Controlled Orientation of Active Sites in a Nanostructured Multienzyme Complex

Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis

Biocatalysis has become an important component of modern organic chemistry, presenting an efficient and environmentally friendly approach to synthetic transformations. Advances in molecular biology, computational modeling, and protein engineering have unlocked the full potential of enzymes in various industrial applications. However, the inherent limitations of the natural building blocks have sparked a revolutionary shift. In vivo genetic incorporation of noncanonical amino acids exceeds the conventional 20 amino acids, opening new avenues for innovation. This review provides a comprehensive overview of applications of noncanonical amino acids in biocatalysis. We aim to examine the field from multiple perspectives, ranging from their impact on enzymatic reactions to the creation of novel active sites, and subsequent catalysis of new-to-nature reactions. Finally, we discuss the challenges, limitations, and promising opportunities within this dynamic research domain.

Noncanonical Amino Acids in Biocatalysis

In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.

Translational fusion of terpene synthases for metabolic engineering: Lessons learned and practical considerations

The step catalyzed by terpene synthases is a well-recognized and significant bottleneck in engineered terpenoid bioproduction. Consequently, substantial efforts have been devoted towards increasing metabolic flux catalyzed by terpene synthases, employing strategies such as gene overexpression and protein engineering. Notably, numerous studies have demonstrated remarkable titer improvements by applying translational fusion, typically by fusing the terpene synthase with a prenyl diphosphate synthase that catalyzes the preceding step in the pathway. The main appeal of the translational fusion approach lies in its simplicity and orthogonality to other metabolic engineering tools. However, there is currently limited understanding of the underlying mechanism of flux enhancement, owing to the unpredictable and often protein-specific effects of translational fusion. In this chapter, we discuss practical considerations when engineering translationally fused terpene synthases, drawing insights from our experience and existing literature. We also provide detailed experimental workflows and protocols based on our previous work in budding yeast (Saccharomyces cerevisiae). Our intention is to encourage further research into the translational fusion of terpene synthases, anticipating that this will contribute mechanistic insights not only into the activity, behavior, and regulation of terpene synthases, but also of other enzymes.

Effect of multimodularity and spatial organization of glycoside hydrolases on catalysis

The wide diversity among the carbohydrate-active enzymes (CAZymes) reflects the equally broad versatility in terms of composition and chemicals bonds found in the plant cell wall polymers on which they are active. This diversity is also expressed through the various strategies developed to circumvent the recalcitrance of these substrates to biological degradation. Glycoside hydrolases (GHs) are the most abundant of the CAZymes and are expressed as isolated catalytic modules or in association with carbohydrate-binding module (CBM), acting in synergism within complex arrays of enzymes. This multimodularity can be even more complex. The cellulosome presents a scaffold protein immobilized to the outer membrane of some microorganisms on which enzymes are grafted to prevent their dispersion and increase catalytic synergism. In polysaccharide utilization loci (PUL), GHs are also distributed across the membranes of some bacteria to co-ordinate the deconstruction of polysaccharides and the internalization of metabolizable carbohydrates. Although the study and characterization of these enzymatic activities need to take into account the entirety of this complex organization-in particular because of the dynamics involved in it-technical problems limit the present study to isolated enzymes. However, these enzymatic complexes also have a spatiotemporal organization, whose still neglected aspect must be considered. In the present review, the different levels of multimodularity that can occur in GHs will be reviewed, from its simplest forms to the most complex. In addition, attempts to characterize or study the effect on catalytic activity of the spatial organization within GHs will be addressed.

Chemical modification of enzymes to improve biocatalytic performance

Improvement in intrinsic enzymatic features is in many instances a prerequisite for the scalable applicability of many industrially important biocatalysts. To this end, various strategies of chemical modification of enzymes are maturing and now considered as a distinct way to improve biocatalytic properties. Traditional chemical modification methods utilize reactivities of amine, carboxylic, thiol and other side chains originating from canonical amino acids. On the other hand, noncanonical amino acid- mediated 'click' (bioorthogoal) chemistry and dehydroalanine (Dha)-mediated modifications have emerged as an alternate and promising ways to modify enzymes for functional enhancement. This review discusses the applications of various chemical modification tools that have been directed towards the improvement of functional properties and/or stability of diverse array of biocatalysts.

Regulating the catalytic activity of multi-Ru-bridged polyoxometalates based on differential active site environments with six-coordinate geometry and five-coordinate geometry transitions

Five-coordinate geometry around ruthenium with highly exposed active sites has attracted intensive scientific interest due to its superior properties and extensive applications. Herein, we report a series of structurally controllable multi-Ru-bridged polyoxometalates, K5NaH10[{Ru4(H2O)n}(WO2)4(AsW9O33)4]·mH2O {1, 1-dehyd-373K, 1-dehyd-473K, 1-dehyd-573K; n = 4, m = 36; n = 4, m = 6; n = 4, m = 0; n = 0, m = 0} fabricated through a feasible assembly strategy using arsenotungstate {2, KNa12H17Cl2(As4W40O140)·29H2O} as a structure-directing unit. Systematic characterization methods identified that the six-coordinate geometry can successfully transform into five-coordinate geometry about active sites (Ru) by removing aqua ligands under high reaction temperatures. All the multi-Ru-bridged polyoxometalates demonstrated strong stability and catalytic effectiveness in the transformation of 1-(4-chlorophenyl)ethanol to 4'-chloroacetophenone under very mild conditions. 1-dehyd-573K, specifically, achieves the best catalytic effectiveness with a turnover frequency (TOF) = 25 100·h-1 owing to its unique five-coordinate geometry on the Ru sites. To our knowledge, 1-dehyd-573K outperforms other POM-based catalysts in the oxidative catalysis of 1-(4-chlorophenyl)ethanol. The heterogeneous polyoxometalates were also proven to be strongly reusable, with their structural integrities well maintained after multiple-cycle catalytic reactions.

Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet

The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.

Nature Inspired Multienzyme Immobilization: Strategies and Concepts

In a biological system, the spatiotemporal arrangement of enzymes in a dense cellular milieu, subcellular compartments, membrane-associated enzyme complexes on cell surfaces, scaffold-organized proteins, protein clusters, and modular enzymes have presented many paradigms for possible multienzyme immobilization designs that were adapted artificially. In metabolic channeling, the catalytic sites of participating enzymes are close enough to channelize the transient compound, creating a high local concentration of the metabolite and minimizing the interference of a competing pathway for the same precursor. Over the years, these phenomena had motivated researchers to make their immobilization approach naturally realistic by generating multienzyme fusion, cluster formation via affinity domain-ligand binding, cross-linking, conjugation on/in the biomolecular scaffold of the protein and nucleic acids, and self-assembly of amphiphilic molecules. This review begins with the discussion of substrate channeling strategies and recent empirical efforts to build it synthetically. After that, an elaborate discussion covering prevalent concepts related to the enhancement of immobilized enzymes' catalytic performance is presented. Further, the central part of the review summarizes the progress in nature motivated multienzyme assembly over the past decade. In this section, special attention has been rendered by classifying the nature-inspired strategies into three main categories: (i) multienzyme/domain complex mimic (scaffold-free), (ii) immobilization on the biomolecular scaffold, and (iii) compartmentalization. In particular, a detailed overview is correlated to the natural counterpart with advances made in the field. We have then discussed the beneficial account of coassembly of multienzymes and provided a synopsis of the essential parameters in the rational coimmobilization design.

Investigating the origin of high efficiency in confined multienzyme catalysis

Biomimetic strategies have successfully been applied to confine multiple enzymes on scaffolds to obtain higher catalytic efficiency of enzyme cascades than freely distributed enzymes. However, the origin of high efficiency is poorly understood. We developed a coarse-grained, particle-based model to understand the origin of high efficiency. We found that a reaction intermediate is the key in affecting reaction kinetics. In the case of unstable intermediates, the confinement of multiple enzymes in clusters enhanced the catalytic efficiency and a shorter distance between enzymes resulted in a higher reaction rate and yield. This understanding was verified by co-encapsulating multiple enzymes in metal-organic framework (MOF) nanocrystals as artificially confined multienzyme complexes. The activity enhancement of multiple enzymes in MOFs depended on the distance between enzymes, when the decay of intermediates existed. The finding of this study is useful for designing in vitro synthetic biology systems based on artificial multienzyme complexes.

Enzyme Fusions in Biocatalysis: Coupling Reactions by Pairing Enzymes

One approach to bringing enzymes together for multienzyme biocatalysis is genetic fusion. This enables the production of multifunctional enzymes that can be used for whole-cell biotransformations or for in vitro (cascade) reactions. In some cases and in some aspects, such as expression and conversions, the fused enzymes outperform a combination of the individual enzymes. In contrast, some enzyme fusions are greatly compromised in activity and/or expression. In this Minireview, we give an overview of studies on fusions between two or more enzymes that were used for biocatalytic applications, with a focus on oxidative enzymes. Typically, the enzymes are paired to facilitate cofactor recycling or cosubstrate supply. In addition, different linker designs are briefly discussed. Although enzyme fusion is a promising tool for some biocatalytic applications, future studies could benefit from integrating the findings of previous studies in order to improve reliability and effectiveness.