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Guo J, Gan C, Cheng B, Cui B, Yi F. Exploration of binding mechanism of apigenin to pepsin: Spectroscopic analysis, molecular docking, enzyme activity and antioxidant assays. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122281. [PMID: 36584639 DOI: 10.1016/j.saa.2022.122281] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/07/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Pepsin plays an important role in nutrient metabolism. Apigenin (AP) is a beneficial polyphenol to human health. To enhance the bioavailability of AP and elucidate the inhibitory effect of AP on pepsin, the interaction mechanism of AP with pepsin was investigated using spectroscopic analysis and molecular docking, and the activity of pepsin and antioxidant activity of AP was also evaluated. Specifically, AP performed static quenching of pepsin and had only one binding site on pepsin. More interestingly, the interaction between AP and pepsin was spontaneous, while hydrogen bonds and van der Waals forces were the main binding forces. Generally, synchronous and three-dimensional fluorescence confirmed that AP induced the conformational changes of pepsin, and molecular docking proved the above results and illustrated the specific binding patterns. Specifically, AP inhibited the activity of pepsin, while pepsin decreased the antioxidant activity of AP. These results provided useful information for elucidating the interactions between AP and pepsin.
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Affiliation(s)
- Jinying Guo
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, PR China.
| | - Chuanfa Gan
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, PR China
| | - Bo Cheng
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, PR China
| | - Bo Cui
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, PR China
| | - Fankai Yi
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, PR China
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Yu Y, Xu S, He R, Liang G. Application of Molecular Simulation Methods in Food Science: Status and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2684-2703. [PMID: 36719790 DOI: 10.1021/acs.jafc.2c06789] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular simulation methods, such as molecular docking, molecular dynamic (MD) simulation, and quantum chemical (QC) calculation, have become popular as characterization and/or virtual screening tools because they can visually display interaction details that in vitro experiments can not capture and quickly screen bioactive compounds from large databases with millions of molecules. Currently, interdisciplinary research has expanded molecular simulation technology from computer aided drug design (CADD) to food science. More food scientists are supporting their hypotheses/results with this technology. To understand better the use of molecular simulation methods, it is necessary to systematically summarize the latest applications and usage trends of molecular simulation methods in the research field of food science. However, this type of review article is rare. To bridge this gap, we have comprehensively summarized the principle, combination usage, and application of molecular simulation methods in food science. We also analyzed the limitations and future trends and offered valuable strategies with the latest technologies to help food scientists use molecular simulation methods.
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Affiliation(s)
- Yuandong Yu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Shiqi Xu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Ran He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
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Nyabadza A, Shan C, Murphy R, Vazquez M, Brabazon D. Laser-synthesised magnesium nanoparticles for amino acid and enzyme immobilisation. OPENNANO 2023. [DOI: 10.1016/j.onano.2023.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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4
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Multi spectroscopy and molecular modeling aspects related to drug interaction of aspirin with alpha chymotrypsin; structural change and protease activity. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Calapoglu F, Sahin S, Ozmen I, Ozbek Yazici S. Investigation of interaction between dexamethasone/pheniramine and trypsin by fluorescence, UV-vis, CD, and molecular docking. J Biomol Struct Dyn 2022; 41:2202-2210. [PMID: 35098895 DOI: 10.1080/07391102.2022.2029565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Antihistamines and glucocorticoids are commonly used to treat allergy symptoms and the inflammatory conditions. In present study, the in-vitro binding interactions a glucocortikoid, dexamethasone/an antihistamine, pheniramine with TSN (TSN) secreted from pancreas to small intestine for protein digestion were investigated by fluorescence emission spectroscopy (FES), UV-Vis spectroscopy, synchronous fluorescence spectroscopy (SFS), CD spectroscopy, FT-IR and molecular modeling methods. Also, the effect of these drugs on the catalytic activity of trypsin (TSN) was determined. The fluorescence quenching experiments indicated that each drugs quenched the intrinsic fluorescence of TSN with their increased concentrations. The results of SFS and UV-Vis spectra proved the interaction of dexamethasone and pheniramine with TSN. CD spectra showed that the secondary structure of enzyme was altered in the presence of the drugs. All these spectroscopy results were validated and explained by molecular docking and molecular dynamic simulation (MD) studies. The IC50 values were determined as 0.0049 mM and 0.0038 mM for dexamethasone and pheniramine, respectively. So, both drugs have inhibition effect on the catalytic activity of TSN. The results of this study can provide valuable information in the field of pharmacokinetics and pharmacodynamics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Furkan Calapoglu
- Faculty of Arts and Sciences, Department of Chemistry, Suleyman Demirel University, Cunur, Isparta, Turkey
| | - Selmihan Sahin
- Faculty of Arts and Sciences, Department of Chemistry, Suleyman Demirel University, Cunur, Isparta, Turkey
| | - Ismail Ozmen
- Faculty of Arts and Sciences, Department of Chemistry, Suleyman Demirel University, Cunur, Isparta, Turkey
| | - Sercan Ozbek Yazici
- Faculty of Health Sciences, Department of Nutrition and Dietetics, Burdur Mehmet Akif Ersoy University, Istiklal Yerleskesi, Burdur, Turkey
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Sahin S, Calapoglu F, Ozbek Yazici S, Ozmen I. Investigation of binding interaction behavior between antiemetic drugs and Trypsin by spectroscopy and molecular docking. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119817. [PMID: 33901946 DOI: 10.1016/j.saa.2021.119817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Antiemetic drugs are used to control excessive vomiting and nausea and generally absorbed through gastrointestinal tract. In present study, the in-vitro binding interactions two of the antiemetic drugs (dimenhydrinate and ondansetron) between Trypsin (Tsn) secreted from pancreas to small intestine for protein digestion were investigated by fluorescence emission spectroscopy (FES), UV-VIS spectroscopy, synchronous fluorescence spectroscopy (SFS), FT-IR spectroscopy and molecular modeling methods. Also, the effect of these drugs on the catalytic activity of Tsn was determined. The fluorescence quenching experiments indicated that each drugs quenched the intrinsic fluorescence of Tsn with their increased concentrations. The results of SFS and UV-VIS spectra proved the interaction of dimenhydrinate and ondansetron with Tsn. FT-IR spectra showed that the secondary structure of enzyme was altered in the presence of the drugs. All these spectroscopy results were validated and explained by molecular docking studies. Both drugs have inhibition effect on the catalytic activity of Tsn and the IC50 values were determined as 2.6 × 10-4 M and 6.4 × 10-4 M for dimenhydrinate and ondansetron, respectively. Docking results revealed that the hydrogen bond interaction of dimenhydrinate with active-site residue Ser195 and ondansetron with active-site residues His57 and Ser195 hydrogen bonds might be cause the inhibition of enzyme activity. The results of this study can provide valuable information in the field of pharmacokinetics and pharmacodynamics.
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Affiliation(s)
- Selmihan Sahin
- Faculty of Arts and Sciences, Department of Chemistry, Suleyman Demirel University, Cunur, Isparta 32260, Turkey.
| | - Furkan Calapoglu
- Faculty of Arts and Sciences, Department of Chemistry, Suleyman Demirel University, Cunur, Isparta 32260, Turkey
| | - Sercan Ozbek Yazici
- Faculty of Health Sciences, Department of Nutrition and Dietetics, Burdur Mehmet Akif Ersoy University, Istiklal Yerleskesi, Burdur 15100, Turkey
| | - Ismail Ozmen
- Faculty of Arts and Sciences, Department of Chemistry, Suleyman Demirel University, Cunur, Isparta 32260, Turkey
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Lin J, Tang M, Meti MD, Liu Y, Han Q, Xu X, Zheng Y, He Z, Hu Z, Xu H. Exploring the binding mechanism of Ginsenoside Rd to Bovine Serum Albumin: Experimental studies and computational simulations. J DISPER SCI TECHNOL 2021. [DOI: 10.1080/01932691.2021.1915154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Jialiang Lin
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Min Tang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Manjunath D. Meti
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yong Liu
- Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Qingguo Han
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xu Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yuan Zheng
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhendan He
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Hong Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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Pramanik U, Khamari L, Shekhar S, Mukherjee S. On the role of hydrophobic interactions between chloramphenicol and bovine pancreatic trypsin: The effect of a strong electrolyte. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137137] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Ying M, Meti MD, Xu H, Wang Y, Lin J, Wu Z, Han Q, Xu X, He Z, Hong W, Hu Z. Binding mechanism of lipase to Ligupurpuroside B extracted from Ku-Ding tea as studied by multi-spectroscopic and molecular docking methods. Int J Biol Macromol 2018; 120:1345-1352. [DOI: 10.1016/j.ijbiomac.2018.09.086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/28/2018] [Accepted: 09/14/2018] [Indexed: 10/28/2022]
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Lin J, Xu Y, Wang Y, Huang S, Li J, Meti MD, Xu X, Hu Z, Liu J, He Z, Xu H. Dissection of binding of trypsin to its natural inhibitor Gensenoside-Rg1 using spectroscopic methods and molecular modeling. J Biomol Struct Dyn 2018; 37:4070-4079. [DOI: 10.1080/07391102.2018.1539411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jialiang Lin
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
| | - Yang Xu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
- School of Science and Engineering, Chinese University of Hong Kong, Shenzhen, China
| | - Yuhan Wang
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
| | - Songyang Huang
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
| | - Junwei Li
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
| | - Manjunath D. Meti
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
| | - Xu Xu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
| | - Zhangli Hu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
| | - Johnson Liu
- School Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Zhendan He
- School of Medicine, Shenzhen University, Shenzhen, China
| | - Hong Xu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
- Key Laboratory of RF Circuits and Systems of Ministry of Education, Hangzhou Dianzi University, Hangzhou, China
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Meti MD, Lin J, Wang Y, Wu Z, Xu H, Xu X, Han Q, Ying M, Hu Z, He Z. Trypsin inhibition by Ligupurpuroside B as studied using spectroscopic, CD, and molecular docking techniques. J Biomol Struct Dyn 2018; 37:3379-3387. [PMID: 30213239 DOI: 10.1080/07391102.2018.1515115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
It is well known that Ligupurpuroside B is a water-soluble polyphenolic compound and used to brew bitter tea with antioxidant activities. It acted as a stimulant to the central nervous system and a diuretic (increase the excretion of urine), was used to treat painful throat and high blood pressure, and also exerted weight-loss function. In this regard, a detailed investigation on the mechanism of interaction between Ligupurpuroside B and trypsin could be of great interest to know the pharmacokinetic behavior of Ligupurpuroside B and for the design of new analogues with effective pharmacological properties. Ligupurpuroside B successfully quenched the intrinsic fluorescence of trypsin via static quenching mechanism. The binding constants (Ka) at three temperatures (288, 298, and 308 K) were 1.7841 × 104, 1.6251 × 104 and 1.5483 × 104 L mol-1, respectively. Binding constants revealed the stronger binding interaction between Ligupurpuroside B and trypsin. The number of binding sites approximated to one, indicating a single class of binding for Ligupurpuroside B in trypsin. The enzyme activity result suggested that Ligupurpuroside B can inhibit trypsin activity. Thermodynamic results revealed that both hydrogen bonds and hydrophobic interactions play main roles in stabilization of Ligupurpuroside B-trypsin complex. Circular dichroism (CD) results showed that the conformation of trypsin changed after bound to ligupurpuroside B. Molecular docking indicated that Ligupurpuroside B can enter the hydrophobic cavity of trypsin and was located near Trp215 and Tyr228 of trypsin. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manjunath D Meti
- a Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , China.,b Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering , Shenzhen University , Shenzhen , China
| | - Jialiang Lin
- a Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , China.,b Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering , Shenzhen University , Shenzhen , China
| | - Yuhan Wang
- a Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , China.,b Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering , Shenzhen University , Shenzhen , China
| | - Zhibing Wu
- a Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , China.,b Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering , Shenzhen University , Shenzhen , China
| | - Hong Xu
- a Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , China.,b Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering , Shenzhen University , Shenzhen , China
| | - Xu Xu
- a Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , China.,b Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering , Shenzhen University , Shenzhen , China
| | - Qingguo Han
- a Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , China.,b Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering , Shenzhen University , Shenzhen , China
| | - Ming Ying
- a Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , China.,b Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering , Shenzhen University , Shenzhen , China
| | - Zhangli Hu
- a Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , China.,b Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering , Shenzhen University , Shenzhen , China
| | - Zhendan He
- c School of Medicine , Shenzhen University , Shenzhen , China
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