1
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Zdun B, Borowiecki P. Vinyl 3-(Dimethylamino)propanoate as an Irreversible Acyl Donor Reagent in a Chromatography-free Lipase-Catalyzed Kinetic Resolution of sec-Alcohols. Chembiochem 2024; 25:e202400394. [PMID: 39031858 DOI: 10.1002/cbic.202400394] [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: 04/30/2024] [Revised: 06/11/2024] [Accepted: 06/18/2024] [Indexed: 07/22/2024]
Abstract
The reported chemoenzymatic strategy involves the employment of vinyl 3-(dimethylamino)propanoate as an irreversible acyl donor in a chromatography-free lipase-catalyzed kinetic resolution (KR) of racemic sec-alcohols. This biotransformation is achieved in a sequential manner using CAL-B to affect the kinetic resolution, followed by a simple acidic extractive work-up furnishing both KR products with excellent enantioselectivity (E>200; up to 98 % ee). The elaborated method eliminates a single-use silica gel chromatographic separation and significantly reduces organic solvent consumption to foster a more environmentally friendly chemical industry.
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Affiliation(s)
- Beata Zdun
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Paweł Borowiecki
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
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2
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Kuroiwa T, Katayama M, Uemoto K, Kanazawa A. Substrate specificity of commercial lipases activated by a hydration-aggregation pretreatment in anhydrous esterification reactions. Enzyme Microb Technol 2024; 180:110497. [PMID: 39154569 DOI: 10.1016/j.enzmictec.2024.110497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 08/01/2024] [Accepted: 08/11/2024] [Indexed: 08/20/2024]
Abstract
Substrate specificity in non-aqueous esterification catalyzed by commercial lipases activated by hydration-aggregation pretreatment was investigated. Four microbial lipases from Rhizopus japonicus, Burkholderia cepacia, Rhizomucor miehei, and Candida antarctica (fraction B) were used to study the effect of the carbon chain length of saturated fatty acid substrates on the esterification activity with methanol in n-hexane. Hydration-aggregation pretreatment had an activation effect on all lipases used, and different chain length dependencies of esterification activity for lipases from different origins were demonstrated. The effects of various acidic substrates with different degrees of unsaturation, aromatic rings, and alcohol substrates with different carbon chain lengths on esterification activity were examined using R. japonicus lipase, which demonstrated the most remarkable activity enhancement after hydration-aggregation pretreatment. Furthermore, in the esterification of myristic acid with methanol catalyzed by the hydrated-aggregated R. japonicus lipase, maximum reaction rate (5.43 × 10-5 mmol/(mg-biocat min)) and Michaelis constants for each substrate (48.5 mM for myristic acid, 24.7 mM for methanol) were determined by kinetic analysis based on the two-substrate Michaelis-Menten model.
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Affiliation(s)
- Takashi Kuroiwa
- Department of Applied Chemistry, Faculty of Science and Engineering, Tokyo City University, 1-28-1 Tamazutsumi, Setagaya-ku, Tokyo 158-8557, Japan.
| | - Maho Katayama
- Department of Applied Chemistry, Faculty of Science and Engineering, Tokyo City University, 1-28-1 Tamazutsumi, Setagaya-ku, Tokyo 158-8557, Japan
| | - Kazuki Uemoto
- Department of Applied Chemistry, Faculty of Science and Engineering, Tokyo City University, 1-28-1 Tamazutsumi, Setagaya-ku, Tokyo 158-8557, Japan
| | - Akihiko Kanazawa
- Department of Applied Chemistry, Faculty of Science and Engineering, Tokyo City University, 1-28-1 Tamazutsumi, Setagaya-ku, Tokyo 158-8557, Japan
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3
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Chong W, Zhang Z, Li Z, Meng S, Nian B, Hu Y. Hook loop dynamics engineering transcended the barrier of activity-stability trade-off and boosted the thermostability of enzymes. Int J Biol Macromol 2024; 278:134953. [PMID: 39181358 DOI: 10.1016/j.ijbiomac.2024.134953] [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: 07/04/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
The improvement of enzyme thermostability often accompanies the decreased activity due to the loss of the key regions' flexibility. As a representative structure, unlocking the potential of loop dynamics will not only provide new ideas for stabilization strategies, but also help to deepen the understanding of the relationship between enzyme structural dynamics and function. In this study, a creative "hook loop dynamics engineering" (HLoD) strategy was successfully proposed for simultaneously improving the thermostability and maintaining activity of the model enzyme, Candida Antarctica lipase B. A small and smart mutant library involving five key residues located at the "hook loop" was meticulously identified and systematically investigated and thus yielded a five-point multiple mutant M1 (L147S/T244P/S250P/T256D/N292D), demonstrating a remarkable 7.0-fold increase in thermostability at 60 °C compared to the wild-type (WT). Furthermore, the activity of M1 remained comparable to that of WT, effectively transcending the barrier of activity-stability trade-off. Molecular dynamics simulations revealed that the precise regulation of hook loop dynamics via intermolecular interactions, such as salt bridges and hydrogen bonding, curbed the excessive flexibility of the pivotal regions α5 and α10 at high temperatures, thus driving the substantial enhancement of the thermostability of M1. Refining the dynamics of the flexible region via HLoD, which transcended the barrier of activity-stability trade-off, exhibited to be a robust and potentially universal strategy for designing enzymes with outstanding thermostability and activity.
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Affiliation(s)
- Wenya Chong
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech university, Nanjing 210009, Jiangsu Province, People's Republic of China
| | - Zihan Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech university, Nanjing 210009, Jiangsu Province, People's Republic of China
| | - Zhongyu Li
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Shuaiqi Meng
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech university, Nanjing 210009, Jiangsu Province, People's Republic of China.
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech university, Nanjing 210009, Jiangsu Province, People's Republic of China.
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4
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Brandolín SE, Scilipoti JA, Magario I. Elucidating solvent effects on lipase-catalyzed peroxyacid synthesis through activity-based kinetics and molecular dynamics. Biotechnol Bioeng 2024; 121:2728-2741. [PMID: 38837223 DOI: 10.1002/bit.28762] [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: 03/12/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
Peroxyacid synthesis is the first step in Prilezhaev epoxidation, which is an industrial method to form epoxides. Motivated by the development of a kinetic model as a tool for solvent selection, the effect of solvent type and acid chain length on the lipase-catalyzed peroxyacid synthesis was studied. A thermodynamic activity-based ping-pong kinetic expression was successfully applied to predict the effect of the reagent loadings in hexane. The activity-based reaction quotients provided a prediction of solvent-independent equilibrium constants. However, this strategy did not achieve satisfactory estimations of initial rates in solvents of higher polarity. The lack of compliance with some assumptions of this methodology could be confirmed through molecular dynamics calculations i.e. independent solvation energies and lack of solvent interaction with the active site. A novel approach is proposed combining the activity-based kinetic expression and the free binding energy of the solvent with the active site to predict kinetics upon solvent change. Di-isopropyl ether generated a strong interaction with the enzyme's active site, which was detrimental to kinetics. On the other hand, toluene or limonene gave moderate interaction with the active site rendering improved catalytic yield compared with less polar solvents, a finding sharpened when peroctanoic acid was produced.
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Affiliation(s)
- Salvador E Brandolín
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada (IPQA), Facultad de Ciencias Exactas, Física y Naturales - Universidad Nacional de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - José A Scilipoti
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada (IPQA), Facultad de Ciencias Exactas, Física y Naturales - Universidad Nacional de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Ivana Magario
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada (IPQA), Facultad de Ciencias Exactas, Física y Naturales - Universidad Nacional de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
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5
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Campodónico PR, Alarcón-Espósito J, Alcázar JJ, Olivares B, Suárez-Rozas C. Analysis of the Behavior of Deep Eutectic Solvents upon Addition of Water: Its Effects over a Catalytic Reaction. Molecules 2024; 29:3296. [PMID: 39064875 PMCID: PMC11279026 DOI: 10.3390/molecules29143296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/21/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
This study presents the potential role of deep eutectic solvents (DESs) in a lipase-catalyzed hydrolysis reaction as a co-solvent in an aqueous solution given by a phosphate buffer. Ammonium salts, such as choline chloride, were paired with hydrogen bond donors, such as urea, 1,2,3-propanetriol, and 1,2 propanediol. The hydrolysis of p-nitrophenyl laureate was carried out with the lipase Candida antarctica Lipase B (CALB) as a reaction model to evaluate the solvent effect and tested in different DES/buffer phosphate mixtures at different % w/w. The results showed that two mixtures of different DES at 25 % w/w were the most promising solvents, as this percentage enhanced the activities of CALB, as evidenced by its higher catalytic efficiency (kcatKM). The solvent analysis shows that the enzymatic reaction requires a reaction media rich in water molecules to enable hydrogen-bond formation from the reaction media toward the enzymatic reaction, suggesting a better interaction between the substrate and the enzyme-active site. This interaction could be attributed to high degrees of freedom influencing the enzyme conformation given by the reaction media, suggesting that CALB acquires a more restrictive structure in the presence of DES or the stabilized network given by the hydrogen bond from water molecules in the mixture improves the enzymatic activity, conferring conformational stability by solvent effects. This study offers a promising approach for applications and further perspectives on genuinely green industrial solvents.
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Affiliation(s)
- Paola R. Campodónico
- Centro de Química Médica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 10021, Chile; (J.J.A.); (B.O.); (C.S.-R.)
| | - Jazmín Alarcón-Espósito
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Jackson J. Alcázar
- Centro de Química Médica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 10021, Chile; (J.J.A.); (B.O.); (C.S.-R.)
| | - Belén Olivares
- Centro de Química Médica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 10021, Chile; (J.J.A.); (B.O.); (C.S.-R.)
| | - Cristian Suárez-Rozas
- Centro de Química Médica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 10021, Chile; (J.J.A.); (B.O.); (C.S.-R.)
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6
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Zhao H, Zhang J, Liu Y, Liu X, Ma L, Zhou L, Gao J, Liu G, Yue X, Jiang Y. Molecular Engineering and Morphology Control of Covalent Organic Frameworks for Enhancing Activity of Metal-Enzyme Cascade Catalysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400730. [PMID: 38654621 PMCID: PMC11220694 DOI: 10.1002/advs.202400730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Metal-enzyme integrated catalysts (MEICs) that combine metal and enzyme offer great potential for sustainable chemoenzymatic cascade catalysis. However, rational design and construction of optimal microenvironments and accessible active sites for metal and enzyme in individual nanostructures are necessary but still challenging. Herein, Pd nanoparticles (NPs) and Candida antarctica lipase B (CALB) are co-immobilized into the pores and surfaces of covalent organic frameworks (COFs) with tunable functional groups, affording Pd/COF-X/CALB (X = ONa, OH, OMe) MEICs. This strategy can regulate the microenvironment around Pd NPs and CALB, and their interactions with substrates. As a result, the activity of the COF-based MEICs in catalyzing dynamic kinetic resolution of primary amines is enhanced and followed COF-OMe > COF-OH > COF-ONa. The experimental and simulation results demonstrated that functional groups of COFs modulated the conformation of CALB, the electronic states of Pd NPs, and the affinity of the integrated catalysts to the substrate, which contributed to the improvement of the catalytic activity of MEICs. Further, the MEICs are prepared using COF with hollow structure as support material, which increased accessible active sites and mass transfer efficiency, thus improving catalytic performance. This work provides a blueprint for rational design and preparation of highly active MEICs.
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Affiliation(s)
- Hao Zhao
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
| | - Jialin Zhang
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
| | - Yunting Liu
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
| | - Xinlong Liu
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
| | - Li Ma
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
| | - Liya Zhou
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
| | - Jing Gao
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
| | - Guanhua Liu
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
| | - Xiaoyang Yue
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
| | - Yanjun Jiang
- National‐Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources UtilizationSchool of Chemical Engineering and TechnologyHebei University of TechnologyTianjin300401China
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7
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Papatola F, Slimani S, Peddis D, Pellis A. Biocatalyst immobilization on magnetic nano-architectures for potential applications in condensation reactions. Microb Biotechnol 2024; 17:e14481. [PMID: 38850268 PMCID: PMC11162105 DOI: 10.1111/1751-7915.14481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 06/10/2024] Open
Abstract
In this review article, a perspective on the immobilization of various hydrolytic enzymes onto magnetic nanoparticles for synthetic organic chemistry applications is presented. After a first part giving short overview on nanomagnetism and highlighting advantages and disadvantages of immobilizing enzymes on magnetic nanoparticles (MNPs), the most important hydrolytic enzymes and their applications were summarized. A section reviewing the immobilization techniques with a particular focus on supporting enzymes on MNPs introduces the reader to the final chapter describing synthetic organic chemistry applications of small molecules (flavour esters) and polymers (polyesters and polyamides). Finally, the conclusion and perspective section gives the author's personal view on further research discussing the new idea of a synergistic rational design of the magnetic and biocatalytic component to produce novel magnetic nano-architectures.
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Affiliation(s)
- F Papatola
- Dipartimento di Chimica e Chimica Industriale, Università di Genova, Genoa, Italy
| | - S Slimani
- Dipartimento di Chimica e Chimica Industriale, Università di Genova, Genoa, Italy
- CNR, Istituto di Struttura Della Materia, nM2-Lab, Monterotondo Scalo (Roma), Italy
| | - D Peddis
- Dipartimento di Chimica e Chimica Industriale, Università di Genova, Genoa, Italy
- CNR, Istituto di Struttura Della Materia, nM2-Lab, Monterotondo Scalo (Roma), Italy
| | - A Pellis
- Dipartimento di Chimica e Chimica Industriale, Università di Genova, Genoa, Italy
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8
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Mu J, Li Z, Zhang B, Zhang Q, Iqbal J, Wadood A, Wei T, Feng Y, Chen HF. Graphormer supervised de novo protein design method and function validation. Brief Bioinform 2024; 25:bbae135. [PMID: 38557677 PMCID: PMC10982952 DOI: 10.1093/bib/bbae135] [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: 10/07/2023] [Revised: 01/31/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Protein design is central to nearly all protein engineering problems, as it can enable the creation of proteins with new biological functions, such as improving the catalytic efficiency of enzymes. One key facet of protein design, fixed-backbone protein sequence design, seeks to design new sequences that will conform to a prescribed protein backbone structure. Nonetheless, existing sequence design methods present limitations, such as low sequence diversity and shortcomings in experimental validation of the designed functional proteins. These inadequacies obstruct the goal of functional protein design. To improve these limitations, we initially developed the Graphormer-based Protein Design (GPD) model. This model utilizes the Transformer on a graph-based representation of three-dimensional protein structures and incorporates Gaussian noise and a sequence random masks to node features, thereby enhancing sequence recovery and diversity. The performance of the GPD model was significantly better than that of the state-of-the-art ProteinMPNN model on multiple independent tests, especially for sequence diversity. We employed GPD to design CalB hydrolase and generated nine artificially designed CalB proteins. The results show a 1.7-fold increase in catalytic activity compared to that of the wild-type CalB and strong substrate selectivity on p-nitrophenyl acetate with different carbon chain lengths (C2-C16). Thus, the GPD method could be used for the de novo design of industrial enzymes and protein drugs. The code was released at https://github.com/decodermu/GPD.
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Affiliation(s)
- Junxi Mu
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, No.5 Yiheyuan Road, Beijing, 100871, China
| | - Zhengxin Li
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Bo Zhang
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qi Zhang
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Ting Wei
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
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9
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Li Y, Guo J, Sun S. Decreasing acid value of fatty acid ethyl ester products using complex enzymes. Front Bioeng Biotechnol 2024; 12:1355009. [PMID: 38390361 PMCID: PMC10882546 DOI: 10.3389/fbioe.2024.1355009] [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: 12/13/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Recently, enzymatic method has been used to prepare biodiesel using various oils. But the high acid value of the biodiesel product using enzyme as a catalyst has been one issue. In this work, an attempt to reduce the acid value of fatty acid ethyl ester (FAEE) product to satisfy the specified requirement (AV ≤ 0.5 mgKOH/g), a complex enzyme-catalyzed method was used for the ethanolysis of Semen Abutili seed oil (SASO) (AV = 5.5 ± 0.3 mgKOH/g). The effects of various variables (constituents of complex enzyme, type and addition of water removal agent, time, temperature, enzyme addition load, substrate ratio) on the enzymatic reaction were investigated. The optimal reaction conditions were: 1% addition of liquid lipase Eversa® Transform 2.0% and 0.8% of enzyme dry powder CALB, reaction temperature 35°C, alcohol-oil ratio 9:1 (mol/mol), 0.8 g/g of 4A-MS and reaction time 24 h. Under the optimal reaction conditions, the FAEE yield was 90.8% ± 1.5% and its acid value was decreased from 12.0 ± 0.2 mgKOH/g to 0.39 ± 0.10 mgKOH/g. In further evaluating the feasibility of preparing FAEE from SASO, the FAEE products obtained under the optimal reaction conditions were purified and evaluated with reference to the ASTM D6751 standard for the main physicochemical indexes. The results obtained were in accordance with the requirements except for the oxidative stability.
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Affiliation(s)
- Yuting Li
- Lipid Technology and Engineering, Henan University of Technology, Zhengzhou, China
| | - Jingjing Guo
- Lipid Technology and Engineering, Henan University of Technology, Zhengzhou, China
| | - Shangde Sun
- Lipid Technology and Engineering, Henan University of Technology, Zhengzhou, China
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10
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Jaito N, Kaewsawat N, Phetlum S, Uengwetwanit T. Metagenomic discovery of lipases with predicted structural similarity to Candida antarctica lipase B. PLoS One 2023; 18:e0295397. [PMID: 38055755 PMCID: PMC10699602 DOI: 10.1371/journal.pone.0295397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
Here we employed sequence-based and structure-based screening for prospecting lipases that have structural homolog to Candida antarctica lipase B (CalB). CalB, a widely used biocatalyst, was used as structural template reference because of its enzymatic properties. Structural homolog could aid in the discovery of novel wild-type enzymes with desirable features and serve as a scaffold for further biocatalyst design. The available metagenomic data isolated from various environments was leveraged as a source for bioprospecting. We identified two bacteria lipases that showed high structural similarity to CalB with <40% sequence identity. Partial purification was conducted. In comparison to CalB, the enzymatic characteristics of two potential lipases were examined. A candidate exhibited optimal pH of 8 and temperature of 50°C similar to CalB. The second lipase candidate demonstrated an optimal pH of 8 and a higher optimal temperature of 55°C. Notably, this candidate sustained considerable activity at extreme conditions, maintaining high activity at 70°C or pH 9, contrasting with the diminished activity of CalB under similar conditions. Further comprehensive experimentation is warranted to uncover and exploit these novel enzymatic properties for practical biotechnological purposes.
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Affiliation(s)
- Nongluck Jaito
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nattha Kaewsawat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Suthathip Phetlum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Tanaporn Uengwetwanit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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11
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Zieniuk B, Stępniewski TM, Fabiszewska A. Do they make a good match? Molecular dynamics studies on CALB-catalyzed esterification of 3-phenylpropionic and cinnamic acids. Arch Biochem Biophys 2023; 750:109807. [PMID: 37923242 DOI: 10.1016/j.abb.2023.109807] [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: 07/03/2023] [Revised: 10/07/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Lipases are versatile catalysts widely used in industrial biotransformations and laboratory-scale developed reactions with industrial potential. Despite the fact that lipase B from Candida antarctica (CALB) is one of the most widely used lipolytic enzymes, its substrate specificity is still poorly understood. One observed trend is that reactions carried out with carboxylic acids containing a double bond are less efficient on average. Here, we have utilized a combination of in vitro and in silico techniques, to better understand the negative impact of a double bond on CALB-mediated esterification. Then through extensive molecular dynamics (MD) simulations, we were able to map the entry pathway of cinnamic acid and its derivative into the CALB active site, and their interactions with catalytic residues. We observed a 2 step binding mechanism of studied compounds, where they first penetrate the enzyme pocket in a conformation where their carboxylic groups are extended towards the solvent. This is followed by further penetration of the acid into the enzymatic active pocket, and a full rotation within the active site, which orients the acid in a conformation that allows further steps of the esterification reaction. As acids containing a double bond are more rigid, their mobility and thus ability to rotate in the narrow CALB active site is hampered, which provides a structural explanation for the decreased efficiency of such acids. Our data provide insight into the substrate specificity of CALB-mediated esterification, providing important structural guidelines to better understand and potentially improve the efficiency of such reactions.
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Affiliation(s)
- Bartłomiej Zieniuk
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, 159c Nowoursynowska Street, 02-776, Warsaw, Poland.
| | - Tomasz Maciej Stępniewski
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Pompeu Fabra University (UPF), 08003, Barcelona, Spain; InterAx Biotech AG, PARK InnovAARE, 5234, Villigen, Switzerland.
| | - Agata Fabiszewska
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, 159c Nowoursynowska Street, 02-776, Warsaw, Poland.
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12
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Pedro KCNR, da Silva JVV, Cipolatti EP, Manoel EA, Campisano ISP, Henriques CA, Langone MAP. Adsorption of lipases on porous silica-based materials for esterification in a solvent-free system. 3 Biotech 2023; 13:380. [PMID: 37900269 PMCID: PMC10600090 DOI: 10.1007/s13205-023-03801-x] [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: 04/01/2023] [Accepted: 10/03/2023] [Indexed: 10/31/2023] Open
Abstract
This study deals with lipase immobilization on micro- and mesoporous silica-based materials. The effects of the type of support (silica MCM-41, zeolite HZSM-5 (SAR 25), zeolite HZSM-5 (SAR 280), and the silica-aluminas Siral 10, Siral 20, and Siral 40) were investigated on the immobilization of lipase B from Candida antarctica (CALB) and lipase from Rhizomucor miehei (RML). The supports that allowed the highest immobilization efficiencies for the CALB were Siral 40 (91.4%), HZSM-5 (SAR 280) (90.6%), and MCM-41 (89.4%). Siral 20 allowed the highest immobilization efficiency for RML (97.6%), followed by HZSM-5 (SAR 25) (77.1%) and HZSM-5 (SAR 280) (62.7%). The effect of protein concentration on lipase immobilization was investigated, and the results adjusted well on the Langmuir isotherm model (R2 > 0.9). The maximum protein adsorption capacity of the support determined by the Langmuir model was equal to 10.64 and 20.97 mgprotein gsupport-1 for CALB and RML, respectively. The effects of pH (pH 7.0 and pH 11.0) and phosphate buffer solution concentration (5 and 100 mmol L-1) were also investigated on lipase immobilization. The immobilization efficiency for both lipases was similar for the different pH values. The use of 100 mmol L-1 phosphate buffer decreased the lipase immobilization efficiency. The biocatalysts (CALB-Siral 40 and RML-Siral 20) were tested in the ethyl oleate synthesis. The conversion of 61.7% was obtained at 60 °C in the reaction catalyzed by CALB-Siral 40. Both heterogeneous biocatalysts showed increased thermal stability compared with their free form. Finally, the reuse of the biocatalysts was studied. CALB-Siral 40 and RML-Siral 20 maintained about 30% of the initial conversion after 3 batches of ethyl oleate synthesis. Silica-aluminas (Siral 20 and 40) proved to be a support that allowed a high efficiency of immobilization of lipases and activity for esterification reaction.
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Affiliation(s)
- Kelly C N R Pedro
- Departamento de Química Analítica, Instituto de Química, Universidade do Estado do Rio de Janeiro (UERJ), Rua São Francisco Xavier, 524, 20550-900 Rio de Janeiro, RJ Brasil
| | - João V V da Silva
- Departamento de Química Analítica, Instituto de Química, Universidade do Estado do Rio de Janeiro (UERJ), Rua São Francisco Xavier, 524, 20550-900 Rio de Janeiro, RJ Brasil
| | - Eliane P Cipolatti
- Departamento de Engenharia Química, Instituto de Tecnologia, Universidade Federal Rural Do Rio de Janeiro, Rodovia BR 465, Km 07- Zona Rural, 23890-000 Seropédica, RJ Brasil
| | - Evelin A Manoel
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro (UFRJ), 21941-170 Rio de Janeiro, RJ Brasil
| | - Ivone S P Campisano
- Departamento de Química Analítica, Instituto de Química, Universidade do Estado do Rio de Janeiro (UERJ), Rua São Francisco Xavier, 524, 20550-900 Rio de Janeiro, RJ Brasil
| | - Cristiane A Henriques
- Departamento de Química Analítica, Instituto de Química, Universidade do Estado do Rio de Janeiro (UERJ), Rua São Francisco Xavier, 524, 20550-900 Rio de Janeiro, RJ Brasil
| | - Marta A P Langone
- Departamento de Química Analítica, Instituto de Química, Universidade do Estado do Rio de Janeiro (UERJ), Rua São Francisco Xavier, 524, 20550-900 Rio de Janeiro, RJ Brasil
- Instituto Federal de Educação, Ciência e Tecnologia Do Rio de Janeiro, Rua Senador Furtado, 121, 20260-100 Rio de Janeiro, RJ Brasil
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13
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Monteiro RRC, Berenguer-Murcia Á, Rocha-Martin J, Vieira RS, Fernandez-Lafuente R. Biocatalytic production of biolubricants: Strategies, problems and future trends. Biotechnol Adv 2023; 68:108215. [PMID: 37473819 DOI: 10.1016/j.biotechadv.2023.108215] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/22/2023]
Abstract
The increasing worries by the inadequate use of energy and the preservation of nature are promoting an increasing interest in the production of biolubricants. After discussing the necessity of producing biolubricants, this review focuses on the production of these interesting molecules through the use of lipases, discussing the different possibilities (esterification of free fatty acids, hydroesterification or transesterification of oils and fats, transesterification of biodiesel with more adequate alcohols, estolides production, modification of fatty acids). The utilization of discarded substrates has special interest due to the double positive ecological impact (e.g., oil distillated, overused oils). Pros and cons of all these possibilities, together with general considerations to optimize the different processes will be outlined. Some possibilities to overcome some of the problems detected in the production of these interesting compounds will be also discussed.
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Affiliation(s)
- Rodolpho R C Monteiro
- Departamento de Engenharia Química, Universidade Federal do Ceará, Campus do Pici, 60455760 Fortaleza, Brazil
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, 03080 Alicante, Spain
| | - Javier Rocha-Martin
- Departamento de Bioquímica y Biología Molecular, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - Rodrigo S Vieira
- Departamento de Engenharia Química, Universidade Federal do Ceará, Campus do Pici, 60455760 Fortaleza, Brazil.
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14
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Tjørnelund HD, Vind J, Brask J, Woodley JM, Peters GH. Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations. Comput Struct Biotechnol J 2023; 21:5451-5462. [PMID: 38022691 PMCID: PMC10665702 DOI: 10.1016/j.csbj.2023.10.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Applications of lipases in low-water environments are found across a broad range of industries, including the pharmaceutical and oleochemical sectors. This includes condensation reactions in organic solvents where the enzyme activity has been found to depend strongly on both the solvent and the water activity (aw). Despite several experimental and computational studies, knowledge is largely empirical, and a general predictive approach is much needed. To close this gap, we chose native Candida antarctica lipase B (CALB) and two mutants thereof and used molecular dynamics (MD) simulations to gain a molecular understanding of the effect of aw on the specific activity of CALB in hexane. Based on the simulations, we propose four criteria to understand the performance of CALB in organic media, which is supported by enzyme kinetics experiments. First, the lipase must be stable in the organic solvent, which was the case for native CALB and the two mutants studied here. Secondly, water clusters that form and grow close to the active site must not block the path of substrate molecules into the active site. Thirdly, the lipase's lid must not cover the active site. Finally, mutations and changes in aw must not disrupt the geometry of the active site. We show that mutating specific residues close to the active site can hinder water cluster formation and growth, making the lipase resistant to changes in aw. Our computational screening criteria could potentially be used to screen in-silico designed variants, so only promising candidates could be pushed forward to characterisation.
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Affiliation(s)
- Helena D. Tjørnelund
- Department of Chemistry, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | | | | | - John M. Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Günther H.J. Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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15
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Chan KK, Sundaram V, Tan J, Ho YK, Ramanan RN, Ooi CW. Enhanced activity of Candida antarctica lipase B in cholinium aminoate ionic liquids: a combined experimental and computational analysis. J Biomol Struct Dyn 2023:1-15. [PMID: 37787564 DOI: 10.1080/07391102.2023.2262590] [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: 07/18/2023] [Accepted: 09/16/2023] [Indexed: 10/04/2023]
Abstract
As a class of ionic liquids with higher biocompatibility, cholinium aminoates ([Cho][AA]) hold potential as solvation media for enzymatic bioprocessing. Herein, solvation effect of [Cho][AA] on structural stability and enzymatic activity of Candida antarctica lipase B (CALB) was evaluated using experimental and computational approaches. Influence of [Cho][AA] on CALB stability was investigated using amino acid anions ([AA]-) with varying hydrophobicity levels. Choline phenylalaninate ([Cho][Phe]) resulted in 109.1% and 110.4% of relative CALB activity to buffer medium at 25 °C and 50 °C, respectively. Simulation results revealed the improvement of CALB's enzymatic activities by [AA]- with a strong hydrophobic character. Shielding of CALB from water molecules by [AA]- was observed. The level of CALB activity was governed by accumulation level of [AA]- at CALB's first hydration layer. The stronger interaction between His224 and Asp187 was postulated to be driven by [Cho][AA], resulting in the activity enhancement of CALB. The slight improvement of CALB activity in 0.05 M [Cho][Phe] at 50 °C could be due to the larger size of entrance to the catalytic site and the stronger interaction between the catalytic residues. The promising effect of [Cho][Phe] on CALB activation may stimulate research efforts in designing a 'fully green' bioreaction for various industrial applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kam Khong Chan
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
| | - Vidya Sundaram
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India
| | - Jully Tan
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
| | - Yong Kuen Ho
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
| | - Ramakrishnan Nagasundara Ramanan
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
| | - Chien Wei Ooi
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
- Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
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16
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Martin Del Campo M, Gómez-Secundino O, Camacho-Ruíz RM, Mateos Díaz JC, Müller-Santos M, Rodríguez JA. Effects of kosmotropic, chaotropic, and neutral salts on Candida antarctica B lipase: An analysis of the secondary structure and its hydrolytic activity on triglycerides. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159380. [PMID: 37591327 DOI: 10.1016/j.bbalip.2023.159380] [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: 04/11/2023] [Revised: 07/22/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023]
Abstract
The effects of different concentrations of Hofmeister salts on the hydrolytic activity on triglycerides and the secondary structure of lipase B from Candida antarctica (CALB) were investigated. Structural changes after short- and long-time incubation at high salt concentrations were determined using circular dichroism (CD), fluorescence, and RMSD-RMSF simulations. At 5.2 M NaCl, the hydrolytic activity of CALB on tributyrin (TC4) and trioctanoin (TC8) was enhanced by 1.5 (from 817 ± 3.9 to 1228 ± 4.3 U/mg)- and 8.7 (from 25 ± 0.3 to 218 ± 2.3 U/mg)-folds compared with 0.15 M NaCl, respectively at pH 7.0 and 40 °C. An activity activation was seen with other salts tested; however, long-time incubation (24 h) did not result in retention of the activation effect for any of the salts tested. Secondary structure CD and fluorescence spectra showed that long-time incubation with NaCl, KCl, and CsCl provokes a compact structure without loss of native conformation, whereas chaotropic LiCl and CaCl2 induced an increase in the α-helical content, and kosmotropic Na2SO4 provoked a molten globule state with rich β-sheet content. The RMSD-RMSF simulation agreed with the CD analysis, highlighting a principal salt-induced effect at the α-helix 5 region, promoting two different conformational states (open and closed) depending on the type and concentration of salt. Lastly, an increase in the interfacial tension occurred when high salt concentrations were added to the reaction media, affecting the catalytic properties. The results indicate that high-salt environments, such as 2-5.2 M NaCl, can be used to increase the lipolytic activity of CALB on TC4 and TC8.
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Affiliation(s)
- Martha Martin Del Campo
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C, Camino el arenero 1227, El Bajío del arenal, 45019 Zapopan, Jalisco, Mexico; Fundamentos del Conocimiento, Centro Universitario del Norte, Universidad de Guadalajara, 46200 Colotlán, Jalisco, Mexico.
| | - Osvaldo Gómez-Secundino
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C, Camino el arenero 1227, El Bajío del arenal, 45019 Zapopan, Jalisco, Mexico.
| | - Rosa M Camacho-Ruíz
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C, Camino el arenero 1227, El Bajío del arenal, 45019 Zapopan, Jalisco, Mexico.
| | - Juan C Mateos Díaz
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C, Camino el arenero 1227, El Bajío del arenal, 45019 Zapopan, Jalisco, Mexico.
| | - Marcelo Müller-Santos
- Departamento de Bioquímica e Biología Molecular, Universidade Federal do Paraná, CP 19046, CEP 81531-980 Curitiba, PR, Brazil.
| | - Jorge A Rodríguez
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C, Camino el arenero 1227, El Bajío del arenal, 45019 Zapopan, Jalisco, Mexico.
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17
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Fernandez-Lopez L, Roda S, Robles-Martín A, Muñoz-Tafalla R, Almendral D, Ferrer M, Guallar V. Enhancing the Hydrolytic Activity of a Lipase towards Larger Triglycerides through Lid Domain Engineering. Int J Mol Sci 2023; 24:13768. [PMID: 37762071 PMCID: PMC10530837 DOI: 10.3390/ijms241813768] [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: 08/03/2023] [Revised: 08/23/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Lipases have valuable potential for industrial use, particularly those mostly active against water-insoluble substrates, such as triglycerides composed of long-carbon chain fatty acids. However, in most cases, engineered variants often need to be constructed to achieve optimal performance for such substrates. Protein engineering techniques have been reported as strategies for improving lipase characteristics by introducing specific mutations in the cap domain of esterases or in the lid domain of lipases or through lid domain swapping. Here, we improved the lipase activity of a lipase (WP_075743487.1, or LipMRD) retrieved from the Marine Metagenomics MarRef Database and assigned to the Actinoalloteichus genus. The improvement was achieved through site-directed mutagenesis and by substituting its lid domain (FRGTEITQIKDWLTDA) with that of Rhizopus delemar lipase (previously R. oryzae; UniProt accession number, I1BGQ3) (FRGTNSFRSAITDIVF). The results demonstrated that the redesigned mutants gain activity against bulkier triglycerides, such as glyceryl tridecanoate and tridodecanoate, olive oil, coconut oil, and palm oil. Residue W89 (LipMRD numbering) appears to be key to the increase in lipase activity, an increase that was also achieved with lid swapping. This study reinforces the importance of the lid domains and their amino acid compositions in determining the substrate specificity of lipases, but the generalization of the lid domain swapping between lipases or the introduction of specific mutations in the lid domain to improve lipase activity may require further investigation.
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Affiliation(s)
- Laura Fernandez-Lopez
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain; (L.F.-L.); (D.A.)
| | - Sergi Roda
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
| | - Ana Robles-Martín
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
- PhD Programme, Faculty of Pharmacy and Food Science, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - Rubén Muñoz-Tafalla
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
- PhD Programme, Faculty of Pharmacy and Food Science, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - David Almendral
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain; (L.F.-L.); (D.A.)
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain; (L.F.-L.); (D.A.)
| | - Víctor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
- Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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18
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Abellanas-Perez P, Carballares D, Fernandez-Lafuente R, Rocha-Martin J. Glutaraldehyde modification of lipases immobilized on octyl agarose beads: Roles of the support enzyme loading and chemical amination of the enzyme on the final enzyme features. Int J Biol Macromol 2023; 248:125853. [PMID: 37460068 DOI: 10.1016/j.ijbiomac.2023.125853] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
Lipase B from Candida antarctica (CALB) and lipase from Thermomyces lanuginosus (TLL) have been immobilized on octyl agarose at low loading and at a loading exceeding the maximum support capacity. Then, the enzymes have been treated with glutaraldehyde and inactivated at pH 7.0 in Tris-HCl, sodium phosphate and HEPES, giving different stabilities. Stabilization (depending on the buffer) of the highly loaded biocatalysts was found, very likely as a consequence of the detected intermolecular crosslinkings. This did not occur for the lowly loaded biocatalysts. Next, the enzymes were chemically aminated and then treated with glutaraldehyde. In the case of TLL, the intramolecular crosslinkings (visible by the apparent reduction of the protein size) increased enzyme stability of the lowly loaded biocatalysts, an effect that was further increased for the highly loaded biocatalysts due to intermolecular crosslinkings. Using CALB, the intramolecular crosslinkings were less intense, and the stabilization was lower, even though the intermolecular crosslinkings were quite intense for the highly loaded biocatalyst. The stabilization detected depended on the inactivation buffer. The interactions between enzyme loading and inactivating buffer on the effects of the chemical modifications suggest that the modification and inactivation studies must be performed under the target biocatalysts and conditions.
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Affiliation(s)
| | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
| | | | - Javier Rocha-Martin
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid Spain.
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19
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Lu Z, Chen M, Jin T, Nian B, Hu Y. Immobilization of Candida antarctica lipase B on ILs modified CNTs with different chain lengths: Regulation of substrate tunnel "Leucine gating". Int J Biol Macromol 2023; 248:125894. [PMID: 37479200 DOI: 10.1016/j.ijbiomac.2023.125894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023]
Abstract
Ionic liquids (ILs) have been widely used as chemical modifiers to modify the carriers and thus improve the efficiency, activity and stability of the enzymes. However, as thousands of ILs have been found up to date, it's a huge work for screening and designing suitable ILs for immobilization of enzymes. Moreover, the mechanism of improving enzymes catalytic performance is still remain ambiguous. Thus, this study investigated the impact of ILs with different chain lengths on the enzymatic properties of Candida antarctica lipase B (CALB). Molecular dynamics simulations were employed to examine the interaction between ILs modified CNTs and CALB, as well as their effects on CALB's structure. The results revealed that ILs with different chain lengths significantly influenced the absorption orientation of CALB. Tunnel analysis identified a key role for Leu278 in regulating the open or closed state of Tunnel 2 during CALB's catalytic cycle. The weak interaction analysis demonstrated that ILs with suitable chain lengths provided spatial freedom and formed strong interactions with CNTs and ILs (vdW and hbond). This led to a conformational flip of Leu278, stabilizing the open state of Tunnel 2 and improving the activity and stability of immobilized CALB. This study provides novel insights into the design of new green modifiers to modulate carrier performance and obtain immobilized enzymes with better performance, and establishes a theoretical basis for the design and selection of modifiers for ILs in future work.
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Affiliation(s)
- Zeping Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China
| | - Mei Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China
| | - Tongtong Jin
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China
| | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China.
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China.
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20
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Wijaya T, Kitao A. Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM. J Phys Chem B 2023; 127:7431-7441. [PMID: 37562019 PMCID: PMC10476181 DOI: 10.1021/acs.jpcb.3c02041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/21/2023] [Indexed: 08/12/2023]
Abstract
The conformational dynamics of Candida antarctica lipase B (CALB) was investigated by molecular dynamics (MD) simulation, parallel cascade selection MD (PaCS-MD), and the Markov state model (MSM) and mainly focused on the lid-opening motion closely related to substrate binding. All-atom MD simulation of CALB was conducted in water and on the interface of water and tricaprylin. CALB initially situated in water and separated by layers of water from the interface is spontaneously adsorbed onto the tricaprylin surface during MD simulation. The opening and closing motions of the lid are simulated by PaCS-MD, and subsequent MSM analysis provided the free-energy landscape and time scale of the conformational transitions among the closed, semiopen, and open states. The closed state is the most stable in the water system, but the stable conformation in the interface system shifts to the semiopen state. These effects could explain the energetics and kinetics origin of the previously reported interfacial activation of CALB. These findings could help expand the application of CALB toward a wide variety of substrates.
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Affiliation(s)
- Tegar
N. Wijaya
- School
of Life Science and Technology, Tokyo Institute
of Technology. 2-12-1
Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department
of Chemistry, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug, Jakarta 12220, Indonesia
| | - Akio Kitao
- School
of Life Science and Technology, Tokyo Institute
of Technology. 2-12-1
Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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21
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Williams GB, Ma H, Khusnutdinova AN, Yakunin AF, Golyshin PN. Harnessing extremophilic carboxylesterases for applications in polyester depolymerisation and plastic waste recycling. Essays Biochem 2023; 67:715-729. [PMID: 37334661 PMCID: PMC10423841 DOI: 10.1042/ebc20220255] [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: 03/19/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
The steady growth in industrial production of synthetic plastics and their limited recycling have resulted in severe environmental pollution and contribute to global warming and oil depletion. Currently, there is an urgent need to develop efficient plastic recycling technologies to prevent further environmental pollution and recover chemical feedstocks for polymer re-synthesis and upcycling in a circular economy. Enzymatic depolymerization of synthetic polyesters by microbial carboxylesterases provides an attractive addition to existing mechanical and chemical recycling technologies due to enzyme specificity, low energy consumption, and mild reaction conditions. Carboxylesterases constitute a diverse group of serine-dependent hydrolases catalysing the cleavage and formation of ester bonds. However, the stability and hydrolytic activity of identified natural esterases towards synthetic polyesters are usually insufficient for applications in industrial polyester recycling. This necessitates further efforts on the discovery of robust enzymes, as well as protein engineering of natural enzymes for enhanced activity and stability. In this essay, we discuss the current knowledge of microbial carboxylesterases that degrade polyesters (polyesterases) with focus on polyethylene terephthalate (PET), which is one of the five major synthetic polymers. Then, we briefly review the recent progress in the discovery and protein engineering of microbial polyesterases, as well as developing enzyme cocktails and secreted protein expression for applications in the depolymerisation of polyester blends and mixed plastics. Future research aimed at the discovery of novel polyesterases from extreme environments and protein engineering for improved performance will aid developing efficient polyester recycling technologies for the circular plastics economy.
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Affiliation(s)
- Gwion B Williams
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Hairong Ma
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Anna N Khusnutdinova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Alexander F Yakunin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
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22
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Yu H, Qin L, Zhou J. Effect of Oil Polarity on the Protein Adsorption at Oil-Water Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:10701-10710. [PMID: 37470337 DOI: 10.1021/acs.langmuir.3c01541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Protein adsorption at oil-water interfaces has received much attention in applications of food emulsion and biocatalysis. The protein activity is influenced by the protein orientation and conformation. The oil polarity is expected to influence the orientation and conformation of adsorbed proteins by modulating intermolecular interactions. Hence, it is possible to tune the protein emulsion stability and activity by varying the oil polarity. Martini v3.0-based coarse-grained molecular dynamics (CGMD) simulations were employed to investigate the effect of oil polarity on the orientation and conformation of hydrophobin (HFBI) and Candida antarctica lipase B (CALB) adsorbed at triolein-water, hexadecane-water, and octanol-water interfaces for the first time. The protein adsorption orientation was predicted through the hydrophobic dipole, indicating that protein adsorption exists in preferred orientations at hydrophobic oil interfaces. The conformation of the adsorbed HFBI is well conserved, whereas relatively larger conformational changes occur during the CALB adsorption as the oil hydrophobicity increases. Comparisons on the adsorption interaction energy of proteins with oils confirm the relationship between the oil polarity and the interaction strength of proteins with oils. In addition, CGMD simulations allow longer time scale simulations of the behaviors of protein adsorption at oil-water interfaces.
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Affiliation(s)
- Hai Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Lanlan Qin
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
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23
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Giraldo L, Gómez-Granados F, Moreno-Piraján JC. Biodiesel Production Using Palm Oil with a MOF-Lipase B Biocatalyst from Candida Antarctica: A Kinetic and Thermodynamic Study. Int J Mol Sci 2023; 24:10741. [PMID: 37445919 DOI: 10.3390/ijms241310741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/11/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
This research presents the results of the immobilization of Candida Antarctica Lipase B (CALB) on MOF-199 and ZIF-8 and its use in the production of biodiesel through the transesterification reaction using African Palm Oil (APO). The results show that the highest adsorption capacity, the 26.9 mg·g-1 Lipase, was achieved using ZIF-8 at 45 °C and an initial protein concentration of 1.20 mg·mL-1. The results obtained for the adsorption equilibrium studies allow us to infer that CALB was physically adsorbed on ZIF-8 while chemically adsorbed with MOF-199. It was determined that the adsorption between Lipase and the MOFs under study better fit the Sips isotherm model. The results of the kinetic studies show that adsorption kinetics follow the Elovich model for the two synthesized biocatalysts. This research shows that under the experimental conditions in which the studies were carried out, the adsorption processes are a function of the intraparticle and film diffusion models. According to the results, the prepared biocatalysts showed a high efficiency in the transesterification reaction to produce biodiesel, with methanol as a co-solvent medium. In this work, the catalytic studies for the imidazolate, ZIF-8, presented more catalytic activity when used with CALB. This system presented 95% biodiesel conversion, while the biocatalyst formed by MOF-199 and CALB generated a catalytic conversion percentage of 90%. Although both percentages are high, it should be noted that CALB-MOF-199 presented better reusability, which is due to chemical interactions.
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Affiliation(s)
- Liliana Giraldo
- Facultad de Ciencias, Departamento de Química, Universidad Nacional de Colombia, Bogotá 111231, Colombia
| | - Fernando Gómez-Granados
- Facultad de Ciencias, Departamento de Química, Universidad Nacional de Colombia, Bogotá 111231, Colombia
| | - Juan Carlos Moreno-Piraján
- Grupo de Investigación en Sólidos Porosos y Calorimetría, Facultad de Ciencias, Departamento de Química, Universidad de los Andes, Bogotá 111711, Colombia
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24
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Wu Z, Shi W, Jin M, Zhou W. Efficient enzymatic synthesis of chiral 2,3-dihydro-1,4-benzodioxane motif using engineered Candida antarctica lipase B. RSC Adv 2023; 13:18953-18959. [PMID: 37350861 PMCID: PMC10284148 DOI: 10.1039/d3ra02623j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Chiral motifs of 2,3-dihydro-1,4 benzodioxane are extensively utilized in diverse medicinal substances and bioactive natural compounds, exhibiting significant biological activities. Notable examples of such therapeutic agents include prosympal, dibozane, piperoxan, and doxazosin. In this work, using 1,4-benzodioxane-2-carboxylic acid methyl ester as the substrate, after screening 38 CALB covariant residues, we found that mutants A225F and A225F/T103A can catalyze the kinetic resolution of the substrate. The effect of temperature, cosolvent, and cosolvent concentration on kinetic resolution was investigated, revealing that the best results were achieved at 30 °C with 20% n-butanol as a cosolvent, resulting in an optimal resolution (e.e.s 97%, E = 278) at 50 mM substrate concentration. Structure analysis showed that mutation sites 225 and 103 are not among the sites that interact directly with the substrate, which means that covariant amino acids that interact remotely with the substrate also regulate enzyme catalysis. This research may provide us with a new strategy for enzyme evolution.
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Affiliation(s)
- Zhiyun Wu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University Changzhou Jiangsu 213003 China
| | - Weifeng Shi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University Changzhou Jiangsu 213003 China
| | - Ming Jin
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University Changzhou Jiangsu 213003 China
| | - Wei Zhou
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University Changzhou Jiangsu 213003 China
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25
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Świderek K, Velasco-Lozano S, Galmés MÀ, Olazabal I, Sardon H, López-Gallego F, Moliner V. Mechanistic studies of a lipase unveil effect of pH on hydrolysis products of small PET modules. Nat Commun 2023; 14:3556. [PMID: 37321996 PMCID: PMC10272158 DOI: 10.1038/s41467-023-39201-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Biocatalysis is a key technology enabling plastic recycling. However, despite advances done in the development of plastic-degrading enzymes, the molecular mechanisms that govern their catalytic performance are poorly understood, hampering the engineering of more efficient enzyme-based technologies. In this work, we study the hydrolysis of PET-derived diesters and PET trimers catalyzed by the highly promiscuous lipase B from Candida antarctica (CALB) through QM/MM molecular dynamics simulations supported by experimental Michaelis-Menten kinetics. The computational studies reveal the role of the pH on the CALB regioselectivity toward the hydrolysis of bis-(hydroxyethyl) terephthalate (BHET). We exploit this insight to perform a pH-controlled biotransformation that selectively hydrolyzes BHET to either its corresponding diacid or monoesters using both soluble and immobilized CALB. The discoveries presented here can be exploited for the valorization of BHET resulting from the organocatalytic depolymerization of PET.
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Affiliation(s)
- Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castellón, Spain.
| | - Susana Velasco-Lozano
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón, 182, 20014 Donostia-San Sebastián, Spain
| | - Miquel À Galmés
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castellón, Spain
| | - Ion Olazabal
- POLYMAT, Department of Polymer Science and Technology, University of the Basque Country UPV/EHU, Manuel de Lardizabal, 3, 20018, Donostia-San Sebastián, Spain
| | - Haritz Sardon
- POLYMAT, Department of Polymer Science and Technology, University of the Basque Country UPV/EHU, Manuel de Lardizabal, 3, 20018, Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón, 182, 20014 Donostia-San Sebastián, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castellón, Spain.
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26
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Hanreich S, Bonandi E, Drienovská I. Design of Artificial Enzymes: Insights into Protein Scaffolds. Chembiochem 2023; 24:e202200566. [PMID: 36418221 DOI: 10.1002/cbic.202200566] [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: 09/27/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
The design of artificial enzymes has emerged as a promising tool for the generation of potent biocatalysts able to promote new-to-nature reactions with improved catalytic performances, providing a powerful platform for wide-ranging applications and a better understanding of protein functions and structures. The selection of an appropriate protein scaffold plays a key role in the design process. This review aims to give a general overview of the most common protein scaffolds that can be exploited for the generation of artificial enzymes. Several examples are discussed and categorized according to the strategy used for the design of the artificial biocatalyst, namely the functionalization of natural enzymes, the creation of a new catalytic site in a protein scaffold bearing a wide hydrophobic pocket and de novo protein design. The review is concluded by a comparison of these different methods and by our perspective on the topic.
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Affiliation(s)
- Stefanie Hanreich
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Elisa Bonandi
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Ivana Drienovská
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
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27
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Jawale PV, Bhanage BM. Synthesis of decanoate compounds in deep eutectic solvent using lipase: Optimization using response surface methodology, kinetic and docking study. J INDIAN CHEM SOC 2023. [DOI: 10.1016/j.jics.2023.100950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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28
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Mohanan N, Wong MCH, Budisa N, Levin DB. Polymer-Degrading Enzymes of Pseudomonas chloroaphis PA23 Display Broad Substrate Preferences. Int J Mol Sci 2023; 24:ijms24054501. [PMID: 36901931 PMCID: PMC10003648 DOI: 10.3390/ijms24054501] [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: 01/02/2023] [Revised: 01/27/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Although many bacterial lipases and PHA depolymerases have been identified, cloned, and characterized, there is very little information on the potential application of lipases and PHA depolymerases, especially intracellular enzymes, for the degradation of polyester polymers/plastics. We identified genes encoding an intracellular lipase (LIP3), an extracellular lipase (LIP4), and an intracellular PHA depolymerase (PhaZ) in the genome of the bacterium Pseudomonas chlororaphis PA23. We cloned these genes into Escherichia coli and then expressed, purified, and characterized the biochemistry and substrate preferences of the enzymes they encode. Our data suggest that the LIP3, LIP4, and PhaZ enzymes differ significantly in their biochemical and biophysical properties, structural-folding characteristics, and the absence or presence of a lid domain. Despite their different properties, the enzymes exhibited broad substrate specificity and were able to hydrolyze both short- and medium-chain length polyhydroxyalkanoates (PHAs), para-nitrophenyl (pNP) alkanoates, and polylactic acid (PLA). Gel Permeation Chromatography (GPC) analyses of the polymers treated with LIP3, LIP4, and PhaZ revealed significant degradation of both the biodegradable as well as the synthetic polymers poly(ε-caprolactone) (PCL) and polyethylene succinate (PES).
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Affiliation(s)
- Nisha Mohanan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Michael C.-H. Wong
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, MB R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, MB R3T 2N2, Canada
- Biocatalysis Group, Technical University of Berlin, Müller-Breslau-Str. 10, D-10623 Berlin, Germany
- Correspondence: or (N.B.); (D.B.L.); Tel.: +1-204-474-7429
| | - David B. Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
- Correspondence: or (N.B.); (D.B.L.); Tel.: +1-204-474-7429
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29
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Feiten MC, Morigi I, Di Luccio M, Oliveira JV. Activity and stability of lipase from Candida Antarctica after treatment in pressurized fluids. Biotechnol Lett 2023; 45:287-298. [PMID: 36592260 DOI: 10.1007/s10529-022-03335-x] [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: 03/14/2022] [Revised: 10/13/2022] [Accepted: 11/28/2022] [Indexed: 01/03/2023]
Abstract
Lipase B from Candida antarctica (CalB) is one of the biocatalysts most used in organic synthesis due to its ability to act in several medium, wide substrate specificity and enantioselectivity, tolerance to non-aqueous environment, and resistance to thermal deactivation. Thus, the objective of this work was to treat CalB in supercritical carbon dioxide (SC-CO2) and liquefied petroleum gas (LPG), and measure its activity before and after high-pressure treatment. Residual specific hydrolytic activities of 132% and 142% were observed when CalB was exposed to SC-CO2 at 35 ℃, 75 bar and 1 h and to LPG at 65 ℃, 30 bar and 1 h, respectively. Residual activity of the enzyme treated at high pressure was still above 100% until the 20th day of storage at low temperatures. There was no difference on the residual activity loss of CalB treated with LPG and stored at different temperatures over time. Greater difference was observed between CalB treated with CO2 and flash-frozen in liquid nitrogen (- 196 ℃) followed by storage in freezer (- 10 ℃) and CalB stored in freezer at - 10 ℃. Such findings encourage deeper studies on CalB as well as other enzymes behavior under different types of pressurized fluids aiming at industrial application.
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Affiliation(s)
- Mirian Cristina Feiten
- Department of Technology, State University of Maringá (UEM), Angelo Moreira da Fonseca Ave, Umuarama, Paraná, 87506-370, Brazil.
| | - Iasmin Morigi
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), Technology Center/C.P. 476, Florianópolis, Santa Catarina, 88040-900, Brazil
| | - Marco Di Luccio
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), Technology Center/C.P. 476, Florianópolis, Santa Catarina, 88040-900, Brazil
| | - José Vladimir Oliveira
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), Technology Center/C.P. 476, Florianópolis, Santa Catarina, 88040-900, Brazil
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30
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Costa IO, Rios NS, Lima PJM, Gonçalves LRB. Synthesis of organic-inorganic hybrid nanoflowers of lipases from Candida antarctica type B (CALB) and Thermomyces lanuginosus (TLL): Improvement of thermal stability and reusability. Enzyme Microb Technol 2023; 163:110167. [DOI: 10.1016/j.enzmictec.2022.110167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/20/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
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31
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Butyl-esters synthesis from palm fatty acid distillate catalyzed by immobilized lipases in solvent-free system – optimization using a simplified method (SER). Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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32
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Lai J, Huang H, Lin M, Xu Y, Li X, Sun B. Enzyme catalyzes ester bond synthesis and hydrolysis: The key step for sustainable usage of plastics. Front Microbiol 2023; 13:1113705. [PMID: 36713200 PMCID: PMC9878459 DOI: 10.3389/fmicb.2022.1113705] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Petro-plastic wastes cause serious environmental contamination that require effective solutions. Developing alternatives to petro-plastics and exploring feasible degrading methods are two solving routes. Bio-plastics like polyhydroxyalkanoates (PHAs), polylactic acid (PLA), polycaprolactone (PCL), poly (butylene succinate) (PBS), poly (ethylene furanoate) s (PEFs) and poly (ethylene succinate) (PES) have emerged as promising alternatives. Meanwhile, biodegradation plays important roles in recycling plastics (e.g., bio-plastics PHAs, PLA, PCL, PBS, PEFs and PES) and petro-plastics poly (ethylene terephthalate) (PET) and plasticizers in plastics (e.g., phthalate esters, PAEs). All these bio- and petro-materials show structure similarity by connecting monomers through ester bond. Thus, this review focused on bio-plastics and summarized the sequences and structures of the microbial enzymes catalyzing ester-bond synthesis. Most of these synthetic enzymes belonged to α/β-hydrolases with conserved serine catalytic active site and catalyzed the polymerization of monomers by forming ester bond. For enzymatic plastic degradation, enzymes about PHAs, PBS, PCL, PEFs, PES and PET were discussed, and most of the enzymes also belonged to the α/β hydrolases with a catalytic active residue serine, and nucleophilically attacked the ester bond of substrate to generate the cleavage of plastic backbone. Enzymes hydrolysis of the representative plasticizer PAEs were divided into three types (I, II, and III). Type I enzymes hydrolyzed only one ester-bond of PAEs, type II enzymes catalyzed the ester-bond of mono-ester phthalates, and type III enzymes hydrolyzed di-ester bonds of PAEs. Divergences of catalytic mechanisms among these enzymes were still unclear. This review provided references for producing bio-plastics, and degrading or recycling of bio- and petro-plastics from an enzymatic point of view.
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Affiliation(s)
- Jinghui Lai
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Huiqin Huang
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Mengwei Lin
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Youqiang Xu
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Xiuting Li
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
| | - Baoguo Sun
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
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33
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Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection. BIOTECH (BASEL (SWITZERLAND)) 2023; 12:biotech12010006. [PMID: 36648832 PMCID: PMC9844320 DOI: 10.3390/biotech12010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023]
Abstract
Enzymes have been highly demanded in diverse applications such as in the food, pharmaceutical, and industrial fuel sectors. Thus, in silico bioprospecting emerges as an efficient strategy for discovering new enzyme candidates. A new program called ProspectBIO was developed for this purpose as it can find non-annotated sequences by searching for homologs of a model enzyme directly in genomes. Here we describe the ProspectBIO software methodology and the experimental validation by prospecting for novel lipases by sequence homology to Candida antarctica lipase B (CaLB) and conserved motifs. As expected, we observed that the new bioprospecting software could find more sequences (1672) than a conventional similarity-based search in a protein database (733). Additionally, the absence of patent protection was introduced as a criterion resulting in the final selection of a putative lipase-encoding gene from Ustilago hordei (UhL). Expression of UhL in Pichia pastoris resulted in the production of an enzyme with activity towards a tributyrin substrate. The recombinant enzyme activity levels were 4-fold improved when lowering the temperature and increasing methanol concentrations during the induction phase in shake-flask cultures. Protein sequence alignment and structural modeling showed that the recombinant enzyme has high similarity and capability of adjustment to the structure of CaLB. However, amino acid substitutions identified in the active pocket entrance may be responsible for the differences in the substrate specificities of the two enzymes. Thus, the ProspectBIO software allowed the finding of a new promising lipase for biotechnological application without the need for laborious and expensive conventional bioprospecting experimental steps.
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34
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Novel CAL-B catalyzed synthetic protocols for pyridodipyrimidines and mercapto oxadiazoles. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02116-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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35
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Souza PMP, Carballares D, Gonçalves LRB, Fernandez-Lafuente R, Rodrigues S. Immobilization of Lipase B from Candida antarctica in Octyl-Vinyl Sulfone Agarose: Effect of the Enzyme-Support Interactions on Enzyme Activity, Specificity, Structure and Inactivation Pathway. Int J Mol Sci 2022; 23:ijms232214268. [PMID: 36430745 PMCID: PMC9697615 DOI: 10.3390/ijms232214268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/21/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022] Open
Abstract
Lipase B from Candida antarctica was immobilized on heterofunctional support octyl agarose activated with vinyl sulfone to prevent enzyme release under drastic conditions. Covalent attachment was established, but the blocking step using hexylamine, ethylenediamine or the amino acids glycine (Gly) and aspartic acid (Asp) altered the results. The activities were lower than those observed using the octyl biocatalyst, except when using ethylenediamine as blocking reagent and p-nitrophenol butyrate (pNPB) as substrate. The enzyme stability increased using these new biocatalysts at pH 7 and 9 using all blocking agents (much more significantly at pH 9), while it decreased at pH 5 except when using Gly as blocking agent. The stress inactivation of the biocatalysts decreased the enzyme activity versus three different substrates (pNPB, S-methyl mandelate and triacetin) in a relatively similar fashion. The tryptophane (Trp) fluorescence spectra were different for the biocatalysts, suggesting different enzyme conformations. However, the fluorescence spectra changes during the inactivation were not too different except for the biocatalyst blocked with Asp, suggesting that, except for this biocatalyst, the inactivation pathways may not be so different.
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Affiliation(s)
- Priscila M. P. Souza
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
- Food Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 858, Fortaleza CEP 60440-900, CE, Brazil
| | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
| | - Luciana R. B. Gonçalves
- Chemical Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 709, Fortaleza CEP 60440-900, CE, Brazil
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
- Center of Excellence in Bionanoscience Research, Member of the External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (R.F.-L.); (S.R.)
| | - Sueli Rodrigues
- Food Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 858, Fortaleza CEP 60440-900, CE, Brazil
- Correspondence: (R.F.-L.); (S.R.)
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36
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Han Y, Kinfu BM, Blombach F, Cackett G, Zhang H, Pérez-García P, Krohn I, Salomon J, Besirlioglu V, Mirzaeigarakani T, Schwaneberg U, Chow J, Werner F, Streit WR. A novel metagenome-derived viral RNA polymerase and its application in a cell-free expression system for metagenome screening. Sci Rep 2022; 12:17882. [PMID: 36284144 PMCID: PMC9596486 DOI: 10.1038/s41598-022-22383-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/13/2022] [Indexed: 01/20/2023] Open
Abstract
The mining of genomes from non-cultivated microorganisms using metagenomics is a powerful tool to discover novel proteins and other valuable biomolecules. However, function-based metagenome searches are often limited by the time-consuming expression of the active proteins in various heterologous host systems. We here report the initial characterization of novel single-subunit bacteriophage RNA polymerase, EM1 RNAP, identified from a metagenome data set obtained from an elephant dung microbiome. EM1 RNAP and its promoter sequence are distantly related to T7 RNA polymerase. Using EM1 RNAP and a translation-competent Escherichia coli extract, we have developed an efficient medium-throughput pipeline and protocol allowing the expression of metagenome-derived genes and the production of proteins in cell-free system is sufficient for the initial testing of the predicted activities. Here, we have successfully identified and verified 12 enzymes acting on bis(2-hydroxyethyl) terephthalate (BHET) in a completely clone-free approach and proposed an in vitro high-throughput metagenomic screening method.
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Affiliation(s)
- Yuchen Han
- grid.9026.d0000 0001 2287 2617Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Birhanu M. Kinfu
- grid.9026.d0000 0001 2287 2617Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany ,grid.9764.c0000 0001 2153 9986Present Address: Institute for General Microbiology, Christian-Albrechts-University, 24118 Kiel, Germany
| | - Fabian Blombach
- grid.83440.3b0000000121901201Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Gwenny Cackett
- grid.83440.3b0000000121901201Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Hongli Zhang
- grid.9026.d0000 0001 2287 2617Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Pablo Pérez-García
- grid.9026.d0000 0001 2287 2617Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Ines Krohn
- grid.9026.d0000 0001 2287 2617Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Jesper Salomon
- grid.10582.3e0000 0004 0373 0797Novozymes A/S, Microbial Discovery, Bagsværd, Denmark
| | - Volkan Besirlioglu
- grid.1957.a0000 0001 0728 696XChair of Biotechnology, RWTH Aachen, Worringerweg 3, 52074 Aachen, Germany
| | - Tayebeh Mirzaeigarakani
- grid.1957.a0000 0001 0728 696XChair of Biotechnology, RWTH Aachen, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- grid.1957.a0000 0001 0728 696XChair of Biotechnology, RWTH Aachen, Worringerweg 3, 52074 Aachen, Germany
| | - Jennifer Chow
- grid.9026.d0000 0001 2287 2617Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Finn Werner
- grid.83440.3b0000000121901201Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Wolfgang R. Streit
- grid.9026.d0000 0001 2287 2617Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
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Öten AM, Atak E, Taktak Karaca B, Fırtına S, Kutlu A. Discussing the roles of proline and glycine from the perspective of cold adaptation in lipases and cellulases. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2124111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Ahmet Melih Öten
- Biology Education Center, Faculty of Science and Technology, Uppsala University, Uppsala, Sweden
| | - Evren Atak
- Bioinformatics and System Biology, Bioengineering Department, Gebze Technical University, Kocaeli, Turkey
| | - Banu Taktak Karaca
- Molecular Biology & Genetics Department, Faculty of Natural Science and Engineering, Atlas University, Istanbul, Turkey
| | - Sinem Fırtına
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
| | - Aslı Kutlu
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
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38
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Pazol J, Weiss TM, Martínez CD, Quesada O, Nicolau E. The influence of calcium ions (Ca 2+) on the enzymatic hydrolysis of lipopolysaccharide aggregates to liberate free fatty acids (FFA) in aqueous solution. JCIS OPEN 2022; 7:100058. [PMID: 37593195 PMCID: PMC10433262 DOI: 10.1016/j.jciso.2022.100058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
The chemical environment in aqueous solutions greatly influences the ability of amphiphilic molecules such as lipopolysaccharides (LPS) to aggregate into different structural phases in aqueous solutions. Understanding the substrate's morphology and conditions of aqueous solution that favor both enzymatic activity and the disruption of LPS aggregates are crucial in developing agents that can counteract the new trend of multidrug resistance by gram-negative bacteria. In this study, we developed two LPS morphologies using LPS from Escherichia coli as a model to study the in vitro hydrolytic response when using a lipase treatment. The hydrolysis was performed using lipase b from Candida antarctica to understand the catalytic effect in removing fatty acids from its lipid A moiety on different LPS aggregates. Physical and chemical characterizations of the products included dynamic light scattering, small angle X-ray scattering, Fourier transform infrared spectroscopy, thin-layer chromatography, and gas chromatography. Our results suggest a trend of prominent hydrolytic response (72% enhancement) upon the addition of calcium ions to induce LPS aggregates into bilayer formations. Moreover, our results revealed the detection of myristic acid (C14:0) as the product of the hydrolysis when using RaLPS in its aggregate forms.
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Affiliation(s)
- Jessika Pazol
- Department of Chemistry, University of Puerto Rico, Rio Piedras Campus, 17 Ave. Universidad Ste. 1701, San Juan, PR, USA, 00925-2537
- Molecular Science Research Center, University of Puerto Rico, 1390 Ponce De Leon Ave, Suite 2, San Juan, PR, USA, 00931-3346
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA, 94025
| | - Cristian D. Martínez
- Molecular Science Research Center, University of Puerto Rico, 1390 Ponce De Leon Ave, Suite 2, San Juan, PR, USA, 00931-3346
| | - Orestes Quesada
- Molecular Science Research Center, University of Puerto Rico, 1390 Ponce De Leon Ave, Suite 2, San Juan, PR, USA, 00931-3346
- Departments of Physical Sciences and Chemistry, University of Puerto Rico, Rio Piedras Campus, 17 Ave. Universidad Ste. 1701, San Juan, PR, USA, 00925-2537
| | - Eduardo Nicolau
- Department of Chemistry, University of Puerto Rico, Rio Piedras Campus, 17 Ave. Universidad Ste. 1701, San Juan, PR, USA, 00925-2537
- Molecular Science Research Center, University of Puerto Rico, 1390 Ponce De Leon Ave, Suite 2, San Juan, PR, USA, 00931-3346
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39
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Visualizing Hydrophobic and Hydrophilic Enzyme Interactions during Immobilization by Means of Infrared Microscopy. Catalysts 2022. [DOI: 10.3390/catal12090989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A novel Fourier transform infrared (FT-IR) microscopy method was developed and used to analyze the diffusion of lipase CalB in two different resins during immobilization. The method consisted of a streamlined sample preparation process and an automated transmission FT-IR microscopic measurement using a commercial benchtop device. The immobilization of CalB was performed on a hydrophobic resin containing aromatic groups (ECR1030M based on divinylbenzene) and on a hydrophilic resin containing ester groups and thus oxygen (ECR8204M based on methacrylate) and FT-IR revealed that the kinetic of immobilization and the distribution of the enzyme on the two resins were completely different. Furthermore, the technique revealed that CalB was immobilized on the external surface only in the case of the hydrophobic ECR1030M in a layer of about 50–70 µm, whereas when immobilized on the hydrophilic carrier ECR8204M the interaction of the enzyme with the carrier was uniform over the full diameter of the polymer bead. The enzyme activity however was higher on the hydrophobic support ECR1030M.
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40
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Remonatto D, Fantatto RR, Pietro RCLR, Monti R, Oliveira JV, de Paula AV, Bassan JC. Enzymatic synthesis of geranyl acetate in batch and fed-batch reactors and evaluation of its larvicidal activity against Rhipicephalus (Boophilus) microplus. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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41
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Monhemi H, Hoang HN, Standley DM, Matsuda T, Housaindokht MR. The protein-stabilizing effects of TMAO in aqueous and non-aqueous conditions. Phys Chem Chem Phys 2022; 24:21178-21187. [PMID: 36039911 DOI: 10.1039/d2cp01279k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a new water-dependent molecular mechanism for the widely-used protein stabilizing osmolyte, trimethylamine N-oxide (TMAO), whose mode of action has remained controversial. Classical interpretations, such as osmolyte exclusion from the vicinity of protein, cannot adequately explain the behavior of this osmolyte and were challenged by recent data showing the direct interactions of TMAO with proteins, mainly via hydrophobic binding. Solvent effect theories also fail to propose a straightforward mechanism. To explore the role of water and the hydrophobic association, we disabled osmolyte-protein hydrophobic interactions by replacing water with hexane and using lipase enzyme as an anhydrous-stable protein. Biocatalysis experiments showed that under this non-aqueous condition, TMAO does not act as a stabilizer, but strongly deactivates the enzyme. Molecular dynamics (MD) simulations reveal that TMAO accumulates near the enzyme and makes many hydrogen bonds with it, like denaturing osmolytes. Some TMAO molecules even reach the active site and interact strongly with the catalystic traid. In aqueous solvent, the enzyme functions well: the extent of TMAO interactions is reduced and can be divided into both polar and non-polar terms. Structural analysis shows that in water, some TMAO molecules bind to the enzyme surface like a surfactant. We show that these interactions limit water-protein hydrogen bonds and unfavorable water-hydrophobic surface contacts. Moreover, a more hydrophobic environment is formed in the solvation layer, which reduces water dynamics and subsequently, rigidifies the backbone in aqueous solution. We show that osmolyte amphiphilicity and protein surface heterogeneity can address the weaknesses of exclusion and solvent effect theories about the TMAO mechanism.
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Affiliation(s)
- Hassan Monhemi
- Department of Chemistry, University of Neyshabur, Neyshabur, Iran. .,Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hai Nam Hoang
- Department of Food Technology, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Vietnam.,Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Daron M Standley
- Laboratory of Systems Immunology, WPI Immunology Frontier Research Center Osaka University, Osaka 565-0871, Japan
| | - Tomoko Matsuda
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Mohammad Reza Housaindokht
- Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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42
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Heiligenthal L, van der Loh M, Polack M, Blaha ME, Moschütz S, Keim A, Sträter N, Belder D. Analysis of double-emulsion droplets with ESI mass spectrometry for monitoring lipase-catalyzed ester hydrolysis at nanoliter scale. Anal Bioanal Chem 2022; 414:6977-6987. [PMID: 35995875 PMCID: PMC9436884 DOI: 10.1007/s00216-022-04266-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 11/11/2022]
Abstract
Microfluidic double-emulsion droplets allow the realization and study of biphasic chemical processes such as chemical reactions or extractions on the nanoliter scale. Double emulsions of the rare type (o1/w/o2) are used here to realize a lipase-catalyzed reaction in the non-polar phase. The surrounding aqueous phase induces the transfer of the hydrophilic product from the core oil phase, allowing on-the-fly MS analysis in single double droplets. A microfluidic two-step emulsification process is developed to generate the (o1/w/o2) double-emulsion droplets. In this first example of microfluidic double-emulsion MS coupling, we show in proof-of-concept experiments that the chemical composition of the water layer can be read online using ESI–MS. Double-emulsion droplets were further employed as two-phase micro-reactors for the hydrolysis of the lipophilic ester p-nitrophenyl palmitate catalyzed by the Candida antarctica lipase B (CalB). Finally, the formation of the hydrophilic reaction product p-nitrophenol within the double-emulsion droplet micro-reactors is verified by subjecting the double-emulsion droplets to online ESI–MS analysis.
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Affiliation(s)
- Laura Heiligenthal
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany
| | - Marie van der Loh
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany
| | - Matthias Polack
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany
| | - Maximilian E Blaha
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany
| | - Susanne Moschütz
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Antje Keim
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany.
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43
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Almeida BC, Figueiredo PR, Dourado DF, Paul S, Sousa AF, Silvestre AJ, Quinn DJ, Moody TS, Carvalho AT. Development of Enzymatic Variants for the Synthesis of Bioresorbable Polyesters. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Beatriz C. Almeida
- CNC─Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra 3004-504, Portugal
| | - Pedro R. Figueiredo
- CNC─Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra 3004-504, Portugal
| | - Daniel F.A.R. Dourado
- Almac Sciences, Department of Biocatalysis and Isotope Chemistry, Almac House, 20 Seagoe Industrial Estate, Craigavon, Northern Ireland BT63 5QD, U.K
| | - Stephanie Paul
- Almac Sciences, Department of Biocatalysis and Isotope Chemistry, Almac House, 20 Seagoe Industrial Estate, Craigavon, Northern Ireland BT63 5QD, U.K
| | - Andreia F. Sousa
- CICECO─Aveiro Institute of Materials and Department of Chemistry, Aveiro 3810-193, Portugal
| | - Armando J.D. Silvestre
- CICECO─Aveiro Institute of Materials and Department of Chemistry, Aveiro 3810-193, Portugal
| | - Derek J. Quinn
- Almac Sciences, Department of Biocatalysis and Isotope Chemistry, Almac House, 20 Seagoe Industrial Estate, Craigavon, Northern Ireland BT63 5QD, U.K
- Arran Chemical Company, Unit 1 Monksland Industrial Estate, Roscommon, Athlone, Co. N37 DN24, Ireland
| | - Thomas S. Moody
- Almac Sciences, Department of Biocatalysis and Isotope Chemistry, Almac House, 20 Seagoe Industrial Estate, Craigavon, Northern Ireland BT63 5QD, U.K
- Arran Chemical Company, Unit 1 Monksland Industrial Estate, Roscommon, Athlone, Co. N37 DN24, Ireland
| | - Alexandra T.P. Carvalho
- CNC─Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra 3004-504, Portugal
- Almac Sciences, Department of Biocatalysis and Isotope Chemistry, Almac House, 20 Seagoe Industrial Estate, Craigavon, Northern Ireland BT63 5QD, U.K
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Kovács A, Yusupov M, Cornet I, Billen P, Neyts EC. Effect of natural deep eutectic solvents of non-eutectic compositions on enzyme stability. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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Extracting extremophilic lipases from aqueous streams by using biocompatible ionic liquids. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Nazarian Z, Arab SS. Solvent-dependent activity of Candida antarctica lipase B and its correlation with a regioselective mono aza-Michael addition - experimental and molecular dynamics simulation studies. Heliyon 2022; 8:e10336. [PMID: 36090210 PMCID: PMC9449572 DOI: 10.1016/j.heliyon.2022.e10336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/21/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
With the aim of gaining understanding of the molecular basis of commercially available Candida antarctica lipase B (CALB) immobilized on polyacrylic resin catalyzed regioselective mono aza-Michael addition of Benzhydrazide to Diethyl maleate we decided to carry out molecular dynamics (MD) simulation studies in parallel with our experimental study. We found a correlation between the activity of CALB and the choice of solvent. Our study showed that solvent affects the performance of the enzyme due to the binding of solvent molecules to the enzyme active site region, and the solvation energy of substrates in the different solvents. We also found that CALB is only active in nonpolar solvent (i.e. Hexane), and therefore we investigated the influence of Hexane on the catalytic activity of CALB for the reaction. The results of this study and related experimental validation from our studies have been discussed here.
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Affiliation(s)
- Zohreh Nazarian
- Faculty of Biological Sciences, Tarbiat Modares University, Jalal Highway, Tehran 14115-154, Iran
- Department of Chemistry and Petroleum Sciences, Shahid Beheshti University, Evin, Tehran 1983963113, Iran
- Corresponding author.
| | - Seyed Shahriar Arab
- Faculty of Biological Sciences, Tarbiat Modares University, Jalal Highway, Tehran 14115-154, Iran
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47
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Sampaio CS, Angelotti JAF, Fernandez-Lafuente R, Hirata DB. Lipase immobilization via cross-linked enzyme aggregates: Problems and prospects - A review. Int J Biol Macromol 2022; 215:434-449. [PMID: 35752332 DOI: 10.1016/j.ijbiomac.2022.06.139] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/20/2022] [Indexed: 02/08/2023]
Abstract
In this review we have focused on the preparation of cross-linked enzyme aggregates (CLEAs) from lipases, as these are among the most used enzyme in bioprocesses. This immobilization method is considered very attractive due to preparation simplicity, non-use of supports and the possibility of using crude enzyme extracts. CLEAs provide lipase stabilization under extreme temperature or pH conditions or in the presence of organic solvents, in addition to preventing enzyme leaching in aqueous medium. However, it presents some problems in the preparation and limitations in their use. The problems in preparation refer mainly to the crosslinking step, and may be solved using an aminated feeder. The problems in handling have been tackled designing magnetic-CLEAs or trapping the CLEAs in particles with better mechanical properties, the substrate diffusion problems has been reduced by producing more porous-CLEAs, etc. The enzyme co-immobilization using combi-CLEAs is also a new tendency. Therefore, this review explores the CLEAs methodology aimed at lipase immobilization and its applications.
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Affiliation(s)
- Camila S Sampaio
- Postgraduate Program in Biotechnology, Federal University of Alfenas, 37130-001 Alfenas, MG, Brazil
| | - Joelise A F Angelotti
- Postgraduate Program in Biotechnology, Federal University of Alfenas, 37130-001 Alfenas, MG, Brazil
| | - Roberto Fernandez-Lafuente
- Department of Biocatalysis, ICP-CSIC, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain.; Center of Excellence in Bionanoscience Research, Member of The External Scientific Advisory Board, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Daniela B Hirata
- Postgraduate Program in Biotechnology, Federal University of Alfenas, 37130-001 Alfenas, MG, Brazil.
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48
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Toledo MV, Briand LE, Ferreira ML. A Simple Molecular Model to Study the Substrate Diffusion into the Active Site of a Lipase-Catalyzed Esterification of Ibuprofen and Ketoprofen with Glycerol. Top Catal 2022. [DOI: 10.1007/s11244-022-01636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Vivek K, Sandhia GS, Subramaniyan S. Extremophilic lipases for industrial applications: A general review. Biotechnol Adv 2022; 60:108002. [PMID: 35688350 DOI: 10.1016/j.biotechadv.2022.108002] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/09/2022] [Accepted: 06/02/2022] [Indexed: 01/10/2023]
Abstract
With industrialization and development in modern science enzymes and their applications increased widely. There is always a hunt for new proficient enzymes with novel properties to meet specific needs of various industrial sectors. Along with the high efficiency, the green and eco-friendly side of enzymes attracts human attention, as they form a true answer to counter the hazardous and toxic conventional industrial catalyst. Lipases have always earned industrial attention due to the broad range of hydrolytic and synthetic reactions they catalyse. When these catalytic properties get accompanied by features like temperature stability, pH stability, and solvent stability lipases becomes an appropriate tool for use in many industrial processes. Extremophilic lipases offer the same, thermostable: hot and cold active thermophilic and psychrophilic lipases, acid and alkali resistant and active acidophilic and alkaliphilic lipases, and salt tolerant halophilic lipases form excellent biocatalyst for detergent formulations, biofuel synthesis, ester synthesis, food processing, pharmaceuticals, leather, and paper industry. An interesting application of these lipases is in the bioremediation of lipid waste in harsh environments. The review gives a brief account on various extremophilic lipases with emphasis on thermophilic, psychrophilic, halophilic, alkaliphilic, and acidophilic lipases, their sources, biochemical properties, and potential applications in recent decades.
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Affiliation(s)
- K Vivek
- Postgraduate Department of Botany and Research Centre (University of Kerala), University College, Thiruvananthapuram 695034, India
| | - G S Sandhia
- Postgraduate Department of Botany and Research Centre (University of Kerala), University College, Thiruvananthapuram 695034, India
| | - S Subramaniyan
- Postgraduate Department of Botany and Research Centre (University of Kerala), University College, Thiruvananthapuram 695034, India.
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Moosavi F, Ahrari F, Ahmadian G, Mohammadi M. Sortase-mediated immobilization of Candida antarctica lipase B (CalB) on graphene oxide; comparison with chemical approach. BIOTECHNOLOGY REPORTS 2022; 34:e00733. [PMID: 35686009 PMCID: PMC9171452 DOI: 10.1016/j.btre.2022.e00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/25/2022]
Abstract
Sortase A was used for the oriented immobilization of CalB on graphene oxide nanosheets Random attachment of CalB on GO nanosheets were performed by chemical immobilization The immobilized CalB were used for the enrichment of omega-3 fatty acids in fish oil The derivative obtained from oriented immobilization showed improved selectivity
In this study, Candida antarctica lipase B (CalB) was covalently immobilized on the surface of graphene oxide (GO) nanoparticles by sortase-mediated immobilization as well as a chemical attachment approach. Sortase is a transpeptidase that provides one-step purification and targeted immobilization of CalB from one specific site, presenting oriented attachment of the enzyme to a solid support. Chemical immobilization, on the other hand, is considered as a random immobilization, in which the protein can bind to the support from different regions of the protein surface. In this approach, amine-functionalized GO was further modified with glutaraldehyde to facilitate the covalent binding of CalB via its amine residues. The applied methods produced 60% and 100% immobilization yields and presented 0.106 U/mg and 0.085 U/mg of specific activities for the oriented and random immobilization, respectively. The stabilized enzyme with the sortase-mediated approach retained approximately 80% of its initial activity at 50°C.
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