Phosphopeptide isomer separation using capillary zone electrophoresis for the study of protein kinases and phosphatases

Separation Abilities of Capillary Electrophoresis Coupled with Ion Mobility Mass Spectrometry for the Discrete Detection of Sequence Isomeric Peptides

The separation and discrete detection of isomeric sequence peptides with similar properties are important tasks for analytical science. Three different peptide isomers of 12 amino-acid residues long, containing direct and reverse regions of the alanine-valine-proline-isoleucine (AVPI) motif, were partially separated and discretely detected from their mixture using two approaches. Capillary electrophoresis enabled the separation and optical detection of the peptide sequence isomers close to the baseline. The ability to separate these sequence isomers from the mixture and discretely identify them from mass spectra has also been demonstrated by ion-mobility tandem mass spectrometry. Moreover, for the first time, capillary electrophoresis and ion-mobility mass spectrometry connected online have shown their ability for a discrete detection of the multidirectional sequence isomers.

Rapid separation of phosphopeptides by microchip electrophoresis-electrospray ionization mass spectrometry

Protein phosphorylation is a significant biological process, but separation of phosphorylated peptide isomers is often challenging for many analytical techniques. We developed a microchip electrophoresis (MCE) method for rapid separation of phosphopeptides with on-chip electrospray ionization (ESI) facilitating online sample introduction to the mass spectrometer (MS). With the method, two monophosphorylated positional isomers of insulin receptor peptide (IR1A and IR1B) and a triply phosphorylated insulin receptor peptide (IR3), all with the same amino acid sequence, were separated from the nonphosphorylated peptide (IR0) in less than one minute. For efficient separation of the positional peptide isomers from each other derivatization with 9-fluorenylmethyl reagents (either chloroformate, Fmoc-Cl, or N-succinimidyl carbonate, Fmoc-OSu) was required before the analysis. The derivatization improved not only the separation of the monophosphorylated positional peptide isomers in MCE, but also identification of the phosphorylation site based on MS/MS.

Site-specific separation and detection of phosphopeptide isomers with pH-mediated stacking capillary electrophoresis-electrospray ionization-tandem mass spectrometry

This study reported a pH-mediated stacking CE coupled with ESI MS/MS method to determine the phosphorylation sites of three synthetic phosphopeptides containing structural isomers. These phosphopeptides mimic the phosphopeptides (amino acid residues 12-25) derived from the trypsin-digested products of human lamin A/C protein. The LODs were determined to be 118, 132 and 1240 fmol for SGAQASS(19)TpPL(22)SPTR, SGAQASS(19)TPL(22)SpPTR, and SGAQASS(19)TpPL(22)SpPTR, respectively. The established method was employed to analyze the phosphorylation sites of the trypsin-digested products of glutathione S-transferase-lamin A/C (1-57) fusion protein that had been phosphorylated in vitro by cyclin-dependent kinase 1. The results indicated that this method is feasible to specifically determine the phosphorylation site from phosphopeptide isomers in the trypsin-digested products of a kinase-catalyzed phosphoprotein, which should benefit the investigation of protein kinase-mediated cellular signal transduction.

A CE-based assay for human protein kinase CK2 activity measurement and inhibitor screening

A new assay for protein kinase CK2 activity determination based on the quantification of a phosphorylated substrate was developed. The common CK2 substrate peptide RRRDDDSDDD, conjugated with the fluorophore 5-[(2-aminoethyl)amino]naphthalene-1-sulfonic acid at the C-terminus served as the analyte. By means of CZE using 2 mol/L acetic acid as electrolyte and UV detection at 214 nm, the non-phosphorylated and the phosphorylated peptide variants could be resolved within 6 min from a complex assay mixture. By this means, activity of human CK2 could be monitored by a kinetic, as well as an endpoint, method. Inhibition of human recombinant CK2 holoenzyme by 6-methyl-1,3,8-trihydroxyanthraquinone and 4,5,6,7-tetrabromobenzotriazole resulted in IC(50) values of 1.33 and 0.27 microM, respectively, which were similar to those obtained with the standard radiometric assay. These results suggest that the CE/UV strategy described here is a straightforward assay for CK2 inhibitor testing.

Separations in poly(dimethylsiloxane) microchips coated with supported bilayer membranes

Hybrid microchannels composed of poly(dimethylsiloxane) and glass were coated with supported bilayer membranes (SBMs) by the process of vesicle fusion. The electroosmotic mobility (mu(eo)) of zwitterionic, positively charged, and negatively charged phospholipid membranes was measured over a 4 h time to evaluate the stability of the coatings in an electric field. Coated microchips with a simple cross design were used to separate the fluorescent dyes fluorescein and Oregon Green. Migration time reproducibility was better than 5% RSD over 70 min of continuous separations. Separation of Oregon Green and fluorescein in channels coated with zwitterionic phosphatidylcholine (PC) membranes yielded efficiencies of 611,000 and 499,000 plates/m and a resolution of 2.4 within 2 s. Both zwitterionic and negatively charged membranes were used to separate peptide substrates from their phosphorylated analogues with efficiencies of 200,000-400,000 plates/m. Notably, separations of fluorescently labeled ABL substrate peptide from its phosphorylated counterpart were achieved using a high-salt physiological buffer with near-baseline resolution in 10 s. PC-coated devices were used to successfully separate enhanced green fluorescent protein (eGFP) from a fusion protein (eGFP-Crakl) with an efficiency of 358,000 and 278,000 plates/m respectively in less than 12 s. These SBM-based coatings may enable the separation of a broad range of analytes and may be ideal in biological applications for microfluidics.

Monitoring phosphatase reactions of multiple phosphorylated substrates by reversed-phase HPLC

In an approach to gain insight into the sequence-dependent dephosphorylation of multiple phosphotyrosyl-containing peptides by the phosphatases SHP-1 and PTP1B, we applied a chromatographic technique for the analysis of the dephosphorylation products. Mono-, bi- and triphosphorylated reference peptides corresponding to positions 1999-2014 in the activation loop of the receptor tyrosine kinase Ros were first analyzed by reversed-phase HPLC and MALDI-TOF/TOF mass spectrometry. Then, the respective products from enzymatic treatment were investigated by HPLC and compared to the standard peptides. The results obtained in this study emphasize the advantage of monitoring phosphatase reactions for mono- and biphosphorylated peptides using the described procedure rather than spectrophotometric and fluorimetric methods that do not allow for a clear identification of the products formed.

Capillary electrophoresis of signaling molecules

The emerging field of quantitative systems biology uses high-throughput bioanalytical measurements to gain a deeper understanding of biological phenomena. With the advent of instrumentation platforms, capillary electrophoresis spans a very wide range of biological applications. This short article focuses on the exploitation of capillary electrophoresis for the systems-level analysis of cell signaling molecules.

Highly efficient protein separations in capillary electrophoresis using a supported bilayer/diblock copolymer coating

A surfactant/polymer wall coating consisting of the doubly chained cationic surfactant dimethyldioctadecylammonium bromide (DODAB) and polyoxyethylene (POE) 40 stearate is investigated. The coating is formed by simply rinsing a capillary with a solution containing DODAB and POE 40 stearate. The resultant coating is semi-permanent--demonstrating stable electroosmotic flow (EOF) even after a 60 min high pressure rinse with buffer. The EOF (-0.45+/-(0.23) x 10(-4) cm(2) V(-1) s(-1) at pH 7.4) is suppressed by more than a factor of ten compared to that observed for DODAB alone. Model protein mixtures were separated over a pH range of 3-10 with efficiencies of up to greater than 1 million plates/m for the basic proteins cytochrome c, lysozyme, ribonuclease A and alpha-lactalbumin, and the acidic proteins insulin chain A, trypsin inhibitor, and alpha-chymotrypsinogen A. Migration time reproducibility was 0.5-4.0% from run to run and 0.6-4.3% from day to day. Protein recoveries with this coating ranged from 84% to 97%.

Separation of mixtures of acidic and basic peptides at neutral pH

Mixtures of acidic and basic peptides composed of the phosphorylated and nonphosphorylated forms of peptide substrates for kinases and a phosphatase were separated by capillary electrophoresis (CE) in buffer conditions compatible with live mammalian cells. The separation of such mixtures was especially challenging given the high salt and neutral pH of the requisite physiologic buffers. Due to poor peak reproducibility in bare capillaries, several strategies were implemented to improve the electrophoretic separation of the peptide mixtures. Covalent coating of the capillary with the neutral polymer poly(dimethylacrylamide) (PDMA) resulted in a 2-fold improvement in the migration time RSD, but required the use of hydrodynamic flow to overcome the differing electrophoretic mobilities (microeo) of the peptides at neutral pH. This parabolic fluid flow diminished separation efficiency almost 5-fold. Polarity switching during the CE run was used to overcome the opposed microeo, but required the retention of hydrodynamic flow and consequent reduction in separation efficiency. The most efficient separations were seen with the use of covalently-linked, charged polymer coatings to maintain electroosmotic flow and to reduce wall interactions. Two such coatings were tested in the current study. Relative to the PDMA coating, an anionic poly(acrylate) improved the average migration time RSD of six peptides from 1.3 to 0.85% and average separation efficiency from 4.8 to 18.0 (x 10(4) plates/m). Likewise, cationic poly([3-(methacryloylamino)propyl]-trimethylammonium) improved the average migration time RSD of eight peptides from 1.2 to 1.1% and average separation efficiency from 4.8 to 33.9 (x 10(4) plates/m). These findings will be of value to the growing number of applications for analytical techniques utilizing CE for cellular analysis and biochemical studies.

Application of multiplexed capillary electrophoresis with laser-induced fluorescence (MCE-LIF) detection for the rapid measurement of endogenous extracellular signal-regulated protein kinase (ERK) levels in cell extracts

Multiplexed (96-lane) capillary electrophoresis with laser-induced fluorescence (MCE-LIF) detection was used for the rapid analysis of extracellular signal-regulated protein kinase (ERK) levels from in vitro cell extracts. The levels of ERK enzyme in cell extracts were determined by monitoring the conversion of a fluorescent-labeled peptide substrate to a phosphorylated fluorescent-labeled peptide product using MCE-LIF. The incorporation of a fluorescent internal standard was found to improve the precision of the analysis. The enzyme assay conditions including substrate concentration, reaction time and enzyme linear range were rapidly optimized using the MCE-LIF approach for both direct and immunoprecipitation-based ERK assays. The levels of ERK from in vitro cell extracts stimulated with angiopoietin 1 (Ang1*) were determined using the MCE-LIF approach. The advantages of MCE-LIF for developing and applying enzyme assays, as well as the figures of merit for the direct and immunoprecipitation ERK assays, are discussed.

Determination of endogenous extracellular signal-regulated protein kinase by microchip capillary electrophoresis

The application of microchip capillary electrophoresis (CE) to the assay of extracellular signal-regulated protein kinase (ERK) is presented. In this assay, ERK catalyzes the transfer of gamma-phosphate from adenosine 5(')-triphosphate to the threonine residue of a fluorescently labeled nonapeptide (APRTPGGRR), and the phosphorylated and nonphosphorylated peptides were detected by fluorescence. The phosphorylated and nonphosphorylated peptides and the internal standard were separated within 20s, and the increase in magnitude of the phosphorylated peptide peak was monitored to assess ERK activity. ERK reactions were prepared off-chip and analyzed on a single-lane glass microchip fabricated by standard methods. It was demonstrated that microchip CE could be used to measure endogenous amounts of ERK by spiking known concentrations of recombinant ERK2 into the lysates of serum-starved human umbilical vein endothelial cells (HUVEC) and recovering between 90 and 100% for all samples. Endogenous ERK activity was determined by microchip where HUVEC were stimulated with 500pM vascular endothelial growth factor (VEGF) at different times before cell lysis. The results showed a transient VEGF-mediated ERK activation that peaked at 10min, which was consistent with previous reports using conventional techniques. The microchip assay provided a rapid, accurate, and precise alternative to conventional methods of determining endogenous ERK activity.

Determination of protein phosphorylation by extracellular signal-regulated kinase using capillary electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Extracellular signal-regulated kinase (ERK) is a key regulatory enzyme mediating cell responses to mitogenic stimulation and is one of the key components in linking growth factor receptor activation to serine/threonine protein phosphorylation processes. Phosphorylation reaction by ERK plays an important role in many signal transduction pathways. ERK phosphorylates numerous substrates such as MBP, microtubule-associated protein 2 (MAP2) and nuclear protein. In particular, MBP is a substrate commonly employed for the detection of ERK activity and contains the consensus primary sequence PRT97P. In this paper, we compared the degree of the phosphorylation reaction of MBP substrate peptides by ERK with the three different MBP substrate peptides, MBP1(KNIVTPRTPPPSQGK), MBP2(VPRTPGGRR) and MBP3(APRTPGGRR) in order to select an efficient substrate peptide for phosphorylation reaction by ERK. The results showed that the MBP3 peptide is the most efficient substrate for phosphorylation reaction by ERK. Using MBP3 peptide, the phosphorylation reaction of MBP by ERK was monitored with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and capillary electrophoresis (CE). Our results demonstrate the feasibility of the CE method, the method being a simple and reliable technique in determining and characterizing various kinds of enzyme reaction especially including kinase enzymes.

Determination of dissociation constant of phosphinate group in phosphinic pseudopeptides by capillary zone electrophoresis

Capillary zone electrophoresis (CZE) was used for determination of dissociation constant of phosphinate group in phosphinic pseudopeptides, i.e. peptides where one peptide bond is substituted by phosphinic acid moiety -PO2--CH2-. The dissociation constants were determined for a set of newly synthesized pseudopeptides derived from a structure N-Ac-Val-Ala(psi)(PO2--CH2)Leu-His-NH2 by nonlinear regression of experimentally measured pH dependence of their effective electrophoretic mobilities. CZE experiments were carried out in Tris-phosphate background electrolytes in the pH range 1.4-3.2. The pseudopeptides were synthesized as a mixture of four diastereomers, the separation of which was achieved in most cases. Moreover, differences of the effective mobilities of the pseudopeptide diastereomers enabled simultaneous determination of the dissociation constant of their phosphinate group without necessity of previous isolation of individual isomers.

Analysis and characterization of phosphinic pseudopeptides by capillary zone electrophoresis

Capillary zone electrophoresis (CZE) was applied to analysis and characterization of phosphinic pseudopeptides with the general structure N-Ac-Val-Ala(psi)(PO2(-)-CH(2)) Leu-Xaa-NH(2), where Xaa represents one of 20 proteinogenic amino acid residues. Pseudopeptides containing neutral or acidic amino acid residues in position Xaa were analyzed as anions in weakly alkaline (pH 8.1) Tris-Tricine background electrolyte (BGE), pseudopeptides with basic amino acid residues in position Xaa were analyzed as cations in acid BGEs (Tris-phosphate buffers). Acidity of phosphinic acid moiety in peptides with basic amino acid residues was determined from the dependence of effective mobility of these peptides on pH in the acid pH region (pH 1.4-2.8). Additionally, separation of diastereomers of some peptides was achieved.

Recent advances in capillary electrophoresis of peptides

The article gives a comprehensive review on the recent developments in the applications of high-performance capillary electromigration methods, including zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography and electrochromatography, to analysis, preparation and physicochemical characterization of peptides. The article presents new approaches to the theoretical description and experimental verification of electromigration behavior of peptides, and covers the methodological aspects of capillary electroseparations of peptides, such as strategy and rules for the rational selection of separation mode and experimental conditions, sample treatment, suppression of peptide adsorption to the inner capillary wall, new developments in individual separation modes and new designs of detection systems. Several types of applications of capillary electromigration methods to peptide analysis are presented: conventional qualitative and quantitative analysis for determination of purity, determination in biomatrices, monitoring of physical and chemical changes and enzymatic conversions, amino acid and sequence analysis and peptide mapping of proteins. Some examples of micropreparative peptide separations are given and capabilities of capillary electromigration techniques to provide important physicochemical characteristics of peptides are demonstrated.

Purification and characterization of the human PDE4A catalytic domain (PDE4A330-723) expressed in Sf9 cells

The human PDE4A catalytic domain (PDE4A330-723) expressed in Sf9 cells was found to be heavily phosphorylated on both serines of the conserved SPS motif by mass spectrometric analysis. The purified protein exists as a tetramer at a concentration approximately 1 mg/ml from light scattering measurement and has a Km of 2 microM in hydrolyzing cAMP. In comparison, a partially purified PDE4A330-723 expressed in Escherichia coli has an apparent Km of 10 microM. The EC50 values for the Mg2+- or Co2+-mediated cAMP hydrolysis between the two enzymes differed by less than twofold. In addition, both enzymes exhibit similar sensitivities toward inhibition by a diverse set of inhibitors. Together with the fact that its adjacent peptide was covalently labeled by an electrophilic cAMP analogue, these results support that the SPS motif is not part of but is positioned near the active site. An efficient purification protocol that provides a highly purified PDE4A catalytic domain suitable for crystallization study is described.

Improved capillary electrophoresis conditions for the separation of kinase substrates by the laser micropipet system

Phosphorylated and nonphosphorylated forms of peptide substrates for protein kinase C (PKC) and calcium-calmodulin activated kinase II (CamKII) were separated by capillary zone electrophoresis. Electrophoresis of the peptide substrates and products in biologic buffer solutions in uncoated capillaries yielded asymmetric analyte peaks with substantial peak tailing. Some of the peptides also exhibited broad peaks with unstable migration times. To improve the electrophoretic separation of the peptides, several strategies were implemented: extensive washing of the capillary with a base, adding betaine to the electrophoretic buffer, and coating the capillaries with polydimethylacrylamide (PDMA). Prolonged rinsing of the capillaries with a base substantially improved the migration time reproducibility and decreased peak tailing. Addition of betaine to the electrophoretic buffer enhanced both the migration time stability as well as the theoretical plate numbers of the peaks. Finally PDMA-coated capillaries brought about significant improvements in the resolving power of the separations. These modifications all utilized an electrophoretic buffer that was compatible with a living biologic cell. Consequently they should be adaptable for the new capillary electrophoresis-based methods to measure kinase activation in single cells.

Rapid dephosphorylation of H1 histones after apoptosis induction

H1 histones are involved in the formation of higher order chromatin structures and in the modulation of gene expression. Changes in chromatin structure are a characteristic initial feature of apoptosis. We therefore have investigated the histone H1 pattern of the human leukemic cell line HL60 undergoing programmed cell death, as induced by topoisomerase I inhibition. Histone H1 proteins were isolated and analyzed by high performance liquid chromatography and capillary zone electrophoresis. DNA fragmentation after apoptosis induction was monitored by agarose gel electrophoresis. The patterns of the three H1 histone subtypes extractable from apoptotic HL60 cells significantly differed from those of control cells in showing a decrease of phosphorylated H1 subtypes and an increase of the respective dephosphorylated forms. This dephosphorylation of H1 histones could be observed already 45 min after apoptosis induction and preceded internucleosomal DNA cleavage by approximately 2 h. We conclude that during apoptotic DNA fragmentation, the H1 histones become rapidly dephosphorylated by a yet unknown protein phosphatase.