Chemical modifications by ionic liquid-inspired cations improve the activity and the stability of formate dehydrogenase in [MMIm][Me2PO4]

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.

Applications of Ionic Liquids in Whole-Cell and Isolated Enzyme Biocatalysis

Ionic liquids have unique chemical properties that have fascinated scientists in many fields. The effects of adding ionic liquids to biocatalysts are many and varied. The uses of ionic liquids in biocatalysis include improved separations and phase behaviour, reduction in toxicity, and stabilization of protein structures. As the ionic liquid state of the art has progressed, concepts of what can be achieved in biocatalysis using ionic liquids have evolved and more beneficial effects have been discovered. In this review ionic liquids for whole-cell and isolated enzyme biocatalysis will be discussed with an emphasis on the latest developments, and a look to the future.

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.

Ionic liquids for regulating biocatalytic process: Achievements and perspectives

Biocatalysis has found enormous applications in sorts of fields as an alternative to chemical catalysis. In the pursue of green and sustainable chemistry, ionic liquids (ILs) have been considered as promising reaction media for biocatalysis, owing to their unique characteristics, such as nonvolatility, inflammability and tunable properties as regards polarity and water miscibility behavior, compared to organic solvents. In recent years, great developments have been achieved in respects to biocatalysis in ILs, especially for preparing various chemicals. This review tends to give illustrative examples with a focus on representative chemicals production by biocatalyst in ILs and elucidate the possible mechanism in such systems. It also discusses how to regulate the catalytic efficiency from several aspects and finally provides an outlook on the opportunities to broaden biocatalysis in ILs.

What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization

Enzyme activity in nonaqueous media (e.g. conventional organic solvents) is typically lower than in water by several orders of magnitude. There is a rising interest of developing new nonaqueous solvent systems that are more "water-like" and more biocompatible. Therefore, we need to learn from the current state of nonaqueous biocatalysis to overcome its bottleneck and provide guidance for new solvent design. This review firstly focuses on the discussion of how organic solvent properties (such as polarity and hydrophobicity) influence the enzyme activity and stability, and how these properties impact the enzyme's conformation and dynamics. While hydrophobic organic solvents usually lead to the maintenance of enzyme activity, solvents carrying functional groups like hydroxys and ethers (including crown ethers and cyclodextrins) can lead to enzyme activation. Ionic liquids (ILs) are designable solvents that can conveniently incorporate these functional groups. Therefore, we systematically survey these ether- and/or hydroxy-functionalized ILs, and find most of them are highly compatible with enzymes leading to high activity and stability. In particular, ILs carrying both ether and tert-alcohol groups are among the most enzyme-activating solvents. Future direction is to learn from enzyme behaviors in both water and nonaqueous media to design biocompatible "water-like" solvents.

Hybrid molecular/enzymatic catalytic cascade for complete electro-oxidation of glycerol using a promiscuous NAD-dependent formate dehydrogenase from Candida boidinii

The formate dehydrogenase from Candida boidinii was combined with NH₂-TEMPO to form a novel hybrid anode to oxidize glycerol to carbon dioxide at near-neutral pH.

A bioinspired ionic liquid tagged cobalt-salophen complex for nonenzymatic detection of glucose

The development of efficient and cost effective nonenzymatic biosensors with remarkable sensitivity, selectivity and stability for the detection of biomolecules, especially glucose is one of the major challenges in materials- and electrochemistry. Herein, we report the design and preparation of nonenzymatic biosensor based on an ionic liquid tagged cobalt-salophen metal complex (Co-salophen-IL) immobilized on electrochemically reduced graphene oxide (ERGO) for the detection of glucose via an electrochemical oxidation. The bioinspired Co-salophen-IL complex has been synthesized and immobilized on ERGO, which was previously deposited on a screen printed carbon electrode (SPE) to form the Co-salophen-IL/ERGO/SPE nonenzymatic biosensor. The electrochemical behaviour of this modified electrode was studied using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Notably, the Co-salophen-IL/ERGO/SPE biosensor exhibited excellent electrocatalytic activity towards glucose oxidation in 0.1M NaOH, based on which an amperometric sensor has been developed. The modified electrode has shown prominent performance towards glucose detection over a wide linear range from 0.2µM to 1.8mM with a detection limit and sensitivity of 0.79µM and 62µAmM^-1 respectively. The detection was carried out at 0.40V and such a less working potential excludes the interference from the coexisting oxidizable analytes. The role of Co-salophen, IL and ERGO in the electrocatalytic activity has been systematically investigated. Furthermore, the biosensor demonstrated high stability with good reproducibility.

Elimination of a Free Cysteine by Creation of a Disulfide Bond Increases the Activity and Stability of Candida boidinii Formate Dehydrogenase

NAD⁺-dependent formate dehydrogenase (FDH; EC 1.2.1.2) is an industrial enzyme widely used for NADH regeneration. However, enzyme inactivation caused by the oxidation of cysteine residues is a flaw of native FDH. In this study, we relieved the oxidation of the free cysteine of FDH from Candida boidinii (CboFDH) through the construction of disulfide bonds between A10 and C23 as well as I239 and C262. Variants A10C, I239C, and A10C/I239C were obtained by the site-directed mutagenesis and their properties were studied. Results showed that there were no significant changes in the optimum temperature and pH between variants and wild-type CboFDH. However, the stabilities of all variant enzymes were improved. Specifically, the CboFDH variant A10C (A10C_fdh) showed a significant increase in copper ion resistance and acid resistance, a 6.7-fold increase in half-life at 60°C, and a 1.4-fold increase in catalytic efficiency compared with the wild type. Asymmetric synthesis of l-tert-leucine indicated that the process time was reduced by 40% with variant A10C_fdh, which benefited from the increase in catalytic efficiency. Circular dichroism analysis and molecular dynamics simulation indicated that variants that contained disulfide bonds lowered the overall root mean square deviation (RMSD) and consequently increased the protein rigidity without affecting the secondary structure of enzyme. This work is expected to provide a viable strategy to avoid the microbial enzyme inactivation caused by the oxidation of the free cysteine residues and improving their performances.

IMPORTANCE

FDH is widely used for NADH regeneration in dehydrogenase-based synthesis of optically active compounds to decrease the cost of production. This study highlighted a viable strategy that was used to eliminate the oxidation of free cysteine residues of FDH from Candida boidinii by the introduction of disulfide bonds. Using this strategy, we obtained a variant FDH with improved activity and stability. The improvement of activity and stability of FDH is expected to reduce its price and then further to decrease the cost of its application.

Protein Stabilization and Enzyme Activation in Ionic Liquids: Specific Ion Effects

There are still debates on whether the hydration of ions perturbs the water structure, and what is the degree of such disturbance; therefore, the origin of Hofmeister effect on protein stabilization continues being questioned. For this reason, it is suggested to use the 'specific ion effect' instead of other misleading terms such as Hofmeister effect, Hofmeister series, lyotropic effect, and lyotropic series. In this review, we firstly discuss the controversial aspect of inorganic ion effects on water structures, and several possible contributors to the specific ion effect of protein stability. Due to recent overwhelming attraction of ionic liquids (ILs) as benign solvents in many enzymatic reactions, we further evaluate the structural properties and molecular-level interactions in neat ILs and their aqueous solutions. Next, we systematically compare the specific ion effects of ILs on enzyme stability and activity, and conclude that (a) the specificity of many enzymatic systems in diluted aqueous IL solutions is roughly in line with the traditional Hofmeister series albeit some exceptions; (b) however, the specificity follows a different track in concentrated or neat ILs because other factors (such as hydrogen-bond basicity, nucelophilicity, and hydrophobicity, etc) are playing leading roles. In addition, we demonstrate some examples of biocatalytic reactions in IL systems that are guided by the empirical specificity rule.

Peroxide detected in imidazolium-based ionic liquids and approaches for reducing its presence in aqueous and non-aqueous environments

Peroxide species appearing in imidazolium-based ionic liquids could be removed by salen–manganese complexes or the enzyme catalase.

Directed evolution of a formate dehydrogenase for increased tolerance to ionic liquids reveals a new site for increasing the stability

The formate dehydrogenase (FDH) from Candida boidinii is a well-known enzyme in biocatalysis for NADH regeneration. Nevertheless, it has low activity in a water-miscible ionic liquid (1,3-dimethylimidazolium dimethyl phosphate, [MMIm][Me2 PO4 ]). In this work, this enzyme was subjected to directed evolution by using error-prone PCR, and a mutant (N187S/T321S) displaying higher activity was obtained following selection based on the formazan-based colorimetric assay. The mutation N187S is responsible for improved activity both in aqueous solution and in [MMIm][Me2 PO4 ], through an enhancement of the kcat value by a factor of 5.8. Fluorescence experiments performed in the presence of a quenching agent revealed that the mutant does not unfold in the presence of 50 % (v/v) [MMIm][Me2 PO4 ] whereas the wild-type enzyme does. Molecular modelling revealed that the mutation is located at the monomer-monomer interface and causes an increase in the pKa of residue E163 from 4.8 to 5.5. Calculation of the pKa of this residue in other microbial FDHs showed that thermostable FDHs have a highly basic glutamate at this position (pKa up to 6.2). We have identified a new site for improving FDH thermostability and tolerance to ionic liquids, and it is linked to the local charge of the enzymes in this class.

Ether- and alcohol-functionalized task-specific ionic liquids: attractive properties and applications

In recent years, the designer nature of ionic liquids (ILs) has driven their exploration and exploitation in countless fields among the physical and chemical sciences. A fair measure of the tremendous attention placed on these fluids has been attributed to their inherent designer nature. And yet, there are relatively few examples of reviews that emphasize this vital aspect in an exhaustive or meaningful way. In this critical review, we systematically survey the physicochemical properties of the collective library of ether- and alcohol-functionalized ILs, highlighting the impact of ionic structure on features such as viscosity, phase behavior/transitions, density, thermostability, electrochemical properties, and polarity (e.g. hydrophilicity, hydrogen bonding capability). In the latter portions of this review, we emphasize the attractive applications of these functionalized ILs across a range of disciplines, including their use as electrolytes or functional fluids for electrochemistry, extractions, biphasic systems, gas separations, carbon capture, carbohydrate dissolution (particularly, the (ligno)celluloses), polymer chemistry, antimicrobial and antielectrostatic agents, organic synthesis, biomolecular stabilization and activation, and nanoscience. Finally, this review discusses anion-functionalized ILs, including sulfur- and oxygen-functionalized analogs, as well as choline-based deep eutectic solvents (DESs), an emerging class of fluids which can be sensibly categorized as semi-molecular cousins to the IL. Finally, the toxicity and biodegradability of ether- and alcohol-functionalized ILs are discussed and cautiously evaluated in light of recent reports. By carefully summarizing literature examples on the properties and applications of oxy-functional designer ILs up till now, it is our intent that this review offers a barometer for gauging future advances in the field as well as a trigger to spur further contemplation of these seemingly inexhaustible and--relative to their potential--virtually untouched fluids. It is abundantly clear that these remarkable fluidic materials are here to stay, just as certain design rules are slowly beginning to emerge. However, in fairness, serendipity also still plays an undeniable role, highlighting the need for both expanded in silico studies and a beacon to attract bright, young researchers to the field (406 references).