1
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Hoque NJ, Rivera S, Young PG, Weinert EE, Liu Y. Heme pocket hydrogen bonding residue interactions within the Pectobacterium Diguanylate cyclase-containing globin coupled sensor: A resonance Raman study. J Inorg Biochem 2024; 260:112686. [PMID: 39106644 DOI: 10.1016/j.jinorgbio.2024.112686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/09/2024]
Abstract
Heme-based sensor proteins are used by organisms to control signaling and physiological effects in response to their gaseous environment. Globin-coupled sensors (GCS) are oxygen-sensing proteins that are widely distributed in bacteria. These proteins consist of a heme globin domain linked by a middle domain to various output domains, including diguanylate cyclase domains, which are responsible for synthesizing c-di-GMP, a bacterial second messenger crucial for regulating biofilm formation. To understand the roles of heme pocket residues in controlling activity of the diguanylate cyclase domain, variants of the Pectobacterium carotovorum GCS (PccGCS) were characterized by enzyme kinetics and resonance Raman (rR) spectroscopy. Results of these studies have identified roles for hydrogen bonding and heme edge residues in modulating heme pocket conformation and flexibility. Better understanding of the ligand-dependent GCS signaling mechanism and the residues involved may allow for future development of methods to control O2-dependent c-di-GMP production.
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Affiliation(s)
- Nushrat J Hoque
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Shannon Rivera
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Paul G Young
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Emily E Weinert
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Yilin Liu
- Department of Chemistry, University of Akron, Akron, OH 44325, USA.
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2
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Reynolds MF. New insights into the signal transduction mechanism of O 2-sensing FixL and other biological heme-based sensor proteins. J Inorg Biochem 2024; 259:112642. [PMID: 38908215 DOI: 10.1016/j.jinorgbio.2024.112642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024]
Abstract
Recent structural and biophysical studies of O2-sensing FixL, NO-sensing soluble guanylate cyclase, and other biological heme-based sensing proteins have begun to reveal the details of their molecular mechanisms and shed light on how nature regulates important biological processes such as nitrogen fixation, blood pressure, neurotransmission, photosynthesis and circadian rhythm. The O2-sensing FixL protein from S. meliloti, the eukaryotic NO-sensing protein sGC, and the CO-sensing CooA protein from R. rubrum transmit their biological signals through gas-binding to the heme domain of these proteins, which inhibits or activates the regulatory, enzymatic domain. These proteins appear to propagate their signal by specific structural changes in the heme sensor domain initiated by the appropriate gas binding to the heme, which is then propagated through a coiled-coil linker or other domain to the regulatory, enzymatic domain that sends out the biological signal. The current understanding of the signal transduction mechanisms of O2-sensing FixL, NO-sensing sGC, CO-sensing CooA and other biological heme-based gas sensing proteins and their mechanistic themes are discussed, with recommendations for future work to further understand this rapidly growing area of biological heme-based gas sensors.
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Affiliation(s)
- Mark F Reynolds
- Department of Chemistry and Biochemistry, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131, United States of America.
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3
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Yoo BK, Kruglik SG, Lambry JC, Lamarre I, Raman CS, Nioche P, Negrerie M. The H-NOX protein structure adapts to different mechanisms in sensors interacting with nitric oxide. Chem Sci 2023; 14:8408-8420. [PMID: 37564404 PMCID: PMC10411614 DOI: 10.1039/d3sc01685d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Some classes of bacteria within phyla possess protein sensors identified as homologous to the heme domain of soluble guanylate cyclase, the mammalian NO-receptor. Named H-NOX domain (Heme-Nitric Oxide or OXygen-binding), their heme binds nitric oxide (NO) and O2 for some of them. The signaling pathways where these proteins act as NO or O2 sensors appear various and are fully established for only some species. Here, we investigated the reactivity of H-NOX from bacterial species toward NO with a mechanistic point of view using time-resolved spectroscopy. The present data show that H-NOXs modulate the dynamics of NO as a function of temperature, but in different ranges, changing its affinity by changing the probability of NO rebinding after dissociation in the picosecond time scale. This fundamental mechanism provides a means to adapt the heme structural response to the environment. In one particular H-NOX sensor the heme distortion induced by NO binding is relaxed in an ultrafast manner (∼15 ps) after NO dissociation, contrarily to other H-NOX proteins, providing another sensing mechanism through the H-NOX domain. Overall, our study links molecular dynamics with functional mechanism and adaptation.
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Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Sergei G Kruglik
- Laboratoire Jean Perrin, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS 75005 Paris France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - C S Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore Maryland 21201 USA
| | - Pierre Nioche
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, UMR S1124, Centre Universitaire des Saints-Pères, Université Paris Descartes 75006 Paris France
- Structural and Molecular Analysis Platform, BioMedTech Facilities, INSERM US36-CNRS-UMS2009, Paris Université Paris France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
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4
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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.
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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.
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5
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Takeda H, Shimba K, Horitani M, Kimura T, Nomura T, Kubo M, Shiro Y, Tosha T. Trapping of a Mononitrosyl Nonheme Intermediate of Nitric Oxide Reductase by Cryo-Photolysis of Caged Nitric Oxide. J Phys Chem B 2023; 127:846-854. [PMID: 36602896 DOI: 10.1021/acs.jpcb.2c05852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Characterization of short-lived reaction intermediates is essential for elucidating the mechanism of the reaction catalyzed by metalloenzymes. Here, we demonstrated that the photolysis of a caged compound under cryogenic temperature followed by thermal annealing is an invaluable technique for trapping of short-lived reaction intermediates of metalloenzymes through the study of membrane-integrated nitric oxide reductase (NOR) that catalyzes reductive coupling of two NO molecules to N2O at its heme/nonheme FeB binuclear center. Although NO produced by the photolysis of caged NO did not react with NOR under cryogenic temperature, annealing to ∼160 K allowed NO to diffuse and react with NOR, which was evident from the appearance of EPR signals assignable to the S = 3/2 state. This indicates that the nonheme FeB-NO species can be trapped as the intermediate. Time-resolved IR spectroscopy with the use of the photolysis of caged NO as a reaction trigger showed that the intermediate formed at 10 μs gave the NO stretching frequency at 1683 cm-1 typical of nonheme Fe-NO, confirming that the combination of the cryo-photolysis of caged NO and annealing enabled us to trap the reaction intermediate. Thus, the cryo-photolysis of the caged compound has great potential for the characterization of short-lived reaction intermediates.
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Affiliation(s)
- Hanae Takeda
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
| | - Kanji Shimba
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry & Food Science, Saga University, Saga 840-8502, Japan.,The United Graduate School of Agricultural Science, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
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6
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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.
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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.
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7
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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.
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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
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8
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Patterson DC, Liu Y, Das S, Yennawar NH, Armache JP, Kincaid JR, Weinert EE. Heme-Edge Residues Modulate Signal Transduction within a Bifunctional Homo-Dimeric Sensor Protein. Biochemistry 2021; 60:3801-3812. [PMID: 34843212 DOI: 10.1021/acs.biochem.1c00581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bifunctional enzymes, which contain two domains with opposing enzymatic activities, are widely distributed in bacteria, but the regulatory mechanism(s) that prevent futile cycling are still poorly understood. The recently described bifunctional enzyme, DcpG, exhibits unusual heme properties and is surprisingly able to differentially regulate its two cyclic dimeric guanosine monophosphate (c-di-GMP) metabolic domains in response to heme gaseous ligands. Mutagenesis of heme-edge residues was used to probe the heme pocket and resulted in decreased O2 dissociation kinetics, identifying roles for these residues in modulating DcpG gas sensing. In addition, the resonance Raman spectra of the DcpG wild type and heme-edge mutants revealed that the mutations alter the heme electrostatic environment, vinyl group conformations, and spin state population. Using small-angle X-ray scattering and negative stain electron microscopy, the heme-edge mutations were demonstrated to cause changes to the protein conformation, which resulted in altered signaling transduction and enzyme kinetics. These findings provide insights into molecular interactions that regulate DcpG gas sensing as well as mechanisms that have evolved to control multidomain bacterial signaling proteins.
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Affiliation(s)
- Dayna C Patterson
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Sayan Das
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Emily E Weinert
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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9
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Phelan BT, Mara MW, Chen LX. Excited-state structural dynamics of nickel complexes probed by optical and X-ray transient absorption spectroscopies: insights and implications. Chem Commun (Camb) 2021; 57:11904-11921. [PMID: 34695174 DOI: 10.1039/d1cc03875c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Excited states of nickel complexes undergo a variety of photochemical processes, such as charge transfer, ligation/deligation, and redox reactions, relevant to solar energy conversion and photocatalysis. The efficiencies of the aforementioned processes are closely coupled to the molecular structures in the ground and excited states. The conventional optical transient absorption spectroscopy has revealed important excited-state pathways and kinetics, but information regarding the metal center, in particular transient structural and electronic properties, remains limited. These deficiencies are addressed by X-ray transient absorption (XTA) spectroscopy, a detailed probe of 3d orbital occupancy, oxidation state and coordination geometry. The examples of excited-state structural dynamics of nickel porphyrin and nickel phthalocyanine have been described from our previous studies with highlights on the unique structural information obtained by XTA spectroscopy. We close by surveying prospective applications of XTA spectroscopy to active areas of Ni-based photocatalysis based on the knowledge gained from our previous studies.
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Affiliation(s)
- Brian T Phelan
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA.
| | - Michael W Mara
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA. .,Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Lin X Chen
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA. .,Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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10
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Dent MR, DeMartino AW, Tejero J, Gladwin MT. Endogenous Hemoprotein-Dependent Signaling Pathways of Nitric Oxide and Nitrite. Inorg Chem 2021; 60:15918-15940. [PMID: 34313417 PMCID: PMC9167621 DOI: 10.1021/acs.inorgchem.1c01048] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interdisciplinary research at the interface of chemistry, physiology, and biomedicine have uncovered pivotal roles of nitric oxide (NO) as a signaling molecule that regulates vascular tone, platelet aggregation, and other pathways relevant to human health and disease. Heme is central to physiological NO signaling, serving as the active site for canonical NO biosynthesis in nitric oxide synthase (NOS) enzymes and as the highly selective NO binding site in the soluble guanylyl cyclase receptor. Outside of the primary NOS-dependent biosynthetic pathway, other hemoproteins, including hemoglobin and myoglobin, generate NO via the reduction of nitrite. This auxiliary hemoprotein reaction unlocks a "second axis" of NO signaling in which nitrite serves as a stable NO reservoir. In this Forum Article, we highlight these NO-dependent physiological pathways and examine complex chemical and biochemical reactions that govern NO and nitrite signaling in vivo. We focus on hemoprotein-dependent reaction pathways that generate and consume NO in the presence of nitrite and consider intermediate nitrogen oxides, including NO2, N2O3, and S-nitrosothiols, that may facilitate nitrite-based signaling in blood vessels and tissues. We also discuss emergent therapeutic strategies that leverage our understanding of these key reaction pathways to target NO signaling and treat a wide range of diseases.
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Affiliation(s)
- Matthew R Dent
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Anthony W DeMartino
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Jesús Tejero
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Mark T Gladwin
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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11
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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.
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12
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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.
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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.
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13
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Germani F, Nardini M, De Schutter A, Cuypers B, Berghmans H, Van Hauwaert ML, Bruno S, Mozzarelli A, Moens L, Van Doorslaer S, Bolognesi M, Pesce A, Dewilde S. Structural and Functional Characterization of the Globin-Coupled Sensors of Azotobacter vinelandii and Bordetella pertussis. Antioxid Redox Signal 2020; 32:378-395. [PMID: 31559835 DOI: 10.1089/ars.2018.7690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aims: Structural and functional characterization of the globin-coupled sensors (GCSs) from Azotobacter vinelandii (AvGReg) and Bordetella pertussis (BpeGReg). Results: Ultraviolet/visible and resonance Raman spectroscopies confirm the presence in AvGReg and BpeGReg of a globin domain capable of reversible gaseous ligand binding. In AvGReg, an influence of the transmitter domain on the heme proximal region of the globin domain can be seen, and k'CO is higher than for other GCSs. The O2 binding kinetics suggests the presence of an open and a closed conformation. As for BpeGReg, the fully oxygenated AvGReg show a very high diguanylate cyclase activity. The carbon monoxide rebinding to BpeGReg indicates that intra- and intermolecular interactions influence the ligand binding. The globin domains of both proteins (AvGReg globin domain and BpeGRegGb with cysteines (Cys16, 45, 114, 154) mutated to serines [BpeGReg-Gb*]) share the same GCS fold, a similar proximal but a different distal side structure. They homodimerize through a G-H helical bundle as in other GCSs. However, BpeGReg-Gb* shows also a second dimerization mode. Innovation: This article extends our knowledge on the GCS proteins and contributes to a better understanding of the GCSs role in the formation of bacterial biofilms. Conclusions:AvGReg and BpeGReg conform to the GCS family, share a similar overall structure, but they have different properties in terms of the ligand binding. In particular, AvGReg shows an open and a closed conformation that in the latter form will very tightly bind oxygen. BpeGReg has only one closed conformation. In both proteins, it is the fully oxygenated GCS form that catalyzes the production of the second messenger.
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Affiliation(s)
- Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | - Amy De Schutter
- Department of Physics, University of Antwerp, Wilrijk, Belgium
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Wilrijk, Belgium
| | - Herald Berghmans
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | | | - Stefano Bruno
- Department of Food and Drugs, University of Parma, Parma, Italy
| | | | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | | | | | | | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
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14
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Belvin BR, Musayev FN, Burgner J, Scarsdale JN, Escalante CR, Lewis JP. Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR. Acta Crystallogr D Struct Biol 2019; 75:437-450. [PMID: 30988260 PMCID: PMC6465984 DOI: 10.1107/s205979831900264x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/21/2019] [Indexed: 11/10/2022] Open
Abstract
Although the HcpR regulator plays a vital step in initiation of the nitrosative stress response in many Gram-negative anaerobic bacteria, the molecular mechanisms that it uses to mediate gas sensing are not well understood. Here, a 2.6 Å resolution crystal structure of the N-terminal sensing domain of the anaerobic periodontopathogen Porphyromonas gingivalis HcpR is presented. The protein has classical features of the regulators belonging to the FNR-CRP family and contains a hydrophobic pocket in its N-terminal sensing domain. It is shown that heme bound to HcpR exhibits heme iron as a hexacoordinate system in the absence of nitric oxide (NO) and that upon nitrosylation it transitions to a pentacoordinate system. Finally, small-angle X-ray scattering experiments on full-length HcpR reveal that the C-terminal DNA-binding domain of HcpR has a high degree of interdomain flexibility.
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Affiliation(s)
- B. Ross Belvin
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Faik N. Musayev
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - John Burgner
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J. Neel Scarsdale
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Carlos R. Escalante
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Janina P. Lewis
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
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15
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Rahaman MM, Nguyen AT, Miller MP, Hahn SA, Sparacino-Watkins C, Jobbagy S, Carew NT, Cantu-Medellin N, Wood KC, Baty CJ, Schopfer FJ, Kelley EE, Gladwin MT, Martin E, Straub AC. Cytochrome b5 Reductase 3 Modulates Soluble Guanylate Cyclase Redox State and cGMP Signaling. Circ Res 2017; 121:137-148. [PMID: 28584062 DOI: 10.1161/circresaha.117.310705] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 12/17/2022]
Abstract
RATIONALE Soluble guanylate cyclase (sGC) heme iron, in its oxidized state (Fe3+), is desensitized to NO and limits cGMP production needed for downstream activation of protein kinase G-dependent signaling and blood vessel dilation. OBJECTIVE Although reactive oxygen species are known to oxidize the sGC heme iron, the basic mechanism(s) governing sGC heme iron recycling to its NO-sensitive, reduced state remain poorly understood. METHODS AND RESULTS Oxidant challenge studies show that vascular smooth muscle cells have an intrinsic ability to reduce oxidized sGC heme iron and form protein-protein complexes between cytochrome b5 reductase 3, also known as methemoglobin reductase, and oxidized sGC. Genetic knockdown and pharmacological inhibition in vascular smooth muscle cells reveal that cytochrome b5 reductase 3 expression and activity is critical for NO-stimulated cGMP production and vasodilation. Mechanistically, we show that cytochrome b5 reductase 3 directly reduces oxidized sGC required for NO sensitization as assessed by biochemical, cellular, and ex vivo assays. CONCLUSIONS Together, these findings identify new insights into NO-sGC-cGMP signaling and reveal cytochrome b5 reductase 3 as the first identified physiological sGC heme iron reductase in vascular smooth muscle cells, serving as a critical regulator of cGMP production and protein kinase G-dependent signaling.
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Affiliation(s)
- Mizanur M Rahaman
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Anh T Nguyen
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Megan P Miller
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Scott A Hahn
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Courtney Sparacino-Watkins
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Soma Jobbagy
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Nolan T Carew
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Nadiezhda Cantu-Medellin
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Katherine C Wood
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Catherine J Baty
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Francisco J Schopfer
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Eric E Kelley
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Mark T Gladwin
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Emil Martin
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.)
| | - Adam C Straub
- From the Heart, Lung, Blood and Vascular Medicine Institute (M.M.R., A.T.N., M.P.M., S.A.H., C.S.-W., N.T.C., N.C.-M., K.C.W., M.T.G., A.C.S.), Division of Pulmonary, Allergy and Critical Care Medicine (C.S.-W., M.T.G.), Department of Pharmacology and Chemical Biology (S.J., C.J.B., F.J.S., A.C.S.), and Division of Renal-Electrolyte (C.J.B.), University of Pittsburgh, PA; Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown (E.E.K.); and Department of Internal Medicine, Division of Cardiology, University of Texas Houston Medical School (E.M.).
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16
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Xu H, Zhang Y, Chen L, Li Y, Li C, Liu L, Ogura T, Kitagawa T, Li Z. Entry of water into the distal heme pocket of soluble guanylate cyclase β1 H-NOX domain alters the ligated CO structure: a resonance Raman and in silico simulation study. RSC Adv 2016. [DOI: 10.1039/c6ra06515e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Water accessing into the heme pocket and alters the structures of CO–sGC (heme), exhibiting two different vFe–CO stretching modes.
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Affiliation(s)
- Haoran Xu
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Yuebin Zhang
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Lei Chen
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Yan Li
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Chen Li
- Picobiology Institute
- Graduate School of Life Science
- University of Hyogo
- RSC-UH Leading Program Center
- Hyogo 679-5148
| | - Li Liu
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Takashi Ogura
- Picobiology Institute
- Graduate School of Life Science
- University of Hyogo
- RSC-UH Leading Program Center
- Hyogo 679-5148
| | - Teizo Kitagawa
- Picobiology Institute
- Graduate School of Life Science
- University of Hyogo
- RSC-UH Leading Program Center
- Hyogo 679-5148
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
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17
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Li J, Peng Q, Oliver A, Alp EE, Hu MY, Zhao J, Sage JT, Scheidt WR. Comprehensive Fe-ligand vibration identification in {FeNO}6 hemes. J Am Chem Soc 2014; 136:18100-10. [PMID: 25490350 PMCID: PMC4295236 DOI: 10.1021/ja5105766] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Indexed: 01/06/2023]
Abstract
Oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS) has been used to obtain all iron vibrations in two {FeNO}(6) porphyrinate complexes, five-coordinate [Fe(OEP)(NO)]ClO4 and six-coordinate [Fe(OEP)(2-MeHIm)(NO)]ClO4. A new crystal structure was required for measurements of [Fe(OEP)(2-MeHIm)(NO)]ClO4, and the new structure is reported herein. Single crystals of both complexes were oriented to be either parallel or perpendicular to the porphyrin plane and/or axial imidazole ligand plane. Thus, the FeNO bending and stretching modes can now be unambiguously assigned; the pattern of shifts in frequency as a function of coordination number can also be determined. The pattern is quite distinct from those found for CO or {FeNO}(7) heme species. This is the result of unchanging Fe-N(NO) bonding interactions in the {FeNO}(6) species, in distinct contrast to the other diatomic ligand species. DFT calculations were also used to obtain detailed predictions of vibrational modes. Predictions were consistent with the intensity and character found in the experimental spectra. The NRVS data allow the assignment and observation of the challenging to obtain Fe-Im stretch in six-coordinate heme derivatives. NRVS data for this and related six-coordinate hemes with the diatomic ligands CO, NO, and O2 reveal a strong correlation between the Fe-Im stretch and Fe-N(Im) bond distance that is detailed for the first time.
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Affiliation(s)
- Jianfeng Li
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, YanQi Lake, HuaiRou District, Beijing 101408, China
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Qian Peng
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Allen
G. Oliver
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - E. Ercan Alp
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael Y. Hu
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - J. Timothy Sage
- Department
of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 120 Forsyth Street, Boston, Massachusetts 02115, United States
| | - W. Robert Scheidt
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
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18
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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.
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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
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19
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Weak coordination of neutral S- and O-donor proximal ligands to a ferrous porphyrin nitrosyl. Characterization of 6-coordinate complexes at low T. J Inorg Biochem 2013; 121:129-33. [PMID: 23376554 DOI: 10.1016/j.jinorgbio.2012.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 12/27/2012] [Accepted: 12/28/2012] [Indexed: 11/23/2022]
Abstract
The interaction of the S- and O-donor ligands tetrahydrothiophen (THT) and tetrahydrofuran (THF) with the ferrous nitrosyl complex Fe(TTP)(NO) (TTP(2-) is meso-tetra-p-tolyl-porphyrinatodianion) was studied at various temperatures both in solid state and solution using electronic and infrared absorption spectroscopy. Upon addition of these ligands to a cryostat containing sublimed layers of Fe(TTP)(NO), no complex formation was detected at room temperature. However, upon lowering the temperature, spectral changes were observed that are consistent with ligand binding in axial position trans to the NO (the proximal site) and formation of the six-coordinate adducts. Analogous behavior was observed in solution. In both media, the six-coordinate adducts are stable only at low temperature and dissociate to the 5-coordinate nitrosyl complexes upon warming. The NO stretching frequencies of the six-coordinate thioether and ether complexes were recorded and binding constants for the weak bonding of proximal THF and THT ligands were determined from the spectral changes. These parameters are compared with those obtained for the N-donor ligand pyrrolidine.
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20
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Franke A, van Eldik R. Factors That Determine the Mechanism of NO Activation by Metal Complexes of Biological and Environmental Relevance. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201201111] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Makino R, Yazawa S, Hori H, Shiro Y. Interactions of soluble guanylate cyclase with a P-site inhibitor: effects of gaseous heme ligands, azide, and allosteric activators on the binding of 2'-deoxy-3'-GMP. Biochemistry 2012; 51:9277-89. [PMID: 23106307 DOI: 10.1021/bi3004044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Nitric oxide (NO) elicits a wide variety of physiological responses by binding to the heme in soluble guanylate cyclase (sGC) to stimulate cGMP production. Although nucleotides, such as ATP or GTP analogues, have been reported to regulate the signaling of NO binding from the heme site to the catalytic site, the other regulatory functions of nucleotides remain unexamined. Among the nucleotides tested, we found that 2'-d-3'-GMP acted as a potent noncompetitive inhibitor with respect to Mn-GTP, when the ferrous enzyme combined with NO, CO, or allosteric activator BAY 41-2272. 2'-d-3'-GMP also displayed nearly identical patterns of inhibition for the ferric enzyme, in which the binding of N(3)(-) or BAY 41-2272 significantly increased the inhibitory effects of the nucleotide. Equilibrium dialysis measurements using the CO-ligated enzyme in the presence of allosteric activators demonstrated that 2'-d-3'-GMP exclusively binds to the catalytic site of sGC. Furthermore, the affinity of 2'-d-3'-GMP for the enzyme was found to increase upon addition of foscarnet, an analogue of PP(i). These findings together with other kinetic results imply that 2'-d-3'-GMP acts as a P-site inhibitor probably by forming a dead-end complex, sGC-2'-d-3'-GMP-PP(i), in the catalytic reaction. The formation of the complex of the enzyme with 2'-d-3'-GMP does not seem to be associated with changes in the Fe-proximal His bond strength, because the CO coordination state or the redox potentials of the enzyme-heme complex are virtually unaffected.
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Affiliation(s)
- Ryu Makino
- Department of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro 3-34-1, Toshima-ku, Tokyo 171-8501, Japan.
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22
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Tsai AL, Martin E, Berka V, Olson JS. How do heme-protein sensors exclude oxygen? Lessons learned from cytochrome c', Nostoc puntiforme heme nitric oxide/oxygen-binding domain, and soluble guanylyl cyclase. Antioxid Redox Signal 2012; 17:1246-63. [PMID: 22356101 PMCID: PMC3430480 DOI: 10.1089/ars.2012.4564] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Ligand selectivity for dioxygen (O(2)), carbon monoxide (CO), and nitric oxide (NO) is critical for signal transduction and is tailored specifically for each heme-protein sensor. Key NO sensors, such as soluble guanylyl cyclase (sGC), specifically recognized low levels of NO and achieve a total O(2) exclusion. Several mechanisms have been proposed to explain the O(2) insensitivity, including lack of a hydrogen bond donor and negative electrostatic fields to selectively destabilize bound O(2), distal steric hindrance of all bound ligands to the heme iron, and restriction of in-plane movements of the iron atom. RECENT ADVANCES Crystallographic structures of the gas sensors, Thermoanaerobacter tengcongensis heme-nitric oxide/oxygen-binding domain (Tt H-NOX(1)) or Nostoc puntiforme (Ns) H-NOX, and measurements of O(2) binding to site-specific mutants of Tt H-NOX and the truncated β subunit of sGC suggest the need for a H-bonding donor to facilitate O(2) binding. CRITICAL ISSUES However, the O(2) insensitivity of full length sGC with a site-specific replacement of isoleucine by a tyrosine on residue 145 and the very slow autooxidation of Ns H-NOX and cytochrome c' suggest that more complex mechanisms have evolved to exclude O(2) but retain high affinity NO binding. A combined graphical analysis of ligand binding data for libraries of heme sensors, globins, and model heme shows that the NO sensors dramatically inhibit the formation of six-coordinated NO, CO, and O(2) complexes by direct distal steric hindrance (cyt c'), proximal constraints of in-plane iron movement (sGC), or combinations of both following a sliding scale rule. High affinity NO binding in H-NOX proteins is achieved by multiple NO binding steps that produce a high affinity five-coordinate NO complex, a mechanism that also prevents NO dioxygenation. FUTURE DIRECTIONS Knowledge advanced by further extensive test of this "sliding scale rule" hypothesis should be valuable in guiding novel designs for heme based sensors.
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Affiliation(s)
- Ah-Lim Tsai
- Division of Hematology, University of Texas Health Science Center at Houston, Houston, Texas 77225, USA.
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Yoo BK, Lamarre I, Martin JL, Negrerie M. Quaternary structure controls ligand dynamics in soluble guanylate cyclase. J Biol Chem 2012; 287:6851-9. [PMID: 22223482 PMCID: PMC3307277 DOI: 10.1074/jbc.m111.299297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 01/03/2012] [Indexed: 11/06/2022] Open
Abstract
Soluble guanylate cyclase (sGC) is the mammalian endogenous nitric oxide (NO) receptor. The mechanisms of activation and deactivation of this heterodimeric enzyme are unknown. For deciphering them, functional domains can be overexpressed. We have probed the dynamics of the diatomic ligands NO and CO within the isolated heme domain β(1)(190) of human sGC by piconanosecond absorption spectroscopy. After photo-excitation of nitrosylated sGC, only NO geminate rebinding occurs in 7.5 ps. In β(1)(190), both photo-dissociation of 5c-NO and photo-oxidation occur, contrary to sGC, followed by NO rebinding (7 ps) and back-reduction (230 ps and 2 ns). In full-length sGC, CO geminate rebinding to the heme does not occur. In contrast, CO geminately rebinds to β(1)(190) with fast multiphasic process (35, 171, and 18 ns). We measured the bimolecular association rates k(on) = 0.075 ± 0.01 × 10(6) M(-1) · S(-1) for sGC and 0.83 ± 0.1 × 10(6) M(-1) · S(-1) for β(1)(190). These different dynamics reflect conformational changes and less proximal constraints in the isolated heme domain with respect to the dimeric native sGC. We concluded that the α-subunit and the β(1)(191-619) domain exert structural strains on the heme domain. These strains are likely involved in the transmission of the energy and relaxation toward the activated state after Fe(2+)-His bond breaking. This also reveals the heme domain plasticity modulated by the associated domains and subunit.
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Affiliation(s)
- Byung-Kuk Yoo
- From the Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645 Ecole Polytechnique, 91128 Palaiseau, France
| | - Isabelle Lamarre
- From the Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645 Ecole Polytechnique, 91128 Palaiseau, France
| | - Jean-Louis Martin
- From the Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645 Ecole Polytechnique, 91128 Palaiseau, France
| | - Michel Negrerie
- From the Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645 Ecole Polytechnique, 91128 Palaiseau, France
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24
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Hishiki T, Yamamoto T, Morikawa T, Kubo A, Kajimura M, Suematsu M. Carbon monoxide: impact on remethylation/transsulfuration metabolism and its pathophysiologic implications. J Mol Med (Berl) 2012; 90:245-54. [PMID: 22331189 PMCID: PMC3296020 DOI: 10.1007/s00109-012-0875-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 01/27/2012] [Accepted: 01/31/2012] [Indexed: 01/08/2023]
Abstract
Carbon monoxide (CO) is a gaseous product generated by heme oxygenase (HO), which oxidatively degrades heme. While the stress-inducible HO-1 has well been recognized as an anti-oxidative defense mechanism under stress conditions, recent studies suggest that cancer cells utilize the reaction for their survival. HO-2, the constitutive isozyme, also plays protective roles as a tonic regulator for neurovascular function. Although protective roles of the enzyme reaction and CO have extensively been studied, little information is available on the molecular mechanisms by which the gas exerts its biological actions. Recent studies using metabolomics revealed that CO inhibits cystathionine β-synthase (CBS), which generates H2S, another gaseous mediator. The CO-dependent CBS inhibition may impact on the remethylation cycle and related metabolic pathways including the methionine salvage pathway and polyamine synthesis. This review focuses on the gas-responsive regulation of metabolic systems, particularly the remethylation and transsulfuration pathways, and their putative implications for cancer and ischemic diseases.
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Affiliation(s)
- Takako Hishiki
- Department of Biochemistry, JST, ERATO, Suematsu Gas Biology Project, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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25
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Abstract
Nitric oxide (NO) is an essential signaling molecule in biological systems. In mammals, the diatomic gas is critical to the cyclic guanosine monophosphate (cGMP) pathway as it functions as the primary activator of soluble guanylate cyclase (sGC). NO is synthesized from l-arginine and oxygen (O(2)) by the enzyme nitric oxide synthase (NOS). Once produced, NO rapidly diffuses across cell membranes and binds to the heme cofactor of sGC. sGC forms a stable complex with NO and carbon monoxide (CO), but not with O(2). The binding of NO to sGC leads to significant increases in cGMP levels. The second messenger then directly modulates phosphodiesterases (PDEs), ion-gated channels, or cGMP-dependent protein kinases to regulate physiological functions, including vasodilation, platelet aggregation, and neurotransmission. Many studies are focused on elucidating the molecular mechanism of sGC activation and deactivation with a goal of therapeutic intervention in diseases involving the NO/cGMP-signaling pathway. This review summarizes the current understanding of sGC structure and regulation as well as recent developments in NO signaling.
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Affiliation(s)
- Emily R Derbyshire
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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26
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He C, Neya S, Knipp M. Breaking the Proximal FeII–NHis Bond in Heme Proteins through Local Structural Tension: Lessons from the Heme b Proteins Nitrophorin 4, Nitrophorin 7, and Related Site-Directed Mutant Proteins. Biochemistry 2011; 50:8559-75. [DOI: 10.1021/bi201073t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Chunmao He
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470
Mülheim an der Ruhr, Germany
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Image-Yayoi,
Chiba 263-8522, Japan
| | - Markus Knipp
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470
Mülheim an der Ruhr, Germany
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27
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Tran R, Weinert EE, Boon EM, Mathies RA, Marletta MA. Determinants of the heme-CO vibrational modes in the H-NOX family. Biochemistry 2011; 50:6519-30. [PMID: 21714509 DOI: 10.1021/bi200551s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Heme Nitric oxide/OXygen binding (H-NOX) family of proteins have important functions in gaseous ligand signaling in organisms from bacteria to humans, including nitric oxide (NO) sensing in mammals, and provide a model system for probing ligand selectivity in hemoproteins. A unique vibrational feature that is ubiquitous throughout the H-NOX family is the presence of a high C-O stretching frequency. To investigate the cause of this spectroscopic characteristic, the Fe-CO and C-O stretching frequencies were probed in the H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX) using resonance Raman (RR) spectroscopy. Four classes of heme pocket mutants were generated to assess the changes in stretching frequency: (i) the distal H-bonding network, (ii) the proximal histidine ligand, (iii) modulation of the heme conformation via Ile-5 and Pro-115, and (iv) the conserved Tyr-Ser-Arg (YxSxR) motif. These mutations revealed important electrostatic interactions that dampen the back-donation of the Fe(II) d(π) electrons into the CO π* orbitals. The most significant change occurred upon disruption of the H-bonds between the strictly conserved YxSxR motif and the heme propionate groups, producing two dominant CO-bound heme conformations. One conformer was structurally similar to Tt H-NOX WT, whereas the other displayed a decrease in ν(C-O) of up to ∼70 cm(-1) relative to the WT protein, with minimal changes in ν(Fe-CO). Taken together, these results show that the electrostatic interactions in the Tt H-NOX binding pocket are primarily responsible for the high ν(C-O) by decreasing the Fe d(π) → CO π* back-donation and suggest that the dominant mechanism by which this family modulates the Fe(II)-CO bond likely involves the YxSxR motif.
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Affiliation(s)
- Rosalie Tran
- Department of Chemistry, University of California , Berkeley, California 94720, United States
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28
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Quintas PO, Catarino T, Todorovic S, Turner DL. Highly selective ligand binding by Methylophilus methylotrophus cytochrome c''. Biochemistry 2011; 50:5624-32. [PMID: 21599015 DOI: 10.1021/bi200480a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c'' (cyt c'') from Methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. Despite cyt c'' having an axial site available for binding small ligands, we show here that only NO binds readily to the ferrous cyt c''. Binding of CO, as well as CN(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. Standard free energies for the binding of NO and CO reveal high selectivity of the ferrous cyt c'' for NO, indicating its putative physiological role. In this work, we characterize in detail the kinetics of NO binding and the structural features of the Fe(2+)-NO adduct by stopped-flow and resonance Raman spectroscopy, respectively.
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Affiliation(s)
- Pedro O Quintas
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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29
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Derbyshire ER, Winter MB, Ibrahim M, Deng S, Spiro TG, Marletta MA. Probing domain interactions in soluble guanylate cyclase. Biochemistry 2011; 50:4281-90. [PMID: 21491957 DOI: 10.1021/bi200341b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eukaryotic nitric oxide (NO) signaling involves modulation of cyclic GMP (cGMP) levels through activation of the soluble isoform of guanylate cyclase (sGC). sGC is a heterodimeric hemoprotein that contains a Heme-Nitric oxide and OXygen binding (H-NOX) domain, a Per/ARNT/Sim (PAS) domain, a coiled-coil (CC) domain, and a catalytic domain. To evaluate the role of these domains in regulating the ligand binding properties of the heme cofactor of NO-sensitive sGC, we constructed chimeras by swapping the rat β1 H-NOX domain with the homologous region of H-NOX domain-containing proteins from Thermoanaerobacter tengcongensis, Vibrio cholerae, and Caenorhabditis elegans (TtTar4H, VCA0720, and Gcy-33, respectively). Characterization of ligand binding by electronic absorption and resonance Raman spectroscopy indicates that the other rat sGC domains influence the bacterial and worm H-NOX domains. Analysis of cGMP production in these proteins reveals that the chimeras containing bacterial H-NOX domains exhibit guanylate cyclase activity, but this activity is not influenced by gaseous ligand binding to the heme cofactor. The rat-worm chimera containing the atypical sGC Gcy-33 H-NOX domain was weakly activated by NO, CO, and O(2), suggesting that atypical guanylate cyclases and NO-sensitive guanylate cyclases have a common molecular mechanism for enzyme activation. To probe the influence of the other sGC domains on the mammalian sGC heme environment, we generated heme pocket mutants (Pro118Ala and Ile145Tyr) in the β1 H-NOX construct (residues 1-194), the β1 H-NOX-PAS-CC construct (residues 1-385), and the full-length α1β1 sGC heterodimer (β1 residues 1-619). Spectroscopic characterization of these proteins shows that interdomain communication modulates the coordination state of the heme-NO complex and the heme oxidation rate. Taken together, these findings have important implications for the allosteric mechanism of regulation within H-NOX domain-containing proteins.
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Affiliation(s)
- Emily R Derbyshire
- Department of Molecular and Cell Biology, University of California-Berkeley, CA 94720, USA
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30
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Makino R, Park SY, Obayashi E, Iizuka T, Hori H, Shiro Y. Oxygen binding and redox properties of the heme in soluble guanylate cyclase: implications for the mechanism of ligand discrimination. J Biol Chem 2011; 286:15678-87. [PMID: 21385878 DOI: 10.1074/jbc.m110.177576] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Soluble guanylate cyclase is an NO-sensing hemoprotein that serves as a NO receptor in NO-mediated signaling pathways. It has been believed that this enzyme displays no measurable affinity for O(2), thereby enabling the selective NO sensing in aerobic environments. Despite the physiological significance, the reactivity of the enzyme-heme for O(2) has not been examined in detail. In this paper we demonstrated that the high spin heme of the ferrous enzyme converted to a low spin oxyheme (Fe(2+)-O(2)) when frozen at 77 K in the presence of O(2). The ligation of O(2) was confirmed by EPR analyses using cobalt-substituted enzyme. The oxy form was produced also under solution conditions at -7 °C, with the extremely low affinity for O(2). The low O(2) affinity was not caused by a distal steric protein effect and by rupture of the Fe(2+)-proximal His bond as revealed by extended x-ray absorption fine structure. The midpoint potential of the enzyme-heme was +187 mV, which is the most positive among high spin protoheme-hemoproteins. This observation implies that the electron density of the ferrous heme iron is relatively low by comparison to those of other hemoproteins, presumably due to the weak Fe(2+)-proximal His bond. Based on our results, we propose that the weak Fe(2+)-proximal His bond is a key determinant for the low O(2) affinity of the heme moiety of soluble guanylate cyclase.
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Affiliation(s)
- Ryu Makino
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan.
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31
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Abstract
YybT family proteins (COG3887) are functionally unknown proteins that are widely distributed among the firmicutes, including the human pathogens Staphylococcus aureus and Listeria monocytogenes. Recent studies suggested that YybT family proteins are crucial for the in vivo survival of bacterial pathogens during host infection. YybT family proteins contain an N-terminal domain that shares minimum sequence homology with Per-ARNT-Sim (PAS) domains. Despite the lack of an apparent residue for heme coordination, the putative PAS domains of BsYybT and GtYybT, two representative members of the YybT family proteins from Bacillus subtilis and Geobacillus thermodenitrificans, respectively, are found to bind b-type heme with 1:1 stoichiometry. Heme binding suppresses the catalytic activity of the DHH/DHHA1 phosphodiesterase domain and the degenerate GGDEF domain. Absorption spectroscopic studies indicate that YybT proteins do not form stable oxyferrous complexes due to the rapid oxidation of the ferrous iron upon O(2) binding. The ferrous heme, however, forms a hexacoordinated complex with carbon monoxide (CO) and a pentacoordinated complex with nitric oxide (NO). The coordination of NO, but not CO, to the heme stimulates the phosphodiesterase activity. These results suggest that YybT family proteins function as stress-signaling proteins for monitoring cellular heme or the NO level by using a heme-binding PAS domain that features an unconventional heme coordination environment.
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De La Cruz C, Sheppard N. A structure-based analysis of the vibrational spectra of nitrosyl ligands in transition-metal coordination complexes and clusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 78:7-28. [PMID: 21123107 DOI: 10.1016/j.saa.2010.08.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 07/17/2010] [Accepted: 08/02/2010] [Indexed: 05/30/2023]
Abstract
The vibrational spectra of nitrogen monoxide or nitric oxide (NO) bonded to one or to several transition-metal (M) atom(s) in coordination and cluster compounds are analyzed in relation to the various types of such structures identified by diffraction methods. These structures are classified in: (a) terminal (linear and bent) nitrosyls, [M(σ-NO)] or [M(NO)]; (b) twofold nitrosyl bridges, [M2(μ2-NO)]; (c) threefold nitrosyl bridges, [M3(μ3-NO)]; (d) σ/π-dihaptonitrosyls or "side-on" nitrosyls; and (e) isonitrosyls (oxygen-bonded nitrosyls). Typical ranges for the values of internuclear N-O and M-N bond-distances and M-N-O bond-angles for linear nitrosyls are: 1.14-1.20 Å/1.60-1.90 Å/180-160° and for bent nitrosyls are 1.16-1.22 Å/1.80-2.00 Å/140-110°. The [M2(μ2-NO)] bridges have been divided into those that contain one or several metal-metal bonds and those without a formal metal/metal bond (M⋯M). Typical ranges for the M-M, N-O, M-N bond distances and M-N-M bond angles for the normal twofold NO bridges are: 2.30-3.00 Å/1.18-1.22 Å/1.80-2.00 Å/90-70°, whereas for the analogous ranges of the long twofold NO bridges these are 3.10-3.40 Å/1.20-1.24 Å/1.90-2.10 Å/130-110°. In both situations the N-O vector is approximately at right angle to the M-M (or M⋯M) vector within the experimental error; i.e. the NO group is symmetrical bonded to the two metal atoms. In contrast the threefold NO bridges can be symmetrically or unsymmetrically bonded to an M3-plane of a cluster compound. Characteristic values for the N-O and M-N bond-distances of these NO bridges are: 1.24-1.28 Å/1.80-1.90 Å, respectively. As few dihaptonitrosyl and isonitrosyl complexes are known, the structural features of these are discussed on an individual basis. The very extensive vibrational spectroscopy literature considered gives emphasis to the data from linearly bonded NO ligands in stable closed-shell metal complexes; i.e. those which are consistent with the "effective atomic number (EAN)" or "18-electron" rule. In the paucity of enough vibrational spectroscopic data from complexes with only nitrosyl ligands, it turned out to be very advantageous to use wavenumbers from the spectra of uncharged and saturated nitrosyl/carbonyl metal complexes as references, because the presence of a carbonyl ligand was found to be neutral in its effect on the ν(NO)-values. The wide wavenumber range found for the ν(NO) values of linear MNO complexes are then presented in terms of the estimated effects of net ionic charges, or of electron-withdrawing or electron-donating ligands bonded to the same metal atom. Using this approach we have found that: (a) the effect for a unit positive charge is [plus 100 cm(-1)] whereas for a unit negative charge it is [minus 145 cm(-1)]. (b) For electron-withdrawing co-ligands the estimated effects are: terminal CN [plus 50 cm(-1)]; terminal halogens [plus 30 cm(-1)]; bridging or quasi-bridging halogens [plus 15 cm(-1)]. (c) For electro donating co-ligands they are: PF3 [plus 10 cm(-1)]; P(OPh)3 [-30 cm(-1)]; P(OR)3 (R=alkyl group) [-40 cm(-1)]; PPh3 [-55 cm(-1)]; PR3 (R=alkyl group) [-70 cm(-1)]; and η5-C5H5 [-60 cm(-1)]; η5-C5H4Me [-70 cm(-1)]; η5-C5Me5 [-80 cm(-1)]. These values were mostly derived from the spectra of nitrosyl complexes that have been corrected for the presence of only a single electronically-active co-ligand. After making allowance for ionic charges or strongly-perturbing ligands on the same metal atom, the adjusted 'neutral-co-ligand' ν(NO)*-values (in cm(-1)) are for linear nitrosyl complexes with transition metals of Period 4 of the Periodic Table, i.e. those with atomic orbitals (…4s3d4p): [ca. 1750, Cr(NO)]; [1775,Mn(NO)]; [1796,Fe(NO)]; [1817,Co(NO)]; [ca. 1840, Ni(NO)]. Period 5 (…5s4d5p): [1730 Mo(NO)]; [-, Tc(NO)]; [1745,Ru(NO)]; [1790,Rh(NO)]; [ca. 1845, Pd(NO)]. Period 6 (…6s4f5d6p), [1720,W(NO)]; [1730,Re(NO)]; [1738,Os(NO)]; [1760,Ir(NO)]; [-, Pt] respectively. Environmental differences to these values, e.g. data taken in polar solutions or in the crystalline state, can cause ν(NO)* variations (mostly reductions) of up to ca. 30 cm(-1). Three spectroscopic criteria are used to distinguish between linear and bent NO groups. These are: (i) the values of ν(14NO) themselves, and (ii) the isotopic band shift--(IBS)--parameter which is defined as [ν(14NO)-ν(15NO)], and, (iii) the isotopic band ratio--(IBR)--given by [ν(15NO/ν14NO)]. The former is illustrated with the ν(14NO)-data from trigonal bipyramidal (TBP) and tetragonal pyramidal (TP) structures of [M(NO(L)4] complexes (where M=Fe, Co, Ru, Rh, Os, Ir and L=ligand). These values indicate that linear (180-170°) and strongly bent (130-120°) NO groups in these compounds absorb over the 1862-1690 cm(-1) and 1720-1525 cm(-1)-regions, respectively. As was explicitly demonstrated for the linear nitrosyls, these extensive regions reflect the presence in different complexes of a very wide range of co-ligands or ionic charges associated with the metal atom of the nitrosyl group. A plot of the IBS parameter against M-N-O bond-angle for compounds with general formulae [M(NO)(L)y] (y=4, 5, 6) reveals that the IBS-values are clustered between 45 and 30 cm(-1) or between 37 and 25 cm(-1) for linear or bent NO groups, respectively. A plot of IBR shows a less well defined pattern. Overall it is suggested that bent nitrosyls absorb ca. 60-100 cm(-1) below, and have smaller co-ligand band-shifts, than their linear counterparts. Spectroscopic ν(NO) data of the bridging or other types of NO ligands are comparatively few and therefore it has not been possible to give other than general ranges for 'neutral co-ligand' values. Moreover the bridging species data often depend on corrections for the effects of electronically-active co-ligands such as cyclopentadienyl-like groups. The derived neutral co-ligand estimates, ν(NO)*, are: (a) twofold bridged nitrosyls with a metal-metal bond order of one, or greater than one, absorb at ca. 1610-1490 cm(-1); (b) twofold bridged nitrosyl ligands with a longer non-bonding M⋯M distance, ca. 1520-1490 cm(-1); (c) threefold bridged nitrosyls, ca. 1470-1410 cm(-1); (d) σ/π dihaptonitrosyl, [M(η2-NO)], where M=Cr, Mn and Ni; ca. 1490-1440 cm(-1). Isonitrosyls, from few examples, appear to absorb below ca. 1100 cm(-1). To be published DFT calculations of the infrared and Raman spectra of complexes with formulae [M(NO)4-n(CO)n] (M=Cr, Mn, Fe, Co, Ni, and n=0, 1, 2, 3, 4, respectively) are used as models for the assignments of the ν(MN) and δ(MNO) bands from more complex metal nitrosyls.
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Affiliation(s)
- Carlos De La Cruz
- Laboratorio de Espectroscopía Molecular y Atómica, Departamento de Química, Facultad Experimental de Ciencias, La Universidad del Zulia, Maracaibo, Estado Zulia, República Bolivariana de Venezuela
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Lukat-Rodgers GS, Correia C, Botuyan MV, Mer G, Rodgers KR. Heme-based sensing by the mammalian circadian protein CLOCK. Inorg Chem 2010; 49:6349-65. [PMID: 20666392 DOI: 10.1021/ic902388q] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Heme is emerging as a key player in the synchrony of circadian-coupled transcriptional regulation. Current evidence suggests that levels of circadian-linked transcription are regulated in response to both the availability of intracellular heme and heme-based sensing of carbon monoxide (CO) and possibly nitric oxide (NO). The protein CLOCK is central to the regulation and maintenance of circadian rhythms in mammals. CLOCK comprises two PAS domains, each with a heme binding site. Our studies focus on the functionality of the murine CLOCK PAS-A domain (residues 103-265). We show that CLOCK PAS-A binds iron(III) protoporhyrin IX to form a complex with 1:1 stoichiometry. Optical absorbance and resonance Raman studies reveal that the heme of ferric CLOCK PAS-A is a six-coordinate, low-spin complex whose resonance Raman signature is insensitive to pH over the range of protein stability. Ferrous CLOCK PAS-A is a mixture of five-coordinate, high-spin and six-coordinate, low-spin complexes. Ferrous CLOCK PAS-A forms complexes with CO and NO. Ferric CLOCK PAS-A undergoes reductive nitrosylation in the presence of NO to generate a CLOCK PAS-A-NO, which is a five-coordinate {FeNO}(7) complex. Formation of the highly stable {FeNO}(7) heme complex from either ferrous or ferric heme makes possible the binding of NO at very low concentration, a characteristic of NO sensors. Comparison of the spectroscopic properties and CO-binding kinetics of CLOCK PAS-A with other CO sensor proteins reveals that CLOCK PAS-A exhibits chemical properties consistent with a heme-based gas sensor protein.
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Affiliation(s)
- Gudrun S Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
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34
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Ibrahim M, Derbyshire ER, Soldatova AV, Marletta MA, Spiro TG. Soluble guanylate cyclase is activated differently by excess NO and by YC-1: resonance Raman spectroscopic evidence. Biochemistry 2010; 49:4864-71. [PMID: 20459051 DOI: 10.1021/bi100506j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Modulation of soluble guanylate cyclase (sGC) activity by nitric oxide (NO) involves two distinct steps. Low-level activation of sGC is achieved by the stoichiometric binding of NO (1-NO) to the heme cofactor, while much higher activation is achieved by the binding of additional NO (xsNO) at a non-heme site. Addition of the allosteric activator YC-1 to the 1-NO form leads to activity comparable to that of the xsNO state. In this study, the mechanisms of sGC activation were investigated using electronic absorption and resonance Raman (RR) spectroscopic methods. RR spectroscopy confirmed that the 1-NO form contains five-coordinate NO-heme and showed that the addition of NO to the 1-NO form has no significant effect on the spectrum. In contrast, addition of YC-1 to either the 1-NO or xsNO forms alters the RR spectrum significantly, indicating a protein-induced change in the heme geometry. This change in the heme geometry was also observed when BAY 41-2272 was added to the xsNO form. Bands assigned to bending and stretching motions of the vinyl and propionate substituents undergo changes in intensity in a pattern suggesting altered tilting of the pyrrole rings to which they are attached. In addition, the N-O stretching frequency increases, with no change in the Fe-NO stretching frequency, an effect modeled via DFT calculations as resulting from a small opening of the Fe-N-O angle. These spectral differences demonstrate different mechanisms of activation by synthetic activators, such as YC-1 and BAY 41-2272, and excess NO.
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Affiliation(s)
- Mohammed Ibrahim
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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35
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Scheidt WR, Barabanschikov A, Pavlik JW, Silvernail NJ, Sage JT. Electronic structure and dynamics of nitrosyl porphyrins. Inorg Chem 2010; 49:6240-52. [PMID: 20666384 PMCID: PMC2919577 DOI: 10.1021/ic100261b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) is a signaling molecule employed to regulate essential physiological processes. Thus, there is great interest in understanding the interaction of NO with heme, which is found at the active site of many proteins that recognize NO, as well as those involved in its creation and elimination. We summarize what we have learned from investigations of the structure, vibrational properties, and conformational dynamics of NO complexes with ferrous porphyrins, as well as computational investigations in support of these experimental studies. Multitemperature crystallographic data reveal variations in the orientational disorder of the nitrosyl ligand. In some cases, equilibria among NO orientations can be analyzed using the van't Hoff relationship and the free energy and enthalpy of the solid-state transitions evaluated experimentally. Density functional theory (DFT) calculations predict that intrinsic barriers to torsional rotation are smaller than thermal energies at physiological temperatures, and the coincidence of observed NO orientations with minima in molecular mechanics potentials indicates that nonbonded interactions with other chemical groups control the conformational freedom of the bound NO. In favorable cases, reduced disorder at low temperatures exposes subtle structural features including off-axis tilting of the Fe-NO bond and anisotropy of the equatorial Fe-N bonds. We also present the results of nuclear resonance vibrational spectroscopy measurements on oriented single crystals of [Fe(TPP)(NO)] and [Fe(TPP)(1-MeIm)(NO)]. These describe the anisotropic vibrational motion of iron in five- and six-coordinate heme-NO complexes and reveal vibrations of all Fe-ligand bonds as well as low-frequency molecular distortions associated with the doming of the heme upon ligand binding. A quantitative comparison with predicted frequencies, amplitudes, and directions facilitates identification of the vibrational modes but also suggests that commonly used DFT functionals are not fully successful at capturing the trans interaction between the axial NO and imidazole ligands. This supports previous conclusions that heme-NO complexes exhibit an unusual degree of variability with respect to the computational method, and we speculate that this variability hints at a genuine electronic instability that a protein can exploit to tune its reactivity. We anticipate that ongoing characterization of heme-NO complexes will deepen our understanding of their structure, dynamics, and reactivity.
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Affiliation(s)
- W. Robert Scheidt
- To whom correspondence should be addressed: WRS: , Fax (574) 631-6652; JTS , FAX (617)-373-2943
| | | | | | | | - J. Timothy Sage
- To whom correspondence should be addressed: WRS: , Fax (574) 631-6652; JTS , FAX (617)-373-2943
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36
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H-NOX domains display different tunnel systems for ligand migration. J Mol Graph Model 2010; 28:814-9. [DOI: 10.1016/j.jmgm.2010.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2009] [Revised: 02/25/2010] [Accepted: 02/25/2010] [Indexed: 11/18/2022]
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37
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Ibrahim M, Derbyshire ER, Marletta MA, Spiro TG. Probing soluble guanylate cyclase activation by CO and YC-1 using resonance Raman spectroscopy. Biochemistry 2010; 49:3815-23. [PMID: 20353168 DOI: 10.1021/bi902214j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Soluble guanylate cyclase (sGC) is weakly activated by carbon monoxide (CO) but is significantly activated by the binding of YC-1 to the sGC-CO complex. In this report, resonance Raman (RR) spectroscopy was used to study selected sGC variants. Addition of YC-1 to the sGC-CO complex alters the intensity pattern of RR bands assigned to the vinyl and propionate heme substituents, suggesting changes in the tilting of the pyrrole rings to which they are attached. YC-1 also shifts the RR intensity of the nu(FeC) and nu(CO) bands from 473 and 1985 cm(-1) to 487 and 1969 cm(-1), respectively, and induces an additional nu(FeC) band, at 521 cm(-1), assigned to five-coordinate heme-CO. Site-directed variants in the proximal heme pocket (P118A) or in the distal heme pocket (V5Y and I149Y) reduce the extent of YC-1 activation, along with the 473 cm(-1) band intensity. These lower-activity sGC variants display another nu(FeC) band at 493 cm(-1) which is insensitive to YC-1 addition and is attributed to protein that cannot be activated by the allosteric activator. The results are consistent with a model in which YC-1 binding to the sGC-CO complex results in a conformational change that activates the protein. Specifically, YC-1 binding alters the heme geometry via peripheral nonbonded contacts and also relieves an intrinsic electronic effect that weakens FeCO backbonding in the native, YC-1 responsive protein. This electronic effect might involve neutralization of the heme propionates via H-bond contacts or negative polarization by a distal cysteine residue. YC-1 binding also strains the Fe-histidine bond, leading to a population of the five-coordinate sGC-CO complex in addition to a conformationally distinct population of the six-coordinate sGC-CO complex. The loss of YC-1 activation in the sGC variants might involve a weakening of the heme-protein contacts that are thought to be critical to a YC-1-induced conformational change.
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Affiliation(s)
- Mohammed Ibrahim
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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38
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Derbyshire ER, Deng S, Marletta MA. Incorporation of tyrosine and glutamine residues into the soluble guanylate cyclase heme distal pocket alters NO and O2 binding. J Biol Chem 2010; 285:17471-8. [PMID: 20231286 DOI: 10.1074/jbc.m109.098269] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nitric oxide (NO) is the physiologically relevant activator of the mammalian hemoprotein soluble guanylate cyclase (sGC). The heme cofactor of alpha1beta1 sGC has a high affinity for NO but has never been observed to form a complex with oxygen. Introduction of a key tyrosine residue in the sGC heme binding domain beta1(1-385) is sufficient to produce an oxygen-binding protein, but this mutation in the full-length enzyme did not alter oxygen affinity. To evaluate ligand binding specificity in full-length sGC we mutated several conserved distal heme pocket residues (beta1 Val-5, Phe-74, Ile-145, and Ile-149) to introduce a hydrogen bond donor in proximity to the heme ligand. We found that the NO coordination state, NO dissociation, and enzyme activation were significantly affected by the presence of a tyrosine in the distal heme pocket; however, the stability of the reduced porphyrin and the proteins affinity for oxygen were unaltered. Recently, an atypical sGC from Drosophila, Gyc-88E, was shown to form a stable complex with oxygen. Sequence analysis of this protein identified two residues in the predicted heme pocket (tyrosine and glutamine) that may function to stabilize oxygen binding in the atypical cyclase. The introduction of these residues into the rat beta1 distal heme pocket (Ile-145 --> Tyr and Ile-149 --> Gln) resulted in an sGC construct that oxidized via an intermediate with an absorbance maximum at 417 nm. This absorbance maximum is consistent with globin Fe(II)-O(2) complexes and is likely the first observation of a Fe(II)-O(2) complex in the full-length alpha1beta1 protein. Additionally, these data suggest that atypical sGCs stabilize O(2) binding by a hydrogen bonding network involving tyrosine and glutamine.
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Affiliation(s)
- Emily R Derbyshire
- Department of Molecular and Cell Biology, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA
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39
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Shaban SY, van Eldik R. Mechanistic Information on the Reversible Binding of NO to Mono‐ and Dinuclear Fe
II
Complexes of a Biomimetic S
4
N Ligand. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.200900807] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shaban Y. Shaban
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen‐Nürnberg, Egerlandstr. 1, 91058 Erlangen, Germany
- Chemistry Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Rudi van Eldik
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen‐Nürnberg, Egerlandstr. 1, 91058 Erlangen, Germany
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40
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Efficient expression of human soluble guanylate cyclase in Escherichia coli and its signaling-related interaction with nitric oxide. Amino Acids 2010; 39:399-408. [DOI: 10.1007/s00726-009-0453-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2009] [Accepted: 12/17/2009] [Indexed: 01/02/2023]
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41
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Salazar-Salinas K, Jauregui LA, Kubli-Garfias C, Seminario JM. Molecular biosensor based on a coordinated iron complex. J Chem Phys 2009; 130:105101. [DOI: 10.1063/1.3070235] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Abstract
Nitric oxide (NO) functions in biology as both a critical cytotoxic agent and an essential signaling molecule. The toxicity of the diatomic gas has long been accepted; however, it was not known to be a signaling molecule until it was identified as the endothelium-derived relaxing factor (EDRF). Since this discovery, the physiological signaling pathways that are regulated by NO have been the focus of numerous studies. Many of the cellular responses that NO modulates are mediated by the heme protein soluble guanylate cyclase (sGC). NO binds to sGC at a diffusion controlled rate, and leads to a several 100-fold increase in the synthesis of the second messenger cGMP from GTP. Other diatomic gases either do not bind (dioxygen), or do not significantly activate (carbon monoxide) sGC. This provides selectivity and efficiency for NO even in an aerobic environment, which is critical due to the high reactivity of NO. Several biochemical studies have focused on elucidating the mechanism of NO activation and O(2) discrimination. Significant advances in our understanding of these topics have occurred with the identification and characterization of the sGC-like homologues termed Heme-Nitric oxide and OXygen binding (H-NOX) proteins.
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43
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Abstract
Cyclic GMP, guanosine 3',5'-cyclic monophosphate, is a critical and multifunctional second-messenger molecule that mediates diverse physiological and pathophysiological functions in cardiac and vascular tissues. Synthesized through nitric oxide, carbon monoxide, and/or natriuretic peptide-mediated guanylate cyclase stimulation and guanosine triphosphate dephosphorylation, cyclic GMP is capable of stimulating a cascade of serine/threonine kinase events, including signaling through cyclic GMP- and/or cyclic AMP-dependent protein kinases, eliciting protein kinase-independent actions such as modulation of ion channels or transporters, or undergoing hydrolytic degradation through actions of cyclic GMP-regulated phosphodiesterases. Substrates, enzymes, cofactors, and associated variables in this multifaceted system have historically been targets of vital pharmacotherapies with perhaps most common the use of vascular smooth muscle-targeting organonitrates in cardiac patients and phosphodiesterase inhibitors in individuals with erectile dysfunction. Accumulating basic science and clinical evidence, however, suggests that cyclic GMP signaling is compromised under conditions of disease or elevated physiological stresses. Moreover, nitric oxide can stimulate an array of cytotoxic effects and nitric oxide-based therapies can be limited by diminished bioactivity and the development of tachyphylaxis or tolerance after prolonged use. Consequently, an emerging area for clinical drug development and therapeutic drug evaluation for conditions of cardiovascular adversity has focused on identification of cyclic GMP signaling pathways that act under oxidized or nitric oxide-unresponsive conditions and/or that operate irrespective of nitric oxide-induced complications. The aim of this therapeutic review is to describe novel, nitric oxide-alternate avenues for cyclic GMP signaling in vascular smooth muscle growth with particular emphasis on pharmacotherapeutics of recently characterized cyclic GMP-specific approaches.
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44
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Volti GL, Vanella L, Gazzolo D, Galvano F. Carbon monoxide: vasoconstrictor or vasodilator? That's the question. Am J Physiol Renal Physiol 2008; 295:F901-3. [PMID: 18684884 DOI: 10.1152/ajprenal.90441.2008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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45
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Abstract
The occurrence, role and consequences of CO and NO in biological systems are reviewed. This includes their syntheses by heme oxygenases and NO synthases, their biological targets and the physiological effects of their signals. The use of CO and NO gases in medicine are discussed and methods of delivery are illustrated with particular emphasis on the therapeutic properties of compounds that generate controlled amounts of NO and CO in vivo.
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Affiliation(s)
- Brian E Mann
- Department of Chemistry, University of Sheffield, Sheffield, UK.
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46
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Derbyshire ER, Gunn A, Ibrahim M, Spiro TG, Britt RD, Marletta MA. Characterization of two different five-coordinate soluble guanylate cyclase ferrous-nitrosyl complexes. Biochemistry 2008; 47:3892-9. [PMID: 18302323 DOI: 10.1021/bi7022943] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Soluble guanylate cyclase (sGC), a hemoprotein, is the primary nitric oxide (NO) receptor in higher eukaryotes. The binding of NO to sGC leads to the formation of a five-coordinate ferrous-nitrosyl complex and a several hundred-fold increase in cGMP synthesis. NO activation of sGC is influenced by GTP and the allosteric activators YC-1 and BAY 41-2272. Electron paramagnetic resonance (EPR) spectroscopy shows that the spectrum of the sGC ferrous-nitrosyl complex shifts in the presence of YC-1, BAY 41-2272, or GTP in the presence of excess NO relative to the heme. These molecules shift the EPR signal from one characterized by g 1 = 2.083, g 2 = 2.036, and g 3 = 2.012 to a signal characterized by g 1 = 2.106, g 2 = 2.029, and g 3 = 2.010. The truncated heme domain constructs beta1(1-194) and beta2(1-217) were compared to the full-length enzyme. The EPR spectrum of the beta2(1-217)-NO complex is characterized by g 1 = 2.106, g 2 = 2.025, and g 3 = 2.010, indicating the protein is a good model for the sGC-NO complex in the presence of the activators, while the spectrum of the beta1(1-194)-NO complex resembles the EPR spectrum of sGC in the absence of the activators. Low-temperature resonance Raman spectra of the beta1(1-194)-NO and beta2(1-217)-NO complexes show that the Fe-NO stretching vibration of the beta2(1-217)-NO complex (535 cm (-1)) is significantly different from that of the beta1(1-194)-NO complex (527 cm (-1)). This shows that sGC can adopt different five-coordinate ferrous nitrosyl conformations and suggests that the Fe-NO conformation characterized by this unique EPR signal and Fe-NO stretching vibration represents a highly active sGC state.
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Affiliation(s)
- Emily R Derbyshire
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3320, USA
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47
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Xu C, Ibrahim M, Spiro TG. DFT analysis of axial and equatorial effects on heme-CO vibrational modes: applications to CooA and H-NOX heme sensor proteins. Biochemistry 2008; 47:2379-87. [PMID: 18217776 DOI: 10.1021/bi702254y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Determinants of the Fe-CO and C-O stretching frequencies in (imidazole)heme-CO adducts have been investigated via density functional theory (DFT) analysis, in connection with puzzling characteristics of the heme sensor protein CooA and of the H-NOX (Heme-Nitric Oxide and/or OXygen binding) family of proteins, including soluble guanylate cyclase (sGC). The computations show that two mechanisms of Fe-histidine bond weakening have opposite effects on the nuFeC/nuCO pattern. Mechanical tension is expected to raise nuFeC with little change in nuCO whereas the weakening of H-bond donation from the imidazole ligand has the opposite effect. Data on CooA indicate imidazole H-bond weakening associated with heme displacement, as part of the activation mechanism. The computations also reveal that protein-induced distortion of the porphyrin ring, a prominent structural feature of the H-NOX protein TtTar4H (Thermoanaerobacter tengcongensis Tar4 protein heme domain), has surprisingly little effect on nuFeC or nuCO. However, another structural feature, strong H-bonding to the propionates, is suggested to account for the weakened back bonding that is evident in sGC. TtTar4H-CO itself has an elevated nuFeC, which is successfully modeled as a compression effect, resulting from steric crowding in the distal pocket. nuFeC/nuCO data, in conjunction with modeling, can provide valuable insight into mechanisms for heme-protein modulation.
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Affiliation(s)
- Changliang Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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48
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Moënne-Loccoz P. Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins. Nat Prod Rep 2007; 24:610-20. [PMID: 17534533 PMCID: PMC3028592 DOI: 10.1039/b604194a] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitric oxide (NO) plays an important role in cell signalling and in the mammalian immune response to infection. On its own, NO is a relatively inert radical, and when it is used as a signalling molecule, its concentration remains within the picomolar range. However, at infection sites, the NO concentration can reach the micromolar range, and reactions with other radical species and transition metals lead to a broad toxicity. Under aerobic conditions, microorganisms cope with this nitrosative stress by oxidizing NO to nitrate (NO3−). Microbial hemoglobins play an essential role in this NO-detoxifying process. Under anaerobic conditions, detoxification occurs via a 2-electron reduction of two NO molecules to N2O. In many bacteria and archaea, this NO-reductase reaction is catalyzed by diiron proteins. Despite the importance of this reaction in providing microorganisms with a resistance to the mammalian immune response, its mechanism remains ill-defined. Because NO is an obligatory intermediate of the denitrification pathway, respiratory NO reductases also provide resistance to toxic concentrations of NO. This family of enzymes is the focus of this review. Respiratory NO reductases are integral membrane protein complexes that contain a norB subunit evolutionarily related to subunit I of cytochrome c oxidase (Cc O). NorB anchors one high-spin heme b3 and one non-heme iron known as FeB, i.e ., analogous to CuB in Cc O. A second group of diiron proteins with NO-reductase activity is comprised of the large family of soluble flavoprotein A found in strict and facultative anaerobic bacteria and archaea. These soluble detoxifying NO reductases contain a non-heme diiron cluster with a Fe–Fe distance of 3.4 Å and are only briefly mentioned here as a promising field of research. This article describes possible mechanisms of NO reduction to N2O in denitrifying NO-reductase (NOR) proteins and critically reviews recent experimental results. Relevant theoretical model calculations and spectroscopic studies of the NO-reductase reaction in heme/copper terminal oxidases are also overviewed.
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Affiliation(s)
- Pierre Moënne-Loccoz
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health and Science University, 20,000 NW Walker Road, Beaverton, Oregon 97006-8921, USA.
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49
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Monien BH, Drepper F, Sommerhalter M, Lubitz W, Haehnel W. Detection of heme oxygenase activity in a library of four-helix bundle proteins: towards the de novo synthesis of functional heme proteins. J Mol Biol 2007; 371:739-53. [PMID: 17585935 DOI: 10.1016/j.jmb.2007.05.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 05/16/2007] [Accepted: 05/18/2007] [Indexed: 11/23/2022]
Abstract
Design and chemical synthesis of de novo heme proteins with enzymatic activity on cellulose membranes is described. 352 antiparallel four-helix bundle proteins with a single histidine for heme ligation were assembled from three different sets of short amphipathic helices on membrane-bound peptide templates. The templates were coupled by linkers to cellulose membranes of microplate format, which could be cleaved for control of intermediate and final products. The incorporation of heme and the heme oxygenase activity of the 352 proteins were monitored by measuring UV-visible spectra directly on the cellulose. The kinetics of the heme oxygenase reaction was studied by monitoring the decrease of the Soret band and the transient absorbance of verdoheme being an intermediate product in the formation of biliverdin. Four of the proteins covering a broad range of the enzymatic rate constants were selected and synthesized in solution for further characterization. Detailed studies by redox potentiometry, analytical ultracentrifugation, and electron paramagnetic resonance spectroscopy yielded information about the aggregation state of the proteins, the spin state and the putative coordination environment of the iron. The amount of five-coordinated high-spin iron and a positive reduction potential were found to promote the oxygenase activity of the proteins.
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Affiliation(s)
- Bernhard H Monien
- Institute of Biology II / Biochemistry, Albert-Ludwigs-Universität Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany.
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50
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Ioanoviciu A, Yukl ET, Moënne-Loccoz P, Ortiz de Montellano PR. DevS, a heme-containing two-component oxygen sensor of Mycobacterium tuberculosis. Biochemistry 2007; 46:4250-60. [PMID: 17371046 PMCID: PMC2518089 DOI: 10.1021/bi602422p] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis can exist in the actively growing state of the overt disease or in a latent quiescent state that can be induced, among other things, by anaerobiosis. Eradication of the latent state is particularly difficult with the available drugs and requires prolonged treatment. DevS is a member of the DevS-DevR two-component regulatory system that is thought to mediate the cellular response to anaerobiosis. Here we report the cloning, expression, and initial characterization of a truncated version of DevS (DevS642) containing only the N-terminal GAF sensor domain (GAF-A) and of the full-length protein DevS. The DevS truncated construct quantitatively binds heme in a 1:1 stoichiometry, and the complex of the protein with ferrous heme reversibly binds O2, NO, and CO. UV-vis and resonance Raman spectroscopy of the wild-type protein and the H149A mutant confirm that His149 is the proximal ligand to the heme iron atom. While the heme-CO complex is present as two conformers in the GAF-A domain, a single set of [Fe-C-O] vibrations is observed with the full-length protein, suggesting that interactions between domains within DevS influence the distal pocket environment of the heme in the GAF-A domain.
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Affiliation(s)
- Alexandra Ioanoviciu
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94158-2517
| | - Erik T. Yukl
- Department of Environmental & Biomolecular Systems, 20,000 NW Walker Road, OGI School of Science and Engineering, Oregon Health & Sciences University, Beaverton, Oregon 97006-8921
| | - Pierre Moënne-Loccoz
- Department of Environmental & Biomolecular Systems, 20,000 NW Walker Road, OGI School of Science and Engineering, Oregon Health & Sciences University, Beaverton, Oregon 97006-8921
| | - Paul R. Ortiz de Montellano
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94158-2517
- To whom editorial correspondence should be addressed: Dr. Paul Ortiz de Montellano, University of California, Genentech Hall GH-N572D, 600 16 Street, Box 2280, San Francisco, CA 94158-2517, TEL: (415) 476-2903, FAX: (415) 502-4728, e-mail:
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