[Using peptide strategy for study functions and structure of signal proteins with enzymatic activity]

The peptide strategy, a new direction of molecular endocrinology, includes the synthesis of peptides corresponding to functional regions of signal proteins, the use of the peptides for study of the molecular mechanisms of transduction of hormonal signal into cell ant the development of selective regulators of hormonal signaling systems on the basis of these peptides. The peptide strategy is used for study a wide spectrum of the proteins, components of signal systems, the proteins possessing the catalytic activity in particular, such as tyrosine kinases receptors, the enzymes generating the second messengers, serine/threonine protein kinase, phosphatases. In the first time in the review the data concerning the synthetic peptides, derivatives of the primary structure of proteins with the enzymatic activity, their application for study of the structural-functional organization and the molecular mechanisms of action of signal proteins, and the construction of regulators of fundamental cell processes on the basis of these peptides are analyzed and summarized.

Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes

All reactions are accelerated by an increase in temperature, but the magnitude of that effect on very slow reactions does not seem to have been fully appreciated. The hydrolysis of polysaccharides, for example, is accelerated 190,000-fold when the temperature is raised from 25 to 100 °C, while the rate of hydrolysis of phosphate monoester dianions increases 10,300,000-fold. Moreover, the slowest reactions tend to be the most heat-sensitive. These tendencies collapse, by as many as five orders of magnitude, the time that would have been required for early chemical evolution in a warm environment. We propose, further, that if the catalytic effect of a "proto-enzyme"--like that of modern enzymes--were mainly enthalpic, then the resulting rate enhancement would have increased automatically as the environment became cooler. Several powerful nonenzymatic catalysts of very slow biological reactions, notably pyridoxal phosphate and the ceric ion, are shown to meet that criterion. Taken together, these findings greatly reduce the time that would have been required for early chemical evolution, countering the view that not enough time has passed for life to have evolved to its present level of complexity.

Nitrite biosensing via selective enzymes--a long but promising route

The last decades have witnessed a steady increase of the social and political awareness for the need of monitoring and controlling environmental and industrial processes. In the case of nitrite ion, due to its potential toxicity for human health, the European Union has recently implemented a number of rules to restrict its level in drinking waters and food products. Although several analytical protocols have been proposed for nitrite quantification, none of them enable a reliable and quick analysis of complex samples. An alternative approach relies on the construction of biosensing devices using stable enzymes, with both high activity and specificity for nitrite. In this paper we review the current state-of-the-art in the field of electrochemical and optical biosensors using nitrite reducing enzymes as biorecognition elements and discuss the opportunities and challenges in this emerging market.

Ascorbate and plasma membrane electron transport--enzymes vs efflux

Transplasma membrane electron transport (tPMET) systems transfer electrons across the plasma membrane, resulting in the net reduction of extracellular oxidants (e.g., ferricyanide) at the expense of intracellular reductants such as NADH and ascorbate. In mammalian tPMET systems, the major proximal electron donor is ascorbate. The classical description of ascorbate-dependent tPMET views ascorbate as a restrictively intracellular electron donor to a transplasma membrane enzymatic activity that transfers electrons across the plasma membrane to various physiological acceptors (e.g., ferric iron and the ascorbyl radical). Candidate proteins involved in this process include members of the cytochrome b(561) family (e.g., duodenal cytochrome b). However, mounting evidence suggests that cellular export of ascorbate (and concomitant import of its two-electron oxidation product, dehydroascorbate) may constitute a novel and physiologically relevant form of ascorbate-dependent tPMET. As with enzymatic tPMET, cellular ascorbate export results in net electron transfer from the cytoplasm to the extracellular space. The mechanisms of ascorbate release from cells are ill-defined, though volume-sensitive anion channels and exocytosis remain promising candidates. Cellular ascorbate release is implicated in various homeostatic processes including ascorbate maintenance in blood and brain, and the uptake of non-transferrin-bound iron by cells. Recent insights into the "duality" of ascorbate-dependent tPMET are discussed.

Quantum catalysis in enzymes: beyond the transition state theory paradigm. A Discussion Meeting held at the Royal Society on 14 and 15 November 2005

How do enzymes work? What is the physical basis of the phenomenal rate enhancements achieved by enzymes? Do we have a theoretical framework that accounts for observed catalytic rates? These are the foremost questions-with particular emphasis on tunnelling phenomena-debated at this Discussion Meeting by the leading practitioners in the field.

EFICAz2: enzyme function inference by a combined approach enhanced by machine learning

BACKGROUND

We previously developed EFICAz, an enzyme function inference approach that combines predictions from non-completely overlapping component methods. Two of the four components in the original EFICAz are based on the detection of functionally discriminating residues (FDRs). FDRs distinguish between member of an enzyme family that are homofunctional (classified under the EC number of interest) or heterofunctional (annotated with another EC number or lacking enzymatic activity). Each of the two FDR-based components is associated to one of two specific kinds of enzyme families. EFICAz exhibits high precision performance, except when the maximal test to training sequence identity (MTTSI) is lower than 30%. To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment.

RESULTS

We have developed two new EFICAz components, analogs to the two FDR-based components, where the discrimination between homo and heterofunctional members is based on the evaluation, via Support Vector Machine models, of all the aligned positions between the query sequence and the multiple sequence alignments associated to the enzyme families. Benchmark results indicate that: i) the new SVM-based components outperform their FDR-based counterparts, and ii) both SVM-based and FDR-based components generate unique predictions. We developed classification tree models to optimally combine the results from the six EFICAz components into a final EC number prediction. The new implementation of our approach, EFICAz2, exhibits a highly improved prediction precision at MTTSI < 30% compared to the original EFICAz, with only a slight decrease in prediction recall. A comparative analysis of enzyme function annotation of the human proteome by EFICAz2 and KEGG shows that: i) when both sources make EC number assignments for the same protein sequence, the assignments tend to be consistent and ii) EFICAz2 generates considerably more unique assignments than KEGG.

CONCLUSION

Performance benchmarks and the comparison with KEGG demonstrate that EFICAz2 is a powerful and precise tool for enzyme function annotation, with multiple applications in genome analysis and metabolic pathway reconstruction. The EFICAz2 web service is available at: http://cssb.biology.gatech.edu/skolnick/webservice/EFICAz2/index.html.

Enzyme function prediction with interpretable models

Enzymes play central roles in metabolic pathways, and the prediction of metabolic pathways in newly sequenced genomes usually starts with the assignment of genes to enzymatic reactions. However, genes with similar catalytic activity are not necessarily similar in sequence, and therefore the traditional sequence similarity-based approach often fails to identify the relevant enzymes, thus hindering efforts to map the metabolome of an organism.Here we study the direct relationship between basic protein properties and their function. Our goal is to develop a new tool for functional prediction (e.g., prediction of Enzyme Commission number), which can be used to complement and support other techniques based on sequence or structure information. In order to define this mapping we collected a set of 453 features and properties that characterize proteins and are believed to be related to structural and functional aspects of proteins. We introduce a mixture model of stochastic decision trees to learn the set of potentially complex relationships between features and function. To study these correlations, trees are created and tested on the Pfam classification of proteins, which is based on sequence, and the EC classification, which is based on enzymatic function. The model is very effective in learning highly diverged protein families or families that are not defined on the basis of sequence. The resulting tree structures highlight the properties that are strongly correlated with structural and functional aspects of protein families, and can be used to suggest a concise definition of a protein family.

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system containing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calculating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. The data in BRENDA are manually curated from more than 79,000 primary literature references. Each entry is clearly linked to a literature reference, the origin organism and, where available, to the protein sequence of the enzyme protein. A new search option provides the access to protein-specific data. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are additional databases created by continuously improved text-mining procedures. These databases ought to provide a complete survey on enzyme data of the literature collection of PubMed. The web service via a SOAP (Simple Object Access Protocol) interface for access to the BRENDA data has been further enhanced.

Porcine preadipocyte proliferation and differentiation: a role for leptin?

The present study was designed to determine whether porcine leptin can alter the proliferation and differentiation of the porcine preadipocyte. The stromal vascular cell fraction of neonatal pig s.c. adipose tissue was isolated by collagenase digestion, filtration, and subsequent centrifugation. For differentiation studies, cells were seeded on six-well tissue culture plates and proliferated to confluency in 10% (vol/vol) fetal bovine serum (FBS) in Dulbecco's modified Eagle medium/F12 (DMEM/F12; 50:50). Cultures were differentiated using 2.5% pig serum (vol/vol) and recombinant porcine leptin at concentrations of 0 to 1,000 ng/mL alone or in combination with porcine insulin (100 nM), dexamethasone (1 microM), or IGF-1 (250 ng/mL). After 7 d of lipid filling, cultures were harvested for analysis of sn-glycerol 3 phosphate dehydrogenase (GPDH) and lipoprotein lipase (LPL). The GPDH and LPL activities are measures of preadipocyte differentiation. Data were corrected for protein content of the cultures. For proliferation experiments, 24 h after seeding cells with 10% FBS in DMEM/F12 in 25-cm2 tissue culture flasks, cells were switched to 5% FBS and supplemented with 0 to 1,000 ng of porcine leptin or 1,000 ng of murine leptin. Cell proliferation was measured by 3H-thymidine incorporation in preconfluent cultures over 24 h on d 4 of culture. At confluency, cells were switched to a medium to promote differentiation and lipid filling (2.5% pig serum, 100 nM insulin, 1 microM dexamethasone) for 7 d. Cells were harvested from the flasks and adipocytes were separated from stromal cells by Percoll gradient centrifugation. In a series of experiments, leptin alone or in combination with insulin, dexamethasone, or IGF-I did not affect differentiation as measured by the activity of GPDH and LPL. Leptin at any concentration did not inhibit differentiation induced by insulin, dexamethasone, or IGF-I; however, leptin at 1,000 ng/mL stimulated a 30% increase in preadipocyte proliferation (P = 0.007; n = 6) and a 27% increase in stromal cell proliferation (P < 0.001; n = 6). These results indicate that, at most, porcine leptin may contribute to the recruitment of new adipocytes within the adipose tissue.

Transient stress and stress enzyme responses have practical impacts on parameters of embryo development, from IVF to directed differentiation of stem cells

In this review, we discuss the expression, regulation, downstream mechanisms, and function of stress-induced stress enzymes in mammalian oocytes, peri-implantation embryos, and the stem cells derived from those embryos. Recent reports suggest that stress enzymes mediate developmental functions during early mammalian development, in addition to the homeostatic functions shared with somatic cells. Stress-induced enzymes appear to insure that necessary developmental events occur: many of these events may occur at a slower rate, although some may occur more rapidly. Developmental events induced by stress may be mediated by a single dominant enzyme, but there are examples of responses that require the integration of more than one stress enzyme. The discussion focuses on the consequences of stress as a function of duration and magnitude, and this includes an emerging understanding of the threshold levels of duration and magnitude that lead to pathology. Other topics discussed are the reversibility of the developmental as well as homeostatic consequences of stress, the further problems with readaptation after stress subsides, and the mechanisms and functions of stress enzymes during early mammalian development. The analyses are done with specific concern for their practical impact in assisted reproductive technology (ART) and stem cell technologies.

Adrenal androgens in humans and nonhuman primates: production, zonation and regulation

The synthesis and secretion of large quantities of the adrenal androgens, dehydroepiandrosterone (DHEA) and its sulfoconjugate DHEA sulfate (DS), is a phenomenon that appears limited to humans and some nonhuman primates. Both hydroxylase and lyase activities of the enzyme 17alpha-hydroxylase/17,20-lyase cytochrome P450 (P450c17) are necessary for DHEA production and are differentially regulated during adrenal development. Production of DHEA and DS occurs in the zona reticularis (ZR) of adults and the fetal zone of fetal primate adrenal glands, which is the primary substrate for maternal estrogen production during pregnancy. The onset of adrenal androgen production in childhood, referred to as adrenarche, corresponds with the establishment of the ZR: but the process is poorly understood, largely due to the lack of accessible animal models. Several nonhuman primates have been used to study adrenal function and remodeling, though none completely recapitulates human adrenarche, developmentally, functionally or temporally. This review will summarize the variations in adrenal androgen production and adrenal zonation in humans and nonhuman primates throughout life. It is hoped that recent studies demonstrating adrenarche in the rhesus will put in proper context the significance of adrenal zonation in nonhuman primates as valid models for human adrenal development and function.

Steroidogenic enzymes

The enzymes and pathways of steroidogenesis are familiar to most endocrinologists, but the biochemistry and molecular biology of these processes are still being studied. This chapter outlines current knowledge about each enzyme. The quantitative regulation of steroidogenesis occurs at the first step, the conversion of cholesterol to pregnenolone. Chronic regulation is principally at the level of transcription of the gene for P450 side chain cleave (P450scc), which is the enzymatically rate-limiting step. Acute regulation is mediated by steroidogenic acute regulatory protein, which facilitates the rapid influx of cholesterol into mitochondria, where P450scc resides. Qualitative regulation, determining the class of steroid produced, is principally determined by P450c17. In the absence of P450c17 in the zona glomerulosa, C21 deoxy steroids are produced, leading to the mineralocorticoid aldosterone. In the presence of the 17alpha-hydroxylase but not the 17,20 lyase activity of P450c17 in the zona fasciculata, C21, 17-hydroxy steroids are produced, leading to the glucocorticoid cortisol. When both the 17alpha-hydroxylase and 17,20 lyase activities of P450c17 are present in the zona reticularis, the androgen precursor dehydroepiandrosterone is produced. The discrimination between 17alpha-hydroxylase and 17,20 lyase activities is regulated by two posttranslational events, the serine phosphorylation of P450c17 and the allosteric action of cytochrome b5, both of which act to optimize the interaction of P450c17 with its obligatory electron donor, P450 oxidoreductase.

Cardiac sodium channel Nav1.5 and its associated proteins

The main cardiac voltage-gated Na+ channel, Nav1.5, plays a key role in generation of the cardiac action potential (cardiac excitability) and propagation of the electrical impulse in the heart (cardiac conduction). During the past decade, numerous mutations in SCN5A, the gene, encoding Nav1.5, were found in patients with different pathologic cardiac phenotypes such as the congenital long QT syndrome type 3, Brugada syndrome, and progressive cardiac conduction defect (or Lenègre-Lev disease). These mutations define a sub-group of Nav1.5 / SCN5A-related cardiac channelopathies. Recent works have suggested that Nav1.5 is part of several multi-protein complexes located in different membrane compartments of the cardiac cells. In some instances, the genes of these regulatory proteins were also found to be mutated in patients with inherited forms of cardiac arrhythmias. The proteins that associate with Nav1.5, and form these complexes, can be classified as 1) anchoring/adaptor proteins, 2) enzymes interacting with and modifying the channel, and 3) proteins modulating the biophysical properties of Nav1.5 upon binding. The purpose of this short article is to review the proposed roles of these interactions. These recent observations indicate that the expression level, cellular localization, and activity of Nav1.5 are finely regulated by complex molecular mechanisms that we are only starting to elucidate.

Mechanism of cell surface expression of the Streptococcus mitis platelet binding proteins PblA and PblB

PblA and PblB are prophage-encoded proteins of Streptococcus mitis strain SF100 that mediate binding to human platelets. The mechanism for surface expression of these proteins has been unknown, as they do not contain signal sequences or cell wall sorting motifs. We therefore assessed whether expression of these proteins was linked the lytic cycle of the prophage. Deletion of either the holin or lysin gene resulted in retention of PblA and PblB in the cytoplasm, and loss of these proteins from the cell wall. Flow cytometric analysis revealed that induction of phage replication in SF100 produced a subpopulation of cells with increased permeability. This effect was abrogated by disruption of the holin and lysin genes. Treatment of these mutants with exogenous PblA and PblB restored surface expression, apparently via binding of the proteins to cell wall choline. Loss of PblA and PblB expression was associated with decreased platelet binding in vitro, and reduced virulence in an animal model of endocarditis. Thus, expression of PblA and PblB occurs via a novel mechanism, whereby phage induction increases bacterial permeability and release of the proteins, followed by their binding to surface of viable cells. This mechanism may be important for endovascular infection.

Genome-wide analysis of enzyme structure-function combination across three domains of life

To investigate diverse enzyme structure-function combination (SFC) types in different species, 34 different genome sequences were annotated using the protein catalytic domain database SCOPEC (http://www.enzome.com/enzome/), in which both the structure and function for each entry are known. Annotated enzymes with catalytic domains from the same SCOP superfamily are considered to have an identical structure. Annotated enzymes sharing the identical three-digit EC number are considered to have the same enzymatic function. Results reveal that the different SFC types for enzymes identified in archaea, bacteria and eukaryota are 137, 300 and 313, respectively. About 80% of the SFCs identified in archaea can be consistently found in bacteria and eukaryota species, whereas 28% and 35% combination types in bacteria and eukaryota respectively are unique to their corresponding groups. The number of functions per structure and the number of structures per function for the annotated sequences were measured in different species. Furthermore, a new concept was proposed to represent enzymatic structures as a functional similarity network. Thus, the current study will be helpful to enhance the global view on the evolution of enzymatic structure and function.

Isolation and properties of a levo-lactonase from Fusarium proliferatum ECU2002: a robust biocatalyst for production of chiral lactones

A fungus strain ECU2002, capable of enantioselectively hydrolyzing chiral lactones to optically pure hydroxy acids, was newly isolated from soil samples through two steps of screening and identified as Fusarium proliferatum (Matsushima) Nirenberg. From the crude extract of F. proliferatum ECU2002, a novel levo-lactonase was purified to homogeneity, with a purification factor of 460-folds and an overall yield of 9.7%, by ultrafiltration, acetone precipitation, and chromatographic separation through DEAE-Toyopearl, Butyl-Toyopearl, Hydroxyapatite, Toyoscreen-Super Q, and TSK-gel columns. The purified enzyme is a monomer; with a molecular mass of ca 68 kDa and a pI of 5.7 as determined by two-dimensional electrophoresis. The catalytic performance of the partially purified levo-lactonase was investigated, giving temperature and pH optima at 50 degrees C and 7.5, respectively, for gamma-butyrolactone hydrolysis. The substrate specificity of the partially purified lactonase was also examined using several useful lactones, among which alpha-hydroxy-gamma-butyrolactone was the best substrate, with 448-fold higher lactonase activity as compared to gamma-butyrolactone. The F. proliferatum lactonase preferentially hydrolyzed the levo enantiomer of butyrolactones, including beta-butyrolactone, alpha-hydroxy-gamma-butyrolactone, alpha-hydroxy-beta,beta-dimethyl-gamma-butyrolactone (pantolactone), and beta-hydroxy-gamma-butyrolactone, affording (+)-hydroxy acids in high (94.8 approximately 98.2%) enantiomeric excesses (ee) and good conversions (38.2 approximately 44.2%). A simple immobilization of the crude lactonase with glutaraldehyde cross-linking led to a stable and easy-to-handle biocatalyst for catalytic resolution of chiral lactones. The immobilized lactonase also performed quite well in repeated batch resolution of dl-pantolactone at a concentration of 35% (w/v), retaining 67% of initial activity after ten cycles of reaction (corresponding to a half life of 20 cycles) and affording the product in 94 approximately 97% ee, which can be easily enhanced to >99% ee after the d-hydroxy acid was chemically converted into l-lactone and crystallized.

Enzymes and pharmacogenetics of cardiovascular drugs

To select the best drug for a patient, physicians can use pharmacogenomics to optimize the effective drug and to minimize adverse reactions. Many enzymes are involved in the pharmacokinetic and pharmacodynamic sources of cardiovascular drugs. Taking the antihypertensive drugs as an example, the variability in blood pressure response is very high in different individuals, some of them having an increase in blood pressure. The most important proteins involved in the patient response to a drug are cytochrome P450 (CYP) 2D6, CYP2C19, CYP3A4 and the ABCB1 transporter. These enzymes, at the origin of important side effects or drug interactions, are responsible, at a great extent, of the cardiovascular drug response variability. Genotyping of the most important CYP today is easy while no reliable tool has been developed for the ABC transporters ATPase dependent and linked to the other phase I and phase II enzymes. The second relevant group of enzymes are involved in pharmacodynamic action of cardiovascular drugs: enzymes of the renin-angiotensin system and enzymes of the lipid metabolism. Angiotensin converting enzyme (ACE) is the most studied target with a relevant insertion deletion polymorphism. Contradictory reported data could be explained by ethnic differences or patient sample size which are often too small.

Selection strategies for improved biocatalysts

Enzymes have become an attractive alternative to conventional catalysts in numerous industrial processes. However, their properties do not always meet the criteria of the application of interest. Directed evolution is a powerful tool for adopting the characteristics of an enzyme. However, selection of the evolved variants is a critical step, and therefore new strategies to enable selection of the desired enzymatic activity have been developed. This review focuses on these novel strategies for selecting enzymes from large libraries, in particular those that are used in the synthesis of pharmaceutical intermediates and pharmaceuticals.