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Yun D, de Serrano V, Ghiladi RA. Oxidation of bisphenol A (BPA) and related compounds by the multifunctional catalytic globin dehaloperoxidase. J Inorg Biochem 2023; 238:112020. [PMID: 36272837 DOI: 10.1016/j.jinorgbio.2022.112020] [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: 08/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Dehaloperoxidase (DHP) from the marine polychaete Amphitrite ornata is a multifunctional enzyme that possesses peroxidase, peroxygenase, oxidase and oxygenase activities. Herein, we investigated the reactivity of DHP B with bisphenol A (BPA) and related compounds (bisphenol E, bisphenol F, tetrachlorobisphenol A, 2,2'-biphenol, 3,3'-biphenol, 4,4'-biphenol, and 3,3'-dibromo-4,4'-biphenol). As a previously unknown substrate for DHP B, BPA (as a representative substrate) is an endocrine disruptor widely used in polycarbonate and epoxy resins, thus resulting in human exposure. Reactivity studies with these substrates were investigated using high performance liquid chromatography (HPLC), and their corresponding oxidation products were determined by mass spectrometry (GC-MS/ LC-MS). BPA undergoes oxidation in the presence of DHP B and hydrogen peroxide yielding two cleavage products (4-isopropenylphenol and 4-(2-hydroxypropan-2-yl)phenol), and oligomers with varying degrees of oxidation. 18O-labeling studies confirmed that the O-atom incorporated into the products was derived exclusively from water, consistent with substrate oxidation via a peroxidase-based mechanism. The X-ray crystal structures of DHP bound with bisphenol E (1.48 Å), bisphenol F (1.75 Å), 2,2'-biphenol (1.90 Å) and 3,3'-biphenol (1.30 Å) showed substrate binding sites are in the distal pocket of the heme cofactor, similar to other previously studied DHP substrates. Stopped-flow UV-visible spectroscopy was utilized to investigate the mechanistic details and enzyme oxidation states during substrate turnover, and a reaction mechanism is proposed. The data presented here strongly suggest that DHP B can catalyze the oxidation of bisphenols and biphenols, thus providing evidence of how infaunal invertebrates can contribute to the biotransformation of these marine pollutants.
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Affiliation(s)
- Dongju Yun
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States.
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2
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Siriboe MG, Vargas DA, Fasan R. Dehaloperoxidase Catalyzed Stereoselective Synthesis of Cyclopropanol Esters. J Org Chem 2022. [PMID: 36542602 DOI: 10.1021/acs.joc.2c02030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chiral cyclopropanols are highly desirable building blocks for medicinal chemistry, but the stereoselective synthesis of these molecules remains challenging. Here, a novel strategy is reported for the diastereo- and enantioselective synthesis of cyclopropanol derivatives via the biocatalytic asymmetric cyclopropanation of vinyl esters with ethyl diazoacetate (EDA). A dehaloperoxidase enzyme from Amphitrite ornata was repurposed to catalyze this challenging cyclopropanation reaction, and its activity and stereoselectivity were optimized via protein engineering. Using this system, a broad range of electron-deficient vinyl esters were efficiently converted to the desired cyclopropanation products with up to 99.5:0.5 diastereomeric and enantiomeric ratios. In addition, the engineered dehaloperoxidase-based biocatalyst is able to catalyze a variety of other abiological carbene transfer reactions, including N-H/S-H carbene insertion with EDA as well as cyclopropanation with diazoacetonitrile, thus adding to the multifunctionality of this enzyme and defining it as a valuable new scaffold for the development of novel carbene transferases.
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Affiliation(s)
- Mary G Siriboe
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York14627, United States
| | - David A Vargas
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York14627, United States
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3
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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4
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Han C, Zhu W, Ma G, Chen Y, Li X, Wei X, Yu H. Computational insight into biotransformation of halophenols by cytochrome P450: Mechanism and reactivity for epoxidation. CHEMOSPHERE 2022; 286:131708. [PMID: 34352543 DOI: 10.1016/j.chemosphere.2021.131708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/11/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Halophenols (XPs) have aroused great interests due to their high toxicity and low biodegradability. Previous experimental studies have shown that XPs can be catalytically transformed into epoxides and haloquinones by cytochrome P450 enzymes (CYPs). However, these metabolites have never been detected directly. Moreover, the effects of the reaction site and the type and number of halogen substituents on the biotransformation reactivity of halophenols still remain unknown. In this work, we performed density functional theory (DFT) calculations to simulate the CYP-mediated biotransformation of 36 XPs with mono-, di-, and tri-halogen (F, Cl, and Br) substitutions to unravel the mechanism and relevant kinetics of XPs epoxidation. The whole epoxidation process consists of initial rate-determining O-addition and subsequent ring-closure steps. The simulation results show that the epoxidation in low-spin (LS) state is kinetically preferred over that in high-spin (HS) state, and the formation of epoxide metabolite is strongly exothermic. For all XPs, the epoxidation reactivity follows the order of ortho/para O-addition > meta O-addition. Moreover, the O-addition with higher energy barriers roughly corresponds to chlorophenols and fluorophenols with more halogen atoms. Compared with dichlorophenols, the additional ortho-Cl substitution on trichlorophenols can slightly increase the energy barriers of meta O-addition. By contrast, the additional inclusion of an ortho-Cl to monochlorophenols enhances the meta O-addition reactivity of dichlorophenols. Overall, the present work clarifies the biotransformation routes of XPs to produce epoxides, and identifies the key factors affecting the epoxidation reactivity, which are beneficial in understanding comprehensively the metabolic fate and toxicity of XPs.
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Affiliation(s)
- Cenyang Han
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China
| | - Wenyou Zhu
- School of Materials and Chemical Engineering, Xuzhou University of Technology, Xuzhou, Jiangsu, 221018, China
| | - Guangcai Ma
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China.
| | - Yewen Chen
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China
| | - Xinqi Li
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China
| | - Xiaoxuan Wei
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China.
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6
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Tsukakoshi K, Yamagishi Y, Kanazashi M, Nakama K, Oshikawa D, Savory N, Matsugami A, Hayashi F, Lee J, Saito T, Sode K, Khunathai K, Kuno H, Ikebukuro K. G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol. Nucleic Acids Res 2021; 49:6069-6081. [PMID: 34095949 PMCID: PMC8216272 DOI: 10.1093/nar/gkab388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/25/2021] [Accepted: 06/03/2021] [Indexed: 01/07/2023] Open
Abstract
Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol. Using in vitro selection, one G4-forming aptamer that enhanced chemiluminescence from luminol by myoglobin's peroxidase activity was discovered. Through our strategy—in silico maturation, which is a genetic algorithm-aided sequence manipulation method, the enhancing activity of the aptamer was improved by introducing mutations to the aptamer sequences. The best aptamer conserved the parallel G4 property with over 300-times higher luminol chemiluminescence from peroxidase activity more than myoglobin alone at an optimal pH of 5.0. Furthermore, using hemin and hemin-binding aptamers, we demonstrated that the binding property of the G4 aptamers to heme in myoglobin might be necessary to exert the enhancing effect. Structure determination for one of the aptamers revealed a parallel-type G4 structure with propeller-like loops, which might be useful for a rational design of aptasensors utilizing the G4 aptamer-myoglobin pair.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yasuko Yamagishi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Mana Kanazashi
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kenta Nakama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daiki Oshikawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Akimasa Matsugami
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Fumiaki Hayashi
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jinhee Lee
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Taiki Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | | | - Hitoshi Kuno
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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7
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Lin YW. Biodegradation of aromatic pollutants by metalloenzymes: A structural-functional-environmental perspective. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213774] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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8
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Chen SF, Liu XC, Xu JK, Li L, Lang JJ, Wen GB, Lin YW. Conversion of Human Neuroglobin into a Multifunctional Peroxidase by Rational Design. Inorg Chem 2021; 60:2839-2845. [PMID: 33539081 DOI: 10.1021/acs.inorgchem.0c03777] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein design has received much attention in the last decades. With an additional disulfide bond to enhance the protein stability, human A15C neuroglobin (Ngb) is an ideal protein scaffold for heme enzyme design. In this study, we rationally converted A15C Ngb into a multifunctional peroxidase by replacing the heme axial His64 with an Asp residue, where Asp64 and the native Lys67 at the heme distal site were proposed to act as an acid-base catalytic couple for H2O2 activation. Kinetic studies showed that the catalytic efficiency of A15C/H64D Ngb was much higher (∼50-80-fold) than that of native dehaloperoxidase, which even exceeds (∼3-fold) that of the most efficient native horseradish peroxidase. Moreover, the dye-decolorizing peroxidase activity was also comparable to that of some native enzymes. Electron paramagnetic resonance, molecular docking, and isothermal titration calorimetry studies provided valuable information for the substrate-protein interactions. Therefore, this study presents the rational design of an efficient multifunctional peroxidase based on Ngb with potential applications such as in bioremediation for environmental sustainability.
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Affiliation(s)
- Shun-Fa Chen
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Xi-Chun Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Jia-Kun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, China
| | - Jia-Jia Lang
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang 421001, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China Medical School, 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, University of South China Medical School, Hengyang 421001, China
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9
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Malewschik T, de Serrano V, McGuire AH, Ghiladi RA. The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants. Arch Biochem Biophys 2019; 673:108079. [PMID: 31445024 DOI: 10.1016/j.abb.2019.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 01/25/2023]
Abstract
The multifunctional catalytic hemoglobin dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of EPA Priority Pollutants (4-Me-o-cresol, 4-Cl-m-cresol and pentachlorophenol) and EPA Toxic Substances Control Act compounds (o-, m-, p-cresol and 4-Cl-o-cresol). Biochemical assays (HPLC/LC-MS) indicated formation of multiple oxidation products, including the corresponding catechol, 2-methylbenzoquinone (2-MeBq), and oligomers with varying degrees of oxidation and/or dehalogenation. Using 4-Br-o-cresol as a representative substrate, labeling studies with 18O confirmed that the O-atom incorporated into the catechol was derived exclusively from H2O2, whereas the O-atom incorporated into 2-MeBq was from H2O, consistent with this single substrate being oxidized by both peroxygenase and peroxidase mechanisms, respectively. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the peroxygenase mechanism leading to catechol formation, and for Compounds I and ES in the peroxidase mechanism that yields the 2-MeBq product. The X-ray crystal structures of DHP bound with 4-F-o-cresol (1.42 Å; PDB 6ONG), 4-Cl-o-cresol (1.50 Å; PDB 6ONK), 4-Br-o-cresol (1.70 Å; PDB 6ONX), 4-NO2-o-cresol (1.80 Å; PDB 6ONZ), o-cresol (1.60 Å; PDB 6OO1), p-cresol (2.10 Å; PDB 6OO6), 4-Me-o-cresol (1.35 Å; PDB 6ONR) and pentachlorophenol (1.80 Å; PDB 6OO8) revealed substrate binding sites in the distal pocket in close proximity to the heme cofactor, consistent with both oxidation mechanisms. The findings establish cresols as a new class of substrate for DHP, demonstrate that multiple oxidation mechanisms may exist for a given substrate, and provide further evidence that different substituents can serve as functional switches between the different activities performed by dehaloperoxidase. More broadly, the results demonstrate the complexities of marine pollution where both microbial and non-microbial systems may play significant roles in the biotransformations of EPA-classified pollutants, and further reinforces that heterocyclic compounds of anthropogenic origin should be considered as environmental stressors of infaunal organisms.
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Affiliation(s)
- Talita Malewschik
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Ashlyn H McGuire
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA.
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10
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Lin Y. Rational design of heme enzymes for biodegradation of pollutants toward a green future. Biotechnol Appl Biochem 2019; 67:484-494. [DOI: 10.1002/bab.1788] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Ying‐Wu Lin
- School of Chemistry and Chemical Engineering University of South China Hengyang People's Republic of China
- Laboratory of Protein Structure and Function University of South China Hengyang People's Republic of China
- Hunan Key Laboratory for the Design and Application of Actinide Complexes University of South China Hengyang People's Republic of China
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11
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Yin L, Yuan H, Liu C, He B, Gao SQ, Wen GB, Tan X, Lin YW. A Rationally Designed Myoglobin Exhibits a Catalytic Dehalogenation Efficiency More than 1000-Fold That of a Native Dehaloperoxidase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02979] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lu−Lu Yin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Can Liu
- 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 and 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, University of South China, Hengyang 421001, China
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12
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McGuire AH, Carey LM, de Serrano V, Dali S, Ghiladi RA. Peroxidase versus Peroxygenase Activity: Substrate Substituent Effects as Modulators of Enzyme Function in the Multifunctional Catalytic Globin Dehaloperoxidase. Biochemistry 2018; 57:4455-4468. [DOI: 10.1021/acs.biochem.8b00540] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ashlyn H. McGuire
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Leiah M. Carey
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Safaa Dali
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
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13
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Carey LM, Gavenko R, Svistunenko DA, Ghiladi RA. How nature tunes isoenzyme activity in the multifunctional catalytic globin dehaloperoxidase from Amphitrite ornata. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:230-241. [DOI: 10.1016/j.bbapap.2017.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/05/2017] [Accepted: 11/07/2017] [Indexed: 01/29/2023]
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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.
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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
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15
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Design of artificial metalloproteins/metalloenzymes by tuning noncovalent interactions. J Biol Inorg Chem 2017; 23:7-25. [DOI: 10.1007/s00775-017-1506-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/20/2017] [Indexed: 12/12/2022]
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16
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Bindings of NO, CO, and O 2 to multifunctional globin type dehaloperoxidase follow the 'sliding scale rule'. Biochem J 2017; 474:3485-3498. [PMID: 28899945 DOI: 10.1042/bcj20170515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 01/09/2023]
Abstract
Dehaloperoxidase-hemoglobin (DHP), a multifunctional globin protein, not only functions as an oxygen carrier as typical globins such as myoglobin and hemoglobin, but also as a peroxidase, a mono- and dioxygenase, peroxygenase, and an oxidase. Kinetics of DHP binding to NO, CO, and O2 were characterized for wild-type DHP A and B and the H55D and H55V DHP A mutants using stopped-flow methods. All three gaseous ligands bind to DHP significantly more weakly than sperm whale myoglobin (SWMb). Both CO and NO bind to DHP in a one-step process to form a stable six-coordinate complex. Multiple-step NO binding is not observed in DHP, which is similar to observations in SWMb, but in contrast with many heme sensor proteins. The weak affinity of DHP for O2 is mainly due to a fast O2 dissociation rate, in accordance with a longer εN-Fe distance between the heme iron and distal histidine in DHP than that in Mb, and an open-distal pocket that permits ligand escape. Binding affinities in DHP show the same 3-4 orders separation between the pairs NO/CO and CO/O2, consistent with the 'sliding scale rule' hypothesis. Strong gaseous ligand discrimination by DHP is very different from that observed in typical peroxidases, which show poor gaseous ligand selectivity, correlating with a neutral proximal imidazole ligand rather than an imidazolate. The present study provides useful insights into the rationale for DHP to function both as mono-oxygenase and oxidase, and is the first example of a globin peroxidase shown to follow the 'sliding scale rule' hypothesis in gaseous ligand discrimination.
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McCombs NL, Smirnova T, Ghiladi RA. Oxidation of Pyrrole by Dehaloperoxidase-Hemoglobin: Chemoenzymatic Synthesis of Pyrrolin-2-Ones. Catal Sci Technol 2017; 7:3104-3118. [PMID: 29158890 PMCID: PMC5693384 DOI: 10.1039/c7cy00781g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of oxidoreductases as biocatalysts in the syntheses of functionalized, monomeric pyrroles has been a challenge owing to, among a number of factors, undesired polypyrrole formation. Here, we have investigated the ability of dehaloperoxidase (DHP), the coelomic hemoglobin from the terebellid polychaete Amphitrite ornata, to catalyze the H2O2-dependent oxidation of pyrroles as a new class of substrate for this enzyme. Substrate oxidation was observed for all compounds employed (pyrrole, N-methylpyrrole, 2-methylpyrrole, 3-methylpyrrole and 2,5-dimethylpyrrole) under both aerobic and anaerobic conditions. Using pyrrole as a representative substrate, only a single oxidation product, 4-pyrrolin-2-one, was observed, and notably without formation of polypyrrole. Reactivity could be initiated from all three biologically relevant oxidation states for this catalytic globin: ferric, ferrous and oxyferrous. Isotope labeling studies determined that the O-atom incorporated into the 4-pyrrolin-2-one product was derived exclusively from H2O2, indicative of a peroxygenase mechanism. Consistent with this observation, single- and double-mixing stopped-flow UV-visible spectroscopic studies supported Compound I, but not Compounds ES or II, as the catalytically-relevant ferryl intermediate involved in pyrrole oxidation. Electrophilic addition of the ferryl oxygen to pyrrole is proposed as the mechanism of O-atom transfer. The results demonstrate the breadth of chemical reactivity afforded by dehaloperoxidase, and provide further evidence for establishing DHP as a multifunctional globin with practical applications as a biocatalyst.
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Affiliation(s)
- Nikolette L McCombs
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204 USA. Tel: +1 919 513 0680
| | - Tatyana Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204 USA. Tel: +1 919 513 0680
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204 USA. Tel: +1 919 513 0680
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18
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McCombs NL, Moreno-Chicano T, Carey LM, Franzen S, Hough MA, Ghiladi RA. Interaction of Azole-Based Environmental Pollutants with the Coelomic Hemoglobin from Amphitrite ornata: A Molecular Basis for Toxicity. Biochemistry 2017; 56:2294-2303. [PMID: 28387506 DOI: 10.1021/acs.biochem.7b00041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The toxicities of azole pollutants that have widespread agricultural and industrial uses are either poorly understood or unknown, particularly with respect to how infaunal organisms are impacted by this class of persistent organic pollutant. To identify a molecular basis by which azole compounds may have unforeseen toxicity on marine annelids, we examine here their impact on the multifunctional dehaloperoxidase (DHP) hemoglobin from the terebellid polychaete Amphitrite ornata. Ultraviolet-visible and resonance Raman spectroscopic studies showed an increase in the six-coordinate low-spin heme population in DHP isoenzyme B upon binding of imidazole, benzotriazole, and benzimidazole (Kd values of 52, 82, and 110 μM, respectively), suggestive of their direct binding to the heme-Fe. Accordingly, atomic-resolution X-ray crystal structures, supported by computational studies, of the DHP B complexes of benzotriazole (1.14 Å), benzimidazole (1.08 Å), imidazole (1.08 Å), and indazole (1.12 Å) revealed two ligand binding motifs, one with direct ligand binding to the heme-Fe, and another in which the ligand binds in the hydrophobic distal pocket without coordinating the heme-Fe. Taken together, the results demonstrate a new mechanism by which azole pollutants can potentially disrupt hemoglobin function, thereby improving our understanding of their impact on infaunal organisms in marine and aquatic environments.
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Affiliation(s)
- Nikolette L McCombs
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
| | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester, Essex CO4 3SQ, U.K
| | - Leiah M Carey
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
| | - Michael A Hough
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester, Essex CO4 3SQ, U.K
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
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19
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Liao F, He B, Du KJ, Gao SQ, Wen GB, Lin YW. Enhanced Dehaloperoxidase Activity of F43Y Myoglobin with a Novel Thyrosine–Heme Crosslink. CHEM LETT 2016. [DOI: 10.1246/cl.160461] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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21
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Manganese-Substituted Myoglobin: Characterization and Reactivity of an Oxidizing Intermediate towards a Weak C-H Bond. INORGANICS 2015. [DOI: 10.3390/inorganics3020219] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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22
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Zhao J, Moretto J, Le P, Franzen S. Measurement of Internal Substrate Binding in Dehaloperoxidase–Hemoglobin by Competition with the Heme–Fluoride Binding Equilibrium. J Phys Chem B 2015; 119:2827-38. [DOI: 10.1021/jp512996v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jing Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Justin Moretto
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Peter Le
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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23
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Le P, Zhao J, Franzen S. Correlation of Heme Binding Affinity and Enzyme Kinetics of Dehaloperoxidase. Biochemistry 2014; 53:6863-77. [DOI: 10.1021/bi5005975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Le
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jing Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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Wang C, Lovelace LL, Sun S, Dawson JH, Lebioda L. Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity. ACTA ACUST UNITED AC 2014; 70:2833-9. [DOI: 10.1107/s1399004714017787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 08/01/2014] [Indexed: 11/10/2022]
Abstract
Sperm whale myoglobin (Mb) functions as an oxygen-storage protein, but in the ferric state it possesses a weak peroxidase activity which enables it to carry out H2O2-dependent dehalogenation reactions. Hemoglobin/dehaloperoxidase fromAmphitrite ornata(DHP) is a dual-function protein represented by two isoproteins DHP A and DHP B; its peroxidase activity is at least ten times stronger than that of Mb and plays a physiological role. The `DHP A-like' K42Y Mb mutant (K42Y) and the `DHP B-like' K42N mutant (K42N) were engineered in sperm whale Mb to mimic the extended heme environments of DHP A and DHP B, respectively. The peroxidase reaction rates increased ∼3.5-fold and ∼5.5-fold in K42Y and K42NversusMb, respectively. The crystal structures of the K42Y and K42N mutants revealed that the substitutions at position 42 slightly elongate not only the distances between the distal His55 and the heme iron but also the hydrogen-bonding distances between His55 and the Fe-coordinated water. The enhanced peroxidase activity of K42Y and K42N thus might be attributed in part to the weaker binding of the axial water molecule that competes with hydrogen peroxide for the binding site at the heme in the ferric state. This is likely to be the mechanism by which the relationship `longer distal histidine to Fe distance – better peroxidase activity', which was previously proposed for heme proteins by Matsuiet al.(1999) (J. Biol. Chem.274, 2838–2844), works. Furthermore, positive cooperativity in K42N was observed when its dehaloperoxidase activity was measured as a function of the concentration of the substrate trichlorophenol. This serendipitously engineered cooperativity was rationalized by K42N dimerization through the formation of a dityrosine bond induced by excess H2O2.
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Sun S, Sono M, Du J, Dawson JH. Evidence of the Direct Involvement of the Substrate TCP Radical in Functional Switching from Oxyferrous O2 Carrier to Ferric Peroxidase in the Dual-Function Hemoglobin/Dehaloperoxidase from Amphitrite ornata. Biochemistry 2014; 53:4956-69. [DOI: 10.1021/bi5002757] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shengfang Sun
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Masanori Sono
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jing Du
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - John H. Dawson
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- School
of Medicine, University of South Carolina, Columbia, South Carolina 29208, United States
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Zhao J, de Serrano V, Franzen S. A model for the flexibility of the distal histidine in dehaloperoxidase-hemoglobin A based on X-ray crystal structures of the carbon monoxide adduct. Biochemistry 2014; 53:2474-82. [PMID: 24670063 PMCID: PMC4203366 DOI: 10.1021/bi5001905] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Dehaloperoxidase
hemoglobin A (DHP A) is a multifunctional hemoglobin
that appears to have evolved oxidative pathways for the degradation
of xenobiotics as a protective function that complements the oxygen
transport function. DHP A possesses at least two internal binding
sites, one for substrates and one for inhibitors, which include various
halogenated phenols and indoles. Herein, we report the X-ray crystallographic
structure of the carbonmonoxy complex (DHPCO). Unlike other DHP structures
with 6-coordinated heme, the conformation of the distal histidine
(H55) in DHPCO is primarily external or solvent exposed, despite the
fact that the heme Fe is 6-coordinated. As observed generally in globins,
DHP exhibits two distal histidine conformations (one internal and
one external). In previous structural studies, we have shown that
the distribution of H55 conformations is weighted strongly toward
the external position when the DHP heme Fe is 5-coordinated. The large
population of the external conformation of the distal histidine observed
in DHPCO crystals at pH 6.0 indicates that some structural factor
in DHP must account for the difference from other globins, which exhibit
a significant external conformation only when pH < 4.5. While the
original hypothesis suggested that interaction with a heme-Fe-bound
ligand was the determinant of H55 conformation, the current study
forces a refinement of that hypothesis. The external or open conformation
of H55 is observed to have interactions with two propionate groups
in heme, at distances of 3.82 and 2.73 Å, respectively. A relatively
weak hydrogen bonding interaction between H55 and CO, combined with
strong interactions with heme propionate (position 6), is hypothesized
to strengthen the external conformation of H55. Density function theory
(DFT) calculations were conducted to test whether there is a weaker
hydrogen bond interaction between H55 and heme bonded CO or O2. Molecular dynamics simulations were conducted to examine
how the tautomeric forms of H55 affect the dynamic motions of the
distal histidine that govern the switching between open and closed
conformations. The calculations support the modified hypothesis suggesting
a competition between the strength of interactions with heme ligand
and the heme propionates as the factors that determine the conformation
of the distal histidine.
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Affiliation(s)
- Junjie Zhao
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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27
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Lin Y, Wang J, Lu Y. Functional tuning and expanding of myoglobin by rational protein design. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5063-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sun S, Sono M, Wang C, Du J, Lebioda L, Dawson JH. Influence of heme environment structure on dioxygen affinity for the dual function Amphitrite ornata hemoglobin/dehaloperoxidase. Insights into the evolutional structure-function adaptations. Arch Biochem Biophys 2014; 545:108-15. [PMID: 24440609 DOI: 10.1016/j.abb.2014.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/08/2014] [Accepted: 01/10/2014] [Indexed: 11/28/2022]
Abstract
Sea worm, Amphitrite ornata, has evolved its globin (an O(2) carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whale myoglobin (SW Mb) revealed some structural factors that influence the dehaloperoxidase activities (significantly lower for Mb) of both proteins. Using an isocyanide/O(2) partition constant measurement method in this study, we have examined the effects of these structural factors on the O(2) equilibrium constants (KO2) of DHP, SW Mb, and their mutants. A clear trend of decreasing O(2) affinity and increasing catalytic activity along with the increase in the distal His N(ε)-heme iron distance is observed. An H93K/T95H Mb double mutant mimicking the DHP proximal His positioning exhibited markedly enhanced O(2) affinity, confirming the essential effect of proximal His rotation on the globin function of DHP. For DHP, the L100F, T56G and M86E variants showed the effects of distal volume, distal His flexibility and proximal electronic push, respectively, on the O(2) affinity. This study provides insights into how DHP has evolved its heme environment to gain significantly enhanced peroxidase capability without compromising its primary function as an O(2) carrier.
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Affiliation(s)
- Shengfang Sun
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Masanori Sono
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States.
| | - Chunxue Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Jing Du
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Lukasz Lebioda
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States.
| | - John H Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States; School of Medicine, University of South Carolina, United States.
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The role of T56 in controlling the flexibility of the distal histidine in dehaloperoxidase-hemoglobin from Amphitrite ornata. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2020-9. [DOI: 10.1016/j.bbapap.2013.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 06/07/2013] [Accepted: 06/10/2013] [Indexed: 11/23/2022]
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30
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Wang C, Lovelace LL, Sun S, Dawson JH, Lebioda L. Complexes of Dual-Function Hemoglobin/Dehaloperoxidase with Substrate 2,4,6-Trichlorophenol Are Inhibitory and Indicate Binding of Halophenol to Compound I. Biochemistry 2013; 52:6203-10. [DOI: 10.1021/bi400627w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chunxue Wang
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Leslie L. Lovelace
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Shengfang Sun
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - John H. Dawson
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- School
of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Lukasz Lebioda
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- Center
for Colon Cancer Research, University of South Carolina, Columbia, South Carolina 29209, United States
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31
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Peroxidase activity of a myoglobin mutant with three distal histidines forming a metal-binding site: Implications for the cross-reactivity of cytochrome c oxidase. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Watt WB. Specific-gene studies of evolutionary mechanisms in an age of genome-wide surveying. Ann N Y Acad Sci 2013; 1289:1-17. [PMID: 23679204 DOI: 10.1111/nyas.12139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The molecular tools of genomics have great power to reveal patterns of genetic difference within or among species, but must be complemented by the mechanistic study of the genetic variants found if these variants' evolutionary meaning is to be well understood. Central to this purpose is knowledge of the organisms' genotype-phenotype-environment interactions, which embody biological adaptation and constraint and thus drive natural selection. The history of this approach is briefly reviewed. Strategies embracing the complementarity of genomics and specific-gene studies in evolution are considered. Implementation of these strategies, and examples showing their feasibility and power, are discussed. Initial generalizations emphasize: (1) reproducibility of adaptive mechanisms; (2) evolutionary co-importance of variation in protein sequences and expression; (3) refinement of rudimentary molecular functions as an origin of evolutionary innovations; (4) identification of specific-gene mechanisms as underpinnings of genomic or quantitative genetic variation; and (5) multiple forms of adaptive or constraining epistasis among genes. Progress along these lines will advance understanding of evolution and support its use in addressing urgent medical and environmental applications.
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Affiliation(s)
- Ward B Watt
- Department of Biology, Stanford University, Stanford, California and Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA.
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Plummer A, Thompson MK, Franzen S. Role of Polarity of the Distal Pocket in the Control of Inhibitor Binding in Dehaloperoxidase-Hemoglobin. Biochemistry 2013; 52:2218-27. [DOI: 10.1021/bi301509r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ashlee Plummer
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - Matthew K. Thompson
- Department
of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee
37232, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
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34
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Sumithran S, Sono M, Raner GM, Dawson JH. Single turnover studies of oxidative halophenol dehalogenation by horseradish peroxidase reveal a mechanism involving two consecutive one electron steps: Toward a functional halophenol bioremediation catalyst. J Inorg Biochem 2012; 117:316-21. [DOI: 10.1016/j.jinorgbio.2012.09.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 09/18/2012] [Accepted: 09/18/2012] [Indexed: 10/27/2022]
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35
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Huang X, Wang C, Celeste LR, Lovelace LL, Sun S, Dawson JH, Lebioda L. Complex of myoglobin with phenol bound in a proximal cavity. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1465-71. [PMID: 23192025 PMCID: PMC3509966 DOI: 10.1107/s1744309112045514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/03/2012] [Indexed: 11/10/2022]
Abstract
Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with Cβ and Cγ of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It appears that the ligand enters the proximal cavity through a gate formed by the flexible loops 79-86 and 93-103. TCP and 4-IP do not bind to Mb in this manner under similar conditions; however, it appears to be likely that dimethyl sulfoxide (DMSO), which was used at a concentration of 0.8 M to facilitate 4-IP dissolution, binds in the phenol/Xe1 binding site. In this structure, a water molecule coordinated to the heme iron was replaced by an oxygen molecule, reflecting the reduction of the heme. Crystals of Mb and G65T Mb soaked for 5-10 min did not show bound phenol. Kinetic studies of TCP dechlorination showed that phenol has a dual effect: it acts as a competitive inhibitor that is likely to interfere with TCP binding at the heme edge and as a weak activator, likely through binding in the proximal cavity. The lack of phenol bound at the heme edge in the crystal structures suggests that its inhibitory binding only takes place when the heme is activated by hydrogen peroxide.
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Affiliation(s)
- Xiao Huang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - Chunxue Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - Lesa R. Celeste
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - Leslie L. Lovelace
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - Shenfang Sun
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - John H. Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
- School of Medicine, University of South Carolina, Columbia, SC 20208, USA
| | - Lukasz Lebioda
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
- South Carolina Colon Cancer Center, University of South Carolina, Columbia, SC 29210, USA
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