51
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Wales JA, Chen CY, Breci L, Weichsel A, Bernier SG, Sheppeck JE, Solinga R, Nakai T, Renhowe PA, Jung J, Montfort WR. Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase. J Biol Chem 2017; 293:1850-1864. [PMID: 29222330 DOI: 10.1074/jbc.ra117.000457] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/18/2017] [Indexed: 11/06/2022] Open
Abstract
Soluble guanylyl cyclase (sGC) is the receptor for nitric oxide and a highly sought-after therapeutic target for the management of cardiovascular diseases. New compounds that stimulate sGC show clinical promise, but where these stimulator compounds bind and how they function remains unknown. Here, using a photolyzable diazirine derivative of a novel stimulator compound, IWP-051, and MS analysis, we localized drug binding to the β1 heme domain of sGC proteins from the hawkmoth Manduca sexta and from human. Covalent attachments to the stimulator were also identified in bacterial homologs of the sGC heme domain, referred to as H-NOX domains, including those from Nostoc sp. PCC 7120, Shewanella oneidensis, Shewanella woodyi, and Clostridium botulinum, indicating that the binding site is highly conserved. The identification of photoaffinity-labeled peptides was aided by a signature MS fragmentation pattern of general applicability for unequivocal identification of covalently attached compounds. Using NMR, we also examined stimulator binding to sGC from M. sexta and bacterial H-NOX homologs. These data indicated that stimulators bind to a conserved cleft between two subdomains in the sGC heme domain. L12W/T48W substitutions within the binding pocket resulted in a 9-fold decrease in drug response, suggesting that the bulkier tryptophan residues directly block stimulator binding. The localization of stimulator binding to the sGC heme domain reported here resolves the longstanding question of where stimulators bind and provides a path forward for drug discovery.
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Affiliation(s)
- Jessica A Wales
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
| | - Cheng-Yu Chen
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
| | - Linda Breci
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
| | - Andrzej Weichsel
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
| | | | | | - Robert Solinga
- Ironwood Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Takashi Nakai
- Ironwood Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Paul A Renhowe
- Ironwood Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Joon Jung
- Ironwood Pharmaceuticals, Cambridge, Massachusetts 02142
| | - William R Montfort
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
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52
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Regulation of nitric oxide signaling by formation of a distal receptor-ligand complex. Nat Chem Biol 2017; 13:1216-1221. [PMID: 28967923 PMCID: PMC5698159 DOI: 10.1038/nchembio.2488] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/28/2017] [Indexed: 12/23/2022]
Abstract
The binding of nitric oxide (NO) to the heme cofactor of heme-nitric oxide/oxygen binding (H-NOX) proteins can lead to the dissociation of the heme-ligating histidine residue and yield a five-coordinate nitrosyl complex, which is an important step for NO-dependent signaling. In the five-coordinate nitrosyl complex, NO can reside either on the distal or proximal side of the heme, which could have a profound influence over the lifetime of the in vivo signal. To investigate this central molecular question, the Shewanella oneidensis H-NOX (So H-NOX)–NO complex was biophysically characterized under limiting and excess NO. The results show that So H-NOX preferably forms a distal NO species under both limiting and excess NO. Therefore, signal strength and complex lifetime in vivo will be dictated by the dissociation rate of NO from the distal complex and the return of the histidine ligand to the heme.
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53
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Gaseous ligand selectivity of the H-NOX sensor protein from Shewanella oneidensis and comparison to those of other bacterial H-NOXs and soluble guanylyl cyclase. Biochimie 2017; 140:82-92. [PMID: 28655588 DOI: 10.1016/j.biochi.2017.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/23/2017] [Indexed: 01/11/2023]
Abstract
To delineate the commonalities and differences in gaseous ligand discrimination among the heme-based sensors with Heme Nitric oxide/OXygen binding protein (H-NOX) scaffold, the binding kinetic parameters for gaseous ligands NO, CO, and O2, including KD, kon, and koff, of Shewanella oneidensis H-NOX (So H-NOX) were characterized in detail in this study and compared to those of previously characterized H-NOXs from Clostridium botulinum (Cb H-NOX), Nostoc sp. (Ns H-NOX), Thermoanaerobacter tengcongensis (Tt H-NOX), Vibrio cholera (Vc H-NOX), and human soluble guanylyl cyclase (sGC), an H-NOX analogue. The KD(NO) and KD(CO) of each bacterial H-NOX or sGC follow the "sliding scale rule"; the affinities of the bacterial H-NOXs for NO and CO vary in a small range but stronger than those of sGC by at least two orders of magnitude. On the other hand, each bacterial H-NOX exhibits different characters in the stability of its 6c NO complex, reactivity with secondary NO, stability of oxyferrous heme and autoxidation to ferric heme. A facile access channel for gaseous ligands is also identified, implying that ligand access has only minimal effect on gaseous ligand selectivity of H-NOXs or sGC. This comparative study of the binding parameters of the bacterial H-NOXs and sGC provides a basis to guide future new structural and functional studies of each specific heme sensor with the H-NOX protein fold.
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54
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Follmann M, Ackerstaff J, Redlich G, Wunder F, Lang D, Kern A, Fey P, Griebenow N, Kroh W, Becker-Pelster EM, Kretschmer A, Geiss V, Li V, Straub A, Mittendorf J, Jautelat R, Schirok H, Schlemmer KH, Lustig K, Gerisch M, Knorr A, Tinel H, Mondritzki T, Trübel H, Sandner P, Stasch JP. Discovery of the Soluble Guanylate Cyclase Stimulator Vericiguat (BAY 1021189) for the Treatment of Chronic Heart Failure. J Med Chem 2017; 60:5146-5161. [PMID: 28557445 DOI: 10.1021/acs.jmedchem.7b00449] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The first-in-class soluble guanylate cyclase (sGC) stimulator riociguat was recently introduced as a novel treatment option for pulmonary hypertension. Despite its outstanding pharmacological profile, application of riociguat in other cardiovascular indications is limited by its short half-life, necessitating a three times daily dosing regimen. In our efforts to further optimize the compound class, we have uncovered interesting structure-activity relationships and were able to decrease oxidative metabolism significantly. These studies resulting in the discovery of once daily sGC stimulator vericiguat (compound 24, BAY 1021189), currently in phase 3 trials for chronic heart failure, are now reported.
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Affiliation(s)
- Markus Follmann
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Jens Ackerstaff
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Gorden Redlich
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Frank Wunder
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Dieter Lang
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Armin Kern
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Peter Fey
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Nils Griebenow
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Walter Kroh
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | | | - Axel Kretschmer
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Volker Geiss
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Volkhart Li
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Alexander Straub
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | | | - Rolf Jautelat
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Hartmut Schirok
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | | | - Klemens Lustig
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Michael Gerisch
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Andreas Knorr
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Hanna Tinel
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Thomas Mondritzki
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Hubert Trübel
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Peter Sandner
- Drug Discovery, Bayer AG , Aprather Weg 18a, 42113 Wuppertal, Germany
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55
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Bioelectrochemical monitoring of soluble guanylate cyclase inhibition by the natural β-carboline canthin-6-one. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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56
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Abstract
Low concentrations of nitric oxide (NO) modulate varied behaviours in bacteria including biofilm dispersal and quorum sensing-dependent light production. H-NOX (haem-nitric oxide/oxygen binding) is a haem-bound protein domain that has been shown to be involved in mediating these bacterial responses to NO in several organisms. However, many bacteria that respond to nanomolar concentrations of NO do not contain an annotated H-NOX domain. Nitric oxide sensing protein (NosP), a newly discovered bacterial NO-sensing haemoprotein, may fill this role. The focus of this review is to discuss structure, ligand binding, and activation of H-NOX proteins, as well as to discuss the early evidence for NO sensing and regulation by NosP domains. Further, these findings are connected to the regulation of bacterial biofilm phenotypes and symbiotic relationships.
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Affiliation(s)
- Bezalel Bacon
- Stony Brook University, Stony Brook, NY, United States
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57
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Rao M, Herzik MA, Iavarone AT, Marletta MA. Nitric Oxide-Induced Conformational Changes Govern H-NOX and Histidine Kinase Interaction and Regulation in Shewanella oneidensis. Biochemistry 2017; 56:1274-1284. [PMID: 28170222 DOI: 10.1021/acs.biochem.6b01133] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nitric oxide (NO) is implicated in biofilm regulation in several bacterial families via heme-nitric oxide/oxygen binding (H-NOX) protein signaling. Shewanella oneidensis H-NOX (So H-NOX) is associated with a histidine kinase (So HnoK) encoded on the same operon, and together they form a multicomponent signaling network whereby the NO-bound state of So H-NOX inhibits So HnoK autophosphorylation activity, affecting the phosphorylation state of three response regulators. Although the conformational changes of So H-NOX upon NO binding have been structurally characterized, the mechanism of HnoK inhibition by NO-bound So H-NOX remains unclear. In the present study, the molecular details of So H-NOX and So HnoK interaction and regulation are characterized. The N-terminal domain in So HnoK was determined to be the site of H-NOX interaction, and the binding interface on So H-NOX was identified using a combination of hydrogen-deuterium exchange mass spectrometry and surface-scanning mutagenesis. Binding kinetics measurements and analytical gel filtration revealed that NO-bound So H-NOX has a tighter affinity for So HnoK compared that of H-NOX in the unliganded state, correlating binding affinity with kinase inhibition. Kinase activity assays with binding-deficient H-NOX mutants further indicate that while formation of the H-NOX-HnoK complex is required for HnoK to be catalytically active, H-NOX conformational changes upon NO-binding are necessary for HnoK inhibition.
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Affiliation(s)
- Minxi Rao
- Department of Chemistry, ‡Department of Molecular and Cell Biology, §QB3 Institute, University of California , Berkeley, California 94720, United States
| | - Mark A Herzik
- Department of Chemistry, ‡Department of Molecular and Cell Biology, §QB3 Institute, University of California , Berkeley, California 94720, United States
| | - Anthony T Iavarone
- Department of Chemistry, ‡Department of Molecular and Cell Biology, §QB3 Institute, University of California , Berkeley, California 94720, United States
| | - Michael A Marletta
- Department of Chemistry, ‡Department of Molecular and Cell Biology, §QB3 Institute, University of California , Berkeley, California 94720, United States
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58
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Montfort WR, Wales JA, Weichsel A. Structure and Activation of Soluble Guanylyl Cyclase, the Nitric Oxide Sensor. Antioxid Redox Signal 2017; 26:107-121. [PMID: 26979942 PMCID: PMC5240008 DOI: 10.1089/ars.2016.6693] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE Soluble guanylyl/guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) and is central to the physiology of blood pressure regulation, wound healing, memory formation, and other key physiological activities. sGC is increasingly implicated in disease and is targeted by novel therapeutic compounds. The protein displays a rich evolutionary history and a fascinating signal transduction mechanism, with NO binding to an N-terminal heme-containing domain, which activates the C-terminal cyclase domains. Recent Advances: Crystal structures of individual sGC domains or their bacterial homologues coupled with small-angle x-ray scattering, electron microscopy, chemical cross-linking, and Förster resonance energy transfer measurements are yielding insight into the overall structure for sGC, which is elongated and likely quite dynamic. Transient kinetic measurements reveal a role for individual domains in lowering NO affinity for heme. New sGC stimulatory drugs are now in the clinic and appear to function through binding near or directly to the sGC heme domain, relieving inhibitory contacts with other domains. New sGC-activating drugs show promise for recovering oxidized sGC in diseases with high inflammation by replacing lost heme. CRITICAL ISSUES Despite the many recent advances, sGC regulation, NO activation, and mechanisms of drug binding remain unclear. Here, we describe the molecular evolution of sGC, new molecular models, and the linked equilibria between sGC NO binding, drug binding, and catalytic activity. FUTURE DIRECTIONS Recent results and ongoing studies lay the foundation for a complete understanding of structure and mechanism, and they open the door for new drug discovery targeting sGC. Antioxid. Redox Signal. 26, 107-121.
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Affiliation(s)
- William R Montfort
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona
| | - Jessica A Wales
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona
| | - Andrzej Weichsel
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona
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59
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An essential role for bacterial nitric oxide synthase in Staphylococcus aureus electron transfer and colonization. Nat Microbiol 2016; 2:16224. [PMID: 27892921 DOI: 10.1038/nmicrobiol.2016.224] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 10/12/2016] [Indexed: 11/08/2022]
Abstract
Nitric oxide (NO•) is a ubiquitous molecular mediator in biology. Many signalling actions of NO• generated by mammalian NO• synthase (NOS) result from targeting of the haem moiety of soluble guanylate cyclase. Some pathogenic and environmental bacteria also produce a NOS that is evolutionary related to the mammalian enzymes, but a bacterial haem-containing receptor for endogenous enzymatically generated NO• has not been identified previously. Here, we show that NOS of the human pathogen Staphylococcus aureus, in concert with an NO•-metabolizing flavohaemoprotein, regulates electron transfer by targeting haem-containing cytochrome oxidases under microaerobic conditions to maintain membrane bioenergetics. This process is essential for staphylococcal nasal colonization and resistance to the membrane-targeting antibiotic daptomycin and demonstrates the conservation of NOS-derived NO•-haem receptor signalling between bacteria and mammals.
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60
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Andrew CR, Petrova ON, Lamarre I, Lambry JC, Rappaport F, Negrerie M. The Dynamics Behind the Affinity: Controlling Heme-Gas Affinity via Geminate Recombination and Heme Propionate Conformation in the NO Carrier Cytochrome c'. ACS Chem Biol 2016; 11:3191-3201. [PMID: 27709886 DOI: 10.1021/acschembio.6b00599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) sensors are heme proteins which may also bind CO and O2. Control of heme-gas affinity and their discrimination are achieved by the structural properties and reactivity of the heme and its distal and proximal environments, leading to several energy barriers. In the bacterial NO sensor cytochrome c' from Alcaligenes xylosoxidans (AXCP), the single Leu16Ala distal mutation boosts the affinity for gas ligands by a remarkable 106-108-fold, transforming AXCP from one of the lowest affinity gas binding proteins to one of the highest. Here, we report the dynamics of diatomics after photodissociation from wild type and L16A-AXCP over 12 orders of magnitude in time. For the L16A variant, the picosecond geminate rebinding of both CO and NO appears with an unprecedented 100% yield, and no exit of these ligands from protein to solvent could be observed. Molecular dynamic simulations saliently demonstrate that dissociated CO stays within 4 Å from Fe2+, in contrast to wild-type AXCP. The L16A mutation confers a heme propionate conformation and docking site which traps the diatomics, maximizing the probability of recombination and directly explaining the ultrahigh affinities for CO, NO, and O2. Overall, our results point to a novel mechanism for modulating heme-gas affinities in proteins.
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Affiliation(s)
- Colin R. Andrew
- Department
of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Olga N. Petrova
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Isabelle Lamarre
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Fabrice Rappaport
- Laboratoire
de Physiologie Membranaire et Moléculaire du Chloroplaste, CNRS, Université Pierre et Marie Curie, 75005 Paris, France
| | - Michel Negrerie
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
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61
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Vijayaraghavan J, Kramp K, Harris ME, van den Akker F. Inhibition of soluble guanylyl cyclase by small molecules targeting the catalytic domain. FEBS Lett 2016; 590:3669-3680. [PMID: 27654641 DOI: 10.1002/1873-3468.12427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/29/2016] [Accepted: 09/09/2016] [Indexed: 12/23/2022]
Abstract
Soluble guanylyl cyclase (sGC) plays a crucial role in cyclic nucleotide signaling that regulates numerous important physiological processes. To identify new sGC inhibitors that may prevent the formation of the active catalytic domain conformation, we carried out an in silico docking screen targeting a 'backside pocket' of the inactive sGC catalytic domain structure. Compounds 1 and 2 were discovered to inhibit sGC even at high/saturating nitric oxide concentrations. Both compounds also inhibit the BAY 58-2667-activated sGC as well as BAY 41-2272-stimulated sGC activity. Additional biochemical analyses showed that compound 2 also inhibits the isolated catalytic domain, thus demonstrating functional binding to this domain. Both compounds have micromolar affinity for sGC and are potential leads to develop more potent sGC inhibitors.
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Affiliation(s)
| | - Kristopher Kramp
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA.
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62
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Abstract
Nitric oxide (NO) is a freely diffusible, radical gas that has now been established as an integral signaling molecule in eukaryotes and bacteria. It has been demonstrated that NO signaling is initiated upon ligation to the heme iron of an H-NOX domain in mammals and in some bacteria. Bacterial H-NOX proteins have been found to interact with enzymes that participate in signaling pathways and regulate bacterial processes such as quorum sensing, biofilm formation, and symbiosis. Here, we review the biochemical characterization of these signaling pathways and, where available, describe how ligation of NO to H-NOX specifically regulates the activity of these pathways and their associated bacterial phenotypes.
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Affiliation(s)
- Lisa-Marie Nisbett
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY, 11794-3400
| | - Elizabeth M. Boon
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY, 11794-3400
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY, 11794-3400
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63
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Hespen CW, Bruegger JJ, Phillips-Piro CM, Marletta MA. Structural and Functional Evidence Indicates Selective Oxygen Signaling in Caldanaerobacter subterraneus H-NOX. ACS Chem Biol 2016; 11:2337-46. [PMID: 27328180 DOI: 10.1021/acschembio.6b00431] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Acute and specific sensing of diatomic gas molecules is an essential facet of biological signaling. Heme nitric oxide/oxygen binding (H-NOX) proteins are a family of gas sensors found in diverse classes of bacteria and eukaryotes. The most commonly characterized bacterial H-NOX domains are from facultative anaerobes and are activated through a conformational change caused by formation of a 5-coordinate Fe(II)-NO complex. Members of this H-NOX subfamily do not bind O2 and therefore can selectively ligate NO even under aerobic conditions. In contrast, H-NOX domains encoded by obligate anaerobes do form stable 6-coordinate Fe(II)-O2 complexes by utilizing a conserved H-bonding network in the ligand-binding pocket. The biological function of O2-binding H-NOX domains has not been characterized. In this work, the crystal structures of an O2-binding H-NOX domain from the thermophilic obligate anaerobe Caldanaerobacter subterraneus (Cs H-NOX) in the Fe(II)-NO, Fe(II)-CO, and Fe(II)-unliganded states are reported. The Fe(II)-unliganded structure displays a conformational shift distinct from the NO-, CO-, and previously reported O2-coordinated structures. In orthogonal signaling assays using Cs H-NOX and the H-NOX signaling effector histidine kinase from Vibrio cholerae (Vc HnoK), Cs H-NOX regulates Vc HnoK in an O2-dependent manner and requires the H-bonding network to distinguish O2 from other ligands. The crystal structures of Fe(II) unliganded and NO- and CO-bound Cs H-NOX combined with functional assays herein provide the first evidence that H-NOX proteins from obligate anaerobes can serve as O2 sensors.
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Affiliation(s)
- Charles W. Hespen
- Department
of Molecular and Cell Biology, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
| | - Joel J. Bruegger
- QB3
Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California, 94720-3220, United States
| | - Christine M. Phillips-Piro
- Department of Chemistry, HAC 416 Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, United States
| | - Michael A. Marletta
- Department
of Molecular and Cell Biology, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
- Department
of Chemistry Department of Molecular and Cell Biology QB3 Institute, University of California—Berkeley, 374B Stanley Hall, Berkeley, California 94720-3220, United States
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64
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Liao F, Yuan H, Du KJ, You Y, Gao SQ, Wen GB, Lin YW, Tan X. Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin. MOLECULAR BIOSYSTEMS 2016; 12:3139-45. [PMID: 27476534 DOI: 10.1039/c6mb00537c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hydrogen-bond (H-bond) network, specifically a Tyr-associated H-bond network, plays key roles in regulating the structure and function of proteins, as exemplified by abundant heme proteins in nature. To explore an approach for fine-tuning the structure and function of artificial heme proteins, we herein used myoglobin (Mb) as a model protein and introduced a Tyr residue in the secondary sphere of the heme active site at two different positions (107 and 138). We performed X-ray crystallography, UV-Vis spectroscopy, stopped-flow kinetics, and electron paramagnetic resonance (EPR) studies for the two single mutants, I107Y Mb and F138Y Mb, and compared to that of wild-type Mb under the same conditions. The results showed that both Tyr107 and Tyr138 form a distinct H-bond network involving water molecules and neighboring residues, which fine-tunes ligand binding to the heme iron and enhances the protein stability, respectively. Moreover, the Tyr107-associated H-bond network was shown to fine-tune both H2O2 binding and activation. With two cases demonstrated for Mb, this study suggests that the Tyr-associated H-bond network has distinct roles in regulating the protein structure, properties and functions, depending on its location in the protein scaffold. Therefore, it is possible to design a Tyr-associated H-bond network in general to create other artificial heme proteins with improved properties and functions.
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Affiliation(s)
- Fei Liao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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65
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Senge MO, MacGowan SA, O'Brien JM. Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles. Chem Commun (Camb) 2016; 51:17031-63. [PMID: 26482230 DOI: 10.1039/c5cc06254c] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.
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Affiliation(s)
- Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland and Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
| | - Stuart A MacGowan
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Jessica M O'Brien
- Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
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66
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Sun Y, Benabbas A, Zeng W, Muralidharan S, Boon EM, Champion PM. Kinetic Control of O2 Reactivity in H-NOX Domains. J Phys Chem B 2016; 120:5351-8. [PMID: 27229134 DOI: 10.1021/acs.jpcb.6b03348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transient absorption, resonance Raman, and vibrational coherence spectroscopies are used to investigate the mechanisms of NO and O2 binding to WT Tt H-NOX and its P115A mutant. Vibrational coherence spectra of the oxy complexes provide clear evidence for the enhancement of an iron-histidine mode near 217 cm(-1) following photoexcitation, which indicates that O2 can be dissociated in these proteins. However, the quantum yield of O2 photolysis is low, particularly in the wild type (≲3%). Geminate recombination of O2 and NO in both of these proteins is very fast (∼1.4 × 10(11) s(-1)) and highly efficient. We show that the distal heme pocket of the H-NOX system forms an efficient trap that limits the O2 off-rate and determines the overall affinity. The distal pocket hydrogen bond, which appears to be stronger in the P115A mutant, may help retard the O2 ligand from escaping into the solvent following either photoinduced or thermal dissociation. This, along with a strengthening of the Fe-O2 bond that is correlated with the significant heme ruffing and saddling distortions, explains the unusually high O2 affinity of WT Tt H-NOX and the even higher affinity found in the P115A mutant.
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Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Weiqiao Zeng
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Sandhya Muralidharan
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, United States
| | - Elizabeth M Boon
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, United States
| | - Paul M Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
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67
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Liu Q, Zhou X, Liu H, Zhang X, Zhou Z. Fractional transfer of a free unpaired electron to overcome energy barriers in the formation of Fe(4+) from Fe(3+) during the core contraction of macrocycles: implication for heme distortion. Org Biomol Chem 2016; 13:2939-46. [PMID: 25609455 DOI: 10.1039/c4ob02429j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The free unpaired electron in Fe(3+) ions cannot be directly removed, and needs a transfer pathway with at least four steps to overcome the high energy barriers to form Fe(4+) ions. Fine changes in the electronic structure of Fe(3+) ions on spin conversion were identified through a deeper analysis of the diffraction, spectral and electrochemical data for six non-planar iron porphyrins. Fe(3+) ions can form four d electron tautomers as the compression of the central ion is increased. This indicates that the Fe(3+) ion undergoes a multistep electron transfer where the total energy gap of electron transfer is split into several smaller gaps to form high-valent Fe(4+) ions. We find that the interchange of these four electron tautomers is clearly related to the core size of the macrocycle in the current series. The large energy barrier to produce iron(iv) complexes is overcome through a gradient effect of multiple energy levels. In addition, a possible porphyrin Fe(3+)˙ radical may be formed from its stable isoelectronic form, porphyrin Fe(3+), under strong core contraction. These results indicate the important role of heme distortion in its catalytic oxidation functions.
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Affiliation(s)
- Qiuhua Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of 'Theoretical Organic Chemistry and Function Molecule' of the Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.
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Yan DJ, Yuan H, Li W, Xiang Y, He B, Nie CM, Wen GB, Lin YW, Tan X. How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin. Dalton Trans 2016; 44:18815-22. [PMID: 26458300 DOI: 10.1039/c5dt03040d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A heme-protein cross-link is a key post-translational modification (PTM) of heme proteins. Meanwhile, the structural and functional consequences of heme-protein cross-links are not fully understood, due to limited studies on a direct comparison of the same protein with and without the cross-link. A Tyr-heme cross-link with a C-O bond is a newly discovered PTM of heme proteins, and is spontaneously formed in F43Y myoglobin (Mb) between the Tyr hydroxyl group and the heme 4-vinyl group in vivo. In this study, we found that with an additional distal His29 introduced in the heme pocket, the double mutant L29H/F43Y Mb can form two distinct forms under different protein purification conditions, with and without a novel Tyr-heme cross-link. By solving the X-ray structures of both forms of L29H/F43Y Mb and performing spectroscopic studies, we made a direct structural and functional comparison in the same protein scaffold. It revealed that the Tyr-heme cross-link regulates the heme distal hydrogen-bonding network, and fine-tunes not only the spectroscopic and ligand binding properties, but also the protein reactivity. Moreover, the formation of the Tyr-heme cross-link in the double mutant L29H/F43Y Mb was investigated in vitro. This study addressed the key issue of how Tyr-heme cross-link fine-tunes the structure and functions of the heme protein, and provided a plausible mechanism for the formation of the newly discovered Tyr-heme cross-link.
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Affiliation(s)
- Dao-Jing Yan
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Hong Yuan
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
| | - Wei Li
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
| | - Yu Xiang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Bo He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Chang-Ming Nie
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
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Abstract
The formation of the organized bacterial community called biofilm is a crucial event in bacterial physiology. Given that biofilms are often refractory to antibiotics and disinfectants to which planktonic bacteria are susceptible, their formation is also an industrially and medically relevant issue. Pseudomonas aeruginosa, a well-known human pathogen causing acute and chronic infections, is considered a model organism to study biofilms. A large number of environmental cues control biofilm dynamics in bacterial cells. In particular, the dispersal of individual cells from the biofilm requires metabolic and morphological reprogramming in which the second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) plays a central role. The diatomic gas nitric oxide (NO), a well-known signaling molecule in both prokaryotes and eukaryotes, is able to induce the dispersal of P. aeruginosa and other bacterial biofilms by lowering c-di-GMP levels. In this review, we summarize the current knowledge on the molecular mechanisms connecting NO sensing to the activation of c-di-GMP-specific phosphodiesterases in P. aeruginosa, ultimately leading to c-di-GMP decrease and biofilm dispersal.
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70
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Xu H, Zhang Y, Chen L, Li Y, Li C, Liu L, Ogura T, Kitagawa T, Li Z. Entry of water into the distal heme pocket of soluble guanylate cyclase β1 H-NOX domain alters the ligated CO structure: a resonance Raman and in silico simulation study. RSC Adv 2016. [DOI: 10.1039/c6ra06515e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Water accessing into the heme pocket and alters the structures of CO–sGC (heme), exhibiting two different vFe–CO stretching modes.
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Affiliation(s)
- Haoran Xu
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Yuebin Zhang
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Lei Chen
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Yan Li
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Chen Li
- Picobiology Institute
- Graduate School of Life Science
- University of Hyogo
- RSC-UH Leading Program Center
- Hyogo 679-5148
| | - Li Liu
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Takashi Ogura
- Picobiology Institute
- Graduate School of Life Science
- University of Hyogo
- RSC-UH Leading Program Center
- Hyogo 679-5148
| | - Teizo Kitagawa
- Picobiology Institute
- Graduate School of Life Science
- University of Hyogo
- RSC-UH Leading Program Center
- Hyogo 679-5148
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
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71
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Wu G, Liu W, Berka V, Tsai AL. H-NOX from Clostridium botulinum, like H-NOX from Thermoanaerobacter tengcongensis, Binds Oxygen but with a Less Stable Oxyferrous Heme Intermediate. Biochemistry 2015; 54:7098-109. [PMID: 26574914 DOI: 10.1021/acs.biochem.5b00994] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Heme nitric oxide/oxygen binding protein isolated from the obligate anaerobe Clostridium botulinum (Cb H-NOX) was previously reported to bind NO with a femtomolar K(D) (Nioche, P. et al. Science 2004, 306, 1550-1553). On the other hand, no oxyferrous Cb H-NOX was observed despite full conservation of the key residues that stabilize the oxyferrous complex in the H-NOX from Thermoanaerobacter tengcongensis (Tt H-NOX) (the same study). In this study, we re-measured the kinetics/affinities of Cb H-NOX for CO, NO, and O2. K(D)(CO) for the simple one-step equilibrium binding was 1.6 × 10(-7) M. The K(D)(NO) of Cb H-NOX was 8.0 × 10(-11) M for the first six-coordinate NO complex, and the previous femtomolar K(D)(NO) was actually an apparent K(D) for its multiple-step NO binding. An oxyferrous Cb H-NOX was clearly observed with a K(D)(O2) of 5.3 × 10(-5) M, which is significantly higher than Tt H-NOX's K(D)(O2) = 4.4 × 10(-8) M. The gaseous ligand binding of Cb H-NOX provides another supportive example for the "sliding scale rule" hypothesis (Tsai, A.-L. et al. Antioxid. Redox Signal. 2012, 17, 1246-1263), and the presence of hydrogen bond donor Tyr139 in Cb H-NOX selectively enhanced its affinity for oxygen.
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Affiliation(s)
- Gang Wu
- Division of Hematology, Department of Internal Medicine, The University of Texas-Medical School at Houston , 6431 Fannin Street, Houston, Texas 77030, United States
| | - Wen Liu
- Division of Hematology, Department of Internal Medicine, The University of Texas-Medical School at Houston , 6431 Fannin Street, Houston, Texas 77030, United States
| | - Vladimir Berka
- Division of Hematology, Department of Internal Medicine, The University of Texas-Medical School at Houston , 6431 Fannin Street, Houston, Texas 77030, United States
| | - Ah-Lim Tsai
- Division of Hematology, Department of Internal Medicine, The University of Texas-Medical School at Houston , 6431 Fannin Street, Houston, Texas 77030, United States
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72
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Zhou Z, Zhou X, Liu Q, Zhang X, Liu H. Fixation of Zinc(II) Ion to Dioxygen in a Highly Deformed Porphyrin: Implications for the Oxygen Carrier Mechanism of Distorted Heme. Org Lett 2015; 17:4078-81. [DOI: 10.1021/acs.orglett.5b02010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zaichun Zhou
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xiaochun Zhou
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Qiuhua Liu
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xi Zhang
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Haomin Liu
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
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73
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Shimizu T, Huang D, Yan F, Stranava M, Bartosova M, Fojtíková V, Martínková M. Gaseous O2, NO, and CO in signal transduction: structure and function relationships of heme-based gas sensors and heme-redox sensors. Chem Rev 2015; 115:6491-533. [PMID: 26021768 DOI: 10.1021/acs.chemrev.5b00018] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Toru Shimizu
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
- §Research Center for Compact Chemical System, National Institute of Advanced Industrial Science and Technology (AIST), Sendai 983-8551, Japan
| | - Dongyang Huang
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Fang Yan
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Martin Stranava
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Martina Bartosova
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Veronika Fojtíková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Markéta Martínková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
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74
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Arora DP, Hossain S, Xu Y, Boon EM. Nitric Oxide Regulation of Bacterial Biofilms. Biochemistry 2015; 54:3717-28. [PMID: 25996573 DOI: 10.1021/bi501476n] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Biofilms are surface-associated, multicellular communities of bacteria. Once established, they are extremely difficult to eradicate by antimicrobial treatment. It has been demonstrated in many species that biofilm formation may be regulated by the diatomic signaling molecule nitric oxide (NO). Although this is still a relatively new area of research, we review here the literature reporting an effect of NO on bacterial biofilm formation, emphasizing dose-dependent responses to NO concentrations when possible. Where it has been investigated, the underlying NO sensors or signaling pathways are also discussed. Most of the examples of NO-mediated biofilm regulation have been documented with exogenously applied NO, but we also survey possible natural sources of NO in biofilm regulation, including endogenously generated NO. Finally, because of the apparent broad-spectrum, antibiofilm effects of NO, NO-releasing materials and prodrugs have also been explored in this minireview.
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Affiliation(s)
- Dhruv P Arora
- †Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Sajjad Hossain
- §Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Yueming Xu
- †Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Elizabeth M Boon
- †Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.,§Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
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75
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Nitric Oxide Mediates Biofilm Formation and Symbiosis in Silicibacter sp. Strain TrichCH4B. mBio 2015; 6:e00206-15. [PMID: 25944856 PMCID: PMC4436077 DOI: 10.1128/mbio.00206-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED Nitric oxide (NO) plays an important signaling role in all domains of life. Many bacteria contain a heme-nitric oxide/oxygen binding (H-NOX) protein that selectively binds NO. These H-NOX proteins often act as sensors that regulate histidine kinase (HK) activity, forming part of a bacterial two-component signaling system that also involves one or more response regulators. In several organisms, NO binding to the H-NOX protein governs bacterial biofilm formation; however, the source of NO exposure for these bacteria is unknown. In mammals, NO is generated by the enzyme nitric oxide synthase (NOS) and signals through binding the H-NOX domain of soluble guanylate cyclase. Recently, several bacterial NOS proteins have also been reported, but the corresponding bacteria do not also encode an H-NOX protein. Here, we report the first characterization of a bacterium that encodes both a NOS and H-NOX, thus resembling the mammalian system capable of both synthesizing and sensing NO. We characterized the NO signaling pathway of the marine alphaproteobacterium Silicibacter sp. strain TrichCH4B, determining that the NOS is activated by an algal symbiont, Trichodesmium erythraeum. NO signaling through a histidine kinase-response regulator two-component signaling pathway results in increased concentrations of cyclic diguanosine monophosphate, a key bacterial second messenger molecule that controls cellular adhesion and biofilm formation. Silicibacter sp. TrichCH4B biofilm formation, activated by T. erythraeum, may be an important mechanism for symbiosis between the two organisms, revealing that NO plays a previously unknown key role in bacterial communication and symbiosis. IMPORTANCE Bacterial nitric oxide (NO) signaling via heme-nitric oxide/oxygen binding (H-NOX) proteins regulates biofilm formation, playing an important role in protecting bacteria from oxidative stress and other environmental stresses. Biofilms are also an important part of symbiosis, allowing the organism to remain in a nutrient-rich environment. In this study, we show that in Silicibacter sp. strain TrichCH4B, NO mediates symbiosis with the alga Trichodesmium erythraeum, a major marine diazotroph. In addition, Silicibacter sp. TrichCH4B is the first characterized bacteria to harbor both the NOS and H-NOX proteins, making it uniquely capable of both synthesizing and sensing NO, analogous to mammalian NO signaling. Our study expands current understanding of the role of NO in bacterial signaling, providing a novel role for NO in bacterial communication and symbiosis.
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76
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Domingos P, Prado AM, Wong A, Gehring C, Feijo JA. Nitric oxide: a multitasked signaling gas in plants. MOLECULAR PLANT 2015; 8:506-20. [PMID: 25680232 DOI: 10.1016/j.molp.2014.12.010] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/11/2014] [Accepted: 12/14/2014] [Indexed: 05/20/2023]
Abstract
Nitric oxide (NO) is a gaseous reactive oxygen species (ROS) that has evolved as a signaling hormone in many physiological processes in animals. In plants it has been demonstrated to be a crucial regulator of development, acting as a signaling molecule present at each step of the plant life cycle. NO has also been implicated as a signal in biotic and abiotic responses of plants to the environment. Remarkably, despite this plethora of effects and functional relationships, the fundamental knowledge of NO production, sensing, and transduction in plants remains largely unknown or inadequately characterized. In this review we cover the current understanding of NO production, perception, and action in different physiological scenarios. We especially address the issues of enzymatic and chemical generation of NO in plants, NO sensing and downstream signaling, namely the putative cGMP and Ca(2+) pathways, ion-channel activity modulation, gene expression regulation, and the interface with other ROS, which can have a profound effect on both NO accumulation and function. We also focus on the importance of NO in cell-cell communication during developmental processes and sexual reproduction, namely in pollen tube guidance and embryo sac fertilization, pathogen defense, and responses to abiotic stress.
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Affiliation(s)
| | | | - Aloysius Wong
- Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Christoph Gehring
- Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jose A Feijo
- Instituto Gulbenkian de Ciência, P-2780-156 Oeiras, Portugal; Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Building, College Park, MD 20742-5815, USA.
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77
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Motion of proximal histidine and structural allosteric transition in soluble guanylate cyclase. Proc Natl Acad Sci U S A 2015; 112:E1697-704. [PMID: 25831539 DOI: 10.1073/pnas.1423098112] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We investigated the changes of heme coordination in purified soluble guanylate cyclase (sGC) by time-resolved spectroscopy in a time range encompassing 11 orders of magnitude (from 1 ps to 0.2 s). After dissociation, NO either recombines geminately to the 4-coordinate (4c) heme (τG1 = 7.5 ps; 97 ± 1% of the population) or exits the heme pocket (3 ± 1%). The proximal His rebinds to the 4c heme with a 70-ps time constant. Then, NO is distributed in two approximately equal populations (1.5%). One geminately rebinds to the 5c heme (τG2 = 6.5 ns), whereas the other diffuses out to the solution, from where it rebinds bimolecularly (τ = 50 μs with [NO] = 200 μM) forming a 6c heme with a diffusion-limited rate constant of 2 × 10(8) M(-1)⋅s(-1). In both cases, the rebinding of NO induces the cleavage of the Fe-His bond that can be observed as an individual reaction step. Saliently, the time constant of bond cleavage differs depending on whether NO binds geminately or from solution (τ5C1 = 0.66 μs and τ5C2 = 10 ms, respectively). Because the same event occurs with rates separated by four orders of magnitude, this measurement implies that sGC is in different structural states in both cases, having different strain exerted on the Fe-His bond. We show here that this structural allosteric transition takes place in the range 1-50 μs. In this context, the detection of NO binding to the proximal side of sGC heme is discussed.
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78
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Wobst J, Rumpf PM, Dang TA, Segura-Puimedon M, Erdmann J, Schunkert H. Molecular variants of soluble guanylyl cyclase affecting cardiovascular risk. Circ J 2015; 79:463-9. [PMID: 25746521 DOI: 10.1253/circj.cj-15-0025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Soluble guanylyl cyclase (sGC) is the physiological receptor for nitric oxide (NO) and NO-releasing drugs, and is a key enzyme in several cardiovascular signaling pathways. Its activation induces the synthesis of the second messenger cGMP. cGMP regulates the activity of various downstream proteins, including cGMP-dependent protein kinase G, cGMP-dependent phosphodiesterases and cyclic nucleotide gated ion channels leading to vascular relaxation, inhibition of platelet aggregation, and modified neurotransmission. Diminished sGC function contributes to a number of disorders, including cardiovascular diseases. Knowledge of its regulation is a prerequisite for understanding the pathophysiology of deficient sGC signaling. In this review we consolidate the available information on sGC signaling, including the molecular biology and genetics of sGC transcription, translation and function, including the effect of rare variants, and present possible new targets for the development of personalized medicine in vascular diseases.
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Affiliation(s)
- Jana Wobst
- Department of Cardiovascular Diseases, German Heart Center Munich, Technical University Munich
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Papapetropoulos A, Hobbs AJ, Topouzis S. Extending the translational potential of targeting NO/cGMP-regulated pathways in the CVS. Br J Pharmacol 2015; 172:1397-414. [PMID: 25302549 DOI: 10.1111/bph.12980] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 09/08/2014] [Accepted: 10/05/2014] [Indexed: 02/06/2023] Open
Abstract
The discovery of NO as both an endogenous signalling molecule and as a mediator of the cardiovascular effects of organic nitrates was acknowledged in 1998 by the Nobel Prize in Physiology/Medicine. The characterization of its downstream signalling, mediated through stimulation of soluble GC (sGC) and cGMP generation, initiated significant translational interest, but until recently this was almost exclusively embodied by the use of PDE5 inhibitors in erectile dysfunction. Since then, research progress in two areas has contributed to an impressive expansion of the therapeutic targeting of the NO-sGC-cGMP axis: first, an increased understanding of the molecular events operating within this complex pathway and second, a better insight into its dys-regulation and uncoupling in human disease. Already-approved PDE5 inhibitors and novel, first-in-class molecules, which up-regulate the activity of sGC independently of NO and/or of the enzyme's haem prosthetic group, are undergoing clinical evaluation to treat pulmonary hypertension and myocardial failure. These molecules, as well as combinations or second-generation compounds, are also being assessed in additional experimental disease models and in patients in a wide spectrum of novel indications, such as endotoxic shock, diabetic cardiomyopathy and Becker's muscular dystrophy. There is well-founded optimism that the modulation of the NO-sGC-cGMP pathway will sustain the development of an increasing number of successful clinical candidates for years to come.
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80
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Ishizuka T, Fukuzumi S, Kojima T. Molecular assemblies based on strong axial coordination in metal complexes of saddle-distorted dodecaphenylporphyrins. J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424615500273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this mini-review, we have highlighted our works on metal complexes having saddle-distorted dodecaphenylporphyrin (DPP) and its derivative as ligands in the light of enhancement of the Lewis acidity of a metal center coordinated by the porphyrin. The important point through this mini-review is ill-overlap of the out-of-plane lone pairs of pyrrole nitrogen atoms with σ-orbitals of the metal center bound to the saddle-distorted porphyrin core. The enhanced Lewis acidity of the central metal ions enabled us to construct stable molecular complexes through axial coordination using metal–DPP (M(DPP)) moieties ( M = Mo V or Sn IV ) and molecular or ionic entities with Lewis-basic coordination sites, including Keggin-type polyoxometallates (POM), which are known to have weak Lewis basicity and thus hard to coordinate to metal ions. A discrete 1:2 complex with a Ru -substituted POM performs catalytic substrate oxidation reactions in organic solvents. A 1:1 complex between Sn IV ( DPP ) and a Keggin-type POM exhibited photoinduced electron transfer, in which the Sn IV ( DPP ) moiety acts as an electron donor and the POM as an electron acceptor. Besides POM, other electron acceptors, including μ3-oxo trinuclear Ru III clusters and anthraquinone, having carboxyl groups as a linker unit also formed stable complexes with DPP-metal complexes as axial ligands to perform photoinduced electron transfer. Successful photoreactions of the M(DPP)-acceptor complexes are mainly enabled by the enhanced Lewis acidity of the DPP-metal complexes for the stabilization of the assemblies and also by lowering the oxidation potential of the porphyrin ligand to gain larger driving force of electron transfer to form an electron-transfer state with avoiding intersystem crossing. The stability and photochemical behavior are in sharp contrast to those for metal complexes with planar porphyrins as ligands.
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Affiliation(s)
- Tomoya Ishizuka
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University and ALCA, Japan Science and Technology Agency (JST), 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Takahiko Kojima
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
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81
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Herzik MA, Jonnalagadda R, Kuriyan J, Marletta MA. Structural insights into the role of iron-histidine bond cleavage in nitric oxide-induced activation of H-NOX gas sensor proteins. Proc Natl Acad Sci U S A 2014; 111:E4156-64. [PMID: 25253889 PMCID: PMC4210026 DOI: 10.1073/pnas.1416936111] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heme-nitric oxide/oxygen (H-NOX) binding domains are a recently discovered family of heme-based gas sensor proteins that are conserved across eukaryotes and bacteria. Nitric oxide (NO) binding to the heme cofactor of H-NOX proteins has been implicated as a regulatory mechanism for processes ranging from vasodilation in mammals to communal behavior in bacteria. A key molecular event during NO-dependent activation of H-NOX proteins is rupture of the heme-histidine bond and formation of a five-coordinate nitrosyl complex. Although extensive biochemical studies have provided insight into the NO activation mechanism, precise molecular-level details have remained elusive. In the present study, high-resolution crystal structures of the H-NOX protein from Shewanella oneidensis in the unligated, intermediate six-coordinate and activated five-coordinate, NO-bound states are reported. From these structures, it is evident that several structural features in the heme pocket of the unligated protein function to maintain the heme distorted from planarity. NO-induced scission of the iron-histidine bond triggers structural rearrangements in the heme pocket that permit the heme to relax toward planarity, yielding the signaling-competent NO-bound conformation. Here, we also provide characterization of a nonheme metal coordination site occupied by zinc in an H-NOX protein.
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Affiliation(s)
- Mark A Herzik
- Departments of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Rohan Jonnalagadda
- Departments of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - John Kuriyan
- Departments of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; Chemistry, University of California, Berkeley, CA 94720; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720; and Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Michael A Marletta
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037;
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82
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Narang BK, Roy S, Sharma R, Singh V, Rawal RK. Riociguat as a treatment regime for pulmonary arterial hypertension: a review. Clin Exp Hypertens 2014; 37:323-31. [PMID: 25268409 DOI: 10.3109/10641963.2014.960976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Pulmonary arterial hypertension (PAH) and chronic thromboembolic pulmonary hypertension (CTEPH) is a life-threatening condition distinguished by elevated pressure of pulmonary arteries and increased vascular resistance. The management of patients with PAH and CTEPH has advanced rapidly over last decade but despite the progress in the treatment, the survival of suffering patients remain unsatisfactory and there is no cure for the diseases. However, surgery is not a first choice for patients. Furthermore, some patients who undergo surgery have persistent pulmonary hypertension (HTN) as a side effect after surgery. Therefore, the search for an "ideal" therapy still goes on and it lead to the approval of riociguat as a potential agent for the treatment. It acts directly on soluble guanylate cyclase, exciting the enzyme, and elevating sensitivity to lower levels of NO. Riociguat, therefore, has potential as a novel therapy for PAH and CTEPH. This review is focused on various aspects of the recently approved "riociguat" including its efficacy and safety profiles with the clinical data highlighting its importance in the present scenario.
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Affiliation(s)
- Bawneet K Narang
- Department of Pharmaceutical Chemistry, Indo-Soviet Friendship College of Pharmacy , Ghal Kalan, Moga, Punjab , India and
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83
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Rogers NM, Seeger F, Garcin ED, Roberts DD, Isenberg JS. Regulation of soluble guanylate cyclase by matricellular thrombospondins: implications for blood flow. Front Physiol 2014; 5:134. [PMID: 24772092 PMCID: PMC3983488 DOI: 10.3389/fphys.2014.00134] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/18/2014] [Indexed: 01/16/2023] Open
Abstract
Nitric oxide (NO) maintains cardiovascular health by activating soluble guanylate cyclase (sGC) to increase cellular cGMP levels. Cardiovascular disease is characterized by decreased NO-sGC-cGMP signaling. Pharmacological activators and stimulators of sGC are being actively pursued as therapies for acute heart failure and pulmonary hypertension. Here we review molecular mechanisms that modulate sGC activity while emphasizing a novel biochemical pathway in which binding of the matricellular protein thrombospondin-1 (TSP1) to the cell surface receptor CD47 causes inhibition of sGC. We discuss the therapeutic implications of this pathway for blood flow, tissue perfusion, and cell survival under physiologic and disease conditions.
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Affiliation(s)
- Natasha M Rogers
- Department of Medicine, Vascular Medicine Institute, University of Pittsburgh School of Medicine Pittsburgh, PA, USA
| | - Franziska Seeger
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County Baltimore, MD, USA
| | - Elsa D Garcin
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County Baltimore, MD, USA
| | - David D Roberts
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, NIH Bethesda, MD, USA
| | - Jeffrey S Isenberg
- Department of Medicine, Vascular Medicine Institute, University of Pittsburgh School of Medicine Pittsburgh, PA, USA ; Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine Pittsburgh, PA, USA
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84
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Molecular mechanisms of heme based sensors from sediment organisms capable of extracellular electron transfer. J Inorg Biochem 2014; 133:104-9. [DOI: 10.1016/j.jinorgbio.2013.10.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/15/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022]
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85
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Seeger F, Quintyn R, Tanimoto A, Williams GJ, Tainer JA, Wysocki VH, Garcin ED. Interfacial residues promote an optimal alignment of the catalytic center in human soluble guanylate cyclase: heterodimerization is required but not sufficient for activity. Biochemistry 2014; 53:2153-65. [PMID: 24669844 PMCID: PMC3985721 DOI: 10.1021/bi500129k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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Soluble guanylate cyclase (sGC) plays
a central role in the cardiovascular
system and is a drug target for the treatment of pulmonary hypertension.
While the three-dimensional structure of sGC is unknown, studies suggest
that binding of the regulatory domain to the catalytic domain maintains
sGC in an autoinhibited basal state. The activation signal, binding
of NO to heme, is thought to be transmitted via the regulatory and
dimerization domains to the cyclase domain and unleashes the full
catalytic potential of sGC. Consequently, isolated catalytic domains
should show catalytic turnover comparable to that of activated sGC.
Using X-ray crystallography, activity measurements, and native mass
spectrometry, we show unambiguously that human isolated catalytic
domains are much less active than basal sGC, while still forming heterodimers.
We identified key structural elements regulating the dimer interface
and propose a novel role for residues located in an interfacial flap
and a hydrogen bond network as key modulators of the orientation of
the catalytic subunits. We demonstrate that even in the absence of
the regulatory domain, additional sGC domains are required to guide
the appropriate conformation of the catalytic subunits associated
with high activity. Our data support a novel regulatory mechanism
whereby sGC activity is tuned by distinct domain interactions that
either promote or inhibit catalytic activity. These results further
our understanding of heterodimerization and activation of sGC and
open additional drug discovery routes for targeting the NO–sGC–cGMP
pathway via the design of small molecules that promote a productive
conformation of the catalytic subunits or disrupt inhibitory domain
interactions.
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Affiliation(s)
- Franziska Seeger
- University of Maryland Baltimore County , Baltimore, Maryland 21250, United States
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86
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Lahiri T, Luan B, Raleigh DP, Boon EM. A structural basis for the regulation of an H-NOX-associated cyclic-di-GMP synthase/phosphodiesterase enzyme by nitric oxide-bound H-NOX. Biochemistry 2014; 53:2126-35. [PMID: 24628400 PMCID: PMC3985513 DOI: 10.1021/bi401597m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Biofilms
are surface-attached communities of bacteria enclosed
in a polysaccharide matrix. Bacteria in a biofilm are extremely resistant
to antibiotics. Several recent reports have linked the signaling molecule
nitric oxide (NO) with biofilm dispersal. We have previously reported
that an H-NOX (heme-nitric oxide/oxygen binding) protein in the biofilm-dwelling
bacterium Shewanella woodyi mediates NO-induced biofilm
dispersal. In S. woodyi, H-NOX (SwH-NOX) is cocistronic with a gene encoding a dual-functioning diguanylate
cyclase/phosphodiesterase
enzyme, designated here as HaCE (H-NOX-associated cyclic-di-GMP processing
enzyme). Enzymes such as these are responsible for regulating the
intracellular concentrations of cyclic-di-GMP, a secondary signaling
molecule essential to biofilm formation in bacteria. We have demonstrated
that NO-bound SwH-NOX regulates both enzymatic activities
of SwHaCE, resulting in decreased cellular cyclic-di-GMP
levels and disruption of biofilm formation. Thus, H-NOX/HaCE represents
a potential drug target for regulating biofilm formation. In this
work, the SwH-NOX surface residues critical for the
formation of a protein complex with SwHaCE are identified
using nuclear magnetic resonance, fluorescence quenching, and cosedimentation.
Enzyme assays confirm this protein–protein interface and its
importance for H-NOX/HaCE function.
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Affiliation(s)
- Tanaya Lahiri
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
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87
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Nierth A, Marletta MA. Directmeso-Alkynylation of Metalloporphyrins Through Gold Catalysis for Hemoprotein Engineering. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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88
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Nierth A, Marletta MA. Direct meso-alkynylation of metalloporphyrins through gold catalysis for hemoprotein engineering. Angew Chem Int Ed Engl 2014; 53:2611-4. [PMID: 24481709 DOI: 10.1002/anie.201310145] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 01/02/2023]
Abstract
A method was developed for the direct functionalization of metalloporphyrins at the methine protons (meso positions) to yield asymmetric alkynylated derivatives by using gold catalysis and hypervalent iodine reagents. This single-step procedure was applied to b-type heme and the product was incorporated into a gas-sensor heme protein. The terminal alkyne allows fluorophore labeling through copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Hemoproteins with this type of engineered cofactor have several potential applications in labeling and imaging technologies. Additionally, the alkyne provides a handle for modulating porphyrin electron density, which affects cofactor redox potential and ligand affinity. This method will be helpful for investigating the chemistry of natural heme proteins and for designing artificial variants with altered properties and reactivities.
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Affiliation(s)
- Alexander Nierth
- Department of Chemistry, Beckman Center for Chemical Sciences, BCC-556, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.scripps.edu/marletta
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89
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Purohit R, Fritz BG, The J, Issaian A, Weichsel A, David CL, Campbell E, Hausrath AC, Rassouli-Taylor L, Garcin ED, Gage MJ, Montfort WR. YC-1 binding to the β subunit of soluble guanylyl cyclase overcomes allosteric inhibition by the α subunit. Biochemistry 2013; 53:101-14. [PMID: 24328155 DOI: 10.1021/bi4015133] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Soluble guanylate cyclase (sGC) is a heterodimeric heme protein and the primary nitric oxide receptor. NO binding stimulates cyclase activity, leading to regulation of cardiovascular physiology and making sGC an attractive target for drug discovery. YC-1 and related compounds stimulate sGC both independently and synergistically with NO and CO binding; however, where the compounds bind and how they work remain unknown. Using linked equilibrium binding measurements, surface plasmon resonance, and domain truncations in Manduca sexta and bovine sGC, we demonstrate that YC-1 binds near or directly to the heme-containing domain of the β subunit. In the absence of CO, YC-1 binds with a Kd of 9-21 μM, depending on the construct. In the presence of CO, these values decrease to 0.6-1.1 μM. Pfizer compound 25 bound ∼10-fold weaker than YC-1 in the absence of CO, whereas compound BAY 41-2272 bound particularly tightly in the presence of CO (Kd = 30-90 nM). Additionally, we found that CO binds much more weakly to heterodimeric sGC proteins (Kd = 50-100 μM) than to the isolated heme domain (Kd = 0.2 μM for Manduca β H-NOX/PAS). YC-1 greatly enhanced binding of CO to heterodimeric sGC, as expected (Kd ∼ 1 μM). These data indicate the α subunit induces a heme pocket conformation with a lower affinity for CO and NO. YC-1 family compounds bind near the heme domain, overcoming the α subunit effect and inducing a heme pocket conformation with high affinity. We propose this high-affinity conformation is required for the full-length protein to achieve high catalytic activity.
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Affiliation(s)
- Rahul Purohit
- Department of Chemistry and Biochemistry, The University of Arizona , Tucson, Arizona 85721, United States
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90
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Wu G, Liu W, Berka V, Tsai AL. The selectivity of Vibrio cholerae H-NOX for gaseous ligands follows the "sliding scale rule" hypothesis. Ligand interactions with both ferrous and ferric Vc H-NOX. Biochemistry 2013; 52:9432-46. [PMID: 24351060 DOI: 10.1021/bi401408x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Vc H-NOX (or VCA0720) is an H-NOX (heme-nitric oxide and oxygen binding) protein from facultative aerobic bacterium Vibrio cholerae. It shares significant sequence homology with soluble guanylyl cyclase (sGC), a NO sensor protein commonly found in animals. Similar to sGC, Vc H-NOX binds strongly to NO and CO with affinities of 0.27 nM and 0.77 μM, respectively, but weakly to O2. When positioned on a "sliding scale" plot [Tsai, A.-l., et al. (2012) Biochemistry 51, 172-186], the line connecting log K(D)(NO) and log K(D)(CO) of Vc H-NOX can almost be superimposed with that of Ns H-NOX. Therefore, the measured affinities and kinetic parameters of gaseous ligands to Vc H-NOX provide more evidence to validate the "sliding scale rule" hypothesis. Like sGC, Vc H-NOX binds NO in multiple steps, forming first a six-coordinate heme-NO complex at a rate of 1.1 × 10(9) M(-1) s(-1), and then converts to a five-coordinate heme-NO complex at a rate that is also dependent on NO concentration. Although the formation of oxyferrous Vc H-NOX cannot be detected at a normal atmospheric oxygen level, ferrous Vc H-NOX is oxidized to the ferric form at a rate of 0.06 s(-1) when mixed with O2. Ferric Vc H-NOX exists as a mixture of high- and low-spin states and is influenced by binding to different ligands. Characterization of both ferric and ferrous Vc H-NOX and their complexes with various ligands lays the foundation for understanding the possible dual roles in gas and redox sensing of Vc H-NOX.
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Affiliation(s)
- Gang Wu
- Division of Hematology, Department of Internal Medicine, The University of Texas-Medical School at Houston , 6431 Fannin Street, Houston, Texas 77030, United States
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91
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Nitric oxide-sensing H-NOX proteins govern bacterial communal behavior. Trends Biochem Sci 2013; 38:566-75. [PMID: 24113192 DOI: 10.1016/j.tibs.2013.08.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 11/22/2022]
Abstract
Heme-nitric oxide/oxygen binding (H-NOX) domains function as sensors for the gaseous signaling agent nitric oxide (NO) in eukaryotes and bacteria. Mammalian NO signaling is well characterized and involves the H-NOX domain of soluble guanylate cyclase. In bacteria, H-NOX proteins interact with bacterial signaling proteins in two-component signaling systems or in cyclic-di-GMP metabolism. Characterization of several downstream signaling processes has shown that bacterial H-NOX proteins share a common role in controlling important bacterial communal behaviors in response to NO. The H-NOX pathways regulate motility, biofilm formation, quorum sensing, and symbiosis. Here, we review the latest structural and mechanistic studies that have elucidated how H-NOX domains selectively bind NO and transduce ligand binding into conformational changes that modulate activity of signaling partners. Furthermore, we summarize the recent advances in understanding the physiological function and biochemical details of the H-NOX signaling pathways.
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92
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Purohit R, Weichsel A, Montfort WR. Crystal structure of the Alpha subunit PAS domain from soluble guanylyl cyclase. Protein Sci 2013; 22:1439-44. [PMID: 23934793 DOI: 10.1002/pro.2331] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 03/31/2013] [Accepted: 08/05/2013] [Indexed: 12/26/2022]
Abstract
Soluble guanylate cyclase (sGC) is a heterodimeric heme protein of ≈ 150 kDa and the primary nitric oxide receptor. Binding of NO stimulates cyclase activity, leading to regulation of cardiovascular physiology and providing attractive opportunities for drug discovery. How sGC is stimulated and where candidate drugs bind remains unknown. The α and β sGC chains are each composed of Heme-Nitric Oxide Oxygen (H-NOX), Per-ARNT-Sim (PAS), coiled-coil and cyclase domains. Here, we present the crystal structure of the α1 PAS domain to 1.8 Å resolution. The structure reveals the binding surfaces of importance to heterodimer function, particularly with respect to regulating NO binding to heme in the β1 H-NOX domain. It also reveals a small internal cavity that may serve to bind ligands or participate in signal transduction.
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Affiliation(s)
- Rahul Purohit
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721
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93
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Liao MS, Huang MJ, Watts JD. Binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins. A theoretical study. J Phys Chem B 2013; 117:10103-14. [PMID: 23926882 PMCID: PMC3810174 DOI: 10.1021/jp403998u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins has been investigated with DFT as well as dispersion-corrected DFT methods. The local protein environment was accounted for by including the six nearest surrounding residues in the studied systems. Attention was also paid to the effects of the protein environment, particularly the distal Tyr140, on the proximal iron-histidine (Fe-His) binding. The Heme-AB (AB = O2, NO) and Fe-His binding energies in iron porphyrin FeP(His)(AB), myoglobin Mb(AB), H-NOX(AB), and Tyr140 → Phe mutated H-NOX[Y140F(AB)] were determined for comparison. The calculated stabilization of bound O2 is even higher in H-NOX than that in a myoglobin (Mb), consistent with the observation that the H-NOX domain of T. tengcongensis has a very high affinity for its oxygen molecule. Among the two different X-ray crystal structures for the Tt H-NOX protein, the calculated results for both AB = O2 and NO appear to support the crystal structure with the PDB code 1XBN , where the Trp9 and Asn74 residues do not form a hydrogen-bonding network with Tyr140. A hydrogen bond interaction from the polar residue does not have obvious effects on the Fe-His binding strength, but a dispersion contribution to Ebind(Fe-His) may be significant, depending on the crystal structure used. We speculate that the Fe-His binding strength in the deoxy form of a native protein could be an important factor in determining whether the bond of His to Fe is broken or maintained upon binding of NO to Fe.
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Affiliation(s)
- Meng-Sheng Liao
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - Ming-Ju Huang
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - John D. Watts
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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94
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Insights into the distal heme pocket of H-NOX using fluoride as a probe for H-bonding interactions. J Inorg Biochem 2013; 126:91-5. [DOI: 10.1016/j.jinorgbio.2013.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/23/2013] [Accepted: 05/24/2013] [Indexed: 11/19/2022]
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95
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Follmann M, Griebenow N, Hahn MG, Hartung I, Mais FJ, Mittendorf J, Schäfer M, Schirok H, Stasch JP, Stoll F, Straub A. The chemistry and biology of soluble guanylate cyclase stimulators and activators. Angew Chem Int Ed Engl 2013; 52:9442-62. [PMID: 23963798 DOI: 10.1002/anie.201302588] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Indexed: 12/14/2022]
Abstract
The vasodilatory properties of nitric oxide (NO) have been utilized in pharmacotherapy for more than 130 years. Still today, NO-donor drugs are important in the management of cardiovascular diseases. However, inhaled NO or drugs releasing NO and organic nitrates are associated with noteworthy therapeutic shortcomings, including resistance to NO in some disease states, the development of tolerance during long-term treatment, and nonspecific effects, such as post-translational modification of proteins. The beneficial actions of NO are mediated by stimulation of soluble guanylate cyclase (sGC), a heme-containing enzyme which produces the intracellular signaling molecule cyclic guanosine monophosphate (cGMP). Recently, two classes of compounds have been discovered that amplify the function of sGC in a NO-independent manner, the so-called sGC stimulators and sGC activators. The most advanced drug, the sGC stimulator riociguat, has successfully undergone Phase III clinical trials for different forms of pulmonary hypertension.
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Affiliation(s)
- Markus Follmann
- Bayer Pharma Aktiengesellschaft, Global Drug Discovery, Aprather Weg 18a, 42113 Wuppertal, Germany.
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96
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Follmann M, Griebenow N, Hahn MG, Hartung I, Mais FJ, Mittendorf J, Schäfer M, Schirok H, Stasch JP, Stoll F, Straub A. Chemie und Biologie der Stimulatoren und Aktivatoren der löslichen Guanylatcyclase. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302588] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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97
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Wirth AJ, Gruebele M. Quinary protein structure and the consequences of crowding in living cells: leaving the test-tube behind. Bioessays 2013; 35:984-93. [PMID: 23943406 DOI: 10.1002/bies.201300080] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Although the importance of weak protein-protein interactions has been understood since the 1980s, scant attention has been paid to this "quinary structure". The transient nature of quinary structure facilitates dynamic sub-cellular organization through loose grouping of proteins with multiple binding partners. Despite our growing appreciation of the quinary structure paradigm in cell biology, we do not yet understand how the many forces inside the cell--the excluded volume effect, the "stickiness" of the cytoplasm, and hydrodynamic interactions--perturb the weakest functional protein interactions. We discuss the unresolved problem of how the forces in the cell modulate quinary structure, and to what extent the cell has evolved to exert control over the weakest biomolecular interactions. We conclude by highlighting the new experimental and computational tools coming on-line for in vivo studies, which are a critical next step if we are to understand quinary structure in its native environment.
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Affiliation(s)
- Anna Jean Wirth
- Department of Chemistry, University of Illinois, Urbana, IL, USA
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98
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Weinert EE, Phillips-Piro CM, Marletta MA. Porphyrin π-stacking in a heme protein scaffold tunes gas ligand affinity. J Inorg Biochem 2013; 127:7-12. [PMID: 23831583 DOI: 10.1016/j.jinorgbio.2013.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022]
Abstract
The role of π-stacking in controlling redox and ligand binding properties of porphyrins has been of interest for many years. The recent discovery of H-NOX domains has provided a model system to investigate the role of porphyrin π-stacking within a heme protein scaffold. Removal of a phenylalanine-porphyrin π-stack dramatically increased O2, NO, and CO affinities and caused changes in redox potential (~40mV) without any structural changes. These results suggest that small changes in redox potential affect ligand affinity and that π-stacking may provide a novel route to engineer heme protein properties for new functions.
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Affiliation(s)
- Emily E Weinert
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
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99
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Abstract
Heme is a prosthetic group best known for roles in oxygen transport, oxidative catalysis, and respiratory electron transport. Recent years have seen the roles of heme extended to sensors of gases such as O2 and NO and cell redox state, and as mediators of cellular responses to changes in intracellular levels of these gases. The importance of heme is further evident from identification of proteins that bind heme reversibly, using it as a signal, e.g. to regulate gene expression in circadian rhythm pathways and control heme synthesis itself. In this minireview, we explore the current knowledge of the diverse roles of heme sensor proteins.
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Affiliation(s)
- Hazel M. Girvan
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Andrew W. Munro
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
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100
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Zhang Y, Liu L, Wu L, Li S, Li F, Li Z. Theoretical investigation on the diatomic ligand migration process and ligand binding properties in non-O2-binding H-NOX domain. Proteins 2013; 81:1363-76. [PMID: 23504767 DOI: 10.1002/prot.24279] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 02/08/2013] [Accepted: 02/23/2013] [Indexed: 01/26/2023]
Abstract
The Nostoc sp (Ns) H-NOX (heme-nitric oxide or OXygen-binding) domain shares 35% sequence identity with soluble guanylate cyclase (sGC) and exhibits similar ligand binding property with the sGC. Previously, our molecular dynamic (MD) simulation work identified that there exists a Y-shaped tunnel system hosted in the Ns H-NOX interior, which servers for ligand migration. The tunnels were then confirmed by Winter et al. [PNAS 2011;108(43):E 881-889] recently using x-ray crystallography with xenon pressured conditions. In this work, to further investigate how the protein matrix of Ns H-NOX modulates the ligand migration process and how the distal residue composition affects the ligand binding prosperities, the free energy profiles for nitric oxide (NO), carbon monooxide (CO), and O2 migration are explored using the steered MDs simulation and the ligand binding energies are calculated using QM/MM schemes. The potential of mean force profiles suggest that the longer branch of the tunnel would be the most favorable route for NO migration and a second NO trapping site other than the distal heme pocket along this route in the Ns H-NOX was identified. On the contrary, CO and O2 would prefer to diffuse via the shorter branch of the tunnel. The QM/MM (quantum mechanics/molecular mechanics) calculations suggest that the hydrophobic distal pocket of Ns H-NOX would provide an approximately vacuum environment and the ligand discrimination would be determined by the intrinsic binding properties of the diatomic gas ligand to the heme group.
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Affiliation(s)
- Yuebin Zhang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, College of Life Sciences, Jilin University, Chang Chun 130012, People's Republic of China
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