1
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Imai M, Colas K, Suga H. Protein Grafting Techniques: From Peptide Epitopes to Lasso-Grafted Neobiologics. Chempluschem 2024:e202400152. [PMID: 38693599 DOI: 10.1002/cplu.202400152] [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: 02/26/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
Protein engineering techniques have vastly expanded their domain of impact, notably following the success of antibodies. Likewise, smaller peptide therapeutics have carved an increasingly significant niche for themselves in the pharmaceutical landscape. The concept of grafting such peptides onto larger protein scaffolds, thus harvesting the advantages of both, has given rise to a variety of protein engineering strategies that are reviewed herein. We also describe our own "Lasso-Grafting" approach, which combines traditional grafting concepts with mRNA display to streamline the production of multiple grafted drug candidates for virtually any target.
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Affiliation(s)
- Mikio Imai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kilian Colas
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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2
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Agosto-Maldonado A, Guo J, Niu W. Engineering carboxylic acid reductases and unspecific peroxygenases for flavor and fragrance biosynthesis. J Biotechnol 2024; 385:1-12. [PMID: 38428504 PMCID: PMC11062483 DOI: 10.1016/j.jbiotec.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
Emerging consumer demand for safer, more sustainable flavors and fragrances has created new challenges for the industry. Enzymatic syntheses represent a promising green production route, but the broad application requires engineering advancements for expanded diversity, improved selectivity, and enhanced stability to be cost-competitive with current methods. This review discusses recent advances and future outlooks for enzyme engineering in this field. We focus on carboxylic acid reductases (CARs) and unspecific peroxygenases (UPOs) that enable selective productions of complex flavor and fragrance molecules. Both enzyme types consist of natural variants with attractive characteristics for biocatalytic applications. Applying protein engineering methods, including rational design and directed evolution in concert with computational modeling, present excellent examples for property improvements to unleash the full potential of enzymes in the biosynthesis of value-added chemicals.
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Affiliation(s)
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States.
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3
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Zhao Y, Chen K, Yang H, Wang Y, Liao X. Semirational Design Based on Consensus Sequences to Balance the Enzyme Activity-Stability Trade-Off. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6454-6462. [PMID: 38477968 DOI: 10.1021/acs.jafc.3c08620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
In this study, the phenomenon of the stability-activity trade-off, which is increasingly recognized in enzyme engineering, was explored. Typically, enhanced stability in enzymes correlates with diminished activity. Utilizing Rosa roxburghii copper-zinc superoxide dismutase (RrCuZnSOD) as a model, single-site mutations were introduced based on a semirational design derived from consensus sequences. The initial set of mutants was selected based on activity, followed by combinatorial mutation. This approach yielded two double-site mutants, D25/A115T (18,688 ± 206 U/mg) and A115T/S135P (18,095 ± 1556 U/mg), exhibiting superior enzymatic properties due to additive and synergistic effects. These mutants demonstrated increased half-lives (T1/2) at 80 °C by 1.2- and 1.6-fold, respectively, and their melting temperatures (Tm) rose by 3.4 and 2.5 °C, respectively, without any loss in activity relative to the wild type. Via an integration of structural analysis and molecular dynamics simulations, we elucidated the underlying mechanism facilitating the concurrent enhancement of both thermostability and enzymatic activity.
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Affiliation(s)
- Yang Zhao
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Sichuan Advanced Agricultural and Industrial Institute, China Agricultural University, Chengdu 611400, China
| | - Kun Chen
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Haixia Yang
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yongtao Wang
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaojun Liao
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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4
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Fusco F, Pires MC, Lopes APY, Alves VDS, Gonçalves VM. Influence of the mRNA initial region on protein production: a case study using recombinant detoxified pneumolysin as a model. Front Bioeng Biotechnol 2024; 11:1304965. [PMID: 38260740 PMCID: PMC10800503 DOI: 10.3389/fbioe.2023.1304965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Recombinant proteins are of great importance in modern society, mostly as biopharmaceutical products. However, challenging and complex processes with low production yield are major drawbacks. Normally, the optimization to overcome these obstacles is focused on bioreactor and purification processes, and the biomolecular aspects are neglected, seen as less important. In this work, we present how the 5' mRNA secondary structure region can be relevant for translation and, therefore, protein production. For this, Escherichia coli BL21(DE3) clones, producing recombinant detoxified pneumolysin (PdT) with and without the N-terminal His-tag, were cultivated in 10-L bioreactors. Another version of the pdt gene (version 2) with synonymous changes in the 5'-end nucleotide sequence was also obtained. Protein production, plasmid stability, carbon sources, and acetic acid were quantified during the cultures. Furthermore, in silico mRNA analyses were performed using TIsigner and RNAfold. The results showed that the His-tag presence at the N-terminus generated a minimum 1.5-fold increase in target protein synthesis, which was explained by the in silico mRNA analyses that returned an mRNA secondary structure easier to translate and, therefore, higher protein production than without the His-tag. The pdt gene version 2 showed lower 5' mRNA opening energy than version 1, allowing higher PdT production even without a tag. This work reveals that simple mRNA analyses during heterologous gene design and production steps can help reach high-recombinant protein titers in a shorter time than using only traditional bioprocess optimization strategies.
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Affiliation(s)
- Filipe Fusco
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | - Manuella Cazelato Pires
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Vítor dos Santos Alves
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
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5
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Ma Z, Mu K, Zhu J, Xiao M, Wang L, Jiang X. Molecular dynamics simulations identify the topological weak spots of a protease CN2S8A. J Mol Graph Model 2023; 124:108571. [PMID: 37487372 DOI: 10.1016/j.jmgm.2023.108571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
Thermophilic enzymes are highly desired in industrial applications due to their efficient catalytic activity at high temperature. However, most enzymes exhibit inferior thermostability and it remains challenging to identify the optimal sites for designing mutations to improve protein stability. To tackle this issue, we integrated topological analysis and all-atom molecular dynamics simulations to efficiently pinpoint the thermally-unstable regions in protein structures. Using a protease CN2S8A as the model, we analyzed the intramolecular hydrogen bonding interactions between adjacent secondary structure elements, and then identified the topological weak spots of CN2S8A where weak hydrogen bonding interactions were formed. To examine the role of these sites in protein structural stability, we designed three virtual mutations at different weak spots and characterized the effects of these mutations on the structural properties of CN2S8A. The results showed that all three mutations increased the protein structural stability. In conclusion, these findings provide a novel method to identify the topological weak spots of proteins, with implications in the rational design of biocatalysts with superior thermostability.
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Affiliation(s)
- Zhenyu Ma
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Kaijie Mu
- Biomedicine Discovery Institute, Monash University, Melbourne, 3500, Australia
| | - Jingyi Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China.
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6
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Golinski AW, Schmitz ZD, Nielsen GH, Johnson B, Saha D, Appiah S, Hackel BJ, Martiniani S. Predicting and Interpreting Protein Developability Via Transfer of Convolutional Sequence Representation. ACS Synth Biol 2023; 12:2600-2615. [PMID: 37642646 PMCID: PMC10829850 DOI: 10.1021/acssynbio.3c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Engineered proteins have emerged as novel diagnostics, therapeutics, and catalysts. Often, poor protein developability─quantified by expression, solubility, and stability─hinders utility. The ability to predict protein developability from amino acid sequence would reduce the experimental burden when selecting candidates. Recent advances in screening technologies enabled a high-throughput (HT) developability dataset for 105 of 1020 possible variants of protein ligand scaffold Gp2. In this work, we evaluate the ability of neural networks to learn a developability representation from a HT dataset and transfer this knowledge to predict recombinant expression beyond observed sequences. The model convolves learned amino acid properties to predict expression levels 44% closer to the experimental variance compared to a non-embedded control. Analysis of learned amino acid embeddings highlights the uniqueness of cysteine, the importance of hydrophobicity and charge, and the unimportance of aromaticity, when aiming to improve the developability of small proteins. We identify clusters of similar sequences with increased recombinant expression through nonlinear dimensionality reduction and we explore the inferred expression landscape via nested sampling. The analysis enables the first direct visualization of the fitness landscape and highlights the existence of evolutionary bottlenecks in sequence space giving rise to competing subpopulations of sequences with different developability. The work advances applied protein engineering efforts by predicting and interpreting protein scaffold expression from a limited dataset. Furthermore, our statistical mechanical treatment of the problem advances foundational efforts to characterize the structure of the protein fitness landscape and the amino acid characteristics that influence protein developability.
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Affiliation(s)
- Alexander W. Golinski
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Zachary D. Schmitz
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Gregory H. Nielsen
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Bryce Johnson
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Diya Saha
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Sandhya Appiah
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Stefano Martiniani
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY 10003
- Simons Center for Computational Physical Chemistry, Departments of Chemistry, New York University, New York, NY 10003
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10003
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7
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Qin H, King GJ, Borpatragohain P, Zou J. Developing multifunctional crops by engineering Brassicaceae glucosinolate pathways. PLANT COMMUNICATIONS 2023:100565. [PMID: 36823985 PMCID: PMC10363516 DOI: 10.1016/j.xplc.2023.100565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Glucosinolates (GSLs), found mainly in species of the Brassicaceae family, are one of the most well-studied classes of secondary metabolites. Produced by the action of myrosinase on GSLs, GSL-derived hydrolysis products (GHPs) primarily defend against biotic stress in planta. They also significantly affect the quality of crop products, with a subset of GHPs contributing unique food flavors and multiple therapeutic benefits or causing disagreeable food odors and health risks. Here, we explore the potential of these bioactive functions, which could be exploited for future sustainable agriculture. We first summarize our accumulated understanding of GSL diversity and distribution across representative Brassicaceae species. We then systematically discuss and evaluate the potential of exploited and unutilized genes involved in GSL biosynthesis, transport, and hydrolysis as candidate GSL engineering targets. Benefiting from available information on GSL and GHP functions, we explore options for multifunctional Brassicaceae crop ideotypes to meet future demand for food diversification and sustainable crop production. An integrated roadmap is subsequently proposed to guide ideotype development, in which maximization of beneficial effects and minimization of detrimental effects of GHPs could be combined and associated with various end uses. Based on several use-case examples, we discuss advantages and limitations of available biotechnological approaches that may contribute to effective deployment and could provide novel insights for optimization of future GSL engineering.
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Affiliation(s)
- Han Qin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | | | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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8
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Yu H, Luo X. IPPF-FE: an integrated peptide and protein function prediction framework based on fused features and ensemble models. Brief Bioinform 2023; 24:6834141. [PMID: 36403184 DOI: 10.1093/bib/bbac476] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/23/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022] Open
Abstract
The prediction of peptide and protein function is important for research and industrial applications, and many machine learning methods have been developed for this purpose. The existing models have encountered many challenges, including the lack of effective and comprehensive features and the limited applicability of each model. Here, we introduce an Integrated Peptide and Protein function prediction Framework based on Fused features and Ensemble models (IPPF-FE), which can accurately capture the relationship between features and labels. The results indicated that IPPF-FE outperformed existing state-of-the-art (SOTA) models on more than 8 different categories of peptide and protein tasks. In addition, t-distributed Stochastic Neighbour Embedding demonstrated the advantages of IPPF-FE. We anticipate that our method will become a versatile tool for peptide and protein prediction tasks and shed light on the future development of related models. The model is open source and available in the GitHub repository https://github.com/Luo-SynBioLab/IPPF-FE.
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Affiliation(s)
- Han Yu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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9
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Mathieu‐Gaedke M, Böker A, Glebe U. How to Characterize the Protein Structure and Polymer Conformation in Protein‐Polymer Conjugates – a Perspective. MACROMOL CHEM PHYS 2023. [DOI: 10.1002/macp.202200353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Maria Mathieu‐Gaedke
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Alexander Böker
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Ulrich Glebe
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
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10
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Rational engineering of a metalloprotease to enhance thermostability and activity. Enzyme Microb Technol 2023; 162:110123. [DOI: 10.1016/j.enzmictec.2022.110123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022]
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11
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Keshavarzi B, Krause T, Schwarzenberger K, Eckert K, Ansorge-Schumacher MB, Heitkam S. Wash water addition on protein foam for removal of soluble impurities in foam fractionation process. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.130215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Panchal N, Jain V, Elliott R, Flint Z, Worsley P, Duran C, Banerjee T, Santra S. Plasmon-Enhanced Bimodal Nanosensors: An Enzyme-Free Signal Amplification Strategy for Ultrasensitive Detection of Pathogens. Anal Chem 2022; 94:13968-13977. [PMID: 36153970 DOI: 10.1021/acs.analchem.2c03215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Increasing foodborne illnesses have led to global health and economic burdens. E. coli O157:H7 is one of the most common disease-provoking pathogens and known to be lethal Shiga toxin-producing E. coli (STEC) strains. With a low infection dose in addition to person-to-person transmission, STEC infections are easily spread. As a result, specific and rapid testing methods to identify foodborne pathogens are urgently needed. Nanozymes have emerged as enzyme-mimetic nanoparticles, demonstrating intrinsic catalytic activity that could allow for rapid, specific, and accurate pathogen identification in the agrifood industry. In this study, we developed a sensitive nanoplatform based on the traditional ELISA assay with the synergistic properties of gold and iron oxide nanozymes, replacing the conventional enzyme horseradish peroxidase (HRP). We designed an easily interchangeable sandwich ELISA composed of a novel, multifunctional magneto-plasmonic nanosensor (MPnS) with target antibodies (MPnS-Ab). Our experiments demonstrate a 100-fold increase in catalytic activity in comparison to HRP with observable color changes within 15 min. Results further indicate that the MPnS-Ab is highly specific for E. coli O157:H7. Additionally, effective translatability of catalytic activity of the MPnS technology in the lateral flow assay (LFA) platform is also demonstrated for E. coli O157:H7 detection. As nanozymes display more stability, tunable activity, and multi-functionality than natural enzymes, our platform could provide customizable, low-cost assay that combines high specificity with rapid detection for a variety of pathogens in a point-of-care setup.
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Affiliation(s)
- Nilamben Panchal
- Department of Chemistry, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, Kansas 66762, United States
| | - Vedant Jain
- Department of Chemistry, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, Kansas 66762, United States
| | - Rebekah Elliott
- Department of Chemistry, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, Kansas 66762, United States
| | - Zachary Flint
- Department of Chemistry and Biochemistry, Missouri State University, 901 S. National Avenue, Springfield, Missouri 65897, United States
| | - Paul Worsley
- Department of Chemistry, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, Kansas 66762, United States
| | - Caine Duran
- Department of Chemistry, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, Kansas 66762, United States
| | - Tuhina Banerjee
- Department of Chemistry and Biochemistry, Missouri State University, 901 S. National Avenue, Springfield, Missouri 65897, United States
| | - Santimukul Santra
- Department of Chemistry, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, Kansas 66762, United States
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13
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Kim D, Noh MH, Park M, Kim I, Ahn H, Ye DY, Jung GY, Kim S. Enzyme activity engineering based on sequence co-evolution analysis. Metab Eng 2022; 74:49-60. [PMID: 36113751 DOI: 10.1016/j.ymben.2022.09.001] [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: 05/17/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
The utility of engineering enzyme activity is expanding with the development of biotechnology. Conventional methods have limited applicability as they require high-throughput screening or three-dimensional structures to direct target residues of activity control. An alternative method uses sequence evolution of natural selection. A repertoire of mutations was selected for fine-tuning enzyme activities to adapt to varying environments during the evolution. Here, we devised a strategy called sequence co-evolutionary analysis to control the efficiency of enzyme reactions (SCANEER), which scans the evolution of protein sequences and direct mutation strategy to improve enzyme activity. We hypothesized that amino acid pairs for various enzyme activity were encoded in the evolutionary history of protein sequences, whereas loss-of-function mutations were avoided since those are depleted during the evolution. SCANEER successfully predicted the enzyme activities of beta-lactamase and aminoglycoside 3'-phosphotransferase. SCANEER was further experimentally validated to control the activities of three different enzymes of great interest in chemical production: cis-aconitate decarboxylase, α-ketoglutaric semialdehyde dehydrogenase, and inositol oxygenase. Activity-enhancing mutations that improve substrate-binding affinity or turnover rate were found at sites distal from known active sites or ligand-binding pockets. We provide SCANEER to control desired enzyme activity through a user-friendly webserver.
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Affiliation(s)
- Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Minhyuk Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Inhae Kim
- ImmunoBiome Inc., Pohang, South Korea
| | - Hyunsoo Ahn
- Graduate School of Artificial Intelligence, Pohang University of Science and Technology, Pohang, South Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, South Korea; Institute of Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, South Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea.
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea; Graduate School of Artificial Intelligence, Pohang University of Science and Technology, Pohang, South Korea; Institute of Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, South Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea.
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14
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Unlocking the access to oxidized coenzyme A via a single-step green membrane-based purification. Sci Rep 2022; 12:12991. [PMID: 35906370 PMCID: PMC9338019 DOI: 10.1038/s41598-022-17250-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022] Open
Abstract
A new membrane-based strategy to purify oxidized coenzyme A ((CoAS)2) from adenosine triphosphate (ATP), adenosine diphosphate (ADP) and adenosine monophosphate (AMP) has been developed. Commercially available membranes were screened and studied (permeate flux and overall compounds retention) which allowed the identification of one efficient membrane (GK from Suez Water Technologies & Solutions). Different total compounds concentrations solutions were used in the system in order to find the following working conditions: 4 bars with a total compounds solution of 5.19 g L−1. Applying these conditions to a dia-filtration set-up allowed us to reach 68% pure (CoAS)2 in 4.8 diafiltration volumes (DV) and a 95% (CoAS)2 purity can be predicted in 8.5 DV. A comparative study of green metrics—i.e. process mass index (PMI)—of the classic chromatography vs the membrane-based one demonstrated the great advantages of the latter in terms of sustainability. This strategy unlocks the access to the essential and central cofactor that is coenzyme A.
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15
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Horne J, Shukla D. Recent Advances in Machine Learning Variant Effect Prediction Tools for Protein Engineering. Ind Eng Chem Res 2022; 61:6235-6245. [DOI: 10.1021/acs.iecr.1c04943] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jesse Horne
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
- Department of Bioengineering, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
- Department of Plant Biology, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
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16
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Microbial Peptidase in Food Processing: Current State of the Art and Future Trends. Catal Letters 2022. [DOI: 10.1007/s10562-022-03965-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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17
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Bailey AO, Huguet R, Mullen C, Syka JEP, Russell WK. Ion-Ion Charge Reduction Addresses Multiple Challenges Common to Denaturing Intact Mass Analysis. Anal Chem 2022; 94:3930-3938. [PMID: 35189062 DOI: 10.1021/acs.analchem.1c04973] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Complete LC-MS-based protein primary sequence characterization requires measurement of intact protein profiles under denaturing and/or reducing conditions. To address issues of protein overcharging of unstructured proteins under acidic, denaturing conditions and sample heterogeneity (macro- and micro-scales) which often confound denaturing intact mass analysis of a wide variety of protein samples, we propose the use of broadband isolation of entire charge state distributions of intact proteins followed by ion-ion proton transfer charge reduction, which we have termed "full scan PTCR" (fsPTCR). Using rapid denaturing size exclusion chromatography coupled to fsPTCR-Orbitrap MS and time-resolved deconvolution data analysis, we demonstrate a strategy for method optimization, leading to significant analytical advantages over conventional MS1. Denaturing analysis of the flexible bacterial translation initiation factor 2 (91 kDa) using fsPTCR reduced overcharging and showed an 11-fold gain in S/N compared to conventional MS1. Analysis by fsPTCR-MS of the microheterogeneous glycoprotein fetuin revealed twice as many proteoforms as MS1 (112 vs 56). In a macroheterogeneous mixture of proteins ranging from 14 to 148 kDa, fsPTCR provided more than 10-fold increased sensitivity and quantitative accuracy for diluted bovine serum albumin (66 kDa). Finally, our analysis shows that collisional gas pressure is a key parameter which can be utilized during fsPTCR to retain or remove larger proteins from acquired spectra.
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Affiliation(s)
- Aaron O Bailey
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Christopher Mullen
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - John E P Syka
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - William K Russell
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
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18
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Freitas AI, Domingues L, Aguiar TQ. Tag-mediated single-step purification and immobilization of recombinant proteins toward protein-engineered advanced materials. J Adv Res 2022; 36:249-264. [PMID: 35127175 PMCID: PMC8799874 DOI: 10.1016/j.jare.2021.06.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Background The potential applications of protein-engineered functional materials are so wide and exciting that the interest in these eco-friendly advanced materials will further expand in the future. Tag-mediated protein purification/immobilization technologies have emerged as green and cost-effective approaches for the fabrication of such materials. Strategies that combine the purification and immobilization of recombinant proteins/peptides onto/into natural, synthetic or hybrid materials in a single-step are arising and attracting increasing interest. Aim of Review This review highlights the most significant advances of the last 5 years within the scope of tag-mediated protein purification/immobilization and elucidates their contributions for the development of efficient single-step purification and immobilization strategies. Recent progresses in the field of protein-engineered materials created using innovative protein-tag combinations and future opportunities created by these new technologies are also summarized and identified herein. Key Scientific Concepts of Review Protein purification/immobilization tags present a remarkable ability to establish specific non-covalent/covalent interactions between solid materials and biological elements, which prompted the creation of tailor-made and advanced functional materials, and of next-generation hybrid materials. Affinity tags can bind to a wide range of materials (of synthetic, natural or hybrid nature), being most suitable for protein purification. Covalently binding tags are most suitable for long-term protein immobilization, but can only bind naturally to protein-based materials. Hybrid affinity-covalently binding tags have allowed efficient one-step purification and immobilization of proteins onto different materials, as well as the development of innovative protein-engineered materials. Self-aggregating tags have been particularly useful in combination with other tags for generating protein-engineered materials with self-assembling, flexible and/or responsive properties. While these tags have been mainly explored for independent protein purification, immobilization or functionalization purposes, efficient strategies that combine tag-mediated purification and immobilization/functionalization in a single-step will be essential to guarantee the sustainable manufacturing of advanced protein-engineered materials.
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Affiliation(s)
- Ana I. Freitas
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Tatiana Q. Aguiar
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
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19
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20
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Liu X, Liu J, Lei D, Zhao GR. Modular metabolic engineering for production of phloretic acid, phloretin and phlorizin in Escherichia coli. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2021.116931] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Protein-like particles through nanoprecipitation of mixtures of polymers of opposite charge. J Colloid Interface Sci 2021; 607:1786-1795. [PMID: 34600342 DOI: 10.1016/j.jcis.2021.09.080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/23/2022]
Abstract
HYPOTHESIS Polymer nanoparticles (NPs) have a very high potential for applications notably in the biomedical field. However, synthetic polymer NPs cannot yet concurrence the functionalities of proteins, their natural counterparts, notably in terms of size, control over internal structure and interactions with biological environments. We hypothesize that kinetic trapping of polymers bearing oppositely charged groups in NPs could bring a new level of control and allow mimicking the surfaces of proteins. EXPERIMENTS Here, the assembly of mixed-charge polymer NPs through nanoprecipitation of mixtures of oppositely charged polymers is studied. Two series of copolymers made of ethyl methacrylate and 1 to 25 mol% of either methacrylic acid or a trimethylammonium bearing methacrylate are synthesized. These carboxylic acid or trimethylammonium bearing polymers are then mixed in different ratios and nanoprecipitated. The influence of the charge fraction, mixing ratio of the polymers, and precipitation conditions on NP size and surface charge is studied. FINDINGS Using this approach, NPs of less than 25 nm with tunable surface charge from +40 mV to -40 mV are assembled. The resulting NPs are sensitive to pH and certain NP formulations have an isoelectric point allowing repeated charge reversal. Encapsulation of fluorescent dyes yields very bright fluorescent NPs, whose interactions with cells are studied through fluorescence microscopy. The obtained results show the potential of nanoprecipitation of oppositely charged polymers for the design of NPs with precisely tuned surface properties.
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22
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Wu H, Chen Q, Zhang W, Mu W. Overview of strategies for developing high thermostability industrial enzymes: Discovery, mechanism, modification and challenges. Crit Rev Food Sci Nutr 2021; 63:2057-2073. [PMID: 34445912 DOI: 10.1080/10408398.2021.1970508] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biocatalysts such as enzymes are environmentally friendly and have substrate specificity, which are preferred in the production of various industrial products. However, the strict reaction conditions in industry including high temperature, organic solvents, strong acids and bases and other harsh environments often destabilize enzymes, and thus substantially compromise their catalytic functions, and greatly restrict their applications in food, pharmaceutical, textile, bio-refining and feed industries. Therefore, developing industrial enzymes with high thermostability becomes very important in industry as thermozymes have more advantages under high temperature. Discovering new thermostable enzymes using genome sequencing, metagenomics and sample isolation from extreme environments, or performing molecular modification of the existing enzymes with poor thermostability using emerging protein engineering technology have become an effective means of obtaining thermozymes. Based on the thermozymes as biocatalytic chips in industry, this review systematically analyzes the ways to discover thermostable enzymes from extreme environment, clarifies various interaction forces that will affect thermal stability of enzymes, and proposes different strategies to improve enzymes' thermostability. Furthermore, latest development in the thermal stability modification of industrial enzymes through rational design strategies is comprehensively introduced from structure-activity relationship point of view. Challenges and future research perspectives are put forward as well.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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23
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Kikani BA, Singh SP. Amylases from thermophilic bacteria: structure and function relationship. Crit Rev Biotechnol 2021; 42:325-341. [PMID: 34420464 DOI: 10.1080/07388551.2021.1940089] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Amylases hydrolyze starch to diverse products including dextrins and progressively smaller polymers of glucose units. Thermally stable amylases account for nearly 25% of the enzyme market. This review highlights the structural attributes of the α-amylases from thermophilic bacteria. Heterologous expression of amylases in suitable hosts is discussed in detail. Further, specific value maximization approaches, such as protein engineering and immobilization of the amylases are discussed in order to improve its suitability for varied applications on a commercial scale. The review also takes into account of the immobilization of the amylases on nanomaterials to increase the stability and reusability of the enzymes. The function-based metagenomics would provide opportunities for searching amylases with novel characteristics. The review is expected to explore novel amylases for future potential applications.
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Affiliation(s)
- Bhavtosh A Kikani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, India.,P.D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Changa, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, India
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24
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Selective Adsorption and Separation of Proteins by Ligand-Modified Nanofiber Fabric. Polymers (Basel) 2021; 13:polym13142313. [PMID: 34301069 PMCID: PMC8309411 DOI: 10.3390/polym13142313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/10/2021] [Accepted: 07/11/2021] [Indexed: 01/14/2023] Open
Abstract
Electrospun polyvinyl alcohol (PVA) nanofiber fabric was modified by Cibacron Blue F3GA (CB) to enhance the affinity of the fabric. Batch experiments were performed to study the nanofiber fabric's bovine hemoglobin (BHb) adsorption capacity at different protein concentrations before and after modification. The maximum BHb adsorption capacity of the modified nanofiber fabric was 686 mg/g, which was much larger than the 58 mg/g of the original fabric. After that, the effect of feed concentration and permeation rate on the dynamic adsorption behaviors for BHb of the nanofiber fabric was investigated. The pH impact on BHb and bovine serum albumin (BSA) adsorption was examined by static adsorption experiments of single protein solutions. The selective separation experiments of the BHb-BSA binary solution were carried out at the optimal pH value, and a high selectivity factor of 5.45 for BHb was achieved. Finally, the reusability of the nanofiber fabric was examined using three adsorption-elution cycle tests. This research demonstrated the potential of the CB-modified PVA nanofiber fabric in protein adsorption and selective separation.
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25
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Adebami GE, Kuila A, Ajunwa OM, Fasiku SA, Asemoloye MD. Genetics and metabolic engineering of yeast strains for efficient ethanol production. J FOOD PROCESS ENG 2021. [DOI: 10.1111/jfpe.13798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Arindam Kuila
- Department of Bioscience and Biotechnology Banasthali University Vanasthali India
| | - Obinna M. Ajunwa
- Department of Microbiology Modibbo Adama University of Technology Yola Nigeria
| | - Samuel A. Fasiku
- Department of Biological Sciences Ajayi Crowther University Oyo Nigeria
| | - Michael D. Asemoloye
- Department of Pharmaceutical Science and Technology Tianjin University Tianjin China
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26
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Recent applications of bio-engineering principles to modulate the functionality of proteins in food systems. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.04.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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27
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Victorino da Silva Amatto I, Gonsales da Rosa-Garzon N, Antônio de Oliveira Simões F, Santiago F, Pereira da Silva Leite N, Raspante Martins J, Cabral H. Enzyme engineering and its industrial applications. Biotechnol Appl Biochem 2021; 69:389-409. [PMID: 33555054 DOI: 10.1002/bab.2117] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 01/03/2023]
Abstract
Recently, there has been an increase in the demand for enzymes with modified activity, specificity, and stability. Enzyme engineering is an important tool to meet the demand for enzymes adjusted to different industrial processes. Knowledge of the structure and function of enzymes guides the choice of the best strategy for engineering enzymes. Each enzyme engineering strategy, such as rational design, directed evolution, and semi-rational design, has specific applications, as well as limitations, which must be considered when choosing a suitable strategy. Engineered enzymes can be optimized for different industrial applications by choosing the appropriate strategy. This review features engineered enzymes that have been applied in food, animal feed, pharmaceuticals, medical applications, bioremediation, biofuels, and detergents.
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Affiliation(s)
- Isabela Victorino da Silva Amatto
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Nathalia Gonsales da Rosa-Garzon
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Flávio Antônio de Oliveira Simões
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Pharmaceutical Sciences Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Fernanda Santiago
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Nathália Pereira da Silva Leite
- Pharmaceutical Sciences Program, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, XUniversity of São Paulo, Ribeirão Preto, SP, Brazil
| | - Júlia Raspante Martins
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Pharmaceutical Sciences Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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28
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Ming H, Zhu MF, Li L, Liu QB, Yu WH, Wu ZQ, Liu YM. A review of solvent freeze-out technology for protein crystallization. CrystEngComm 2021. [DOI: 10.1039/d1ce00005e] [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
In this review, we summarize important advances in solvent freeze-out (SFO) technology for protein crystallization, including the background of SFO, its fundamental principle, and some crucial conditions and factors for optimizing SFO technology.
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Affiliation(s)
- Hui Ming
- School of Bioengineering
- Sichuan University of Science and Engineering
- Zigong 643000
- PR China
| | - Ming-Fu Zhu
- School of Physics
- Zhengzhou University
- Zhengzhou
- PR China
- Henan Chuitian Technology Co. Ltd
| | - Lu Li
- School of Bioengineering
- Sichuan University of Science and Engineering
- Zigong 643000
- PR China
| | - Qing-Bin Liu
- School of Bioengineering
- Sichuan University of Science and Engineering
- Zigong 643000
- PR China
| | - Wen-Hua Yu
- Sichuan Food Fermentation Industry Research and Design Institute
- Chengdu 611130
- PR China
| | - Zi-Qing Wu
- School of Medical Engineering
- Xinxiang Medical University
- Xinxiang 453003
- PR China
| | - Yong-Ming Liu
- School of Bioengineering
- Sichuan University of Science and Engineering
- Zigong 643000
- PR China
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29
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Abstract
Many flavin-dependent phenolic hydroxylases (monooxygenases) have been extensively investigated. Their crystal structures and reaction mechanisms are well understood. These enzymes belong to groups A and D of the flavin-dependent monooxygenases and can be classified as single-component and two-component flavin-dependent monooxygenases. The insertion of molecular oxygen into the substrates catalyzed by these enzymes is beneficial for modifying the biological properties of phenolic compounds and their derivatives. This chapter provides an in-depth discussion of the structural features of single-component and two-component flavin-dependent phenolic hydroxylases. The reaction mechanisms of selected enzymes, including 3-hydroxy-benzoate 4-hydroxylase (PHBH) and 3-hydroxy-benzoate 6-hydroxylase as representatives of single-component enzymes and 3-hydroxyphenylacetate 4-hydroxylase (HPAH) as a representative of two-component enzymes, are discussed in detail. This chapter comprises the following four main parts: general reaction, structures, reaction mechanisms, and enzyme engineering for biocatalytic applications. Enzymes belonging to the same group catalyze similar reactions but have different unique structural features to control their reactivity to substrates and the formation and stabilization of C4a-hydroperoxyflavin. Protein engineering has been employed to improve the ability to use these enzymes to synthesize valuable compounds. A thorough understanding of the structural and mechanistic features controlling enzyme reactivity is useful for enzyme redesign and enzyme engineering for future biocatalytic applications.
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Affiliation(s)
- Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, Thailand.
| | - Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand; Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Nakhon Pathom, Thailand
| | - Chanakan Tongsook
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
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30
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Agarwal PK, Bernard DN, Bafna K, Doucet N. Enzyme dynamics: Looking beyond a single structure. ChemCatChem 2020; 12:4704-4720. [PMID: 33897908 PMCID: PMC8064270 DOI: 10.1002/cctc.202000665] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 12/23/2022]
Abstract
Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.
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Affiliation(s)
- Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma 74078
- Arium BioLabs, 2519 Caspian Drive, Knoxville, Tennessee 37932
| | - David N. Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
| | - Khushboo Bafna
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
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31
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32
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Maluf JU, Fiorese ML, Maestre KL, Dos Passos FR, Finkler JK, Fleck JF, Borba CE. Optimization of the porcine liver enzymatic hydrolysis conditions. J FOOD PROCESS ENG 2020. [DOI: 10.1111/jfpe.13370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- José U. Maluf
- Chemical Engineering Postgraduate Program, State University of West Paraná, UNIOESTE Toledo Paraná Brazil
| | - Mônica L. Fiorese
- Chemical Engineering Postgraduate Program, State University of West Paraná, UNIOESTE Toledo Paraná Brazil
| | - Keiti L. Maestre
- Chemical Engineering Postgraduate Program, State University of West Paraná, UNIOESTE Toledo Paraná Brazil
| | - Fernanda R. Dos Passos
- Chemical Engineering Postgraduate Program, State University of West Paraná, UNIOESTE Toledo Paraná Brazil
| | - Joana K. Finkler
- Fishing Resources and Fishing Engineering Postgraduate Program, State University of West Paraná, UNIOESTE Toledo Paraná Brazil
| | | | - Carlos E. Borba
- Chemical Engineering Postgraduate Program, State University of West Paraná, UNIOESTE Toledo Paraná Brazil
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33
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Kamble A, Singh H. Different Methods of Soil DNA Extraction. Bio Protoc 2020. [DOI: 10.21769/bioprotoc.3521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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34
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Bilal M, Iqbal HMN. State-of-the-art strategies and applied perspectives of enzyme biocatalysis in food sector - current status and future trends. Crit Rev Food Sci Nutr 2020; 60:2052-2066. [PMID: 31210055 DOI: 10.1080/10408398.2019.1627284] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With the recent progress in biotechnology, a wide variety of novel enzymes with unique physicochemical properties and diverse applications has been introduced, and new application list continues to extend in the future. Enzymes obtained from microorganisms, including bacteria, fungi, yeast are widely applied in numerous food formulations for intensifying their texture and taste. Owing to several desirable characteristics such as easy, cost-efficient and stable production, microbial-derived enzymes are preferred source in contrast to animals or plants. Enzymatic processes have a considerable impact in controlling the characteristics such as (1) physiochemical properties, (2) rheological functionalities, (3) facile process as compared to the chemical-based processing, (4) no or minimal consumption of harsh chemicals, (5) overall cost-effective ratio, (6) sensory and flavor qualities, and (7) intensifying the stability, shelf life and overall quality of the product, etc. in the food industry. Also, enzyme-catalyzed processing has also been designed for new food applications such as extraction of bioactive compounds, nutrient-rich and texture improved foods production, and eliminating food safety hazards. Herein, we reviewed recent applications of food-processing enzymes and highlighted promising technologies to diversify their application range in food industries. Immobilization technology enabled biocatalysts to be used cost-effectively due to reusability with negligible or no activity loss. Integrated progress in novel enzyme discovery, and recombinant DNA technology, as well as protein engineering and bioprocess engineering strategies, are believed to rapidly propagate biocatalysis at industrial-scale food processing or green and sustainable chemical manufacturing.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Hafiz M N Iqbal
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, N.L., Mexico
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35
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Construction of a synthetic protein using PCR with a high essential amino acid content for nutritional purposes. Mol Biol Rep 2019; 46:1593-1601. [DOI: 10.1007/s11033-019-04604-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/16/2019] [Indexed: 01/08/2023]
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36
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Louwagie M, Kieffer-Jaquinod S, Brun V. Ultrasensitive Quantification of Recombinant Proteins Using AAA-MS. Methods Mol Biol 2019; 2030:1-10. [PMID: 31347105 DOI: 10.1007/978-1-4939-9639-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recombinant proteins are essential components of therapeutic, biotechnological, food, and household products. In some cases, recombinant proteins must be purified and their quantity and/or concentration precisely determined. In this chapter, we describe a protocol for the quantification of purified recombinant proteins. The protocol is based on a microwave-assisted acidic hydrolysis of the target protein followed by high-resolution mass spectrometry (HRMS) analysis of the hydrolytic products. Absolute quantification is obtained by adding controlled amounts of labeled amino acids that serve as standards.
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Affiliation(s)
| | | | - Virginie Brun
- Univ. Grenoble Alpes, CEA, Inserm, U1038 BIG-BGE, Grenoble, France.
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37
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38
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Childers MC, Daggett V. Insights from molecular dynamics simulations for computational protein design. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2017; 2:9-33. [PMID: 28239489 PMCID: PMC5321087 DOI: 10.1039/c6me00083e] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
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Affiliation(s)
| | - Valerie Daggett
- Corresponding author: , Phone: 1.206.685.7420, Fax: 1.206.685.3300
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