Rationalization of stereoselectivity in enzyme reactions

A Practical Guide to Computational Tools for Engineering Biocatalytic Properties

The growing demand for efficient, selective, and stable enzymes has fueled advancements in computational enzyme engineering, a field that complements experimental methods to accelerate enzyme discovery. With a plethora of software and tools available, researchers from different disciplines often face challenges in selecting the most suitable method that meets their requirements and available starting data. This review categorizes the computational tools available for enzyme engineering based on their capacity to enhance the following specific biocatalytic properties of biotechnological interest: (i) protein-ligand affinity/selectivity, (ii) catalytic efficiency, (iii) thermostability, and (iv) solubility for recombinant enzyme production. By aligning tools with their respective scoring functions, we aim to guide researchers, particularly those new to computational methods, in selecting the appropriate software for the design of protein engineering campaigns. De novo enzyme design, involving the creation of novel proteins, is beyond this review's scope. Instead, we focus on practical strategies for fine-tuning enzymatic performance within an established reference framework of natural proteins.

Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

To unravel why computational design fails in creating viable enzymes, while directed evolution (DE) succeeds, our research delves into the laboratory evolution of protoglobin. DE has adapted this protein to efficiently catalyze carbene transfer reactions. We show that the previously proposed enhanced substrate access and binding alone cannot account for increased yields during DE. The 3D electric field in the entire active site is tracked through protein dynamics, clustered using the affinity propagation algorithm, and subjected to principal component analysis. This analysis reveals notable changes in the electric field with DE, where distinct field topologies influence transition state energetics and mechanism. A chemically meaningful field component emerges and takes the lead during DE and facilitates crossing the barrier to carbene transfer. Our findings underscore intrinsic electric field dynamic's influence on enzyme function, the ability of the field to switch mechanisms within the same protein, and the crucial role of the field in enzyme design.

Peptide hydrogels: Synthesis, properties, and applications in food science

Due to the unique and excellent biological, physical, and chemical properties of peptide hydrogels, their application in the biomedical field is extremely wide. The applications of peptide hydrogels are closely related to their unique responsiveness and excellent properties. However, its defects in mechanical properties, stability, and toxicity limit its application in the food field. In this review, we focus on the fabrication methods of peptide hydrogels through the physical, chemical, and biological stimulations. In addition, the functional design of peptide hydrogels by the incorporation with materials is discussed. Meanwhile, the excellent properties of peptide hydrogels such as the stimulus responsiveness, biocompatibility, antimicrobial properties, rheology, and stability are reviewed. Finally, the application of peptide hydrogel in the food field is summarized and prospected.

Computer-aided understanding and engineering of enzymatic selectivity

Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.