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Barati F, Hosseini F, Vafaee R, Sabouri Z, Ghadam P, Arab SS, Shadfar N, Piroozmand F. In silico approaches to investigate enzyme immobilization: a comprehensive systematic review. Phys Chem Chem Phys 2024; 26:5744-5761. [PMID: 38294035 DOI: 10.1039/d3cp03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems. Bioinformatics tools can often correctly predict immobilization outcomes, resulting in a cost-effective experimental phase with the least time consumed. This study provides an overview of in silico methods predicting immobilization processes via a comprehensive systematic review of published articles till 11 December 2022. It also mentions the strengths and weaknesses of the processes and explains the computational analyses in each method that are required for immobilization assessment. In this regard, Web of Science and Scopus databases were screened to gain relevant publications. After screening the gathered documents (n = 3873), 60 articles were selected for the review. The selected papers have applied in silico procedures including only molecular dynamics (MD) simulations (n = 20), parallel tempering Monte Carlo (PTMC) and MD simulations (n = 3), MD and docking (n = 1), density functional theory (DFT) and MD (n = 1), only docking (n = 11), metal ion binding site prediction (MIB) server and docking (n = 2), docking and DFT (n = 1), docking and analysis of enzyme surfaces (n = 1), only DFT (n = 1), only MIB server (n = 2), analysis of an enzyme structure and surface (n = 12), rational design of immobilized derivatives (RDID) software (n = 3), and dissipative particle dynamics (DPD; n = 2). In most included studies (n = 51), enzyme immobilization was investigated experimentally in addition to in silico evaluation.
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Affiliation(s)
- Farzaneh Barati
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Fakhrisadat Hosseini
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Rayeheh Vafaee
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Sabouri
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Parinaz Ghadam
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Najmeh Shadfar
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Firoozeh Piroozmand
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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Sorokin AV, Goncharova SS, Lavlinskaya MS, Holyavka MG, Faizullin DA, Zuev YF, Kondratyev MS, Artyukhov VG. Complexation of Bromelain, Ficin, and Papain with the Graft Copolymer of Carboxymethyl Cellulose Sodium Salt and N-Vinylimidazole Enhances Enzyme Proteolytic Activity. Int J Mol Sci 2023; 24:11246. [PMID: 37511006 PMCID: PMC10379864 DOI: 10.3390/ijms241411246] [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: 06/21/2023] [Revised: 07/01/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
This study investigates the features of interactions between cysteine proteases (bromelain, ficin, and papain) and a graft copolymer of carboxymethyl cellulose sodium salt with N-vinylimidazole. The objective is to understand the influence of this interactions on the proteolytic activity and stability of the enzymes. The enzymes were immobilized through complexation with the carrier. The interaction mechanism was examined using Fourier-transform infrared spectroscopy and flexible molecular docking simulations. The findings reveal that the enzymes interact with the functional groups of the carrier via amino acid residues, resulting in the formation of secondary structure elements and enzyme's active sites. These interactions induce modulation of active site of the enzymes, leading to an enhancement in their proteolytic activity. Furthermore, the immobilized enzymes demonstrate superior stability compared to their native counterparts. Notably, during a 21-day incubation period, no protein release from the conjugates was observed. These results suggest that the complexation of the enzymes with the graft copolymer has the potential to improve their performance as biocatalysts, with applications in various fields such as biomedicine, pharmaceutics, and biotechnology.
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Affiliation(s)
- Andrey V Sorokin
- Biophysics and Biotechnology Department, Voronezh State University, 1 Universitetskaya Square, 394018 Voronezh, Russia
- Bioresource Potential of the Seaside Territory Laboratory, Sevastopol State University, 33 Studencheskaya Street, 299053 Sevastopol, Russia
| | - Svetlana S Goncharova
- Biophysics and Biotechnology Department, Voronezh State University, 1 Universitetskaya Square, 394018 Voronezh, Russia
| | - Maria S Lavlinskaya
- Biophysics and Biotechnology Department, Voronezh State University, 1 Universitetskaya Square, 394018 Voronezh, Russia
- Bioresource Potential of the Seaside Territory Laboratory, Sevastopol State University, 33 Studencheskaya Street, 299053 Sevastopol, Russia
| | - Marina G Holyavka
- Biophysics and Biotechnology Department, Voronezh State University, 1 Universitetskaya Square, 394018 Voronezh, Russia
- Bioresource Potential of the Seaside Territory Laboratory, Sevastopol State University, 33 Studencheskaya Street, 299053 Sevastopol, Russia
| | - Dzhigangir A Faizullin
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky Street, 420111 Kazan, Russia
| | - Yuriy F Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky Street, 420111 Kazan, Russia
- Alexander Butlerov Chemical Institute, Kazan Federal University, Kremlevskaya Street 18, 420008 Kazan, Russia
| | - Maxim S Kondratyev
- Biophysics and Biotechnology Department, Voronezh State University, 1 Universitetskaya Square, 394018 Voronezh, Russia
- Institute of Cell Biophysics of the RAS, 3 Institutskaya Street, 142290 Pushchino, Russia
| | - Valeriy G Artyukhov
- Biophysics and Biotechnology Department, Voronezh State University, 1 Universitetskaya Square, 394018 Voronezh, Russia
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De Santis P, Petrovai N, Meyer LE, Hobisch M, Kara S. A holistic carrier-bound immobilization approach for unspecific peroxygenase. Front Chem 2022; 10:985997. [PMID: 36110138 PMCID: PMC9468545 DOI: 10.3389/fchem.2022.985997] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are among the most studied enzymes in the last decade and their well-deserved fame owes to the enzyme’s ability of catalyzing the regio- and stereospecific hydroxylation of non-activated C–H bonds at the only expense of H2O2. This leads to more direct routes for the synthesis of different chiral compounds as well as to easier oxyfunctionalization of complex molecules. Unfortunately, due to the high sensitivity towards the process conditions, UPOs’ application at industrial level has been hampered until now. However, this challenge can be overcome by enzyme immobilization, a valid strategy that has been proven to give several benefits. Within this article, we present three different immobilization procedures suitable for UPOs and two of them led to very promising results. The immobilized enzyme, indeed, shows longer stability and increased robustness to reaction conditions. The immobilized enzyme half-life time is 15-fold higher than for the free AaeUPO PaDa-I and no enzyme deactivation occurred when incubated in organic media for 120 h. Moreover, AaeUPO PaDa-I is proved to be recycled and reused up to 7 times when immobilized.
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Affiliation(s)
- Piera De Santis
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Noémi Petrovai
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Lars-Erik Meyer
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Markus Hobisch
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Selin Kara
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
- *Correspondence: Selin Kara,
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