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Molecular Docking and Site-Directed Mutagenesis of Dichloromethane Dehalogenase to Improve Enzyme Activity for Dichloromethane Degradation. Appl Biochem Biotechnol 2019; 190:487-505. [DOI: 10.1007/s12010-019-03106-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/18/2019] [Indexed: 10/26/2022]
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Fan N, Liu R, Ma P, Wang X, Li C, Li J. The On-Off chiral mesoporous silica nanoparticles for delivering achiral drug in chiral environment. Colloids Surf B Biointerfaces 2019; 176:122-129. [DOI: 10.1016/j.colsurfb.2018.12.065] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/06/2018] [Accepted: 12/25/2018] [Indexed: 01/12/2023]
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Zhou J, Zhu F, Li J, Wang Y. Concealed body mesoporous silica nanoparticles for orally delivering indometacin with chiral recognition function. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2018; 90:314-324. [DOI: 10.1016/j.msec.2018.04.071] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 12/20/2022]
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Ni H, Zeng S, Qin X, Sun X, Zhang S, Zhao X, Yu Z, Li L. Molecular docking and site-directed mutagenesis of a Bacillus thuringiensis chitinase to improve chitinolytic, synergistic lepidopteran-larvicidal and nematicidal activities. Int J Biol Sci 2015; 11:304-15. [PMID: 25678849 PMCID: PMC4323370 DOI: 10.7150/ijbs.10632] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/24/2014] [Indexed: 11/05/2022] Open
Abstract
Bacterial chitinases are useful in the biocontrol of agriculturally important pests and fungal pathogens. However, the utility of naturally occurring bacterial chitinases is often limited by their low enzyme activity. In this study, we constructed mutants of a Bacillus thuringiensis chitinase with enhanced activity based on homology modeling, molecular docking, and the site-directed mutagenesis of target residues to modify spatial positions, steric hindrances, or hydrophilicity/hydrophobicity. We first identified a gene from B. thuringiensis YBT-9602 that encodes a chitinase (Chi9602) belonging to glycosyl hydrolase family 18 with conserved substrate-binding and substrate-catalytic motifs. We constructed a structural model of a truncated version of Chi9602 (Chi960235-459) containing the substrate-binding domain using the homologous 1ITX protein of Bacillus circulans as the template. We performed molecular docking analysis of Chi960235-459 using di-N-acetyl-D-glucosamine as the ligand. We then selected 10 residues of interest from the docking area for the site-directed mutagenesis experiments and expression in Escherichia coli. Assays of the chitinolytic activity of the purified chitinases revealed that the three mutants exhibited increased chitinolytic activity. The ChiW50A mutant exhibited a greater than 60 % increase in chitinolytic activity, with similar pH, temperature and metal ion requirements, compared to wild-type Chi9602. Furthermore, ChiW50A exhibited pest-controlling activity and antifungal activity. Remarkable synergistic effects of this mutant with B. thuringiensis spore-crystal preparations against Helicoverpa armigera and Caenorhabditis elegans larvae and obvious activity against several plant-pathogenic fungi were observed.
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Affiliation(s)
- Hong Ni
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China ; 2. Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, Hubei, China
| | - Siquan Zeng
- 2. Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, Hubei, China
| | - Xu Qin
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xiaowen Sun
- 2. Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, Hubei, China
| | - Shan Zhang
- 2. Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, Hubei, China
| | - Xiuyun Zhao
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Ziniu Yu
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Lin Li
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Woodward JD, Wepf RA. Macromolecular 3D SEM reconstruction strategies: signal to noise ratio and resolution. Ultramicroscopy 2014; 144:43-9. [PMID: 24830764 DOI: 10.1016/j.ultramic.2014.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 04/16/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
Abstract
Three-dimensional scanning electron microscopy generates quantitative volumetric structural data from SEM images of macromolecules. This technique provides a quick and easy way to define the quaternary structure and handedness of protein complexes. Here, we apply a variety of preparation and imaging methods to filamentous actin in order to explore the relationship between resolution, signal-to-noise ratio, structural preservation and dataset size. This information can be used to define successful imaging strategies for different applications.
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Affiliation(s)
- J D Woodward
- Department of Molecular and Cell Biology, University of Cape Town, South Africa; Electron Microscope Unit, University of Cape Town, South Africa.
| | - R A Wepf
- Electron Microscopy (EMEZ), ETH, Zürich, Switzerland
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Miller JL, Woodward J, Chen S, Jaffer M, Weber B, Nagasaki K, Tomaru Y, Wepf R, Roseman A, Varsani A, Sewell T. Three-dimensional reconstruction of Heterocapsa circularisquama RNA virus by electron cryo-microscopy. J Gen Virol 2011; 92:1960-1970. [PMID: 21562120 DOI: 10.1099/vir.0.031211-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Heterocapsa circularisquama RNA virus is a non-enveloped icosahedral ssRNA virus infectious to the harmful bloom-forming dinoflagellate, H. circularisquama, and which is assumed to be the major natural agent controlling the host population. The viral capsid is constructed from a single gene product. Electron cryo-microscopy revealed that the virus has a diameter of 34 nm and T = 3 symmetry. The 180 quasi-equivalent monomers have an unusual arrangement in that each monomer contributes to a 'bump' on the surface of the protein. Though the capsid protein probably has the classic 'jelly roll' β-sandwich fold, this is a new packing arrangement and is distantly related to the other positive-sense ssRNA virus capsid proteins. The handedness of the structure has been determined by a novel method involving high resolution scanning electron microscopy of the negatively stained viruses and secondary electron detection.
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Affiliation(s)
- Jennifer L Miller
- Electron Microscope Unit, Division of Medical Biochemistry, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Jeremy Woodward
- Electron Microscope Unit, Division of Medical Biochemistry, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Shaoxia Chen
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | - Mohammed Jaffer
- Electron Microscope Unit, Division of Medical Biochemistry, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Brandon Weber
- Electron Microscope Unit, Division of Medical Biochemistry, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Keizo Nagasaki
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, Hiroshima 739-0452, Japan
| | - Yuji Tomaru
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, Hiroshima 739-0452, Japan
| | - Roger Wepf
- Electron Microscopy ETH Zurich (EMEZ), 8093 Zurich, Switzerland
| | - Alan Roseman
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Electron Microscope Unit, Division of Medical Biochemistry, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Trevor Sewell
- Electron Microscope Unit, Division of Medical Biochemistry, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
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Tomography of asymmetric bulk specimens imaged by scanning electron microscopy. Ultramicroscopy 2009; 110:170-5. [PMID: 19945223 DOI: 10.1016/j.ultramic.2009.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Revised: 10/18/2009] [Accepted: 11/03/2009] [Indexed: 11/19/2022]
Abstract
The scanning electron microscope produces nanometer-resolution surface images of biological samples preserved in a life-like state. Extracting three-dimensional information from these two-dimensional images has been the subject of long and ongoing research. We present here a general method and theoretical basis for reconstructing the surfaces of SEM specimens imaged from multiple directions by back-projection. The resulting reconstructions are faithful representations of the original specimen geometry, even when the input images are blurred and have low signal-to-noise ratio.
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