1
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Cozzi M, Failla M, Gianquinto E, Kovachka S, Buoli Comani V, Compari C, De Bei O, Giaccari R, Marchesani F, Marchetti M, Ronda L, Rolando B, Baroni M, Cruciani G, Campanini B, Bettati S, Faggiano S, Lazzarato L, Spyrakis F. Identification of small molecules affecting the interaction between human hemoglobin and Staphylococcus aureus IsdB hemophore. Sci Rep 2024; 14:8272. [PMID: 38594253 PMCID: PMC11003968 DOI: 10.1038/s41598-024-55931-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/29/2024] [Indexed: 04/11/2024] Open
Abstract
Human hemoglobin (Hb) is the preferred iron source of Staphylococcus aureus. This pathogenic bacterium exploits a sophisticated protein machinery called Iron-regulated surface determinant (Isd) system to bind Hb, extract and internalize heme, and finally degrade it to complete iron acquisition. IsdB, the surface exposed Hb receptor, is a proven virulence factor of S. aureus and the inhibition of its interaction with Hb can be pursued as a strategy to develop new classes of antimicrobials. To identify small molecules able to disrupt IsdB:Hb protein-protein interactions (PPIs), we carried out a structure-based virtual screening campaign and developed an ad hoc immunoassay to screen the retrieved set of commercially available compounds. Saturation-transfer difference (STD) NMR was applied to verify specific interactions of a sub-set of molecules, chosen based on their efficacy in reducing the amount of Hb bound to IsdB. Among molecules for which direct binding was verified, the best hit was submitted to ITC analysis to measure the binding affinity to Hb, which was found to be in the low micromolar range. The results demonstrate the viability of the proposed in silico/in vitro experimental pipeline to discover and test IsdB:Hb PPI inhibitors. The identified lead compound will be the starting point for future SAR and molecule optimization campaigns.
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Affiliation(s)
- Monica Cozzi
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Sandra Kovachka
- Department of Drug Science and Technology, University of Turin, Turin, Italy
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | | | - Omar De Bei
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Institute of Biophysics, National Research Council, Pisa, Italy
| | - Barbara Rolando
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Massimo Baroni
- Molecular Discovery Ltd, Kisnetic Business Centre, Elstree, Borehamwood, Hertfordshire, UK
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | | | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Institute of Biophysics, National Research Council, Pisa, Italy
| | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy.
- Institute of Biophysics, National Research Council, Pisa, Italy.
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, Italy.
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2
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Suzuki Y, Arakida Y, Sakai H, Enoki Y, Matsumoto K, Taguchi K. Elucidating the binding properties of methemoglobin in red blood cell to cyanide, hydrosulfide, and azide ions using artificial red blood cell. Toxicol Appl Pharmacol 2023; 481:116752. [PMID: 37956930 DOI: 10.1016/j.taap.2023.116752] [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: 10/07/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Methemoglobin (metHb), the oxidized form of hemoglobin, lacks the ability of reversible oxygen binding; however, it has a high binding affinity to toxic substances such as cyanide, hydrosulfide, and azide. This innate property of metHb offers the clinical option to treat patients poisoned with these toxins, by oxidizing the endogenous hemoglobin in the red blood cells (RBCs). The binding properties of naked metHb (isolated from RBC) with these toxins has been studied; however, the binding behaviors of metHb under the intracellular conditions of RBC are unclear because of the difficulty in detecting metHb status changes in RBC. This study aimed to elucidate the binding properties of metHb in RBC under physiological and poisoned conditions using artificial RBC, which was hemoglobin encapsulated in a liposome. The mimic-circumstances of metHb in RBC (metHb-V) was prepared by oxidizing the hemoglobin in artificial RBC. Spectroscopic analysis indicated that the metHb in metHb-V exhibited a binding behavior different from that of naked metHb, depending on the toxic substance: When the pH decreased, (i) the cyanide binding affinity of metHb-V remained unchanged, but that of naked metHb decreased (ii) the hydrosulfide binding affinity was increased in metHb-V but was decreased in naked metHb. (iii) Azide binding was increased in metHb-V, which was similar to that in naked metHb, irrespective of the pH change. Thus, the binding behavior of intracellular metHb in the RBC with cyanide, hydrosulfide, and azide under physiological and pathological conditions were partly elucidated using the oxidized artificial RBC.
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Affiliation(s)
- Yuto Suzuki
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Yo Arakida
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Hiromi Sakai
- Department of Chemistry, Nara Medical University, Shijo-cho 840, Kashihara, Nara 634-8521, Japan
| | - Yuki Enoki
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Kazuaki Matsumoto
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Kazuaki Taguchi
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
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3
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Freindorf M, Antonio J, Kraka E. Hydrogen Sulfide Ligation in Hemoglobin I of Lucina pectinata─A QM/MM and Local Mode Study. J Phys Chem A 2023; 127:8316-8329. [PMID: 37774120 DOI: 10.1021/acs.jpca.3c04399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
In this study, we investigated the interaction between the H2S ligand and the heme pocket of hemoglobin I (HbI) of Lucina pectinata for the wild-type protein; three known mutations where distal glutamine is replaced by hydrophobic valine (Gln64Val) and hydrophilic histidine in both protonation forms (Gln64Hisϵ and Gln64Hisδ); five known mutations of the so-called phenyl cage, replacing the hydrophobic phenylalanines Phe29 and Phe43 with tyrosine (Tyr), valine (Val), or leucine (Leu); and two additional mutations, Phe68Tyr and Phe68Val, in order to complement previous studies with new insights about the binding mechanism at the molecular level. A particular focus was on the intrinsic strengths of the chemical bonds involved, utilizing local vibrational force constants based on combined quantum mechanical-molecular mechanical calculations. Wild-type protein and mutations clustered into two distinct groups: Group 1 protein systems with a proton acceptor in the distal protein pocket, close to one of the H2S bonds, and Group 2 protein systems without a hydrogen acceptor close by in the active site of the protein. According to our results, the interactions between H2S and HbI of Lucina pectinata involve two important elements, namely, binding of H2S to Fe of the heme group, followed by the proton transfer from the HS bond to the distal residue. The distal residue is additionally stabilized by a second proton transfer from the distal residue to COO- of the propionate group in heme. We could identify the FeS bond as a key player and discovered that the strength of this bond depends on two mutual factors, namely, the strength of the HS bond involved in the proton transfer and the electrostatic field of the protein pocket qualifying the FeS bond as a sensitive probe for monitoring changes in H2S ligation upon protein mutations. We hope our study will inspire and guide future experimental studies, targeting new promising mutations such as Phe68Tyr, Phe68Val, or Phe43Tyr/Phe68Val.
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Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Juliana Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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4
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Palermo JC, Carllinni Colombo M, Semelak JA, Scocozza MF, Boubeta FM, Murgida DH, Estrin DA, Bari SE. Autocatalytic Mechanism in the Anaerobic Reduction of Metmyoglobin by Sulfide Species. Inorg Chem 2023; 62:11304-11317. [PMID: 37439562 DOI: 10.1021/acs.inorgchem.3c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The mechanism of the metal centered reduction of metmyoglobin (MbFeIII) by sulfide species (H2S/HS-) under an argon atmosphere has been studied by a combination of spectroscopic, kinetic, and computational methods. Asymmetric S-shaped time-traces for the formation of MbFeII at varying ratios of excess sulfide were observed at pH 5.3 < pH < 8.0 and 25 °C, suggesting an autocatalytic reaction mechanism. An increased rate at more alkaline pHs points to HS- as relevant reactive species for the reduction. The formation of the sulfanyl radical (HS•) in the slow initial phase was assessed using the spin-trap phenyl N-tert-butyl nitrone. This radical initiates the formation of S-S reactive species as disulfanuidyl/ disulfanudi-idyl radical anions and disulfide (HSSH•-/HSS•2- and HSS-, respectively). The autocatalysis has been ascribed to HSS-, formed after HSSH•-/HSS•2- disproportionation, which behaves as a fast reductant toward the intermediate complex MbFeIII(HS-). We propose a reaction mechanism for the sulfide-mediated reduction of metmyoglobin where only ferric heme iron initiates the oxidation of sulfide species. Beside the chemical interest, this insight into the MbFeIII/sulfide reaction under an argon atmosphere is relevant for the interpretation of biochemical aspects of ectopic myoglobins found on hypoxic tissues toward reactive sulfur species.
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Affiliation(s)
- Juan Cruz Palermo
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Melisa Carllinni Colombo
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Jonathan A Semelak
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Magalí F Scocozza
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Fernando M Boubeta
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Daniel H Murgida
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Darío A Estrin
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Sara E Bari
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
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5
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Domán A, Dóka É, Garai D, Bogdándi V, Balla G, Balla J, Nagy P. Interactions of reactive sulfur species with metalloproteins. Redox Biol 2023; 60:102617. [PMID: 36738685 PMCID: PMC9926313 DOI: 10.1016/j.redox.2023.102617] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Reactive sulfur species (RSS) entail a diverse family of sulfur derivatives that have emerged as important effector molecules in H2S-mediated biological events. RSS (including H2S) can exert their biological roles via widespread interactions with metalloproteins. Metalloproteins are essential components along the metabolic route of oxygen in the body, from the transport and storage of O2, through cellular respiration, to the maintenance of redox homeostasis by elimination of reactive oxygen species (ROS). Moreover, heme peroxidases contribute to immune defense by killing pathogens using oxygen-derived H2O2 as a precursor for stronger oxidants. Coordination and redox reactions with metal centers are primary means of RSS to alter fundamental cellular functions. In addition to RSS-mediated metalloprotein functions, the reduction of high-valent metal centers by RSS results in radical formation and opens the way for subsequent per- and polysulfide formation, which may have implications in cellular protection against oxidative stress and in redox signaling. Furthermore, recent findings pointed out the potential role of RSS as substrates for mitochondrial energy production and their cytoprotective capacity, with the involvement of metalloproteins. The current review summarizes the interactions of RSS with protein metal centers and their biological implications with special emphasis on mechanistic aspects, sulfide-mediated signaling, and pathophysiological consequences. A deeper understanding of the biological actions of reactive sulfur species on a molecular level is primordial in H2S-related drug development and the advancement of redox medicine.
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Affiliation(s)
- Andrea Domán
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, 1122, Budapest, Hungary
| | - Éva Dóka
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, 1122, Budapest, Hungary
| | - Dorottya Garai
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, 1122, Budapest, Hungary,Kálmán Laki Doctoral School, University of Debrecen, 4012, Debrecen, Hungary
| | - Virág Bogdándi
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, 1122, Budapest, Hungary
| | - György Balla
- Kálmán Laki Doctoral School, University of Debrecen, 4012, Debrecen, Hungary,Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary,ELKH-UD Vascular Pathophysiology Research Group, 11003, University of Debrecen, 4012, Debrecen, Hungary
| | - József Balla
- Kálmán Laki Doctoral School, University of Debrecen, 4012, Debrecen, Hungary,ELKH-UD Vascular Pathophysiology Research Group, 11003, University of Debrecen, 4012, Debrecen, Hungary,Department of Nephrology, Institute of Internal Medicine, Faculty of Medicine, University of Debrecen, 4012, Debrecen, Hungary
| | - Péter Nagy
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, 1122, Budapest, Hungary; Department of Anatomy and Histology, ELKH Laboratory of Redox Biology, University of Veterinary Medicine, 1078, Budapest, Hungary; Chemistry Institute, University of Debrecen, 4012, Debrecen, Hungary.
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6
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Sevalkar RR, Glasgow JN, Pettinati M, Marti MA, Reddy VP, Basu S, Alipour E, Kim-Shapiro DB, Estrin DA, Lancaster JR, Steyn AJC. Mycobacterium tuberculosis DosS binds H 2S through its Fe 3+ heme iron to regulate the DosR dormancy regulon. Redox Biol 2022; 52:102316. [PMID: 35489241 PMCID: PMC9062744 DOI: 10.1016/j.redox.2022.102316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/16/2022] [Indexed: 01/14/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) senses and responds to host-derived gasotransmitters NO and CO via heme-containing sensor kinases DosS and DosT and the response regulator DosR. Hydrogen sulfide (H2S) is an important signaling molecule in mammals, but its role in Mtb physiology is unclear. We have previously shown that exogenous H2S can modulate expression of genes in the Dos dormancy regulon via an unknown mechanism(s). Here, we test the hypothesis that Mtb senses and responds to H2S via the DosS/T/R system. Using UV-Vis and EPR spectroscopy, we show that H2S binds directly to the ferric (Fe3+) heme of DosS (KDapp = 5.30 μM) but not the ferrous (Fe2+) form. No interaction with DosT(Fe2+-O2) was detected. We found that the binding of sulfide can slowly reduce the DosS heme iron to the ferrous form. Steered Molecular Dynamics simulations show that H2S, and not the charged HS- species, can enter the DosS heme pocket. We also show that H2S increases DosS autokinase activity and subsequent phosphorylation of DosR, and H2S-mediated increases in Dos regulon gene expression is lost in Mtb lacking DosS. Finally, we demonstrate that physiological levels of H2S in macrophages can induce DosR regulon genes via DosS. Overall, these data reveal a novel mechanism whereby Mtb senses and responds to a third host gasotransmitter, H2S, via DosS(Fe3+). These findings highlight the remarkable plasticity of DosS and establish a new paradigm for how bacteria can sense multiple gasotransmitters through a single heme sensor kinase.
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Affiliation(s)
- Ritesh R Sevalkar
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joel N Glasgow
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Martín Pettinati
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Marcelo A Marti
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica (IQUIBICEN), Buenos Aires, Argentina
| | - Vineel P Reddy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Swati Basu
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - Elmira Alipour
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | | | - Dario A Estrin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Jack R Lancaster
- Department of Pharmacology & Chemical Biology, Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Adrie J C Steyn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA; Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA; Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.
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7
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Mantle D, Yang G. Hydrogen sulfide and metal interaction: the pathophysiological implications. Mol Cell Biochem 2022; 477:2235-2248. [PMID: 35461429 DOI: 10.1007/s11010-022-04443-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/08/2022] [Indexed: 11/27/2022]
Abstract
Hydrogen sulfide (H2S), previously recognized as a toxic gas, has emerged as an important gaseous signaling molecule along with nitric oxide, carbon monoxide and also hydrogen. H2S can be endogenously produced in the mammalian body at a very low level for various pathophysiological processes. Notably, H2S can interact with several essential metals in the body such as iron, copper, nickel, and zinc to carry out specific functions. The interactions of H2S with metal-binding proteins have been shown to aid in its signal transduction and cellular metabolism. In addition, H2S is capable of providing a cytoprotective role against metal toxicity. As the research in the field of H2S signaling in biology and medicine increases, much progresses have been developed for detecting H2S via interaction with metals. In this review, the interaction of H2S with metals, specifically in regard to metal-driven metabolism of H2S, the protection against metal toxicity by H2S and the detection of H2S using metals will be discussed. Discovering the interactions of this gasotransmitter with metals is important for determining the mechanisms underlying the cellular functions of H2S as well as developing novel therapeutic avenues.
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Affiliation(s)
- Devin Mantle
- School of Natural Sciences, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
- Cardiovascular and Metabolic Research Unit, Laurentian University, Sudbury, Canada
| | - Guangdong Yang
- School of Natural Sciences, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada.
- Cardiovascular and Metabolic Research Unit, Laurentian University, Sudbury, Canada.
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8
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Rahman MA, Glasgow JN, Nadeem S, Reddy VP, Sevalkar RR, Lancaster JR, Steyn AJC. The Role of Host-Generated H 2S in Microbial Pathogenesis: New Perspectives on Tuberculosis. Front Cell Infect Microbiol 2020; 10:586923. [PMID: 33330130 PMCID: PMC7711268 DOI: 10.3389/fcimb.2020.586923] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/13/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, hydrogen sulfide (H2S) was considered primarily as a poisonous gas and environmental hazard. However, with the discovery of prokaryotic and eukaryotic enzymes for H2S production, breakdown, and utilization, H2S has emerged as an important signaling molecule in a wide range of physiological and pathological processes. Hence, H2S is considered a gasotransmitter along with nitric oxide (•NO) and carbon monoxide (CO). Surprisingly, despite having overlapping functions with •NO and CO, the role of host H2S in microbial pathogenesis is understudied and represents a gap in our knowledge. Given the numerous reports that followed the discovery of •NO and CO and their respective roles in microbial pathogenesis, we anticipate a rapid increase in studies that further define the importance of H2S in microbial pathogenesis, which may lead to new virulence paradigms. Therefore, this review provides an overview of sulfide chemistry, enzymatic production of H2S, and the importance of H2S in metabolism and immunity in response to microbial pathogens. We then describe our current understanding of the role of host-derived H2S in tuberculosis (TB) disease, including its influences on host immunity and bioenergetics, and on Mycobacterium tuberculosis (Mtb) growth and survival. Finally, this review discusses the utility of H2S-donor compounds, inhibitors of H2S-producing enzymes, and their potential clinical significance.
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Affiliation(s)
| | - Joel N Glasgow
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sajid Nadeem
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Vineel P Reddy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ritesh R Sevalkar
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jack R Lancaster
- Department of Pharmacology and Chemical Biology, Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Adrie J C Steyn
- Africa Health Research Institute, Durban, South Africa.,Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States.,Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, United States
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9
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Foglia NO, Bari SE, Estrin DA. In Silico Insight into the Reductive Nitrosylation of Ferric Hemeproteins. Inorg Chem 2020; 59:3631-3641. [DOI: 10.1021/acs.inorgchem.9b03198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nicolás O. Foglia
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Quı́mica de los Materiales, Medio Ambiente y Energı́a, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica, Buenos Aires, Argentina
| | - Sara E. Bari
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Quı́mica de los Materiales, Medio Ambiente y Energı́a, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
| | - Darío A. Estrin
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Quı́mica de los Materiales, Medio Ambiente y Energı́a, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica, Buenos Aires, Argentina
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10
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Foglia NO, González Lebrero MC, Biekofsky RR, Estrin DA. Reaction Path Analysis from Potential Energy Contributions Using Forces: An Accessible Estimator of Reaction Coordinate Adequacy. J Chem Theory Comput 2020; 16:1618-1629. [PMID: 31999449 DOI: 10.1021/acs.jctc.9b01081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The calculation of potential energy and free-energy profiles along complex chemical reactions or rare event processes is of great interest because of their importance for many areas in chemistry, molecular biology, and material science. One typical way to generate these profiles is to add a bias potential to modify the energy surface, which can act on a selected degree of freedom in the system. However, in these cases, the quality of the result is strongly dependent on the selection of the degree of freedom over which this bias potential acts. The present work introduces a simple method for the analysis of the degree of freedom selected to describe a chemical process. The proposed methodology is based on the decomposition of contributions to the potential energy profiles by the integration of forces along a reaction path, which allows evaluating the different contributions to the energy change. This could be useful for discriminating the contributions to the energy arising from different regions of the system, which is particularly useful in systems with complex environments that must be represented using hybrid quantum mechanics/molecular mechanics schemes. Furthermore, this methodology allows in generating a quick and simple analysis of the degree of freedom which is used to describe the potential energy profile associated with the reactive process. This is computationally more accessible than the corresponding free-energy profile and can therefore be used as a simple estimator of reaction coordinate adequacy.
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Affiliation(s)
- Nicolás O Foglia
- Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Mariano C González Lebrero
- Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Rodolfo R Biekofsky
- Moebius Research Ltd., Systems Biomedicine, 24 Chedworth House, West Green Rd, N15 5EH London, U.K
| | - Darío A Estrin
- Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
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11
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Boubeta FM, Bieza SA, Bringas M, Palermo JC, Boechi L, Estrin DA, Bari SE. Hemeproteins as Targets for Sulfide Species. Antioxid Redox Signal 2020; 32:247-257. [PMID: 31530164 DOI: 10.1089/ars.2019.7878] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Significance: Sulfides are endogenous and ubiquitous signaling species that share the hemeproteins as biochemical targets with O2, nitric oxide, and carbon monoxide. The description of the binding mechanisms is mandatory to anticipate the biochemical relevance of the interaction. Recent Advances: The binding of sulfide to ferric hemeproteins has been described in more than 40 systems, including native proteins, mutants, and model systems. Mechanisms of sulfide binding to ferric hemeproteins have been examined by a combination of kinetic and computational experiments. The distal control of the association process, dissected into the migration of the ligand to the active site and the binding event, reveals that neutral hydrogen sulfide (H2S) reaches the active site and is the predominant binding ligand, while the HS- is excluded by the protein matrix. Experiments with model compounds, devoid of a protein scaffold, reveal that both H2S and HS- can bind the ferric heme if accessing the site. A critical role of the proximal ligand in the prevention of the metal-centered reduction has been experimentally assessed. For metmyoglobin and methemoglobin, the coordination of sulfide leads to noncanonical functions: sulfide storage and its oxidative detoxification have been evidenced under physiological and excess sulfide concentrations, respectively. Critical Issues: The bound species is suggested to predominate in the monoprotonated form, although spectroscopic evidence is pending. Future Directions: A description of the role of hemeproteins as biochemical targets for inorganic sulfide requires understanding the reactivity of bound sulfide, for example: the metal-centered reduction, the reaction with excess sulfide, oxidants, or other gasotransmitters, among other biomolecules.
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Affiliation(s)
- Fernando Martín Boubeta
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía. (INQUIMAE) CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Silvina Andrea Bieza
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía. (INQUIMAE) CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauro Bringas
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía. (INQUIMAE) CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan Cruz Palermo
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía. (INQUIMAE) CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leonardo Boechi
- Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Darío Ariel Estrin
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía. (INQUIMAE) CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sara Elizabeth Bari
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía. (INQUIMAE) CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
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12
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Jensen B, Fago A. A Novel Possible Role for Met Hemoglobin as Carrier of Hydrogen Sulfide in the Blood. Antioxid Redox Signal 2020; 32:258-265. [PMID: 31530173 DOI: 10.1089/ars.2019.7877] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Significance: Along with other gasotransmitters nitric oxide (NO) and carbon monoxide, hydrogen sulfide (H2S) has recently emerged as an important signaling molecule with a particularly complex metabolism. Endogenous H2S reacts with multiple cellular targets, including protein ferric heme groups, to elicit physiological responses, such as regulation of local blood flow. Recent Advances: Recent in vitro evidence suggests that H2S at low physiological concentrations is carried in the blood as bound to the small fraction of oxidized ferric hemoglobin (metHb). A relatively stable metHb-sulfide complex forms when H2S and purified metHb react in vitro, with an affinity within the in vivo physiological range of sulfide in the blood. Formation and subsequent redox metabolism of metHb-sulfide complex have also been confirmed in isolated intact red blood cells (RBCs) containing enhanced metHb levels. Thus, H2S may function as an endocrine signaling molecule and elicit responses at sites away from the site of production. In addition, metHb, considered as an inert or pathological hemoglobin derivative, may have a novel potential physiological role in the transport of H2S in the blood. Critical Issues: The transport of H2S in the blood mediated by metHb would represent an O2-independent pH-dependent mechanism for the blood-mediated control of blood flow and as such it is critical to understand the in vivo significance of this transport. Future Directions: Major challenges must be resolved to understand how metHb may carry H2S in the RBCs, in particular determination of metHb-sulfide levels in the blood and identification of targets in the vasculature.
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Affiliation(s)
- Birgitte Jensen
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Angela Fago
- Department of Bioscience, Aarhus University, Aarhus, Denmark
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13
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Mot AC, Puscas C, Dorneanu SA, Silaghi-Dumitrescu R. EPR detection of sulfanyl radical during sulfhemoglobin formation - Influence of catalase. Free Radic Biol Med 2019; 137:110-115. [PMID: 31035002 DOI: 10.1016/j.freeradbiomed.2019.04.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/18/2022]
Abstract
Hemoglobin in its ferryl form oxidizes hydrogen sulfide and is transformed to sulfhemoglobin, where the sulfur is inserted covalently at the heme edge. Shown here is evidence that-as previously proposed by others-this process involves oxidation of hydrogen sulfide to a sulfanyl radical detectable by spin-trapping in electron paramagnetic resonance (EPR) spectroscopy. The yields and rates of formation of sulfhemoglobin as well as of the sulfanyl radical are affected by the same factors that affect the reactivity of hemoglobin ferryl, in bovine hemoglobin and in phytoglobins as well. A freely-diffusing sulfanyl radical is thus proposed to be involved in sulfhemoglobin formation. Catalase is shown to accelerate this process due to a previously described hydrogen sulfide oxidase activity, within which EPR evidence for sulfanyl generation is shown here for the first time. The reaction of preformed ferryl with hydrogen sulfide-in absence of hydrogen peroxide-is studied by stopped-flow at several pH values and explained in light of reactivity and redox potential control.
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Affiliation(s)
- Augustin C Mot
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania.
| | - Cristina Puscas
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Sorin Aurel Dorneanu
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Radu Silaghi-Dumitrescu
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania.
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14
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Boubeta FM, Contestín García RM, Lorenzo EN, Boechi L, Estrin D, Sued M, Arrar M. Lessons learned about steered molecular dynamics simulations and free energy calculations. Chem Biol Drug Des 2019; 93:1129-1138. [PMID: 30793836 DOI: 10.1111/cbdd.13485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/18/2018] [Accepted: 12/22/2018] [Indexed: 01/30/2023]
Abstract
The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM-MM tools, ligand migration, and conformational rearrangements that can be modeled using classical potentials. The use of steered molecular dynamics (sMD) together with the Jarzynski equality is a popular approach in calculating free energy profiles. Here, we first briefly review the application of the Jarzynski equality to sMD simulations, then revisit the so-called stiff-spring approximation and the consequent expectation of Gaussian work distributions and, finally, reiterate the practical utility of the second-order cumulant expansion, as it coincides with the parametric maximum-likelihood estimator in this scenario. We illustrate this procedure using simulations of CO, both in aqueous solution and in a carbon nanotube as a model system for biologically relevant nanoheterogeneous environments. We conclude the use of the second-order cumulant expansion permits the use of faster pulling velocities in sMD simulations, without introducing bias due to large dispersion in the non-equilibrium work distribution.
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Affiliation(s)
- Fernando Martín Boubeta
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rocío María Contestín García
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ezequiel Norberto Lorenzo
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leonardo Boechi
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario Estrin
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariela Sued
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mehrnoosh Arrar
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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15
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Arrar M, Boubeta FM, Szretter ME, Sued M, Boechi L, Rodriguez D. On the accurate estimation of free energies using the jarzynski equality. J Comput Chem 2018; 40:688-696. [DOI: 10.1002/jcc.25754] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/18/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Mehrnoosh Arrar
- Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
| | - Fernando Martín Boubeta
- Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
| | - Maria Eugenia Szretter
- Departamento de Matemática, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina, Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
| | - Mariela Sued
- Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
| | - Leonardo Boechi
- Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
| | - Daniela Rodriguez
- Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
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16
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Characterization of Recombinant His-Tag Protein Immobilized onto Functionalized Gold Nanoparticles. SENSORS 2018; 18:s18124262. [PMID: 30518079 PMCID: PMC6308469 DOI: 10.3390/s18124262] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/19/2018] [Accepted: 11/30/2018] [Indexed: 12/18/2022]
Abstract
The recombinant polyhistidine-tagged hemoglobin I ((His)₆-rHbI) from the bivalve Lucina pectinata is an ideal biocomponent for a hydrogen sulfide (H₂S) biosensor due to its high affinity for H₂S. In this work, we immobilized (His)₆-rHbI over a surface modified with gold nanoparticles functionalized with 3-mercaptopropionic acid complexed with nickel ion. The attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) analysis of the modified-gold electrode displays amide I and amide II bands characteristic of a primarily α-helix structure verifying the presence of (His)₆-rHbI on the electrode surface. Also, X-ray photoelectron spectroscopy (XPS) results show a new peak after protein interaction corresponding to nitrogen and a calculated overlayer thickness of 5.3 nm. The functionality of the immobilized hemoprotein was established by direct current potential amperometry, using H₂S as the analyte, validating its activity after immobilization. The current response to H₂S concentrations was monitored over time giving a linear relationship from 30 to 700 nM with a corresponding sensitivity of 3.22 × 10-3 nA/nM. These results confirm that the analyzed gold nanostructured platform provides an efficient and strong link for polyhistidine-tag protein immobilization over gold and glassy carbon surfaces for a future biosensors development.
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17
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Dulac M, Melet A, Galardon E. Reversible Detection and Quantification of Hydrogen Sulfide by Fluorescence Using the Hemoglobin I from Lucina pectinata. ACS Sens 2018; 3:2138-2144. [PMID: 30204417 DOI: 10.1021/acssensors.8b00701] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new detection system for the endogenous gaseous transmitter and environmental pollutant hydrogen sulfide is presented. It is based on the modulation of the fluorescence spectrum of a coumarin dye by the absorption spectrum of the recombinant hemoglobin I from clam Lucina pectinata upon coordination of the analyte. While we establish that the reported affinity of rHbI for H2S has been overestimated, the association of the protein with an appropriate fluorophore allows fast, easy, and reversible detection and quantification of hydrogen sulfide in buffer as well as biological fluids such as human plasma, with a quantification limit around 200 nM at pH 7.4.
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Affiliation(s)
- Martin Dulac
- UMR 8601, LCBPT, CNRS-Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Sts Pères, 75006 Paris, France
| | - Armelle Melet
- UMR 8601, LCBPT, CNRS-Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Sts Pères, 75006 Paris, France
| | - Erwan Galardon
- UMR 8601, LCBPT, CNRS-Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Sts Pères, 75006 Paris, France
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18
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Boubeta FM, Boechi L, Estrin D, Patrizi B, Di Donato M, Iagatti A, Giordano D, Verde C, Bruno S, Abbruzzetti S, Viappiani C. Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125. J Phys Chem B 2018; 122:11649-11661. [PMID: 30230844 DOI: 10.1021/acs.jpcb.8b07682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologues, resulting in enhanced reaction rates at low temperatures. In this context, protein-bound water molecules were suggested to play a major role, and their weaker interactions at protein active sites have been associated with cold adaptation. In this work, we tested this hypothesis on truncated hemoglobins (a family of microbial heme-proteins of yet-unclear function) applying molecular dynamics simulations and ligand-rebinding kinetics on a protein from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in comparison with its thermophilic Thermobifida fusca homologue. The CO rebinding kinetics of the former highlight several geminate phases, with an unusually long-lived geminate intermediate. An articulated tunnel with at least two distinct docking sites was identified by analysis of molecular dynamics simulations and was suggested to be at the origin of the unusual geminate rebinding phase. Water molecules are present in the distal pocket, but their stabilization by TrpG8, TyrB10, and HisCD1 is much weaker than in thermophilic Thermobifida fusca truncated hemoglobin, resulting in a faster geminate rebinding. Our results support the hypothesis that weaker water-molecule interactions at the reaction site are associated with cold adaptation.
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Affiliation(s)
- Fernando M Boubeta
- Instituto de Quimica Fisica de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET, and Universidad de Buenos Aires , C1428EHA Buenos Aires , Argentina
| | - Leonardo Boechi
- Instituto de Calculo, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , C1428EGA Buenos Aires , Argentina
| | - Dario Estrin
- Instituto de Quimica Fisica de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET, and Universidad de Buenos Aires , C1428EHA Buenos Aires , Argentina
| | - Barbara Patrizi
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy.,INO-CNR, Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche , Largo Fermi 6 , 50125 Florence , Italy
| | - Mariangela Di Donato
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy.,INO-CNR, Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche , Largo Fermi 6 , 50125 Florence , Italy
| | - Alessandro Iagatti
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR , Via Pietro Castellino 111 , I-80131 Naples , Italy.,Stazione Zoologica Anton Dohrn , Villa Comunale , 80121 Naples , Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR , Via Pietro Castellino 111 , I-80131 Naples , Italy.,Stazione Zoologica Anton Dohrn , Villa Comunale , 80121 Naples , Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , Parco Area delle Scienze 23A , 43124 , Parma , Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche , Università di Parma , Parco Area delle Scienze 7A , 43124 , Parma , Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche , Università di Parma , Parco Area delle Scienze 7A , 43124 , Parma , Italy
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19
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Ostojić B, Schwerdtfeger P, Đorđević D. Modeling the hydrogen sulfide binding to heme. J Inorg Biochem 2018; 184:108-114. [DOI: 10.1016/j.jinorgbio.2018.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 10/17/2022]
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20
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Boubeta FM, Bieza SA, Bringas M, Estrin DA, Boechi L, Bari SE. Mechanism of Sulfide Binding by Ferric Hemeproteins. Inorg Chem 2018; 57:7591-7600. [DOI: 10.1021/acs.inorgchem.8b00478] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fernando M. Boubeta
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | - Silvina A. Bieza
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | - Mauro Bringas
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | - Darío A. Estrin
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | | | - Sara E. Bari
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
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21
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Reactions of ferric hemoglobin and myoglobin with hydrogen sulfide under physiological conditions. J Inorg Biochem 2018; 182:133-140. [DOI: 10.1016/j.jinorgbio.2018.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/18/2018] [Accepted: 02/07/2018] [Indexed: 12/15/2022]
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22
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Feis A, Howes BD, Milazzo L, Coppola D, Smulevich G. Structural determinants of ligand binding in truncated hemoglobins: Resonance Raman spectroscopy of the native states and their carbon monoxide and hydroxide complexes. Biopolymers 2018; 109:e23114. [DOI: 10.1002/bip.23114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Alessandro Feis
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| | - Barry D. Howes
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| | - Lisa Milazzo
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| | - Daniela Coppola
- Dipartimento di Scienze bio-agroalimentari del CNR (DiSBA-CNR), CNR, Via Pietro Castellino 111; Naples I-80131 Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
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23
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Coexistence of multiple globin genes conferring protection against nitrosative stress to the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Nitric Oxide 2018; 73:39-51. [DOI: 10.1016/j.niox.2017.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 12/07/2017] [Accepted: 12/18/2017] [Indexed: 11/20/2022]
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24
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Mot AC, Bischin C, Damian G, Attia AAA, Gal E, Dina N, Leopold N, Silaghi-Dumitrescu R. Fe(III) - Sulfide interaction in globins: Characterization and quest for a putative Fe(IV)-sulfide species. J Inorg Biochem 2017; 179:32-39. [PMID: 29156293 DOI: 10.1016/j.jinorgbio.2017.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 10/16/2017] [Accepted: 10/31/2017] [Indexed: 01/06/2023]
Abstract
The present study reports findings regarding the contrast between H2S interaction with bovine hemoglobin (Hb) and horse heart myoglobin (Mb), in terms of binding and dissociation kinetics, affinities, and mechanism. At pH9.5, oxidation of ferric-sulfide adducts in presence of no free sulfide, using hexachloroiridate as oxidant is examined using stopped-flow UV-vis, EPR, vibrational spectroscopy and mass spectrometry. Oxidation of the ferric-sulfide adduct in such conditions occurs with a putative unstable Fe(IV)-sulfide adduct as intermediate that finally leads to a paramagnetic ferric species with distinct EPR features. As detected by MS spectrometry, this final species appears to be a truncated form of globin at a distinct Tyr. In case of Hb, only β-chain is truncated at Tyr144.
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Affiliation(s)
- Augustin C Mot
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania.
| | - Cristina Bischin
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Grigore Damian
- Faculty of Physics, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Amr A A Attia
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Emese Gal
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Nicoleta Dina
- National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Nicolae Leopold
- Faculty of Physics, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Radu Silaghi-Dumitrescu
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania.
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