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Li Z, Li C, Cheng P, Yu G. Rhodotorula mucilaginosa—alternative sources of natural carotenoids, lipids, and enzymes for industrial use. Heliyon 2022; 8:e11505. [DOI: 10.1016/j.heliyon.2022.e11505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/19/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
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Rahmatabadi SS, Sadeghian I, Ghasemi Y, Sakhteman A, Hemmati S. Identification and characterization of a sterically robust phenylalanine ammonia-lyase among 481 natural isoforms through association of in silico and in vitro studies. Enzyme Microb Technol 2018; 122:36-54. [PMID: 30638507 DOI: 10.1016/j.enzmictec.2018.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 11/14/2018] [Accepted: 12/09/2018] [Indexed: 10/27/2022]
Abstract
The enzyme phenylalanine ammonia lyase (PAL) is of special importance for the treatment of phenylketonuria patients. The aim of this study was to find a stable recombinant PAL with suitable kinetic properties among all natural PAL producing species using in silico and experimental approaches. To find such a stable PAL among 481 natural isoforms, 48,000 of 3-D models were predicted using the Modeller 9.10 program and evaluated by Ramachandran plot. Correlation analysis between Ramachandran plot and the energy of different thermodynamic components indicated that this plot could be an appropriate tool to predict protein stability. Hence, PAL6 from Lotus japonicus (LjPAL6) was selected as a stable isoform. Molecular dynamic (MD) simulation for 50 ns and docking has been conducted for LjPAL6-phenylalanine complex. The best PAL-phenylalanine frame was selected by re-docking with l-phenylalanine (L-Phe) and root-mean-square deviation (RMSD) value. MD simulation showed that the complex has a good stability, depicted by the low RMSD value, binding free energy and hydrogen bindings. Docking results showed that LjPAL6 has a high affinity toward l-Phe according to the low level of binding free energy. By overexpressing Ljpal6 in E. coli BL21, a total of 33.5 mg/l of protein was obtained, which has been increased to 83.7 mg/l via the optimization of LjPAL6 production using response surface methodology. The optimal pH and temperature were 8.5 and 50 °C, respectively. LjPAL6 showed a specific activity of 42 nkat/mg protein, with Km, Kcat and Kcat/Km values of 0.483 mM, 7 S-1 and 14.5 S-1 mM-1 for l-phe, respectively. In conclusion, finding models with the most reasonable stereo-chemical quality and lowest numbers of steric clashes would result in easier folding. Hence, in silico analyses of bulk data from natural origin will lead one to find an optimal model for in vitro studies and drug design.
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Affiliation(s)
- Seyyed Soheil Rahmatabadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Issa Sadeghian
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Yuferova AA. The Impact of Different Drying Modes of Scyphozoan JellyfishRhopilema EsculentumandAurelia Auritaon the Protein and Carbohydrate Components in their Composition and the Possibility of Their Use as Dried Prepared Food. J FOOD PROCESS ENG 2015. [DOI: 10.1111/jfpe.12326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mesoporous CLEAs-silica composite microparticles with high activity and enhanced stability. Sci Rep 2015; 5:14203. [PMID: 26374188 PMCID: PMC4570996 DOI: 10.1038/srep14203] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 08/20/2015] [Indexed: 12/29/2022] Open
Abstract
A novel enzyme immobilization approach was used to generate mesoporous enzymes-silica composite microparticles by co-entrapping gelatinized starch and cross-linked phenylalanine ammonia lyase (PAL) aggregates (CLEAs) containing gelatinized starch into biomemitic silica and subsequently removing the starch by α-amylase treatment. During the preparation process, the gelatinzed starch served as a pore-forming agent to create pores in CLEAs and biomimetic silica. The resulting mesoporous CLEAs-silica composite microparticles exhibited higher activity and stability than native PAL, conventional CLEAs, and PAL encapsulated in biomimetic silica. Furthermore, the mesoporous CLEAs-silica composite microparticles displayed good reusability due to its suitable size and mechanical properties, and had excellent stability for storage. The superior catalytic performances were attributed to the combinational unique structure from the intra-cross-linking among enzyme aggregates and hard mesoporous silica shell, which not only decreased the enzyme-support negative interaction and mass-transfer limitations, but also improved the mechanical properties and monodispersity. This approach will be highly beneficial for preparing various bioactive mesoporous composites with excellent catalytic performance.
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Cui J, Liang L, Han C, Lin Liu R. Stabilization of Phenylalanine Ammonia Lyase from Rhodotorula glutinis by Encapsulation in Polyethyleneimine-Mediated Biomimetic Silica. Appl Biochem Biotechnol 2015; 176:999-1011. [PMID: 25906687 DOI: 10.1007/s12010-015-1624-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/06/2015] [Indexed: 02/03/2023]
Abstract
Phenylalanine ammonia lyase (PAL) from Rhodotorula glutinis was encapsulated within polyethyleneimine-mediated biomimetic silica. The main factors in the preparation of biomimetic silica were optimized by response surface methodology (RSM). Compared to free PAL (about 2 U), the encapsulated PAL retained more than 43 % of their initial activity after 1 h of incubation time at 60 °C, whereas free PAL lost most of activity in the same conditions. It was clearly indicated that the thermal stability of PAL was improved by encapsulation. Moreover, the encapsulated PAL exhibited the excellent stability of the enzyme against denaturants and storage stability, and pH stability was improved by encapsulation. Operational stability of 7 reaction cycles showed that the encapsulated PAL was stable. Nevertheless, the K m value of encapsulated PAL in biomimetic silica was higher than that of the free PAL due to lower total surface area and increased mass transfer resistance.
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Affiliation(s)
- Jiandong Cui
- Research Center for Fermentation Engineering of Hebei, College of Bioscience and Bioengineering, Hebei University of Science and Technology, 70 Yuhua East Road, Shijiazhang, 050018, People's Republic of China,
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Cui JD, Li LL, Zhao YM. Simple Technique for Preparing Stable and Recyclable Cross-Linked Enzyme Aggregates with Crude-Pored Microspherical Silica Core. Ind Eng Chem Res 2014. [DOI: 10.1021/ie5021206] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jian Dong Cui
- Research
Center for Fermentation Engineering of Hebei, College of Bioscience
and Bioengineering, Hebei University of Science and Technology, 26 YuXiang Street, Shijiazhang 050000, P. R. China
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, HaiDian District, Beijing, 100080, P. R. China
- Key
Laboratory of Industry Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, 29 Thirteenth Street, Tianjin 300457, P. R. China
| | - Lian Lian Li
- Research
Center for Fermentation Engineering of Hebei, College of Bioscience
and Bioengineering, Hebei University of Science and Technology, 26 YuXiang Street, Shijiazhang 050000, P. R. China
| | - Ya Min Zhao
- Research
Center for Fermentation Engineering of Hebei, College of Bioscience
and Bioengineering, Hebei University of Science and Technology, 26 YuXiang Street, Shijiazhang 050000, P. R. China
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Cui JD, Cui LL, Zhang SP, Zhang YF, Su ZG, Ma GH. Hybrid magnetic cross-linked enzyme aggregates of phenylalanine ammonia lyase from Rhodotorula glutinis. PLoS One 2014; 9:e97221. [PMID: 24825453 PMCID: PMC4019550 DOI: 10.1371/journal.pone.0097221] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/16/2014] [Indexed: 11/18/2022] Open
Abstract
Novel hybrid magnetic cross-linked enzyme aggregates of phenylalanine ammonia lyase (HM-PAL-CLEAs) were developed by co-aggregation of enzyme aggregates with magnetite nanoparticles and subsequent crosslinking with glutaraldehyde. The HM-PAL-CLEAs can be easily separated from the reaction mixture by using an external magnetic field. Analysis by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) indicated that PAL-CLEAs were inlayed in nanoparticle aggregates. The HM-PAL-CLEAs revealed a broader limit in optimal pH compared to free enzyme and PAL-CLEAs. Although there is no big difference in Km of enzyme in CLEAs and HM-PAL-CLEAs, Vmax of HM-PAL-CLEAs is about 1.75 times higher than that of CLEAs. Compared with free enzyme and PAL-CLEAs, the HM-PAL-CLEAs also exhibited the highest thermal stability, denaturant stability and storage stability. The HM-PAL-CLEAs retained 30% initial activity even after 11 cycles of reuse, whereas PAL-CLEAs retained 35% of its initial activity only after 7 cycles. These results indicated that hybrid magnetic CLEAs technology might be used as a feasible and efficient solution for improving properties of immobilized enzyme in industrial application.
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Affiliation(s)
- Jian dong Cui
- Research Center for Fermentation Engineering of Hebei, College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhang, P R China
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, HaiDian district, Beijing, P R China
- Key Laboratory of Industry Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tai Da Development Area, Tianjin, P R China
| | - Li li Cui
- Research Center for Fermentation Engineering of Hebei, College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhang, P R China
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, HaiDian district, Beijing, P R China
| | - Song ping Zhang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, HaiDian district, Beijing, P R China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Yu fei Zhang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, HaiDian district, Beijing, P R China
| | - Zhi guo Su
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, HaiDian district, Beijing, P R China
| | - Guang hui Ma
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, HaiDian district, Beijing, P R China
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