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Duan R, Wang S, Li Z, Zhang W, Wu J, Jiang Y, Lin Q, Yuan P, Yue X, Yao Y, Xiao X, Xiao Y, Wang Z. Computer-assisted semi-rational design enhanced the enzymatic activity and protein stability of Proteinase K in calcium-free conditions. Biochem Biophys Res Commun 2024; 721:150109. [PMID: 38762932 DOI: 10.1016/j.bbrc.2024.150109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Wild-type Proteinase K binds to two Ca2+ ions, which play an important role in regulating enzymaticactivity and maintaining protein stability. Therefore, a predetermined concentration of Ca2+ must be added during the use of Proteinase K, which increases its commercial cost. Herein, we addressed this challenge using a computational strategy to engineer a Proteinase K mutant that does not require Ca2+ and exhibits high enzymatic activity and protein stability. In the absence of Ca2+, the best mutant, MT24 (S17W-S176N-D260F), displayed an activity approximately 9.2-fold higher than that of wild-type Proteinase K. It also exhibited excellent protein stability, retaining 56.2 % of its enzymatic activity after storage at 4 °C for 5 days. The residual enzymatic activity was 65-fold higher than that of the wild-type Proteinase K under the same storage conditions. Structural analysis and molecular dynamics simulations suggest that the introduction of new hydrogen bond and π-π stacking at the Ca2+ binding sites due to the mutation may be the reasons for the increased enzymatic activity and stability of MT24.
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Affiliation(s)
- Rongdi Duan
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Shen Wang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Zhetao Li
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Wenjun Zhang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Junteng Wu
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yifei Jiang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Qinting Lin
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Peixiong Yuan
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Xiaoyan Yue
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yunxiao Yao
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Xiaoyue Xiao
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yunjie Xiao
- School of Life Sciences, Tianjin University, Tianjin, 300072, China.
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China.
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Asad M, Liao J, Chen J, Munir F, Pang S, Abbas AN, Yang G. Exploring the role of the ovary-serine protease gene in the female fertility of the diamondback moth using CRISPR/Cas9. PEST MANAGEMENT SCIENCE 2024. [PMID: 38348909 DOI: 10.1002/ps.8022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/24/2023] [Accepted: 02/11/2024] [Indexed: 03/01/2024]
Abstract
BACKGROUND Oogenesis is a complex pathway necessary for proper female reproduction in insects. Ovary-serine protease (Osp) is a homologous gene of serine protease Nudel (SpNudel) and plays an essential role in the oogenesis and ovary development of Drosophila melanogaster. However, the function of Osp is not determined in Plutella xylostella, a highly destructive pest of cruciferous crops. RESULTS The PxOsp gene comprises a 5883-bp open-reading frame that encodes a protein consisting of 1994 amino acids, which contain four conserved domains. PxOsp exhibited a high relative expression in adult females with a specific expression in the ovary. Through the utilization of CRISPR/Cas9 technology, homozygous mutants of PxOsp were generated. These homozygous mutant females produced fewer eggs (average of 56 eggs/female) than wild-type (WT) females (average of 97 eggs/female) when crossed with WT males, and these eggs failed to hatch. Conversely, mutant males produced normal progeny when crossed with WT females. The ovarioles in homozygous mutant females were significantly shorter (5.02 mm in length) and contained fewer eggs (average of 3 eggs/ovariole) than WT ovarioles (8.09 mm in length with an average of 8 eggs/ovariole). Moreover, eggs laid by homozygous mutant females were fragile, with irregular shapes, and were unable to maintain structural integrity due to eggshell ruptures. However, no significant differences were observed between WT and mutant individuals regarding developmental duration, pupal weight, and mating behavior. CONCLUSION Our study suggesteds that PxOsp plays a vital role in female reproduction, particularly in ovary and egg development. Disrupting PxOsp results in recessive female sterility while leaving the male reproductive capability unaffected. This report represents the first study of a haplosufficient gene responsible for female fertility in lepidopteran insects. Additionally, these findings emphasize PxOsp as a potential target for genetically-based pest management of P. xylostella. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Muhammad Asad
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Jianying Liao
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Jing Chen
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Faisal Munir
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Senbo Pang
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Anam Noreen Abbas
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
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3
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Brown M, Badzinski TD, Pardoe E, Ehlebracht M, Maurer-Jones MA. UV Light Degradation of Polylactic Acid Kickstarts Enzymatic Hydrolysis. ACS MATERIALS AU 2024; 4:92-98. [PMID: 38221918 PMCID: PMC10786133 DOI: 10.1021/acsmaterialsau.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 01/16/2024]
Abstract
Polylactic acid (PLA) and bioplastics alike have a designed degradability to avoid the environmental buildup that petroplastics have created. Yet, this designed biotic-degradation has typically been characterized in ideal conditions. This study seeks to relate the abiotic to the biotic degradation of PLA to accurately represent the degradation pathways bioplastics will encounter, supposing their improper disposal in the environment. Enzymatic hydrolysis was used to study the biodegradation of PLA with varying stages of photoaging. Utilizing a fluorescent tag to follow enzyme hydrolysis, it was determined that increasing the amount of irradiation yielded greater amounts of total enzymatic hydrolysis by proteinase K after 8 h of enzyme incubation. While photoaging of the polymers causes minimal changes in chemistry and increasing amounts of crystallinity, the trends in biotic degradation appear to primarily be driven by photoinduced reduction in molecular weight. The relationship between photoaging and enzyme hydrolysis appears to be independent of enzyme type, though commercial product degradation may be impacted by the presence of additives. Overall, this work reveals the importance of characterizing biodegradation with relevant samples that ultimately can inform optimization of production and disposal.
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Affiliation(s)
- Margaret
H. Brown
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, 1038 University Dr, Duluth, Minnesota 55812, United States
| | - Thomas D. Badzinski
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, 1038 University Dr, Duluth, Minnesota 55812, United States
| | - Elizabeth Pardoe
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, 1038 University Dr, Duluth, Minnesota 55812, United States
| | - Molly Ehlebracht
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, 1038 University Dr, Duluth, Minnesota 55812, United States
| | - Melissa A. Maurer-Jones
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, 1038 University Dr, Duluth, Minnesota 55812, United States
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4
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Cowan RM, Birch E, Nisbet G, Onyeiwu C, Campbell C, Archer I, Campopiano DJ. An improved, optimised and robust keratin azure assay for accurate assessment of keratinase activity. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:6468-6475. [PMID: 37982303 DOI: 10.1039/d3ay01433a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Keratin, in the form of coarse sheep wool, has been identified as an undervalued natural resource, which with the appropriate tools (e.g. a keratinase biocatalyst) can be repurposed for various textile and industrial biotechnology applications. For these purposes, we describe a novel method for identifying keratinase activity through the use of α-keratin azure (KA), an anthraquinone dyed substrate. A colourimetric method monitored the keratinase activity of Proteinase K (PK), which degrades the KA substrate and releases soluble products that are observed at 595 nm. Initially, the azure dye standard, Remazol Brilliant Blue R (RBBR), was used to calibrate the assay and allowed the kinetics of the keratinase-catalysed reaction to be determined. The assay was also used to investigate substrate pre-treatment, as well as different reaction quenching/work up conditions. Milling and washing of the KA substrate provided the best reproducibility and centrifugation was the most effective method for removing unreacted starting material. This assay was then applied to investigate the reduction of the keratin disulfide bond on keratinase-catalysed degradation. This optimised, improved and robust method will enable identification of keratinases ideally suited for application in the valorisation of the α-keratin found in natural wool fibres.
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Affiliation(s)
- Rhona M Cowan
- School of Chemistry, University of Edinburgh, David Brewster Road, King's Buildings, Edinburgh, EH9 3FJ, UK
| | - Eleanor Birch
- School of Chemistry, University of Edinburgh, David Brewster Road, King's Buildings, Edinburgh, EH9 3FJ, UK
| | - Grace Nisbet
- School of Chemistry, University of Edinburgh, David Brewster Road, King's Buildings, Edinburgh, EH9 3FJ, UK
| | | | - Clare Campbell
- Prickly Thistle Scotland Ltd, Evanton Industrial Estate, Beechwood Rd, Evanton, Alness IV16 9XJ, UK
| | - Ian Archer
- Industrial Biotechnology Innovation Centre (IBioIC), Inovo Building, 121 George Street, Glasgow G1 1RD, UK
| | - Dominic J Campopiano
- School of Chemistry, University of Edinburgh, David Brewster Road, King's Buildings, Edinburgh, EH9 3FJ, UK
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5
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Altoé LSC, de Araújo Costa E, Tavares GP, Rocha MS, Queiroz JHD, Gonçalves JBC, de Figueiredo SG, de Araújo JV. On the interactions involving serine proteases obtained from Monacrosporium thaumasium (Ascomycota: Orbiliomycetes) and deoxyribonucleic acid (DNA): biological macromolecules in action. Arch Microbiol 2023; 205:208. [PMID: 37103635 DOI: 10.1007/s00203-023-03551-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023]
Abstract
The use of force spectroscopy approaches performed with optical tweezers can be very useful in determining the binding modes and the physical chemistry of DNA interactions with ligands, from small drugs to proteins. Helminthophagous fungi, on the other hand, have important enzyme secretion mechanisms for various purposes, and the interactions between such enzymes and nucleic acids are very poorly studied. Therefore, the main goal of the present work was to investigate, at the molecular level, the mechanisms of interaction between fungal serine proteases and the double-stranded (ds) DNA molecule. Experimental assays performed with this single molecule technique consist in exposing different concentrations of the protease of this fungus to dsDNA until saturation while monitoring the changes on the mechanical properties of the macromolecular complexes formed, from where the physical chemistry of the interaction can be deduced. It was found that the protease binds strongly to the double-helix, forming aggregates and changing the persistence length of the DNA molecule. The present work thus allowed us to infer information at the molecular level on the pathogenicity of these proteins, an important class of biological macromolecules, when applied to a target specimen.
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Affiliation(s)
| | - Ethe de Araújo Costa
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Márcio Santos Rocha
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - José Humberto de Queiroz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Suely Gomes de Figueiredo
- Departamento de Ciências Fisiológicas, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
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Yang J, Chu N, Chen X. Preparation of Polyoxometalate-Based Composite by Solidification of Highly Active Cobalt-Containing Polytungstate on Polymeric Ionic Liquid for the Efficient Isolation of Proteinase K. Molecules 2023; 28:molecules28083307. [PMID: 37110541 PMCID: PMC10142915 DOI: 10.3390/molecules28083307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
A novel porous polyoxometalate (POM)-based composite (Co4PW-PDDVAC) was prepared via the solidification of water-soluble polytungstate (Co4PW) on the polymeric ionic liquid dimethyldodecyl-4-polyethylene benzyl ammonium chloride (PDDVAC) via a cation-exchange reaction. The solidification was confirmed by EDS, SEM, FT-IR, TGA, and so on. The strong covalent coordination and hydrogen-bonding interaction between the highly active Co2+ of the Co4PW and the aspartic acid residues of proteinase K endowed the obtained Co4PW-PDDVAC composite with excellent proteinase K adsorption properties. Thermodynamic investigations indicate that the adsorption behavior of proteinase K was consistent with the linear Langmuir isothermal model, giving an adsorption capacity as high as 1428 mg g-1. The Co4PW-PDDVAC composite was applied in the selective isolation of highly active proteinase K from Tritirachium album Limber crude enzyme fluid.
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Affiliation(s)
- Jiaxuan Yang
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Ning Chu
- Bayuquan Customs District of the People's Republic of China, Yingkou 115007, China
| | - Xuwei Chen
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
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7
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Wang X, Qin X, Tong L, Zheng J, Dong T, Wang X, Wang Y, Huang H, Yao B, Zhang H, Luo H. Improving the catalytic activity of a detergent-compatible serine protease by rational design. Microb Biotechnol 2023; 16:947-960. [PMID: 36636777 PMCID: PMC10128134 DOI: 10.1111/1751-7915.14218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/14/2023] Open
Abstract
Serine proteases are among the most important biological additives in various industries such as detergents, leather, animal feed and food. A serine protease gene, Fgapt4, from Fusarium graminearum 2697 was identified, cloned and expressed in Pichia pastoris. The optimal pH and temperature of FgAPT4 were 8.5 and 40°C, respectively. The relative activity was >30% even at 10°C. It had a wide range of pH stability (4.0-12.0) and detergent compatibility. To improve the catalytic activity, a strategy combining molecular docking and evolutionary analysis was adopted. Twelve amino acid residue sites and three loops (A, B and C) were selected as potential hot spots that might play critical roles in the enzyme's functional properties. Twenty-eight mutants targeting changes in individual sites or loops were designed, and mutations with good performance were combined. The best mutant was FgAPT4-M3 (Q70N/D142S/A143S/loop C). The specific activity and catalytic efficiency of FgAPT4-M3 increased by 1.6 (1008.5 vs. 385.9 U/mg) and 2.2-fold (3565.1 vs. 1106.3/s/mM), respectively. Computational analyses showed that the greater flexibility of the substrate pocket may be responsible for the increased catalytic activity. In addition, its application in detergents indicated that FgAPT4-M3 has great potential in washing.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lige Tong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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De la Cruz-Torres LF, Rodríguez-Celestino V, Centeno-Leija S, Serrano-Posada H, Ceballos-Magaña SG, Aguilar-Padilla J, Mancilla-Margalli NA, Osuna-Castro JA. Development of a rapid, high-sensitivity, low-cost fluorescence method for protein surface hydrophobicity determination using a Nanodrop fluorospectrometer. Food Chem 2022; 396:133681. [PMID: 35853375 DOI: 10.1016/j.foodchem.2022.133681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/18/2022] [Accepted: 07/09/2022] [Indexed: 11/27/2022]
Abstract
A microvolumetric method for surface hydrophobicity (H0) determination of proteins using a Nanodrop fluorospectrometer was developed. This method reduces the protein and fluorophore quantities that are necessary for sample preparations and readings by two and three orders of magnitude, respectively, compared to conventional methods. In addition, readings can be obtained in just 2-6 s. Bovine serum albumin (BSA) and 1-anilino 8-naphthalene sulfonic acid (ANS) were used for the first optimization of appropriate fluorophore-protein conditions for H0 determination (20 μM ANS, 0.5-4 μM BSA, pH 5). Based on validation guidelines, the novel method shows linear behavior, good intraday precision, accuracy, and sensitivity. This method was robust against several factors, as determined by a Youden-Steiner test. Additional surface hydrophobicity determinations using several proteins demonstrate suitable method applicability. The present microvolumetric method provides a reliable technique to determine the H0 of proteins for pharmaceutical, biotechnological, and food applications.
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Affiliation(s)
- Luis Fernando De la Cruz-Torres
- Facultad de Ciencias Químicas, Universidad de Colima, Carr. Colima-Coquimatlán km. 9, C.P. 28400 Coquimatlán, Colima, Mexico; Facultad de Ciencias Biológicas y Agropecuarias, Universidad de Colima, Carr. Colima-Manzanillo km. 40, C.P. 28100 Tecomán, Colima, Mexico; Consejo Nacional de Ciencia y Tecnología, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, C.P. 28629 Colima, Colima, Mexico
| | - Verónica Rodríguez-Celestino
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad de Colima, Carr. Colima-Manzanillo km. 40, C.P. 28100 Tecomán, Colima, Mexico; Consejo Nacional de Ciencia y Tecnología, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, C.P. 28629 Colima, Colima, Mexico; Centro Nacional de Referencia de Control Biológico, Carr. Tecomán-Estación FFCC km 1.5, Col. Tepeyac, C.P. 28110 Tecomán, Colima, Mexico
| | - Sara Centeno-Leija
- Consejo Nacional de Ciencia y Tecnología, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, C.P. 28629 Colima, Colima, Mexico
| | - Hugo Serrano-Posada
- Consejo Nacional de Ciencia y Tecnología, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, C.P. 28629 Colima, Colima, Mexico
| | - Silvia G Ceballos-Magaña
- Facultad de Ciencias, Universidad de Colima, c/ Bernal Díaz del Castillo 340, C.P. 28045 Colima, Colima, Mexico.
| | - Jorge Aguilar-Padilla
- Facultad de Ciencias Químicas, Universidad de Colima, Carr. Colima-Coquimatlán km. 9, C.P. 28400 Coquimatlán, Colima, Mexico; Facultad de Ciencias Biológicas y Agropecuarias, Universidad de Colima, Carr. Colima-Manzanillo km. 40, C.P. 28100 Tecomán, Colima, Mexico; Consejo Nacional de Ciencia y Tecnología, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, C.P. 28629 Colima, Colima, Mexico
| | - Norma Alejandra Mancilla-Margalli
- Tecnológico Nacional de México, Instituto Tecnológico de Tlajomulco, Carr. a San Miguel Cuyutlán km. 10, Tlajomulco de Zúñiga, Jalisco C.P. 45650, Mexico
| | - Juan Alberto Osuna-Castro
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad de Colima, Carr. Colima-Manzanillo km. 40, C.P. 28100 Tecomán, Colima, Mexico.
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9
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Catechol Mediated Synthesis of Monometallic and Bimetallic Nanoparticles and Catalytic Efficiency of Monometallic Nanoparticles. Catal Letters 2022. [DOI: 10.1007/s10562-022-04095-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Li R, Liu Z, Jiang F, Zhao Y, Yang G, Hong L. Enhancement of thermal stability of proteinase K by biocompatible cholinium-based ionic liquids. Phys Chem Chem Phys 2022; 24:13057-13065. [PMID: 35583879 DOI: 10.1039/d1cp04782e] [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
Proteinase K (PK) is a proteolytic enzyme that has been widely used in nucleic acid purification, leather production, environmental protection, and other industrial applications. However, this biocatalyst cannot tolerate high temperatures which has severely restricted its wider application. As reported in previous studies, cholinium-based ionic liquids (ILs) have gained tremendous attention serving as a promising media to stabilize and preserve proteins, DNA, and other biomolecules due to their environmentally benign nature and biocompatibility. In this work, we chose 13 different kinds of cholinium-based ILs to examine their effects on the thermal stability and enzymatic activity of PK. We found that biocompatible cholinium-based ions with appropriately chosen anions can greatly improve the thermal stability of PK, whose melting temperature (Tm) is increased from ∼74.4 °C to 87.7 °C. However, the enzymatic activity is slightly reduced in the presence of ILs. Further comparison of our results with other literature findings suggests that kosmotropic anions of cholinium-based ILs are crucial to maintain the thermal stability of proteins. However, to achieve the best performance, the choice of IL anions is protein specific.
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Affiliation(s)
- Rui Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. .,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. .,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Zhao
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. .,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
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11
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Kawai A, Hamamoto N, Sasanuma Y. Conformational characteristics and conformation-dependent properties of poly(ε-caprolactone). Phys Chem Chem Phys 2022; 24:11382-11394. [PMID: 35502818 DOI: 10.1039/d2cp01273a] [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
Structures and properties of isolated and crystalline poly(ε-caprolactone) (PCL) chains have been investigated. Ab initio molecular orbital (MO) calculations were conducted for methyl 6-acetoxyhexanoate (MAH), a model compound of PCL, to yield Gibbs free energies of all its existent conformers. Bond conformations of its seven bonds corresponding to the repeating unit of PCL were calculated therefrom; two C-C bonds close to the ester group show gauche preferences owing to intramolecular C-H⋯O attractions, and the other five prefer trans forms. 1H and 13C NMR vicinal coupling constants of 13C-labeled MAH yielded bond conformations consistent with the MO calculations. The rotational isomeric state (RIS) calculations on PCL led to the characteristic ratios (4.1-4.5) that agree with those estimated experimentally from the Stockmayer-Fixman plots. Periodic density functional theory calculations on PCL crystals yielded the optimum structures and Young's moduli in the a-, b-, and c (fiber)-axis directions. The fiber-axis modulus (252 GPa) falls short of that (333 GPa) of polyethylene but exceeds that (182 GPa) of poly(ethylene terephthalate), whereas the three-dimensionally averaged Young's modulus (10.7 GPa) of PCL is the smallest of those of representative polymers investigated so far. The enzymatic selectivity of biodegradable polyesters is discussed herein in terms of their conformational characteristics and surface structures of enzymes.
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Affiliation(s)
- Azumi Kawai
- Department of Applied Chemistry and Biotechnology, Graduate School and Faculty of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Naoki Hamamoto
- Department of Applied Chemistry and Biotechnology, Graduate School and Faculty of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Yuji Sasanuma
- Department of Applied Chemistry and Biotechnology, Graduate School and Faculty of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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12
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Martin-Garcia JM, Botha S, Hu H, Jernigan R, Castellví A, Lisova S, Gil F, Calisto B, Crespo I, Roy-Chowdhury S, Grieco A, Ketawala G, Weierstall U, Spence J, Fromme P, Zatsepin N, Boer DR, Carpena X. Serial macromolecular crystallography at ALBA Synchrotron Light Source. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:896-907. [PMID: 35511023 PMCID: PMC9070724 DOI: 10.1107/s1600577522002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15-30 µm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and α-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 µm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.
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Affiliation(s)
- Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Hao Hu
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Rebecca Jernigan
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Albert Castellví
- Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Fernando Gil
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Isidro Crespo
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | - Shatabdi Roy-Chowdhury
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Alice Grieco
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Gihan Ketawala
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - John Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
- ARC Centre of Excellence in Advance Molecular Physics, La Trobe Institute for Molecular ScienceImaging, Department of Chemistry and Physics, La Trobe University, Melbourne, Australia
| | | | - Xavi Carpena
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
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13
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Paudyal S, Sigdel G, Shah SK, Sharma SK, Grubb JD, Micic M, Caseli L, Leblanc RM. Interfacial behavior of Proteinase K enzyme at air-saline subphase. J Colloid Interface Sci 2022; 616:701-708. [PMID: 35247808 DOI: 10.1016/j.jcis.2022.02.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/04/2022] [Accepted: 02/19/2022] [Indexed: 10/19/2022]
Abstract
This study investigates the interfacial behavior of the proteinase K enzyme at air-water interface. Adsorption of enzyme on the surface was induced using saline subphase. The surface packing and stability of the enzyme was investigated using of surface pressure-area (π-A) and surface potential-area (ΔV-A) isotherms. Proteinase K enzyme forms film at air-aqueous interface and demonstrates good stability as shown through compression-decompression cycle experiments. To characterize the surface assembly morphology of the interfacial enzymes UV-vis and fluorescence spectroscopic techniques were used. The data revealed that the enzyme Langmuir monolayer has good homogeneity with no evidence of aggregates during compression. The secondary structure of the enzyme at interface was determined to be α-helix using p-polarized infrared-reflection absorption spectroscopy. This was confirmed through Circular dichroism spectra of the enzyme Langmuir-Blodgett (LB) film which showed that the major conformation present were α-helices.
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Affiliation(s)
- Suraj Paudyal
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Ganesh Sigdel
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Sujit K Shah
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA; Department of Chemistry, Mahendra Morang Adarsh Multiple Campus, Tribhuvan University, Biratnagar 56613, Nepal
| | - Shiv K Sharma
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - John D Grubb
- Gojira Fine Chemicals LLC, 5386 Majestic Pkwy , Suite #7, Bedford Heights, OH 44146, USA
| | - Miodrag Micic
- Gojira Fine Chemicals LLC, 5386 Majestic Pkwy , Suite #7, Bedford Heights, OH 44146, USA; Department of Engineering Design Technology, Cerritos College, 11110, Alondra Blvd, Norwalk, CA 90650, USA
| | - Luciano Caseli
- Department of Chemistry, Federal University of São Paulo, Diadema, Sao Paulo, Brazil
| | - Roger M Leblanc
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA.
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14
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Xu X, Wang Y, Chen J, Du X, Yao L, Xu J, Zhang Y, Huang Y, Wang Y. Mutation of Serine protease 1 Induces Male Sterility in Bombyx mori. Front Physiol 2022; 13:828859. [PMID: 35222089 PMCID: PMC8867212 DOI: 10.3389/fphys.2022.828859] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/17/2022] [Indexed: 01/19/2023] Open
Abstract
Serine proteases are important in reproduction, embryonic development, cell differentiation, apoptosis, and immunity. The genes encoding some serine proteases are essential for male fertility in both humans and rodents and are functionally conserved among metazoan. For example, the Serine protease 1 (Ser1) gene determines male reproductive success in the model lepidopteran insect Bombyx mori. In this study, we explored the function of BmSer1 through transgenic CRISPR/Cas9 technology-mediated mutations in silkworm. We found that the mutation of BmSer1 gene resulted in male sterility but had no effect on female fertility. Male mutants produce normal eupyrene sperm bundles, but the sperm bundles do not dissociate into single sperm. Male sterility caused by the BmSer1 gene mutation was inherited stably through female individuals. Therefore, the serine protease encoded by BmSer1 is essential for male reproductive success in lepidopterans and is a potential target gene for biological reproductive regulation.
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Affiliation(s)
- Xia Xu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaohui Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jine Chen
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xin Du
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lusong Yao
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jun Xu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yong Zhang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Yongping Huang,
| | - Yongqiang Wang
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Yongqiang Wang,
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15
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Bijlani S, Parker C, Singh NK, Sierra MA, Foox J, Wang CCC, Mason CE, Venkateswaran K. Genomic Characterization of the Titan-like Cell Producing Naganishia tulchinskyi, the First Novel Eukaryote Isolated from the International Space Station. J Fungi (Basel) 2022; 8:jof8020165. [PMID: 35205919 PMCID: PMC8875396 DOI: 10.3390/jof8020165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 12/25/2022] Open
Abstract
Multiple strains of a novel yeast belonging to genus Naganishia were isolated from environmental surfaces aboard the International Space Station (ISS). These strains exhibited a phenotype similar to Titan cell (~10 µm diameter) morphology when grown under a combination of simulated microgravity and 5% CO2 conditions. Confocal, scanning, and transmission electron microscopy revealed distinct morphological differences between the microgravity-grown cells and the standard Earth gravity-grown cells, including larger cells and thicker cell walls, altered intracellular morphology, modifications to extracellular fimbriae, budding, and the shedding of bud scars. Phylogenetic analyses via multi-locus sequence typing indicated that these ISS strains represented a single species in the genus Naganishia and were clustered with Naganishia diffluens. The name Naganishia tulchinskyi is proposed to accommodate these strains, with IF6SW-B1T as the holotype. The gene ontologies were assigned to the cell morphogenesis, microtubule-based response, and response to UV light, suggesting a variety of phenotypes that are well suited to respond to microgravity and radiation. Genomic analyses also indicated that the extracellular region, outer membrane, and cell wall were among the highest cellular component results, thus implying a set of genes associated with Titan-like cell plasticity. Finally, the highest molecular function matches included cytoskeletal motor activity, microtubule motor activity, and nuclear export signal receptor activity.
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Affiliation(s)
- Swati Bijlani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; (S.B.); (C.C.C.W.)
| | - Ceth Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
| | - Maria A. Sierra
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA;
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Jonathan Foox
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; (S.B.); (C.C.C.W.)
| | - Christopher E. Mason
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
- Correspondence: (C.E.M.); (K.V.); Tel.: +1-(203)-668-1448 (C.E.M.); +1-(818)-393-1481 (K.V.); Fax: +1-(646)-962-00383 (C.E.M.); +1-(818)-393-4176 (K.V.)
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
- Correspondence: (C.E.M.); (K.V.); Tel.: +1-(203)-668-1448 (C.E.M.); +1-(818)-393-1481 (K.V.); Fax: +1-(646)-962-00383 (C.E.M.); +1-(818)-393-4176 (K.V.)
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16
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Li Q. Structure, Application, and Biochemistry of Microbial Keratinases. Front Microbiol 2021; 12:674345. [PMID: 34248885 PMCID: PMC8260994 DOI: 10.3389/fmicb.2021.674345] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 12/17/2022] Open
Abstract
Keratinases belong to a class of proteases that are able to degrade keratins into amino acids. Microbial keratinases play important roles in turning keratin-containing wastes into value-added products by participating in the degradation of keratin. Keratin is found in human and animal hard tissues, and its complicated structures make it resistant to degradation by common proteases. Although breaking disulfide bonds are involved in keratin degradation, keratinase is responsible for the cleavage of peptides, making it attractive in pharmaceutical and feather industries. Keratinase can serve as an important tool to convert keratin-rich wastes such as feathers from poultry industry into diverse products applicable to many fields. Despite of some progress made in isolating keratinase-producing microorganisms, structural studies of keratinases, and biochemical characterization of these enzymes, effort is still required to expand the biotechnological application of keratinase in diverse fields by identifying more keratinases, understanding the mechanism of action and constructing more active enzymes through molecular biology and protein engineering. Herein, this review covers structures, applications, biochemistry of microbial keratinases, and strategies to improve its efficiency in keratin degradation.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
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17
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Tuning Transport Phenomena in Agarose Gels for the Control of Protein Nucleation Density and Crystal Form. CRYSTALS 2021. [DOI: 10.3390/cryst11050466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Agarose gels provide the ideal environment for studying the nucleation step of complex biomacromolecules under diffusion-controlled conditions. In the present paper, we characterized the influence of agarose on the nucleation of three model proteins, i.e., lysozyme, insulin, and proteinase K, as a function of the agarose concentration using a batch method set-up inside flat capillaries. By using this set-up, we were able to directly count the number of crystals in a given volume and correlate it with the amount of agarose and with the average crystal size. We also studied the crystallization behavior of proteinase K with free-interface diffusion so that batch conditions were achieved through slow diffusion of the precipitant. Thanks to the control over the protein mass transport imposed by the network, a previously unknown crystal form, P212121, was obtained, and the three-dimensional structure was determined at a 1.6 Å resolution. Overall, the versatility of agarose gels makes them ideal candidates for the preparation of microcrystalline suspensions of biopharmaceuticals with precise and reproducible crystal attributes or for the exploration of the existence of different polymorphs.
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18
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Microbial enzymes catalyzing keratin degradation: Classification, structure, function. Biotechnol Adv 2020; 44:107607. [PMID: 32768519 PMCID: PMC7405893 DOI: 10.1016/j.biotechadv.2020.107607] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022]
Abstract
Keratin is an insoluble and protein-rich epidermal material found in e.g. feather, wool, hair. It is produced in substantial amounts as co-product from poultry processing plants and pig slaughterhouses. Keratin is packed by disulfide bonds and hydrogen bonds. Based on the secondary structure, keratin can be classified into α-keratin and β-keratin. Keratinases (EC 3.4.-.- peptide hydrolases) have major potential to degrade keratin for sustainable recycling of the protein and amino acids. Currently, the known keratinolytic enzymes belong to at least 14 different protease families: S1, S8, S9, S10, S16, M3, M4, M14, M16, M28, M32, M36, M38, M55 (MEROPS database). The various keratinolytic enzymes act via endo-attack (proteases in families S1, S8, S16, M4, M16, M36), exo-attack (proteases in families S9, S10, M14, M28, M38, M55) or by action only on oligopeptides (proteases in families M3, M32), respectively. Other enzymes, particularly disulfide reductases, also play a key role in keratin degradation as they catalyze the breakage of disulfide bonds for better keratinase catalysis. This review aims to contribute an overview of keratin biomass as an enzyme substrate and a systematic analysis of currently sequenced keratinolytic enzymes and their classification and reaction mechanisms. We also summarize and discuss keratinase assays, available keratinase structures and finally examine the available data on uses of keratinases in practical biorefinery protein upcycling applications.
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19
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Jafari A, Shareghi B, Hosseini-Koupaei M, Farhadian S. Characterization of osmolyte-enzyme interactions using different spectroscopy and molecular dynamic techniques: Binding of sucrose to proteinase K. Int J Biol Macromol 2020; 151:1250-1258. [DOI: 10.1016/j.ijbiomac.2019.10.171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 12/20/2022]
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20
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Sang P, Liu SQ, Yang LQ. New Insight into Mechanisms of Protein Adaptation to High Temperatures: A Comparative Molecular Dynamics Simulation Study of Thermophilic and Mesophilic Subtilisin-Like Serine Proteases. Int J Mol Sci 2020; 21:E3128. [PMID: 32354206 PMCID: PMC7247438 DOI: 10.3390/ijms21093128] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/19/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022] Open
Abstract
In high-temperature environments, thermophilic proteins must possess enhanced thermal stability in order to maintain their normal biological functions. However, the physicochemical basis of the structural stability of thermophilic proteins at high temperatures remains elusive. In this study, we performed comparative molecular dynamics simulations on thermophilic serine protease (THM) and its homologous mesophilic counterpart (PRK). The comparative analyses of dynamic structural and geometrical properties suggested that THM adopted a more compact conformation and exhibited more intramolecular interactions and lower global flexibility than PRK, which could be in favor of its thermal stability in high-temperature environments. Comparison between protein solvent interactions and the hydrophobicity of these two forms of serine proteases showed that THM had more burial of nonpolar areas, and less protein solvent hydrogen bonds (HBs), indicating that solvent entropy maximization and mobility may play a significant role in THM's adaption to high temperature environments. The constructed funnel-like free energy landscape (FEL) revealed that, in comparison to PRK, THM had a relatively flat and narrow free energy surface, and a lower minimum free energy level, suggesting that the thermophilic form had lower conformational diversity and flexibility. Combining the FEL theory and our simulation results, we conclude that the solvent (entropy force) plays a significant role in protein adaption at high temperatures.
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Affiliation(s)
- Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali 671000, China;
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650000, China
| | - Li-Quan Yang
- College of Agriculture and Biological Science, Dali University, Dali 671000, China;
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21
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High-resolution crystal structures of a “half sandwich”-type Ru(II) coordination compound bound to hen egg-white lysozyme and proteinase K. J Biol Inorg Chem 2020; 25:635-645. [DOI: 10.1007/s00775-020-01786-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/24/2020] [Indexed: 12/29/2022]
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22
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The modifier action of NiO nanoparticles on the activity, structure, and stability of proteinase K. MONATSHEFTE FUR CHEMIE 2020. [DOI: 10.1007/s00706-020-02552-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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23
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Ahmad MS, Akbar Z, Choudhary MI. Insight into the binding affinity of thiourea in the calcium binding pocket of proteinase K, through high resolution X-ray crystallography. Bioorg Chem 2019; 94:103443. [PMID: 31812259 DOI: 10.1016/j.bioorg.2019.103443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/20/2019] [Accepted: 11/13/2019] [Indexed: 12/01/2022]
Abstract
Proteinase K is a stable serine protease, crystallized and extensively used in the study of molecular interactions at the atomic level. During the current study, crystal structure of proteinase K with thiourea (TU) was solved at 1.45 Å (angstrom) resolution. Proteinase K showed its binding affinity with thiourea after soaking with 200 mM (millimolar) concentration of thiourea solution for 6 h. The binding affinity of proteinase K was evaluated with three different molecules i.e., thiourea, acetamide, and thiosemicarbazide. Interestingly, only the thiourea went into the calcium-binding region, and showed interactions with those amino acids which have also displayed interactions with calcium previously. Pro175 (proline 175), Ser197 (Serine 197), Val198 (valine 198), and Asp200 (aspartic acid 200) were the key amino acids involved in the binding of thiourea with proteinase K. Thiourea showed strong hydrogen bondings with Pro175 (2.85 Å), Ser197 (2.88 Å), and Asp200 (2.90 Å, and 3.30 Å), as the key interactions involved in the binding of thiourea with proteinase K. This study provides an insight into the binding mechanism of thiourea with calcium-binding pocket of proteinase K, and thus can be extrapolated to other calcium-binding proteins.
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Affiliation(s)
- Malik Shoaib Ahmad
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Zeeshan Akbar
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - M Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21412, Saudi Arabia
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24
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Meewan I, Zhang X, Roy S, Ballatore C, O’Donoghue AJ, Schooley RT, Abagyan R. Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant. ACS OMEGA 2019; 4:16999-17008. [PMID: 31646247 PMCID: PMC6796237 DOI: 10.1021/acsomega.9b02491] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/02/2019] [Indexed: 06/01/2023]
Abstract
Hepatitis C virus (HCV) is a human pathogen with high morbidity. The HCV NS3/4A protease is essential for viral replication and is one of the top three drug targets. Several drugs targeting the protease have been developed, but drug-resistant mutant strains emerged. Here, we screened a library and synthesized a novel class of small molecules based on a tryptophan derivative scaffold identified as HCV NS3/4A protease inhibitors that are active against both wild type and mutant form of the protease. Only the compounds with predicted binding poses not affected by the most frequent mutations in the active site were selected for experimental validation. The antiviral activities were evaluated by replicon and enzymatic assays. Twenty-two compounds were found to inhibit HCV with EC50 values ranging between 0.64 and 63 μM with compound 22 being the most active. In protease assays, 22 had a comparable inhibition profile for the common mutant HCV GT1b D168A and the wild-type enzyme. However, in the same assay, the potency of the approved drug, simeprevir, decreased 5.7-fold for the mutant enzyme relative to the wild type. The top three inhibitors were also tested against four human serine proteases and were shown to be specific to the viral protease. The fluorescence-based cell viability assay demonstrated a sufficient therapeutic range for the top three candidates.
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Affiliation(s)
- Ittipat Meewan
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Xingquan Zhang
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Suchismita Roy
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Carlo Ballatore
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Robert T. Schooley
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Ruben Abagyan
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
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25
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Lieske J, Cerv M, Kreida S, Komadina D, Fischer J, Barthelmess M, Fischer P, Pakendorf T, Yefanov O, Mariani V, Seine T, Ross BH, Crosas E, Lorbeer O, Burkhardt A, Lane TJ, Guenther S, Bergtholdt J, Schoen S, Törnroth-Horsefield S, Chapman HN, Meents A. On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies. IUCRJ 2019; 6:714-728. [PMID: 31316815 PMCID: PMC6608620 DOI: 10.1107/s2052252519007395] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/21/2019] [Indexed: 05/18/2023]
Abstract
Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, 'naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds.
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Affiliation(s)
- Julia Lieske
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maximilian Cerv
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stefan Kreida
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Kemicentrum, 221 00 Lund, Sweden
| | - Dana Komadina
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janine Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Tim Pakendorf
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas Seine
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- EMBL, Notkestrasse 85, 22607 Hamburg, Germany
| | - Breyan H. Ross
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Eva Crosas
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Olga Lorbeer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anja Burkhardt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas J. Lane
- Bioscience Division and Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sebastian Guenther
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Julian Bergtholdt
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Silvan Schoen
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Susanna Törnroth-Horsefield
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Kemicentrum, 221 00 Lund, Sweden
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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26
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Evaluation of maltose binding to proteinase K: Insights from spectroscopic and computational approach. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Andreis FC, Schrank A, Thompson CE. Molecular evolution of Pr1 proteases depicts ongoing diversification in Metarhizium spp. Mol Genet Genomics 2019; 294:901-917. [DOI: 10.1007/s00438-019-01546-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/08/2019] [Indexed: 10/27/2022]
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28
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Iqbal M, Dubey M, Gudmundsson M, Viketoft M, Jensen DF, Karlsson M. Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea. BMC Evol Biol 2018; 18:171. [PMID: 30445903 PMCID: PMC6240243 DOI: 10.1186/s12862-018-1291-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 11/06/2018] [Indexed: 11/18/2022] Open
Abstract
Background The ascomycete fungus Clonostachys rosea (order Hypocreales) can control several important plant diseases caused by plant pathogenic fungi and nematodes. Subtilisin-like serine proteases are considered to play an important role in pathogenesis in entomopathogenic, mycoparasitic, and nematophagous fungi used for biological control. In this study, we analysed the evolutionary histories of protease gene families, and investigated sequence divergence and regulation of serine protease genes in C. rosea. Results Proteases of selected hypocrealean fungal species were classified into families based on the MEROPS peptidase database. The highest number of protease genes (590) was found in Fusarium solani, followed by C. rosea with 576 genes. Analysis of gene family evolution identified non-random changes in gene copy numbers in the five serine protease gene families S1A, S8A, S9X, S12 and S33. Four families, S1A, S8A, S9X, and S33, displayed gene gains in C. rosea. A gene-tree / species-tree reconciliation analysis of the S8A family revealed that the gene copy number increase in C. rosea was primarily associated with the S08.054 (proteinase K) subgroup. In addition, regulatory and predicted structural differences, including twelve sites evolving under positive selection, among eighteen C. rosea S8A serine protease paralog genes were also observed. The C. rosea S8A serine protease gene prs6 was induced during interaction with the plant pathogenic species F. graminearum. Conclusions Non-random increases in S8A, S9X and S33 serine protease gene numbers in the mycoparasitic species C. rosea, Trichoderma atroviride and T. virens suggests an involvement in fungal-fungal interactions. Regulatory and predicted structural differences between C. rosea S8A paralogs indicate that functional diversification is driving the observed increase in gene copy numbers. The induction of prs6 expression in C. rosea during confrontation with F. graminearum suggests an involvement of the corresponding protease in fungal-fungal interactions. The results pinpoint the importance of serine proteases for ecological niche adaptation in C. rosea, including a potential role in the mycoparasitic attack on fungal prey. Electronic supplementary material The online version of this article (10.1186/s12862-018-1291-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mudassir Iqbal
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
| | - Maria Viketoft
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, SE-75007, Uppsala, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
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29
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Hosseini-Koupaei M, Shareghi B, Saboury AA, Davar F, Sirotkin VA, Hosseini-Koupaei MH, Enteshari Z. Catalytic activity, structure and stability of proteinase K in the presence of biosynthesized CuO nanoparticles. Int J Biol Macromol 2018; 122:732-744. [PMID: 30408449 DOI: 10.1016/j.ijbiomac.2018.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/14/2018] [Accepted: 11/01/2018] [Indexed: 12/18/2022]
Abstract
Here, CuO nanoparticles were synthesized using Sambucus nigra (elderberry) fruit extract. Further, the binding of proteinase K, as a model enzyme with green synthesized nanoparticles was investigated. The results demonstrated that the structural changes in enzyme were induced by the binding of nanoparticles. These changes were accompanied by the decrease in the Michaelis-Menten constant at 298 K. This means that the enzyme affinity for the substrate was increased. Thermodynamic parameters of protein stability and protein-ligand binding were estimated from the spectroscopic measurements at 298-333 K. Depending on the temperature, CuO nanoparticles showed a dual effect on the thermodynamic stability and binding affinity of enzyme. Nanoparticles increase the stability of the native state of enzyme at room temperature. On the other hand, nanoparticles stabilize the unfolded state of enzyme at 310-333 K. An overall favorable Gibbs energy change was observed for the binding process at 298-333 K. The enzyme-nanoparticle binding is enthalpically driven at room temperature. It was concluded that hydrogen bonding plays a key role in the interaction of enzyme with nanoparticles at 298-310 K. At higher temperatures, the protein-ligand binding is entropically driven. This means that hydrophobic association plays a major role in the proteinase K-CuO binding at 310-333 K.
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Affiliation(s)
- Mansoore Hosseini-Koupaei
- Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O. Box .115, Iran; Department of Biology, Naghshe Jahan Institute of Higher Education, Isfahan, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O. Box .115, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Fatemeh Davar
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
| | - Vladimir A Sirotkin
- Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kremlevskaya str., 18, Kazan 420008, Russia
| | | | - Zahra Enteshari
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
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30
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Botha S, Baitan D, Jungnickel KEJ, Oberthür D, Schmidt C, Stern S, Wiedorn MO, Perbandt M, Chapman HN, Betzel C. De novo protein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography. IUCRJ 2018; 5:524-530. [PMID: 30224955 PMCID: PMC6126645 DOI: 10.1107/s2052252518009223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/26/2018] [Indexed: 05/30/2023]
Abstract
During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.
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Affiliation(s)
- S. Botha
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - D. Baitan
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
- Xtal Concepts GmbH, Marlowring 19, 22525 Hamburg, Germany
| | - K. E. J. Jungnickel
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
| | - D. Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - C. Schmidt
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
| | - S. Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - M. O. Wiedorn
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - M. Perbandt
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - H. N. Chapman
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - C. Betzel
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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31
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Zhang J, Zhang Q, Lou Y, Fu Q, Chen Q, Wei T, Yang J, Tang J, Wang J, Chen Y, Zhang X, Zhang J, Bai X, Liang T. Hypoxia-inducible factor-1α/interleukin-1β signaling enhances hepatoma epithelial-mesenchymal transition through macrophages in a hypoxic-inflammatory microenvironment. Hepatology 2018; 67:1872-1889. [PMID: 29171040 DOI: 10.1002/hep.29681] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 10/31/2017] [Accepted: 11/17/2017] [Indexed: 02/06/2023]
Abstract
UNLABELLED The development and progression of hepatocellular carcinoma (HCC) are dependent on its local microenvironment. Hypoxia and inflammation are two critical factors that shape the HCC microenvironment; however, the interplay between the two factors and the involvement of cancer cells under such conditions remain poorly understood. We found that tumor-associated macrophages, the primary proinflammatory cells within tumors, secreted more interleukin 1β (IL-1β) under moderate hypoxic conditions due to increased stability of hypoxia inducible factor 1α (HIF-1α). Under persistent and severe hypoxia, we found that the necrotic debris of HCC cells induced potent IL-1β release by tumor-associated macrophages with an M2 phenotype. We further confirmed that the necrotic debris-induced IL-1β secretion was mediated through Toll-like receptor 4/TIR domain-containing adapter-inducing interferon-β/nuclear factor kappa-light-chain-enhancer of activated B cells signaling in a similar, but not identical, fashion to lipopolysaccharide-induced inflammation. Using mass spectrometry, we identified a group of proteins with O-linked glycosylation to be responsible for the necrotic debris-induced IL-1β secretion. Following the increase of IL-1β in the local microenvironment, the synthesis of HIF-1α was up-regulated by IL-1β in HCC cells through cyclooxygenase-2. The epithelial-mesenchymal transition of HCC cells was enhanced by overexpression of HIF-1α. We further showed that IL-1β promoted HCC metastasis in mouse models and was predictive of poor prognosis in HCC patients. CONCLUSION Our findings revealed an HIF-1α/IL-1β signaling loop between cancer cells and tumor-associated macrophages in a hypoxic microenvironment, resulting in cancer cell epithelial-mesenchymal transition and metastasis; more importantly, our results suggest a potential role of an anti-inflammatory strategy in HCC treatment. (Hepatology 2018;67:1872-1889).
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Affiliation(s)
- Jingying Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Yu Lou
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Qihan Fu
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Qi Chen
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Jiaqi Yang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Jinlong Tang
- Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianxin Wang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Yiwen Chen
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Xiaoyu Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Jian Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine.,Zhejiang Provincial Key Laboratory of Pancreatic Disease.,Zhejiang University, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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32
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Xia YL, Sun JH, Ai SM, Li Y, Du X, Sang P, Yang LQ, Fu YX, Liu SQ. Insights into the role of electrostatics in temperature adaptation: a comparative study of psychrophilic, mesophilic, and thermophilic subtilisin-like serine proteases. RSC Adv 2018; 8:29698-29713. [PMID: 35547280 PMCID: PMC9085296 DOI: 10.1039/c8ra05845h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/15/2018] [Indexed: 11/21/2022] Open
Abstract
To investigate the role of electrostatics in different temperature adaptations, we performed a comparative study on subtilisin-like serine proteases from psychrophilic Vibrio sp. PA-44 (VPR), mesophilic Engyodontium album (Tritirachium album) (PRK), and thermophilic Thermus aquaticus (AQN) using multiple-replica molecular dynamics (MD) simulations combined with continuum electrostatics calculations. The results reveal that although salt bridges are not a crucial factor in determining the overall thermostability of these three proteases, they on average provide the greatest, moderate, and least electrostatic stabilization to AQN, PRK, and VPR, respectively, at the respective organism growth temperatures. Most salt bridges in AQN are effectively stabilizing and thus contribute to maintaining the overall structural stability at 343 K, while nearly half of the salt bridges in VPR interconvert between being stabilizing and being destabilizing, likely aiding in enhancing the local conformational flexibility at 283 K. The individual salt bridges, salt-bridge networks, and calcium ions contribute differentially to local stability and flexibility of these three enzyme structures, depending on their spatial distributions and electrostatic strengths. The shared negatively charged surface potential at the active center of the three enzymes may provide the active-center flexibility necessary for nucleophilic attack and proton transfer. The differences in distributions of the electro-negative, electro-positive, and electro-neutral potentials, particularly over the back surfaces of the three proteases, may modulate/affect not only protein solubility and thermostability but also structural stability and flexibility/rigidity. These results demonstrate that electrostatics contributes to both heat and cold adaptation of subtilisin-like serine proteases through fine-tuning, either globally or locally, the structural stability and conformational flexibility/rigidity, thus providing a foundation for further engineering and mutagenesis studies. Differently charged surface patches contribute to temperature adaptation of subtilisin-like serine proteases through affecting/modulating the protein solubility and thermostability and the structural flexibility/rigidity/stability.![]()
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Affiliation(s)
- Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Jian-Hong Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Shi-Meng Ai
- Department of Applied Mathematics
- Yunnan Agricultural University
- Kunming
- P. R. China
| | - Yi Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Xing Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Peng Sang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Yun-Xin Fu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
- Human Genetics Center and Division of Biostatistics
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
- Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province
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33
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Zhang Y, Ultsch M, Skelton NJ, Burdick DJ, Beresini MH, Li W, Kong-Beltran M, Peterson A, Quinn J, Chiu C, Wu Y, Shia S, Moran P, Di Lello P, Eigenbrot C, Kirchhofer D. Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists. Nat Struct Mol Biol 2017; 24:848-856. [DOI: 10.1038/nsmb.3453] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/20/2017] [Indexed: 12/31/2022]
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34
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Hosseini-Koupaei M, Shareghi B, Saboury AA. Conjugation of biogenic polyamine (putrescine) with proteinase K: Spectroscopic and theoretical insights. Int J Biol Macromol 2017; 98:150-158. [DOI: 10.1016/j.ijbiomac.2017.01.111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/21/2017] [Accepted: 01/25/2017] [Indexed: 11/27/2022]
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35
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Masuda T, Suzuki M, Inoue S, Song C, Nakane T, Nango E, Tanaka R, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Mikami B, Nureki O, Numata K, Iwata S, Sugahara M. Atomic resolution structure of serine protease proteinase K at ambient temperature. Sci Rep 2017; 7:45604. [PMID: 28361898 PMCID: PMC5374539 DOI: 10.1038/srep45604] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/01/2017] [Indexed: 01/24/2023] Open
Abstract
Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.
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Affiliation(s)
- Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.,RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mamoru Suzuki
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigeyuki Inoue
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Changyong Song
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Physics, POSTECH, Pohang 790-784, Korea
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Bunzo Mikami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keiji Numata
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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36
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Sang P, Du X, Yang LQ, Meng ZH, Liu SQ. Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms. RSC Adv 2017. [DOI: 10.1039/c6ra23230b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The physicochemical bases for enzyme cold-adaptation remain elusive.
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Affiliation(s)
- Peng Sang
- Laboratory of Molecular Cardiology
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
| | - Xing Du
- Laboratory for Conservation and Utilization of Bio-Resources
- Yunnan University
- Kunming
- P. R. China
- Department of Biochemistry and Molecular Biology
| | - Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Zhao-Hui Meng
- Laboratory of Molecular Cardiology
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
| | - Shu-Qun Liu
- Laboratory of Molecular Cardiology
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
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37
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Hosseini-Koupaei M, Shareghi B, Saboury AA, Davar F. Molecular investigation on the interaction of spermine with proteinase K by multispectroscopic techniques and molecular simulation studies. Int J Biol Macromol 2017; 94:406-414. [DOI: 10.1016/j.ijbiomac.2016.10.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/30/2016] [Accepted: 10/14/2016] [Indexed: 11/17/2022]
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38
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Zhang D, Fu X, Dai X, Chen Y, Dai L. A new biological process for short-chain fatty acid generation from waste activated sludge improved by Clostridiales enhancement. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:23972-23982. [PMID: 27638799 DOI: 10.1007/s11356-016-7579-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
Short-chain fatty acids (SCFAs), the carbon source of biological nutrient removal, can be produced by waste activated sludge (WAS) anaerobic fermentation. To get more SCFAs from sludge, most studies in literature focused on the mechanical process control or the structure of microbial community; little attention has been paid to the key microorganisms and their function related to SCFA generation. In this study, a different sludge pretreated method, i.e., pretreating sludge by proteinase K for 2 days followed by pretreating at pH 10 for 4 days, is reported, by which the proportion of Clostridiales was increased and SCFA generation was enhanced. First, the effects of different proteinase K concentrations and initial pH on sludge hydrolysis and SCFA generation were investigated. The optimal conditions showed the highest SCFA generation (352.91 mg COD per gram of volatile suspended solids), which was 2.89-fold of the blank (un-pretreated). Further, the new biological pretreatment process led to the conversion of other SCFAs to acetic acid. Acetic acid accounted for 60.8 % of total SCFAs with the new biological pretreatment process compared with 44.9 % in the blank test. Then, the investigation on the key microorganisms related to SCFA production with 16S rRNA gene clone library and fluorescence in situ hybridization (FISH) indicated that there were much greater active Clostridiales when SCFAs were generated with the proteinase K and pH 10 pretreated sludge. Further, the mechanisms for the optimal conditions significantly enhancing SCFA generation were investigated. It was found that pretreating sludge by proteinase K and pH 10 caused the greatest key enzyme activities, organic consumption, and inhibition of methane generation. Graphical abstract A new biological process for short-chain fatty acid generation from waste activated sludge improved by Clostridiales enhancement.
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Affiliation(s)
- Dong Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xiang Fu
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Lingling Dai
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
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39
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Ghéczy N, Küchler A, Walde P. Proteinase K activity determination with β-galactosidase as sensitive macromolecular substrate. Anal Biochem 2016; 513:54-60. [DOI: 10.1016/j.ab.2016.08.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 01/12/2023]
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40
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Yan EK, Lu QQ, Zhang CY, Liu YL, He J, Chen D, Wang B, Zhou RB, Wu P, Yin DC. Preparation of cross-linked hen-egg white lysozyme crystals free of cracks. Sci Rep 2016; 6:34770. [PMID: 27703210 PMCID: PMC5050519 DOI: 10.1038/srep34770] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/19/2016] [Indexed: 11/29/2022] Open
Abstract
Cross-linked protein crystals (CLPCs) are very useful materials in applications such as biosensors, catalysis, and X-ray crystallography. Hence, preparation of CLPCs is an important research direction. During the preparation of CLPCs, an often encountered problem is that cracks may appear in the crystals, which may finally lead to shattering of the crystals into small pieces and cause problem in practical applications. To avoid cross-link induced cracking, it is necessary to study the cracking phenomenon in the preparation process. In this paper, we present an investigation on how to avoid cracking during preparation of CLPCs. An orthogonal experiment was designed to study the phenomenon of cross-link induced cracking of hen-egg white lysozyme (HEWL) crystals against five parameters (temperature, solution pH, crystal growth time, glutaraldehyde concentration, and cross-linking time). The experimental results showed that, the solution pH and crystal growth time can significantly affect cross-link induced cracking. The possible mechanism was studied, and optimized conditions for obtaining crack-free CLPCs were obtained and experimentally verified.
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Affiliation(s)
- Er-Kai Yan
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
| | - Qin-Qin Lu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
| | - Chen-Yan Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
| | - Ya-Li Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
| | - Jin He
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
| | - Da Chen
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
| | - Bo Wang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
| | - Ren-Bin Zhou
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
| | - Ping Wu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, P. R. China
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41
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Du X, Sang P, Xia YL, Li Y, Liang J, Ai SM, Ji XL, Fu YX, Liu SQ. Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:1500-1517. [PMID: 27485684 DOI: 10.1080/07391102.2016.1188155] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Molecular dynamics (MD) simulations of a subtilisin-like serine protease VPR from the psychrophilic marine bacterium Vibrio sp. PA-44 and its mesophilic homologue, proteinase K (PRK), have been performed for 20 ns at four different temperatures (300, 373, 473, and 573 K). The comparative analyses of MD trajectories reveal that at almost all temperatures, VPR exhibits greater structural fluctuations/deviations, more unstable regular secondary structural elements, and higher global flexibility than PRK. Although these two proteases follow similar unfolding pathways at high temperatures, VPR initiates unfolding at a lower temperature and unfolds faster at the same high temperatures than PRK. These observations collectively indicate that VPR is less stable and more heat-labile than PRK. Analyses of the structural/geometrical properties reveal that, when compared to PRK, VPR has larger radius of gyration (Rg), less intramolecular contacts and hydrogen bonds (HBs), more protein-solvent HBs, and smaller burial of nonpolar area and larger exposure of polar area. These suggest that the increased flexibility of VPR would be most likely caused by its reduced intramolecular interactions and more favourable protein-solvent interactions arising from the larger exposure of the polar area, whereas the enhanced stability of PRK could be ascribed to its increased intramolecular interactions arising from the better optimized hydrophobicity. The factors responsible for the significant differences in local flexibility between these two proteases were also analyzed and ascertained. This study provides insights into molecular basis of thermostability of homologous serine proteases adapted to different temperatures.
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Affiliation(s)
- Xing Du
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Peng Sang
- b Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming 650032 , PR China
| | - Yuan-Ling Xia
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Yi Li
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Jing Liang
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Shi-Meng Ai
- c Department of Applied Mathematics , Yunnan Agricultural University , Kunming 650201 , PR China
| | - Xing-Lai Ji
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.,d Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province, School of Life Sciences , Yunnan University , Kunming 650223 , PR China
| | - Yun-Xin Fu
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.,e Human Genetics Center and Division of Biostatistics, School of Public Health , The University of Texas Health Science Center , Houston , TX , 77030 , USA
| | - Shu-Qun Liu
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.,d Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province, School of Life Sciences , Yunnan University , Kunming 650223 , PR China
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42
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Singh N, Bhattacharyya D. Cholesterol and Its Derivatives Reversibly Inhibit Proteinase K. J Cell Physiol 2016; 232:596-609. [DOI: 10.1002/jcp.25457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/13/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Namrata Singh
- Division of Structural Biology and Bioinformatics; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata India
| | - Debasish Bhattacharyya
- Division of Structural Biology and Bioinformatics; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata India
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43
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Khan S, Nadir S, Wang X, Khan A, Xu J, Li M, Tao L, Khan S, Karunarathna SC. Using in silico techniques: Isolation and characterization of an insect cuticle-degrading-protease gene from Beauveria bassiana. Microb Pathog 2016; 97:189-97. [PMID: 27287496 DOI: 10.1016/j.micpath.2016.05.024] [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: 03/07/2016] [Revised: 05/05/2016] [Accepted: 05/29/2016] [Indexed: 10/21/2022]
Abstract
Cuticle-degrading-proteases (CDPs) secreted by Beauveria spp. are pivotal biocontrol substances, possessing commercial potential for developing bio-pesticides. Therefore, a thoughtful and contemplative understanding and assessment of the structural and functional features of these proteases would markedly assist the development of biogenic pesticides. Computational molecular biology is a new facile alternative approach to the tedious experimental molecular biology; therefore, by using bioinformatics tools, we isolated and characterized an insect CDP gene from Beauveria bassiana 70 s.l. genomic DNA. The CDP gene (1240 bp with GeneBank accession no. KT804651.1) consisted of three introns and four CDS exons, and shared 74-100% sequence identity to the reference CDP genes. Its phylogenetic tree results showed a unique evolution pattern, and the predicted amino acid peptide (PAAP) consisted of 344 amino acid residues with pI, molecular weight, instability index, grand average hydropathicity value and aliphatic index of 7.2, 35.4 kDa, 24.45, -0.149, and 76.63, respectively. The gene possessed 74-89% amino acid sequence similarity to the 12 reference strains. Three motifs (Peptidase_S8 subtilase family) were detected in the PAAP, and the computed 3D structure possessed 79.09% structural identity to alkaline serine proteases. The PAAP had four (three serine proteases and one Pyridoxal-dependent decarboxylase) conserved domains, a disulfide bridge, two calcium binding sites, MY domain, and three predicted active sites in the serine family domains. These results will set the groundwork for further exploitation of proteases and understanding the mechanism of disease caused by cuticle-degrading-serine-proteases from entomopathogenic fungi.
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Affiliation(s)
- Sehroon Khan
- World Agroforestry Centre, East and Central Asia Office, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Rd, Heilongtan, Kunming 650201, Yunnan, China; Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
| | - Sadia Nadir
- Department of Chemistry, Faculty of Sciences, University of Science and Technology Bannu, 28100 Bannu, Khyber Pakhtunkhwa, Pakistan; Rice Research Institute, Yunnan Agriculture University, Heilongtan, Kunming 650201, Yunnan, China
| | - Xuewen Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China.
| | - Afsar Khan
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan
| | - Jianchu Xu
- World Agroforestry Centre, East and Central Asia Office, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Rd, Heilongtan, Kunming 650201, Yunnan, China; Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Meng Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China
| | - Lihong Tao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China
| | - Siraj Khan
- School of Software, Beijing Institute of Technology, Beijing, China
| | - Samantha C Karunarathna
- World Agroforestry Centre, East and Central Asia Office, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Rd, Heilongtan, Kunming 650201, Yunnan, China
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44
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Sang P, Yang Q, Du X, Yang N, Yang LQ, Ji XL, Fu YX, Meng ZH, Liu SQ. Effect of the Solvent Temperatures on Dynamics of Serine Protease Proteinase K. Int J Mol Sci 2016; 17:254. [PMID: 26907253 DOI: 10.3390/ijms17020254] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 01/21/2016] [Accepted: 02/06/2016] [Indexed: 11/16/2022] Open
Abstract
To obtain detailed information about the effect of the solvent temperatures on protein dynamics, multiple long molecular dynamics (MD) simulations of serine protease proteinase K with the solute and solvent coupled to different temperatures (either 300 or 180 K) have been performed. Comparative analyses demonstrate that the internal flexibility and mobility of proteinase K are strongly dependent on the solvent temperatures but weakly on the protein temperatures. The constructed free energy landscapes (FELs) at the high solvent temperatures exhibit a more rugged surface, broader spanning range, and higher minimum free energy level than do those at the low solvent temperatures. Comparison between the dynamic hydrogen bond (HB) numbers reveals that the high solvent temperatures intensify the competitive HB interactions between water molecules and protein surface atoms, and this in turn exacerbates the competitive HB interactions between protein internal atoms, thus enhancing the conformational flexibility and facilitating the collective motions of the protein. A refined FEL model was proposed to explain the role of the solvent mobility in facilitating the cascade amplification of microscopic motions of atoms and atomic groups into the global collective motions of the protein.
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Affiliation(s)
- Peng Sang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
| | - Qiong Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Xing Du
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Nan Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Li-Quan Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- College of Agriculture and Biological Science, Dali University, Dali 671003, China.
| | - Xing-Lai Ji
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Yun-Xin Fu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Human Genetics Center, School of Public Health, the University of Texas Health Science Center, Houston, TX 77030, USA.
| | - Zhao-Hui Meng
- Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
| | - Shu-Qun Liu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
- Key Laboratory for Tumor molecular biology of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming 650091, China.
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45
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Hosseini-Koupaei M, Shareghi B, Saboury AA, Davar F, Raisi F. The effect of spermidine on the structure, kinetics and stability of proteinase K: spectroscopic and computational approaches. RSC Adv 2016. [DOI: 10.1039/c6ra20975k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Polyamines (such as spermidine) are low molecular weight compounds which can be used as cosolvents in biological and industrial applications.
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Affiliation(s)
| | - Behzad Shareghi
- Department of Biology
- Faculty of Science
- University of Shahrekord
- Shahrekord
- Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
- Center of Excellence in Biothermodynamics
| | - Fatemeh Davar
- Department of Chemistry
- Isfahan University of Technology
- Isfahan
- Iran
| | - Fatame Raisi
- Young Researchers and Elites Club
- Islamic Azad University
- Shahrekord
- Iran
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46
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Koupaei MH, Shareghi B, Saboury AA, Davar F, Semnani A, Evini M. Green synthesis of zinc oxide nanoparticles and their effect on the stability and activity of proteinase K. RSC Adv 2016. [DOI: 10.1039/c5ra24862k] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The use of environmentally benign materials for the synthesis of zinc oxide nanoparticles offers numerous benefits of eco-friendliness and compatibility for pharmaceutical, biotechnological and biological applications.
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Affiliation(s)
| | - Behzad Shareghi
- Department of Biology
- Faculty of Science
- University of Shahrekord
- Shahrekord
- Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
- Center of Excellence in Biothermodynamics
| | - Fateme Davar
- Department of Chemistry
- Isfahan University of Technology
- Isfahan
- Iran
| | - Aboulfazl Semnani
- Department of Chemistry
- Faculty of Science
- University of Shahrekord
- Shahrekord
- Iran
| | - Mina Evini
- Center of Excellence in Biothermodynamics
- University of Tehran
- Tehran
- Iran
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47
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Last D, Müller J, Dawood AWH, Moldenhauer EJ, Pavlidis IV, Bornscheuer UT. Highly efficient and easy protease-mediated protein purification. Appl Microbiol Biotechnol 2015; 100:1945-1953. [DOI: 10.1007/s00253-015-7206-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/25/2015] [Accepted: 11/28/2015] [Indexed: 11/29/2022]
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Juntunen K, Mäkinen S, Isoniemi S, Valtakari L, Pelzer A, Jänis J, Paloheimo M. A New Subtilase-Like Protease Deriving from Fusarium equiseti with High Potential for Industrial Applications. Appl Biochem Biotechnol 2015; 177:407-30. [DOI: 10.1007/s12010-015-1752-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/06/2015] [Indexed: 11/28/2022]
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Abstract
The proof of concept that proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibition affects cholesterol levels was first established after the demonstration that PCSK9 loss-of-function mutations result in a significant drop in circulating LDL cholesterol levels. Subsequent studies revealed that PCSK9 binds the epidermal growth factor precursor homology domain-A on the surface LDL Receptor (LDLR) and directs LDLR and PCSK9 for lysosomal degradation. Alirocumab (also known as SAR236553/REGN727) is a monoclonal antibody that binds circulating PCSK9 and blocks its interactions with surface LDLR. Alirocumab clinical trials with different doses on different administration schedules were shown to significantly reduce LDL cholesterol both as a mono-therapy and in combination with statins or ezetimibe. Although there is great potential for anti-PCSK9 therapies in the management of cholesterol metabolism, there is no clear evidence yet that blocking PCSK9 reduces cardiovascular disease outcome. This is being investigated in ongoing Phase III clinical trials with alirocumab.
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Affiliation(s)
- Hagai Tavori
- Knight Cardiovascular Institute, Center for Preventive Cardiology, Oregon Health and Science University, Portland, OR, USA.
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50
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Hou H, Liu Y, Wang B, Jiang F, Tao HR, Hu SY, Yin DC. Recrystallization: a method to improve the quality of protein crystals. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715005129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The quality of protein crystals is an important parameter for structural determination with X-ray crystallography. Indeed, a prerequisite for obtaining high-resolution diffraction data is that the crystals be of sufficient quality. However, obtaining high-quality protein crystals is a well known bottleneck to protein structural determination that remains a difficult task. In this paper, it is demonstrated that recrystallization can be an effective method of improving the quality of protein crystals. Five proteins, lysozyme, proteinase K, concanavalin A, thaumatin and catalase, were used for this investigation, and the crystal quality of these proteins was examined using X-ray diffraction before and after recrystallization. Comparisons of the crystals before and after recrystallization verified that recrystallization not only enhanced the morphology of the crystals but also improved crystal quality. Therefore, it is proposed that recrystallization might be a useful alternative method for obtaining protein crystals with enhanced diffraction.
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