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Xi Y, Ye L, Yu H. Enhanced thermal and alkaline stability of L-lysine decarboxylase CadA by combining directed evolution and computation-guided virtual screening. BIORESOUR BIOPROCESS 2022; 9:24. [PMID: 38647777 PMCID: PMC10992825 DOI: 10.1186/s40643-022-00510-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/23/2022] [Indexed: 12/30/2022] Open
Abstract
As an important monomer for bio-based nylons PA5X, cadaverine is mainly produced by enzymatic decarboxylation of L-lysine. A key issue with this process is the instability of L-lysine decarboxylase (CadA) during the reaction due to the dissociation of CadA subunits with the accumulation of alkaline cadaverine. In this work, we attempted to improve the thermal and alkaline stability of CadA by combining directed evolution and computation-guided virtual screening. Interestingly, site 477 residue located at the protein surface and not the decamer interface was found as a hotspot in directed evolution. By combinatorial mutagenesis of the positive mutations obtained by directed evolution and virtual screening with the previously reported T88S mutation, K477R/E445Q/T88S/F102V was generated as the best mutant, delivering 37% improvement of cadaverine yield at 50 ºC and pH 8.0. Molecular dynamics simulations suggested the improved rigidity of regional structures, increased number of salt bridges, and enhancement of hydrogen bonds at the multimeric interface as possible origins of the improved stability of the mutant. Using this four-point mutant, 160.7 g/L of cadaverine was produced from 2.0 M Lysine hydrochloride at 50 °C without pH regulation, with a conversion of 78.5%, whereas the wild type produced 143.7 g/L cadaverine, corresponding to 70% conversion. This work shows the combination of directed evolution and virtual screening as an efficient protein engineering strategy.
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Affiliation(s)
- Yang Xi
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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Acıkgoz-Erkaya I, Bayramoglu G, Akbulut A, Arica MY. Immobilization of Candida rugosa Lipase on Magnetic Biosilica Particles: Hydrolysis and Transesterification Studies. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0387-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Jacob AG, Wahab RA, Misson M. Operational Stability, Regenerability, and Thermodynamics Studies on Biogenic Silica/Magnetite/Graphene Oxide Nanocomposite-Activated Candida rugosa Lipase. Polymers (Basel) 2021; 13:polym13213854. [PMID: 34771409 PMCID: PMC8587300 DOI: 10.3390/polym13213854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 11/24/2022] Open
Abstract
Inorganic biopolymer-based nanocomposites are useful for stabilizing lipases for enhanced catalytic performance and easy separation. Herein, we report the operational stability, regenerability, and thermodynamics studies of the ternary biogenic silica/magnetite/graphene oxide nanocomposite (SiO2/Fe3O4/GO) as a support for Candida rugosa lipase (CRL). The X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), field-electron scanning electron microscopy (FESEM), vibrating sample magnetometry (VSM), and nitrogen adsorption/desorption data on the support and biocatalyst corroborated their successful fabrication. XPS revealed the Fe3O4 adopted Fe2+ and Fe3+ oxidation states, while XRD data of GO yielded a peak at 2θ = 11.67°, with the SiO2/Fe3O4/GO revealing a high surface area (≈261 m2/g). The fourier transform infrared (FTIR) spectra affirmed the successful fabricated supports and catalyst. The half-life and thermodynamic parameters of the superparamagnetic immobilized CRL (CRL/SiO2/Fe3O4/GO) improved over the free CRL. The microwave-regenerated CRL/SiO2/Fe3O4/GO (≈82%) exhibited higher catalytic activity than ultrasonic-regenerated (≈71%) ones. Lower activation (Ea) and higher deactivation energies (Ed) were also noted for the CRL/SiO2/Fe3O4/GO (13.87 kJ/mol, 32.32 kJ/mol) than free CRL (15.26 kJ/mol, 27.60 kJ/mol). A peak at 4.28 min in the gas chromatograph-flame ionization detection (GC-FID) chromatogram of the purified ethyl valerate supported the unique six types of 14 hydrogen atoms of the ester (CAS: 539-82-2) in the proton nuclear magnetic resonance (1H-NMR) data. The results collectively demonstrated the suitability of SiO2/Fe3O4/GO in stabilizing CRL for improved operational stability and thermodynamics and permitted biocatalyst regenerability.
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Affiliation(s)
- Adikwu Gowon Jacob
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia (UTM), Johor Bahru 81310, Johor, Malaysia;
- Department of Applied Chemistry, Federal University Dutsin-Ma (FUDMA), Dutsin-Ma P.M.B. 5001, Katsina State, Nigeria
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia (UTM), Johor Bahru 81310, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia (UTM), Johor Bahru 81310, Johor, Malaysia;
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia (UTM), Johor Bahru 81310, Johor, Malaysia
- Advanced Membrane Technology Research Centre (AMTEC), Universiti Teknologi Malaysia (UTM), Johor Bahru 81310, Johor, Malaysia
- Correspondence: or (R.A.W.); (M.M.)
| | - Mailin Misson
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
- Correspondence: or (R.A.W.); (M.M.)
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Amalia S, Angga SC, Iftitah ED, Septiana D, Anggraeny BOD, Warsito, Hasanah AN, Sabarudin A. Immobilization of trypsin onto porous methacrylate-based monolith for flow-through protein digestion and its potential application to chiral separation using liquid chromatography. Heliyon 2021; 7:e07707. [PMID: 34401587 PMCID: PMC8350527 DOI: 10.1016/j.heliyon.2021.e07707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/11/2021] [Accepted: 07/26/2021] [Indexed: 10/27/2022] Open
Abstract
Monolithic columns for analytical applications have attracted the researcher's attention. In this work, the laboratory-made organic-polymer monolithic column is modified with trypsin and further applied as a nanobiocatalyst microreactor and a stationary phase for separating chiral compounds by liquid chromatography. The monolith was synthesized by in-situ copolymerization of glycidyl methacrylate (GMA) and ethylene glycol dimethacrylate (EDMA) or trimethylolpropane trimethacrylate (TRIM) as a crosslinking agent, with porogen of 1,4-butanediol/propanol/water (4:7:1 v/v) and AIBN as the radical polymerization initiator inside PEEK and silicosteel tubings (1.0 mm i.d × 100 mm) at 60 °C for 12 h. A total monomer ratio (%T) and crosslinking agent (%C) of 40:25 and 28:12 were applied to prepare poly-(GMA-co-EDMA) and poly-(GMA-co-TRIM), respectively. The produced monoliths were further modified by introducing trypsin (10 mg/L) through the ring-opening reaction of the epoxide group existing in the monolithic column. The trypsin-immobilized poly-(GMA-co-EDMA) monolithic column was applied as the nanobiocatalyst microreactor for online/flow-through and rapid digestion of β-casein sample into its peptide fragments. The trypsin-immobilized poly-(GMA-co-TRIM) column has potential application to be used as the HPLC stationary phase for the separation of R/S-citronellal enantiomers.
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Affiliation(s)
- Suci Amalia
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia.,Department of Chemistry, Faculty of Science and Technology, Maulana Malik Ibrahim Islamic State University, Malang, 65144, Indonesia
| | - Stevin Carolius Angga
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia
| | - Elvina Dhiaul Iftitah
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia
| | - Dias Septiana
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia
| | | | - Warsito
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia
| | - Aliya Nur Hasanah
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Akhmad Sabarudin
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia.,Research Center for Advanced System and Material Technology (ASMAT), Brawijaya University, Malang, 65145, Indonesia
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Pagolu R, Singh R, Shanmugam R, Kondaveeti S, Patel SKS, Kalia VC, Lee JK. Site-directed lysine modification of xylanase for oriented immobilization onto silicon dioxide nanoparticles. BIORESOURCE TECHNOLOGY 2021; 331:125063. [PMID: 33813167 DOI: 10.1016/j.biortech.2021.125063] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Enhanced covalent immobilization of xylanase from Chaetomium globosum (XylCg) onto SiO2 nanoparticles was achieved by the modification of surface residues. The mutation of surface residues to lysine by site-directed mutagenesis increased the immobilization efficiency (IE) and immobilization yield (IY). The immobilized mutant XylCg (N172K-H173K-S176K-K133A-K148A) exhibited an IY of 99.5% and IE of 135%, which were 1.8- and 4.3-fold higher than immobilized wildtype (WT). Regarding the catalytic properties, the kcat and kcat/Km values were 1850 s-1 and 2030 mL mg-1 s-1 for the immobilized mutant, and 331 s-1 and 404 mL mg-1 s-1 for the immobilized WT, respectively. Additionally, the immobilized mutant exhibited four times higher thermal stability than the immobilized WT at 60 °C. These results suggest that surface-mutated lysine residues confer good stability and orientation on the support matrix, thus improving the overall performance of xylanase.
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Affiliation(s)
- Raviteja Pagolu
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Raushan Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Sanath Kondaveeti
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea.
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Features of adsorption human Ig on the surface of magnetically sensitive nanocomposites. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01692-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Bayramoglu G, Akbulut A, Arica MY. Utilization of immobilized horseradish peroxidase for facilitated detoxification of a benzidine based azo dye. Chem Eng Res Des 2021. [DOI: 10.1016/j.cherd.2020.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Flow-Through Macroporous Polymer Monoliths Containing Artificial Catalytic Centers Mimicking Chymotrypsin Active Site. Catalysts 2020. [DOI: 10.3390/catal10121395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Synthetic catalysts that could compete with enzymes in term of the catalytic efficiency but surpass them in stability have a great potential for the practical application. In this work, we have developed a novel kind of organic catalysts based on flow-through macroporous polymer monoliths containing catalytic centers that mimic the catalytic site of natural enzyme chymotrypsin. It is known that chymotrypsin catalytic center consists of L-serine, L-histidine, and L-aspartic acid and has specificity to C-terminal residues of hydrophobic amino acids (L-phenylalanine, L-tyrosine, and L-tryptophan). In this paper, we have prepared the macroporous polymer monoliths bearing grafted polymer layer on their surface. The last one was synthesized via copolymerization of N-methacryloyl-L-serine, N-methacryloyl-L-histidine, and N-methacryloyl-L-aspartic acid. The spatial orientation of amino acids in the polymer layer, generated on the surface of monolithic framework, was achieved by coordinating amino acid-polymerizable derivatives with cobalt (II) ions without substrate-mimicking template and with its use. The conditions for the preparation of mimic materials were optimized to achieve a mechanically stable system. Catalytic properties of the developed systems were evaluated towards the hydrolysis of ester bond in a low molecular substrate and compared to the results of using chymotrypsin immobilized on the surface of a similar monolithic framework. The effect of flow rate increase and temperature elevation on the hydrolysis efficiency were evaluated for both mimic monolith and column with immobilized enzyme.
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