A new intrinsic thermal parameter for enzymes reveals true temperature optima

Two established thermal properties of enzymes are the Arrhenius activation energy and thermal stability. Arising from anomalies found in the variation of enzyme activity with temperature, a comparison has been made of experimental data for the activity and stability properties of five different enzymes with theoretical models. The results provide evidence for a new and fundamental third thermal parameter of enzymes, T(eq), arising from a subsecond timescale-reversible temperature-dependent equilibrium between the active enzyme and an inactive (or less active) form. Thus, at temperatures above its optimum, the decrease in enzyme activity arising from the temperature-dependent shift in this equilibrium is up to two orders of magnitude greater than what occurs through thermal denaturation. This parameter has important implications for our understanding of the connection between catalytic activity and thermostability and of the effect of temperature on enzyme reactions within the cell. Unlike the Arrhenius activation energy, which is unaffected by the source ("evolved") temperature of the enzyme, and enzyme stability, which is not necessarily related to activity, T(eq) is central to the physiological adaptation of an enzyme to its environmental temperature and links the molecular, physiological, and environmental aspects of the adaptation of life to temperature in a way that has not been described previously. We may therefore expect the effect of evolution on T(eq) with respect to enzyme temperature/activity effects to be more important than on thermal stability. T(eq) is also an important parameter to consider when engineering enzymes to modify their thermal properties by both rational design and by directed enzyme evolution.     

Biosensors based on acrylic microgels: a comparative study of immobilized glucose oxidase and tyrosinase

Acrylic microgels are proposed as enzyme immobilizing support in amperometric biosensors. Two enzymes, glucose oxidase and tyrosinase, were entrapped in this matrix and their behaviour is compared. The optimum cross-linking of the polymeric matrix required to retain the enzyme, and to allow the diffusion of the substrate is different for each enzyme, 3.2% for glucose oxidase and 4.5% for tyrosinase. The effect of pH and temperature on the biosensor responses has been studied by experimental design methodology and predictions have been compared with independently performed experimental measurements. A quadratic effect of the variables studied (pH and T) on the biosensor response and the small or null interaction between them was confirmed. The pH results obtained with both methods are coincident revealing an reversible effect on the enzyme. However, the temperature optimum value obtained by experimental design was 10 degrees C lower as a result of an activity decay due to irreversible thermal denaturation of both enzymes.     

Computational modeling of carbohydrate processing enzymes reactions

Carbohydrate processing enzymes are of biocatalytic interest. Glycoside hydrolases and the recently discovered lytic polysaccharide monooxygenase for their use in biomass degradation to obtain biofuels or valued chemical entities. Glycosyltransferases or engineered glycosidases and phosphorylases for the synthesis of carbohydrates and glycosylated products. Quantum mechanics-molecular mechanics (QM/MM) methods are highly contributing to establish their different chemical reaction mechanisms. Other computational methods are also used to study enzyme conformational changes, ligand pathways, and processivity, e.g. for processive glycosidases like cellobiohydrolases. There is still a long road to travel to fully understand the role of conformational dynamics in enzyme activity and also to disclose the variety of reaction mechanisms these enzymes employ. Additionally, computational tools for enzyme engineering are beginning to be applied to evaluate substrate specificity or aid in the design of new biocatalysts with increased thermostability or tailored activity, a growing field where molecular modeling is finding its way.     

Kinetic characterization of an enzymatic irreversible inhibition measured in the presence of coupling enzymes. The inhibition of adenosine triphosphatase from sarcoplasmic reticulum by fluorescein isothiocyanate

A kinetic study of the irreversible inhibition of an enzyme measured in the presence of a coupling enzyme system has been carried out to assess the type of mechanism of the irreversible inhibition. By using the algebraic criteria proposed here it should be possible to discriminate between these mechanisms and to calculate their corresponding kinetic constants. An experimental design has been developed and applied to fluorescein isothiocyanate as inhibitor of the ATPase activity from sarcoplasmic reticulum.     

Function and biotechnology of extremophilic enzymes in low water activity

ABSTRACT: Enzymes from extremophilic microorganisms usually catalyze chemical reactions in non-standard conditions. Such conditions promote aggregation, precipitation, and denaturation, reducing the activity of most non-extremophilic enzymes, frequently due to the absence of sufficient hydration. Some extremophilic enzymes maintain a tight hydration shell and remain active in solution even when liquid water is limiting, e.g. in the presence of high ionic concentrations, or at cold temperature when water is close to the freezing point. Extremophilic enzymes are able to compete for hydration via alterations especially to their surface through greater surface charges and increased molecular motion. These properties have enabled some extremophilic enzymes to function in the presence of non-aqueous organic solvents, with potential for design of useful catalysts. In this review, we summarize the current state of knowledge of extremophilic enzymes functioning in high salinity and cold temperatures, focusing on their strategy for function at low water activity. We discuss how the understanding of extremophilic enzyme function is leading to the design of a new generation of enzyme catalysts and their applications to biotechnology.     

4-Thiazolidinones: novel inhibitors of the bacterial enzyme MurB

4-Thiazolidinones were synthesized and evaluated for their ability to inhibit the bacterial enzyme MurB. Selected 4-thiazolidinones displayed activity against the enzyme in vitro. This activity, coupled with the design principles of the thiazolidinones, supports the postulate that 4-thiazolidinones may be recognized as diphosphate mimics by a biological selector.     

Physics‐based enzyme design: Predicting binding affinity and catalytic activity

Computational enzyme design is an emerging field that has yielded promising success stories, but where numerous challenges remain. Accurate methods to rapidly evaluate possible enzyme design variants could provide significant value when combined with experimental efforts by reducing the number of variants needed to be synthesized and speeding the time to reach the desired endpoint of the design. To that end, extending our computational methods to model the fundamental physical–chemical principles that regulate activity in a protocol that is automated and accessible to a broad population of enzyme design researchers is essential. Here, we apply a physics‐based implicit solvent MM‐GBSA scoring approach to enzyme design and benchmark the computational predictions against experimentally determined activities. Specifically, we evaluate the ability of MM‐GBSA to predict changes in affinity for a steroid binder protein, catalytic turnover for a Kemp eliminase, and catalytic activity for α‐Gliadin peptidase variants. Using the enzyme design framework developed here, we accurately rank the most experimentally active enzyme variants, suggesting that this approach could provide enrichment of active variants in real‐world enzyme design applications. Proteins 2014; 82:3397–3409. © 2014 Wiley Periodicals, Inc.     

Influence of alternansucrase-derived oligosaccharides and other carbohydrates on alpha-galactosidase and alpha-glucosidase activity in Bifidobacterium adolescentis.

AIMS: To determine the influence of alternansucrase-derived oligosaccharides (AOS) and other carbohydrates on alpha-galactosidase and alpha-glucosidase activity in Bifidobacterium adolescentis. METHODS AND RESULTS: Activities for alpha-galactosidase and alpha-glucosidase were determined from cell extracts of B. adolescentis grown on 18 test carbohydrates including AOS. alpha-galactosidase activity was enhanced on a variety of alpha-linked or beta-linked carbohydrates regardless of a galactoside or glucoside. alpha-glucosidase, however, was enhanced only on alpha-linked carbohydrates. AOS significantly enhanced enzyme activity compared with most of the carbohydrates tested. Most of the AOS showed significant increases in activity for both enzymes over that displayed by their corresponding acceptor carbohydrates. CONCLUSIONS: alpha-galactosidase may serve as a biomarker for microbial metabolic activity within the large intestine for potential prebiotics composed of alpha-linked or beta-linked oligosaccharides whereas alpha-glucosidase activity may be restricted to assessing the influence of only alpha-linked carbohydrates. The AOS synthesis process provided a value-added component to carbohydrates by increasing metabolic activity (via alpha-galactosidase and alpha-glucosidase) over certain acceptor carbohydrates. SIGNIFICANCE AND IMPACT OF THE STUDY: Fundamental knowledge of enzyme activity in Bifidobacterium may aid in the design of more effective prebiotics and may also help identify enzyme indicators of metabolic activity when assessing influence within the intestine.     

酶分子设计常用策略和进展

酶分子的生物学功能很大程度上是由其三维空间结构和所处溶剂环境共同决定的。因此,优化酶分子的结构性质以及探索其性质最优的溶剂环境是改善酶分子功能以及进行理性设计的一个可行途径。从实际应用的角度来看,分子设计方法可以为酶工程提供一种有效的解决方案。目前,酶分子设计有两个重要的研究方向,包括提高酶分子的催化活力和优化其稳定性。同时,对酶分子设计方法的研究也有助于对蛋白质生物学机理的探索。在近些年的学术界酶分子设计案例中,生物信息学方法得到广泛的应用。本文系统地总结基于生物信息学的酶分子设计方法的背景、策略和一些经典案例。     

Milestones in directed enzyme evolution

Directed evolution has now been used for over two decades as an alternative to rational design for protein engineering. Protein function, however, is complex, and modifying enzyme activity is a tall order. We can now improve existing enzyme activity, change enzyme selectivity and evolve function de novo using directed evolution. Although directed evolution is now used routinely to improve existing enzyme activity, there are still only a handful of examples where substrate selectivity has been modified sufficiently for practical application, and the de novo evolution of function largely eludes us.     

Thermodynamically based solvent design for enzymatic saccharide acylation with hydroxycinnamic acids in non-conventional media

Enzyme-catalyzed synthesis has been widely studied with lipases (EC 3.1.1.3), but feruloyl esterases (FAEs; EC 3.1.1.73) may provide advantages such as higher substrate affinity and regioselectivity in the synthesis of hydroxycinnamate saccharide esters. These compounds are interesting because of their amphiphilicity and antioxidative potential. Synthetic reactions using mono- or disaccharides as one of the substrates may moreover direct new routes for biomass upgrading in the biorefinery. The paper reviews the available data for enzymatic hydroxycinnamate saccharide ester synthesis in organic solvent systems as well as other enzymatic hydroxycinnamate acylations in ionic liquid systems. The choice of solvent system is highly decisive for enzyme stability, selectivity, and reaction yields in these synthesis reactions. To increase the understanding of the reaction environment and to facilitate solvent screening as a crucial part of the reaction design, the review explores the use of activity coefficient models for describing these systems and - more importantly - the use of group contribution model UNIFAC and quantum chemistry based COSMO-RS for thermodynamic predictions and preliminary solvent screening. Surfactant-free microemulsions of a hydrocarbon, a polar alcohol, and water are interesting solvent systems because they accommodate different substrate and product solubilities and maintain enzyme stability. Ionic liquids may provide advantages as solvents in terms of increased substrate and product solubility, higher reactivity and selectivity, as well as tunable physicochemical properties, but their design should be carefully considered in relation to enzyme stability. The treatise shows that thermodynamic modeling tools for solvent design provide a new toolbox to design enzyme-catalyzed synthetic reactions from biomass sources.     

Effect of active site residues in barnase on activity and stability.

We have mutated residues in the active site of the ribonuclease, barnase, in order to determine their effects on both enzyme activity and protein stability. Mutation of several of the positively charged residues that interact with the negatively charged RNA substrate (Lys27----Ala, Arg59----Ala and His102----Ala) causes large decreases in activity. This is accompanied, however, by an increase in stability. There is presumably electrostatic strain in the active site where positively charged side-chains are clustered. Mutation of several residues that make hydrogen bonds (Ser57----Ala, Asn58----Asp and Tyr103----Phe) causes smaller decreases in activity, but increases or has no effect on stability. Deletion of hydrogen bonding groups elsewhere in proteins has been found previously to decrease stability by 0.5 to 1.5 kcal mol-1. Conversely, we find that two mutations (Asp54----Asn and Gln104----Ala) decrease stability and increase activity. Another mutation (Glu73----Ala) decreases both activity and stability. It is clear that many residues in the active site do not contribute to stability and that for some, but not all, of the residues there is a compromise between activity and stability. This suggests that certain types of local instability may be necessary for substrate binding and catalysis by barnase. This has implications for the understanding of enzyme activity and the design of enzymes.     

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

Computational enzyme design holds promise for the production of renewable fuels, drugs and chemicals. De novo enzyme design has generated catalysts for several reactions, but with lower catalytic efficiencies than naturally occurring enzymes. Here we report the use of game-driven crowdsourcing to enhance the activity of a computationally designed enzyme through the functional remodeling of its structure. Players of the online game Foldit were challenged to remodel the backbone of a computationally designed bimolecular Diels-Alderase to enable additional interactions with substrates. Several iterations of design and characterization generated a 24-residue helix-turn-helix motif, including a 13-residue insertion, that increased enzyme activity >18-fold. X-ray crystallography showed that the large insertion adopts a helix-turn-helix structure positioned as in the Foldit model. These results demonstrate that human creativity can extend beyond the macroscopic challenges encountered in everyday life to molecular-scale design problems.     

Sorting out molecules reacting with acetylcholinesterase by enzyme encapsulation in liposome

Enzymes are considered as providential molecules for biosensor design because of their sensitivity and the high specificity of the reactions they catalyse. However, their active sites often display low selectivity, a lot of molecules may enter and interfere with catalysis. These molecules may be either competitive inhibitors, activators or molecules which change the physico-chemical environment of the enzyme (pH, ionic strength). They produce the "matrix effect" that lowers the reliability of biosensors. We show here that encapsulation of enzymes in liposomes inserts a barrier between the enzyme and the external environment and protects the enzyme in a stable nano-environment for an optimal activity. This barrier sorts out the molecules that could react with the enzyme according to their hydrophobicity. Acetylcholinesterase is used to detect organophosphorous and carbamate insecticide residues but several molecules (reversible inhibitors, pH and ionic strength modifiers) generate matrix effects in free conditions. These perturbations were completely ineffective following enzyme encapsulation.     

Activity-based proteomics: enzymatic activity profiling in complex proteomes

Summary. In the postgenomic era new technologies are emerging for global analysis of protein function. The introduction of active site-directed chemical probes for enzymatic activity profiling in complex mixtures, known as activity-based proteomics has greatly accelerated functional annotation of proteins. Here we review probe design for different enzyme classes including serine hydrolases, cysteine proteases, tyrosine phosphatases, glycosidases, and others. These probes are usually detected by their fluorescent, radioactive or affinity tags and their protein targets are analyzed using established proteomics techniques. Recent developments, such as the design of probes for in vivo analysis of proteomes, as well as microarray technologies for higher throughput screenings of protein specificity and the application of activity-based probes for drug screening are highlighted. We focus on biological applications of activity-based probes for target and inhibitor discovery and discuss challenges for future development of this field.     

A tetrameric structure is not essential for activity in dihydrodipicolinate synthase (DHDPS) from Mycobacterium tuberculosis

Dihydrodipicolinate synthase (DHDPS) is a validated antibiotic target for which a new approach to inhibitor design has been proposed: disrupting native tetramer formation by targeting the dimer–dimer interface. In this study, rational design afforded a variant of Mycobacterium tuberculosis, Mtb-DHDPS-A204R, with disrupted quaternary structure. X-ray crystallography (at a resolution of 2.1 Å) revealed a dimeric protein with an identical fold and active-site structure to the tetrameric wild-type enzyme. Analytical ultracentrifugation confirmed the dimeric structure in solution, yet the dimeric mutant has similar activity to the wild-type enzyme. Although the affinity for both substrates was somewhat decreased, the high catalytic competency of the enzyme was surprising in the light of previous results showing that dimeric variants of the Escherichia coli and Bacillus anthracis DHDPS enzymes have dramatically reduced activity compared to their wild-type tetrameric counterparts. These results suggest that Mtb-DHDPS-A204R is similar to the natively dimeric enzyme from Staphylococcus aureus, and highlight our incomplete understanding of the role played by oligomerisation in relating protein structure and function.     

Osmolyte-induced folding enhances tryptic enzyme activity

Osmolytes form a class of naturally occurring small compounds known to protect proteins in their native folded and functional states. Among the osmolytes, trimethylamine-N-oxide (TMAO) has received special interest lately because it has shown an extraordinary capability to support folding of denatured to native-like species, which show significant functional activity. Most enzymes and/or proteins are commonly stored in glycerol to maintain their activity/function. In the present study, we tested whether TMAO can be a better solute than glycerol for two commonly used proteases, trypsin and chymotrypsin. Our enzyme kinetic data suggest that the enzyme activity of trypsin is significantly enhanced in TMAO compared to glycerol, whereas chymotrypsin activity is not significantly changed in either case. These results are in accordance with the osmolyte effects on the folding of these enzymes, as judged by data from fluorescence emission spectroscopy. These results suggest that TMAO may be a better solute than glycerol to maintain optimal tryptic enzyme activity.     

Purification and properties of a proteolytic enzyme from French beans.

1. A proteolytic enzyme with some features of a carboxypeptidase has been purified some 1180-fold from the sap of French beans (Phaseolus vulgaris var. Prince). A bright blue protein, plastocyanin, was separated from the enzyme by DEAE-cellulose chromatography. 2. Unlike carboxypeptidase A or B of animal origin, there is no evidence that the enzyme is a metalloprotein. There was no stimulation of activity by a number of metal ions, reducing agents or 2-mercapto-ethanol. Neither EDTA nor 1,10-o-phenanthroline inhibited the enzyme. 3. The proteolytic enzyme from beans, readily soluble at neutral or slightly acidic pH values, has a pH optimum of pH5.6 for the hydrolysis of leucine from benzyloxy-carbonylglycyl-l-leucine. Solutions of the enzyme in 0.1m-sodium acetate, pH5.5, lose about 2% of their activity/week at 4 degrees . Virtually no loss of activity results after prolonged storage at -15 degrees . 4. Incubation of the bean enzyme with peptides indicates that the enzyme will release acidic, neutral and basic amino acid residues as well as proline, although adjacent acidic residues in a peptide appear to inhibit the enzyme. The possibility of endopeptidase activity in the purified preparation requires further examination.     

Discovery of novel regulators of aldehyde dehydrogenase isoenzymes

Over the past three years we have been involved in high-throughput screening in an effort to discover novel small molecular modulators of aldehyde dehydrogenase (ALDH) activity. In particular, we have been interested in both the activation and inhibition of the three commonly studied isoenzymes, ALDH1A1, ALDH2 and ALDH3A1, as their distinct, yet overlapping substrate specificities, present a particularly difficult challenge for inhibitor discovery and design. Activation of ALDH2 has been shown to benefit cardiovascular outcome following periods of ischemia and renewed interest in specific inhibition of ALDH2 has application for alcohol aversion therapy, and more recently, in cocaine addiction. In contrast, inhibition of either ALDH1A1 or ALDH3A1 has application in cancer treatments where the isoenzymes are commonly over-expressed and serve as markers for cancer stem cells. We are taking two distinct approaches for these screens: in vitro enzyme activity screens using chemical libraries and virtual computational screens using the structures of the target enzymes as filters for identifying potential inhibitors, followed by in vitro testing of their ability to inhibit their intended targets. We have identified selective inhibitors of each of these three isoenzymes with inhibition constants in the high nanomolar to low micromolar range from these screening procedures. Together, these inhibitors provide proof for concept that selective inhibition of these broad specificity general detoxication enzymes through small molecule discovery and design is possible.     

Directed evolution of enzymes and biosynthetic pathways

Directed evolution is an important tool for overcoming the limitations of natural enzymes as biocatalysts. Recent advances have focused on applying directed evolution to a variety of enzymes, such as epoxide hydrolase, glyphosate N-acetyltransferase, xylanase and phosphotriesterase, in order to improve their activity, selectivity, stability and solubility. The focus has also shifted to manipulating biosynthetic pathways for the production of many naturally synthesized compounds, as well as the production of novel 'unnatural' compounds. A combined directed evolution and computational design approach is becoming increasingly important in exploring enzyme sequence-space and creating improved or novel enzymes. Fueled by recent breakthroughs in genomics and metagenomics, these developments should help expand the use of biocatalysts in industry.