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Purcarea C, Ruginescu R, Banciu RM, Vasilescu A. Extremozyme-Based Biosensors for Environmental Pollution Monitoring: Recent Developments. BIOSENSORS 2024; 14:143. [PMID: 38534250 DOI: 10.3390/bios14030143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Extremozymes combine high specificity and sensitivity with the ability to withstand extreme operational conditions. This work presents an overview of extremozymes that show potential for environmental monitoring devices and outlines the latest advances in biosensors utilizing these unique molecules. The characteristics of various extremozymes described so far are presented, underlining their stability and operational conditions that make them attractive for biosensing. The biosensor design is discussed based on the detection of photosynthesis-inhibiting herbicides as a case study. Several biosensors for the detection of pesticides, heavy metals, and phenols are presented in more detail to highlight interesting substrate specificity, applications or immobilization methods. Compared to mesophilic enzymes, the integration of extremozymes in biosensors faces additional challenges related to lower availability and high production costs. The use of extremozymes in biosensing does not parallel their success in industrial applications. In recent years, the "collection" of recognition elements was enriched by extremozymes with interesting selectivity and by thermostable chimeras. The perspectives for biosensor development are exciting, considering also the progress in genetic editing for the oriented immobilization of enzymes, efficient folding, and better electron transport. Stability, production costs and immobilization at sensing interfaces must be improved to encourage wider applications of extremozymes in biosensors.
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Affiliation(s)
- Cristina Purcarea
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Robert Ruginescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Roberta Maria Banciu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
- Department of Analytical and Physical Chemistry, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania
| | - Alina Vasilescu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
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A Key Role in Catalysis and Enzyme Thermostability of a Conserved Helix H5 Motif of Human Glutathione Transferase A1-1. Int J Mol Sci 2023; 24:ijms24043700. [PMID: 36835112 PMCID: PMC9959719 DOI: 10.3390/ijms24043700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Glutathione transferases (GSTs) are promiscuous enzymes whose main function is the detoxification of electrophilic compounds. These enzymes are characterized by structural modularity that underpins their exploitation as dynamic scaffolds for engineering enzyme variants, with customized catalytic and structural properties. In the present work, multiple sequence alignment of the alpha class GSTs allowed the identification of three conserved residues (E137, K141, and S142) at α-helix 5 (H5). A motif-directed redesign of the human glutathione transferase A1-1 (hGSTA1-1) was performed through site-directed mutagenesis at these sites, creating two single- and two double-point mutants (E137H, K141H, K141H/S142H, and E137H/K141H). The results showed that all the enzyme variants displayed enhanced catalytic activity compared to the wild-type enzyme hGSTA1-1, while the double mutant hGSTA1-K141H/S142H also showed improved thermal stability. X-ray crystallographic analysis revealed the molecular basis of the effects of double mutations on enzyme stability and catalysis. The biochemical and structural analysis presented here will contribute to a deeper understanding of the structure and function of alpha class GSTs.
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Immobilized Enzyme-based Novel Biosensing System for Recognition of Toxic Elements in the Aqueous Environment. Top Catal 2023. [DOI: 10.1007/s11244-023-01786-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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4
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A Review on Recent Trends in Advancement of Bio-Sensory Techniques Toward Pesticide Detection. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02382-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Perperopoulou F, Poudel N, Papageorgiou AC, Ataya FS, Labrou NE. Structural and Functional Characterization of Camelus dromedarius Glutathione Transferase M1-1. LIFE (BASEL, SWITZERLAND) 2022; 12:life12010106. [PMID: 35054499 PMCID: PMC8780062 DOI: 10.3390/life12010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/30/2022]
Abstract
Glutathione transferases (GSTs; EC. 2.5.1.18) are a large family of multifunctional enzymes that play crucial roles in the metabolism and inactivation of a broad range of xenobiotic compounds. In the present work, we report the kinetic and structural characterization of the isoenzyme GSTM1-1 from Camelus dromedarius (CdGSTM1-1). The CdGSΤM1-1 was expressed in E. coli BL21 (DE3) and was purified by affinity chromatography. Kinetics analysis showed that the enzyme displays a relative narrow substrate specificity and restricted ability to bind xenobiotic compounds. The crystal structures of CdGSΤM1-1 were determined by X-ray crystallography in complex with the substrate (GSH) or the reaction product (S-p-nitrobenzyl-GSH), providing snapshots of the induced-fit catalytic mechanism. The thermodynamic stability of CdGSTM1-1 was investigated using differential scanning fluorimetry (DSF) in the absence and in presence of GSH and S-p-nitrobenzyl-GSH and revealed that the enzyme’s structure is significantly stabilized by its ligands. The results of the present study advance the understanding of camelid GST detoxification mechanisms and their contribution to abiotic stress adaptation in harsh desert conditions.
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Affiliation(s)
- Fereniki Perperopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece;
| | - Nirmal Poudel
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20521 Turku, Finland; (N.P.); (A.C.P.)
| | - Anastassios C. Papageorgiou
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20521 Turku, Finland; (N.P.); (A.C.P.)
| | - Farid S. Ataya
- Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece;
- Correspondence: ; Tel.: +30-210-5294308
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Zhao M, Wang M, Zhang X, Zhu Y, Cao J, She Y, Cao Z, Li G, Wang J, Abd El-Aty AM. Recognition elements based on the molecular biological techniques for detecting pesticides in food: A review. Crit Rev Food Sci Nutr 2021:1-24. [PMID: 34852703 DOI: 10.1080/10408398.2021.2009762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Excessive use of pesticides can cause contamination of the environment and agricultural products that are directly threatening human life and health. Therefore, in the process of food safety supervision, it is crucial to conduct sensitive and rapid detection of pesticide residues. The recognition element is the vital component of sensors and methods for fast testing pesticide residues in food. Improper recognition elements may lead to defects of testing methods, such as poor stability, low sensitivity, high economic costs, and waste of time. We can use the molecular biological technique to address these challenges as a good strategy for recognition element production and modification. Herein, we review the molecular biological methods of five specific recognition elements, including aptamers, genetic engineering antibodies, DNAzymes, genetically engineered enzymes, and whole-cell-based biosensors. In addition, the application of these identification elements combined with biosensor and immunoassay methods in actual detection was also discussed. The purpose of this review was to provide a valuable reference for further development of rapid detection methods for pesticide residues.
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Affiliation(s)
- Mingqi Zhao
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Miao Wang
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Xiaoguang Zhang
- Hebei Xiangzhi Testing Technology Co., Ltd, Shijiazhuang, China.,Core Facilities and Centers of Hebei Medical University, Shijiazhuang, China
| | - Yongan Zhu
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Jing Cao
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Yongxin She
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Zhen Cao
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wang
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.,Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum, Turkey
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Platis M, Vlachakis D, Foudah AI, Muharram MM, Alqarni MH, Papageorgiou AC, Labrou NE. The Interaction of Schistosoma Japonicum Glutathione Transferase with Cibacron Blue 3GA and its Fragments. Med Chem 2021; 17:332-343. [PMID: 32242785 DOI: 10.2174/1573406416666200403074742] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/22/2020] [Accepted: 03/04/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The 26kDa glutathione transferase (GST, EC 2.5.1.18) from Schistosoma japonicum (SjGST) is recognized as the major detoxification enzyme of S. japonicum, a pathogenic helminth causing schistosomiasis. OBJECTIVE In the present study, the interaction of the chlorotriazine dye Cibacron blue 3GA (CB3GA) and its structural analogues with SjGST was investigated. The work aimed to shed light on the non-substrate ligand-binding properties of the enzyme. METHODS Kinetic inhibition analysis, affinity labelling experiments and molecular modelling studies were employed. RESULTS The results showed that CB3GA is a potent inhibitor (IC50 0.057 ± 0.003 μM) towards SjGST. The enzyme was specifically and irreversibly inactivated by the dichlorotriazine-analogue of CB3GA (IC50 0.190 ± 0.024 μM), following a biphasic pseudo-first-order saturation kinetics with approximately 1 mol of inhibitor per mol of the dimeric enzyme being incorporated. All other monochlorotriazine analogues behave as reversible inhibitors with lower inhibition potency (IC50 5.2-82.3 μM). Kinetic inhibition studies, together with molecular modelling and molecular dynamics simulations, established that the CB3GA binding site overlaps both the G- and H-sites. Both hydrophobic/ polar interactions, as well as steric effects, have decisive roles in determining the inhibitory strength of CB3GA and its analogues. CONCLUSION The results of the present study might be useful in future drug design and development efforts towards SjGST.
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Affiliation(s)
- Michalis Platis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855-Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855-Athens, Greece
| | - Ahmed I Foudah
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942 Al Kharj, Saudi Arabia
| | - Magdy M Muharram
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Alkharj, Saudi Arabia
| | - Mohamed H Alqarni
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Alkharj, Saudi Arabia
| | | | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855-Athens, Greece
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Liu W, Li C, Shan J, Wang Y, Chen G. Insights into the aggregation mechanism of RNA recognition motif domains in TDP-43: a theoretical exploration. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210160. [PMID: 34457335 PMCID: PMC8371369 DOI: 10.1098/rsos.210160] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/19/2021] [Indexed: 05/10/2023]
Abstract
The transactive response DNA-binding protein 43 (TDP-43) is associated with several diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) due to pathogenic aggregations. In this work, we examined the dimer, tetramer and hexamer models built from the RRM domains of TDP-43 using molecular dynamics simulations in combination with the protein-protein docking. Our results showed that the formations of the dimer models are mainly achieved by the interactions of the RRM1 domains. The parallel β-sheet layers between the RRM1 domains provide most of the binding sites in these oligomer models, and thus play an important role in the aggregation process. The approaching of the parallel β-sheet layers from small oligomer models gradually expand to large ones through the allosteric communication between the α1/α2 helices of the RRM1 domains, which maintains the binding affinities and interactions in the larger oligomer models. Using the repeatable-superimposing method based on the tetramer models, we proposed a new aggregation mechanism of RRM domains in TDP-43, which could well characterize the formation of the large aggregation models with the repeated, helical and rope-like structures. These new insights help to understand the amyloid-like aggregation phenomena of TDP-43 protein in ALS and FTLD diseases.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Chaoqun Li
- Hebei Key Laboratory of Heterocyclic Compounds, College of Chemistry, Chemical Engineering and Materials, Handan University, Handan 056005, Hebei Province, People's Republic of China
| | - Jiankai Shan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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Vaish S, Gupta D, Mehrotra R, Mehrotra S, Basantani MK. Glutathione S-transferase: a versatile protein family. 3 Biotech 2020; 10:321. [PMID: 32656054 PMCID: PMC7320970 DOI: 10.1007/s13205-020-02312-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
Glutathione-S transferase (GST) is a most ancient protein superfamily of multipurpose roles and evolved principally from gene duplication of an ancestral GSH binding protein. They have implemented in diverse plant functions such as detoxification of xenobiotic, secondary metabolism, growth and development, and majorly against biotic and abiotic stresses. The vital structural features of GSTs like highly divergent functional topographies, conserved integrated architecture with separate binding pockets for substrates and ligand, the stringent structural fidelity with high Tm values (50º-60º), and stress-responsive cis-regulatory elements in the promoter region offer this protein as most flexible plant protein for plant breeding approaches, biotechnological applications, etc. This review article summarizes the recent information of GST evolution, and their distribution and structural features with emphasis on the assorted roles of Ser and Cys GSTs with the signature motifs in their active sites, alongside their recent biotechnological application in the area of agriculture, environment, and nanotechnology have been highlighted.
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Affiliation(s)
- Swati Vaish
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh 225003 India
| | - Divya Gupta
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh 225003 India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science, KK Birla Goa Campus, NH-17B, Zuarinagar, Goa 403726 India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science, KK Birla Goa Campus, NH-17B, Zuarinagar, Goa 403726 India
| | - Mahesh Kumar Basantani
- Faculty of Bioscience, Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, Uttar Pradesh India
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Tsagkaris A, Nelis J, Ross G, Jafari S, Guercetti J, Kopper K, Zhao Y, Rafferty K, Salvador J, Migliorelli D, Salentijn G, Campbell K, Marco M, Elliot C, Nielen M, Pulkrabova J, Hajslova J. Critical assessment of recent trends related to screening and confirmatory analytical methods for selected food contaminants and allergens. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115688] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Valiūnienė A, Virbickas P, Medvikytė G, Ramanavičius A. Urea Biosensor Based on Electrochromic Properties of Prussian Blue. ELECTROANAL 2019. [DOI: 10.1002/elan.201900556] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Aušra Valiūnienė
- Department of Physical Chemistry, Faculty of Chemistry and GeosciencesVilnius University Naugarduko 24 LT-03225 Vilnius Lithuania
| | - Povilas Virbickas
- Department of Physical Chemistry, Faculty of Chemistry and GeosciencesVilnius University Naugarduko 24 LT-03225 Vilnius Lithuania
| | - Giedrė Medvikytė
- Department of Physical Chemistry, Faculty of Chemistry and GeosciencesVilnius University Naugarduko 24 LT-03225 Vilnius Lithuania
| | - Arūnas Ramanavičius
- Department of Physical Chemistry, Faculty of Chemistry and GeosciencesVilnius University Naugarduko 24 LT-03225 Vilnius Lithuania
- Laboratory of NanotechnologyState Research Institute Center for Physical Sciences and Technology Sauletekio-avenue 3 LT-10257 Vilnius Lithuania
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