaciguat occupies the haem pocket in the ß H-NOX domain and sGC shows both inactive and active conformations. These structures suggest a converged mechanism of sGC activation by pharmacological compounds.


Assuntos
Ativadores de Enzimas/farmacologia , Guanilil Ciclase Solúvel/metabolismo , Animais , Benzoatos/química , Benzoatos/farmacologia , Sítios de Ligação , Linhagem Celular , Microscopia Crioeletrônica , Ativação Enzimática/efeitos dos fármacos , Ativadores de Enzimas/química , Humanos , Indazóis/química , Indazóis/farmacologia , Modelos Moleculares , Óxido Nítrico/farmacologia , Multimerização Proteica , Pirazóis/química , Pirazóis/farmacologia , Pirimidinas/química , Pirimidinas/farmacologia , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/ultraestrutura
7.
J Med Chem ; 64(9): 5323-5344, 2021 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-33872507

RESUMO

Herein we describe the discovery, mode of action, and preclinical characterization of the soluble guanylate cyclase (sGC) activator runcaciguat. The sGC enzyme, via the formation of cyclic guanosine monophoshphate, is a key regulator of body and tissue homeostasis. sGC activators with their unique mode of action are activating the oxidized and heme-free and therefore NO-unresponsive form of sGC, which is formed under oxidative stress. The first generation of sGC activators like cinaciguat or ataciguat exhibited limitations and were discontinued. We overcame limitations of first-generation sGC activators and identified a new chemical class via high-throughput screening. The investigation of the structure-activity relationship allowed to improve potency and multiple solubility, permeability, metabolism, and drug-drug interactions parameters. This program resulted in the discovery of the oral sGC activator runcaciguat (compound 45, BAY 1101042). Runcaciguat is currently investigated in clinical phase 2 studies for the treatment of patients with chronic kidney disease and nonproliferative diabetic retinopathy.


Assuntos
Desenho de Fármacos , Ativadores de Enzimas/química , Guanilil Ciclase Solúvel/química , Animais , Sítios de Ligação , Cristalografia por Raios X , Citocromo P-450 CYP3A/química , Citocromo P-450 CYP3A/metabolismo , Cães , Ativadores de Enzimas/metabolismo , Ativadores de Enzimas/farmacologia , Ativadores de Enzimas/uso terapêutico , Meia-Vida , Frequência Cardíaca/efeitos dos fármacos , Hemodinâmica/efeitos dos fármacos , Hipertensão/tratamento farmacológico , Hipertensão/patologia , Simulação de Dinâmica Molecular , Ratos , Ratos Endogâmicos SHR , Solubilidade , Guanilil Ciclase Solúvel/metabolismo , Relação Estrutura-Atividade
8.
J Inorg Biochem ; 214: 111267, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33099233

RESUMO

Nitric oxide (NO), carbon monoxide (CO), and oxygen (O2) are important physiological messengers whose concentrations vary in a remarkable range, [NO] typically from nM to several µM while [O2] reaching to hundreds of µM. One of the machineries evolved in living organisms for gas sensing is sensor hemoproteins whose conformational change upon gas binding triggers downstream response cascades. The recently proposed "sliding scale rule" hypothesis provides a general interpretation for gaseous ligand selectivity of hemoproteins, identifying five factors that govern gaseous ligand selectivity. Hemoproteins have intrinsic selectivity for the three gases due to a neutral proximal histidine ligand while proximal strain of heme and distal steric hindrance indiscriminately adjust the affinity of these three gases for heme. On the other hand, multiple-step NO binding and distal hydrogen bond donor(s) specifically enhance affinity for NO and O2, respectively. The "sliding scale rule" hypothesis provides clear interpretation for dramatic selectivity for NO over O2 in soluble guanylate cyclase (sGC) which is an important example of sensor hemoproteins and plays vital roles in a wide range of physiological functions. The "sliding scale rule" hypothesis has so far been validated by all experimental data and it may guide future designs for heme-based gas sensors.


Assuntos
Monóxido de Carbono/metabolismo , Hemeproteínas/metabolismo , Óxido Nítrico/metabolismo , Oxigênio/metabolismo , Guanilil Ciclase Solúvel/metabolismo , Monóxido de Carbono/química , Hemeproteínas/química , Óxido Nítrico/química , Oxigênio/química , Guanilil Ciclase Solúvel/química
9.
Eur J Pharmacol ; 881: 173203, 2020 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-32446711

RESUMO

Soluble guanylyl cyclase (sGC), the major receptor for nitric oxide (NO), is a heterodimer consisting of two subunits, the α and the ß subunit. The NO/sGC/cGMP signaling pathway is protective in different disease pathomechanisms including angina pectoris, pulmonary hypertension and fibrotic diseases. The natural ligand heme has two carboxylic acids which interact in the ß1 heme nitric oxide oxygen binding (HNOX) domain with the amino acids of the highly conserved Y-x-S-x-R motif. The Y-x-S-x-R motif is also involved in binding of the dicarboxylic activators cinaciguat and BAY 60-2770 as indicated by crystallization studies of sGC activator and bacterial HNOX homologs. To what extent the Y-x-S-x-R motif hydrogen bond network contributes to binding of monocarboxylic acids has not been examined so far. In the current paper, the chemical structural formula of the novel monocarboxylic drug BAY-543 is described for the first time. Using this novel drug, we evaluate the importance of the amino acids Y135 and R139 for thermostabilization and activation in comparison to the dicarboxylic acid BAY 60-2770. Measurements with point mutated sGC variants demonstrate tyrosine 135 as exclusive binding site of the monocarboxylic acid BAY-543 but not the dicarboxylic BAY 60-2770.


Assuntos
Ativadores de Enzimas/farmacologia , Guanilil Ciclase Solúvel/metabolismo , Motivos de Aminoácidos , Animais , Benzoatos/metabolismo , Benzoatos/farmacologia , Sítios de Ligação , Compostos de Bifenilo/metabolismo , Compostos de Bifenilo/farmacologia , Ativação Enzimática , Ativadores de Enzimas/química , Ativadores de Enzimas/metabolismo , Células HEK293 , Humanos , Hidrocarbonetos Fluorados/metabolismo , Hidrocarbonetos Fluorados/farmacologia , Óxido Nítrico/metabolismo , Óxido Nítrico/farmacologia , Mutação Puntual , Ligação Proteica , Conformação Proteica , Subunidades Proteicas , Células Sf9 , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/genética , Relação Estrutura-Atividade , Tirosina
10.
J Pharm Biomed Anal ; 181: 113065, 2020 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-32032919

RESUMO

Thermal shift assay is a fluorescence dye based biochemical method to determine the melting point of a protein. It can be used to investigate the ligand-induced stabilization of proteins and helps to increase the likelihood of crystallization in biological samples. Dimeric proteins like soluble guanylyl cyclase (sGC) have specific structural and functional properties which may pose a challenge in thermal shift measurements. In this paper, thermal shift assay was used to examine ligand-induced thermostabilization of the dimeric heme-containing protein soluble guanylyl cyclase. Adjustment of the parameters buffer solution, pH, protein / dye ratio and protein amount per well yielded a one-phase melting curve of sGC with a sharp transition and high reproducibility. We found that thermal shift measurement is not affected by heme state or heme content of the enzyme preparation. We used the method to investigate the thermostabilization of sGC induced by the heme-mimetic activator drugs cinaciguat, BAY 60-2770 and BR 11257 in combination with non-hydrolyzable nucleotides. Measurements with the dicarboxylic drugs cinaciguat and BAY 60-2770 yielded steep melting curves with high amplitudes. In contrast, in the presence of the monocarboxylic sGC activator BR 11257, melting curves appear flattened in the dye-based measurements. In the present paper, we show that activity-based thermostability measurements are superior to dye-based measurements in detecting the thermostabilizing influence of sGC activator drugs.


Assuntos
Análise Diferencial Térmica/métodos , Estabilidade Enzimática/efeitos dos fármacos , Guanilil Ciclase Solúvel/química , Benzoatos/farmacologia , Compostos de Bifenilo/farmacologia , Hidrocarbonetos Fluorados/farmacologia , Ligantes , Nucleotídeos/farmacologia , Temperatura de Transição
11.
J Biol Chem ; 294(48): 18451-18464, 2019 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-31645439

RESUMO

Soluble guanylyl cyclase (sGC) is the main receptor for nitric oxide (NO) and a central component of the NO-cGMP pathway, critical to cardiovascular function. NO binding to the N-terminal sensor domain in sGC enhances the cyclase activity of the C-terminal catalytic domain. Our understanding of the structural elements regulating this signaling cascade is limited, hindering structure-based drug design efforts that target sGC to improve the management of cardiovascular diseases. Conformational changes are thought to propagate the NO-binding signal throughout the entire sGC heterodimer, via its coiled-coil domain, to reorient the catalytic domain into an active conformation. To identify the structural elements involved in this signal transduction cascade, here we optimized a cGMP-based luciferase assay that reports on heterologous sGC activity in Escherichia coli and identified several mutations that activate sGC. These mutations resided in the dorsal flaps, dimer interface, and GTP-binding regions of the catalytic domain. Combinations of mutations from these different elements synergized, resulting in even greater activity and indicating a complex cross-talk among these regions. Molecular dynamics simulations further revealed conformational changes underlying the functional impact of these mutations. We propose that the interfacial residues play a central role in the sGC activation mechanism by coupling the coiled-coil domain to the active site via a series of hot spots. Our results provide new mechanistic insights not only into the molecular pathway for sGC activation but also for other members of the larger nucleotidyl cyclase family.


Assuntos
GMP Cíclico/metabolismo , Simulação de Dinâmica Molecular , Mutação , Óxido Nítrico/metabolismo , Guanilil Ciclase Solúvel/genética , Sequência de Aminoácidos , Animais , Domínio Catalítico , GMP Cíclico/química , Ativação Enzimática/genética , Humanos , Cinética , Óxido Nítrico/química , Ligação Proteica , Conformação Proteica , Multimerização Proteica , Subunidades Proteicas/química , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Homologia de Sequência de Aminoácidos , Transdução de Sinais , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/metabolismo
12.
Nature ; 574(7777): 206-210, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31514202

RESUMO

Soluble guanylate cyclase (sGC) is the primary sensor of nitric oxide. It has a central role in nitric oxide signalling and has been implicated in many essential physiological processes and disease conditions. The binding of nitric oxide boosts the enzymatic activity of sGC. However, the mechanism by which nitric oxide activates the enzyme is unclear. Here we report the cryo-electron microscopy structures of the human sGCα1ß1 heterodimer in different functional states. These structures revealed that the transducer module bridges the nitric oxide sensor module and the catalytic module. Binding of nitric oxide to the ß1 haem-nitric oxide and oxygen binding (H-NOX) domain triggers the structural rearrangement of the sensor module and a conformational switch of the transducer module from bending to straightening. The resulting movement of the N termini of the catalytic domains drives structural changes within the catalytic module, which in turn boost the enzymatic activity of sGC.


Assuntos
Microscopia Crioeletrônica , Guanilil Ciclase Solúvel/metabolismo , Guanilil Ciclase Solúvel/ultraestrutura , Animais , Dissulfetos/química , Dissulfetos/metabolismo , Drosophila melanogaster , Ativação Enzimática , Células HEK293 , Heme/metabolismo , Humanos , Hidrazinas/farmacologia , Camundongos , Modelos Moleculares , Óxido Nítrico/metabolismo , Doadores de Óxido Nítrico/metabolismo , Oxigênio/metabolismo , Domínios Proteicos , Multimerização Proteica , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/genética
13.
Protein Sci ; 28(10): 1830-1839, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31411784

RESUMO

How nitric oxide (NO) activates its primary receptor, α1/ß1 soluble guanylyl cyclase (sGC or GC-1), remains unknown. Likewise, how stimulatory compounds enhance sGC activity is poorly understood, hampering development of new treatments for cardiovascular disease. NO binding to ferrous heme near the N-terminus in sGC activates cyclase activity near the C-terminus, yielding cGMP production and physiological response. CO binding can also stimulate sGC, but only weakly in the absence of stimulatory small-molecule compounds, which together lead to full activation. How ligand binding enhances catalysis, however, has yet to be discovered. Here, using a truncated version of sGC from Manduca sexta, we demonstrate that the central coiled-coil domain, the most highly conserved region of the ~150,000 Da protein, not only provides stability to the heterodimer but is also conformationally active in signal transduction. Sequence conservation in the coiled coil includes the expected heptad-repeating pattern for coiled-coil motifs, but also invariant positions that disfavor coiled-coil stability. Full-length coiled coil dampens CO affinity for heme, while shortening of the coiled coil leads to enhanced CO binding. Introducing double mutation αE447L/ßE377L, predicted to replace two destabilizing glutamates with leucines, lowers CO binding affinity while increasing overall protein stability. Likewise, introduction of a disulfide bond into the coiled coil results in reduced CO affinity. Taken together, we demonstrate that the heme domain is greatly influenced by coiled-coil conformation, suggesting communication between heme and catalytic domains is through the coiled coil. Highly conserved structural imperfections in the coiled coil provide needed flexibility for signal transduction.


Assuntos
Transdução de Sinais , Guanilil Ciclase Solúvel/química , Animais , Manduca/enzimologia , Modelos Moleculares , Óxido Nítrico/metabolismo , Estabilidade Proteica , Guanilil Ciclase Solúvel/metabolismo
14.
J Mol Graph Model ; 90: 109-119, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31055154

RESUMO

The human soluble Guanylate Cyclase (hsGC) is a heterodimeric heme-containing enzyme which regulates many important physiological processes. In eukaryotes, hsGC is the only known receptor for nitric oxide (NO) signaling. Improper NO signaling results in various disease conditions such as neurodegeneration, hypertension, stroke and erectile dysfunction. To understand the mechanisms of these diseases, structure determination of the hsGC dimer complex is crucial. However, so far all the attempts for the experimental structure determination of the protein were unsuccessful. The current study explores the possibility to model the quaternary structure of hsGC using a hybrid approach that combines state-of-the-art protein structure prediction tools with cryo-EM experimental data. The resultant 3D model shows close consistency with structural and functional insights extracted from biochemistry experiment data. Overall, the atomic-level complex structure determination of hsGC helps to unveil the inter-domain communication upon NO binding, which should be of important usefulness for elucidating the biological function of this important enzyme and for developing new treatments against the hsGC associated human diseases.


Assuntos
Óxido Nítrico/química , Óxido Nítrico/metabolismo , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/metabolismo , Sequência de Aminoácidos , Simulação por Computador , Microscopia Crioeletrônica/métodos , Heme/química , Heme/metabolismo , Humanos , Alinhamento de Sequência , Transdução de Sinais/fisiologia
15.
Biochemistry ; 58(17): 2250-2259, 2019 04 30.
Artigo em Inglês | MEDLINE | ID: mdl-30946781

RESUMO

Signaling pathways that involve diatomic gases in photosynthetic organisms are not well understood. Exposure to nitric oxide or carbon monoxide is known to elicit certain responses in some photosynthetic organisms. For example, Chlamydomonas reinhardtii grown in low-iron media responds to exogenous carbon monoxide by increasing cell growth and intracellular chlorophyll levels. Here, we characterize Cyg11, a gas-responsive soluble guanylate cyclase from the eukaryotic green alga C. reinhardtii that converts GTP to cGMP. Cyg11 transcription is upregulated when C. reinhardtii is grown in iron-limited media, suggesting its importance in nutrient-limited environments. Cyg11 is purified as a homodimer and is activated by nitric oxide (2.5-fold over basal activity) and carbon monoxide (6.3-fold). The heme binding stoichiometry of Cyg11 was found to be one heme per homodimer, an unexpected result based on the sequence and oligomerization state of the enzyme. Gas binding properties, the kinetics of gas binding, and the ligand-modulated activity of Cyg11 are consistent with CO as the relevant physiological ligand.


Assuntos
Proteínas de Algas/metabolismo , Monóxido de Carbono/metabolismo , Chlamydomonas reinhardtii/enzimologia , Guanilil Ciclase Solúvel/metabolismo , Proteínas de Algas/química , Proteínas de Algas/genética , Dióxido de Carbono/metabolismo , Chlamydomonas reinhardtii/genética , Heme/química , Heme/metabolismo , Cinética , Óxido Nítrico/metabolismo , Ligação Proteica , Multimerização Proteica , Transdução de Sinais , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/genética , Regulação para Cima
16.
Int J Mol Sci ; 20(3)2019 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-30736292

RESUMO

Soluble guanylate cyclase (sGC) regulates numerous physiological processes. The ß 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, ß, 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.


Assuntos
Heme/química , Óxido Nítrico/química , Oxigênio/química , Heme/metabolismo , Humanos , Ligação de Hidrogênio , Ligantes , Conformação Molecular , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Óxido Nítrico/metabolismo , Oxigênio/metabolismo , Ligação Proteica , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/metabolismo
17.
Curr Med Chem ; 26(15): 2730-2747, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30621555

RESUMO

The soluble guanylate cyclase (sGC) is the physiological sensor for nitric oxide and alterations of its function are actively implicated in a wide variety of pathophysiological conditions. Intense research efforts over the past 20 years have provided significant information on its regulation, culminating in the rational development of approved drugs or investigational lead molecules, which target and interact with sGC through novel mechanisms. However, there are numerous questions that remain unanswered. Ongoing investigations, with the critical aid of structural chemistry studies, try to further elucidate the enzyme's structural characteristics that define the association of "stimulators" or "activators" of sGC in the presence or absence of the heme moiety, respectively, as well as the precise conformational attributes that will allow the design of more innovative and effective drugs. This review relates the progress achieved, particularly in the past 10 years, in understanding the function of this enzyme, and focusses on a) the rationale and results of its therapeutic targeting in disease situations, depending on the state of enzyme (oxidized or not, heme-carrying or not) and b) the most recent structural studies, which should permit improved design of future therapeutic molecules that aim to directly upregulate the activity of sGC.


Assuntos
Ativadores de Enzimas/uso terapêutico , Guanilil Ciclase Solúvel/metabolismo , Animais , Doenças Cardiovasculares/tratamento farmacológico , GMP Cíclico/metabolismo , Ativadores de Enzimas/farmacologia , Humanos , Nefropatias/tratamento farmacológico , Óxido Nítrico/metabolismo , Domínios Proteicos , Transdução de Sinais/efeitos dos fármacos , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/fisiologia
18.
Molecules ; 23(9)2018 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-30149624

RESUMO

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 ß, 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.


Assuntos
Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Heme/química , Óxido Nítrico/química , Oxigênio/química , Domínios e Motivos de Interação entre Proteínas , Guanilil Ciclase Solúvel/antagonistas & inibidores , Guanilil Ciclase Solúvel/química , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Humanos , Ligação de Hidrogênio , Conformação Molecular , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Ligação Proteica , Guanilil Ciclase Solúvel/metabolismo
19.
Nitric Oxide ; 77: 53-64, 2018 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-29702251

RESUMO

Soluble guanylyl cyclase (GC-1) is the primary receptor of nitric oxide (NO) in smooth muscle cells and maintains vascular function by inducing vasorelaxation in nearby blood vessels. GC-1 converts guanosine 5'-triphosphate (GTP) into cyclic guanosine 3',5'-monophosphate (cGMP), which acts as a second messenger to improve blood flow. While much work has been done to characterize this pathway, we lack a mechanistic understanding of how NO binding to the heme domain leads to a large increase in activity at the C-terminal catalytic domain. Recent structural evidence and activity measurements from multiple groups have revealed a low-activity cyclase domain that requires additional GC-1 domains to promote a catalytically-competent conformation. How the catalytic domain structurally transitions into the active conformation requires further characterization. This review focuses on structure/function studies of the GC-1 catalytic domain and recent advances various groups have made in understanding how catalytic activity is regulated including small molecules interactions, Cys-S-NO modifications and potential interactions with the NO-sensor domain and other proteins.


Assuntos
Domínio Catalítico , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/metabolismo , Animais , Biocatálise , Humanos , Óxido Nítrico/metabolismo , Conformação Proteica , Relação Estrutura-Atividade
20.
Biochim Biophys Acta Proteins Proteom ; 1866(5-6): 702-711, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29653192

RESUMO

Nitric oxide sensitive guanylyl cyclase (NOsGC) is a heterodimeric enzyme consisting of one α and one ß subunit. Each subunit consists of four domains: the N-terminal heme-nitric oxide oxygen binding (HNOX) domain, a PAS domain, a coiled-coil domain and the C-terminal catalytic domain. Upon activation by the endogenous ligand NO or activating drugs, NOsGC catalyses the conversion of GTP to cGMP. Although several crystal structures of the isolated domains are known, the structure of the full-length enzyme and the interdomain conformational changes during activation remain unsolved to date. In the current study, we performed protein thermal shift assays of purified NOsGC to identify discrete conformational states amenable to further analysis e.g. by crystallisation. A non-hydrolysable substrate analogue binding to the catalytic domain led to a subtle change in melting temperature. An activator drug binding to the HNOX domain led to a small increase. However, the combination of substrate analogue and activator drug led to a marked synergistic increase from 51 °C to 60 °C. This suggests reciprocal communication between HNOX domain and catalytic domain and formation of a stable activated conformation amenable to further biophysical characterization.


Assuntos
Benzoatos/farmacologia , Ativadores de Enzimas/farmacologia , Guanosina Trifosfato/farmacologia , Heme/metabolismo , Guanilil Ciclase Solúvel/metabolismo , Sítios de Ligação , Domínio Catalítico , Cloretos/farmacologia , GMP Cíclico/metabolismo , Relação Dose-Resposta a Droga , Sinergismo Farmacológico , Ativação Enzimática , Estabilidade Enzimática , Guanosina Trifosfato/análogos & derivados , Guanosina Trifosfato/metabolismo , Heme/química , Humanos , Compostos de Manganês/farmacologia , Ligação Proteica , Conformação Proteica , Desnaturação Proteica , Guanilil Ciclase Solúvel/química , Guanilil Ciclase Solúvel/genética , Relação Estrutura-Atividade , Temperatura de Transição
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