1
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Heng S, Sutheeworapong S, Wangnai C, Champreda V, Kosugi A, Ratanakhanokchai K, Tachaapaikoon C, Ceballos RM. Hydrolysis of ionic liquid-treated substrate with an Iocasia fonsfrigidae strain SP3-1 endoglucanase. Appl Microbiol Biotechnol 2024; 108:63. [PMID: 38189956 PMCID: PMC10774164 DOI: 10.1007/s00253-023-12918-1] [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: 07/26/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024]
Abstract
Recently, we reported the discovery of a novel endoglucanase of the glycoside hydrolase family 12 (GH12), designated IfCelS12A, from the haloalkaliphilic anaerobic bacterium Iocasia fonsfrigidae strain SP3-1, which was isolated from a hypersaline pond in the Samut Sakhon province of Thailand (ca. 2017). IfCelS12A exhibits high substrate specificity on carboxymethyl cellulose and amorphous cellulose but low substrate specificity on b-1,3;1,4-glucan. Unlike some endoglucanases of the GH12 family, IfCelS12A does not exhibit hydrolytic activity on crystalline cellulose (i.e., Avicel™). High-Pressure Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC) analyses of products resulting from IfCelS12-mediated hydrolysis indicate mode of action for this enzyme. Notably, IfCelS12A preferentially hydrolyzes cellotetraoses, cellopentaoses, and cellohexaoses with negligible activity on cellobiose or cellotriose. Kinetic analysis with cellopentaose and barely b-D-glucan as cellulosic substrates were conducted. On cellopentaose, IfCelS12A demonstrates a 16-fold increase in activity (KM = 0.27 mM; kcat = 0.36 s-1; kcat/KM = 1.34 mM-1 s-1) compared to the enzymatic hydrolysis of barley b-D-glucan (KM: 0.04 mM, kcat: 0.51 s-1, kcat/KM = 0.08 mM-1 s-1). Moreover, IfCelS12A enzymatic efficacy is stable in hypersaline sodium chlorids (NaCl) solutions (up to 10% NaCl). Specifically, IfCel12A retains notable activity after 24 h at 2M NaCl (10% saline solution). IfCelS12A used as a cocktail component with other cellulolytic enzymes and in conjunction with mobile sequestration platform technology offers additional options for deconstruction of ionic liquid-pretreated cellulosic feedstock. KEY POINTS: • IfCelS12A from an anaerobic alkaliphile Iocasia fronsfrigidae shows salt tolerance • IfCelS12A in cocktails with other enzymes efficiently degrades cellulosic biomass • IfCelS12A used with mobile enzyme sequestration platforms enhances hydrolysis.
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Affiliation(s)
- Sobroney Heng
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chinnapong Wangnai
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road Klong Luang, Pathumthani, 12120, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
| | - Ruben Michael Ceballos
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA.
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA.
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2
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Zhang J, Chen J, Sha Y, Deng J, Wu J, Yang P, Zou F, Ying H, Zhuang W. Water-mediated active conformational transitions of lipase on organic solvent interfaces. Int J Biol Macromol 2024; 277:134056. [PMID: 39074702 DOI: 10.1016/j.ijbiomac.2024.134056] [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: 04/15/2024] [Revised: 05/31/2024] [Accepted: 07/19/2024] [Indexed: 07/31/2024]
Abstract
When it comes to enzyme stability and their application in organic solvents, enzyme biocatalysis has emerged as a popular substitute for conventional chemical processes. However, the demand for enzymes exhibiting improved stability remains a persistent challenge. Organic solvents can significantly impacts enzyme properties, thereby limiting their practical application. This study focuses on Lipase Thermomyces lanuginose, through molecular dynamics simulations and experiments, we quantified the effect of different solvent-lipase interfaces on the interfacial activation of lipase. Revealed molecular views of the complex solvation processes through the minimum distance distribution function. Solvent-protein interactions were used to interpret the factors influencing changes in lipase conformation and enzyme activity. We found that water content is crucial for enzyme stability, and the optimum water content for lipase activity was 35 % in the presence of benzene-water interface, which is closely related to the increase of its interfacial activation angle from 78° to 102°. Methanol induces interfacial activation in addition to significant competitive inhibition and denaturation at low water content. Our findings shed light on the importance of understanding solvent effects on enzyme function and provide practical insights for enzyme engineering and optimization in various solvent-lipase interfaces.
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Affiliation(s)
- Jihang Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jiale Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Yu Sha
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jiawei Deng
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jinglan Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Pengpeng Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Fengxia Zou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
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3
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Li R, Wu Z, Liu X, Chen H, Li X, Fan D, Wu Z. Increasing Multienzyme Cascade Efficiency and Stability of MOF via Partitioning Immobilization. ACS APPLIED MATERIALS & INTERFACES 2024; 16:33235-33245. [PMID: 38885355 DOI: 10.1021/acsami.4c07487] [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: 06/20/2024]
Abstract
Enhancing the stability of multienzyme cascade reactions in metal-organic frameworks (MOFs) is a challenging task in the fields of biotechnology and chemistry. However, addressing this challenge could yield far-reaching benefits across the application range in the biomedical, food, and environmental sectors. In this study, multienzyme partitioning immobilization that sequentially immobilizes cascade enzymes with hierarchical MOFs is proposed to reduce substrate diffusion resistance. Conversion results of ginsenosides indicate that this strategy improves the cascade efficiency up to 1.26 times. The substrate diffusion model is used to investigate the dual-interenzyme mass transfer behavior of substrates in the restricted domain space and evaluate the substrate channeling effect under partitioning immobilization. Molecular docking and kinetic simulations reveal that the MOFs effectively limit the conformational changes of cascade enzymes at high temperatures and in organic solvents while maintaining a large pocket of active centers. This phenomenon increased efficient substrate docking to the enzyme molecules, further optimizing cascade efficiency. The results of the immobilization of GOX and horseradish peroxidase as model enzymes indicate that the partitioned MOF immobilization strategy could be used for universal adaptation of cascade enzymes.
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Affiliation(s)
- Runze Li
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, P. R. China
- School of Chemistry and Chemical Engineering, Shihezi University/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, Shihezi 832003, P. R. China
| | - Zheng Wu
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, P. R. China
| | - Xiaochen Liu
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, P. R. China
| | - Hongxiu Chen
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, P. R. China
| | - Xue Li
- School of Chemical Engineering, Shaanxi Key Laboratory of Degradable Biomedical Materials, Northwest University, Xi'an 710069, P. R. China
| | - Daidi Fan
- School of Chemical Engineering, Shaanxi Key Laboratory of Degradable Biomedical Materials, Northwest University, Xi'an 710069, P. R. China
| | - Zhansheng Wu
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, P. R. China
- School of Chemistry and Chemical Engineering, Shihezi University/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, Shihezi 832003, P. R. China
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4
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Yüksek G, Taş DO, Ubay-Cokgor E, Jones JP, Gosselin M, Cabana H. Effects of potential inducers to enhance laccase production and evaluating concomitant enzyme immobilisation. ENVIRONMENTAL TECHNOLOGY 2024; 45:3517-3532. [PMID: 37259795 DOI: 10.1080/09593330.2023.2219851] [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: 03/20/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
This work investigated non-polar solvent hexane and polar solvents methanol and ethanol as inducers besides a well-known inducer, copper, for laccase production with and without mesoporous silica-covered plastic packing under sterilised and unsterilised conditions. The potential of waste-hexane water, which is generated during the mesoporous silica production process, was also investigated as a laccase inducer. During the study, the free and immobilised laccase activity on the packing was measured. The results showed that the highest total laccase activity, approximately 10,000 Units, was obtained under sterilised conditions with 0.5 mM copper concentration. However, no immobilised laccase activity was detected except in the copper and ethanol sets under unsterilised conditions. The maximum immobilised laccase activity of the sets that used waste hexane as an inducer was 1.25 U/mg packing. According to its significant performance, waste hexane can be an alternative inducer under sterilised conditions. Concomitant immobilised packing showed satisfactory laccase activities and could be a promising method to reduce operation costs and improve the cost-efficiency of enzymatic processes in wastewater treatment plants.
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Affiliation(s)
- Gülten Yüksek
- Sherbrooke University Water Research Group, Department of Civil and Building Engineering, Université de Sherbrooke, Sherbrooke, Canada
- Faculty of Civil Engineering, Department of Environmental Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Didem Okutman Taş
- Faculty of Civil Engineering, Department of Environmental Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Emine Ubay-Cokgor
- Faculty of Civil Engineering, Department of Environmental Engineering, Istanbul Technical University, Istanbul, Turkey
| | - J Peter Jones
- Department of Chemical and Biotechnology Engineering, Université de Sherbrooke, Sherbrooke, Canada
| | | | - Hubert Cabana
- Sherbrooke University Water Research Group, Department of Civil and Building Engineering, Université de Sherbrooke, Sherbrooke, Canada
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5
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Zhang S, Gan Y, Wang H, Qi X, Su P, Song J, Yang Y. Enhancing Chymotrypsin Activity and Stability of Capillary Immobilized Enzyme Microreactors Using Zeolitic Imidazolate Frameworks as Encapsulation Materials. Anal Chem 2024; 96:9228-9235. [PMID: 38779801 DOI: 10.1021/acs.analchem.4c01425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Open-tubular immobilized enzyme microreactors (OT-IMERs) are some of the most widely used enzyme reaction devices due to the advantages of simple preparation and fast sample processing. However, the traditional approaches for OT-IMERs preparation had some defects such as limited enzyme loading amount, susceptibility to complex sample interference, and less stability. Here, we report a strategy for the preparation of highly active and stable OT-IMERs, in which the single-stranded DNA-enzyme composites were immobilized in capillaries and then encapsulated in situ in the capillaries via zeolitic imidazolate frameworks (ZIF-L). The phosphate groups of the DNA adjusted the surface potential of the enzyme to negative values, which could attract cations, such as Zn2+, to promote the formation of ZIF-L for enzyme encapsulation. Using chymotrypsin (ChT) as a model enzyme, the prepared ChT@ZIF-L-IMER has higher activity and better affinity than the free enzyme and ChT-IMER. Moreover, the thermal stability, pH stability, and organic solvent stability of ChT@ZIF-L-IMER were much higher than those of free enzyme and ChT-IMER. Furthermore, the activity of ChT@ZIF-L-IMER was much higher than that of ChT-IMER after ten consecutive reactions. To demonstrate the versatility of this preparation method, we replaced ChT with glucose oxidase (GOx). The stability of GOx@ZIF-L-IMER was also experimentally demonstrated to be superior to that of GOx and GOx-IMER. Finally, ChT@ZIF-L-IMER was used for proteolytic digestion analysis. The results showed that ChT@ZIF-L-IMER had a short digestion time and high digestive efficiency compared with the free enzyme. The present study broadened the synthesis method of OT-IMERs, effectively integrating the advantages of metal-organic frameworks and IMER, and the prepared OT-IMERs significantly improved enzyme stability. All of the results indicated that the IMER prepared by this method had a broad application prospect in capillary electrophoresis-based high-performance enzyme analysis.
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Affiliation(s)
- Shuyi Zhang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yijia Gan
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Han Wang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Xingyi Qi
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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6
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Zhang J, Lin L, Wei W, Wei D. Identification, Characterization, and Computer-Aided Rational Design of a Novel Thermophilic Esterase from Geobacillus subterraneus, and Application in the Synthesis of Cinnamyl Acetate. Appl Biochem Biotechnol 2024; 196:3553-3575. [PMID: 37713064 DOI: 10.1007/s12010-023-04697-2] [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] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
Investigation of a novel thermophilic esterase gene from Geobacillus subterraneus DSMZ 13552 indicated a high amino acid sequence similarity of 25.9% to a reported esterase from Geobacillus sp. A strategy that integrated computer-aided rational design tools was developed to select mutation sites. Six mutants were selected from four criteria based on the simulated saturation mutation (including 19 amino acid residues) results. Of these, the mutants Q78Y and G119A were found to retain 87% and 27% activity after incubation at 70 °C for 20 min, compared with the 19% activity for the wild type. Subsequently, a double-point mutant (Q78Y/G119A) was obtained and identified with optimal temperature increase from 65 to 70 °C and a 41.51% decrease in Km. The obtained T1/2 values of 42.2 min (70 °C) and 16.9 min (75 °C) for Q78Y/G119A showed increases of 340% and 412% compared with that in the wild type. Q78Y/G119A was then employed as a biocatalyst to synthesize cinnamyl acetate, for which the conversion rate reached 99.40% with 0.3 M cinnamyl alcohol at 60 °C. The results validated the enhanced enzymatic properties of the mutant and indicated better prospects for industrial application as compared to that in the wild type. This study reported a method by which an enzyme could evolve to achieve enhanced thermostability, thereby increasing its potential for industrial applications, which could also be expanded to other esterases.
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Affiliation(s)
- Jin Zhang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Lin Lin
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
- Research Laboratory for Functional Nanomaterial, National Engineering Research Center for Nanotechnology, Shanghai, 200241, People's Republic of China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
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7
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Chen M, Jin T, Nian B, Cheng W. Solvent Tolerance Improvement of Lipases Enhanced Their Applications: State of the Art. Molecules 2024; 29:2444. [PMID: 38893320 PMCID: PMC11173743 DOI: 10.3390/molecules29112444] [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: 04/15/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Lipases, crucial catalysts in biochemical synthesis, find extensive applications across industries such as food, medicine, and cosmetics. The efficiency of lipase-catalyzed reactions is significantly influenced by the choice of solvents. Polar organic solvents often result in a decrease, or even loss, of lipase activity. Conversely, nonpolar organic solvents induce excessive rigidity in lipases, thereby affecting their activity. While the advent of new solvents like ionic liquids and deep eutectic solvents has somewhat improved the activity and stability of lipases, it fails to address the fundamental issue of lipases' poor solvent tolerance. Hence, the rational design of lipases for enhanced solvent tolerance can significantly boost their industrial performance. This review provides a comprehensive summary of the structural characteristics and properties of lipases in various solvent systems and emphasizes various strategies of protein engineering for non-aqueous media to improve lipases' solvent tolerance. This study provides a theoretical foundation for further enhancing the solvent tolerance and industrial properties of lipases.
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Affiliation(s)
| | | | | | - Wenjun Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China; (M.C.); (T.J.); (B.N.)
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8
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Zheng Y, Ren Q. Nuclear spin alignment of sodium ions via electric field gradients in phospholipid membranes. Phys Chem Chem Phys 2024; 26:13374-13382. [PMID: 38646714 DOI: 10.1039/d3cp06207d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The electric field gradient (EFG) has the potential to control both the direction and energy levels of nuclear spins greater than 1/2, a phenomenon known as nuclear electric resonance. Sodium ions on phospholipid membranes, having a nuclear spin of 3/2, can be influenced by surrounding EFGs. Driven by the complex behavior of anisotropic rotation and diffusion of phospholipid molecules, we conducted theoretical investigations and molecular dynamics simulations to study the characteristics of the EFG in this unique environment. Our results demonstrate a tendency for the principal axis of the maximum component of the effective EFG to align orthogonally to the membrane at the position of sodium ions coordinated with phospholipids. This alignment provides a unified precession axis for the nuclear spins of sodium ions, which potentially leads to a consistent definition of quantum information across the membrane. The values of the effective EFG's maximum component suggest energy level gaps of the nuclear spins in the range of tens of kHz, frequencies that have been identified in nerve electromagnetic waves. Consequently, such coherent directionality and energy levels may influence nearby proton and phosphorus nuclear spins, opening the possibility of constructing biological quantum computing systems based on membrane-associated spin interactions and evolutions.
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Affiliation(s)
- Yu Zheng
- School of Electronics, Peking University, Beijing 100871, China.
| | - Quansheng Ren
- School of Electronics, Peking University, Beijing 100871, China.
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9
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Lee YL, Jaafar NR, Ling JG, Huyop F, Abu Bakar FD, Rahman RA, Illias RM. Cross-linked enzyme aggregates of polyethylene terephthalate hydrolyse (PETase) from Ideonella sakaiensis for the improvement of plastic degradation. Int J Biol Macromol 2024; 263:130284. [PMID: 38382786 DOI: 10.1016/j.ijbiomac.2024.130284] [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: 12/04/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Polyethylene terephthalate (PET) is one of the most produced plastics globally and its accumulation in the environment causes harm to the ecosystem. Polyethylene terephthalate hydrolyse (PETase) is an enzyme that can degrade PET into its monomers. However, free PETase lacks operational stabilities and is not reusable. In this study, development of cross-linked enzyme aggregate (CLEA) of PETase using amylopectin (Amy) as cross-linker was introduced to solve the limitations of free PETase. PETase-Amy-CLEA exhibited activity recovery of 81.9 % at its best immobilization condition. Furthermore, PETase-Amy-CLEA exhibited 1.37-, 2.75-, 2.28- and 1.36-fold higher half-lives than free PETase at 50 °C, 45 °C, 40 °C and 35 °C respectively. Moreover, PETase-Amy-CLEA showed broader pH stability from pH 5 to 10 and could be reused up to 5 cycles. PETase-Amy-CLEA retained >70 % of initial activity after 40 days of storage at 4 °C. In addition, lower Km of PETase-Amy-CLEA indicated better substrate affinity than free enzyme. PETase-Amy-CLEA corroded PET better and products yielded was 66.7 % higher than free PETase after 32 h of treatment. Hence, the enhanced operational stabilities, storage stability, reusability and plastic degradation ability are believed to make PETase-Amy-CLEA a promising biocatalyst in plastic degradation.
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Affiliation(s)
- Yi Lin Lee
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Nardiah Rizwana Jaafar
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Jonathan Guyang Ling
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
| | - Roshanida A Rahman
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia; Institute of Bioproduct Development, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Rosli Md Illias
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia; Institute of Bioproduct Development, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
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10
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Bittner JP, Smirnova I, Jakobtorweihen S. Investigating Biomolecules in Deep Eutectic Solvents with Molecular Dynamics Simulations: Current State, Challenges and Future Perspectives. Molecules 2024; 29:703. [PMID: 38338447 PMCID: PMC10856712 DOI: 10.3390/molecules29030703] [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: 12/06/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Deep eutectic solvents (DESs) have recently gained increased attention for their potential in biotechnological applications. DESs are binary mixtures often consisting of a hydrogen bond acceptor and a hydrogen bond donor, which allows for tailoring their properties for particular applications. If produced from sustainable resources, they can provide a greener alternative to many traditional organic solvents for usage in various applications (e.g., as reaction environment, crystallization agent, or storage medium). To navigate this large design space, it is crucial to comprehend the behavior of biomolecules (e.g., enzymes, proteins, cofactors, and DNA) in DESs and the impact of their individual components. Molecular dynamics (MD) simulations offer a powerful tool for understanding thermodynamic and transport processes at the atomic level and offer insights into their fundamental phenomena, which may not be accessible through experiments. While the experimental investigation of DESs for various biotechnological applications is well progressed, a thorough investigation of biomolecules in DESs via MD simulations has only gained popularity in recent years. Within this work, we aim to provide an overview of the current state of modeling biomolecules with MD simulations in DESs and discuss future directions with a focus for optimizing the molecular simulations and increasing our fundamental knowledge.
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Affiliation(s)
- Jan Philipp Bittner
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
| | - Irina Smirnova
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
| | - Sven Jakobtorweihen
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
- Institute of Chemical Reaction Engineering, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
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11
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Akhlaghi Bagherjeri M, Monhemi H, Haque ANMA, Naebe M. Molecular mechanism of cellulose dissolution in N-methyl morpholine-N-oxide: A molecular dynamics simulation study. Carbohydr Polym 2024; 323:121433. [PMID: 37940258 DOI: 10.1016/j.carbpol.2023.121433] [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: 07/21/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 11/10/2023]
Abstract
N-methyl morpholine-N-oxide (NMMO) is the only commercialised solvent to dissolve cellulose and produce lyocell. However, the molecular mechanism of NMMO-induced cellulose solubilisation is unknown which limits further process development. In this work, and for the first time the complete dissolution process of a large cellulose bunch was simulated in NMMO monohydrate using long microsecond molecular dynamic simulations. The dissolution process was also simulated in 1-ethyl-3-methylimidazolium acetate (EmimAc) as an efficient ionic liquid in cellulose dissolution and the results were compared with the aqueous conditions. While the cellulose bunch showed a stable and insoluble structure in pure water, it was completely and efficiently dissolved in both NMMO monohydrate and EmimAc. It was shown that the dissolution time of cellulose in NMMO monohydrate is almost twice that in EmimAc, which is in agreement with the experimental observations. Although it is revealed that hydrogen bonding is the main driving force of cellulose dissolution in NMMO monohydrate, one cannot explain the complete molecular mechanism of NMMO-induced cellulose dissolution only by considering hydrogen bonds. A straightforward molecular mechanism was proposed, in which the interactions of NMMO molecules, not with cellulose, but with the other NMMO molecules play a critical role in the dissolution process.
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Affiliation(s)
| | - Hassan Monhemi
- Department of Chemistry, University of Neyshabur, Neyshabur, Iran
| | | | - Maryam Naebe
- Deakin University, Institute for Frontier Materials, Geelong, Victoria 3216, Australia.
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12
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Wang S, Mo L, Wu B, Ma C, Wang H. Effect of structural stability of lipase in acetonitrile on its catalytic activity in EGCG esterification reaction: FTIR and MD simulation. Int J Biol Macromol 2024; 255:128266. [PMID: 37984584 DOI: 10.1016/j.ijbiomac.2023.128266] [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: 09/12/2023] [Revised: 11/05/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
In this study, (-)-Epigallocatechin-3-O-gallate (EGCG) esterification reaction was catalyzed by Novozym 435, Lipozyme RM, Lipozyme TLIM, and lipase Amano 30SD in acetonitrile. Fourier transform infrared spectroscopy (FTIR) and molecular dynamic (MD) simulations were used to analyze the structural stability of different lipases in acetonitrile and their effect on EGCG esterification reaction. The results showed that conversion rate of EGCG catalyzed by Lipozyme RM was the highest, followed by Lipozyme TLIM. FTIR indicated that the secondary structure of Lipozyme RM was the most stable. MD simulations suggested that whole structural stability of Lipozyme RM in acetonitrile was superior to Novozym 435 and lipase Amano 30SD and similar to Lipozyme TLIM due to their similar conformation, while the active site of Lipozyme RM is more flexible than that of Lipozyme TLIM, which indicated that lipase with stable whole structure and flexible active site may be more conducive to the esterification of EGCG in acetonitrile. This study provided a direction for rapidly screening lipase to synthetize EGCG or other polyphenols esterified derivatives.
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Affiliation(s)
- Shan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ling Mo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Guilin Medical University, No.1 Zhiyuan Road, Lingui District, Guilin City, Guangxi 541004, China
| | - Beiqi Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chaoyang Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Hongxin Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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13
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Huang A, Tong L, Kou X, Gao R, Li ZW, Huang S, Zhu F, Chen G, Ouyang G. Structural and Functional Insights into the Biomineralized Zeolite Imidazole Frameworks. ACS NANO 2023; 17:24130-24140. [PMID: 38015792 DOI: 10.1021/acsnano.3c09118] [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: 11/30/2023]
Abstract
Biomineralization is a natural process of mineral formation mediated by biomacromolecules, allowing access to hierarchical structures integrating biological, chemical, and material properties. In this contribution, we comprehensively investigate the biomineralization of zeolite imidazole frameworks (ZIFs) for one-step synthesis of an enzyme-MOF biocomposite, in terms of differential crystallization behaviors, fine microstructure of resultant ZIF biominerals, the enzyme's conformation evolution, and protective effect of ZIF mineral. We discover that the biomineralization ability is ZIF organic linker dependent and the biocatalytic function is highly related to the ZIF mineral species and their distinguishable topologies and defect structures. Importantly, a side-by-side analysis suggests that the protective effect of ZIF mineral toward the hosted enzyme is highly associated with the synergistic effect of size dimension and chemical microenvironment of the ZIF pores. This work provides important insight into the ZIF-dependent biomineralization behaviors and highlights the important role of the ZIF microstructure in its biocatalytic activity and durability, which has been underestimated previously.
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Affiliation(s)
- Anlian Huang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Linjing Tong
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Xiaoxue Kou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Rui Gao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Zhi-Wei Li
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Siming Huang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, People's Republic of China
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Guosheng Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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14
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Vahidi SH, Monhemi H, Hassani Sabzevar B, Eftekhari M. Electrostatic interactions of enzymes in non-aqueous conditions: insights from molecular dynamics simulations. J Biomol Struct Dyn 2023:1-14. [PMID: 37965802 DOI: 10.1080/07391102.2023.2280775] [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: 05/29/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
Electrostatic interactions of enzymes and their effects on enzyme activity and stability are poorly understood in non-aqueous conditions. Here, we investigate the contribution of the electrostatic interactions on the stability and activity of enzymes in the non-aqueous environment using molecular dynamics simulations. Lipase was selected as active and lysozyme as inactive model enzymes in non-aqueous media. Hexane was used as a common non-aqueous solvent model. In agreement with the previous experiments, simulations show that lysozyme has more structural instabilities than lipase in hexane. The number of hydrogen bonds and salt bridges of both enzymes is dramatically increased in hexane. In contrast to the other opinions, we show that the increase of the electrostatic interactions in non-aqueous media is not so favorable for enzymatic function and stability. In this condition, the newly formed hydrogen bonds and salt bridges can partially denature the local structure of the enzymes. For lysozyme, the changes in electrostatic interactions occur in all domains including the active site cleft, which leads to enzyme inactivation and destabilization. Interestingly, most of the changes in electrostatic interactions of lipase occur far from the active site regions. Therefore, the active site entrance regions remain functional in hexane. The results of this study reveal how the changes in electrostatic interactions can affect enzyme stability and activity in non-aqueous conditions. Moreover, we show for the first time how some enzymes, such as lipase, remain active in a non-aqueous environment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Hooman Vahidi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Hassan Monhemi
- Department of Chemistry, Faculty of Sciences, University of Neyshabur, Neyshabur, Iran
| | | | - Mohammad Eftekhari
- Department of Chemistry, Faculty of Sciences, University of Neyshabur, Neyshabur, Iran
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15
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Godase VP, Kumar VR, Kumar AR. Potential of Y. lipolytica epoxide hydrolase for efficient production of enantiopure (R)-1,2-octanediol. AMB Express 2023; 13:77. [PMID: 37495892 PMCID: PMC10371975 DOI: 10.1186/s13568-023-01584-1] [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: 03/28/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
The recombinant Yleh from a tropical marine yeast Yarrowia lipolytica NCIM 3589 exhibited a high epoxide hydrolase activity of 9.34 ± 1.80 µmol min-1 mg-1 protein towards 1,2-epoxyoctane (EO), at pH 8.0 and 30 °C. The reaction product was identified as 1,2-Octanediol (OD) by GC-MS using EO and H2O18 as substrate, affirming the functionality of Yleh as an epoxide hydrolase. For EO, the Km, Vmax, and kcat/Km values were 0.43 ± 0.017 mM, 0.042 ± 0.003 mM min-1, and 467.17 ± 39.43 mM-1 min-1, respectively. To optimize the reaction conditions for conversion of racemic EO by Yleh catalyst to enantiopure (R)-1,2-octanediol, initially, Response Surface Methodology was employed. Under optimized reaction conditions of 15 mM EO, 150 µg purified Yleh at 30 °C a maximal diol production of 7.11 mM was attained in a short span of 65 min with a yield of 47.4%. Green technology using deep eutectic solvents for the hydrophobic substrate (EO) were tested as co-solvents in Yleh catalyzed EO hydrolysis. Choline chloride-Glycerol, produced 9.08 mM OD with an increased OD yield of 60.5%. Thus, results showed that deep eutectic solvents could be a promising solvent for Yleh-catalyzed reactions making Yleh a potential biocatalyst for the biosynthesis of enantiopure synthons.
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Affiliation(s)
- Vijaya P Godase
- Biochemistry Research Laboratory, Department of Biotechnology (Formerly Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, 411007, Pune, India
- Department of Biochemistry, Shivaji University, 416004, Kolhapur, India
| | - V Ravi Kumar
- Chemical Engineering and Process Development Division, National Chemical Laboratory, 411008, Pune, India
| | - Ameeta Ravi Kumar
- Biochemistry Research Laboratory, Department of Biotechnology (Formerly Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, 411007, Pune, India.
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16
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Wang KY, Zhang J, Hsu YC, Lin H, Han Z, Pang J, Yang Z, Liang RR, Shi W, Zhou HC. Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis. Chem Rev 2023; 123:5347-5420. [PMID: 37043332 PMCID: PMC10853941 DOI: 10.1021/acs.chemrev.2c00879] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Indexed: 04/13/2023]
Abstract
Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.
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Affiliation(s)
- Kun-Yu Wang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaqi Zhang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Chuan Hsu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hengyu Lin
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zongsu Han
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiandong Pang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- School
of Materials Science and Engineering, Tianjin Key Laboratory of Metal
and Molecule-Based Material Chemistry, Nankai
University, Tianjin 300350, China
| | - Zhentao Yang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rong-Ran Liang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wei Shi
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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17
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Tian Y, Yang L, Peng X, Qi W, Wang M. A covalent crosslinking strategy to construct a robust peptide-based artificial esterase. SOFT MATTER 2023; 19:3458-3463. [PMID: 37129250 DOI: 10.1039/d3sm00284e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Peptide-based artificial enzymes derived from the supramolecular assembly of short peptides have attracted growing attention in recent years. However, the stability of these artificial enzymes is still a problem since their noncovalent supramolecular structure is quite sensitive and frail under environmental conditions. In this study, we reported a covalent crosslinking strategy for the fabrication of a robust peptide-based artificial esterase. Inspired by the di-tyrosine bonds in many natural structural proteins, multi-tyrosines were designed into a peptide sequence with histidine as the catalytic residue for the ester hydrolysis reaction. Upon the photo-induced oxidation reaction, the short peptide YYHYY rapidly transferred into nanoparticle-shaped aggregates (CL-YYHYY) and displayed improved esterase-like catalytic activity than some previously reported noncovalent-based artificial esterases. Impressively, CL-YYHYY showed outstanding reusability and superior stability under high temperature, strong acid and alkaline and organic solvent conditions. This study provides a promising approach to improving the catalytic activity and stability of peptide-based artificial enzymes.
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Affiliation(s)
- Yi Tian
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
| | - Lijun Yang
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
| | - Xin Peng
- School of Life Sciences, Tianjin University, Tianjin 300072, P. R. China.
| | - Wei Qi
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
- The Co-Innovation Centre of Chemistry and Chemical Engineering of Tianjin, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300350, P. R. China
| | - Mengfan Wang
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
- School of Life Sciences, Tianjin University, Tianjin 300072, P. R. China.
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300350, P. R. China
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18
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Wang S, Lei H, Ji Z. Exploring Oxidoreductases from Extremophiles for Biosynthesis in a Non-Aqueous System. Int J Mol Sci 2023; 24:ijms24076396. [PMID: 37047370 PMCID: PMC10094897 DOI: 10.3390/ijms24076396] [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: 10/30/2022] [Revised: 03/19/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Organic solvent tolerant oxidoreductases are significant for both scientific research and biomanufacturing. However, it is really challenging to obtain oxidoreductases due to the shortages of natural resources and the difficulty to obtained it via protein modification. This review summarizes the recent advances in gene mining and structure-functional study of oxidoreductases from extremophiles for non-aqueous reaction systems. First, new strategies combining genome mining with bioinformatics provide new insights to the discovery and identification of novel extreme oxidoreductases. Second, analysis from the perspectives of amino acid interaction networks explain the organic solvent tolerant mechanism, which regulate the discrete structure-functional properties of extreme oxidoreductases. Third, further study by conservation and co-evolution analysis of extreme oxidoreductases provides new perspectives and strategies for designing robust enzymes for an organic media reaction system. Furthermore, the challenges and opportunities in designing biocatalysis non-aqueous systems are highlighted.
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Affiliation(s)
- Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen 361005, China
| | - Hangbin Lei
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhehui Ji
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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19
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Kikani B, Patel R, Thumar J, Bhatt H, Rathore DS, Koladiya GA, Singh SP. Solvent tolerant enzymes in extremophiles: Adaptations and applications. Int J Biol Macromol 2023; 238:124051. [PMID: 36933597 DOI: 10.1016/j.ijbiomac.2023.124051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/05/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Non-aqueous enzymology has always drawn attention due to the wide range of unique possibilities in biocatalysis. In general, the enzymes do not or insignificantly catalyze substrate in the presence of solvents. This is due to the interfering interactions of the solvents between enzyme and water molecules at the interface. Therefore, information about solvent-stable enzymes is scarce. Yet, solvent-stable enzymes prove quite valuable in the present day biotechnology. The enzymatic hydrolysis of the substrates in solvents synthesizes commercially valuable products, such as peptides, esters, and other transesterification products. Extremophiles, the most valuable yet not extensively explored candidates, can be an excellent source to investigate this avenue. Due to inherent structural attributes, many extremozymes can catalyze and maintain stability in organic solvents. In the present review, we aim to consolidate information about the solvent-stable enzymes from various extremophilic microorganisms. Further, it would be interesting to learn about the mechanism adapted by these microorganisms to sustain solvent stress. Various approaches to protein engineering are used to enhance catalytic flexibility and stability and broaden biocatalysis's prospects under non-aqueous conditions. It also describes strategies to achieve optimal immobilization with minimum inhibition of the catalysis. The proposed review would significantly aid our understanding of non-aqueous enzymology.
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Affiliation(s)
- Bhavtosh Kikani
- Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India; Department of Biological Sciences, P.D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Changa 388 421, Gujarat, India
| | - Rajesh Patel
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395 007, Gujarat, India
| | - Jignasha Thumar
- Government Science College, Gandhinagar 382 016, Gujarat, India
| | - Hitarth Bhatt
- Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India; Department of Microbiology, Faculty of Science, Atmiya University, Rajkot 360005, Gujarat, India
| | - Dalip Singh Rathore
- Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India; Gujarat Biotechnology Research Centre, Gandhinagar 382 010, Gujarat, India
| | - Gopi A Koladiya
- Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India
| | - Satya P Singh
- Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India.
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20
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Dudkaitė V, Kairys V, Bagdžiūnas G. Understanding the activity of glucose oxidase after exposure to organic solvents. J Mater Chem B 2023; 11:2409-2416. [PMID: 36806466 DOI: 10.1039/d2tb02605h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Long-term stability of enzymes in organic solvents is one of the most challenging problems in modern biotechnology and chemical industries. However, the resistance of enzymes to organic solvents is not very well understood so far. Herein, the effects of apolar, chlorinated, and polar organic solvents on the activity and structure of glucose oxidase from Aspergillus niger were systemically investigated using spectrophotometric activity assay of this enzyme and absorption and chiroptical spectroscopy. Molecular dynamics simulations and correlation of the activity with properties of the organic solvents were employed to understand the effects of organic solvents on the enzyme. The experimental and theoretical results showed that apolar solvents reduce the enzyme activity because they facilitate its aggregation through inter-enzymatic salt bridges. Moreover, polar solvents strongly coordinate with amino acid residues in the glucose binding pocket and prevent binding of the substrates. We found that this enzyme is stable in pure apolar and chlorinated solvents and these solvents can be used for the functionalization of its residues. This work provides an in depth understanding at the molecular level of the impact of various pure organic solvents on the structure and dynamics of glucose oxidase and the regulation of its catalytic activity.
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Affiliation(s)
- Vygailė Dudkaitė
- Group of Supramolecular Analysis, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania.
| | - Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Gintautas Bagdžiūnas
- Group of Supramolecular Analysis, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania.
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21
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Zan Q, Long M, Zheng N, Zhang Z, Zhou H, Xu X, Osire T, Xia X. Improving ethanol tolerance of ethyl carbamate hydrolase by diphasic high pressure molecular dynamic simulations. AMB Express 2023; 13:32. [PMID: 36920541 PMCID: PMC10017909 DOI: 10.1186/s13568-023-01538-7] [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: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 03/16/2023] Open
Abstract
Ethyl carbamate (EC) is mainly found in fermented foods and fermented alcoholic beverages, which could cause carcinogenic potential to humans. Reducing EC is one of the key research priorities to address security of fermented foods. Enzymatic degradation of EC with EC hydrolase in food is the most reliable and efficient method. However, poor tolerance to ethanol severely hinders application of EC hydrolase. In this study, the mutants of EC hydrolase were screened by diphasic high pressure molecular dynamic simulations (dHP-MD). The best variant with remarkable improvement in specific activity and was H68A/K70R/S325N, whose specific activity was approximately 3.42-fold higher than WT, and relative enzyme activity under 20% (v/v) was 5.02-fold higher than WT. Moreover, the triple mutant increased its stability by acquiring more hydration shell and forming extra hydrogen bonds. Furthermore, the ability of degrading EC of the immobilized triple mutant was both detected in mock wine and under certain reaction conditions. The stability of immobilized triple mutant and WT were both improved, and immobilized triple mutant degraded nearly twice as much EC as that of immobilized WT. Overall, dHP-MD was proved to effectively improve enzyme activity and ethanol tolerance for extent application at industrial scale.
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Affiliation(s)
- Qijia Zan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Mengfei Long
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Nan Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zehua Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Huimin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xinjie Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Tolbert Osire
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, 518172, Guangdong, China
| | - Xiaole Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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22
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Zdarta J, Kołodziejczak-Radzimska A, Bachosz K, Rybarczyk A, Bilal M, Iqbal HMN, Buszewski B, Jesionowski T. Nanostructured supports for multienzyme co-immobilization for biotechnological applications: Achievements, challenges and prospects. Adv Colloid Interface Sci 2023; 315:102889. [PMID: 37030261 DOI: 10.1016/j.cis.2023.102889] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/14/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
The synergistic combination of current biotechnological and nanotechnological research has turned to multienzyme co-immobilization as a promising concept to design biocatalysis engineering. It has also intensified the development and deployment of multipurpose biocatalysts, for instance, multienzyme co-immobilized constructs, via biocatalysis/protein engineering to scale-up and fulfil the ever-increasing industrial demands. Considering the characteristic features of both the loaded multienzymes and nanostructure carriers, i.e., selectivity, specificity, stability, resistivity, induce activity, reaction efficacy, multi-usability, high catalytic turnover, optimal yield, ease in recovery, and cost-effectiveness, multienzyme-based green biocatalysts have become a powerful norm in biocatalysis/protein engineering sectors. In this context, the current state-of-the-art in enzyme engineering with a synergistic combination of nanotechnology, at large, and nanomaterials, in particular, are significantly contributing and providing robust tools to engineer and/or tailor enzymes to fulfil the growing catalytic and contemporary industrial needs. Considering the above critics and unique structural, physicochemical, and functional attributes, herein, we spotlight important aspects spanning across prospective nano-carriers for multienzyme co-immobilization. Further, this work comprehensively discuss the current advances in deploying multienzyme-based cascade reactions in numerous sectors, including environmental remediation and protection, drug delivery systems (DDS), biofuel cells development and energy production, bio-electroanalytical devices (biosensors), therapeutical, nutraceutical, cosmeceutical, and pharmaceutical oriented applications. In conclusion, the continuous developments in nano-assembling the multienzyme loaded co-immobilized nanostructure carriers would be a unique way that could act as a core of modern biotechnological research.
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Affiliation(s)
- Jakub Zdarta
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
| | - Agnieszka Kołodziejczak-Radzimska
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Karolina Bachosz
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Agnieszka Rybarczyk
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Torun, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
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23
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Cui H, Vedder M, Zhang L, Jaeger K, Schwaneberg U, Davari MD. Polar Substitutions on the Surface of a Lipase Substantially Improve Tolerance in Organic Solvents. CHEMSUSCHEM 2022; 15:e202102551. [PMID: 35007408 PMCID: PMC9305861 DOI: 10.1002/cssc.202102551] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Indexed: 06/09/2023]
Abstract
Biocatalysis in organic solvents (OSs) enables more efficient routes to the synthesis of various valuable chemicals. However, OSs often reduce enzymatic activity, which limits the use of enzymes in OSs. Herein, we report a comprehensive understanding of interactions between surface polar substitutions and DMSO by integrating molecular dynamics (MD) simulations of 45 variants from Bacillus subtilis lipase A (BSLA) and substitution landscape into a "BSLA-SSM" library. By systematically analyzing 39 structural-, solvation-, and interaction energy-based observables, we discovered that hydration shell maintenance, DMSO reduction, and decreased local flexibility simultaneously govern the stability of polar variants in OS. Moreover, the fingerprints of 1631 polar-related variants in three OSs demonstrated that substituting aromatic to polar amino acid(s) hold great potential to highly improve OSs resistance. Hence, surface polar engineering is a powerful strategy to generate OS-tolerant lipases and other enzymes, thereby adapting the catalyst to the desired reaction and process with OSs.
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Affiliation(s)
- Haiyang Cui
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 3Aachen52074Germany
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstraße 50Aachen52074Germany
- University of Illinois at Urbana-Champaign Carl R. Woese Institute for Genomic Biology1206 West Gregory DriveUrbana, IL61801USA
| | - Markus Vedder
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 3Aachen52074Germany
| | - Lingling Zhang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesWest 7th Avenue 32, Tianjin Airport Economic AreaTianjin300308P. R. China
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine University DüsseldorfWilhelm Johnen StrasseJülich52426Germany
- Institute of Bio-and Geosciences IBG 1: BiotechnologyForschungszentrum Jülich GmbHWilhelm Johnen StrasseJülich52426Germany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 3Aachen52074Germany
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstraße 50Aachen52074Germany
| | - Mehdi D. Davari
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryWeinberg 306120HalleGermany
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24
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Lin Y, Wang F, Yu J, Zhang X, Lu GP. Iron single-atom anchored N-doped carbon as a 'laccase-like' nanozyme for the degradation and detection of phenolic pollutants and adrenaline. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127763. [PMID: 34801307 DOI: 10.1016/j.jhazmat.2021.127763] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 05/09/2023]
Abstract
To solve the inherent defects of laccase, the first iron single-atom anchored N-doped carbon material (Fe1@CN-20) as a laccase mimic was disclosed. The FeN4 structure of this material can well mimic the catalytic activity of laccase. Although Fe1@CN-20 has a lower metal content (2.9 wt%) than any previously reported laccase mimics, it exhibits kinetic constants comparable to those of laccase, as its Km (Michaelis constant) and Vmax (maximum rate) are 0.070 mM and 2.25 µM/min respectively, which are similar to those of laccase (0.078 mM, 2.49 µM/min). This catalyst displays excellent stability even under extreme pH (2-9), high temperature (100 °C), strong ionic strength (500 mM of NaCl), high ethanol concentration (volume ratio 40%) and long storage time (2 months). Additionally, it can be reused for at least 7 times with only a slight loss in activity. Therefore, this material has a much lower price and better stability and recyclability than laccase, which has been applied in the detection and degradation of a series of phenolic compounds. In the detection of adrenaline, Fe1@CN-20 achieved a detection limit of 1.3 µM, indicating it is more sensitive than laccase (3.9 µM).
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Affiliation(s)
- Yamei Lin
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Fei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Jie Yu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Guo-Ping Lu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei Street, Nanjing 210094, PR China.
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25
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Monica P, Mutturi S, Kapoor M. Truncation of C-terminal amino acids of GH26 endo-mannanase (ManB-1601) affects biochemical properties and stability against anionic surfactants. Enzyme Microb Technol 2022; 157:110031. [DOI: 10.1016/j.enzmictec.2022.110031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/18/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022]
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26
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Feng W, Shi H, Xu W, Song P. Heterologous expression and physicochemical characteristics identification of Kunitz protease inhibitor in Brassica napus. 3 Biotech 2022; 12:81. [PMID: 35251883 PMCID: PMC8882505 DOI: 10.1007/s13205-022-03149-8] [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: 11/07/2021] [Accepted: 02/11/2022] [Indexed: 11/01/2022] Open
Abstract
A Kunitz protease inhibitor gene (RTI; rti) was cloned from rapeseed and expressed in a Pichia pastoris expression system for the first time. After isolation and purification, the physical and chemical characteristics of the inhibitor were analyzed. The results showed that the induced expression level of the recombinant RTI reached 628 mg/L, and the specific activity of the inhibitor reached 69.6 TIU/mg protein at the shake flask fermentation level; the recombinant RTI retained more than 70% inhibitory activity between 30 and 90 °C and more than 80% inhibitory activity between pH 2.0-11.0. The metal ions Cu2+ and CO2+ and the organic reagents methanol, ethanol, acetone, and chloroform inhibit its activity. The recombinant RTI interacts with trypsin in a noncompetitive manner and has a strong and specific inhibitory effect on trypsin, a typical Kunitz trypsin inhibitor from plants. Combined with its good physical and chemical properties, recombinant RTI has the potential to be developed into an insect resistance protein.
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Affiliation(s)
- Wei Feng
- grid.411351.30000 0001 1119 5892School of Life Sciences, Liaocheng University, Liaocheng, 252000 China
| | - Haiying Shi
- grid.411351.30000 0001 1119 5892School of Life Sciences, Liaocheng University, Liaocheng, 252000 China
| | - Wei Xu
- grid.411351.30000 0001 1119 5892School of Life Sciences, Liaocheng University, Liaocheng, 252000 China
| | - Peng Song
- grid.411351.30000 0001 1119 5892School of Life Sciences, Liaocheng University, Liaocheng, 252000 China
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27
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Theoretical design and experimental study of new aptamers with the enhanced binding affinity relying on colorimetric assay for tetracycline detection. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Radhakrishnan R, Manna B, Ghosh A. Solvent induced conformational changes for the altered activity of laccase: A molecular dynamics study. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127123. [PMID: 34530268 DOI: 10.1016/j.jhazmat.2021.127123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The growing demands of solvent-based industries like paint, pharmaceutical, petrochemical, paper and pulp, etc., have directly increased the release of effluents that are rich in hazardous aromatic compounds in the environment. A sustainable biotechnological approach utilizing laccases as biocatalyst enable in biodegradation of these aromatic toxin-rich effluents. However, this enzymatic process is ineffective as laccases lose their stability and catalytic activity at high organic solvent concentrations. In this study, molecular dynamic simulations of a novel solvent tolerant laccase, DLac from Cerrena sp. RSD1 was performed to explore the molecular-level understanding of DLac in 30%(v/v) acetone and acetonitrile. Solvent-induced conformational changes were analyzed via protein structure network, which was illustrated with respect to cliques and communities. In the presence of acetonitrile, the cliques around the active site and substrate-binding site were disjoined, thus the communities lost their network integrity. Whereas with acetone, the community near the substrate-binding site gained new residues and formed a rigidified network that corresponded to enhanced DLac's activity. Moreover, prominent solvent binding sites were speculated, which can be probable mutation targets to further improve solvent tolerance and catalytic activity. The molecular basis behind solvent induced catalytic activity will further aid in engineering laccase for its industrial application.
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Affiliation(s)
- Rokesh Radhakrishnan
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Bharat Manna
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India; School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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29
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Cui H, Vedder M, Schwaneberg U, Davari MD. Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents. Methods Mol Biol 2022; 2397:179-202. [PMID: 34813065 DOI: 10.1007/978-1-0716-1826-4_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biocatalysis in organic solvents (OSs) is very appealing for the industry in producing bulk and/or fine chemicals, such as pharmaceuticals, biodiesel, and fragrances. The poor performance of enzymes in OSs (e.g., reduced activity, insufficient stability, and deactivation) negates OSs' excellent solvent properties. Molecular dynamics (MD) simulations provide a complementary method to study the relationship between enzymes dynamics and the stability in OSs. Here we describe computational procedure for MD simulation of enzymes in OSs with an example of Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO) cosolvent with software GROMACS. We discuss main essential practical issues considered (such as choice of force field, parameterization, simulation setup, and trajectory analysis). The core part of this protocol (enzyme-OS system setup, analysis of structural-based and solvation-based observables) is transferable to other enzymes and any OS systems. Combining with experimental studies, the obtained molecular knowledge is most likely to guide researchers to access rational protein engineering approaches to tailor OS resistant enzymes and expand the scope of biocatalysis in OS media. Finally, we discuss potential solutions to overcome the remaining challenges of computational biocatalysis in OSs and briefly draw future directions for further improvement in this field.
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Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Markus Vedder
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany.
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30
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Morris P, García-Arrazola R, Rios-Solis L, Dalby PA. Biophysical characterization of the inactivation of E. coli transketolase by aqueous co-solvents. Sci Rep 2021; 11:23584. [PMID: 34880340 PMCID: PMC8654844 DOI: 10.1038/s41598-021-03001-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Transketolase (TK) has been previously engineered, using semi-rational directed evolution and substrate walking, to accept increasingly aliphatic, cyclic, and then aromatic substrates. This has ultimately led to the poor water solubility of new substrates, as a potential bottleneck to further exploitation of this enzyme in biocatalysis. Here we used a range of biophysical studies to characterise the response of both E. coli apo- and holo-TK activity and structure to a range of polar organic co-solvents: acetonitrile (AcCN), n-butanol (nBuOH), ethyl acetate (EtOAc), isopropanol (iPrOH), and tetrahydrofuran (THF). The mechanism of enzyme deactivation was found to be predominantly via solvent-induced local unfolding. Holo-TK is thermodynamically more stable than apo-TK and yet for four of the five co-solvents it retained less activity than apo-TK after exposure to organic solvents, indicating that solvent tolerance was not simply correlated to global conformational stability. The co-solvent concentrations required for complete enzyme inactivation was inversely proportional to co-solvent log(P), while the unfolding rate was directly proportional, indicating that the solvents interact with and partially unfold the enzyme through hydrophobic contacts. Small amounts of aggregate formed in some cases, but this was not sufficient to explain the enzyme inactivation. TK was found to be tolerant to 15% (v/v) iPrOH, 10% (v/v) AcCN, or 6% (v/v) nBuOH over 3 h. This work indicates that future attempts to engineer the enzyme to better tolerate co-solvents should focus on increasing the stability of the protein to local unfolding, particularly in and around the cofactor-binding loops.
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Affiliation(s)
- Phattaraporn Morris
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
- Chemical Metrology and Biometry Department, National Institute of Metrology, 3/4-5 Moo 3, Klong 5, Klong Luang, 12120, Pathumthani, Thailand
| | - Ribia García-Arrazola
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, UK
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, King's Buildings, Edinburgh, EH9 3JL, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
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31
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Ingenbosch KN, Vieyto-Nuñez JC, Ruiz-Blanco YB, Mayer C, Hoffmann-Jacobsen K, Sanchez-Garcia E. Effect of Organic Solvents on the Structure and Activity of a Minimal Lipase. J Org Chem 2021; 87:1669-1678. [PMID: 34706196 DOI: 10.1021/acs.joc.1c01136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lipases are ubiquitously used in chemo-enzymatic synthesis and industrial applications. Nevertheless, the modulation of the activity of lipases by organic solvents still is not fully understood at the molecular level. We systematically investigated the activity and structure of lipase A from Bacillus subtilis in binary water-organic solvent mixtures of dimethyl sulfoxide (DMSO), acetonitrile (ACN), and isopropyl alcohol (IPA) using activity assays, fluorescence spectroscopy, molecular dynamics (MD) simulations, and FRET/MD analysis. The enzymatic activity strongly depended on the type and amount of organic solvent in the reaction media. Whereas IPA and ACN reduced the activity of the enzyme, small concentrations of DMSO led to lipase activation via an uncompetitive mechanism. DMSO molecules did not directly interfere with the binding of the substrate in the active site, contrary to what is known for other solvents and enzymes. We propose that the His156-Asp133 interaction, the binding of organic molecules to the active site, and the water accessibility of the substrate are key factors modulating the catalytic activity. Furthermore, we rationalized the role of solvent descriptors on the regulation of enzymatic activity in mixtures with low concentrations of the organic molecule, with prospective implications for the optimization of biocatalytic processes via solvent tuning.
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Affiliation(s)
- Kim N Ingenbosch
- Department of Chemistry and Institute for Coatings and Surface Chemistry, Niederrhein University of Applied Sciences, Adlerstrasse 32, 47798 Krefeld, Germany.,Institute for Physical Chemistry, University Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Julio Cesar Vieyto-Nuñez
- Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Christian Mayer
- Institute for Physical Chemistry, University Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Kerstin Hoffmann-Jacobsen
- Department of Chemistry and Institute for Coatings and Surface Chemistry, Niederrhein University of Applied Sciences, Adlerstrasse 32, 47798 Krefeld, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
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32
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Li SF, Xie JY, Qiu S, Xu SY, Cheng F, Wang YJ, Zheng YG. Semirational engineering of an aldo-keto reductase KmAKR for overcoming trade-offs between catalytic activity and thermostability. Biotechnol Bioeng 2021; 118:4441-4452. [PMID: 34374988 DOI: 10.1002/bit.27913] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 01/05/2023]
Abstract
Enzyme engineering usually generates trade-offs between activity, stability, and selectivity. Herein, we report semirational engineering of an aldo-keto reductase (AKR) KmAKR for simultaneously enhancing its thermostability and catalytic activity. Previously, we constructed KmAKRM9 (W297H/Y296W/K29H/Y28A/T63M/A30P/T302S/N109K/S196C), which showed outstanding activity towards t-butyl 6-chloro-(3R,5S)-dihydroxyhexanoate ((3R,5S)-CDHH), and t-butyl 6-cyano-(3R,5R)-dihydroxyhexanoate, the key chiral building blocks of rosuvastatin and atorvastatin. Under the guidance of computer-aided design including consensus residues analysis and molecular dynamics (MD) simulations, K164, S182, S232, and Q266 were dug out for their thermostability conferring roles, generating the "best" mutant KmAKRM13 (W297H/Y296W/K29H/Y28A/T63M/A30P/T302S/N109K/S196C/K164E/S232A/S182H/Q266D). The Tm and T50 15 values of KmAKRM13 were 10.4 and 6.1°C higher than that of KmAKRM9 , respectively. Moreover, it displayed a significantly elevated organic solvent tolerance over KmAKRM9 . Structural analysis indicated that stabilization of the α-helixes mainly contributed to thermostability enhancement. Under the optimized conditions, KmAKRM13 completely asymmetrically reduced 400 g/l t-butyl 6-chloro-(5S)-hydroxy-3-oxohexanoate ((5S)-CHOH) in 8.0 h at a high substrate to catalyst ratio (S/C) of 106.7 g/g, giving diastereomerically pure (3R,5S)-CDHH (>99.5% d.e.P ) with a space-time yield (STY) of 449.2 g/l·d.
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Affiliation(s)
- Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Jian-Yong Xie
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Shuai Qiu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
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33
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Ma Y, Velioğlu S, Yin Z, Wang R, Chew JW. Molecular dynamics investigation of membrane fouling in organic solvents. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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34
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Wang S, Xu Y, Yu XW. Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? Biomolecules 2021; 11:848. [PMID: 34200257 PMCID: PMC8226779 DOI: 10.3390/biom11060848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Water content is an important factor in lipase-catalyzed reactions in organic media but is frequently ignored in the study of lipases by molecular dynamics (MD) simulation. In this study, Candida antarctica lipase B, Candida rugosa lipase and Rhizopus chinensis lipase were used as research models to explore the mechanisms of lipase in micro-aqueous organic solvent (MAOS) media. MD simulations indicated that lipases in MAOS systems showed unique conformations distinguished from those seen in non-aqueous organic solvent systems. The position of water molecules aggregated on the protein surface in MAOS media is the major determinant of the unique conformations of lipases and particularly impacts the distribution of hydrophilic and hydrophobic amino acids on the lipase surface. Additionally, two maxima were observed in the water-lipase radial distribution function in MAOS systems, implying the formation of two water shells around lipase in these systems. The energy landscapes of lipases along solvent accessible areas of catalytic residues and the minimum energy path indicated the dynamic open states of lipases in MAOS systems differ from those in other solvent environments. This study confirmed the necessity of considering the influence of the microenvironment on MD simulations of lipase-catalyzed reactions in organic media.
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Affiliation(s)
| | | | - Xiao-Wei Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (S.W.); (Y.X.)
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Ardila-Leal LD, Monterey-Gutiérrez PA, Poutou-Piñales RA, Quevedo-Hidalgo BE, Galindo JF, Pedroza-Rodríguez AM. Recombinant laccase rPOXA 1B real-time, accelerated and molecular dynamics stability study. BMC Biotechnol 2021; 21:37. [PMID: 34088291 PMCID: PMC8178886 DOI: 10.1186/s12896-021-00698-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/24/2021] [Indexed: 12/28/2022] Open
Abstract
Background Laccases (EC 1.10.3.2) are multi-copper oxidoreductases with great biotechnological importance due to their high oxidative potential and utility for removing synthetic dyes, oxidizing phenolic compounds, and degrading pesticides, among others. Methods A real-time stability study (RTS) was conducted for a year, by using enzyme concentrates from 3 batches (L1, L3, and L4). For which, five temperatures 243.15, 277.15, 298.15, 303.15, 308.15, and 313.15 K were assayed. Using RTS data and the Arrhenius equation, we calculated the rPOXA 1B accelerated stability (AS). Molecular dynamics (MD) computational study results were very close to those obtained experimentally at four different temperatures 241, 278, 298, and 314 K. Results In the RTS, 101.16, 115.81, 75.23, 46.09, 5.81, and 4.83% of the relative enzyme activity were recovered, at respective assayed temperatures. AS study, showed that rPOXA 1B is stable at 240.98 ± 5.38, 277.40 ± 1.32 or 297.53 ± 3.88 K; with t1/2 values of 230.8, 46.2, and 12.6 months, respectively. Kinetic and thermodynamic parameters supported the high stability of rPOXA 1B, with an Ed value of 41.40 KJ mol− 1, a low variation of KM and Vmax, at 240.98 ± 5.38, and 297.53 ± 3.88 K, and ∆G values showing deactivation reaction does not occur. The MD indicates that fluctuations in loop, coils or loops with hydrophilic or intermediate polarity amino acids as well as in some residues of POXA 1B 3D structure, increases with temperature; changing from three fluctuating residues at 278 K to six residues at 298 K, and nine residues at 314 K. Conclusions Laccase rPOXA 1B demonstrated experimentally and computationally to be a stable enzyme, with t1/2 of 230.8, 46.2 or 12.6 months, if it is preserved impure without preservatives at temperatures of 240.98 ± 5.38, 277.40 ± 1.32 or 297.53 ± 3.88 K respectively; this study could be of great utility for large scale producers. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00698-3.
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Affiliation(s)
- Leidy D Ardila-Leal
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia
| | - Pedro A Monterey-Gutiérrez
- Vicerrectoría Académica. Universidad Antonio Nariño, Programa de Maestría y Doctorado en Educación Matemática, Bogotá, D.C, Colombia
| | - Raúl A Poutou-Piñales
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia.
| | - Balkys E Quevedo-Hidalgo
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ), Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia.
| | - Johan F Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá, D.C, Colombia.
| | - Aura M Pedroza-Rodríguez
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia
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Peng B, Luo T, Chen F, Wang M, Fu JH, Zheng LF, Li J, Deng ZY. Stability comparison of four lipases and catalytic mechanism during the synthesis of 1,3-di-oleic-2-medium chain triacylglycerols in a trace water-in-oil system: Experimental analyses and computational simulations. J Food Biochem 2021; 45:e13667. [PMID: 33837552 DOI: 10.1111/jfbc.13667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/02/2021] [Accepted: 01/25/2021] [Indexed: 11/28/2022]
Abstract
In the present study, a kind of structured lipids, namely 1,3-di-oleic-2-medium chain (OMO) triacylglycerols, were synthesized through lipase-catalyzed reactions using coconut oil and rapeseed acid as materials in a trace water-in-oil system. Experimental analysis and computational simulations were undertaken to compare the stability of four lipases including Lipozyme RMIM, Lipozyme TLIM, Novozym 435, and Aspergillus oryzae immobilized lipase (AOIM), and illustrate catalytic mechanism of Novozym 435 during the synthesis of OMO. Fourier transform infrared and molecular dynamics simulation results demonstrated that a decrease in ordered structure (α-helix and β-sheet) led to a reduction in enzyme activity. Compared with Lipozyme RMIM and Novozym 435, Lipozyme TLIM and AOIM exhibited better stability due to a short-chain lid in TLIM, which covers activity sites, and hydrogen bonds formed between activity center of AOIM and water. Among four lipases, AOIM exhibited best catalytic performance: a OMO yield of 30.7% at 3 hr and a good stability of long term (48 hr). Density functional theory results demonstrated that specifically, during the synthesis of OMO triacylglycerol, the addition of Novozym 435 (derived from Candida antarctica lipase B, CALB) substantially lowered reaction barriers (64.4 KJ/mol with CALB vs. 332.7 KJ/mol with no lipase), aiding in the generation of OMO because of the formations of transitional tetrahedral intermediates. A trace water-in-oil system was a green and efficient alternative for lipase-catalyzed production of OMO, and this study provided crucial insights into the stability/instability and catalytic mechanisms of lipase in the synthesis of structured lipids. PRACTICAL APPLICATIONS: We compared the stability of Lipozyme RMIM, Lipozyme 435, Lipozyme TLIM, and AOIM during the synthesis of the OMO triacylglycerols in a trace water-in-oil system, where exhibited a high catalytic activity of lipase in water-oil interface. AOIM had the highest stability and showed the best catalytic performance due to the formation of hydrogen bonds. Besides, for the first time, the transition tetrahedral structure was revealed in the enzymatic synthesis of medium- and long-chain triacylglycerols. This study provides a rational approach to compare lipase stability and a possible hint to choose appropriate enzyme in a specific catalytic condition.
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Affiliation(s)
- Bin Peng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Ting Luo
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Fang Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,School of Public Health, Nanchang University, Nanchang, China
| | - Mei Wang
- The State Centre of Quality Supervision and Inspection for Camellia Products, Ganzhou, China
| | - Jin-Heng Fu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Liu-Feng Zheng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Jing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Ze-Yuan Deng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
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Changing the residues interaction pattern as a universal mechanism for enzyme inactivation and denaturation in supercritical CO2. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Wang S, Xu Y, Yu XW. A phenylalanine dynamic switch controls the interfacial activation of Rhizopus chinensis lipase. Int J Biol Macromol 2021; 173:1-12. [PMID: 33476612 DOI: 10.1016/j.ijbiomac.2021.01.086] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 01/10/2023]
Abstract
The catalytic mechanism of most lipases involves a step called "interfacial activation" which significantly increases lipases activity beyond the critical micellar concentration (CMC) of substrate. In the present study, Rhizopus chinensis lipase (RCL) was used as a research model to explore the mechanism of lipase interfacial activation beyond the CMC. Molecular dynamic (MD) simulations indicated the open- and closed-lid transitions and revealed that Phe113 was the critical site for RCL activation by its dynamic flipping. Such putative switch affecting interfacial activation has not been reported in lipase so far. The function of Phe113 was subsequently verified by mutation experiments. The F113W mutant increases the lipase catalytic efficiency (1.9 s-1·μM-1) to 280% at the optimum temperature (40 °C) and pH 8.5 with the addition of 0.12 μg protein in the 200 μL reaction system. MD simulations indicated that the fast flipping rate from the closed to the open state, the high open state proportion, and the exposure of the catalytic triad are the main reasons for the lipase activation. The mutual corroboration of simulations and site-directed mutagenesis results revealed the vital role of Phe113 in the lipase activation.
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Affiliation(s)
- Shang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Xiao-Wei Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
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Simulation of the Reactivation of Partially Inactivated Biocatalysts in Sequential Batch Reactors. Processes (Basel) 2020. [DOI: 10.3390/pr8111419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The enzymatic reactivation process enables the recovery of catalytic activity for inactive biocatalysts. However, its effect on the specific productivity of the processes has not been studied. The main objective of this work was to evaluate the specific productivity of the processes with and without reactivation using the program Spyder Python (3.7). Using fixed values for all of the parameters, the global specific productivity was 8 mM/h·gbiocat for the process without reactivation, and 4 mM/h·gbiocat for the process with reactivation. Random numbers were generated to use as different values for parameters, and the results yielded a global specific productivity of 3.79 mM/h·gbiocat for the process with reactivation and 3.68 mM/h·gbiocat for the process without reactivation. ANOVA tests showed that there were significant differences between the specific global productivities of the two processes. Reactivation has great potential for use when the biocatalyst is of high cost.
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Biocatalysis at Extreme Temperatures: Enantioselective Synthesis of both Enantiomers of Mandelic Acid by Transesterification Catalyzed by a Thermophilic Lipase in Ionic Liquids at 120 °C. Catalysts 2020. [DOI: 10.3390/catal10091055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The use of biocatalysts in organic chemistry for catalyzing chemo-, regio- and stereoselective transformations has become an usual tool in the last years, both at lab and industrial scale. This is not only because of their exquisite precision, but also due to the inherent increase in the process sustainability. Nevertheless, most of the interesting industrial reactions involve water-insoluble substrates, so the use of (generally not green) organic solvents is generally required. Although lipases are capable of maintaining their catalytic precision working in those solvents, reactions are usually very slow and consequently not very appropriate for industrial purposes. Increasing reaction temperature would accelerate the reaction rate, but this should require the use of lipases from thermophiles, which tend to be more enantioselective at lower temperatures, as they are more rigid than those from mesophiles. Therefore, the ideal scenario would require a thermophilic lipase capable of retaining high enantioselectivity at high temperatures. In this paper, we describe the use of lipase from Geobacillus thermocatenolatus as catalyst in the ethanolysis of racemic 2-(butyryloxy)-2-phenylacetic to furnish both enantiomers of mandelic acid, an useful intermediate in the synthesis of many drugs and active products. The catalytic performance at high temperature in a conventional organic solvent (isooctane) and four imidazolium-based ionic liquids was assessed. The best results were obtained using 1-ethyl-3-methyl imidazolium tetrafluoroborate (EMIMBF4) and 1-ethyl-3-methyl imidazolium hexafluorophosphate (EMIMPF6) at temperatures as high as 120 °C, observing in both cases very fast and enantioselective kinetic resolutions, respectively leading exclusively to the (S) or to the (R)-enantiomer of mandelic acid, depending on the anion component of the ionic liquid.
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Counterbalance of Stability and Activity Observed for Thermostable Transaminase from Thermobaculum terrenum in the Presence of Organic Solvents. Catalysts 2020. [DOI: 10.3390/catal10091024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pyridoxal-5’-phosphate-dependent transaminases catalyze stereoselective amination of organic compounds and are highly important for industrial applications. Catalysis by transaminases often requires organic solvents to increase the solubility of reactants. However, natural transaminases are prone to inactivation in the presence of water-miscible organic solvents. Here, we present the solvent tolerant thermostable transaminase from Thermobaculum terrenum (TaTT) that catalyzes transamination between L-leucine and alpha-ketoglutarate with an optimum at 75 °C and increases the activity ~1.8-fold upon addition of 15% dimethyl sulfoxide or 15% methanol at high but suboptimal temperature, 50 °C. The enhancement of the activity correlates with a decrease in the thermal denaturation midpoint temperature. The blue-shift of tryptophan fluorescence suggested that solvent molecules penetrate the hydration shell of the enzyme. Analysis of hydrogen bonds in the TaTT dimer revealed a high number of salt bridges and surface hydrogen bonds formed by backbone atoms. The latter are sensitive to the presence of organic solvents; they rearrange, conferring the relaxation of some constraints inherent to a thermostable enzyme at low temperatures. Our data support the idea that the counterbalance of stability and activity is crucial for the catalysis under given conditions; the obtained results may be useful for fine-tuning biocatalyst efficiency.
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Monhemi H, Tabaee SS. The effects of mutation and modification on the structure and stability of human lysozyme: A molecular link between carbamylation and atherosclerosis. J Mol Graph Model 2020; 100:107703. [PMID: 32799051 DOI: 10.1016/j.jmgm.2020.107703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/01/2020] [Accepted: 07/18/2020] [Indexed: 01/09/2023]
Abstract
Amino acid mutations in some proteins such as lysozyme lead to genetically disorder variants and adverse pathogenic consequences. Recently, amino acid modifications were known as a risk factor in many related diseases such as uremia and atherosclerosis, showing the importance of these surface-structure changes. Although the structural consequences of the hereditary proteins have been examined extensively, such effects for the protein modifications are known to a lesser extent. One drawback in the examination of protein modifications is hardness in experimental detection of modifications by techniques such as NMR and crystallography. Molecular modeling and simulation can help to understand such phenomena at the molecular levels. It is more rational that the effects of both mutation and modification can be compared in a single protein model. Here, molecular dynamics simulation is used to compare the effects of a disease-related carbamylation modification and an amyloidogenic mutation (D67H) in human lysozyme as a model protein. The results show that the carbamylation adversely effects on the tertiary structure, leading to the similar unfolding pathway to the hereditary amyloidogenic form. The carbamylation leads to the instability of the overall protein conformation, especially on the β-domain, which is a characteristic of hereditary amyloidosis in human lysozymes. The aggregation behaviors of both modified and mutant lysozyme were examined by molecular docking calculations. The results showed that the partially unfolded lysozyme might form tight protein aggregates upon carbamylation similar to the amyloidogenic variant. Both single and all-residues carbamylations impose serious conformational changes to the tertiary structure of lysozyme. It was obtained that carbamylation of lysozyme strongly effects on the stability of N-terminal β-sheet, which can produce a highly unstable conformation. The results of this study not only show the adverse structural consequences of a disease-associated post-translational modification, but it also may be very helpful to understand the molecular basis for many carbamylation-related diseases such as atherosclerosis in ESRD patients. The results show that non-native post-translational modifications may be as structurally important as hereditary mutations.
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Affiliation(s)
- Hassan Monhemi
- Department of Chemistry, University of Neyshabur, Neyshabur, Iran.
| | - Seyedeh Samaneh Tabaee
- Healthy Ageing Research Centre, Neyshabur University of Medical Sciences, Neyshabur, Iran; Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran.
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Wang R, Wang S, Xu Y, Yu X. Enhancing the thermostability of Rhizopus chinensis lipase by rational design and MD simulations. Int J Biol Macromol 2020; 160:1189-1200. [PMID: 32485250 DOI: 10.1016/j.ijbiomac.2020.05.243] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 01/16/2023]
Abstract
To improve the thermostability of r27RCL from Rhizopus chinensis and broaden its industrial applications, we used rational design (FoldX) according to ΔΔG calculation to predict mutations. Four thermostable variants S142A, D217V, Q239F, and S250Y were screened out and then combined together to generate a quadruple-mutation (S142A/D217V/Q239F/S250Y) variant, called m31. m31 exhibited enhanced thermostability with a 41.7-fold longer half-life at 60 °C, a 5 °C higher of topt, and 15.8 °C higher of T5030 compared to that of r27RCL expressed in Pichiapastoris. Molecular dynamics simulations were conducted to analyze the mechanism of the thermostable mutant. The results indicated that the rigidity of m31 was improved due to the decreased solvent accessible surface area, a newly formed salt bridge of Glu292:His171, and the increased ΔΔG of m31. According to the root-mean-square-fluctuation analysis, three positive mutations S142A, D217V, and Q239F located in the thermal weak regions and greatly decreased the distribution of thermal-fluctuated regions of m31, compared to that of r27RCL. These results suggested that to simultaneously implement MD simulations and ΔΔG-based rational approaches will be more accurate and efficient for the improvement of enzyme thermostability.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Pharmaceutical Science, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Shang Wang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaowei Yu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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Khoshbin Z, Housaindokht MR. Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach. J Biomol Struct Dyn 2020; 39:3071-3079. [PMID: 32323612 DOI: 10.1080/07391102.2020.1760133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This study introduces a computational method to design a new aptamer with higher binding affinity to a special target in comparison with the experimentally available aptamers. The method is called step by step mutation based on MD simulation, which includes some steps. First, MD simulation is performed for the SELEX-introduced (native) aptamer in the presence of the target. Afterwards, conformational factor (Pi) is calculated for the simulated system, which obtains the affinity of the aptamer residues to the target. A nucleotide exchange is done for the residue with the least Pi parameter to the nucleotide with the highest Pi value that results in a mutant aptamer. MD simulation is performed for the target-mutant complex, and Pi values are calculated again. The nucleotide exchange is performed similarly, and the designing process is proceeded repeatedly that results in a mutant with the improved specificity to the target. The aptamer affinity to the target is also determined in each step through calculating the binding Gibbs energy (ΔGBind) as a reliable parameter. The introduced strategy is utilized efficiently to design a mutant aptamer with improved specificity toward sulfadimethoxine (SDM) antibiotic as a case study. The great difference in the ΔGBind values about 579.856 kJ mol-1 highlights that the M5 mutant possesses the improved specificity toward SDM in comparison with the native aptamer. Besides, the selectivity of the M5 aptamer toward SDM is examined among some conventional interfering compounds by using MD simulation that confirms the applicability of the designed aptamer for further experimental studies.
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Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Wang Y, Li S, Jin M, Han Q, Liu S, Chen X, Han Y. Enhancing the Thermo-Stability and Anti-Bacterium Activity of Lysozyme by Immobilization on Chitosan Nanoparticles. Int J Mol Sci 2020; 21:ijms21051635. [PMID: 32121010 PMCID: PMC7084273 DOI: 10.3390/ijms21051635] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/20/2020] [Accepted: 02/23/2020] [Indexed: 12/19/2022] Open
Abstract
The recent emergence of antibiotic-resistant bacteria requires the development of new antibiotics or new agents capable of enhancing antibiotic activity. Lysozyme degrades bacterial cell wall without involving antibiotic resistance and has become a new antibacterial strategy. However, direct use of native, active proteins in clinical settings is not practical as it is fragile under various conditions. In this study, lysozyme was integrated into chitosan nanoparticles (CS-NPs) by the ionic gelation technique to obtain lysozyme immobilized chitosan nanoparticles (Lys-CS-NPs) and then characterized by dynamic light scattering (DLS) and transmission electron microscopy (TEM), which showed a small particle size (243.1 ± 2.1 nm) and positive zeta potential (22.8 ± 0.2 mV). The immobilization significantly enhanced the thermal stability and reusability of lysozyme. In addition, compared with free lysozyme, Lys-CS-NPs exhibited superb antibacterial properties according to the results of killing kinetics in vitro and measurement of the minimum inhibitory concentration (MIC) of CS-NPs and Lys-CS-NPs against Pseudomonas aeruginosa (P. aeruginosa), Klebsiella pneumoniae (K. pneumoniae), Escherichia coli (E. coli), and Staphylococcus aureus (S. aureus). These results suggest that the integration of lysozyme into CS-NPs will create opportunities for the further potential applications of lysozyme as an anti-bacterium agent.
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Zhou Z, Gao Z, Shen H, Li M, He W, Su P, Song J, Yang Y. Metal-Organic Framework in Situ Post-Encapsulating DNA-Enzyme Composites on a Magnetic Carrier with High Stability and Reusability. ACS APPLIED MATERIALS & INTERFACES 2020; 12:7510-7517. [PMID: 31971363 DOI: 10.1021/acsami.9b23526] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In recent years, metal-organic frameworks (MOFs) have been extensively studied as candidate enzyme immobilization platforms. However, conventional MOF-enzyme composites usually exhibit low controllability and reusability. In this study, a novel and stable strategy for enzyme immobilization was designed by use of ZIF-8 to encapsulate in situ DNA-enzyme composites on the surface of magnetic particles (MPs). The mechanism of in situ encapsulation was discussed in detail. It was found that immobilized enzymes were involved in the growth of ZIF-8, and the DNA cross-linking agents promoted the growth of ZIF-8 on the surface of MP. The thermal, chemical, and physical stabilities of horseradish peroxidase (HRP) were all significantly enhanced after in situ encapsulation. Most importantly, this strategy was proven to be a general platform that can be used to stabilize various proteins. The in situ encapsulation strategy was expanded to immobilize a cascade of enzymes, and ZIF-8@MPGOx-HRP possessed high selectivity and a wide linear range (25-500 μM) for glucose detection.
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Affiliation(s)
- Zixin Zhou
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Zijing Gao
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Hao Shen
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Mengqi Li
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Wenting He
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry , Beijing University of Chemical Technology , Beijing 100029 , China
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47
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Theoretical design and experimental study of new aptamers with the improved target-affinity: New insights into the Pb2+-specific aptamers as a case study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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