1
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Chatterjee S, Nochebuena J, Cisneros GA. Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity. J Am Chem Soc 2024; 146:13247-13257. [PMID: 38701006 DOI: 10.1021/jacs.4c01100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A previous report indicated that peroxidases can have an enhancement in initial enzymatic activity in an aqueous solution of 0.26 M 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) at neutral pH. However, the atomistic details remain elusive. In the enzymatic landscape of HRP, compound II (Cpd II) plays a key role and involves a histidine (H42) residue. Cpd II exists as oxoferryl (2a) or hydroxoferryl (2b(FeIV)) forms, where 2a is the predominantly observed form in experimental studies. Intriguingly, the ferric 2b(FeIII) form seen in synthetic complexes has not been observed in HRP. Here, we have investigated the structure and dynamics of HRP in pure water and aqueous [EMIm][EtSO4] (0.26 M), as well as the reaction mechanism of 2a to 2b conversion using polarizable molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations. When HRP is solvated in aq [EMIm][EtSO4], the catalytic water displaces, and H42 directly orients over the ferryl moiety, allowing a direct proton transfer (PT) with a significant energy barrier reduction. Conversely, in neat water, the reaction of 2a to 2b follows the previously reported mechanism. We further investigated the deprotonated form of H42. Analysis of the electric fields at the active site indicates that the aq [EMIm][EtSO4] medium facilitates the reaction by providing a more favorable environment compared with the system solvated in neat water. Overall, the atomic level supports the previous experimental observations and underscores the importance of favorable electric fields in the active site to promote catalysis.
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Affiliation(s)
- Shubham Chatterjee
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
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2
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Zhang X, Liu Y. Computational Insights into the Catalysis of the pH Dependence of Bromite Decomposition Catalyzed by Chlorite Dismutase from Dechloromonas aromatica ( DaCld). Inorg Chem 2024; 63:6776-6786. [PMID: 38572830 DOI: 10.1021/acs.inorgchem.4c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The heme-containing chlorite dismutases catalyze the rapid and efficient decomposition of chlorite (ClO2-) to yield Cl- and O2, and the catalytic efficiency of chlorite dismutase from Dechloromonas aromatica (DaCld) in catalyzing the decomposition of bromite (BrO2-) was dependent on pH, which was supposed to be caused by the conversion of active Cpd I to the inactive Cpd II by proton-coupled electron transfer (PCET) from the pocket Tyr118 to the propionate side chain of heme at high pH. However, the direct evidence of PCET and how the pH affects the efficiency of DaCld, as well as whether Cpd II is really inactive, are still poorly understood. Here, on the basis of the high-resolution crystal structures, the computational models in both acidic (pH 5.0) and alkaline (pH 9.0) environments were constructed, and a series of quantum mechanical/molecular mechanical calculations were performed. On the basis of our calculation results, the O-Br bond cleavage of BrO2- always follows the homolytic mode to generate Cpd II rather than Cpd I. It is different from the O-O cleavage of O2/H2O2 or peracetic acid catalyzed by the other heme-containing enzymes. Thus, in the subsequent O-O rebound reaction, it is the Fe(IV)═O in Cpd II that combines with the O-Br radical. Because the porphyrin ring in Cpd II does not bear an unpaired electron, the previously suggested PCET from Tyr118 to the propionate side chain of heme was not theoretically recognized in an alkaline environment. In addition, the O-O rebound step in an alkaline solution corresponds to an energy barrier that is larger than that in an acidic environment, which can well explain the pH dependence of the activity of DaCld. In addition, the protonation state of the propionic acid side chains of heme and the surrounding hydrogen bond networks were calculated to have a significant impact on the barriers of the O-O rebound step, which is mainly achieved by affecting the reactivity of the Fe(IV)═O group in Cpd II. In an acidic environment, the relatively weaker coordination of the O2 atom to Fe leads to its higher reactivity toward the O-O rebound reaction. These observations may provide useful information for understanding the catalysis of chlorite dismutases.
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Affiliation(s)
- Xianghui Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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3
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Pandey AK, Trivedi V. Role Transformation of HSPA8 to Heme-peroxidase After Binding Hemin to Catalyze Heme Polymerization. Protein J 2024; 43:48-61. [PMID: 38066289 DOI: 10.1007/s10930-023-10167-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2023] [Indexed: 02/29/2024]
Abstract
Hemin, a byproduct of hemoglobin degradation, inflicts oxidative insult to cells. Following its accumulation, several proteins are recruited for heme detoxification with heme oxygenase playing the key role. Chaperones play a protective role primarily by preventing protein degradation and unfolding. They also are known to have miscellaneous secondary roles during similar situations. To discover a secondary role of chaperones during heme stress we studied the role of the chaperone HSPA8 in the detoxification of hemin. In-silico studies indicated that HSPA8 has a well-defined biophoric environment to bind hemin. Through optical difference spectroscopy, we found that HSPA8 binds hemin through its N-terminal domain with a Kd value of 5.9 ± 0.04 µM and transforms into a hemoprotein. The hemoprotein was tested for exhibiting peroxidase activity using guaiacol as substrate. The complex formed reacts with H2O2 and exhibits classical peroxidase activity with an ability to oxidize aromatic and halide substrates. HSPA8 is dose-dependently catalyzing heme polymerization through its N-terminal domain. The IR results reveal that the polymer formed exhibits structural similarities to β-hematin suggesting its covalent nature. The polymerization mechanism was tested through optical spectroscopy, spin-trap, and activity inhibition experiments. The results suggest that the polymerization occurs through a peroxidase-H2O2 system involving a one-electron transfer mechanism, and the formation of free radical and radical-radical interaction. It highlights a possible role of the HSPA8-hemin complex in exhibiting cytoprotective function during pathological conditions like malaria, sickle cell disease, etc.
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Affiliation(s)
- Alok Kumar Pandey
- Malaria Research Group, Department of Bioscience and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, Assam, 781039, India
| | - Vishal Trivedi
- Malaria Research Group, Department of Bioscience and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, Assam, 781039, India.
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4
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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.
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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
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5
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Wang J, Yang J, Huang W, Huang W, Jia R. A mutant R70V/E166A of short manganese peroxidase showing Mn 2+-independent dye decolorization. Appl Microbiol Biotechnol 2023; 107:2303-2319. [PMID: 36843195 DOI: 10.1007/s00253-023-12438-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/28/2023]
Abstract
Il-MnP1, a short-type manganese peroxidase from Irpex lacteus F17, can oxidize some substrates in the absence of Mn2+, but the catalysis was much lower than in the presence of Mn2+. Here, we report a mutant R70V/E166A of Il-MnP1 with some unique properties, which possessed clearly higher catalysis for the decolorization of anthraquinone and azo dyes in the absence of Mn2+ than that of Il-MnP1. Importantly, the optimum pH of R70V/E166A for decolorization of anthraquinone dyes (Reactive Blue 19, RB19) was 6.5, and the mutant achieved high decolorization activities in the range of pH 4.0-7.0, whereas Il-MnP1 only showed decolorization for RB19 at pH 3.5-4.0. In addition, the optimum H2O2 concentration of R70V/E166A for RB19 decolorization was eight times that of Il-MnP1 and the H2O2 stability has improved 1.4 times compared with Il-MnP1. Furthermore, Mn2+ competitively inhibited the oxidation of RB19 by R70V/E166A, explaining the higher catalytic activity of the mutant R70V/E166A in the absence of Mn2+. Molecular docking results suggested that RB19 binds to the distal side of the heme plane in mutant R70V/E166A, which extended from the heme δ-side to the heme γ-side, and close to the mutated residues of R70V and E166A, whereas RB19 could not access the heme pocket of Il-MnP1 due to the steric hindrance of the side-chain group of Arg 70. Thus, this study constructed a useful mutant R70V/E166A and analyzed its higher Mn2+-independent activity, which is very important for better understanding the Mn2+-independent catalytic mechanism for short manganese peroxidases. KEY POINTS: • The mutant R70V/E166A of atypical MnP1 of I. lacteus F17 shows unique catalytic properties. • At pH 6.5, the R70V/E166A had a strong ability to decolorize anthraquinone dyes in the absence of Mn2+. • The binding sites of Reactive Blue 19 in mutant R70V/E166A were elucidated.
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Affiliation(s)
- Junli Wang
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Jun Yang
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Wenhan Huang
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Wenting Huang
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Rong Jia
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601.
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China.
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6
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Zhou W, Lai R, Cheng Y, Bao Y, Miao W, Cao X, Jia G, Li G, Li C. Insights into How NH 4+ Ions Enhance the Activity of Dimeric G-Quadruplex/Hemin DNAzyme. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Wenqin Zhou
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Rui Lai
- State Key Laboratory of Molecular Reaction Dynamics, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Cheng
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Bao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Wenhui Miao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Xupeng Cao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Can Li
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
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7
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Zhang X, Qiu D, Chen J, Zhang Y, Wang J, Chen D, Liu Y, Cheng M, Monchaud D, Mergny JL, Ju H, Zhou J. Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase. J Am Chem Soc 2023; 145:4517-4526. [PMID: 36795970 DOI: 10.1021/jacs.2c11318] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Chimeric peptide-DNAzyme (CPDzyme) is a novel artificial peroxidase that relies on the covalent assembly of DNA, peptides, and an enzyme cofactor in a single scaffold. An accurate control of the assembly of these different partners allows for the design of the CPDzyme prototype G4-Hemin-KHRRH, found to be >2000-fold more active (in terms of conversion number kcat) than the corresponding but non-covalent G4/Hemin complex and, more importantly, >1.5-fold more active than the corresponding native peroxidase (horseradish peroxidase) when considering a single catalytic center. This unique performance originates in a series of gradual improvements, thanks to an accurate selection and arrangement of the different components of the CPDzyme, in order to benefit from synergistic interactions between them. The optimized prototype G4-Hemin-KHRRH is efficient and robust as it can be used under a wide range of non-physiologically relevant conditions [organic solvents, high temperature (95 °C), and in a wide range of pH (from 2 to 10)], thus compensating for the shortcomings of the natural enzymes. Our approach thus opens broad prospects for the design of ever more efficient artificial enzymes.
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Affiliation(s)
- Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiawei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Desheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
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8
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Abedanzadeh S, Karimi B, Moosavi-Movahedi Z, Pourshiani O, Badiei A, Moosavi-Movahedi AA. Artificial metalloenzyme with peroxidase-like activity based on periodic mesoporous organosilica with ionic-liquid framework. MICROPOROUS AND MESOPOROUS MATERIALS 2023; 348:112384. [DOI: 10.1016/j.micromeso.2022.112384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
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9
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Bissaro B, Kodama S, Nishiuchi T, Díaz-Rovira AM, Hage H, Ribeaucourt D, Haon M, Grisel S, Simaan AJ, Beisson F, Forget SM, Brumer H, Rosso MN, Guallar V, O’Connell R, Lafond M, Kubo Y, Berrin JG. Tandem metalloenzymes gate plant cell entry by pathogenic fungi. SCIENCE ADVANCES 2022; 8:eade9982. [PMID: 36542709 PMCID: PMC9770985 DOI: 10.1126/sciadv.ade9982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Global food security is endangered by fungal phytopathogens causing devastating crop production losses. Many of these pathogens use specialized appressoria cells to puncture plant cuticles. Here, we unveil a pair of alcohol oxidase-peroxidase enzymes to be essential for pathogenicity. Using Colletotrichum orbiculare, we show that the enzyme pair is cosecreted by the fungus early during plant penetration and that single and double mutants have impaired penetration ability. Molecular modeling, biochemical, and biophysical approaches revealed a fine-tuned interplay between these metalloenzymes, which oxidize plant cuticular long-chain alcohols into aldehydes. We show that the enzyme pair is involved in transcriptional regulation of genes necessary for host penetration. The identification of these infection-specific metalloenzymes opens new avenues on the role of wax-derived compounds and the design of oxidase-specific inhibitors for crop protection.
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Affiliation(s)
- Bastien Bissaro
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Sayo Kodama
- Faculty of Agriculture, Setsunan University, 573-0101 Osaka, Japan
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, 920-0934 Kanazawa, Japan
| | | | - Hayat Hage
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - David Ribeaucourt
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
- V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France
| | - Mireille Haon
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Sacha Grisel
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - A. Jalila Simaan
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Fred Beisson
- CEA, CNRS, Aix Marseille Université, Institut de Biosciences et Biotechnologies d’Aix-Marseille (UMR7265), CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Stephanie M. Forget
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Marie-Noëlle Rosso
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Victor Guallar
- Barcelona Supercomputing Center, Plaça Eusebi Güell, 1-3, E-08034 Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Richard O’Connell
- INRAE, UMR BIOGER, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Mickaël Lafond
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Yasuyuki Kubo
- Faculty of Agriculture, Setsunan University, 573-0101 Osaka, Japan
- Corresponding author. (Y.K.); (J.-G.B.)
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
- Corresponding author. (Y.K.); (J.-G.B.)
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10
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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11
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Amanullah S, Saha P, Dey A. Recent developments in the synthesis of bio-inspired iron porphyrins for small molecule activation. Chem Commun (Camb) 2022; 58:5808-5828. [PMID: 35474535 DOI: 10.1039/d2cc00430e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nature utilizes a diverse set of tetrapyrrole-based macrocycles (referred to as porphyrinoids) for catalyzing various biological processes. Investigation of the differences in electronic structure and reactivity in these reactions have revealed striking differences that lead to diverse reactivity from, apparently, similar looking active sites. Therefore, the role of the different heme cofactors as well as the distal superstructure in the proteins is important to understand. This article summarizes the role of a few synthetic metallo-porphyrinoids towards catalyzing several small molecule activation reactions, such as the ORR, NiRR, CO2RR, etc. The major focus of the article is to enlighten the synthetic routes to the well-decorated active-site mimic in a tailor-made fashion pursuing a retrosynthetic approach, learning from the biosynthesis of the cofactors. Techniques and the role of the second-sphere residues on the reaction rate, selectivity, etc. are incorporated emulating the basic amino acid residues fencing the active sites. These bioinspired mimics play an important role towards understanding the role of the prosthetic groups as well as the basic residues towards any reaction occurring in Nature.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB 700032, India.
| | - Paramita Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB 700032, India.
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB 700032, India.
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12
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Wang T, Bi X, Wang L, Liu M, Yu WW, Zhu Z, Sui N. Biomimetic design of graphdiyne supported hemin for enhanced peroxidase-like activity. J Colloid Interface Sci 2021; 607:470-478. [PMID: 34509729 DOI: 10.1016/j.jcis.2021.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 02/07/2023]
Abstract
Effective electronic interactions between molecular catalysts and supports are critical for heterogeneous enzyme mimics, yet they are frequently neglected in most catalyst designs. Taking the enzyme mimics of hemin immobilized on graphdiyne (Hemin-GDY) as an example, we explicate for the first time the underlying role of GDY as a co-catalyst. Based on the robust conjugation between GDY and hemin, the delocalized π-electrons in GDY act as a ligand for Fe ions so that the orbital interactions including electron transport from GDY → Fe can induce the formation of an electron-rich Fe center and an electron-deficient π-electron conjugated system. This mechanism was validated by electron paramagnetic resonance (EPR), Raman spectroscopy, and DFT calculations. Moreover, both EPR spetra and Lineweaver-Burk plots revealed that Hemin-GDY could efficiently catalyze the decomposition of hydrogen peroxide (H2O2) to produce hydroxyl radical (•OH) and superoxide anion (O2•-) by a ping-pong type catalytic mechanism, and particularly, the catalytic activity was increased by 2.3-fold comparing to that of hemin immobilized on graphene (Hemin-GR). In addition, Hemin-GDY with the exceptional activity and stability was demonstrated for efficient catalytic degradation of organic pollutants under acidic conditions. Collectively, this work provides a theoretical basis for the design of GDY supported catalysts and renders great promises of the GDY based enzyme mimics.
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Affiliation(s)
- Tao Wang
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China
| | - Xuelong Bi
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China; College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China
| | - Lina Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Manhong Liu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China
| | - William W Yu
- Department of Chemistry and Physics, Louisiana State University Shreveport, Shreveport, LA 71115, USA
| | - Zhiling Zhu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Ning Sui
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
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13
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Lučić M, Wilson MT, Svistunenko DA, Owen RL, Hough MA, Worrall JAR. Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of Fe IV = O formation in bacterial dye-decolorizing peroxidases. J Biol Inorg Chem 2021; 26:743-761. [PMID: 34477969 PMCID: PMC8463360 DOI: 10.1007/s00775-021-01896-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (FeIV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, Oxfordshire, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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14
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Pandey VP, Tyagi A, Ali S, Yadav K, Yadav A, Shasany AK, Dwivedi UN. Recombinant Expression and Characterization of Lemon (Citrus limon) Peroxidase. Protein Pept Lett 2021; 28:469-479. [PMID: 32981494 DOI: 10.2174/0929866527666200925114054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Class III plant peroxidases play important role in a number of physiological processes in plants such as lignin biosynthesis, suberization, cell wall biosynthesis, reactive oxygen species metabolism and plant defense against pathogens. Peroxidases are also of significance in several industrial applications. In view of this, the production and identification of novel peroxidases having resistance towards temperature, pH, salts is desirable. OBJECTIVE The objective of the present work was to clone and characterize a novel plant peroxidase suitable for industrial application. METHODS A full length cDNA clone of lemon peroxidase was isolated using PCR and RACE approaches, characterized and heterologously expressed in Escherichia coli using standard protocols. The expressed peroxidase was purified using Ni-NTA agarose column and biochemically characterized using standard protocols. The peroxidase was also in-silico characterized at nucleotide as well as protein levels using standard protocols. RESULTS A full length cDNA clone of lemon peroxidase was isolated and expressed heterologously in E. coli. The expressed recombinant lemon peroxidase (LPRX) was activated by in-vitro refolding and purified. The purified LPRX exhibited pH and temperature optima of pH 7.0 and 50°C, respectively. The LPRX was found to be activated by metal ions (Na+, Ca2+, Mg2+ and Mn2+) at lower concentration. The expressional analysis of the transcripts suggested involvement of lemon peroxidase in plant defense. The lemon peroxidase was in silico modelled and docked with the substrates guaiacol, and pyrogallol and shown the favourability of pyrogallol over guaiacol, which is in agreement with the in-vitro findings. The protein function annotation analyses suggested the involvement of lemon peroxidase in the phenylpropanoid biosynthesis pathway and plant defense mechanisms. CONCLUSION Based on the biochemical characterization, the purified peroxidase was found to be resistant towards the salts and thus, might be a good candidate for industrial exploitation. The in-silico protein function annotation and transcript analyses highlighted the possible involvement of the lemon peroxidase in plant defense response.
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Affiliation(s)
- Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow-226007, India
| | - Apoorvi Tyagi
- Department of Biochemistry, University of Lucknow, Lucknow-226007, India
| | - Shagoofa Ali
- Department of Biochemistry, University of Lucknow, Lucknow-226007, India
| | - Kusum Yadav
- Department of Biochemistry, University of Lucknow, Lucknow-226007, India
| | - Anurag Yadav
- College of Basic Sciences & Humanities, Sardarkrushinagar Agricultural University Dantiwada, District-Banaskantha, Gujarat, India
| | - Ajit K Shasany
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow-226015, India
| | - Upendra N Dwivedi
- Department of Biochemistry, University of Lucknow, Lucknow-226007, India
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15
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Rai A, Klare JP, Reinke PYA, Englmaier F, Fohrer J, Fedorov R, Taft MH, Chizhov I, Curth U, Plettenburg O, Manstein DJ. Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum. Int J Mol Sci 2021; 22:ijms22126265. [PMID: 34200865 PMCID: PMC8230527 DOI: 10.3390/ijms22126265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 05/29/2021] [Accepted: 06/05/2021] [Indexed: 12/23/2022] Open
Abstract
A novel cytoplasmic dye-decolorizing peroxidase from Dictyostelium discoideum was investigated that oxidizes anthraquinone dyes, lignin model compounds, and general peroxidase substrates such as ABTS efficiently. Unlike related enzymes, an aspartate residue replaces the first glycine of the conserved GXXDG motif in Dictyostelium DyPA. In solution, Dictyostelium DyPA exists as a stable dimer with the side chain of Asp146 contributing to the stabilization of the dimer interface by extending the hydrogen bond network connecting two monomers. To gain mechanistic insights, we solved the Dictyostelium DyPA structures in the absence of substrate as well as in the presence of potassium cyanide and veratryl alcohol to 1.7, 1.85, and 1.6 Å resolution, respectively. The active site of Dictyostelium DyPA has a hexa-coordinated heme iron with a histidine residue at the proximal axial position and either an activated oxygen or CN- molecule at the distal axial position. Asp149 is in an optimal conformation to accept a proton from H2O2 during the formation of compound I. Two potential distal solvent channels and a conserved shallow pocket leading to the heme molecule were found in Dictyostelium DyPA. Further, we identified two substrate-binding pockets per monomer in Dictyostelium DyPA at the dimer interface. Long-range electron transfer pathways associated with a hydrogen-bonding network that connects the substrate-binding sites with the heme moiety are described.
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Affiliation(s)
- Amrita Rai
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Johann P. Klare
- Department of Physics, University of Osnabrueck, Barbarastrasse 7, D-49076 Osnabrück, Germany;
| | - Patrick Y. A. Reinke
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
- Center for Free-Electron Laser Science, German Electron Synchrotron (DESY), Notkestr. 85, D-22607 Hamburg, Germany
| | - Felix Englmaier
- Institute of Medicinal Chemistry, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany; (F.E.); (O.P.)
- Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1b, D-30167 Hannover, Germany;
| | - Jörg Fohrer
- Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1b, D-30167 Hannover, Germany;
- NMR Department of the Department of Chemistry, Technical University Darmstadt, Clemens Schöpf Institute for Organic Chemistry and Biochemistry, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Roman Fedorov
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
| | - Manuel H. Taft
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany; (F.E.); (O.P.)
- Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1b, D-30167 Hannover, Germany;
| | - Dietmar J. Manstein
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
- RESiST, Cluster of Excellence 2155, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
- Correspondence: ; Tel.: +49-511-5323700
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16
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Guo WJ, Xu JK, Liu JJ, Lang JJ, Gao SQ, Wen GB, Lin YW. Biotransformation of Lignin by an Artificial Heme Enzyme Designed in Myoglobin With a Covalently Linked Heme Group. Front Bioeng Biotechnol 2021; 9:664388. [PMID: 34136471 PMCID: PMC8201792 DOI: 10.3389/fbioe.2021.664388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
The conversion of Kraft lignin in plant biomass into renewable chemicals, aiming at harvesting aromatic compounds, is a challenge process in biorefinery. Comparing to the traditional chemical methods, enzymatic catalysis provides a gentle way for the degradation of lignin. Alternative to natural enzymes, artificial enzymes have been received much attention for potential applications. We herein achieved the biodegradation of Kraft lignin using an artificial peroxidase rationally designed in myoglobin (Mb), F43Y/T67R Mb, with a covalently linked heme cofactor. The artificial enzyme of F43Y/T67R Mb has improved catalytic efficiencies at mild acidic pH for phenolic and aromatic amine substrates, including Kraft lignin and the model lignin dimer guaiacylglycerol-β-guaiacyl ether (GGE). We proposed a possible catalytic mechanism for the biotransformation of lignin catalyzed by the enzyme, based on the results of kinetic UV-Vis studies and UPLC-ESI-MS analysis, as well as molecular modeling studies. With the advantages of F43Y/T67R Mb, such as the high-yield by overexpression in E. coli cells and the enhanced protein stability, this study suggests that the artificial enzyme has potential applications in the biodegradation of lignin to provide sustainable bioresource.
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Affiliation(s)
- Wen-Jie Guo
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Jia-Kun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao, China
| | - Jing-Jing Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Jia-Jia Lang
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
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17
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Markel U, Sauer DF, Wittwer M, Schiffels J, Cui H, Davari MD, Kröckert KW, Herres-Pawlis S, Okuda J, Schwaneberg U. Chemogenetic Evolution of a Peroxidase-like Artificial Metalloenzyme. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Daniel F. Sauer
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Malte Wittwer
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Johannes Schiffels
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Konstantin W. Kröckert
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Sonja Herres-Pawlis
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI—Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
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18
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Uchida T, Omura I, Umetsu S, Ishimori K. Radical transfer but not heme distal residues is essential for pH dependence of dye-decolorizing activity of peroxidase from Vibrio cholerae. J Inorg Biochem 2021; 219:111422. [PMID: 33756393 DOI: 10.1016/j.jinorgbio.2021.111422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 02/02/2021] [Accepted: 03/07/2021] [Indexed: 02/08/2023]
Abstract
Dye-decolorizing peroxidase (DyP) is a heme-containing enzyme that catalyzes the degradation of anthraquinone dyes. A main feature of DyP is the acidic optimal pH for dye-decolorizing activity. In this study, we constructed several mutant DyP enzymes from Vibrio cholerae (VcDyP), with a view to identifying the decisive factor of the low pH preference of DyP. Initially, distal Asp144, a conserved residue, was replaced with His, which led to significant loss of dye-decolorizing activity. Introduction of His into a position slightly distant from heme resulted in restoration of activity but no shift in optimal pH, indicating that distal residues do not contribute to the pH dependence of catalytic activity. His178, an essential residue for dye decolorization, is located near heme and forms hydrogen bonds with Asp138 and Thr278. While Trp and Tyr mutants of His178 were inactive, the Phe mutant displayed ~35% activity of wild-type VcDyP, indicating that this position is a potential radical transfer route from heme to the active site on the protein surface. The Thr278Val mutant displayed similar enzymatic properties as WT VcDyP, whereas the Asp138Val mutant displayed significantly increased activity at pH 6.5. On the basis of these findings, we propose that neither distal amino acid residues, including Asp144, nor hydrogen bonds between His178 and Thr278 are responsible while the hydrogen bond between His178 and Asp138 plays a key role in the pH dependence of activity.
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Affiliation(s)
- Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan.
| | - Issei Omura
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Sayaka Umetsu
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
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19
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Metal complexes that bind to the amyloid-β peptide of relevance to Alzheimer’s disease. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213255
expr 886172045 + 931245952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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20
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Gomes LM, Bataglioli JC, Storr T. Metal complexes that bind to the amyloid-β peptide of relevance to Alzheimer’s disease. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213255] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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21
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Bhunia S, Rana A, Dey SG, Ivancich A, Dey A. A designed second-sphere hydrogen-bond interaction that critically influences the O-O bond activation for heterolytic cleavage in ferric iron-porphyrin complexes. Chem Sci 2020; 11:2681-2695. [PMID: 34084327 PMCID: PMC8157560 DOI: 10.1039/c9sc04388h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/26/2020] [Indexed: 12/18/2022] Open
Abstract
Heme hydroperoxidases catalyze the oxidation of substrates by H2O2. The catalytic cycle involves the formation of a highly oxidizing species known as Compound I, resulting from the two-electron oxidation of the ferric heme in the active site of the resting enzyme. This high-valent intermediate is formed upon facile heterolysis of the O-O bond in the initial FeIII-OOH complex. Heterolysis is assisted by the histidine and arginine residues present in the heme distal cavity. This chemistry has not been successfully modeled in synthetic systems up to now. In this work, we have used a series of iron(iii) porphyrin complexes (FeIIIL2(Br), FeIIIL3(Br) and FeIIIMPh(Br)) with covalently attached pendent basic groups (pyridine and primary amine) mimicking the histidine and arginine residues in the distal-pocket of natural heme enzymes. The presence of pendent basic groups, capable of 2nd sphere hydrogen bonding interactions, leads to almost 1000-fold enhancement in the rate of Compound I formation from peracids relative to analogous complexes without these residues. The short-lived Compound I intermediate formed at cryogenic temperatures could be detected using UV-vis electronic absorption spectroscopy and also trapped to be unequivocally identified by 9 GHz EPR spectroscopy at 4 K. The broad (2000 G) and axial EPR spectrum of an exchange-coupled oxoferryl-porphyrin radical species, [FeIV[double bond, length as m-dash]O Por˙+] with g eff ⊥ = 3.80 and g eff ‖ = 1.99, was observed upon a reaction of the FeIIIL3(Br) porphyrin complex with m-CPBA. The characterization of the reactivity of the FeIII porphyrin complexes with a substrate in the presence of an oxidant like m-CPBA by UV-vis electronic absorption spectroscopy showed that they are capable of oxidizing two equivalents of inorganic and organic substrate(s) like ferrocene, 2,4,6-tritertiary butyl phenol and o-phenylenediamine. These oxidations are catalytic with a turnover number (TON) as high as 350. Density Functional Theory (DFT) calculations show that the mechanism of O-O bond activation by 2nd sphere hydrogen bonding interaction from these pendent basic groups, which are protonated by a peracid, involves polarization of the O-O σ-bond, leading to lowering of the O-O σ*-orbital allowing enhanced back bonding from the iron center. These results demonstrate how inclusion of 2nd sphere hydrogen bonding interaction can play a critical role in O-O bond heterolysis.
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Affiliation(s)
- Sarmistha Bhunia
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
| | - Atanu Rana
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
| | - Somdatta Ghosh Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
| | - Anabella Ivancich
- CNRS, Aix-Marseille Univ, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479 Marseille France
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
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22
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Uchida T, Dojun N, Ota K, Sekine Y, Nakamura Y, Umetsu S, Ishimori K. Role of conserved arginine in the heme distal site of HutZ from Vibrio cholerae in the heme degradation reaction. Arch Biochem Biophys 2019; 677:108165. [PMID: 31689379 DOI: 10.1016/j.abb.2019.108165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 10/25/2022]
Abstract
HutZ from Vibrio cholerae is a dimeric enzyme that catalyzes degradation of heme. The highly conserved Arg92 residue in the HutZ family is proposed to interact with an iron-bound water molecule in the distal heme pocket. To clarify the specific role of Arg92 in the heme degradation reaction, the residue was substituted with alanine, leucine, histidine or lysine to modulate electrostatic interactions with iron-bound ligand. All four Arg92 mutants reacted with hydrogen peroxide to form verdoheme, a prominent intermediate in the heme degradation process. However, when ascorbic acid was used as an electron source, iron was not released even at pH 6.0 despite a decrease in the Soret band, indicating that non-enzymatic heme degradation occurred. Comparison of the rates of heme reduction, ligand binding and verdoheme formation suggested that proton transfer to the reduced oxyferrous heme, a potential rate-limiting step of heme degradation in HutZ, is hampered by mutation. In our previous study, we found that the increase in the distance between heme and Trp109 from 16 to 18 Å upon lowering the pH from 8.0 to 6.0 leads to activation of ascorbic acid-assisted heme degradation by HutZ. The distance in Arg92 mutants was >19 Å at pH 6.0, suggesting that subunit-subunit interactions at this pH are not suitable for heme degradation, similar to Asp132 and His63 mutants. These results suggest that interactions of Arg92 with heme-bound ligand induce alterations in the distance between subunits, which plays a key role in controlling the heme degradation activity of HutZ.
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Affiliation(s)
- Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan.
| | - Nobuhiko Dojun
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuki Ota
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yukari Sekine
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuina Nakamura
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Sayaka Umetsu
- Division of Chemistry, School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
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23
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Nye DB, Johnson EA, Mai MH, Lecomte JTJ. Replacement of the heme axial lysine as a test of conformational adaptability in the truncated hemoglobin THB1. J Inorg Biochem 2019; 201:110824. [PMID: 31514090 DOI: 10.1016/j.jinorgbio.2019.110824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
Amino acid replacement is a useful strategy to assess the roles of axial heme ligands in the function of native heme proteins. THB1, the protein product of the Chlamydomonas reinhardtii THB1 gene, is a group 1 truncated hemoglobin that uses a lysine residue in the E helix (Lys53, at position E10 by reference to myoglobin) as an iron ligand at neutral pH. Phylogenetic evidence shows that many homologous proteins have a histidine, methionine or arginine at the same position. In THB1, these amino acids would each be expected to convey distinct reactive properties if replacing the native lysine as an axial ligand. To explore the ability of the group 1 truncated Hb fold to support alternative ligation schemes and distal pocket conformations, the properties of the THB1 variants K53A as a control, K53H, K53M, and K53R were investigated by electronic absorption, EPR, and NMR spectroscopies. We found that His53 is capable of heme ligation in both the Fe(III) and Fe(II) states, that Met53 can coordinate only in the Fe(II) state, and that Arg53 stabilizes a hydroxide ligand in the Fe(III) state. The data illustrate that the group 1 truncated Hb fold can tolerate diverse rearrangement of the heme environment and has a strong tendency to use two protein side chains as iron ligands despite accompanying structural perturbations. Access to various redox pairs and different responses to pH make this protein an excellent test case for energetic and dynamic studies of heme ligation.
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Affiliation(s)
- Dillon B Nye
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Melissa H Mai
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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24
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Wang Z, Li Y, Wang H, Wan K, Liu Q, Shi X, Ding B. Enzyme Mimic Based on a Self‐Assembled Chitosan/DNA Hybrid Exhibits Superior Activity and Tolerance. Chemistry 2019; 25:12576-12582. [DOI: 10.1002/chem.201902509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/15/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Zhen‐Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- State Key Laboratory of Organic-Inorganic CompositesBeijing University of Chemical Technology Beijing 100029 China
| | - Yunzhe Li
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
| | - Kaiwei Wan
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
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25
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Wu W, Wang Q, Chen J, Huang L, Zhang H, Rong K, Dong S. Biomimetic design for enhancing the peroxidase mimicking activity of hemin. NANOSCALE 2019; 11:12603-12609. [PMID: 31232410 DOI: 10.1039/c9nr03506k] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although various nanomaterials have been found to exhibit intrinsic enzyme-like activity, to date, there is no general strategy for designing nanozymes, and their catalytic mechanism has not been studied in depth. To realize the desired enzymatic properties, imitating the structure of natural enzymes is a commendable way to develop effective nanozymes. Inspired by the structure of natural horseradish peroxidase (HRP), we loaded hemin onto amino-modified single-walled carbon nanotubes (SWNT-NH2) to prepare an effective peroxidase-like nanozyme (SWNT-NH2@hemin). The peroxidase-like activity of hemin was enhanced by SWNT through π-π interactions, and the positively charged -NH2 groups played a similar role to arginine in HRP and stabilized the intermediate during catalysis and facilitated the cleavage of the O-O bond. This is instructive for the development of a variety of highly efficient nanozymes by simulating the adjacent environment of the active center in natural enzymes. In addition, dual sensor platforms consisting of a colorimetric method and electrochemical method were developed based on SWNT-NH2@hemin.
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Affiliation(s)
- Weiwei Wu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China. and University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Qingqing Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China.
| | - Jinxing Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China. and University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Liang Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China. and University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - He Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China. and University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Kai Rong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China. and University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China. and University of Science and Technology of China, Hefei, Anhui 230026, PR China
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26
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Liu C, Yuan H, Liao F, Wei CW, Du KJ, Gao SQ, Tan X, Lin YW. Unique Tyr-heme double cross-links in F43Y/T67R myoglobin: an artificial enzyme with a peroxidase activity comparable to that of native peroxidases. Chem Commun (Camb) 2019; 55:6610-6613. [PMID: 31119219 DOI: 10.1039/c9cc02714a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The X-ray crystal structure of F43Y/T67R myoglobin revealed unique Tyr-heme double cross-links between Tyr43 and the heme 4-vinyl group, which represents a novel post-translational modification of heme proteins. Moreover, with the feature of a distal His-Arg pair, the designed artificial enzyme exhibited a peroxidase activity comparable to that of native peroxidases, such as the most efficient horseradish peroxidase.
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Affiliation(s)
- Can Liu
- 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
| | - Fei Liao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Chuan-Wan Wei
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Ke-Jie Du
- 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
| | - 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. and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
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27
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Bhakta S, Nayek A, Roy B, Dey A. Induction of Enzyme-like Peroxidase Activity in an Iron Porphyrin Complex Using Second Sphere Interactions. Inorg Chem 2019; 58:2954-2964. [DOI: 10.1021/acs.inorgchem.8b02707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Snehadri Bhakta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhijit Nayek
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Bijan Roy
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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28
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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: 132] [Impact Index Per Article: 22.0] [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.
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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
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29
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Pfanzagl V, Nys K, Bellei M, Michlits H, Mlynek G, Battistuzzi G, Djinovic-Carugo K, Van Doorslaer S, Furtmüller PG, Hofbauer S, Obinger C. Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage. J Biol Chem 2018; 293:14823-14838. [PMID: 30072383 PMCID: PMC6153280 DOI: 10.1074/jbc.ra118.004773] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/26/2018] [Indexed: 11/06/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) represent the most recently classified hydrogen peroxide-dependent heme peroxidase family. Although widely distributed with more than 5000 annotated genes and hailed for their biotechnological potential, detailed biochemical characterization of their reaction mechanism remains limited. Here, we present the high-resolution crystal structures of WT B-class DyP from the pathogenic bacterium Klebsiella pneumoniae (KpDyP) (1.6 Å) and the variants D143A (1.3 Å), R232A (1.9 Å), and D143A/R232A (1.1 Å). We demonstrate the impact of elimination of the DyP-typical, distal residues Asp-143 and Arg-232 on (i) the spectral and redox properties, (ii) the kinetics of heterolytic cleavage of hydrogen peroxide, (iii) the formation of the low-spin cyanide complex, and (iv) the stability and reactivity of an oxoiron(IV)porphyrin π-cation radical (Compound I). Structural and functional studies reveal that the distal aspartate is responsible for deprotonation of H2O2 and for the poor oxidation capacity of Compound I. Elimination of the distal arginine promotes a collapse of the distal heme cavity, including blocking of one access channel and a conformational change of the catalytic aspartate. We also provide evidence of formation of an oxoiron(IV)-type Compound II in KpDyP with absorbance maxima at 418, 527, and 553 nm. In summary, a reaction mechanism of the peroxidase cycle of B-class DyPs is proposed. Our observations challenge the idea that peroxidase activity toward conventional aromatic substrates is related to the physiological roles of B-class DyPs.
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Affiliation(s)
- Vera Pfanzagl
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Kevin Nys
- the Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium
| | | | - Hanna Michlits
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Georg Mlynek
- the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Gianantonio Battistuzzi
- Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and
| | - Kristina Djinovic-Carugo
- the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | | | - Paul G Furtmüller
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Stefan Hofbauer
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Christian Obinger
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria,
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30
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Wang ZG, Wang H, Liu Q, Duan F, Shi X, Ding B. Designed Self-Assembly of Peptides with G-Quadruplex/Hemin DNAzyme into Nanofibrils Possessing Enzyme-Mimicking Active Sites and Catalytic Functions. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00896] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Fangyuan Duan
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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31
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Köktepe T, Altın S, Tohma H, Gülçin İ, Köksal E. Purification, characterization and selected inhibition properties of peroxidase from haricot bean (Phaseolus vulgaris L.). INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2017. [DOI: 10.1080/10942912.2017.1360903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tubanur Köktepe
- Department of Chemistry, Faculty of Science and Arts, Erzincan University, Erzincan, Turkey
| | - Sevgi Altın
- Department of Chemistry, Faculty of Science and Arts, Erzincan University, Erzincan, Turkey
| | - Hatice Tohma
- Department of Chemistry, Faculty of Science and Arts, Erzincan University, Erzincan, Turkey
| | - İlhami Gülçin
- Department of Chemistry, Faculty of Science, Atatürk University, Erzincan, Turkey
| | - Ekrem Köksal
- Department of Chemistry, Faculty of Science and Arts, Erzincan University, Erzincan, Turkey
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32
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Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme. Nat Commun 2017; 8:358. [PMID: 28842561 PMCID: PMC5572459 DOI: 10.1038/s41467-017-00541-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 07/07/2017] [Indexed: 11/08/2022] Open
Abstract
Although catalytic mechanisms in natural enzymes are well understood, achieving the diverse palette of reaction chemistries in re-engineered native proteins has proved challenging. Wholesale modification of natural enzymes is potentially compromised by their intrinsic complexity, which often obscures the underlying principles governing biocatalytic efficiency. The maquette approach can circumvent this complexity by combining a robust de novo designed chassis with a design process that avoids atomistic mimicry of natural proteins. Here, we apply this method to the construction of a highly efficient, promiscuous, and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2. The maquette exhibits kinetics that match and even surpass those of certain natural peroxidases, retains its activity at elevated temperature and in the presence of organic solvents, and provides a simple platform for interrogating catalytic intermediates common to natural heme-containing enzymes.Catalytic mechanisms of enzymes are well understood, but achieving diverse reaction chemistries in re-engineered proteins can be difficult. Here the authors show a highly efficient and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2.
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33
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Chreifi G, Dejam D, Poulos TL. Crystal structure and functional analysis of Leishmania major pseudoperoxidase. J Biol Inorg Chem 2017; 22:919-927. [PMID: 28584975 DOI: 10.1007/s00775-017-1469-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/23/2017] [Indexed: 11/25/2022]
Abstract
Leishmania major pseudoperoxidase (LmPP) is a recently discovered heme protein expressed by the human pathogen. Previous in vivo and in vitro studies suggest that LmPP is a crucial element of the pathogen's defense mechanism against the reactive nitrogen species peroxynitrite produced during the host immune response. To shed light on the potential mechanism of peroxynitrite detoxification, we have determined the 1.76-Å X-ray crystal structure of LmPP, revealing a striking degree of homology with heme peroxidases. The most outstanding structural feature is a Cys/His heme coordination, which corroborates previous spectroscopic and mutagenesis studies. We also used a combination of stopped-flow and electron paramagnetic spectroscopies that together suggest that peroxynitrite is not a substrate for LmPP catalysis, leaving the function of LmPP an open question.
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Affiliation(s)
- Georges Chreifi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Dillon Dejam
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Thomas L Poulos
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-3900, USA.
- Department of Chemistry, University of California, Irvine, CA, USA.
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA.
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34
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Zhang Y, Schmid YRF, Luginbühl S, Wang Q, Dittrich PS, Walde P. Spectrophotometric Quantification of Peroxidase with p-Phenylene-diamine for Analyzing Peroxidase-Encapsulating Lipid Vesicles. Anal Chem 2017; 89:5484-5493. [PMID: 28415842 PMCID: PMC5681863 DOI: 10.1021/acs.analchem.7b00423] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A spectrophotometric assay for the determination of horseradish peroxidase (HRP) in aqueous solution with p-phenylenediamine (PPD, benzene-1,4-diamine) as electron donor substrate and hydrogen peroxide (H2O2) as oxidant was developed. The oxidation of PPD by HRP/H2O2 leads to the formation of Bandrowski's base ((3E,6E)-3,6-bis[(4-aminophenyl)imino]cyclohexa-1,4-diene-1,4-diamine), which can be quantified by following the increase in absorbance at 500 nm. The assay was applied for monitoring the activity of HRP inside ≈180 nm-sized lipid vesicles (liposomes), prepared from POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and purified by size exclusion chromatography. Because of the high POPC bilayer permeability of PPD and H2O2, the HRP-catalyzed oxidation of PPD occurs inside the vesicles once PPD and H2O2 are added to the vesicle suspension. In contrast, if instead of PPD the bilayer-impermeable substrate ABTS2- (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate)) is used, the oxidation of ABTS2- inside the vesicles does not occur. Therefore, using PPD and ABTS2- in separate assays allows distinguishing between vesicle-trapped HRP and HRP in the external bulk solution. In this way, the storage stability of HRP-containing POPC vesicles was investigated in terms of HRP leakage and activity of entrapped HRP. It was found that pH 7.0 suspensions of POPC vesicles (2.2 mM POPC) containing on average about 12 HRP molecules per vesicle are stable for at least 1 month without any significant HRP leakage, if stored at 4 °C. Such high stability is beneficial not only for bioanalytical applications but also for exploring the kinetic properties of vesicle-entrapped HRP through simple spectrophotometric absorption measurements with PPD as a sensitive and cheap substrate.
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Affiliation(s)
- Ya Zhang
- Polymer Chemistry Group, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
- Key Laboratory of Science and Technology of Eco-Textile, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Yannick R. F. Schmid
- Bioanalytics Group, Department of Biosystems Science and Engineering, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Sandra Luginbühl
- Polymer Chemistry Group, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
| | - Qiang Wang
- Key Laboratory of Science and Technology of Eco-Textile, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Petra S. Dittrich
- Bioanalytics Group, Department of Biosystems Science and Engineering, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Peter Walde
- Polymer Chemistry Group, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
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35
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Brissos V, Tavares D, Sousa AC, Robalo MP, Martins LO. Engineering a Bacterial DyP-Type Peroxidase for Enhanced Oxidation of Lignin-Related Phenolics at Alkaline pH. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03331] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vânia Brissos
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Diogo Tavares
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Ana Catarina Sousa
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Maria Paula Robalo
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Lígia O. Martins
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
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36
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Chaplin AK, Wilson MT, Worrall JAR. Kinetic characterisation of a dye decolourising peroxidase from Streptomyces lividans: new insight into the mechanism of anthraquinone dye decolourisation. Dalton Trans 2017; 46:9420-9429. [DOI: 10.1039/c7dt01144j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A dye decolourising haem peroxidase fromStreptomyces lividansdecolourises the anthraquinone dye RB19 through a disproportionation mechanism.
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37
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Lee C, Lee SY. Hemin-bound cysteinyl bolaamphiphile self-assembly as a horseradish peroxidase-mimetic catalyst. RSC Adv 2017. [DOI: 10.1039/c7ra06547g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
A horseradish peroxidase (HRP) mimetic catalyst was constructed by tethering hemin to the cysteinyl bolaamphiphile assembly through thiol–Fe bond. The prepared catalyst showed high catalytic activity comparable to HRP even at the high temperature.
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Affiliation(s)
- Chaemyeong Lee
- Department of Chemical and Biomolecular Engineering
- Yonsei University
- Seoul
- South Korea
| | - Sang-Yup Lee
- Department of Chemical and Biomolecular Engineering
- Yonsei University
- Seoul
- South Korea
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38
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Long A, Rothenberg P, Patel D, MacDougall J, Hartings MR. The structure and peroxidase activity of myoglobin in alcoholic solvents. Polyhedron 2016. [DOI: 10.1016/j.poly.2015.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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39
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Uchida T, Sasaki M, Tanaka Y, Ishimori K. A Dye-Decolorizing Peroxidase from Vibrio cholerae. Biochemistry 2015; 54:6610-21. [PMID: 26431465 DOI: 10.1021/acs.biochem.5b00952] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The dye-decolorizing peroxidase (DyP) protein from Vibrio cholerae (VcDyP) was expressed in Escherichia coli, and its DyP activity was assayed by monitoring degradation of a typical anthraquinone dye, reactive blue 19 (RB19). Its kinetic activity was obtained by fitting the data to the Michaelis-Menten equation, giving kcat and Km values of 1.3 ± 0.3 s(-1) and 50 ± 20 μM, respectively, which are comparable to those of other DyP enzymes. The enzymatic activity of VcDyP was highest at pH 4. A mutational study showed that two distal residues, Asp144 and Arg230, which are conserved in a DyP family, are essential for the DyP reaction. The crystal structure and resonance Raman spectra of VcDyP indicate the transfer of a radical from heme to the protein surface, which was supported by the formation of the intermolecular covalent bond in the reaction with H2O2. To identify the radical site, each of nine tyrosine or two tryptophan residues was substituted. It was clarified that Tyr129 and Tyr235 are in the active site of the dye degradation reaction at lower pH, while Tyr109 and Tyr133 are the sites of an intermolecular covalent bond at higher pH. VcDyP degrades RB19 at lower pH, while it loses activity under neutral or alkaline conditions because of a change in the radical transfer pathway. This finding suggests the presence of a pH-dependent switch of the radical transfer pathway, probably including His178. Although the physiological function of the DyP reaction is unclear, our findings suggest that VcDyP enhances the DyP activity to survive only when it is placed under a severe condition such as being in gastric acid.
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Affiliation(s)
- Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University , Sapporo 060-0810, Japan
| | - Miho Sasaki
- Graduate School of Chemical Sciences and Engineering, Hokkaido University , Sapporo 060-0810, Japan
| | - Yoshikazu Tanaka
- Faculty of Advanced Life Science, Hokkaido University , Sapporo 060-0808, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University , Sapporo 060-0810, Japan
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40
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Zhao J, Lu C, Franzen S. Distinct Enzyme–Substrate Interactions Revealed by Two Dimensional Kinetic Comparison between Dehaloperoxidase-Hemoglobin and Horseradish Peroxidase. J Phys Chem B 2015; 119:12828-37. [DOI: 10.1021/acs.jpcb.5b07126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Zhao
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Chang Lu
- Department
of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Stefan Franzen
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department
of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
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41
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Martins D, Bakas I, McIntosh K, English AM. Peroxynitrite and hydrogen peroxide elicit similar cellular stress responses mediated by the Ccp1 sensor protein. Free Radic Biol Med 2015; 85:138-47. [PMID: 25881547 DOI: 10.1016/j.freeradbiomed.2015.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/03/2015] [Accepted: 04/06/2015] [Indexed: 12/30/2022]
Abstract
Peroxynitrite [ONOO(H)] is an oxidant associated with deleterious effects in cells. Because it is an inorganic peroxide that reacts rapidly with peroxidases, we speculated that cells may respond to ONOO(H) and H2O2 challenge in a similar manner. We exposed yeast cells to SIN-1, a well-characterized ONOO(H) generator, and observed stimulation of catalase and peroxiredoxin (Prx) activities. Previously, we reported that H2O2 challenge increases these activities in wild-type cells and in cells producing the hyperactive mutant H2O2 sensor Ccp1(W191F) but not in Ccp1-knockout cells (ccp1Δ). We find here that the response of ccp1Δ and ccp1(W191F) cells to SIN-1 mirrors that to H2O2, identifying Ccp1 as a sensor of both peroxides. SIN-1 simultaneously releases (•)NO and O2(•-), which react to form ONOO(H), but exposure of the three strains separately to an (•)NO donor (spermine-NONOate) or an O2(•-) generator (paraquat) mainly depresses catalase or Prx activity, whereas co-challenge with the NONOate and paraquat stimulates these activities. Because Ccp1 appears to sense ONOO(H) in cells, we examined its reaction with ONOO(H) in vitro and found that peroxynitrous acid (ONOOH) rapidly (k2>10(6)M(-1)s(-1)) oxidizes purified Ccp1 to an intermediate with spectral and ferrocytochrome-oxidizing properties indistinguishable from those of its well-characterized compound I formed with H2O2. Importantly, the nitrite released from ONOOH is not oxidized to (•)NO2 by Ccp1(׳)s compound I, unlike peroxidases involved in immune defense. Overall, our results reveal that yeast cells mount a common antioxidant response to ONOO(H) and H2O2, with Ccp1 playing a pivotal role as an inorganic peroxide sensor.
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Affiliation(s)
- Dorival Martins
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada H4B 1R6; PROTEO, the FRQ-NT Network for Research on Protein Function, Structure, and Engineering, Québec, QC, Canada
| | - Iolie Bakas
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada H4B 1R6
| | - Kelly McIntosh
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada H4B 1R6
| | - Ann M English
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada H4B 1R6; PROTEO, the FRQ-NT Network for Research on Protein Function, Structure, and Engineering, Québec, QC, Canada.
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42
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Chen C, Shrestha R, Jia K, Gao PF, Geisbrecht BV, Bossmann SH, Shi J, Li P. Characterization of Dye-decolorizing Peroxidase (DyP) from Thermomonospora curvata Reveals Unique Catalytic Properties of A-type DyPs. J Biol Chem 2015. [PMID: 26205819 DOI: 10.1074/jbc.m115.658807] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) comprise a new family of heme peroxidases, which has received much attention due to their potential applications in lignin degradation. A new DyP from Thermomonospora curvata (TcDyP) was identified and characterized. Unlike other A-type enzymes, TcDyP is highly active toward a wide range of substrates including model lignin compounds, in which the catalytic efficiency with ABTS (kcat(app)/Km(app) = (1.7 × 10(7)) m(-1) s(-1)) is close to that of fungal DyPs. Stopped-flow spectroscopy was employed to elucidate the transient intermediates as well as the catalytic cycle involving wild-type (wt) and mutant TcDyPs. Although residues Asp(220) and Arg(327) are found necessary for compound I formation, His(312) is proposed to play roles in compound II reduction. Transient kinetics of hydroquinone (HQ) oxidation by wt-TcDyP showed that conversion of the compound II to resting state is a rate-limiting step, which will explain the contradictory observation made with the aspartate mutants of A-type DyPs. Moreover, replacement of His(312) and Arg(327) has significant effects on the oligomerization and redox potential (E°') of the enzyme. Both mutants were found to promote the formation of dimeric state and to shift E°' to a more negative potential. Not only do these results reveal the unique catalytic property of the A-type DyPs, but they will also facilitate the development of these enzymes as lignin degraders.
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Affiliation(s)
| | | | | | - Philip F Gao
- the Protein Production Group, University of Kansas, Lawrence, Kansas 66045
| | | | | | - Jishu Shi
- Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506 and
| | - Ping Li
- From the Departments of Chemistry,
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43
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Genaro-Mattos TC, Queiroz RF, Cunha D, Appolinario PP, Di Mascio P, Nantes IL, Augusto O, Miyamoto S. Cytochrome c Reacts with Cholesterol Hydroperoxides To Produce Lipid- and Protein-Derived Radicals. Biochemistry 2015; 54:2841-50. [DOI: 10.1021/bi501409d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Thiago C. Genaro-Mattos
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - Raphael F. Queiroz
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
- Departamento
de Química e Exatas, Universidade Estadual do Sudoeste da Bahia, Jequié, BA 45200-000, Brazil
| | - Daniela Cunha
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - Patricia P. Appolinario
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - Paolo Di Mascio
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - Iseli L. Nantes
- Centro
de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210-580, Brazil
| | - Ohara Augusto
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - Sayuri Miyamoto
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
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44
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Mendes S, Brissos V, Gabriel A, Catarino T, Turner DL, Todorovic S, Martins LO. An integrated view of redox and catalytic properties of B-type PpDyP from Pseudomonas putida MET94 and its distal variants. Arch Biochem Biophys 2015; 574:99-107. [PMID: 25797439 DOI: 10.1016/j.abb.2015.03.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 10/23/2022]
Abstract
PpDyP from Pseudomonas putida MET94 is an extremely versatile B-type dye-decolourising peroxidase (DyP) capable of efficient oxidation of a wide range of anthraquinonic and azo dyes, phenolic substrates, the non-phenolic veratryl alcohol and even manganese and ferrous ions. In reaction with H2O2 it forms a stable Compound I at a rate of (1.4±0.3)×10(6)M(-1)s(-1), comparable to those of classical peroxidases and other DyPs. We provide the first report of standard redox potential (E(0')) of the Compound I/Native redox couple in a DyP-type peroxidase. The value of E(0')Cpd I/N=1.10±0.04 (V) is similar to those found in peroxidases from the mammalian superfamily but higher than in peroxidases from the plant superfamily. Site-directed mutagenesis has been used to investigate the role of conserved distal residues, i.e. to replace aspartate 132 by asparagine, and arginine 214 and asparagine 136 by leucine. The structural, redox and catalytic properties of variants are addressed by spectroscopic, electrochemical and kinetic measurements. Our data point to the importance of the distal arginine in the catalytic mechanism of PpDyP, as also observed in DyPB from Rhodococcus jostii RHA1 but not in DyPs from the A and D subfamilies. This work reinforces the idea of existence of mechanistic variations among members of the different sub-families of DyPs with direct implications for their enzymatic properties and potential for biotechnological applications.
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Affiliation(s)
- Sónia Mendes
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Antonieta Gabriel
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - David L Turner
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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45
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The multihued palette of dye-decolorizing peroxidases. Arch Biochem Biophys 2015; 574:56-65. [PMID: 25743546 DOI: 10.1016/j.abb.2015.01.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/11/2015] [Accepted: 01/16/2015] [Indexed: 12/31/2022]
Abstract
Dye-decolorizing peroxidases (DyPs; EC 1.11.1.19) are heme enzymes that comprise a family of the dimeric α+β barrel structural superfamily of proteins. The first DyP, identified relatively recently in the fungus Bjerkandera adusta, was characterized for its ability to catalyze the decolorization of anthraquinone-based industrial dyes. These enzymes are now known to be present in all three domains of life, but do not appear to occur in plants or animals. They are involved in a range of physiological processes, although in many cases their roles remain unknown. This has not prevented the development of their biocatalytic potential, which includes the transformation of lignin. This review highlights the functional diversity of DyPs in the light of phylogenetic, structural and biochemical data. The phylogenetic analysis reveals the existence of at least five classes of DyPs. Their potential physiological roles are discussed based in part on synteny analyses. Finally, the considerable biotechnological potential of DyPs is summarized.
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46
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Mendes S, Catarino T, Silveira C, Todorovic S, Martins LO. The catalytic mechanism of A-type dye-decolourising peroxidase BsDyP: neither aspartate nor arginine is individually essential for peroxidase activity. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00478k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BsDyP from Bacillus subtilis belongs to the new dye-decolourising peroxidase (DyP) family. Here, we use transient kinetics to provide details on the catalytic cycle of BsDyP.
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Affiliation(s)
- S. Mendes
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
| | - T. Catarino
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
- Departamento de Química
- Faculdade de Ciências e Tecnologia
| | - C. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
| | - S. Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
| | - L. O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
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47
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Vitale R, Lista L, Cerrone C, Caserta G, Chino M, Maglio O, Nastri F, Pavone V, Lombardi A. An artificial heme-enzyme with enhanced catalytic activity: evolution, functional screening and structural characterization. Org Biomol Chem 2015; 13:4859-68. [DOI: 10.1039/c5ob00257e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rational refinement of function into the heme-protein model Mimochrome VI (MC6) resulted in a new analogue, FeIII-E2L(TD)-MC6, with an improved peroxidase activity.
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Affiliation(s)
- Rosa Vitale
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | - Liliana Lista
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | - Corinne Cerrone
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | | | - Marco Chino
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | - Ornella Maglio
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
- IBB
| | - Flavia Nastri
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
- IMAST Scarl
| | - Angela Lombardi
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
- IMAST Scarl
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48
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Baker M, Zhao H, Sakharov IY, Li QX. Amino acid sequence of anionic peroxidase from the windmill palm tree Trachycarpus fortunei. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:11941-8. [PMID: 25383699 PMCID: PMC4334278 DOI: 10.1021/jf504511h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 05/09/2023]
Abstract
Palm peroxidases are extremely stable and have uncommon substrate specificity. This study was designed to fill in the knowledge gap about the structures of a peroxidase from the windmill palm tree Trachycarpus fortunei. The complete amino acid sequence and partial glycosylation were determined by MALDI-top-down sequencing of native windmill palm tree peroxidase (WPTP), MALDI-TOF/TOF MS/MS of WPTP tryptic peptides, and cDNA sequencing. The propeptide of WPTP contained N- and C-terminal signal sequences which contained 21 and 17 amino acid residues, respectively. Mature WPTP was 306 amino acids in length, and its carbohydrate content ranged from 21% to 29%. Comparison to closely related royal palm tree peroxidase revealed structural features that may explain differences in their substrate specificity. The results can be used to guide engineering of WPTP and its novel applications.
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Affiliation(s)
- Margaret
R. Baker
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Hongwei Zhao
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
- School
of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Ivan Yu. Sakharov
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Qing X. Li
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
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49
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Navapour L, Mogharrab N, Amininasab M. How modification of accessible lysines to phenylalanine modulates the structural and functional properties of horseradish peroxidase: a simulation study. PLoS One 2014; 9:e109062. [PMID: 25313804 PMCID: PMC4196758 DOI: 10.1371/journal.pone.0109062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 09/09/2014] [Indexed: 11/19/2022] Open
Abstract
Horseradish Peroxidase (HRP) is one of the most studied peroxidases and a great number of chemical modifications and genetic manipulations have been carried out on its surface accessible residues to improve its stability and catalytic efficiency necessary for biotechnological applications. Most of the stabilized derivatives of HRP reported to date have involved chemical or genetic modifications of three surface-exposed lysines (K174, K232 and K241). In this computational study, we altered these lysines to phenylalanine residues to model those chemical modifications or genetic manipulations in which these positively charged lysines are converted to aromatic hydrophobic residues. Simulation results implied that upon these substitutions, the protein structure becomes less flexible. Stability gains are likely to be achieved due to the increased number of stable hydrogen bonds, improved heme-protein interactions and more integrated proximal Ca2+ binding pocket. We also found a new persistent hydrogen bond between the protein moiety (F174) and the heme prosthetic group as well as two stitching hydrogen bonds between the connecting loops GH and F′F″ in mutated HRP. However, detailed analysis of functionally related structural properties and dynamical features suggests reduced reactivity of the enzyme toward its substrates. Molecular dynamics simulations showed that substitutions narrow the bottle neck entry of peroxide substrate access channel and reduce the surface accessibility of the distal histidine (H42) and heme prosthetic group to the peroxide and aromatic substrates, respectively. Results also demonstrated that the area and volume of the aromatic-substrate binding pocket are significantly decreased upon modifications. Moreover, the hydrophobic patch functioning as a binding site or trap for reducing aromatic substrates is shrunk in mutated enzyme. Together, the results of this simulation study could provide possible structural clues to explain those experimental observations in which the protein stability achieved concurrent with a decrease in enzyme activity, upon manipulation of charge/hydrophobicity balance at the protein surface.
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Affiliation(s)
- Leila Navapour
- Biophysics and Computational Biology Laboratory, Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Navid Mogharrab
- Biophysics and Computational Biology Laboratory, Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
- * E-mail:
| | - Mehriar Amininasab
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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50
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Affiliation(s)
- Thomas L. Poulos
- Departments of Molecular Biology & Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California Irvine, Irvine, California 92697-3900
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