1
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Tronnet A, Salas-Ambrosio P, Roman R, Bravo-Anaya LM, Ayala M, Bonduelle C. Star-Like Polypeptides as Simplified Analogues of Horseradish Peroxidase (HRP) Metalloenzymes. Macromol Biosci 2024:e2400155. [PMID: 39122460 DOI: 10.1002/mabi.202400155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/19/2024] [Indexed: 08/12/2024]
Abstract
Peroxidases, like horseradish peroxidase (HRP), are heme metalloenzymes that are powerful biocatalysts for various oxidation reactions. By using simple grafting-from approach, ring-opening polymerization (ROP), and manganese porphyrins, star-shaped polypeptides analogues of HRP capable of catalyzing oxidation reactions with H2O2 is successfully prepared. Like their protein model, these simplified analogues show interesting Michaelis-Menten constant (KM) in the mM range for the oxidant. Interestingly, the polymer structures are more resistant to denaturation (heat, proteolysis and oxidant concentration) than HRP, opening up interesting prospects for their use in catalysis or in biosensing devices.
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Affiliation(s)
- Antoine Tronnet
- CNRS, LCPO (Laboratoire de Chimie des Polymères Organiques (UMR5629)), University of Bordeaux, Bordeaux INP, 16 avenue Pey Berland, Pessac, F-33600, France
- CNRS, LCC (Laboratoire de Chimie de Coordination (UPR8241)), University of Toulouse, 205 route de Narbonne, Toulouse, F-31077, France
| | - Pedro Salas-Ambrosio
- CNRS, LCPO (Laboratoire de Chimie des Polymères Organiques (UMR5629)), University of Bordeaux, Bordeaux INP, 16 avenue Pey Berland, Pessac, F-33600, France
| | - Rosa Roman
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología UNAM. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos
| | | | - Marcela Ayala
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología UNAM. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos
| | - Colin Bonduelle
- CNRS, LCPO (Laboratoire de Chimie des Polymères Organiques (UMR5629)), University of Bordeaux, Bordeaux INP, 16 avenue Pey Berland, Pessac, F-33600, France
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2
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Okawa Y, Endo K, Hakamata Y, Watanabe S, Yokoyama A, Sugimori T, Takagi HD, Inamo M. Thermal and photoinduced electron transfer reactions of phthalocyanine complexes of Zn(II) and Cu(II) in acetonitrile. Dalton Trans 2022; 51:15393-15402. [PMID: 36155701 DOI: 10.1039/d2dt02498e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phthalocyanine that has four peripheral 2-methoxyphenyl substituents at the α-position and its Zn(II) and Cu(II) complexes were synthesized. Chemical oxidation by the Cu(II) ion and electrochemical oxidation of these metal complexes were investigated spectrophotometrically in acetonitrile. The UV-visible absorption spectra of these metal complexes and their one-electron oxidized π-cation radicals showed no concentration dependence, indicating that these species exist as monomers in solution. Kinetics of the thermal electron transfer reaction from each phthalocyanine complex to Cu2+ and the photoinduced electron transfer reaction of the Zn(II) phthalocyanine complex with V(V) and V(IV) Schiff base complexes were studied using conventional spectrophotometric and transient absorption techniques, and the electron transfer rate constants were analysed using the Marcus cross relationship. The obtained rate constants of the electron self-exchange reaction between the parent phthalocyanine complexes and their π-cation radicals were in the order of 109 to 1011 M-1 s-1 at T = 298.2 K. These large electron self-exchange rate constants are consistent with the phthalocyanine-centred redox reactions where small reorganization energies are required with little structural change during the electron transfer process.
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Affiliation(s)
- Yui Okawa
- Department of Chemistry, Aichi University of Education, Kariya 448-8542, Japan.
| | - Kousuke Endo
- Department of Chemistry, Aichi University of Education, Kariya 448-8542, Japan.
| | - Yukihiko Hakamata
- Department of Chemistry, Aichi University of Education, Kariya 448-8542, Japan.
| | - Shingo Watanabe
- Department of Chemistry, Aichi University of Education, Kariya 448-8542, Japan.
| | - Aika Yokoyama
- Department of Chemistry, Aichi University of Education, Kariya 448-8542, Japan.
| | - Tamotsu Sugimori
- Institute of Liberal Arts and Sciences, University of Toyama, Toyama 930-8555, Japan
| | - Hideo D Takagi
- Research Centre for Materials Science, Nagoya University, Nagoya 464-8602, Japan
| | - Masahiko Inamo
- Department of Chemistry, Aichi University of Education, Kariya 448-8542, Japan.
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3
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Kondo HX, Fujii M, Tanioka T, Kanematsu Y, Yoshida T, Takano Y. Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket. J Chem Inf Model 2022; 62:775-784. [PMID: 35157473 DOI: 10.1021/acs.jcim.1c01315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme proteins play diverse and important biological roles, from electron transfer and chemical catalysis to oxygen transport and/or storage. Although the distortion of heme porphyrin correlates with the physical properties of heme, such as the redox potential and oxygen affinity, the relationship between heme distortion and the heme protein environment is unclear. Here, we tested the hypothesis that the protein environment of the heme-binding pocket determines heme distortion (conformation). We analyzed the correlations between the amino acid composition of the heme-binding pocket and the magnitude of heme distortion along 12 vibrational modes using machine learning. A correlation was detected in the three lowest vibrational modes. Analysis of heme distortions in nearly the same environments of the heme-binding pocket supported this notion. Our analyses indicate that the heme-binding pocket environment is a major factor impacting the distortion of heme porphyrin along the three lowest vibrational modes. In addition, statistical analysis of the distortion of heme porphyrin revealed that the peaks of distributions of the ruffling and breathing distortions are shifted from 0 (the equilibrium structure). Both the ruffling and breathing distortions are correlated with the redox potential of heme, so that heme molecules with these distortions have a lower redox potential than planar molecules. These findings explain the structure-function relationship of heme.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan.,Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Masanori Fujii
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Takuma Tanioka
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yusuke Kanematsu
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Takashi Yoshida
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
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4
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Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin. Life (Basel) 2022; 12:life12020210. [PMID: 35207496 PMCID: PMC8880375 DOI: 10.3390/life12020210] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
Heme is located in the active site of proteins and has diverse and important biological functions, such as electron transfer and oxygen transport and/or storage. The distortion of heme porphyrin is considered an important factor for the diverse functions of heme because it correlates with the physical properties of heme, such as oxygen affinity and redox potential. Therefore, clarification of the relationship between heme distortion and the protein environment is crucial in protein science. Here, we analyzed the fluctuation in heme distortion in the protein environment for hemoglobin and myoglobin using molecular dynamics (MD) simulations and quantum mechanical (QM) calculations as well as statistical analysis of the protein structures of hemoglobin and myoglobin stored in Protein Data Bank. Our computation and statistical analysis showed that the protein environment for hemoglobin and myoglobin prominently affects the doming distortion of heme porphyrin, which correlates with its oxygen affinity, and that the magnitude of distortion is different between hemoglobin and myoglobin. These results suggest that heme distortion is affected by its protein environment and fluctuates around its fitted conformation, leading to physical properties that are appropriate for protein functions.
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5
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Krüger A, Keppel M, Sharma V, Frunzke J. The diversity of heme sensor systems - heme-responsive transcriptional regulation mediated by transient heme protein interactions. FEMS Microbiol Rev 2022; 46:6506450. [PMID: 35026033 DOI: 10.1093/femsre/fuac002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/21/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Heme is a versatile molecule that is vital for nearly all cellular life by serving as prosthetic group for various enzymes or as nutritional iron source for diverse microbial species. However, elevated levels of heme molecule are toxic to cells. The complexity of this stimulus has shaped the evolution of diverse heme sensor systems, which are involved in heme-dependent transcriptional regulation in eukaryotes and prokaryotes. The functions of these systems are manifold - ranging from the specific control of heme detoxification or uptake systems to the global integration of heme and iron homeostasis. This review focuses on heme sensor systems, regulating heme homeostasis by transient heme protein interaction. We provide an overview of known heme-binding motifs in prokaryotic and eukaryotic transcription factors. Besides the central ligands, the surrounding amino acid environment was shown to play a pivotal role in heme binding. The diversity of heme-regulatory systems therefore illustrates that prediction based on pure sequence information is hardly possible and requires careful experimental validation. Comprehensive understanding of heme-regulated processes is not only important for our understanding of cellular physiology, but also provides a basis for the development of novel antibacterial drugs and metabolic engineering strategies.
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Affiliation(s)
- Aileen Krüger
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Marc Keppel
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Vikas Sharma
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Julia Frunzke
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
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6
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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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7
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Koebke KJ, Kühl T, Lojou E, Demeler B, Schoepp-Cothenet B, Iranzo O, Pecoraro VL, Ivancich A. The pH-Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α-Helical Metalloprotein. Angew Chem Int Ed Engl 2020; 60:3974-3978. [PMID: 33215801 DOI: 10.1002/anie.202012673] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/19/2020] [Indexed: 11/09/2022]
Abstract
De Novo metalloprotein design assesses the relationship between metal active site architecture and catalytic reactivity. Herein, we use an α-helical scaffold to control the iron coordination geometry when a heme cofactor is allowed to bind to either histidine or cysteine ligands, within a single artificial protein. Consequently, we uncovered a reversible pH-induced switch of the heme axial ligation within this simplified scaffold. Characterization of the specific heme coordination modes was done by using UV/Vis and Electron Paramagnetic Resonance spectroscopies. The penta- or hexa-coordinate thiolate heme (9≤pH≤11) and the penta-coordinate imidazole heme (6≤pH≤8.5) reproduces well the heme ligation in chloroperoxidases or cyt P450 monooxygenases and peroxidases, respectively. The stability of heme coordination upon ferric/ferrous redox cycling is a crucial property of the construct. At basic pHs, the thiolate mini-heme protein can catalyze O2 reduction when adsorbed onto a pyrolytic graphite electrode.
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Affiliation(s)
- Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Toni Kühl
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Barbara Schoepp-Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Olga Iranzo
- Institut des Sciences Moléculaires de Marseille (iSm2), Centrale Marseille, Aix-Marseille Univ., CNRS, Marseille, France
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anabella Ivancich
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
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8
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Koebke KJ, Kühl T, Lojou E, Demeler B, Schoepp‐Cothenet B, Iranzo O, Pecoraro VL, Ivancich A. The pH‐Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α‐Helical Metalloprotein. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Toni Kühl
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Borries Demeler
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge AB T1K 3M4 Canada
| | - Barbara Schoepp‐Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Olga Iranzo
- Institut des Sciences Moléculaires de Marseille (iSm2) Centrale Marseille Aix-Marseille Univ. CNRS Marseille France
| | | | - Anabella Ivancich
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
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9
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Kondo HX, Kanematsu Y, Masumoto G, Takano Y. PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins. Database (Oxford) 2020; 2023:baaa066. [PMID: 33002111 PMCID: PMC10755257 DOI: 10.1093/database/baaa066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/09/2020] [Accepted: 07/24/2020] [Indexed: 11/14/2022]
Abstract
Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation and so on. While the mechanism of each function has been investigated for many heme proteins, the origin of the diversity of the heme functions is still unclear and a crucial scientific issue. We have constructed a database of heme proteins, named Python-based database and analyzer for DIStortion of Heme porphyrin (PyDISH), which also contains some analysis tools. The aim of PyDISH is to integrate the information on the structures of hemes and heme proteins and the functions of heme proteins. This database will provide the structure-function relationships focusing on heme porphyrin distortion and lead to the elucidation of the origin of the functional diversity of heme proteins. In addition, the insights obtained from the database can be used for the design of protein function. PyDISH contains the structural data of more than 13 000 hemes extracted from the Protein Data Bank, including heme porphyrin distortion, axial ligands coordinating to the heme and the orientation of the propionate sidechains of heme. PyDISH also has information about the protein domains, including Uniprot ID, protein fold by CATH ID, organism, coordination distance and so on. The analytical tools implemented in PyDISH allow users to not only browse and download the data but also analyze the structures of heme porphyrin by using the analytical tools implemented in PyDISH. PyDISH users will be able to utilize the obtained results for the design of protein function. Database URL: http://pydish.bio.info.hiroshima-cu.ac.jp/.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita 565-0874, Japan and
| | - Yusuke Kanematsu
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
| | - Gen Masumoto
- Information Systems Division, RIKEN Head Office for Information Systems and Cybersecurity, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
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10
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Sitte E, Senge MO. The Red Color of Life Transformed - Synthetic Advances and Emerging Applications of Protoporphyrin IX in Chemical Biology. European J Org Chem 2020; 2020:3171-3191. [PMID: 32612451 PMCID: PMC7319466 DOI: 10.1002/ejoc.202000074] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 01/10/2023]
Abstract
Protoporphyrin IX (PPIX) is the porphyrin scaffold of heme b, a ubiquitous prosthetic group of proteins responsible for oxygen binding (hemoglobin, myoglobin), electron transfer (cytochrome c) and catalysis (cytochrome P450, catalases, peroxidases). PPIX and its metallated derivatives frequently find application as therapeutic agents, imaging tools, catalysts, sensors and in light harvesting. The vast toolkit of accessible porphyrin functionalization reactions enables easy synthetic modification of PPIX to meet the requirements for its multiple uses. In the past few years, particular interest has arisen in exploiting the interaction of PPIX and its synthetic derivatives with biomolecules such as DNA and heme-binding proteins to evolve molecular devices with new functions as well as to uncover potential therapeutic toeholds. This review strives to shine a light on the most recent developments in the synthetic chemistry of PPIX and its uses in selected fields of chemical biology.
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Affiliation(s)
- Elisabeth Sitte
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse Street2DublinIreland
| | - Mathias O. Senge
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse Street2DublinIreland
- Institute for Advanced Study (TUM‐IAS)Technische Universität MünchenLichtenberg‐Str. 2a85748GarchingGermany
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11
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Louropoulou E, Gledhill M, Achterberg EP, Browning TJ, Honey DJ, Schmitz RA, Tagliabue A. Heme b distributions through the Atlantic Ocean: evidence for "anemic" phytoplankton populations. Sci Rep 2020; 10:4551. [PMID: 32165723 PMCID: PMC7067765 DOI: 10.1038/s41598-020-61425-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 02/24/2020] [Indexed: 11/09/2022] Open
Abstract
Heme b is an iron-containing cofactor in hemoproteins that participates in the fundamental processes of photosynthesis and respiration in phytoplankton. Heme b concentrations typically decline in waters with low iron concentrations but due to lack of field data, the distribution of heme b in particulate material in the ocean is poorly constrained. Here we report particulate heme b distributions across the Atlantic Ocean (59.9°N to 34.6°S). Heme b concentrations in surface waters ranged from 0.10 to 33.7 pmol L-1 (median = 1.47 pmol L-1, n = 974) and were highest in regions with a high biomass. The ratio of heme b to particulate organic carbon (POC) exhibited a mean value of 0.44 μmol heme b mol-1 POC. We identified the ratio of 0.10 µmol heme b mol-1 POC as the cut-off between heme b replete and heme b deficient (anemic) phytoplankton. By this definition, we observed anemic phytoplankton populations in the Subtropical South Atlantic and Irminger Basin. Comparison of observed and modelled heme b suggested that heme b could account for between 0.17-9.1% of biogenic iron. Our large scale observations of heme b relative to organic matter provide further evidence of the impact of changes in iron supply on phytoplankton iron status across the Atlantic Ocean.
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Affiliation(s)
- Evangelia Louropoulou
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany. .,Institute for General Microbiology, Christian-Albrechts-Universität, Kiel, Germany.
| | - Martha Gledhill
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | | | - David J Honey
- School of Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität, Kiel, Germany
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12
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Huang J, Ferlez BH, Young EJ, Kerfeld CA, Kramer DM, Ducat DC. Functionalization of Bacterial Microcompartment Shell Proteins With Covalently Attached Heme. Front Bioeng Biotechnol 2020; 7:432. [PMID: 31993414 PMCID: PMC6962350 DOI: 10.3389/fbioe.2019.00432] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022] Open
Abstract
Heme is a versatile redox cofactor that has considerable potential for synthetic biology and bioelectronic applications. The capacity to functionalize non-heme-binding proteins with covalently bound heme moieties in vivo could expand the variety of bioelectronic materials, particularly if hemes could be attached at defined locations so as to facilitate position-sensitive processes like electron transfer. In this study, we utilized the cytochrome maturation system I to develop a simple approach that enables incorporation of hemes into the backbone of target proteins in vivo. We tested our methodology by targeting the self-assembling bacterial microcompartment shell proteins, and inserting functional hemes at multiple locations in the protein backbone. We found substitution of three amino acids on the target proteins promoted heme attachment with high occupancy. Spectroscopic measurements suggested these modified proteins covalently bind low-spin hemes, with relative low redox midpoint potentials (about -210 mV vs. SHE). Heme-modified shell proteins partially retained their self-assembly properties, including the capacity to hexamerize, and form inter-hexamer attachments. Heme-bound shell proteins demonstrated the capacity to integrate into higher-order shell assemblies, however, the structural features of these macromolecular complexes was sometimes altered. Altogether, we report a versatile strategy for generating electron-conductive cytochromes from structurally-defined proteins, and provide design considerations on how heme incorporation may interface with native assembly properties in engineered proteins.
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Affiliation(s)
- Jingcheng Huang
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Bryan H. Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Eric J. Young
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David M. Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
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13
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Louropoulou E, Gledhill M, Browning TJ, Desai DK, Barraqueta JLM, Tonnard M, Sarthou G, Planquette H, Bowie AR, Schmitz RA, LaRoche J, Achterberg EP. Regulation of the Phytoplankton Heme b Iron Pool During the North Atlantic Spring Bloom. Front Microbiol 2019; 10:1566. [PMID: 31354666 PMCID: PMC6637849 DOI: 10.3389/fmicb.2019.01566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Heme b is an iron-containing co-factor in hemoproteins. Heme b concentrations are low (<1 pmol L-1) in iron limited phytoplankton in cultures and in the field. Here, we determined heme b in marine particulate material (>0.7 μm) from the North Atlantic Ocean (GEOVIDE cruise - GEOTRACES section GA01), which spanned several biogeochemical regimes. We examined the relationship between heme b abundance and the microbial community composition, and its utility for mapping iron limited phytoplankton. Heme b concentrations ranged from 0.16 to 5.1 pmol L-1 (median = 2.0 pmol L-1, n = 62) in the surface mixed layer (SML) along the cruise track, driven mainly by variability in biomass. However, in the Irminger Basin, the lowest heme b levels (SML: median = 0.53 pmol L-1, n = 12) were observed, whilst the biomass was highest (particulate organic carbon, median = 14.2 μmol L-1, n = 25; chlorophyll a: median = 2.0 nmol L-1, n = 23) pointing to regulatory mechanisms of the heme b pool for growth conservation. Dissolved iron (DFe) was not depleted (SML: median = 0.38 nmol L-1, n = 11) in the Irminger Basin, but large diatoms (Rhizosolenia sp.) dominated. Hence, heme b depletion and regulation is likely to occur during bloom progression when phytoplankton class-dependent absolute iron requirements exceed the available ambient concentration of DFe. Furthermore, high heme b concentrations found in the Iceland Basin and Labrador Sea (median = 3.4 pmol L-1, n = 20), despite having similar DFe concentrations to the Irminger Basin, were attributed to an earlier growth phase of the extant phytoplankton populations. Thus, heme b provides a snapshot of the cellular activity in situ and could both be used as indicator of iron limitation and contribute to understanding phytoplankton adaptation mechanisms to changing iron supplies.
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Affiliation(s)
- Evangelia Louropoulou
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martha Gledhill
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Dhwani K Desai
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Jan-Lukas Menzel Barraqueta
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Department of Earth Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Manon Tonnard
- UMR 6539/LEMAR/IUEM, CNRS, UBO, IRD, Ifremer, Brest, France.,Antarctic Climate and Ecosystems Cooperative Research Centre, Hobart, TAS, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | | | - Andrew R Bowie
- Antarctic Climate and Ecosystems Cooperative Research Centre, Hobart, TAS, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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14
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Núñez G, Sakamoto K, Soares MP. Innate Nutritional Immunity. THE JOURNAL OF IMMUNOLOGY 2019; 201:11-18. [PMID: 29914937 DOI: 10.4049/jimmunol.1800325] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/06/2018] [Indexed: 12/12/2022]
Abstract
Iron (Fe) is an essential micronutrient for both microbes and their hosts. The biologic importance of Fe derives from its inherent ability to act as a universal redox catalyst, co-opted in a variety of biochemical processes critical to maintain life. Animals evolved several mechanisms to retain and limit Fe availability to pathogenic microbes, a resistance mechanism termed "nutritional immunity." Likewise, pathogenic microbes coevolved to deploy diverse and efficient mechanisms to acquire Fe from their hosts and in doing so overcome nutritional immunity. In this review, we discuss how the innate immune system regulates Fe metabolism to withhold Fe from pathogenic microbes and how strategies used by pathogens to acquire Fe circumvent these resistance mechanisms.
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Affiliation(s)
- Gabriel Núñez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109; .,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109; and
| | - Kei Sakamoto
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109.,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109; and
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15
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Yaseen M, Farooq Z, Mahmood MHR, Ahmad SA, Nazir S, Anjum KM, Naqvi SAR. Synthesis of Novel Symmetric Porphyrin Schiff Base Dimers by Solid–Liquid Reaction Methodology. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Muhammad Yaseen
- Department of ChemistryUniversity of Education (Lahore) Faisalabad Campus Faisalabad Pakistan
| | - Zahid Farooq
- Department of PhysicsUniversity of Education (Lahore) Faisalabad Campus Faisalabad Pakistan
| | - Mian H. R. Mahmood
- Department of ChemistryUniversity of Education (Lahore) Faisalabad Campus Faisalabad Pakistan
| | - Sheikh Asrar Ahmad
- Division of Science and Technology, Department of ChemistryUniversity of Education Lahore Pakistan
| | - Shahbaz Nazir
- Department of EducationGovernment of Punjab Pakistan
| | - Khalid Mahmood Anjum
- Department of Wildlife and EcologyUniversity of Veterinary and Animal Sciences Lahore Pakistan
| | - Syed Ali Raza Naqvi
- Department of ChemistryGovernment College University, Faisalabad 38000 Faisalabad Pakistan
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16
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Bilyk KT, Zhuang X, Murphy KR, Cheng CHC. A tale of two genes: divergent evolutionary fate of haptoglobin and hemopexin in hemoglobinless antarctic icefishes. J Exp Biol 2019; 222:jeb.188573. [DOI: 10.1242/jeb.188573] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 02/06/2019] [Indexed: 12/31/2022]
Abstract
Evolution of Antarctic notothenioid fishes in the isolated freezing Southern Ocean have led to remarkable trait gains and losses. One of the most extraordinary was the loss of the major oxygen carrier hemoglobin (Hb) in the icefishes (family Channichthyidae). While the mechanisms of this loss and the resulting compensatory changes have been well studied, the impact of Hb loss on the network of genes that once supported its recycling and disposal has remained unexplored. Here we report the functional fate and underlying molecular changes of two such key Hb-supporting proteins across the icefish family - haptoglobin (Hp) and hemopexin (Hx), crucial in removing cytotoxic free Hb and heme respectively. Hp plays a critical role in binding free Hb for intracellular recycling and absent its primary client, icefish Hp transcription is now vanishingly little and translation into a functional protein is nearly silenced. Hp genotype degeneration has manifested in separate lineages of the icefish phylogeny with three distinct nonsense mutations and a deletion-frameshift, as well as mutated polyadenylation signal sequences. Thus, Hb loss appears to have diminished selective constraint on Hp maintenance, resulting in its stochastic, co-evolutionary drift towards extinction. Hx binds free heme for iron recycling in hepatocytes. In contrast to Hp, Hx genotype integrity is preserved in the icefishes and transcription occurs at comparable levels to the red-blooded notothenioids. The persistence of Hx likely owes to continued selective pressure for its function from mitochondrial and non-Hb cellular hemoproteins.
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Affiliation(s)
- Kevin T. Bilyk
- Department of Biology, Western Kentucky University, USA
- Department of Animal Biology, University of Illinois, Urbana Champaign, USA
| | - Xuan Zhuang
- Department of Ecology & Evolution, University of Chicago, USA
| | - Katherine R. Murphy
- Department of Animal Biology, University of Illinois, Urbana Champaign, USA
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, USA
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17
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Mashima T, Oohora K, Hayashi T. Substitution of an amino acid residue axially coordinating to the heme molecule in hexameric tyrosine-coordinated hemoprotein to enhance peroxidase activity. J PORPHYR PHTHALOCYA 2018. [DOI: 10.1142/s1088424617500936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To convert an originally tyrosine-coordinated heme to histidine-coordinated heme in hexameric tyrosine-coordinated hemoprotein, HTHP, Tyr45, a residue coordinating to the heme cofactor, and Arg25 located in the distal site are replaced with Phe45 and His25, respectively in each of the subunits of the protein. The obtained HTHP mutant (HTHP[Formula: see text] was characterized by SDS-PAGE, ESI-TOF MS, dynamic light scattering measurements and size exclusion chromatography. These analyses indicate that HTHP[Formula: see text] maintains its stable hexameric structure with the altered ligation of each of the heme cofactors. Comparison of UV-vis absorption spectra of the ferric-, ferrous-, CO- and CN-forms of HTHP[Formula: see text] with those of several well-known His-ligated hemoproteins indicates that heme is coordinated by the His25 residue. The reaction of HTHP[Formula: see text] with cumene hydroperoxide produces both cumyl alcohol and acetophenone in a 2.3:1 ratio, indicating that heterolytic O–O bond cleavage dominantly occurs to form the two-electron oxidized species known as compound I. Peroxidase activity of HTHP[Formula: see text] is found to follow Michaelis–Menten kinetics. The [Formula: see text] values of HTHP[Formula: see text] for H[Formula: see text]O[Formula: see text]-dependent oxidation of ABTS and guaiacol are 10- and 100-fold higher, respectively, than those of wild type HTHP (HTHP[Formula: see text]. The [Formula: see text]/[Formula: see text] values of HTHP[Formula: see text] for both substrates are increased 30-fold relative to that of HTHP[Formula: see text]. Moreover, HTHP[Formula: see text] is capable of promoting catalytic sulfoxidation of thioanisole with H[Formula: see text]O[Formula: see text] with a turnover number ca. 2-fold higher than that of HTHP[Formula: see text]. The present findings demonstrate that proximal His ligation to the heme is significantly effective to increase the peroxidase activity in the HTHP matrix.
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Affiliation(s)
- Tsuyoshi Mashima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
- Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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18
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Bren KL. Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome
c. Isr J Chem 2016. [DOI: 10.1002/ijch.201600021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kara L. Bren
- Department of Chemistry University of Rochester Rochester NY 14627-0216 USA
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19
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Senge MO, MacGowan SA, O'Brien JM. Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles. Chem Commun (Camb) 2016; 51:17031-63. [PMID: 26482230 DOI: 10.1039/c5cc06254c] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.
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Affiliation(s)
- Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland and Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
| | - Stuart A MacGowan
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Jessica M O'Brien
- Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
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20
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Utilization of heme as an iron source by marine Alphaproteobacteria in the Roseobacter clade. Appl Environ Microbiol 2013; 79:5753-62. [PMID: 23872569 DOI: 10.1128/aem.01562-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microorganisms have rarely been examined. This study used Ruegeria sp. strain TrichCH4B as a model organism to study heme acquisition by a member of the Roseobacter clade. Analogs of known heme transporter proteins were found within the Ruegeria sp. TrichCH4B genome. The identified heme uptake and utilization system appears to be functional, as the heme genes were upregulated under iron stress, the bacterium could grow on ferric-porphyrin complexes as the sole iron source, and internalization of (55) Fe from ferric protoporphyrin IX was observed. The potential ability to utilize heme in the Roseobacter clade appears to be common, as half of the isolates in the RoseoBase database were found to have a complete heme uptake system. A degenerate primer set was designed and successfully used to identify the putative heme oxygenase gene (hmus) in the roseobacter heme uptake system from diverse nonenriched marine environments. This study found that members of the Roseobacter clade are capable of utilizing heme as an iron source and that this capability may be present in all types of marine environments. The results of this study add a new perspective to the current picture of iron cycling in marine systems, whereby relatively refractory intracellular pools of heme-bound iron may be taken up quickly and directly reincorporated into living bacteria without previous degradation or the necessity of a siderophore intermediate.
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21
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Myradalyyev S, Limpanuparb T, Wang X, Hirao H. Comparative computational analysis of binding energies between several divalent first-row transition metals (Cr2+, Mn2+, Fe2+, Co2+, Ni2+, and Cu2+) and ligands (porphine, corrin, and TMC). Polyhedron 2013. [DOI: 10.1016/j.poly.2012.11.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Bose M, Saha R, Sen Santara S, Mukherjee S, Roy J, Adak S. Protection against peroxynitrite by pseudoperoxidase from Leishmania major. Free Radic Biol Med 2012; 53:1819-28. [PMID: 22985938 DOI: 10.1016/j.freeradbiomed.2012.08.583] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 08/23/2012] [Accepted: 08/23/2012] [Indexed: 11/22/2022]
Abstract
Heme proteins share the ability to detoxify reactive nitrogen intermediates (NO and peroxynitrite). But, to date, no heme-containing enzymatic defense against toxic reactive nitrogen intermediates has been discovered in Leishmania species. We have cloned, expressed, and characterized a pseudoperoxidase from Leishmania major (LmPP) that is capable of detoxifying peroxynitrite (ONOO(-)). Optical, EPR, and resonance Raman spectral studies demonstrate that ONOO(-) can rapidly convert the six-coordinate ferric low-spin to a ferric high-spin form at neutral pH. Western blotting and immunofluorescence studies with anti-LmPP antibody show that the mature enzyme is located at the plasma membrane of amastigotes and is expressed eightfold higher in amastigotes compared to promastigotes. Moreover, to further investigate its exact physiological role in Leishmania, we have created LmPP-knockout mutants by gene replacement in L. major strains. IC(50) values for exogenously added H(2)O(2) or 3-morpholinosydnonimine (SIN1) show that deletion of LmPP in L. major renders the cell more susceptible to SIN1. The null mutant cells exhibit a marked decrease in virulence on infection with activated macrophages as well as inoculation into BALB/c mice. Collectively, these data provide strong evidence that LmPP plays an important role in the enzymatic defense against ONOO(-) within macrophages.
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Affiliation(s)
- Moumita Bose
- Division of Structural Biology and Bio-informatics, Indian Institute of Chemical Biology, Kolkata, India
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23
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Jelić D, Tatić I, Trzun M, Hrvačić B, Brajša K, Verbanac D, Tomašković M, Čulić O, Antolović R, Glojnarić I, Weygand-Đurašević I, Vladimir-Knežević S, Mildner B. Porphyrins as new endogenous anti-inflammatory agents. Eur J Pharmacol 2012; 691:251-60. [PMID: 22687816 DOI: 10.1016/j.ejphar.2012.05.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/18/2012] [Accepted: 05/24/2012] [Indexed: 10/28/2022]
Abstract
A series of porphyrins, tetrapyrrole natural organic compounds, are evaluated here as endogenous anti-inflammatory agents. They directly inhibit the activity of Fyn, a non-receptor Src-family tyrosine kinase, triggering anti-inflammatory events associated with down-regulation of T-cell receptor signal transduction, leading to inhibition of tumor necrosis factor alpha (TNF-α) production. This is one of the major pro-inflammatory cytokines, associated with diseases such as diabetes, tumorigenesis, rheumatoid arthritis, and inflammatory bowel disease. Porphyrins, as a chemical class, inhibited Fyn kinase activity in a non-competitive, linear-mixed fashion. In cell-based in vitro experiments on polymorphonuclear cells, porphyrins inhibited TNF-α cytokine production, T-cell proliferation, and the generation of free radicals in the oxidative burst, in a concentration-related manner. In vivo, lipopolysaccharide-induced TNF-α production in mice was inhibited by several of the porphyrins. These findings may be very important for the overall understanding of the role(s) of porphyrins in inflammation and their possible application as new anti-inflammatory agents.
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Affiliation(s)
- Dubravko Jelić
- GlaxoSmithKline Research Centre Zagreb, Prilaz baruna Filipovića 29, HR-10000 Zagreb, Croatia.
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24
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Affiliation(s)
- Tatyana E. Shubina
- a Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander Universität Erlangen-Nürnberg , Nägelsbachstraße 25, 91052 Erlangen, Germany
| | - Timothy Clark
- a Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander Universität Erlangen-Nürnberg , Nägelsbachstraße 25, 91052 Erlangen, Germany
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25
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Shubina TE. Computational Studies on Properties, Formation, and Complexation of M(II)-Porphyrins. ADVANCES IN INORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0898-8838(10)62007-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Zheng Z, Gunner MR. Analysis of the electrochemistry of hemes with E(m)s spanning 800 mV. Proteins 2009; 75:719-34. [PMID: 19003997 DOI: 10.1002/prot.22282] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The free energy of heme reduction in different proteins is found to vary over more than 18 kcal/mol. It is a challenge to determine how proteins manage to achieve this enormous range of E(m)s with a single type of redox cofactor. Proteins containing 141 unique hemes of a-, b-, and c-type, with bis-His, His-Met, and aquo-His ligation were calculated using Multi-Conformation Continuum Electrostatics (MCCE). The experimental E(m)s range over 800 mV from -350 mV in cytochrome c(3) to 450 mV in cytochrome c peroxidase (vs. SHE). The quantitative analysis of the factors that modulate heme electrochemistry includes the interactions of the heme with its ligands, the solvent, the protein backbone, and sidechains. MCCE calculated E(m)s are in good agreement with measured values. Using no free parameters the slope of the line comparing calculated and experimental E(m)s is 0.73 (R(2) = 0.90), showing the method accounts for 73% of the observed E(m) range. Adding a +160 mV correction to the His-Met c-type hemes yields a slope of 0.97 (R(2) = 0.93). With the correction 65% of the hemes have an absolute error smaller than 60 mV and 92% are within 120 mV. The overview of heme proteins with known structures and E(m)s shows both the lowest and highest potential hemes are c-type, whereas the b-type hemes are found in the middle E(m) range. In solution, bis-His ligation lowers the E(m) by approximately 205 mV relative to hemes with His-Met ligands. The bis-His, aquo-His, and His-Met ligated b-type hemes all cluster about E(m)s which are approximately 200 mV more positive in protein than in water. In contrast, the low potential bis-His c-type hemes are shifted little from in solution, whereas the high potential His-Met c-type hemes are raised by approximately 300 mV from solution. The analysis shows that no single type of interaction can be identified as the most important in setting heme electrochemistry in proteins. For example, the loss of solvation (reaction field) energy, which raises the E(m), has been suggested to be a major factor in tuning in situ E(m)s. However, the calculated solvation energy vs. experimental E(m) shows a slope of 0.2 and R(2) of 0.5 thus correlates weakly with E(m)s. All other individual interactions show even less correlation with E(m). However the sum of these terms does reproduce the range of observed E(m)s. Therefore, different proteins use different aspects of their structures to modulate the in situ heme electrochemistry. This study also shows that the calculated E(m)s are relatively insensitive to different heme partial charges and to the protein dielectric constant used in the simulation.
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Affiliation(s)
- Zhong Zheng
- Department of Physics, The City College of New York, New York, NY, USA
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27
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Engineering heme binding sites in monomeric rop. J Biol Inorg Chem 2009; 14:497-505. [PMID: 19152012 DOI: 10.1007/s00775-009-0465-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 12/26/2008] [Indexed: 10/21/2022]
Abstract
Heme ligands were introduced in the hydrophobic core of an engineered monomeric ColE1 repressor of primer (rop-S55) in two different layers of the heptad repeat. Mutants rop-L63M/F121H (layer 1) and rop-L56H/L113H (layer 3) were found to bind heme with a K (D) of 1.1 +/- 0.2 and 0.47 +/- 0.07 microM, respectively. The unfolding of heme-bound and heme-free mutants, in the presence of guanidinium hydrochloride, was monitored by both circular dichroism and fluorescence spectroscopy. For the heme-bound rop mutants, the total free energy change was 0.5 kcal/mol higher in the layer 3 mutant compared with that in the layer1 mutant. Heme binding also stabilized these mutants by increasing the [DGobsH2O] by 1.4 and 1.8 kcal/mol in rop-L63M/F121H and rop-L56H/L113H, respectively. The reduction potentials measured by spectroelectrochemical titrations were calculated to be -154 +/- 2 mV for rop-56H/113H and -87.5 +/- 1.2 mV for rop-L63M/F121H. The mutant designed to bind heme in a more buried environment (layer 3) showed tighter heme binding, a higher stability, and a different reduction potential compared with the mutant designed to bind heme in layer 1.
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28
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Fufezan C, Zhang J, Gunner MR. Ligand preference and orientation in b- and c-type heme-binding proteins. Proteins 2008; 73:690-704. [PMID: 18491383 DOI: 10.1002/prot.22097] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hemes are often incorporated into designed proteins. The importance of the heme ligand type and its orientation is still a matter of debate. Here, heme ligands and ligand orientation were investigated using a nonredundant (87 structures) and a redundant (1503 structures) set of structures to compare and contrast design features of natural b- and c-type heme-binding proteins. Histidine is the most common ligand. Marked differences in ligation motifs between b- and c-type hemes are higher occurrence of His-Met in c-type heme binding motifs (16.4% vs. 1.4%) and higher occurrence of exchangeable, small molecules in b-type heme binding motifs (67.6% vs. 9.9%). Histidine ligands that are part of the c-type CXXCH heme-binding motif show a distinct asymmetric distribution of orientation. They tend to point between either the heme propionates or between the NA and NB heme nitrogens. Molecular mechanics calculations show that this asymmetry is due to the bonded constraints of the covalent attachment between the heme and the protein. In contrast, the orientations of b-type hemes histidine ligands are found evenly distributed with no preference. Observed histidine heme ligand orientations show no dominating influence of electrostatic interactions between the heme propionates and the ligands. Furthermore, ligands in bis-His hemes are found more frequently perpendicular rather than parallel to each other. These correlations support energetic constraints on ligands that can be used in designing proteins.
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Affiliation(s)
- Christian Fufezan
- Physics Department, City College of New York, New York, New York 10031, USA.
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van Niftrik L, Geerts WJC, van Donselaar EG, Humbel BM, Webb RI, Fuerst JA, Verkleij AJ, Jetten MSM, Strous M. Linking ultrastructure and function in four genera of anaerobic ammonium-oxidizing bacteria: cell plan, glycogen storage, and localization of cytochrome C proteins. J Bacteriol 2008; 190:708-17. [PMID: 17993524 PMCID: PMC2223682 DOI: 10.1128/jb.01449-07] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 10/31/2007] [Indexed: 11/20/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) is an ecologically and industrially important process and is performed by a clade of deeply branching Planctomycetes. Anammox bacteria possess an intracytoplasmic membrane-bounded organelle, the anammoxosome. In the present study, the ultrastructures of four different genera of anammox bacteria were compared with transmission electron microscopy and electron tomography. The four anammox genera shared a common cell plan and contained glycogen granules. Differences between the four genera included cell size (from 800 to 1,100 nm in diameter), presence or absence of cytoplasmic particles, and presence or absence of pilus-like appendages. Furthermore, cytochrome c proteins were detected exclusively inside the anammoxosome. This detection provides further support for the hypothesis that this organelle is the locus of anammox catabolism.
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Affiliation(s)
- Laura van Niftrik
- Department of Microbiology, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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Reedy CJ, Elvekrog MM, Gibney BR. Development of a heme protein structure-electrochemical function database. Nucleic Acids Res 2007; 36:D307-13. [PMID: 17933771 PMCID: PMC2238922 DOI: 10.1093/nar/gkm814] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Proteins containing heme, iron(protoporphyrin IX) and its variants, continue to be one of the most-studied classes of biomolecules due to their diverse range of biological functions. The literature is abundant with reports of structural and functional characterization of individual heme proteins which demonstrate that heme protein reduction potential values, Em, span the range from –550 mV to +450 mV versus SHE. In order to unite these data for the purposes of global analysis, a new web-based resource of heme protein structure–function relationships is presented: the Heme Protein Database (HPD). This database is the first of its kind to combine heme protein structural classifications including protein fold, heme type and heme axial ligands, with heme protein reduction potential values in a web-searchable format. The HPD is located at http://heme.chem.columbia.edu/heme.php. The data illustrate that heme protein Em values are modulated over a 300 mV range by the type of global protein fold, a 600 mV range by the type of porphyrin and an 800 mV range by the axial ligands. Thus, the 1 V range observed in heme protein reduction potential values in biological systems arises from subtle combinations of these various factors.
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Affiliation(s)
- Charles J Reedy
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3121, New York, NY 10027, USA
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31
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Shubina TE, Marbach H, Flechtner K, Kretschmann A, Jux N, Buchner F, Steinrück HP, Clark T, Gottfried JM. Principle and mechanism of direct porphyrin metalation: joint experimental and theoretical investigation. J Am Chem Soc 2007; 129:9476-83. [PMID: 17625856 DOI: 10.1021/ja072360t] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The direct metalation of tetraphenylporphyrin with bare metal atoms (Co and Zn) was studied with X-ray photoelectron spectroscopy, scanning tunneling microscopy, and temperature-programmed reaction measurements on ordered monolayer films of the molecules adsorbed on a Ag(111) surface. The mechanism of this novel type of surface reaction was investigated using density functional theory (DFT) calculations for the related gas-phase reactions of the unsubstituted porphyrin with the metals Fe, Co, Ni, Cu, and Zn. The reaction starts with the formation of an initial complex, in which the metal atom is coordinated by the intact unreduced porphyrin. This complex resembles the sitting-atop complex proposed for porphyrin metalation with metal ions in solution. In two subsequent steps, the pyrrolic hydrogen atoms are transferred to the metal atom, forming H2, which is eventually released. The activation barriers of the H-transfer steps vary for the different metal atoms. DFT calculations suggest that metalations with Fe, Co, and Ni show two-state reactivity, while those with Cu and Zn proceed on a single potential energy surface. For metalation with Zn, we calculated a barrier of the first hydrogen transfer step of 32.6 kcal mol(-1), in good agreement with the overall experimental activation energy of 31 kcal mol(-1).
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Affiliation(s)
- Tatyana E Shubina
- Computer-Chemie-Centrum, Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, Erlangen, Germany
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32
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Schneider S, Marles-Wright J, Sharp KH, Paoli M. Diversity and conservation of interactions for binding heme in b-type heme proteins. Nat Prod Rep 2007; 24:621-30. [PMID: 17534534 DOI: 10.1039/b604186h] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Sabine Schneider
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, England, UK
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33
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Marritt SJ, van Wonderen JH, Cheesman MR, Butt JN. Magnetic circular dichroism of hemoproteins with in situ control of electrochemical potential: “MOTTLE”. Anal Biochem 2006; 359:79-83. [PMID: 16996021 DOI: 10.1016/j.ab.2006.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 08/16/2006] [Accepted: 08/17/2006] [Indexed: 10/24/2022]
Abstract
Hemoproteins have been recognized for nearly a century and are ubiquitous components of cellular organisms. Despite our familiarity with these proteins, defining the functional role of a given heme can still present considerable challenges. In this situation, magnetic circular dichroism (MCD) is a technique of choice because it has the capacity to define heme oxidation, spin, and ligation states in solution and at ambient temperature. Unfortunately, the resolving power of MCD rarely has been brought to bare on the intermediate redox states accessible to multiheme proteins. This is due in large part to the time-consuming procedure of magnetic field cycling required each time a sample is introduced into the magnet and the risk that control over, and knowledge of, the potential will be lost between sample preparation and spectral acquisition. Here we present a solution to this problem in the form of MCD-compatible optically transparent thin-layer electrochemistry (MOTTLE). MOTTLE defines redox behavior for cytochrome c in good agreement with the literature. In addition, MOTTLE reproduces the redox-driven transformation of heme ligand sets reported for cytochrome bd. Thus, MOTTLE provides a robust analytical tool for the dissection of heme properties with resolution across the electrochemical potential domain.
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Affiliation(s)
- Sophie J Marritt
- School of Chemical Sciences and Pharmacy, Centre for Metalloprotein Spectroscopy and Biology, University of East Anglia, Norwich NR4 7TJ, UK
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34
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Yen WN, Lo SS, Kuo MC, Mai CL, Lee GH, Peng SM, Yeh CY. Synthesis, Structure, and Optical and Electrochemical Properties of Star-Shaped Porphyrin−Triarylamine Conjugates. Org Lett 2006; 8:4239-42. [PMID: 16956196 DOI: 10.1021/ol061478w] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of novel star-shaped porphyrin-triarylamine conjugates were synthesized by palladium-catalyzed cross-coupling reactions. The spectroscopic and electrochemical studies show that pi-conjugation of the porphyrin core is extended to the triarylamine moieties.
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Affiliation(s)
- Wei-Nan Yen
- Department of Chemistry and Center of Nanoscience and Nanotechnology, National Chung Hsing University, Taichung 402, Taiwan
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35
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Sacquin-Mora S, Lavery R. Investigating the local flexibility of functional residues in hemoproteins. Biophys J 2006; 90:2706-17. [PMID: 16428284 PMCID: PMC1414562 DOI: 10.1529/biophysj.105.074997] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is now widely accepted that protein function depends not only on structure, but also on flexibility. However, the way mechanical properties contribute to catalytic mechanisms remains unclear. Here, we propose a method for investigating local flexibility within protein structures that combines a reduced protein representation with Brownian dynamics simulations. An analysis of residue fluctuations during the dynamics simulation yields a rigidity profile for the protein made up of force constants describing the ease of displacing each residue with respect to the rest of the structure. This approach has been applied to the analysis of a set of hemoproteins, one of the functionally most diverse protein families. Six proteins containing one or two heme groups have been studied, paying particular attention to the mechanical properties of the active-site residues. The calculated rigidity profiles show that active site residues are generally associated with high force constants and thus rigidly held in place. This observation also holds for diheme proteins if their mechanical properties are analyzed domain by domain. We note, however, that residues other than those in the active site can also have high force constants, as in the case of residues belonging to the folding nucleus of c-type hemoproteins.
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Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, Paris, France
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36
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Atteia A, van Lis R, Beale SI. Enzymes of the heme biosynthetic pathway in the nonphotosynthetic alga Polytomella sp. EUKARYOTIC CELL 2005; 4:2087-97. [PMID: 16339726 PMCID: PMC1317499 DOI: 10.1128/ec.4.12.2087-2097.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Accepted: 09/25/2005] [Indexed: 11/20/2022]
Abstract
Heme biosynthesis involves a number of enzymatic steps which in eukaryotes take place in different cell compartments. Enzyme compartmentalization differs between photosynthetic and nonphotosynthetic eukaryotes. Here we investigated the structures and subcellular localizations of three enzymes involved in the heme pathway in Polytomella sp., a colorless alga evolutionarily related to the green alga Chlamydomonas reinhardtii. Functional complementation of Escherichia coli mutant strains was used to isolate cDNAs encoding three heme biosynthetic enzymes, glutamate-1-semialdehyde aminotransferase, protoporphyrinogen IX oxidase, and ferrochelatase. All three proteins show highest similarity to their counterparts in photosynthetic organisms, including C. reinhardtii. All three proteins have N-terminal extensions suggestive of intracellular targeting, and immunoblot studies indicate their enrichment in a dense cell fraction that is enriched in amyloplasts. These results suggest that even though the plastids of Polytomella sp. are not photosynthetically active, they are the major site of heme biosynthesis. The presence of a gene for glutamate-1-semialdehyde aminotransferase suggests that Polytomella sp. uses the five-carbon pathway for synthesis of the heme precursor 5-aminolevulinic acid.
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Affiliation(s)
- Ariane Atteia
- Division of Biology and Medicine, Brown University, Providence, RI 02912, USA
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37
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Affiliation(s)
- Charles J Reedy
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3121, New York, New York 10027, USA
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38
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Singh R, Chauhan SMS. Electron transfer in natural and unnatural flavoporphyrins. Bioorg Chem 2004; 32:140-69. [PMID: 15110193 DOI: 10.1016/j.bioorg.2003.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2003] [Indexed: 11/24/2022]
Abstract
The development of chemical models for enzymes and their chemical and physical studies constitutes an important area of research from a scientific as well as an industrial point of view. Covalently linked flavin and porphyrin (flavoporphyrins) have attracted attention due to their applications as chemical models for flavoproteins and related enzymes. In this review, the literature has been surveyed to provide a comprehensive coverage of the synthetic methodology and characterization techniques of various types of synthetic flavoporphyrins.
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Affiliation(s)
- Ram Singh
- Department of Chemistry, University of Delhi, Delhi 110 007, India.
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39
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Fuziwara S, Sagami I, Rozhkova E, Craig D, Noble MA, Munro AW, Chapman SK, Shimizu T. Catalytically functional flavocytochrome chimeras of P450 BM3 and nitric oxide synthase. J Inorg Biochem 2002; 91:515-26. [PMID: 12237219 DOI: 10.1016/s0162-0134(02)00478-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
P450 BM3 and the nitric oxide synthases are related classes of flavocytochrome mono-oxygenase enzymes, containing NADPH-dependent FAD- and FMN-containing oxidoreductase modules fused to heme b-containing oxygenase domains. Domain-swap hybrids of these two multi-domain enzymes were created by genetic engineering of different segments of reductase and heme domains from neuronal nitric oxide synthase and P450 BM3, as a means of investigating the catalytic competence and substrate-binding properties of the fusions and the influence of tetrahydrpbiopterin and calmodulin binding regions on the electron transfer kinetics of the chimeras. Despite marked differences in hybrid stability and solubility, four catalytically functional chimeras were created that retained good reductase activity and which could be expressed successfully in Escherichia coli and purified. All of the BM3 reductase domain chimeras (chimeras I-III) exhibited inefficient flavin-to-heme inter-domain electron transfer, diminishing their oxygenase activity. However, the chimera containing the neuronal nitric oxide synthase reductase domain (chimera IV) showed good oxygenase domain activity, indicating that the flavin-to-heme electron transfer reaction is relatively efficient in this case. The data reinforce the importance of the nature of inter-domain linker constitution in multi-domain enzymes, and the difficulties posed in attempts to create chimeric enzymes with enhanced catalytic properties.
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Affiliation(s)
- Shigeyoshu Fuziwara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
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40
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Abstract
Biological systems rely on heme-proteins to carry out a number of basic functions essential for their survival. Hemes, or iron-porphyrin complexes, are the versatile and ubiquitous active centers of these proteins. In the past decade, discovery of new heme-proteins, together with functional and structural research, provided a wealth of information on these diverse and biologically important molecules. Structure determination work has shown that nature has used a variety of different scaffolds and architectures to bind heme and modulate functions such as redox properties. Structural data have also provided insights into the heme-linked protein conformational changes required in many regulatory heme-proteins. Remarkable efforts have been made towards the understanding of factors governing redox potentials. Site-directed mutagenesis studies and theoretical calculations on heme environments investigated the roles of hydrophobic and electrostatic residues, and analyzed the effect of heme solvent accessibility. This review focuses on the structure-function relationships underlying the association of heme in signaling and iron metabolism proteins. In addition, an account is given about molecular features affecting heme's redox properties; this briefly revisits previous conclusions in the light of some more recent reports.
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Affiliation(s)
- Massimo Paoli
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK.
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41
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Marques HM, Brown KL. Molecular mechanics and molecular dynamics simulations of porphyrins, metalloporphyrins, heme proteins and cobalt corrinoids. Coord Chem Rev 2002. [DOI: 10.1016/s0010-8545(01)00411-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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Yeh CY, Chang CJ, Nocera DG. "Hangman" porphyrins for the assembly of a model heme water channel. J Am Chem Soc 2001; 123:1513-4. [PMID: 11456732 DOI: 10.1021/ja003245k] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C Y Yeh
- Department of Chemistry, 6-335, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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43
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Patchkovskii S, Ziegler T. Structural origin of two paramagnetic species in six-coordinated nitrosoiron(II) porphyrins revealed by density functional theory analysis of the g tensors. Inorg Chem 2000; 39:5354-64. [PMID: 11154592 DOI: 10.1021/ic0005691] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potential energy and electron paramagnetic resonance (EPR) g tensor surfaces of model five- and six-coordinated porphyrins were examined. For both types of complexes, the NO ligand is preferably coordinated end-on, with a Fe-N-O bond angle of approximately 140 degrees. In the free five-coordinated structure, NO undergoes free rotation around the axial Fe-N(NO) bond. This motion is strongly coupled to the saddle-type distortion of the porphyrin ligand. Coordination by the second axial ligand (imidazole) raises the calculated barrier for NO rotation to about 1 kcal/mol, which is further increased by displacements of imidazole from the ideal axial position. The potential energy surface for the dissociation of the weakly coordinated imidazole ligand is exceptionally flat, with variation of the Fe-N(Im) bond length between 2.1 and 2.5 A changing the energy by less than 1 kcal/mol. Experimental orientations of both axial ligands, as well as the Fe-N(Im) bond length, are therefore likely to be determined by the environment of the complex. In contrast to the total energy, calculated EPR g-tensors are sensitive to the orientation of the NO ligand and to the Fe-N(Im) bond length. Contrary to a common assumption, the g tensor component closest to the free-electron value does not coincide with the direction of the Fe-N(NO) bond. From comparison of the calculated and experimental g-tensor components for a range of structures, the rhombic ("type I") EPR signal is assigned to a static structure with NO oriented toward the meso-C atom of the prophyrin ring, and RFe-N(Im) approximately 2.1 A (calcd g1 = 1.95, g2 = 2.00, g3 = 2.04; exptl g1 = 1.96-1.98, g2 = 2.00, g3 = 2.06-2.08). The axial ("type II") EPR signal cannot correspond to any of the static structures studied presently. It is tentatively assigned to a partially dissociated six-coordinated complex (RFe-N(Im) > 2.5 A), with a freely rotating NO ligand (calcd g parallel = 2.00, g perpendicular = 2.03; exptl g parallel = 1.99-2.00, g perpendicular = 2.02-2.03).
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Affiliation(s)
- S Patchkovskii
- Department of Chemistry, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4 Canada
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Fedurco M. Redox reactions of heme-containing metalloproteins: dynamic effects of self-assembled monolayers on thermodynamics and kinetics of cytochrome c electron-transfer reactions. Coord Chem Rev 2000. [DOI: 10.1016/s0010-8545(00)00292-7] [Citation(s) in RCA: 200] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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45
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Electronic structures of active sites in electron transfer metalloproteins: contributions to reactivity. Coord Chem Rev 2000. [DOI: 10.1016/s0010-8545(00)00332-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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46
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Morgan WT, Smith A. Binding and transport of iron-porphyrins by hemopexin. ADVANCES IN INORGANIC CHEMISTRY 2000. [DOI: 10.1016/s0898-8838(00)51004-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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