Anatomy of lipase binding sites: the scissile fatty acid binding site

Cold active microbial lipases: some hot issues and recent developments

Lipases are glycerol ester hydrolases that catalyze the hydrolysis of triglycerides to free fatty acids and glycerol. Lipases catalyze esterification, interesterification, acidolysis, alcoholysis and aminolysis in addition to the hydrolytic activity on triglycerides. The temperature stability of lipases has regarded as the most important characteristic for use in industry. Psychrophilic lipases have lately attracted attention because of their increasing use in the organic synthesis of chiral intermediates due to their low optimum temperature and high activity at very low temperatures, which are favorable properties for the production of relatively frail compounds. In addition, these enzymes have an advantage under low water conditions due to their inherent greater flexibility, wherein the activity of mesophilic and thermophilic enzymes are severely impaired by an excess of rigidity. Cold-adapted microorganisms are potential source of cold-active lipases and they have been isolated from cold regions and studied. Compared to other lipases, relatively smaller numbers of cold active bacterial lipases were well studied. Lipases isolated from different sources have a wide range of properties depending on their sources with respect to positional specificity, fatty acid specificity, thermostability, pH optimum, etc. Use of industrial enzymes allows the technologist to develop processes that closely approach the gentle, efficient processes in nature. Some of these processes using cold active lipase from C. antarctica have been patented by pharmaceutical, chemical and food industries. Cold active lipases cover a broad spectrum of biotechnological applications like additives in detergents, additives in food industries, environmental bioremediations, biotransformation, molecular biology applications and heterologous gene expression in psychrophilic hosts to prevent formation of inclusion bodies. Cold active enzymes from psychrotrophic microorganisms showing high catalytic activity at low temperatures can be highly expressed in such recombinant strains. Thus, cold active lipases are today the enzymes of choice for organic chemists, pharmacists, biophysicists, biochemical and process engineers, biotechnologists, microbiologists and biochemists.

The proinflammatory cytokine response to Chlamydia trachomatis elementary bodies in human macrophages is partly mediated by a lipoprotein, the macrophage infectivity potentiator, through TLR2/TLR1/TLR6 and CD14

Chlamydiae components and signaling pathway(s) responsible for the production of proinflammatory cytokines by human monocytes/macrophages are not clearly identified. To this aim, Chlamydia trachomatis-inactivated elementary bodies (EB) as well as the following seven individual Ags were tested for their ability to induce the production of proinflammatory cytokines by human monocytes/macrophages and THP-1 cells: purified LPS, recombinant heat shock protein (rhsp)70, rhsp60, rhsp10, recombinant polypeptide encoded by open reading frame 3 of the plasmid (rpgp3), recombinant macrophage infectivity potentiator (rMip), and recombinant outer membrane protein 2 (rOmp2). Aside from EB, rMip displayed the highest ability to induce release of IL-1beta, TNF-alpha, IL-6, and IL-8. rMip proinflammatory activity could not be attributed to Escherichia coli LPS contamination as determined by the Limulus Amoebocyte lysate assay, insensitivity to polymyxin B (50 microg/ml), and different serum requirement. We have recently demonstrated that Mip is a "classical" bacterial lipoprotein, exposed at the surface of EB. The proinflammatory activity of EB was significantly attenuated in the presence of polyclonal Ab to rMip. Native Mip was able to induce TNF-alpha and IL-8 secretion, whereas a nonlipidated C20A rMip variant was not. Proinflammatory activity of rMip was unaffected by heat or proteinase K treatments but was greatly reduced by treatment with lipases, supporting a role of lipid modification in this process. Stimulating pathways appeared to involve TLR2/TLR1/TLR6 with the help of CD14 but not TLR4. These data support a role of Mip lipoprotein in pathogenesis of C. trachomatis-induced inflammatory responses.

Multiple tandem gene duplications in a neutral lipase gene cluster in Drosophila

We have examined a highly dynamic section of the Drosophila melanogaster genome which contains neutral lipase family genes that have undergone multiple tandem duplication events. We have identified the orthologous clusters, encoding between five and eight apparently functional lipases, in other Drosophila genomes: yakuba, ananassae, pseudoobscura, virilis, mojavensis, persimilis, grimshawi and willistoni. We examined their gene structure, duplication and pseudogene formation, and the presence of transposable elements. Based on phylogenetic comparisons, the lipase genes contained in each of the clusters fall into four distinct clades. Clades I and II have distinct evolutionary constraints to clades III and IV. Multiple gene duplications have occurred in different lineages of clades I and II while clades III and IV contain a single lipase gene from each species. Compared with lipases from other clades, clade IV genes contain an additional 3' domain of tandemly repeated sequence of varying length and composition, and a substitution in the residue adjacent to the key catalytic serine in the encoded proteins. A comparison of non-synonymous to synonymous nucleotide substitution (dN/dS) rates within each clade showed the highest rate of divergence was between paralogous lipase gene pairs suggesting selection pressure on duplicated genes. Analysis of the encoded lipase protein sequences within each species using PAML identified positively selected sites; structure homology modeling based on human pancreatic lipase indicated many of these residues formed part of the active site of the enzyme. As some of the cluster lipase genes are known to be expressed in the insect midgut and respond to changes in dietary components, we propose that the lipase cluster has undergone dynamic evolutionary changes to maximize absorption of lipid nutrients from the diet.

Microbial carbohydrate esterases in cold adapted environments

Psychrophiles produce cold-evolved enzymes that display a high catalytic efficiency, associated with a low thermal stability. In recent years, these enzymes have attracted the attention of scientists because of their peculiar properties that render them particularly useful in investigating the relationship existing between enzyme stability and flexibility on one hand, and enzyme activity on the other hand. Among these enzymes, the esterases, and particularly the feruloyl esterases, have potential uses over a broad range of applications in the agro-food industries. In recent years, the number of microbial feruloyl esterase activities has increased in the growing genome databases. Based on substrate utilization data and supported by primary sequence identity, four subclasses of esterase have been characterized so far. Up to the present, ten genomes from psychrophilic bacteria have been completely sequenced and additional fourteen genomes are under investigation. From the bacteria strains whose genome has been completely sequenced, we analyzed the presence of esterase genes, both the putative genes and the determined experimentally genes, and performed a ClustalW analysis for feruloyl esterases. Major details will be presented for the ORF PSHAa1385 from P. haloplanktis TAC125 that recently has been studied in our research group. In addition, the potential biotechnology applications of this class of enzymes will be discussed.

Enthalpie and Entropie Contributions in the Transesterification of Sucrose: Computational Study of Lipases and Subtilisin

Transesterification of sucrose with fatty acids catalyzed by subtilisin Carlsberg occurs with regioselectivity that is different from that in lipases. Thermomyces lanuginosus lipase (TlL) and Candida antarctica lipase B (CALB) catalyze synthesis at positions 6 and 6', with differing abilities, while subtilisin catalysis leads to the 1'-acylated sucrose. The catalytic machinery in lipases is approximately mirrored in subtilisins but different pocket morphologies including size, shape, and rearrangement of the catalytic elements underlies the differing regioselectivities. The thermodynamic consequences of these differences on the above reactions have been explored systematically using computational methods, determining the free energies of interaction of the putative transition-state adducts. Analysis of the conformers with the lowest transition state energies (protein-ligand interactions and vibrational entropy contributions) indicates that enthalpic factors control specificities in lipases while entropic factors are more important in subtilisin.

The allosteric modulation of lipases and its possible biological relevance

Background

During the development of an enantioselective synthesis using the lipase from Mucor miehei an unusual reaction course was observed, which was analyzed precisely. For the first time an allosteric modulation of a lipase changing its selectivity was shown.

Theory

Considering the biological relevance of the discovered regulation mechanism we developed a theory that describes the regulation of energy homeostasis and fat metabolism.

Conclusion

This theory represents a new approach to explain the cause of the metabolic syndrome and provides an innovative basis for further research activity.

Novel and highly regioselective route for synthesis of 5-fluorouridine lipophilic ester derivatives by lipozyme TL IM

For the first time, lipozyme TL IM, an inexpensive lipase from Thermomyces lanuginosa, was successfully applied to the regioselective synthesis of lipophilic 5-fluorouridine ester derivatives. The ESI-MS and (13)C NMR analysis confirmed that the end products of the acylation were 5'-O-acyl 5-fluorouridines, more powerful anti-tumor drugs than 5-fluorouridine itself. Notably, the chain length of acyl donors had an obvious effect on the initial rate and the maximum substrate conversion of the regioselective acylation. The acylation of 5-fluorouridine with vinyl laurate was used as a model to explore the influence of various factors on the reaction with respect to the initial rate, the maximum substrate conversion and the regioselectivity. The optimum water activity, the molar ratio of vinyl laurate to 5-fluorouridine, reaction temperature and shaking rate were 0.07, 15/1, 45 degrees C and 200rpm, respectively, under which the maximum substrate conversion and the regioselectivity were as high as 98.4 and >99%, respectively, after a reaction time of around 6h.

Inhibition or activation of Pseudomonas species lipase by 1,2-ethylene-di-N-alkylcarbamates in detergents

1,2-Ethylene-di-N-n-propylcarbamate (1) is characterized as an essential activator of Pseudomonas species lipase while 1,2-ethylene-di-N-n-butyl-, t-butyl-, n-heptyl-, and n-octyl-carbamates (2-5) are characterized as the pseudo substrate inhibitors of the enzyme in the presence of the detergent taurocholate or triton X-100. The inhibition and activation reactions are more sensitive in taurocholate than in triton X-100. From CD studies, the enzyme changes conformations in the presence of the detergent and further alters conformations by addition of the carbamate activator or inhibitor into the enzyme-detergent adduct. Therefore, this study suggests that the conformational change of lipase during interfacial activation is a continuous process to expose the active site of the enzyme to substrate. From 600 MHz (1)H NMR studies, the conformations of the alpha- and beta-methylene moieties of the activator 1,2-ethylene-di-N-n-propylcarbamate in the presence of substrate change after adding taurocholate into the mixture, and the conformations of the beta-methylene moieties of the inhibitor 1,2-ethylene-di-N-n-butylcarbamate in the presence of substrate alter after adding taurocholate into the mixture.

Kinetic model of 1,3-specific triacylglycerols alcoholysis catalyzed by lipases

A new model of enzymatic 1,3-specific alcoholysis of triacylglycerols has been developed. The irreversibility of the acyl bounds cleavage in glycerides, a reversible monoglycerides isomerization and an irreversible enzyme deactivation have been assumed. The Ping Pong Bi Bi mechanism with competitive inhibition by alcohol has been applied to describe rates of acyl bonds cleavage. The enzymatic propanolysis and iso-propanolysis of triacetin and tricaprylin catalyzed by immobilized lipase B from Candida antarctica (Novozym 435) have been investigated to verify the model. Good agreement between experimental data and calculations has been obtained. It was shown that the rate of tricaprylin alcoholysis is higher than the triacetin alcoholysis and that the rate of iso-propanolysis reactions are higher than propanolysis. The irreversible enzyme deactivation affects the conversion of glycerides whereas the competitive alcohol inhibition may be neglected. Empirical correlations of rates for monoglycerides isomerization and enzyme deactivation have been proposed.

Molecular Basis for the Enhanced Lipase-Catalyzed N-Acylation of 1-Phenylethanamine with Methoxyacetate

One of the commercial methods for preparing enantiopure amines is lipase-catalyzed kinetic resolution, although lipases catalyze aminolysis with only low activity. Interestingly, in 1997 Balkenhohl et al. used ethyl methoxyacetate instead of ethyl butyrate as an acylation reagent for the aminolysis of 1-phenylethanamine and increased the reaction rate more than a 100-fold. This method has been applied to other aminolysis reactions, but the molecular basis for the enhanced rate is not understood. A molecular-modeling study of the transition-state analogue for the aminolysis showed that an interaction between the beta-oxygen atom in methoxyacetate and the amine nitrogen atom might be a key factor in the rate enhancement. Other acylation reagents, such as methyl 3-methoxypropionate and methyl 4-methoxybutyrate, were chosen to test the influence of this interaction because these molecules can be spatially arranged to have similar interactions. The results were similar to that in the acylation with methoxyacetate. The initial aminolysis rates were improved (11-fold and sixfold, respectively) compared to that with butyrate. In contrast, alcoholysis with 1-phenylethanol afforded the same rate with all acyl donors.

Structure-activity analysis of base and enzyme-catalyzed 4-hydroxybenzoyl coenzyme A hydrolysis

In this study, the second-order rate constant k2 of base-catalyzed hydrolysis and the values of kcat, Km and kcat/Km of wild-type Pseudomonas sp. CBS3 4-hydroxybenzoyl coenzyme A (4-HBA-CoA) thioesterase-catalyzed hydrolysis of 4-HBA-CoA and its para-substituted analogs were measured. For the base-catalyzed hydrolysis, the plot of logk2 vs the sigma value of the para-substituents was linear with a slope (rho) of 1.5. In the case of the enzyme-catalyzed hydrolysis, the kcat/Km values measured for the para-substituted analogs defined substrate specificity. Asp32 was shown to play a key role in substrate recognition, and in particular, in the discrimination between the targeted substrate and other cellular benzoyl-CoA thioesters.

Computational methods to rationalize experimental strategies in biocatalysis

Computational methods are more and more widely applied in biocatalysis to gain rational guidelines, to orient experimental planning and, ultimately, to avoid expensive and time-consuming experiments. In this respect, molecular modelling, multivariate statistical analysis and chemometrics in general are useful computational tools, although they follow completely different investigative approaches.

Understanding Candida rugosa lipases: an overview

Candida rugosa lipase (CRL) is one of the enzymes most frequently used in biotransformations. However, there are some irreproducibility problems inherent to this biocatalyst, attributed either to differences in lipase loading and isoenzymatic profile or to other medium-engineering effects (temperature, a(w), choice of solvent, etc.). In addition, some other properties (influence of substrate and reaction conditions on the lid movement, differences in the glycosylation degree, post-translational modifications) should not be ruled out. In the present paper the recent developments published in the CRL field are overviewed, focusing on: (a) comparison of structural and biochemical data among isoenzymes (Lip1-Lip5), and their influence in the biocatalytical performance; (b) developments in fermentation technology to achieve new crude C. rugosa lipases; (c) biocatalytical reactivity of each isoenzyme, and methods for characterising them in crude CRL; (d) state-of-the-art of new applications performed with recombinant CRLs, both in CRL-second generation (wild-type recombinant enzymes), as well as in CRL-third generation, (mutants of the wt-CRL).

Novel Fluorescent Phosphonic Acid Esters for Discrimination of Lipases and Esterases

Lipases and esterases are responsible for carboxylester hydrolysis inside and outside cells and are useful biocatalysts for (stereo)selective modification of synthetic substrates. Here we describe novel fluorescent suicide inhibitors that differ in structure and polarity for screening and discrimination of lipolytic enzymes in enzyme preparations. The inhibitors covalently react with the enzymes to form fluorescent lipid-protein complexes that can be resolved by gel electrophoresis. The selectivities of the inhibitors were determined by using different (phospho)lipase, esterase and cholesterol esterase preparations. The results indicate that formation of an inhibitor-enzyme complex is highly dependent on the chemical structure of the inhibitor. We identified inhibitors with very low specificity, and other derivatives that were highly specific for certain subgroups of lipolytic enzymes such as lipases and cholesterol esterases. A combination of these substrate-analogous activity probes represents a useful toolbox for rapid identification and classification of serine hydrolase enzymes.

Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26

Haloalkane dehalogenases are microbial enzymes that cleave a carbon-halogen bond in halogenated compounds. The haloalkane dehalogenase LinB, isolated from Sphingomonas paucimobilis UT26, is a broad-specificity enzyme. Fifty-five halogenated aliphatic and cyclic hydrocarbons were tested for dehalogenation with the LinB enzyme. The compounds for testing were systematically selected using a statistical experimental design. Steady-state kinetic constants K(m) and k(cat) were determined for 25 substrates that showed detectable cleavage by the enzyme and low abiotic hydrolysis. Classical quantitative structure-activity relationships (QSARs) were used to correlate the kinetic constants with molecular descriptors and resulted in a model that explained 94% of the experimental data variability. The binding affinity of the tested substrates for this haloalkane dehalogenase correlated with hydrophobicity, molecular surface, dipole moment, and volume:surface ratio. Binding of the substrate molecules in the active site pocket of LinB depends nonlinearly on the size of the molecules. Binding affinity increases with increasing substrate size up to a chain length of six carbon atoms and then decreases. Comparative binding energy (COMBINE) analysis was then used to identify amino acid residues in LinB that modulate its substrate specificity. A model with three statistically significant principal components explained 95% of the experimental data variability. van der Waals interactions between substrate molecules and the enzyme dominated the COMBINE model, in agreement with the importance of substrate size in the classical QSAR model. Only a limited number of protein residues (6-8%) contribute significantly to the explanation of variability in binding affinities. The amino acid residues important for explaining variability in binding affinities are as follows: (i) first-shell residues Asn38, Asp108, Trp109, Glu132, Ile134, Phe143, Phe151, Phe169, Val173, Trp207, Pro208, Ile211, Leu248, and His272, (ii) tunnel residues Pro144, Asp147, Leu177, and Ala247, and (iii) second-shell residues Pro39 and Phe273. The tunnel and the second-shell residues represent the best targets for modulating specificity since their replacement does not lead to loss of functionality by disruption of the active site architecture. The mechanism of molecular adaptation toward a different specificity is discussed on the basis of quantitative comparison of models derived for two protein family members.

Mutations in the “lid” region affect chain length specificity and thermostability of aPseudomonas fragilipase

The cold-adapted Pseudomonas fragi lipase (PFL) displays highest activity on short-chain triglyceride substrates and is rapidly inactivated at moderate temperature. Sequence and structure comparison with homologous lipases endowed with different substrate specificity and stability, pointed to three polar residues in the lid region, that were replaced with the amino acids conserved at equivalent positions in the reference lipases. Substitutions at residues T137 and T138 modified the lipase chain-length preference profile, increasing the relative activity towards C8 substrates. Moreover, mutations conferred to PFL higher temperature stability. On the other hand, replacement of the serine at position 141 by glycine destabilized the protein.

Specificity in lipases: a computational study of transesterification of sucrose

Computational conformational searches of putative transition states of the reaction of sucrose with vinyl laurate catalyzed by lipases from Candida antarctica B and Thermomyces lanuginosus have been carried out. The dielectric of the media have been varied to understand the role of protein plasticity in modulating the observed regioselective transesterification. The binding pocket of lipase from Candida adapts to the conformational variability of the various substates of the substrates by small, local adjustments within the binding pocket. In contrast, the more constrained pocket of the lipase from Thermomyces adapts by adjusting through concerted global motions between subdomains. This leads to the identification of one large pocket in Candida that accommodates both the sucrose and the lauroyl moieties of the transition state, whereas in Thermomyces the binding pocket is smaller, leading to the localization of the two moieties in two distinct pockets; this partly rationalizes the broader specificity of the former relative to the latter. Mutations have been suggested to exploit the differences towards changing the observed selectivities.

A rate determining step change in the pre-steady state of acetylcholinesterase inhibitions by 1,n-alkane-di-N-butylcarbamates

Alkane-1-N-butylcarbamate-n-ols (1-7) and 1,n-alkane-di-N-butylcarbamates (8-14) are potent pseudo-substrate inhibitors of acetylcholinesterase. For inhibitors 1-7, the pre-steady state -logK(s) values and steady state -logK(i), values are linearly correlated with the tether length (N). However, for inhibitors 8-14, correlation of the -logK(s) or -logK(i) values against N deviates from linearity. A discontinuity of the -logK(s) versus N plot, concave downwards, is indicative of a rate determining step change in the pre-steady state of acetylcholinesterase inhibitions by inhibitors 8-14.

Production and applications of esterases

Esterase plays a major role in the degradation of natural materials and industrial pollutants, viz., cereal wastes, plastics, and other toxic chemicals. It is useful in the synthesis of optically pure compounds, perfumes, and antioxidants. The potential applications of esterase with reference to agriculture, food, and pharmaceutical industries, are discussed in this review. Promising applications in this avenue can be supported by appropriate production strategies.

Computational Approach to Solvent-Free Synthesis of Ethyl Oleate Using Candida rugosa and Candida antarctica B Lipases. I. Interfacial Activation and Substrate (Ethanol, Oleic Acid) Adsorption

This paper presents the results of a MM2 study of the adsorption of oleic acid and ethanol/water in the tunnel and active-site models of lipases from Candida rugosa and Candida antarctica B. The role of an interface polar/no polar in the opening of C. rugosa lipase's lid is also addressed, discussed and analyzed at the level of the conformational changes needed to achieve the lipase open form. The adsorption of oleic acid and alcohols considering C. antarctica B, a lipase not interfacially activated, is also presented. In this case, the tunnel is shorter than in case of C. rugosa lipase. Two different pockets can be visualized at the active site-tunnel model of C. antarctica B lipase: one for the acyl group and another for the alcohol. Wrong location of alcohol and oleic acid severely hinders reaction because it hinders the H-transfer to histidine, a key step in the reaction mechanism. Right location of alcohol decreases the possibility of alcohol inhibition. In the case of C. rugosa, no restrictions for ethanol/water location are found. For that lipase, a second adsorption site for oleic acid (outside the tunnel) is presented. This site is the exit tunnel of the ester product when oleic acid is adsorbed in the tunnel. Experimental results of our own that correlate with this study are presented.

Model studies on the formation of monochloropropanediols in the presence of lipase

The formation of chloropropanols was investigated using model systems comprised of lipase, vegetable oil or fat, water, and sodium chloride. The results showed that measurable levels of the foodborne carcinogen 3-chloro-1,2-propanediol (3-MCPD) are formed in the presence of commercially available lipases of mammalian, vegetable, and fungal origins, incubated at temperatures of 40 degrees C. The highest yield of 3-MCPD was obtained in reaction mixtures containing lipase from Rhizopus oryzae, and all the lipases studied exhibited a high hydrolytic activity toward triglycerides from palm and peanut oil. In contrast, hydrolysis over time and the yield of 3-MCPD in olive and sunflower oils were significantly lower (up to 10-fold), possibly linked to the relatively lower amount (<18%) of saturated fatty acids in these oils. We provide here for the first time evidence that lipases are able to induce the formation of chloropropanols under model system conditions. However, the key intermediates and precise mechanistic aspects governing the formation of 3-MCPD in the presence of lipase still need to be elucidated.

Sequence and structure of epoxide hydrolases: a systematic analysis

Epoxide hydrolases (EC 3.3.2.3) are ubiquitous enzymes that catalyze the hydrolysis of epoxides to the corresponding vicinal diols. More than 100 epoxide hydrolases (EH) have been identified or predicted, and 3 structures are available. Although they catalyze the same chemical reaction, sequence similarity is low. To identify conserved regions, all EHs were aligned. Phylogenetic analysis identified 12 homologous families, which were grouped into 2 major superfamilies: the microsomal EH superfamily, which includes the homologous families of Mammalian, Insect, Fungal, and Bacterial EHs, and the cytosolic EH superfamily, which includes Mammalian, Plant, and Bacterial EHs. Bacterial EHs show a high sequence diversity. Based on structure comparison of three known structures from Agrobacterium radiobacter AD1 (cytosolic EH), Aspergillus niger (microsomal EH), Mus musculus (cytosolic EH), and multisequence alignment and phylogenetic analysis of 95 EHs, the modular architecture of this enzyme family was analyzed. Although core and cap domain are highly conserved, the structural differences between the EHs are restricted to only two loops: the NC-loop connecting the core and the cap and the cap-loop, which is inserted into the cap domain. EHs were assigned to either of three clusters based on loop length. By using this classification, core and cap region of all EHs, NC-loops and cap-loops of 78% and 89% of all EHs, respectively, could be modeled. Representative models are available from the Lipase Engineering Database, http://www.led.uni-stuttgart.de.