Protein and Peptide Letters - Volume 16, Issue 10, 2009

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The α/βhydrolase superfamily has rapidly expanded in recent years and continues to do so at an expeditious pace. According to the ESTHER database (http://bioweb.ensam.inra.fr/ESTHER) 29000 papers have been published cataloguing 89 family groups, comprising a total of 15438 gene loci and 666 structures. This paper presents a snapshot of the current family taxonomy, catalytic chemistries, structural topologies and useful technologies emerging from the knowledge base at the current time.

Carboxylesterases (Carboxyl ester hydrolase) include two groups of enzymes, namely non-specific esterases (EC 3.1.1.1) and lipases (EC 3.1.1.3) which have been early differentiated on the basis of their substrate specificity. Esterases hydrolyse solutions of water-soluble short acyl chain esters and are inactive against water-insoluble long chain triacylglycerols which, in turn, are specifically hydrolyzed by lipases. Based on the comparison of the primary structures, three families of sequence-related carboxylesterases, namely the lipoprotein lipase family (L-family), the hormonesensitive lipase family (H-family) and the cholinesterase family (C-family) have been identified. Using solutions and emulsions of vinyl, glyceryl and p-nitrophenyl esters, we have reinvestigated the kinetic properties of some esterases and lipases of the H- and C-families. Results indicate that esterases and lipases, which are both active on soluble esters, can be differentiated by their value of Km. Moreover, esterase, unlike lipases, are inactive against water-insoluble esters as vinyl laurate and trioctanoylglycerol. From the the comparison of structural features of sequence-related esterases and lipases, it appears that lipases, unlike esterases, display a significant difference in the distribution of hydrophobic amino acid residues at vicinity of their active site. This observation supports the hypothesis of the existence in lipases of a particular surface domain that specifically interacts with lipid-water interfaces and contributes to the transfer a single substrate molecule from the organized lipid-water interface (supersubstrate) to the catalytic site of the enzyme.

In the past few years a considerable number of mutagenesis methods and high-throughput screening (HTS) systems have been developed and improved. In parallel, computer programs or software packages for molecular modeling have been further investigated. Thus, the number of examples for successful directed evolution and rational design is increasing constantly. In this review the essential mutagenesis methods and HTS systems, especially for esterases, are described and various examples for the application of these protein engineering tools are provided.

Micro-organisms that thrive at low temperatures produce cold-adapted enzymes which display high catalytic efficiency, generally associated with low thermal stability. In the recent past, researchers and industries have focused the attention on cold-adapted enzymes, whose peculiar properties make them particularly interesting either for investigating stability/flexibility relationships, or for their potential application in industrial processes. Among these enzymes, lipases and esterases, have potential utilisations in a broad range of biotechnological applications. In fact, these biocatalysts represent the most widely used enzymes in biotechnology and organic chemistry. Modern methods of genetic engineering combined with growing knowledge of structure and function allow further adaptation to industrial needs and exploration of novel applications. Hence, in this review we attempt to offer an overview on some psychrophilic esterases and lipases; major details will be presented for ORF PSHAa0051 from Pseudoalteromonas haloplanktis TAC125, recently investigated by our team. In addition, potential biotechnological applications will be discussed.

Carboxylesterases (EC 3.1.1.1) distribute broadly in insects, and play an important role in the metabolism with various functions. This paper reviews the insect carboxylesterases including the definitions and reaction mechanism, classification, structural context, functions especially on insecticide resistance, and its application.

Thermophilic and hyperthermophilic carboxylesterases (EC 3.1.1.1) are excellent model systems for studying structure function relationships as well as in vitro and in vivo evolution and possible biotechnological applications. In this paper we review the main aspect of one of most studied microbial representative of the hormone sensitive lipase family (HSL), namely carboxylesterase 2 (EST2) from Alicyclobacillus acidocaldarius.

In the last years we have performed a series of studies to characterize the conformational stability of three esterases from thermophilic and mesophilic sources: Aes esterase from Escherichia coli, EST2 from Alicyclobacillus acidocaldarius and AFEST from Archeoglobus fulgidus. These three esterases belong to the Hormone-sensitive lipase group of the superfamily of carboxylester hydrolases. The conformational stability of the three enzymes against temperature, urea and GuHCl has been determined by means of circular dichroism, fluorescence and differential scanning calorimetry measurements. Analysis of experimental data coupled with available structural information allowed us to suggest that the optimization of charge-charge interactions on the protein surface could be one of the mechanisms to increase the thermal stability for the three esterases. This idea has been tested in the case of EST2, which shows a fully reversible thermal unfolding, by producing and studying variant forms of wild type enzyme in which a charged residue has been mutated. In the present article the obtained results are critically recollected in order to provide a clear and unified scenario.

Carboxylesterases belong to Phase I group of drug metabolizing enzymes. They hydrolyze a variety of drug esters, amides, carbamates and similar structures. There are five ‘carboxylesterase’ genes listed in the Human Genome Organization database. In this review, we will focus on the CES1, CES2 and CES3 genes and their protein products that have been partially characterized. Several variants of these three CESs result from alternate splicing, single nucleotide polymorphisms and multiple copy variants. The three CESs, are largely localized to tissues that are major sites of drug metabolism like the mucosa of the gastrointestinal tract, lungs and liver but, they differ in tissue-specific expression. The amino acid alignment of the three CESs reveals important conserved catalytic and structural residues. There are interesting insertions and deletions that may affect enzymatic function as determined by homology modeling of CES3 using the CES1 three-dimensional structure. A comparison of the substrate specificity of CES1 versus CES2 reveals broad but distinct substrate preferences. There is little information on the substrate specificity of CES3 but it seems to have a lower catalytic efficiency than the other two CESs for selected substrates.

Human butyrylcholinesterase (BuChE) is a serine enzyme present in most organs and plasma. No clear physiological function has yet been assigned to BuChE, but it is a pharmacologically and toxicologically important enzyme that plays a role in degradation of numerous ester-containing drugs and poisonous esters. Thus, BuChE-based bioscavengers are an alternative for prophylaxis and treatments of intoxications by these compounds. Also, BuChE has been integrated in biosensors for detection of organophosphorus compounds and other cholinesterase inhibitors.

The quest for a quick and easy detection of the neurotoxin levels in the environment has fostered the search for systems alternative to currently employed analytical methods such as spectrophotometry, gas-liquid chromatography, thin-layer chromatography, and more recently mass spectrometry. These drawbacks lead to intense research efforts to develop biosensor devices for the determination of these compounds. In this review, we present an overview of the actual development of research in neurotoxin detection by using enzymatic biosensors based on esterase activity, in particular cholinesterases, and carboxylesterases. Detection by enzymatic activity could be carried out measuring the hydrolysis products or the residual enzymatic activity after inhibition, using a transducer system that makes possible the correlation between the determined activity and the analyte concentration. Several transducer systems were adopted for the neurotoxins identification using esterases, including electrochemical, optical, conductimetric and piezoelectric procedures. The differences in the used transducer determine the final sensitivity and specificity of the biosensor. Moreover, a brief description of immobilization procedure, that is an important step in the biosensor development and could affect the final characteristic of biosensor (sensibility, stability, response time and reproducibility), was accomplished. Final considerations on advantages and problems, related to actual development of these technologies, and its prospective were discussed.

The milk fat is an essential component for the development of correct flavour in cheese. The lipolysis and catabolism of fatty acids are two biochemical events very important on flavour development of some cheese varieties. The role and characteristics of various lipolytic agents during cheese ripening is reviewed and discused. Before starting with the specific study about formation of flavour compounds from milk fat during cheese ripening, a brief review of the technological aspects of cheese production is needed.

We showed that Tspan-1, a tetraspanin overexpressed in many human cancers, harbours oligosaccharides at all four potential N-glycosylation sites. Its most abundant form contained only mannose-rich sugar chains but two distinct glycosylation sites could also contain complex carbohydrates. Glycosylation seemed to be required for correct folding and subsequent transition through the endoplasmic reticulum.

Oxidized human galectin-1 plays a role in the immune response to injured axons. Over-expression of galectin-1 by cancer, in combination with cancer associated oxidative stress suggests oxidized human galectin-1 may also play a role(s) in tumourigenesis. Here we generate milligram quantities of oxidized human galectin-1 and undertake biophysical characterization. The protein adopts a number of different states. Two separable oxidized forms are identified that exist as largely mono-disperse solutions at higher milligram/ml concentrations. The presence of disulphide bonds is confirmed for these two protein forms, as is their change in overall shape and loss of lectin activity. Our studies lead to production of a particular mono-disperse oxidized human galectin-1 species that is anticipated most optimal for investigations requiring milligram/ml concentrations such as X-ray crystallography.

A previously uncharacterized member of the M1 family of zinc metallopeptidases, arginyl aminopeptidase-like 1 (RNPEPL1; EC 3.4.11.1), was cloned and expressed, and the recombinant enzyme characterized. RNPEPL1 was a broad specificity aminopeptidase with preference for a P1 methionine, glutamine, or citrulline residue, and exhibited a broad pH preference, with maximal activity observed between pH 6.6 and 8.0. The enzyme was inhibited by calcium ions but unaffected by chloride ions, and was insensitive to specific inhibitors of the closely-related arginyl aminopeptidase, indicating similarity to leukotriene A4 hydrolase. RT-PCR analysis of RNPEPL1 expression revealed a ubiquitous tissue distribution, consistent with a general housekeeping function, but also revealed alternative splicing of the mRNA in all tissues examined. The inclusion of intron 5 was predicted to result in a truncated protein product, while an alternative 3’ splice site of exon 9 of the reference sequence was predicted to result in the omission of a conserved eleven amino acid stretch from the C-terminal domain.

To fix the large and expanding gap between sequence known proteins and structure known proteins, it is important to study on protein structural class prediction (PSCP) for its foundation and usefulness in protein structure analysis. In this paper, the d-interval conditional probability index was proposed to reflect the long-term correlation between amino acids. Based on this index, the impact of residues' long-term relationship on PSCP was analyzed. Two new information theory based algorithms were proposed and were used combining with the long-term information between residues to predict protein structural class (PSC). The dataset 5714 was tested for its low sequence similarity and high reliability. The result showed that the new index was 3-6% higher than traditional index by use of the same algorithms, and the PSCP accuracy was 4-10% improved using the new algorithms. The presented index, algorithms and the long-term relationship of residues on PSCP can be extensively applied in other sequence based protein structure analysis.