Use of a native affinity ligand for the detection of G proteins by capillary isoelectric focusing with laser-induced fluorescence detection

Affinity probe capillary isoelectric focusing (CIEF) with laser-induced fluorescence was explored for detection of Ras-like G proteins. In the assay, a fluorescent BODIPY FL GTP analogue (BGTPgammaS) and G protein were incubated resulting in formation of BGTPgammaS-G protein complex. Excess BGTPgammaS was separated from BGTPgammaS-G protein complex by CIEF using a 3-10 pH gradient and detected in whole-column imaging mode. In other cases, a single point detector was used to detect zones during the focusing step of CIEF using a 2.5-5 pH gradient. In this case, analyte peaks passed the detector in approximately 5 min at an electric field of 350 V/cm. Detection during focusing allowed for more reproducible assays at shorter times but with a sacrifice in sensitivity compared to detection during mobilization. Resolution was adequate to separate BGTPgammaS-Ras and BGTPgammaS-Rab3A complexes. Formation of specific complexes was confirmed by adding GTPgammaS to samples containing BGTPgammaS-G protein. GTPgammaS competed with BGTPgammaS for G protein binding sites resulting in decreased BGTPgammaS-G protein peak heights. The concentrating effect of CIEF enabled detection limits of 30 pM.     

A CE assay for the detection of agonist-stimulated adenylyl cyclase activity

A CE assay was developed for the detection of adenylyl cyclase (AC) activity stimulated at the AC and G protein-coupled receptor (GPCR) level. In the assay, cell membranes overexpressing GPCR and/or AC were incubated with modulators and substrate ATP to produce cAMP in a dose-dependent manner. In both the CE-UV and a radiochemical assay, the addition of forskolin (FSK) resulted in a two- to three-fold maximum increase in AC activity with EC50s of 4.2 +/- 0.7 and 2.4 +/- 0.7 microM, respectively, demonstrating that similar results were obtained by both assays. GPCR activation was also detected using cell membranes overexpressing AC and the beta2-adrenergic receptor (beta2AR) fused to the stimulatory G protein. Terbutaline (beta2AR agonist) increased the basal rate of cAMP formation 1.7 +/- 0.1-fold resulting in an EC50 of 62 +/- 10 nM. The assay's ability to detect antagonists is demonstrated by the expected right-shifted EC50 of terbutaline by the beta2AR antagonist propranolol. The CE-UV assay offers advantages over the traditional radioactivity assay in terms of safety and labor.     

Homogeneous fluorescence assay for cyclic AMP

The objective of these studies was to develop a new homogeneous fluorescence assay for determining the concentrations of cAMP in biological samples. The assay is based on a novel general concept of using ligand-dependent sequence-specific DNA binding proteins as sensors for their respective ligands. CAP protein, a bacterial DNA binding protein whose DNA binding activity depends on cAMP, was used to develop the assay. In the presence of cAMP, DNA binding activity of CAP is greatly increased. Signaling of cAMP presence was achieved by detecting cAMP-dependent formation of CAP-DNA complex using a recently developed fluorescence assay for DNA binding proteins (Heyduk, T., and Heyduk, E. Nature Biotechnology 20,171-176, 2002). Both 96-well and 384-well black microplate formats of the assay were developed and used to detect cAMP in low nanomolar concentrations. The assay involves mixing of the sample with the assay solution containing all necessary components for cAMP determination followed by fluorescence intensity readout; no washing or reagent addition steps are necessary. Excellent reproducibility of fluorescence signal change as a function of cAMP concentration was observed. Experiments with HEK 293 cells stimulated with forskolin were performed to demonstrate that the assay could be used for cAMP determination in cellular extracts. In summary, the obtained data fully validated the new homogenous assay for measuring cAMP based on cAMP-dependent DNA binding activity of CAP protein. It is expected that the development of assays for many other ligands of DNA binding proteins will be possible using the same overall assay design developed for cAMP.     

Structural insights into calmodulin/adenylyl cyclase 8 interaction

Calmodulin (CaM) is a highly conserved intracellular Ca²⁺-binding protein that exerts important functions in many cellular processes. Prominent examples of CaM-regulated proteins are adenylyl cyclases (ACs), which synthesize cAMP as a central second messenger. The interaction of ACs with CaM represents the link between Ca²⁺-signaling and cAMP-signaling pathways. Thereby, different AC isoforms stimulated by CaM, comprise diverse mechanisms of regulation by the Ca²⁺ sensor. To extend the structural information about the detailed mechanisms underlying the regulation of AC8 by CaM, we employed an integrated approach combining chemical cross-linking and mass spectrometry with two peptides representing the CaM-binding regions of AC8. These experiments reveal that the structures of CaM/AC8 peptide complexes are similar to that of the CaM/skeletal muscle myosin light chain kinase peptide complex where CaM is collapsed around the target peptide that binds to CaM in an antiparallel orientation. Cross-linking experiments were complemented by investigating the binding of AC8 peptides to CaM thermodynamically with isothermal titration calorimetry. There were no hints on a complex, in which both AC8 peptides bind simultaneously to CaM, refining our current understanding of the interaction between CaM and AC8.

Activation of the hippocampal AC‐cAMP‐PKA‐CREB‐BDNF signaling pathway using WTKYR in depression model rats

Depression, also called “depression disorder,” is characterized by a significant and persistent low mood. It has become a major refractory disease in the 21st century. In recent years, Chinese medicine has shown some important clinical value in the treatment of depression. Among them, the Warming and “Tonifying” Kidney‐Yang Recipe (WTKYR) has been demonstrated to have obvious effects in the clinical treatments of depression; however, the mechanism remains unclear. This study is based on the adenylyl cyclase (AC)—cyclic adenosine monophosphate (cAMP)—protein kinase A (PKA)—cAMP response element‐binding protein (CREB)—brain derived neurotrophic factor (BDNF) signaling pathway, aiming to investigate the mechanism of WTKYR. The results showed that WTKYR can upregulate AC‐cAMP‐PKA‐CREB‐BDNF in the hippocampus of depression model rats and alleviate its depressive symptoms, which may be the mechanism of WTKYR.     

8-Hydroxyquinoline-substituted boron-dipyrromethene compounds: synthesis, structure, and OFF-ON-OFF type of pH-sensing properties

A series of four novel 8-hydroxyquinoline-substituted boron-dipyrromethene derivatives, namely 4,4-difluoro-8-(5-(8-hydroxyquinoline))-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (1), 4,4-difluoro-8-(5-(8-hydroxyquinoline))-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (2), 4,4-difluoro-8-(5-azastyryl-(8-hydroxyquinoline))-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (3), and 4,4-difluoro-8-(5-azastyryl-(8-hydroxyquinoline))-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (4), have been synthesized and characterized by a series of spectroscopic methods. The molecular structures of 1 and 2 have been determined by single-crystal X-ray diffraction analyses. The two methyl substituents attached at C-1 and C-7 positions of boron-dipyrromethene (Bodipy) in compound 2 was revealed to prevent the free rotation of the 8-hydroxyquinoline (8-HQ) moiety, resulting in an almost vertical 8-HQ-Bodipy configuration of this compound. This is obviously different from those for 1 with the dihedral angle between 8-hydroxyquinoline and Bodipy moieties of 65.44 and 66.79° due to the lack of methyl substituents in the latter compound. The intense fluorescence from the Bodipy subunit of these compounds was revealed to gradually get diminished along with either decreasing or increasing the pH value under acidic and basic conditions, respectively, in particular for 1, 2, and 4 because of the photoinduced intramolecular electron transfer from excited Bodipy moiety to 8-HQ unit and just an opposite process. This renders these compounds the first OFF-ON-OFF type of pH-dependent fluorescent sensors. Nevertheless, both the intrinsic fluorescence of these compounds and their fluorescent quenching properties along with the change in the pH value have been found to depend on the steric configuration as well as the linking group between 8-hydroxyquinoline and Bodipy moieties, revealing the effect of molecular structure on their fluorescence properties.     

Fluorescence polarization is a useful technology for reagent reduction in assay miniaturization

The use of fluorescence polarization (FP) has increased significantly in the development of sensitive and robust assays for high throughput screening of chemical compound libraries during the past few years. In this study, we show that FP is a useful assay miniaturization technology for reagent reduction during high throughput screening. We developed and optimized several FP assays for binding to estrogen receptor alpha and two protein kinases with an assay volume of 100 microl. Without any re-optimization, a consistent signal window was maintained in 384- or 1536-well format when the assay volume varied from 2.5-100 microl at constant concentrations of all assay components. In contrast, the signal window decreased with decreasing assay volume at constant reagent concentration in the protein kinase C scintillation proximity assay (SPA) and prompt fluorescence assay. In addition, the effect of evaporation on the signal window was minimal for the FP assays. Our study suggests that FP is superior to SPA and prompt fluorescence in terms of reagent reduction in the miniaturized assay format.     

Determination of the DNA methylation level in tumor cells by capillary electrophoresis and laser-induced fluorescence detection

An analytical method to determine the genome-wide DNA methylation in only 100 ng DNA is presented. The analysis is based on DNA isolation and hydrolysis followed by derivatization of the 2'-desoxyribonucleoside-3'-monophosphates with a fluorescence dye (4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionyl ethylene diamine hydrochloride, Bodipy FL EDA). The separation of the derivatives was carried out by micellar electrokinetic chromatography, and laser-induced fluorescence was used for detection. To calculate the methylation level, the derivatization factor and the quantum yields of the Bodipy conjugates of 2'-desoxycytidine-3'-monophosphate (dCMP) and 2'-desoxy-5-methylcytidine-3'-monophosphate (5m-dCMP) were determined by measurement of methylated Lambda DNA. The assignment was made by cochromatography with the synthesized and characterized standard compound 5m-dCMP. After optimization of the method it was possible to determine the methylation level in 100-ng DNA samples with a standard deviation of less than 5%.     

Biochemical Characterization of the Engineered Soluble Photoactivated Guanylate Cyclases from Microbes Expands Optogenetic Tools

Cyclic nucleotide, such as cyclic GMP, is a secondary messenger that regulates a wide range of biological process via the diverse signaling cascades. Photoactivated adenylyl cyclases (PACs), constituted of blue light utilizing flavin (BLUF) and cyclase homology domain (CHD), are used as an optogenetic tool to modulate the cyclic AMP (cAMP) level and to study cAMP-mediated signal transduction mechanisms. Here, we have engineered photoactivated adenylyl cyclases (PACs) from microbes to photoactivated guanylyl cyclases (PGCs) via mutagenesis of the substrate binding-specific residues in cyclase homology domain. We demonstrate purification, photodynamic, and detailed biochemical characterization of the engineered PGCs that can serve as optogenetic tool for manipulation of cGMP level in the cells. Engineered PGCs show typical BLUF photoreceptor properties with different recovery kinetics and varying light-regulated guanylyl cyclase activities.     

A phytochrome-like protein AphC triggers the cAMP signaling induced by far-red light in the cyanobacterium Anabaena sp. strain PCC7120

In the filamentous, nitrogen-fixing cyanobacterium Anabaena sp. PCC7120, red light (630 nm) decreased, whereas far-red light (720 nm) increased cellular adenosine 3',5'-cyclic monophosphate (cAMP) content. To find a red and far-red light photoreceptor that triggers the cAMP signal cascade, we disrupted 10 open reading frame having putative chromophore-binding GAF domains. The response of the cellular cAMP concentration to red and far-red light in each open reading frame disruptant was determined. It was found that only the mutant of the gene all2699 failed to respond to far-red light. The open reading frame named as aphC encoded a protein with 920 amino acids including GAF domains similar to those involved in Cph2, a photoreceptor of Synechocystis sp. PCC6803. To determine which adenylate cyclase (AC) is responsible for far-red light signal, we disrupted all AC genes and found that CyaC was the candidate. The enzymatic activity of CyaC might be controlled by a far-red light photoreceptor through the phosphotransfer reaction. The site-specific mutant of the Asp59 residue of the receiver (R1) domain of CyaC lost its light-response capability. It was suggested that the far-red light signal was received by AphC and then transferred to the N-terminal response regulator domain of CyaC. Then its catalytic activity was stimulated, which increased the cellular cAMP concentration and drove the subsequent signal transduction cascade.     

High-throughput screening of small molecules in miniaturized mammalian cell-based assays involving post-translational modifications

BACKGROUND: Fully adapting a forward genetic approach to mammalian systems requires efficient methods to alter systematically gene products without prior knowledge of gene sequences, while allowing for the subsequent characterization of these alterations. Ideally, these methods would also allow function to be altered in a temporally controlled manner. RESULTS: We report the development of a miniaturized cell-based assay format that enables a genetic-like approach to understanding cellular pathways in mammalian systems using small molecules, rather than mutations, as the source of gene-product alterations. This whole-cell immunodetection assay can sensitively detect changes in specific cellular macromolecules in high-density arrays of mammalian cells. Furthermore, it is compatible with screening large numbers of small molecules in nanoliter to microliter culture volumes. We refer to this assay format as a 'cytoblot', and demonstrate the use of cytoblotting to monitor biosynthetic processes such as DNA synthesis, and post-translational processes such as acetylation and phosphorylation. Finally, we demonstrate the applicability of these assays to natural-product screening through the identification of marine sponge extracts exhibiting genotype-specific inhibition of 5-bromodeoxyuridine incorporation and suppression of the anti-proliferative effect of rapamycin. CONCLUSIONS: We show that cytoblots can be used for high-throughput screening of small molecules in cell-based assays. Together with small-molecule libraries, the cytoblot assay can be used to perform chemical genetic screens analogous to those used in classical genetics and thus should be applicable to understanding a wide variety of cellular processes, especially those involving post-transitional modifications.     

Promising fast energy transfer system via an easy synthesis: Bodipy-porphyrin dyads connected via a cyanuric chloride bridge, their synthesis, and electrochemical and photophysical investigations

The boron dipyrrin (Bodipy) chromophore was combined with either a free-base or a Zn porphyrin moiety (H(2)P and ZnP respectively), via an easy synthesis involving a cyanuric chloride bridging unit, yielding dyads Bodipy-H(2)P (4) and Bodipy-ZnP (5). The photophysical properties of Bodipy-H(2)P (4) and Bodipy-ZnP (5) were investigated by UV-Vis absorption and emission spectroscopy, cyclic voltammetry, and femtosecond transient absorption spectroscopy. The comparison of the absorption spectra and cyclic voltammograms of dyads Bodipy-H(2)P (4) and Bodipy-ZnP (5) with those of their model compounds Bodipy, H(2)P, and ZnP shows that the spectroscopic and electrochemical properties of the constituent chromophores are essentially retained in the dyads indicating negligible interaction between them in the ground state. In addition, luminescence and transient absorption experiments show that excitation of the Bodipy unit in Bodipy-H(2)P (4) and Bodipy-ZnP (5) into its first singlet excited state results in rapid Bodipy to porphyrin energy transfer-k(4) = 2.9 × 10(10) s(-1) and k(5) = 2.2 × 10(10) s(-1) for Bodipy-H(2)P (4) and Bodipy-ZnP (5), respectively-generating the first porphyrin-based singlet excited state. The porphyrin-based singlet excited states give rise to fluorescence or undergo intersystem crossing to the corresponding triplet excited states. The title complexes could also be used as precursors for further substitution on the third chlorine atom on the cyanuric acid moiety.     

The mechanism of sugar-dependent repression of synthesis of catabolic enzymes in Escherichia coli.

Previous studies have indicated that the Escherichia coli adenylate cyclase (AC) activity is controlled by an interaction with the phosphoenolpyruvate (PEP): sugar phosphotransferase system (PTS). A model for the regulation of AC involving the phosphorylation state of the PTS is described. Kinectic studies support the concept that the velocity of AC is determined by the opposing contributions of PEP-dependent phosphorylation (V1) and sugar-dependent dephosphorylation (V2) of the PTS proteins according to the expression percent VAC=100/[1 + (Max V2/Max V1)]. Physiological parameters influencing the rate of the PTS are discussed in the framework of their effects on cAMP metabolism. Factors that increase cellular concentration of PEP (and stimulate V1) appear to enhance AC activity while increases in extracellular sugar concentration (which stimulate V2) or internal levels of pyruvate (which inhibit V1) inhibit the activity of this enzyme.     

Ultrafast Energy Transfer in Triptycene‐Grafted Bodipy Scaffoldings

A series of new compounds in which various Bodipy dyes are grafted logically on triptycene rigid structures are synthesized and characterized, and their absorption spectra and photophysical properties are studied, also by pump‐probe transient absorption spectroscopy. The studied compounds are: the mono‐Bodipy species TA, TB, and TC (where A, B, and C identify different Bodipy subunits absorbing and emitting at different wavelengths), the multichromophore species TA₃, which bears three identical A subunits, and the three multichromophoric species TAB, TBC, and TABC, all of them containing at least two different types of Bodipy subunits. The triptycene moiety plays the role of a rigid scaffold, keeping the various dyes at predetermined distances and allowing for a three‐dimensional structural arrangement of the multichromophoric species. The absorption spectra of the multichromophoric Bodipy species are essentially additive, indicating that negligible inter‐chromophoric interaction takes place at the ground state. Luminescence properties and transient absorption spectroscopy indicate that a very fast (on the picosecond time scale) and efficient photoinduced energy transfer occurs in all the multi‐Bodipy species, with the lower‐energy Bodipy subunits of each multi‐Bodipy compounds playing the role of an electronic energy collector. In TAB, an energy transfer from the A‐type Bodipy subunit to the B‐type one takes place with a rate constant of 1.6×10¹⁰ s^?1, whereas in TBC an energy transfer from the B‐type Bodipy subunit to the C‐type subunit is bi‐exponential, exhibiting rate constants of 1.7×10¹¹ and 1.9×10¹⁰ s^?1; the possible presence of different conformers with different donor–acceptor distances in this bichromophoric species is proposed to cause the bi‐exponential energy‐transfer process. Interpretation of the intricate energy‐transfer pathways occurring in TABC is made with the help of the processes identified in the bichromophoric compounds. In all cases, the measured energy‐transfer rate constants agree with a Förster mechanism for the energy‐transfer processes.     

Implementation of droplet-membrane-droplet liquid-phase microextraction under stagnant conditions for lab-on-a-chip applications

In the current work, droplet-membrane-droplet liquid-phase microextraction (LPME) under totally stagnant conditions was presented for the first time. Subsequently, implementation of this concept on a microchip was demonstrated as a miniaturized, on-line sample preparation method. The performance level of the lab-on-a-chip system with integrated microextraction, capillary electrophoresis (CE) and laser-induced fluorescence (LIF) detection in a single miniaturized device was preliminarily investigated and characterized. Extractions under stagnant conditions were performed from 3.5 to 15 μL sample droplets, through a supported liquid membrane (SLM) sustained in the pores of a small piece of a flat polypropylene membrane, and into 3.5-15 μL of acceptor droplet. The basic model analytes pethidine, nortriptyline, methadone, haloperidol, and loperamide were extracted from alkaline sample droplets (pH 12), through 1-octanol as SLM, and into acidified acceptor droplets (pH 2) with recoveries ranging between 13 and 66% after 5 min of operation. For the acidic model analytes Bodipy FL C₅ and Oregon Green 488, the pH conditions were reversed, utilizing an acidic sample droplet and an alkaline acceptor droplet, and 1-octanol as SLM. As a result, recoveries for Bodipy FL C₅ and Oregon Green 488 from human urine were 15 and 25%, respectively.     

Automated high content screening for phosphoinositide 3 kinase inhibition using an AKT 1 redistribution assay

High Content Screening (HCS), a combination of fluorescence microscopic imaging and automated image analysis, has become a frequently applied tool to study test compound effects in cellular disease-modelling systems. In this work, we established a medium to high throughput HCS assay in the 384-well format to measure cellular type I phosphoinositide 3 kinase (PI3K) activity. Type I PI3K is involved in several intracellular pathways such as cell survival, growth and differentiation as well as immunological responses. As a cellular model system we used Chinese Hamster Ovary (CHO) cells that had been stably transfected with human insulin receptor (hIR) and an AKT1-enhanced green fluorescent protein (EGFP) fusion construct. Upon stimulation of the hIR with insulin-like growth factor-1 (IGF-1), PI3K was activated to phosphorylate phosphatidylinositol (PtdIns)-4,5-bisphosphate at the 3-position, resulting in the recruitment of AKT1-EGFP to the plasma membrane. The AKT1-EGFP redistribution assay was robust and displayed little day-to-day variability, the quantification of the fluorescence intensity associated with plasma membrane spots delivered good Z' statistics. A novel format of compound dose-response testing was employed using serial dilutions of test compounds across consecutive microtiter plates (MTPs). The dose response testing of a PI3K inhibitor series provided reproducible IC50 values. The profiling of the redistribution assay with isoform-selective inhibitors indicates that PI3Kalpha is the main isoform activated in the CHO host cells after IGF-1 stimulation. Toxic compound side effects could be determined using automated image analysis. We conclude that the AKT1-EGFP redistribution assay represents a solid medium/high throughput screening (MTS/HTS) format to determine the cellular activity of PI3K inhibitors under conditions of growth factor stimulation.     

Fluorescence resonance energy transfer assay for high-throughput screening of ADAMTS1 inhibitors

A disintegrin and metalloprotease with thrombospondin type I motifs-1 (ADAMTS1) plays a crucial role in inflammatory joint diseases and its inhibitors are potential candidates for anti-arthritis drugs. For the purposes of drug discovery, we reported the development and validation of fluorescence resonance energy transfer (FRET) assay for high-throughput screening (HTS) of the ADAMTS1 inhibitors. A FRET substrate was designed for a quantitative assay of ADAMTS1 activity and enzyme kinetics studies. The assay was developed into a 50-μL, 384-well assay format for high throughput screening of ADAMTS1 inhibitors with an overall Z' factor of 0.89. ADAMTS1 inhibitors were screened against a diverse library of 40,960 total compounds with the established HTS system. Four structurally related hits, naturally occurring compounds, kuwanon P, kuwanon X, albafuran C and mulberrofuran J, extracted from the Chinese herb Morus alba L., were identified for further investigation. The results suggest that this FRET assay is an excellent tool, not only for measurement of ADAMTS1 activity but also for discovery of novel ADAMTS1 inhibitors with HTS.     

Contribution of the cAMP-Dependent Signal Pathway to Circadian Synchrony of Motility and Resting Membrane Potential in Paramecium

It is known that the ciliated protozoan Paramecium multimicronucleatum has synchronized circadian rhythms of motility, resting membrane potential and cyclic adenosine 3',5'-monophosphate (cAMP) and cyclic guanosine 3',5'-monophosphate (cGMP) concentrations. The present study shows that (1) extracellularly added 4 m M tetraethylammonium (TEA)⁺ (a K⁺ channel blocker) almost completely abolishes the diurnal oscillation of intracellular cAMP concentrations; (2) even 32 m^M TEA⁺ fails to abolish the circadian motility rhythm; but (3) the motility rhythm is highly damped when 4 m^M TEA⁺ and 100 μ^M CdCl₂ (a Ca²⁺ channel blocker) are added simultaneously. A cAMP analogue ( N ⁶-monobutyryl-cAMP) added extracellularly accelerates swimming velocity. Both a K⁺ channel blocker ( e.g . TEA⁺) and an inhibitor (trifluoperazine) of adenylate cyclase (AC) suppress cAMP formation, supporting the hypothesis that AC in Paramecium has dual functions, as a K⁺ channel and as an enzyme for cAMP formation. It is hypothesized that the circadian synchrony is due to circadian fluctuations of AC causing separate circadian changes both in ciliary motion and membrane potential through a cAMP-dependent signal pathway that forms a sophisticated network of second messengers to govern the synchrony together with Ca²⁺- and cGMP-dependent pathways in a manner antiphasic and/or complementary to one another.