Structure-driven protein engineering for production of valuable natural products

Wang, Yun; Yu, Luyao; Shao, Jie; Zhu, Zhanpin; Zhang, Lei

doi:10.1016/j.tplants.2022.11.004

Cited by 8 publications

(6 citation statements)

References 59 publications

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“…The core of protein engineering is the change in the function of a protein according to its structure. In most enzymes, the substrate pocket is the core region to perform catalytic functions . The residues that make up the substrate pocket determine the physicochemical properties of the substrate, such as its charge, shape, and size .…”

Section: Resultsmentioning

confidence: 99%

“…In most enzymes, the substrate pocket is the core region to perform catalytic functions. 30 The residues that make up the substrate pocket determine the physicochemical properties of the substrate, such as its charge, shape, and size. 9 By determining the substrate pocket of the enzyme and formulating effective transformation strategies, the enzyme's catalytic rate, specificity, and promiscuity can be optimized.…”

Section: Resultsmentioning

confidence: 99%

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Computer-Aided Semi-Rational Design to Enhance the Activity of l-Sorbosone Dehydrogenase from Gluconobacter oxidans WSH-004

Li,

Wang,

Huo

et al. 2024

J. Agric. Food Chem.

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The titer of the microbial fermentation products can be increased by enzyme engineering. L-Sorbosone dehydrogenase (SNDH) is a key enzyme in the production of 2-keto-L-gulonic acid (2-KLG), which is the precursor of vitamin C. Enhancing the activity of SNDH may have a positive impact on 2-KLG production. In this study, a computer-aided semirational design of SNDH was conducted. Based on the analysis of SNDH's substrate pocket and multiple sequence alignment, three modification strategies were established: (1) expanding the entrance of SNDH's substrate pocket, (2) engineering the residues within the substrate pocket, and (3) enhancing the electron transfer of SNDH. Finally, mutants S453A, L460V, and E471D were obtained, whose specific activity was increased by 20, 100, and 10%, respectively. In addition, the ability of Gluconobacter oxidans WSH-004 to synthesize 2-KLG was improved by eliminating H 2 O 2 . This study provides mutant enzymes and metabolic engineering strategies for the microbial-fermentation-based production of 2-KLG.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Computer-Aided Semi-Rational Design to Enhance the Activity of l-Sorbosone Dehydrogenase from Gluconobacter oxidans WSH-004

Li,

Wang,

Huo

et al. 2024

J. Agric. Food Chem.

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show abstract

“…In the articles mentioned above, the optimization of fermentation was achieved by changing the fermentation media composition, induction time, temperature optimization, etc. Still, there are also trials increasing the fermentation yield of these enzymes by using state-of-the-art technologies such as precision fermentation [82], directed evolution [83], protein and strain engineering [84], high-throughput screening methods based on in vitro compartmentalization [85], flow cytometry, and microfluidics.…”

Section: State-of-the-art Technologies For Increasing Recombinant Pro...mentioning

confidence: 99%

State of the Art Technologies for High Yield Heterologous Expression and Production of Oxidoreductase Enzymes: Glucose Oxidase, Cellobiose Dehydrogenase, Horseradish Peroxidase, and Laccases in Yeasts P. pastoris and S. cerevisiae

Crnoglavac Popović,

Stanišić,

Prodanović

2024

Fermentation

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Oxidoreductase (OXR) enzymes are in high demand for biocatalytic applications in the food industry and cosmetics (glucose oxidase (GOx) and cellobiose dehydrogenase (CDH)), bioremediations (horseradish peroxidase (HRP) and laccase (LAC)), and medicine for biosensors and miniature biofuel cells (GOx, CDH, LAC, and HRP). They can be used in a soluble form and/or within the yeast cell walls expressed as chimeras on the surface of yeast cells (YSD), such as P. pastoris and S. cerevisiae. However, most of the current studies suffer from either low yield for soluble enzyme expression or low enzyme activity when expressed as chimeric proteins using YSD. This is always the case in studies dealing with the heterologous expression of oxidoreductase enzymes, since there is a requirement not only for multiple OXR gene integrations into the yeast genome (super transformations), and codon optimization, but also very careful design of fermentation media composition and fermentation conditions during expression due to the need for transition metals (copper and iron) and metabolic precursors of FAD and heme. Therefore, scientists are still trying to find the optimal formula using the above-mentioned approaches; most recently, researcher started using protein engineering and directed evolution to increase in the yield of recombinant enzyme production. In this review article, we will cover all the current state-of-the-art technologies and most recent advances in the field that yielded a high expression level for some of these enzymes in specially designed expression/fermentation systems. We will also tackle and discuss new possibilities for further increases in fermentation yield using cutting-edge technologies such as directed evolution, protein and strain engineering, high-throughput screening methods based on in vitro compartmentalization, flow cytometry, and microfluidics.

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“…The use of X-ray crystallography to determine protein structure provides an opportunity to understand the molecular mechanisms underlying biology at the atomic level [1][2][3][4]. This structural information offers insights into the development of new drugs [5][6][7] and into protein engineering for the improvement of industrial enzyme applications [8][9][10]. In typical macromolecular crystallography, diffraction data are collected in cryogenic environments using cryocrystallography to reduce radiation damage [11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of Room Temperature Structures Determined by Macromolecular and Serial Crystallography

Nam

2024

Crystals

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Temperature directly influences the function and structure of proteins. Crystal structures determined at room temperature offer more biologically relevant structural information regarding flexibility, rigidity, and thermal motion than those determined by conventional cryocrystallography. Crystal structures can be determined at room temperature using conventional macromolecular crystallography (MX) or serial crystallography (SX) techniques. Among these, MX may theoretically be affected by radiation damage or X-ray heating, potentially resulting in differences between the room temperature structures determined by MX and SX, but this has not been fully elucidated. In this study, the room temperature structure of xylanase GH11 from Thermoanaerobacterium saccharolyticum was determined by MX (RT-TsaGH11-MX). The RT-TsaGH11-MX exhibited both the open and closed conformations of the substrate-binding cleft within the β-sandwich fold. The RT-TsaGH11-MX showed distinct structural changes and molecular flexibility when compared with the RT-TsaGH11 determined via serial synchrotron crystallography. The notable molecular conformation and flexibility of the RT-TsaGH11-MX may be induced by radiation damage and X-ray heating. These findings will broaden our understanding of the potential limitations of room temperature structures determined by MX.

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Structure-driven protein engineering for production of valuable natural products

Cited by 8 publications

References 59 publications

Computer-Aided Semi-Rational Design to Enhance the Activity of l-Sorbosone Dehydrogenase from Gluconobacter oxidans WSH-004

Computer-Aided Semi-Rational Design to Enhance the Activity of l-Sorbosone Dehydrogenase from Gluconobacter oxidans WSH-004

State of the Art Technologies for High Yield Heterologous Expression and Production of Oxidoreductase Enzymes: Glucose Oxidase, Cellobiose Dehydrogenase, Horseradish Peroxidase, and Laccases in Yeasts P. pastoris and S. cerevisiae

Comparative Analysis of Room Temperature Structures Determined by Macromolecular and Serial Crystallography

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