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Zhang J, Chen J, Sha Y, Deng J, Wu J, Yang P, Zou F, Ying H, Zhuang W. Water-mediated active conformational transitions of lipase on organic solvent interfaces. Int J Biol Macromol 2024; 277:134056. [PMID: 39074702 DOI: 10.1016/j.ijbiomac.2024.134056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/31/2024] [Accepted: 07/19/2024] [Indexed: 07/31/2024]
Abstract
When it comes to enzyme stability and their application in organic solvents, enzyme biocatalysis has emerged as a popular substitute for conventional chemical processes. However, the demand for enzymes exhibiting improved stability remains a persistent challenge. Organic solvents can significantly impacts enzyme properties, thereby limiting their practical application. This study focuses on Lipase Thermomyces lanuginose, through molecular dynamics simulations and experiments, we quantified the effect of different solvent-lipase interfaces on the interfacial activation of lipase. Revealed molecular views of the complex solvation processes through the minimum distance distribution function. Solvent-protein interactions were used to interpret the factors influencing changes in lipase conformation and enzyme activity. We found that water content is crucial for enzyme stability, and the optimum water content for lipase activity was 35 % in the presence of benzene-water interface, which is closely related to the increase of its interfacial activation angle from 78° to 102°. Methanol induces interfacial activation in addition to significant competitive inhibition and denaturation at low water content. Our findings shed light on the importance of understanding solvent effects on enzyme function and provide practical insights for enzyme engineering and optimization in various solvent-lipase interfaces.
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Affiliation(s)
- Jihang Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jiale Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Yu Sha
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jiawei Deng
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jinglan Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Pengpeng Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Fengxia Zou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
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2
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Papanikolaou A, Chatzikonstantinou AV, Fotiadou R, Tsakni A, Houhoula D, Polydera AC, Pavlidis IV, Stamatis H. A Study on the Regioselective Acetylation of Flavonoid Aglycons Catalyzed by Immobilized Lipases. Biomolecules 2024; 14:897. [PMID: 39199285 PMCID: PMC11352720 DOI: 10.3390/biom14080897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 09/01/2024] Open
Abstract
This study aimed to explore the capacity of immobilized lipases on the acetylation of six aglycon flavonoids, namely myricetin, quercetin, luteolin, naringenin, fisetin and morin. For this purpose, lipase B from Candida antarctica (CaLB) and lipase from Thermomyces lanuginosus (TLL) were immobilized onto the surface of ZnOFe nanoparticles derived from an aqueous olive leaf extract. Various factors affecting the conversion of substrates and the formation of monoesterified and diesterified products, such as the amount of biocatalyst and the molar ratio of the substrates and reaction solvents were investigated. Both CaLB and TLL-ZnOFe achieved 100% conversion yield of naringenin to naringenin acetate after 72 h of reaction time, while TLL-ZnOFe achieved higher conversion yields of quercetin, morin and fisetin (73, 85 and 72% respectively). Notably, CaLB-ZnOFe displayed significantly lower conversion yields for morin compared with TLL-ZnOFe. Molecular docking analysis was used to elucidate this discrepancy, and it was revealed that the position of the hydroxyl groups of the B ring on morin introduced hindrances on the active site of CaLB. Finally, selected flavonoid esters showed significantly higher antimicrobial activity compared with the original compound. This work indicated that these lipase-based nanobiocatalysts can be successfully applied to produce lipophilic derivatives of aglycon flavonoids with improved antimicrobial activity.
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Affiliation(s)
- Angelos Papanikolaou
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (R.F.); (A.C.P.)
| | - Alexandra V. Chatzikonstantinou
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (R.F.); (A.C.P.)
| | - Renia Fotiadou
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (R.F.); (A.C.P.)
| | - Aliki Tsakni
- Department of Food Science and Technology, University of West Attica, 12243 Athens, Greece; (A.T.); (D.H.)
| | - Dimitra Houhoula
- Department of Food Science and Technology, University of West Attica, 12243 Athens, Greece; (A.T.); (D.H.)
| | - Angeliki C. Polydera
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (R.F.); (A.C.P.)
| | - Ioannis V. Pavlidis
- Department of Chemistry, University of Crete, Voutes University Campus, 70013 Heraklion, Greece;
| | - Haralambos Stamatis
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (R.F.); (A.C.P.)
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3
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Bittner JP, Smirnova I, Jakobtorweihen S. Investigating Biomolecules in Deep Eutectic Solvents with Molecular Dynamics Simulations: Current State, Challenges and Future Perspectives. Molecules 2024; 29:703. [PMID: 38338447 PMCID: PMC10856712 DOI: 10.3390/molecules29030703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Deep eutectic solvents (DESs) have recently gained increased attention for their potential in biotechnological applications. DESs are binary mixtures often consisting of a hydrogen bond acceptor and a hydrogen bond donor, which allows for tailoring their properties for particular applications. If produced from sustainable resources, they can provide a greener alternative to many traditional organic solvents for usage in various applications (e.g., as reaction environment, crystallization agent, or storage medium). To navigate this large design space, it is crucial to comprehend the behavior of biomolecules (e.g., enzymes, proteins, cofactors, and DNA) in DESs and the impact of their individual components. Molecular dynamics (MD) simulations offer a powerful tool for understanding thermodynamic and transport processes at the atomic level and offer insights into their fundamental phenomena, which may not be accessible through experiments. While the experimental investigation of DESs for various biotechnological applications is well progressed, a thorough investigation of biomolecules in DESs via MD simulations has only gained popularity in recent years. Within this work, we aim to provide an overview of the current state of modeling biomolecules with MD simulations in DESs and discuss future directions with a focus for optimizing the molecular simulations and increasing our fundamental knowledge.
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Affiliation(s)
- Jan Philipp Bittner
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
| | - Irina Smirnova
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
| | - Sven Jakobtorweihen
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
- Institute of Chemical Reaction Engineering, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
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4
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Kumar P, Kermanshahi-Pour A, Brar SK, He QS, Rainey JK. Influence of elevated pressure and pressurized fluids on microenvironment and activity of enzymes. Biotechnol Adv 2023; 68:108219. [PMID: 37488056 DOI: 10.1016/j.biotechadv.2023.108219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023]
Abstract
Enzymes have great potential in bioprocess engineering due to their green and mild reaction conditions. However, there are challenges to their application, such as enzyme extraction and purification costs, enzyme recovery, and long reaction time. Enzymatic reaction rate enhancement and enzyme immobilization have the potential to overcome some of these challenges. Application of high pressure (e.g., hydrostatic pressure, supercritical carbon dioxide) has been shown to increase the activity of some enzymes, such as lipases and cellulases. Under high pressure, enzymes undergo multiple alterations simultaneously. High pressure reduces the bond lengths of molecules of reaction components and causes a reduction in the activation volume of enzyme-substrate complex. Supercritical CO2 interacts with enzyme molecules, catalyzes structural changes, and removes some water molecules from the enzyme's hydration layer. Interaction of scCO2 with the enzyme also leads to an overall change in secondary structure content. In the extreme, such changes may lead to enzyme denaturation, but enzyme activation and stabilization have also been observed. Immobilization of enzymes onto silica and zeolite-based supports has been shown to further stabilize the enzyme and provide resistance towards perturbation under subjection to high pressure and scCO2.
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Affiliation(s)
- Pawan Kumar
- Biorefining and Remediation Laboratory, Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3J 1Z1, Canada
| | - Azadeh Kermanshahi-Pour
- Biorefining and Remediation Laboratory, Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3J 1Z1, Canada.
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario M3J 1P3, Canada
| | - Quan Sophia He
- Department of Engineering, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Jan K Rainey
- Department of Biochemistry & Molecular Biology, Department of Chemistry, and School of Biomedical Engineering, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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Li W, Bilal M, Singh AK, Sher F, Ashraf SS, Franco M, Américo-Pinheiro JHP, Iqbal HMN. Broadening the Scope of Biocatalysis Engineering by Tailoring Enzyme Microenvironment: A Review. Catal Letters 2022. [DOI: 10.1007/s10562-022-04065-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Radhakrishnan R, Manna B, Ghosh A. Solvent induced conformational changes for the altered activity of laccase: A molecular dynamics study. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127123. [PMID: 34530268 DOI: 10.1016/j.jhazmat.2021.127123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The growing demands of solvent-based industries like paint, pharmaceutical, petrochemical, paper and pulp, etc., have directly increased the release of effluents that are rich in hazardous aromatic compounds in the environment. A sustainable biotechnological approach utilizing laccases as biocatalyst enable in biodegradation of these aromatic toxin-rich effluents. However, this enzymatic process is ineffective as laccases lose their stability and catalytic activity at high organic solvent concentrations. In this study, molecular dynamic simulations of a novel solvent tolerant laccase, DLac from Cerrena sp. RSD1 was performed to explore the molecular-level understanding of DLac in 30%(v/v) acetone and acetonitrile. Solvent-induced conformational changes were analyzed via protein structure network, which was illustrated with respect to cliques and communities. In the presence of acetonitrile, the cliques around the active site and substrate-binding site were disjoined, thus the communities lost their network integrity. Whereas with acetone, the community near the substrate-binding site gained new residues and formed a rigidified network that corresponded to enhanced DLac's activity. Moreover, prominent solvent binding sites were speculated, which can be probable mutation targets to further improve solvent tolerance and catalytic activity. The molecular basis behind solvent induced catalytic activity will further aid in engineering laccase for its industrial application.
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Affiliation(s)
- Rokesh Radhakrishnan
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Bharat Manna
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India; School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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7
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Cui H, Vedder M, Schwaneberg U, Davari MD. Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents. Methods Mol Biol 2022; 2397:179-202. [PMID: 34813065 DOI: 10.1007/978-1-0716-1826-4_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biocatalysis in organic solvents (OSs) is very appealing for the industry in producing bulk and/or fine chemicals, such as pharmaceuticals, biodiesel, and fragrances. The poor performance of enzymes in OSs (e.g., reduced activity, insufficient stability, and deactivation) negates OSs' excellent solvent properties. Molecular dynamics (MD) simulations provide a complementary method to study the relationship between enzymes dynamics and the stability in OSs. Here we describe computational procedure for MD simulation of enzymes in OSs with an example of Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO) cosolvent with software GROMACS. We discuss main essential practical issues considered (such as choice of force field, parameterization, simulation setup, and trajectory analysis). The core part of this protocol (enzyme-OS system setup, analysis of structural-based and solvation-based observables) is transferable to other enzymes and any OS systems. Combining with experimental studies, the obtained molecular knowledge is most likely to guide researchers to access rational protein engineering approaches to tailor OS resistant enzymes and expand the scope of biocatalysis in OS media. Finally, we discuss potential solutions to overcome the remaining challenges of computational biocatalysis in OSs and briefly draw future directions for further improvement in this field.
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Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Markus Vedder
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany.
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Xu H, Li X, Xin X, Mo L, Zou Y, Zhao G. Efficient Enzymatic Synthesis of Lipophilic Phenolic Glycoside Azelaic Acid Esters and Their Depigmenting Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13102-13112. [PMID: 34705451 DOI: 10.1021/acs.jafc.1c03092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this paper, an enzymatic route for synthesizing phenolic glycoside azelaic acid esters was successfully set up via lipase-catalyzed esterification and transesterification. Among the lipases tested, Candida antarctica lipase B (Novozyme 435) showed the highest activity in catalyzing esterification and Thermomyces lanuginosus (Lipozyme TLIM) gave the highest substrate conversion in catalyzing transesterification for the synthesis of ester. The addition of 4A molecular sieves into the reaction system is found to be an effective method for in situ absorption of the byproduct water and methanol, with which the substrate conversions of the enzymatic esterification and transesterification were 98.7 and 95.1%, respectively. Also, the main product ratios in transesterification were above 99.0% with lipozyme TLIM as a catalyst because the hydrolysis reaction was hindered. The results of the physical and biological properties indicate that all esters had higher Clog p values than their parent compounds. Also, the esters showed higher intracellular tyrosinase inhibitory and depigmentating activities than phenolic glycosides, azelaic acid (AA), and their physical mixtures due to their higher membrane penetration and tyrosinase inhibitory effects. In particular, piceid 6″-O-azelaic acid ester (PIA) showed the strongest inhibitory effect against melanin production. Its inhibitory rate was 77.4% at a concentration of 0.25 mM, about 4.2 times higher than that of arbutin (18.5%).
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Affiliation(s)
- Haixia Xu
- School of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou 510640, China
| | - Xiaofeng Li
- School of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou 510640, China
| | - Xuan Xin
- School of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou 510640, China
| | - Lan Mo
- School of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou 510640, China
| | - Yucong Zou
- School of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou 510640, China
| | - Guanglei Zhao
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China
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Fotiadou R, Chatzikonstantinou AV, Hammami MA, Chalmpes N, Moschovas D, Spyrou K, Polydera AC, Avgeropoulos A, Gournis D, Stamatis H. Green Synthesized Magnetic Nanoparticles as Effective Nanosupport for the Immobilization of Lipase: Application for the Synthesis of Lipophenols. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:458. [PMID: 33670153 PMCID: PMC7916844 DOI: 10.3390/nano11020458] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 11/16/2022]
Abstract
In this work, hybrid zinc oxide-iron oxide (ZnOFe) magnetic nanoparticles were synthesized employing Olea europaea leaf aqueous extract as a reducing/chelating and capping medium. The resulting magnetic nanoparticles were characterized by basic spectroscopic and microscopic techniques, namely, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), fourier-transform infrared (FTIR) and atomic force microscopy (AFM), exhibiting a spherical shape, average size of 15-17 nm, and a functionalized surface. Lipase from Thermomyces lanuginosus (TLL) was efficiently immobilized on the surface of ZnOFe nanoparticles through physical absorption. The activity of immobilized lipase was found to directly depend on the enzyme to support the mass ratio, and also demonstrated improved pH and temperature activity range compared to free lipase. Furthermore, the novel magnetic nanobiocatalyst (ZnOFe-TLL) was applied to the preparation of hydroxytyrosyl fatty acid esters, including derivatives with omega-3 fatty acids, in non-aqueous media. Conversion yields up to 90% were observed in non-polar solvents, including hydrophobic ionic liquids. Different factors affecting the biocatalyst performance were studied. ZnOFe-TLL was reutilized for eight subsequent cycles, exhibiting 90% remaining esterification activity (720 h of total operation at 50 °C). The green synthesized magnetic nanoparticles, reported here for the first time, are excellent candidates as nanosupports for the immobilization of enzymes with industrial interest, giving rise to nanobiocatalysts with elevated features.
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Affiliation(s)
- Renia Fotiadou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece; (R.F.); (A.V.C.); (A.C.P.)
| | - Alexandra V. Chatzikonstantinou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece; (R.F.); (A.V.C.); (A.C.P.)
| | - Mohamed Amen Hammami
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY 14853, USA;
| | - Nikolaos Chalmpes
- Department of Materials Science and Engineering, University of Ioannina, 45110 Ioannina, Greece; (N.C.); (D.M.); (K.S.); (A.A.); (D.G.)
| | - Dimitrios Moschovas
- Department of Materials Science and Engineering, University of Ioannina, 45110 Ioannina, Greece; (N.C.); (D.M.); (K.S.); (A.A.); (D.G.)
| | - Konstantinos Spyrou
- Department of Materials Science and Engineering, University of Ioannina, 45110 Ioannina, Greece; (N.C.); (D.M.); (K.S.); (A.A.); (D.G.)
| | - Angeliki C. Polydera
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece; (R.F.); (A.V.C.); (A.C.P.)
| | - Apostolos Avgeropoulos
- Department of Materials Science and Engineering, University of Ioannina, 45110 Ioannina, Greece; (N.C.); (D.M.); (K.S.); (A.A.); (D.G.)
| | - Dimitrios Gournis
- Department of Materials Science and Engineering, University of Ioannina, 45110 Ioannina, Greece; (N.C.); (D.M.); (K.S.); (A.A.); (D.G.)
| | - Haralambos Stamatis
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece; (R.F.); (A.V.C.); (A.C.P.)
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Cicco L, Dilauro G, Perna FM, Vitale P, Capriati V. Advances in deep eutectic solvents and water: applications in metal- and biocatalyzed processes, in the synthesis of APIs, and other biologically active compounds. Org Biomol Chem 2021; 19:2558-2577. [DOI: 10.1039/d0ob02491k] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review highlights recent advances in metal- and biocatalyzed transformations, in the synthesis of APIs and other biologically active compounds, when employing deep eutectic solvents and water as environmentally responsible solvents.
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Affiliation(s)
- Luciana Cicco
- Dipartimento di Farmacia-Scienze del Farmaco
- Università di Bari “Aldo Moro”
- Consorzio C.I.N.M.P.I.S
- Bari
- Italy
| | - Giuseppe Dilauro
- Dipartimento di Farmacia-Scienze del Farmaco
- Università di Bari “Aldo Moro”
- Consorzio C.I.N.M.P.I.S
- Bari
- Italy
| | - Filippo Maria Perna
- Dipartimento di Farmacia-Scienze del Farmaco
- Università di Bari “Aldo Moro”
- Consorzio C.I.N.M.P.I.S
- Bari
- Italy
| | - Paola Vitale
- Dipartimento di Farmacia-Scienze del Farmaco
- Università di Bari “Aldo Moro”
- Consorzio C.I.N.M.P.I.S
- Bari
- Italy
| | - Vito Capriati
- Dipartimento di Farmacia-Scienze del Farmaco
- Università di Bari “Aldo Moro”
- Consorzio C.I.N.M.P.I.S
- Bari
- Italy
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11
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Cui H, Zhang L, Eltoukhy L, Jiang Q, Korkunç SK, Jaeger KE, Schwaneberg U, Davari MD. Enzyme Hydration Determines Resistance in Organic Cosolvents. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03233] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Lingling Zhang
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Lobna Eltoukhy
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Qianjia Jiang
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Seval Kübra Korkunç
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Wilhelm Johnen Strasse, Jülich 52426, Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, Jülich 52426, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstrasse 50, Aachen 52074, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
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12
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Zhao H. What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization. Biotechnol Adv 2020; 45:107638. [PMID: 33002582 DOI: 10.1016/j.biotechadv.2020.107638] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/05/2020] [Accepted: 09/25/2020] [Indexed: 12/16/2022]
Abstract
Enzyme activity in nonaqueous media (e.g. conventional organic solvents) is typically lower than in water by several orders of magnitude. There is a rising interest of developing new nonaqueous solvent systems that are more "water-like" and more biocompatible. Therefore, we need to learn from the current state of nonaqueous biocatalysis to overcome its bottleneck and provide guidance for new solvent design. This review firstly focuses on the discussion of how organic solvent properties (such as polarity and hydrophobicity) influence the enzyme activity and stability, and how these properties impact the enzyme's conformation and dynamics. While hydrophobic organic solvents usually lead to the maintenance of enzyme activity, solvents carrying functional groups like hydroxys and ethers (including crown ethers and cyclodextrins) can lead to enzyme activation. Ionic liquids (ILs) are designable solvents that can conveniently incorporate these functional groups. Therefore, we systematically survey these ether- and/or hydroxy-functionalized ILs, and find most of them are highly compatible with enzymes leading to high activity and stability. In particular, ILs carrying both ether and tert-alcohol groups are among the most enzyme-activating solvents. Future direction is to learn from enzyme behaviors in both water and nonaqueous media to design biocompatible "water-like" solvents.
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Affiliation(s)
- Hua Zhao
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO 80639, United States.
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13
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Shehata M, Unlu A, Sezerman U, Timucin E. Lipase and Water in a Deep Eutectic Solvent: Molecular Dynamics and Experimental Studies of the Effects of Water-In-Deep Eutectic Solvents on Lipase Stability. J Phys Chem B 2020; 124:8801-8810. [DOI: 10.1021/acs.jpcb.0c07041] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Mohamed Shehata
- Institute of Health Science, Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Aise Unlu
- Department of Chemistry, Gebze Technical University, Gebze 41400, Kocaeli, Turkey
| | - Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
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14
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15
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Development of a new Geobacillus lipase variant GDlip43 via directed evolution leading to identification of new activity-regulating amino acids. Int J Biol Macromol 2020; 151:1194-1204. [DOI: 10.1016/j.ijbiomac.2019.10.163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
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16
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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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17
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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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18
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A novel strategy to improve the aromatic alcohols tolerance of enzyme for preparative-scale synthesis of natural glycosides. CATAL COMMUN 2017. [DOI: 10.1016/j.catcom.2017.07.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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19
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Singh A, Vanga SK, Orsat V, Raghavan V. Application of molecular dynamic simulation to study food proteins: A review. Crit Rev Food Sci Nutr 2017; 58:2779-2789. [DOI: 10.1080/10408398.2017.1341864] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ashutosh Singh
- School of Engineering, University of Guelph, Guelph, Ontario, Canada
| | - Sai Kranthi Vanga
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Valerie Orsat
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Vijaya Raghavan
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
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20
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Effect of Water Clustering on the Activity of Candida antarctica Lipase B in Organic Medium. Catalysts 2017. [DOI: 10.3390/catal7080227] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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21
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Verma R, Mitchell-Koch K. In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function. Catalysts 2017; 7:212. [PMID: 30464857 PMCID: PMC6241538 DOI: 10.3390/catal7070212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.
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Affiliation(s)
- Rajni Verma
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| | - Katie Mitchell-Koch
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
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22
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Maiangwa J, Mohamad Ali MS, Salleh AB, Rahman RNZRA, Normi YM, Mohd Shariff F, Leow TC. Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents. PeerJ 2017; 5:e3341. [PMID: 28533982 PMCID: PMC5438581 DOI: 10.7717/peerj.3341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 04/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity.
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Affiliation(s)
- Jonathan Maiangwa
- Department of Cell and Molecular Biology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Serlangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Department of Biochemistry/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Department of Biochemistry/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Department of Microbiology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Department of Cell and Molecular Biology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Serlangor, Malaysia
| | - Fairolniza Mohd Shariff
- Department of Microbiology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Department of Cell and Molecular Biology/Enzyme and Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science/Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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23
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Are Directed Evolution Approaches Efficient in Exploring Nature’s Potential to Stabilize a Lipase in Organic Cosolvents? Catalysts 2017. [DOI: 10.3390/catal7050142] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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24
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Cao H, Jiang Y, Zhang H, Nie K, Lei M, Deng L, Wang F, Tan T. Enhancement of methanol resistance of Yarrowia lipolytica lipase 2 using β-cyclodextrin as an additive: Insights from experiments and molecular dynamics simulation. Enzyme Microb Technol 2017; 96:157-162. [DOI: 10.1016/j.enzmictec.2016.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 10/05/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
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25
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Dutta Banik S, Nordblad M, Woodley JM, Peters GH. A Correlation between the Activity of Candida antarctica Lipase B and Differences in Binding Free Energies of Organic Solvent and Substrate. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02073] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sindrila Dutta Banik
- Department
of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, Building
207, 2800 Kongens
Lyngby, Denmark
| | - Mathias Nordblad
- Department
of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kongens Lyngby, Denmark
| | - John M. Woodley
- Department
of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kongens Lyngby, Denmark
| | - Günther H. Peters
- Department
of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, Building
207, 2800 Kongens
Lyngby, Denmark
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26
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Dahanayake JN, Gautam DN, Verma R, Mitchell-Koch KR. To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent. MOLECULAR SIMULATION 2016; 42:1001-1013. [PMID: 27403032 DOI: 10.1080/08927022.2016.1139108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results.
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Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Devaki N Gautam
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Rajni Verma
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Katie R Mitchell-Koch
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
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27
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28
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Catalytic activity and structural stability of three different Bacillus enzymes in water/organic co-solvent mixtures. J Taiwan Inst Chem Eng 2016. [DOI: 10.1016/j.jtice.2015.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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29
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Sirotkin VA, Dudkina EV. A study of the hydration of lysozyme in neat organic solvents using isothermal calorimetry: Effect of water solvation. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Tong X, Busk PK, Lange L, Pang J. New insights into the molecular mechanism of methanol-induced inactivation ofThermomyces lanuginosuslipase: a molecular dynamics simulation study. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1059938] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Li L, Ji F, Wang J, Li Y, Bao Y. Esterification degree of fructose laurate exerted by Candida antarctica lipase B in organic solvents. Enzyme Microb Technol 2015; 69:46-53. [DOI: 10.1016/j.enzmictec.2014.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 12/03/2014] [Accepted: 12/07/2014] [Indexed: 01/30/2023]
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32
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Makshakova ON, Faizullin DA, Zuev YF. Structure of complexes of poly-γ-benzyl-L-glutamate with water and dioxane molecules studied by IR spectroscopy and quantum chemical calculations. J STRUCT CHEM+ 2015. [DOI: 10.1134/s0022476614080265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Benson SP, Pleiss J. Solvent Flux Method (SFM): A Case Study of Water Access to Candida antarctica Lipase B. J Chem Theory Comput 2014; 10:5206-14. [DOI: 10.1021/ct500791e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Mohammad Latif MA, Micaêlo NM, Abdul Rahman MB. Influence of anion–water interactions on the behaviour of lipases in room temperature ionic liquids. RSC Adv 2014. [DOI: 10.1039/c4ra07460b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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35
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Jiang Y, Li L, Zhang H, Feng W, Tan T. Lid Closure Mechanism of Yarrowia lipolytica Lipase in Methanol Investigated by Molecular Dynamics Simulation. J Chem Inf Model 2014; 54:2033-41. [DOI: 10.1021/ci500163y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yang Jiang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingli Li
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haiyang Zhang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Feng
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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36
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Purification and characterization of solvent stable, alkaline protease from Bacillus firmus CAS 7 by microbial conversion of marine wastes and molecular mechanism underlying solvent stability. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.03.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Yang W, Zhang L, Li M, Pu X, Zhao N. Effects of Non‐specific and Specific Solvation on Adsorption of BPTI on Au Surface: Insight from Molecular Dynamics Simulation. CHINESE J CHEM PHYS 2013. [DOI: 10.1063/1674-0068/26/05/558-568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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38
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Latif MA, Tejo BA, Abedikargiban R, Abdul Rahman MB, Micaêlo NM. Modeling stability and flexibility of α-Chymotrypsin in room temperature ionic liquids. J Biomol Struct Dyn 2013; 32:1263-73. [DOI: 10.1080/07391102.2013.813411] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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39
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Park HJ, Park K, Yoo YJ. Understanding the effect of tert-butanol onCandida antarcticalipase B using molecular dynamics simulations. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.758850] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Meng Y, Yuan Y, Zhu Y, Guo Y, Li M, Wang Z, Pu X, Jiang L. Effects of organic solvents and substrate binding on trypsin in acetonitrile and hexane media. J Mol Model 2013; 19:3749-66. [DOI: 10.1007/s00894-013-1900-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/27/2013] [Indexed: 11/29/2022]
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41
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Stepankova V, Damborsky J, Chaloupkova R. Organic co-solvents affect activity, stability and enantioselectivity of haloalkane dehalogenases. Biotechnol J 2013; 8:719-29. [PMID: 23420811 DOI: 10.1002/biot.201200378] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/21/2013] [Accepted: 02/12/2013] [Indexed: 01/12/2023]
Abstract
Haloalkane dehalogenases are microbial enzymes with a wide range of biotechnological applications, including biocatalysis. The use of organic co-solvents to solubilize their hydrophobic substrates is often necessary. In order to choose the most compatible co-solvent, the effects of 14 co-solvents on activity, stability and enantioselectivity of three model enzymes, DbjA, DhaA, and LinB, were evaluated. All co-solvents caused at high concentration loss of activity and conformational changes. The highest inactivation was induced by tetrahydrofuran, while more hydrophilic co-solvents, such as ethylene glycol and dimethyl sulfoxide, were better tolerated. The effects of co-solvents at low concentration were different for each enzyme-solvent pair. An increase in DbjA activity was induced by the majority of organic co-solvents tested, while activities of DhaA and LinB decreased at comparable concentrations of the same co-solvent. Moreover, a high increase of DbjA enantioselectivity was observed. Ethylene glycol and 1,4-dioxane were shown to have the most positive impact on the enantioselectivity. The favorable influence of these co-solvents on both activity and enantioselectivity makes DbjA suitable for biocatalytic applications. This study represents the first investigation of the effects of organic co-solvents on the biocatalytic performance of haloalkane dehalogenases and will pave the way for their broader use in industrial processes.
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Affiliation(s)
- Veronika Stepankova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Masaryk University, Brno, Czech Republic
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42
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Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation. J Mol Model 2013; 19:2525-38. [PMID: 23455930 DOI: 10.1007/s00894-013-1807-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
Abstract
The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 % v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution and H-bonding are analyzed in the two organic media. Our results show that the changes in overall structure of the protein almost display a clear correlation with the water content in hexane media while to some extent U-shaped/bell-shaped dependence on the water content is observed in acetonitrile media with a minimum/maximum at 10-20 % water content. In contrast, the water content change in the two organic solvents does not play an observable role in the stability of catalytic hydrogen-bond network, which still exhibits high stability in all hydration levels, different from observations on the free enzyme system [Zhu L, Yang W, Meng YY, Xiao X, Guo Y, Pu X, Li M (2012) J Phys Chem B 116(10):3292-3304]. In low hydration levels, most water molecules mainly distribute near the protein surface and an increase in the water content could not fully exclude the organic solvent from the protein surface. However, the acetonitrile solvent displays a stronger ability to strip off water molecules from the protein than the hexane. In a summary, the difference in the calculated properties between the two organic solvents is almost significant in low water content (<10 %) and become to be small with increasing water content. In addition, some structural properties at 10 ~ 20 % v/v hydration zone, to large extent, approach to those in aqueous solution.
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43
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Park HJ, Joo JC, Park K, Kim YH, Yoo YJ. Prediction of the solvent affecting site and the computational design of stable Candida antarctica lipase B in a hydrophilic organic solvent. J Biotechnol 2013. [DOI: 10.1016/j.jbiotec.2012.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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Xu J, Zhuang Y, Wu B, Su L, He B. Calcium-ion-induced stabilization of the protease from Bacillus cereus WQ9-2 in aqueous hydrophilic solvents: effect of calcium ion binding on the hydration shell and intramolecular interactions. J Biol Inorg Chem 2013; 18:211-221. [PMID: 23322168 DOI: 10.1007/s00775-012-0966-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/24/2012] [Indexed: 01/12/2023]
Abstract
The neutral protease WQ from Bacillus cereus is stable in various aqueous organic mixtures, with the exception of those containing acetonitrile (ACN) and dimethylformamide (DMF). The stability of the enzyme in aqueous hydrophilic solvents was dramatically enhanced with the addition of calcium ions, with the degree of improvement in the half-life relative to different solutions ranging from fourfold to more than 70-fold. Studies of the kinetic constants showed that calcium ions induced slight conformational changes in the active site of the enzyme in aqueous ACN. We investigated the molecular mechanisms underlying this stabilizing effect by employing a combination of biophysical techniques and molecular dynamics simulation. In aqueous ACN, the intrinsic fluorescence and circular dichroism analysis demonstrated that the addition of calcium ions induced a relatively compact conformation and maintained both the native-like microenvironment near the tryptophan residues and the secondary structure. Alternatively, homology modeling confirmed the location of four calcium-ion-binding sites in the enzyme, and molecular dynamics simulation revealed that three other calcium ions were bound to the surface of the enzyme. Calcium ions, known as a type of kosmotrope, can strongly bond with water molecules, thus aiding in the formation of the regional hydration shell required for the maintenance of enzyme activity. In addition, the introduction of calcium ions resulted in the formation of additional ionic interactions, providing propitious means for protein stabilization. Thus, the stronger intramolecular interactions were also expected to contribute partially to the enhanced stability of the enzyme in an aqueous organic solvent.
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Affiliation(s)
- Jiaxing Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Yu Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Long Su
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China.
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Lousa D, Baptista AM, Soares CM. A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies. Phys Chem Chem Phys 2013; 15:13723-36. [DOI: 10.1039/c3cp51761f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Abildskov J, van Leeuwen M, Boeriu C, van den Broek L. Computer-aided solvent screening for biocatalysis. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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47
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Makshakova ON, Faĭzullin DA, Zuev IF. [Influence of dioxane on the hydration shell of polypeptides]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 38:300-5. [PMID: 22997701 DOI: 10.1134/s1068162012030107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Our interest in modifying influence of the low-molecular organic compounds on the hydration shell of biopolymers is due to a well-known fact that the former can act as regulators of the enzymatic activity changed the hydration shell of the latter. Dioxane was chosen because of its wide application in non-aqueous biocatalysis. In the present study we investigate the mechanisms of the dioxane influence on water of the first hydration layer of the model polypeptides by FTIR-spectroscopy during simultaneous sorption of water-dioxane vapors into the polypeptide films at low water activity. It was found that modification of the hydration shell of the studied polypeptides was mainly due to the indirect ordering ofpolypeptide secondary structure at penetration of dioxane molecules at these conditions.
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48
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Interaction of organic solvents with protein structures at protein-solvent interface. J Mol Model 2012; 19:4701-11. [DOI: 10.1007/s00894-012-1507-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
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Kazenwadel C, Eiben S, Maurer S, Beuttler H, Wetzl D, Hauer B, Koschorreck K. Thiol-functionalization of acrylic ester monomers catalyzed by immobilized Humicola insolens cutinase. Enzyme Microb Technol 2012; 51:9-15. [DOI: 10.1016/j.enzmictec.2012.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/23/2012] [Accepted: 03/26/2012] [Indexed: 11/26/2022]
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50
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Lousa D, Cianci M, Helliwell JR, Halling PJ, Baptista AM, Soares CM. Interaction of Counterions with Subtilisin in Acetonitrile: Insights from Molecular Dynamics Simulations. J Phys Chem B 2012; 116:5838-48. [DOI: 10.1021/jp303008g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diana Lousa
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras,
Portugal
| | - Michele Cianci
- European Molecular
Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestraße 85, 22603 Hamburg, Germany
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United
Kingdom
| | - Peter J. Halling
- WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras,
Portugal
| | - Cláudio M. Soares
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras,
Portugal
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