From directed evolution to computational enzyme engineering—A review

Abstract

Nature relies on a wide range of enzymes with specific biocatalytic roles to carry out much of the chemistry needed to sustain life. Enzymes catalyze the interconversion of a vast array of molecules with high specificity-from molecular nitrogen fixation to the synthesis of highly specialized hormones and quorum-sensing molecules. Ever increasing emphasis on renewable sources for energy and waste minimization has turned enzymes into key industrial workhorses for targeted chemical conversions. Modern enzymology is central to not only food and beverage manufacturing processes but also finds relevance in countless consumer product formulations such as proteolytic enzymes in detergents, amylases for excess bleach removal from textiles, proteases in meat tenderization, and lactoperoxidases in dairy products. Herein, we present an overview of enzyme science and engineering milestones and the emergence of directed evolution of enzymes for which the 2018 Nobel Prize in Chemistry was awarded to Dr. Frances Arnold. K E Y W O R D Sbiocatalysis, computational protein design, directed evolution, enzyme engineering, mutagenesis

Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals

“…Advances in the fields of structural bioinformatics, computational modeling, and the availability of huge amounts of DNA sequence data have led to the development of a variety of computational tools that can speed up enzyme engineering for biotechnological application. Computational enzyme engineering and design methodology has been reviewed recently for altering properties such as stability, substrate specificity, or activity of biocatalysts ( Ebert and Pelletier, 2017 ; Chowdhury and Maranas, 2020 ; Sequeiros-Borja et al, 2020 ). Here, we describe which enzymatic features are important for enzyme engineering and design and how recently published computational tools ( Table 1 ) can facilitate the required steps from preparing the input structure complexes to screening designed variants for best performance.…”

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

“…The genetic improving of enzymes by means of rational (or semirational) design [32][33][34][35][36][37], directed evolution [4,[38][39][40][41][42][43][44][45] or even de novo enzyme design [46][47][48][49] helped with machine-learning technologies [50][51][52][53], a very powerful (although rather complex) approach. The chemical modification of enzymes is also a usual technique to improve enzyme features [54][55][56][57].…”

Artificial Enzymes for Diels‐Alder Reactions

“…[65] This example emphasizes both the power of enzyme computational design and the requirement for catalyst optimization after the initial design. Recent progresses in directed evolution techniques [124][125][126][127] together with the development of more and more accurate computational tools [73] should allow improving the catalytic proficiency and stability of artificial enzymes, and many examples presented in this review should be considered as proof-of-concepts. Figure 20.…”