1
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Wijaya T, Kitao A. Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM. J Phys Chem B 2023; 127:7431-7441. [PMID: 37562019 PMCID: PMC10476181 DOI: 10.1021/acs.jpcb.3c02041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/21/2023] [Indexed: 08/12/2023]
Abstract
The conformational dynamics of Candida antarctica lipase B (CALB) was investigated by molecular dynamics (MD) simulation, parallel cascade selection MD (PaCS-MD), and the Markov state model (MSM) and mainly focused on the lid-opening motion closely related to substrate binding. All-atom MD simulation of CALB was conducted in water and on the interface of water and tricaprylin. CALB initially situated in water and separated by layers of water from the interface is spontaneously adsorbed onto the tricaprylin surface during MD simulation. The opening and closing motions of the lid are simulated by PaCS-MD, and subsequent MSM analysis provided the free-energy landscape and time scale of the conformational transitions among the closed, semiopen, and open states. The closed state is the most stable in the water system, but the stable conformation in the interface system shifts to the semiopen state. These effects could explain the energetics and kinetics origin of the previously reported interfacial activation of CALB. These findings could help expand the application of CALB toward a wide variety of substrates.
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Affiliation(s)
- Tegar
N. Wijaya
- School
of Life Science and Technology, Tokyo Institute
of Technology. 2-12-1
Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department
of Chemistry, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug, Jakarta 12220, Indonesia
| | - Akio Kitao
- School
of Life Science and Technology, Tokyo Institute
of Technology. 2-12-1
Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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2
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Feiten MC, Morigi I, Di Luccio M, Oliveira JV. Activity and stability of lipase from Candida Antarctica after treatment in pressurized fluids. Biotechnol Lett 2023; 45:287-298. [PMID: 36592260 DOI: 10.1007/s10529-022-03335-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 10/13/2022] [Accepted: 11/28/2022] [Indexed: 01/03/2023]
Abstract
Lipase B from Candida antarctica (CalB) is one of the biocatalysts most used in organic synthesis due to its ability to act in several medium, wide substrate specificity and enantioselectivity, tolerance to non-aqueous environment, and resistance to thermal deactivation. Thus, the objective of this work was to treat CalB in supercritical carbon dioxide (SC-CO2) and liquefied petroleum gas (LPG), and measure its activity before and after high-pressure treatment. Residual specific hydrolytic activities of 132% and 142% were observed when CalB was exposed to SC-CO2 at 35 ℃, 75 bar and 1 h and to LPG at 65 ℃, 30 bar and 1 h, respectively. Residual activity of the enzyme treated at high pressure was still above 100% until the 20th day of storage at low temperatures. There was no difference on the residual activity loss of CalB treated with LPG and stored at different temperatures over time. Greater difference was observed between CalB treated with CO2 and flash-frozen in liquid nitrogen (- 196 ℃) followed by storage in freezer (- 10 ℃) and CalB stored in freezer at - 10 ℃. Such findings encourage deeper studies on CalB as well as other enzymes behavior under different types of pressurized fluids aiming at industrial application.
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Affiliation(s)
- Mirian Cristina Feiten
- Department of Technology, State University of Maringá (UEM), Angelo Moreira da Fonseca Ave, Umuarama, Paraná, 87506-370, Brazil.
| | - Iasmin Morigi
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), Technology Center/C.P. 476, Florianópolis, Santa Catarina, 88040-900, Brazil
| | - Marco Di Luccio
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), Technology Center/C.P. 476, Florianópolis, Santa Catarina, 88040-900, Brazil
| | - José Vladimir Oliveira
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), Technology Center/C.P. 476, Florianópolis, Santa Catarina, 88040-900, Brazil
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3
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Tu H, Gao K, Zhang B, Chen Z, Wang P, Li Z. Comparative study of poly tannic acid functionalized magnetic particles before and after modification for immobilized penicillin G acylase. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2022; 33:823-846. [PMID: 34935604 DOI: 10.1080/09205063.2021.2021352] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this work, Fe3O4 nanoparticles (NPs) was synthesized by inverting microemulsion method. After that, based on the physical and chemical properties of tannic acid (TA), poly tannic acid (PTA) was coated on Fe3O4 NPs surface. Fe3O4 NPs coated with PTA, on the one hand, was used to immobilize Penicillin G acylase (PGA) by physical adsorption. On the other hand, it was modified by glutaraldehyde (GA). GA grafting rate (Gr-GA) was optimized, and the Gr-GA was 30.0% under the optimum conditions. Then, through the Schiff base reaction between the glutaraldehyde group and PGA amino group, this covalent immobilization of PGA was further realized under mild conditions. Finally, the structures of every stage of magnetic composites were characterized by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), vibration magnetometer (VSM) and transmission electron microscopy (TEM), respectively. The results indicated that the enzyme activity (EA), enzyme activity recovery (EAR) and maximum load (ELC) of the immobilized PGA were 26843 U/g, 80.2% and 125 mg/g, respectively. Compared to the physical immobilization of PGA by only coating PTA nanoparticles, further modified nanoparticles by GA showed higher catalytic stability, reusability and storage stability.
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Affiliation(s)
- Hongyi Tu
- School of Materials Science and Engineering, Lanzhou University of Technology, Lanzhou, China.,State Key Laboratory of Advanced progressing and Recycling of Nonferrous Metal Materials, Lanzhou University of Technology, Lanzhou, China
| | - Kaikai Gao
- School of Materials Science and Engineering, Lanzhou University of Technology, Lanzhou, China.,State Key Laboratory of Advanced progressing and Recycling of Nonferrous Metal Materials, Lanzhou University of Technology, Lanzhou, China
| | - Boyuan Zhang
- School of Materials Science and Engineering, Lanzhou University of Technology, Lanzhou, China.,State Key Laboratory of Advanced progressing and Recycling of Nonferrous Metal Materials, Lanzhou University of Technology, Lanzhou, China
| | - Zhenbin Chen
- School of Materials Science and Engineering, Lanzhou University of Technology, Lanzhou, China.,State Key Laboratory of Advanced progressing and Recycling of Nonferrous Metal Materials, Lanzhou University of Technology, Lanzhou, China
| | - Pingbo Wang
- School of Materials Science and Engineering, Lanzhou University of Technology, Lanzhou, China.,State Key Laboratory of Advanced progressing and Recycling of Nonferrous Metal Materials, Lanzhou University of Technology, Lanzhou, China
| | - Zhizhong Li
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
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4
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Abstract
In relation to the development of environmentally-friendly processing technologies for the continuously growing market of plastics, enzymes play an important role as green and sustainable biocatalysts. The present study reports the use of heterogeneous immobilized biocatalysts in solvent-free systems for the synthesis of aliphatic oligoesters with Mws and monomer conversions up to 1500 Da and 74%, respectively. To improve the accessibility of hydrophilic and hydrophobic substrates to the surface of the biocatalyst and improve the reaction kinetic and the chain elongation, two different binding modules were fused on the surface of cutinase 1 from Thermobifida cellulosilytica. The fusion enzymes were successfully immobilized (>99% of bound protein) via covalent bonding onto epoxy-activated beads. To the best of our knowledge, this is the first example where fused enzymes are used to catalyze transesterification reactions for polymer synthesis purposes.
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5
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Meena J, Gupta A, Ahuja R, Singh M, Panda AK. Recent advances in nano-engineered approaches used for enzyme immobilization with enhanced activity. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116602] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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6
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Criteria for Engineering Cutinases: Bioinformatics Analysis of Catalophores. Catalysts 2021. [DOI: 10.3390/catal11070784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cutinases are bacterial and fungal enzymes that catalyze the hydrolysis of natural cutin, a three-dimensional inter-esterified polyester with epoxy-hydroxy fatty acids with chain lengths between 16 and 18 carbon atoms. Due to their ability to accept long chain substrates, cutinases are also effective in catalyzing in vitro both the degradation and synthesis of several synthetic polyesters and polyamides. Here, we present a bioinformatics study that intends to correlate the structural features of cutinases with their catalytic properties to provide rational basis for their effective exploitation, particularly in polymer synthesis and biodegradation. The bioinformatics study used the BioGPS method (Global Positioning System in Biological Space) that computed molecular descriptors based on Molecular Interaction Fields (MIFs) described in the GRID force field. The information was used to generate catalophores, spatial representations of the ability of each enzymatic active site to establish hydrophobic and electrostatic interactions. These tools were exploited for comparing cutinases to other serine-hydrolases enzymes, namely lipases, esterases, amidases and proteases, and for highlighting differences and similarities that might guide rational engineering strategies. Structural features of cutinases with their catalytic properties were correlated. The “catalophore” of cutinases indicate shared features with lipases and esterases.
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7
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Different strategies for the lipase immobilization on the chitosan based supports and their applications. Int J Biol Macromol 2021; 179:170-195. [PMID: 33667561 DOI: 10.1016/j.ijbiomac.2021.02.198] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 01/15/2023]
Abstract
Immobilized enzymes have received incredible interests in industry, pharmaceuticals, chemistry and biochemistry sectors due to their various advantages such as ease of separation, multiple reusability, non-toxicity, biocompatibility, high activity and resistant to environmental changes. This review in between various immobilized enzymes focuses on lipase as one of the most practical enzyme and chitosan as a preferred biosupport for lipase immobilization and provides a broad range of studies of recent decade. We highlight several aspects of lipase immobilization on the surface of chitosan support containing various types of lipase and immobilization techniques from physical adsorption to covalent bonding and cross-linking with their benefits and drawbacks. The recent advances and future perspectives that can improve the present problems with lipase and chitosan such as high-price of lipase and low mechanical resistance of chitosan are also discussed. According to the literature, optimization of immobilization methods, combination of these methods with other techniques, physical and chemical modifications of chitosan, co-immobilization and protein engineering can be useful as a solution to overcome the mentioned limitations.
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8
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Ismail AR, Baek KH. Lipase immobilization with support materials, preparation techniques, and applications: Present and future aspects. Int J Biol Macromol 2020; 163:1624-1639. [DOI: 10.1016/j.ijbiomac.2020.09.021] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/19/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022]
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9
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Verma N, Dollinger P, Kovacic F, Jaeger KE, Gohlke H. The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A. J Comput Chem 2019; 41:500-512. [PMID: 31618459 DOI: 10.1002/jcc.26085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/22/2019] [Accepted: 09/25/2019] [Indexed: 12/19/2022]
Abstract
Lipases are essential and widely used biocatalysts. Hence, the production of lipases requires a detailed understanding of the molecular mechanism of its folding and secretion. Lipase A from Pseudomonas aeruginosa, PaLipA, constitutes a prominent example that has additional relevance because of its role as a virulence factor in many diseases. PaLipA requires the assistance of a membrane-integrated steric chaperone, the lipase-specific foldase Lif, to achieve its enzymatically active state. However, the molecular mechanism of how Lif activates its cognate lipase has remained elusive. Here, we show by molecular dynamics simulations at the atomistic level and potential of mean force computations that Lif catalyzes the activation process of PaLipA by structurally stabilizing an intermediate PaLipA conformation, particularly a β-sheet in the region of residues 17-30, such that the opening of PaLipA's lid domain is facilitated. This opening allows substrate access to PaLipA's catalytic site. A surprising and so far not fully understood aspect of our study is that the open state of PaLipA is unstable compared to the closed one according to our computational and in vitro biochemical results. We thus speculate that further interactions of PaLipA with the Xcp secretion machinery and/or components of the extracellular matrix contribute to the remaining activity of secreted PaLipA. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Neha Verma
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätstr. 1, 40225, Düsseldorf, Germany
| | - Peter Dollinger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätstr. 1, 40225, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
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10
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Ferrario V, Fischer M, Zhu Y, Pleiss J. Modelling of substrate access and substrate binding to cephalosporin acylases. Sci Rep 2019; 9:12402. [PMID: 31455800 PMCID: PMC6712217 DOI: 10.1038/s41598-019-48849-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/14/2019] [Indexed: 01/16/2023] Open
Abstract
Semisynthetic cephalosporins are widely used antibiotics currently produced by different chemical steps under harsh conditions, which results in a considerable amount of toxic waste. Biocatalytic synthesis by the cephalosporin acylase from Pseudomonas sp. strain N176 is a promising alternative. Despite intensive engineering of the enzyme, the catalytic activity is still too low for a commercially viable process. To identify the bottlenecks which limit the success of protein engineering efforts, a series of MD simulations was performed to study for two acylase variants (WT, M6) the access of the substrate cephalosporin C from the bulk to the active site and the stability of the enzyme-substrate complex. In both variants, cephalosporin C was binding to a non-productive substrate binding site (E86α, S369β, S460β) at the entrance to the binding pocket, preventing substrate access. A second non-productive binding site (G372β, W376β, L457β) was identified within the binding pocket, which competes with the active site for substrate binding. Noteworthy, substrate binding to the protein surface followed a Langmuir model resulting in binding constants K = 7.4 and 9.2 mM for WT and M6, respectively, which were similar to the experimentally determined Michaelis constants KM = 11.0 and 8.1 mM, respectively.
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Affiliation(s)
- Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Mona Fischer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Yushan Zhu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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11
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Buchholz PCF, Ferrario V, Pohl M, Gardossi L, Pleiss J. Navigating within thiamine diphosphate-dependent decarboxylases: Sequences, structures, functional positions, and binding sites. Proteins 2019; 87:774-785. [PMID: 31070804 DOI: 10.1002/prot.25706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/23/2019] [Accepted: 05/05/2019] [Indexed: 11/10/2022]
Abstract
Thiamine diphosphate-dependent decarboxylases catalyze both cleavage and formation of CC bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP-dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP-dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences.
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Affiliation(s)
- Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.,Laboratory of Applied and Computational Biocatalysis, Department of Chemical and Pharmaceutical Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Martina Pohl
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany
| | - Lucia Gardossi
- Laboratory of Applied and Computational Biocatalysis, Department of Chemical and Pharmaceutical Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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12
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Rice Husk as an Inexpensive Renewable Immobilization Carrier for Biocatalysts Employed in the Food, Cosmetic and Polymer Sectors. Catalysts 2018. [DOI: 10.3390/catal8100471] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The high cost and environmental impact of fossil-based organic carriers represent a critical bottleneck to their use in large-scale industrial processes. The present study demonstrates the applicability of rice husk as inexpensive renewable carrier for the immobilization of enzymes applicable sectors where the covalent anchorage of the protein is a pre-requisite for preventing protein contamination while assuring the recyclability. Rice husk was oxidized and then functionalized with a di-amino spacer. The morphological characterization shed light on the properties that affect the functionalization processes. Lipase B from Candida antarctica (CaLB) and two commercial asparaginases were immobilized covalently achieving higher immobilization yield than previously reported. All enzymes were immobilized also on commercial epoxy methacrylic resins and the CaLB immobilized on rice husk demonstrated a higher efficiency in the solvent-free polycondensation of dimethylitaconate. CaLB on rice husk appears particularly suitable for applications in highly viscous processes because of the unusual combination of its low density and remarkable mechanical robustness. In the case of the two asparaginases, the biocatalyst immobilized on rice husk performed in aqueous solution at least as efficiently as the enzyme immobilized on methacrylic resins, although the rice husk loaded a lower amount of protein.
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13
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Ferrario V, Pleiss J. Simulation of protein diffusion: a sensitive probe of protein-solvent interactions. J Biomol Struct Dyn 2018; 37:1534-1544. [PMID: 29667536 DOI: 10.1080/07391102.2018.1461689] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein-water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (RS), which was derived from the diffusion coefficient and the viscosity. RS was compared to the geometric radius (RG) of CALB, which was derived from the protein density. RS and RG differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein-water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.
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Affiliation(s)
- Valerio Ferrario
- a Institute of Biochemistry and Technical Biochemistry , University of Stuttgart , Allmandring 31, Stuttgart 70569 , Germany
| | - Jürgen Pleiss
- a Institute of Biochemistry and Technical Biochemistry , University of Stuttgart , Allmandring 31, Stuttgart 70569 , Germany
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14
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A General Overview of Support Materials for Enzyme Immobilization: Characteristics, Properties, Practical Utility. Catalysts 2018. [DOI: 10.3390/catal8020092] [Citation(s) in RCA: 459] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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15
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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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16
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Soni S, Dwivedee BP, Sharma VK, Patel G, Banerjee UC. Exploration of the expeditious potential of Pseudomonas fluorescens lipase in the kinetic resolution of racemic intermediates and its validation through molecular docking. Chirality 2017; 30:85-94. [PMID: 29064594 DOI: 10.1002/chir.22771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/28/2017] [Accepted: 09/03/2017] [Indexed: 11/05/2022]
Abstract
A profoundly time-efficient chemoenzymatic method for the synthesis of (S)-3-(4-chlorophenoxy)propan-1,2-diol and (S)-1-chloro-3-(2,5-dichlorophenoxy)propan-2-ol, two important pharmaceutical intermediates, was successfully developed using Pseudomonas fluorescens lipase (PFL). Kinetic resolution was successfully achieved using vinyl acetate as acylating agent, toluene/hexane as solvent, and reaction temperature of 30°C giving high enantioselectivity and conversion. Under optimized condition, PFL demonstrated 50.2% conversion, enantiomeric excess of 95.0%, enantioselectivity (E = 153) in an optimum time of 1 hour and 50.3% conversion, enantiomeric excess of 95.2%, enantioselectivity (E = 161) in an optimum time of 3 hours, for the two racemic alcohols, respectively. Docking of the R- and S-enantiomers of the intermediates demonstrated stronger H-bond interaction between the hydroxyl group of the R-enantiomer and the key binding residues of the catalytic site of the lipase, while the S-enantiomer demonstrated lesser interaction. Thus, docking study complemented the experimental outcome that PFL preferentially acylated the R form of the intermediates. The present study demonstrates a cost-effective and expeditious biocatalytic process that can be applied in the enantiopure synthesis of pharmaceutical intermediates and drugs.
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Affiliation(s)
- Surbhi Soni
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Bharat P Dwivedee
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Vishnu K Sharma
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Gopal Patel
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Uttam C Banerjee
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Punjab, India
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17
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Benson SP, Pleiss J. Self-Assembly Nanostructures of Triglyceride-Water Interfaces Determine Functional Conformations of Candida antarctica Lipase B. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3151-3159. [PMID: 28274117 DOI: 10.1021/acs.langmuir.6b04570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Candida antarctica lipase B (CalB) acts as a lipase when adsorbed to an acylglyceride interface and as an esterase when exposed to an aqueous environment. The effect of the molecular self-assembly nanostructure of triglyceride-water interfaces on structural conformations of adsorbed CalB and the implications to its catalytic function were studied by molecular dynamics simulations. Systems of CalB adsorbed to interfaces and solvated in water were compared. The two environments induced relative motions of helices α5 and α10 that resulted in open and closed conformations. The open conformation was stabilized by interactions between the polar and nonpolar amino acids of α5 and α10 and the nanostructure of triglyceride aggregates, which self-assembled into crystalline-like patterns of alternating polar and nonpolar lamellae. Thus, the structure of CalB has been adapted by evolution to the geometric constraints imposed by the interface nanostructure for optimized catalytic activity. Helices α5 and α10 have two functions. As mobile elements, they ensure access of bulky substrates to the active site in the open conformation. As a part of the active site pocket, they ensure binding of substrate molecules in a productive orientation near the active site. In water, access to the binding site is limited, and the smaller substrate binding site is beneficial for the binding of small, water-soluble substrates. The CalB crystal structure commonly used for protein engineering studies represents an intermediate state between open and closed, and may thus not be adequate to assess the function of CalB, neither as lipase nor as esterase.
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Affiliation(s)
- Sven P Benson
- Institute of Technical Biochemistry, University of Stuttgart , Allmandring 31, D - 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart , Allmandring 31, D - 70569 Stuttgart, Germany
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18
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Soni S, Dwivedee BP, Sharma VK, Banerjee UC. Kinetic resolution of (RS)-1-chloro-3-(4-(2-methoxyethyl)phenoxy)propan-2-ol: a metoprolol intermediate and its validation through homology model of Pseudomonas fluorescens lipase. RSC Adv 2017. [DOI: 10.1039/c7ra06499c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Kinetic resolution of (±)-1-chloro-3-(4-(2-methoxyethyl)phenoxy)propan-2-ol: a metoprolol intermediate and its validation through homology model of Pseudomonas fluorescens lipase.
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Affiliation(s)
- Surbhi Soni
- Department of Biotechnology
- National Institute of Pharmaceutical Education and Research
- S.A.S. Nagar
- India
| | - Bharat P. Dwivedee
- Department of Pharmaceutical Technology (Biotechnology)
- National Institute of Pharmaceutical Education and Research
- S.A.S. Nagar 160062
- India
| | - Vishnu K. Sharma
- Department of Pharmacoinformatics
- National Institute of Pharmaceutical Education and Research
- S.A.S. Nagar 160062
- India
| | - Uttam C. Banerjee
- Department of Pharmaceutical Technology (Biotechnology)
- National Institute of Pharmaceutical Education and Research
- S.A.S. Nagar 160062
- India
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19
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Nature Inspired Solutions for Polymers: Will Cutinase Enzymes Make Polyesters and Polyamides Greener? Catalysts 2016. [DOI: 10.3390/catal6120205] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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de Souza TC, de S. Fonseca T, da Costa JA, Rocha MVP, de Mattos MC, Fernandez-Lafuente R, Gonçalves LR, S. dos Santos JC. Cashew apple bagasse as a support for the immobilization of lipase B from Candida antarctica: Application to the chemoenzymatic production of (R)-Indanol. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.05.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Corici L, Ferrario V, Pellis A, Ebert C, Lotteria S, Cantone S, Voinovich D, Gardossi L. Large scale applications of immobilized enzymes call for sustainable and inexpensive solutions: rice husks as renewable alternatives to fossil-based organic resins. RSC Adv 2016. [DOI: 10.1039/c6ra12065b] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Rice husk for physical and covalent immobilization of enzymes: a sustainable and economic alternative to fossil-based organic resins.
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Affiliation(s)
| | - V. Ferrario
- Laboratory of Applied and Computational Biocatalysis
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- Trieste
- Italy
| | - A. Pellis
- Laboratory of Applied and Computational Biocatalysis
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- Trieste
- Italy
| | - C. Ebert
- Laboratory of Applied and Computational Biocatalysis
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- Trieste
- Italy
| | - S. Lotteria
- Laboratory of Applied and Computational Biocatalysis
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- Trieste
- Italy
| | | | - D. Voinovich
- Laboratory of Applied and Computational Biocatalysis
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- Trieste
- Italy
| | - L. Gardossi
- Laboratory of Applied and Computational Biocatalysis
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- Trieste
- Italy
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22
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Pellis A, Ferrario V, Zartl B, Brandauer M, Gamerith C, Herrero Acero E, Ebert C, Gardossi L, Guebitz GM. Enlarging the tools for efficient enzymatic polycondensation: structural and catalytic features of cutinase 1 from Thermobifida cellulosilytica. Catal Sci Technol 2016. [DOI: 10.1039/c5cy01746g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic and structural properties make cutinase 1 from Thermobifida cellulosilytica a more efficient biocatalyst for polycondensations, also of short-chain monomers.
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Affiliation(s)
- A. Pellis
- University of Natural Resources and Life Sciences
- Institute for Environmental Biotechnology
- 3430 Tulln an der Donau
- Austria
| | - V. Ferrario
- Laboratory of Applied and Computational Biocatalysis
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- Trieste
- Italy
| | - B. Zartl
- University of Natural Resources and Life Sciences
- Institute for Environmental Biotechnology
- 3430 Tulln an der Donau
- Austria
| | - M. Brandauer
- Austrian Centre of Industrial Biotechnology GmbH
- Division Enzymes and Polymers
- 3430 Tulln an der Donau
- Austria
| | - C. Gamerith
- Austrian Centre of Industrial Biotechnology GmbH
- Division Enzymes and Polymers
- 3430 Tulln an der Donau
- Austria
| | - E. Herrero Acero
- Austrian Centre of Industrial Biotechnology GmbH
- Division Enzymes and Polymers
- 3430 Tulln an der Donau
- Austria
| | - C. Ebert
- Laboratory of Applied and Computational Biocatalysis
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- Trieste
- Italy
| | - L. Gardossi
- Laboratory of Applied and Computational Biocatalysis
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- Trieste
- Italy
| | - G. M. Guebitz
- University of Natural Resources and Life Sciences
- Institute for Environmental Biotechnology
- 3430 Tulln an der Donau
- Austria
- Austrian Centre of Industrial Biotechnology GmbH
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23
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Wikmark Y, Engelmark Cassimjee K, Lihammar R, Bäckvall JE. Removing the Active-Site Flap in Lipase A fromCandida antarcticaProduces a Functional Enzyme without Interfacial Activation. Chembiochem 2015; 17:141-5. [DOI: 10.1002/cbic.201500471] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Ylva Wikmark
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Karim Engelmark Cassimjee
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Richard Lihammar
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Jan-E. Bäckvall
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
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24
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Ferrario V, Chernykh A, Fiorindo F, Kolomytseva M, Sinigoi L, Myasoedova N, Fattor D, Ebert C, Golovleva L, Gardossi L. Investigating the Role of Conformational Effects on Laccase Stability and Hyperactivation under Stress Conditions. Chembiochem 2015; 16:2365-72. [DOI: 10.1002/cbic.201500339] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Valerio Ferrario
- Department of Chemical and Pharmaceutical Sciences; University of Trieste; Piazzale Europa 1 34127 Trieste Italy
| | - Alexey Chernykh
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; 5 Prospekt Nauki Pushchino Moscow Region 142290 Russia
| | - Federica Fiorindo
- Department of Chemical and Pharmaceutical Sciences; University of Trieste; Piazzale Europa 1 34127 Trieste Italy
| | - Marina Kolomytseva
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; 5 Prospekt Nauki Pushchino Moscow Region 142290 Russia
| | - Loris Sinigoi
- Department of Chemical and Pharmaceutical Sciences; University of Trieste; Piazzale Europa 1 34127 Trieste Italy
| | - Nina Myasoedova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; 5 Prospekt Nauki Pushchino Moscow Region 142290 Russia
| | - Diana Fattor
- Department of Chemical and Pharmaceutical Sciences; University of Trieste; Piazzale Europa 1 34127 Trieste Italy
| | - Cynthia Ebert
- Department of Chemical and Pharmaceutical Sciences; University of Trieste; Piazzale Europa 1 34127 Trieste Italy
| | - Ludmila Golovleva
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; 5 Prospekt Nauki Pushchino Moscow Region 142290 Russia
| | - Lucia Gardossi
- Department of Chemical and Pharmaceutical Sciences; University of Trieste; Piazzale Europa 1 34127 Trieste Italy
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25
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Stauch B, Fisher SJ, Cianci M. Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation. J Lipid Res 2015; 56:2348-58. [PMID: 26447231 PMCID: PMC4655990 DOI: 10.1194/jlr.m063388] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 11/20/2022] Open
Abstract
Lipases (EC 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates, such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of considerable physiological significance with high interest also for their industrial applications. The hydrolysis reaction follows a two-step mechanism, or “interfacial activation,” with adsorption of the enzyme to a heterogeneous interface and subsequent enhancement of the lipolytic activity. Among lipases, Candida antarctica lipase B (CALB) has never shown any significant interfacial activation, and a closed conformation of CALB has never been reported, leading to the conclusion that its behavior was due to the absence of a lid regulating the access to the active site. The lid open and closed conformations and their protonation states are observed in the crystal structure of CALB at 0.91 Å resolution. Having the open and closed states at atomic resolution allows relating protonation to the conformation, indicating the role of Asp145 and Lys290 in the conformation alteration. The findings explain the lack of interfacial activation of CALB and offer new elements to elucidate this mechanism, with the consequent implications for the catalytic properties and classification of lipases.
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Affiliation(s)
- Benjamin Stauch
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Robinson College, University of Cambridge, Cambridge CB3 9AN, United Kingdom
| | - Stuart J Fisher
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Michele Cianci
- European Molecular Biology Laboratory (EMBL), Deutsches Elektronen-Synchrotron (DESY), Hamburg 22607, Germany
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26
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Zhang WW, Jia JQ, Wang N, Hu CL, Yang SY, Yu XQ. Improved activity of lipase immobilized in microemulsion-based organogels for ( R, S)-ketoprofen ester resolution: Long-term stability and reusability. ACTA ACUST UNITED AC 2015. [PMID: 28626708 PMCID: PMC5466060 DOI: 10.1016/j.btre.2015.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Microemulsion-based organogels (MBGs) were effectively employed for the immobilization of four commonly used lipases. During the asymmetric hydrolysis of ketoprofen vinyl ester at 30 °C for 24 h, lipase from Rhizomucor miehei and Mucor javanicus immobilized in microemulsion-based organogels (RML MBGs and MJL MBGs) maintained good enantioselectivities (eep were 86.2% and 99.2%, respectively), and their activities increased 12.8-fold and 7.8-fold, respectively, compared with their free forms. They gave higher yields compared with other lipase MBGs and exhibited better enantioselectivity than commercial immobilized lipases. Immobilization considerably increased the tolerance to organic solvents and high temperature. Both MJL MBGs and RML MBGs showed excellent reusability during 30 cycles of repeated 24 h reactions at 30 °C (over 40 days). The system maintained yields of greater than 50%, while the ees values of RML MBGs and MJL MBGs remained nearly constant at 95% and 88%, respectively.
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Affiliation(s)
- Wei-Wei Zhang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Jun-Qi Jia
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Na Wang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Cheng-Li Hu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Sheng-Yong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610064, PR China
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
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27
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Chen PC, Huang XJ, Xu ZK. Activation and deformation of immobilized lipase on self-assembled monolayers with tailored wettability. Phys Chem Chem Phys 2015; 17:13457-65. [DOI: 10.1039/c5cp00802f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relationships between the activity of immobilized lipase and its adsorption behavior, distribution, and structure were revealed for the first time.
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Affiliation(s)
- Peng-Cheng Chen
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Xiao-Jun Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Zhi-Kang Xu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
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28
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Steudle AK, Subinya M, Nestl BM, Stubenrauch C. Hydrolysis of Hydrophobic Esters in a Bicontinuous Microemulsion Catalysed by Lipase B fromCandida antarctica. Chemistry 2014; 21:2691-700. [DOI: 10.1002/chem.201405335] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 11/08/2022]
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29
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BioGPS descriptors for rational engineering of enzyme promiscuity and structure based bioinformatic analysis. PLoS One 2014; 9:e109354. [PMID: 25353170 PMCID: PMC4212942 DOI: 10.1371/journal.pone.0109354] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/27/2014] [Indexed: 11/20/2022] Open
Abstract
A new bioinformatic methodology was developed founded on the Unsupervised Pattern Cognition Analysis of GRID-based BioGPS descriptors (Global Positioning System in Biological Space). The procedure relies entirely on three-dimensional structure analysis of enzymes and does not stem from sequence or structure alignment. The BioGPS descriptors account for chemical, geometrical and physical-chemical features of enzymes and are able to describe comprehensively the active site of enzymes in terms of “pre-organized environment” able to stabilize the transition state of a given reaction. The efficiency of this new bioinformatic strategy was demonstrated by the consistent clustering of four different Ser hydrolases classes, which are characterized by the same active site organization but able to catalyze different reactions. The method was validated by considering, as a case study, the engineering of amidase activity into the scaffold of a lipase. The BioGPS tool predicted correctly the properties of lipase variants, as demonstrated by the projection of mutants inside the BioGPS “roadmap”.
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30
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Villo L, Metsala A, Tamp S, Parve J, Vallikivi I, Järving I, Samel N, Lille Ü, Pehk T, Parve O. Thermomyces lanuginosusLipase with Closed Lid Catalyzes Elimination of Acetic Acid from 11-Acetyl-Prostaglandin E2. ChemCatChem 2014. [DOI: 10.1002/cctc.201400019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Ferrario V, Ebert C, Svendsen A, Besenmatter W, Gardossi L. An integrated platform for automatic design and screening of virtual mutants based on 3D-QSAR analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Nalder TD, Marshall S, Pfeffer FM, Barrow CJ. Characterisation of lipase fatty acid selectivity using novel omega-3 pNP-acyl esters. J Funct Foods 2014. [DOI: 10.1016/j.jff.2013.10.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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33
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Ferrario V, Veny H, De Angelis E, Navarini L, Ebert C, Gardossi L. Lipases immobilization for effective synthesis of biodiesel starting from coffee waste oils. Biomolecules 2013; 3:514-34. [PMID: 24970178 PMCID: PMC4030945 DOI: 10.3390/biom3030514] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/04/2013] [Accepted: 08/06/2013] [Indexed: 11/18/2022] Open
Abstract
Immobilized lipases were applied to the enzymatic conversion of oils from spent coffee ground into biodiesel. Two lipases were selected for the study because of their conformational behavior analysed by Molecular Dynamics (MD) simulations taking into account that immobilization conditions affect conformational behavior of the lipases and ultimately, their efficiency upon immobilization. The enzymatic synthesis of biodiesel was initially carried out on a model substrate (triolein) in order to select the most promising immobilized biocatalysts. The results indicate that oils can be converted quantitatively within hours. The role of the nature of the immobilization support emerged as a key factor affecting reaction rate, most probably because of partition and mass transfer barriers occurring with hydrophilic solid supports. Finally, oil from spent coffee ground was transformed into biodiesel with yields ranging from 55% to 72%. The synthesis is of particular interest in the perspective of developing sustainable processes for the production of bio-fuels from food wastes and renewable materials. The enzymatic synthesis of biodiesel is carried out under mild conditions, with stoichiometric amounts of substrates (oil and methanol) and the removal of free fatty acids is not required.
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Affiliation(s)
- Valerio Ferrario
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Piazzale Europa 1, Trieste 34127, Italy.
| | - Harumi Veny
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, Malaysia.
| | | | | | - Cynthia Ebert
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Piazzale Europa 1, Trieste 34127, Italy.
| | - Lucia Gardossi
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Piazzale Europa 1, Trieste 34127, Italy.
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34
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Lipase from Pseudomonas stutzeri: Purification, homology modelling and rational explanation of the substrate binding mode. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Cantone S, Ferrario V, Corici L, Ebert C, Fattor D, Spizzo P, Gardossi L. Efficient immobilisation of industrial biocatalysts: criteria and constraints for the selection of organic polymeric carriers and immobilisation methods. Chem Soc Rev 2013; 42:6262-76. [DOI: 10.1039/c3cs35464d] [Citation(s) in RCA: 351] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Ganjalikhany MR, Ranjbar B, Taghavi AH, Tohidi Moghadam T. Functional motions of Candida antarctica lipase B: a survey through open-close conformations. PLoS One 2012; 7:e40327. [PMID: 22808134 PMCID: PMC3393743 DOI: 10.1371/journal.pone.0040327] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 06/07/2012] [Indexed: 12/02/2022] Open
Abstract
Candida antarctica lipase B (CALB) belongs to psychrophilic lipases which hydrolyze carboxyl ester bonds at low temperatures. There have been some features reported about cold-activity of the enzyme through experimental methods, whereas there is no detailed information on its mechanism of action at molecular level. Herein, a comparative molecular dynamics simulation and essential dynamics analysis have been carried out at three temperatures (5, 35 and 50°C) to trace the dominant factors in the psychrophilic properties of CALB under cold condition. The results clearly describe the effect of temperature on CALB with meaningful differences in the flexibility of the lid region (α5 helix), covering residues 141–147. Open- closed conformations have been obtained from different sets of long-term simulations (60 ns) at 5°C gave two reproducible distinct forms of CALB. The starting open conformation became closed immediately at 35 and 50°C during 60 ns of simulation, while a sequential open-closed form was observed at 5°C. These structural alterations were resulted from α5 helical movements, where the closed conformation of active site cleft was formed by displacement of both helix and its side chains. Analysis of normal mode showed concerted motions that are involved in the movement of both α5 and α10 helices. It is suggested that the functional motions needed for lypolytic activity of CALB is constructed from short-range movement of α5, accompanied by long-range movement of the domains connected to the lid region.
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Affiliation(s)
| | - Bijan Ranjbar
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail:
| | - Amir Hossein Taghavi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Tahereh Tohidi Moghadam
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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