1
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Somchob B, Promphet N, Rodthongkum N, Hoven VP. Zwitterionic hydrogel for preserving stability and activity of oxidase enzyme for electrochemical biosensor. Talanta 2024; 270:125510. [PMID: 38128281 DOI: 10.1016/j.talanta.2023.125510] [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: 08/20/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
Enzymatic electrochemical biosensor is the most common analytical platform for medical diagnosis. To mimic the biological environment of the enzyme for maintaining the function of biosensor, zwitterionic hydrogels have been recognized as effective matrices for enzymatic immobilization. Herein, a zwitterionic hydrogel derived from a copolymer, poly[2-methacryloyloxyethyl phosphorylcholine (MPC)-co-N-methacryloyloxyethyl tyrosine methylester (MAT)] (PMM) was firstly applied as versatile coating to preserve stability and activity of oxidase enzymes, glucose oxidase (GOx) and lactate oxidase (LOx) for enzymatic electrochemical sensor. A screen-printed carbon electrode (SPCE) was sequentially coated with nitrogen-doped graphene (NDG), oxidase enzyme, and PMM mixed with Ru(II)bpy32+ and (NH4)2S2O8 followed by visible light irradiation for 3 min to induce PMM gelation. Electrochemical detection of glucose and lactate using the modified SPCE was performed via amperometry in the presence of hydrogen peroxide. The activity of both GOx and LOx immobilized on the modified SPCE was well maintained for 49 days at 87 and 80 %, respectively. Additionally, two different electrodes, a screen-printed graphene electrode (SPGE), and a screen-printed silver electrode (SPAgE), similarly modified gave the same satisfactory detection of spiked glucose and lactate in human plasma and sweat with 93-118 % recovery. This indicates the potential of the PMM hydrogel as a universal platform for preservation of enzymes which can be easily fabricated without the need for specific chemical modification of the electrode.
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Affiliation(s)
- Benjawan Somchob
- Program in Petrochemistry and Polymer Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nadtinan Promphet
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Road, Wangmai, Patumwan, Bangkok, 10330, Thailand
| | - Nadnudda Rodthongkum
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Road, Wangmai, Patumwan, Bangkok, 10330, Thailand; Center of Excellence in Responsive Wearable Materials, Chulalongkorn University, Soi Chula 12, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Voravee P Hoven
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Center of Excellence in Materials and Bio-interfaces, Chulalongkorn University, Bangkok, 10330, Thailand.
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2
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Skendrović D, Primožič M, Rezić T, Vrsalović Presečki A. Mesocellular Silica Foam as Immobilization Carrier for Production of Statin Precursors. Int J Mol Sci 2024; 25:1971. [PMID: 38396648 PMCID: PMC10887991 DOI: 10.3390/ijms25041971] [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: 01/16/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
The employment of 2-deoxyribose-5-phosphate aldolase (DERA) stands as a prevalent biocatalytic route for synthesizing statin side chains. The main problem with this pathway is the low stability of the enzyme. In this study, mesocellular silica foam (MCF) with different pore sizes was used as a carrier for the covalent immobilization of DERA. Different functionalizing and activating agents were tested and kinetic modeling was subsequently performed. The use of succinic anhydride as an activating agent resulted in an enzyme hyperactivation of approx. 140%, and the stability almost doubled compared to that of the free enzyme. It was also shown that the pore size of MCF has a decisive influence on the stability of the DERA enzyme.
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Affiliation(s)
- Dino Skendrović
- Faculty of Chemical Engineering and Technology, University of Zagreb, HR-10000 Zagreb, Croatia;
| | - Mateja Primožič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, 2000 Maribor, Slovenia;
| | - Tonči Rezić
- Faculty of Food Technology and Biotechnology, University of Zagreb, HR-10000 Zagreb, Croatia;
| | - Ana Vrsalović Presečki
- Faculty of Chemical Engineering and Technology, University of Zagreb, HR-10000 Zagreb, Croatia;
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3
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Wu K, Yan J, Liu Q, Wang X, Wu P, Cao Y, Lu X, Xu Y, Huang J, Shao L. Computational design of an imine reductase: mechanism-guided stereoselectivity reversion and interface stabilization. Chem Sci 2024; 15:1431-1440. [PMID: 38274081 PMCID: PMC10806680 DOI: 10.1039/d3sc04636b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Imine reductases (IREDs) are important biocatalysts in the asymmetric synthesis of chiral amines. However, a detailed understanding of the stereocontrol mechanism of IRED remains incomplete, making the design of IRED for producing the desired amine enantiomers challenging. In this study, we investigated the stereoselective catalytic mechanism and designed an (R)-stereoselective IRED from Paenibacillus mucilaginosus (PmIR) using pharmaceutically relevant 2-aryl-substituted pyrrolines as substrates. A putative mechanism for controlling stereoselectivity was proposed based on the crucial role of electrostatic interactions in controlling iminium cation orientation and employed to achieve complete inversion of stereoselectivity in PmIR using computational design. The variant PmIR-Re (Q138M/P140M/Y187E/Q190A/D250M/R251N) exhibited opposite (S)-stereoselectivity, with >96% enantiomeric excess (ee) towards tested 2-aryl-substituted pyrrolines. Computational tools were employed to identify stabilizing mutations at the interface between the two subunits. The variant PmIR-6P (P140A/Q190S/R251N/Q217E/A257R/T277M) showed a nearly 5-fold increase in activity and a 12 °C increase in melting temperature. The PmIR-6P successfully produced (R)-2-(2,5-difluorophenyl)-pyrrolidine, a key chiral pharmaceutical intermediate, at a concentration of 400 mM with an ee exceeding 99%. This study provides insight into the stereocontrol elements of IREDs and demonstrates the potential of computational design for tailored stereoselectivity and thermal stability.
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Affiliation(s)
- Kai Wu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Jinrong Yan
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry 285 Gebaini Rd. Shanghai 200040 China
| | - Qinde Liu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
- Shanghai University of Traditional Chinese Medicine 1200 Cailun Road Shanghai 201203 China
| | - Xiaojing Wang
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Piaoru Wu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Yiyang Cao
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Xiuhong Lu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Yixin Xu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Junhai Huang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry 285 Gebaini Rd. Shanghai 200040 China
| | - Lei Shao
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry 285 Gebaini Rd. Shanghai 200040 China
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4
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Xu SY, Zhou L, Xu Y, Hong HY, Dai C, Wang YJ, Zheng YG. Recent advances in structure-based enzyme engineering for functional reconstruction. Biotechnol Bioeng 2023; 120:3427-3445. [PMID: 37638646 DOI: 10.1002/bit.28540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
Structural information can help engineer enzymes. Usually, specific amino acids in particular regions are targeted for functional reconstruction to enhance the catalytic performance, including activity, stereoselectivity, and thermostability. Appropriate selection of target sites is the key to structure-based design, which requires elucidation of the structure-function relationships. Here, we summarize the mutations of residues in different specific regions, including active center, access tunnels, and flexible loops, on fine-tuning the catalytic performance of enzymes, and discuss the effects of altering the local structural environment on the functions. In addition, we keep up with the recent progress of structure-based approaches for enzyme engineering, aiming to provide some guidance on how to take advantage of the structural information.
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Affiliation(s)
- Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Chen Dai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
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5
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Komp E, Alanzi HN, Francis R, Vuong C, Roberts L, Mosallanejad A, Beck DAC. Homologous Pairs of Low and High Temperature Originating Proteins Spanning the Known Prokaryotic Universe. Sci Data 2023; 10:682. [PMID: 37805601 PMCID: PMC10560248 DOI: 10.1038/s41597-023-02553-w] [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: 06/30/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
Stability of proteins at high temperature has been a topic of interest for many years, as this attribute is favourable for applications ranging from therapeutics to industrial chemical manufacturing. Our current understanding and methods for designing high-temperature stability into target proteins are inadequate. To drive innovation in this space, we have curated a large dataset, learn2thermDB, of protein-temperature examples, totalling 24 million instances, and paired proteins across temperatures based on homology, yielding 69 million protein pairs - orders of magnitude larger than the current largest. This important step of pairing allows for study of high-temperature stability in a sequence-dependent manner in the big data era. The data pipeline is parameterized and open, allowing it to be tuned by downstream users. We further show that the data contains signal for deep learning. This data offers a new doorway towards thermal stability design models.
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Affiliation(s)
- Evan Komp
- Department of Chemical Engineering, University of Washington, Seattle, USA.
| | - Humood N Alanzi
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Ryan Francis
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Chau Vuong
- Department of Biochemistry, University of Washington, Seattle, USA
| | - Logan Roberts
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Amin Mosallanejad
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, USA.
- eScience Institute, University of Washington, Seattle, USA.
- Paul G. Allen School of Computer Science, University of Washington, Seattle, USA.
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6
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Abellanas-Perez P, Carballares D, Fernandez-Lafuente R, Rocha-Martin J. Glutaraldehyde modification of lipases immobilized on octyl agarose beads: Roles of the support enzyme loading and chemical amination of the enzyme on the final enzyme features. Int J Biol Macromol 2023; 248:125853. [PMID: 37460068 DOI: 10.1016/j.ijbiomac.2023.125853] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
Lipase B from Candida antarctica (CALB) and lipase from Thermomyces lanuginosus (TLL) have been immobilized on octyl agarose at low loading and at a loading exceeding the maximum support capacity. Then, the enzymes have been treated with glutaraldehyde and inactivated at pH 7.0 in Tris-HCl, sodium phosphate and HEPES, giving different stabilities. Stabilization (depending on the buffer) of the highly loaded biocatalysts was found, very likely as a consequence of the detected intermolecular crosslinkings. This did not occur for the lowly loaded biocatalysts. Next, the enzymes were chemically aminated and then treated with glutaraldehyde. In the case of TLL, the intramolecular crosslinkings (visible by the apparent reduction of the protein size) increased enzyme stability of the lowly loaded biocatalysts, an effect that was further increased for the highly loaded biocatalysts due to intermolecular crosslinkings. Using CALB, the intramolecular crosslinkings were less intense, and the stabilization was lower, even though the intermolecular crosslinkings were quite intense for the highly loaded biocatalyst. The stabilization detected depended on the inactivation buffer. The interactions between enzyme loading and inactivating buffer on the effects of the chemical modifications suggest that the modification and inactivation studies must be performed under the target biocatalysts and conditions.
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Affiliation(s)
| | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
| | | | - Javier Rocha-Martin
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid Spain.
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7
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Hertel JS, Bitterwolf P, Kröll S, Winterhalter A, Weber AJ, Grösche M, Walkowsky LB, Heißler S, Schwotzer M, Wöll C, van de Kamp T, Zuber M, Baumbach T, Rabe KS, Niemeyer CM. Biocatalytic Foams from Microdroplet-Formulated Self-Assembling Enzymes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303952. [PMID: 37358068 DOI: 10.1002/adma.202303952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/16/2023] [Indexed: 06/27/2023]
Abstract
Industrial biocatalysis plays an important role in the development of a sustainable economy, as enzymes can be used to synthesize an enormous range of complex molecules under environmentally friendly conditions. To further develop the field, intensive research is being conducted on process technologies for continuous flow biocatalysis in order to immobilize large quantities of enzyme biocatalysts in microstructured flow reactors under conditions that are as gentle as possible in order to realize efficient material conversions. Here, monodisperse foams consisting almost entirely of enzymes covalently linked via SpyCatcher/SpyTag conjugation are reported. The biocatalytic foams are readily available from recombinant enzymes via microfluidic air-in-water droplet formation, can be directly integrated into microreactors, and can be used for biocatalytic conversions after drying. Reactors prepared by this method show surprisingly high stability and biocatalytic activity. The physicochemical characterization of the new materials is described and exemplary applications in biocatalysis are shown using two-enzyme cascades for the stereoselective synthesis of chiral alcohols and the rare sugar tagatose.
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Affiliation(s)
- Julian S Hertel
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Patrick Bitterwolf
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Sandra Kröll
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Astrid Winterhalter
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Annika J Weber
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Maximilian Grösche
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Laurenz B Walkowsky
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Heißler
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Matthias Schwotzer
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof Wöll
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Thomas van de Kamp
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), D-76344, Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), D-76131, Karlsruhe, Germany
| | - Marcus Zuber
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), D-76344, Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), D-76131, Karlsruhe, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), D-76344, Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), D-76131, Karlsruhe, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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8
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Aguirre ME, Ramírez CL, Di Iorio Y. Stable and Reusable Fe 3 O 4 /ZIF-8 Composite for Encapsulation of FDH Enzyme under Mild Conditions Applicable to CO 2 Reduction. Chemistry 2023; 29:e202301113. [PMID: 37294852 DOI: 10.1002/chem.202301113] [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: 04/07/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/11/2023]
Abstract
The enzymatic reduction of carbon dioxide presents limited applicability due to denaturation and the impossibility of biocatalyst recovery; disadvantages that can be minimized by its immobilization. Here, a recyclable bio-composed system was constructed by in-situ encapsulation under mild conditions using formate dehydrogenase in a ZIF-8 metalorganic framework (MOF) in the presence of magnetite. The partial dissolution of ZIF-8 in the enzyme's operation medium can be relatively inhibited if the concentration of magnetic support used exceeds 10 mg mL-1 . The bio-friendly environment for immobilization does not harm the integrity of the biocatalyst, and the production of formic acid is improved 3.4-fold compared to the free enzyme because the MOFs act as concentrators of the enzymatic cofactor. Furthermore, the bio-composed system retains 86 % of its activity after a long time of five cycles, thus indicating an excellent magnetic recovery and a good reusability.
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Affiliation(s)
- Matías E Aguirre
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3350, 7600, Mar del Plata, Buenos Aires, Argentina
- Instituto de Investigaciones Fisicas de Mar del Plata, Universidad Nacional de Mar del Plata, Funes 3350, 7600, Mar del Plata, Buenos Aires, Argentina
| | - Cristina L Ramírez
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3350, 7600, Mar del Plata, Buenos Aires, Argentina
| | - Yesica Di Iorio
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3350, 7600, Mar del Plata, Buenos Aires, Argentina
- Instituto de Investigaciones Fisicas de Mar del Plata, Universidad Nacional de Mar del Plata, Funes 3350, 7600, Mar del Plata, Buenos Aires, Argentina
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9
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Suderman RJ, Gibson SD, Strecker M, Bonner AM, Chao DM. Protein engineering of a nanoCLAMP antibody mimetic scaffold as a platform for producing bioprocess-compatible affinity capture ligands. J Biol Chem 2023; 299:104910. [PMID: 37315789 PMCID: PMC10404686 DOI: 10.1016/j.jbc.2023.104910] [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: 12/23/2022] [Revised: 05/17/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Abstract
Protein A affinity chromatography is widely used for the large-scale purification of antibodies because of its high yield, selectivity, and compatibility with NaOH sanitation. A general platform to produce robust affinity capture ligands for proteins beyond antibodies would improve bioprocessing efficiency. We previously developed nanoCLAMPs (nano Clostridial Antibody Mimetic Proteins), a class of antibody mimetic proteins useful as lab-scale affinity capture reagents. This work describes a protein engineering campaign to develop a more robust nanoCLAMP scaffold compatible with harsh bioprocessing conditions. The campaign generated an improved scaffold with dramatically improved resistance to heat, proteases, and NaOH. To isolate additional nanoCLAMPs based on this scaffold, we constructed a randomized library of 1 × 1010 clones and isolated binders to several targets. We then performed an in-depth characterization of nanoCLAMPs recognizing yeast SUMO, a fusion partner used for the purification of recombinant proteins. These second-generation nanoCLAMPs typically had a Kd of <80 nM, a Tm of >70 °C, and a t1/2 in 0.1 mg/ml trypsin of >20 h. Affinity chromatography resins bearing these next-generation nanoCLAMPs enabled single-step purifications of SUMO fusions. Bound target proteins could be eluted at neutral or acidic pH. These affinity resins maintained binding capacity and selectivity over 20 purification cycles, each including 10 min of cleaning-in-place with 0.1 M NaOH, and remained functional after exposure to 100% DMF and autoclaving. The improved nanoCLAMP scaffold will enable the development of robust, high-performance affinity chromatography resins against a wide range of protein targets.
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Affiliation(s)
| | - Shane D Gibson
- Nectagen, Inc, Kansas City, Kansas, USA; University of Washington, Seattle, Washington, USA
| | - Mary Strecker
- Nectagen, Inc, Kansas City, Kansas, USA; Two Dot Consulting, Arvada, Colorado, USA
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10
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Llowarch P, Usselmann L, Ivanov D, Holdgate GA. Thermal unfolding methods in drug discovery. BIOPHYSICS REVIEWS 2023; 4:021305. [PMID: 38510342 PMCID: PMC10903397 DOI: 10.1063/5.0144141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/13/2023] [Indexed: 03/22/2024]
Abstract
Thermal unfolding methods, applied in both isolated protein and cell-based settings, are increasingly used to identify and characterize hits during early drug discovery. Technical developments over recent years have facilitated their application in high-throughput approaches, and they now are used more frequently for primary screening. Widespread access to instrumentation and automation, the ability to miniaturize, as well as the capability and capacity to generate the appropriate scale and quality of protein and cell reagents have all played a part in these advances. As the nature of drug targets and approaches to their modulation have evolved, these methods have broadened our ability to provide useful chemical start points. Target proteins without catalytic function, or those that may be difficult to express and purify, are amenable to these methods. Here, we provide a review of the applications of thermal unfolding methods applied in hit finding during early drug discovery.
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Affiliation(s)
- Poppy Llowarch
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Laura Usselmann
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Delyan Ivanov
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Geoffrey A. Holdgate
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
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11
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Du C, Tan S, Liu L, Zhou Y, Wu P, Zhang G. Improving the specific activity and stability of alkaline pectinase PEL3 through SpyTag/SpyCatcher cyclization. Biotechnol Lett 2023:10.1007/s10529-023-03385-9. [PMID: 37171698 DOI: 10.1007/s10529-023-03385-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 04/11/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023]
Abstract
OBJECTIVES PEL3, an alkaline pectinase, exhibited the highest activity among documented alkaline pectate lyases reported in our early study. Unfortunately, undesired thermal stability hampering its industrial application. The purpose of this study is to enhance the performance of wild-type PEL3 (W-PEL3) based on SpyTag/SpyCatcher-mediated cyclization. RESULTS The cyclized PEL3 (C-PEL3) was observed to fold correctly and generate a spatial conformation in a head-to-tail manner in E. coli. C-PEL3 exhibited comparable optimum pH and temperature to those of W-PEL3. Moreover, the catalytic activity of C-PEL3 increased by 23% compared to W-PEL3, and the kcat/Km of C-PEL3 was 1.5-fold greater than that of the W-PEL3. Importantly, C-PEL3 showed improved stability compared to W-PEL3. Firstly, C-PEL3 displayed a 65% increase in residual activity after treatment at 55 °C for 30 min. Secondly, C-PEL3 was prone to resist heat-induced protein aggregation. Thirdly, C-PEL3 exhibited metal ion stability. Circular dichroism analysis revealed that C-PEL3 was more capable of maintaining its secondary structures than W-PEL3 upon heat treatment. CONCLUSIONS C-PEL3, the initial example of a circular pectinase through SpyTag/SpyCatcher cyclization, exhibits superior performance and represents a highly encouraging contender for industrial utilization.
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Affiliation(s)
- Chao Du
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Siqin Tan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Lin Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yuling Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Pan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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12
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Rao D, Huo R, Yan Z, Guo Z, Liu W, Lu M, Luo H, Tao X, Yang W, Su L, Chen S, Wang L, Wu J. Multiple approaches of loop region modification for thermostability improvement of 4,6-α-glucanotransferase from Limosilactobacillus fermentum NCC 3057. Int J Biol Macromol 2023; 233:123536. [PMID: 36740130 DOI: 10.1016/j.ijbiomac.2023.123536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
4,6-α-glucanotransferase (4,6-α-GT), as a member of the glycoside hydrolase 70 (GH70) family, converts starch/maltooligosaccharides into α,1-6 bond-containing α-glucan and possesses potential applications in food, medical and related industries but does not satisfy the high-temperature requirement due to its poor thermostability. In this study, a 4,6-α-GT (ΔGtfB) from Limosilactobacillus fermentum NCC 3057 was used as a model enzyme to improve its thermostability. The loops of ΔGtfB as the target region were optimized using directed evolution, sequence alignment, and computer-aided design. A total of 11 positive mutants were obtained and iteratively combined to obtain a combined mutant CM9, with high resistance to temperature (50 °C). The activity of mutant CM9 was 2.08-fold the activity of the wild type, accompanied by a 5 °C higher optimal temperature, a 5.76 °C higher melting point (Tm, 59.46 °C), and an 11.95-fold longer half-life time (t1/2). The results showed that most of the polar residues in the loop region of ΔGtfB are mutated into rigid proline residues. Molecular dynamics simulation demonstrated that the root mean square fluctuation of CM9 significantly decreased by "Breathing" movement reduction of the loop region. This study provides a new strategy for improving the thermostability of 4,6-α-GT through rational loop region modification.
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Affiliation(s)
- Deming Rao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Runtian Huo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhengfei Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhiyong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Weiqiong Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Mengwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Hui Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xiumei Tao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Weikang Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
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13
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Switzer HJ, Howard CA, Halonski JF, Peairs EM, Smith N, Zamecnik MP, Verma S, Young DD. Employing non-canonical amino acids towards the immobilization of a hyperthermophilic enzyme to increase protein stability. RSC Adv 2023; 13:8496-8501. [PMID: 36926306 PMCID: PMC10012417 DOI: 10.1039/d3ra00392b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/12/2023] [Indexed: 03/16/2023] Open
Abstract
A carboxylesterase derived from Sulfolobus solfataricus P1 was immobilized onto an epoxy-activated Sepharose resin via non-canonical amino acids. The immobilized enzyme exhibited heightened performance in organic solvents, recyclability, and stability at room temperature for over two years. The incorporation of a non-canonical amino acid afforded a high degree of control over the bioorthogonal immobilization reaction. These results indicate that the specificity conferred by genetic code expansion produces advantages in protein immobilization and broadens the utility of such proteins to non-biological settings.
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Affiliation(s)
| | | | | | - Emily M Peairs
- Department of Chemistry, William & Mary Williamsburg VA USA
| | - Nolan Smith
- Department of Chemistry, William & Mary Williamsburg VA USA
| | | | - Sanjana Verma
- Department of Chemistry, William & Mary Williamsburg VA USA
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14
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Peccati F, Alunno-Rufini S, Jiménez-Osés G. Accurate Prediction of Enzyme Thermostabilization with Rosetta Using AlphaFold Ensembles. J Chem Inf Model 2023; 63:898-909. [PMID: 36647575 PMCID: PMC9930118 DOI: 10.1021/acs.jcim.2c01083] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Thermostability enhancement is a fundamental aspect of protein engineering as a biocatalyst's half-life is key for its industrial and biotechnological application, particularly at high temperatures and under harsh conditions. Thermostability changes upon mutation originate from modifications of the free energy of unfolding (ΔGu), making thermostabilization extremely challenging to predict with computational methods. In this contribution, we combine global conformational sampling with energy prediction using AlphaFold and Rosetta to develop a new computational protocol for the quantitative prediction of thermostability changes upon laboratory evolution of acyltransferase LovD and lipase LipA. We highlight how using an ensemble of protein conformations rather than a single three-dimensional model is mandatory for accurate thermostability predictions. By comparing our approaches with existing ones, we show that ensembles based on AlphaFold models provide more accurate and robust calculated thermostability trends than ensembles based solely on crystallographic structures as the latter introduce a strong distortion (scaffold bias) in computed thermostabilities. Eliminating this bias is critical for computer-guided enzyme design and evaluating the effect of multiple mutations on protein stability.
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Affiliation(s)
- Francesca Peccati
- Basque
Research and Technology Alliance (BRTA), Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Building
800, 48160Derio, Spain,
| | - Sara Alunno-Rufini
- Basque
Research and Technology Alliance (BRTA), Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Building
800, 48160Derio, Spain
| | - Gonzalo Jiménez-Osés
- Basque
Research and Technology Alliance (BRTA), Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Building
800, 48160Derio, Spain,Ikerbasque, Basque
Foundation for Science, 48013Bilbao, Spain,
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15
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Lin J, Cheng Y, La,i O, Tan C, Panpipat W, Shen C, Cheong L. Biomimetic Mineralization of Metal Ion‐Doped Lipase into ZIF‐8 Framework for Enhanced Hydrolytic Activity in Biphasic System. ChemistrySelect 2022. [DOI: 10.1002/slct.202202721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jiale Lin
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition College of Food and Pharmaceutical Sciences Ningbo University Ningbo 315211 China
| | - Yongfa Cheng
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition College of Food and Pharmaceutical Sciences Ningbo University Ningbo 315211 China
| | - Oi‐Ming La,i
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition College of Food and Pharmaceutical Sciences Ningbo University Ningbo 315211 China
- Department of Bioprocess Technology Faculty of Biotechnology and Biomolecular Sciences University Putra Malaysia Serdang Selangor 43400 Malaysia
- Institute of Bioscience University Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Chin‐Ping Tan
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition College of Food and Pharmaceutical Sciences Ningbo University Ningbo 315211 China
- Department of Food Technology Faculty of Food Science and Technology University Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Worawan Panpipat
- Food Technology and Innovation Research Center of Excellence Department of Agro-Industry, School of Agricultural Technology Walailak University Thasala, Nakhon Si Thammarat 80161 Thailand
| | - Cai Shen
- China Beacons Institute University of Nottingham Ningbo China Ningbo 315100 China
| | - Ling‐Zhi Cheong
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition College of Food and Pharmaceutical Sciences Ningbo University Ningbo 315211 China
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16
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Unifying views on catalyst deactivation. Nat Catal 2022. [DOI: 10.1038/s41929-022-00842-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Jorgensen MD, Chmielewski J. Recent advances in coiled-coil peptide materials and their biomedical applications. Chem Commun (Camb) 2022; 58:11625-11636. [PMID: 36172799 DOI: 10.1039/d2cc04434j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive research has gone into deciphering the sequence requirements for peptides to fold into coiled-coils of varying oligomeric states. More recently, additional signals have been introduced within coiled-coils to promote higher order assembly into biomaterials with a rich distribution of morphologies. Herein we describe these strategies for association of coiled-coil building blocks and biomedical applications. With many of the systems described herein having proven use in protein storage, cargo binding and delivery, three dimensional cell culturing and vaccine development, the future potential of coiled-coil materials to have significant biomedical impact is highly promising.
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Affiliation(s)
- Michael D Jorgensen
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
| | - Jean Chmielewski
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
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18
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Hormozi Jangi SR, Akhond M. Introducing a covalent thiol-based protected immobilized acetylcholinesterase with enhanced enzymatic performances for biosynthesis of esters. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Engineering of enzymes using non-natural amino acids. Biosci Rep 2022; 42:231590. [PMID: 35856922 PMCID: PMC9366748 DOI: 10.1042/bsr20220168] [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: 05/16/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
In enzyme engineering, the main targets for enhancing properties are enzyme activity, stereoselective specificity, stability, substrate range, and the development of unique functions. With the advent of genetic code extension technology, non-natural amino acids (nnAAs) are able to be incorporated into proteins in a site-specific or residue-specific manner, which breaks the limit of 20 natural amino acids for protein engineering. Benefitting from this approach, numerous enzymes have been engineered with nnAAs for improved properties or extended functionality. In this review, we focus on applications and strategies for using nnAAs in enzyme engineering. Notably, approaches to computational modelling of enzymes with nnAAs are also addressed. Finally, we discuss the bottlenecks that currently need to be addressed in order to realise the broader prospects of this genetic code extension technique.
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20
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Dworakowska S, Lorandi F, Gorczyński A, Matyjaszewski K. Toward Green Atom Transfer Radical Polymerization: Current Status and Future Challenges. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2106076. [PMID: 35175001 PMCID: PMC9259732 DOI: 10.1002/advs.202106076] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Indexed: 05/13/2023]
Abstract
Reversible-deactivation radical polymerizations (RDRPs) have revolutionized synthetic polymer chemistry. Nowadays, RDRPs facilitate design and preparation of materials with controlled architecture, composition, and functionality. Atom transfer radical polymerization (ATRP) has evolved beyond traditional polymer field, enabling synthesis of organic-inorganic hybrids, bioconjugates, advanced polymers for electronics, energy, and environmentally relevant polymeric materials for broad applications in various fields. This review focuses on the relation between ATRP technology and the 12 principles of green chemistry, which are paramount guidelines in sustainable research and implementation. The green features of ATRP are presented, discussing the environmental and/or health issues and the challenges that remain to be overcome. Key discoveries and recent developments in green ATRP are highlighted, while providing a perspective for future opportunities in this area.
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Affiliation(s)
- Sylwia Dworakowska
- Department of ChemistryCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
- Faculty of Chemical Engineering and TechnologyCracow University of TechnologyWarszawska 24Cracow31‐155Poland
| | - Francesca Lorandi
- Department of ChemistryCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
- Department of Industrial EngineeringUniversity of Padovavia Marzolo 9Padova35131Italy
| | - Adam Gorczyński
- Department of ChemistryCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
- Faculty of ChemistryAdam Mickiewicz UniversityUniwersytetu Poznańskiego 8Poznań61‐614Poland
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21
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Iannuzzelli J, Bacik JP, Moore EJ, Shen Z, Irving EM, Vargas DA, Khare SD, Ando N, Fasan R. Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization. Biochemistry 2022; 61:1041-1054. [PMID: 35612958 PMCID: PMC9178789 DOI: 10.1021/acs.biochem.2c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/04/2022] [Indexed: 11/30/2022]
Abstract
Enhancing the thermostability of enzymes without impacting their catalytic function represents an important yet challenging goal in protein engineering and biocatalysis. We recently introduced a novel method for enzyme thermostabilization that relies on the computationally guided installation of genetically encoded thioether "staples" into a protein via cysteine alkylation with the noncanonical amino acid O-2-bromoethyl tyrosine (O2beY). Here, we demonstrate the functionality of an expanded set of electrophilic amino acids featuring chloroacetamido, acrylamido, and vinylsulfonamido side-chain groups for protein stapling using this strategy. Using a myoglobin-based cyclopropanase as a model enzyme, our studies show that covalent stapling with p-chloroacetamido-phenylalanine (pCaaF) provides higher stapling efficiency and enhanced stability (thermodynamic and kinetic) compared to the other stapled variants and the parent protein. Interestingly, molecular simulations of conformational flexibility of the cross-links show that the pCaaF staple allows fewer energetically feasible conformers than the other staples, and this property may be a broader indicator of stability enhancement. Using this strategy, pCaaF-stapled variants with significantly enhanced stability against thermal denaturation (ΔTm' = +27 °C) and temperature-induced heme loss (ΔT50 = +30 °C) were obtained while maintaining high levels of catalytic activity and stereoselectivity. Crystallographic analyses of singly and doubly stapled variants provide key insights into the structural basis for stabilization, which includes both direct interactions of the staples with protein residues and indirect interactions through adjacent residues involved in heme binding. This work expands the toolbox of protein stapling strategies available for protein stabilization.
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Affiliation(s)
- Jacob
A. Iannuzzelli
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - John-Paul Bacik
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Eric J. Moore
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Zhuofan Shen
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Ellen M. Irving
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - David A. Vargas
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sagar D. Khare
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Nozomi Ando
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Rudi Fasan
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
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22
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Rogers TA, Encarnación-Gómez LG, Bommarius AS. Long-Term Biocatalyst Performance: Mechanistic Prediction and Continuous Non-Isothermal Testing. CHEMSUSCHEM 2022; 15:e202102701. [PMID: 35441829 DOI: 10.1002/cssc.202102701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The assessment of the operational stability of biocatalysts by conventional direct determination of the total turnover number (TTN), a useful indicator of lifetime biocatalyst productivity, via continuous isothermal experiments tends to be time-consuming, material-intensive, and prone to disturbances, especially in case of rather stable catalysts. In the present work, we present and validate two alternative methods for estimating the TTN of a biocatalyst for any desired operating temperature. The first method is a mechanistic approach, built upon mathematical derivation of enzyme deactivation models derived from first principles, in which TTN can be calculated from two straightforward isothermal biochemical batch measurements. The second method relies on a few non-isothermal, continuous-mode experiments in conjunction with mathematical modeling to determine the intrinsic deactivation parameters of the biocatalyst. We verify both methods on the test case of TEM-1 β-lactamase-catalyzed penicillin G (Pen G) hydrolysis. Both alternative methods provide estimates of TTN which are typically within a factor of two to five or less of the values measured directly via lengthy, costly, and error-prone conventional isothermal aging tests. Therefore, both the mechanistic approach and the non-isothermal continuous approach are extremely valuable tools to enable calculation of catalyst cost contribution in continuous processing and to eliminate underperforming candidates in search of the most stable biocatalyst.
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Affiliation(s)
- Thomas A Rogers
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
- Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, 30332-0363, USA
- MilliporeSigma, 6211 El Camino Real, Carlsbad, CA 92009, USA
| | - Luis G Encarnación-Gómez
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Andreas S Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
- Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, 30332-0363, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
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23
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Chu M, Liu Y, Lou X, Zhang Q, Chen J. Rational Design of Chemical Catalysis for Plastic Recycling. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01286] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mingyu Chu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Yu Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Xiangxi Lou
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Qiao Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Jinxing Chen
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
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24
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Thermostabilizing ketoreductase ChKRED20 by consensus mutagenesis at dimeric interfaces. Enzyme Microb Technol 2022; 158:110052. [DOI: 10.1016/j.enzmictec.2022.110052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/15/2022] [Accepted: 04/17/2022] [Indexed: 11/19/2022]
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25
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Immobilization of Urokinase onto Magnetically Directed Micromotors. Appl Biochem Biotechnol 2022; 194:3351-3364. [PMID: 35353317 DOI: 10.1007/s12010-022-03878-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/14/2022] [Indexed: 11/02/2022]
Abstract
In this presented work, a new micromotor was prepared for urokinase immobilization. A covalent bond was constructed between the urokinase and the carboxyl groups of the graphene oxide, which is located at the outer layer of micromotors by EDC/NHS chemistry. The inner nickel layer gave magnetic properties to the micromotors and enables them to be separated from the reaction medium with the help of a simple magnet. For promising in vivo applications in the future, these micromotors do not require any fuel for their movement. The structures of the synthesized micromotors were illuminated by SEM and EDX analysis, and the movements of the micromotors were observed under an optical microscope with camera equipment. The immobilization yield of urokinase was found to be 68.07% (0.073 mg/100 µL micromotor solution) using the Bradford protein assay. In addition, to compare the activities of the immobilized and free enzymes, Lineweaver-Burk plots were constructed, and the kinetic parameters were calculated. Km values for free urokinase and immobilized urokinase were 2.0964 mM and 0.5602 mM, respectively. The maximum velocities of free and immobilized urokinase were found to be 25.25 µmol/min and 30.12 µmol/min, respectively. Also, storage stability profiles of the immobilized and free urokinase were monitored for 40-day incubation at + 4 °C, and the immobilized enzyme has 88% of its initial activity, while the free urokinase demonstrated only 30% of its initial activity. As a result, the experiments were carried out in human commercial serum, and specific activity values for free urokinase and immobilized urokinase were found to be 38.06 and 169.84 µmolmg-1 min-1, respectively.
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26
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Remonatto D, Miotti Jr. RH, Monti R, Bassan JC, de Paula AV. Applications of immobilized lipases in enzymatic reactors: A review. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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27
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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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28
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Partipilo M, Ewins EJ, Frallicciardi J, Robinson T, Poolman B, Slotboom DJ. Minimal Pathway for the Regeneration of Redox Cofactors. JACS AU 2021; 1:2280-2293. [PMID: 34984417 PMCID: PMC8717395 DOI: 10.1021/jacsau.1c00406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 06/14/2023]
Abstract
Effective metabolic pathways are essential for the construction of in vitro systems mimicking the biochemical complexity of living cells. Such pathways require the inclusion of a metabolic branch that ensures the availability of reducing equivalents. Here, we built a minimal enzymatic pathway confinable in the lumen of liposomes, in which the redox status of the nicotinamide cofactors NADH and NADPH is controlled by an externally provided formate. Formic acid permeates the membrane where a luminal formate dehydrogenase uses NAD+ to form NADH and carbon dioxide. Carbon dioxide diffuses out of the liposomes, leaving only the reducing equivalents in the lumen. A soluble transhydrogenase subsequently utilizes NADH for reduction of NADP+ thereby making NAD+ available again for the first reaction. The pathway is functional in liposomes ranging from a few hundred nanometers in diameter (large unilamellar vesicles) up to several tens of micrometers (giant unilamellar vesicles) and remains active over a period of 7 days. We demonstrate that the downstream biochemical process of reduction of glutathione disulfide can be driven by the transfer of reducing equivalents from formate via NAD(P)H, thereby providing a versatile set of electron donors for reductive metabolism.
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Affiliation(s)
- Michele Partipilo
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Eleanor J. Ewins
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jacopo Frallicciardi
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Tom Robinson
- Department
of Theory & Bio-Systems, Max Planck
Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Bert Poolman
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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29
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Enhanced Thermostability of Pseudomonas nitroreducens Isoeugenol Monooxygenase by the Combinatorial Strategy of Surface Residue Replacement and Consensus Mutagenesis. Catalysts 2021. [DOI: 10.3390/catal11101199] [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
Vanillin has many applications in industries. Isoeugenol monooxygenase (IEM) can catalyze the oxidation of isoeugenol to vanillin in the presence of oxygen under mild conditions. However, the low thermal stability of IEM limits its practical application in the biosynthesis of natural vanillin. Herein, two rational strategies were combined to improve the thermostability of IEM from Pseudomonas nitroreducens Jin1. Two variants (K83R and K95R) with better thermostability and one mutant (G398A) with higher activity were identified from twenty candidates based on the Surface Residue Replacement method. According to the Consensus Mutagenesis method, one mutant (I352R) with better thermostability and another mutant (L273F) with higher activity were also identified from nine candidates. After combinatorial mutation, a triple mutant K83R/K95R/L273F with the best thermostability and catalytic efficiency was generated. Compared with the wild-type IEM, the thermal inactivation half-lives (t1/2) of K83R/K95R/L273F at 25 °C, 30 °C, and 35 °C increased 2.9-fold, 11.9-fold, and 24.7-fold, respectively. Simultaneously, it also exhibited a 4.8-fold increase in kcat, leading to a 1.2-fold increase in catalytic efficiency (kcat/Km). When the whole cell of K83R/K95R/L273F was applied to the biotransformation of isoeugenol on preparative scale, the vanillin concentration reached 240.1 mM with space-time yield of 109.6 g/L/d, and vanillin was achieved in 77.6% isolated yield and >99% purity.
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30
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Jones K, Snodgrass HM, Belsare K, Dickinson BC, Lewis JC. Phage-Assisted Continuous Evolution and Selection of Enzymes for Chemical Synthesis. ACS CENTRAL SCIENCE 2021; 7:1581-1590. [PMID: 34584960 PMCID: PMC8461764 DOI: 10.1021/acscentsci.1c00811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 05/04/2023]
Abstract
Ligand-dependent biosensors are valuable tools for coupling the intracellular concentrations of small molecules to easily detectable readouts such as absorbance, fluorescence, or cell growth. While ligand-dependent biosensors are widely used for monitoring the production of small molecules in engineered cells and for controlling or optimizing biosynthetic pathways, their application to directed evolution for biocatalysts remains underexplored. As a consequence, emerging continuous evolution technologies are rarely applied to biocatalyst evolution. Here, we develop a panel of ligand-dependent biosensors that can detect a range of small molecules. We demonstrate that these biosensors can link enzymatic activity to the production of an essential phage protein to enable biocatalyst-dependent phage-assisted continuous evolution (PACE) and phage-assisted continuous selection (PACS). By combining these phage-based evolution and library selection technologies, we demonstrate that we can evolve enzyme variants with improved and expanded catalytic properties. Finally, we show that the genetic diversity resulting from a highly mutated PACS library is enriched for active enzyme variants with altered substrate scope. These results lay the foundation for using phage-based continuous evolution and selection technologies to engineer biocatalysts with novel substrate scope and reactivity.
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Affiliation(s)
- Krysten
A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Ketaki Belsare
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- E-mail:
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
- E-mail:
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31
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Cirujano FG, Dhakshinamoorthy A. Challenges and Opportunities for the Encapsulation of Enzymes over Porous Solids for Biodiesel Production and Cellulose Valorization into Glucose. ChemCatChem 2021. [DOI: 10.1002/cctc.202100943] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Francisco G. Cirujano
- Institute of Molecular Science (ICMOL) Universidad de Valencia 46980 Paterna Valencia Spain
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32
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Dube S, Rawtani D. Understanding intricacies of bioinspired organic-inorganic hybrid nanoflowers: A quest to achieve enhanced biomolecules immobilization for biocatalytic, biosensing and bioremediation applications. Adv Colloid Interface Sci 2021; 295:102484. [PMID: 34358991 DOI: 10.1016/j.cis.2021.102484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/10/2023]
Abstract
The immobilization of biomolecules has been a subject of interest for scientists for a long time. The organic-inorganic hybrid nanoflowers are a new class of nanostructures that act as a host platform for the immobilization of such biomolecules. It provides better practical applicability to these functional biomolecules while also providing superior activity and reusability when catalysis is involved. These nanostructures have a versatile and straightforward synthesis process and also exhibit enzyme mimicking activity in many cases. However, this facile synthesis involves many intricacies that require in-depth analysis to fully attain its potential as an immobilization technique. A complete account of all the factors involving the synthesis process optimisation is essential to be studied to make it commercially viable. This paper explores all the different aspects of hybrid nanoflowers which sets them apart from the conventional immobilization techniques while also giving an overview of its wide range of applications in industries.
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33
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Wu H, Chen Q, Zhang W, Mu W. Overview of strategies for developing high thermostability industrial enzymes: Discovery, mechanism, modification and challenges. Crit Rev Food Sci Nutr 2021; 63:2057-2073. [PMID: 34445912 DOI: 10.1080/10408398.2021.1970508] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biocatalysts such as enzymes are environmentally friendly and have substrate specificity, which are preferred in the production of various industrial products. However, the strict reaction conditions in industry including high temperature, organic solvents, strong acids and bases and other harsh environments often destabilize enzymes, and thus substantially compromise their catalytic functions, and greatly restrict their applications in food, pharmaceutical, textile, bio-refining and feed industries. Therefore, developing industrial enzymes with high thermostability becomes very important in industry as thermozymes have more advantages under high temperature. Discovering new thermostable enzymes using genome sequencing, metagenomics and sample isolation from extreme environments, or performing molecular modification of the existing enzymes with poor thermostability using emerging protein engineering technology have become an effective means of obtaining thermozymes. Based on the thermozymes as biocatalytic chips in industry, this review systematically analyzes the ways to discover thermostable enzymes from extreme environment, clarifies various interaction forces that will affect thermal stability of enzymes, and proposes different strategies to improve enzymes' thermostability. Furthermore, latest development in the thermal stability modification of industrial enzymes through rational design strategies is comprehensively introduced from structure-activity relationship point of view. Challenges and future research perspectives are put forward as well.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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34
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Humer D, Furlanetto V, Schruef AK, Wlodarczyk A, Kuttke M, Divne C, Spadiut O. Potential of unglycosylated horseradish peroxidase variants for enzyme prodrug cancer therapy. Biomed Pharmacother 2021; 142:112037. [PMID: 34392084 DOI: 10.1016/j.biopha.2021.112037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/07/2021] [Indexed: 12/17/2022] Open
Abstract
Fighting cancer still relies on chemo- and radiation therapy, which is a trade-off between effective clearance of malignant cells and severe side effects on healthy tissue. Targeted cancer treatment on the other hand is a promising and refined strategy with less systemic interference. The enzyme horseradish peroxidase (HRP) exhibits cytotoxic effects on cancer cells in combination with indole-3-acetic acid (IAA). However, the plant-derived enzyme is out of bounds for medical purposes due to its foreign glycosylation pattern and resulting rapid clearance and immunogenicity. In this study, we generated recombinant, unglycosylated HRP variants in Escherichia coli using random mutagenesis and investigated their biochemical properties and suitability for cancer treatment. The cytotoxicity of the HRP-IAA enzyme prodrug system was assessed in vitro with HCT-116 human colon, FaDu human nasopharyngeal squamous cell carcinoma and murine colon adenocarcinoma cells (MC38). Extensive cytotoxicity was shown in all three cancer cell lines: the cell viability of HCT-116 and MC38 cells treated with HRP-IAA was below 1% after 24 h incubation and the surviving fraction of FaDu cells was ≤ 10% after 72 h. However, no cytotoxic effect was observed upon in vivo intratumoral application of HRP-IAA on a MC38 tumor model in C57BL/6J mice. However, we expect that targeting of HRP to the tumor by conjugation to specific antibodies or antibody fragments will reduce HRP clearance and thereby enhance therapy efficacy.
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Affiliation(s)
- Diana Humer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Valentina Furlanetto
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health Department of Industrial Biotechnology, AlbaNova, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden
| | - Anna-Katharina Schruef
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Angelika Wlodarczyk
- Austrian Research Institute for Chemistry and Engineering (OFI), Franz-Grill-Straße 5, Objekt 213, 1030 Vienna, Austria
| | - Mario Kuttke
- Medical University of Vienna, Institute for Vascular Biology and Thrombosis Research, Center for Pharmacology and Physiology, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Christina Divne
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health Department of Industrial Biotechnology, AlbaNova, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria.
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35
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Ellis LD, Rorrer NA, Sullivan KP, Otto M, McGeehan JE, Román-Leshkov Y, Wierckx N, Beckham GT. Chemical and biological catalysis for plastics recycling and upcycling. Nat Catal 2021. [DOI: 10.1038/s41929-021-00648-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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36
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Hasan S, Naeem A. The modulation of structural stability of horseradish peroxidase as a consequence of macromolecular crowding. J Mol Recognit 2021; 34:e2902. [PMID: 34013591 DOI: 10.1002/jmr.2902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/24/2021] [Accepted: 04/05/2021] [Indexed: 11/07/2022]
Abstract
Macromolecular crowding plays an inevitable role in all biological processes influencing association, conformation, and other characteristics of proteins. Present study is based on the effect of macromolecular crowding on structure of horseradish peroxidase (HRP) enzyme. Concentration-dependent conformational changes induced by crowding agents, dextran 70 and polyethylene glycol (PEG)-4000, were monitored employing a range of biophysical techniques. The intrinsic fluorescence spectra showed transition of protein from native to unfolded state. Marked increase in 8-Anilino-1-naphthalene-sulphonoic acid and Thioflavin T fluorescence indicated presence of non-native moieties with 80 mg/mL dextran. Enhanced absorbance in turbidity, Soret, and Congo red in corroboration with scattering intensity at 350nm results revealed incidence of HRP aggregates. A new peak around 218 nm in CD spectra pointed towards change in secondary structure towards β-sheets. Significant loss of enzyme activity upon structural disruption was seen. Comet assay demonstrated DNA damage and genotoxic nature of HRP aggregates, supporting spectroscopic, and fluorescence results. The normalized results were obtained with 120 mg/mL PEG-4000 close to that of native HRP implying no disruptive effect on structure. It can be hypothesized that macromolecular crowding is a vital element, which can have diverse effects. In this study, dextran 70 was observed to have pro-aggregatory effect while enhanced stability of native enzyme was witnessed with PEG. Hence, it can be stated that PEG has potentially better crowder as it helps retain the native enzyme structure. Routine addition of crowding agents is recommended if biological molecules are to be studied under more physiologically appropriate environments.
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Affiliation(s)
- Samra Hasan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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37
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Xylooligosaccharides production by crude and partially purified xylanase from Aureobasidium pullulans: Biochemical and thermodynamic properties of the enzymes and their application in xylan hydrolysis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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38
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Athapattu US, Amarasekara CA, Immel JR, Bloom S, Barany F, Nagel AC, Soper SA. Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing. Nucleic Acids Res 2021; 49:e41. [PMID: 33511416 PMCID: PMC8053086 DOI: 10.1093/nar/gkab001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 01/29/2023] Open
Abstract
Modifications in RNA are numerous (∼170) and in higher numbers compared to DNA (∼5) making the ability to sequence an RNA molecule to identify these modifications highly tenuous using next generation sequencing (NGS). The ability to immobilize an exoribonuclease enzyme, such as XRN1, to a solid support while maintaining its activity and capability to cleave both the canonical and modified ribonucleotides from an intact RNA molecule can be a viable approach for single-molecule RNA sequencing. In this study, we report an enzymatic reactor consisting of covalently attached XRN1 to a solid support as the groundwork for a novel RNA exosequencing technique. The covalent attachment of XRN1 to a plastic solid support was achieved using EDC/NHS coupling chemistry. Studies showed that the solid-phase digestion efficiency of model RNAs was 87.6 ± 2.8%, while the XRN1 solution-phase digestion for the same model was 78.3 ± 4.4%. The ability of immobilized XRN1 to digest methylated RNA containing m6A and m5C ribonucleotides was also demonstrated. The processivity and clipping rate of immobilized XRN1 secured using single-molecule fluorescence measurements of a single RNA transcript demonstrated a clipping rate of 26 ± 5 nt s-1 and a processivity of >10.5 kb at 25°C.
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Affiliation(s)
| | | | - Jacob R Immel
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Steven Bloom
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | | | | | - Steven A Soper
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
- Sunflower Genomics, Inc., Lawrence, KS 66047, USA
- Department of Mechanical Engineering and Bioengineering, University of Kansas, Lawrence, KS 66045, USA
- Department of Cancer Biology and KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
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39
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Abstract
Bioelectrocatalysis using redox enzymes appears as a sustainable way for biosensing, electricity production, or biosynthesis of fine products. Despite advances in the knowledge of parameters that drive the efficiency of enzymatic electrocatalysis, the weak stability of bioelectrodes prevents large scale development of bioelectrocatalysis. In this review, starting from the understanding of the parameters that drive protein instability, we will discuss the main strategies available to improve all enzyme stability, including use of chemicals, protein engineering and immobilization. Considering in a second step the additional requirements for use of redox enzymes, we will evaluate how far these general strategies can be applied to bioelectrocatalysis.
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40
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Atkins DL, Magana JR, Sproncken CCM, van Hest JCM, Voets IK. Single Enzyme Nanoparticles with Improved Biocatalytic Activity through Protein Entrapment in a Surfactant Shell. Biomacromolecules 2021; 22:1159-1166. [PMID: 33630590 PMCID: PMC7944482 DOI: 10.1021/acs.biomac.0c01663] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A polymeric corona
consisting of an alkyl-glycolic acid ethoxylate
(CXEOY) surfactant
offers a promising approach toward endowing proteins with thermotropic
phase behavior and hyperthermal activity. Typically, preparation of
protein–surfactant biohybrids is performed via chemical modification of acidic residues followed by electrostatic
conjugation of an anionic surfactant to encapsulate single proteins.
While this procedure has been applied to a broad range of proteins,
modification of acidic residues may be detrimental to function for
specific enzymes. Herein, we report on the one-pot preparation of
biohybrids via covalent conjugation of surfactants
to accessible lysine residues. We entrap the model enzyme hen egg-white
lysozyme (HEWL) in a shell of carboxyl-functionalized C12EO10 or C12EO22 surfactants. With
fewer surfactants, our covalent biohybrids display similar thermotropic
phase behavior to their electrostatically conjugated analogues. Through
a combination of small-angle X-ray scattering and circular dichroism
spectroscopy, we find that both classes of biohybrids consist of a
folded single-protein core decorated by surfactants. Whilst traditional
biohybrids retain densely packed surfactant coronas, our biohybrids
display a less dense and heterogeneously distributed surfactant coverage
located opposite to the catalytic cleft of HEWL. In solution, this
surfactant coating permits 7- or 3.5-fold improvements in activity
retention for biohybrids containing C12EO10 or
C12EO22, respectively. The reported alternative
pathway for biohybrid preparation offers a new horizon to expand upon
the library of proteins for which functional biohybrid materials can
be prepared. We also expect that an improved understanding of the
distribution of tethered surfactants in the corona will be crucial
for future structure–function investigations.
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Affiliation(s)
- Dylan L Atkins
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - J Rodrigo Magana
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Christian C M Sproncken
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Jan C M van Hest
- Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Laboratory of Bio-Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ilja K Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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41
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Stourac J, Dubrava J, Musil M, Horackova J, Damborsky J, Mazurenko S, Bednar D. FireProtDB: database of manually curated protein stability data. Nucleic Acids Res 2021; 49:D319-D324. [PMID: 33166383 PMCID: PMC7778887 DOI: 10.1093/nar/gkaa981] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 10/12/2020] [Indexed: 01/13/2023] Open
Abstract
The majority of naturally occurring proteins have evolved to function under mild conditions inside the living organisms. One of the critical obstacles for the use of proteins in biotechnological applications is their insufficient stability at elevated temperatures or in the presence of salts. Since experimental screening for stabilizing mutations is typically laborious and expensive, in silico predictors are often used for narrowing down the mutational landscape. The recent advances in machine learning and artificial intelligence further facilitate the development of such computational tools. However, the accuracy of these predictors strongly depends on the quality and amount of data used for training and testing, which have often been reported as the current bottleneck of the approach. To address this problem, we present a novel database of experimental thermostability data for single-point mutants FireProtDB. The database combines the published datasets, data extracted manually from the recent literature, and the data collected in our laboratory. Its user interface is designed to facilitate both types of the expected use: (i) the interactive explorations of individual entries on the level of a protein or mutation and (ii) the construction of highly customized and machine learning-friendly datasets using advanced searching and filtering. The database is freely available at https://loschmidt.chemi.muni.cz/fireprotdb.
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Affiliation(s)
- Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Juraj Dubrava
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Jana Horackova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
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42
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Bi J, Jing X, Wu L, Zhou X, Gu J, Nie Y, Xu Y. Computational design of noncanonical amino acid-based thioether staples at N/C-terminal domains of multi-modular pullulanase for thermostabilization in enzyme catalysis. Comput Struct Biotechnol J 2021; 19:577-585. [PMID: 33510863 PMCID: PMC7811066 DOI: 10.1016/j.csbj.2020.12.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 12/14/2022] Open
Abstract
Enzyme thermostabilization is considered a critical and often obligatory step in biosynthesis, because thermostability is a significant property of enzymes that can be used to evaluate their feasibility for industrial applications. However, conventional strategies for thermostabilizing enzymes generally introduce non-covalent interactions and/or natural covalent bonds caused by natural amino acid substitutions, and the trade-off between the activity and stability of enzymes remains a challenge. Here, we developed a computationally guided strategy for constructing thioether staples by incorporating noncanonical amino acid (ncAA) into the more flexible N/C-terminal domains of the multi-modular pullulanase from Bacillus thermoleovorans (BtPul) to enhance its thermostability. First, potential thioether staples located in the N/C-terminal domains of BtPul were predicted using RosettaMatch. Next, eight variants involving stable thioether staples were precisely predicted using FoldX and Rosetta ddg_monomer. Six positive variants were obtained, of which T73(O2beY)-171C had a 157% longer half-life at 70 °C and an increase of 7.0 °C in T m, when compared with the wild-type (WT). T73(O2beY)-171C/T126F/A72R exhibited an even more improved thermostability, with a 211% increase in half-life at 70 °C and a 44% enhancement in enzyme activity compared with the WT, which was attributed to further optimization of the local interaction network. This work introduces and validates an efficient strategy for enhancing the thermostability and activity of multi-modular enzymes.
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Affiliation(s)
- Jiahua Bi
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiaoran Jing
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xia Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jie Gu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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43
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The fabrication of a high performance enzymatic hybrid membrane reactor (EHMR) containing immobilized Candida rugosa lipase (CRL) onto graphene oxide nanosheets-blended polyethersulfone membrane. J Memb Sci 2020. [DOI: 10.1016/j.memsci.2020.118435] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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44
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Optimizing the linker length for fusing an alcohol dehydrogenase with a cyclohexanone monooxygenase. Methods Enzymol 2020; 647:107-143. [PMID: 33482986 DOI: 10.1016/bs.mie.2020.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The use of enzymes in organic synthesis is highly appealing due their remarkably high chemo-, regio- and enantioselectivity. Nevertheless, for biosynthetic routes to be industrially useful, the enzymes must fulfill several requirements. Particularly, in case of cofactor-dependent enzymes self-sufficient systems are highly valuable. This can be achieved by fusing enzymes with complementary cofactor dependency. Such bifunctional enzymes are also relatively easy to handle, may enhance stability, and promote product intermediate channeling. However, usually the characteristics of the linker, fusing the target enzymes, are not thoroughly evaluated. A poor linker design can lead to detrimental effects on expression levels, enzyme stability and/or enzyme performance. In this chapter, the effect of the length of a glycine-rich linker was explored for the case study of ɛ-caprolactone synthesis through an alcohol dehydrogenase-cyclohexanone monooxygenase fusion system. The procedure includes cloning of linker variants, expression analysis, determination of thermostability and effect on activity and conversion levels of 15 variants of different linker sizes. The protocols can also be used for the creation of other protein-protein fusions.
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45
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Monica P, Kapoor M. Alkali-stable GH11 endo-β-1,4 xylanase (XynB) from Bacillus subtilis strain CAM 21: application in hydrolysis of agro-industrial wastes, fruit/vegetable peels and weeds. Prep Biochem Biotechnol 2020; 51:475-487. [PMID: 33043796 DOI: 10.1080/10826068.2020.1830416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
GH11 endo-xylanases, due to their inherent structural and biochemical properties, are the key to efficient bioconversion of lignocellulosic biomass into value-added products. A GH11 endo-xylanase (XynB) from Bacillus subtilis strain CAM 21 was cloned, over-expressed and purified (Mw∼24 kDa) using Ni-NTA affinity chromatography. XynB showed optimum activity at pH 7.0 and 50°C and was stable (>88%) in a broad range of pH (4-11). The apparent Km, Kcat and Kcat/Km of XynB were 2.9 mg/ml, 1961.2/sec, and 675.62 ml/mg/sec, respectively using birchwood xylan as substrate. XynB was a classical endo-xylanase as it hydrolyzed birchwood xylan to xylo-oligosaccharides and not xylose. Kinetic stability of XynB at 45-53°C was between 43-182 min. Secondary structure analysis of XynB using far-UV CD spectroscopy revealed presence of 51.85% β strands and 2.64% α helix and was consistent with the homology modeling studies. XynB hydrolyzed the xylan extracted from agro-industrial wastes and fruit/vegetable peels by releasing up to 670 mg/g of reducing sugars. The xylan extracted from weeds (Ageratum conyzoides, Achyranthes aspera and Tridax procumbens) had characteristic signatures of hemicelluloses and after XynB hydrolysis showed cracks, peeling and release of up to 135.2 mg/g reducing sugars.
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Affiliation(s)
- P Monica
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR - Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, India
| | - Mukesh Kapoor
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR - Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, India
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46
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Chen C, Su L, Wu L, Zhou J, Wu J. Enhanced the catalytic efficiency and thermostability of maltooligosyltrehalose synthase from Arthrobacter ramosus by directed evolution. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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47
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Gul I, Wang Q, Jiang Q, Fang R, Tang L. Enzyme immobilization on glass fiber membrane for detection of halogenated compounds. Anal Biochem 2020; 609:113971. [PMID: 32979368 DOI: 10.1016/j.ab.2020.113971] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 01/19/2023]
Abstract
Enzyme immobilization using inorganic membranes has enticed increased attention as they not only improve enzyme stability, but also furnish user-friendly biodevices that can be tailored to different applications. Herein, we explored the suitability of the glass fiber membrane for enzyme immobilization and its application for halocarbon detection. For this, halohydrin dehalogenase (HheC) and bovine serum albumin were crosslinked and immobilized on a glass fiber membrane without membrane functionalization. Immobilized HheC exhibited higher storage stability than its free counterpart over 60 days at 4 °C (67% immobilized vs. 8.1% free) and 30 °C (77% immobilized vs. 57% free). Similarly, the thermal endurance of the immobilized HheC was significantly improved. The practical utility of the membrane-immobilized enzyme was demonstrated by colorimetric detection of 1,3-dichloro-2-propanol (1,3-DCP) and 2,3-dibromo-1-propanol (2,3-DBP) as model analytes. Under optimized conditions, the detection limits of 0.06 mM and 0.09 mM were achieved for 1,3-DCP and 2,3-DBP, respectively. The satisfactory recoveries were observed with spiked river and lake water samples, which demonstrate the application potential of immobilized HheC for screening contaminants in water samples. Our results revealed that the proposed frugal and facile approach could be useful for enzyme stabilization, and mitigation of halocarbon pollution.
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Affiliation(s)
- Ijaz Gul
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Qian Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Qifa Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Ruiqin Fang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
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48
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Counterbalance of Stability and Activity Observed for Thermostable Transaminase from Thermobaculum terrenum in the Presence of Organic Solvents. Catalysts 2020. [DOI: 10.3390/catal10091024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pyridoxal-5’-phosphate-dependent transaminases catalyze stereoselective amination of organic compounds and are highly important for industrial applications. Catalysis by transaminases often requires organic solvents to increase the solubility of reactants. However, natural transaminases are prone to inactivation in the presence of water-miscible organic solvents. Here, we present the solvent tolerant thermostable transaminase from Thermobaculum terrenum (TaTT) that catalyzes transamination between L-leucine and alpha-ketoglutarate with an optimum at 75 °C and increases the activity ~1.8-fold upon addition of 15% dimethyl sulfoxide or 15% methanol at high but suboptimal temperature, 50 °C. The enhancement of the activity correlates with a decrease in the thermal denaturation midpoint temperature. The blue-shift of tryptophan fluorescence suggested that solvent molecules penetrate the hydration shell of the enzyme. Analysis of hydrogen bonds in the TaTT dimer revealed a high number of salt bridges and surface hydrogen bonds formed by backbone atoms. The latter are sensitive to the presence of organic solvents; they rearrange, conferring the relaxation of some constraints inherent to a thermostable enzyme at low temperatures. Our data support the idea that the counterbalance of stability and activity is crucial for the catalysis under given conditions; the obtained results may be useful for fine-tuning biocatalyst efficiency.
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49
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Adebar N, Gröger H. Heterogeneous Catalysts “on the Move”: Flow Chemistry with Fluid Immobilised (Bio)Catalysts. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000705] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Niklas Adebar
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
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50
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Exploring the Role of Phenylalanine Residues in Modulating the Flexibility and Topography of the Active Site in the Peroxygenase Variant PaDa-I. Int J Mol Sci 2020; 21:ijms21165734. [PMID: 32785123 PMCID: PMC7460833 DOI: 10.3390/ijms21165734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 11/28/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are fungal heme-thiolate enzymes able to catalyze a wide range of oxidation reactions, such as peroxidase-like, catalase-like, haloperoxidase-like, and, most interestingly, cytochrome P450-like. One of the most outstanding properties of these enzymes is the ability to catalyze the oxidation a wide range of organic substrates (both aromatic and aliphatic) through cytochrome P450-like reactions (the so-called peroxygenase activity), which involves the insertion of an oxygen atom from hydrogen peroxide. To catalyze this reaction, the substrate must access a channel connecting the bulk solution to the heme group. The composition, shape, and flexibility of this channel surely modulate the catalytic ability of the enzymes in this family. In order to gain an understanding of the role of the residues comprising the channel, mutants derived from PaDa-I, a laboratory-evolved UPO variant from Agrocybe aegerita, were obtained. The two phenylalanine residues at the surface of the channel, which regulate the traffic towards the heme active site, were mutated by less bulky residues (alanine and leucine). The mutants were experimentally characterized, and computational studies (i.e., molecular dynamics (MD)) were performed. The results suggest that these residues are necessary to reduce the flexibility of the region and maintain the topography of the channel.
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