Low-concentration trypsin detection from a metal-enhanced fluorescence (MEF) platform: Towards the development of ultra-sensitive and rapid detection of proteolytic enzymes

Proteolytic enzymes, which serve to degrade proteins to their amino acid building blocks, provide a distinct challenge for both diagnostics and biological research fields. Due to their ubiquitous presence in a wide variety of organisms and their involvement in disease, proteases have been identified as biomarkers for various conditions. Additionally, low-levels of proteases may interfere with biological investigation, as contamination with these enzymes can physically alter the protein of interest to researchers, resulting in protein concentration loss or subtler polypeptide clipping that leads to a loss of functionality. Low levels of proteolytic degradation also reduce the shelf-life of commercially important proteins. Many detection platforms have been developed to achieve low-concentration or low-activity detection of proteases, yet many suffer from limitations in analysis time, label stability, and ultimately sensitivity. Herein we demonstrate the potential utility of fluorescein derivatives as fluorescent labels in a new, turn-off enzymatic assay based on the principles of metal-enhanced fluorescence (MEF). For fluorescein sodium salt alone on nano-slivered 96-well plates, or Quanta Plates™, we report up to 11,000x enhancement for fluorophores within the effective coupling or enhancement volume region, defined as ~100 nm from the silver surface. We also report a 9% coefficient of variation, and detection on the picomolar concentration scale. Further, we demonstrate the use of fluorescein isothiocyanate-labeled YebF protein as a coating layer for a MEF-based, Quanta Plate™ enzymatic activity assay using trypsin as the model enzyme. From this MEF assay we achieve a detection limit of ~1.89 ng of enzyme (2.8 mBAEE activity units) which corresponds to a minimum fluorescence signal decrease of 10%. The relative success of this MEF assay sets the foundation for further development and the tuning of MEF platforms for proteolytic enzyme sensing not just for trypsin, but other proteases as well. In addition, we discuss the future development of ultra-fast detection of proteases via microwave-accelerated MEF (MAMEF) detection technologies.

CT2108A and B: New fatty acid synthase inhibitors as antifungal agents

A systematic screen for new natural products that displayed antifungal activity by inhibition of fungal fatty acid synthase (FAS) led to the discovery of two new fungal metabolites, designated CT2108A (1) and CT2108B (2). The metabolites were produced by Penicillium solitum (Westling) strain CT2108 and were classified as azaphilones. The structures of these new metabolites were determined using a variety of 1D and 2D NMR experiments, including COSY, HMQC, and HMBC. The chemical conversion of CT2108A to CT2108B was effected using WCl(6). The related metabolite, patulodin (3), was also isolated from the fermentation culture of this P. solitum isolate. Both new compounds inhibited fungal FAS, and neither was found to significantly inhibit human FAS activity.

Phenolic compounds from Nymphaea odorata

Assay-guided fractionation of the ethanol extract of Nymphaea odorata resulted in the identification of two lignans, one new (1) and one known (2), together with six known flavonol glycosides (3-8). The structures of 1-8 were established by spectroscopic analysis as nymphaeoside A (1), icariside E(4) (2), kaempferol 3-O-alpha-l-rhamnopyranoside (afzelin, 3), quercetin 3-O-alpha-l-rhamnopyranoside (4), myricetin 3-O-alpha-l-rhamnopyranoside (myricitrin, 5), quercetin 3-O-(6' '-O-acetyl)-beta-d-galactopyranoside (6), myricetin 3-O-beta-d-galactopyranoside (7), and myricetin 3-O-(6' '-O-acetyl)-beta-d-galactopyranoside (8). Compounds 3, 4, and 7 showed marginal inhibitory effect against fatty acid synthase with IC(50) values of 45, 50, and 25 microg/mL, respectively.

Flavanone glycosides from Miconia trailii

Assay-guided fractionation of the ethanol extract of the twigs and leaves of Miconia trailii yielded two new flavanone glycosides, matteucinol 7-O-alpha-l-arabinopyranosyl(1-->6)-beta-d-glucopyranoside (miconioside A, 1) and farrerol 7-O-beta-d-apiofuranosyl(1-->6)-beta-d-glucopyranoside (miconioside B, 2), along with the known compounds matteucinol 7-O-beta-d-apiofuranosyl(1-->6)-beta-d-glucopyranoside (3), matteucinol (4), 2alpha,3beta,19alpha-trihydroxyolean-12-ene-24,28-dioic acid (bartogenic acid, 5), 2alpha,3beta,23-trihydroxyolean-12-ene-28-oic acid (arjunolic acid, 6), 2alpha,3alpha,19alpha, 23-tetrahydroxyurs-12-ene-28-oic acid (myrianthic acid, 7), and stigmast-4-ene-3,6-dione (8). The structures of 1-8 were elucidated by spectroscopic methods, including 2D NMR.

Fatty acid synthase inhibitors from plants: isolation, structure elucidation, and SAR studies

Fatty acid synthase (FAS) has been identified as a potential antifungal target. FAS prepared from Saccharomyces cerevisiae was employed for bioactivity-guided fractionation of Chlorophora tinctoria,Paspalum conjugatum, Symphonia globulifera, Buchenavia parviflora, and Miconia pilgeriana. Thirteen compounds (1-13), including three new natural products (1, 4, 12), were isolated and their structures identified by spectroscopic interpretation. They represented five chemotypes, namely, isoflavones, flavones, biflavonoids, hydrolyzable tannin-related derivatives, and triterpenoids. 3'-Formylgenistein (1) and ellagic acid 4-O-alpha-l-rhamnopyranoside (9) were the most potent compounds against FAS, with IC(50) values of 2.3 and 7.5 microg/mL, respectively. Furthermore, 43 (14-56) analogues of the five chemotypes from our natural product repository and commercial sources were tested for their FAS inhibitory activity. Structure-activity relationships for some chemotypes were investigated. All these compounds were further evaluated for antifungal activity against Candida albicans and Cryptococcus neoformans. Although there were several antifungal compounds in the set, correlation between the FAS inhibitory activity and antifungal activity could not be defined.

Mechanical and chemical unfolding of a single protein: a comparison

Is the mechanical unraveling of protein domains by atomic force microscopy (AFM) just a technological feat or a true measurement of their unfolding? By engineering a protein made of tandem repeats of identical Ig modules, we were able to get explicit AFM data on the unfolding rate of a single protein domain that can be accurately extrapolated to zero force. We compare this with chemical unfolding rates for untethered modules extrapolated to 0 M denaturant. The unfolding rates obtained by the two methods are the same. Furthermore, the transition state for unfolding appears at the same position on the folding pathway when assessed by either method. These results indicate that mechanical unfolding of a single protein by AFM does indeed reflect the same event that is observed in traditional unfolding experiments. The way is now open for the extensive use of AFM to measure folding reactions at the single-molecule level. Single-molecule AFM recordings have the added advantage that they define the reaction coordinate and expose rare unfolding events that cannot be observed in the absence of chemical denaturants.

Avirulence of Candida albicans FAS2 mutants in a mouse model of systemic candidiasis

Disruption of both alleles of the Candida albicans FAS2 gene abolishes the ability of the organism to establish infection in a murine model of systemic candidiasis. Within 72 h all mice inoculated with 10(6) CFU of the parental C. albicans strain had died. In contrast, all animals inoculated with the mutant strain CFD2 survived for the course of the experiment (21 days). Animals infected with either mutant strain CFD1 or CFD3, in which only one FAS2 allele was disrupted, also succumbed to infection, but mortality was not observed until 4 days postinfection and survivors remained for up to 20 days postinfection. The results demonstrate that FAS2 is required for successful C. albicans infection.

Requirement for the Candida albicans FAS2 gene for infection in a rat model of oropharyngeal candidiasis

The virulence of Candida albicans strains deficient in fatty acid synthase activity by virtue of disruption/deletion of the FAS2 gene was examined in a rat model of oropharyngeal candidiasis. The FAS2 alleles of C. albicans CAI4 (delta ura3::imm434/delta ura3::imm434) were sequentially disrupted with a cassette that included a portion of FAS2 from which a 984 bp fragment containing the FAS condensing reaction domain was deleted and replaced with hisG-URA3-hisG sequences. Verification of fatty acid synthase inactivation was obtained from assays of enzyme activity. Strains in which a single allele was disrupted (CFD1 and CFD3) exhibited an approximately 20% reduction in activity, when compared to wild-type. In addition, fatty acid synthase activity was abolished in a FAS2 null mutant strain (CFD2), and growth of CFD2 occurred only when the growth medium was supplemented with Tween 40 and certain fatty acids. Strain CFD2 was avirulent in the rat model, indicating that fatty acid synthase activity is required for C. albicans oropharyngeal infection. Strains with a single FAS2 allele disruption colonized the oral cavity, but the number of cells recovered from infected animals was approximately fivefold less than for the parental strain. The results suggest that FAS may be exploited as a possible target for the development of new antifungal agents.

Growth-phase-dependent induction of 6-phosphogluconate dehydrogenase and glucose 6-phosphate dehydrogenase in the cyanobacterium Synechococcus sp. PCC7942

In most cyanobacteria, the only known pathway for oxidation of stored carbohydrate in the dark or under energy-limiting conditions is the hexose monophosphate shunt. To determine whether the increased use of the shunt under these conditions derives from an increase in the activity level of the respective enzymes, we measured the effect of growth phase during the growth of batch cultures of Synechococcus sp. strain PCC7942 on the specific activity of 6-phosphogluconate dehydrogenase (6PGD) and glucose 6-phosphate dehydrogenase. The specific activities were constant during the exponential growth phase of the culture, but they increased about fivefold during the transition into stationary phase. As an approach to determining the level of expression at which the growth-phase-dependent regulation of 6PGD level is exerted, we constructed operon and gene fusions between the gnd gene, which encodes 6PGD, and the Escherichia coli lacZ gene, which encodes beta-galactosidase (beta Gal). Strains harboring the fusions integrated into the cyanobacterial chromosome were prepared, and the growth-phase dependence of beta Gal level was determined. The specific activity of beta Gal in cultures of both types of fusion strains increased during the transition into stationary phase, indicating that the growth-phase-dependent regulation is on the gnd mRNA level. Characterization of the growth-phase-dependent induction of 6PGD in strains carrying differing amounts of DNA upstream from the gnd structural gene led to the localization of the promoter and the regulatory site on the restriction map of the gene, whose sequence has previously been determined.(ABSTRACT TRUNCATED AT 250 WORDS)

Genetic tagging, cloning, and DNA sequence of the Synechococcus sp. strain PCC 7942 gene (gnd) encoding 6-phosphogluconate dehydrogenase

A genetic approach was used for the cloning of the Synechococcus sp. strain PCC 7942 (Synechococcus strain R2) gnd gene which encodes 6-phosphogluconate dehydrogenase (6PGD). A restriction map of the gnd locus was prepared by Southern analysis using the Escherichia coli gene as a heterologous probe. The Synechococcus strain R2 gene was genetically tagged by restriction site-specific insertion of the nptII gene of Tn903 into a pUC19 plasmid library of Synechococcus strain R2 chromosomal DNA. Synechococcus strain R2 was transformed with this insertion mutation library, and isolates carrying the gnd::nptII gene were identified as mutants hypersensitive to incubation in the dark. The interrupted gene was cloned from one of the mutants. A plasmid carrying the gnd::nptII gene was reintroduced into Synechococcus strain R2, and kanamycin-resistant transformants were selected. Transformants arising by gene replacement were dark sensitive and missing 6PGD activity. Transformants arising by plasmid insertion were dark resistant and had 6PGD activity. The wild-type gene was then cloned from a transformant containing a plasmid insertion, making use of the restriction map derived from the interrupted gene. Synechococcus strain R2 6PGD was expressed in E. coli when the cloned gnd gene was transcribed from the lacZ promoter resident on the vector. The boundaries of the gene and the direction of transcription were determined from the phenotypes conferred by plasmids carrying deletions entering gnd from either end. The nucleotide sequence was determined. The deduced amino acid sequence of Synechococcus strain R2 6PGD has 56% homology to that of the E. coli K-12 enzyme.