Enzyme engineering and its industrial applications

Amatto, Isabela Victorino da Silva; Rosa-Garzon, Nathália Gonsales da; Simões, Fernando Carmona; Santiago, Fernanda L.B.; Leite, Nathália Pereira da Silva; Martins, Júlia Raspante; Cabral, Hamilton

doi:10.1002/bab.2117

Cited by 63 publications

(36 citation statements)

References 117 publications

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“…Many efforts have been made to tackle this challenge, but there is no one-size-fits-all strategy. Known strategies are directed evolution , and sequence-based phylogenetic analysis to identify thermostable analogous and structure-guided site-directed mutagenesis. , Increased protein stability will result in lower process costs per unit of product and make biocatalytic transformations a real alternative to chemical processes.…”

mentioning

confidence: 99%

Mutations Increasing Cofactor Affinity, Improve Stability and Activity of a Baeyer–Villiger Monooxygenase

et al. 2022

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The typically low thermodynamic and kinetic stability of enzymes is a bottleneck for their application in industrial synthesis. Baeyer–Villiger monooxygenases, which oxidize ketones to lactones using aerial oxygen, among other activities, suffer particularly from these instabilities. Previous efforts in protein engineering have increased thermodynamic stability but at the price of decreased activity. Here, we solved this trade-off by introducing mutations in a cyclohexanone monooxygenase from Acinetobacter sp., guided by a combination of rational and structure-guided consensus approaches. We developed variants with improved activity (1.5- to 2.5-fold) and increased thermodynamic (+5 °C T m ) and kinetic stability (8-fold). Our analysis revealed a crucial position in the cofactor binding domain, responsible for an 11-fold increase in affinity to the flavin cofactor, and explained using MD simulations. This gain in affinity was compatible with other mutations. While our study focused on a particular model enzyme, previous studies indicate that these findings are plausibly applicable to other BVMOs, and possibly to other flavin-dependent monooxygenases. These new design principles can inform the development of industrially robust, flavin-dependent biocatalysts for various oxidations.

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confidence: 99%

Mutations Increasing Cofactor Affinity, Improve Stability and Activity of a Baeyer–Villiger Monooxygenase

et al. 2022

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“…This has been achieved due to the advancement of bioinformatics, which allows the protein structure to be visualized in a three-dimensional way and, thus, achieve a rational design that allows the introduction of disulfide bridges, replacing the N terminal and increasing the number of hydrogen bonds [105]. Table 3 shows some enzymes designed from these techniques, taken from Victorino da Silva Amatto et al [106]. The design of enzymes has also led to the choice of the expression system for the production of recombinant proteins, using mainly bacteria (Escherichia coli, Bacillus spp., Lactobacillus lactis), filamentous fungi (Aspergillus spp.)…”

Section: Production Of Enzymes For Animal Feedingmentioning

confidence: 99%

Exogenous Enzymes as Zootechnical Additives in Animal Feed: A Review

et al. 2021

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Enzymes are widely used in the food industry. Their use as a supplement to the raw material for animal feed is a current research topic. Although there are several studies on the application of enzyme additives in the animal feed industry, it is necessary to search for new enzymes, as well as to utilize bioinformatics tools for the design of specific enzymes that work in certain environmental conditions and substrates. This will allow the improvement of the productive parameters in animals, reducing costs and making the processes more efficient. Technological needs have considered these catalysts as essential in many industrial sectors and research is constantly being carried out to optimize their use in those processes. This review describes the enzymes used in animal nutrition, their mode of action, their production and new sources of production as well as studies on different animal models to evaluate their effect on the productive performance intended for the production of animal feed.

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“…Enzymes catalyze biochemical reactions and are applied in engineered microbes to biosynthesize a wide range of industrial chemicals, pharmaceuticals, and food additives. , Discovery and engineering of novel enzymes are necessary to increase the scope of target compounds that can be covered by the rapidly developing fields of genetic engineering, synthetic biology, and metabolic engineering. − Existing enzymes may be capable of reacting with newly characterized substrates to synthesize new products in addition to known natural reactions. Furthermore, novel enzymes can be harnessed to catalyze previously unknown reactions.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Machine Learning Prediction of Extensive Enzymatic Reactions

et al. 2022

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New enzyme functions exist within the increasing number of unannotated protein sequences. Novel enzyme discovery is necessary to expand the pathways that can be accessed by metabolic engineering for the biosynthesis of functional compounds. Accordingly, various machine learning models have been developed to predict enzymatic reactions. However, the ability to predict unknown reactions that are not included in the training data has not been clarified. In order to cover uncertain and unknown reactions, a wider range of reaction types must be demonstrated by the models. Here, we establish 16 expanded enzymatic reaction prediction models developed using various machine learning algorithms, including deep neural network. Improvements in prediction performances over that of our previous study indicate that the updated methods are more effective for the prediction of enzymatic reactions. Overall, the deep neural network model trained with combined substrate−enzyme−product information exhibits the highest prediction accuracy with Macro F 1 scores up to 0.966 and with robust prediction of unknown enzymatic reactions that are not included in the training data. This model can predict more extensive enzymatic reactions in comparison to previously reported models. This study will facilitate the discovery of new enzymes for the production of useful substances.

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Enzyme engineering and its industrial applications

Cited by 63 publications

References 117 publications

Mutations Increasing Cofactor Affinity, Improve Stability and Activity of a Baeyer–Villiger Monooxygenase

Mutations Increasing Cofactor Affinity, Improve Stability and Activity of a Baeyer–Villiger Monooxygenase

Exogenous Enzymes as Zootechnical Additives in Animal Feed: A Review

Comprehensive Machine Learning Prediction of Extensive Enzymatic Reactions

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