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Barati F, Hosseini F, Vafaee R, Sabouri Z, Ghadam P, Arab SS, Shadfar N, Piroozmand F. In silico approaches to investigate enzyme immobilization: a comprehensive systematic review. Phys Chem Chem Phys 2024; 26:5744-5761. [PMID: 38294035 DOI: 10.1039/d3cp03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems. Bioinformatics tools can often correctly predict immobilization outcomes, resulting in a cost-effective experimental phase with the least time consumed. This study provides an overview of in silico methods predicting immobilization processes via a comprehensive systematic review of published articles till 11 December 2022. It also mentions the strengths and weaknesses of the processes and explains the computational analyses in each method that are required for immobilization assessment. In this regard, Web of Science and Scopus databases were screened to gain relevant publications. After screening the gathered documents (n = 3873), 60 articles were selected for the review. The selected papers have applied in silico procedures including only molecular dynamics (MD) simulations (n = 20), parallel tempering Monte Carlo (PTMC) and MD simulations (n = 3), MD and docking (n = 1), density functional theory (DFT) and MD (n = 1), only docking (n = 11), metal ion binding site prediction (MIB) server and docking (n = 2), docking and DFT (n = 1), docking and analysis of enzyme surfaces (n = 1), only DFT (n = 1), only MIB server (n = 2), analysis of an enzyme structure and surface (n = 12), rational design of immobilized derivatives (RDID) software (n = 3), and dissipative particle dynamics (DPD; n = 2). In most included studies (n = 51), enzyme immobilization was investigated experimentally in addition to in silico evaluation.
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Affiliation(s)
- Farzaneh Barati
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Fakhrisadat Hosseini
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Rayeheh Vafaee
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Sabouri
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Parinaz Ghadam
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Najmeh Shadfar
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Firoozeh Piroozmand
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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Qu Y, Zhang X, Shen W, Ma Q, You S, Pei X, Li S, Ma F, Zhou J. Illumina MiSeq sequencing reveals long-term impacts of single-walled carbon nanotubes on microbial communities of wastewater treatment systems. BIORESOURCE TECHNOLOGY 2016; 211:209-215. [PMID: 27017131 DOI: 10.1016/j.biortech.2016.03.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
Abstract
In this study, phenol wastewater treatment systems treated with different concentrations of single-walled carbon nanotubes (SWCNTs) (0-3.5g/L) were exposed to phenol and carbon nanotubes (CNTs) shock loadings to investigate the long-term impacts of SWCNTs on microbial communities. Phenol removal remained high efficiency (>98%) in SWCNTs-treated groups but decreased in non-treated group (85.1±1.9%) when exposed to high concentration of phenol (500mg/L). However, secondary dosing of SWCNTs in SWCNTs-treated groups would decrease the phenol removal efficiency. Illumina MiSeq sequencing revealed that the diversity, richness and structure of microbial communities were shifted under phenol shock loading, especially under high phenol concentration, but not under CNTs shock loading. In response to phenol and CNTs shock loadings, Rudaea, Burkholderia, Sphingomonas, Acinetobacter, Methylocystis and Thauera became dominant genera, which should be involved in phenol removal. These results suggested that a proper amount of SWCNTs might have positive effects on phenol wastewater treatment systems.
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Affiliation(s)
- Yuanyuan Qu
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xuwang Zhang
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Wenli Shen
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qiao Ma
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Shengnan You
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaofang Pei
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Shuzhen Li
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Jiti Zhou
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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Qu Y, Ma Q, Deng J, Shen W, Zhang X, He Z, Van Nostrand JD, Zhou J, Zhou J. Responses of microbial communities to single-walled carbon nanotubes in phenol wastewater treatment systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4627-4635. [PMID: 25751159 DOI: 10.1021/es5053045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The expanding use of single-walled carbon nanotubes (SWCNTs) raises environmental concerns. Wastewater treatment systems are potential recipients of SWCNTs containing influent, yet the impacts of SWCNTs on these systems are poorly documented. In this study, the microbial responses to SWCNTs in simulated phenol wastewater treatment systems were investigated. The phenol removal rates were improved in all SWCNTs-treated sequencing batch reactors during the first 20 days, but when facing higher phenol concentration (1000 mg/L) after 60 days, reactors with the highest concentration (3.5 g/L) of SWCNTs exhibited a notably decreased phenol removal capacity. Cell viability tests, scanning electron microscopy analysis and DNA leakage data suggested that SWCNTs protected microbes from inactivation, possibly by producing more bound extracellular polymeric substances (EPS), which could create a protective barrier for the microbes. Illumina sequencing of 16S rRNA gene amplicons revealed that the bacterial diversity did not change significantly except for a minor reduction after the immediate addition of SWCNTs. Bacterial community structure significantly shifted after SWCNTs addition and did not recover afterward. Zoogloea increased significantly upon SWCNTs shocking. At the final stage, Rudaea and Mobilicoccus increased, while Burkholderia, Singulisphaera, Labrys and Mucilaginibacter decreased notably. The shifts of these dominant genera may be associated with altered sludge settling, aromatic degradation and EPS production. This study suggested that SWCNTs exerted protective rather than cytotoxic effects on sludge microbes of phenol wastewater treatment systems and they affected the bacterial community structure and diversity at test concentrations. These findings provide new insights into our understanding of the potential effects of SWCNTs on wastewater treatment processes.
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Affiliation(s)
- Yuanyuan Qu
- †Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
- ‡Institute for Environmental Genomics (IEG), Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Qiao Ma
- †Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
- ‡Institute for Environmental Genomics (IEG), Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jie Deng
- ‡Institute for Environmental Genomics (IEG), Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Wenli Shen
- †Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xuwang Zhang
- †Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhili He
- ‡Institute for Environmental Genomics (IEG), Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Joy D Van Nostrand
- ‡Institute for Environmental Genomics (IEG), Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jiti Zhou
- †Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jizhong Zhou
- ‡Institute for Environmental Genomics (IEG), Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- §Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- ⊥State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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Ma Q, Qu Y, Shen W, Wang J, Zhang Z, Zhang X, Zhou H, Zhou J. Activated sludge microbial community responses to single-walled carbon nanotubes: community structure does matter. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2015; 71:1235-1240. [PMID: 25909735 DOI: 10.2166/wst.2015.095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ecological effects of carbon nanotubes (CNTs) have been a worldwide research focus due to their extensive release and accumulation in environment. Activated sludge acting as an important gathering place will inevitably encounter and interact with CNTs, while the microbial responses have been rarely investigated. Herein, the activated sludges from six wastewater treatment plants were acclimated and treated with single-walled carbon nanotubes (SWCNTs) under identical conditions. Illumina high-throughput sequencing was applied to in-depth analyze microbial changes and results showed SWCNTs differently perturbed the alpha diversity of the six groups (one increase, two decrease, three no change). Furthermore, the microbial community structures were shifted, and specific bacterial performance in each group was different. Since the environmental and operational factors were identical in each group, it could be concluded that microbial responses to SWCNTs were highly depended on the original community structures.
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Affiliation(s)
- Qiao Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road No. 2, 116024 Dalian, Liaoning, China E-mail:
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road No. 2, 116024 Dalian, Liaoning, China E-mail:
| | - Wenli Shen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road No. 2, 116024 Dalian, Liaoning, China E-mail:
| | - Jingwei Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road No. 2, 116024 Dalian, Liaoning, China E-mail:
| | - Zhaojing Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road No. 2, 116024 Dalian, Liaoning, China E-mail:
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road No. 2, 116024 Dalian, Liaoning, China E-mail:
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road No. 2, 116024 Dalian, Liaoning, China E-mail:
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road No. 2, 116024 Dalian, Liaoning, China E-mail:
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Catalytic transformation of HODAs using an efficient meta-cleavage product hydrolase-spore surface display system. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhou H, Qu Y, Kong C, Li D, Shen E, Ma Q, Zhang X, Wang J, Zhou J. Catalytic performance and molecular dynamic simulation of immobilized CC bond hydrolase based on carbon nanotube matrix. Colloids Surf B Biointerfaces 2014; 116:365-71. [DOI: 10.1016/j.colsurfb.2014.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/31/2013] [Accepted: 01/13/2014] [Indexed: 12/17/2022]
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