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Li S, Zhang T, Zheng H, Dong X, Leong YK, Chang JS. Advances and challenges in the removal of organic pollutants via sulfate radical-based advanced oxidation processes by Fe-based metal-organic frameworks: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171885. [PMID: 38527540 DOI: 10.1016/j.scitotenv.2024.171885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/03/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
Organic contaminants, notorious for their complexity and resistance to degradation, are prevalent in aquatic environments, posing severe threats to ecosystems. Sulfate radical-based advanced oxidation processes (SR-AOPs), known for their stability and high effectiveness, have become a common choice for treating organic wastewater. Metal-organic framework materials (MOFs) have garnered substantial attention due to their facile chemical manipulation, unique structural configurations, and other favorable properties. Therefore, this article critically reviews recent advances in research involving the utilization of Fe-based MOFs (Fe-MOFs) and their derivatives in SR-AOPs. Specifically, it highlights the manipulation of influencing factors within the system to enhance the degradation of organic pollutants. The mechanisms and applications underlying the degradation of organic pollutants in the SR-AOPs system are also elucidated.
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Affiliation(s)
- Shuo Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China
| | - Tianqi Zhang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China
| | - Heshan Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China.
| | - Xu Dong
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China
| | - Yoong Kit Leong
- Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan; Department of Chemical Engineering, National Cheng-Kung University, Tainan, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, 32003, Taiwan.
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2
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Yang J, Liu S, Liu Y, Zhou L, Wen H, Wei H, Shen R, Wu X, Jiang J, Li B. Review and perspectives on TS-1 catalyzed propylene epoxidation. iScience 2024; 27:109064. [PMID: 38375219 PMCID: PMC10875142 DOI: 10.1016/j.isci.2024.109064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Titanium silicate zeolite (TS-1) is widely used in the research on selective oxidations of organic substrates by H2O2. Compared with the chlorohydrin process and the hydroperoxidation process, the TS-1 catalyzed hydroperoxide epoxidation of propylene oxide (HPPO) has advantages in terms of by-products and environmental friendliness. This article reviews the latest progress in propylene epoxidation catalyzed by TS-1, including the HPPO process and gas phase epoxidation. The preparation and modification of TS-1 for green and sustainable production are summarized, including the use of low-cost feedstocks, the development of synthetic routes, strategies to enhance mass transfer in TS-1 crystal and the enhancement of catalytic performance after modification. In particular, this article summarizes the catalytic mechanisms and advanced characterization techniques for propylene epoxidation in recent years. Finally, the present situation, development prospect and challenge of propylene epoxidation catalyzed by TS-1 were prospected.
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Affiliation(s)
- Jimei Yang
- College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou 450001, P.R. China
| | - Shuling Liu
- College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou 450001, P.R. China
| | - Yanyan Liu
- College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou 450001, P.R. China
- College of Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou 450002, P.R. China
- Institute of Chemical Industry of Forest Products, CAF, National Engineering Lab for Biomass Chemical Utilization, Nanjing 210042, P.R. China
| | - Limin Zhou
- College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou 450001, P.R. China
- Institute of Chemical Industry of Forest Products, CAF, National Engineering Lab for Biomass Chemical Utilization, Nanjing 210042, P.R. China
| | - Hao Wen
- College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou 450001, P.R. China
| | - Huijuan Wei
- College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou 450001, P.R. China
| | - Ruofan Shen
- College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou 450001, P.R. China
| | - Xianli Wu
- College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou 450001, P.R. China
| | - Jianchun Jiang
- Institute of Chemical Industry of Forest Products, CAF, National Engineering Lab for Biomass Chemical Utilization, Nanjing 210042, P.R. China
| | - Baojun Li
- College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou 450001, P.R. China
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3
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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4
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Chen J, Zhao K, Wu Y, Liu J, Wang R, Yang Y, Liu Y. Improved bioelectrochemical performance of MnO 2 nanorods modified cathode in microbial fuel cell. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49052-49059. [PMID: 36764990 DOI: 10.1007/s11356-023-25787-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/03/2023] [Indexed: 04/16/2023]
Abstract
The property of cathode in the microbial fuel cell (MFC) was one of the key factors limiting its output performance. MnO2 nanorods were prepared by a simple hydrothermal method as cathode catalysts for MFCs. There were a number of typical characteristic crystal planes of MnO2 nanorods like (110), (310), (121), and (501). Additionally, there were great many hydroxyl groups on the surface of nanorod-like MnO2, which provided a rich set of active adsorption sites. The maximum power density (Pmax) of MnO2-MFC was 180 mW/m2, which was 1.51 times that of hydrothermally synthesized MnO2 (119.07 mW/m2), 4.28 times that of naturally synthesized MnO2 (42.05 mW/m2), and 5.61 times that of the bare cathode (32.11 mW/m2). The maximum voltage was 234 mV and the maximum stabilization time was 4 days. The characteristics of MnO2, including rod-like structure, high specific surface area, and high conductivity, were conducive to providing more active sites for oxygen reduction reaction (ORR). Therefore, the air cathode modified by MnO2 nanorods was a kind of fuel cell electrode with great application potential.
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Affiliation(s)
- Junfeng Chen
- School of Life Sciences, Qufu Normal University, Qufu, 273165, People's Republic of China.
| | - Kunqi Zhao
- School of Life Sciences, Qufu Normal University, Qufu, 273165, People's Republic of China
| | - Yiqun Wu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, People's Republic of China
| | - Jinyu Liu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, People's Republic of China
| | - Renjun Wang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, People's Republic of China
| | - Yuewei Yang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, People's Republic of China
| | - Yanyan Liu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, People's Republic of China
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5
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Berhanu A, Mutanda I, Taolin J, Qaria MA, Yang B, Zhu D. A review of microbial degradation of per- and polyfluoroalkyl substances (PFAS): Biotransformation routes and enzymes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160010. [PMID: 36356780 DOI: 10.1016/j.scitotenv.2022.160010] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Since the 1950s, copious amounts of per- and polyfluoroalkyl substances (PFAS) (dubbed "forever chemicals") have been dumped into the environment, causing heavy contamination of soil, surface water, and groundwater sources. Humans, animals, and the environment are frequently exposed to PFAS through food, water, consumer products, as well as waste streams from PFAS-manufacturing industries. PFAS are a large group of synthetic organic fluorinated compounds with widely diverse chemical structures that are extremely resistant to microbial degradation. Their persistence, toxicity to life on earth, bioaccumulation tendencies, and adverse health and ecological effects have earned them a "top priority pollutant" designation by regulatory bodies. Despite that a number of physicochemical methods exist for PFAS treatment, they suffer from major drawbacks regarding high costs, use of high energy and incomplete mineralization (destruction of the CF bond). Consequently, microbial degradation and enzymatic treatment of PFAS are highly sought after as they offer a complete, cheaper, sustainable, and environmentally friendly alternative. In this critical review, we provide an overview of the classification, properties, and interaction of PFAS within the environment relevant to microbial degradation. We discuss latest developments in the biodegradation of PFAS by microbes, transformation routes, transformation products and degradative enzymes. Finally, we highlight the existing challenges, limitations, and prospects of bioremediation approaches in treating PFAS and proffer possible solutions and future research directions.
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Affiliation(s)
- Ashenafi Berhanu
- Biofuels Institute, School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Haramaya Institute of Technology, Department of Chemical Engineering, Haramaya University, Dire Dawa, Ethiopia
| | - Ishmael Mutanda
- Biofuels Institute, School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Ji Taolin
- Biofuels Institute, School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Majjid A Qaria
- Biofuels Institute, School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Bin Yang
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA 99354, USA
| | - Daochen Zhu
- Biofuels Institute, School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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6
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Gashi A, Parmentier J, Fioux P, Marsalek R. Tuning the C/N Ratio of C‐Rich Graphitic Carbon Nitride (g‐C
3
N
4
) Materials by the Melamine/Carboxylic Acid Adduct Route. Chemistry 2022; 28:e202103605. [DOI: 10.1002/chem.202103605] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Arianit Gashi
- Department of Chemistry University of Ostrava 30. Dubna 22 Ostrava 701 03 Czech Republic
- Institut de Science des Matériaux de Mulhouse (IS2 M) Université de Strasbourg, Université de Haute-Alsace 15 rue Jean Starcky, BP 2488 68057 Mulhouse Cedex France
| | - Julien Parmentier
- Institut de Science des Matériaux de Mulhouse (IS2 M) Université de Strasbourg, Université de Haute-Alsace 15 rue Jean Starcky, BP 2488 68057 Mulhouse Cedex France
| | - Philippe Fioux
- Institut de Science des Matériaux de Mulhouse (IS2 M) Université de Strasbourg, Université de Haute-Alsace 15 rue Jean Starcky, BP 2488 68057 Mulhouse Cedex France
| | - Roman Marsalek
- Department of Chemistry University of Ostrava 30. Dubna 22 Ostrava 701 03 Czech Republic
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7
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Chen X, Xu Y, Xu G. Modification of graphite carbon nitride by adding an ultra-micro amount of triaminotriphenylamine for superior photocatalytic hydrogen evolution. NEW J CHEM 2022. [DOI: 10.1039/d2nj00393g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electron–hole pairs separated effectively by intermolecular charge transfer between triphenylamine and heptazine of doped g-C3N4 improve photocatalytic hydrogen evolution.
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Affiliation(s)
- Xiaona Chen
- School of Environment and Chemical Engineering, Shenyang University of Technology, 110870 Shenyang, P. R. China
| | - Yanheng Xu
- School of Environment and Chemical Engineering, Shenyang University of Technology, 110870 Shenyang, P. R. China
| | - Ge Xu
- School of Environment and Chemical Engineering, Shenyang University of Technology, 110870 Shenyang, P. R. China
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8
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Kang H, Zheng M. Influence of the quantum mechanical region size in QM/MM modelling: A case study of fluoroacetate dehalogenase catalyzed C F bond cleavage. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Yue Y, Fan J, Xin G, Huang Q, Wang JB, Li Y, Zhang Q, Wang W. Comprehensive Understanding of Fluoroacetate Dehalogenase-Catalyzed Degradation of Fluorocarboxylic Acids: A QM/MM Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9817-9825. [PMID: 34080849 DOI: 10.1021/acs.est.0c08811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorochemicals are persistent, bioaccumulative, and toxic compounds that are widely tributed in the environment. Developing efficient biodegradation strategies to decompose the fluorochemicals via breaking the inert C-F bonds presents a holistic challenge. As a promising biodegradation enzyme candidate, fluoroacetate dehalogenase (FAcD) has been reported as the only non-metallic enzyme to catalyze the cleavage of the strong C-F bond. Here, we systematically investigated the catalytic actions of FAcD toward its natural substrate fluoroacetate using molecular dynamics simulations and quantum mechanism/molecular mechanism calculations. We propose that the enzymatic transformation involves four elementary steps, (I) C-F bond activation, (II) nucleophilic attack, (III) C-O bond cleavage, and (IV) proton transfer. Our results show that nucleophilic attack is the rate-determining step. However, for difluoroacetate and trifluoroacetate, C-F bond activation, instead of nucleophilic attack, becomes the rate-determining step. We show that FAcD, originally recognized as α-fluorocarboxylic acid degradation enzyme, can catalyze the defluorination of difluoroacetate to glyoxylate, which is captured by our high-resolution mass spectrometry experiments. In addition, we employed amino acid electrostatic analysis method to screen potential mutation hotspots for tuning FAcD's electrostatic environment to favor substrate conversion. The comprehensive understanding of catalytic mechanism will inform a rational enzyme engineering strategy to degrade fluorochemicals for benefits of environmental sustainability.
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Affiliation(s)
- Yue Yue
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Jiaqian Fan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P. R. China
| | - Guoqing Xin
- Wuhan National High Magnetic Field Center (WHMFC), Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Qun Huang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P. R. China
| | - Jian-Bo Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P. R. China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
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10
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Abstract
2,5-furandicarboxylic acid (2,5-FDCA) is a biomass derivate of high importance that is used as a building block in the synthesis of green polymers such as poly(ethylene furandicarboxylate) (PEF). PEF is presumed to be an ideal substitute for the predominant polymer in industry, the poly(ethylene terephthalate) (PET). Current routes for 2,5-FDCA synthesis require 5-hydroxymethylfurfural (HMF) as a reactant, which generates undesirable co-products due to the complicated oxidation step. Therefore, direct CO2 carboxylation of furoic acid salts (FA, produced from furfural, derivate of inedible lignocellulosic biomass) to 2,5-FDCA is potentially a good alternative. Herein, we present the primary results obtained on the carboxylation reaction of potassium 2-furoate (K2F) to synthesize 2,5-FDCA, using heterogeneous catalysts. An experimental setup was firstly validated, and then several operation conditions were optimized, using heterogeneous catalysts instead of the semi-heterogeneous counterparts (molten salts). Ag/SiO2 catalyst showed interesting results regarding the K2F conversion and space–time yield of 2,5-FDCA.
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11
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Oyewusi HA, Wahab RA, Huyop F. Dehalogenase-producing halophiles and their potential role in bioremediation. MARINE POLLUTION BULLETIN 2020; 160:111603. [PMID: 32919122 DOI: 10.1016/j.marpolbul.2020.111603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
This review aims to briefly describe the potential role of dehalogenase-producing halophilic bacteria in decontamination of organohalide pollutants. Hypersaline habitats pose challenges to life because of low water activity (water content) and is considered as the largest and ultimate sink for pollutants due to naturally and anthropogenic activities in which a substantial amount of ecological contaminants are organohalides. Several such environments appear to host and support substantial diversity of extremely halophilic and halotolerant bacteria as well as halophilic archaea. Biodegradation of several toxic inorganic and organic compounds in both aerobic and anaerobic conditions are carried out by halophilic microbes. Therefore, remediation of polluted marine/hypersaline environments are the main scorching issues in the field of biotechnology. Although many microbial species are reported as effective pollutants degrader, but little has been isolated from marine/hypersaline environments. Therefore, more novel microbial species with dehalogenase-producing ability are still desired.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, PMB, 5351, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia.
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12
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Yue Y, Chen J, Bao L, Wang J, Li Y, Zhang Q. Fluoroacetate dehalogenase catalyzed dehalogenation of halogenated carboxylic acids: A QM/MM approach. CHEMOSPHERE 2020; 254:126803. [PMID: 32361540 DOI: 10.1016/j.chemosphere.2020.126803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/11/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
Dehalogenation is one of the most important reactions in environmental pollution control, for instance, the degradation of persistent organic pollutants (POPs). Recently, fluoroacetate dehalogenase (FAcD) has been reported to catalyze the dehalogenation reactions, which shows great potential in treating halogenated pollutants. Here the dehalogenation mechanism catalyzed by FAcD was fully deciphered with the aid of quantum mechanics/molecular mechanics method. The results show that FAcD catalyzed dehalogenation efficiency follows the order of defluorination > dechlorination > debromination. The corresponding Boltzmann-weighted average barriers are 10.1, 19.7, and 20.9 kcal mol-1. Positive/negative correlations between activation barriers and structural parameters (e.g. distance and angle) for FAcD catalyzed dechlorination and debromination were established. Based on the structure-energy relationship, we propose that mutation of the binding pocket amino acids (e.g. His155, Trp156, Tyr219) to smaller proton donor amino acids (e.g. Serine, Threonine, Cysteine, Asparagine) may increase the efficiency for dechlorination and debromination. The results may of practical value for the efficient degradation of chlorined and bromined pollutants by harnessing FAcD.
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Affiliation(s)
- Yue Yue
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
| | - Jinfeng Chen
- School of Life Sciences, Westlake University, Hangzhou, 310000, PR China
| | - Lei Bao
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
| | - Junjie Wang
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Jinan, 250100, PR China.
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
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13
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Song Z, Yue Y, Feng S, Sun H, Li Y, Xu F, Zhang Q, Wang W. Cysteine dioxygenase catalyzed C F bond cleavage: An in silico approach. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Zhou J, Zhu L, Chen J, Wang W, Zhang R, Li Y, Zhang Q, Wang W. Degradation mechanism for Zearalenone ring-cleavage by Zearalenone hydrolase RmZHD: A QM/MM study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:135897. [PMID: 31887512 DOI: 10.1016/j.scitotenv.2019.135897] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/01/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
The danger of zearalenone (ZEN) as an endocrine disruptor to humans and the environment has aroused increasing attention. In this study, we implemented the quantum mechanics/molecular mechanics (QM/MM) method to investigate the degradation mechanism of ZEN hydrolase (RmZHD) toward ZEN at the atomic level. The degradation process involves two concerted reaction pathways, where the active site contains a Ser-His-Glu triplet as a proton donor. With the Boltzmann-weighted average potential barriers of 18.1 and 21.5 kcal/mol, the process undergoes proton transfer and nucleophilic-substituted ring opening to form a hydroxyl product. Non-covalent interaction analyses elucidated hydrogen bonding between key amino acids with ZEN. The electrostatic influence analysis of 16 amino acids proposes residues Asp34 and His128 as the possible mutation target for future mutation design of enzyme RmZHD. An in-depth investigation of the protein environment of RmZHD can improve the bioremediation efficiency of endocrine disrupting chemicals.
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Affiliation(s)
- Jie Zhou
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Ledong Zhu
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Jinfeng Chen
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wei Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Ruiming Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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15
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Johnson BM, Shu YZ, Zhuo X, Meanwell NA. Metabolic and Pharmaceutical Aspects of Fluorinated Compounds. J Med Chem 2020; 63:6315-6386. [PMID: 32182061 DOI: 10.1021/acs.jmedchem.9b01877] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The applications of fluorine in drug design continue to expand, facilitated by an improved understanding of its effects on physicochemical properties and the development of synthetic methodologies that are providing access to new fluorinated motifs. In turn, studies of fluorinated molecules are providing deeper insights into the effects of fluorine on metabolic pathways, distribution, and disposition. Despite the high strength of the C-F bond, the departure of fluoride from metabolic intermediates can be facile. This reactivity has been leveraged in the design of mechanism-based enzyme inhibitors and has influenced the metabolic fate of fluorinated compounds. In this Perspective, we summarize the literature associated with the metabolism of fluorinated molecules, focusing on examples where the presence of fluorine influences the metabolic profile. These studies have revealed potentially problematic outcomes with some fluorinated motifs and are enhancing our understanding of how fluorine should be deployed.
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Affiliation(s)
- Benjamin M Johnson
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Yue-Zhong Shu
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Xiaoliang Zhuo
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Nicholas A Meanwell
- Discovery Chemistry Platforms, Small Molecule Drug Discovery, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
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Zhang H, Tian S, Yue Y, Li M, Tong W, Xu G, Chen B, Ma M, Li Y, Wang JB. Semirational Design of Fluoroacetate Dehalogenase RPA1163 for Kinetic Resolution of α-Fluorocarboxylic Acids on a Gram Scale. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04804] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Hongxia Zhang
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University Changsha 410081, People’s Republic of China
| | - Shaixiao Tian
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University Changsha 410081, People’s Republic of China
| | - Yue Yue
- Environment Research Institute, Shandong University, Qingdao 266237, People’s Republic of China
| | - Min Li
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University Changsha 410081, People’s Republic of China
| | - Wei Tong
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University Changsha 410081, People’s Republic of China
| | - Guangyu Xu
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University Changsha 410081, People’s Republic of China
| | - Bo Chen
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University Changsha 410081, People’s Republic of China
| | - Ming Ma
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University Changsha 410081, People’s Republic of China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, People’s Republic of China
| | - Jian-bo Wang
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University Changsha 410081, People’s Republic of China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 368 Youyi Road, Wuchang Wuhan 430062, People’s Republic of China
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17
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Li Y, Yue Y, Zhang H, Yang Z, Wang H, Tian S, Wang JB, Zhang Q, Wang W. Harnessing fluoroacetate dehalogenase for defluorination of fluorocarboxylic acids: in silico and in vitro approach. ENVIRONMENT INTERNATIONAL 2019; 131:104999. [PMID: 31319293 DOI: 10.1016/j.envint.2019.104999] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
Widely distributed fluorocarboxylic acids have aroused worldwide environmental concerns due to its toxicity, persistence, and bioaccumulation. Enzyme-based eco-friendly biodegradation techniques have become increasingly important in treating fluorocarboxylic acids. Here we utilized in silico and in vitro approaches to investigate the defluorination mechanism of fluoroacetate dehalogenase (FAcD) toward monofluoropropionic acids at atomic-level. The experimentally determined kcat and kM for defluorination of 2-fluoropropionic acid are 330 ± 60 min-1 and 6.12 ± 0.13 mM. The in silico results demonstrated positive/negative correlations between activation barriers and structural parameters (e.g. distance and angle) under different enzymatic conformations. We also screened computationally and tested in vitro (enzyme assay and kinetic study) the catalytic proficiency of FAcD toward polyfluoropropionic acids and perfluoropropionic acids which are known to be challenging for enzymatic degradation. The results revealed potential degradation activity of FAcD enzyme toward 2,3,3,3-tetrafluoropropionic acids. Our work will initiate the development of a new "integrated approach" for enzyme engineering to degrade environmentally persistent fluorocarboxylic acids.
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Affiliation(s)
- Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Yue Yue
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Hongxia Zhang
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China; Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China
| | - Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Hui Wang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Shaixiao Tian
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China; Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China
| | - Jian-Bo Wang
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China; Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China.
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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18
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Calixto AR, Ramos MJ, Fernandes PA. Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway. Chem Sci 2019; 10:7212-7221. [PMID: 31588289 PMCID: PMC6677113 DOI: 10.1039/c9sc01464k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/10/2019] [Indexed: 02/04/2023] Open
Abstract
The role of conformational diversity in enzyme catalysis has been a matter of analysis in recent studies. Pre-organization of the active site has been pointed out as the major source for enzymes' catalytic power. Following this line of thought, it is becoming clear that specific, instantaneous, non-rare enzyme conformations that make the active site perfectly pre-organized for the reaction lead to the lowest activation barriers that mostly contribute to the macroscopically observed reaction rate. The present work is focused on exploring the relationship between structure and catalysis in HIV-1 protease (PR) with an adiabatic mapping method, starting from different initial structures, collected from a classical MD simulation. The first, rate-limiting step of the HIV-1 PR catalytic mechanism was studied with the ONIOM QM/MM methodology (B3LYP/6-31G(d):ff99SB), with activation and reaction energies calculated at the M06-2X/6-311++G(2d,2p):ff99SB level of theory, in 19 different enzyme:substrate conformations. The results showed that the instantaneous enzyme conformations have two independent consequences on the enzyme's chemistry: they influence the barrier height, something also observed in the past in other enzymes, and they also influence the specific reaction pathway, which is something unusual and unexpected, challenging the "one enzyme-one substrate-one reaction mechanism" paradigm. Two different reaction mechanisms, with similar reactant probabilities and barrier heights, lead to the same gem-diol intermediate. Subtle nanosecond-timescale rearrangements in the active site hydrogen bonding network were shown to determine which reaction the enzyme follows. We named this phenomenon chemical disorder. The results make us realize the unexpected mechanistic consequences of conformational diversity in enzymatic reactivity.
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Affiliation(s)
- Ana Rita Calixto
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Maria João Ramos
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Pedro Alexandrino Fernandes
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
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19
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Cui S, Zhang X, Liu J, Zhou L, Shang Y, Zhang C, Liu W, Zhuang S. Natural sunlight-driven aquatic toxicity enhancement of 2,6-di-tert-butylphenol toward Photobacterium phosphoreum. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 251:66-71. [PMID: 31071634 DOI: 10.1016/j.envpol.2019.04.123] [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: 01/29/2019] [Revised: 04/03/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
The tert-butylphenols (TBPs) are one group of alkylated phenolic compounds with wide applications in UV absorbers and antioxidants. They are becoming contaminants of emerging concern with residues frequently detected in natural surface water or drinking water. The direct sunlight may photolyze TBPs in waters and affect their aquatic toxicities; however, such data are very limited. In the present study, we investigate the photodegradation of 2,6-DTBP by direct sunlight in water and compare the aquatic toxicities of 2,6-DTBP with that of its product toward Photobacterium phosphoreum. 2,6-DTBP is photodegraded by 71.31 ± 2.64% under simulated sunlight following a pseudo-first-order kinetics with rate constant (k) of 0.061 h-1. Density functional theory simulations at M06-2X/def2-SVP level reveal that the photodegradation occurred sequentially through oxidation, photo-isomerization and hydrogenation. The degradation product 2,5-DTBP is toxic to P. phosphoreum (EC50 3.389 × 10-5 mol/L) whereas 2,6-DTBP is not harmful (EC50 3.917 × 10-3 mol/L) as designated by the European Union Standard, indicating the enhanced toxicities driven by the direct sunlight photodegradation. We demonstrate the enhanced toxicities of 2,6-DTBP by natural sunlight, suggesting that negligence of photodegradation of TBPs-related contaminants will underestimate the comprehensive risk of these emerging contaminant in natural waters.
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Affiliation(s)
- Shixuan Cui
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaofang Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinsong Liu
- Zhejiang Province Environmental Monitoring Center, Hangzhou, 310005, China
| | - Lihong Zhou
- Institute of Environment, Chengdu University of Technology, Chengdu, 610059, China
| | - Yukun Shang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chunlong Zhang
- Department of Environmental Sciences, University of Houston-Clear Lake, 2700 Bay Area Boulevard, Houston, TX, 77058, USA
| | - Weiping Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shulin Zhuang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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20
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Catalysis mechanism of oxidized polyvinyl alcohol by pseudomonas hydrolase: Insights from molecular dynamics and QM/MM analysis. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.02.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
The application of native enzymes may not be economical owing to the stability factor. A smaller protein molecule may be less susceptible to external stresses. Haloalkane dehalogenases (HLDs) that act on toxic haloalkanes may be incorporated as bioreceptors to detect haloalkane contaminants. Therefore, this study aims to develop mini proteins of HLD as an alternative bioreceptor which was able to withstand extreme conditions. Initially, the mini proteins were designed through computer modeling. Based on the results, five designed mini proteins were deemed to be viable stable mini proteins. They were then validated through experimental study. The smallest mini protein (model 5) was chosen for subsequent analysis as it was expressed in soluble form. No dehalogenase activity was detected, thus the specific binding interaction of between 1,3-dibromopropane with mini protein was investigated using isothermal titration calorimetry. Higher binding affinity between 1,3-dibromopropane and mini protein was obtained than the native. Thermal stability study with circular dichroism had proven that the mini protein possessed two times higher Tm value at 83.73 °C than the native at 43.97 °C. In conclusion, a stable mini protein was successfully designed and may be used as bioreceptors in the haloalkane sensor that is suitable for industrial application.
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22
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Lu J, Ma X, Singh V, Zhang Y, Wang P, Feng J, Ma P, Niu J, Wang J. Facile CO2 Cycloaddition to Epoxides by Using a Tetracarbonyl Metal Selenotungstate Derivate [{Mn(CO)3}4(Se2W11O43)]8–. Inorg Chem 2018; 57:14632-14643. [DOI: 10.1021/acs.inorgchem.8b02321] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jingkun Lu
- Henan Key Laboratory of Polyoxometalate, Institute of Molecular and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004 Henan, PR China
| | - Xinyi Ma
- Henan Key Laboratory of Polyoxometalate, Institute of Molecular and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004 Henan, PR China
| | - Vikram Singh
- Henan Key Laboratory of Polyoxometalate, Institute of Molecular and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004 Henan, PR China
| | - Yujiao Zhang
- Henan Key Laboratory of Polyoxometalate, Institute of Molecular and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004 Henan, PR China
| | - Ping Wang
- Henan Key Laboratory of Polyoxometalate, Institute of Molecular and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004 Henan, PR China
| | - Junwei Feng
- Henan Key Laboratory of Polyoxometalate, Institute of Molecular and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004 Henan, PR China
| | - Pengtao Ma
- Henan Key Laboratory of Polyoxometalate, Institute of Molecular and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004 Henan, PR China
| | - Jingyang Niu
- Henan Key Laboratory of Polyoxometalate, Institute of Molecular and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004 Henan, PR China
| | - Jingping Wang
- Henan Key Laboratory of Polyoxometalate, Institute of Molecular and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004 Henan, PR China
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23
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Ge P, Luo G, Luo Y, Huang W, Xie H, Chen J, Qu J. Molecular understanding of the interaction of amino acids with sulfuric acid in the presence of water and the atmospheric implication. CHEMOSPHERE 2018; 210:215-223. [PMID: 30005342 DOI: 10.1016/j.chemosphere.2018.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
Amino acids are important components of atmospheric aerosols. Despite the diversity of amino acids structures, however, the role of amino acids with additional non-characteristic functional groups in new particle formation (NPF) has almost remained unexplored. Herein, the interaction of serine (Ser) and threonine (Thr), which feature a hydroxyl group and differ by a methyl-substitution, with sulfuric acid (SA) and up to three water (W) molecules has been investigated at the M06-2X/6-311++G (3df, 3pd) level of theory. The effects of structural differences of amino acids on the structure and properties of clusters were also pointed out. Results show that serine may play more important role in stabilizing sulfuric acid to promote NPF in initial steps compared with threonine, glycine and alanine. Meanwhile, threonine may participate in ion-induced nucleation due to the high dipole moment of (Thr) (SA) isomers. Moreover, the effects of structure differences of amino acids can be seen in several aspects. Firstly, methyl substitution and hydroxyl group of amino acids have great influence on the structure of clusters. Secondly, hydrated (Ser) (SA) and (Tur) (SA) clusters could retain water even at low relative humidity, which may due to the hydroxyl group in serine and threonine. In addition, the Rayleigh light scattering intensities of amino acid-containing clusters are higher than trimethylamine, monoethanolamine and oxalic acid-involved counterparts. The effect of carboxyl group and methyl substitution on optical properties of clusters is also discussed. This study may bring new insight into the role of amino acids with additional non-characteristic functional groups in initial steps of NPF.
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Affiliation(s)
- Pu Ge
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Gen Luo
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Yi Luo
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, 116024, China.
| | - Wei Huang
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Hongbin Xie
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jingping Qu
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, 116024, China
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24
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QM/MM study of the reaction mechanism of Cl-cis,cis-muconate with muconate lactonizing enzyme. Bioorg Chem 2018; 80:453-460. [DOI: 10.1016/j.bioorg.2018.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/09/2018] [Accepted: 05/10/2018] [Indexed: 11/18/2022]
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25
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Liu Y, Huang YT, Wang WL. Reaction probability and defluorination mechanisms of a potent greenhouse gas SF 5CF 3 attacked by CH 3 radical: a theoretical study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1469798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Yan Liu
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, People’s Republic of China
- Shaanxi Engineering Research Center of Coal Conversion Alcohol, College of Chemistry and Material, Weinan Normal University, Weinan, People’s Republic of China
| | - Yue-tian Huang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, People’s Republic of China
| | - Wen-liang Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, People’s Republic of China
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26
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Wang J, Tang X, Li Y, Zhang R, Zhu L, Chen J, Sun Y, Zhang Q, Wang W. Computational evidence for the degradation mechanism of haloalkane dehalogenase LinB and mutants of Leu248 to 1-chlorobutane. Phys Chem Chem Phys 2018; 20:20540-20547. [PMID: 30051124 DOI: 10.1039/c8cp03561j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The catalytic degradation ability of the haloalkane dehalogenase LinB toward 1-chlorobutane (1-CB) was studied using a combined quantum mechanics/molecular mechanics (QM/MM) approach. Two major processes are involved in the LinB-catalyzed removal of halogens: dechlorination and hydrolyzation. The present study confirmed the experimentally proposed reaction path at the molecular level. Moreover, based on nucleophilic substitution mechanism (SN2 reaction), dechlorination was found to be the rate-determining step of the entire reaction process. In this study, the Boltzmann-weighted average barrier for dechlorination was determined to be 17.0 kcal mol-1, which is fairly close to the experimental value (17.4 kcal mol-1). The state of His107 and the influence of Leu248 on the dechlorination process were also explored. In addition, an intriguing phenomenon was discovered: the potential energy barrier decreased by 7.5 kcal mol-1 when the Leu248 residue was mutated into Phe248. This discovery might be of great help to design new mutant enzymes or novel biocatalysts.
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Affiliation(s)
- Junjie Wang
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China.
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27
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Computational investigation of M1/W6S8 (M = Fe, Ru, and Os) single-atom catalysts for CO2 hydrogenation. CATALYSIS SURVEYS FROM ASIA 2018. [DOI: 10.1007/s10563-018-9252-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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Ang TF, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018; 23:E1100. [PMID: 29735886 PMCID: PMC6100074 DOI: 10.3390/molecules23051100] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.
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Affiliation(s)
- Thiau-Fu Ang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Jonathan Maiangwa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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29
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Santos-Martins D, Calixto AR, Fernandes PA, Ramos MJ. A Buried Water Molecule Influences Reactivity in α-Amylase on a Subnanosecond Time Scale. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Diogo Santos-Martins
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Ana R. Calixto
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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30
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Miranda-Rojas S, Fernández I, Kästner J, Toro-Labbé A, Mendizábal F. Unraveling the Nature of the Catalytic Power of Fluoroacetate Dehalogenase. ChemCatChem 2018. [DOI: 10.1002/cctc.201701517] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastián Miranda-Rojas
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; Av. República 275 Santiago Chile
| | - Israel Fernández
- Departamento de Química Orgánica I and Centro de Innovación en, Química Avanzada (ORFEO-CINQA); Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040- Madrid Spain
| | - Johannes Kästner
- Institut für Theoretische Chemie; Universität Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional; Facultad de Química; Pontifica Universidad Católica de Chile; Av. Vicuña Mackenna 4860, Macul Santiago Chile
| | - Fernando Mendizábal
- Departamento de Química; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Ñuñoa Santiago Chile
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31
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Yan J, Shi K, Zhao C, Ding L, Jiang S, Yang L, Zhong G. NHC-catalyzed [4+2] cycloaddition reactions for the synthesis of 3′-spirocyclic oxindoles via a C–F bond cleavage protocol. Chem Commun (Camb) 2018; 54:1567-1570. [DOI: 10.1039/c7cc08048d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A chiral NHC-catalyzed cycloaddition of γ-fluoroenals is developed. The nucleophilic γ-carbon generated via C–F bond cleavage undergoes highly enantioselective cycloaddition (up to >99% ee) to isatins and provides 3′-spirocyclic oxindoles in good yields (up to 91%).
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Affiliation(s)
- Jun Yan
- College of Material
- Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310018
- China
| | - Kuangxi Shi
- College of Material
- Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310018
- China
| | - Chengtao Zhao
- College of Material
- Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310018
- China
| | - Liyuan Ding
- College of Material
- Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310018
- China
| | - Shengsheng Jiang
- College of Material
- Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310018
- China
| | - Limin Yang
- College of Material
- Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310018
- China
| | - Guofu Zhong
- College of Material
- Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310018
- China
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32
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Zhang H, Wei X, Song X, Shah S, Chen J, Liu J, Hao C, Chen Z. Photophysical and photochemical insights into the photodegradation of sulfapyridine in water: A joint experimental and theoretical study. CHEMOSPHERE 2018; 191:1021-1027. [PMID: 29145130 DOI: 10.1016/j.chemosphere.2017.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
For organic pollutants, photodegradation, as a major abiotic elimination process and of great importance to the environmental fate and risk, involves rather complicated physical and chemical processes of excited molecules. Herein, we systematically studied the photophysical and photochemical processes of a widely used antibiotic, namely sulfapyridine. By means of density functional theory (DFT) computations, we examined the rate constants and the competition of both photophysical and photochemical processes, elucidated the photochemical reaction mechanism, calculated reaction quantum yield (Φ) based on both photophysical and photochemical processes, and subsequently estimated the photodegradation rate constant. We further conducted photolysis experiments to measure the photodegradation rate constant of sulfapyridine. Our computations showed that sulfapyridine at the lowest excited singlet state (S1) mainly undergoes internal conversion to its ground state, and is difficult to transfer to the lowest excited triplet states (T1) via intersystem crossing (ISC) and emit fluorescence. In T1 state, compared with phosphorescence emission and ISC, chemical reaction is much easier to initiate. Encouragingly, the theoretically predicted photodegradation rate constant is close to the experimentally observed value, indicating that quantum chemistry computation is powerful enough to study photodegradation involving ultra-fast photophysical and photochemical processes.
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Affiliation(s)
- Heming Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Xiaoxuan Wei
- Department of Chemistry, University of Puerto Rico, Rio Piedras Campus, San Juan, PR 00931, USA
| | - Xuedan Song
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Shaheen Shah
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jianhui Liu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Ce Hao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.
| | - Zhongfang Chen
- Department of Chemistry, University of Puerto Rico, Rio Piedras Campus, San Juan, PR 00931, USA.
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33
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Ryde U. How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging. J Chem Theory Comput 2017; 13:5745-5752. [DOI: 10.1021/acs.jctc.7b00826] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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34
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Li W, Guo S, Guo L. Theoretical Investigation of Reverse Water Gas Shift Reaction Catalyzed by Ruthenium Halogen Carbonyl Complexes. CATALYSIS SURVEYS FROM ASIA 2017. [DOI: 10.1007/s10563-017-9236-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Bayat A, Fattahi A. The free radical scavenging activity of lespedezacoumestan toward ˙OH radical: A quantum chemical and computational kinetics study. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3755] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ahmad Bayat
- Department of Chemistry; Sharif University of Technology; Tehran Iran
| | - Alireza Fattahi
- Department of Chemistry; Sharif University of Technology; Tehran Iran
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36
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Tang X, Wang J, Zhao N, Zhang Q, Wang W. Theoretical study on the hydrolytic step in the biotransformation of β-hexachlorocyclohexane degraded by haloalkane dehalogenase LinB. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The hydrolytic process of LinB-catalyzed biotransformation of a notorious contaminant β-HCH was investigated in atomistic detail with a combined quantum mechanics/molecular mechanics approach. The Boltzmann-weighted averaging method amended by disproportionate effect analysis was showed to capture the fluctuation of a single molecule enzyme reaction. With the potential barriers of 18.7 and 2.6 kcal/mol, two elementary steps that refer to formation and decomposition of a tetrahedral intermediate are involved in the hydrolytic reaction, respectively. Polarized by Glu132, His272 serves as a proton carrier along the whole hydrolysis reaction. The electrostatic influence analysis highlighted residue Leu248 as a possible mutation target for rational design of LinB in enzyme modification. Further spatial location analysis provided explanation for the opposite effect of Asn38 toward the two elementary steps. Getting insight into the catalytic details and the structure and function of LinB can enrich the knowledge of it and promote its application in bioremediation of chlorinated hydrocarbon pollutants.
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Affiliation(s)
- Xiaowen Tang
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
| | - Junjie Wang
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
| | - Nan Zhao
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
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37
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Leong LEX, Khan S, Davis CK, Denman SE, McSweeney CS. Fluoroacetate in plants - a review of its distribution, toxicity to livestock and microbial detoxification. J Anim Sci Biotechnol 2017; 8:55. [PMID: 28674607 PMCID: PMC5485738 DOI: 10.1186/s40104-017-0180-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/11/2017] [Indexed: 02/08/2023] Open
Abstract
Fluoroacetate producing plants grow worldwide and it is believed they produce this toxic compound as a defence mechanism against grazing by herbivores. Ingestion by livestock often results in fatal poisonings, which causes significant economic problems to commercial farmers in many countries such as Australia, Brazil and South Africa. Several approaches have been adopted to protect livestock from the toxicity with limited success including fencing, toxic plant eradication and agents that bind the toxin. Genetically modified bacteria capable of degrading fluoroacetate have been able to protect ruminants from fluoroacetate toxicity under experimental conditions but concerns over the release of these microbes into the environment have prevented the application of this technology. Recently, a native bacterium from an Australian bovine rumen was isolated which can degrade fluoroacetate. This bacterium, strain MFA1, which belongs to the Synergistetes phylum degrades fluoroacetate to fluoride ions and acetate. The discovery and isolation of this bacterium provides a new opportunity to detoxify fluoroacetate in the rumen. This review focuses on fluoroacetate toxicity in ruminant livestock, the mechanism of fluoroacetate toxicity, tolerance of some animals to fluoroaceate, previous attempts to mitigate toxicity, aerobic and anaerobic microbial degradation of fluoroacetate, and future directions to overcome fluoroacetate toxicity.
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Affiliation(s)
- Lex Ee Xiang Leong
- School of Chemistry and Molecular Bioscience, University of Queensland, St Lucia, 4072 QLD Australia
| | - Shahjalal Khan
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, 4072 QLD Australia
| | - Carl K Davis
- School of Chemistry and Molecular Bioscience, University of Queensland, St Lucia, 4072 QLD Australia
| | - Stuart E Denman
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, 4072 QLD Australia
| | - Chris S McSweeney
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, 4072 QLD Australia
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38
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Zhang H, Kupiainen-Määttä O, Zhang X, Molinero V, Zhang Y, Li Z. The enhancement mechanism of glycolic acid on the formation of atmospheric sulfuric acid–ammonia molecular clusters. J Chem Phys 2017. [DOI: 10.1063/1.4982929] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Tang X, Zhang R, Li Y, Zhang Q, Wang W. Enantioselectivity of haloalkane dehalogenase LinB on the degradation of 1,2-dichloropropane: A QM/MM study. Bioorg Chem 2017; 73:16-23. [PMID: 28527381 DOI: 10.1016/j.bioorg.2017.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/08/2017] [Accepted: 04/10/2017] [Indexed: 11/26/2022]
Abstract
The hydrolysis dechlorination mechanism of a chiral organochlorinepollutant, 1,2-dichloropropane (DCP), catalyzed by haloalkane dehalogenase LinB has been investigated by using a combined quantum mechanics/molecular mechanics method. LinB was confirmed to be enantioselective towards the catabolism of the racemic mixture. Based on the SN2 nucleophilic substitution mechanism, the dechlorination process was identified as the rate-determining step in LinB-catalyzed degradation of 1,2-dichloropropane, the Boltzmann-weighted average potential barrier of which is 18.8kcal/mol for the (R)-isomer and 24.0kcal/mol for the (S)-isomer. A particular water molecule near (S)-DCP in the reaction system can strongly disturb the dechlorination process, which can account for the enantioselectivity of LinB. Further electrostatic influence analysis indicates that proper mutation of Gly37 may improve the catalytic efficiency of LinB towards DCP.
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Affiliation(s)
- Xiaowen Tang
- Environment Research Institute, Shandong University, Jinan 250100, PR China
| | - Ruiming Zhang
- Environment Research Institute, Shandong University, Jinan 250100, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Jinan 250100, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Jinan 250100, PR China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Jinan 250100, PR China
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40
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Esrafili MD, Mohammadirad N. A first-principles study on the adsorption behaviour of methanol and ethanol over C59B heterofullerene. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1311423] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Department of Chemistry, Laboratory of Theoretical Chemistry, University of Maragheh, Maragheh, Iran
| | - Nafiseh Mohammadirad
- Department of Chemistry, Laboratory of Theoretical Chemistry, University of Maragheh, Maragheh, Iran
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41
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Luo C, Yu Q, Wang H. DFT study of the formation mechanism of anthraquinone from the reaction of NO 2 and anthracene on NaCl clusters: the role of NaNO 3. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2016; 18:1500-1507. [PMID: 27812561 DOI: 10.1039/c6em00420b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and oxygenated-PAHs are globally worrisome air pollutants because of their highly direct-acting mutagenicity and carcinogenicity. The formation of oxygenated-PAHs is of crucial importance for the prevention of their atmospheric pollution successfully. In this paper, the formation mechanism of oxygenated-PAHs from the heterogeneous reaction of NO2 with anthracene on the surface of NaCl was studied by density functional theory (DFT) calculations. At first, the various adsorption configurations of NO2 and N2O4 on NaCl were investigated. The chemical conversion mechanisms among these configurations were also investigated. It is found that these structures can easily interconvert due to their low energy barriers. NaNO3 was found to be the main product of the reaction of NO2/N2O4 on NaCl. Then the oxidation mechanism of anthracene by NO2 on the NaCl surface showed that NaNO3 is able to oxidize anthracene and plays a catalytic role in the reaction process. This means that the formation of NaNO3 is very important to promote the formation of 9,10-anthraquinone from the heterogeneous reaction of NO2 with anthracene. Our calculations also showed that the introduction of water can greatly accelerate this reaction process.
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Affiliation(s)
- Chao Luo
- School of Resources Environmental and Chemical Engineering, Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi, 330031 China.
| | - Qiming Yu
- School of Resources Environmental and Chemical Engineering, Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi, 330031 China.
| | - Hongming Wang
- School of Resources Environmental and Chemical Engineering, Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi, 330031 China.
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42
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Li Y, Zhang R, Du L, Zhang Q, Wang W. How Many Conformations of Enzymes Should Be Sampled for DFT/MM Calculations? A Case Study of Fluoroacetate Dehalogenase. Int J Mol Sci 2016; 17:E1372. [PMID: 27556449 PMCID: PMC5000767 DOI: 10.3390/ijms17081372] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 11/16/2022] Open
Abstract
The quantum mechanics/molecular mechanics (QM/MM) method (e.g., density functional theory (DFT)/MM) is important in elucidating enzymatic mechanisms. It is indispensable to study "multiple" conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue. The criteria were tested by defluorination reaction catalyzed by fluoroacetate dehalogenase. The results suggest that at least 20 conformations of enzymatic residues are required for convergence using DFT/MM calculations. We also tested the correlation of energy barriers between small QM regions and big QM regions. A roughly positive correlation was found. This kind of correlation has not been reported in the literature. The correlation inspires us to propose a protocol for more efficient sampling. This saves 50% of the computational cost in our current case.
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Affiliation(s)
- Yanwei Li
- Environment Research Institute, Shandong University, Jinan 250100, China.
| | - Ruiming Zhang
- Environment Research Institute, Shandong University, Jinan 250100, China.
| | - Likai Du
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China..
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Jinan 250100, China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Jinan 250100, China.
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43
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Zhao Y, Han C, Huang Y, Qin W, Zhang X, Kan Y, Ye Y. New all-solid-state carbonate ion-selective electrode with Ag2CO3-BaCO3 as sensitive films. Chem Res Chin Univ 2016. [DOI: 10.1007/s40242-016-6062-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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An X, Guo L, Li A, Cao Z, Liu N. Theoretical Study of the Water-Gas Shift Reaction Catalyzed by Tungsten Carbonyls. CATALYSIS SURVEYS FROM ASIA 2016. [DOI: 10.1007/s10563-016-9212-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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