1
|
De Simone G, di Masi A, Sbardella D, Ascenzi P, Coletta M. Nitric Oxide Binding Geometry in Heme-Proteins: Relevance for Signal Transduction. Antioxidants (Basel) 2024; 13:666. [PMID: 38929104 PMCID: PMC11201058 DOI: 10.3390/antiox13060666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Nitric oxide (NO) synthesis, signaling, and scavenging is associated to relevant physiological and pathological events. In all tissues and organs, NO levels and related functions are regulated at different levels, with heme proteins playing pivotal roles. Here, we focus on the structural changes related to the different binding modes of NO to heme-Fe(II), as well as the modulatory effects of this diatomic messenger on heme-protein functions. Specifically, the ability of heme proteins to bind NO at either the distal or proximal side of the heme and the transient interchanging of the binding site is reported. This sheds light on the regulation of O2 supply to tissues with high metabolic activity, such as the retina, where a precise regulation of blood flow is necessary to meet the demand of nutrients.
Collapse
Affiliation(s)
- Giovanna De Simone
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
| | - Alessandra di Masi
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
- Centro Linceo Interdisciplinare “Beniamino Segre”, Accademia dei Lincei, 00165 Rome, Italy
| | | | - Paolo Ascenzi
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
- Accademia Nazionale dei Lincei, 00165 Rome, Italy
| | | |
Collapse
|
2
|
Adams HR, Svistunenko DA, Wilson MT, Fujii S, Strange RW, Hardy ZA, Vazquez PA, Dabritz T, Streblow GJ, Andrew CR, Hough MA. A Heme Pocket Aromatic Quadrupole Modulates Gas Binding to Cytochrome c'-β: Implications for NO Sensors. J Biol Chem 2023:104742. [PMID: 37100286 DOI: 10.1016/j.jbc.2023.104742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023] Open
Abstract
The structural basis by which gas-binding heme proteins control their interactions with NO, CO, and O2, is fundamental to enzymology, biotechnology and human health. Cytochromes c´ (cyts c´) are a group of putative NO-binding heme proteins that fall into two families: the well characterised four alpha helix bundle fold (cyts c´-α) and an unrelated family with a largely beta sheet fold (cyts c´-β) resembling that of cytochromes P460. A recent structure of cyt c´-β from Methylococcus capsulatus Bath (McCP-β) revealed two heme pocket phenylalanine residues (Phe 32 and Phe 61) positioned near the distal gas binding site. This feature, dubbed the "Phe cap", is highly conserved within the sequences of other cyts c´-β, but is absent in their close homologues, the hydroxylamine oxidizing cytochromes P460, although some do contain a single Phe residue. Here we report an integrated structural, spectroscopic, and kinetic characterization of McCP-β complexes with diatomic gases, focusing on the interaction of the Phe cap with NO and CO. Significantly, crystallographic and resonance Raman data show that orientation of the electron rich aromatic ring face of Phe 32 towards distally-bound NO or CO is associated with weakened backbonding and higher off rates. Moreover, we propose that an aromatic quadrupole also contributes to the unusually weak backbonding reported for some heme-based gas sensors, including the mammalian NO-sensor, soluble guanylate cyclase (sGC). Collectively, this study sheds light on the influence of highly conserved distal Phe residues on heme-gas complexes of cytochrome c'-β, including the potential for aromatic quadrupoles to modulate NO and CO binding in other heme proteins.
Collapse
Affiliation(s)
- Hannah R Adams
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima, Hiroshima, 739-8528, Japan; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Richard W Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Zoe A Hardy
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Priscilla A Vazquez
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Tyler Dabritz
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Gabriel J Streblow
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Colin R Andrew
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA.
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| |
Collapse
|
3
|
Liu R, Kang Y, Chen L. NO binds to the distal site of haem in the fully activated soluble guanylate cyclase. Nitric Oxide 2023; 134-135:17-22. [PMID: 36972843 DOI: 10.1016/j.niox.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/09/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO). The binding of NO to the haem of sGC induces a large conformational change in the enzyme and activates its cyclase activity. However, whether NO binds to the proximal site or the distal site of haem in the fully activated state remains under debate. Here, we present cryo-EM maps of sGC in the NO-activated state at high resolutions, allowing the observation of the density of NO. These cryo-EM maps show the binding of NO to the distal site of haem in the NO-activated state.
Collapse
Affiliation(s)
- Rui Liu
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, 100871, China; National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Yunlu Kang
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, 100871, China; National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Lei Chen
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, 100871, China; National Biomedical Imaging Center, Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| |
Collapse
|
4
|
Karaa A, Klopstock T. Clinical trials in mitochondrial diseases. HANDBOOK OF CLINICAL NEUROLOGY 2023; 194:229-250. [PMID: 36813315 DOI: 10.1016/b978-0-12-821751-1.00002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Primary mitochondrial diseases are some of the most common and complex inherited inborn errors of metabolism. Their molecular and phenotypic diversity has led to difficulties in finding disease-modifying therapies and clinical trial efforts have been slow due to multiple significant challenges. Lack of robust natural history data, difficulties in finding specific biomarkers, absence of well-validated outcome measures, and small patient numbers have made clinical trial design and conduct difficult. Encouragingly, new interest in treating mitochondrial dysfunction in common diseases and regulatory incentives to develop therapies for rare conditions have led to significant interest and efforts to develop drugs for primary mitochondrial diseases. Here, we review past and present clinical trials and future strategies of drug development in primary mitochondrial diseases.
Collapse
Affiliation(s)
- Amel Karaa
- Mitochondrial Disease Program, Division of Medical Genetics and Metabolism, Massachusetts General Hospital, Boston, MA, United States; Department of Pediatrics, Harvard Medical School, Boston, MA, United States.
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; German Network for mitochondrial disorders (mitoNET), Munich, Germany
| |
Collapse
|
5
|
Sharina I, Martin E. Cellular Factors That Shape the Activity or Function of Nitric Oxide-Stimulated Soluble Guanylyl Cyclase. Cells 2023; 12:471. [PMID: 36766813 PMCID: PMC9914232 DOI: 10.3390/cells12030471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
NO-stimulated guanylyl cyclase (SGC) is a hemoprotein that plays key roles in various physiological functions. SGC is a typical enzyme-linked receptor that combines the functions of a sensor for NO gas and cGMP generator. SGC possesses exclusive selectivity for NO and exhibits a very fast binding of NO, which allows it to function as a sensitive NO receptor. This review describes the effect of various cellular factors, such as additional NO, cell thiols, cell-derived small molecules and proteins on the function of SGC as cellular NO receptor. Due to its vital physiological function SGC is an important drug target. An increasing number of synthetic compounds that affect SGC activity via different mechanisms are discovered and brought to clinical trials and clinics. Cellular factors modifying the activity of SGC constitute an opportunity for improving the effectiveness of existing SGC-directed drugs and/or the creation of new therapeutic strategies.
Collapse
Affiliation(s)
| | - Emil Martin
- Department of Internal Medicine, Cardiology Division, The University of Texas—McGovern Medical School, 1941 East Road, Houston, TX 77054, USA
| |
Collapse
|
6
|
Wu G, Sharina I, Martin E. Soluble guanylyl cyclase: Molecular basis for ligand selectivity and action in vitro and in vivo. Front Mol Biosci 2022; 9:1007768. [PMID: 36304925 PMCID: PMC9592903 DOI: 10.3389/fmolb.2022.1007768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/27/2022] [Indexed: 01/14/2023] Open
Abstract
Nitric oxide (NO), carbon monoxide (CO), oxygen (O2), hydrogen sulfide (H2S) are gaseous molecules that play important roles in the physiology and pathophysiology of eukaryotes. Tissue concentrations of these physiologically relevant gases vary remarkable from nM range for NO to high μM range of O2. Various hemoproteins play a significant role in sensing and transducing cellular signals encoded by gaseous molecules or in transporting them. Soluble guanylyl cyclase (sGC) is a hemoprotein that plays vital roles in a wide range of physiological functions and combines the functions of gaseous sensor and signal transducer. sGC uniquely evolved to sense low non-toxic levels of NO and respond to elevated NO levels by increasing its catalytic ability to generate the secondary signaling messenger cyclic guanosine monophosphate (cGMP). This review discusses sGC's gaseous ligand selectivity and the molecular basis for sGC function as high-affinity and selectivity NO receptor. The effects of other gaseous molecules and small molecules of cellular origin on sGC's function are also discussed.
Collapse
Affiliation(s)
- Gang Wu
- Hematology-Oncology Division, Department of Internal Medicine, The University of Texas—McGovern Medical School, Houston, TX, United States,*Correspondence: Gang Wu, ; Emil Martin,
| | - Iraida Sharina
- Cardiology Division, Department of Internal Medicine, The University of Texas—McGovern Medical School, Houston, TX, United States
| | - Emil Martin
- Cardiology Division, Department of Internal Medicine, The University of Texas—McGovern Medical School, Houston, TX, United States,*Correspondence: Gang Wu, ; Emil Martin,
| |
Collapse
|
7
|
Rozza AM, Papp M, McFarlane NR, Harvey JN, Oláh J. The Mechanism of Biochemical NO-Sensing: Insights from Computational Chemistry. Chemistry 2022; 28:e202200930. [PMID: 35670519 PMCID: PMC9542423 DOI: 10.1002/chem.202200930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/22/2022]
Abstract
The binding of small gas molecules such as NO and CO plays a major role in the signaling routes of the human body. The sole NO-receptor in humans is soluble guanylyl cyclase (sGC) - a histidine-ligated heme protein, which, upon NO binding, activates a downstream signaling cascade. Impairment of NO-signaling is linked, among others, to cardiovascular and inflammatory diseases. In the present work, we use a combination of theoretical tools such as MD simulations, high-level quantum chemical calculations and hybrid QM/MM methods to address various aspects of NO binding and to elucidate the most likely reaction paths and the potential intermediates of the reaction. As a model system, the H-NOX protein from Shewanella oneidensis (So H-NOX) homologous to the NO-binding domain of sGC is used. The signaling route is predicted to involve NO binding to form a six-coordinate intermediate heme-NO complex, followed by relatively facile His decoordination yielding a five-coordinate adduct with NO on the distal side with possible isomerization to the proximal side through binding of a second NO and release of the first one. MD simulations show that the His sidechain can quite easily rotate outward into solvent, with this motion being accompanied in our simulations by shifts in helix positions that are consistent with this decoordination leading to significant conformational change in the protein.
Collapse
Affiliation(s)
- Ahmed M. Rozza
- Department of Inorganic and Analytical ChemistryBudapest University of Technology and Economics1111Budapest Műegyetem rakpart 3.Hungary
- Department of BiotechnologyFaculty of AgricultureAl-Azhar UniversityCairo11651Egypt
| | - Marcell Papp
- Department of Inorganic and Analytical ChemistryBudapest University of Technology and Economics1111Budapest Műegyetem rakpart 3.Hungary
| | - Neil R. McFarlane
- Department of ChemistryKU Leuven3001LeuvenCelestijnenlaan 200 f- box 2404Belgium
| | - Jeremy N. Harvey
- Department of ChemistryKU Leuven3001LeuvenCelestijnenlaan 200 f- box 2404Belgium
| | - Julianna Oláh
- Department of Inorganic and Analytical ChemistryBudapest University of Technology and Economics1111Budapest Műegyetem rakpart 3.Hungary
| |
Collapse
|
8
|
Lu W, Yang X, Wang B. Carbon monoxide signaling and soluble guanylyl cyclase: Facts, myths, and intriguing possibilities. Biochem Pharmacol 2022; 200:115041. [PMID: 35447132 DOI: 10.1016/j.bcp.2022.115041] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/12/2022]
Abstract
The endogenous signaling roles of carbon monoxide (CO) have been firmly established at the pathway level. For CO's molecular mechanism(s) of actions, hemoproteins are generally considered as possible targets. Importantly, soluble guanylyl cyclase (sGC) is among the most widely referenced molecular targets. However, the affinity of CO for sGC (Kd: 240 μM) is much lower than for other highly abundant hemoproteins in the body, such as myoglobin (Kd: 29 nM) and hemoglobin (Kd: 0.7 nM-4.5 μM), which serve as CO reservoirs. Further, most of the mechanistic studies involving sGC activation by CO were based on in-vitro or ex-vivo studies using CO concentrations not readily attenable in vivo and in the absence of hemoglobin as a competitor in binding. As such, whether such in-vitro/ex-vivo results can be directly extrapolated to in-vivo studies is not clear because of the need for CO to be transferred from a high-affinity binder (e.g., hemoglobin) to a low-affinity target if sGC is to be activated in vivo. In this review, we discuss literature findings of sGC activation by CO and the experimental conditions; examine the myths in the disconnect between the low affinity of sGC for CO and the reported activation of sGC by CO; and finally present several possibilities that may lead to additional studies to improve our understanding of this direct CO-sGC axis, which is yet to be convincingly established as playing generally critical roles in CO signaling in vivo.
Collapse
Affiliation(s)
- Wen Lu
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| |
Collapse
|
9
|
Kamkin AG, Kamkina OV, Shim AL, Bilichenko A, Mitrokhin VM, Kazansky VE, Filatova TS, Abramochkin D, Mladenov MI. The role of activation of two different sGC binding sites by NO-dependent and NO-independent mechanisms in the regulation of SACs in rat ventricular cardiomyocytes. Physiol Rep 2022; 10:e15246. [PMID: 35384354 PMCID: PMC8981922 DOI: 10.14814/phy2.15246] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 04/18/2023] Open
Abstract
The mechanoelectrical feedback (MEF) mechanism in the heart that plays a significant role in the occurrence of arrhythmias, involves cation flux through cation nonselective stretch-activated channels (SACs). It is well known that nitric oxide (NO) can act as a regulator of MEF. Here we addressed the possibility of SAC's regulation along NO-dependent and NO-independent pathways, as well as the possibility of S-nitrosylation of SACs. In freshly isolated rat ventricular cardiomyocytes, using the patch-clamp method in whole-cell configuration, inward nonselective stretch-activated cation current ISAC was recorded through SACs, which occurs during dosed cell stretching. NO donor SNAP, α1-subunit of sGC activator BAY41-2272, sGC blocker ODQ, PKG blocker KT5823, PKG activator 8Br-cGMP, and S-nitrosylation blocker ascorbic acid, were employed. We concluded that the physiological concentration of NO in the cell is a necessary condition for the functioning of SACs. An increase in NO due to SNAP in an unstretched cell causes the appearance of a Gd3+ -sensitive nonselective cation current, an analog of ISAC , while in a stretched cell it eliminates ISAC . The NO-independent pathway of sGC activation of α subunit, triggered by BAY41-2272, is also important for the regulation of SACs. Since S-nitrosylation inhibitor completely abolishes ISAC , this mechanism occurs. The application of BAY41-2272 cannot induce ISAC in a nonstretched cell; however, the addition of SNAP on its background activates SACs, rather due to S-nitrosylation. ODQ eliminates ISAC , but SNAP added on the background of stretch increases ISAC in addition to ODQ. This may be a result of the lack of NO as a result of inhibition of NOS by metabolically modified ODQ. KT5823 reduces PKG activity and reduces SACs phosphorylation, leading to an increase in ISAC . 8Br-cGMP reduces ISAC by activating PKG and its phosphorylation. These results demonstrate a significant contribution of S-nitrosylation to the regulation of SACs.
Collapse
Affiliation(s)
- Andre G. Kamkin
- Department of PhysiologyPirogov Russian National Research Medical UniversityMoscowRussia
| | - Olga V. Kamkina
- Department of PhysiologyPirogov Russian National Research Medical UniversityMoscowRussia
| | - Andrey L. Shim
- Department of PhysiologyPirogov Russian National Research Medical UniversityMoscowRussia
| | - Andrey Bilichenko
- Department of PhysiologyPirogov Russian National Research Medical UniversityMoscowRussia
| | - Vadim M. Mitrokhin
- Department of PhysiologyPirogov Russian National Research Medical UniversityMoscowRussia
| | - Viktor E. Kazansky
- Department of PhysiologyPirogov Russian National Research Medical UniversityMoscowRussia
| | - Tatiana S. Filatova
- Department of PhysiologyPirogov Russian National Research Medical UniversityMoscowRussia
- Department of Human and Animal PhysiologyLomonosov Moscow State UniversityMoscowRussia
| | - Denis V. Abramochkin
- Department of PhysiologyPirogov Russian National Research Medical UniversityMoscowRussia
- Department of Human and Animal PhysiologyLomonosov Moscow State UniversityMoscowRussia
| | - Mitko I. Mladenov
- Department of PhysiologyPirogov Russian National Research Medical UniversityMoscowRussia
- Faculty of Natural Sciences and MathematicsInstitute of Biology, “Ss. Cyril and Methodius” UniversitySkopjeMacedonia
| |
Collapse
|
10
|
Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
Collapse
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
11
|
A new paradigm for gaseous ligand selectivity of hemoproteins highlighted by soluble guanylate cyclase. J Inorg Biochem 2020; 214:111267. [PMID: 33099233 DOI: 10.1016/j.jinorgbio.2020.111267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/23/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023]
Abstract
Nitric oxide (NO), carbon monoxide (CO), and oxygen (O2) are important physiological messengers whose concentrations vary in a remarkable range, [NO] typically from nM to several μM while [O2] reaching to hundreds of μM. One of the machineries evolved in living organisms for gas sensing is sensor hemoproteins whose conformational change upon gas binding triggers downstream response cascades. The recently proposed "sliding scale rule" hypothesis provides a general interpretation for gaseous ligand selectivity of hemoproteins, identifying five factors that govern gaseous ligand selectivity. Hemoproteins have intrinsic selectivity for the three gases due to a neutral proximal histidine ligand while proximal strain of heme and distal steric hindrance indiscriminately adjust the affinity of these three gases for heme. On the other hand, multiple-step NO binding and distal hydrogen bond donor(s) specifically enhance affinity for NO and O2, respectively. The "sliding scale rule" hypothesis provides clear interpretation for dramatic selectivity for NO over O2 in soluble guanylate cyclase (sGC) which is an important example of sensor hemoproteins and plays vital roles in a wide range of physiological functions. The "sliding scale rule" hypothesis has so far been validated by all experimental data and it may guide future designs for heme-based gas sensors.
Collapse
|
12
|
Geeraerts Z, Heskin AK, DuBois J, Rodgers KR, Lukat-Rodgers GS. Structure and reactivity of chlorite dismutase nitrosyls. J Inorg Biochem 2020; 211:111203. [PMID: 32768737 PMCID: PMC7749827 DOI: 10.1016/j.jinorgbio.2020.111203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 11/28/2022]
Abstract
Ferric nitrosyl ({FeNO}6) and ferrous nitrosyl ({FeNO}7) complexes of the chlorite dismutases (Cld) from Klebsiella pneumoniae and Dechloromonas aromatica have been characterized using UV-visible absorbance and Soret-excited resonance Raman spectroscopy. Both of these Clds form kinetically stable {FeNO}6 complexes and they occupy a unique region of ν(Fe-NO)/ν(N-O) correlation space for proximal histidine liganded heme proteins, characteristic of weak Fe-NO and N-O bonds. This location is attributed to admixed FeIII-NO character of the {FeNO}6 ground state. Cld {FeNO}6 complexes undergo slow reductive nitrosylation to yield {FeNO}7 complexes. The effects of proximal and distal environment on reductive nitroylsation rates for these dimeric and pentameric Clds are reported. The ν(Fe-NO) and ν(N-O) frequencies for Cld {FeNO}7 complexes reveal both six-coordinate (6c) and five-coordinate (5c) nitrosyl hemes. These 6c and 5c forms are in a pH dependent equilibrium. The 6c and 5c {FeNO}7 Cld frequencies provided positions of both Clds on their respective ν(Fe-NO) vs ν(N-O) correlation lines. The 6c {FeNO}7 complexes fall below (along the ν(Fe-NO) axis) the correlation line that reports hydrogen-bond donation to NNO, which is consistent with a relatively weak Fe-NO bond. Kinetic and spectroscopic evidence is consistent with the 5c {FeNO}7 Clds having NO coordinated on the proximal side of the heme, analogous to 5c {FeNO}7 hemes in proteins known to have NO sensing functions.
Collapse
Affiliation(s)
- Zachary Geeraerts
- North Dakota State University, Fargo, ND 58108, United States of America
| | - Alisa K Heskin
- North Dakota State University, Fargo, ND 58108, United States of America
| | - Jennifer DuBois
- Montana State University, Bozeman, MT 59717, United States of America
| | - Kenton R Rodgers
- North Dakota State University, Fargo, ND 58108, United States of America.
| | | |
Collapse
|
13
|
Almannai M, El-Hattab AW, Ali M, Soler-Alfonso C, Scaglia F. Clinical trials in mitochondrial disorders, an update. Mol Genet Metab 2020; 131:1-13. [PMID: 33129691 PMCID: PMC7537630 DOI: 10.1016/j.ymgme.2020.10.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/02/2020] [Indexed: 12/11/2022]
Abstract
Mitochondrial disorders comprise a molecular and clinically diverse group of diseases that are associated with mitochondrial dysfunction leading to multi-organ disease. With recent advances in molecular technologies, the understanding of the pathomechanisms of a growing list of mitochondrial disorders has been greatly expanded. However, the therapeutic approaches for mitochondrial disorders have lagged behind with treatment options limited mainly to symptom specific therapies and supportive measures. There is an increasing number of clinical trials in mitochondrial disorders aiming for more specific and effective therapies. This review will cover different treatment modalities currently used in mitochondrial disorders, focusing on recent and ongoing clinical trials.
Collapse
Affiliation(s)
- Mohammed Almannai
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - May Ali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Claudia Soler-Alfonso
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, Shatin, Hong Kong.
| |
Collapse
|
14
|
Rozza AM, Menyhárd DK, Oláh J. Gas Sensing by Bacterial H-NOX Proteins: An MD Study. Molecules 2020; 25:molecules25122882. [PMID: 32585836 PMCID: PMC7356049 DOI: 10.3390/molecules25122882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 01/08/2023] Open
Abstract
Gas sensing is crucial for both prokaryotes and eukaryotes and is primarily performed by heme-based sensors, including H-NOX domains. These systems may provide a new, alternative mode for transporting gaseous molecules in higher organisms, but for the development of such systems, a detailed understanding of the ligand-binding properties is required. Here, we focused on ligand migration within the protein matrix: we performed molecular dynamics simulations on three bacterial (Ka, Ns and Cs) H-NOX proteins and studied the kinetics of CO, NO and O2 diffusion. We compared the response of the protein structure to the presence of ligands, diffusion rate constants, tunnel systems and storage pockets. We found that the rate constant for diffusion decreases in the O2 > NO > CO order in all proteins, and in the Ns > Ks > Cs order if single-gas is considered. Competition between gases seems to seriously influence the residential time of ligands spent in the distal pocket. The channel system is profoundly determined by the overall fold, but the sidechain pattern has a significant role in blocking certain channels by hydrophobic interactions between bulky groups, cation-π interactions or hydrogen bonding triads. The majority of storage pockets are determined by local sidechain composition, although certain functional cavities, such as the distal and proximal pockets are found in all systems. A major guideline for the design of gas transport systems is the need to chemically bind the gas molecule to the protein, possibly joining several proteins with several heme groups together.
Collapse
Affiliation(s)
- Ahmed M. Rozza
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Budapest Szent Gellért tér 4, H-1111 Budapest, Hungary;
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and Biology & MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Correspondence: (D.K.M.); (J.O.)
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Budapest Szent Gellért tér 4, H-1111 Budapest, Hungary;
- Correspondence: (D.K.M.); (J.O.)
| |
Collapse
|
15
|
Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
Collapse
Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
| |
Collapse
|
16
|
Adams HR, Krewson C, Vardanega JE, Fujii S, Moreno-Chicano T, Moreno T, Chicano, Sambongi Y, Svistunenko D, Paps J, Andrew CR, Hough MA. One fold, two functions: cytochrome P460 and cytochrome c'-β from the methanotroph Methylococcus capsulatus (Bath). Chem Sci 2019; 10:3031-3041. [PMID: 30996884 PMCID: PMC6427953 DOI: 10.1039/c8sc05210g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/20/2019] [Indexed: 11/21/2022] Open
Abstract
Nature is adept at utilising highly similar protein folds to carry out very different functions, yet the mechanisms by which this functional divergence occurs remain poorly characterised. In certain methanotrophic bacteria, two homologous pentacoordinate c-type heme proteins have been identified: a cytochrome P460 (cyt P460) and a cytochrome c'-β (cyt cp-β). Cytochromes P460 are able to convert hydroxylamine to nitrous oxide (N2O), a potent greenhouse gas. This reactivity is similar to that of hydroxylamine oxidoreductase (HAO), which is a key enzyme in nitrifying and methanotrophic bacteria. Cyt P460 and HAO both have unusual protein-heme cross-links, formed by a Tyr residue in HAO and a Lys in cyt P460. In contrast, cyts cp-β (the only known cytochromes c' with a β-sheet fold) lack this crosslink and appears to be optimized for binding non-polar molecules (including NO and CO) without enzymatic conversion. Our bioinformatics analysis supports the proposal that cyt cp-β may have evolved from cyt P460 via a gene duplication event. Using high-resolution X-ray crystallography, UV-visible absorption, electron paramagnetic resonance (EPR) and resonance Raman spectroscopy, we have characterized the overall protein folding and active site structures of cyt cp-β and cyt P460 from the obligate methanotroph, Methylococcus capsulatus (Bath). These proteins display a similar β-sheet protein fold, together with a pattern of changes to the heme pocket regions and localised tertiary structure that have converted a hydroxylamine oxidizing enzyme into a gas-binding protein. Structural comparisons provide insights relevant to enzyme redesign for synthetic enzymology and engineering of gas sensor proteins. We also show the widespread occurrence of cyts cp-β and characterise their phylogeny.
Collapse
Affiliation(s)
- Hannah R Adams
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Callie Krewson
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Jenny E Vardanega
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Sotaro Fujii
- Graduate School of Biosphere Science , Hiroshima University , Kagamiyama 1-4-4, Higashi-Hiroshima , Hiroshima , 739-8528 , Japan
| | | | - Tadeo Moreno
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Chicano
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science , Hiroshima University , Kagamiyama 1-4-4, Higashi-Hiroshima , Hiroshima , 739-8528 , Japan
| | - Dimitri Svistunenko
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Jordi Paps
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Colin R Andrew
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Michael A Hough
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| |
Collapse
|
17
|
Zhang L, Zhou J, Ma F, Wang Q, Xu H, Ju H, Lei J. Single‐Sided Competitive Axial Coordination of G‐Quadruplex/Hemin as Molecular Switch for Imaging Intracellular Nitric Oxide. Chemistry 2018; 25:490-494. [DOI: 10.1002/chem.201804897] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/03/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Lei Zhang
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
- School of Chemistry and Molecular Engineering, Institute of, Advanced SynthesisJiangsu National Synergetic Innovation Center for, Advanced MaterialsNanjing Tech University Nanjing 211816 P.R. China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| | - Fengjiao Ma
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| | - Quanbo Wang
- Laboratory of Immunology for Environment and HealthShandong Analysis and Test CenterShandong Academy of Sciences Jinan 250014 P.R. China
| | - Hui Xu
- School of Chemistry and Molecular Engineering, Institute of, Advanced SynthesisJiangsu National Synergetic Innovation Center for, Advanced MaterialsNanjing Tech University Nanjing 211816 P.R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| |
Collapse
|
18
|
Guo Y, Marletta MA. Structural Insight into H‐NOX Gas Sensing and Cognate Signaling Protein Regulation. Chembiochem 2018; 20:7-19. [DOI: 10.1002/cbic.201800478] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Yirui Guo
- California Institute for Quantitative BiosciencesUniversity of California, Berkeley Berkeley, CA 94720 USA
| | - Michael A. Marletta
- California Institute for Quantitative BiosciencesUniversity of California, Berkeley Berkeley, CA 94720 USA
- Department of Molecular and Cell BiologyUniversity of California, Berkeley Berkeley, CA 94720 USA
- Department of ChemistryUniversity of California, Berkeley Berkeley, CA 94720 USA
| |
Collapse
|
19
|
Bacon BA, Liu Y, Kincaid JR, Boon EM. Spectral Characterization of a Novel NO Sensing Protein in Bacteria: NosP. Biochemistry 2018; 57:6187-6200. [PMID: 30272959 DOI: 10.1021/acs.biochem.8b00451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A novel family of bacterial hemoproteins named NosP has been discovered recently; its members are proposed to function as nitric oxide (NO) responsive proteins involved in bacterial group behaviors such as quorum sensing and biofilm growth and dispersal. Currently, little is known about molecular activation mechanisms in NosP. Here, functional studies were performed utilizing the distinct spectroscopic characteristics associated with the NosP heme cofactor. NosPs from Pseudomonas aeruginosa ( Pa), Vibrio cholerae ( Vc), and Legionella pneumophila ( Lpg) were studied in their ferrous unligated forms as well as their ferrous CO, ferrous NO, and ferric CN adducts. The resonance Raman (rR) data collected on the ferric forms strongly support the existence of a distorted heme cofactor, which is a common feature in NO sensors. The ferrous spectra exhibit a 213 cm-1 feature, which is assigned to the Fe-Nhis stretching mode. The Fe-C and C-O frequencies in the spectra of ferrous CO NosP complexes are inversely correlated with relatively similar frequencies, consistent with a proximal histidine ligand and a relatively hydrophobic environment. The rR spectra obtained for isotopically labeled ferrous NO adducts provide evidence of formation of a 5-coordinate NO complex, resulting from proximal Fe-Nhis cleavage, which is believed to play a role in biological heme-NO signal transduction. Additionally, we found that of the three NosPs studied, Lpg NosP contains the most electropositive ligand binding pocket, while Pa NosP has the most electronegative ligand binding pocket. This pattern is also observed in the measured heme reduction potentials for these three proteins, which may indicate distinct functions for each.
Collapse
Affiliation(s)
- Bezalel A Bacon
- Graduate program in Biochemistry and Structural Biology , Stony Brook University , Stony Brook , New York 11790-3400 , United States
| | - Yilin Liu
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - James R Kincaid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Elizabeth M Boon
- Graduate program in Biochemistry and Structural Biology , Stony Brook University , Stony Brook , New York 11790-3400 , United States.,Department of Chemistry and Institute of Chemical Biology and Drug Discovery , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| |
Collapse
|
20
|
Horst BG, Marletta MA. Physiological activation and deactivation of soluble guanylate cyclase. Nitric Oxide 2018; 77:65-74. [PMID: 29704567 PMCID: PMC6919197 DOI: 10.1016/j.niox.2018.04.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 01/24/2023]
Abstract
Soluble guanylate cyclase (sGC) is responsible for transducing the gaseous signaling molecule nitric oxide (NO) into the ubiquitous secondary signaling messenger cyclic guanosine monophosphate in eukaryotic organisms. sGC is exquisitely tuned to respond to low levels of NO, allowing cells to respond to non-toxic levels of NO. In this review, the structure of sGC is discussed in the context of sGC activation and deactivation. The sequence of events in the activation pathway are described into a comprehensive model of in vivo sGC activation as elucidated both from studies with purified enzyme and those done in cells. This model is then used to discuss the deactivation of sGC, as well as the molecular mechanisms of pathophysiological deactivation.
Collapse
Affiliation(s)
- Benjamin G Horst
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Michael A Marletta
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
| |
Collapse
|
21
|
Sömmer A, Behrends S. Methods to investigate structure and activation dynamics of GC-1/GC-2. Nitric Oxide 2018; 78:S1089-8603(17)30348-8. [PMID: 29705716 DOI: 10.1016/j.niox.2018.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/19/2018] [Accepted: 04/23/2018] [Indexed: 12/18/2022]
Abstract
Soluble guanylyl cyclase (sGC) is a heterodimeric enzyme consisting of one α and one β subunit. The α1β1 (GC-1) and α2β1 (GC-2) heterodimers are important for NO signaling in humans and catalyse the conversion from GTP to cGMP. Each sGC subunit consists of four domains. Several crystal structures of the isolated domains are available. However, crystals of full-length sGC have failed to materialise. In consequence, the detailed three dimensional structure of sGC remains unknown to date. Different techniques including stopped-flow spectroscopy, Förster-resonance energy transfer, direct fluorescence, analytical ultracentrifugation, chemical cross-linking, small-angle X-ray scattering, electron microscopy, hydrogen-deuterium exchange and protein thermal shift assays, were used to collect indirect information. Taken together, this circumstantial evidence from different groups brings forth a plausible model of sGC domain arrangement, spatial orientation and dynamic rearrangement upon activation. For analysis of the active conformation the stable binding mode of sGC activators has a significant methodological advantage over the transient, elusive, complex and highly concentration dependent effects of NO in many applications. The methods used and the results obtained are reviewed and discussed in this article.
Collapse
Affiliation(s)
- Anne Sömmer
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig - Institute of Technology, Germany.
| | - Sönke Behrends
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig - Institute of Technology, Germany.
| |
Collapse
|
22
|
Childers KC, Garcin ED. Structure/function of the soluble guanylyl cyclase catalytic domain. Nitric Oxide 2018; 77:53-64. [PMID: 29702251 PMCID: PMC6005667 DOI: 10.1016/j.niox.2018.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
Abstract
Soluble guanylyl cyclase (GC-1) is the primary receptor of nitric oxide (NO) in smooth muscle cells and maintains vascular function by inducing vasorelaxation in nearby blood vessels. GC-1 converts guanosine 5′-triphosphate (GTP) into cyclic guanosine 3′,5′-monophosphate (cGMP), which acts as a second messenger to improve blood flow. While much work has been done to characterize this pathway, we lack a mechanistic understanding of how NO binding to the heme domain leads to a large increase in activity at the C-terminal catalytic domain. Recent structural evidence and activity measurements from multiple groups have revealed a low-activity cyclase domain that requires additional GC-1 domains to promote a catalytically-competent conformation. How the catalytic domain structurally transitions into the active conformation requires further characterization. This review focuses on structure/function studies of the GC-1 catalytic domain and recent advances various groups have made in understanding how catalytic activity is regulated including small molecules interactions, Cys-S-NO modifications and potential interactions with the NO-sensor domain and other proteins.
Collapse
Affiliation(s)
- Kenneth C Childers
- University of Maryland Baltimore County, Department of Chemistry and Biochemistry, Baltimore, USA
| | - Elsa D Garcin
- University of Maryland Baltimore County, Department of Chemistry and Biochemistry, Baltimore, USA.
| |
Collapse
|
23
|
Makino R, Obata Y, Tsubaki M, Iizuka T, Hamajima Y, Kato-Yamada Y, Mashima K, Shiro Y. Mechanistic Insights into the Activation of Soluble Guanylate Cyclase by Carbon Monoxide: A Multistep Mechanism Proposed for the BAY 41-2272 Induced Formation of 5-Coordinate CO-Heme. Biochemistry 2018; 57:1620-1631. [PMID: 29461815 DOI: 10.1021/acs.biochem.7b01240] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Soluble guanylate cyclase (sGC) is a heme-containing enzyme that catalyzes cGMP production upon sensing NO. While the CO adduct, sGC-CO, is much less active, the allosteric regulator BAY 41-2272 stimulates the cGMP productivity to the same extent as that of sGC-NO. The stimulatory effect has been thought to be likely associated with Fe-His bond cleavage leading to 5-coordinate CO-heme, but the detailed mechanism remains unresolved. In this study, we examined the mechanism under the condition including BAY 41-2272, 2'-deoxy-3'-GMP and foscarnet. The addition of these effectors caused the original 6-coordinate CO-heme to convert to an end product that was an equimolar mixture of a 5- and a new 6-coordinate CO-heme, as assessed by IR spectral measurements. The two types of CO-hemes in the end product were further confirmed by CO dissociation kinetics. Stopped-flow measurements under the condition indicated that the ferrous sGC bound CO as two reversible steps, where the primary step was assigned to the full conversion of the ferrous enzyme to the 6-coordinate CO-heme, and subsequently followed by the slower second step leading a partial conversion of the 6-coordinate CO-heme to the 5-coordinate CO-heme. The observed rates for both steps linearly depended on CO concentrations. The unexpected CO dependence of the rates in the second step supports a multistep mechanism, in which the 5-coordinate CO-heme is led by CO release from a putative bis-carbonyl intermediate that is likely provided by the binding of a second CO to the 6-coordinate CO-heme. This mechanism provides a new aspect on the activation of sGC by CO.
Collapse
Affiliation(s)
- Ryu Makino
- Department of Life Science, College of Science , Rikkyo University , Nishi-ikebukuro 3-34-1 , Toshima-ku, Tokyo 171-8501 , Japan
| | - Yuji Obata
- Department of Life Science, College of Science , Rikkyo University , Nishi-ikebukuro 3-34-1 , Toshima-ku, Tokyo 171-8501 , Japan
| | - Motonari Tsubaki
- Department of Chemistry, Graduate School of Science , Kobe University , Kobe , Hyogo 657-8501 , Japan
| | - Tetsutaro Iizuka
- RIKEN Harima Institute/Spring8 , 1-1-1 Kouto , Mikazuki-cho, Sayo-gun , Hyogo 679-5148 , Japan
| | - Yuki Hamajima
- Department of Life Science, College of Science , Rikkyo University , Nishi-ikebukuro 3-34-1 , Toshima-ku, Tokyo 171-8501 , Japan
| | - Yasuyuki Kato-Yamada
- Department of Life Science, College of Science , Rikkyo University , Nishi-ikebukuro 3-34-1 , Toshima-ku, Tokyo 171-8501 , Japan
| | - Keisuke Mashima
- Department of Life Science, College of Science , Rikkyo University , Nishi-ikebukuro 3-34-1 , Toshima-ku, Tokyo 171-8501 , Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science , University of Hyogo , 3-2-1 Kouto , Kamigori-cho, Ako-gun , Hyogo 678-1297 , Japan
| |
Collapse
|
24
|
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.
Collapse
|
25
|
Abstract
Soluble guanylyl cyclase (sGC) is the principal enzyme in mediating the biological actions of nitric oxide. On activation, sGC converts guanosine triphosphate to guanosine 3',5'-cyclic monophosphate (cGMP), which mediates diverse physiological processes including vasodilation, platelet aggregation, and myocardial functions predominantly by acting on cGMP-dependent protein kinases. Cyclic GMP has long been considered as the sole second messenger for sGC action. However, emerging evidence suggests that, in addition to cGMP, other nucleoside 3',5'-cyclic monophosphates (cNMPs) are synthesized by sGC in response to nitric oxide stimulation, and some of these nucleoside 3',5'-cyclic monophosphates are involved in various physiological activities. For example, inosine 3',5'-cyclic monophosphate synthesized by sGC may play a critical role in hypoxic augmentation of vasoconstriction. The involvement of cytidine 3',5'-cyclic monophosphate and uridine 3',5'-cyclic monophosphate in certain cardiovascular activities is also implicated.
Collapse
|
26
|
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.
Collapse
|
27
|
Sharina IG, Martin E. The Role of Reactive Oxygen and Nitrogen Species in the Expression and Splicing of Nitric Oxide Receptor. Antioxid Redox Signal 2017; 26:122-136. [PMID: 26972233 PMCID: PMC7061304 DOI: 10.1089/ars.2016.6687] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Nitric oxide (NO)-dependent signaling is critical to many cellular functions and physiological processes. Soluble guanylyl cyclase (sGC) acts as an NO receptor and mediates the majority of NO functions. The signaling between NO and sGC is strongly altered by reactive oxygen and nitrogen species. Recent Advances: Besides NO scavenging, sGC is affected by oxidation/loss of sGC heme, oxidation, or nitrosation of cysteine residues and phosphorylation. Apo-sGC or sGC containing oxidized heme is targeted for degradation. sGC transcription and the stability of sGC mRNA are also affected by oxidative stress. CRITICAL ISSUES Studies cited in this review suggest the existence of compensatory processes that adapt cellular processes to diminished sGC function under conditions of short-term or moderate oxidative stress. Alternative splicing of sGC transcripts is discussed as a mechanism with the potential to both enhance and reduce sGC function. The expression of α1 isoform B, a functional and stable splice variant of human α1 sGC subunit, is proposed as one of such compensatory mechanisms. The expression of dysfunctional splice isoforms is discussed as a contributor to decreased sGC function in vascular disease. FUTURE DIRECTIONS Targeting the process of sGC splicing may be an important approach to maintain the composition of sGC transcripts that are expressed in healthy tissues under normal conditions. Emerging new strategies that allow for targeted manipulations of RNA splicing offer opportunities to use this approach as a preventive measure and to control the composition of sGC splice isoforms. Rational management of expressed sGC splice forms may be a valuable complementary treatment strategy for existing sGC-directed therapies. Antioxid. Redox Signal. 26, 122-136.
Collapse
Affiliation(s)
- Iraida G Sharina
- 1 Division of Cardiology, Department of Internal Medicine, The University of Texas Health Science Center in Houston Medical School , Houston, Texas
| | - Emil Martin
- 1 Division of Cardiology, Department of Internal Medicine, The University of Texas Health Science Center in Houston Medical School , Houston, Texas.,2 School of Science and Technology, Nazarbayev University , Astana, Kazakhstan
| |
Collapse
|
28
|
Gambaryan S, Subramanian H, Kehrer L, Mindukshev I, Sudnitsyna J, Reiss C, Rukoyatkina N, Friebe A, Sharina I, Martin E, Walter U. Erythrocytes do not activate purified and platelet soluble guanylate cyclases even in conditions favourable for NO synthesis. Cell Commun Signal 2016; 14:16. [PMID: 27515066 PMCID: PMC4982240 DOI: 10.1186/s12964-016-0139-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/01/2016] [Indexed: 01/28/2023] Open
Abstract
Background Direct interaction between Red blood cells (RBCs) and platelets is known for a long time. The bleeding time is prolonged in anemic patients independent of their platelet count and could be corrected by transfusion of RBCs, which indicates that RBCs play an important role in hemostasis and platelet activation. However, in the last few years, opposing mechanisms of platelet inhibition by RBCs derived nitric oxide (NO) were proposed. The aim of our study was to identify whether RBCs could produce NO and activate soluble guanylate cyclase (sGC) in platelets. Methods To test whether RBCs could activate sGC under different conditions (whole blood, under hypoxia, or even loaded with NO), we used our well-established and highly sensitive models of NO-dependent sGC activation in platelets and activation of purified sGC. The activation of sGC was monitored by detecting the phosphorylation of Vasodilator Stimulated Phosphoprotein (VASPS239) by flow cytometry and Western blot. ANOVA followed by Bonferroni’s test and Student’s t-test were used as appropriate. Results We show that in the whole blood, RBCs prevent NO-mediated inhibition of ADP and TRAP6-induced platelet activation. Likewise, coincubation of RBCs with platelets results in strong inhibition of NO-induced sGC activation. Under hypoxic conditions, incubation of RBCs with NO donor leads to Hb-NO formation which inhibits sGC activation in platelets. Similarly, RBCs inhibit activation of purified sGC, even under conditions optimal for RBC-mediated generation of NO from nitrite. Conclusions All our experiments demonstrate that RBCs act as strong NO scavengers and prevent NO-mediated inhibition of activated platelets. In all tested conditions, RBCs were not able to activate platelet or purified sGC.
Collapse
Affiliation(s)
- Stepan Gambaryan
- Institute of Clinical Biochemistry and Pathobiochemistry, University of Wuerzburg, Grombuehlstraße 12, D-97080, Wuerzburg, Germany. .,Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez pr. 44, St, Petersburg, 194223, Russia. .,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Mainz, Germany.
| | - Hariharan Subramanian
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Linda Kehrer
- Institute of Physiology, University of Wuerzburg, Wuerzburg, Germany
| | - Igor Mindukshev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez pr. 44, St, Petersburg, 194223, Russia
| | - Julia Sudnitsyna
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez pr. 44, St, Petersburg, 194223, Russia
| | - Cora Reiss
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Mainz, Germany
| | - Natalia Rukoyatkina
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez pr. 44, St, Petersburg, 194223, Russia
| | - Andreas Friebe
- Institute of Physiology, University of Wuerzburg, Wuerzburg, Germany
| | - Iraida Sharina
- Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School, Houston, USA
| | - Emil Martin
- Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School, Houston, USA
| | - Ulrich Walter
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Mainz, Germany.,German Centre for Cardiovascular Research (DZHK) RheinMain, Mainz, Germany
| |
Collapse
|
29
|
Zhou Z, Martin E, Sharina I, Esposito I, Szabo C, Bucci M, Cirino G, Papapetropoulos A. Regulation of soluble guanylyl cyclase redox state by hydrogen sulfide. Pharmacol Res 2016; 111:556-562. [PMID: 27378567 DOI: 10.1016/j.phrs.2016.06.029] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/07/2016] [Accepted: 06/30/2016] [Indexed: 01/09/2023]
Abstract
Soluble guanylate cyclase (sGC) is a receptor for nitric oxide (NO). Binding of NO to ferrous (Fe(2+)) heme increases its catalytic activity, leading to the production of cGMP from GTP. Hydrogen sulfide (H2S) is a signaling molecule that exerts both direct and indirect anti-oxidant effects. In the present, study we aimed to determine whether H2S could regulate sGC redox state and affect its responsiveness to NO-releasing agents and sGC activators. Using cultured rat aortic smooth muscle cells, we observed that treatment with H2S augmented the response to the NO donor DEA/NO, while attenuating the response to the heme-independent activator BAY58-2667 that targets oxidized sGC. Similarly, overexpression of H2S-synthesizing enzyme cystathionine-γ lyase reduced the ability of BAY58-2667 to promote cGMP accumulation. In experiments with phenylephrine-constricted mouse aortic rings, treatment with rotenone (a compound that increases ROS production), caused a rightward shift of the DEA/NO concentration-response curve, an effect partially restored by H2S. When rings were pre-treated with H2S, the concentration-response curve to BAY 58-2667 shifted to the right. Using purified recombinant human sGC, we observed that treatment with H2S converted ferric to ferrous sGC enhancing NO-donor-stimulated sGC activity and reducing BAY 58-2667-triggered cGMP formation. The present study identified an additional mechanism of cross-talk between the NO and H2S pathways at the level of redox regulation of sGC. Our results provide evidence that H2S reduces sGC heme Fe, thus, facilitating NO-mediated cellular signaling events.
Collapse
Affiliation(s)
- Zongmin Zhou
- 1st Department of Critical Care and Pulmonary Services, Faculty of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, Greece
| | - Emil Martin
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical School at Houston, TX, USA
| | - Iraida Sharina
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical School at Houston, TX, USA
| | - Iolanda Esposito
- Department of Experimental Pharmacology, Faculty of Pharmacy, University of NaplesFederico II, Italy
| | - Csaba Szabo
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mariarosaria Bucci
- Department of Experimental Pharmacology, Faculty of Pharmacy, University of NaplesFederico II, Italy
| | - Giuseppe Cirino
- Department of Experimental Pharmacology, Faculty of Pharmacy, University of NaplesFederico II, Italy
| | - Andreas Papapetropoulos
- 1st Department of Critical Care and Pulmonary Services, Faculty of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, Greece; Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece; Center of Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation of the Academy of Athens, Greece.
| |
Collapse
|
30
|
Vicente JB, Malagrinò F, Arese M, Forte E, Sarti P, Giuffrè A. Bioenergetic relevance of hydrogen sulfide and the interplay between gasotransmitters at human cystathionine β-synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1127-1138. [PMID: 27039165 DOI: 10.1016/j.bbabio.2016.03.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/07/2016] [Accepted: 03/28/2016] [Indexed: 12/27/2022]
Abstract
Merely considered as a toxic gas in the past, hydrogen sulfide (H2S) is currently viewed as the third 'gasotransmitter' in addition to nitric oxide (NO) and carbon monoxide (CO), playing a key signalling role in human (patho)physiology. H2S can either act as a substrate or, similarly to CO and NO, an inhibitor of mitochondrial respiration, in the latter case by targeting cytochrome c oxidase (CcOX). The impact of H(2)S on mitochondrial energy metabolism crucially depends on the bioavailability of this gaseous molecule and its interplay with the other two gasotransmitters. The H(2)S-producing human enzyme cystathionine β-synthase (CBS), sustaining cellular bioenergetics in colorectal cancer cells, plays a role in the interplay between gasotransmitters. The enzyme was indeed recently shown to be negatively modulated by physiological concentrations of CO and NO, particularly in the presence of its allosteric activator S-adenosyl-l-methionine (AdoMet). These newly discovered regulatory mechanisms are herein reviewed. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
Collapse
Affiliation(s)
- João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República (EAN), 2780-156 Oeiras, Portugal.
| | - Francesca Malagrinò
- Department of Biochemical Sciences and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Marzia Arese
- Department of Biochemical Sciences and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Elena Forte
- Department of Biochemical Sciences and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Paolo Sarti
- Department of Biochemical Sciences and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Alessandro Giuffrè
- CNR Institute of Molecular Biology and Pathology, Piazzale Aldo Moro 5, I-00185 Rome, Italy.
| |
Collapse
|
31
|
Matsumura H, Chakraborty S, Reed J, Lu Y, Moënne-Loccoz P. Effect of Outer-Sphere Side Chain Substitutions on the Fate of the trans Iron-Nitrosyl Dimer in Heme/Nonheme Engineered Myoglobins (Fe(B)Mbs): Insights into the Mechanism of Denitrifying NO Reductases. Biochemistry 2016; 55:2091-9. [PMID: 27003474 DOI: 10.1021/acs.biochem.5b01109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Denitrifying NO reductases are transmembrane protein complexes that utilize a heme/nonheme diiron center at their active sites to reduce two NO molecules to the innocuous gas N2O. Fe(B)Mb proteins, with their nonheme iron sites engineered into the heme distal pocket of sperm whale myoglobin, are attractive models for studying the molecular details of the NO reduction reaction. Spectroscopic and structural studies of Fe(B)Mb constructs have confirmed that they reproduce the metal coordination spheres observed at the active site of the cytochrome c-dependent NO reductase from Pseudomonas aeruginosa. Exposure of Fe(B)Mb to excess NO, as examined by analytical and spectroscopic techniques, results primarily in the formation of a five-coordinate heme-nitrosyl complex without N2O production. However, substitution of the outer-sphere residue Ile107 with a glutamic acid (i.e., I107E) decreases the formation rate of the five-coordinate heme-nitrosyl complex and allows for the substoichiometric production of N2O. Here, we aim to better characterize the formation of the five-coordinate heme-nitrosyl complex and to explain why the level of N2O production increases with the I107E substitution. We follow the formation of the five-coordinate heme-nitrosyl inhibitory complex through the sequential exposure of Fe(B)Mb to different NO isotopomers using rapid-freeze-quench resonance Raman spectroscopy. The data show that the complex is formed by the displacement of the proximal histidine by a new NO molecule after the weakening of the Fe(II)-His bond in the intermediate six-coordinate low-spin (6cLS) heme-nitrosyl complex. These results lead us to explore diatomic migration within the scaffold of myoglobin and whether substitutions at residue 107 can be sufficient to control access to the proximal heme cavities. Results on a new Fe(B)Mb construct with an I107F substitution (Fe(B)Mb3) show an increased rate for the formation of the five-coordinate low-spin heme-nitrosyl complex without N2O production. Taken together, our results suggest that production of N2O from the [6cLS heme {FeNO}(7)/{Fe(B)NO}(7)] trans iron-nitrosyl dimer intermediate requires a proton transfer event facilitated by an outer-sphere residue such as E107 in Fe(B)Mb2 and E280 in P. aeruginosa cNOR.
Collapse
Affiliation(s)
- Hirotoshi Matsumura
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Saumen Chakraborty
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Julian Reed
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Pierre Moënne-Loccoz
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| |
Collapse
|
32
|
Arora D, Jain P, Singh N, Kaur H, Bhatla SC. Mechanisms of nitric oxide crosstalk with reactive oxygen species scavenging enzymes during abiotic stress tolerance in plants. Free Radic Res 2016; 50:291-303. [PMID: 26554526 DOI: 10.3109/10715762.2015.1118473] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nitric oxide (NO) acts in a concentration and redox-dependent manner to counteract oxidative stress either by directly acting as an antioxidant through scavenging reactive oxygen species (ROS), such as superoxide anions (O(2)(-)*), to form peroxynitrite (ONOO(-)) or by acting as a signaling molecule, thereby altering gene expression. NO can interact with different metal centres in proteins, such as heme-iron, zinc-sulfur clusters, iron-sulfur clusters, and copper, resulting in the formation of a stable metal-nitrosyl complex or production of varied biochemical signals, which ultimately leads to modification of protein structure/function. The thiols (ferrous iron-thiol complex and nitrosothiols) are also involved in the metabolism and mobilization of NO. Thiols bind to NO and transport it to the site of action whereas nitrosothiols release NO after intercellular diffusion and uptake into the target cells. S-nitrosoglutathione (GSNO) also has the ability to transnitrosylate proteins. It is an NO˙ reservoir and a long-distance signaling molecule. Tyrosine nitration of proteins has been suggested as a biomarker of nitrosative stress as it can lead to either activation or inhibition of target proteins. The exact molecular mechanism(s) by which exogenous and endogenously generated NO (or reactive nitrogen species) modulate the induction of various genes affecting redox homeostasis, are being extensively investigated currently by various research groups. Present review provides an in-depth analysis of the mechanisms by which NO interacts with and modulates the activity of various ROS scavenging enzymes, particularly accompanying ROS generation in plants in response to varied abiotic stress.
Collapse
Affiliation(s)
- Dhara Arora
- a Laboratory of Plant Physiology and Biochemistry, Department of Botany , University of Delhi , Delhi , India
| | - Prachi Jain
- a Laboratory of Plant Physiology and Biochemistry, Department of Botany , University of Delhi , Delhi , India
| | - Neha Singh
- a Laboratory of Plant Physiology and Biochemistry, Department of Botany , University of Delhi , Delhi , India
| | - Harmeet Kaur
- a Laboratory of Plant Physiology and Biochemistry, Department of Botany , University of Delhi , Delhi , India
| | - Satish C Bhatla
- a Laboratory of Plant Physiology and Biochemistry, Department of Botany , University of Delhi , Delhi , India
| |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Hunt AP, Lehnert N. Heme-nitrosyls: electronic structure implications for function in biology. Acc Chem Res 2015; 48:2117-25. [PMID: 26114618 DOI: 10.1021/acs.accounts.5b00167] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The question of why mammalian systems use nitric oxide (NO), a potentially hazardous and toxic diatomic, as a signaling molecule to mediate important functions such as vasodilation (blood pressure control) and nerve signal transduction initially perplexed researchers when this discovery was made in the 1980s. Through extensive research over the past two decades, it is now well rationalized why NO is used in vivo for these signaling functions, and that heme proteins play a dominant role in NO signaling in mammals. Key insight into the properties of heme-nitrosyl complexes that make heme proteins so well poised to take full advantage of the unique properties of NO has come from in-depth structural, spectroscopic, and theoretical studies on ferrous and ferric heme-nitrosyls. This Account highlights recent findings that have led to greater understanding of the electronic structures of heme-nitrosyls, and the contributions that model complex studies have made to elucidate Fe-NO bonding are highlighted. These results are then discussed in the context of the biological functions of heme-nitrosyls, in particular in soluble guanylate cyclase (sGC; NO signaling), nitrophorins (NO transport), and NO-producing enzymes. Central to this Account is the thermodynamic σ-trans effect of NO, and how this relates to the activation of the universal mammalian NO sensor sGC, which uses a ferrous heme as the high affinity "NO detection unit". It is shown via detailed spectroscopic and computational studies that the strong and very covalent Fe(II)-NO σ-bond is at the heart of the strong thermodynamic σ-trans effect of NO, which greatly weakens the proximal Fe-NHis (or Fe-SCys) bond in six-coordinate ferrous heme-nitrosyls. In sGC, this causes the dissociation of the proximally bound histidine ligand upon NO binding to the ferrous heme, inducing a significant conformational change that activates the sGC catalytic domain for the production of cGMP. This, in turn, leads to vasodilation and nerve signal transduction. Studies on ferrous heme-nitrosyl model complexes have allowed for a quantification of this thermodynamic σ-trans effect of NO, through the use of high-resolution crystal structures, binding constant studies, single-crystal vibrational spectroscopy and density functional theory (DFT) calculations. These studies have further identified the singly occupied molecular orbital (SOMO) of the NO complexes as the key MO that mediates the thermodynamic σ-trans effect of NO. In comparison to ferrous heme-nitrosyls, ferric heme-nitrosyls display thermodynamically much weaker Fe-NO bonds (from NO binding constants), but at the same time much stronger Fe-NO bonds in their ground states (from vibrational spectroscopy). Using spectroscopic investigations coupled to DFT calculations, this apparent contradiction has been rationalized with the involvement of at least three different electronic states in the binding/dissociation of NO to/from ferric hemes. This is of key significance for the release of NO from NO-producing enzymes like NOS, and further forms the basis for ferric hemes to serve as NO transporters in biological systems.
Collapse
Affiliation(s)
- Andrew P. Hunt
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicolai Lehnert
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
35
|
Ghafoor DD, Kekilli D, Abdullah GH, Dworkowski FSN, Hassan HG, Wilson MT, Strange RW, Hough MA. Hydrogen bonding of the dissociated histidine ligand is not required for formation of a proximal NO adduct in cytochrome c'. J Biol Inorg Chem 2015; 20:949-56. [PMID: 26100643 DOI: 10.1007/s00775-015-1278-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/04/2015] [Indexed: 11/28/2022]
Abstract
Cytochromes c', that occur in methanotrophic, denitrifying and photosynthetic bacteria, form unusual proximal penta-coordinate NO complexes via a hexa-coordinate distal NO intermediate. Their NO binding properties are similar to those of the eukaryotic NO sensor, soluble guanylate cyclase, for which they provide a valuable structural model. Previous studies suggested that hydrogen bonding between the displaced proximal histidine (His120) ligand (following its dissociation from heme due to trans effects from the distally bound NO) and a conserved aspartate residue (Asp121) could play a key role in allowing proximal NO binding to occur. We have characterized three variants of Alcaligenes xylosoxidans cytochrome c' (AXCP) where Asp121 has been replaced by Ala, Ile and Gln, respectively. In all variants, hydrogen bonding between residue 121 and His120 is abolished yet 5-coordinate proximal NO species are still formed. Our data therefore demonstrate that the His120-Asp121 bond is not essential for proximal NO binding although it likely provides an energy minimum for the displaced His ligand. All variants have altered proximal pocket structure relative to native AXCP.
Collapse
Affiliation(s)
- Dlzar D Ghafoor
- Faculty of Science and Education Science, University of Sulaimani, Sulaymaniyah, Iraq
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Servid AE, McKay AL, Davis CA, Garton EM, Manole A, Dobbin PS, Hough MA, Andrew CR. Resonance Raman Spectra of Five-Coordinate Heme-Nitrosyl Cytochromes c′: Effect of the Proximal Heme-NO Environment. Biochemistry 2015; 54:3320-7. [DOI: 10.1021/acs.biochem.5b00227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amy E. Servid
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Alison L. McKay
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Cherry A. Davis
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Elizabeth M. Garton
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Andreea Manole
- School
of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Paul S. Dobbin
- School
of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Michael A. Hough
- School
of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Colin R. Andrew
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| |
Collapse
|
37
|
Sürmeli NB, Müskens FM, Marletta MA. The Influence of Nitric Oxide on Soluble Guanylate Cyclase Regulation by Nucleotides: ROLE OF THE PSEUDOSYMMETRIC SITE. J Biol Chem 2015; 290:15570-15580. [PMID: 25907555 DOI: 10.1074/jbc.m115.641431] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 01/09/2023] Open
Abstract
Activation of soluble guanylate cyclase (sGC) by the signaling molecule nitric oxide (NO) leads to formation of the second messenger cGMP, which mediates numerous physiological processes. NO activates sGC by binding to the ferrous heme cofactor; the relative amount of NO with respect to sGC heme affects the enzyme activity. ATP can also influence the activity by binding to an allosteric site, most likely the pseudosymmetric site located in the catalytic domain. Here, the role of the pseudosymmetric site on nucleotide regulation was investigated by point mutations at this site. ATP inhibition kinetics of wild type and a pseudosymmetric site (α1-C594A/β1-D477A) variant of sGC was determined at various levels of NO. Results obtained show that in the presence of less than 1 eq of NO, there appears to be less than complete activation and little change in the nucleotide binding parameters. The most dramatic effects are observed for the addition of excess NO, which results in an increase in the affinity of GTP at the catalytic site and full activation of sGC. The pseudosymmetric site mutation only affected nucleotide affinities in the presence of excess NO; there was a decrease in the affinity for ATP in both the allosteric and catalytic sites. These observations led to a new kinetic model for sGC activity in the presence of excess NO. This model revealed that the active and allosteric sites show cooperativity. This new comprehensive model gives a more accurate description of sGC regulation by NO and nucleotides in vivo.
Collapse
Affiliation(s)
- Nur Başak Sürmeli
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037
| | - Frederike M Müskens
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CG Utrecht, The Netherlands
| | - Michael A Marletta
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037.
| |
Collapse
|
38
|
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.
Collapse
|
39
|
Conformational control of the binding of diatomic gases to cytochrome c'. J Biol Inorg Chem 2015; 20:675-86. [PMID: 25792378 DOI: 10.1007/s00775-015-1253-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/06/2015] [Indexed: 10/23/2022]
Abstract
The cytochromes c' (CYTcp) are found in denitrifying, methanotrophic and photosynthetic bacteria. These proteins are able to form stable adducts with CO and NO but not with O2. The binding of NO to CYTcp currently provides the best structural model for the NO activation mechanism of soluble guanylate cyclase. Ligand binding in CYTcps has been shown to be highly dependent on residues in both the proximal and distal heme pockets. Group 1 CYTcps typically have a phenylalanine residue positioned close to the distal face of heme, while for group 2, this residue is typically leucine. We have structurally, spectroscopically and kinetically characterised the CYTcp from Shewanella frigidimarina (SFCP), a protein that has a distal phenylalanine residue and a lysine in the proximal pocket in place of the more common arginine. Each monomer of the SFCP dimer folds as a 4-alpha-helical bundle in a similar manner to CYTcps previously characterised. SFCP exhibits biphasic binding kinetics for both NO and CO as a result of the high level of steric hindrance from the aromatic side chain of residue Phe 16. The binding of distal ligands is thus controlled by the conformation of the phenylalanine ring. Only a proximal 5-coordinate NO adduct, confirmed by structural data, is observed with no detectable hexacoordinate distal NO adduct.
Collapse
|
40
|
Hough MA, Andrew CR. Cytochromes c': Structure, Reactivity and Relevance to Haem-Based Gas Sensing. Adv Microb Physiol 2015; 67:1-84. [PMID: 26616515 DOI: 10.1016/bs.ampbs.2015.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cytochromes c' are a group of class IIa cytochromes with pentacoordinate haem centres and are found in photosynthetic, denitrifying and methanotrophic bacteria. Their function remains unclear, although roles in nitric oxide (NO) trafficking during denitrification or in cellular defence against nitrosoative stress have been proposed. Cytochromes c' are typically dimeric with each c-type haem-containing monomer folding as a four-α-helix bundle. Their hydrophobic and crowded distal sites impose severe restrictions on the binding of distal ligands, including diatomic gases. By contrast, NO binds to the proximal haem face in a similar manner to that of the eukaryotic NO sensor, soluble guanylate cyclase and bacterial analogues. In this review, we focus on how structural features of cytochromes c' influence haem spectroscopy and reactivity with NO, CO and O2. We also discuss the relevance of cytochrome c' to understanding the mechanisms of gas binding to haem-based sensor proteins.
Collapse
|
41
|
Dasgupta A, Bowman L, D'Arsigny CL, Archer SL. Soluble guanylate cyclase: a new therapeutic target for pulmonary arterial hypertension and chronic thromboembolic pulmonary hypertension. Clin Pharmacol Ther 2014; 97:88-102. [PMID: 25670386 DOI: 10.1002/cpt.10] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/03/2014] [Indexed: 01/08/2023]
Abstract
Nitric oxide (NO) activates soluble guanylate cyclase (sGC) by binding its prosthetic heme group, thereby catalyzing cyclic guanosine monophosphate (cGMP) synthesis. cGMP causes vasodilation and may inhibit smooth muscle cell proliferation and platelet aggregation. The NO-sGC-cGMP pathway is disordered in pulmonary arterial hypertension (PAH), a syndrome in which pulmonary vascular obstruction, inflammation, thrombosis, and constriction ultimately lead to death from right heart failure. Expression of sGC is increased in PAH but its function is reduced by decreased NO bioavailability, sGC oxidation and the related loss of sGC's heme group. Two classes of sGC modulators offer promise in PAH. sGC stimulators (e.g., riociguat) require heme-containing sGC to catalyze cGMP production, whereas sGC activators (e.g., cinaciguat) activate heme-free sGC. Riociguat is approved for PAH and yields functional and hemodynamic benefits similar to other therapies. Its main serious adverse effect is dose-dependent hypotension. Riociguat is also approved for inoperable chronic thromboembolic pulmonary hypertension.
Collapse
Affiliation(s)
- A Dasgupta
- Department of Medicine, Queen's University, Etherington Hall, Kingston, Ontario, Canada
| | | | | | | |
Collapse
|
42
|
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.
Collapse
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;
| |
Collapse
|
43
|
Structures of soluble guanylate cyclase: implications for regulatory mechanisms and drug development. Biochem Soc Trans 2014; 42:108-13. [PMID: 24450636 PMCID: PMC3901396 DOI: 10.1042/bst20130228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Activation of cGMP synthesis leads to vasodilation, and is an important mechanism in clinical treatment of angina, heart failure, and severe peripheral and pulmonary hypertension. The nitric oxide-responsive sGC (soluble guanylate cyclase) has been the target of recent drug discovery efforts. The present review surveys recent data on the structure and regulation of sGC, and the prospects of new avenues for therapeutic intervention.
Collapse
|
44
|
Lobato L, Bouzhir-Sima L, Yamashita T, Wilson MT, Vos MH, Liebl U. Dynamics of the heme-binding bacterial gas-sensing dissimilative nitrate respiration regulator (DNR) and activation barriers for ligand binding and escape. J Biol Chem 2014; 289:26514-26524. [PMID: 25037216 DOI: 10.1074/jbc.m114.571398] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
DNR (dissimilative nitrate respiration regulator) is a heme-binding transcription factor that is involved in the regulation of denitrification in Pseudomonas aeruginosa. In the ferrous deoxy state, the heme is 6-coordinate; external NO and CO can replace an internal ligand. Using fluorescence anisotropy, we show that high-affinity sequence-specific DNA binding occurs only when the heme is nitrosylated, consistent with the proposed function of DNR as NO sensor and transcriptional activator. This role is moreover supported by the NO "trapping" properties revealed by ultrafast spectroscopy that are similar to those of other heme-based NO sensor proteins. Dissociated CO-heme pairs rebind in an essentially barrierless way. This process competes with migration out of the heme pocket. The latter process is thermally activated (Ea ∼ 7 kJ/mol). This result is compared with other heme proteins, including the homologous CO sensor/transcription factor CooA, variants of the 5-coordinate mycobacterial sensor DosT and the electron transfer protein cytochrome c. This comparison indicates that thermal activation of ligand escape from the heme pocket is specific for systems where an external ligand replaces an internal one. The origin of this finding and possible implications are discussed.
Collapse
Affiliation(s)
- Laura Lobato
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France
| | - Latifa Bouzhir-Sima
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France
| | - Taku Yamashita
- Laboratory of Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan, and
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester C04 3SQ, United Kingdom
| | - Marten H Vos
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France,.
| | - Ursula Liebl
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France,.
| |
Collapse
|
45
|
Kekilli D, Dworkowski FSN, Pompidor G, Fuchs MR, Andrew CR, Antonyuk S, Strange RW, Eady RR, Hasnain SS, Hough MA. Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy. ACTA ACUST UNITED AC 2014; 70:1289-96. [PMID: 24816098 DOI: 10.1107/s1399004714004039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 02/20/2014] [Indexed: 11/10/2022]
Abstract
It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.
Collapse
Affiliation(s)
- Demet Kekilli
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | | | - Guillaume Pompidor
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Martin R Fuchs
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Colin R Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, OR 97850-2899, USA
| | - Svetlana Antonyuk
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Richard W Strange
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Robert R Eady
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - S Samar Hasnain
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| |
Collapse
|
46
|
Vicente JB, Colaço HG, Mendes MIS, Sarti P, Leandro P, Giuffrè A. NO* binds human cystathionine β-synthase quickly and tightly. J Biol Chem 2014; 289:8579-87. [PMID: 24515102 DOI: 10.1074/jbc.m113.507533] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hexa-coordinate heme in the H2S-generating human enzyme cystathionine β-synthase (CBS) acts as a redox-sensitive regulator that impairs CBS activity upon binding of NO(•) or CO at the reduced iron. Despite the proposed physiological relevance of this inhibitory mechanism, unlike CO, NO(•) was reported to bind at the CBS heme with very low affinity (Kd = 30-281 μm). This discrepancy was herein reconciled by investigating the NO(•) reactivity of recombinant human CBS by static and stopped-flow UV-visible absorption spectroscopy. We found that NO(•) binds tightly to the ferrous CBS heme, with an apparent Kd ≤ 0.23 μm. In line with this result, at 25 °C, NO(•) binds quickly to CBS (k on ∼ 8 × 10(3) m(-1) s(-1)) and dissociates slowly from the enzyme (k off ∼ 0.003 s(-1)). The observed rate constants for NO(•) binding were found to be linearly dependent on [NO(•)] up to ∼ 800 μm NO(•), and >100-fold higher than those measured for CO, indicating that the reaction is not limited by the slow dissociation of Cys-52 from the heme iron, as reported for CO. For the first time the heme of human CBS is reported to bind NO(•) quickly and tightly, providing a mechanistic basis for the in vivo regulation of the enzyme by NO(•). The novel findings reported here shed new light on CBS regulation by NO(•) and its possible (patho)physiological relevance, enforcing the growing evidence for an interplay among the gasotransmitters NO(•), CO, and H2S in cell signaling.
Collapse
Affiliation(s)
- João B Vicente
- From the Metabolism and Genetics Group, Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal
| | | | | | | | | | | |
Collapse
|
47
|
Matsumura H, Hayashi T, Chakraborty S, Lu Y, Moënne-Loccoz P. The production of nitrous oxide by the heme/nonheme diiron center of engineered myoglobins (Fe(B)Mbs) proceeds through a trans-iron-nitrosyl dimer. J Am Chem Soc 2014; 136:2420-31. [PMID: 24432820 PMCID: PMC4004238 DOI: 10.1021/ja410542z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Denitrifying NO reductases are transmembrane
protein complexes
that are evolutionarily related to heme/copper terminal oxidases.
They utilize a heme/nonheme diiron center to reduce two NO molecules
to N2O. Engineering a nonheme FeB site within
the heme distal pocket of sperm whale myoglobin has offered well-defined
diiron clusters for the investigation of the mechanism of NO reduction
in these unique active sites. In this study, we use FTIR spectroscopy
to monitor the production of N2O in solution and to show
that the presence of a distal FeBII is not sufficient
to produce the expected product. However, the addition of a glutamate
side chain peripheral to the diiron site allows for 50% of a productive
single-turnover reaction. Unproductive reactions are characterized
by resonance Raman spectroscopy as dinitrosyl complexes, where one
NO molecule is bound to the heme iron to form a five-coordinate low-spin
{FeNO}7 species with ν(FeNO)heme and ν(NO)heme at 522 and 1660 cm–1, and a second NO
molecule is bound to the nonheme FeB site with a ν(NO)FeB at 1755 cm–1. Stopped-flow UV–vis
absorption coupled with rapid-freeze-quench resonance Raman spectroscopy
provide a detailed map of the reaction coordinates leading to the
unproductive iron-nitrosyl dimer. Unexpectedly, NO binding to FeB is kinetically favored and occurs prior to the binding of
a second NO to the heme iron, leading to a (six-coordinate low-spin
heme-nitrosyl/FeB-nitrosyl) transient dinitrosyl complex
with characteristic ν(FeNO)heme at 570 ± 2 cm–1 and ν(NO)FeB at 1755 cm–1. Without the addition of a peripheral glutamate, the dinitrosyl
complex is converted to a dead-end product after the dissociation
of the proximal histidine of the heme iron, but the added peripheral
glutamate side chain in FeBMb2 lowers the rate of dissociation
of the promixal histidine which in turn allows the (six-coordinate
low-spin heme-nitrosyl/FeB-nitrosyl) transient dinitrosyl
complex to decay with production of N2O at a rate of 0.7
s–1 at 4 °C. Taken together, our results support
the proposed trans mechanism of NO reduction in NORs.
Collapse
Affiliation(s)
- Hirotoshi Matsumura
- Divison of Environmental & Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | | | | | | | | |
Collapse
|
48
|
|
49
|
Hough MA, Silkstone G, Worrall JAR, Wilson MT. NO binding to the proapoptotic cytochrome c-cardiolipin complex. VITAMINS AND HORMONES 2014; 96:193-209. [PMID: 25189388 DOI: 10.1016/b978-0-12-800254-4.00008-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytochrome c is a heme protein that is localized in the compartment between the inner and outer mitochondrial membranes where it functions to transfer electrons between complex III and complex IV of the respiratory chain. It can also form an intimate association with the mitochondrion-specific phospholipid cardiolipin that induces a conformational change in the protein enabling it to act as a peroxidase catalyzing the oxidation of cardiolipin and thereby instigating a chain of events that leads to apoptosis. Unlike the native protein, cytochrome c within the complex binds ligands rapidly; in particular, NO can coordinate to either the ferric or ferrous iron of the heme. Remarkably, in the ferrous form, NO binds preferentially to the proximal side of the heme and thus behaves in a way similar to cytochrome c'-type proteins and to guanylate cyclase. The implications of NO binding to the proapoptotic cytochrome c/cardiolipin complex are discussed in terms of modulating the apoptotic response and buffering NO concentrations. Insights into the structure of the complex are provided by comparison with cytochrome c' for which X-ray structures are available.
Collapse
Affiliation(s)
- Michael A Hough
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Gary Silkstone
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - J A R Worrall
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Colchester, United Kingdom.
| |
Collapse
|
50
|
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.
Collapse
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
| | | | | | | |
Collapse
|