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Wang L, Lei Z, Zhang Z, Yang X, Chen R. Deciphering the role of extracellular polymeric substances in the adsorption and biotransformation of organic micropollutants during anaerobic wastewater treatment. WATER RESEARCH 2024; 257:121718. [PMID: 38723358 DOI: 10.1016/j.watres.2024.121718] [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: 02/28/2024] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024]
Abstract
Extracellular polymeric substances (EPS) participate in the removal of organic micropollutants (OMPs), but the primary pathways of removal and detailed mechanisms remain elusive. We evaluated the effect of EPS on removal for 16 distinct chemical classes of OMPs during anaerobic digestion (AD). The results showed that hydrophobic OMPs (HBOMPs) could not be removed by EPS, while hydrophilic OMPs (HLOMPs) were amenable to removal via adsorption and biotransformation of EPS. The adsorption and biotransformation of HLOMPs by EPS accounted up to 19.4 ± 0.9 % and 6.0 ± 0.8 % of total removal, respectively. Further investigations into the adsorption and biotransformation mechanisms of HLOMPs by EPS were conducted utilizing spectral, molecular dynamics simulation, and electrochemical analysis. The results suggested that EPS provided abundant binding sites for the adsorption of HLOMPs. The binding of HLOMPs to tryptophan-like proteins in EPS formed nonfluorescent complexes. Hydrogen bonds, hydrophobic interactions and water bridges were key to the binding processes and helped stabilize the complexes. The biotransformation of HLOMPs by EPS may be attributed to the presence of extracellular redox active components (c-type cytochromes (c-Cyts), c-Cyts-bound flavins). This study enhanced the comprehension for the role of EPS on the OMPs removal in anaerobic wastewater treatment.
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Affiliation(s)
- Lianxu Wang
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, PR China
| | - Zhen Lei
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, PR China
| | - Zixin Zhang
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, PR China
| | - Xiaohuan Yang
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, PR China
| | - Rong Chen
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, PR China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, PR China.
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2
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Bavadi M, Zhu Z, Zhang B. Evaluation of surfactant-aided polycyclic aromatic hydrocarbon biodegradation by molecular docking and molecular dynamic simulation in the marine environment. CHEMOSPHERE 2024; 358:142171. [PMID: 38714247 DOI: 10.1016/j.chemosphere.2024.142171] [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: 08/02/2023] [Revised: 03/27/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
Abstract
Marine oil spills directly cause polycyclic aromatic hydrocarbons (PAHs) pollution and affect marine organisms due to their toxic property. Chemical and bio-based dispersants composed of surfactants and solvents are considered effective oil spill-treating agents. Dispersants enhance oil biodegradation in the marine environment by rapidly increasing their solubility in the water column. However, the effect of dispersants, especially surfactants, on PAHs degradation by enzymes produced by microorganisms has not been studied at the molecular level. The role of the cytochrome P450 (CYP) enzyme in converting contaminants into reactive metabolites during the biodegradation process has been evidenced, but the activity in the presence of surfactants is still ambiguous. Thus, this study focused on the evaluation of the impact of chemical and bio-surfactants (i.e., Tween 80 (TWE) and Surfactin (SUC)) on the biodegradation of naphthalene (NAP), chrysene (CHR), and pyrene (PYR), the representative components of PAHs, with CYP enzyme from microalgae Parachlorella kessleri using molecular docking and molecular dynamics (MD) simulation. The molecular docking analysis revealed that PAHs bound to residues at the CYP active site through hydrophobic interactions for biodegradation. The MD simulation showed that the surfactant addition changed the enzyme conformation in the CYP-PAH complexes to provide more interactions between the enzyme and PAHs. This led to an increase in the enzyme's capability to degrade PAHs. Binding free energy (ΔGBind) calculations confirmed that surfactant treatment could enhance PAHs degradation by the enzyme. The SUC gave a better result on NAP and PYR biodegradation based on ΔGBind, while TWE facilitated the biodegradation of CHR. The research outputs could greatly facilitate evaluating the behaviors of oil spill-treating agents and oil spill response operations in the marine environment.
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Affiliation(s)
- Masoumeh Bavadi
- Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, A1B 3X5, Canada
| | - Zhiwen Zhu
- Oceans Science, Fisheries and Oceans Canada, Ottawa, ON, K1A 0E6, Canada
| | - Baiyu Zhang
- Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, A1B 3X5, Canada.
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3
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González-Durruthy M, Rial R, Ruso JM. Decoding the conformational binding of drug mixtures on ovalbumin: An integrated multimodal network. Int J Biol Macromol 2024; 261:129866. [PMID: 38302030 DOI: 10.1016/j.ijbiomac.2024.129866] [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: 12/12/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
This research addresses the crucial necessity for a deeper understanding of the binding interactions between surfactants and proteins, with a specific focus on ovalbumin. Considering ovalbumin's role in diverse biochemical processes, it remains a subject of significant interest for drug discovery and design. To fill existing knowledge gaps, we investigated the binding interaction between dicloxacillin and cetyltrimethylammonium bromide (CTAB) on ovalbumin, employing a comprehensive approach that combines computational modeling with experimental validations. Using the ezPocket tool, the computational phase predicted ten relevant binding sites on ovalbumin's surface. The isobologram combination index (CI) heatmap strongly suggested a complex interplay of antagonistic and synergistic effects. Besides, a conformational drug-drug interaction network was proposed to explore the stability of the surfactant mixture within specific binding sites of ovalbumin, revealing a dynamic landscape of suggested antagonist effects. Experimental validations through UV-vis, Fluorescence, and circular dichroism (CD) spectroscopy further corroborated the computational findings, confirming the formation of stable complexes. Finally, this study not only advances our comprehension of ovalbumin's interactions with surfactants but also offers a multidimensional perspective and an advanced methodological framework for efficient therapeutic strategies, opening new avenues for future applications in drug development and applied biochemistry.
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Affiliation(s)
- Michael González-Durruthy
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics and Institute of Materials (iMATUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; NanoSafety Group, International Iberian Nanotechnology Laboratory, Braga 4715-330, Portugal.
| | - Ramón Rial
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics and Institute of Materials (iMATUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Juan M Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics and Institute of Materials (iMATUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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4
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Wu J, Lv J, Zhao L, Zhao R, Gao T, Xu Q, Liu D, Yu Q, Ma F. Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167028. [PMID: 37704131 DOI: 10.1016/j.scitotenv.2023.167028] [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: 07/02/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ruofan Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Tian Gao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China
| | - Qi Xu
- PetroChina Fushun Petrochemical Company, Fushun 113000, China
| | - Dongbo Liu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Qiqi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China.
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5
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Wang H, Rao P, Qiu Y, Xiang L. Interaction mechanism between hydroxychloroquine sulfate and collagen: Insights from multi-spectroscopy, molecular docking, and molecular dynamic simulation methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123155. [PMID: 37480720 DOI: 10.1016/j.saa.2023.123155] [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: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Hydroxychloroquine sulfate (HCQ) can be used to treat various connective tissue diseases. Collagen, which is not only an important drug delivery carrier but also the main component in the connective tissue, is the focus of this study. Here, the interaction mechanism of HCQ with collagen was investigated through various spectroscopic and computational methods. It is found that HCQ binds to collagen spontaneously, primarily via hydrophobic interactions and some hydrogen bonds. The findings of X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) verified that formation of HCQ-collagen complex and the amorphous structure, secondary structures, and microstructure of collagen were changed after HCQ binding. A decrease in the relaxation time of free water was observed in the collagen system when HCQ was added. Molecular docking demonstrated that HCQ was almost buried in the cavity of collagen via some hydrophobic interactions with one hydrogen bond, which conforms to the findings of the fluorescence and FTIR analyses. Molecular dynamic (MD) simulations further revealed the structural change information in the docking process. Hopefully, the information generated in this study can provide some useful insights for the research on the pharmacological mechanisms of HCQ in the treatment of the connective tissue diseases and the application of collagen as a drug carrier.
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Affiliation(s)
- Hailin Wang
- College of Food and Bioengineering, Fujian Polytechnic Normal University, Fuqing, Fujian, China; Food Nutrition Science Centre, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Pingfan Rao
- Food Nutrition Science Centre, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Yunjie Qiu
- College of Food and Bioengineering, Fujian Polytechnic Normal University, Fuqing, Fujian, China
| | - Leiwen Xiang
- College of Food and Bioengineering, Fujian Polytechnic Normal University, Fuqing, Fujian, China.
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6
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Silva MC, de Castro AA, Lopes KL, Ferreira IFL, Bretz RR, Ramalho TC. Combining computational tools and experimental studies towards endocrine disruptors mitigation: A review of biocatalytic and adsorptive processes. CHEMOSPHERE 2023; 344:140302. [PMID: 37788749 DOI: 10.1016/j.chemosphere.2023.140302] [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: 08/03/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
The endocrine disruptors (EDCs) are an important group of emerging contaminants, and their mitigation has been a huge challenge due to their chemistry complexity and variety of these compounds. The traditional treatments are inefficient to completely remove EDCs, and adsorptive processes are the major alternative investigated on their removal. Also, the use of EDCs degrading enzymes has been encouraged due to ecofriendly approach of biocatalytic processes. This paper highlights the occurrence, classification, and toxicity of EDCs with special focus in the use of enzyme-based and adsorptive technologies in the elimination of EDCs from ambiental matrices. Numerous prior reviews have focused on the discussions toward these technologies. However, the literature lacks theoretical discussions about important aspects of these methods such as the mechanisms of EDCs adsorption on the adsorbent surface or the interactions between degrading enzymes - EDCs. In this sense, theoretical calculations combined to experimental studies may help in the development of more efficient technologies to EDCs mitigation. In this review, we point out how computational tools such as molecular docking and molecular dynamics have to contribute to the design of new adsorbents and efficient catalytic processes towards endocrine disruptors mitigation.
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Affiliation(s)
- Maria Cristina Silva
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil.
| | | | - Karla Lara Lopes
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil
| | - Igor F Lara Ferreira
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil
| | - Raphael Resende Bretz
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil
| | - Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
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7
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Pant R, Kumar R, Sharma S, Karuppasamy R, Veerappapillai S. Exploring the potential of Halalkalibacterium halodurans laccase for endosulfan and chlorophacinone degradation: insights from molecular docking and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-15. [PMID: 37990551 DOI: 10.1080/07391102.2023.2283165] [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: 03/27/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023]
Abstract
Pesticides are widely used in agriculture but at the same time, a majority of them are known to cause serious harm to health and the environment. In the recent past, laccases have been reported as key enzymes having the ability to degrade pollutants by converting them into less toxic forms. In this investigation, laccase from polyextremophilic bacterium Halalkalibacterium halodurans C-125 was analyzed for its structural, physicochemical, and functional characterization using in silico approaches. The 3D model of the said enzyme is unknown; therefore, the model was generated by template-independent modeling using ROBETTA, I-TASSER, and Alphafold server. The best-generated model from Alphafold with a confidence of 0.95 was validated from ERRAT and Verify 3D scores of 89.95 and 91.80%, respectively. The Ramachandran plot generated using the PROCHECK server further predicted the accuracy of the model with 93.7% and 5.9% of residues present in most favored and additional allowed regions of the plot respectively. The active sites, ion binding sites, and subcellular localization of laccase were also predicted. The generated model was docked with 121 pollutants (pesticides, insecticides, herbicides, fungicides, and rodenticides) for its degradation potential towards these pollutants. Two ligands chlorophacinone (based on the highest binding energy) and endosulfan (based on agricultural uses) were selected for molecular dynamic simulation studies. Endosulfan as a pesticide is banned but in some countries governments allow its use for special purposes which need serious consideration on developing bioremediation approaches for endosulfan degradation. MD simulation studies revealed that both chlorophacinone and endosulfan form hydrogen bonds and hydrophobic bonds with the active site of laccase and chlorophacinone-laccase complex were more stable in comparison to endosulfan. The present investigation provides insight into the structural features of laccase and its potential for the degradation of pesticides which can be further validated by experimental data.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajat Pant
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Ravi Kumar
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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8
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Zhang W, Zhang Y, Lu Z, Nian B, Yang S, Hu Y. Enhanced stability and catalytic performance of laccase immobilized on magnetic graphene oxide modified with ionic liquids. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 346:118975. [PMID: 37716172 DOI: 10.1016/j.jenvman.2023.118975] [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: 06/26/2023] [Revised: 08/23/2023] [Accepted: 09/09/2023] [Indexed: 09/18/2023]
Abstract
Graphite oxide (GO) is an excellent laccase immobilization material. However, the electrostatic interaction between graphene leads to the accumulation of GO, as well as the interaction with the surface of enzyme molecules causing protein denaturation and deactivation, which limits its further industrial application. In this study, the ionic liquids (ILs) modification strategy was proposed to improve the stability and catalytic performance of immobilized laccase. The laccase-ILs-MGO exhibited remarkable enzymatic properties, with significant enhancements in organic solvent tolerance, thermal and operational stability. The laccase-ILs-MGO system exhibited a remarkable removal efficiency of 95.5% towards 2,4-dichlorophenol (2,4-DCP) within 12 h and maintained over 70.0% removal efficiency after seven reaction cycles. In addition, the efficient elimination of other phenolic compounds and recalcitrant polycyclic aromatic hydrocarbons could also be accomplished. Molecular dynamics simulation and molecular docking studies demonstrated that immobilized laccase exhibited superior structural rigidity and stronger hydrogen bond interactions with substrates compared to free laccase, which was beneficial for the stability of both the laccase and substrate degradation efficiency. Therefore, this study proposed a simple and practical strategy for modifying GO with ILs, providing novel insights into developing efficient enzyme immobilization techniques.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Yifei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Zeping Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Shipin Yang
- College of Electrical Engineering and Control Science, Nanjing Tech University, Nanjing, China.
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China.
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Li Y, Chen L, Li J, Zhao B, Jing T, Wang R. Computational explorations of the interaction between laccase and bisphenol A: influence of surfactant and different organic solvents. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:963-981. [PMID: 38009185 DOI: 10.1080/1062936x.2023.2280584] [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: 08/08/2023] [Accepted: 10/30/2023] [Indexed: 11/28/2023]
Abstract
Bisphenol A (BPA), as an environmental endocrine disruptor can cause damage to the reproductive, nervous and immune systems. Laccase can be used to degrade BPA. However, laccase is easily deactivated, especially in organic solvents, but the specific details are not clear. Molecular dynamics simulations were used to investigate the reasons for changes in laccase activity in acetonitrile (ACN) and dimethyl formamide (DMF) solutions. In addition, the effects of ACN and DMF on the activity of laccase and surfactant rhamnolipid (RL) on the degradation of BPA by laccase were investigated. Results showed that addition of ACN changed the structure of the laccase, not only decreasing the van der Waals interaction that promoted the binding of laccase with BPA, but also increasing the polar solvation free energy that hindered the binding of laccase with BPA, so it weakened the laccase activity. DMF greatly enhanced the van der Waals interaction between laccase and BPA, and played a positive role in their binding. The addition of surfactant RL alleviated the effect of organic solvent on the activity of laccase by changing the polar solvation energy. The mechanism of surfactant RL affecting laccase activity in ACN and DMF is described, providing support for understanding the effect of organic solvents on laccase.
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Affiliation(s)
- Y Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
| | - L Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
| | - J Li
- Transportation Class in the first operation area of the Fourth Oil Production Plant of Daqing Oilfield of CNPC, Daqing, P. R. China
| | - B Zhao
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
- Heilongjiang Provincial Key Laboratory of Surface Active Agent and Auxiliary, Qiqihar University, Qiqihar, P. R. China
| | - T Jing
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
| | - R Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
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Vaidyanathan VK, Kumar PS, Singh I, Singh I, Rangasamy G, Saratale RG, Saratale GD. Removal of pentachlorophenol and phenanthrene from lignocellulosic biorefinery wastewater by a biocatalytic/biosurfactant system comprising cross-linked laccase aggregates and rhamnolipid. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121635. [PMID: 37085105 DOI: 10.1016/j.envpol.2023.121635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/01/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Synthesis and characterization of highly active cross-linked laccase aggregates (CLLAs) were performed and evaluated for removal of pentachlorophenol and phenanthrene from lignocellulosic biorefinery wastewater. Laccase from Tramates versicolor MTCC 138 was insolubilized as CLLAs via precipitation with 70% ammonium sulphate and simultaneous cross-linking with 5 mM glutaraldehyde to obtain activity recovery of 89.1%. Compared to the free laccase, the pH and thermal stability of the prepared CLLAs were significantly higher. At a high temperature of 60 °C, free laccase had a half-life of 0.25 h, while CLLAs had a half-life of 6.2 h. In biorefinery wastewater (pH 7.0), the free and CLLAs were stored for 3 day at a temperature of 30 °C. Free laccase completely lost their initial activity after 60 h; however, the CLLAs retained 39% activity till 72 h. Due to its excellent stability, free laccase and CLLAs were assessed for removing pentachlorophenol and phenanthrene in wastewater. CLLAs could remove 51-58% of pentachlorophenol (PCP) and phenanthrene (PHE) in 24 h. Biosurfactants, including surfactin, sophorolipid, and rhamnolipid, were assessed for their aptitude to improve the removal of organic contaminants in wastewater. Biorefinery wastewater incubated with all surfactants enhanced PCP and PHE removal compared to the no-surfactant controls. Further, 1 μM rhamnolipid significantly amplified pentachlorophenol and phenanthrene removal to 81-93% for free laccase and CLLAs, respectively.
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Affiliation(s)
- Vinoth Kumar Vaidyanathan
- Integrated Bioprocessing Laboratory, Department of Biotechnology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur , 603203, Chengalpattu District, Tamil Nadu, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, 603110, Tamil Nadu, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, 603 110, Tamil Nadu, India; School of Engineering, Lebanese American University, Byblos, Lebanon
| | - Isita Singh
- Integrated Bioprocessing Laboratory, Department of Biotechnology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur , 603203, Chengalpattu District, Tamil Nadu, India
| | - Ishani Singh
- Integrated Bioprocessing Laboratory, Department of Biotechnology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur , 603203, Chengalpattu District, Tamil Nadu, India
| | - Gayathri Rangasamy
- School of Engineering, Lebanese American University, Byblos, Lebanon; Department of Sustainable Engineering, Institute of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India; University Centre for Research and Development & Department of Civil Engineering, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Rijuta Ganesh Saratale
- Research Institute of Integrative Life Sciences, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggido, 10326, Republic of Korea
| | - Ganesh Dattatraya Saratale
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggido, 10326, Republic of Korea.
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11
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Venkataraman S, Vaidyanathan VK. Synthesis of magnetically recyclable porous cross-linked aggregates of Tramates versicolor MTCC 138 laccase for the efficient removal of pentachlorophenol from aqueous solution. ENVIRONMENTAL RESEARCH 2023; 229:115899. [PMID: 37076027 DOI: 10.1016/j.envres.2023.115899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 03/14/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
The primary objective of this study is to synthesize the magnetically separable highly active porous immobilized laccase for the removal of pentachlorophenol (PCP) in an aqueous solution. Magnetic porous cross-linked enzyme aggregates (Mp-CLEAs) of laccase were synthesized using 1% starch solution with 5 mM glutaraldehyde followed by 10 h of cross-linking time with an activity recovery of 90.85 ± 0.2%. The biocatalytic efficiency of magnetic porous CLEAs (Mp-CLEAs) was 2-fold higher than that of magnetic CLEAs. The synthesized Mp-CLEAs were mechanically stable with enhanced catalytic efficiency, and reusability thus overcoming the mass transfer limitations and enzyme loss. At 40 °C, the thermal stability of the magnetic porous immobilized laccase was improved, with a 602 min half-life compared to 207 min half-life for the free enzyme. Using 40 U/mL of laccase for the removal of 100 ppm of PCP, M-CLEAs, and Mp-CLEAs removed 60.44% and 65.53% of PCP, respectively. Furthermore, to enhance PCP removal, a laccase-aided system was harnessed by optimizing various surfactants and mediators. Of these, 0.1 mM of rhamnolipid and 2,3 dimethoxy phenol had the highest PCP removal rates of 95.12% and 99.41%, respectively, for Mp-CLEAs. This study demonstrates the efficacy of the laccase-surfactant-mediator system for the removal of PCP from the aqueous solution, which can also be proposed for real-time application.
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Affiliation(s)
- Swethaa Venkataraman
- Integrated Bioprocessing Laboratory, Department of Biotechnology, SRM Institute of Science, And Technology, Chennai, Tamil Nadu, 603203, India
| | - Vinoth Kumar Vaidyanathan
- Integrated Bioprocessing Laboratory, Department of Biotechnology, SRM Institute of Science, And Technology, Chennai, Tamil Nadu, 603203, India.
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12
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Li N, Zeng Z, Zhang Y, Zhang H, Tang N, Guo Y, Lu L, Li X, Zhu Z, Gao X, Liang J. Higher toxicity induced by co-exposure of polystyrene microplastics and chloramphenicol to Microcystis aeruginosa: Experimental study and molecular dynamics simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161375. [PMID: 36621494 DOI: 10.1016/j.scitotenv.2022.161375] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/23/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
Antibiotics and microplastics (MPs) inevitably coexist in natural waters, but their combined effect on aquatic organisms is still ambiguous. This study investigated the individual and combined toxicity of chloramphenicol (CAP) and micro-polystyrene (mPS) particles to Microcystis aeruginosa by physiological biomarkers, related gene expression, and molecular dynamics simulation. The results indicated that both individual and joint treatments threatened algal growth, while combined toxicity was higher than the former. Photosynthetic pigments and gene expression were inhibited by single CAP and mPS exposure, but CAP dominated and aggravated photosynthetic toxicity in combined exposure. Additionally, mPS damaged cell membranes and induced oxidative stress, which might further facilitate the entry of CAP into cells during co-exposure. The synergistic effect of CAP and mPS might be explained by the common photosynthetic toxicity target of CAP and mPS as well as oxidative stress. Furthermore, the molecular dynamics simulation revealed that CAP altered conformations of photosynthetic assembly protein YCF48 and SOD enzyme, and competed for functional sites of SOD, thus disturbing photosynthesis and antioxidant systems. These findings provide useful insights into the combined toxicity mechanism of antibiotics and MPs as well as highlight the importance of co-pollutant toxicity in the aquatic environment.
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Affiliation(s)
- Na Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Zhuotong Zeng
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, PR China
| | - Yafei Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Hui Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Ning Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Yihui Guo
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Lan Lu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Xin Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Ziqian Zhu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Xiang Gao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Jie Liang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environment Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China.
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13
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Wang F, Zhang L, Zhang D, Wu X, Deng S. Binding of Anionic Polyacrylamide with Amidase and Laccase under 298, 303, and 308 K: Docking and Molecular Dynamics Simulation Studies Combined with Experiments. ACS OMEGA 2023; 8:10040-10050. [PMID: 36969392 PMCID: PMC10034835 DOI: 10.1021/acsomega.2c07380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Amidase and laccase play a key role in the degradation process of anionic polyacrylamide (HPAM). However, the largest challenge of HPAM enzymatic degradation is whether the enzyme can bind with a substrate for a period of time. Here, the most suitable complexes, namely, Rh Amidase-HPAM-2 and Bacillus subtilis (B. subtilis) laccase-HPAM-3, were obtained by docking, and they were carried out for molecular dynamics simulation (MDS) under 298, 303, and 308 K. MDS result analysis showed that Rh Amidase-HPAM-2 was the most stable at 298 K mainly due to a salt bridge and a hydrogen bond, and B. subtilis laccase-HPAM-3 was the most stable at 298 K mainly due to two electrostatic and hydrogen bonds. The LYS96 in Rh Amidase-HPAM-2 and LYS135 in B. subtilis laccase-HPAM-3 had been the most important in their binding process. The binding of Rh Amidase-HPAM-2 and B. subtilis laccase-HPAM-3 was optimal at 303 and 298 K, respectively. HPAM was degraded by mixed bacteria, and the optimal conditions were determined to be 308 K, initial pH = 7, and an inoculated dosage of 2 mL. Under these conditions, the degradation ratio reached 39.24%. The effect of parameters on the HPAM degradation ratio followed a decreasing order of temperature > initial pH > inoculated dosage. The HPAM codegradation mechanism was supposed by mixed bacteria according to test data. The mixed bacteria secreted both amidase and laccase, and they interacted jointly with HPAM. These results lay a theoretical foundation to design and modify the enzyme through mutation experiments in the future.
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Affiliation(s)
- Fanglue Wang
- School
of Bioengineering, Huainan Normal University, Huainan 232038, China
| | - Liwen Zhang
- School
of Mechanical and Electrical Engineering, Huainan Normal University, Huainan 232038, China
| | - Dongchen Zhang
- School
of Materials Science and Engineering, Anhui
University of Science and Technology, Huainan 232001, China
| | - Xuefeng Wu
- School
of Food and Bioengineering, Hefei University
of Technology, Hefei 230009, China
| | - Shengsong Deng
- School
of Food and Bioengineering, Hefei University
of Technology, Hefei 230009, China
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14
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Bhatt P, Bhatt K, Chen WJ, Huang Y, Xiao Y, Wu S, Lei Q, Zhong J, Zhu X, Chen S. Bioremediation potential of laccase for catalysis of glyphosate, isoproturon, lignin, and parathion: Molecular docking, dynamics, and simulation. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130319. [PMID: 36356521 DOI: 10.1016/j.jhazmat.2022.130319] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/21/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
The present study aimed to investigate the catalytic degradation produced by laccase in the detoxification of glyphosate, isoproturon, lignin polymer, and parathion. We explored laccase-glyphosate, laccase-lignin polymer, laccase-isoproturon, and laccase-parathion using molecular docking (MD) and molecular dynamics simulation (MDS) approaches. The results suggest that laccase interacts well with glyphosate, lignin polymer, isoproturon, and parathion during biodegradation. We calculated the root mean square deviations (RMSD) of laccase-glyphosate, laccase-lignin polymer, laccase-isoproturon, and laccase-parathion as 0.24 ± 0.02, 0.59 ± 0.32, 0.43 ± 0.07, and 0.43 ± 0.06 nm, respectively. In an aqueous solution, the stability of laccase with glyphosate, lignin polymer, isoproturon, and parathion is mediated through the formation of hydrophobic interactions, hydrogen bonds, and van der Waals interactions. The presence of xenobiotic toxic compounds in the active site changed the conformation of laccase. MDS of the laccase-substrate complexes confirmed their stability during catalytic degradation. Laccase assay results confirmed that the degradation of syringol, dihydroconiferyl alcohol, guaiacol, parathion, isoproturon, and glyphosate were 100%, 99.31%, 95.69%, 60.96%, 54.51%, and 48.34% within 2 h, respectively. Taken together, we describe a novel method to understand the molecular-level biodegradation of xenobiotic compounds through laccase and its potential application in contaminant removal.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Department of Agricultural & Biological Engineering, Purdue University, West Lafayette 47906, USA
| | - Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette 47906, USA
| | - Wen-Juan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Ying Xiao
- Institute of Chemical Engineering, Guangdong Academy of Sciences, Guangzhou 510665, China
| | - Siyi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Qiqi Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Jianfeng Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Xixian Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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15
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Continuous, green, and room-temperature synthesis of silver nanowires in a helically-coiled millifluidic reactor. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2022.130806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Pande V, Joshi T, Pandey SC, Sati D, Mathpal S, Pande V, Chandra S, Samant M. Molecular docking and molecular dynamics simulation approaches for evaluation of laccase-mediated biodegradation of various industrial dyes. J Biomol Struct Dyn 2022; 40:12461-12471. [PMID: 34459700 DOI: 10.1080/07391102.2021.1971564] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dyes are being increasingly utilized across the globe, but there is no appropriate method of bioremediation for their full mineralization from the environment. Laccases are key enzymes that help microbes to degrade dyes as well as their intermediate metabolites. Various dyes have been reported to be degraded by bacteria, but it is still unclear how these enzymes function during dye degradation. To effectively eradicate toxic dyes from the system, it is essential to understand the molecular function of enzymes. As a result, the interaction of laccase with different toxic dyes was investigated using molecular docking. Based on the highest binding energy we have screened ten dyes with positive interaction with laccase. Evaluating the MD simulation results, three out of ten dyes were more stable as potential targets for degradation by laccase of Bacillus subtilis. As a result, subsequent research focused solely on the results of three substrates: pigment red, fuchsin base, and Sudan IV. Analysis of MD simulation revealed that pigments red 23, fuchsin base, and Sudan IV form hydrogen and hydrophobic bond as well as Vander Waals interactions with the active site of laccase to keep it stable in aqueous solution. The conformation of laccase is greatly altered by the inclusion of all three substrates in the active site. The MD simulation findings show that laccase complexes remain stable throughout the catalytic reaction. Therefore, this research provides a molecular understanding of laccase expression and its role in the bioremediation of the pigments red 23, fuchsin base, and Sudan IV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Veni Pande
- Cell and Molecular Biology Laboratory, Department of Zoology (DST-FIST sponsored), Kumaun University, Almora, Uttarakhand, India.,Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Satish Chandra Pandey
- Cell and Molecular Biology Laboratory, Department of Zoology (DST-FIST sponsored), Kumaun University, Almora, Uttarakhand, India.,Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Diksha Sati
- Cell and Molecular Biology Laboratory, Department of Zoology (DST-FIST sponsored), Kumaun University, Almora, Uttarakhand, India
| | - Shalini Mathpal
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Mukesh Samant
- Cell and Molecular Biology Laboratory, Department of Zoology (DST-FIST sponsored), Kumaun University, Almora, Uttarakhand, India
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17
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Liu Y, Cheng S, Yang X, Xue A, Li Z, Alessi DS, Konhauser KO, Zhao H. Molecular dynamics simulation study of covalently bound hybrid coagulants (CBHyC): Molecular structure and coagulation mechanisms. CHEMOSPHERE 2022; 307:135863. [PMID: 35961451 DOI: 10.1016/j.chemosphere.2022.135863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/01/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Covalently-bound organic silicate-aluminum hybrid coagulants (CBHyC) have been shown to efficiently remove low molecular weight organic contaminants from wastewater. However, the interaction dynamics and motivations during the coagulation of contaminant molecules by CBHyC are limited. In this study, a molecular dynamics (MD) simulation showed that CBHyC forms core-shell structure with the aliphatic carbon chains gather inside as a core and the hydrophilic quaternary ammonium-Si-Al complexes disperse outside as a shell. This wrapped structure allowed the coagulant to diffuse into solutions easily and capture target contaminants. The adsorption of anionic organic contaminants (e.g., diclofenac) onto the CBHyC aggregates was driven equally by van der Waals forces and electrostatic interactions. Cationic organic contaminants (e.g., tetracycline) were seldom bound to CBHyC because of substantial repulsive forces between cationic molecules and CBHyC. Neutrally-charged organic molecules were generally bound through hydrophobic interactions. For adenine and thymine deoxynucleotide, representatives of antibiotic resistance genes, van der Waals forces and electrostatic interaction became the dominant driving force with further movement for adenine and thymine, respectively. Driving forces between target contaminant and coagulant directly affect the size and stability of formed aggregate, following the coagulation efficiency of wastewater treatment. The findings of this study enrich the database of aggregation behavior between low molecular weight contaminants and CBHyC and contribute to further and efficient application of CBHyC in wastewater treatment.
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Affiliation(s)
- Yuxia Liu
- State Kety Laboratory of Petroleum Pollution Control, State Key Laboratory of Heavy Oil Processing, Department of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, China.
| | - Shihan Cheng
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Xueying Yang
- State Key Laboratory of Petroleum Pollution Control, CNPC Research Institute of Safety and Environmental Technology, Beijing, 102206, China
| | - An Xue
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), Department of Environmental Engineering, Peking University, Beijing, 100871, China.
| | - Zhenshan Li
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Huazhang Zhao
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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18
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Hokmabady L, Fani N. In silico elucidation of the interactions of thymoquinone analogues with phosphatase and tensin homolog (PTEN). J Mol Model 2022; 28:321. [DOI: 10.1007/s00894-022-05318-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022]
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19
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Wang H, Ke L, Zhou J, Li G, Xu T, Rao P. Multi-spectroscopic, molecular docking and molecular dynamic simulation evaluation of hydroxychloroquine sulfate interaction with caseins and whey proteins. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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20
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Disinfection and Photocatalytic Degradation of Organic Contaminants Using Visible Light-Activated GCN/Ag2CrO4 Nanocomposites. Catalysts 2022. [DOI: 10.3390/catal12090943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Visible-light-driven photocatalysts have gained increasing attention in the past few decades in treating emerging contaminants in water and wastewater. In this work, the photocatalytic activity of the coupled graphitic carbon nitride (GCN) and silver chromate (Ag2CrO4), herein denoted as GCN/Ag2CrO4, nanocomposites was evaluated for degrading organic pollutants and inactivating microorganisms under visible light irradiation using a royal blue light-emitting diode (LED). The organic pollutants studied were 2,4-dichlorophenoxyacetic acid (2,4-D) and methyl chlorophenoxy propionic acid (MCPP or Mecoprop-P) present in KillexR, a commercially available herbicide, bovine serum albumin (BSA) protein, and SARS-CoV-2 spike protein. The disinfection experiments were conducted on wastewater secondary effluent. The results showed that over 85% degradation was achieved for both 2,4-D and Mecoprop-P in 120 min while 100% of BSA protein and 77.5% of SARS-CoV-2 protein were degraded in 20 min and 30 min, respectively. Additionally, GCN/Ag2CrO4 nanocomposites led to over one log reduction of cellular ATP (cATP), total coliforms, and E. coli in wastewater treatment plant (WWTP) secondary effluent after 60 min of royal blue LED irradiation. It was observed that the degradation performance of a photocatalyst under light irradiation is contaminant-specific. The binding affinity of the released metal ions from GCN/Ag2CrO4 with protein and ATP functional groups was responsible for the degradation of proteins and the reduction of cATP, while the generated ROS was responsible for the disinfection of total coliforms and E. coli. Overall, the results indicate that GCN/Ag2CrO4 nanocomposite is a promising photocatalyst in degrading organic pollutants and disinfecting microorganisms under visible light irradiation within a reasonable time.
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21
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Wang F, Zhang D, Zhang L, Wu X, Deng S, Yuan X. Biodegradation of anionic polyacrylamide by manganese peroxidase: docking, virtual mutation based on affinity, QM/MM calculation and molecular dynamics simulation. Bioprocess Biosyst Eng 2022; 45:1349-1358. [PMID: 35771268 DOI: 10.1007/s00449-022-02750-8] [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: 03/21/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022]
Abstract
Manganese peroxidase (Mn P) is capable of effectively degrading anionic polyacrylamide (HPAM). However, the interaction of Mn P with HPAM at molecular level is lacking until now. Here, the HPAM model compounds, HPAM-2, HPAM-3, HPAM-4, and HPAM-5, were selected to reveal their binding mechanisms with Mn P. The results showed that the most suitable substrate for Mn P was HPAM-5, and the main reason for MnP-HPAM-5 with maximal affinity was strong hydrogen bond. LYS96 was the important key residue in all complexes, and the number of key residue was largest in MnP-HPAM-5. The optimal THR27ILE mutant may enhance the affinity of Mn P to HPAM-4. The stability of Mn P binding to HPAM-4 was the optimal. These results were helpful in designing highly efficient Mn P against HPAM to protect the ecological environment.
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Affiliation(s)
- Fanglue Wang
- School of Material Science and Engineering, Anhui University of Science and Technology, Huainan, 232001, China.
| | - Dongchen Zhang
- School of Material Science and Engineering, Anhui University of Science and Technology, Huainan, 232001, China
| | - Liwen Zhang
- School of Mechanical and Electrical Engineering, Huainan Normal University, Huainan, 232001, China
| | - Xuefeng Wu
- School of Food and Bioengineering, Hefei University of Technology, Hefei, 230009, China
| | - Shengsong Deng
- School of Food and Bioengineering, Hefei University of Technology, Hefei, 230009, China
| | - Xinyu Yuan
- School of Food and Bioengineering, Hefei University of Technology, Hefei, 230009, China
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22
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Zhou Z, Li R, Ng TB, Huang F, Ye X. Considerations regarding affinity determinants for aflatoxin B 1 in binding cavity of fungal laccase based on in silico mutational and in vitro verification studies. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113412. [PMID: 35304333 DOI: 10.1016/j.ecoenv.2022.113412] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Laccase, a multicopper oxidase, is well known for its industrial potentials to remove environmental pollutants due to its low substrate specificity to oxidize phenols and thus catalytic versatility. Many efforts focused on the metabolic mechanism, yet to decipher the structural determinants responsible for the differentiation between substrates. Aflatoxin B1 (AFB1), a new substrate for laccase, is a mycotoxin with a formidable environmental threat to public health and food safety. In the present study, we combined biochemical, in silico mutational and molecular-docking data to gain an insight to the function of key residues in the active cavity close to the T1 copper site in a characterized recombinant laccase from Cerrena unicolor (rCuL). Kinetic data for computer-assisted virtual mutants established the binding affinity of hydrogen bonds and residues (Asn336, Asp207, Val391, and Thr165) in rCuL to AFB1. The augmented binding affinity to AFB1 may be related to the conformational rearrangements of the laccase and its ability to hydrogen-bond with the substrate. Furthermore, the optimal pH and temperature for rCuL and variants mediated AFB1 degradation may depend on their pH stability and thermostability. Our findings reinforce the importance of the structure-function relationship of fungal laccases in degrading AFB1, providing mechanistic guidance for future biocatalyst and bioengineering applications.
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Affiliation(s)
- Zhimin Zhou
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China; The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou 350116, China; National Engineering Laboratory for High-efficient Enzyme Expression, Fuzhou 350116, China
| | - Renkuan Li
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou 350116, China; National Engineering Laboratory for High-efficient Enzyme Expression, Fuzhou 350116, China
| | - Tzi Bun Ng
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, New Territories 999077, Hong Kong, China
| | - Fang Huang
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou 350116, China; National Engineering Laboratory for High-efficient Enzyme Expression, Fuzhou 350116, China
| | - Xiuyun Ye
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China; The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou 350116, China; National Engineering Laboratory for High-efficient Enzyme Expression, Fuzhou 350116, China.
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23
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Daneshamouz S, Saadati S, Abdelrasoul A. Molecular docking study of biocompatible enzyme interactions for removal of indoxyl sulfate (IS), indole-3-acetic acid (IAA), and p-cresyl sulfate (PCS) protein bound uremic toxins. Struct Chem 2022. [DOI: 10.1007/s11224-022-01905-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Fu W, Yi J, Cheng M, Liu Y, Zhang G, Li L, Du L, Li B, Wang G, Yang X. When bimetallic oxides and their complexes meet Fenton-like process. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127419. [PMID: 34673389 DOI: 10.1016/j.jhazmat.2021.127419] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/09/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The heterogeneous Fenton-like reaction is an advanced oxidation process, which is widely recognized for its efficient removal of recalcitrant organic contaminants. In recent years, the construction of efficient and reusable heterogeneous Fenton-like catalysts has been extensively investigated. Recently, the use of bimetallic oxides and their complexes as catalysts for Fenton-like reaction has attracted intense attention due to their high catalytic performance and excellent stability over a wide pH range. In this article, the fundamental mechanisms of Fenton-like reactions were briefly introduced. The important reports on bimetallic oxides and their complexes are classified in detail, which are mainly divided into Fe-based and Fe-free bimetallic catalysts. We then focused in depth on the performance of their respective applications in Fenton-like reactions. Special consideration has been given to the respective contributions and synergistic mechanisms of the two metals in catalysts. Overall, it is concluded that synergistic effect of the two metals in the bimetallic catalyst can boost the utilization of hydrogen peroxide, provide adequate accessible active sites, which are all beneficial to improve catalytic performance. Finally, the current challenges in this field were proposed. Our review is expected to provide help for the application of bimetallic oxides and their complexes.
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Affiliation(s)
- Wenhong Fu
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Jing Yi
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Min Cheng
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China.
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China.
| | - Gaoxia Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Ling Li
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Li Du
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Bo Li
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Guangfu Wang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Xiaofeng Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
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Gao Y, Li L, Zu W, Sun Y, Guan J, Cao Y, Yu H, Zhang W. Preparation of Dual Z-scheme Bi2MoO6/ZnSnO3/ZnO Heterostructure Photocatalyst for Efficient Visible Light Degradation of Organic Pollutants. J Inorg Organomet Polym Mater 2022. [DOI: 10.1007/s10904-022-02242-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Radhakrishnan R, Manna B, Ghosh A. Solvent induced conformational changes for the altered activity of laccase: A molecular dynamics study. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127123. [PMID: 34530268 DOI: 10.1016/j.jhazmat.2021.127123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The growing demands of solvent-based industries like paint, pharmaceutical, petrochemical, paper and pulp, etc., have directly increased the release of effluents that are rich in hazardous aromatic compounds in the environment. A sustainable biotechnological approach utilizing laccases as biocatalyst enable in biodegradation of these aromatic toxin-rich effluents. However, this enzymatic process is ineffective as laccases lose their stability and catalytic activity at high organic solvent concentrations. In this study, molecular dynamic simulations of a novel solvent tolerant laccase, DLac from Cerrena sp. RSD1 was performed to explore the molecular-level understanding of DLac in 30%(v/v) acetone and acetonitrile. Solvent-induced conformational changes were analyzed via protein structure network, which was illustrated with respect to cliques and communities. In the presence of acetonitrile, the cliques around the active site and substrate-binding site were disjoined, thus the communities lost their network integrity. Whereas with acetone, the community near the substrate-binding site gained new residues and formed a rigidified network that corresponded to enhanced DLac's activity. Moreover, prominent solvent binding sites were speculated, which can be probable mutation targets to further improve solvent tolerance and catalytic activity. The molecular basis behind solvent induced catalytic activity will further aid in engineering laccase for its industrial application.
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Affiliation(s)
- Rokesh Radhakrishnan
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Bharat Manna
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India; School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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Abdi SAH, Alzahrani A, Alghamdi S, Alquraini A, Alghamdi A. Hexaconazole exposure ravages biosynthesis pathway of steroid hormones: revealed by molecular dynamics and interaction. Toxicol Res (Camb) 2022; 11:60-76. [PMID: 35237412 PMCID: PMC8882804 DOI: 10.1093/toxres/tfab113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/05/2021] [Accepted: 11/03/2021] [Indexed: 12/25/2023] Open
Abstract
Widespread application of hexaconazole for agriculture purpose poses a threat to human health by disrupting normal endocrine homeostasis. To avoid adverse health effects on human, it is crucial to identify the effects of hexaconazole on key enzymes responsible for steroidal hormone synthesis. In view of this, present study was conducted to investigate the interaction mechanisms of hexaconazole with key enzymes in comparison with their food drug administration (FDA) approved inhibitor by molecular docking and molecular dynamics simulations. Results indicate that hexaconazole contacts with the active site of the key enzymes required for steroidal hormonal synthesis. Results pertaining to root-mean-square deviation, root-mean-square calculation, radius of gyration, hydrogen bonding and solvent accessible surface area exhibited that the interaction pattern and stability of interaction of hexaconazole was similar to enzyme specific inhibitor. In addition, ligand and enzyme complex interaction energy of hexaconazole was almost similar to key enzyme and FDA-approved enzyme specific inhibitor complex. This study offers a molecular level of understanding of hexaconazole with different enzymes required for steroidal hormonal synthesis. Findings of the study clearly suggest that hexaconazole has efficacy to stably interact with various enzyme required to progress the pathway of hormonal synthesis. If incessant exposure of hexaconazole occurs during agricultural work it may lead to ravage hormonal synthesis or potent endocrine disruption. The result of binding energy and complex interaction energy is depicted in the graphical abstract.
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Affiliation(s)
- Sayed Aliul Hasan Abdi
- Department of Pharmaceutical Chemistry, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia
| | - Abdulaziz Alzahrani
- Department of Pharmaceutical Chemistry, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia
| | - Saleh Alghamdi
- Department of Clinical Pharmacy, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia, Saudi Arabia
| | - Ali Alquraini
- Department of Pharmaceutical Chemistry, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia
| | - Adel Alghamdi
- Department of Pharmaceutical Chemistry, Faculty of Clinical Pharmacy, Albaha University, 1988, Saudi Arabia
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Zdarta J, Jesionowski T, Pinelo M, Meyer AS, Iqbal HMN, Bilal M, Nguyen LN, Nghiem LD. Free and immobilized biocatalysts for removing micropollutants from water and wastewater: Recent progress and challenges. BIORESOURCE TECHNOLOGY 2022; 344:126201. [PMID: 34710611 DOI: 10.1016/j.biortech.2021.126201] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 02/05/2023]
Abstract
Enzymatic conversion of micropollutants into less-toxic derivatives is an important bioremediation strategy. This paper aims to critically review the progress in water and wastewater treatment by both free and immobilized enzymes presenting this approach as highly efficient and performed under environmentally benign and friendly conditions. The review also summarises the effects of inorganic and organic wastewater matrix constituents on enzymatic activity and degradation efficiency of micropollutants. Finally, application of enzymatic reactors facilitate continuous treatment of wastewater and obtaining of pure final effluents. Of a particular note, enzymatic treatment of micropollutants from wastewater has been mostly reported by laboratory scale studies. Thus, this review also highlights key research gaps of the existing techniques and provides future perspectives to facilitate the transfer of the lab-scale solutions to a larger scale and to improve operationability of biodegradation processes.
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Affiliation(s)
- Jakub Zdarta
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo, PL-60965 Poznan, Poland.
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo, PL-60965 Poznan, Poland
| | - Manuel Pinelo
- Process and Systems Engineering Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, DK-2800 Kongens Lyngby, Denmark
| | - Anne S Meyer
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kongens Lyngby, Denmark
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Luong N Nguyen
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia
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Li GF, Ma WJ, Ren ZQ, Wang Y, Li JP, Zhao JW, Li ST, Liu Q, Gu YN, Cheng YF, Huang BC, Jin RC. Molecular Insight into the Binding Property and Mechanism of Sulfamethoxazole to Extracellular Proteins of Anammox Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16627-16635. [PMID: 34889591 DOI: 10.1021/acs.est.1c05203] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibiotics are widely found in nitrogen-containing wastewater, which may affect the operation stability of anaerobic ammonium oxidation (anammox)-based biological treatment systems. Extracellular polymeric substances (EPSs) of anammox sludge play a pivotal role in combining with antibiotics; however, the exact role and how the structure of the leading component of EPSs (i.e., extracellular proteins) changes under antibiotic stress remain to be elucidated. Here, the interaction between sulfamethoxazole and the extracellular proteins of anammox sludge was investigated via multiple spectra and molecular simulation. Results showed that sulfamethoxazole statically quenched the fluorescent components of EPSs, and the quenching constant of the aromatic proteins was the largest, with a value of 1.73 × 104 M-1. The overall binding was an enthalpy-driven process, with ΔH = -75.15 kJ mol-1, ΔS = -0.175 kJ mol-1 K-1, and ΔG = -21.10 kJ mol-1 at 35 °C. The O-P-O and C═O groups responded first under the disturbance of sulfamethoxazole. Excessive sulfamethoxazole (20 mg L-1) would decrease the ratio of α-helix/(β-sheet + random coil) of extracellular proteins, resulting in a loose structure. Molecular docking and dynamic simulation revealed that extracellular proteins would provide abundant sites to bind with sulfamethoxazole, through hydrogen bond and Pi-Akyl hydrophobic interaction forces. Once sulfamethoxazole penetrates into the cell surface and combines with the transmembrane ammonium transport domain, it may inhibit the NH4+ transport. Our findings enhance the understanding on the interaction of extracellular proteins and sulfamethoxazole, which may be valuable for deciphering the response property of anammox sludge under the antibiotic stress.
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Affiliation(s)
- Gui-Feng Li
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Wen-Jie Ma
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Zhi-Qi Ren
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ye Wang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jing-Peng Li
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jia-Wen Zhao
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Shu-Ting Li
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Qi Liu
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ye-Nan Gu
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ya-Fei Cheng
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Bao-Cheng Huang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ren-Cun Jin
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
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Zhao X, Meng X, Ragauskas AJ, Lai C, Ling Z, Huang C, Yong Q. Unlocking the secret of lignin-enzyme interactions: Recent advances in developing state-of-the-art analytical techniques. Biotechnol Adv 2021; 54:107830. [PMID: 34480987 DOI: 10.1016/j.biotechadv.2021.107830] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/07/2021] [Accepted: 08/29/2021] [Indexed: 02/08/2023]
Abstract
Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of the most effective ways to solve the problem of fossil resource shortage, energy security, and environmental challenges. Among the many biorefinery pathways, hydrolysis of lignocellulosics to fermentable monosaccharides by cellulase is arguably the most critical step of lignocellulose bioconversion. In the process of enzymatic hydrolysis, the direct physical contact between enzymes and cellulose is an essential prerequisite for the hydrolysis to occur. However, lignin is considered one of the most recalcitrant factors hindering the accessibility of cellulose by binding to cellulase unproductively, which reduces the saccharification rate and yield of sugars. This results in high costs for the saccharification of carbohydrates. The various interactions between enzymes and lignin have been explored from different perspectives in literature, and a basic lignin inhibition mechanism has been proposed. However, the exact interaction between lignin and enzyme as well as the recently reported promotion of some types of lignin on enzymatic hydrolysis is still unclear at the molecular level. Multiple analytical techniques have been developed, and fully unlocking the secret of lignin-enzyme interactions would require a continuous improvement of the currently available analytical techniques. This review summarizes the current commonly used advanced research analytical techniques for investigating the interaction between lignin and enzyme, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy (FLS), and molecular dynamics (MD) simulations. Interdisciplinary integration of these analytical methods is pursued to provide new insight into the interactions between lignin and enzymes. This review will serve as a resource for future research seeking to develop new methodologies for a better understanding of the basic mechanism of lignin-enzyme binding during the critical hydrolysis process.
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Affiliation(s)
- Xiaoxue Zhao
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Renewable Carbon, Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN 37996, USA; Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chenhuan Lai
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhe Ling
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Caoxing Huang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Yong
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
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Enhancement and analysis of Anthracene degradation by Tween 80 in LMS-HOBt. Sci Rep 2021; 11:13121. [PMID: 34162899 PMCID: PMC8222252 DOI: 10.1038/s41598-021-90609-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/27/2021] [Indexed: 11/30/2022] Open
Abstract
This study examines the specific effect of Tween 80 on the conversion of anthracene (ANT) in laccase medium system regarding surfactant chemical changes and mechanism. The conversion rate and degradation products of ANT were investigated in different concentrations of Tween 80 solution. Between Tween 80 concentration 0–40 critical micelle concentrations (CMC), the kinetic parameter-k (h−1) and corresponding half-life T1/2 decreased with increasing concentration. When Tween 80 was above 20 CMC the laccase-medium system converted > 95% of ANT to anthraquinone within 12 h. During the entire enzymatic reaction, the laccase activity in the system increased with increasing Tween 80 concentration. Combined with GC/MS analysis of the product, it was speculated that hydrogens belonging to the ether-oxygen bond and carbon–carbon double bond α-CH of Tween 80, were removed by the laccase-media system, promoting its degradation. Additionally, enhanced activity caused by oxygen free radicals (ROS) such as RO• and ROO•, continuously oxidized Tween 80, which in turn produced free radicals while converting ANT. This study provides new theoretical support toward the application of surfactants in the elimination of polycyclic aromatic hydrocarbons.
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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Bhatt P, Joshi T, Bhatt K, Zhang W, Huang Y, Chen S. Binding interaction of glyphosate with glyphosate oxidoreductase and C-P lyase: Molecular docking and molecular dynamics simulation studies. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:124927. [PMID: 33450511 DOI: 10.1016/j.jhazmat.2020.124927] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 05/12/2023]
Abstract
Widespread application of glyphosate poses a threat to living organisms. Microbial strains are able to degrade glyphosate via contrasting metabolic pathways with the help of enzymes. Glyphosate oxidoreductase (GOX) and C-P lyase are the key enzymes for the biodegradation of glyphosate and its intermediate metabolite aminomethylphosphonic acid (AMPA) in microbes. The microbial degradation of glyphosate has been reported, but the underlying molecular mechanism is still unclear. Therefore, in this study, the interaction mechanism of GOX and C-P lyase with glyphosate and AMPA were investigated by using molecular docking and molecular dynamics (MD) simulations. The results indicate that glyphosate contacts with the active site of GOX and C-P lyase by hydrogen bonds as well as hydrophobic and van der Waals interactions in aqueous solution to maintain its stability. The presence of glyphosate and AMPA in the active site significantly changes the conformation of GOX and C-P lyase. The results of the MD simulations confirm that GOX and C-P lyase complexes are stable during the catalytic reaction. This study offers a molecular level of understanding of the expression and function of GOX and C-P lyase for the bioremediation of glyphosate.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand 263136, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar, Uttarakhand 249404, India
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Kooravand M, Asadpour S, Haddadi H, Farhadian S. An insight into the interaction between malachite green oxalate with human serum albumin: Molecular dynamic simulation and spectroscopic approaches. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124878. [PMID: 33360194 DOI: 10.1016/j.jhazmat.2020.124878] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/17/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
Cationic triarylmethane dyes such as malachite green are aromatic xenobiotic compounds causing environmental pollution. The affinity between hazardous materials and biomolecules makes it important to understand the properties of such compounds. Accordingly, in this study, the possible molecular interaction between this pollutant and the human serum albumin (HSA) was investigated using a combination of molecular docking, molecular dynamic simulation and multi-spectroscopic approaches. The docking results illustrated that malachite green oxalate (MGO) could bind to some of the HSA amino acids with the estimated free energy = -32.93 kJ/mol. Further, the results of the dynamic simulation revealed that MGO had a steady interaction with the protein though increasing flexibility and decreasing the HSA compactness. These results were, therefore, in agreement with those obtained by spectroscopic techniques. The MGO concentration of 0.0005 mM could quench the HSA's intrinsic fluorescence by %16.88. The protein structural changes also revealed that the binding interaction of MGO-HSA was accompanied by an increase in the α-helix and a decrease in the β-sheet of the protein. Overall, this study indicated the suitable molecular modeling interaction of MGO and HSA.
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Affiliation(s)
- Masoumeh Kooravand
- Department of Chemistry, Faculty of Sciences, Shahrekord University, P. O. Box 115, Shahrekord, Iran
| | - Saeid Asadpour
- Department of Chemistry, Faculty of Sciences, Shahrekord University, P. O. Box 115, Shahrekord, Iran.
| | - Hedayat Haddadi
- Department of Chemistry, Faculty of Sciences, Shahrekord University, P. O. Box 115, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Sciences, Shahrekord University, P. O. Box.115, Shahrekord, Iran
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36
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Onaizi SA. Statistical analyses of the effect of rhamnolipid biosurfactant addition on the enzymatic removal of Bisphenol A from wastewater. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.101929] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Onaizi SA, Alshabib M. The degradation of bisphenol A by laccase: Effect of biosurfactant addition on the reaction kinetics under various conditions. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.117785] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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38
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Liang Q, Liu X, Wang J, Liu Y, Liu Z, Tang L, Shao B, Zhang W, Gong S, Cheng M, He Q, Feng C. In-situ self-assembly construction of hollow tubular g-C 3N 4 isotype heterojunction for enhanced visible-light photocatalysis: Experiments and theories. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123355. [PMID: 32659580 DOI: 10.1016/j.jhazmat.2020.123355] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/09/2020] [Accepted: 06/25/2020] [Indexed: 05/15/2023]
Abstract
A highly reactive hollow tubular g-C3N4 isotype heterojunction (SCN-CN) was designed to enhance visible light absorption and manipulate the directed transfer of electrons and holes. The results of UV-vis DRS, XPS valence band and DFT theoretical calculations indicated S doping increases the visible-light absorption capacity and changed the ba nd gap structure of g-C3N4 (CN), resulting in the transfer of electrons from the CN to the SCN and holes from the SCN to the CN under visible light. In addition, the tubular structure of the SCN-CN facilitated the transfer of electrons in the longitudinal direction, which reduced charge carrier recombination. Furthermore, the optical properties, electronic structure, and electron transfer of SCN-CN were also studied by experiments and theoretical calculations. The antibiotic tetracycline hydrochloride (TCH) and dye Rhodamine B (RHB) were subjected to evaluate the photocatalytic performance of SCN-CN. The scavenger tests and ESR data showed that the h+, ·O2- and ·OH worked together in the photocatalytic process. Moreover, the photocatalytic degradation pathway was analyzed by LC-MS. This study synthesized a hollow tubular CN isotype heterojunction with high visible-light photocatalytic performance and provided a theoretical basis for CN isotype heterojunction.
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Affiliation(s)
- Qinghua Liang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Xiaojuan Liu
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, 410007, PR China
| | - Jiajia Wang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Zhifeng Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China.
| | - Lin Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China.
| | - Binbin Shao
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Wei Zhang
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, 410007, PR China
| | - Shanxi Gong
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, PR China
| | - Min Cheng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Qingyun He
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Chengyang Feng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
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Tang H, Zhang S, Huang T, Cui F, Xing B. pH-Dependent adsorption of aromatic compounds on graphene oxide: An experimental, molecular dynamics simulation and density functional theory investigation. JOURNAL OF HAZARDOUS MATERIALS 2020; 395:122680. [PMID: 32330781 DOI: 10.1016/j.jhazmat.2020.122680] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/11/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
This work provides a comprehensive understanding for the pH-dependent adsorption of aromatic compounds (ACs) on graphene oxide (GO). Isothermal and kinetics experiments indicated both adsorption capacity and adsorption rate were suppressed at higher pH, and the mechanisms were revealed by molecular dynamics simulations and density functional theory calculations. More specifically, π-π, hydrogen bond, vdWs, and water-mediated steric hindrance interactions were examined to reveal how pH affected the adsorption capacity, and microscopic dynamic adsorption process was captured to reveal how pH affected the adsorption rate. Results showed the reduced adsorption capacity at higher pH was mediated by increased electrostatic repulsion, weakened π-π interaction, and increased water-mediated steric hindrance. The pH-dependent behaviour of GO was responsible for the effect of pH on adsorption rate. Self-aggregation of GO at lower pH helped to capture ACs and created more favourable adsorption sites. Upon the adsorption of ACs on GO, GO/water/AC/water/GO sandwich-like structure formed, which was also mediated by solution pH. Overall, pH affects the adsorption of ACs on GO by regulating driving forces, adsorption process, and the configuration property of GOAC complex.
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Affiliation(s)
- Huan Tang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
| | - Shuyan Zhang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Tinglin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
| | - Fuyi Cui
- College of Environment and Ecology, Chongqing University, Chongqing, 40045, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, USA
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Mitusińska K, Raczyńska A, Bzówka M, Bagrowska W, Góra A. Applications of water molecules for analysis of macromolecule properties. Comput Struct Biotechnol J 2020; 18:355-365. [PMID: 32123557 PMCID: PMC7036622 DOI: 10.1016/j.csbj.2020.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/26/2020] [Accepted: 02/01/2020] [Indexed: 01/12/2023] Open
Abstract
Water molecules maintain proteins' structures, functions, stabilities and dynamics. They can occupy certain positions or pass quickly via a protein's interior. Regardless of their behaviour, water molecules can be used for the analysis of proteins' structural features and biochemical properties. Here, we present a list of several software programs that use the information provided by water molecules to: i) analyse protein structures and provide the optimal positions of water molecules for protein hydration, ii) identify high-occupancy water sites in order to analyse ligand binding modes, and iii) detect and describe tunnels and cavities. The analysis of water molecules' distribution and trajectories sheds a light on proteins' interactions with small molecules, on the dynamics of tunnels and cavities, on protein composition and also on the functionality, transportation network and location of functionally relevant residues. Finally, the correct placement of water molecules in protein crystal structures can significantly improve the reliability of molecular dynamics simulations.
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Affiliation(s)
| | | | | | | | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, Gliwice, Poland
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41
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Zhang W, Zeng Z, Liu Z, Huang J, Xiao R, Shao B, Liu Y, Liu Y, Tang W, Zeng G, Gong J, He Q. Effects of carbon nanotubes on biodegradation of pollutants: Positive or negative? ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 189:109914. [PMID: 31761551 DOI: 10.1016/j.ecoenv.2019.109914] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 06/10/2023]
Abstract
Recently, a large quantity of carbon nanotubes (CNTs) enters the environment due to the increasing production and applications. More and more researches are focused on the fate and possible ecological risks of CNTs. Some literatures summarized the effects of CNTs on the chemical behavior and fate of pollutants. However, little reviewed the effects of CNTs on the biodegradation of pollutants. In general, the effects of CNTs on the biodegradation of pollutants and the related mechanisms were summarized in this review. CNTs have positive or negative effects on the biodegradation of contaminants by affecting the functional microorganisms, enzymes and the bioavailability of pollutants. CNTs may affect the microbial growth, activity, biomass, community composition, diversity and the activity of enzymes. The decrease of the bioavailability of pollutants due to the sorption on CNTs also causes the reduction of the biodegradation of contaminants. In addition, the roles of CNTs are controlled by multiple mechanisms, which are divided into three aspects i.e., properties of CNTs, environment condition, and microorganisms themself. The better understanding of the fate of CNTs and their impacts on the biochemical process in the environment is conducive to determine the release of CNTs into the environment.
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Affiliation(s)
- Wei Zhang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Zhuotong Zeng
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, 410007, China
| | - Zhifeng Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China.
| | - Jinhui Huang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China.
| | - Rong Xiao
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, 410007, China
| | - Binbin Shao
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Yujie Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Wangwang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Jilai Gong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Qingyun He
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
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42
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Wu T, Liu X, Liu Y, Cheng M, Liu Z, Zeng G, Shao B, Liang Q, Zhang W, He Q, Zhang W. Application of QD-MOF composites for photocatalysis: Energy production and environmental remediation. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213097] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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43
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Qiu Z, Qu K, Luan F, Liu Y, Zhu Y, Yuan Y, Li H, Zhang H, Hai Y, Zhao C. Binding specificities of estrogen receptor with perfluorinated compounds: A cross species comparison. ENVIRONMENT INTERNATIONAL 2020; 134:105284. [PMID: 31707300 DOI: 10.1016/j.envint.2019.105284] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/15/2019] [Accepted: 10/21/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Perfluorinated compounds (PFCs) were reported to result in the endocrine disruption by activating the estrogen receptor (ER) and inducing ER-mediated transcriptions. OBJECTIVE The aim of the present work was to perform cross-species comparisons on the characteristics of eight PFCs binding to humans ERα and to rats ERα. METHODS In the present work, in vivo tests, including serum estradiol level assay and immunohistochemical staining, fluorescence assay and molecular models were applied. RESULTS Based on the in vivo experiments, the exposure of PFOA and PFOS to female rats was proved to increase the ERα expression in the terus, suggesting that PFCs may act as estrogenic compounds to activate ERα in vivo. The further fluorescence assay presented that these eight PFCs have stronger binding abilities to human ERα than to rat ERα. In addition, the differences in binding specificities between human ERα and rat ERα were identified in the process of molecular dynamics modeling with the term of helix position and the ability of coregulator recruitment. It can be found that more and stronger charge clamps could form between PFCs with human ERα than with rat ERα. Also, the eight PFCs presented lower binding energies in human ERα systems, which proved that eight PFCs presented much stronger binding abilities with human ERα. DISCUSSION In all, it can be concluded that PFCs might be more sensitive to human ERα than to that of rats, which also suggested the greater susceptibility to adverse effects on humans. The present work was a beginning assessment of a cross-species comparison, providing important information on health impacts of PFCs in humans.
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Affiliation(s)
- Zhiqiang Qiu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Kaili Qu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Feng Luan
- College of Chemistry & Chemical Engineering, Yantai University, Yantai 264005, China
| | - Yaquan Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yu Zhu
- Department of Ecology and Environment of Gansu Province, Lanzhou 730000, China
| | - Yongna Yuan
- School of Information Science & Engineering, Lanzhou University, Lanzhou 730000, China
| | - Hongyu Li
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Haixia Zhang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Ying Hai
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Chunyan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
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44
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Peng Z, Liu X, Zhang W, Zeng Z, Liu Z, Zhang C, Liu Y, Shao B, Liang Q, Tang W, Yuan X. Advances in the application, toxicity and degradation of carbon nanomaterials in environment: A review. ENVIRONMENT INTERNATIONAL 2020; 134:105298. [PMID: 31765863 DOI: 10.1016/j.envint.2019.105298] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Carbon nanomaterials (CNMs) are novel nanomaterials with excellent physicochemical properties, which are widely used in biomedicine, energy and sensing. Besides, CNMs also play an important role in environmental pollution control, which can absorb heavy metals, antibiotics and harmful gases. However, CNMs are inevitably entering the environment while they are rapidly developing. They are harmful to living organisms in the environment and are difficult to degrade under natural conditions. Here, we systematically describe the toxicity of carbon nanotubes (CNTs), graphene (GRA) and C60 to cells, animals, humans, and microorganisms. According to the current research results, the toxicity mechanism is summarized, including oxidative stress response, mechanical damage and effects on biological enzymes. In addition, according to the latest research progress, we focus on the two major degradation methods of chemical degradation and biodegradation of CNTs, GRA and C60. Meanwhile, the reaction conditions and degradation mechanisms of degradation are respectively stated. Moreover, we have prospects for the limitations of CNM degradation under non-experimental conditions and their potential application.
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Affiliation(s)
- Zan Peng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xiaojuan Liu
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha 410007, China
| | - Wei Zhang
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha 410007, China
| | - Zhuotong Zeng
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, PR China
| | - Zhifeng Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Chang Zhang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Binbin Shao
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Qinghua Liang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Wangwang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xingzhong Yuan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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45
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Promoting microbial utilization of phenolic substrates from bio-oil. ACTA ACUST UNITED AC 2019; 46:1531-1545. [DOI: 10.1007/s10295-019-02208-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/21/2019] [Indexed: 10/26/2022]
Abstract
Abstract
The economic viability of the biorefinery concept is limited by the valorization of lignin. One possible method of lignin valorization is biological upgrading with aromatic-catabolic microbes. In conjunction, lignin monomers can be produced by fast pyrolysis and fractionation. However, biological upgrading of these lignin monomers is limited by low water solubility. Here, we address the problem of low water solubility with an emulsifier blend containing approximately 70 wt% Tween® 20 and 30 wt% Span® 80. Pseudomonas putida KT2440 grew to an optical density (OD600) of 1.0 ± 0.2 when supplied with 1.6 wt% emulsified phenolic monomer-rich product produced by fast pyrolysis of red oak using an emulsifier dose of 0.076 ± 0.002 g emulsifier blend per g of phenolic monomer-rich product. This approach partially mitigated the toxicity of the model phenolic monomer p-coumarate to the microbe, but not benzoate or vanillin. This study provides a proof of concept that processing of biomass-derived phenolics to increase aqueous availability can enhance microbial utilization.
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46
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Du J, Zhang A, Zhang X, Si X, Cao J. Comparative analysis of rhamnolipid congener synthesis in neotype Pseudomonas aeruginosa ATCC 10145 and two marine isolates. BIORESOURCE TECHNOLOGY 2019; 286:121380. [PMID: 31048264 DOI: 10.1016/j.biortech.2019.121380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
A comparative study of rhamnolipid congener synthesis was performed using the neotype Pseudomonas aeruginosa ATCC 10145 and two marine isolates (1A01151 and 1A00364). Compared with the neotype, 1A01151 and 1A00364 showed increased production of rhamnolipids containing higher proportion of congeners with longer fatty acid chains (C10-C12 and C10-C12:1) and/or di-rhamnose moiety. These could reduce surface tension of water to lower minimum values of 21.3 mN m-1 and 25.7 mN m-1. The comparative profile of rhamnolipid congener composition, fatty acid content and gene expression suggested that elevated expression of rhlAB and rhlC throughout the fermentation process and enhanced accumulation of dTDP-l-rhamnose and fatty acid precursors (C12 and C12:1) at the onset of rhamnolipid accumulation were related to improved rhamnolipid production and surface-active property. This work provides insights into the metabolic relationship between rhamnolipids and related precursor biosynthesis, and could therefore be beneficial for process optimization for efficient rhamnolipid congener production.
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Affiliation(s)
- Jin Du
- The Institute of Seawater Desalination and Multipurpose Utilization, MNR, Tianjin 300192, PR China.
| | - Aijun Zhang
- The Institute of Seawater Desalination and Multipurpose Utilization, MNR, Tianjin 300192, PR China
| | - Xiaoqing Zhang
- The Institute of Seawater Desalination and Multipurpose Utilization, MNR, Tianjin 300192, PR China
| | - Xiaoguang Si
- The Institute of Seawater Desalination and Multipurpose Utilization, MNR, Tianjin 300192, PR China
| | - Junrui Cao
- The Institute of Seawater Desalination and Multipurpose Utilization, MNR, Tianjin 300192, PR China
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47
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Liu Y, Liu Z, Huang D, Cheng M, Zeng G, Lai C, Zhang C, Zhou C, Wang W, Jiang D, Wang H, Shao B. Metal or metal-containing nanoparticle@MOF nanocomposites as a promising type of photocatalyst. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.02.031] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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48
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Yang J, Du Q, Gan N, Chen Y, Yang L, Liu Z, Zhao H, Sun Q, Li H. Exploring the binding pattern between pepsin and deferasirox using detailed experimental and computer simulation methods. RSC Adv 2018; 8:37208-37218. [PMID: 35557832 PMCID: PMC9088941 DOI: 10.1039/c8ra07993e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/30/2018] [Indexed: 01/19/2023] Open
Abstract
Steady-state fluorescence spectroscopy indicated that a ground state complex was formed between deferasirox (DFX) and pepsin. The binding parameters and thermodynamic parameters of pepsin–DFX complex formation suggested the presence of only one high affinity binding site in the binding process of DFX and pepsin and that the binding process was hydrogen bond dominated. According to the MD simulation optimal pepsin–DFX binding model analysis, the binding force between DFX and pepsin was mainly hydrogen bonding, and the hydrophobic interaction was supplemented. Synchronous fluorescence spectroscopy and 3D fluorescence spectroscopy indicated that the binding of DFX to pepsin had minor effect on the protein structure and function. Circular dichroism spectra showed that DFX had no significant effect on the main secondary structure of pepsin. MD analysis also showed that DFX did not affect the looseness of pepsin and the overall secondary structure, but it affected the amino acid residue sequence Leu48-Ala49-Cys50-Ser51-Asp52. Pepsin enzyme activity test showed that the addition of DFX had a slight enhancement effect on the activity of pepsin. Combined with the MD results, DFX bound to pepsin and was closer to the pepsin active site Asp-215, which may affect the electrical environment of Asp-215 residues and enhance the activity of pepsin. Investigation on the binding properties of deferasirox to pepsin.![]()
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Affiliation(s)
- Ji Yang
- School of Chemical Engineering
- Sichuan University
- Chengdu
- China
- R&D Center of China Tobacco Yunnan Industrial Co., Ltd
| | - Qiaohong Du
- School of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Na Gan
- School of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Yongkuan Chen
- R&D Center of China Tobacco Yunnan Industrial Co., Ltd
- Kunming
- China
| | - Liu Yang
- R&D Center of China Tobacco Yunnan Industrial Co., Ltd
- Kunming
- China
| | - Zhihua Liu
- R&D Center of China Tobacco Yunnan Industrial Co., Ltd
- Kunming
- China
| | - Hui Zhao
- R&D Center of China Tobacco Yunnan Industrial Co., Ltd
- Kunming
- China
| | - Qiaomei Sun
- School of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Hui Li
- School of Chemical Engineering
- Sichuan University
- Chengdu
- China
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