Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements.

The measurement of values of apparent equilibrium constants K' for enzyme-catalyzed reactions involve a substantial number of critical details, neglect of which could lead to systematic errors. Here, interferences, impurities in the substances used, and failure to achieve equilibrium are matters of substantial consequence. Careful reporting of results is of great importance if the results are to have archival value. Thus, attention must be paid to the identification of the substances, specification of the reaction(s), the conditions of reaction, the definition of the equilibrium constant(s) and standard states, the use of standard nomenclature, symbols, and units, and uncertainties. This document contains a general discussion of various aspects of these equilibrium measurements as well as STRENDA (Standards for Reporting Enzymology Data) recommendations regarding the measurements and the reporting of results.

Kinetics of enzyme-catalysed desymmetrisation of prochiral substrates: product enantiomeric excess is not always constant.

The kinetics of enzymatic desymmetrisation were analysed for the most common kinetic mechanisms: ternary complex ordered (prochiral ketone reduction); ping-pong second (ketone amination, diol esterification, desymmetrisation in the second half reaction); ping-pong first (diol ester hydrolysis) and ping-pong both (prochiral diacids). For plausible values of enzyme kinetic parameters, the product enantiomeric excess (ee) can decline substantially as the reaction proceeds to high conversion. For example, an ee of 0.95 at the start of the reaction can decline to less than 0.5 at 95% of equilibrium conversion, but for different enzyme properties it will remain almost unchanged. For most mechanisms a single function of multiple enzyme rate constants (which can be termed ee decline parameter, eeDP) accounts for the major effect on the tendency for the ee to decline. For some mechanisms, the concentrations or ratios of the starting materials have an important influence on the fall in ee. For the application of enzymatic desymmetrisation it is important to study if and how the product ee declines at high conversion.

Thermodynamic Favorability of End Products of Anaerobic Glucose Metabolism.

The eQuilibrator component contribution method allows calculation of the overall Gibbs energy changes for conversion of glucose to a wide range of final products in the absence of other oxidants. Values are presented for all possible combinations of products with up to three carbons and selected others. The most negative Gibbs energy change is for the formation of graphite and water (-499 kJ mol-1) followed by CH4 and CO2 (-430 kJ mol-1), the observed final products of anaerobic digestion. Other favored products (with various combinations having Gibbs energy changes between -300 and -367 kJ mol-1) are short-chain alkanes, fatty acids, dicarboxylic acids, and even hexane and benzene. The most familiar products, lactate and ethanol + CO2, are less favored (Gibbs energy changes of -206 and -265 kJ mol-1 respectively). The values presented offer an interesting perspective on observed metabolism and its evolutionary origins as well as on cells engineered for biotechnological purposes.

Highly Active Protein Surfaces Enabled by Plant-Based Polyphenol Coatings.

Proteins represent complex biomolecules capable of wide-ranging but also highly specific functionalities. Their immobilization on material supports can enable broad applications from sensing and industrial biocatalysis to biomedical interfaces and materials. We demonstrate the advantages of using aqueous-processed cross-linked polyphenol coatings for immobilizing proteins, including IgG, avidin, and various single and multidomain enzymes on diverse materials, to enable active biofunctional structures (e.g., ca. 2.2, 1.7, 1.1, and 4.8 mg·m-2 active phosphatase on nanoporous cellulose and alumina, steel mesh, and polyester fabric, respectively). Enzyme assays, X-ray photoelectron spectroscopy, silver staining, supplemented with contact angle, solid-state 13C NMR, HPLC, and ESI-MS measurements were used to characterize the polyphenols, coatings, and protein layers. We show that the functionalization process may be advantageously optimized directly for protein activity rather than the traditional focus on the thickness of the coating layer. Higher activities (by more than an order of magnitude in some cases) and wider process pH and material compatibility are demonstrated with polyphenol coatings than other approaches such as polydopamine. Coatings formed from different plant polyphenol extracts, even at lowered purity (and cost), were also found to be highly functional. Chemically, our results indicate that polyphenol coatings differ from polydopamine mainly because of the elimination of amine groups, and that polyphenol layers with intermediate levels of reactivity may better lead to high immobilized protein activity. Overall, an improved understanding of simple-to-use polyphenol coatings has been obtained, which enabled a significant development in active protein surfaces that may be applied across diverse materials and nanostructured supports.

Two-dimensional 1H and 1H-detected NMR study of a heterogeneous biocatalyst using fast MAS at high magnetic fields.

Nuclear magnetic resonance (NMR) is a powerful tool for investigating atomic-scale structure in heterogeneous or composite materials where long-range order is absent. In this work solid-state 1H and 1H-detected NMR experiments were performed with fast magic angle spinning (νR = 75 kHz) and at high magnetic fields (B0 = 20 T) and used to gain structural insight into a heterogeneous biocatalyst consisting of an enzyme, human carbonic anhydrase II (hCA II), covalently immobilized on epoxy-functionalized silica. Two-dimensional 1H-1H NOESY-type correlation experiments were able to provide information on 1H environments in silica, epoxy-silica and the immobilized enzyme. Two distinct signals originating from water protons were observed: water associated with the surface of the silica and the water associated with the immobilized enzyme. Additional two-dimensional 1H-1H double-single quantum (DQ-SQ) correlation experiments suggested that the immobilized enzyme is not in close contact with the silica surface. Most significantly, comparison of two-dimensional 1H-15N spectra of the immobilized enzyme and the solution-state enzyme confirmed that the structural integrity of the protein is well preserved upon covalent immobilization.

Enzymatic Synthesis of Glucose-Based Fatty Acid Esters in Bisolvent Systems Containing Ionic Liquids or Deep Eutectic Solvents.

Sugar fatty acid esters (SFAEs) are biocompatible nonionic surfactants with broad applications in food, cosmetic, and pharmaceutical industries. They can be synthesized enzymatically with many advantages over their chemical synthesis. In this study, SFAE synthesis was investigated by using two reactions: (1) transesterification of glucose with fatty acid vinyl esters and (2) esterification of methyl glucoside with fatty acids, catalyzed by Lipozyme TLIM and Novozym 435 respectively. Fourteen ionic liquids (ILs) and 14 deep eutectic solvents (DESs) were screened as solvents, and the bisolvent system composed of 1-hexyl-3-methylimidazolium trifluoromethylsulfonate ([HMIm][TfO]) and 2-methyl-2-butanol (2M2B) was the best for both reactions, yielding optimal productivities (769.6 and 397.5 µmol/h/g, respectively) which are superior to those reported in the literature. Impacts of different reaction conditions were studied for both reactions. Response surface methodology (RSM) was employed to optimize the transesterification reaction. Results also demonstrated that as co-substrate, methyl glucoside yielded higher conversions than glucose, and that conversions increased with an increase in the chain length of the fatty acid moieties. DESs were poor solvents for the above reactions presumably due to their high viscosity and high polarity.

Fluid-dynamical model for antisurfactants.

We construct a fluid-dynamical model for the flow of a solution with a free surface at which surface tension acts. This model can describe both classical surfactants, which decrease the surface tension of the solution relative to that of the pure solvent, and antisurfactants (such as many salts when added to water, and small amounts of water when added to alcohol) which increase it. We demonstrate the utility of the model by considering the linear stability of an infinitely deep layer of initially quiescent fluid. In particular, we predict the occurrence of an instability driven by surface-tension gradients, which occurs for antisurfactant, but not for surfactant, solutions.

Supramolecular Fibers in Gels Can Be at Thermodynamic Equilibrium: A Simple Packing Model Reveals Preferential Fibril Formation versus Crystallization.

Low molecular weight gelators are able to form nanostructures, typically fibers, which entangle to form gel-phase materials. These materials have wide-ranging applications in biomedicine and nanotechnology. While it is known that supramolecular gels often represent metastable structures due to the restricted molecular dynamics in the gel state, the thermodynamic nature of the nanofibrous structure is not well understood. Clearly, 3D extended structures will be able to form more interactions than 1D structures. However, self-assembling molecules are typically amphiphilic, thus giving rise to a combination of solvophobic and solvophilic moieties where a level of solvent exposure at the nanostructure surface is favorable. In this study, we introduce a simple packing model, based on prisms with faces of different nature (solvophobic and solvophilic) and variable interaction parameters, to represent amphiphile self-assembly. This model demonstrates that by tuning shape and "self" or "solvent" interaction parameters either the 1D fiber or 3D crystal may represent the thermodynamic minimum. The model depends on parameters that relate to features of experimentally known systems: the number of faces exposed to the solvent or buried in the fiber; the overall shape of the prism; and the free energy penalties associated with the interactions can be adjusted to match their chemical nature. The model is applied to describe the pH-dependent gelation/precipitation of well-known gelator Fmoc-FF. We conclude that, despite the fact that most experimentally produced gels probably represent metastable states, one-dimensional fibers can represent thermodynamic equilibrium. This conclusion has critical implications for the theoretical treatment of gels.

Effect of pore size on the performance of immobilised enzymes.

Porous materials are widely employed as supports in the immobilisation of enzymes. Traditionally macroporous materials with pore diameters >50 nm were believed to be the most suitable support material, ensuring no spatial restrictions upon enzyme molecules entering such large pores. In recent years however, there has been growing emphasis in the use of mesoporous supports with pore diameters ranging between 2 and 50 nm. It is thought this smaller pore range may offer enhanced conformational stability to immobilised enzymes while not being so small as to restrict enzyme access. Despite their increasing popularity, many argue that mesoporous materials have not yet proven superior to traditional macroporous supports for enzyme immobilisation. Through the design and application of a unique confidence rating system we were able to accurately compare data and establish trends between pore characteristics and protein loading. By analysing published data (182 experiments in total) and extracting pore characteristics and protein loading values, we have described three categories of pore diameters in which correlations between pore characteristics and protein loading are noted. With pore diameters less than 10 nm we see a general decrease in protein loading as the enzymes find physical restrictions in accessing the high surface offered in this pore diameter range. At pore sizes greater than 100 nm, protein loading generally decreases due to a concomitant reduction in available surface area. In the pore range of 10-100 nm there it is expected to see a decrease in protein loading level with increasing pore diameter. In fact protein loading in this range remains largely constant, suggesting some degree of protein-protein interaction blocking pores and restricting access to the increasing surface area available at decreasing pore diameters. No trends were established between pore characteristics and retention of activity.

Salt-induced control of supramolecular order in biocatalytic hydrogelation.

Biocatalytic action and specific ion effects are both known to have dramatic effects on molecular self-assembly and hydrogelation. In this paper, we demonstrate that these effects are highly cooperative. Biocatalytic hydrogelation of Fmoc peptides in the presence of salts combines kinetic (through enzymatic catalysis) and thermodynamic (specific ion and protein templating) contributions when applied in combination. Spectroscopic data (obtained by fluorescence spectroscopy and circular dichroism) revealed that hydrophobic interactions are greatly affected, giving rise to differential chiral organization and supramolecular structure formation. The kinetic effects of catalytic action could be removed from the system by applying a heat/cool cycle, giving insight into the thermodynamic influence of both protein and salt on these systems and showing that the effects of catalysis, templating, and salts are cooperative. The variable molecular interactions are expressed as variable material properties, such as thermal stability and mechanical strength of the final gel-phase material. To gain more insight into the role of the enzyme, beyond catalysis, in the underlying mechanism, static light scattering is performed, which indicates the different mode of aggregation of the enzyme molecules in the presence of different salts in aqueous solution that may play a role to direct the assembly via templating. Overall, the results show that the combination of specific salts and enzymatic hydrogelation can give rise to complex self-assembly behaviors that may be exploited to tune hydrogel properties.

Dramatic specific-ion effect in supramolecular hydrogels.

We report on a pronounced specific-ion effect on the intermolecular and chiral organization, supramolecular structure formation, and resulting materials properties for a series of low molecular weight peptide-based hydrogelators, observed in the presence of simple inorganic salts. This effect was demonstrated using aromatic short peptide amphiphiles, based on fluorenylmethoxycarbonyl (Fmoc). Gel-phase materials were formed due to molecular self-assembly, driven by a combination of hydrogen bonding and π-stacking interactions. Pronounced morphological changes were observed by atomic force microscopy (AFM) for Fmoc-YL peptide, ranging from dense fibrous networks to spherical aggregates, depending on the type of anions present. The gels formed had variable mechanical properties, with G' values between 0.8 kPa and 2.4 kPa as determined by rheometry. Spectroscopic analysis provided insights into the differential mode of self-assembly, which was found to be dictated by the hydrophobic interactions of the fluorenyl component, with comparable H-bonding patterns observed in each case. The efficiency of the anions in promoting the hydrophobic interactions and thereby self-assembly was found to be consistent with the Hofmeister anion sequence. Similar effects were observed with other hydrophobic peptides, Fmoc-VL and Fmoc-LL. The effect was found to be less pronounced for a less hydrophobic peptide, Fmoc-AA. To get more insights into the molecular mechanism, the effect of anions on sol-gel equilibrium was investigated, which indicates the observed changes result from the specific-ion effects on gels structure, rather than on the sol-gel equilibrium. Thus, we demonstrate that, by simply changing the ionic environment, structurally diverse materials can be accessed providing an important design consideration in nanofabrication via molecular self-assembly.

Interaction of counterions with subtilisin in acetonitrile: insights from molecular dynamics simulations.

A recent X-ray structure has enabled the location of chloride and cesium ions on the surface of subtilisin Carlsberg in acetonitrile soaked crystals. (1) To complement the previous study and analyze the system in solution, molecular dynamics (MD) simulations, in acetonitrile, were performed using this structure. Additionally, Cl(-) and Cs(+) ions were docked on the protein surface and this system was also simulated. Our results indicate that chloride ions tend to stay close to the protein, whereas cesium ions frequently migrate to the solvent. The distribution of the ions around the enzyme surface is not strongly biased by their initial locations. Replacing cesium by sodium ions showed that the distribution of the two cations is similar, indicating that Cs(+) can be used to find the binding sites of cations like Na(+) and K(+), which, unlike Cs(+), have physiological and biotechnological roles. The Na(+)Cl(-) is more stable than the Cs(+)Cl(-) ion pair, decreasing the probability of interaction between Cl(-) and subtilisin. The comparison of water and acetonitrile simulations indicates that the solvent influences the distribution of the ions. This work provides an extensive theoretical analysis of the interaction between ions and the model enzyme subtilisin in a nonaqueous medium.

Examining structure-activity correlations of some high activity enzyme preparations for low water media.

A first study of the comparison of structures of enzymes (by FT-IR and CD) in different high activity (in low water media) preparations is reported. Using chymotrypsin and subtilisin as models, we have studied various factors that distinguish enzyme precipitated and rinsed with propanol (EPRP), crosslinked enzyme aggregates (CLEA), protein coated microcrystals (PCMC) and crosslinked protein coated microcrystals (CLPCMC). The suspensions in organic media were assayed for catalytic activity, and structures were probed by FT-IR and CD measurements. CD studies of enzyme suspensions were possible by using a rotating cell accessory. There was a generally good correlation between higher catalytic activity and retention of native structures. Activity and retention of native structure was always higher if aqueous enzyme solution was added to propanol rather than vice versa in the precipitation step of these preparations. The work identifies factors which may lead to better biocatalyst designs for low water media.

Enzymatic acylation of starch.

Starch a cheap, abundant and renewable natural material has been chemically modified for many years. The popular modification acylation has been used to adjust rheological properties as well as deliver polymers with internal plasticizers and other potential uses. However the harsh reaction conditions required to produce these esters may limit their use, especially in sensitive applications (foods, pharmaceuticals, etc.). The use of enzymes to catalyse acylation may provide a suitable alternative due to high selectivities and mild reaction conditions. Traditional hydrolase-catalysed synthesis in non-aqueous apolar media is hard due to lack of polysaccharide solubility. However, acylated starch derivatives have recently been successfully produced in other non-conventional systems: (a) surfactant-solubilised subtilisin and suspended amylose in organic media; (b) starch nanoparticles dispersed in organic medium with immobilised lipase; (c) aqueous starch gels with lipase and dispersed fatty acids. We attempt a systematic review that draws parallels between the seemingly unrelated approaches described.

Lipase-catalysed acylation of starch and determination of the degree of substitution by methanolysis and GC.

BACKGROUND: Natural polysaccharides such as starch are becoming increasingly interesting as renewable starting materials for the synthesis of biodegradable polymers using chemical or enzymatic methods. Given the complexity of polysaccharides, the analysis of reaction products is challenging. RESULTS: Esterification of starch with fatty acids has traditionally been monitored by saponification and back-titration, but in our experience this method is unreliable. Here we report a novel GC-based method for the fast and reliable quantitative determination of esterification. The method was used to monitor the enzymatic esterification of different starches with decanoic acid, using lipase from Thermomyces lanuginosus. The reaction showed a pronounced optimal water content of 1.25 mL per g starch, where a degree of substitution (DS) of 0.018 was obtained. Incomplete gelatinization probably accounts for lower conversion with less water. CONCLUSIONS: Lipase-catalysed esterification of starch is feasible in aqueous gel systems, but attention to analytical methods is important to obtain correct DS values.

Guidelines for reporting of biocatalytic reactions.

Enzymes and whole cells are being increasingly applied in research and industry, but the adoption of biocatalysis relies strongly on useful scientific literature. Unfortunately, too many published papers lack essential information needed to reproduce and understand the results. Here, members of the scientific committee of the European Federation of Biotechnology Section on Applied Biocatalysis (ESAB) provide practical guidelines for reporting experiments. The document embraces the recommendations of the STRENDA initiative (Standards for Reporting Enzymology Data) in the context of pure enzymology and provides further guidelines and explanations on topics of crucial relevance for biocatalysis. In particular, guidelines are given on issues such as the selectivity, specificity, productivity and stability of biocatalysts, as well as on methodological problems related to reactions in multiphase systems. We believe that adoption and use of these guidelines could greatly increase the value and impact of published work in biocatalysis, and hence promote the further growth of applications.

Crystallographic analysis of counterion effects on subtilisin enzymatic action in acetonitrile.

When enzymes are in low dielectric nonaqueous media, it would be expected that their charged groups would be more closely associated with counterions. There is evidence that these counterions may then affect enzymatic activity. Published crystal structures of proteins in organic solvents do not show increased numbers of associated counterions, and this might reflect the difficulty of distinguishing cations like Na(+) from water molecules. In this paper, the placement of several Cs(+) and Cl(-) ions in crystals of the serine protease subtilisin Carlsberg is presented. Ions are more readily identified crystallographically through their anomalous diffraction using softer X-rays. The protein conformation is very similar to that of the enzyme without CsCl in acetonitrile, both for the previously reported ( 1SCB ) and our own newly determined model. No fewer than 11 defined sites for Cs(+) cations and 8 Cl(-) anions are identified around the protein molecule, although most of these have partial occupancy and may represent nonspecific binding sites. Two Cs(+) and two Cl(-) ions are close to the mouth of the active site cleft, where they may affect catalysis. In fact, cross-linked CsCl-treated subtilisin crystals transferred to acetonitrile show catalytic activity several fold higher than the reference crystals containing Na(+). Presoaking with another large cation, choline, also increases the enzyme activity. The active site appears only minimally sterically perturbed by the ion presence around it, so alternative activation mechanisms can be suggested: an electrostatic redistribution and/or a larger hydration sphere that enhances the protein domain.

Hofmeister effects on activity and stability of alkaline phosphatase.

We have studied the effects on alkaline phosphatase of adding high concentrations (normally 1.0 M) of simple salts. It is necessary to allow for significant effects of salts on the extinction coefficient of the reaction product, and on the apparent pH of the buffer. Both activity and stability of the enzyme correlate well with the Hofmeister series in terms of the salt's kosmotropic/chaotropic properties, which are assessed by the Jones-Dole viscosity B coefficients (B(+) for cations and B(-) for anions). The catalytic activity or V(max)/K(m) of the enzyme showed a bell-shaped relationship with the (B(-)-B(+)) values of the salts present, being optimal with salts (such as NaCl, KCl, and KNO(3)) where the anion and cation have similar kosmotropic/chaotropic properties. This effect is believed to be enzyme-specific and relates to the impact of both cations and anions on the enzyme's surface pH, active site, and catalytic mechanism. Anions play a more predominant role than cations in affecting enzyme stability. The rate of irreversible thermal inactivation is strongly reduced by addition of kosmotropic anions like SO(4)(2-) (half-life increased from 8 to 580 min at 60 degrees C). This effect is general and the mechanism probably involves the ability of the ions to affect the water solvation layer around the enzyme molecule and to interact with both the surface and internal structure of the enzyme.