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Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023; 66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.
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Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - David Kovar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Yun Ding
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
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2
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Ferreira J, Castro F. High-Throughput Protein Crystallization in an Integrated Droplet-Based Microfluidic Platform. Methods Mol Biol 2023; 2652:347-359. [PMID: 37093486 DOI: 10.1007/978-1-0716-3147-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
We present an integrated droplet-based microfluidic platform for high-throughput protein crystallization experimentation. The device consists of commercially available micro-junctions and PFA tubing assembled for different functions: droplet generation, incubation, and observation. Herein, we describe a complete methodology to generate hundreds of droplets with controlled properties (i.e., size, generation frequency, and composition). Therefore, multiple trials can be carried out under controlled experimental conditions for the screening and optimization of protein crystallization conditions.
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Affiliation(s)
- Joana Ferreira
- CEFT - Transport Phenomena Research Center, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Filipa Castro
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
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3
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Dong J, Wang J, Wang S, Wen J. Experimental Investigation of p-Xylene Crystallization Characteristics and Ultrasound Enhancement Mechanism. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c03204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jiayu Dong
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi710049, China
| | - Jiarui Wang
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi710049, China
| | - Simin Wang
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi710049, China
| | - Jian Wen
- School of Energy and Power Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi710049, China
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4
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Savchenko M, Hurtado M, Lopez-Lopez MT, Rus G, Álvarez de Cienfuegos L, Melchor J, Gavira JA. Lysozyme crystallization in hydrogel media under ultrasound irradiation. ULTRASONICS SONOCHEMISTRY 2022; 88:106096. [PMID: 35868210 PMCID: PMC9305616 DOI: 10.1016/j.ultsonch.2022.106096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 05/20/2023]
Abstract
Sonocrystallization implies the application of ultrasound radiation to control the nucleation and crystal growth depending on the actuation time and intensity. Its application allows to induce nucleation at lower supersaturations than required under standard conditions. Although extended in inorganic and organic crystallization, it has been scarcely explored in protein crystallization. Now, that industrial protein crystallization is gaining momentum, the interest on new ways to control protein nucleation and crystal growth is advancing. In this work we present the development of a novel ultrasound bioreactor to study its influence on protein crystallization in agarose gel. Gel media minimize convention currents and sedimentation, favoring a more homogeneous and stable conditions to study the effect of an externally generated low energy ultrasonic irradiation on protein crystallization avoiding other undesired effects such as temperature increase, introduction of surfaces which induce nucleation, destructive cavitation phenomena, etc. In-depth statistical analysis of the results has shown that the impact of ultrasound in gel media on crystal size populations are statistically significant and reproducible.
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Affiliation(s)
- Mariia Savchenko
- Universidad de Granada (UGR), Departamento de Química Orgánica, Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ), C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain; Universidad de Granada (UGR), Departamento de Física Aplicada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain; Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-UGR), UEQ, Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Manuel Hurtado
- Universidad de Granada (UGR), Departamento de Estadística e Investigación Operativa, Spain; Departamento de Mecánica de Estructuras e Ingeniería Hidráulica, Ultrasonics Lab TEP-959, Universidad de Granada, Spain; Unidad de Excelencia Modeling Nature MNAT, Universidad de Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain
| | - Modesto T Lopez-Lopez
- Universidad de Granada (UGR), Departamento de Física Aplicada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain
| | - Guillermo Rus
- Departamento de Mecánica de Estructuras e Ingeniería Hidráulica, Ultrasonics Lab TEP-959, Universidad de Granada, Spain; Unidad de Excelencia Modeling Nature MNAT, Universidad de Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain
| | - Luis Álvarez de Cienfuegos
- Universidad de Granada (UGR), Departamento de Química Orgánica, Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ), C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain.
| | - Juan Melchor
- Universidad de Granada (UGR), Departamento de Estadística e Investigación Operativa, Spain; Unidad de Excelencia Modeling Nature MNAT, Universidad de Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain.
| | - José A Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-UGR), UEQ, Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain.
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5
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Zhang G, Zhu C, Walayat N, Nawaz A, Ding Y, Liu J. Recent development in evaluation methods, influencing factors and control measures for freeze denaturation of food protein. Crit Rev Food Sci Nutr 2022; 63:5874-5889. [PMID: 34996325 DOI: 10.1080/10408398.2022.2025534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Frozen storage is most widely adopted preservation method to maintain food freshness and nutritional attributes. However, at low temperature, food is prone to chemical changes such as protein denaturation and lipid oxidation. In this review, we discussed the reasons and influencing factors that cause protein denaturation during freezing, such as freezing rate, freezing temperature, freezing method, etc. From the previous literatures, it was found that frozen storage is commonly used to prevent freeze induced protein denaturation by adding cryoprotectants to food. Some widely used cryoprotectants (for example, sucrose and sorbitol) have been reported with higher sweetness and weaker cryoprotective abilities. Therefore, this article comprehensively discusses the new cryopreservation methods and providing comparative study to the conventional frozen storage. Meanwhile, this article sheds light on the freeze induced alterations, such as change in functional and gelling properties. In addition, this article could be helpful for the prolonged frozen storage of food with minimum quality related changes. Meanwhile, it could also improve the commercial values and consumer satisfaction of frozen food as well.
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Affiliation(s)
- Gaopeng Zhang
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, P.R. China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, P.R. China
- National R & D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, P.R. China
| | - Chunyan Zhu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, P.R. China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, P.R. China
- National R & D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, P.R. China
| | - Noman Walayat
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, P.R. China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, P.R. China
- National R & D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, P.R. China
| | - Asad Nawaz
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, P.R. China
| | - Yuting Ding
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, P.R. China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, P.R. China
- National R & D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, P.R. China
| | - Jianhua Liu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, P.R. China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, P.R. China
- National R & D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, P.R. China
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6
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Liu J, Zhang CY, Liu Y, Wu XL, Zhang TD, Zhao FZ, Chen LL, Jin XQ, He JL, Yin DC. The dual function of impurity in protein crystallization. CrystEngComm 2022. [DOI: 10.1039/d1ce01535d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein crystallization could be promoted with a low concentration of impurities and inhibited with a high concentration of impurities, and this inhibition can be weakened by an audible sound.
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Affiliation(s)
- Jie Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR 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, PR China
| | - Yue Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Xiang-Long Wu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Tuo-Di Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Feng-Zhu Zhao
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Liang-Liang Chen
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Xiao-Qian Jin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Jin-Liang He
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR 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, PR China
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7
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Yu F, Mao Y, Zhao H, Zhang X, Wang T, Yuan M, Ding S, Wang N, Huang X, Hao H. Enhancement of Continuous Crystallization of Lysozyme through Ultrasound. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.1c00292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Fei Yu
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yafei Mao
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hongtu Zhao
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiunan Zhang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Ting Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Mingpu Yuan
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Suping Ding
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Na Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xin Huang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hongxun Hao
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
- School of Chemical Engineering and Technology, Hainan University, Haikou 570208, China
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8
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The critical role of agitation in moving from preliminary screening results to reproducible batch protein crystallisation. Chem Eng Res Des 2021. [DOI: 10.1016/j.cherd.2021.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Comparative evaluations of bulk seeded protein crystallization in batch versus continuous slug flow crystallizers. Chem Eng Res Des 2021. [DOI: 10.1016/j.cherd.2021.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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