Salt-activation of nonhydrolase enzymes for use in organic solvents

Exploring Oxidoreductases from Extremophiles for Biosynthesis in a Non-Aqueous System

Organic solvent tolerant oxidoreductases are significant for both scientific research and biomanufacturing. However, it is really challenging to obtain oxidoreductases due to the shortages of natural resources and the difficulty to obtained it via protein modification. This review summarizes the recent advances in gene mining and structure-functional study of oxidoreductases from extremophiles for non-aqueous reaction systems. First, new strategies combining genome mining with bioinformatics provide new insights to the discovery and identification of novel extreme oxidoreductases. Second, analysis from the perspectives of amino acid interaction networks explain the organic solvent tolerant mechanism, which regulate the discrete structure-functional properties of extreme oxidoreductases. Third, further study by conservation and co-evolution analysis of extreme oxidoreductases provides new perspectives and strategies for designing robust enzymes for an organic media reaction system. Furthermore, the challenges and opportunities in designing biocatalysis non-aqueous systems are highlighted.

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.

Reflections on charge state distributions, protein structure, and the mystical mechanism of electrospray ionization

The connection between charge state distributions, protein structure, and mechanistic details of electrospray are discussed in relation to the emerging field of gas phase structural biology. Comparisons are drawn with the established area of enzymatic catalysis in organic solvents, which shares many similar challenges. Charge solvation emerges as a dominant force in both systems that must be dealt with to enable kinetic trapping of native structures in foreign environments. Potential methods for mediating unfavorable charge solvation effects are discussed and, ironically, do not include partial solvation by water. The importance of timescale in relation to the evolution of protein structure during the process of electrospray ionization is discussed. Finally several prospects for future endeavors are highlighted.

Hydrogen/deuterium exchange study of subtilisin Carlsberg during prolonged exposure to organic solvents

It has been previously reported that prolonged exposure of an enzyme to organic solvents leads to substantial decrease of activity. This effect was found to be unrelated to the catalysts' structure or their possible aggregation in organic solvents, and up to the present day the cause for activity loss remains unclear. In the present work, the structural dynamics of the serine protease subtilisin Carlsberg (SC) have been investigated during prolonged exposure to two organic solvents by following hydrogen/deuterium (H/D) exchange of mobile protons. The enzyme, after lyophilization, was incubated in organic solvents at controlled deuteriated water activity for different times and the H/D exchange was allowed to take place. The amount of deuterium exchanged was evaluated by (2)H NMR, which in turn gave us a picture of the changing dynamics of our model enzyme during incubation and under different experimental conditions. Our results show that the flexibility of SC decreases during prolonged storage in 1,4-dioxane (Diox) and acetonitrile (ACN) as indicated by the observed 3- to 10-fold decrease in the apparent rate constants of exchange (k) of fast exchangeable protons (FEP) and slow exchangeable protons (SEP) in the protein. Our study also shows that SC is more flexible in ACN than in Diox (k 3-20 times higher in ACN for the FEP and SEP), suggesting that enzyme dynamics are affected by solvent physicochemical properties. Additionally, the enzyme dynamics are also affected by the method of preparation: decreased flexibility (k decreases 3- to 10-fold for FEP and SEP) is observed when the enzyme is chemically modified with poly ethylene glycol (PEGylated) or colyophilized with crown ethers. A possible relationship between activity, enantioselectivity (E), and structural dynamics is discussed, demonstrating that direct correlations, as have been attempted in the past, are hampered by the multi-variable nature and complexity of the system.

Techno-economic analysis of biocatalytic processes for production of alkene epoxides

A techno-economic analysis of two different bioprocesses was conducted, one for the conversion of propylene to propylene oxide (PO) and other for conversion of styrene to styrene epoxide (SO). The first process was a lipase-mediated chemo-enzymatic reaction, whereas the second one was a one-step enzymatic process using chloroperoxidase. The PO produced through the chemo-enzymatic process is a racemic product, whereas the latter process (based on chloroperoxidase) produces an enantio-pure product. The former process thus falls under the category of high-volume commodity chemical (PO); whereas the latter is a low-volume, high-value product (SO).A simulation of the process was conducted using the bioprocess engineering software SuperPro Designer v6.0 (Intelligen, Inc., Scotch Plains, NJ) to determine the economic feasibility of the process. The purpose of the exercise was to compare biocatalytic processes with existing chemical processes for production of alkene expoxides. The results show that further improvements are needed in improving biocatalyst stability to make these bioprocesses competitive with chemical processes.

Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents

A comprehensive study of the hydration mechanism of an enzyme in nonaqueous media was done using molecular dynamics simulations in five organic solvents with different polarities, namely, hexane, 3-pentanone, diisopropyl ether, ethanol, and acetonitrile. In these solvents, the serine protease cutinase from Fusarium solani pisi was increasingly hydrated with 12 different hydration levels ranging from 5% to 100% (w/w) (weight of water/weight of protein). The ability of organic solvents to 'strip off' water from the enzyme surface was clearly dependent on the nature of the organic solvent. The rmsd of the enzyme from the crystal structure was shown to be lower at specific hydration levels, depending on the organic solvent used. It was also shown that organic solvents determine the structure and dynamics of water at the enzyme surface. Nonpolar solvents enhance the formation of large clusters of water that are tightly bound to the enzyme, whereas water in polar organic solvents is fragmented in small clusters loosely bound to the enzyme surface. Ions seem to play an important role in the stabilization of exposed charged residues, mainly at low hydration levels. A common feature is found for the preferential localization of water molecules at particular regions of the enzyme surface in all organic solvents: water seems to be localized at equivalent regions of the enzyme surface independently of the organic solvent employed.

Horseradish and soybean peroxidases: comparable tools for alternative niches?

Horseradish and soybean peroxidases (HRP and SBP, respectively) are useful biotechnological tools. HRP is often termed the classical plant heme peroxidase and although it has been studied for decades, our understanding has deepened since its cloning and subsequent expression, enabling numerous mutational and protein engineering studies. SBP, however, has been neglected until recently, despite offering a real alternative to HRP: SBP actually outperforms HRP in terms of stability and is now used in numerous biotechnological applications, including biosensors. Review of both is timely. This article summarizes and discusses the main insights into the structure and mechanism of HRP, with special emphasis on HRP mutagenesis, and outlines its use in a variety of applications. It also reviews the current knowledge and applications to date of SBP, particularly biosensors. The final paragraphs speculate on the future of plant heme-based peroxidases, with probable trends outlined and explored.

Protein-coated Microcrystals for use in Organic Solvents: Application to Oxidoreductases

Protein-coated microcrystals (PCMC), a biocatalyst preparation previously demonstrated to display substantially increased transesterification activity of proteases and lipases in organic solvents when compared to their as received counterparts [Kreiner M, Moore BD, Parker MC (2001) Chem. Commun. 12:1096--1097], was applied to oxidoreductases. Horse liver alcohol dehydrogenase (HLADH), catalase (CAT), soybean peroxidase and horseradish peroxidase were immobilised onto K(2)SO(4) crystals and dehydrated in a 1-step process, resulting in PCMC. These PCMC preparations showed enhanced activity in different organic solvents in most types of reactions tested. The highest activation was observed with HLADH (50-fold as active as enzyme as received) and CAT (25-fold).

The use of enzyme mixtures for complex biosyntheses

Biocatalysis is currently employed to produce known substances more economically and for the synthesis of new compounds. Increased production or novel product synthesis can be achieved through the use of mutant organisms, tailored enzymes or novel combinations of enzymes in reactors. These complex biosyntheses, once only in the realm of the biopharmaceutical industry, have now been embraced by the food and textile industries and are finding geochemical and environmental applications. New uses are dictating novel methods of manufacture that utilize knowledge of systems level biology. Increased understanding of the functional interaction of proteins and protein-protein networks is also altering the practice of in vitro biosynthesis.

Enzymes in organic media

Enzyme catalysis in low water containing organic solvents is finding an increasing number of applications in diverse areas. This review focuses on some aspects which have not been reviewed elsewhere. Different strategies for obtaining higher activity and stability in such media are described. In this context, the damaging role of lyophilization and the means of overcoming such effects are discussed. Ultrasonication and microwave assistance are two emerging approaches for enhancing reaction rates in low water media. Control of water activity and medium engineering are two crucial approaches in optimization of catalytic behaviour in nonaqueous enzymology. Organometallics and synthesis/modification of polymers are two areas where nonaqueous enzymology can play a greater role in the coming years. The greater understanding of enzyme behaviour in nonaqueous media is expected to lead to larger and even more diverse kinds of applications.