1
|
Clemen R, Minkus L, Singer D, Schulan P, von Woedtke T, Wende K, Bekeschus S. Multi-Oxidant Environment as a Suicidal Inhibitor of Myeloperoxidase. Antioxidants (Basel) 2023; 12:1936. [PMID: 38001789 PMCID: PMC10668958 DOI: 10.3390/antiox12111936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Tissue inflammation drives the infiltration of innate immune cells that generate reactive species to kill bacteria and recruit adaptive immune cells. Neutrophil activation fosters the release of myeloperoxidase (MPO) enzyme, a heme-containing protein generating hypochlorous acid (HOCl) from hydrogen peroxide (H2O2) and chloride ions. MPO-dependent oxidant formation initiates bioactive oxidation and chlorination products and induces oxidative post-translational modifications (oxPTMs) on proteins and lipid oxidation. Besides HOCl and H2O2, further reactive species such as singlet oxygen and nitric oxide are generated in inflammation, leading to modified proteins, potentially resulting in their altered bioactivity. So far, knowledge about multiple free radical-induced modifications of MPO and its effects on HOCl generation is lacking. To mimic this multi-oxidant microenvironment, human MPO was exposed to several reactive species produced simultaneously via argon plasma operated at body temperature. Several molecular gas admixes were used to modify the reactive species type profiles generated. MPO was investigated by studying its oxPTMs, changes in protein structure, and enzymatic activity. MPO activity was significantly reduced after treatment with all five tested plasma gas conditions. Dynamic light scattering and CD-spectroscopy revealed altered MPO protein morphology indicative of oligomerization. Using mass spectrometry, various oxPTMs, such as +1O, +2O, and +3O, were determined on methionine and cysteine (Cys), and -1H-1N+1O was detected in asparagine (Asp). The modification types identified differed between argon-oxygen and argon-nitrogen plasmas. However, all plasma gas conditions led to the deamidation of Asp and oxidation of Cys residues, suggesting an inactivation of MPO due to oxPTM-mediated conformational changes.
Collapse
Affiliation(s)
- Ramona Clemen
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Lara Minkus
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Debora Singer
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Clinic and Policlinic for Dermatology and Venerology, Rostock University Medical Center, Strempelstr. 13, 18057 Rostock, Germany
| | - Paul Schulan
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Thomas von Woedtke
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Institute for Hygiene and Environmental Medicine, Greifswald University Medical Center, Sauerbruchstr., 17475 Greifswald, Germany
| | - Kristian Wende
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Sander Bekeschus
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Clinic and Policlinic for Dermatology and Venerology, Rostock University Medical Center, Strempelstr. 13, 18057 Rostock, Germany
| |
Collapse
|
2
|
Rivett ED, Addis HG, Dietz JV, Carroll-Deaton JA, Gupta S, Foreman KL, Dang MA, Fox JL, Khalimonchuk O, Hegg EL. Evidence that the catalytic mechanism of heme a synthase involves the formation of a carbocation stabilized by a conserved glutamate. Arch Biochem Biophys 2023; 744:109665. [PMID: 37348627 PMCID: PMC10529832 DOI: 10.1016/j.abb.2023.109665] [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: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
In eukaryotes and many aerobic prokaryotes, the final step of aerobic respiration is catalyzed by an aa3-type cytochrome c oxidase, which requires a modified heme cofactor, heme a. The conversion of heme b, the prototypical cellular heme, to heme o and ultimately to heme a requires two modifications, the latter of which is conversion of a methyl group to an aldehyde, catalyzed by heme a synthase (HAS). The N- and C-terminal halves of HAS share homology, and each half contains a heme-binding site. Previous reports indicate that the C-terminal site is occupied by a heme b cofactor. The N-terminal site may function as the substrate (heme o) binding site, although this has not been confirmed experimentally. Here, we assess the role of conserved residues from the N- and C-terminal heme-binding sites in HAS from prokaryotic (Shewanella oneidensis) and eukaryotic (Saccharomyces cerevisiae) species - SoHAS/CtaA and ScHAS/Cox15, respectively. A glutamate within the N-terminal site is found to be critical for activity in both types of HAS, consistent with the hypothesis that a carbocation forms transiently during catalysis. In contrast, the residue occupying the analogous C-terminal position is dispensable for enzyme activity. In SoHAS, the C-terminal heme ligands are critical for stability, while in ScHAS, substitutions in either heme-binding site have little effect on global structure. In both species, in vivo accumulation of heme o requires the presence of an inactive HAS variant, highlighting a potential regulatory role for HAS in heme o biosynthesis.
Collapse
Affiliation(s)
- Elise D Rivett
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Hannah G Addis
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA
| | - Jonathan V Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA
| | - Jayda A Carroll-Deaton
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA
| | - Shipra Gupta
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Koji L Foreman
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Minh Anh Dang
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jennifer L Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA.
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA; Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, USA; Fred & Pamela Buffett Cancer Center, Omaha, NE, 68198, USA.
| | - Eric L Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
| |
Collapse
|
3
|
Bollmeyer MM, Coleman RE, Majer SH, Ferrao SD, Lancaster KM. Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification. J Am Chem Soc 2023; 145:14404-14416. [PMID: 37338957 PMCID: PMC10431212 DOI: 10.1021/jacs.3c03608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Cytochrome P460s are heme enzymes that oxidize hydroxylamine to nitrous oxide. They bear specialized "heme P460" cofactors that are cross-linked to their host polypeptides by a post-translationally modified lysine residue. Wild-type N. europaea cytochrome P460 may be isolated as a cross-link-deficient proenzyme following anaerobic overexpression in E. coli. When treated with peroxide, this proenzyme undergoes maturation to active enzyme with spectroscopic and catalytic properties that match wild-type cyt P460. This maturation reactivity requires no chaperones─it is intrinsic to the protein. This behavior extends to the broader cytochrome c'β superfamily. Accumulated data reveal key contributions from the secondary coordination sphere that enable selective, complete maturation. Spectroscopic data support the intermediacy of a ferryl species along the maturation pathway.
Collapse
Affiliation(s)
- Melissa M. Bollmeyer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Rachael E. Coleman
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Sean H. Majer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Silas D. Ferrao
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| |
Collapse
|
4
|
Chen L, Yuan H, Wang XJ, Li L, Tan X, Lin YW. Engineering Human Neuroglobin into a Cytochrome c-Like Protein with a Single Thioether Bond in Non-native State. Chembiochem 2022; 23:e202200531. [PMID: 36217897 DOI: 10.1002/cbic.202200531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/10/2022] [Indexed: 01/25/2023]
Abstract
A double mutant of human H64M/V71C neuroglobin (Ngb) was engineered, which formed a single thioether bond as that in atypical cytochrome c, whereas the heme distal Met64 was oxidized to both sulfoxide (SO-Met) and sulfone (SO2 -Met). By contrast, no Cys-heme cross-link was formed in V71C Ngb with His64/His96 coordination, as shown by the X-ray crystal structure, which indicates that an open distal site facilitates the activation of heme iron for structural modifications.
Collapse
Affiliation(s)
- Lei Chen
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China.,Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, 421001, China
| |
Collapse
|
5
|
Theoretical (DFT) study on the hydroxylation mechanism of Sn(IV)porphyrin: How does Sn(IV)porphyrin inhibit heme oxygenase catalysis function. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
6
|
Abstract
Myeloperoxidase participates in innate immune defense mechanism through formation of microbicidal reactive oxidants and diffusible radical species. A unique activity is its ability to use chloride as a cosubstrate with hydrogen peroxide to generate chlorinating oxidants such as hypochlorous acid, a potent antimicrobial agent. However, chronic MPO activation can lead to indiscriminate protein modification causing tissue damage, and has been associated with chronic inflammatory diseases, atherosclerosis, and acute cardiovascular events. This has attracted considerable interest in the development of therapeutically useful MPO inhibitors. Today, based on the profound knowledge of structure and function of MPO and its biochemical and biophysical differences with the other homologous human peroxidases, various rational and high-throughput screening attempts were performed in developing specific irreversible and reversible inhibitors. The most prominent candidates as well as MPO inhibitors already studied in clinical trials are introduced and discussed.
Collapse
|
7
|
Understanding molecular enzymology of porphyrin-binding α + β barrel proteins - One fold, multiple functions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140536. [PMID: 32891739 PMCID: PMC7611857 DOI: 10.1016/j.bbapap.2020.140536] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 11/24/2022]
Abstract
There is a high functional diversity within the structural superfamily of porphyrin-binding dimeric α + β barrel proteins. In this review we aim to analyze structural constraints of chlorite dismutases, dye-decolorizing peroxidases and coproheme decarboxylases in detail. We identify regions of structural variations within the highly conserved fold, which are most likely crucial for functional specificities. The loop linking the two ferredoxin-like domains within one subunit can be of different sequence lengths and can adopt various structural conformations, consequently defining the shape of the substrate channels and the respective active site architectures. The redox cofactor, heme b or coproheme, is oriented differently in either of the analyzed enzymes. By thoroughly dissecting available structures and discussing all available results in the context of the respective functional mechanisms of each of these redox-active enzymes, we highlight unsolved mechanistic questions in order to spark future research in this field.
Collapse
|
8
|
Mori D, Yoneda T, Suzuki M, Hoshino T, Neya S. meso-Diketopyripentaphyrin and Diketopyrihexaphyrin as Macrocyclic Tripyrrinone Ligands for Ni II Ions. Chem Asian J 2019; 14:4169-4173. [PMID: 31777185 DOI: 10.1002/asia.201901375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/24/2019] [Indexed: 12/27/2022]
Abstract
We report expanded porphyrins with pyridine rings and two neighboring carbonyl groups, which allow NiII ions to coordinate to the tripyrrinone-type NNNO coordination structure with Ni-O bonds. The selectivity of tripyrrinone is superior to other pyrrolic or pyridinic cavities of expanded porphyrins. Introduction of α-carbonyl pyridine next to the tripyrrolic conjugated structure is a powerful strategy for regioselective metalation of flexible expanded porphyrinoids.
Collapse
Affiliation(s)
- Daiki Mori
- Department of Pharmaceutical Sciences, Chiba University, Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Tomoki Yoneda
- Department of Pharmaceutical Sciences, Chiba University, Inohana, Chuo-ku, Chiba, 260-8675, Japan.,Current address: Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8 Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Masaaki Suzuki
- Department of Material Sciences, Interdisciplinary Graduate School of Science and Engineering, Shimane University, Matsue, Shimane, 690-8504, Japan
| | - Tyuji Hoshino
- Department of Pharmaceutical Sciences, Chiba University, Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Saburo Neya
- Department of Pharmaceutical Sciences, Chiba University, Inohana, Chuo-ku, Chiba, 260-8675, Japan
| |
Collapse
|
9
|
Rana A, Amanullah S, Das PK, McQuarters AB, Lehnert N, Dey A. Formally Ferric Heme Carbon Monoxide Adduct. J Am Chem Soc 2019; 141:5073-5077. [PMID: 30866627 DOI: 10.1021/jacs.8b09067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formally ferric carbonyl adducts are reported in a series of thiolate-bound iron porphyrins. Resonance Raman data indicate the presence of both Fe-S and Fe-CO bonds, and EPR data of this S = 1/2 species indicate a ligand-based electron hole, giving this complex an Fe(II)-thiyl radical electronic ground state. The FTIR data show that the C-O vibrations are substantially higher than in the corresponding ferrous-thiolate CO adducts. DFT calculations reproduce the spectroscopic features and indicate that backbonding to the low lying π* orbitals of the bound CO stabilizes the Fe 3d orbitals resulting in a stabilization of the ferrous-thiyl radical ground state compared to the five-coordinate ferric-thiolate precursor complexes. Access to stable thiyl radicals will help understand these elusive species that are mostly encountered as short-lived reactive reaction intermediates.
Collapse
Affiliation(s)
- Atanu Rana
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , Kolkata , West Bengal 700032 , India
| | - Sk Amanullah
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , Kolkata , West Bengal 700032 , India
| | - Pradip K Das
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , Kolkata , West Bengal 700032 , India
| | - Ashley B McQuarters
- Department of Chemistry , The University of Michigan , 930 N. University , Ann Arbor , Michigan 48109 , United States
| | - Nicolai Lehnert
- Department of Chemistry , The University of Michigan , 930 N. University , Ann Arbor , Michigan 48109 , United States
| | - Abhishek Dey
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , Kolkata , West Bengal 700032 , India
| |
Collapse
|
10
|
Liu HX, Li L, Yang XZ, Wei CW, Cheng HM, Gao SQ, Wen GB, Lin YW. Enhancement of protein stability by an additional disulfide bond designed in human neuroglobin. RSC Adv 2019; 9:4172-4179. [PMID: 35520156 PMCID: PMC9062612 DOI: 10.1039/c8ra10390a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/28/2019] [Indexed: 12/21/2022] Open
Abstract
Human neuroglobin (Ngb) forms an intramolecular disulfide bond between Cys46 and Cys55, with a third Cys120 near the protein surface, which is a promising protein model for heme protein design. In order to protect the free Cys120 and to enhance the protein stability, we herein developed a strategy by designing an additional disulfide bond between Cys120 and Cys15 via A15C mutation. The design was supported by molecular modeling, and the formation of Cys15–Cys120 disulfide bond was confirmed experimentally by ESI-MS analysis. Molecular modeling, UV-Vis and CD spectroscopy showed that the additional disulfide bond caused minimal structural alterations of Ngb. Meanwhile, the disulfide bond of Cys15–Cys120 was found to enhance both Gdn·HCl-induced unfolding stability (increased by ∼0.64 M) and pH-induced unfolding stability (decreased by ∼0.69 pH unit), as compared to those of WT Ngb with a single native disulfide bond of Cys46–Cys55. Moreover, the half denaturation temperature (Tm) of A15C Ngb was determined to be higher than 100 °C. In addition, the disulfide bond of Cys15–Cys120 has slight effects on protein function, such as an increase in the rate of O2 release by ∼1.4-fold. This study not only suggests a crucial role of the artificial disulfide in protein stabilization, but also lays the groundwork for further investigation of the structure and function of Ngb, as well as for the design of other functional heme proteins, based on the scaffold of A15C Ngb with an enhanced stability. A disulfide bond of Cys120 and Cys15 was rationally designed in human neuroglobin (Ngb) by A15C mutation, which caused minimal structural alterations, whereas enhanced both chemical and pH stability, with a thermal stability higher than 100 °C.![]()
Collapse
Affiliation(s)
- Hai-Xiao Liu
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
| | - Xin-Zhi Yang
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Chuan-Wan Wei
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Hui-Min Cheng
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
- Laboratory of Protein Structure and Function
| |
Collapse
|
11
|
Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
Collapse
Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
12
|
Gheidi M, Safari N, Zahedi M. Density functional theory studies on the conversion of hydroxyheme to iron-verdoheme in the presence of dioxygen. Dalton Trans 2018; 46:2146-2158. [PMID: 28120965 DOI: 10.1039/c6dt04250c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Detailed insight into the second step of heme degradation by heme oxygenase, oxophlorin to verdoheme and biliverdin, is presented. Density functional theory methods are reported for the conversion of oxophlorin to verdoheme. Since it is currently unclear whether dioxygen binding to iron oxophlorin is followed by a reduction or not, in this work we have focused on the difference in reactivity between [(Im)(O2˙)FeIII(PO˙)] (PO˙ is the oxophlorin dianion radical) and [(Im)(O2˙)FeIII(PO)]- (PO is the oxophlorin trianion). Thus, we have shown that in [(Im)(O2˙)FeIII(PO˙)] and [(Im)(O2˙)FeIII(PO)]-, the mechanisms are stepwise with an initial C-O bond activation to form a ring-structure where the oxophlorin is distorted from planarity. This is followed by homolytic dioxygen bond breaking that directly leads to iron-oxo verdoheme products. The [(Im)(O2˙)FeIII(PO˙)] mechanism proceeds via two-state-reactivity patterns on the adjacent doublet and quartet spin state surfaces, whereas the [(Im)(O2˙)FeIII(PO)]- route shows single-state-reactivity on a triplet spin state surface. In both, the rate determining step is the C-O bond activation, with substantially lower barriers on the [(Im)(O2˙)FeIII(PO˙)] surface of 12.15 kcal mol-1 in the gas phase compared to 22.55 kcal mol-1 for the intermediate-spin of [(Im)(O2˙)FeIII(PO)]-. The complete active space self-consistent-field wave functions with second-order multi-reference perturbation theory were also studied. Finally, the effects of the solvent and the medium on the reaction barriers were tested and shown to be considerable.
Collapse
Affiliation(s)
- Mahin Gheidi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran.
| | - Nasser Safari
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran.
| | - Mansour Zahedi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran.
| |
Collapse
|
13
|
Jennings GK, Hsu MH, Shock LS, Johnson EF, Hackett JC. Noncovalent interactions dominate dynamic heme distortion in cytochrome P450 4B1. J Biol Chem 2018; 293:11433-11446. [PMID: 29858244 PMCID: PMC6065186 DOI: 10.1074/jbc.ra118.004044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 05/31/2018] [Indexed: 01/07/2023] Open
Abstract
Cytochrome P450 4B1 (4B1) functions in both xenobiotic and endobiotic metabolism. An ester linkage between Glu-310 in 4B1 and the 5-methyl group of heme facilitates preferential hydroxylation of terminal (ω) methyl groups of hydrocarbons (HCs) and fatty acids compared with ω-1 sites bearing weaker C-H bonds. This preference is retained albeit diminished 4-fold for the E310A mutant, but the reason for this is unclear. Here, a crystal structure of the E310A-octane complex disclosed that noncovalent interactions maintain heme deformation in the absence of the ester linkage. Consistent with the lower symmetry of the heme, resonance Raman (RR) spectroscopy revealed large enhancements of RR peaks for high-spin HC complexes of 4B1 and the E310A mutant relative to P450 3A4. Whereas these enhancements were diminished in RR spectra of a low-spin 4B1-N-hydroxy-N'-(4-butyl-2-methylphenyl)formamidine complex, a crystal structure indicated that this inhibitor does not alter heme ruffling. RR spectra of Fe2+-CO HC complexes revealed larger effects of HC length in E310A than in 4B1, suggesting that reduced rigidity probably underlies increased E310A-catalyzed (ω-1)-hydroxylation. Diminished effects of the HC on the position of the Fe-CO stretching mode in 4B1 suggested that the ester linkage limits substrate access to the CO. Heme ruffling probably facilitates autocatalytic ester formation by reducing inhibitory coordination of Glu-310 with the heme iron. This also positions the 5-methyl for a reaction with the proposed glutamyl radical intermediate and potentially enhances oxo-ferryl intermediate reactivity for generation of the glutamyl radical to initiate ester bond formation and ω-hydroxylation.
Collapse
Affiliation(s)
- Gareth K Jennings
- Massey Cancer Center and Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298
| | - Mei-Hui Hsu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| | - Lisa S Shock
- Massey Cancer Center and Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298
| | - Eric F Johnson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037.
| | - John C Hackett
- Massey Cancer Center and Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298.
| |
Collapse
|
14
|
Fourie R, Kuloyo OO, Mochochoko BM, Albertyn J, Pohl CH. Iron at the Centre of Candida albicans Interactions. Front Cell Infect Microbiol 2018; 8:185. [PMID: 29922600 PMCID: PMC5996042 DOI: 10.3389/fcimb.2018.00185] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/14/2018] [Indexed: 12/27/2022] Open
Abstract
Iron is an absolute requirement for both the host and most pathogens alike and is needed for normal cellular growth. The acquisition of iron by biological systems is regulated to circumvent toxicity of iron overload, as well as the growth deficits imposed by iron deficiency. In addition, hosts, such as humans, need to limit the availability of iron to pathogens. However, opportunistic pathogens such as Candida albicans are able to adapt to extremes of iron availability, such as the iron replete environment of the gastrointestinal tract and iron deficiency during systemic infection. C. albicans has developed a complex and effective regulatory circuit for iron acquisition and storage to circumvent iron limitation within the human host. As C. albicans can form complex interactions with both commensal and pathogenic co-inhabitants, it can be speculated that iron may play an important role in these interactions. In this review, we highlight host iron regulation as well as regulation of iron homeostasis in C. albicans. In addition, the review argues for the need for further research into the role of iron in polymicrobial interactions. Lastly, the role of iron in treatment of C. albicans infection is discussed.
Collapse
Affiliation(s)
- Ruan Fourie
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Oluwasegun O Kuloyo
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Bonang M Mochochoko
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Jacobus Albertyn
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Carolina H Pohl
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| |
Collapse
|
15
|
Nicolussi A, Auer M, Sevcnikar B, Paumann-Page M, Pfanzagl V, Zámocký M, Hofbauer S, Furtmüller PG, Obinger C. Posttranslational modification of heme in peroxidases – Impact on structure and catalysis. Arch Biochem Biophys 2018; 643:14-23. [DOI: 10.1016/j.abb.2018.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 12/16/2022]
|
16
|
Structural basis of activation of mammalian heme peroxidases. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 133:49-55. [DOI: 10.1016/j.pbiomolbio.2017.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 12/27/2022]
|
17
|
Cheng HM, Yuan H, Wang XJ, Xu JK, Gao SQ, Wen GB, Tan X, Lin YW. Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen. J Inorg Biochem 2018; 182:141-149. [PMID: 29477977 DOI: 10.1016/j.jinorgbio.2018.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 12/13/2022]
Abstract
The structure and function of heme proteins are regulated by diverse post-translational modifications including heme-protein cross-links, with the underlying mechanisms not well understood. In this study, we introduced a Cys (K42C) close to the heme 4-vinyl group in sperm whale myoglobin (Mb) and solved its X-ray crystal structure. Interestingly, we found that K42C Mb can partially form a Cys-heme cross-link (termed K42C Mb-X) under dithiothreitol-induced reductive conditions in presence of O2, as suggested by guanidine hydrochloride-induced unfolding and heme extraction studies. Mass spectrometry (MS) studies, together with trypsin digestion studies, further indicated that a thioether bond is formed between Cys42 and the heme 4-vinyl group with an additional mass of 16 Da, likely due to hydroxylation of the α‑carbon. We then proposed a plausible mechanism for the formation of the novel Cys-heme cross-link based on MS, kinetic UV-vis and electron paramagnetic resonance (EPR) studies. Moreover, the Cys-heme cross-link was shown to fine-tune the protein reactivity toward activation of H2O2. This study provides valuable insights into the post-translational modification of heme proteins, and also suggests that the Cys-heme cross-link can be induced to form in vitro, making it useful for design of new heme proteins with a non-dissociable heme and improved functions.
Collapse
Affiliation(s)
- Hui-Min Cheng
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Jia-Kun Xu
- Yellow Sea Fisheries Research Institute, Qingdao 266071, China
| | - Shu-Qin Gao
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Lab of Protein Structure and Function, University of South China, Hengyang 421001, China.
| |
Collapse
|
18
|
Streit BR, Celis AI, Moraski GC, Shisler KA, Shepard EM, Rodgers KR, Lukat-Rodgers GS, DuBois JL. Decarboxylation involving a ferryl, propionate, and a tyrosyl group in a radical relay yields heme b. J Biol Chem 2018; 293:3989-3999. [PMID: 29414780 DOI: 10.1074/jbc.ra117.000830] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/01/2018] [Indexed: 01/02/2023] Open
Abstract
The H2O2-dependent oxidative decarboxylation of coproheme III is the final step in the biosynthesis of heme b in many microbes. However, the coproheme decarboxylase reaction mechanism is unclear. The structure of the decarboxylase in complex with coproheme III suggested that the substrate iron, reactive propionates, and an active-site tyrosine convey a net 2e-/2H+ from each propionate to an activated form of H2O2 Time-resolved EPR spectroscopy revealed that Tyr-145 formed a radical species within 30 s of the reaction of the enzyme-coproheme complex with H2O2 This radical disappeared over the next 270 s, consistent with a catalytic intermediate. Use of the harderoheme III intermediate as substrate or substitutions of redox-active side chains (W198F, W157F, or Y113S) did not strongly affect the appearance or intensity of the radical spectrum measured 30 s after initiating the reaction with H2O2, nor did it change the ∼270 s required for the radical signal to recede to ≤10% of its initial intensity. These results suggested Tyr-145 as the site of a catalytic radical involved in decarboxylating both propionates. Tyr-145• was accompanied by partial loss of the initially present Fe(III) EPR signal intensity, consistent with the possible formation of Fe(IV)=O. Site-specifically deuterated coproheme gave rise to a kinetic isotope effect of ∼2 on the decarboxylation rate constant, indicating that cleavage of the propionate Cβ-H bond was partly rate-limiting. The inferred mechanism requires two consecutive hydrogen atom transfers, first from Tyr-145 to the substrate Fe/H2O2 intermediate and then from the propionate Cβ-H to Tyr-145•.
Collapse
Affiliation(s)
- Bennett R Streit
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Arianna I Celis
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Garrett C Moraski
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Krista A Shisler
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Eric M Shepard
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Kenton R Rodgers
- the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Gudrun S Lukat-Rodgers
- the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| |
Collapse
|
19
|
Alavi FS, Gheidi M, Zahedi M, Safari N, Ryde U. A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations. Dalton Trans 2018; 47:8283-8291. [DOI: 10.1039/c8dt00064f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Heme degradation by heme oxygenase enzymes is important for maintaining iron homeostasis and prevention of oxidative stress.
Collapse
Affiliation(s)
- Fatemeh Sadat Alavi
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Mahin Gheidi
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Mansour Zahedi
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Nasser Safari
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| |
Collapse
|
20
|
Yin LL, Yuan H, Du KJ, He B, Gao SQ, Wen GB, Tan X, Lin YW. Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin. Chem Commun (Camb) 2018; 54:4356-4359. [DOI: 10.1039/c8cc01646a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The V21C/V66C/F46S myoglobin mutant, with a de novo designed intramolecular disulfide bond resembling that in cytoglobin without structural evidence, exhibits a dehalogenation activity exceeding that of a native dehaloperoxidase.
Collapse
Affiliation(s)
- Lu-Lu Yin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Ke-Jie Du
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Bo He
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
- Laboratory of Protein Structure and Function
| |
Collapse
|
21
|
Lee MJY, Wang Y, Jiang Y, Li X, Ma J, Tan H, Turner-Wood K, Rahman MN, Chen G, Jia Z. Function Coupling Mechanism of PhuS and HemO in Heme Degradation. Sci Rep 2017; 7:11273. [PMID: 28900278 PMCID: PMC5596023 DOI: 10.1038/s41598-017-11907-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/31/2017] [Indexed: 12/24/2022] Open
Abstract
Most bacteria possess only one heme-degrading enzyme for obtaining iron, however few bacteria such as Pseudomonas aeruginosa express two, namely PhuS and HemO. While HemO is a well-known heme oxygenase, previously we discovered that PhuS also possesses heme degradation activity and generates verdoheme, an intermediate of heme breakdown. To understand the coexistence of these two enzymes, using the DFT calculation we reveal that PhuS effectively enhances heme degradation through its participation in heme hydroxylation, the rate limiting reaction. Heme is converted to verdoheme in this reaction and the energy barrier for PhuS is substantially lower than for HemO. Thus, HemO is mainly involved in the ring opening reaction which converts verdoheme to biliverdin and free iron. Our kinetics experiments show that, in the presence of both PhuS and HemO, complete degradation of heme to biliverdin is enhanced. We further show that PhuS is more active than HemO using heme as a substrate and generates more CO. Combined experimental and theoretical results directly identify function coupling of this two-enzyme system, resulting in more efficient heme breakdown and utilization.
Collapse
Affiliation(s)
- Michael J Y Lee
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Ye Wang
- College of Chemistry, Beijing Normal University, 100875, Beijing, China
| | - Yafei Jiang
- College of Chemistry, Beijing Normal University, 100875, Beijing, China
| | - Xichen Li
- College of Chemistry, Beijing Normal University, 100875, Beijing, China
| | - Jianqiu Ma
- College of Chemistry, Beijing Normal University, 100875, Beijing, China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, 100875, Beijing, China.
| | - Keegan Turner-Wood
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Mona N Rahman
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, 100875, Beijing, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada. .,College of Chemistry, Beijing Normal University, 100875, Beijing, China.
| |
Collapse
|
22
|
Kitagishi H, Sugaya Y, Komazawa K, Tamaki M, Kano K. Participation of Hydroxyl Radical in the Formation of Verdoheme-type Compound in the Reaction of a Ferric Porphyrin with Hydrogen Peroxide. CHEM LETT 2017. [DOI: 10.1246/cl.161161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321
| | - Yosuke Sugaya
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321
| | - Kozue Komazawa
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321
| | - Mariko Tamaki
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321
| | - Koji Kano
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321
| |
Collapse
|
23
|
Celis AI, Gauss GH, Streit BR, Shisler K, Moraski GC, Rodgers KR, Lukat-Rodgers GS, Peters JW, DuBois JL. Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ). J Am Chem Soc 2017; 139:1900-1911. [PMID: 27936663 PMCID: PMC5348300 DOI: 10.1021/jacs.6b11324] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyrosine, forming Tyr•. This residue then abstracts a net hydrogen atom (H•) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.
Collapse
Affiliation(s)
- Arianna I. Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - George H. Gauss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Bennett R. Streit
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Krista Shisler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Garrett C. Moraski
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050
| | - John W. Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| |
Collapse
|
24
|
Jha JC, Banal C, Chow BSM, Cooper ME, Jandeleit-Dahm K. Diabetes and Kidney Disease: Role of Oxidative Stress. Antioxid Redox Signal 2016; 25:657-684. [PMID: 26906673 PMCID: PMC5069735 DOI: 10.1089/ars.2016.6664] [Citation(s) in RCA: 395] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Intrarenal oxidative stress plays a critical role in the initiation and progression of diabetic kidney disease (DKD). Enhanced oxidative stress results from overproduction of reactive oxygen species (ROS) in the context of concomitant, insufficient antioxidant pathways. Renal ROS production in diabetes is predominantly mediated by various NADPH oxidases (NOXs), but a defective antioxidant system as well as mitochondrial dysfunction may also contribute. Recent Advances: Effective agents targeting the source of ROS generation hold the promise to rescue the kidney from oxidative damage and prevent subsequent progression of DKD. Critical Issues and Future Directions: In the present review, we summarize and critically analyze molecular and cellular mechanisms that have been demonstrated to be involved in NOX-induced renal injury in diabetes, with particular focus on the role of increased glomerular injury, the development of albuminuria, and tubulointerstitial fibrosis, as well as mitochondrial dysfunction. Furthermore, novel agents targeting NOX isoforms are discussed. Antioxid. Redox Signal. 25, 657-684.
Collapse
Affiliation(s)
- Jay C Jha
- 1 Diabetic Complications Division, JDRF Danielle Alberti Memorial Centre for Diabetic Complications, Baker IDI Heart and Diabetes Institute , Melbourne, Australia
| | - Claudine Banal
- 1 Diabetic Complications Division, JDRF Danielle Alberti Memorial Centre for Diabetic Complications, Baker IDI Heart and Diabetes Institute , Melbourne, Australia
| | - Bryna S M Chow
- 1 Diabetic Complications Division, JDRF Danielle Alberti Memorial Centre for Diabetic Complications, Baker IDI Heart and Diabetes Institute , Melbourne, Australia
| | - Mark E Cooper
- 1 Diabetic Complications Division, JDRF Danielle Alberti Memorial Centre for Diabetic Complications, Baker IDI Heart and Diabetes Institute , Melbourne, Australia .,2 Department of Medicine, Monash University , Melbourne, Australia
| | - Karin Jandeleit-Dahm
- 1 Diabetic Complications Division, JDRF Danielle Alberti Memorial Centre for Diabetic Complications, Baker IDI Heart and Diabetes Institute , Melbourne, Australia .,2 Department of Medicine, Monash University , Melbourne, Australia
| |
Collapse
|
25
|
Arbelo-Lopez HD, Simakov NA, Smith JC, Lopez-Garriga J, Wymore T. Homolytic Cleavage of Both Heme-Bound Hydrogen Peroxide and Hydrogen Sulfide Leads to the Formation of Sulfheme. J Phys Chem B 2016; 120:7319-31. [DOI: 10.1021/acs.jpcb.6b02839] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Hector D. Arbelo-Lopez
- Chemistry
Department, University of Puerto Rico, Mayagüez Campus, Mayagüez 00681, Puerto Rico
| | - Nikolay A. Simakov
- Center
for Computational Research, University of Buffalo, Buffalo, New York 14203, United States
| | - Jeremy C. Smith
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Juan Lopez-Garriga
- Chemistry
Department, University of Puerto Rico, Mayagüez Campus, Mayagüez 00681, Puerto Rico
| | - Troy Wymore
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
26
|
Yan DJ, Yuan H, Li W, Xiang Y, He B, Nie CM, Wen GB, Lin YW, Tan X. How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin. Dalton Trans 2016; 44:18815-22. [PMID: 26458300 DOI: 10.1039/c5dt03040d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A heme-protein cross-link is a key post-translational modification (PTM) of heme proteins. Meanwhile, the structural and functional consequences of heme-protein cross-links are not fully understood, due to limited studies on a direct comparison of the same protein with and without the cross-link. A Tyr-heme cross-link with a C-O bond is a newly discovered PTM of heme proteins, and is spontaneously formed in F43Y myoglobin (Mb) between the Tyr hydroxyl group and the heme 4-vinyl group in vivo. In this study, we found that with an additional distal His29 introduced in the heme pocket, the double mutant L29H/F43Y Mb can form two distinct forms under different protein purification conditions, with and without a novel Tyr-heme cross-link. By solving the X-ray structures of both forms of L29H/F43Y Mb and performing spectroscopic studies, we made a direct structural and functional comparison in the same protein scaffold. It revealed that the Tyr-heme cross-link regulates the heme distal hydrogen-bonding network, and fine-tunes not only the spectroscopic and ligand binding properties, but also the protein reactivity. Moreover, the formation of the Tyr-heme cross-link in the double mutant L29H/F43Y Mb was investigated in vitro. This study addressed the key issue of how Tyr-heme cross-link fine-tunes the structure and functions of the heme protein, and provided a plausible mechanism for the formation of the newly discovered Tyr-heme cross-link.
Collapse
Affiliation(s)
- Dao-Jing Yan
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Hong Yuan
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
| | - Wei Li
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
| | - Yu Xiang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Bo He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Chang-Ming Nie
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
| |
Collapse
|
27
|
Lin YW. The broad diversity of heme-protein cross-links: An overview. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:844-59. [DOI: 10.1016/j.bbapap.2015.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/26/2015] [Accepted: 04/17/2015] [Indexed: 12/30/2022]
|
28
|
Shimizu T, Huang D, Yan F, Stranava M, Bartosova M, Fojtíková V, Martínková M. Gaseous O2, NO, and CO in signal transduction: structure and function relationships of heme-based gas sensors and heme-redox sensors. Chem Rev 2015; 115:6491-533. [PMID: 26021768 DOI: 10.1021/acs.chemrev.5b00018] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Toru Shimizu
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
- §Research Center for Compact Chemical System, National Institute of Advanced Industrial Science and Technology (AIST), Sendai 983-8551, Japan
| | - Dongyang Huang
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Fang Yan
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Martin Stranava
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Martina Bartosova
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Veronika Fojtíková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Markéta Martínková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| |
Collapse
|
29
|
Ravlić S, Žučko J, Tanković MS, Fafanđel M, Bihari N. Sequence analysis of novel CYP4 transcripts from Mytilus galloprovincialis. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2015; 40:300-309. [PMID: 26176904 DOI: 10.1016/j.etap.2015.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 05/29/2015] [Accepted: 06/02/2015] [Indexed: 06/04/2023]
Abstract
Cytochrome P450 enzymes (CYPs) are essential components of cellular detoxification system. We identified and characterized seven new cytochrome P450 gene transcript clusters in the populations of bivalve mollusc Mytilus galloprovincialis from three different locations. The phylogenetic analysis identified all transcripts as clusters within the CYP4 branch. Identified clusters, each comprising a number of transcript variants, were designated CYP4Y1, Y2, Y3, Y4, Y5, Y6 and Y7. Transcript clusters CYP4Y2 and Y7, and CYP4Y5 and Y6 showed site specificity, while the transcript clusters CYP4Y1, Y3 and Y4 were present at all investigated locations. The comparison of transcripts deduced amino acid sequences with CYP4s from vertebrate and invertebrate species showed high conservation of the residues and domains essential to the putative function of the enzyme, as terminal ω-hydroxylation and prostaglandin hydroxylation. Our results suggest the great expansion of the CYP4Y cDNAs indicative of CYP4 proteins in the mussel M. galloprovincialis presumably as a response to different environmental conditions.
Collapse
Affiliation(s)
- Sanda Ravlić
- Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia.
| | - Jurica Žučko
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Mirta Smodlaka Tanković
- Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia
| | - Maja Fafanđel
- Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia
| | - Nevenka Bihari
- Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia
| |
Collapse
|
30
|
Spolitak T, Ballou DP. Evidence for catalytic intermediates involved in generating the chromopyrrolic acid scaffold of rebeccamycin by RebO and RebD. Arch Biochem Biophys 2015; 573:111-9. [DOI: 10.1016/j.abb.2015.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 10/23/2022]
|
31
|
Inactivation of myeloperoxidase by benzoic acid hydrazide. Arch Biochem Biophys 2015; 570:14-22. [PMID: 25688920 DOI: 10.1016/j.abb.2015.01.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 01/20/2015] [Accepted: 01/24/2015] [Indexed: 12/12/2022]
Abstract
Myeloperoxidase (MPO) is expressed by myeloid cells for the purpose of catalyzing the formation of hypochlorous acid, from chloride ions and reaction with a hydrogen peroxide-charged heme covalently bound to the enzyme. Most peroxidase enzymes both plant and mammalian are inhibited by benzoic acid hydrazide (BAH)-containing compounds, but the mechanism underlying MPO inhibition by BAH compounds is largely unknown. Recently, we reported MPO inhibition by BAH and 4-(trifluoromethyl)-BAH was due to hydrolysis of the ester bond between MPO heavy chain glutamate 242 ((HC)Glu(242)) residue and the heme pyrrole A ring, freeing the heme linked light chain MPO subunit from the larger remaining heavy chain portion. Here we probed the structure and function relationship behind this ester bond cleavage using a panel of BAH analogs to gain insight into the constraints imposed by the MPO active site and channel leading to the buried protoporphyrin IX ring. In addition, we show evidence that destruction of the heme ring does not occur by tracking the heme prosthetic group and provide evidence that the mechanism of hydrolysis follows a potential attack of the (HC)Glu(242) carbonyl leading to a rearrangement causing the release of the vinyl-sulfonium linkage between (HC)Met(243) and the pyrrole A ring.
Collapse
|
32
|
Yan DJ, Li W, Xiang Y, Wen GB, Lin YW, Tan X. A Novel Tyrosine-Heme CO Covalent Linkage in F43Y Myoglobin: A New Post-translational Modification of Heme Proteins. Chembiochem 2014; 16:47-50. [DOI: 10.1002/cbic.201402504] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Indexed: 12/18/2022]
|
33
|
NADPH oxidases: an overview from structure to innate immunity-associated pathologies. Cell Mol Immunol 2014; 12:5-23. [PMID: 25263488 DOI: 10.1038/cmi.2014.89] [Citation(s) in RCA: 641] [Impact Index Per Article: 64.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 12/11/2022] Open
Abstract
Oxygen-derived free radicals, collectively termed reactive oxygen species (ROS), play important roles in immunity, cell growth, and cell signaling. In excess, however, ROS are lethal to cells, and the overproduction of these molecules leads to a myriad of devastating diseases. The key producers of ROS in many cells are the NOX family of NADPH oxidases, of which there are seven members, with various tissue distributions and activation mechanisms. NADPH oxidase is a multisubunit enzyme comprising membrane and cytosolic components, which actively communicate during the host responses to a wide variety of stimuli, including viral and bacterial infections. This enzymatic complex has been implicated in many functions ranging from host defense to cellular signaling and the regulation of gene expression. NOX deficiency might lead to immunosuppression, while the intracellular accumulation of ROS results in the inhibition of viral propagation and apoptosis. However, excess ROS production causes cellular stress, leading to various lethal diseases, including autoimmune diseases and cancer. During the later stages of injury, NOX promotes tissue repair through the induction of angiogenesis and cell proliferation. Therefore, a complete understanding of the function of NOX is important to direct the role of this enzyme towards host defense and tissue repair or increase resistance to stress in a timely and disease-specific manner.
Collapse
|
34
|
Yamashita KI, Hirano D, Asano MS, Sugiura KI. Oxidation of meso-Diarylporphyrins by a Hypervalent Iodine Compound: Facile Synthesis of meso-Acyloxyporphyrins and Dioxoporphodimethenes. CHEM LETT 2014. [DOI: 10.1246/cl.140219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ken-ichi Yamashita
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University
| | - Daisuke Hirano
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University
| | - Motoko S. Asano
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University
| | - Ken-ichi Sugiura
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University
| |
Collapse
|
35
|
Gheidi M, Safari N, Zahedi M. Chameleonic Nature of Hydroxyheme in Heme Oxygenase and Its Reactivity: A Density Functional Theory Study. Inorg Chem 2014; 53:2766-75. [DOI: 10.1021/ic402754y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mahin Gheidi
- Department of Chemistry, Faculty
of Sciences, Shahid Beheshti University, G. C. Evin, 19839-63113 Tehran, Iran
| | - Nasser Safari
- Department of Chemistry, Faculty
of Sciences, Shahid Beheshti University, G. C. Evin, 19839-63113 Tehran, Iran
| | - Mansour Zahedi
- Department of Chemistry, Faculty
of Sciences, Shahid Beheshti University, G. C. Evin, 19839-63113 Tehran, Iran
| |
Collapse
|
36
|
Garcia-Bosch I, Sharma SK, Karlin KD. A selective stepwise heme oxygenase model system: an iron(IV)-oxo porphyrin π-cation radical leads to a verdoheme-type compound via an isoporphyrin intermediate. J Am Chem Soc 2013; 135:16248-51. [PMID: 24147457 DOI: 10.1021/ja405739m] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The selective oxidation of the α-position of two heme-Fe(III) tetraarylporphryinate complexes occurs when water(hydroxide) attacks their oxidized Cmpd I-type equivalents, high-valent Fe(IV)═O π-cation radical species ((P(+•))Fe(IV)═O). Stepwise intermediate formation occurs, as detected by UV-vis spectroscopic monitoring or mass spectrometric interrogation, being iron(III) isoporphyrins, iron(III) benzoyl-biliverdins, and the final verdoheme-like products. Heme oxygenase (HO) enzymes could proceed through heterolytic cleavage of an iron(III)-hydroperoxo intermediate to form a transient Cmpd I-type species.
Collapse
Affiliation(s)
- Isaac Garcia-Bosch
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | | | | |
Collapse
|
37
|
Unno M, Ardèvol A, Rovira C, Ikeda-Saito M. Structures of the substrate-free and product-bound forms of HmuO, a heme oxygenase from corynebacterium diphtheriae: x-ray crystallography and molecular dynamics investigation. J Biol Chem 2013; 288:34443-58. [PMID: 24106279 DOI: 10.1074/jbc.m113.486936] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe(3+)-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 Å resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe(3+)-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe(3+)-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe(3+)-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit.
Collapse
Affiliation(s)
- Masaki Unno
- From the Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan
| | | | | | | |
Collapse
|
38
|
Preimesberger MR, Wenke BB, Gilevicius L, Pond MP, Lecomte JTJ. Facile heme vinyl posttranslational modification in a hemoglobin. Biochemistry 2013; 52:3478-88. [PMID: 23607716 DOI: 10.1021/bi400289e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron-protoporphyrin IX, or b heme, is utilized as such by a large number of proteins and enzymes. In some cases, notably the c-type cytochromes, this group undergoes a posttranslational covalent attachment to the polypeptide chain, which adjusts the physicochemical properties of the holoprotein. The hemoglobin from the cyanobacterium Synechocystis sp. PCC 6803 (GlbN), contrary to the archetypical hemoglobin, modifies its b heme covalently. The posttranslational modification links His117, a residue that does not coordinate the iron, to the porphyrin 2-vinyl substituent and forms a hybrid b/c heme. The reaction is an electrophilic addition that occurs spontaneously in the ferrous state of the protein. This apparently facile type of heme modification has been observed in only two cyanobacterial GlbNs. To explore the determinants of the reaction, we examined the behavior of Synechocystis GlbN variants containing a histidine at position 79, which is buried against the porphyrin 4-vinyl substituent. We found that L79H/H117A GlbN bound the heme weakly but nevertheless formed a cross-link between His79 Nε2 and the heme 4-Cα. In addition to this linkage, the single variant L79H GlbN also formed the native His117-2-Cα bond yielding an unprecedented bis-alkylated protein adduct. The ability to engineer the doubly modified protein indicates that the histidine-heme modification in GlbN is robust and could be engineered in different local environments. The rarity of the histidine linkage in natural proteins, despite the ease of reaction, is proposed to stem from multiple sources of negative selection.
Collapse
Affiliation(s)
- Matthew R Preimesberger
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | | | | | | | | |
Collapse
|
39
|
Aicart-Ramos C, Valhondo Falcón M, Ortiz de Montellano PR, Rodriguez-Crespo I. Covalent attachment of heme to the protein moiety in an insect E75 nitric oxide sensor. Biochemistry 2012; 51:7403-16. [PMID: 22946928 DOI: 10.1021/bi300848x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have recombinantly expressed and purified the ligand binding domains (LBDs) of four insect nuclear receptors of the E75 family. The Drosophila melanogaster and Bombyx mori nuclear receptors were purified as ferric hemoproteins with Soret maxima at 424 nm, whereas their ferrous forms had a Soret maximum at 425 nm that responds to (•)NO and CO binding. In contrast, the purified LBD of Oncopeltus fasciatus displayed a Soret maximum at 415 nm for the ferric protein that shifted to 425 nm in its ferrous state. Binding of (•)NO to the heme moiety of the D. melanogaster and B. mori E75 LBD resulted in the appearance of a peak at 385 nm, whereas this peak appeared at 416 nm in the case of the O. fasciatus hemoprotein, resembling the behavior displayed by its human homologue, Rev-erbβ. High-performance liquid chromatography analysis revealed that, unlike the D. melanogaster and B. mori counterparts, the heme group of O. fasciatus is covalently attached to the protein through the side chains of two amino acids. The high degree of sequence homology with O. fasciatus E75 led us to clone and express the LBD of Blattella germanica, which established that its spectral properties closely resemble those of O. fasciatus and that it also has the heme group covalently bound to the protein. Hence, (•)NO/CO regulation of the transcriptional activity of these nuclear receptors might be differently controlled among various insect species. In addition, covalent heme binding provides strong evidence that at least some of these nuclear receptors function as diatomic gas sensors rather than heme sensors. Finally, our findings expand the classes of hemoproteins in which the heme group is normally covalently attached to the polypeptide chain.
Collapse
Affiliation(s)
- Clara Aicart-Ramos
- Departamento de Bioquímica y Biología Molecular I, Universidad Complutense, 28040 Madrid, Spain
| | | | | | | |
Collapse
|
40
|
Kamachi T, Nishimi T, Yoshizawa K. A new understanding on how heme metabolism occurs in heme oxygenase: water-assisted oxo mechanism. Dalton Trans 2012; 41:11642-50. [PMID: 22825429 DOI: 10.1039/c2dt30777d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Heme metabolism by heme oxygenase (HO) is investigated with quantum mechanical/molecular mechanical (QM/MM) calculations. A mechanism assisted by water is proposed: (1) an iron-oxo species and a water molecule are generated by the heterolytic cleavage of the O-O bond of an iron-hydroperoxo species in a similar way to P450-mediated reactions, (2) a hydrogen atom abstraction by the iron-oxo species from the generated water molecule and the C-O bond formation between the water molecule and the α-meso carbon take place simultaneously. The water molecule is hydrogen-bonded to the oxo ligand and to the water cluster in the active site of HO. The water cluster can control the position of the generated water molecule to ensure the regioselective oxidation of heme at the α-meso position, at the same time, can facilitate the oxidation by stabilizing a positive charge on the water molecule in the transition state. A key difference between HO and P450 is observed in the structure of the active site; Thr252 in P450 blocks the access of the water molecule to the α-meso position, and can thus suppress the undesired heme oxidation for P450.
Collapse
Affiliation(s)
- Takashi Kamachi
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
| | | | | |
Collapse
|
41
|
Zhou Z, Shen M, Cao C, Liu Q, Yan Z. Opposing Influences of Ruffling and Doming Deformation on the 4-N Cavity Size of Porphyrin Macrocycles: The Role of Heme Deformations Revealed. Chemistry 2012; 18:7675-9. [DOI: 10.1002/chem.201200722] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Indexed: 01/09/2023]
|
42
|
Lai W, Li C, Chen H, Shaik S. Hydrogen-abstraction reactivity patterns from A to Y: the valence bond way. Angew Chem Int Ed Engl 2012; 51:5556-78. [PMID: 22566272 DOI: 10.1002/anie.201108398] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Indexed: 01/06/2023]
Abstract
"Give us insight, not numbers" was Coulson's admonition to theoretical chemists. This Review shows that the valence bond (VB)-model provides insights and some good numbers for one of the fundamental reactions in nature, the hydrogen-atom transfer (HAT). The VB model is applied to over 50 reactions from the simplest H + H(2) process, to P450 hydroxylations and H-transfers among closed-shell molecules; for each system the barriers are estimated from raw data. The model creates a bridge to the Marcus equation and shows that H-atom abstraction by a closed-shell molecule requires a higher barrier owing to the additional promotion energy needed to prepare the abstractor for H-abstraction. Under certain conditions, a closed-shell abstractor can bypass this penalty through a proton-coupled electron transfer (PCET) mechanism. The VB model links the HAT and PCET mechanisms conceptually and shows the consequences that this linking has for H-abstraction reactivity.
Collapse
Affiliation(s)
- Wenzhen Lai
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | | | | | | |
Collapse
|
43
|
Lai W, Li C, Chen H, Shaik S. Wasserstoffatomabstraktion von A bis Y: Reaktionsmuster nach der Valenzstrukturtheorie. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108398] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
44
|
Geoghegan KF, Varghese AH, Feng X, Bessire AJ, Conboy JJ, Ruggeri RB, Ahn K, Spath SN, Filippov SV, Conrad SJ, Carpino PA, Guimarães CRW, Vajdos FF. Deconstruction of Activity-Dependent Covalent Modification of Heme in Human Neutrophil Myeloperoxidase by Multistage Mass Spectrometry (MS4). Biochemistry 2012; 51:2065-77. [DOI: 10.1021/bi201872j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | - Xidong Feng
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | | | - James J. Conboy
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | - Roger B. Ruggeri
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | - Kay Ahn
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | | | | | - Steven J. Conrad
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | | | | | - Felix F. Vajdos
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| |
Collapse
|
45
|
Usharani D, Zazza C, Lai W, Chourasia M, Waskell L, Shaik S. A single-site mutation (F429H) converts the enzyme CYP 2B4 into a heme oxygenase: a QM/MM study. J Am Chem Soc 2012; 134:4053-6. [PMID: 22356576 DOI: 10.1021/ja211905e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The intriguing deactivation of the cytochrome P450 (CYP) 2B4 enzyme induced by mutation of a single residue, Phe429 to His, is explored by quantum mechanical/molecular mechanical calculations of the O-OH bond activation of the (Fe(3+)OOH)(-) intermediate. It is found that the F429H mutant of CYP 2B4 undergoes homolytic instead of heterolytic O-OH bond cleavage. Thus, the mutant acquires the following characteristics of a heme oxygenase enzyme: (a) donation by His429 of an additional NH---S H-bond to the cysteine ligand combined with the presence of the substrate retards the heterolytic cleavage and gives rise to homolytic O-OH cleavage, and (b) the Thr302/water cluster orients nascent OH(•) and ensures efficient meso hydroxylation.
Collapse
Affiliation(s)
- Dandamudi Usharani
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | | | | | | | | | | |
Collapse
|
46
|
Manipulating the proximal triad His–Asn–Arg in human myeloperoxidase. Arch Biochem Biophys 2011; 516:21-8. [DOI: 10.1016/j.abb.2011.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 09/01/2011] [Accepted: 09/13/2011] [Indexed: 12/31/2022]
|
47
|
Wei W, Hu XY, Yan XW, Zhang Q, Cheng M, Ji JX. Direct use of dioxygen as an oxygen source: catalytic oxidative synthesis of amides. Chem Commun (Camb) 2011; 48:305-7. [PMID: 22089138 DOI: 10.1039/c1cc14640h] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The first transition-metal-catalyzed direct oxidative synthesis of amides by using dioxygen as an oxygen source has been developed under mild conditions, in which DBU was used as the key additive. The present methodology, which utilizes dioxygen as an oxidant and oxygen source and cheap copper salts as catalysts, opens up an interesting and attractive avenue for the synthesis of amide functionality.
Collapse
Affiliation(s)
- Wei Wei
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | | | | | | | | | | |
Collapse
|
48
|
Cheng G, Li H, Cao Z, Qiu X, McCormick S, Thannickal VJ, Nauseef WM. Vascular peroxidase-1 is rapidly secreted, circulates in plasma, and supports dityrosine cross-linking reactions. Free Radic Biol Med 2011; 51:1445-53. [PMID: 21798344 PMCID: PMC3439998 DOI: 10.1016/j.freeradbiomed.2011.07.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 06/10/2011] [Accepted: 07/04/2011] [Indexed: 02/07/2023]
Abstract
Members of the peroxidase-cyclooxygenase superfamily catalyze biochemical reactions essential to a broad spectrum of biological processes, including host defense, thyroid hormone biosynthesis, and modification of extracellular matrix, as well as contributing to the pathogenesis of chronic inflammatory diseases. We recently identified a novel member of this family, vascular peroxidase-1 (VPO1), that is highly expressed in the human cardiovascular system. Its biosynthesis and enzymatic properties are largely unknown. Here, we report that VPO1 was rapidly and efficiently secreted into the extracellular space when the gene was stably expressed in human embryonic kidney (HEK) cells. Secreted VPO1 is a monomer with complex N-linked oligosaccharides and exhibits peroxidase activity. Biosynthesis of endogenous VPO1 by cultured human umbilical vein endothelial cells (HUVECs) shares features exhibited by heterologous expression of recombinant VPO1 (rVPO1) in HEK cells. The proinflammatory agents lipopolysaccharide and tumor necrosis factor-α induce expression of VPO1 mRNA and protein in HUVECs. Furthermore, murine and bovine sera and human plasma contain enzymatically active VPO1. rVPO1 exhibits spectral and enzymatic properties characteristic of the peroxidase-cyclooxygenase family, except with regard to its heat stability. rVPO1 catalyzes tyrosyl radical formation and promotes dityrosine cross-linking. Taken together, these data demonstrate that VPO1 is a glycosylated heme peroxidase that is actively secreted into circulating plasma by vascular endothelial cells and shares several features with other members of the peroxidase-cyclooxygenase family, including the catalysis of dityrosine formation.
Collapse
Affiliation(s)
- Guangjie Cheng
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
- Correspondence: Guangjie Cheng, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama School of Medicine, BMR2, Room 410, 1530 3rd Avenue South, Birmingham, AL, 35294 USA; Phone 205-975-8919; Fax 205-975-3043, ; or William M. Nauseef, Inflammation Program, Department of Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa and Veterans Affairs Medical Center, Coralville, Iowa City, IA, USA; Phone 319-335-4278; Fax 319-335-4194;
| | - Hong Li
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Zehong Cao
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Xiaoyun Qiu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Sally McCormick
- Inflammation Program, Department of Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa and Veterans Affairs Medical Center, Coralville, Iowa City, IA, USA
| | - Victor J. Thannickal
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - William M. Nauseef
- Inflammation Program, Department of Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa and Veterans Affairs Medical Center, Coralville, Iowa City, IA, USA
- Correspondence: Guangjie Cheng, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama School of Medicine, BMR2, Room 410, 1530 3rd Avenue South, Birmingham, AL, 35294 USA; Phone 205-975-8919; Fax 205-975-3043, ; or William M. Nauseef, Inflammation Program, Department of Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa and Veterans Affairs Medical Center, Coralville, Iowa City, IA, USA; Phone 319-335-4278; Fax 319-335-4194;
| |
Collapse
|
49
|
Chen H, Lai W, Shaik S. Multireference and multiconfiguration ab initio methods in heme-related systems: what have we learned so far? J Phys Chem B 2011; 115:1727-42. [PMID: 21344948 DOI: 10.1021/jp110016u] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This work reviews the recent applications of ab initio multireference/multiconfiguration (MR/MC) electronic structure methods to heme-related systems, involving tetra-, penta-, and hexa-coordinate species, as well as the high-valent iron-oxo species. The current accuracy of these methods in the various systems is discussed, with special attention to potential sources of systematic errors. Thus, the review summarizes and tries to rationalize the key elements of MR/MC calculations, namely, the choice of the employed active space, especially the so-called double-shell effect that has already been recognized to be important in transition-metal-containing systems, and the impact of these elements on the spin-state energetics of heme species, as well as on the bonding mechanism of small molecules to the heme. It is shown that expansion of the MC wave function into one based on localized orbitals provides a compact and insightful view on some otherwise complex electronic structures. The effects of protein environment on the MR/MC results are summarized for the few available quantum mechanical/molecular mechanical (QM/MM) studies. Comparisons with corresponding DFT results are also made wherever available. Potential future directions are proposed.
Collapse
Affiliation(s)
- Hui Chen
- Institute of Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel.
| | | | | |
Collapse
|
50
|
Miao J, Pan L, Liu N, Xu C, Zhang L. Molecular cloning of CYP4 and GSTpi homologues in the scallop Chlamys farreri and its expression in response to benzo[a]pyrene exposure. Mar Genomics 2011; 4:99-108. [PMID: 21620331 DOI: 10.1016/j.margen.2011.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 02/27/2011] [Accepted: 03/09/2011] [Indexed: 10/18/2022]
Abstract
Cytochrome P450 enzymes (CYP) and glutathione s-transferases (GST) are essential components of cellular detoxification systems. In this study we cloned full-length cDNAs encoding CYP4 and GSTpi homologues from scallop Chlamys farreri. Both sequences were deposited in the GenBank with accession no. ACL80141 for CYP4 and ACL80138 for GSTpi. The sequence called Cf (C. farreri) CYP4 is constituted by an ORF of 1317 bp encoding for a protein of 50.8 kDa. The CfGSTpi is constituted by an ORF of 618 bp encoding for a protein of 23.9 kDa. The comparison of the deduced amino acid sequences with CYP4 and GSTpi from vertebrates showed high conservation of the residues and domains essential to the function of these two enzymes. CfCYP4 and CfGSTpi mRNA expression was detected in digestive gland, gill, mantle, mature female gonad and adductor. We then utilized the real-time PCR to study expression levels of the CfCYP4 and CfGSTpi gene in response to exposure of Benzo[a]pyrene (BaP) (0.01 and 0.2 μg/L) for 10 days. The results showed that during the exposure to BaP, CfCYP4 was significantly decreased in the gill and digestive gland of scallops, and CfGSTpi was increased on day 3 until the end of exposure. The changes in CfGSTpi mRNA levels observed in scallops exposed to BaP indicated that GSTpi could play an important role in the detoxification of BaP.
Collapse
Affiliation(s)
- Jingjing Miao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, China
| | | | | | | | | |
Collapse
|