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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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Galmés MA, Świderek K, Moliner V. Computational Studies Suggest Promiscuous Candida antarctica Lipase B as an Environmentally Friendly Alternative for the Production of Epoxides. J Chem Inf Model 2021; 61:3604-3614. [PMID: 34251205 DOI: 10.1021/acs.jcim.1c00425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Environmentally friendly processes are nowadays a trending topic to get highly desired chemical compounds and, in this sense, the use of enzyme-catalyzed routes is becoming a promising alternative to traditional synthetic methods. In the present paper, a hybrid quantum mechanics/molecular mechanics (QM/MM) computational study on the epoxidation of alkenes catalyzed by the Ser105Ala variant of the promiscuous Candida antarctica lipase B (CALB) is presented in an attempt to search for alternative paths to get useful intermediates in industries. The catalyzed reaction, described at the atomistic level with a model of the full solvated in a box of water molecules, is compared with the alternative epoxidation of alkenes by peroxy acids in chloroform. Free-energy profiles obtained at the density functional theory (DFT)/MM level show how Ser105Ala CALB is capable of epoxide short alkenes in a two-step process with free-energy barriers, in agreement with available experimental data, that are significantly lower than those of the single-step reaction in solution. The possible (R)-enantioselectivity dictated by the binding step, explored by means of alchemical QM/MM free-energy perturbation (FEP) methods, and the preference for the (S)-enantiomer derived from the free-energy landscape of the chemical steps would cancel out, thus predicting the lack of enantioselectivity experimentally observed. In general, our results provide general information on the molecular mechanism employed by a highly promiscuous enzyme, with potential applications in biotechnology.
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Affiliation(s)
- Miquel A Galmés
- BioComp group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Katarzyna Świderek
- BioComp group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- BioComp group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
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Galmés MÀ, Nödling AR, Luk L, Świderek K, Moliner V. Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes. ACS Catal 2021; 11:8635-8644. [PMID: 35875595 PMCID: PMC9299431 DOI: 10.1021/acscatal.1c02150] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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Convergent evolution has resulted in nonhomologous enzymes that
contain similar active sites that catalyze the same primary and secondary
reactions. Comparing how these enzymes achieve their reaction promiscuity
can yield valuable insights to develop functions from the optimization
of latent activities. In this work, we have focused on the promiscuous
amidase activity in the esterase from Bacillus subtilis (Bs2) and compared with the same activity in the promiscuous lipase
B from Candida antarctica (CALB). The
study, combining multiscale quantum mechanics/molecular mechanics
(QM/MM) simulations, deep machine learning approaches, and experimental
characterization of Bs2 kinetics, confirms the amidase activity of
Bs2 and CALB. The computational results indicate that both enzymes
offer a slightly different reaction environment reflected by electrostatic
effects within the active site, thus resulting in a different reaction
mechanism during the acylation step. A convolutional neural network
(CNN) has been used to understand the conserved amino acids among
the evolved protein family and suggest that Bs2 provides a more robust
protein scaffold to perform future mutagenesis studies. Results derived
from this work will help reveal the origin of enzyme promiscuity,
which will find applications in enzyme (re)design, particularly in
creating a highly active amidase.
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Affiliation(s)
- Miquel À. Galmés
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Alexander R. Nödling
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Louis Luk
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Katarzyna Świderek
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
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Peng B, Luo T, Chen F, Wang M, Fu JH, Zheng LF, Li J, Deng ZY. Stability comparison of four lipases and catalytic mechanism during the synthesis of 1,3-di-oleic-2-medium chain triacylglycerols in a trace water-in-oil system: Experimental analyses and computational simulations. J Food Biochem 2021; 45:e13667. [PMID: 33837552 DOI: 10.1111/jfbc.13667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/02/2021] [Accepted: 01/25/2021] [Indexed: 11/28/2022]
Abstract
In the present study, a kind of structured lipids, namely 1,3-di-oleic-2-medium chain (OMO) triacylglycerols, were synthesized through lipase-catalyzed reactions using coconut oil and rapeseed acid as materials in a trace water-in-oil system. Experimental analysis and computational simulations were undertaken to compare the stability of four lipases including Lipozyme RMIM, Lipozyme TLIM, Novozym 435, and Aspergillus oryzae immobilized lipase (AOIM), and illustrate catalytic mechanism of Novozym 435 during the synthesis of OMO. Fourier transform infrared and molecular dynamics simulation results demonstrated that a decrease in ordered structure (α-helix and β-sheet) led to a reduction in enzyme activity. Compared with Lipozyme RMIM and Novozym 435, Lipozyme TLIM and AOIM exhibited better stability due to a short-chain lid in TLIM, which covers activity sites, and hydrogen bonds formed between activity center of AOIM and water. Among four lipases, AOIM exhibited best catalytic performance: a OMO yield of 30.7% at 3 hr and a good stability of long term (48 hr). Density functional theory results demonstrated that specifically, during the synthesis of OMO triacylglycerol, the addition of Novozym 435 (derived from Candida antarctica lipase B, CALB) substantially lowered reaction barriers (64.4 KJ/mol with CALB vs. 332.7 KJ/mol with no lipase), aiding in the generation of OMO because of the formations of transitional tetrahedral intermediates. A trace water-in-oil system was a green and efficient alternative for lipase-catalyzed production of OMO, and this study provided crucial insights into the stability/instability and catalytic mechanisms of lipase in the synthesis of structured lipids. PRACTICAL APPLICATIONS: We compared the stability of Lipozyme RMIM, Lipozyme 435, Lipozyme TLIM, and AOIM during the synthesis of the OMO triacylglycerols in a trace water-in-oil system, where exhibited a high catalytic activity of lipase in water-oil interface. AOIM had the highest stability and showed the best catalytic performance due to the formation of hydrogen bonds. Besides, for the first time, the transition tetrahedral structure was revealed in the enzymatic synthesis of medium- and long-chain triacylglycerols. This study provides a rational approach to compare lipase stability and a possible hint to choose appropriate enzyme in a specific catalytic condition.
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Affiliation(s)
- Bin Peng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Ting Luo
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Fang Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,School of Public Health, Nanchang University, Nanchang, China
| | - Mei Wang
- The State Centre of Quality Supervision and Inspection for Camellia Products, Ganzhou, China
| | - Jin-Heng Fu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Liu-Feng Zheng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Jing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Ze-Yuan Deng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
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Singla P, Bhardwaj RD. Enzyme promiscuity – A light on the “darker” side of enzyme specificity. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1696779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Prabhjot Singla
- Department of Biochemistry, Punjab Agricultural University, Ludhiana, India
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6
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Lind MES, Himo F. Quantum Chemical Modeling of Enantioconvergency in Soluble Epoxide Hydrolase. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01562] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Maria E. S. Lind
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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8
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Świderek K, Moliner V. Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point To Redesign New Diels-Alderases. J Phys Chem B 2015; 120:2053-70. [PMID: 26624234 DOI: 10.1021/acs.jpcb.5b10527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition because of its applications in organic synthesis and the absence of efficient natural enzymes that catalyze it. In this paper, the possibilities of using the highly promiscuous Candida Antarctica lipase B as a protein scaffold to redesign a Diels-Alderase has been explored by means of theoretical quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. Free energy surfaces have been computed for two reactions in the wild-type and in several mutants with hybrid AM1/MM potentials with corrections at M06-2X/MM level. The study of the counterpart reactions in solution has allowed performing comparative analysis that render interesting conclusions. Since the dienophile anchors very well in the oxyanion hole of all tested protein variants, the slight electronic changes from reactant complex to the transition state suggest that mutations should be focused in favoring the formation of reactive conformations of a reactant complex that, in turn, would reduce the energy barrier.
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Affiliation(s)
- Katarzyna Świderek
- Institute of Applied Radiation Chemistry, Lodz University of Technology , 90-924 Lodz, Poland.,Departamento de Química Física y Analítica, Universitat Jaume I , 12071 Castellón, Spain
| | - Vicent Moliner
- Departamento de Química Física y Analítica, Universitat Jaume I , 12071 Castellón, Spain
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