Immobilization of lipases on hydrophobic supports: immobilization mechanism,advantages, problems,and solutions

Lipases are the most widely used enzymes in biocatalysis, and the most utilized method for enzyme immobilization is using hydrophobic supports at low ionic strength. This method allows the one step immobilization, purification, stabilization, and hyperactivation of lipases, and that is the main cause of their popularity. This review focuses on these lipase immobilization supports. First, the advantages of these supports for lipase immobilization will be presented and the likeliest immobilization mechanism (interfacial activation on the support surface) will be revised. Then, its main shortcoming will be discussed: enzyme desorption under certain conditions (such as high temperature, presence of cosolvents or detergent molecules). Methods to overcome this problem include physical or chemical crosslinking of the immobilized enzyme molecules or using heterofunctional supports. Thus, supports containing hydrophobic acyl chain plus epoxy, glutaraldehyde, ionic, vinylsulfone or glyoxyl groups have been designed. This prevents enzyme desorption and improved enzyme stability, but it may have some limitations, that will be discussed and some additional solutions will be proposed (e.g., chemical amination of the enzyme to have a full covalent enzyme-support reaction). These immobilized lipases may be subject to unfolding and refolding strategies to reactivate inactivated enzymes. Finally, these biocatalysts have been used in new strategies for enzyme coimmobilization, where the most stable enzyme could be reutilized after desorption of the least stable one after its inactivation.     

Effects of charged water-soluble polymers on the stability and activity of yeast alcohol dehydrogenase and subtilisin Carlsberg.

Remarkable increases in enzyme catalytic stability resulting from addition of charged water-soluble polymers have recently been reported, suggesting that use of these polymers may be an attractive general strategy for enzyme stabilization. To test the proposed hypothesis that coulombic forces between water-soluble polymers and enzymes are primarily responsible for enzyme stabilization, we examined the catalytic stability and activity of two enzymes in the presence of polymers differing in net charge. All polymers tested increased enzyme lifetimes, regardless of their net charge, suggesting that stabilization of these enzymes by water-soluble polymers is not solely dependent on simple electrostatic interactions between the polymers and enzymes.     

Stabilization of multimeric enzymes: Strategies to prevent subunit dissociation

The moderate stability of enzymes is one of the main drawbacks that hinder general implementation of these interesting biocatalysts at industrial scale. An especially complex problem is the stabilization of multimeric proteins, where dissociation of the subunits produces enzyme inactivation and even product contamination. In this review, different strategies to stabilize multimeric enzymes at different levels are revised. First, the use of proper experimental conditions may facilitate the handling of the enzymes (ions, polymers, etc.). Second, genetic tools may be used to crosslink (via disulfide bonds) or just to reinforce the subunit–subunit interactions. The physical or chemical crosslinking of the enzyme subunits will be also discussed. Finally, the use of immobilization strategies (with or without pre-existing supports) will be discussed. Special emphasis will be put on the new immobilization strategies specifically designed to involve the maximum amount of enzyme subunits in the immobilization (and thus, in the further multipoint covalent attachment).     

Life as aerobes: are there simple rules for activation of dioxygen by enzymes?

Numerous biological systems involve reaction with dioxygen in the absence of readily accessible spectroscopic signals. We have begun to develop a set of "generic" strategies that will allow us to probe the mechanisms of dioxygen activation. In particular, we wish to understand the nature of the dioxygen binding step, the degree to which electron transfer to dioxygen is rate limiting, whether reactive species accumulate during turnover and, finally, whether proton and electron transfer to dioxygen occur as coupled processes. Our strategy will be introduced for an enzyme system that uses only an organic cofactor in dioxygen activation (glucose oxidase). Two key features emerge from studies of glucose oxidase: (1) that formation of the superoxide anion is a major rate-limiting step and (2) that electrostatic stabilization of the superoxide anion plays a key role in catalysis. Similar themes emerge when our protocols are applied to enzymes containing both an active site metal center and an organic cofactor. Finally, enzymes that rely solely on metal centers for substrate functionalization will be discussed. In no instance, thus far, has evidence been found for a direct coupling of proton to electron transfer in the reductive activation of dioxygen.     

Enzyme stability in downstream processing. Part 1: enzyme inactivation, stability and stabilization

In biotechnological recovery processes the instability of the product can lead to large losses in the sequence of recovery processes needed to purify the product. As the cost of the final active product is strongly dependent on the recovery yield, this will lead to an increase in product cost. Therefore knowledge of factors that influence stability is important. This Part 1 contains a review on the factors that influence stability. As stability is very important in enzyme purification this review deals about enzymes and their ability to retain catalytic activity. Inactivation mechanisms and agents are discussed. A short review is given of enzyme structure and stability. This is followed by stabilization strategies and methods.     

Effect of evolution on the kinetic properties of enzymes

1. The likely effect of a selective pressure in the direction of higher reaction fluxes on rate parameters for enzyme reactions confirming to Michaelis-Menten kinetics has been analyzed on the basis of relationships which take into account the changes in metabolite concentrations that must be associated with mutational changes of the kinetic properties of enzymes participating in metabolic pathways. 2. Arguments are presented to show that such a pressure should tend to increase kcat, whereas Km may decrease or increase depending on what stage of evolutionary development the enzyme has reached. While the early evolution of enzymes must have been associated with decreasing Km values, an increase of both kcat and Km is mandatory for enhancement of the rate performance of extensively developed enzymes which exhibit kcat/Km ratios approaching the diffusion-control limit. The latter limit is dependent on the equilibrium constant for the catalysed reaction. 3. Enzymes which have reached the diffusion-control limit for their second-order rate performance cannot be considered as perfectly evolved catalysts, but may well undergo further development towards a higher catalytic efficiency in response to the improvement of other enzymes in the metabolic pathway with regard to the criterion of an enhanced reaction flux. Such evolution is associated with an increase of the metabolite levels in the pathway, and a simple model system is examined in order to illustrate the ultimate limits for the metabolite levels and reaction flux that may obtain. 4. The theoretical evidence presented lends no support to previous proposals that certain enzymes (e.g. triosephosphate isomerase), or enzymes showing certain kinetic characteristics (e.g. kcat/Km quotients approaching 10(9) s-1 M-1), have reached the end of their evolutionary development. A claim that any specific enzyme has reached catalytic perfection would provide the unreasonable inference that all enzymes participating in intermediary metabolism have reached catalytic perfection.     

Functionally-stabilized proteins--a review

The maintenance or stabilization of protein or enzyme function is of vital importance in Biotechnology. Investigations of thermophilic organisms, studies of denaturation and the use of enzymes in organic solvents have each contributed to an understanding of protein stability. Enzymes can reliably and reproducibly be stabilized by variety of means including immobilization, use of additives, chemical modification in solution and protein engineering. Examples of each of these are discussed. With these recent advances it appears that a rational strategy for achieving a particular stabilized enzyme or protein may be within reach.     

Mechanisms of enzyme action and inhibition: Transition state analogues for acid-base catalysis

The theory of absolute reaction rates implies that the grip of a catalyst on a substrate tightens with substrate activation, relaxing later as products are formed and released. Analogs that mimic different kinds of substrate activation can, through the structural details of their complexes with enzymes, indicate how active site residues are involved in the enhancement of reactions rates. In several cases, bonds involved in general acid-base catalysis have been identified tentatively; and recent evidence points to a hydrogen bond of remarkable stability in the transition state in enzymatic deamination of adenosine. Similar approaches have been used to enzymes that act primarily by substrate distortion, nucleophilic catalysis, solvent removal and catalysis by approximation. Two recurring observations, that were not expected in theory, have been the binding of inhibitors in ionized forms that are rare in solution, and changes in enzyme configuration that accompany binding of transition state analogs. Origins and implications of these findings will be discussed with specific reference to the role of solvent water in catalytic phenomena.Supported by Grant GM-18325 from the National Institutes of Health.     

Brought to life: targeted activation of enzyme function with small molecules

Cell-permeable small molecules that are capable of activating particular enzymes would be invaluable tools for studying protein function in complex cell-signaling cascades. But, is it feasible to identify compounds that allow chemical–biology researchers to activate specific enzymes in a cellular context? In this review, we describe some recent advances in achieving targeted enzyme activation with small molecules. In addition to surveying progress in the identification and targeting of enzymes that contain natural allosteric-activation sites, we focus on recently developed protein-engineering strategies that allow researchers to render an enzyme of interest “activatable” by a pre-chosen compound. Three distinct strategies for targeting an engineered enzyme are discussed: direct chemical “rescue” of an intentionally inactivated enzyme, activation of an enzyme by targeting a de novo small-molecule-binding site, and the generation of activatable enzymes via fusion of target enzymes to previously characterized small-molecule-binding domains.     

Pressure Stabilization of Proteins from Extreme Thermophiles

We describe the stabilization by pressure of enzymes, including a hydrogenase from Methanococcus jannaschii, an extremely thermophilic deep-sea methanogen. This is the first published report of proteins from thermophiles being stabilized by pressure. Inactivation studies of partially purified hydrogenases from an extreme thermophile (Methanococcus igneus), a moderate thermophile (Methanococcus thermolithotrophicus), and a mesophile (Methanococcus maripaludis), all from shallow marine sites, show that pressure stabilization is not unique to enzymes isolated from high-pressure environments. These studies suggest that pressure stabilization of an enzyme may be related to its thermophilicity. Further experiments comparing the effects of increased pressure on the stability of α-glucosidases from the hyperthermophile Pyrococcus furiosus and Saccharomyces cerevisiae support this possibility. We have also examined pressure effects on several highly homologous glyceraldehyde-3-phosphate dehydrogenases from mesophilic and thermophilic sources and a rubredoxin from P. furiosus. The results suggest that hydrophobic interactions, which have been implicated in the stabilization of many thermophilic proteins, contribute to the pressure stabilization of enzymes from thermophiles.     

Application of magnetic nanoparticles in smart enzyme immobilization

Immobilization of enzymes enhances their properties for efficient utilization in industrial processes. Magnetic nanoparticles, due to their high surface area, large surface-to-volume ratio and easy separation under external magnetic fields, are highly valued. Significant progress has been made to develop new catalytic systems that are immobilized onto magnetic nanocarriers. This review provides an overview of recent developments in enzyme immobilization and stabilization protocols using this technology. The current applications of immobilized enzymes based on magnetic nanoparticles are summarized and future growth prospects are discussed. Recommendations are also given for areas of future research.     

Rational engineering of enzyme stability

During the past 15 years there has been a continuous flow of reports describing proteins stabilized by the introduction of mutations. These reports span a period from pioneering rational design work on small enzymes such as T4 lysozyme and barnase to protein design, and directed evolution. Concomitantly, the purification and characterization of naturally occurring hyperstable proteins has added to our understanding of protein stability. Along the way, many strategies for rational protein stabilization have been proposed, some of which (e.g. entropic stabilization by introduction of prolines or disulfide bridges) have reasonable success rates. On the other hand, comparative studies and efforts in directed evolution have revealed that there are many mutational strategies that lead to high stability, some of which are not easy to define and rationalize. Recent developments in the field include increasing awareness of the importance of the protein surface for stability, as well as the notion that normally a very limited number of mutations can yield a large increase in stability. Another development concerns the notion that there is a fundamental difference between the "laboratory stability" of small pure proteins that unfold reversibly and completely at high temperatures and "industrial stability", which is usually governed by partial unfolding processes followed by some kind of irreversible inactivation process (e.g. aggregation). Provided that one has sufficient knowledge of the mechanism of thermal inactivation, successful and efficient rational stabilization of enzymes can be achieved.     

The state-of-the-art strategies of protein engineering for enzyme stabilization

Enzymes generated by natural recruitment and protein engineering have greatly contribute in various sets of applications. However, their insufficient stability is a bottleneck that limit the rapid development of biocatalysis. Novel approaches based on precise and global structural dissection, advanced gene manipulation, and combination with the multidisciplinary techniques open a new horizon to generate stable enzymes efficiently. Here, we comprehensively introduced emerging advances of protein engineering strategies for enzyme stabilization. Then, we highlighted practical cases to show importance of enzyme stabilization in pharmaceutical and industrial applications. Combining computational enzyme design with molecular evolution will hold considerable promise in this field.     

结构修饰提高酶稳定性、活性

酶因其特异性和可持续性而成为广泛应用的绿色催化剂，其稳定性和催化活性是决定酶适用性的关键因素。为满足实际应用需求，通过蛋白质结构修饰赋予其所需的催化特性是当前的研究热点。提高热稳定性的策略有：引入非共价/共价相互作用（疏水相互作用、氢键、盐桥、芳香环相互作用、二硫键）、环截短、C端和N端工程，及增加脯氨酸/减少甘氨酸的数目等；获得具有高效性和多样性的生物催化剂的策略有：降低空间位阻、拓宽催化口袋、增加底物亲和力及调节活性位点灵活性等。然而，在稳定性或催化功能改造的过程中，新突变的引入会削弱其他功能，致使进化过程中稳定性和催化活性相互制约。因此，采用基于理性计算优选突变热点、基于多重蛋白质稳定性或活性改造策略的共进化，以及基于高度稳定的蛋白质骨架创造或/和优化蛋白质功能等多种策略克服酶稳定性-活性之间的权衡。本综述重点阐述了结构修饰方法在提高酶稳定性或/和催化活性方面的应用，并展望了该领域的未来发展前景。     

Engineering enzyme access tunnels

Enzymes are efficient and specific catalysts for many essential reactions in biotechnological and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic efficiency, stability or specificity required for these industrial processes. The current enzyme engineering methods offer solutions to this problem, but they mainly target the buried active site where the chemical reaction takes place. Despite being many times ignored, the tunnels and channels connecting the environment with the active site are equally important for the catalytic properties of enzymes. Changes in the enzymatic tunnels and channels affect enzyme activity, specificity, promiscuity, enantioselectivity and stability. This review provides an overview of the emerging field of enzyme access tunnel engineering with case studies describing design of all the aforementioned properties. The software tools for the analysis of geometry and function of the enzymatic tunnels and channels and for the rational design of tunnel modifications will also be discussed. The combination of new software tools and enzyme engineering strategies will provide enzymes with access tunnels and channels specifically tailored for individual industrial processes.     

Strategy for Stabilizing Enzymes Part Two: Increasing Enzyme Stability by Selective Chemical Modification

The molecular mechanisms of change in the thermal stability of proteins modified with low molecular weight reagents are discussed. The choice of stabilization mechanisms to be used as a general strategy for increasing enzyme stability by chemical modification is addressed. Hydrophilization of nonpolar surface areas is the most simple and reliable approach to artificial stabilization of enzymes for use in applied biochemistry and biotechnology.     

Cold adaptation of enzyme reaction rates

A major issue for organisms living at extreme temperatures is to preserve both stability and activity of their enzymes. Cold-adapted enzymes generally have a reduced thermal stability, to counteract freezing, and show a lower enthalpy and a more negative entropy of activation compared to mesophilic and thermophilic homologues. Such a balance of thermodynamic activation parameters can make the reaction rate decrease more linearly, rather than exponentially, as the temperature is lowered, but the structural basis for rate optimization toward low working temperatures remains unclear. In order to computationally address this problem, it is clear that reaction simulations rather than standard molecular dynamics calculations are needed. We have thus carried out extensive computer simulations of the keto-enol(ate) isomerization steps in differently adapted citrate synthases to explore the structure-function relationships behind catalytic rate adaptation to different temperatures. The calculations reproduce the absolute rates of the psychrophilic and mesophilic enzymes at 300 K, as well as the lower enthalpy and more negative entropy of activation of the cold-adapted enzyme, where the latter simulation result is obtained from high-precision Arrhenius plots. The overall catalytic effect originates from electrostatic stabilization of the transition state and enolate and the reduction of reorganization free energy. The simulations, however, show psychrophilic, mesophilic, and hyperthermophilic citrate synthases to have increasingly stronger electrostatic stabilization of the transition state, while the energetic penalty in terms of internal protein interactions follows the reverse order with the cold-adapted enzyme having the most favorable energy term. The lower activation enthalpy and more negative activation entropy observed for cold-adapted enzymes are found to be associated with a decreased protein stiffness. The origin of this effect is, however, not localized to the active site but to other regions of the protein structure.     

A comparative infrared spectroscopic study of glycoside hydrolases from extremophilic archaea revealed different molecular mechanisms of adaptation to high temperatures

The identification of the determinants of protein thermal stabilization is often pursued by comparing enzymes from hyperthermophiles with their mesophilic counterparts while direct structural comparisons among proteins and enzymes from hyperthermophiles are rather uncommon. Here, oligomeric beta-glycosidases from the hyperthermophilic archaea Sulfolobus solfataricus (Ss beta-gly), Thermosphaera aggregans (Ta beta-gly), and Pyrococcus furiosus (Pf beta-gly), have been compared. Studies of FTIR spectroscopy and kinetics of thermal inactivation showed that the three enzymes had similar secondary structure composition, but Ss beta-gly and Ta beta-gly (temperatures of melting 98.1 and 98.4 degrees C, respectively) were less stable than Pf beta-gly, which maintained its secondary structure even at 99.5 degrees C. The thermal denaturation of Pf beta-gly, followed in the presence of SDS, suggested that this enzyme is stabilized by hydrophobic interactions. A detailed inspection of the 3D-structures of these enzymes supported the experimental results: Ss beta-gly and Ta beta-gly are stabilized by a combination of ion-pairs networks and intrasubunit S-S bridges while the increased stability of Pf beta-gly resides in a more compact protein core. The different strategies of protein stabilization give experimental support to recent theories on thermophilic adaptation and suggest that different stabilization strategies could have been adopted among archaea.     

Stabilization of Micrococcal Endonuclease by Immobilization on Agarose Gels Highly Activated with CNBr

The attachment of enzymes, through their amino groups, to CNBr activated agarose gels has been tested as an immobilization stabilization system. By using this system, the development of a strategy to immobilize enzymes through multipoint covalent attachment has been studied. We have prepared different staphylococcal nuclease-Agarose derivatives by using Sepharose 2B gels previously activated with CNBr. Activity and stability of the derivatives obtained were very dependent on the degree of activation of the support. The most stable derivatives, prepared with the most activated supports, were 700 fold more stable than the soluble enzyme in irreversible thermal inactivation experiments, at 40d`C. In contrast, a significant loss of catalytic activity (k_cat decreases down to 40%) was associated with the increase in stability. Colorimetric titration of amine groups in the stabilized derivatives suggested that enzyme-support multipoint attachment was the main reason for the observed stabilizing effect.

Index Entries: micrococcal nuclease immobilization enzyme stabilization enzyme-support multipoint attachment     

Directed evolution of enzyme stability

Modern enzyme development relies to an increasing extent on strategies based on diversity generation followed by screening for variants with optimised properties. In principle, these directed evolution strategies might be used for optimising any enzyme property, which can be screened for in an economically feasible way, even if the molecular basis of that property is not known. Stability is an interesting property of enzymes because (1) it is of great industrial importance, (2) it is relatively easy to screen for, and (3) the molecular basis of stability relates closely to contemporary issues in protein science such as the protein folding problem and protein folding diseases. Thus, engineering enzyme stability is of both commercial and scientific interest. Here, we review how directed evolution has contributed to the development of stable enzymes and to new insight into the principles of protein stability. Several recent examples are described. These examples show that directed evolution is an effective strategy to obtain stable enzymes, especially when used in combination with rational or semi-rational engineering strategies. With respect to the principles of protein stability, some important lessons to learn from recent efforts in directed evolution are (1) that there are many structural ways to stabilize a protein, which are not always easy to rationalize, (2) that proteins may very well be stabilized by optimizing their surfaces, and (3) that high thermal stability may be obtained without forfeiture of catalytic performance at low temperatures.