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Chatterjee J, Bandyopadhyay A, Pattabiraman M, Sarkar R. Discovery and development of tyrosine-click (Y-click) reaction for the site-selective labelling of proteins. Chem Commun (Camb) 2024. [PMID: 38913168 DOI: 10.1039/d4cc01997k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
With the versatile utility of bio-conjugated peptides and proteins in the fields of agriculture, food, cosmetics and pharmaceutical industry, the design of smart protocols to conjugate and modulate biomolecules becomes highly desirable. During this process, the most important consideration for biochemists is the retention of configurational integrity of the biomolecules. Moreover, this type of bioconjugation of peptide and protein becomes frivolous if the reaction is not performed with precise amino acid residues. Hence, chemo-selective, as well as site-selective reactions, that are biocompatible and possess an appropriate level of reactivity are necessary. Based on click chemistry, there are so many tyrosine (Y) conjugation strategies, such as sulfur-fluoride exchange (SuFEx), sulfur-triazole exchange (SuTEx), coupling with π-allyl palladium complexes, diazonium salts, diazodicarboxyamide-based reagents etc. Among these techniques, diazodicarboxyamide-based Y-conjugation, which is commonly known as the "tyrosine-click (Y-click) reaction", has met the expectations of synthetic and biochemists for the tyrosine-specific functionalization of biomolecules. Over the past one and a half decades, significant progress has been made in the classical organic synthesis approach, as well as its biochemical, photochemical, and electrochemical variants. Despite such progress and increasing importance, the Y-click reaction has not been reviewed to document variations in its methodology, applications, and broad utility. The present article aims to provide a summary of the approaches for the modulation of biomolecules at the hotspot of tyrosine residue by employing the Y-click reaction. The article also highlights its application for the mapping of proteins, imaging of living cells, and in the fields of analytical and medicinal chemistry.
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Affiliation(s)
| | - Ayan Bandyopadhyay
- Department of Chemistry, Chapra Government College, Nadia-741123, West Bengal, India
- Department of Higher Education, Government of West Bengal, India.
| | | | - Rajib Sarkar
- Department of Higher Education, Government of West Bengal, India.
- Department of Chemistry, Muragachha Government College, Nadia-741154, West Bengal, India
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2
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Ríos-González BB, Domán A, Ditrói T, Garai D, Crespo LD, Gerfen GJ, Furtmüller PG, Nagy P, López-Garriga J. Lactoperoxidase catalytically oxidize hydrogen sulfide via intermediate formation of sulfheme derivatives. REDOX BIOCHEMISTRY AND CHEMISTRY 2024; 8:100021. [PMID: 38993681 PMCID: PMC11238738 DOI: 10.1016/j.rbc.2024.100021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
The biological chemistry of hydrogen sulfide (H2S) with physiologically important heme proteins is in the focus of redox biology research. In this study, we investigated the interactions of lactoperoxidase (LPO) with H2S in the presence and absence of molecular dioxygen (O2) or hydrogen peroxide (H2O2). Under anaerobic conditions, native LPO forms no heme-H2S complex upon sulfide exposure. However, under aerobic conditions or in the presence of H2O2 the formation of both ferrous and ferric sulfheme (sulfLPO) derivatives was observed based on the appearances of their characteristic optical absorptions at 638 nm and 727 nm, respectively. Interestingly, we demonstrate that LPO can catalytically oxidize H2S by H2O2 via intermediate formation of relatively short-lived ferrous and ferric sulfLPO derivatives. Pilot product analyses suggested that the turnover process generates oxidized sulfide species, which include sulfateS O 4 2 - and inorganic polysulfides (H S x - ; x = 2-5). These results indicated that H2S can serve as a non-classical LPO substrate by inducing a reversible sulfheme-like modification of the heme porphyrin ring during turnover. Furthermore, electron paramagnetic resonance data suggest that H2S can act as a scavenger of H2O2 in the presence of LPO without detectable formation of any carbon-centered protein radical species, suggesting that H2S might be capable of protecting the enzyme from radical-mediated damage. We propose possible mechanisms, which explain our results as well as contrasting observations with other heme proteins, where either no sulfheme formation was observed or the generation of sulfheme derivatives provided a dead end for enzyme functions.
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Affiliation(s)
- Bessie B Ríos-González
- Department of Chemistry, University of Puerto Rico, Mayagüez Campus, P.O. Box 9019, Mayagüez, 00681-9019, Puerto Rico
| | - Andrea Domán
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, Ráth György street 7-9, Budapest, 1122, Hungary
| | - Tamás Ditrói
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, Ráth György street 7-9, Budapest, 1122, Hungary
| | - Dorottya Garai
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, Ráth György street 7-9, Budapest, 1122, Hungary
| | - Leishka D Crespo
- Department of Chemistry, University of Puerto Rico, Mayagüez Campus, P.O. Box 9019, Mayagüez, 00681-9019, Puerto Rico
| | - Gary J Gerfen
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY, 10461, United States
| | - Paul G Furtmüller
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, Vienna, Austria, A-1190
| | - Péter Nagy
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, Ráth György street 7-9, Budapest, 1122, Hungary
- Department of Anatomy and Histology, ELKH Laboratory of Redox Biology, University of Veterinary Medicine, István street 2, Budapest, 1078, Hungary
- Chemistry Institute, University of Debrecen, Egyetem square 1, Debrecen, 4032, Hungary
| | - Juan López-Garriga
- Department of Chemistry, University of Puerto Rico, Mayagüez Campus, P.O. Box 9019, Mayagüez, 00681-9019, Puerto Rico
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3
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Ansari M, Bhattacharjee S, Pantazis DA. Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II. J Am Chem Soc 2024; 146:9640-9656. [PMID: 38530124 PMCID: PMC11009960 DOI: 10.1021/jacs.3c13169] [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] [Received: 11/23/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024]
Abstract
Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.
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Affiliation(s)
- Mursaleem Ansari
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Sinjini Bhattacharjee
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
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4
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Fan S, Cong Z. Emerging Strategies for Modifying Cytochrome P450 Monooxygenases into Peroxizymes. Acc Chem Res 2024. [PMID: 38293787 DOI: 10.1021/acs.accounts.3c00746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
ConspectusCytochrome P450 monooxygenase is a versatile oxidizing enzyme with great potential in synthetic chemistry and biology. However, the dependence of its catalytic function on the nicotinamide cofactor NAD(P)H and redox partner proteins limits the practical catalytic application of P450 in vitro. An alternative to expensive cofactors is low-cost H2O2, which can be used directly to exploit the catalytic potential of P450s. However, the peroxide shunt pathway is generally inefficient at driving P450 catalysis compared to normal NAD(P)H-dependent activity. Over the last few decades, the scientific community has made continuous efforts to use directed evolution or site-directed mutagenesis to modify P450 monooxygenases into their peroxizyme modes─peroxygenase and peroxidase. Despite significant progress, obtaining efficient P450 peroxizymes remains a huge challenge. Here, we summarize our efforts to modulate peroxizyme activity in P450 monooxygenases and exploit their catalytic applications in challenging selective C-H oxidation, oxygenation, and oxyfunctionalization over the past seven years. We first developed a dual-functional small molecule (DFSM) strategy for transforming P450BM3 monooxygenase into peroxygenase. In this strategy, the typical DFSM, such as N-(ω-imidazolyl)-hexanoyl-l-phenylalanine (Im-C6-Phe), binds to the P450BM3 protein with an anchoring group at one end and plays a general acid-base catalytic role in the activation of H2O2 with an imidazolyl group at the other end. Compared with the O-O homolysis mechanism in the absence of DFSM, the addition of DFSM efficiently enables the heterolytic O-O cleavage of the adduct Fe-O-OH, thus being favored for the formation of active species compound I, which has been demonstrated by combining crystallographic and theoretical calculations. Furthermore, protein engineering showed the unique catalytic performance of DFSM-facilitated P450 peroxygenase for the highly difficult selective oxidation of C-H bonds. This catalytic performance was demonstrated during the chemoselective hydroxylation of gaseous alkanes, regioselective O-demethylation of aryl ethers, highly (R)-enantioselective epoxidation of styrene, and regio- and enantiomerically diverse hydroxylation of alkylbenzenes. Second, we demonstrated that DFSM-facilitated P450BM3 peroxygenase could be effectively switched to an efficient peroxidase mode through mechanism-guided protein engineering of redox-sensitive residues. Utilizing the peroxidase function of P450 enabled the direct nitration of unsaturated hydrocarbons including phenols, aromatic amines, and styrene derivatives, which was not only the P450-catalyzed direct nitration of phenols and aromatic amines for the first time but also the first example of the direct biological nitration of olefins. Finally, we report an H2O2 tunnel engineering strategy to enable peroxygenase activity in several different P450 monooxygenases for the first time, providing a general approach for accessing engineered P450 peroxygenases. In this Account, we highlight the emerging strategies we have developed for producing practical P450 peroxizyme biocatalysts. Although the DFSM strategy is primarily applied to P450BM3 to date, both strategies of redox-sensitive residue engineering and H2O2 tunnel engineering show great potential to extend to other P450s. These strategies have expanded the scope of applications of P450 chemistry and catalysis. Additionally, they provide a unique solution to the challenging selective oxidation of inert C-H bonds in synthetic chemistry.
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Affiliation(s)
- Shengxian Fan
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
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5
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Li Y, Shi X, Xu J, Huang X, Feng J, Huang Y, Liu K, Yu F. Proteomics-based analysis on the stress response mechanism of Bidens pilosa L. under cadmium exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132761. [PMID: 37837780 DOI: 10.1016/j.jhazmat.2023.132761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
Bidens pilosa L. (B. pilosa) has great potential for the phytoremediation of cadmium (Cd)-contaminated soils. However, the molecular mechanism underlying Cd tolerance and detoxification in B. pilosa is still unclear. In the present study, a 4D label-free quantification technique combined with liquid chromatography-parallel reaction monitoring mass spectrometry was used to explore the stress response mechanism of B. pilosa. Proteomic analysis revealed 213 and 319 differentially expressed proteins (DEPs) in the roots and leaves of B. pilosa, respectively, and 12 target proteins were selected for further analysis. SWISS-MODEL was used to predict the 3D structures of the target proteins. The cation-ATPase-N structural domain and an ATPase-E1-E2 motif, which help to regulate ATPase function, were detected in the TR10519_c0_g1_ORF protein. In addition, the TR6620_c0_g1_ORF_1 and TR611_c1_g1_ORF proteins contained peroxidase-1 and peroxidase-2 motifs. The TR11239_c0_g1_ORF protein was found to belong to the Fe-SOD family, to have a dimeric structure and to contain a relatively high proportion of α-helices but few β-sheets, which play important roles in reactive oxygen intermediate scavenging. Thus, the current study provides an overview of the proteomic response of B. pilosa in scavenging of Cd-induced reactive oxygen intermediates and reveals key proteins involved in the stress response of B. pilosa under Cd exposure.
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Affiliation(s)
- Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, Guilin 541004, China
| | - Xinwei Shi
- College of Environment and Resources, Guangxi Normal University, Guilin 541004, China
| | - Jie Xu
- College of Life Science, Guangxi Normal University, Guilin 541004, China
| | - Xiaofang Huang
- College of Life Science, Guangxi Normal University, Guilin 541004, China
| | - Jingpei Feng
- College of Environment and Resources, Guangxi Normal University, Guilin 541004, China
| | - Yuanyuan Huang
- College of Environment and Resources, Guangxi Normal University, Guilin 541004, China
| | - Kehui Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Life Science, Guangxi Normal University, Guilin 541004, China
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, Guilin 541004, China.
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6
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López-Gómez P, Buezo J, Urra M, Cornejo A, Esteban R, Fernández de Los Reyes J, Urarte E, Rodríguez-Dobreva E, Chamizo-Ampudia A, Eguaras A, Wolf S, Marino D, Martínez-Merino V, Moran JF. A new oxidative pathway of nitric oxide production from oximes in plants. MOLECULAR PLANT 2024; 17:178-198. [PMID: 38102832 DOI: 10.1016/j.molp.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 09/06/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Nitric oxide (NO) is an essential reactive oxygen species and a signal molecule in plants. Although several studies have proposed the occurrence of oxidative NO production, only reductive routes for NO production, such as the nitrate (NO-3) -upper-reductase pathway, have been evidenced to date in land plants. However, plants grown axenically with ammonium as the sole source of nitrogen exhibit contents of nitrite and NO3-, evidencing the existence of a metabolic pathway for oxidative production of NO. We hypothesized that oximes, such as indole-3-acetaldoxime (IAOx), a precursor to indole-3-acetic acid, are intermediate oxidation products in NO synthesis. We detected the production of NO from IAOx and other oximes catalyzed by peroxidase (POD) enzyme using both 4-amino-5-methylamino-2',7'-difluorescein fluorescence and chemiluminescence. Flavins stimulated the reaction, while superoxide dismutase inhibited it. Interestingly, mouse NO synthase can also use IAOx to produce NO at a lower rate than POD. We provided a full mechanism for POD-dependent NO production from IAOx consistent with the experimental data and supported by density functional theory calculations. We showed that the addition of IAOx to extracts from Medicago truncatula increased the in vitro production of NO, while in vivo supplementation of IAOx and other oximes increased the number of lateral roots, as shown for NO donors, and a more than 10-fold increase in IAOx dehydratase expression. Furthermore, we found that in vivo supplementation of IAOx increased NO production in Arabidopsis thaliana wild-type plants, while prx33-34 mutant plants, defective in POD33-34, had reduced production. Our data show that the release of NO by IAOx, as well as its auxinic effect, explain the superroot phenotype. Collectively, our study reveals that plants produce NO utilizing diverse molecules such as oximes, POD, and flavins, which are widely distributed in the plant kingdom, thus introducing a long-awaited oxidative pathway to NO production in plants. This knowledge has essential implications for understanding signaling in biological systems.
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Affiliation(s)
- Pedro López-Gómez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Javier Buezo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Marina Urra
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Alfonso Cornejo
- Institute for Advanced Materials and Mathematics (INAMAT2), Department of Sciences, Public University of Navarre (UPNA), Campus de Arrosadía, 31006 Pamplona, Spain
| | - Raquel Esteban
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Sarriena s/n, Apdo. 644, 48080 Bilbao, Spain
| | - Jorge Fernández de Los Reyes
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Estibaliz Urarte
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Estefanía Rodríguez-Dobreva
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Alejandro Chamizo-Ampudia
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Alejandro Eguaras
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Sebastian Wolf
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
| | - Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Sarriena s/n, Apdo. 644, 48080 Bilbao, Spain
| | - Victor Martínez-Merino
- Institute for Advanced Materials and Mathematics (INAMAT2), Department of Sciences, Public University of Navarre (UPNA), Campus de Arrosadía, 31006 Pamplona, Spain.
| | - Jose F Moran
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain.
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Wu F, Wang Z, Li X, Wang X. Amide herbicides: Analysis of their environmental fate, combined plant-microorganism soil remediation scheme, and risk prevention and control strategies for sensitive populations. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132452. [PMID: 37683346 DOI: 10.1016/j.jhazmat.2023.132452] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
In this study, we predicted the environmental fate of amide herbicides (AHs) using the EQC (EQuilibrium Criterion) model. We found that the soil phase is the main reservoir of AHs in the environment. Second, a toxicokinetic prediction indicated that butachlor have a low human health risk, while the alachlor, acetochlor, metolachlor, napropamide, and propanil are all uncertain. To address the environmental and human-health-related threats posed by AHs, 27 new proteins/enzymes that easily absorb, degrade, and mineralize AHs were designed. Compared with the target protein/enzyme, the comprehensive evaluation value of the new proteins/enzymes increased significantly: the absorption protein increased by 20.29-113.49%; the degradation enzyme increased by 151.26-425.22%; and the mineralization enzyme increased by 23.70-52.16%. Further experiments revealed that the remediating effect of 13 new proteins/enzymes could be significantly enhanced to facilitate their applicability under real environmental conditions. The hydrophobic interactions, van der Waals forces, and polar solvation are the key factors influencing plant-microorganism remediation. Finally, the simulations revealed that appropriate consumption of kiwifruit or simultaneous consumption of ginseng, carrot, and spinach, and avoiding the simultaneous consumption of maize and carrot/spinach are the most effective means reduce the risk of exhibiting AH-linked toxicity.
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Affiliation(s)
- Fuxing Wu
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Zini Wang
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Xinao Li
- Moe Key Laboratory of Resources and Environmental System Optimization, North China Electric Power University, Beijing 102206, China.
| | - Xiaoli Wang
- College of Plant Science, Jilin University, Changchun 130062, China.
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8
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Ramakrishnan K, Johnson RL, Winter SD, Worthy HL, Thomas C, Humer DC, Spadiut O, Hindson SH, Wells S, Barratt AH, Menzies GE, Pudney CR, Jones DD. Glycosylation increases active site rigidity leading to improved enzyme stability and turnover. FEBS J 2023; 290:3812-3827. [PMID: 37004154 PMCID: PMC10952495 DOI: 10.1111/febs.16783] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/14/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Glycosylation is the most prevalent protein post-translational modification, with a quarter of glycosylated proteins having enzymatic properties. Yet, the full impact of glycosylation on the protein structure-function relationship, especially in enzymes, is still limited. Here, we show that glycosylation rigidifies the important commercial enzyme horseradish peroxidase (HRP), which in turn increases its turnover and stability. Circular dichroism spectroscopy revealed that glycosylation increased holo-HRP's thermal stability and promoted significant helical structure in the absence of haem (apo-HRP). Glycosylation also resulted in a 10-fold increase in enzymatic turnover towards o-phenylenediamine dihydrochloride when compared to its nonglycosylated form. Utilising a naturally occurring site-specific probe of active site flexibility (Trp117) in combination with red-edge excitation shift fluorescence spectroscopy, we found that glycosylation significantly rigidified the enzyme. In silico simulations confirmed that glycosylation largely decreased protein backbone flexibility, especially in regions close to the active site and the substrate access channel. Thus, our data show that glycosylation does not just have a passive effect on HRP stability but can exert long-range effects that mediate the 'native' enzyme's activity and stability through changes in inherent dynamics.
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Affiliation(s)
| | - Rachel L. Johnson
- Molecular Biosciences Division, School of BiosciencesCardiff UniversityUK
| | | | - Harley L. Worthy
- Molecular Biosciences Division, School of BiosciencesCardiff UniversityUK
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterUK
| | | | - Diana C. Humer
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical EngineeringTU WienAustria
| | - Oliver Spadiut
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical EngineeringTU WienAustria
| | | | | | - Andrew H. Barratt
- Molecular Biosciences Division, School of BiosciencesCardiff UniversityUK
| | | | - Christopher R. Pudney
- Department of Biology and BiochemistryUniversity of BathUK
- Centre for Therapeutic InnovationUniversity of BathUK
| | - D. Dafydd Jones
- Molecular Biosciences Division, School of BiosciencesCardiff UniversityUK
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9
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New J, Barsky D, Uhde-Stone C. ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses. Int J Mol Sci 2023; 24:ijms24098297. [PMID: 37176003 PMCID: PMC10179425 DOI: 10.3390/ijms24098297] [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: 03/15/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Participating in both biotic and abiotic stress responses, plant-specific class III peroxidases (PERs) show promise as candidates for crop improvement. The multigenic PER family is known to take part in diverse functions, such as lignin formation and defense against pathogens. Traditionally linked to hydrogen peroxide (H2O2) consumption, PERs can also produce reactive oxygen species (ROS), essential in tissue development, pathogen defense and stress signaling. The amino acid sequences of both orthologues and paralogues of PERs are highly conserved, but discovering correlations between sequence differences and their functional diversity has proven difficult. By combining meta-analysis of transcriptomic data and sequence alignments, we discovered a correlation between three key amino acid positions and gene expression in response to biotic and abiotic stresses. Phylogenetic analysis revealed evolutionary pressure on these amino acids toward stress responsiveness. Using AlphaFold modeling, we found unique interdomain and protein-heme interactions involving those key amino acids in stress-induced PERs. Plausibly, these structural interactions may act as "gate keepers" by preventing larger substrates from accessing the heme and thereby shifting PER function from consumption to the production of ROS.
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Affiliation(s)
- James New
- Department of Biological Sciences, California State University, East Bay, Hayward, CA 94542, USA
| | - Daniel Barsky
- Department of Physics, California State University, East Bay, Hayward, CA 94542, USA
| | - Claudia Uhde-Stone
- Department of Biological Sciences, California State University, East Bay, Hayward, CA 94542, USA
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10
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Liu X, Zhang Q, Li M, Qin S, Zhao Z, Lin B, Ding Y, Xiang Y, Li C. Horseradish peroxidase (HRP) and glucose oxidase (GOX) based dual-enzyme system: Sustainable release of H 2O 2 and its effect on the desirable ping pong bibi degradation mechanism. ENVIRONMENTAL RESEARCH 2023; 229:115979. [PMID: 37119847 DOI: 10.1016/j.envres.2023.115979] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/13/2023] [Accepted: 04/22/2023] [Indexed: 05/05/2023]
Abstract
In this study, an adaptable HRP/GOX-Glu system was established due to the trait, efficient degradation of pollutants in the catalytic process of HRP named the ping-pong bibi mechanism and a sustained release of H2O2 in-situ under the catalysis of glucose oxidase (GOX). Compared with the traditional HRP/H2O2 system, the HRP was more stable in the HRP/GOX-Glu system based on the feature of persistent releasing H2O2 in-situ. Simultaneously, the high valent iron was found out to give a greater contribution to Alizarin Green (AG) removal through ping-pong mechanism, whereas the hydroxyl radical and superoxide free radical generated by Bio-Fenton were also the main active substances for AG degradation. Furthermore, on the basis of effect evaluation of the co-existence of two different degradation mechanisms in the HRP/GOX-Glu system, the degradation pathways of AG were proposed. Moreover, the optimum reaction conditions preferentially triggering ping-pong bibi mechanism instead of Bio-Fenton were determined by single factor analysis and degradation mechanism elaboration. This study would provide a reference for how to give full play to the advantages of ping-pong bibi mechanism in the dual-enzyme system based on HRP to degrade pollutants with high efficiency.
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Affiliation(s)
- Xiangyu Liu
- School of Civil Engineering & Architecture, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Qian Zhang
- School of Civil Engineering & Architecture, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China; Shenzhen Research Institute of Wuhan University of Technology, Shenzhen, 518000, China
| | - Meng Li
- School of Civil Engineering & Architecture, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China; Shenzhen Research Institute of Wuhan University of Technology, Shenzhen, 518000, China
| | - Song Qin
- School of Art and Design, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China.
| | - Ziqi Zhao
- School of Civil Engineering & Architecture, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Bing Lin
- School of Civil Engineering & Architecture, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Yuwei Ding
- School of Civil Engineering & Architecture, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Yutong Xiang
- School of Civil Engineering & Architecture, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Chengwei Li
- Hunan Land and Resources Exploration Institute, Changsha, 410001, China
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11
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Zhao P, Kong F, Jiang Y, Qin X, Tian X, Cong Z. Enabling Peroxygenase Activity in Cytochrome P450 Monooxygenases by Engineering Hydrogen Peroxide Tunnels. J Am Chem Soc 2023; 145:5506-5511. [PMID: 36790023 DOI: 10.1021/jacs.3c00195] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Given prominent physicochemical similarities between H2O2 and water, we report a new strategy for promoting the peroxygenase activity of P450 enzymes by engineering their water tunnels to facilitate H2O2 access to the heme center buried therein. Specifically, the H2O2-driven activities of two native NADH-dependent P450 enzymes (CYP199A4 and CYP153AM.aq) increase significantly (by >183-fold and >15-fold, respectively). Additionally, the amount of H2O2 required for an artificial P450 peroxygenase facilitated by a dual-functional small molecule to obtain the desired product is reduced by 95%-97.5% (with ∼95% coupling efficiency). Structural analysis suggests that mutating the residue at the bottleneck of the water tunnel may open a second pathway for H2O2 to flow to the heme center (in addition to the natural substrate tunnel). This study highlights a promising, generalizable strategy whereby P450 monooxygenases can be modified to adopt peroxygenase activity through H2O2 tunnel engineering, thus broadening the application scope of P450s in synthetic chemistry and synthetic biology.
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Affiliation(s)
- Panxia Zhao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanhui Kong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiping Jiang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Xiangquan Qin
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Xiaoxia Tian
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shandong Energy Institute, Qingdao, Shandong 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
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12
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Szerlauth A, Varga Á, Madácsy T, Sebők D, Bashiri S, Skwarczynski M, Toth I, Maléth J, Szilagyi I. Confinement of Triple-Enzyme-Involved Antioxidant Cascade in Two-Dimensional Nanostructure. ACS MATERIALS LETTERS 2023; 5:565-573. [PMID: 36776691 PMCID: PMC9906813 DOI: 10.1021/acsmaterialslett.2c00580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Application of antioxidant enzymes in medical or industrial processes is limited due to their high sensitivity to environmental conditions. Incorporation of such enzymes in nanostructures provides a promising route to obtain highly efficient and robust biocatalytic system to scavenge reactive oxygen species (ROS). Here, this question was addressed by confinement of superoxide dismutase (SOD), horseradish peroxidase (HRP), and catalase (CAT) enzymes into nanostructures containing polyelectrolyte building blocks (alginate (Alg) and trimethyl chitosan (TMC)) and delaminated layered double hydroxide (dLDH) nanoparticle support. The nanocomposite possessed excellent structural and colloidal stability, while antioxidant tests revealed that the enzymes remained active upon immobilization and the developed composite greatly reduced intracellular oxidative stress in two-dimensional cell cultures. Moreover, it effectively prevented hydrogen peroxide-induced double stranded DNA breaks, which is a common consequence of oxidative stress. The results provide important tools to design complex nanostructures with multienzymatic antioxidant activities for ROS scavenging.
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Affiliation(s)
- Adel Szerlauth
- MTA-SZTE
Lendület Biocolloids Research Group, Interdisciplinary Excellence
Centre, University of Szeged, H-6720 Szeged, Hungary
| | - Árpád Varga
- MTA-SZTE
Lendület Epithelial Cell Signaling and Secretion Research Group,
Interdisciplinary Excellence Centre, University
of Szeged, H-6720 Szeged, Hungary
| | - Tamara Madácsy
- MTA-SZTE
Lendület Epithelial Cell Signaling and Secretion Research Group,
Interdisciplinary Excellence Centre, University
of Szeged, H-6720 Szeged, Hungary
| | - Dániel Sebők
- Department
of Applied and Environmental Chemistry, University of Szeged, H-6720 Szeged, Hungary
| | - Sahra Bashiri
- School
of Chemistry and Molecular Biosciences, University of Queensland, QLD-4072 St. Lucia, Australia
| | - Mariusz Skwarczynski
- School
of Chemistry and Molecular Biosciences, University of Queensland, QLD-4072 St. Lucia, Australia
| | - Istvan Toth
- School
of Chemistry and Molecular Biosciences, University of Queensland, QLD-4072 St. Lucia, Australia
| | - József Maléth
- MTA-SZTE
Lendület Epithelial Cell Signaling and Secretion Research Group,
Interdisciplinary Excellence Centre, University
of Szeged, H-6720 Szeged, Hungary
| | - Istvan Szilagyi
- MTA-SZTE
Lendület Biocolloids Research Group, Interdisciplinary Excellence
Centre, University of Szeged, H-6720 Szeged, Hungary
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13
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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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14
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Madhuresh NKD, Nguyen H, Franzen S. The divergent pH dependence of substrate turnover in dehaloperoxidases A and B. J Inorg Biochem 2023; 238:112029. [PMID: 36371913 DOI: 10.1016/j.jinorgbio.2022.112029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
Abstract
The pH-dependent peroxidase activity in both dehaloperoxidases A and B was studied by a kinetic assay, stopped flow spectroscopy, resonance Raman spectroscopy, and high-performance liquid chromatography at pH 5.0, 6.0, and 7.0. At pH 7.0, both isozymes follow the peroxidase ping-pong kinetic model derived from the three-step reaction scheme using the steady-state approximation. However, deviation from standard saturation behavior is observed at pH < 6.0 and [TCP] > 0.7 mM, owing to multiple processes: a) self-inhibition of TCP by internal binding; b) oxidation of the product by a pH- and concentration-dependent secondary reaction; and c) formation of an inactive species known as compound RH in the absence of oxidizable substrate. Although DHP-A and DHP-B differ by only 5 amino acids, they show a complete trend reversal in their observed peroxidase kinetics and product yields. Although at pH 7.0 DHP-B had higher TCP oxidation activity than DHP-A as reported previously, as pH was lowered, DHP-A appeared to have a higher peroxidase activity than DHP-B. This is an unprecedented result. However, the fact that there are multiple processes contributing to both kinetics and yield of TCP oxidation complicates interpretation of these data. Deactivation via compound RH and self-inhibition are pH dependent reactions that compete with substrate oxidation. Compound RH formation was observed to be rapid at low pH. A complete set of control experiments were conducted to differentiate the various contributions to the observed enzyme kinetics.
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Affiliation(s)
| | - Hilbert Nguyen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America.
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15
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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16
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Schweitzer-Stenner R. Heme-Protein Interactions and Functional Relevant Heme Deformations: The Cytochrome c Case. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248751. [PMID: 36557884 PMCID: PMC9781506 DOI: 10.3390/molecules27248751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Heme proteins are known to perform a plethora of biologically important functions. This article reviews work that has been conducted on various class I cytochrome c proteins over a period of nearly 50 years. The article focuses on the relevance of symmetry-lowering heme-protein interactions that affect the function of the electron transfer protein cytochrome c. The article provides an overview of various, mostly spectroscopic studies that explored the electronic structure of the heme group in these proteins and how it is affected by symmetry-lowering deformations. In addition to discussing a large variety of spectroscopic studies, the article provides a theoretical framework that should enable a comprehensive understanding of the physical chemistry that underlies the function not only of cytochrome c but of all heme proteins.
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17
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Bizeau J, Adam A, Nadal C, Francius G, Siniscalco D, Pauly M, Bégin-Colin S, Mertz D. Protein sustained release from isobutyramide-grafted stellate mesoporous silica nanoparticles. Int J Pharm X 2022; 4:100130. [PMID: 36156982 PMCID: PMC9494245 DOI: 10.1016/j.ijpx.2022.100130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 10/31/2022] Open
Abstract
Proteins are great therapeutic candidates as endogenous biomolecules providing a wide range of applications. However, their delivery suffers from some limitations and specifically designed delivery systems having an efficient protein anchoring and delivery strategy are still needed. In this work, we propose to combine large pore stellate mesoporous silica (STMS) with isobutyramide (IBAM), as a “glue” molecule which has been shown promising for immobilization of various biomacromolecules at silica surface. We address here for the first time the ability of such IBAM-modified NPs to sustainably deliver proteins over a prolonged time. In this work, a quantitative loading study of proteins (serum albumin (HSA), peroxidase (HRP), immunoglobulin (IgG) and polylysine (PLL)) on STMS@IBAM is first presented using three complementary detection techniques to ensure precision and avoid protein quantification issues. The results demonstrated a high loading capacity for HSA and HRP (≥ ca. 350 μg.mg−1) but a moderate one for IgG and PLL. After evaluating the physicochemical properties of the loaded particles and their stability over scaling-up and washings, the ability of STMS@IBAM to release proteins over prolonged time was evaluated in equilibrium (static) and flow mimicking (dynamic) conditions and at different temperatures (25, 37, 45 °C). Results show not only the potential of such “glue” functionalized STMS to release proteins in a sustained way, but also the retention of the biological activity of immobilized and released HRP, used as an enzyme model. Finally, an AFM-force spectroscopy study was conducted to decipher the interactions between IBAM and proteins, showing the involvement of different interactions in the adsorption and release processes. Isobutyramide bound stellate mesoporous silica allow the immobilization of various proteins. Protein release was achieved from the nanoparticles in a sustained way in buffer. Peroxidase activity was retained whether in immobilized or released conditions. Choice of protein detection techniques was shown to be crucial. AFM-spectroscopy was used to investigate IBAM-protein intermolecular bonding.
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18
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Ivanov YD, Tatur VY, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Ivanova ND, Stepanov IN, Lukyanitsa AA, Ziborov VS. The Effect of a Rotating Cone on Horseradish Peroxidase Aggregation on Mica Revealed by Atomic Force Microscopy. MICROMACHINES 2022; 13:1947. [PMID: 36363968 PMCID: PMC9697547 DOI: 10.3390/mi13111947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Our study reported herein aims to determine whether an electromagnetic field, induced triboelectrically by a metallic cone, rotating at a frequency of 167 Hz, has an effect on the properties of the horseradish peroxidase (HRP) enzyme. Atomic force microscopy (AFM) was employed to detect even the most subtle effects on single enzyme molecules. In parallel, a macroscopic method (spectrophotometry) was used to reveal whether the enzymatic activity of HRP in solution was affected. An aqueous solution of the enzyme was incubated at a distance of 2 cm from the rotating cone. The experiments were performed at various incubation times. The control experiments were performed with a non-rotating cone. The incubation of the HRP solution was found to cause the disaggregation of the enzyme. At longer incubation times, this disaggregation was found to be accompanied by the formation of higher-order aggregates; however, no change in the HRP enzymatic activity was observed. The results of our experiments could be of interest in the development of enzyme-based biosensors with rotating elements such as stirrers. Additionally, the results obtained herein are important for the correct interpretation of data obtained with such biosensors.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, 109472 Moscow, Russia
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, 119991 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
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19
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Ivanova IA, Ershova MO, Shumov ID, Valueva AA, Ivanov YD, Pleshakova TO. Atomic Force Microscopy Study of the Temperature and Storage Duration Dependencies of Horseradish Peroxidase Oligomeric State. Biomedicines 2022; 10:biomedicines10102645. [PMID: 36289907 PMCID: PMC9599489 DOI: 10.3390/biomedicines10102645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
This paper presents an investigation of the temperature dependence of the oligomeric state of the horseradish peroxidase (HRP) enzyme on the temperature of its solution, and on the solution storage time, at the single-molecule level. Atomic force microscopy has been employed to determine how the temperature and the storage time of the HRP solution influence its aggregation upon direct adsorption of the enzyme from the solution onto bare mica substrates. In parallel, spectrophotometric measurements have been performed in order to estimate whether the HRP enzymatic activity changes over time upon the storage of the enzyme solution. The temperature dependence of the HRP oligomeric state has been studied within a broad (15–40 °C) temperature range. It has been demonstrated that the storage of the HRP solution for 14 days does not have any considerable effect on the oligomeric state of the enzyme, neither does it affect its activity. At longer storage times, AFM has allowed us to reveal a tendency of HRP to oligomerization during the storage of its buffered solution, while the enzymatic activity remains virtually unchanged even after a 1-month-long storage. By AFM, it has been revealed that after the incubation of a mica substrate in the HRP solution at various temperatures, the content of the mica-adsorbed oligomers increases insignificantly owing to a high-temperature stability of the enzyme.
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20
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He SB, Yang HJ, Yang L, A. A. Noreldeen H, Peng HP, Deng HH, Chen W, Hong GL. Rutin as a coenzyme of Fe-doped silicon nanozyme with enhanced peroxidase-like activity for a colorimetric β-glucuronidase sensor. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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21
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The Effect of a Dodecahedron-Shaped Structure on the Properties of an Enzyme. J Funct Biomater 2022; 13:jfb13040166. [PMID: 36278635 PMCID: PMC9590084 DOI: 10.3390/jfb13040166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/26/2022] Open
Abstract
In this research, the influence of a dodecahedron-shaped structure on the adsorption behavior of a horseradish peroxidase (HRP) enzyme glycoprotein onto mica substrates was studied. In the experiments, samples of an aqueous HRP solution were incubated at various distances (0.03 m, 2 m, 5 m, and control at 20 m) from the dodecahedron surface. After the incubation, the direct adsorption of HRP onto mica substrates immersed in the solutions was performed, and the mica-adsorbed HRP particles were visualized via atomic force microscopy (AFM). The effect of the increased HRP aggregation was only observed after the incubation of the enzyme solution at the 2 m distance from the dodecahedron. In addition, with respect to the control sample, spectrophotometric measurements revealed no change in the HRP enzymatic activity after the incubation at any of the distances studied. The results reported herein can be of use in the modeling of the possible influences of various spatial structures on biological objects in the development of biosensors and other electronic equipment.
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22
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Sosna M, Ferapontova EE. Electron Transfer in Binary Hemin-Modified Alkanethiol Self-Assembled Monolayers on Gold: Hemin's Lateral and Interfacial Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11180-11190. [PMID: 36062334 DOI: 10.1021/acs.langmuir.2c01064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Orientated coupling of redox enzymes to electrodes by their reconstitution onto redox cofactors, such as hemin conjugated to self-assembled monolayers (SAMs) formed on the electrodes, poses the requirements for a SAM design enabling reconstitution. We show that the kinetics of electron transfer (ET) in binary SAMs of alkanethiols on gold composed of in situ hemin-conjugated 11-amino-1-undecanethiol (AUT) and diluting OH-terminated alkanethiols with 11, 6, and 2 methylene groups (MC11OH, MC6OH, and MC2OH) depends on both the SAM composition and surface density of hemin, Γheme. In AUT/MC11OH SAMs composed of equal linker/diluent lengths, the heterogeneous ET rate constant ks decreased with the Γheme and varied between 70 and 500 s-1. For shorter diluents, the ks of 245-330 s-1 (C6) and 300-340 s-1 (C2) showed a little (if any) Γheme dependence. In AUT/MC11OH SAMs, the increasing Γheme resulted in the steric crowding of hemin species and their neighboring lateral interactions in the plane of hemin localization, affecting the potential distribution at the SAM/electrode interface and inducing local electrostatic effects interfering with hemin oxidation. In AUT/MC6OH and AUT/MC2OH SAMs, hemin discharged at the plane of the closest approach to the gold surface, equal to the diluent length and permeable to electrolyte ions, which lessened those effects. All studied binary SAMs provided steric hindrance for protein reconstitution on the hemin cofactor conjugated to the extended AUT linker. Further use of SAM-modified electrodes with the covalently attached hemin as interfaces for heme proteins' reconstitution should consider SAMs with loosely dispersed redox centers terminating more rigid molecular wires. Such wires place hemin at fixed distances from the electrode surface and thus ensure the interfacial properties required for the effective on-surface reconstitution of proteins and enzymes.
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Affiliation(s)
- Maciej Sosna
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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23
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Uchida T, Ota K, Tatsumi A, Takeuchi S, Ishimori K. Metal Sensing by a Glycine-Histidine Repeat Sequence Regulates the Heme Degradation Activity of PM0042 from Pasteurella multocida. Inorg Chem 2022; 61:13543-13553. [PMID: 35960895 DOI: 10.1021/acs.inorgchem.2c02172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PM0042 protein from the Gram-negative bacterial pathogen Pasteurella multocida is homologous to the heme-degrading enzyme HutZ belonging to the pyridoxine-5-phosphate oxidase-like family. A characteristic feature of PM0042 is possession of a glycine-histidine (GH) repeat sequence at the C-terminal region. In this study, we examined the heme degradation ability of PM0042, with a particular focus on the role of the GH repeat sequence. PM0042 was expressed in Escherichia coli and successfully purified using a nickel (Ni2+)-affinity column without a histidine tag, suggesting that its GH motif facilitates binding to Ni2+. Reaction with ascorbic acid induced a significant decrease in the Soret band, suggesting the breakage of heme. While a Fe2+-ferrozine complex was not formed upon addition of ferrozine to the solution after the reaction, prior addition of metal ions to fill the metal binding site in the GH repeat sequence led to increased complex formation. In the presence of Fe2+, the heme degradation rate was accelerated ∼threefold, supporting the theory that Fe2+ binds the PM0042 protein (possibly at the GH repeat sequence) and enhances its heme degradation activity. In contrast to HutZ from Vibrio cholerae in which enzymatic activity is regulated by the protonation status of the heme proximal ligand, heme reduction is not the rate-determining step for PM0042. Rather, proton transfer to reduced oxyheme is affected, as established with the H2O/D2O isotope experiment. Based on the collective findings, the GH repeat sequence of PM0042 is proposed to function as a metal sensor that modulates iron uptake via the heme-degrading process in P. multocida.
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Affiliation(s)
- Takeshi Uchida
- 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
| | - Akinobu Tatsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Syota Takeuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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24
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Akhgar CK, Ebner J, Alcaraz MR, Kopp J, Goicoechea H, Spadiut O, Schwaighofer A, Lendl B. Application of Quantum Cascade Laser-Infrared Spectroscopy and Chemometrics for In-Line Discrimination of Coeluting Proteins from Preparative Size Exclusion Chromatography. Anal Chem 2022; 94:11192-11200. [PMID: 35926134 PMCID: PMC9386682 DOI: 10.1021/acs.analchem.2c01542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
An external-cavity quantum cascade laser (EC-QCL)-based
flow-through
mid-infrared (IR) spectrometer was placed in line with a preparative
size exclusion chromatography system to demonstrate real-time analysis
of protein elutions with strongly overlapping chromatographic peaks.
Two different case studies involving three and four model proteins
were performed under typical lab-scale purification conditions. The
large optical path length (25 μm), high signal-to-noise ratios,
and wide spectral coverage (1350 to 1750 cm–1) of
the QCL-IR spectrometer allow for robust spectra acquisition across
both the amide I and II bands. Chemometric analysis by self-modeling
mixture analysis and multivariate curve resolution enabled accurate
quantitation and structural fingerprinting across the protein elution
transient. The acquired concentration profiles were found to be in
excellent agreement with the off-line high-performance liquid chromatography
reference analytics performed on the collected effluent fractions.
These results demonstrate that QCL-IR detectors can be used effectively
for in-line, real-time analysis of protein elutions, providing critical
quality attribute data that are typically only accessible through
time-consuming and resource-intensive off-line methods.
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Affiliation(s)
- Christopher K Akhgar
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Julian Ebner
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Mirta R Alcaraz
- Laboratorio de Desarrollo Analítico y Quimiometría (LADAQ), Cátedra de Química Analítica I, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB CABA, Argentina
| | - Julian Kopp
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Héctor Goicoechea
- Laboratorio de Desarrollo Analítico y Quimiometría (LADAQ), Cátedra de Química Analítica I, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB CABA, Argentina
| | - Oliver Spadiut
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Andreas Schwaighofer
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Bernhard Lendl
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, Getreidemarkt 9, 1060 Vienna, Austria
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25
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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26
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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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27
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Abendroth J, Buchko GW, Liew FN, Nguyen JN, Kim HJ. Structural Characterization of Cytochrome c'β-Met from an Ammonia-Oxidizing Bacterium. Biochemistry 2022; 61:563-574. [PMID: 35315646 DOI: 10.1021/acs.biochem.1c00640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ammonia-oxidizing bacterium Nitrosomonas europaea expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NH2OH) is converted to nitric oxide (NO) and nitrous oxide (N2O) requiring a unique heme-lysyl cross-link in the catalytic cofactor. In the second, cyt c'β-Met, the cross-link is absent, and the cytochrome instead binds H2O2 forming a ferryl species similar to compound II of peroxidases. Here, we report the 1.80 Å crystal structure of cyt c'β-Met─a well-expressed protein in N. europaea with a lysine to a methionine replacement at the cross-linking position. The structure of cyt c'β-Met is characterized by a large β-sheet typical of P460 members; however, several localized structural differences render cyt c'β-Met distinct. This includes a large lasso-like loop at the "top" of the cytochrome that is not observed in other structurally characterized members. Active site variation is also observed, especially in comparison to its closest homologue cyt c'β from the methane-oxidizing Methylococcus capsulatus Bath, which also lacks the cross-link. The phenylalanine "cap" which is presumed to control small ligand access to the distal heme iron is replaced with an arginine, reminiscent of the strictly conserved distal arginine in peroxidases and to the NH2OH-oxidizing cytochromes P460. A critical proton-transferring glutamate residue required for NH2OH oxidation is nevertheless missing in the active site. This in part explains the inability of cyt c'β-Met to oxidize NH2OH. Our structure also rationalizes the absence of a methionyl cross-link, although the side chain's spatial position in the structure does not eliminate the possibility that it could form under certain conditions.
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Affiliation(s)
- Jan Abendroth
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,UCB Biosciences, Bainbridge Island, Washington 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 98354, United States.,School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Fong Ning Liew
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Joline N Nguyen
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Hyung J Kim
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
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28
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Di S, Fan S, Jiang F, Cong Z. A Unique P450 Peroxygenase System Facilitated by a Dual-Functional Small Molecule: Concept, Application, and Perspective. Antioxidants (Basel) 2022; 11:antiox11030529. [PMID: 35326179 PMCID: PMC8944620 DOI: 10.3390/antiox11030529] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 02/01/2023] Open
Abstract
Cytochrome P450 monooxygenases (P450s) are promising versatile oxidative biocatalysts. However, the practical use of P450s in vitro is limited by their dependence on the co-enzyme NAD(P)H and the complex electron transport system. Using H2O2 simplifies the catalytic cycle of P450s; however, most P450s are inactive in the presence of H2O2. By mimicking the molecular structure and catalytic mechanism of natural peroxygenases and peroxidases, an artificial P450 peroxygenase system has been designed with the assistance of a dual-functional small molecule (DFSM). DFSMs, such as N-(ω-imidazolyl fatty acyl)-l-amino acids, use an acyl amino acid as an anchoring group to bind the enzyme, and the imidazolyl group at the other end functions as a general acid-base catalyst in the activation of H2O2. In combination with protein engineering, the DFSM-facilitated P450 peroxygenase system has been used in various oxidation reactions of non-native substrates, such as alkene epoxidation, thioanisole sulfoxidation, and alkanes and aromatic hydroxylation, which showed unique activities and selectivity. Moreover, the DFSM-facilitated P450 peroxygenase system can switch to the peroxidase mode by mechanism-guided protein engineering. In this short review, the design, mechanism, evolution, application, and perspective of these novel non-natural P450 peroxygenases for the oxidation of non-native substrates are discussed.
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Affiliation(s)
- Siyu Di
- CAS Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.D.); (S.F.); (F.J.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengxian Fan
- CAS Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.D.); (S.F.); (F.J.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengjie Jiang
- CAS Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.D.); (S.F.); (F.J.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.D.); (S.F.); (F.J.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-532-80662758
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29
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Yao Y, Huang L, Xu Y, Li QX. Recombinant Arthromyces ramosus Peroxidase Has Similar Substrate Specificity Profiles as, but a Catalytic Efficiency up to 11-Fold Higher than, Horseradish Peroxidase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:646-655. [PMID: 34981926 DOI: 10.1021/acs.jafc.1c06261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fungal peroxidases are valuable enzymes. Arthromyces ramosus peroxidase (ARP) and horseradish peroxidase (HRP) share a conserved catalytic site. Both native ARP and recombinant ARP (rARP) were not commercially available. The substrate specificity and kinetic parameters of rARP and HRP were not well compared, particularly relevent to structure-activity relationship. In this work, rARP expressed by Komagataella phaffii had a production yield of 6.2 mg/L, up to 155-fold higher than ARP and other recombinant peroxidases, and a specific activity of 3240 units/mg toward 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), up to 29-fold higher than HRP and other peroxidases. The Michaelis constant (Km) and first-order rate constant (kcat) of rARP showed 10-fold substrate affinity and consequently 6-fold catalytic efficiency of HRP toward ABTS. Under optimal conditions, rARP shared similar substrate specificity profiles as commercial HRP; the second-order rate constants (kapp) of rARP showed 2-11-fold catalytic efficiency of HRP toward well-known peroxidase substrates. rARP's higher catalytic efficiency was also in agreement with the shorter binding distance of H/N-His56 in rARP/substrate in comparison to that of HRP/substrate, as illustrated by docking simulation. The rARP had similar substrate specificity profiles as, but higher specific activity and catalytic efficiency than, HRP, which merits its further structure-functional characterization and applications.
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Affiliation(s)
- Yuqun Yao
- School of Medicine, Guangxi University of Science and Technology, Liushi Road 257, Liuzhou 545025, China
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, Hawaii 96822, United States
| | - Li Huang
- School of Medicine, Guangxi University of Science and Technology, Liushi Road 257, Liuzhou 545025, China
| | - Yueqiang Xu
- State Key Laboratory of Biochemical Engineering, Institute of Processing and Engineering, Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, Hawaii 96822, United States
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30
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Harlington AC, Shearwin KE, Bell SG, Whelan F. Efficient O-demethylation of lignin monoaromatics using the peroxygenase activity of cytochrome P450 enzymes. Chem Commun (Camb) 2022; 58:13321-13324. [DOI: 10.1039/d2cc04698a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Selective O-demethylation of the lignin monoaromatics, syringol and guaiacol, using the peroxygenase activity of two distinct cytochrome P450 enzymes.
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Affiliation(s)
- Alix C. Harlington
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Keith E. Shearwin
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephen G. Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Fiona Whelan
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
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31
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Hassan MM, Hettiarachchi M, Kilani M, Gao X, Sankari A, Boyer C, Mao G. Sustained A1 Adenosine Receptor Antagonist Drug Release from Nanoparticles Functionalized by a Neural Tracing Protein. ACS Chem Neurosci 2021; 12:4438-4448. [PMID: 34672533 DOI: 10.1021/acschemneuro.1c00538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Respiratory dysfunction is a major cause of death in people with spinal cord injury (SCI). A remaining unsolved problem in treating SCI is the intolerable side effects of the drugs to patients. In a significant departure from conventional targeted nanotherapeutics to overcome the blood-brain barrier (BBB), this work pursues a drug-delivery approach that uses neural tracing retrograde transport proteins to bypass the BBB and deliver an adenosine A1 receptor antagonist drug, 1,3-dipropyl-8-cyclopentyl xanthine, exclusively to the respiratory motoneurons in the spinal cord and the brainstem. A single intradiaphragmatic injection at one thousandth of the native drug dosage induces prolonged respiratory recovery in a hemisection animal model. To translate the discovery into new treatments for respiratory dysfunction, we carry out this study to characterize the purity and quality of synthesis, stability, and drug-release properties of the neural tracing protein (wheat germ agglutinin chemically conjugated to horseradish peroxidase)-coupled nanoconjugate. We show that the batch-to-batch particle size and drug dosage variations are less than 10%. We evaluate the nanoconjugate size against the spatial constraints imposed by transsynaptic transport from pre to postsynaptic neurons. We determine that the nanoconjugate formulation is capable of sustained drug release lasting for days at physiologic pH, a prerequisite for long-distance transport of the drug from the diaphragm muscle to the brainstem. We model the drug-release profiles using a first-order reaction model and the Noyes-Whitney diffusion model. We confirm via biological electron microscopy that the nanoconjugate particles do not accumulate in the tissues at the injection site. We define the nanoconjugate storage conditions after monitoring the solution dispersion stability under various conditions for 4 months. This study supports further development of neural tracing protein-enabled nanotherapeutics for treating respiratory problems associated with SCI.
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Affiliation(s)
- Md. Musfizur Hassan
- School of Chemical Engineering, University of New South Wales (UNSW Sydney), Sydney, New South Wales 2052, Australia
| | - Malsha Hettiarachchi
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Mohamed Kilani
- School of Chemical Engineering, University of New South Wales (UNSW Sydney), Sydney, New South Wales 2052, Australia
| | - Xiaohua Gao
- School of Medicine, Wayne State University, Detroit, Michigan 48201, United States
| | - Abdulghani Sankari
- School of Medicine, Wayne State University, Detroit, Michigan 48201, United States
| | - Cyrille Boyer
- School of Chemical Engineering, University of New South Wales (UNSW Sydney), Sydney, New South Wales 2052, Australia
- Australian Centre for Nanomedicine, Sydney, New South Wales 2052, Australia
| | - Guangzhao Mao
- School of Chemical Engineering, University of New South Wales (UNSW Sydney), Sydney, New South Wales 2052, Australia
- Australian Centre for Nanomedicine, Sydney, New South Wales 2052, Australia
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32
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Khojastehnezhad A, Taghavi F, Yaghoobi E, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. Recent achievements and advances in optical and electrochemical aptasensing detection of ATP based on quantum dots. Talanta 2021; 235:122753. [PMID: 34517621 DOI: 10.1016/j.talanta.2021.122753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022]
Abstract
The design and fabrication of high sensitive and selective biosensing platforms areessential goals to precisely recognize biomaterials in biological assays. In particular, determination of adenosine triphosphate (ATP) as the main energy currency of the cells and one of the most important biomolecules in living organisms is a pressing need in advanced biological detection. Recently, aptamer-based biosensors are introduced as a new direct strategy in which the aptamers (Apts) directly bind to the different targets and detect them on the basis of conformational changes and physical interactions. They can also be conjugated to optical and electronic probes such as quantum dot (QD) nanomaterials and provide unique QD aptasensing platforms. Currently, these Apt-based biosensors with excellent recognition features have attracted extensive attention due to the high specificity, rapid response and facile construction. Therefore, in this review article, recent achievements and advances in aptasensing detection of ATP based on different detection methods and types of QDs are discussed. In this regard, the optical and electrochemical aptasensors have been categorized based on detection methods; fluorescence (FL), electrochemiluminescence (ECL) and photoelectrochemical (PEC) and they have been also divided to two main groups based on QDs; metal-based (M-based) and carbon-based (C-based) materials. Then, their advantages and limitations have been highlighted, compared and discussed in detail.
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Affiliation(s)
- Amir Khojastehnezhad
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Faezeh Taghavi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elnaz Yaghoobi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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33
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Sáringer S, Valtner T, Varga Á, Maléth J, Szilágyi I. Development of polymer-based multifunctional composite particles of protease and peroxidase activities. J Mater Chem B 2021; 10:2523-2533. [PMID: 34757359 DOI: 10.1039/d1tb01861b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A hybrid material (SL-PPN-HEP-HRP) of dual enzyme function was prepared by co-immobilization of papain (PPN) and horseradish peroxidase (HRP) on sulphate latex (SL) microspheres using heparin (HEP) polyelectrolyte as a building block in the sequential adsorption method. The doses of PPN, HEP and HRP were optimized in each step of the preparation process to achieve high functional and colloidal stability. The enzymes and the polyelectrolyte strongly adsorbed on the oppositely charged surfaces via electrostatic forces, and enzyme leakage was not observed from the hybrid material, as confirmed by colorimetric protein tests and microscopy measurements. It was found that the polyelectrolyte acted as a separator between PPN and HRP to prevent hydrolytic attack on the latter enzyme, which otherwise prevents the joint use of these important biocatalysts. Excellent colloidal stability was obtained for the SL-PPN-HEP-HRP composite and the embedded PPN and HRP showed remarkable protease and peroxidase activities, respectively, at least until five days after preparation. The present results offer a promising approach to develop biocatalytic systems of dual function, which are often required in manufacturing processes in the food industry, where the colloidal stability of such multifunctional materials is a key parameter to achieve remarkable efficiency.
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Affiliation(s)
- Szilárd Sáringer
- MTA-SZTE Lendület Biocolloids Research Group, Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary.
| | - Tamás Valtner
- MTA-SZTE Lendület Biocolloids Research Group, Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary.
| | - Árpád Varga
- HAS-USZ Momentum Epithelial Cell Signaling and Secretion Research Group and HCEMM-SZTE Molecular Gastroenterology Research Group, Department of Medicine, University of Szeged, H-6720 Szeged, Hungary
| | - József Maléth
- HAS-USZ Momentum Epithelial Cell Signaling and Secretion Research Group and HCEMM-SZTE Molecular Gastroenterology Research Group, Department of Medicine, University of Szeged, H-6720 Szeged, Hungary
| | - István Szilágyi
- MTA-SZTE Lendület Biocolloids Research Group, Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary.
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34
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Sun P, Li Y, Li J, Zhang Y. Entrapment of horseradish peroxidase into nanometer-scale metal-organic frameworks: a new nanocarrier for signal amplification in enzyme-linked immunosorbent assay. Mikrochim Acta 2021; 188:409. [PMID: 34739603 DOI: 10.1007/s00604-021-05065-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/12/2021] [Indexed: 11/24/2022]
Abstract
Horseradish peroxidase (HRP) was highly loaded into large holes of nanometer-scale metal-organic frameworks (i.e., PCN-333(Al)) for signal amplification in enzyme-linked immunosorbent assay (ELISA). The enzyme-labeled antibody complex prepared using nanometer-scale PCN-333(Al) maintained a high catalytic efficiency. Its Vm and Kcat values with 3,3',5,5'-Tetramethylbenzidine (TMB)-H2O2 as substrates were 4.84 × 10-5 mM/s and 4.84 × 104 min-1, respectively. We demonstrated an HRP@PCN-333 signal amplification strategy for colorimetric assay of human prostate-specific antigen (PSA). The linear range of PSA detection by using this method was 15-165 pg/mL, and the limit of detection was 6 pg/mL (S/N = 3), indicating the potential application of this method in detecting disease markers under clinical conditions. The presented strategy exhibited the characteristics of significantly increased amount of labeled enzymes, improved stability and utilization of enzymes, simple preparation process of enzyme-labeled antibodies, and low cost.
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Affiliation(s)
- Pengyue Sun
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Changan West Road 620, Xi'an, 710119, China
| | - Yao Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Changan West Road 620, Xi'an, 710119, China
| | - Jing Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Changan West Road 620, Xi'an, 710119, China
| | - Yaodong Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Changan West Road 620, Xi'an, 710119, China.
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35
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Hindson SA, Bunzel HA, Frank B, Svistunenko DA, Williams C, van der Kamp MW, Mulholland AJ, Pudney CR, Anderson JLR. Rigidifying a De Novo Enzyme Increases Activity and Induces a Negative Activation Heat Capacity. ACS Catal 2021; 11:11532-11541. [PMID: 34557328 PMCID: PMC8453482 DOI: 10.1021/acscatal.1c01776] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/29/2021] [Indexed: 12/22/2022]
Abstract
![]()
Conformational sampling
profoundly impacts the overall activity
and temperature dependence of enzymes. Peroxidases have emerged as
versatile platforms for high-value biocatalysis owing to their broad
palette of potential biotransformations. Here, we explore the role
of conformational sampling in mediating activity in the de
novo peroxidase C45. We demonstrate that 2,2,2-triflouoroethanol
(TFE) affects the equilibrium of enzyme conformational states, tending
toward a more globally rigid structure. This is correlated with increases
in both stability and activity. Notably, these effects are concomitant
with the emergence of curvature in the temperature-activity profile,
trading off activity gains at ambient temperature with losses at high
temperatures. We apply macromolecular rate theory (MMRT) to understand
enzyme temperature dependence data. These data point to an increase
in protein rigidity associated with a difference in the distribution
of protein dynamics between the ground and transition states. We compare
the thermodynamics of the de novo enzyme activity
to those of a natural peroxidase, horseradish peroxidase. We find
that the native enzyme resembles the rigidified de novo enzyme in terms of the thermodynamics of enzyme catalysis and the
putative distribution of protein dynamics between the ground and transition
states. The addition of TFE apparently causes C45 to behave more like
the natural enzyme. Our data suggest robust, generic strategies for
improving biocatalytic activity by manipulating protein rigidity;
for functional de novo protein catalysts in particular,
this can provide more enzyme-like catalysts without further rational
engineering, computational redesign, or directed evolution.
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Affiliation(s)
- Sarah A. Hindson
- Department of Biology and Biochemistry, Centre for Sustainable Chemical Technology, University of Bath, Bath BA2 7AY, U.K
| | - H. Adrian Bunzel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
- Centre for Computational Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Bettina Frank
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
- Bristol Centre for Functional Nanomaterials, School of Physics, University of Bristol, Bristol BS8 1TL, U.K
| | | | | | | | | | - Christopher R. Pudney
- Department of Biology and Biochemistry, Centre for Sustainable Chemical Technology, University of Bath, Bath BA2 7AY, U.K
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36
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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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37
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Lukacova Z, Bokor B, Vavrova S, Soltys K, Vaculik M. Divergence of reactions to arsenic (As) toxicity in tobacco (Nicotiana benthamiana) plants: A lesson from peroxidase involvement. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126049. [PMID: 34000701 DOI: 10.1016/j.jhazmat.2021.126049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 03/25/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
To evaluate the multiplicity of reactions to toxic metalloid arsenic (As) with specific emphasis on the role of plant peroxidases, a model plant Nicotiana benthamiana was cultivated in in vitro conditions at various doses of As (applied as As5+ up to 80 μM). After 28-day cultivation, several physiological characteristics such as plant growth, photosynthetic pigment concentration, As concentration, peroxidase (POX) expression levels, and POX activity were evaluated. A newly sequenced gene for POX has been identified, that belongs to the Class III plant extracellular peroxidases, and its relationship to the genus Solanum as the most relative species has been confirmed. In the control and selected As treatments (20As, 50As, and 80As), newly identified POX expression and POX activity were continuously detected during the whole cultivation period. The plant reactions to As stress were distinguished into three groups: low As, moderate As, and high As. A tight relationship was found between the photosynthetic pigments and POX expression. Accumulation of As in roots and shoots showed correlations with POX activities. The results showed that the diversity of reactions depends on As dose and time exposure and indicate an interface of peroxidase functional role with other physiological processes in plants suffering from As toxicity.
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Affiliation(s)
- Zuzana Lukacova
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovak Republic.
| | - Boris Bokor
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovak Republic; Comenius University Science Park, Ilkovičova 8, 841 04 Bratislava, Slovak Republic
| | - Silvia Vavrova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Katarina Soltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Marek Vaculik
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
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38
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Humer D, Furlanetto V, Schruef AK, Wlodarczyk A, Kuttke M, Divne C, Spadiut O. Potential of unglycosylated horseradish peroxidase variants for enzyme prodrug cancer therapy. Biomed Pharmacother 2021; 142:112037. [PMID: 34392084 DOI: 10.1016/j.biopha.2021.112037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/07/2021] [Indexed: 12/17/2022] Open
Abstract
Fighting cancer still relies on chemo- and radiation therapy, which is a trade-off between effective clearance of malignant cells and severe side effects on healthy tissue. Targeted cancer treatment on the other hand is a promising and refined strategy with less systemic interference. The enzyme horseradish peroxidase (HRP) exhibits cytotoxic effects on cancer cells in combination with indole-3-acetic acid (IAA). However, the plant-derived enzyme is out of bounds for medical purposes due to its foreign glycosylation pattern and resulting rapid clearance and immunogenicity. In this study, we generated recombinant, unglycosylated HRP variants in Escherichia coli using random mutagenesis and investigated their biochemical properties and suitability for cancer treatment. The cytotoxicity of the HRP-IAA enzyme prodrug system was assessed in vitro with HCT-116 human colon, FaDu human nasopharyngeal squamous cell carcinoma and murine colon adenocarcinoma cells (MC38). Extensive cytotoxicity was shown in all three cancer cell lines: the cell viability of HCT-116 and MC38 cells treated with HRP-IAA was below 1% after 24 h incubation and the surviving fraction of FaDu cells was ≤ 10% after 72 h. However, no cytotoxic effect was observed upon in vivo intratumoral application of HRP-IAA on a MC38 tumor model in C57BL/6J mice. However, we expect that targeting of HRP to the tumor by conjugation to specific antibodies or antibody fragments will reduce HRP clearance and thereby enhance therapy efficacy.
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Affiliation(s)
- Diana Humer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Valentina Furlanetto
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health Department of Industrial Biotechnology, AlbaNova, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden
| | - Anna-Katharina Schruef
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Angelika Wlodarczyk
- Austrian Research Institute for Chemistry and Engineering (OFI), Franz-Grill-Straße 5, Objekt 213, 1030 Vienna, Austria
| | - Mario Kuttke
- Medical University of Vienna, Institute for Vascular Biology and Thrombosis Research, Center for Pharmacology and Physiology, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Christina Divne
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health Department of Industrial Biotechnology, AlbaNova, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria.
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39
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Araki H, Hagiwara S, Shinomiya R, Momotake A, Kotani H, Kojima T, Ochiai T, Shimada N, Maruyama A, Yamamoto Y. A cationic copolymer as a cocatalyst for a peroxidase-mimicking heme-DNAzyme. Biomater Sci 2021; 9:6142-6152. [PMID: 34346413 DOI: 10.1039/d1bm00949d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heme binds to a parallel-stranded G-quadruplex DNA to form a peroxidase-mimicking heme-DNAzyme. An interpolyelectrolyte complex between the heme-DNAzyme and a cationic copolymer possessing protonated amino groups was characterized and the peroxidase activity of the complex was evaluated to elucidate the effect of the polymer on the catalytic activity of the heme-DNAzyme. We found that the catalytic activity of the heme-DNAzyme is enhanced through the formation of the interpolyelectrolyte complex due to the general acid catalysis of protonated amino groups of the polymer, enhancing the formation of the iron(iv)oxo porphyrin π-cation radical intermediate known as Compound I. This finding indicates that the polymer with protonated amino groups can act as a cocatalyst for the heme-DNAzyme in the oxidation catalysis. We also found that the enhancement of the activity of the heme-DNAzyme by the polymer depends on the local heme environment such as the negative charge density in the proximity of the heme and substrate accessibility to the heme. These findings provide novel insights as to molecular design of the heme-DNAzyme for enhancing its catalytic activity.
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Affiliation(s)
- Haruka Araki
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Shota Hagiwara
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryosuke Shinomiya
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Hiroaki Kotani
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takuro Ochiai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Naohiko Shimada
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Atsushi Maruyama
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan and Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
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40
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Hagiwara S, Momotake A, Ogura T, Yanagisawa S, Suzuki A, Neya S, Yamamoto Y. Effects of Heme Electronic Structure and Local Heme Environment on Catalytic Activity of a Peroxidase-Mimicking Heme-DNAzyme. Inorg Chem 2021; 60:11206-11213. [PMID: 34289695 DOI: 10.1021/acs.inorgchem.1c01179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic cycle of a peroxidase-mimicking heme-DNAzyme involves an iron(IV)oxo porphyrin π-cation radical intermediate known as compound I formed through heterolytic O-O bond cleavage of an Fe3+-bound hydroperoxo ligand (Fe-OOH) in compound 0, like that of a heme enzyme such as horseradish peroxidase (HRP). Peroxidase assaying of complexes composed of chemically modified hemes possessing various electron densities of the heme iron atom (ρFe) and parallel-stranded tetrameric G-quadruplex DNAs of oligonucleotides d(TTAGGG), d(TTAGGGT), and d(TTAGGGA) was performed to elucidate the effects of the heme electronic structure and local heme environment on the catalytic activity of the heme-DNAzyme. The study revealed that the DNAzyme activity is enhanced through an increase in the ρFe and general base catalysis of the adenine base adjacent to the heme, which are reminiscent of the "push" and "pull" mechanisms in the catalytic cycle of HRP, respectively, and that the activity of the heme-DNAzyme can be independently controlled through the heme electronic structure and local heme environment. These findings allow a deeper understanding of the structure-function relationship of the peroxidase-mimicking heme-DNAzyme.
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Affiliation(s)
- Shota Hagiwara
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Sachiko Yanagisawa
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Akihiro Suzuki
- Department of Material Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan.,Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
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41
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Cui X, Wang K, Wang T, Li J, Li C, Wang W, Wang H, Wang Z. Crystal Structure Analysis of Cationic Peroxidase from Proso Millet and Identification of Its Phosphatase Active Sites. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6251-6259. [PMID: 34044543 DOI: 10.1021/acs.jafc.1c01606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proso millet peroxidase (PmPOD) belongs to class III plant peroxidases, which are enzymes typically characterized by their heme coenzymes. PmPOD exhibits not only heme-dependent peroxidase activity but also heme-independent phosphatase activity. Crystal structure analysis and sequence alignment showed that PmPOD contained a phosphatase catalytic loop CXXXXXR in its β-domain that is similar to the active site of a dual-specific phosphatase. Recombinant truncated proso millet peroxidase (tPmPOD), which contained only a conserved catalytic loop CXXXXXR of phosphatase, was found to exhibit phosphatase activity. Five tPmPOD mutants containing five different mutations in the phosphatase active sites exhibited significantly lower phosphatase activity compared to that of tPmPOD, indicating that the five amino acids play important roles in the phosphatase activity of tPmPOD. Finally, nucleophilic amino acid Cys192 formed a disulfide bond with Cys219 to protect the stability of a sulfhydryl group; thus, it may play a decisive role in the phosphatase activity of PmPOD.
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Affiliation(s)
- Xiaodong Cui
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan030006, China
| | - Ke Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan030006, China
| | - Tingfen Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan030006, China
| | - Jiao Li
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Chen Li
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Wenming Wang
- Institute of Molecular Science, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Hongfei Wang
- Institute of Molecular Science, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Zhuanhua Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan030006, China
- School of Life Science, Shanxi University, Taiyuan 030006, China
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42
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Zitare UA, Habib MH, Rozeboom H, Mascotti ML, Todorovic S, Fraaije MW. Mutational and structural analysis of an ancestral fungal dye-decolorizing peroxidase. FEBS J 2021; 288:3602-3618. [PMID: 33369202 PMCID: PMC8248431 DOI: 10.1111/febs.15687] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/31/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) constitute a superfamily of heme-containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A-C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D-type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D-type DyP ancestor, AncDyPD-b1. Expression of AncDyPD-b1 in Escherichia coli results in large amounts of a heme-containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV-Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady-state kinetics and the crystal structure, reveal fine pH-dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long-range electron transfer process. DATABASE: Structural data are available in the PDB database under the accession number 7ANV.
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Affiliation(s)
- Ulises A. Zitare
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE)Departamento de Química Inorgánica, Analítica y Química FísicaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires and CONICETArgentina
| | - Mohamed H. Habib
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Department of Microbiology and ImmunologyFaculty of PharmacyCairo UniversityEgypt
| | | | - Maria L. Mascotti
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- IMIBIO‐SL CONICETFacultad de Química Bioquímica y FarmaciaUniversidad Nacional de San LuisArgentina
| | - Smilja Todorovic
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
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43
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Hasan S, Naeem A. The modulation of structural stability of horseradish peroxidase as a consequence of macromolecular crowding. J Mol Recognit 2021; 34:e2902. [PMID: 34013591 DOI: 10.1002/jmr.2902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/24/2021] [Accepted: 04/05/2021] [Indexed: 11/07/2022]
Abstract
Macromolecular crowding plays an inevitable role in all biological processes influencing association, conformation, and other characteristics of proteins. Present study is based on the effect of macromolecular crowding on structure of horseradish peroxidase (HRP) enzyme. Concentration-dependent conformational changes induced by crowding agents, dextran 70 and polyethylene glycol (PEG)-4000, were monitored employing a range of biophysical techniques. The intrinsic fluorescence spectra showed transition of protein from native to unfolded state. Marked increase in 8-Anilino-1-naphthalene-sulphonoic acid and Thioflavin T fluorescence indicated presence of non-native moieties with 80 mg/mL dextran. Enhanced absorbance in turbidity, Soret, and Congo red in corroboration with scattering intensity at 350nm results revealed incidence of HRP aggregates. A new peak around 218 nm in CD spectra pointed towards change in secondary structure towards β-sheets. Significant loss of enzyme activity upon structural disruption was seen. Comet assay demonstrated DNA damage and genotoxic nature of HRP aggregates, supporting spectroscopic, and fluorescence results. The normalized results were obtained with 120 mg/mL PEG-4000 close to that of native HRP implying no disruptive effect on structure. It can be hypothesized that macromolecular crowding is a vital element, which can have diverse effects. In this study, dextran 70 was observed to have pro-aggregatory effect while enhanced stability of native enzyme was witnessed with PEG. Hence, it can be stated that PEG has potentially better crowder as it helps retain the native enzyme structure. Routine addition of crowding agents is recommended if biological molecules are to be studied under more physiologically appropriate environments.
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Affiliation(s)
- Samra Hasan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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44
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Mishler-Elmore JW, Zhou Y, Sukul A, Oblak M, Tan L, Faik A, Held MA. Extensins: Self-Assembly, Crosslinking, and the Role of Peroxidases. FRONTIERS IN PLANT SCIENCE 2021; 12:664738. [PMID: 34054905 PMCID: PMC8160292 DOI: 10.3389/fpls.2021.664738] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/19/2021] [Indexed: 05/29/2023]
Abstract
The extensin (EXT) network is elaborated by the covalent intermolecular crosslinking of EXT glycoprotein monomers, and its proper assembly is important for numerous aspects of basic wall architecture and cellular defense. In this review, we discuss new advances in the secretion of EXT monomers and the molecular drivers of EXT network self-assembly. Many of the functions of EXTs are conferred through covalent crosslinking into the wall, so we also discuss the different types of known intermolecular crosslinks, the enzymes that are involved, as well as the potential for additional crosslinks that are yet to be identified. EXTs also function in wall architecture independent of crosslinking status, and therefore, we explore the role of non-crosslinking EXTs. As EXT crosslinking is upregulated in response to wounding and pathogen infection, we discuss a potential regulatory mechanism to control covalent crosslinking and its relationship to the subcellular localization of the crosslinking enzymes.
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Affiliation(s)
| | - Yadi Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
| | - Abhijit Sukul
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
| | - Mercedes Oblak
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
| | - Li Tan
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Ahmed Faik
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, United States
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
| | - Michael A. Held
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, United States
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Hu X, Wang X, Liu Q, Wu J, Zhang H, Khalique A, Sun Z, Chen R, Wei J, Li H, Kong D, Zhuang J, Yan X, Huang X. Nanozyme-Powered Giant Unilamellar Vesicles for Mimicry and Modulation of Intracellular Oxidative Stress. ACS APPLIED MATERIALS & INTERFACES 2021; 13:21087-21096. [PMID: 33908764 DOI: 10.1021/acsami.1c05512] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The bottom-up construction of enzyme-based artificial cells is generating increasing interest, but achieving artificial cells for "all artificial modules" remains challenging in synthetic biology. Here, we introduce a fully synthetic cell system by integration of biomimetic nanozymes into giant unilamellar vesicles (GUVs). To mimic native peroxidase for free radical generation by taking advantage of Fenton catalysis reactions, we designed and prepared a de novo artificial nanozyme composed of ferritin heavy-chain scaffold protein and catalytic Fe3O4 nanoparticles as the active center. As two examples in bioapplications, we showed this nanozyme-powered GUV system not only mimics intracellular oxidative stress pathways but also induces tumor cell death by sensing and responding to external chemical signals. Specifically, we recreated intracellular biochemical events, including DNA damage and lipid peroxidation, in the compartmentalized GUVs by taking advantage of nanozyme induction of defined catalytic reactions. Additionally, the GUV system also actively induced DNA double-strand breakage and lipid damage of tumor cells, in response to the high expression of H2O2 within the tumor microenvironment. This concept-of-proof study offers a promising option for defining catalysis in biological systems and gives new insights into the de novo creation of artificial cells in a fully synthetic manner.
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Affiliation(s)
- Xueyan Hu
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Xinyue Wang
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Qiqi Liu
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Jin Wu
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
- College of Medicine, Nankai University, Tianjin 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haoqi Zhang
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
- College of Medicine, Nankai University, Tianjin 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Anila Khalique
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Zhiyuan Sun
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Rui Chen
- School of Materials Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jing Wei
- Beijing Key Laboratory of Construction-Tailorable Advanced Functional Materials and Green Applications, Experimental Center of Advanced Materials School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Hongbo Li
- Beijing Key Laboratory of Construction-Tailorable Advanced Functional Materials and Green Applications, Experimental Center of Advanced Materials School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Deling Kong
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Jie Zhuang
- College of Medicine, Nankai University, Tianjin 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiyun Yan
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin 300071, China
- CAS Engineering Laboratory for Nanozymes, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinglu Huang
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin 300071, China
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Co-immobilization of antioxidant enzymes on titania nanosheets for reduction of oxidative stress in colloid systems. J Colloid Interface Sci 2021; 590:28-37. [DOI: 10.1016/j.jcis.2021.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/07/2023]
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47
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Lin YW. Biodegradation of aromatic pollutants by metalloenzymes: A structural-functional-environmental perspective. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213774] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Singh PK, Sharma P, Bhushan A, Kaur P, Sharma S, Singh TP. Structure of a ternary complex of lactoperoxidase with iodide and hydrogen peroxide at 1.77 Å resolution. J Inorg Biochem 2021; 220:111461. [PMID: 33882424 DOI: 10.1016/j.jinorgbio.2021.111461] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/05/2021] [Accepted: 04/05/2021] [Indexed: 11/16/2022]
Abstract
Lactoperoxidase (LPO) is a mammalian heme peroxidase which catalyzes the conversion of thiocyanate (SCN¯) and iodide (I-) by hydrogen peroxide (H2O2) into antimicrobial hypothiocyanite (OSCN¯) and hypoiodite (IO-). The prosthetic heme group is covalently attached to LPO through two ester linkages involving conserved glutamate and aspartate residues. On the proximal side, His351 is coordinated to heme iron while His 109 is located in the substrate binding site on the distal heme side. We report here the first structure of the ternary complex of LPO with iodide (I-) and H2O2 at 1.77 Å resolution. LPO was crystallized with ammonium iodide and the crystals were soaked in the reservoir solution containing H2O2. Structure determination showed the presence of an iodide ion and a H2O2 molecule in the substrate binding site. The iodide ion occupied the position which is stabilized by the interactions with heme moiety, His109, Arg255 and Glu258 while H2O2 was held between the heme iron and His109. The presence of I- in the distal heme cavity seems to screen the positive charge of Arg255 thus suppressing the proton transfer from H2O2 to His109. This prevents compound I formation and allows trapping of a stable enzyme-substrate (LPO-I--H2O2) ternary complex. This stable geometrical arrangement of H2O2 in the distal heme cavity of LPO is similar to that of H2O2 in the structure of the transient intermediate of the palm tree heme peroxidase. The biochemical studies showed that the catalytic activity of LPO decreased when the samples of LPO were preincubated with ammonium iodide.
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Affiliation(s)
- Prashant K Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Asha Bhushan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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Xi Z, Wei K, Wang Q, Kim MJ, Sun S, Fung V, Xia X. Nickel-Platinum Nanoparticles as Peroxidase Mimics with a Record High Catalytic Efficiency. J Am Chem Soc 2021; 143:2660-2664. [PMID: 33502185 DOI: 10.1021/jacs.0c12605] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
While nanoscale mimics of peroxidase have been extensively developed over the past decade or so, their catalytic efficiency as a key parameter has not been substantially improved in recent years. Herein, we report a class of highly efficient peroxidase mimic-nickel-platinum nanoparticles (Ni-Pt NPs) that consist of nickel-rich cores and platinum-rich shells. The Ni-Pt NPs exhibit a record high catalytic efficiency with a catalytic constant (Kcat) as high as 4.5 × 107 s-1, which is ∼46- and 104-fold greater than the Kcat values of conventional Pt nanoparticles and natural peroxidases, respectively. Density functional theory calculations reveal that the unique surface structure of Ni-Pt NPs weakens the adsorption of key intermediates during catalysis, which boosts the catalytic efficiency. The Ni-Pt NPs were applied to an immunoassay of a carcinoembryonic antigen that achieved an ultralow detection limit of 1.1 pg/mL, hundreds of times lower than that of the conventional enzyme-based assay.
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Affiliation(s)
| | - Kecheng Wei
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Qingxiao Wang
- Department of Materials Science and Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Moon J Kim
- Department of Materials Science and Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Shouheng Sun
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Victor Fung
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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50
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Pavlovic M, Muráth S, Katona X, Alsharif NB, Rouster P, Maléth J, Szilagyi I. Nanocomposite-based dual enzyme system for broad-spectrum scavenging of reactive oxygen species. Sci Rep 2021; 11:4321. [PMID: 33619308 PMCID: PMC7900168 DOI: 10.1038/s41598-021-83819-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
A broad-spectrum reactive oxygen species (ROS)-scavenging hybrid material (CASCADE) was developed by sequential adsorption of heparin (HEP) and poly(L-lysine) (PLL) polyelectrolytes together with superoxide dismutase (SOD) and horseradish peroxidase (HRP) antioxidant enzymes on layered double hydroxide (LDH) nanoclay support. The synthetic conditions were optimized so that CASCADE possessed remarkable structural (no enzyme leakage) and colloidal (excellent resistance against salt-induced aggregation) stability. The obtained composite was active in decomposition of both superoxide radical anions and hydrogen peroxide in biochemical assays revealing that the strong electrostatic interaction with the functionalized support led to high enzyme loadings, nevertheless, it did not interfere with the native enzyme conformation. In vitro tests demonstrated that ROS generated in human cervical adenocarcinoma cells were successfully consumed by the hybrid material. The cellular uptake was not accompanied with any toxicity effects, which makes the developed CASCADE a promising candidate for treatment of oxidative stress-related diseases.
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Affiliation(s)
- Marko Pavlovic
- Department of Colloid Chemistry, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Szabolcs Muráth
- MTA-SZTE Lendület Biocolloids Research Group, Interdisciplinary Excellence Centre, Department of Physical Chemistry and Materials Science, University of Szeged, 6720, Szeged, Hungary
| | - Xénia Katona
- MTA-SZTE Lendület Epithelial Cell Signaling and Secretion Research Group, Interdisciplinary Excellence Centre, University of Szeged, 6720, Szeged, Hungary
| | - Nizar B Alsharif
- MTA-SZTE Lendület Biocolloids Research Group, Interdisciplinary Excellence Centre, Department of Physical Chemistry and Materials Science, University of Szeged, 6720, Szeged, Hungary
| | - Paul Rouster
- Institute of Condensed Matter and Nanosciences-Bio and Soft Matter, Université Catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - József Maléth
- MTA-SZTE Lendület Epithelial Cell Signaling and Secretion Research Group, Interdisciplinary Excellence Centre, University of Szeged, 6720, Szeged, Hungary
| | - Istvan Szilagyi
- MTA-SZTE Lendület Biocolloids Research Group, Interdisciplinary Excellence Centre, Department of Physical Chemistry and Materials Science, University of Szeged, 6720, Szeged, Hungary.
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