Current methods and applications in computational protein design for food industry

Comprehensive Understanding of Laboratory Evolution for Food Enzymes: From Design to Screening Innovations

In the field of food processing, enzymes play a pivotal role in improving product quality and flavor, and extending shelf life. However, the exposure of traditional food enzymes to high temperatures during processing often leads to a decrease in activity or even inactivation, limiting the effectiveness of their application under high-temperature conditions. Therefore, the modification of thermostability and activity of enzymes to adapt to extreme conditions through protein engineering has become a key way to improve the efficiency and economic benefits of industrial production. Directed evolution and semirational design strategies in the laboratory have proven to be broadly applicable frameworks for biochemical researchers in the food field, including those who are beginners. In this review, we systematically summarize semirational design strategies and high-throughput screening strategies, and introduce some intuitive computer simulation software to improve the thermostability and enzyme activity of food enzymes. The application of these strategies and techniques provides a comprehensive guide for the optimization of food enzymes. In addition, the latest hot topics of genetically engineered food enzymes in the field of application are discussed.

Computational Chemistry Strategies to Investigate the Antioxidant Activity of Flavonoids-An Overview

Despite several decades of research, the beneficial effect of flavonoids on health is still enigmatic. Here, we focus on the antioxidant effect of flavonoids, which is elementary to their biological activity. A relatively new strategy for obtaining a more accurate understanding of this effect is to leverage computational chemistry. This review systematically presents various computational chemistry indicators employed over the past five years to investigate the antioxidant activity of flavonoids. We categorize these strategies into five aspects: electronic structure analysis, thermodynamic analysis, kinetic analysis, interaction analysis, and bioavailability analysis. The principles, characteristics, and limitations of these methods are discussed, along with current trends.

Recent advances in biosynthesis of mycotoxin-degrading enzymes and their applications in food and feed

Mycotoxins are secondary metabolites produced by fungi in food and feed, which can cause serious health problems. Bioenzymatic degradation is gaining increasing popularity due to its high specificity, gentle degradation conditions, and environmental friendliness. We reviewed recently reported biosynthetic mycotoxin-degrading enzymes, traditional and novel expression systems, enzyme optimization strategies, food and feed applications, safety evaluation of both degrading enzymes and degradation products, and commercialization potentials. Special emphasis is given to the novel expression systems, advanced optimization strategies, and safety considerations for industrial use. Over ten types of recombinases such as oxidoreductase and hydrolase have been studied in the enzymatic hydrolysis of mycotoxins. Besides traditional expression system of Escherichia coli and yeasts, these enzymes can also be expressed in novel systems such as Bacillus subtilis and lactic acid bacteria. To meet the requirements of industrial applications in terms of degradation efficacy and stability, genetic engineering and computational tools are used to optimize enzymatic expression. Currently, registration and technical difficulties have restricted commercial application of mycotoxin-degrading enzymes. To overcome these obstacles, systematic safety evaluation of both biosynthetic enzymes and their degradation products, in-depth understanding of degradation mechanisms and a comprehensive evaluation of their impact on food and feed quality are urgently needed.

Hot spot-based engineering of ketopantoate hydroxymethyltransferase for the improvement of D-pantothenic acid production in Escherichia coli

D-Pantothenic acid (D-PA) is an essential vitamin with wide applications. However, the biotechnological production of D-PA is still not competitive with the chemical synthesis in terms of production cost. Ketopantoate hydroxymethyltransferase is a crucial enzyme in the D-PA synthetic pathway in Escherichia coli encoded by the panB gene. Here a hot spots study was applied to a ketopantoate hydroxymethyltransferase from Corynebacterium glutamicum (CgKPHMT) to relieve the product inhibitory effect and thus improve the D-PA production. Compared with the wild type, the double-site variant CgKPHMT-K25A/E189S showed 1.8 times higher enzyme activity and 2.1 times higher catalytic efficiency, 1.88 and 3.32 times higher inhibitory constant of α-ketoisovalerate and D-PA, respectively. The D-PA yield using E. coli W3110 adopted the double-site variant was 41.17 g·L^-1 within 48 h, a 9.80 g·L^-1 increase. Structural analysis of K25A/E189S revealed the expansion of the entry channel and the change of the electric charge from negative to uncharged due to the substitution from glutamic acid to serine at site 189. Our study emphasized the positive roles of ketopantoate hydroxymethyltransferase in D-PA production and paved the way by analyzing critical enzymes in the synthetic pathway of E. coli to increase the D-PA yield.

Computational Methods for the Interaction between Cyclodextrins and Natural Compounds: Technology, Benefits, Limitations, and Trends

Cyclodextrins (CDs) have a hollow structure with a hydrophobic interior and hydrophilic exterior. Forming inclusion complexes with CDs will maximize the bioavailability of natural compounds and enable active components to be processed into functional foods, medicines, additives, and so forth. However, experimental methods cannot explain CD-guest binding at the atomic level. Different models have been recently developed to simulate the interaction between CDs and guests to study the binding conformation and analyze noncovalent forces. This review paper summarizes modeling methods of CD-natural compound complexes. The methods include quantitative structure-activity relationships, molecular docking, molecular dynamics simulations, and quantum-chemical calculations. The applications of these methods to enhance the solubility and bioactivities of guest molecules, assist material transportation, and promote compound extraction are also discussed. The purpose of this review is to explore interaction mechanisms of CDs and guests and to help expand new applications of CDs.

Overview of strategies for developing high thermostability industrial enzymes: Discovery, mechanism, modification and challenges

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.

Cold plasma: An emerging pretreatment technology for the drying of jujube slices

Jujube slices were pretreated by cold plasma for 15, 30, and 60 s on each side, followed by hot air drying at 50, 60, and 70 °C. Scanning electron microscopy investigation indicated that the application of cold plasma significantly changed the surface topography of jujube slice by etching larger cavities, which can facilitate moisture transfer and consequently enhance drying rate and effective diffusivity. Modified Henderson & Pabis model and Two-term model were the two most recommended models for describing the drying kinetics of jujube slices. Cold plasma pretreatment improved the contents of procyanidins, flavonoids, and phenolics by 53.81%, 33.89%, and 13.85% at most, respectively, and thereby enhanced antioxidant capacity by 36.85% at most. Besides, cold plasma pretreatment can reduce the production of 5-hydroxymethylfurfural by 52.19% at most. In summary, cold plasma can be used as a promising pretreatment tool for drying processes of jujube slices.

One Pot Use of Combilipases for Full Modification of Oils and Fats: Multifunctional and Heterogeneous Substrates

Lipases are among the most utilized enzymes in biocatalysis. In many instances, the main reason for their use is their high specificity or selectivity. However, when full modification of a multifunctional and heterogeneous substrate is pursued, enzyme selectivity and specificity become a problem. This is the case of hydrolysis of oils and fats to produce free fatty acids or their alcoholysis to produce biodiesel, which can be considered cascade reactions. In these cases, to the original heterogeneity of the substrate, the presence of intermediate products, such as diglycerides or monoglycerides, can be an additional drawback. Using these heterogeneous substrates, enzyme specificity can promote that some substrates (initial substrates or intermediate products) may not be recognized as such (in the worst case scenario they may be acting as inhibitors) by the enzyme, causing yields and reaction rates to drop. To solve this situation, a mixture of lipases with different specificity, selectivity and differently affected by the reaction conditions can offer much better results than the use of a single lipase exhibiting a very high initial activity or even the best global reaction course. This mixture of lipases from different sources has been called “combilipases” and is becoming increasingly popular. They include the use of liquid lipase formulations or immobilized lipases. In some instances, the lipases have been coimmobilized. Some discussion is offered regarding the problems that this coimmobilization may give rise to, and some strategies to solve some of these problems are proposed. The use of combilipases in the future may be extended to other processes and enzymes.