A label-free and sensitive fluorescent assay for one step detection of protein kinase activity and inhibition

In this paper, a label-free, highly sensitive and simple assay for one step detection of protein kinase (PKA) activity and inhibition that avoids the fluorescent dye process has been established. The detection was based on the fluorescence (FL) quenching of peptide-Ag nanoclusters (Ag NCs) caused by antibody modified Au nanoparticles (anti-Au NPs) via fluorescence resonance energy transfer (FRET). With PKA and adenosine 5′-triphosphate (ATP) introduced, the substrate peptide of Ag NCs could react with PKA via targeted phosphorylation, and followed by the linking interactions between peptide-Ag NCs and anti-Au NPs. According to the fluorescence quenching of Ag NCs, the activity of protein kinase can be facilely monitored in the range of 0.1–2000 mU/μL with high sensitivity. The detection limit for PKA is 0.039 mU/μL. We further explored the inhibitory effect of H-89 for protein kinase activity. The developed method was also applied to the investigation of drug-induced PKA activation in HeLa cells, which provides a promising means for screening of kinase-related drugs and the clinical diagnosis of disease.     

Development of a peptide inhibitor-based cantilever sensor assay for cyclic adenosine monophosphate-dependent protein kinase

A highly sensitive nanomechanical cantilever sensor assay based on an electrical measurement has been developed for detecting activated cyclic adenosine monophosphate (cyclic AMP)-dependent protein kinase (PKA). Employing a peptide derived from the heat-stable protein kinase inhibitor (PKI), a magnetic bead system was first selected as a vehicle to immobilize the PKI-(5-24) peptide for capturing PKA catalytic subunit and the activity assay was applied for indirectly assessing the binding. Synergistic interactions of adenosine triphosphate (ATP) and the peptide inhibitor with the kinase were then investigated by a solution phase capillary electrophoretic assay, and by surface plasmon resonance technology which involved immobilization of the peptide inhibitor. After systemically evaluated by a homogeneous direct binding assay, the ATP-dependent recognition of the catalytic subunit of PKA by PKI-(5-24) was successfully transferred on to the nanomechanical cantilevers at protein concentrations of 6.6 pM-66 nM, exhibiting much higher sensitivity and wider dynamic range than the conventional activity assay. Thus, direct assessment of activated kinases using the cantilever sensor system functionalized with specific peptide inhibitors holds great promise in analytical applications and clinical medicine.     

Analysis of protein kinase A activity in insulin-secreting cells using a cell-penetrating protein substrate and capillary electrophoresis

A cell-penetrating, fluorescent protein substrate was developed to monitor intracellular protein kinase A (PKA) activity in cells without the need for cellular transfection. The PKA substrate (PKAS) was prepared with a 6×histidine purification tag, an enhanced green fluorescent protein (EGFP) reporter, an HIV-TAT protein transduction domain for cellular translocation and a pentaphosphorylation motif specific for PKA. PKAS was expressed in Escherichia coli and purified by metal affinity chromatography. Incubation of PKAS in the extracellular media facilitated translocation into the intracellular milieu in HeLa cells, βTC-3 cells and pancreatic islets with minimal toxicity in a time and concentration dependent manner. Upon cellular loading, glucose-dependent phosphorylation of PKAS was observed in both βTC-3 cells and pancreatic islets via capillary zone electrophoresis. In pancreatic islets, maximal PKAS phosphorylation (83 ± 6%) was observed at 12 mM glucose, whereas maximal PKAS phosphorylation (86 ± 4%) in βTC-3 cells was observed at 3 mM glucose indicating a left-shifted glucose sensitivity. Increased PKAS phosphorylation was observed in the presence of PKA stimulators forskolin and 8-Br-cAMP (33% and 16%, respectively), with corresponding decreases in PKAS phosphorylation observed in the presence of PKA inhibitors staurosporine and H-89 (40% and 54%, respectively).     

Electrochemical sensing for the determination of activated cyclic AMP-dependent protein kinase.

A novel electrochemical system has been developed for monitoring the cyclic AMP-dependent protein kinase (PKA) activity. In this method, PKA activity was monitored as the change in the redox current of a ferrocene-pendant PKA substrate peptide (Fe-LRRASLG) on a gold electrode, which had been modified with thioctic acid, using cyclic voltammetry. The phosphrylation of the ferrocene-pendant substrate with PKA changed the net charge from +1 to -1. This caused a decrease in the redox current of the ferrocene unit due to an electrostatic repulsion between the substrate and the anionic surface of the electrode. We expect that this method is potentially useful for monitoring the enzyme activity in medical or pharmacological fields.     

Isoform-specific PKA dynamics revealed by dye-triggered aggregation and DAKAP1alpha-mediated localization in living cells

The tetracysteine sequence YRECCPGCCMWR fused to the N terminus of green fluorescent protein (GFP) self-aggregates upon biarsenical labeling in living cells or in vitro. Such dye-triggered aggregates form temperature-dependent morphologies and are dispersed by photobleaching. Fusion of the biarsenical aggregating GFP to the regulatory (R) or catalytic (C) subunit of PKA traps intact holoenzyme in compact fluorescent puncta upon biarsenical labeling. Contrary to the classical model of PKA activation, elevated cAMP does not allow RIalpha and Calpha to diffuse far apart unless the pseudosubstrate inhibitor PKI or locally concentrated substrate is coexpressed. However, RIIalpha releases Calpha upon elevated cAMP alone, dependent on autophosphorylation of the RIIalpha inhibitory domain. DAKAP1alpha overexpression induced R and C outer mitochondrial colocalization and showed similar regulation. Overall, effective separation of type I PKA is substrate dependent, whereas type II PKA dissociation relies on autophosphorylation.     

Sensitive and versatile electrogenerated chemiluminescence biosensing platform for protein kinase based on Ru(bpy)3 functionalized gold nanoparticles mediated signal transduction

A novel, sensitive and versatile electrogenerated chemiluminescence biosensing platform is developed for monitoring activity and inhibition of protein kinase based on Ru(bpy)₃²⁺ functionalized gold nanoparticles (Ru(bpy)₃²⁺-AuNPs) mediated signal transduction. Ru(bpy)₃²⁺-AuNPs were formed by functionalizing AuNPs with Ru(bpy)₃²⁺ through electrostatic interactions and were used as thiol-versatile signal probe. Casein kinase II (CK2) and cAMP-dependent protein kinase (PKA), two classical protein kinase implicated in disease, were chosen as model protein kinases while a CK2-specific peptide (CRRRADDSDDDDD) and a PKA-specific peptide (CLRRASLG) were employed as molecular substrate for CK2 and PKA, respectively. The specific peptide was self-assembled onto the gold electrode via Au–S bond to form ECL biosensor. Upon thiophosphorylation of the peptide on the electrode in the presence of protein kinase and co-substrate adenosine-5’-(γ-thio)-triphosphate, Ru(bpy)₃²⁺-AuNPs was assembled onto the thiophosphorylated peptides via Au–S bond. The Ru(bpy)₃²⁺-AuNPs attached on electrode surface produce detectable ECL signal in the presence of coreactant tripropylamine. This strategy is promising for multiple protein kinase assay and kinase inhibitor profiling with high sensitivity, good selectivity and versatility. The ECL intensity is proportional to the activity of CK2 in the range of 0.01–0.5 unit/mL with a low detection limit of 0.008 unit/mL and to the activity of PKA in the range of 0.01–0.4 unit/mL with a detection limit of 0.005 unit/mL. Additionally, this assay was applied to the detection of CK2 in serum samples and the inhibition of CK2 and PKA. This work demonstrates that the developed ECL method can provide a sensitive and versatile platform for the detection of kinase activity and drug-screening.     

Simultaneous Analysis of Phosphorylated Peptides by MALDI-TOF-MS

Six peptides with various phosphorylation sensitivities for protein kinase A (PKA) were used for the simultaneous analysis of phosphorylated peptides using matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. The mixture of six peptides was reacted with PKA and was analyzed by MALDI-TOF mass spectrometry. The intensity of all peaks except one phosphorylated peptide peak was very low (<20%). Moreover, we examined whether the addition of diammonium citrate to CHCA matrix at concentrations of 1–20 mg mL^?1 can increase the peak intensity of peptides and phosphorylated peptides. The addition of diammonium citrate increased the peak intensity of peptides and phosphorylated peptides, but an increase in the intensity was unsatisfactory. Our study strongly suggests that MALDI-TOF mass spectrometry is not suitable for the simultaneous analysis of phosphorylated peptides.     

谷胱甘肽和凋亡酶-3响应的环肽分子荧光探针

设计、合成了一类新型谷胱甘肽(glutathione,GSH)和凋亡酶-3(Caspase-3)响应的环肽分子荧光探针.该类探针主要由能量共振转移(FRET)分子荧光对、Caspase-3特异性识别多肽序列和GSH响应双硫键组成,分为不含穿膜肽序列(CP)和包含穿膜肽序列(cp CP)的两种不同环肽分子荧光探针.2种环肽分子荧光探针均能实现在GSH和Caspase-3同时存在情况下的精确成像,同时具有良好的响应性、特异性和高信噪比.该类环肽分子荧光探针在细胞培养环境中具有良好的稳定性和生物相容性.利用该探针,可以实现对星形孢菌素(STS)诱发的细胞凋亡进行实时、原位的成像监测,并对抗肿瘤药物阿霉素(DOX)和顺铂(cisplatin)诱导的细胞凋亡进行成像.这种具有多重响应并能用于精确成像的分子荧光探针将极大地促进疾病的精确诊断.     

How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study

We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reaction catalyzed by PKA is mainly dissociative, and Asp166 serves as the catalytic base to accept the proton delivered by the substrate peptide. Among the key interactions in the active site, the Mg(2+) ions, glycine rich loop, and Lys72 are found to stabilize the transition state through electrostatic interactions. On the other hand, Lys168, Asn171, Asp184, and the conserved waters bound to Mg(2+) ions do not directly contribute to lower the energy barrier of the phosphorylation reaction, and possible roles for these residues are proposed. The QM/MM calculations with different QM/MM partition schemes or different initial structures yield consistent results. In addition, we have carried out 12 ns molecular dynamics simulations on both wild type and K168A mutated PKA, respectively, to demonstrate that the catalytic role of Lys168 is to keep ATP and substrate peptide in the near-attack reactive conformation.     

Monitoring selectivity in kinase-promoted phosphorylation of densely packed peptide monolayers using label-free electrochemical detection

This paper describes remarkably high sensitivities in the label-free detection of kinase-promoted phosphorylation for 14 different peptide substrates on electrode-immobilized monolayers (gold or nitride) using serine/threonine kinases PKA, PKC, and CaMK2. Peptide substrates were preselected using (33)P-labeling in a microarray of 1024 substrates. The three most active peptides (A1-A3, C1-C3, and M1-M3) were investigated using electrochemical impedance spectroscopy (EIS) and ion-sensitive field effect transistors (ISFETs). Some of the peptide substrates, for example, the PKC-specific substrate PPRRSSIRNAH (C1), showed a remarkably high sensitivity in the EIS-based sensor measurements. Our studies revealed that this high sensitivity is primarily due to the monolayer's packing density. Nanoscopic studies demonstrated a distinct disordering of the C1-monolayer upon phosphorylation, while phosphatase-promoted dephosphorylation regenerated the highly ordered peptide monolayer. As a matter of fact, the initial surface packing of the peptide monolayer mainly determined the level of sensitivity, whereas electrostatic repulsion of the redox-active species was found to be much less important.     

Gold Nanoparticle Based Fluorescence Resonance Energy Transfer Immunoassay for the Detection of the Histone Deacetylase Activity using a Fluorescent Peptide Probe

A novel platform for detection of histone deacetylase (HDAC) activity has been developed using a gold nanoparticle based fluorescence resonance energy transfer (FRET) immunoassay. This strategy combined the acetylated fluorescent peptide probe with the anti-acetyl antibody functionalized Au NPs to measure the deacetylation activity of histone deacetylase sirtuin2. Enzymatic deacetylation of the acetylated peptide substrate was detected by a gold nanoparticle labeled anti-acetyl peptide antibody with the formation of the immunocomplex resulting in energy transfer between the fluorescent dyes and the nanoparticles. Due to the highly efficient fluorescence quenching of the gold nanoparticles, the proposed method shows a low background and favorable sensitivity. In addition, this approach can be applied to the evaluation of HDAC inhibitor activity. The proposed platform should facilitate the development of new assays for HDAC activity and other histone modifications.     

Construction of recB-recD genetic fusion and functional analysis of RecBDC fusion enzyme in Escherichia coli

Background

A novel fluorescent cAMP analog (8-[Pharos-575]- adenosine-3', 5'-cyclic monophosphate) was characterized with respect to its spectral properties, its ability to bind to and activate three main isoenzymes of the cAMP-dependent protein kinase (PKA-Iα, PKA-IIα, PKA-IIβ) in vitro, its stability towards phosphodiesterase and its ability to permeate into cultured eukaryotic cells using resonance energy transfer based indicators, and conventional fluorescence imaging.

Results

The Pharos fluorophore is characterized by a Stokes shift of 42 nm with an absorption maximum at 575 nm and the emission peaking at 617 nm. The quantum yield is 30%. Incubation of the compound to RIIα and RIIβ subunits increases the amplitude of excitation and absorption maxima significantly; no major change was observed with RIα. In vitro binding of the compound to RIα subunit and activation of the PKA-Iα holoenzyme was essentially equivalent to cAMP; RII subunits bound the fluorescent analog up to ten times less efficiently, resulting in about two times reduced apparent activation constants of the holoenzymes compared to cAMP. The cellular uptake of the fluorescent analog was investigated by cAMP indicators. It was estimated that about 7 μM of the fluorescent cAMP analog is available to the indicator after one hour of incubation and that about 600 μM of the compound had to be added to intact cells to half-maximally dissociate a PKA type IIα sensor.

Conclusion

The novel analog combines good membrane permeability- comparable to 8-Br-cAMP – with superior spectral properties of a modern, red-shifted fluorophore. GFP-tagged regulatory subunits of PKA and the analog co-localized. Furthermore, it is a potent, PDE-resistant activator of PKA-I and -II, suitable for in vitro applications and spatial distribution evaluations in living cells.     

Fluorescent modification for peptide sequencing by postsource decay-matrix assisted laser desorption/ionization-mass spectrometry

The sequential analysis of a peptide of CDYEGRLI, relating to the nucleic proteins in influenza virus, was performed by the postsource decay (PSD) fragmentation method using matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). The sequence of the peptide was difficult to analyze by MALDI-MS since the PSD fragment ions of the peptide were almost never observed and were not amenable to complete sequence interpretation. The peptide was modified by 4(5)-(iodoacetamide) fluorescent reagent to improve the sensitivity of the MALDI-PSD fragment spectrum. In the spectrum of the fluorescent modified peptide, almost all sequential b-series fragment ions were observed clearly, which was sufficient for complete sequence interpretation. The results indicate the advantage of fluorescent modification for the total sequencing of the peptides by MALDI-MS.     

Hypelcin A,an α-aminoisobutyric acid containing antibiotic peptide,induced fusion of egg yolk-l-α-phosphatidylcholine small unilamellar vesicles

Hypelcin A, an α-aminoisobutyric acid-containing antibiotic peptide inducing fusion of egg yolk-l-α-phosphatidylcholine (egg PC) small unilamellar vesicles (SUVs), was investigated by lipid-mixing assay based on resonanceenergy transfer between fluorescent probes, electron microscopy, light scattering, and¹H-nuclear magnetic-resonance spectroscopy. At a high peptide-to-lipid ratio of approximately 1:5, the peptide fuses several SUVs of 20–30 nm in diameter into a 40–100 nm vesicle. Under mild conditions where the permeability enhancement (leakage of a trapped fluorescent dye, calcein) of lipid bilayers are observed (peptide to lipid ratios around 1/100), the fusion of the SUVs also occurs, although the fusion requires a somewhat larger amount of the peptide than the leakage does. Furthermore, at higher lipid concentrations, where the aggregation step is sufficiently rapid, the fusion rate is determined by the amount of the membrane bound peptide per lipid molecule, as is the leakage rate. In contrast, for egg PC large unilamellar vesicles (110 nm), hypelcin A induces the leakage, but not the fusion. We conclude that the leakage is not due to the fusion.     

Phosphorylation-driven protein-protein interactions: a protein kinase sensing system

A highly flexible protein kinase sensing system is described that furnishes severalfold changes in fluorescence in response to phosphorylation. A library of Src kinase peptide substrates was prepared that contained different environmentally sensitive fluorophores positioned at various sites on the active site directed sequence. Robust changes in fluorescent intensity were observed in the presence of a phosphotyrosine binding domain protein (Lck SH2 domain), which furnishes a hydrophobic environment for the fluorophore. This protein kinase sensing system has the advantages that the fluorescent indicator can be unobtrusively positioned on the peptide substrate, and that different environmentally sensitive fluorophores with distinct photophysical properties can be employed.     

Ratiometric and turn-on monitoring for heavy and transition metal ions in aqueous solution with a fluorescent peptide sensor

A novel fluorescent peptide sensor containing tryptophan (donor) and dansyl fluorophore (acceptor) was synthesized for monitoring heavy and transition metal (HTM) ions on the basis of metal ion binding motif (Cys-X-X-X-Cys). The peptide probe successfully exhibited a turn on and ratiometric response for several heavy metal ions such as Hg²⁺, Cd²⁺, Pb²⁺, Zn²⁺, and Ag⁺ in aqueous solution. The enhancements of emission intensity were achieved in the presence of the HTM ions by fluorescent resonance energy transfer (FRET) and chelation enhanced fluorescence (CHEF) effects. The detection limits of the sensor for Cd²⁺, Pb²⁺, Zn²⁺, and Ag⁺ were lower than the EPA's drinking water maximum contaminant levels (MCL). We described the fluorescent enhancement, binding affinity, and detection limit of the peptide probe for HTM ions.     

Shear stress stimulates phosphorylation of protein kinase A substrate proteins including endothelial nitric oxide synthase in endothelial cells

Fluid shear stress plays a critical role in vascular health and disease. While protein kinase A (PKA) has been implicated in shear-stimulated signaling events in endothelial cells, it remains unclear whether and how PKA is stimulated in response to shear stress. This issue was addressed in the present study by monitoring the phosphorylation of endogenous substrates of PKA. Shear stress stimulated the phosphorylation of cAMP responsive element binding protein (CREB) in a PKA-dependent manner. Western blot analysis using the antibody reactive against the consensus motif of PKA substrates detected two proteins, P135 and P50, whose phosphorylation was increased by shear stress. The phosphorylation of P135 was blocked by a PKA inhibitor, H89, but not by a phosphoinositide 3-kinase inhibitor, wortmannin. Expression of a constitutively active PKA subunit stimulated P135 phosphorylation, supporting the potential of P135 as a PKA substrate. P135 was identified as endothelial nitric oxide synthase (eNOS) by immunoprecipitation study. PKA appeared to mediate shear stress-stimulated eNOS activation. Shear stress stimulated intracellular translocation of PKA activity from 'soluble' to 'particulate' fractions without involving cellular cAMP increase. Taken together, this study suggests that shear stress stimulates PKA-dependent phosphorylation of target proteins including eNOS, probably by enhancing intracellular site-specific interactions between protein kinase and substrates.     

Context-dependent fluorescence detection of a phosphorylated tyrosine residue by a ribonucleopeptide

Tools for selective recognition and sensing of specific phosphorylated tyrosine residues on the protein surface are essential for understanding signal transduction cascades in the cell. A stable complex of RNA and peptide, a ribonucleopeptide (RNP), provides effective approaches to tailor RNP receptors and fluorescent RNP sensors for small molecules. In vitro selection of an RNA-derived pool of RNP afforded RNP receptors specific for a phosphotyrosine residue within a defined amino-acid sequence Gly-Tyr-Ser-Arg. The RNP receptor for the specific phosphotyrosine residue was successfully converted to a fluorescent RNP sensor for sequence-specific recognition of a phosphorylated tyrosine by screening a pool of fluorescent phosphotyrosine-binding RNPs generated by a combination of the RNA subunits of phosphotyrosine-binding RNPs and various fluorophore-modified peptide subunits. The phosphotyrosine-binding RNP receptor and fluorescent RNP sensor constructed from the RNP receptor not only discriminated phosphotyrosine against tyrosine, phosphoserine, or phosphothreonine, but also showed specific recognition of amino acid residues surrounding the phosphotyrosine residue. A fluorescent RNP sensor for one of the tyrosine phosphorylation sites of p100 coactivator showed a binding affinity to the target site ~95-fold higher than the other tyrosine phosphorylation site. The fluorescent RNP sensor has an ability to function as a specific fluorescent sensor for the phosphorylated tyrosine residue within a defined amino-acid sequence in HeLa cell extracts.     

Imaging farnesyl protein transferase using a topologically activated probe

We report on the development and application of a "smart" activatable peptide-based probe for detection of Ras-related farnesyl protein transferase (FPT). Upon farnesylation by FPT, the probe was brought close to a hydrophobic milieu and as a consequence emitted fluorescent light that could be detected by several media, such as fluorescence microscopy, a plate reader, and an optical imaging system. A FPT activity assay confirmed the specificity of the probe (IC50 = 1.2 muM) for FPT compared to that of the native peptide (IC50 = 0.17 muM). In addition, the probe has remarkable binding constant, Kd = 26 nM. The specificity of enzyme activation was proved in pure enzyme assays as well as in cell-based assays. Furthermore, the fluorescent enhancement of the probe was 30-fold stronger than the control peptide in a live cell assay.