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Chen Q, Wu J, Wu Y, Wang Z, Zeng M, He Z, Chen J, Mu W. Rational Design of Loop Dynamics for a Barrel-Shaped Enzyme by Introducing Disulfide Bonds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38848490 DOI: 10.1021/acs.jafc.4c03493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Loop dynamics redesign is an important strategy to manipulate protein function. Cellobiose 2-epimerase (CE) and other members of its superfamily are widely used for diverse industrial applications. The structural feature of the loops connecting barrel helices contributes greatly to the differences in their functional characteristics. Inspired by the in-silico mutation with molecular dynamics (MD) simulation analysis, we propose a strategy for identifying disulfide bond mutation candidates based on the prediction of protein flexibility and residue-residue interaction. The most beneficial mutant with the newly introduced disulfide bond would simultaneously improve both its thermostability and its reaction propensity to the targeting isomerization product. The ratio of the isomerization/epimerization catalytic rate was improved from 4:103 to 9:22. MD simulation and binding free energy calculations were applied to provide insights into molecular recognition upon mutations. The comparative analysis of enzyme/substrate binding modes indicates that the altered catalytic reaction pathway is due to less efficient binding of the native product. The key residue responsible for the observed phenotype was identified by energy decomposition and was further confirmed by the mutation experiment. The rational design of the key loop region might be a promising strategy to alter the catalytic behavior of all (α/α)6-barrel-like proteins.
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Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Junhao Wu
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Yanchang Wu
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Zhaojun Wang
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Maomao Zeng
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Zhiyong He
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Jie Chen
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
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2
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Zhang H, Ye YH, Wang Y, Liu JZ, Jiao QC. A Bibliometric Analysis: Current Perspectives and Potential Trends of Enzyme Thermostability from 1991-2022. Appl Biochem Biotechnol 2024; 196:1211-1240. [PMID: 37382790 DOI: 10.1007/s12010-023-04615-6] [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] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
Thermostability is considered a crucial parameter to evaluate the viability of enzymes in industrial applications. Over the past 31 years, many studies have been reported on the thermostability of enzymes. However, there is no systematic bibliometric analysis of publications on the thermostability of enzymes. In this study, 16,035 publications related to the thermostability of enzymes were searched and collected, showing an increasing annual trend. China contributed the most publications, while the United States had the highest citation count. International Journal of Biological Macromolecules is the most productive journal in the research field. Moreover, Chinese acad sci and Khosro Khajeh are the most active institutions and prolific authors in the field, respectively. Analysis of references with the strongest citation bursts and keyword co-occurrences, magnetic nanoparticles, metal-organic frameworks, molecular dynamics, and rational design are current hot spots and significant future research directions. This study is the first comprehensive bibliometric analysis summarizing trends and developments in enzyme thermostability research. Our findings could provide scholars with an understanding of the fundamental knowledge framework of the field and identify recent potential hotspots and research trends that could facilitate the discovery of collaboration opportunities.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yun-Hui Ye
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yu Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jun-Zhong Liu
- Nanjing Institute for Comprehensive Utilization of Wild Plants, CHINA CO-OP, Nanjing, 211111, China.
| | - Qing-Cai Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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3
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Wu J, Lv J, Zhao L, Zhao R, Gao T, Xu Q, Liu D, Yu Q, Ma F. Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167028. [PMID: 37704131 DOI: 10.1016/j.scitotenv.2023.167028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ruofan Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Tian Gao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China
| | - Qi Xu
- PetroChina Fushun Petrochemical Company, Fushun 113000, China
| | - Dongbo Liu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Qiqi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China.
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4
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Wu C, Yu X, Zheng P, Chen P, Wu D. Rational Redesign of Chitosanase to Enhance Thermostability and Catalytic Activity to Produce Chitooligosaccharides with a Relatively High Degree of Polymerization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15213-15223. [PMID: 37793074 DOI: 10.1021/acs.jafc.3c04542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Chitooligosaccharides (hdpCOS) with a high degree of polymerization (hdp, DP 4-10) generally have greater biological activities than those of low-DP (ldp, DP 2-3) COS. Chitosanase from Bacillus amyloliquefaciens KCP2 (Csn46) can degrade chitosan to more hdpCOS at high temperature (70 °C), but low thermal stability at this temperature makes it unsuitable for industrial application; the wild-type enzyme can only produce COS (DP 2-4) at lower temperatures. Several thermostable mutants were obtained by modifying chitosanase using a comprehensive strategy based on a computer-aided mutant design. A combination of four beneficial single-point mutations (A129L/T175 V/K70T/D34G) to Csn46 was selected to obtain a markedly improved mutant, Mut4, with a half-life at 60 °C extended from 34.31 to 690.80 min, and the specific activity increased from 1671.73 to 3528.77 U/mg. Mut4 produced COS with DPs of 2-4 and 2-7 at 60 and 70 °C, respectively. Therefore, Mut4 has the potential to be applied to the industrial-scale preparation of hdpCOS with high biological activity.
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Affiliation(s)
- Changyun Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Xiaowei Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Pu Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Pengcheng Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Dan Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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5
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Ge F, Chen G, Qian M, Xu C, Liu J, Cao J, Li X, Hu D, Xu Y, Xin Y, Wang D, Zhou J, Shi H, Tan Z. Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14911-14930. [PMID: 37800676 DOI: 10.1021/acs.jafc.3c05029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
With the development of artificial intelligence (AI), tailoring methods for enzyme engineering have been widely expanded. Additional protocols based on optimized network models have been used to predict and optimize lipase production as well as properties, namely, catalytic activity, stability, and substrate specificity. Here, different network models and algorithms for the prediction and reforming of lipase, focusing on its modification methods and cases based on AI, are reviewed in terms of both their advantages and disadvantages. Different neural networks coupled with various algorithms are usually applied to predict the maximum yield of lipase by optimizing the external cultivations for lipase production, while one part is used to predict the molecule variations affecting the properties of lipase. However, few studies have directly utilized AI to engineer lipase by affecting the structure of the enzyme, and a set of research gaps needs to be explored. Additionally, future perspectives of AI application in enzymes, including lipase engineering, are deduced to help the redesign of enzymes and the reform of new functional biocatalysts. This review provides a new horizon for developing effective and innovative AI tools for lipase production and engineering and facilitating lipase applications in the food industry and biomass conversion.
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Affiliation(s)
- Feiyin Ge
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Gang Chen
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Minjing Qian
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Cheng Xu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jiao Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jiaqi Cao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Xinchao Li
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Die Hu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, People's Republic of China
| | - Yangsen Xu
- Dongtai Hanfangyuan Biotechnology Co. Ltd., Yancheng 224241, People's Republic of China
| | - Ya Xin
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Dianlong Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jia Zhou
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Hao Shi
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Zhongbiao Tan
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
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6
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Cheng W, Nian B. Computer-Aided Lipase Engineering for Improving Their Stability and Activity in the Food Industry: State of the Art. Molecules 2023; 28:5848. [PMID: 37570817 PMCID: PMC10421223 DOI: 10.3390/molecules28155848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
As some of the most widely used biocatalysts, lipases have exhibited extreme advantages in many processes, such as esterification, amidation, and transesterification reactions, which causes them to be widely used in food industrial production. However, natural lipases have drawbacks in terms of organic solvent resistance, thermostability, selectivity, etc., which limits some of their applications in the field of foods. In this systematic review, the application of lipases in various food processes was summarized. Moreover, the general structure of lipases is discussed in-depth, and the engineering strategies that can be used in lipase engineering are also summarized. The protocols of some classical methods are compared and discussed, which can provide some information about how to choose methods of lipase engineering. Thermostability engineering and solvent tolerance engineering are highlighted in this review, and the basic principles for improving thermostability and solvent tolerance are summarized. In the future, comput er-aided technology should be more emphasized in the investigation of the mechanisms of reactions catalyzed by lipases and guide the engineering of lipases. The engineering of lipase tunnels to improve the diffusion of substrates is also a promising prospect for further enhanced lipase activity and selectivity.
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Affiliation(s)
| | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China;
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7
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Boukid F, Ganeshan S, Wang Y, Tülbek MÇ, Nickerson MT. Bioengineered Enzymes and Precision Fermentation in the Food Industry. Int J Mol Sci 2023; 24:10156. [PMID: 37373305 DOI: 10.3390/ijms241210156] [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: 05/20/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Enzymes have been used in the food processing industry for many years. However, the use of native enzymes is not conducive to high activity, efficiency, range of substrates, and adaptability to harsh food processing conditions. The advent of enzyme engineering approaches such as rational design, directed evolution, and semi-rational design provided much-needed impetus for tailor-made enzymes with improved or novel catalytic properties. Production of designer enzymes became further refined with the emergence of synthetic biology and gene editing techniques and a plethora of other tools such as artificial intelligence, and computational and bioinformatics analyses which have paved the way for what is referred to as precision fermentation for the production of these designer enzymes more efficiently. With all the technologies available, the bottleneck is now in the scale-up production of these enzymes. There is generally a lack of accessibility thereof of large-scale capabilities and know-how. This review is aimed at highlighting these various enzyme-engineering strategies and the associated scale-up challenges, including safety concerns surrounding genetically modified microorganisms and the use of cell-free systems to circumvent this issue. The use of solid-state fermentation (SSF) is also addressed as a potentially low-cost production system, amenable to customization and employing inexpensive feedstocks as substrate.
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Affiliation(s)
- Fatma Boukid
- ClonBio Group Ltd., 6 Fitzwilliam Pl, D02 XE61 Dublin, Ireland
| | | | - Yingxin Wang
- Saskatchewan Food Industry Development Centre, Saskatoon, SK S7M 5V1, Canada
| | | | - Michael T Nickerson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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8
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Chi H, Zhu X, Shen J, Lu Z, Lu F, Lyu Y, Zhu P. Thermostability enhancement and insight of L-asparaginase from Mycobacterium sp. via consensus-guided engineering. Appl Microbiol Biotechnol 2023; 107:2321-2333. [PMID: 36843197 DOI: 10.1007/s00253-023-12443-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/28/2023]
Abstract
Acrylamide alleviation in food has represented as a critical issue due to its neurotoxic effect on human health. L-Asparaginase (ASNase, EC 3.5.1.1) is considered a potential additive for acrylamide alleviation in food. However, low thermal stability hinders the application of ASNase in thermal food processing. To obtain highly thermal stable ASNase for its industrial application, a consensus-guided approach combined with site-directed saturation mutation (SSM) was firstly reported to engineer the thermostability of Mycobacterium gordonae L-asparaginase (GmASNase). The key residues Gly97, Asn159, and Glu249 were identified for improving thermostability. The combinatorial triple mutant G97T/N159Y/E249Q (TYQ) displayed significantly superior thermostability with half-life values of 61.65 ± 8.69 min at 50 °C and 5.12 ± 1.66 min at 55 °C, whereas the wild-type was completely inactive at these conditions. Moreover, its Tm value increased by 8.59 °C from parent wild-type. Interestingly, TYQ still maintained excellent catalytic efficiency and specific activity. Further molecular dynamics and structure analysis revealed that the additional hydrogen bonds, increased hydrophobic interactions, and favorable electrostatic potential were essential for TYQ being in a more rigid state for thermostability enhancement. These results suggested that our strategy was an efficient engineering approach for improving fundamental properties of GmASNase and offering GmASNase as a potential agent for efficient acrylamide mitigation in food industry. KEY POINTS: • The thermostability of GmASNase was firstly improved by consensus-guided engineering. • The half-life and Tm value of triple mutant TYQ were significantly increased. • Insight on improved thermostability of TYQ was revealed by MD and structure analysis.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunbin Lyu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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9
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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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10
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Wang L, Gu J, Zhao W, Wang M, Ng KR, Lyu X, Yang R. Reshaping the Binding Pocket of Cellobiose 2-Epimerase for Improved Substrate Affinity and Isomerization Activity for Enabling Green Synthesis of Lactulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15879-15893. [PMID: 36475670 DOI: 10.1021/acs.jafc.2c06980] [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] [Indexed: 06/17/2023]
Abstract
Enzymatic isomerization of lactose into lactulose via cellobiose 2-epimerase (CE) could provide an eco-friendly route for the industrial production of lactulose, a valuable food prebiotic. However, poor substrate affinity for lactose and preference for epimerization over isomerization hinder this application. Previous studies on CE improvement have focused on random mutagenesis or active site rational design; little is known about the relationship between substrate binding and enzyme efficacy, which was hence the subject of this study. First, residues 372W and 308W were identified as key for disaccharide recognition in CEs based on crystal structure alignment of the N-acetyl-glucosamine 2-epimerase superfamily and site-directed mutation. This binding domain was then reshaped through site saturation mutagenesis, resulting in seven mutants with enhanced isomerization activity. The optimal mutant CsCE/Q371E had significantly enhanced substrate affinity (Km, 269.65 mM vs Km, 417.5 mM), reduced epimerization activity, and 3.3-fold increased isomerization activity over the original CsCE. Molecular dynamics simulation further revealed that substituting Gln-371 with Glu strengthened the hydrogen-bonding network and altered the active site-substrate interactions, increasing the substrate stability and shifting the catalytic direction. This study uncovered new information about the substrate binding region and its mechanisms and impact on CE catalytic performance, paving the way for potential commercial applications.
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Affiliation(s)
- Lu Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jiali Gu
- College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Wei Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingming Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Kuan Rei Ng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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11
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Modification of nitrile hydratase from Rhodococcus erythropolis CCM2595 by semirational design to enhance its substrate affinity. Biointerphases 2022; 17:061007. [PMID: 36456206 DOI: 10.1116/6.0002061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) is an excellent biocatalyst that catalyzes the hydration of nitrile substances to their corresponding amides. Given its catalytic specificity and eco-friendliness, NHase has extensive applications in the chemical, pharmaceutical, and cosmetic industries. To improve the affinity between Rhodococcus erythropolis CCM2595-derived NHase (ReNHase) and adiponitrile, this study used a semirational design to improve the efficiency of ReNHase in catalyzing the generation of 5-cyanopentanamide from adiponitrile. Enzyme kinetics analysis showed that Km of the mutant ReNHaseB:G196Y was 3.265 mmol l-1, which was lower than that of the wild-type NHase. The affinity of the mutant ReNHaseB:G196Y to adiponitrile was increased by 36.35%, and the efficiency of the mutant ReNHaseB:G196Y in catalyzing adiponitrile to 5-cyanopentamide was increased by 10.11%. The analysis of the enzyme-substrate interaction showed that the hydrogen bond length of the mutant ReNHaseB:G196Y to adiponitrile was shortened by 0.59 Å, which enhanced the interaction between the mutant and adiponitrile and, thereby, increased the substrate affinity. Similarly, the structural analysis showed that the amino acid flexibility near the mutation site of ReNHaseB:G196Y was increased, which enhanced the binding force between the enzyme and adiponitrile. Our work may provide a new theoretical basis for the modification of substrate affinity of NHase and increase the possibility of industrial applications of the enzyme.
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12
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Thermostability Improvement of L-Asparaginase from Acinetobacter soli via Consensus-Designed Cysteine Residue Substitution. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196670. [PMID: 36235209 PMCID: PMC9572581 DOI: 10.3390/molecules27196670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
To extend the application range of L-asparaginase in food pre-processing, the thermostability improvement of the enzyme is essential. Herein, two non-conserved cysteine residues with easily oxidized free sulfhydryl groups, Cys8 and Cys283, of Acinetobacter soli L-asparaginase (AsA) were screened out via consensus design. After saturation mutagenesis and combinatorial mutation, the mutant C8Y/C283Q with highly improved thermostability was obtained with a half-life of 361.6 min at 40 °C, an over 34-fold increase compared with that of the wild-type. Its melting temperature (Tm) value reaches 62.3 °C, which is 7.1 °C higher than that of the wild-type. Molecular dynamics simulation and structure analysis revealed the formation of new hydrogen bonds of Gln283 and the aromatic interaction of Tyr8 formed with adjacent residues, resulting in enhanced thermostability. The improvement in the thermostability of L-asparaginase could efficiently enhance its effect on acrylamide inhibition; the contents of acrylamide in potato chips were efficiently reduced by 86.50% after a mutant C8Y/C283Q treatment, which was significantly higher than the 59.05% reduction after the AsA wild-type treatment. In addition, the investigation of the mechanism behind the enhanced thermostability of AsA could further direct the modification of L-asparaginases for expanding their clinical and industrial applications.
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13
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Fang Y, Zhang Z, Xu W, Zhang W, Guang C, Mu W. Zearalenone lactonase: characteristics, modification, and application. Appl Microbiol Biotechnol 2022; 106:6877-6886. [PMID: 36173450 DOI: 10.1007/s00253-022-12205-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022]
Abstract
Zearalenone (ZEN) and its derivatives are one of the most contaminated fungal toxins worldwide, posing a severe threat to food security and human life. Traditional physical and chemical detoxifying methods are unsatisfactory due to incomplete detoxification, nutrient loss, and secondary pollutants. In recent years, bioremediation for eliminating fungal toxins has been gradually investigated. ZEN lactone hydrolase (lactonase) has been widely studied because of its high activity, mild conditions, and non-toxic product property. This review comprehensively represents the gene mining, characterization, molecular modification, and application of microbial-derived ZEN lactonases. It is aimed to elucidate the advantages and challenges of ZEN lactonases in industrial application, which also provides perspectives on obtaining innovative and promising biocatalysts for ZEN degradation. KEY POINTS: • A timely and concise review related to enzymatic elimination towards ZEN is shown. • The catalytic conditions and mechanism of ZEN lactonase is presented. • The modification and application of ZEN lactonase are exhibited also.
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Affiliation(s)
- Yuanyuan Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhenxia Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
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14
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Wang M, Wang L, Lyu X, Hua X, Goddard JM, Yang R. Lactulose production from lactose isomerization by chemo-catalysts and enzymes: Current status and future perspectives. Biotechnol Adv 2022; 60:108021. [PMID: 35901861 DOI: 10.1016/j.biotechadv.2022.108021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/02/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Lactulose, a semisynthetic nondigestive disaccharide with versatile applications in the food and pharmaceutical industries, has received increasing interest due to its significant health-promoting effects. Currently, industrial lactulose production is exclusively carried out by chemical isomerization of lactose via the Lobry de Bruyn-Alberda van Ekenstein (LA) rearrangement, and much work has been directed toward improving the conversion efficiency in terms of lactulose yield and purity by using new chemo-catalysts and integrated catalytic-purification systems. Lactulose can also be produced by an enzymatic route offering a potentially greener alternative to chemo-catalysis with fewer side products. Compared to the controlled trans-galactosylation by β-galactosidase, directed isomerization of lactose with high isomerization efficiency catalyzed by the most efficient lactulose-producing enzyme, cellobiose 2-epimerase (CE), has gained much attention in recent decades. To further facilitate the industrial translation of CE-based lactulose biotransformation, numerous studies have been reported on improving biocatalytic performance through enzyme mediated molecular modification. This review summarizes recent developments in the chemical and enzymatic production of lactulose. Related catalytic mechanisms are also highlighted and described in detail. Emerging techniques that aimed at advancing lactulose production, such as the boronate affinity-based technique and molecular biological techniques, are reviewed. Finally, perspectives on challenges and opportunities in lactulose production and purification are also discussed.
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Affiliation(s)
- Mingming Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China; College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, China; Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Lu Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiao Hua
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Julie M Goddard
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China.
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15
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Chen H, Ma L, Dai H, Fu Y, Wang H, Zhang Y. Advances in Rational Protein Engineering toward Functional Architectures and Their Applications in Food Science. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4522-4533. [PMID: 35353517 DOI: 10.1021/acs.jafc.2c00232] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein biomolecules including enzymes, cagelike proteins, and specific peptides have been continuously exploited as functional biomaterials applied in catalysis, nutrient delivery, and food preservation in food-related areas. However, natural proteins usually function well in physiological conditions, not industrial conditions, or may possess undesirable physical and chemical properties. Currently, rational protein design as a valuable technology has attracted extensive attention for the rational engineering or fabrication of ideal protein biomaterials with novel properties and functionality. This article starts with the underlying knowledge of protein folding and assembly and is followed by the introduction of the principles and strategies for rational protein design. Basic strategies for rational protein engineering involving experienced protein tailoring, computational prediction, computation redesign, and de novo protein design are summarized. Then, we focus on the recent progress of rational protein engineering or design in the application of food science, and a comprehensive summary ranging from enzyme manufacturing to cagelike protein nanocarriers engineering and antimicrobial peptides preparation is given. Overall, this review highlights the importance of rational protein engineering in food biomaterial preparation which could be beneficial for food science.
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Affiliation(s)
- Hai Chen
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Liang Ma
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Hongjie Dai
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yu Fu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Hongxia Wang
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yuhao Zhang
- College of Food Science, Southwest University, Chongqing 400715, China
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16
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Wu Y, Huang Z, Zhang W, Guang C, Chen Q, Mu W. Characterization of a Novel Mannose Isomerase from Stenotrophomonas rhizophila and Identification of Its Possible Catalytic Residues. Mol Biotechnol 2022; 64:650-659. [PMID: 35048315 DOI: 10.1007/s12033-021-00437-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/06/2021] [Indexed: 10/19/2022]
Abstract
D-Mannose has great value in the treatment of chronic diseases. D-Mannose isomerase can catalyze the bioconversion of D-fructose to D-mannose. Therefore, a novel D-mannose isomerase gene (Strh-MIase) from Stenotrophomonas rhizophila strain IS26 was expressed, purified, and characterized for the industrial production of D-mannose. The specific activities of the Strh-MIase for D-mannose and D-fructose were 437.5 ± 0.8 U/mg and 267.2 ± 0.7 U/mg. Its optimal temperature and pH were 50 °C and 7.0. The enzymatic bioconversion produced 25 g/L D-mannose from concentration D-fructose (100 g/L) in 6 h by recombinant Strh-MIase, resulting in a final yield of 25%. Sodium phosphate inhibition has little influence on D-mannose production when a high concentration of D-fructose is used as substrate. We demonstrate that the metal ions improve the efficiency of D-mannose isomerase because of the enhancement of its thermostability. Moreover, the possible catalytic residues of Strh-MIase were identified by site-directed mutagenesis.
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Affiliation(s)
- Yanchang Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
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17
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Wang X, Du J, Zhao B, Wang H, Rao S, Du G, Zhou J, Chen J, Liu S. Significantly Improving the Thermostability and Catalytic Efficiency of Streptomyces mobaraenesis Transglutaminase through Combined Rational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15268-15278. [PMID: 34874715 DOI: 10.1021/acs.jafc.1c05256] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Streptomyces mobaraenesis transglutaminase has been widely used in food processing. We here significantly improved the catalytic properties of S2P-S23V-Y24N-S199A-K294L (TGm1), a highly stabilized variant of the transglutaminase. First, a virtual proline scan was performed based on folding free energy changes to obtain TGm1 variants with enhanced thermostability. Second, the residues within 15 Å of Cys64 in the enzyme-substrate complex of TGm1 were subjected to virtual saturation mutagenesis to generate the variants with reduced binding free energy and increased activity. After combining the favorable mutations, we obtained the variant FRAPD-TGm1-E28T-A265P-A287P (FRAPD-TGm2), exhibiting 66.9 min of half-life at 60 °C (t1/2(60 °C)), 67.8 °C of melting temperature (Tm), and 71.8 U/mg of specific activity, which are 2-fold, 2.6 °C, and 43.8% higher than those of FRAPD-TGm1, respectively. At last, to increase the surface negative net charge of FRAPD-TGm2, we introduced the mutations N96E-S144E-N163D-R183E-R208E-K325E, yielding FRAPD-TGm3. The latter's t1/2(60 °C), Tm, and specific activity were 122.9 min, 68.6 °C, and 83.7 U/mg, which are 83.8%, 0.8 °C, and 16.6% higher than the former, respectively. FRAPD-TGm3 is thus a robust candidate for transglutaminase application.
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Affiliation(s)
- Xinglong Wang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jianhui Du
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Beichen Zhao
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Haiyan Wang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Shengqi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 214122, China
| | - Guocheng Du
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Song Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
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18
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Samaga YBL, Raghunathan S, Priyakumar UD. SCONES: Self-Consistent Neural Network for Protein Stability Prediction Upon Mutation. J Phys Chem B 2021; 125:10657-10671. [PMID: 34546056 DOI: 10.1021/acs.jpcb.1c04913] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Engineering proteins to have desired properties by mutating amino acids at specific sites is commonplace. Such engineered proteins must be stable to function. Experimental methods used to determine stability at throughputs required to scan the protein sequence space thoroughly are laborious. To this end, many machine learning based methods have been developed to predict thermodynamic stability changes upon mutation. These methods have been evaluated for symmetric consistency by testing with hypothetical reverse mutations. In this work, we propose transitive data augmentation, evaluating transitive consistency with our new Stransitive data set, and a new machine learning based method, the first of its kind, that incorporates both symmetric and transitive properties into the architecture. Our method, called SCONES, is an interpretable neural network that predicts small relative protein stability changes for missense mutations that do not significantly alter the structure. It estimates a residue's contributions toward protein stability (ΔG) in its local structural environment, and the difference between independently predicted contributions of the reference and mutant residues is reported as ΔΔG. We show that this self-consistent machine learning architecture is immune to many common biases in data sets, relies less on data than existing methods, is robust to overfitting, and can explain a substantial portion of the variance in experimental data.
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Affiliation(s)
- Yashas B L Samaga
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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19
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Chen Q, Wu Y, Huang Z, Zhang W, Mu W. Molecular Characterization of a Mesophilic Cellobiose 2-Epimerase That Maintains a High Catalytic Efficiency at Low Temperatures. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8268-8275. [PMID: 34231359 DOI: 10.1021/acs.jafc.1c02025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cellobiose 2-epimerase (CE) can catalyze bioconversion of lactose to its prebiotic derivative epilactose. The catalytic property of a novel CE from Treponema brennaborense (Trbr-CE) was investigated. Trbr-CE showed the highest catalytic efficiency of epimerization toward lactose among all of the previously reported CEs. This enzyme's specific activity could reach as high as 208.5 ± 5.3 U/mg at its optimum temperature, which is 45 °C. More importantly, this enzyme demonstrated a considerably high activity at low temperatures, suggesting Trbr-CE as a promising enzyme for industrial low-temperature production of epilactose. This structurally flexible enzyme exhibited a comparatively high binding affinity toward substrates, which was confirmed by both experimental verification and computational analysis. Molecular dynamics (MD) simulations and binding free energy calculations were applied to provide insights into molecular recognition upon temperature changes. Compared with thermophilic CEs, Trbr-CE presents a more negative enthalpy change and a higher entropy change when the temperature drops.
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Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Yanchang Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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20
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Rao SJA, Shetty NP. Evolutionary selectivity of amino acid is inspired from the enhanced structural stability and flexibility of the folded protein. Life Sci 2021; 281:119774. [PMID: 34197884 DOI: 10.1016/j.lfs.2021.119774] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/18/2022]
Abstract
AIM The present study attempts to decipher the site-specific amino acid alterations at certain positions experiencing preferential selectivity and their effect on proteins' stability and flexibility. The study examines the selection preferences by considering pair-wise non-bonded interaction energies of adjacent and interacting amino acids present at the interacting site, along with their evolutionary history. MATERIALS AND METHODS For the study, variations in the interacting residues of spike protein (S-Protein) receptor-binding domain (RBD) of different coronaviruses were examined. The MD simulation trajectory analysis revealed that, though all the variants studied were structurally stable at their native and bound confirmations, the RBD of 2019-nCoV/SARS-CoV-2 was found to be more flexible and more dynamic. Furthermore, a noticeable change observed in the non-bonded interaction energies of the amino acids interacting with the receptor corroborated their selection at respective positions. KEY FINDINGS The conformational changes exerted by the altered amino acids could be the reason for a broader range of interacting receptors among the selected proteins. SIGNIFICANCE The results envisage a strong indication that the residue selection at certain positions is governed by a well-orchestrated feedback mechanism, which follows increased stability and flexibility in the folded structure compared to its evolutionary predecessor.
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Affiliation(s)
- S J Aditya Rao
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India.
| | - Nandini P Shetty
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
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21
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Song Y, Wu X, Zhao Y, Jiang X, Wang L. Comparative molecular dynamics simulations identify a salt-sensitive loop responsible for the halotolerant activity of GH5 cellulases. J Biomol Struct Dyn 2021; 40:9522-9529. [PMID: 34043936 DOI: 10.1080/07391102.2021.1930167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Halotolerant glycoside hydrolases (GH) have broad application potentials in biorefinery industries. Elucidating the structure-activity relationship underlying the halotolerant catalysis is essential to design superior biocatalysts. Here, we performed molecular dynamics simulations to investigate the structural dynamics of two GH5 cellulases, namely the halotolerant Cel5R and non-halotolerant TfCel5A. Through characterizing the physical properties at different salt concentrations, the results revealed that the overall structures of Cel5R and TfCel5A were marginally affected by the increase in salt concentrations. However, a salt-sensitive loop was identified from both Cel5R and TfCel5A based on its significantly increased flexibility at high salt concentrations. Importantly, compared to TfCel5A the salt-sensitive loop of Cel5R engaged more sodium ions and water molecules around the active site of the enzyme. Besides, the unique residue motif of the salt-sensitive loop in Cel5R formed more intramolecular hydrogen bonds, stabilizing the active architecture of Cel5R at high salt concentrations. Collectively, the structural and dynamic differences may contribute to the various catalytic halotolerance of Cel5R and TfCel5A. These findings provide mechanistic insight into the halotolerant catalysis and will guide the ration design of GH5 cellulases with improved catalytic properties.Communicated by Ramaswamy H. Samy.
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Affiliation(s)
- Yuxuan Song
- Taishan College, Shandong University, Qingdao, China
| | - Xiuyun Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yue Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xukai Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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22
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Wang L, Gu J, Feng Y, Wang M, Tong Y, Liu Y, Lyu X, Yang R. Enhancement of the Isomerization Activity and Thermostability of Cellobiose 2-Epimerase from Caldicellulosiruptor saccharolyticus by Exchange of a Flexible Loop. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1907-1915. [PMID: 33541071 DOI: 10.1021/acs.jafc.0c07073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cellobiose 2-epimerase (CE) offers a promising enzymatic approach to produce lactulose. However, its application is limited by the unsatisfactory isomerization activity and thermostability. Our study attempted to optimize the catalytic performances of CEs by flexible loop exchange, for which four mutants were constructed using CsCE (CE from Caldicellulosiruptor saccharolyticus) as a template. As a result, all mutants maintained the same catalytic directions as the templates. Mutant RmC displayed a 2.2- and 1.34-fold increase in the isomerization activity and catalytic efficiency, respectively. According to the results of molecular dynamics (MD) simulations, it was revealed that the loop exchange in RmC enlarged the entrance of the active site for substrate binding and benefited proton transfer involved in the isomerization process. Besides, the t1/2 of mutant StC at 70 °C was increased from 29.07 to 38.29 h, owing to the abundance of rigid residues (proline) within the flexible loop of StC. Our work demonstrated that the isomerization activity and thermostability of CEs were closely related to the flexible loop surrounding the active site, which provides a new perspective to engineer CEs for higher lactulose production.
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Affiliation(s)
- Lu Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jiali Gu
- College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Yinghui Feng
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingming Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yingjie Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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23
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24
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Alizadeh AA, Jafari B, Dastmalchi S. Application of bioinformatics and molecular dynamics simulation approaches for identification of fibroblast growth factor 10 analogues with potentially improved thermostability. Growth Factors 2020; 38:197-209. [PMID: 34121575 DOI: 10.1080/08977194.2021.1881501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Fibroblast growth factor 10 functions as a paracrine mesenchymal molecule to initiate signalling pathways regarding to cellular development and health. However, the low thermal stability restricts it's functionality in the human body and the shelf-life of FGF10-based formulations. The current study aimed to employ rational design and bioinformatics approaches to identify some point mutations which may improve the thermal stability of FGF10. Bioinformatics analyses resulted in N105D, C106F, K144R, K153M and I156R as the potential stability conferring mutations. The identified mutants were subjected to MD simulation indicating that all mutations are both structurally and energetically favoured. Finally, the effects of the identified mutations on receptor binding of FGF10 were predicted and the results showed that K144R and K153M mutations may increase the binding affinity relative to the wild type. The findings of the current study propose potentially improved FGF10 analogues for further experimental investigations.
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Affiliation(s)
- Ali Akbar Alizadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Jafari
- Department of Medicinal Chemistry, School of Pharmacy, Urmia University of Medical Sciences, Urmia, Iran
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Pharmacy, Near East University, Nicosia, Turkey
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