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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. [PMID: 38837223 DOI: 10.1002/bit.28762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [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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2
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Delavault A, Opochenska O, Schönrock S, Hollenbach R, Ochsenreither K, Syldatk C. Intensification of Enzymatic Sorbityl Laurate Production in Dissolved and Neat Systems under Conventional and Microwave Heating. ACS OMEGA 2024; 9:17163-17173. [PMID: 38645351 PMCID: PMC11024949 DOI: 10.1021/acsomega.3c10004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 04/23/2024]
Abstract
Glycolipids such as sugar alcohol esters have been demonstrated to be relevant for numerous applications across various domains of specialty. The use of organic solvents and, more recently, deep eutectic solvents (DESs) to mediate lipase-supported bioconversions is gaining potential for industrial application. However, many challenges and limitations remain such as extensive time of production and relatively low productivities among others, which must be solved to strengthen such a biocatalytic process in industry. In this context, this study focuses on the intensification of sorbityl laurate production, as a model biocatalyzed reaction using Novozym 435, investigating the relevance of temperature, heating method, and solvent system. By increasing the reaction temperature from 50 to 90 °C, the space-time yield and product yield were considerably enhanced for reactions in DES and the organic solvent 2M2B, irrespective of the heating method (conventional or microwave heating). However, positive effects in 2M2B were more pronounced with conventional heating as 98% conversion yield was reached within 90 min at 90 °C, equating thus to a nearly 4-fold increase in performance yielding 118.0 ± 3.6 g/(L·h) productivity. With DES, the overall yield and space-time yield were lower with both heating methods. However, microwave heating enabled a 2-fold increase in both performance parameters when the reaction temperature was increased from 50 to 90 °C. Compared to conventional heating, a 7-fold increase in space-time yield at 50 °C and a 16-fold increase at 90 °C were achieved in DES by microwave heating. Furthermore, microwave irradiation enabled the usage of a neat, solvent-free system, representing an initial proof of concept with productivities of up to 13.3 ± 2.3 g/(L·h).
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Affiliation(s)
- André Delavault
- Technical
Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Oleksandra Opochenska
- Technical
Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Sonja Schönrock
- Technical
Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Rebecca Hollenbach
- Biotechnological
Conversion, Technikum Laubholz GmbH, Göppingen 73033, Germany
| | | | - Christoph Syldatk
- Technical
Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
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3
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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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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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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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Wang H, Li H, Lee CK, Mat Nanyan NS, Tay GS. Recent Advances in the Enzymatic Synthesis of Polyester. Polymers (Basel) 2022; 14:polym14235059. [PMID: 36501454 PMCID: PMC9740404 DOI: 10.3390/polym14235059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Polyester is a kind of polymer composed of ester bond-linked polybasic acids and polyol. This type of polymer has a wide range of applications in various industries, such as automotive, furniture, coatings, packaging, and biomedical. The traditional process of synthesizing polyester mainly uses metal catalyst polymerization under high-temperature. This condition may have problems with metal residue and undesired side reactions. As an alternative, enzyme-catalyzed polymerization is evolving rapidly due to the metal-free residue, satisfactory biocompatibility, and mild reaction conditions. This article presented the reaction modes of enzyme-catalyzed ring-opening polymerization and enzyme-catalyzed polycondensation and their combinations, respectively. In addition, the article also summarized how lipase-catalyzed the polymerization of polyester, which includes (i) the distinctive features of lipase, (ii) the lipase-catalyzed polymerization and its mechanism, and (iii) the lipase stability under organic solvent and high-temperature conditions. In addition, this article also focused on the advantages and disadvantages of enzyme-catalyzed polyester synthesis under different solvent systems, including organic solvent systems, solvent-free systems, and green solvent systems. The challenges of enzyme optimization and process equipment innovation for further industrialization of enzyme-catalyzed polyester synthesis were also discussed in this article.
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Affiliation(s)
- Hong Wang
- Bioresource Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
| | - Hongpeng Li
- Tangshan Jinlihai Biodiesel Co. Ltd., Tangshan 063000, China
| | - Chee Keong Lee
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
- Renewable Biomass Transformation Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
| | - Noreen Suliani Mat Nanyan
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
- Renewable Biomass Transformation Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
| | - Guan Seng Tay
- Bioresource Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
- Green Biopolymer, Coatings & Packaging Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
- Correspondence:
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Posada NC, Sierra CA, Perez LD. An Evaluation of the Effect of Reaction Conditions in the Enzymatically Catalyzed Synthesis of Poly(ϵ‐Caprolactone). ChemistrySelect 2022. [DOI: 10.1002/slct.202202372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Cesar A. Sierra
- Departamento de Química Universidad Nacional de Colombia Bogotá D.C
| | - Leon D. Perez
- Departamento de Química Universidad Nacional de Colombia Bogotá D.C
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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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Reactivity of a Recombinant Esterase from Thermus thermophilus HB27 in Aqueous and Organic Media. Microorganisms 2022; 10:microorganisms10050915. [PMID: 35630360 PMCID: PMC9143606 DOI: 10.3390/microorganisms10050915] [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: 03/02/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/16/2022] Open
Abstract
The thermoalkalophilic membrane-associated esterase E34Tt from Thermus thermophilus HB27 was cloned and expressed in Kluyveromyces lactis (KLEST-3S esterase). The recombinant enzyme was tested as a biocatalyst in aqueous and organic media. It displayed a high thermal stability and was active in the presence of 10% (v/v) organic solvents and 1% (w/v) detergents. KLEST-3S hydrolysed triglycerides of various acyl chains, which is a rare characteristic among carboxylic ester hydrolases from extreme thermophiles, with maximum activity on tributyrin. It also displayed interfacial activation towards triacetin. KLEST-3S was also tested as a biocatalyst in organic media. The esterase provided high yields for the acetylation of alcohols. In addition, KLEST-3S catalyzed the stereoselective hydrolysis of (R,S)-ibuprofen methyl ester (87% ee). Our results indicate that KLEST-3S may be a robust and efficient biocatalyst for application in industrial bioconversions.
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In Silico Core Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pyogenes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111355. [PMID: 34769873 PMCID: PMC8582943 DOI: 10.3390/ijerph182111355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 12/18/2022]
Abstract
Streptococcus pyogenes is a significant pathogen that causes skin and upper respiratory tract infections and non-suppurative complications, such as acute rheumatic fever and post-strep glomerulonephritis. Multidrug resistance has emerged in S. pyogenes strains, making them more dangerous and pathogenic. Hence, it is necessary to identify and develop therapeutic methods that would present novel approaches to S. pyogenes infections. In the current study, a subtractive proteomics approach was employed to core proteomes of four strains of S. pyogenes using several bioinformatic software tools and servers. The core proteome consists of 1324 proteins, and 302 essential proteins were predicted from them. These essential proteins were analyzed using BLASTp against human proteome, and the number of potential targets was reduced to 145. Based on subcellular localization prediction, 46 proteins with cytoplasmic localization were chosen for metabolic pathway analysis. Only two cytoplasmic proteins, i.e., chromosomal replication initiator protein DnaA and two-component response regulator (TCR), were discovered to have the potential to be novel drug target candidates. Three-dimensional (3D) structure prediction of target proteins was carried out via the Swiss Model server. Molecular docking approach was employed to screen the library of 1000 phytochemicals against the interacting residues of the target proteins through the MOE software. Further, the docking studies were validated by running molecular dynamics simulation and highly popular binding free energy approaches of MM-GBSA and MM-PBSA. The findings revealed a promising candidate as a novel target against S. pyogenes infections.
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Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches. BIOLOGY 2021; 10:biology10100997. [PMID: 34681096 PMCID: PMC8533590 DOI: 10.3390/biology10100997] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022]
Abstract
Chlamydia trachomatis, a Gram-negative bacterium that infects the rectum, urethra, congenital sites, and columnar epithelium of the cervix. It is a major cause of preventable blindness, ectopic pregnancy, and bacterial sexually transmitted infections worldwide. There is currently no licensed multi-epitope vaccination available for this pathogen. This study used core proteomics, immuno-informatics, and subtractive proteomics approaches to identify the best antigenic candidates for the development of a multi-epitope-based vaccine (MEBV). These approaches resulted in six vaccine candidates: Type III secretion system translocon subunit CopD2, SctW family type III secretion system gatekeeper subunit CopN, SycD/LcrH family type III secretion system chaperone Scc2, CT847 family type III secretion system effector, hypothetical protein CTDEC_0668, and CHLPN 76kDa-like protein. A variety of immuno-informatics tools were used to predict B and T cell epitopes from vaccine candidate proteins. An in silico vaccine was developed using carefully selected epitopes (11 CTL, 2 HTL & 10 LBL) and then docked with the MHC molecules (MHC I & MHC II) and human TLR4. The vaccine was coupled with Cholera toxin subunit B (CTB) adjuvant to boost the immune response. Molecular dynamics (MD) simulations, molecular docking, and MMGBSA analysis were carried out to analyze the molecular interactions and binding affinity of MEBV with TLR4 and MHC molecules. To achieve the highest level of vaccine protein expression, the MEBV was cloned and reverse-translated in Escherichia coli. The highest level of expression was achieved, and a CAI score of 0.97 was reported. Further experimental validation of the MEBV is required to prove its efficacy. The vaccine developed will be useful in preventing infections caused by C. trachomatis.
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Ethanol as additive enhance the performance of immobilized lipase LipA from Pseudomonas aeruginosa on polypropylene support. ACTA ACUST UNITED AC 2021; 31:e00659. [PMID: 34367924 PMCID: PMC8326728 DOI: 10.1016/j.btre.2021.e00659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022]
Abstract
Immobilization is practical to upgrade enzymes, increasing their performance and expanding their applications. The recombinant, solvent tolerant lipase LipA PSA01 from Pseudomonas aeruginosa was immobilized on polypropylene Accurel® MP1004 to improve its performance. We investigated the effect of ethanol as an additive during the immobilization process at three concentrations (20%, 25%, and 30%) on the operational behavior of the enzyme. The immobilization efficiency was higher than 92%, and the immobilized enzymes showed hyperactivation and thermal resistance depending on the concentration of ethanol. For example, at 70 °C, the free enzyme lost the activity, while the prepared one with ethanol 25% conserved a residual activity of up to 73.3% (∆ T15 50 = 27.1 °C). LipA immobilized had an optimal pH value lower than that of the free enzyme, and the organic solvent tolerance of the immobilized enzymes depended on the ethanol used. Hence, the immobilized enzyme with ethanol 25% showed hyperactivation to more solvents than the soluble enzyme. Remarkable stability towards methanol (up to 8 folds) was evidenced in all the immobilized preparations. The immobilized enzyme changed their chemo preference, and it hydrolyzed oils preferentially with short-chain than those with long-chain. LipA had a notable shelf-life after one year, keeping its activity up to 87%. Ethanol facilitated the access of the enzyme to the hydrophobic support and increased its activity and stability according to the amount of ethanol added.
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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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15
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Changing the residues interaction pattern as a universal mechanism for enzyme inactivation and denaturation in supercritical CO2. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Miguel-Ruano V, Rivera I, Rajkovic J, Knapik K, Torrado A, Otero JM, Beneventi E, Becerra M, Sánchez-Costa M, Hidalgo A, Berenguer J, González-Siso MI, Cruces J, Rúa ML, Hermoso JA. Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family. Comput Struct Biotechnol J 2021; 19:1214-1232. [PMID: 33680362 PMCID: PMC7905190 DOI: 10.1016/j.csbj.2021.01.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/31/2022] Open
Abstract
A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60°C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester. The tridimensional structures of EstD11 and the inactive mutant have been determined at atomic resolutions. Structural and bioinformatic analysis, confirm that EstD11 belongs to the family IV, the hormone-sensitive lipase (HSL) family, from the α/β-hydrolase superfamily. The canonical α/β-hydrolase domain is completed by a cap domain, composed by two subdomains that can unmask of the active site to allow the substrate to enter. Eight crystallographic complexes were solved with different substrates and reaction products that allowed identification of the hot-spots in the active site underlying the specificity of the protein. Crystallization and/or incubation of EstD11 at high temperature provided unique information on cap dynamics and a first glimpse of enzymatic activity in vivo. Very interestingly, we have discovered a unique Met zipper lining the active site and the cap domains that could be essential in pivotal aspects as thermo-stability and substrate promiscuity in EstD11.
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Key Words
- CHCA, cyclohexane carboxylic acid
- CMC, critical micellar concentration
- CV, column volume
- Crystal structure
- DMSO, dimethyl sulfoxide
- DSF, Differential scanning fluorimetry
- Enzyme-substrate complex
- FLU, fluorescein
- HSL, hormone-sensitive lipase
- LDAO, N,N-dimethyldodecylamine N-oxide
- MNP, methyl-naproxen
- Metagenomic
- NP, naproxen
- PPL, Porcine Pancreatic Lipase
- Thermophilic esterase
- pNP, 4-nitrophenol
- α/β hydrolase fold
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Affiliation(s)
- Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
| | - Ivanna Rivera
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
| | - Jelena Rajkovic
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | - Kamila Knapik
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | - Ana Torrado
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | | | | | - Manuel Becerra
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | - Mercedes Sánchez-Costa
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Aurelio Hidalgo
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - José Berenguer
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - María-Isabel González-Siso
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | | | - María L. Rúa
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
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17
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Seo J, Shin M, Lee J, Lee T, Oh JM, Park C. Novel and highly efficient lipase-catalyzed esterification of formic acid with hexanol for waste gas reutilization. J IND ENG CHEM 2021. [DOI: 10.1016/j.jiec.2020.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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First biocatalytic Groebke-Blackburn-Bienaymé reaction to synthesize imidazo[1,2-a]pyridine derivatives using lipase enzyme. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131643] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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19
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Zhang Y, Ren W, Zhao Q, Lv K, Sun Y, Gao X, Wang F, Liu J. One-pot three-step enzymatic ROP in situ to form polycaprolactone from cyclohexanone: Optimizing and kinetic modeling. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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20
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Facile One-Pot Immobilization of a Novel Esterase and Its Application in Cinnamyl Acetate Synthesis. Catal Letters 2020. [DOI: 10.1007/s10562-020-03168-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Chen ZS, Wu YD, Hao JH, Liu YJ, He KP, Jiang WH, Xiong MJ, Lv YS, Cao SL, Zhu J. Molecular Dynamic Simulation of the Porcine Pancreatic Lipase in Non-aqueous Organic Solvents. Front Bioeng Biotechnol 2020; 8:676. [PMID: 32766212 PMCID: PMC7381131 DOI: 10.3389/fbioe.2020.00676] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/01/2020] [Indexed: 11/13/2022] Open
Abstract
This paper investigates the conformational stability of porcine pancreatic lipase (PPL) in three non-aqueous organic solvents, including dimethyl sulfoxide (DMSO), propylene glycol (PRG), and ethanol (EtOH) through molecular dynamic (MD) simulation. The root mean square deviations (RMSDs), radius of gyration (Rg), solution accessible surface area (SASA), radial distribution function (RDF), hydrogen bond (H-bond), Ramachandran plot analysis, secondary structure, and enzyme substrate affinity of the PPL in the various organic solvents were comparatively investigated. The results showed that the backbone and active pocket RMSD, and hydrophilic ASA of PPL in three solvents increase with the increase in the solvent LogP, while the Rg, hydrophobic ASA, and H-bond between the solvent and PPL decrease. Among the three organic solvents, DMSO acts as a better solvent, in which the PPL can be loose and extended, and retains its native backbone in DMSO compared to PRG and EtOH. Moreover, Ramachandran plot analysis indicated that the PPL structure quality in DMSO was higher than that in PRG and EtOH. Also, the molecular docking results showed that PPL in DMSO exhibited the highest enzyme-substrate affinity.
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Affiliation(s)
- Zi-Shi Chen
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Yi-Da Wu
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Jin-Heng Hao
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Yu-Jia Liu
- School of Chemical Engineering and Energy Technology, Engineering Research Center of Health Food Design and Nutrition Regulation, Dongguan University of Technology, Dongguan, China
| | - Kang-Ping He
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Wen-Hao Jiang
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Mei-Jie Xiong
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Yong-Si Lv
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Shi-Lin Cao
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China.,Sustainable Biochemical and Biosynthetic Engineering Center, Foshan Wu-Yuan Biotechnology Co., Ltd., Guangdong Biomedical Industrial Base, Foshan, China
| | - Jie Zhu
- School of Chemical Engineering and Energy Technology, Engineering Research Center of Health Food Design and Nutrition Regulation, Dongguan University of Technology, Dongguan, China
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22
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Cui H, Stadtmüller THJ, Jiang Q, Jaeger K, Schwaneberg U, Davari MD. How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000422] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Tom H. J. Stadtmüller
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Qianjia Jiang
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf and Research Center Jülich Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstraße 50 52074 Aachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
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23
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Facile One-Pot Immobilization of a Novel Thermostable Carboxylesterase from Geobacillus uzenensis for Continuous Pesticide Degradation in a Packed-Bed Column Reactor. Catalysts 2020. [DOI: 10.3390/catal10050518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The novel carboxylesterase gene (est741) was cloned from Geobacillus uzenensis. The optimal pH and temperature of Est741 were 8.0 and 50 °C. Through site-directed mutation, the optimum temperature of the mutant M160K(EstM160K) was increased from 50 to 60 °C, and showed enhanced T1/2 of 2.5 h at 70 °C in comparison to the wild type (1.3 h). EstM160K was successfully expressed Pichia pastoris and EstM160K fermentation broth was directly immobilized on epoxy-functionalized supports via a one-pot strategy to obtain the immobilized enzyme lx-EstM160K. Additionally, lx-EstM160K showed enhanced T1/2 of 36.8 h at 70 °C in comparison to free enzyme. lx-EstM160K could degrade various pyrethroid pesticides. After 40 min reaction with 50 U of the lx-EstM160K, the malathion removal was 95.8% with a malathion concentration of 20 mg/L. When 2.5 g lx-EstM160K was added to the 10 mL column reactor with the concentration of bifenthrin was 500 mg/L and the transfer rate of the pump was 0.7 mL/min, the degradation rate of lx-EstM160K to bifenthrin was 90.4%. lx-EstM160K exhibited high operational stability and maintained 72% initial activity after ten batches of continuous reaction for bifenthrin pesticide biodegradation.
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24
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Mangiagalli M, Carvalho H, Natalello A, Ferrario V, Pennati ML, Barbiroli A, Lotti M, Pleiss J, Brocca S. Diverse effects of aqueous polar co-solvents on Candida antarctica lipase B. Int J Biol Macromol 2020; 150:930-940. [DOI: 10.1016/j.ijbiomac.2020.02.145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 02/04/2023]
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25
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Huang L, Bittner JP, Domínguez de María P, Jakobtorweihen S, Kara S. Modeling Alcohol Dehydrogenase Catalysis in Deep Eutectic Solvent/Water Mixtures. Chembiochem 2020; 21:811-817. [PMID: 31605652 PMCID: PMC7154551 DOI: 10.1002/cbic.201900624] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Indexed: 11/17/2022]
Abstract
The use of oxidoreductases (EC1) in non-conventional reaction media has been increasingly explored. In particular, deep eutectic solvents (DESs) have emerged as a novel class of solvents. Herein, an in-depth study of bioreduction with an alcohol dehydrogenase (ADH) in the DES glyceline is presented. The activity and stability of ADH in mixtures of glyceline/water with varying water contents were measured. Furthermore, the thermodynamic water activity and viscosity of mixtures of glyceline/water have been determined. For a better understanding of the observations, molecular dynamics simulations were performed to quantify the molecular flexibility, hydration layer, and intraprotein hydrogen bonds of ADH. The behavior of the enzyme in DESs follows the classic dependence of water activity (aW ) in non-conventional media. At low aW values (<0.2), ADH does not show any activity; at higher aW values, the activity was still lower than that in pure water due to the high viscosities of the DES. These findings could be further explained by increased enzyme flexibility with increasing water content.
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Affiliation(s)
- Lei Huang
- Department of EngineeringBiocatalysis and Bioprocessing GroupAarhus UniversityGustav Wieds Vej 108000AarhusDenmark
| | - Jan Philipp Bittner
- Institute of Thermal Separation ProcessesHamburg University of TechnologyEißendorfer Strasse 3821073HamburgGermany
| | | | - Sven Jakobtorweihen
- Institute of Thermal Separation ProcessesHamburg University of TechnologyEißendorfer Strasse 3821073HamburgGermany
| | - Selin Kara
- Department of EngineeringBiocatalysis and Bioprocessing GroupAarhus UniversityGustav Wieds Vej 108000AarhusDenmark
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26
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Martínez R, Bernal C, Álvarez R, Concha C, Araya F, Cabrera R, Dhoke GV, Davari MD. Deletion and Randomization of Structurally Variable Regions in B. subtilis Lipase A (BSLA) Alter Its Stability and Hydrolytic Performance Against Long Chain Fatty Acid Esters. Int J Mol Sci 2020; 21:ijms21061990. [PMID: 32183336 PMCID: PMC7139672 DOI: 10.3390/ijms21061990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
The continuous search for novel enzyme backbones and the engineering of already well studied enzymes for biotechnological applications has become an increasing challenge, especially by the increasing potential diversity space provided by directed enzyme evolution approaches and the demands of experimental data generated by rational design of enzymes. In this work, we propose a semi-rational mutational strategy focused on introducing diversity in structurally variable regions in enzymes. The identified sequences are subjected to a progressive deletion of two amino acids and the joining residues are subjected to saturation mutagenesis using NNK degenerate codons. This strategy offers a novel library diversity approach while simultaneously decreasing enzyme size in the variable regions. In this way, we intend to identify and reduce variable regions found in enzymes, probably resulting from neutral drift evolution, and simultaneously studying the functional effect of said regions. This strategy was applied to Bacillus. subtilis lipase A (BSLA), by selecting and deleting six variable enzyme regions (named regions 1 to 6) by the deletion of two amino acids and additionally randomizing the joining amino acid residues. After screening, no active variants were found in libraries 1% and 4%, 15% active variants were found in libraries 2% and 3%, and 25% for libraries 5 and 6 (n = 3000 per library, activity detected using tributyrin agar plates). Active variants were assessed for activity in microtiter plate assay (pNP-butyrate), thermal stability, substrate preference (pNP-butyrate, -palmitate), and compared to wildtype BSLA. From these analyses, variant P5F3 (F41L-ΔW42-ΔD43-K44P), from library 3 was identified, showing increased activity towards longer chain p-nitrophenyl fatty acid esters, when compared to BSLA. This study allowed to propose the targeted region 3 (positions 40-46) as a potential modulator for substrate specificity (fatty acid chain length) in BSLA, which can be further studied to increase its substrate spectrum and selectivity. Additionally, this variant showed a decreased thermal resistance but interestingly, higher isopropanol and Triton X-100 resistance. This deletion-randomization strategy could help to expand and explore sequence diversity, even in already well studied and characterized enzyme backbones such as BSLA. In addition, this strategy can contribute to investigate and identify important non-conserved regions in classic and novel enzymes, as well as generating novel biocatalysts with increased performance in specific processes, such as enzyme immobilization.
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Affiliation(s)
- Ronny Martínez
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
- Correspondence: ; Tel.: +56-51-2334661; Fax: +56-51-2204446
| | - Claudia Bernal
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
| | - Rodrigo Álvarez
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
- Escuela de Tecnología Médica, Facultad de Salud, Sede La Serena, Universidad Santo Tomás, La Serena 1710172, Chile
| | - Christopher Concha
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
| | - Fernando Araya
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile; (F.A.); (R.C.)
| | - Ricardo Cabrera
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile; (F.A.); (R.C.)
| | - Gaurao V. Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (G.V.D.); (M.D.D.)
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (G.V.D.); (M.D.D.)
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27
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Chen X, Zhang H, Hemar Y, Li N, Zhou P. Glycerol induced stability enhancement and conformational changes of β-lactoglobulin. Food Chem 2020; 308:125596. [DOI: 10.1016/j.foodchem.2019.125596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 11/26/2022]
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28
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Gagnon C, Godin É, Minozzi C, Sosoe J, Pochet C, Collins SK. Biocatalytic synthesis of planar chiral macrocycles. Science 2020; 367:917-921. [DOI: 10.1126/science.aaz7381] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/21/2020] [Indexed: 12/25/2022]
Abstract
Macrocycles can restrict the rotation of substituents through steric repulsions, locking in conformations that provide or enhance the activities of pharmaceuticals, agrochemicals, aroma chemicals, and materials. In many cases, the arrangement of substituents in the macrocycle imparts an element of planar chirality. The difficulty in predicting when planar chirality will arise, as well as the limited number of synthetic methods to impart selectivity, have led to planar chirality being regarded as an irritant. We report a strategy for enantio- and atroposelective biocatalytic synthesis of planar chiral macrocycles. The macrocycles can be formed with high enantioselectivity from simple building blocks and are decorated with functionality that allows one to further modify the macrocycles with diverse structural features.
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Affiliation(s)
- Christina Gagnon
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Éric Godin
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Clémentine Minozzi
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Johann Sosoe
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Corentin Pochet
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Shawn K. Collins
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
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29
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Kaabel S, Friščić T, Auclair K. Mechanoenzymatic Transformations in the Absence of Bulk Water: A More Natural Way of Using Enzymes. Chembiochem 2019; 21:742-758. [PMID: 31651073 DOI: 10.1002/cbic.201900567] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Sandra Kaabel
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montreal QC H3A 0B8 Canada
| | - Tomislav Friščić
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montreal QC H3A 0B8 Canada
| | - Karine Auclair
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montreal QC H3A 0B8 Canada
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30
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Wilk M, Trzepizur D, Koszelewski D, Brodzka A, Ostaszewski R. Synthesis of (E)-α,β-unsaturated carboxylic esters derivatives from cyanoacetic acid via promiscuous enzyme-promoted cascade esterification/Knoevenagel reaction. Bioorg Chem 2019; 93:102816. [DOI: 10.1016/j.bioorg.2019.02.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
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31
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Pérez‐Venegas M, Tellez‐Cruz MM, Solorza‐Feria O, López‐Munguía A, Castillo E, Juaristi E. Thermal and Mechanical Stability of Immobilized
Candida antarctica
Lipase B: an Approximation to Mechanochemical Energetics in Enzyme Catalysis. ChemCatChem 2019. [DOI: 10.1002/cctc.201901714] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Mario Pérez‐Venegas
- Department of ChemistryCentro de Investigación y de Estudios Avanzados Av. IPN 2508 Ciudad de México 07360 Mexico
| | - Miriam M. Tellez‐Cruz
- Department of ChemistryCentro de Investigación y de Estudios Avanzados Av. IPN 2508 Ciudad de México 07360 Mexico
| | - Omar Solorza‐Feria
- Department of ChemistryCentro de Investigación y de Estudios Avanzados Av. IPN 2508 Ciudad de México 07360 Mexico
| | - Agustín López‐Munguía
- Department of cellular engineering and biocatalysisUniversidad Nacional Autónoma de México Av. Universidad 2001 Col. Chamilpa 62210 Cuernavaca Mexico
| | - Edmundo Castillo
- Department of cellular engineering and biocatalysisUniversidad Nacional Autónoma de México Av. Universidad 2001 Col. Chamilpa 62210 Cuernavaca Mexico
| | - Eusebio Juaristi
- Department of ChemistryCentro de Investigación y de Estudios Avanzados Av. IPN 2508 Ciudad de México 07360 Mexico
- El Colegio Nacional Luis Gonzáles Obregón 23 Ciudad de México 06020 Mexico
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Zieniuk B, Fabiszewska A, Białecka-Florjańczyk E. Screening of solvents for favoring hydrolytic activity of Candida antarctica Lipase B. Bioprocess Biosyst Eng 2019; 43:605-613. [PMID: 31734716 DOI: 10.1007/s00449-019-02252-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/08/2019] [Indexed: 02/04/2023]
Abstract
Lipases are a group of enzymes of considerable significance in organic synthesis, among which Candida antarctica lipase B (CALB) is one of the most widely studied enzymes. The activity of the biocatalyst has been intensively characterized in many organic media, but this paper aimed to compare the effect of 20 different solvents on the activity of CALB in the hydrolysis of p-nitrophenyl laurate. Nonpolar, polar aprotic, and polar protic solvents were used for enzyme pretreatment and then entered the composition of mixed solvents reaction medium. An impact of solvents on solvation processes affecting the catalysis steps, protein denaturation, and changes of its conformation was discussed. Moreover the hydrolytic activity of CALB with partition coefficient (logP) of the solvent used was correlated. It was emphasized that the substrate solubility plays an important role in solvent selection. In the presence of hydrophobic solvents, hydration layer becomes more hydrophobic facilitating the substrate access to the enzyme surface. In turn, polar compounds are good solvents for organic substrates facilitating the penetration of the aqueous layer that surrounds the surface of the enzyme. Two variants proved to be favorable for ester hydrolysis reaction: isooctane or polar solvent such as acetone, tert -butyl methyl ether, tert-butanol or acetonitrile.
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Affiliation(s)
- Bartłomiej Zieniuk
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 159c Nowoursynowska St., 02-776, Warsaw, Poland.
| | - Agata Fabiszewska
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 159c Nowoursynowska St., 02-776, Warsaw, Poland
| | - Ewa Białecka-Florjańczyk
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 159c Nowoursynowska St., 02-776, Warsaw, Poland
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Immobilization of a Novel ESTBAS Esterase from Bacillus altitudinis onto an Epoxy Resin: Characterization and Regioselective Synthesis of Chloramphenicol Palmitate. Catalysts 2019. [DOI: 10.3390/catal9070620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Novel gene estBAS from Bacillus altitudinis, encoding a 216-amino acid esterase (EstBAS) with a signal peptide (SP), was expressed in Escherichia coli. EstBASΔSP showed the highest activity toward p-nitrophenyl hexanoate at 50 °C and pH 8.0 and had a half-life (T1/2) of 6 h at 50 °C. EstBASΔSP was immobilized onto a novel epoxy resin (Lx-105s) with a high loading of 96 mg/g. Fourier transform infrared (FTIR) spectroscopy showed that EstBASΔSP was successfully immobilized onto Lx-105s. In addition, immobilization improved its enzymatic performance by widening the tolerable ranges of pH and temperature. The optimum temperature of immobilized EstBASΔSP (Lx-EstBASΔSP) was higher, 60 °C, and overall thermostability improved. T1/2 of Lx-EstBASΔSP and free EstBASΔSP at 60 °C was 105 and 28 min, respectively. Lx-EstBASΔSP was used as a biocatalyst to synthesize chloramphenicol palmitate by regioselective modification at the primary hydroxyl group. Conversion efficiency reached 94.7% at 0.15 M substrate concentration after 24 h. Lx-EstBASΔSP was stable and could be reused for seven cycles, after which it retained over 80% of the original activity.
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34
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SreeHarsha N, Ghorpade RV, Alzahrani AM, Al-Dhubiab BE, Venugopala KN. Immobilization studies of Candida Antarctica lipase B on gallic acid resin-grafted magnetic iron oxide nanoparticles. Int J Nanomedicine 2019; 14:3235-3244. [PMID: 31118633 PMCID: PMC6504639 DOI: 10.2147/ijn.s203547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/19/2019] [Indexed: 11/23/2022] Open
Abstract
Purpose: Here, we present the successful preparation of a highly efficient gallic acid resin grafted with magnetic nanoparticles (MNPs) and containing a branched brush polymeric shell. Methods: Using a convenient co-precipitation method, we prepared Fe3O4 nanoparticles stabilized by citric acid. These nanoparticles underwent further silica modification and amino functionalization followed by gallic acid functionalization on their surface. Under alkaline conditions, we used a condensation reaction that combined formaldehyde and gallic, to graft the gallic acid-formaldehyde resin on the surface. We then evaluated the polymer-grafted MNPs to assay the Candida Antarctica B lipase(Cal-B) immobilization via physical adsorption. Conclusion: Furthermore, during optimization of parameters that defined conditions of immobilization, we found that the optimum immobilization was achieved in 15 mins. Also, optimal immobilization temperature and pH were 38ºC and 7.5, respectively. In addition, the reusability study of immobilized lipase polymer-grafted MNPs was done by isolating the MNPs from the reaction medium using magnetic separation, which showed that grafted MNPs reached 5 cycles with 91% activity retention.
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Affiliation(s)
- Nagaraja SreeHarsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Ravindra V Ghorpade
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune411 008, India
| | - Abdullah Mossa Alzahrani
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Bandar E Al-Dhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban4001, South Africa
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35
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Yuan X, Zhang P, Xu W, Tang K. Kinetic study on enantioselective resolution of (
R,S
)‐2‐phenylpropionic acid through Novozyme 435–catalyzed esterification. INT J CHEM KINET 2019. [DOI: 10.1002/kin.21274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Xin Yuan
- Department of Chemistry and Chemical EngineeringHunan Institute of Science and Technology Yueyang Hunan China
| | - Panliang Zhang
- Department of Chemistry and Chemical EngineeringHunan Institute of Science and Technology Yueyang Hunan China
| | - Weifeng Xu
- Department of Chemistry and Chemical EngineeringHunan Institute of Science and Technology Yueyang Hunan China
| | - Kewen Tang
- Department of Chemistry and Chemical EngineeringHunan Institute of Science and Technology Yueyang Hunan China
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36
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Gesse P, Müller TJJ. Consecutive Five-Component Ugi-4CR-CAL B-Catalyzed Aminolysis Sequence and Concatenation with Transition Metal Catalysis in a One-Pot Fashion to Substituted Triamides. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Pascal Gesse
- Institut für Organische Chemie und Makromolekulare Chemie; Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf; Germany
| | - Thomas J. J. Müller
- Institut für Organische Chemie und Makromolekulare Chemie; Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf; Germany
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37
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Rathankumar AK, SaiLavanyaa S, Saikia K, Gururajan A, Sivanesan S, Gosselin M, Vaidyanathan VK, Cabana H. Systemic Concocting of Cross‐Linked Enzyme Aggregates of
Candida antarctica
Lipase B (Novozyme 435) for the Biomanufacturing of Rhamnolipids. J SURFACTANTS DETERG 2019. [DOI: 10.1002/jsde.12266] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Abiram Karanam Rathankumar
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of BioengineeringSRM Institute of Science and Technology Kattankulathur, Chennai, 603 203 India
| | - Sundar SaiLavanyaa
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of BioengineeringSRM Institute of Science and Technology Kattankulathur, Chennai, 603 203 India
| | - Kongkona Saikia
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of BioengineeringSRM Institute of Science and Technology Kattankulathur, Chennai, 603 203 India
| | - Anusha Gururajan
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of BioengineeringSRM Institute of Science and Technology Kattankulathur, Chennai, 603 203 India
| | - Subramanian Sivanesan
- Department of Applied Science and Technology, Environment Management LaboratoryAC Tech, Anna University Chennai, 600025 India
| | - Mathilde Gosselin
- Materium Innovations INC.Boulevard Industriel 790 J2G 9J5, Granby Canada
| | - Vinoth Kumar Vaidyanathan
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of BioengineeringSRM Institute of Science and Technology Kattankulathur, Chennai, 603 203 India
- Laboratoire de génie de l'environnement, Faculté de génieUniversité de Sherbrooke 2500 boul. de l'Université, Sherbrooke, Québec, J1K 2R1 Canada
| | - Hubert Cabana
- Laboratoire de génie de l'environnement, Faculté de génieUniversité de Sherbrooke 2500 boul. de l'Université, Sherbrooke, Québec, J1K 2R1 Canada
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38
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Fu Z, Xu W, Chen G, Wang Z, Lu D, Wu J, Liu Z. Molecular dynamics simulations reveal how graphene oxide stabilizes and activates lipase in an anhydrous gas. Phys Chem Chem Phys 2019; 21:25425-25430. [DOI: 10.1039/c9cp05271b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction between Candida antarctica lipase B (CALB) and graphene oxide (GO) in an anhydrous gas was studied using molecular dynamics (MD) simulations augmented with a simulated annealing procedure to accelerate relaxation towards equilibrium.
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Affiliation(s)
- Zhongwang Fu
- Key Lab for Industrial Biocatalysis
- Ministry of Education
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
| | - Weina Xu
- Key Lab for Industrial Biocatalysis
- Ministry of Education
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
| | - Gong Chen
- Key Lab for Industrial Biocatalysis
- Ministry of Education
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
| | - Zheyu Wang
- Key Lab for Industrial Biocatalysis
- Ministry of Education
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
| | - Diannan Lu
- Key Lab for Industrial Biocatalysis
- Ministry of Education
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
| | - Jianzhong Wu
- Department of Chemical and Environmental Engineering
- University of California
- Riverside
- USA
| | - Zheng Liu
- Key Lab for Industrial Biocatalysis
- Ministry of Education
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
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39
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Sadaf A, Grewal J, Jain I, Kumari A, Khare SK. Stability and structure of Penicillium chrysogenum lipase in the presence of organic solvents. Prep Biochem Biotechnol 2018; 48:977-983. [PMID: 30461349 DOI: 10.1080/10826068.2018.1525566] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The present work describes the enzymatic properties of Penicillium chrysogenum lipase and its behavior in the presence of organic solvents. The temperature and pH optima of the purified lipase was found to be 55 °C and pH 8.0 respectively. The lipase displayed remarkable stability in both polar and non-polar solvents upto 50% (v/v) concentrations for 72 h. A structural perspective of the purified lipase in different organic solvents was gained by using circular dichroism and intrinsic fluorescence spectroscopy. The native lipase consisted of a predominant α-helix structure which was maintained in both polar and non-polar solvents with the exception of ethyl butyrate where the activity was decreased and the structure was disrupted. The quenching of fluorescence intensity in the presence of organic solvents indicated the transformation of the lipase microenviroment P. chrysogenum lipase offers an interesting system for understanding the solvent stability mechanisms which could be used for rationale designing of engineered lipase biocatalysts for application in organic synthesis in non-aqueous media.
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Affiliation(s)
- Ayesha Sadaf
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
| | - Jasneet Grewal
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
| | - Isha Jain
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
| | - Arti Kumari
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
| | - Sunil K Khare
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
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40
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Mathpati AC, Bhanage BM. Prediction of enantioselectivity of lipase catalyzed kinetic resolution using umbrella sampling. J Biotechnol 2018; 283:70-80. [DOI: 10.1016/j.jbiotec.2018.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/21/2018] [Accepted: 07/18/2018] [Indexed: 12/21/2022]
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41
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Fu J, Wang Z, Luo W, Xing S, Lv P, Wang Z, Yuan Z. Novel Sanger's Reagent-like Styrene Polymer for the Immobilization of Burkholderia cepacia Lipase. ACS APPLIED MATERIALS & INTERFACES 2018; 10:30973-30982. [PMID: 30141613 DOI: 10.1021/acsami.8b09225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sanger's reaction, which was originally developed for amino acid detection, was utilized for enzyme immobilization. The newly synthesized polymer support, which was called polymer NO2-4-fluorostyrene-divinylbenzene (pNFD), was embedded with a Sanger's reagent-like functional group for immobilizing enzymes covalently under mild reaction conditions. Using Burkholderia cepacia lipase (BCL) as the target enzyme, the immobilization efficiency and activity of pNFD-BCL reached as high as 1.2 mg·g-1 and 33.21 U·g-1 (a specific activity of 27 675 U·g-1), respectively, realizing 90% activity recovery. It also improved the optimal reaction temperature of BCL from 40 to 65 °C, under which its full activity could be retained for 4 h. The new carrier also widened the pH-adaptive range of BCL as 6.5-10.0, allowing the lipase to operate normally in weak acid environment. Reusability of pNFD-BCL was significantly improved as almost no activity and/or enantioselectivity loss was observed in 200 h of triglyceride hydrolysis reaction and 17 batches of ( R, S)-1-phenylethanol resolution reaction.
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Affiliation(s)
| | | | | | | | - Pengmei Lv
- Collaborative Innovation Center of Biomass Energy , Zhengzhou 450002 , Henan , China
| | | | - Zhenhong Yuan
- Collaborative Innovation Center of Biomass Energy , Zhengzhou 450002 , Henan , China
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42
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Zhang Y, Lu P, Sun Q, Li T, Zhao L, Gao X, Wang F, Liu J. Lipase-mediated direct in situ ring-opening polymerization of ε-caprolactone formed by a chemo-enzymatic method. J Biotechnol 2018; 281:74-80. [PMID: 29908204 DOI: 10.1016/j.jbiotec.2018.06.338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 12/27/2022]
Abstract
A novel method to synthesize poly(ε-caprolactone) (PCL) through a three-step, lipase-mediated chemo-enzymatic reaction from cyclohexanone using an immobilized lipase from Trichosporon laibacchii (T. laibacchii) CBS5791 was developed. The immobilized preparation with 1280 U· g-1 used here was obtained by a method of purification and in situ immobilization where the crude intracellular lipase (cell homogenate) was subjected to partial purification by an aqueous two-phase system (ATPS) consisting of 12% (w/w) polyethylene glycol (PEG) 4000 and 13% (w/w) potassium phosphate (K2HPO4) and then in situ immobilization directly on diatomite from the top PEG-rich phase of ATPS. In this multi-step process, the ε-caprolactone (ε-CL) produced by lipase-mediated one-pot two-step chemo-enzymatic oxidation of cyclohexanone was directly subjected to in situ ring-opening polymerization (ROP) started by adding highly hydrophobic solvents. It is necessary to note that ε-CL synthesis and its subsequent ROP were catalyzed by the same lipase. The impact of various reaction parameters, e.g., solvent, cyclohexanone: hydrogen peroxide molar ratio, hydrogen peroxide forms and reaction temperature were investigated. Toluene was selected as a preferred solvent due to supporting the highest molecular weight (Mn = 2168) and moderate ε-CL conversion (65.42%). Through the optimization of reaction conditions, PCL was produced with a Mn of 2283 at 50 °C for 24 h. These results reveal that this lipase-mediated direct ring-opening polymerization of in situ formed ε-CL is an alternative route to the conventional synthesis of PCL.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Pharmaceutics, College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Peiyu Lu
- Department of Pharmaceutics, College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Qinghua Sun
- Department of Pharmaceutics, College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Tao Li
- Department of Pharmaceutics, College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Lanjie Zhao
- Department of Pharmaceutics, College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Xin Gao
- Department of Pharmaceutics, College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Fanye Wang
- Department of Pharmaceutics, College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
| | - Junhong Liu
- Department of Pharmaceutics, College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
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43
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Foukis A, Gkini OA, Stergiou PY, Papamichael EM. New insights and tools for the elucidation of lipase catalyzed esterification reaction mechanism in n-hexane: The synthesis of ethyl butyrate. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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44
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Zhang H, Jiang Y, Cui Z, Yin C. Force Field Benchmark of Amino Acids. 2. Partition Coefficients between Water and Organic Solvents. J Chem Inf Model 2018; 58:1669-1681. [DOI: 10.1021/acs.jcim.8b00493] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Ziheng Cui
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Chunhua Yin
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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45
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Dahanayake JN, Mitchell-Koch KR. How Does Solvation Layer Mobility Affect Protein Structural Dynamics? Front Mol Biosci 2018; 5:65. [PMID: 30057902 PMCID: PMC6053501 DOI: 10.3389/fmolb.2018.00065] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations. Data was obtained for the enzyme in acetonitrile, cyclohexane, n-butanol, and tert-butanol, in addition to water. Protein dynamics and solvation shell dynamics are characterized regionally: for each α-helix, β-sheet, and loop or connector region. Correlations are seen between solvent mobility and protein flexibility. So, does local viscosity explain the relationship between protein structural dynamics and solvation layer dynamics? Halle and Davidovic presented a cogent analysis of data describing the global hydrodynamics of a protein (tumbling in solution) that fits a model in which the protein's interfacial viscosity is higher than that of bulk water's, due to retarded water dynamics in the hydration layer (measured in NMR τ2 reorientation times). Numerous experiments have shown coupling between protein and solvation layer dynamics in site-specific measurements. Our data provides spatially-resolved characterization of solvent shell dynamics, showing correlations between regional solvation layer dynamics and protein dynamics in both aqueous and organic solvents. Correlations between protein flexibility and inverse solvent viscosity (1/η) are considered across several protein regions and for a rather disparate collection of solvents. It is seen that the correlation is consistently higher when local solvent shell dynamics are considered, rather than bulk viscosity. Protein flexibility is seen to correlate best with either the local interfacial viscosity or the ratio of the mobility of an organic solvent in a regional solvation layer relative to hydration dynamics around the same region. Results provide insight into the function of aqueous proteins, while also suggesting a framework for interpreting and predicting enzyme structural dynamics in non-aqueous solvents, based on the mobility of solvents within the solvation layer. We suggest that Kramers' theory may be used in future work to model protein conformational transitions in different solvents by incorporating local viscosity effects.
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46
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Jahangiri A, Møller AH, Danielsen M, Madsen B, Joernsgaard B, Vaerbak S, Adlercreutz P, Dalsgaard TK. Hydrophilization of bixin by lipase-catalyzed transesterification with sorbitol. Food Chem 2018; 268:203-209. [PMID: 30064749 DOI: 10.1016/j.foodchem.2018.06.085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 10/28/2022]
Abstract
Bixin is one of the most used yellow-orange food colorants in the food industry. The polyene chain of bixin makes it highly hydrophobic and less suitable for water-based food formulations. Lipase-catalyzed reactions of bixin with sorbitol were studied to synthesize a new derivative of bixin with potential hydrophilic properties. Interestingly, we show that the lipase-catalyzed reaction of bixin leads to a transesterification reaction and formation of a transesterified product, sorbitol ester of norbixin (SEN). The reaction efficiency was optimized with various immobilized lipases at different water activity levels in the organic solvent, 2-methyl-2-butanol. Among the examined lipases, immobilized Candida antarctica lipase B (Novozyme 435) provided the highest reaction yield at a water activity close to zero. Tetrahydrofuran (THF) was used as co-solvent to improve bixin solubility. The optimization of the reaction conditions with 20% THF lead to a total reaction yield of 50% of SEN.
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Affiliation(s)
- Amita Jahangiri
- Department of Food Science, Aarhus University, DK-8830 Tjele, Denmark
| | | | | | - Bjoern Madsen
- Chr. Hansen Natural Colors A/S, Hoejbakkegaard Alle, 30, 2630 Taastrup, Denmark
| | - Bjarne Joernsgaard
- Chr. Hansen Natural Colors A/S, Hoejbakkegaard Alle, 30, 2630 Taastrup, Denmark
| | - Signe Vaerbak
- Chr. Hansen Natural Colors A/S, Hoejbakkegaard Alle, 30, 2630 Taastrup, Denmark
| | - Patrick Adlercreutz
- Department of Chemistry, Division of Biotechnology, Lund University, SE-221 00 Lund, Sweden
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47
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Das S, Balasubramanian S. pH-Induced Rotation of Lidless Lipase LipA from Bacillus subtilis at Lipase-Detergent Interface. J Phys Chem B 2018; 122:4802-4812. [PMID: 29623706 DOI: 10.1021/acs.jpcb.8b02296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Lipases exhibit a unique process during the catalysis of the hydrolysis of triglyceride substrates called interfacial activation. Surfactants are used as cosolvents with water not only to offer a less polar environment to the lipases needed for their interfacial activation but also to solvate the substrate which are poorly soluble in water. However, the presence of detergent in the medium can affect both the lipase and the substrate, making the construction of a microkinetic model for lipase activity in the presence of the detergent difficult. Herein, we study the interfacial activation of a lidless lipase LipA from Bacillus subtilis using extensive atomistic molecular dynamics simulations at different concentrations of the surfactant, Thesit (C12E8), at two pH values. Residues which bind to the monomeric detergent are found to be the same as the ones which have been reported earlier to bind to the substrate. Very importantly, a pH-induced rotation of the enzyme with respect to surfactant aggregate has been observed which not only explains the experimentally observed pH-dependent enzymatic activity of this lidless lipase, but also suggests its reorientation at an aqueous-lipodophilic interface.
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Affiliation(s)
- Sudip Das
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064 , India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064 , India
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48
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Frauenkron-Machedjou VJ, Fulton A, Zhao J, Weber L, Jaeger KE, Schwaneberg U, Zhu L. Exploring the full natural diversity of single amino acid exchange reveals that 40–60% of BSLA positions improve organic solvents resistance. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-017-0188-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Baheti P, Gimello O, Bouilhac C, Lacroix-Desmazes P, Howdle SM. Sustainable synthesis and precise characterisation of bio-based star polycaprolactone synthesised with a metal catalyst and with lipase. Polym Chem 2018. [DOI: 10.1039/c8py01266k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Development of a sustainable route for the synthesis of star-shaped poly(ε-caprolactone) using renewable feedstocks in clean solvents (scCO2 and bulk) with the catalysts Sn(Oct)2 or the enzyme Novozym 435.
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Affiliation(s)
| | | | | | | | - Steven M. Howdle
- School of Chemistry
- University of Nottingham
- University Park
- Nottingham NG7 2RD
- UK
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Chiplunkar PP, Zhao X, Tomke PD, Noro J, Xu B, Wang Q, Silva C, Pratap AP, Cavaco-Paulo A. Ultrasound-assisted lipase catalyzed hydrolysis of aspirin methyl ester. ULTRASONICS SONOCHEMISTRY 2018; 40:587-593. [PMID: 28946463 DOI: 10.1016/j.ultsonch.2017.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/02/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
The ultrasound-assisted hydrolysis of aspirin methyl ester (AME) was investigated using immobilized Candida antarctica lipase B (CALB) (1%) in the presence of solvents like triolein, chloroform (CHCl3) and dichloromethane (DCM). The effect of ultrasound and the role of water on the conversion rates have also been investigated. Proton nuclear magnetic resonance spectroscopic (1H NMR) was chosen to calculate hydrolysis convertion rates. We observed that lipase-ultrasound assisted hydrolysis of AME in the presence of triolein and water showed the highest hydrolysis conversion rate (65.3%). Herein low water amount played an important role as a nucleophile being crucial for the hydrolysis yields obtained. Lipase activity was affected by the conjugated action of ultrasound and solvents (35.75% of decrease), however not disturbing its hydrolytic efficiency. It was demonstrated that lipase is able to hydrolyse AME to methyl 2-hydroxy benzoate (methyl salicylate), which applications include fragrance agents in food, beverages and cosmetics, or analgesic agent in liniments.
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Affiliation(s)
- Pranali P Chiplunkar
- International Joint Research Laboratory for Textile and Fiber Bioprocesses, Jiangnan University, Wuxi 214122, China; Department of Oils, Oleochemicals and Surfactants Technology, Institute of Chemical Technology, Matunga (E), Mumbai 400019, India
| | - Xiaoman Zhao
- International Joint Research Laboratory for Textile and Fiber Bioprocesses, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Technology Research Center for Functional Textiles, Institute of Chemical Technology, Matunga (E), Mumbai 400019, India; Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Prerana D Tomke
- International Joint Research Laboratory for Textile and Fiber Bioprocesses, Jiangnan University, Wuxi 214122, China; Department of Chemical Engineering, Institute of Chemical Technology, Matunga (E), Mumbai 400019, India
| | - Jennifer Noro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Bo Xu
- International Joint Research Laboratory for Textile and Fiber Bioprocesses, Jiangnan University, Wuxi 214122, China
| | - Qiang Wang
- International Joint Research Laboratory for Textile and Fiber Bioprocesses, Jiangnan University, Wuxi 214122, China
| | - Carla Silva
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Amit P Pratap
- Department of Oils, Oleochemicals and Surfactants Technology, Institute of Chemical Technology, Matunga (E), Mumbai 400019, India
| | - Artur Cavaco-Paulo
- International Joint Research Laboratory for Textile and Fiber Bioprocesses, Jiangnan University, Wuxi 214122, China; Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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