Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling

Protein kinases represent a family of enzymes that are critical in cell signaling. One mechanism by which protein kinases are regulated is via autophosphorylation. In the studies described here, we have examined the mechanism of autophosphosphorylation at serine 338 in the regulation of protein kinase A (PKA). Expressed protein ligation allowed for the covalent linkage of an ATP moiety to a Ser mimic at this phosphorylation site. Using a combination of size exclusion chromatography, fluorescence nucleotide binding, kinase measurements, and limited proteolysis assays on this semisynthetic ATP-linked protein, we have obtained unique evidence for an intramolecular autophosphorylation mechanism in PKA regulation. Computational analysis provided a plausible model for a PKA conformation consistent with intramolecular phosphoryl transfer. This approach could be applied to other autoprocessing enzymes by exploiting appropriate transition state analogue motifs in the context of protein semisynthesis.     

Synthesis of functionalized rab GTPases by a combination of solution- or solid-phase lipopeptide synthesis with expressed protein ligation

Prenylated proteins with non-native functionalities are generally very difficult to obtain by recombinant or enzymatic means. The semisynthesis of preparative amounts of prenylated Rab guanosine triphosphatases (GTPases) from recombinant proteins and synthetic prenylated peptides depends largely on the availability of functionalised prenylated peptides corresponding to the proteins' native structure or modifications thereof. Here, we describe and compare solution-phase and solid-phase strategies for the generation of peptides corresponding to the prenylated C terminus of Rab7 GTPase. The solid-phase with utilisation of a hydrazide linker emerges as the more favourable approach. It allows a fast and practical synthesis of pure peptides and gives a high degree of flexibility in their modification. To facilitate the analysis of semisynthetic proteins, the synthesised peptides were equipped with a fluorescent group. Using the described approach, we introduced fluorophores at several different positions of the Rab7 C terminus. The position of the incorporated fluorescent groups in the peptides did not influence the protein-ligation reaction, as the generated peptides could be ligated onto thioester-tagged Rab7. However, it was found that the positioning of the fluorescent group had an influence on the functionality of the Rab7 proteins; analysis of the interaction of the semisynthetic Rab7 proteins with REP (Rab escort protein) and GDI (guanosine diphosphate dissociation inhibitor) molecules revealed that modification of the peptide side chains or of the C-terminal isoprenoid did not significantly interfere with complex formation. However, functionalisation of the C terminus was found to have an adverse effect on complex formation and stability, possibly reflecting low structural flexibility of the Rab GDI/REP molecules in the vicinity of the lipid-binding site.     

Water-soluble phosphinothiols for traceless staudinger ligation and integration with expressed protein ligation

The traceless Staudinger ligation is an effective means to synthesize an amide bond between two groups of otherwise orthogonal reactivity: a phosphinothioester and an azide. An important application of the Staudinger ligation is in the ligation of peptides at a variety of residues. Here, we demonstrate that the traceless Staudinger ligation can be achieved in water with a water-soluble reagent. Those reagents that provide a high yield of amide product discourage protonation of the nitrogen in the key iminophosphorane intermediate. The most efficacious reagent, bis(p-dimethylaminoethyl)phosphinomethanethiol, mediates the rapid ligation of equimolar substrates in water. This reagent is also able to perform a transthioesterification reaction with the thioester intermediate formed during intein-mediated protein splicing. Hence, the traceless Staudinger ligation can be integrated with expressed protein ligation, extending the reach of modern protein chemistry.     

Protein synthesis by solid-phase chemical ligation using a safety catch linker

The native chemical ligation reaction has been used extensively for the synthesis of the large polypeptides that correspond to folded proteins and domains. The efficiency of the synthesis of the target protein is highly dependent on the number of peptide segments in the synthesis. Assembly of proteins from multiple components requires repeated purification and lyophilization steps that give rise to considerable handling losses. In principle, performing the ligation reactions on a solid support would eliminate these inefficient steps and increase the yield of the protein assembly. A new strategy is described for the assembly of large polypeptides on a solid support that utilizes a highly stable safety catch acid-labile linker. This amide generating linker is compatible with a wide range of N-terminal protecting groups and ligation chemistries. The utility of the methodology is demonstrated by a three-segment synthesis of vMIP I, a chemokine that contains all 20 natural amino acids and has two disulfide bonds. The crude polypeptide product was recovered quantitatively from the solid support and purified in 20%-recovered yield. This strategy should facilitate the synthesis of large polypeptides and should find useful applications in the assembly of protein libraries.     

Semisynthesis of dimeric proteins by expressed protein ligation

A one-pot synthesis of homodimeric proteins is described. The synthetic strategy is based on a double expressed protein ligation reaction between thioester peptides and a new bis-cysteinyl linker. The protocol was also applied to the synthesis of heterodimers.     

Synthesis of protein-nucleic acid conjugates by expressed protein ligation

The synthesis of covalent conjugates of proteins and polyamide nucleic acids (PNA) is accomplished by expressed protein ligation of intein-fusion proteins and a PNA-cysteine conjugate.     

Strategies and solid-phase formats for the analysis of protein and peptide phosphorylation employing a novel fluorescent phosphorylation sensor dye

Protein kinases represent one of the largest families of regulatory enzymes, with more than 2,000 of them being encoded for by the human genome. Many cellular processes are regulated by the reversible phosphorylation of proteins and upwards of 30% of the proteins comprising the eukaryotic proteome are likely to be phosphorylated at some point during their existence. In the past, analysis of global protein phosphorylation has been accomplished through radiolabelling of samples with inorganic (32P or [gamma-32)P] ATP. The approach is limited to specimens amenable to radiolabelling and poses certain safety and disposal problems. Alternatively, immunodetection with antibodies to the common phosphoamino acids may be employed, but the antibodies are relatively expensive and exhibit limited specificity and a certain degree of cross-reactivity. Pro-Q Diamond dye is a new fluorescent phosphosensor technology suitable for the detection of phosphoserine-, phosphothreonine- and phosphotyrosine-containing proteins directly in isoelectric focusing gels, SDS-polyacrylamide gels and two-dimensional gels. Additionally, the technology is appropriate for the detection of phosphoproteins or phosphopeptides arrayed on protein chips or affixed to beads. Dye-stained proteins and peptides can be excited with a laser-based light source of 532 or 543 nm or with a xenon-arc lamp-based system equipped with appropriate band pass filters. Alternatively, ultraviolet light of about 302 nm may be employed, providing that sufficiently long exposure times are used to collect the fluorescence signal. Pro-Q Diamond dye emits maximally at approximately 580 nm. The fluorescence-based detection technology is easy to conduct, cost effective and allows rapid large-scale screening of protein and peptide phosphorylation in a variety of solid-phase assay formats.     

Cyanogen bromide cleavage generates fragments suitable for expressed protein and glycoprotein ligation

Herein cyanogen bromide is employed for the efficient production of N-terminal cysteine containing protein fragments for expressed protein ligation (EPL) from polyhistidine-tagged precursors. We provide three examples of efficient CNBr cleavage of fragments of the glycoprotein erythropoietin that can be ligated with peptides or glycopeptide mimetics potentially giving rise to semisynthetic glycoprotein therapeutics.     

Site-specific labeling of DNA-protein conjugates by means of expressed protein ligation

Site-specific bioconjugation of protein thioesters with a DNA oligonucleotide was achieved by Expressed Protein Ligation (EPL) and the new thiol group formed upon EPL in the conjugate was selectively coupled with small molecule labels using maleimide chemistry.     

Chlorophyll fluorescence biosensor for the detection of herbicides

A biosensor is described for the detection of triazine and phenylurea herbicides in drinking water by kinetic measurements of endogenous chlorophyll fluorescence in isolated chloroplasts from higher plants. The pocket-size device uses a diode laser for simultaneous excitation of sample and reference channels, and photodiodes for detection of the emitted light. The biological material can be supplied as a freeze-dried powder, stable for 21 days at room temperature, for 6 weeks at 4 ( degrees )C or for at least 9 months at -20 ( degrees )C. The detection of 0.1 microg/l of a single herbicide, as required by European Community legislation on drinking water quality, can be achieved without prior extraction of the sample.     

Sortase-mediated protein ligation: a new method for protein engineering

Sortase (SrtA), a transpeptidase from Staphylococcus aureus, catalyzes a cell-wall sorting reaction at an LPXTG motif by cleaving between threonine and glycine and subsequently joining the carboxyl group of threonine to an amino group of pentaglycine on the cell wall peptidoglycan. We have applied this transpeptidyl activity of sortase to in vitro protein ligation. We found that in the presence of sortase, protein/peptide with an LPXTG motif can be specifically ligated to an aminoglycine protein/peptide via an amide bond. Additionally, sortase can even conjugate substrates such as (d)-peptides, synthetic branched peptides, and aminoglycine-derivatized small molecules to the C terminus of a recombinant protein. The sortase-mediate protein ligation is robust, specific, and easy to perform, and can be widely applied to specific protein conjugation with polypeptides or molecules of unique biochemical and biophysical properties.     

Enzymatic cleavage and mass amplification strategy for small molecule detection using aptamer-based fluorescence polarization biosensor

Fluorescence polarization (FP) assays incorporated with fluorophore-labeled aptamers have attracted great interest in recent years. However, detecting small molecules through the use of FP assays still remains a challenge because small-molecule binding only results in negligible changes in the molecular weight of the fluorophore-labeled aptamer. To address this issue, we herein report a fluorescence polarization (FP) aptamer assay that incorporates a novel signal amplification strategy for highly sensitive detection of small molecules. In the absence of adenosine, our model target, free FAM-labeled aptamer can be digested by nuclease, resulting in the release of FAM-labeled nucleotide segments from the dT-biotin/streptavidin complex with weak background signal. However, in the presence of target, the FAM-labeled aptamer–target complex protects the FAM-labeled aptamer from nuclease cleavage, allowing streptavidin to act as a molar mass amplifier. The resulting increase in molecular mass and FP intensity of the aptamer–target complex provides improved sensitivity for concentration measurement. The probe could detect adenosine from 0.5 μM to 1000 μM, with a detection limit of 500 nM, showing that the sensitivity of the probe is superior to aptamer-based FP approaches previously reported for adenosine. Importantly, FP could resist environmental interferences, making it useful for complex biological samples without any tedious sample pretreatments. Our results demonstrate that this dual-amplified, aptamer-based strategy can be used to design fluorescence polarization probes for rapid, sensitive, and selective measurement of small molecules in complicated biological environment.     

Determination of urea in serum by a fiber-optic fluorescence biosensor

A new fiber-optic biosensor for urea has been developed, based on immobilized urease coupled to a fluorescence ammonia sensor. The enzymatically generated ammonia diffuses through the membrane into a solution of the fluorescent pH indicator trisodium 8-hydroxypyrene-1,3,6-trisulfonate. The sensor has been successfully used for the determination of urea in serum samples, with results in good agreement with those reported by a local hospital. The proposed sensor is reversible and selective to urea. The ease of construction of the sensor tip offers the possibility of designing disposable tips for use in clinical applications.     

Optimisation of chemical protein cleavage for erythropoietin semi-synthesis using native chemical ligation

Selective protein cleavage at methionine residues is a useful method for the production of bacterially derived protein fragments containing an N-terminal cysteine residue required for native chemical ligation. Here we describe an optimised procedure for cyanogen bromide-mediated protein cleavage, and ligation of the resulting fragments to afford biologically active proteins.     

Single-label kinase and phosphatase assays for tyrosine phosphorylation using nanosecond time-resolved fluorescence detection

The collision-induced fluorescence quenching of a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) by hydrogen atom abstraction from the tyrosine residue in peptide substrates was introduced as a single-labeling strategy to assay the activity of tyrosine kinases and phosphatases. The assays were tested for 12 different combinations of Dbo-labeled substrates and with the enzymes p60c-Src Src kinase, EGFR kinase, YOP protein tyrosine phosphatase, as well as acid and alkaline phosphatases, thereby demonstrating a broad application potential. The steady-state fluorescence changed by a factor of up to 7 in the course of the enzymatic reaction, which allowed for a sufficient sensitivity of continuous monitoring in steady-state experiments. The fluorescence lifetimes (and intensities) were found to be rather constant for the phosphotyrosine peptides (ca. 300 ns in aerated water), while those of the unphosphorylated peptides were as short as 40 ns (at pH 7) and 7 ns (at pH 13) as a result of intramolecular quenching. Owing to the exceptionally long fluorescence lifetime of Dbo, the assays were alternatively performed by using nanosecond time-resolved fluorescence (Nano-TRF) detection, which leads to an improved discrimination of background fluorescence and an increased sensitivity. The potential for inhibitor screening was demonstrated through the inhibition of acid and alkaline phosphatases by molybdate.     

A simple and rapid detection of viral protein using RNA oligonucleotide in a biosensor

The monitoring of non-structural viral protein 3 (NS3) has been of considerable interest in developing simple and reliable methods for detection of hepatitis C virus (HCV) for applications in diagnostic medicine. Although enzyme-linked immunosorbent assay (ELISA) is the most general method in HCV detection, using antibody brings problems. This method is temperature-sensitive and requires specific reactions condition. In addition, secondary antibody conjugated with enzyme and fluorescent dye is required. To overcome these bottlenecks, we designed a streptavidin-biotin conjugation method, namely, the RNA oligonucleotide sensor system that could monitor viral protein with detection limit of 500 pg/mL by using biotin-tagged RNA oligonucleotide in forteBio??s Octet optical biosensor system. In this study, we proposed an efficient method for simple and convenient detection of HCV viral protein, with the advantage of target specific monitoring.     

Chemoselective attachment of biologically active proteins to surfaces by expressed protein ligation and its application for "protein chip" fabrication

The present work describes a general method for the selective attachment of proteins to solid surfaces through their C-termini that can be used for the efficient creation of protein chips. Our method is based in the chemoselective reaction between a protein C-terminal alpha-thioester and a modified surface containing N-terminal Cys residues. alpha-Thioester proteins can be obtained using standard recombinant techniques by using expression vectors containing engineered inteins. This new method was used to immobilize two fluorescent proteins and a functional SH3 domain using a protein microarrayer.     

Development of an analytical method for eight fluoroquinolones using solid-phase extraction and liquid chromatography with fluorescence detection

In this study, a practicable and effective analytical method based on solid-phase-extraction and reversed-phase liquid chromatography with fluorescence detection (SPE-LC-FLD) was developed and partially validated for routine analysis of eight FQs in wastewater at the trace level. Different SPE materials, pH conditions and eluents were modified to find an economic and effective SPE conditions. In our work, it is the first time that well-known commercially available SPE sorbent are compared to ‘generic’ cheap SPE sorbent. Aqueous samples (pH 2–3) were extracted using Anpel? MEP cartridges where they were subsequently eluted by 6?mL of 2% formic acid in MeOH. The aqueous extracts were analysed by gradient elution LC-FLD, whose initial mobile phase was composed of ACN and 10?mmol?L^?1 tetrabutyl ammonium bromide (4/96, v/v, pH 3). The LODs and LOQs of the wastewater were as low as 0.32–2.12?ng?L^?1 and 1.07–7.07?ng?L^?1, respectively. The precisions of the overall method (RSD, n?=?3) using wastewater were below 10%. The method was used to quantify FQs in influents and effluents of several typical sewage treatment plants (STPs) in Shanghai. The extraction recoveries of 100?mL influent, 500?mL effluent and 500?mL of river water samples were between 88.6 and 102.6%, 79.2 and 109.2%, 80.0 and 105.5% and 87.4 and 99.4%, respectively. FQs of interest except sarafloxacin were identified in the influents, effluents and river waters with concentrations varying from 0.012–1.163?µg?L^?1, 0.003–0.291?µg?L^?1, and 0.002–0.040?µg?L^?1, respectively. The method can serve as a tool to obtain detailed information on occurrence, behaviour and fate of FQs in the aquatic environment. Occurrence of FQs detected in summer is higher than in spring at STPs, and those detected in the suburban area are less than those in the urban area. Complete removal of FQs is not achieved from the STPs, indicating domestic wastewater and STP discharge is the source of FQs in the surface water.