Protein phosphorylation: technologies for the identification of phosphoamino acids

Morphine increases myocardial triacylglycerol through regulating adipose triglyceride lipase S406 phosphorylation

AIMS

Morphine, a commonly used drug for anesthesia, affects lipid metabolism in different tissues, but the mechanism is currently unclear. Adipose triglyceride lipase (ATGL) is the rate-limiting enzyme responsible for the first step of triglyceride (TG) hydrolysis. Here we aim to investigate whether ATGL phosphorylation is involved in morphine-induced TG accumulation.

MAIN METHODS

Oil red O staining and TG content analysis were used to detect the effect of morphine on lipid storage. A series of ATGL phosphoamino acid site mutant plasmids were constructed by gene synthesis and transfected to HL-1 cells to evaluate the phosphorylation levels of ATGL phosphoamino acid in morphine-treated HL-1 cells with immunoprecipitation and immunoblotting assay.

KEY FINDINGS

Morphine acute treatment induced excessive accumulation of TG and decreased the phosphorylation level of ATGL Ser406 in HL-1 cells. Of note, the phosphorylation positive mutation of ATGL Ser406 to aspartic acid effectively reversed morphine-induced excessive accumulation of TG in HL-1 cells.

SIGNIFICANCE

This discovery will help to fully understand the lipid regulation function of morphine in a new scope. In addition, it will expand the phosphorylation research of ATGL more comprehensively and provide powerful clues for lipid metabolism regulation.

Multiple phosphorylated protein selective analysis via fluorous derivatization and liquid chromatography-electrospray ionization-mass spectrometry analysis

Post-translational modification of proteins is involved in protein function and higher-order structure. Among such modification, phosphorylation is an important intracellular signal transduction pathway. Many studies on phosphorylated protein analysis using liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) have been developed. However, there are few reports on the analysis of highly phosphorylated proteins because of their handling difficulty. Hence, we developed an analytical method that converts multiple phosphate groups contained in the peptides into perfluoroalkyl groups for selective analysis using fluorous affinity. Here, tryptic digested β-casein fragment peptides [RELEELNVPGEIVE(pSer)L(pSer)(pSer)(pSer)EESITR and FQ(pSer)EEQQQTEDELQDK] were used as model phosphorylated peptides. 1H,1H,2H,2H-Perfluorooctanethiol (PFOT) and 2,2,2-trifluoroethanethiol (TFET) were used as derivatization reagents for mono-phosphorylated peptides and multi-phosphorylated peptides, respectively, to derivatize via β-elimination/Michael addition. The derivatives were analyzed by LC-ESI-MS. A fluorous LC column is typically used to selectively retain the fluorous-derivatized peptides, which are expected to be separated from contaminants and non-phosphorylated peptides. When this method was applied to β-casein, TFET- and PFOT-derivatized peptides were strongly retained in the fluorous LC column and clearly separated from non-phosphorylated peptides on the chromatogram. Therefore, the developed method enables quantification of mono- and multi-phosphorylated peptides and is suitable for application in proteomics.

Protein Phosphorylation Response to Abiotic Stress in Plants

Plants are an important part of nature because as photoautotrophs, they provide a nutrient source for many other living organisms. Due to their sessile nature, to overcome both biotic and abiotic stresses, plants have developed intricate mechanisms for perception of and reaction to these stresses, both on an external level (perception) and on an internal level (reaction). Specific proteins found within cells play crucial roles in stress mitigation by enhancing cellular processes that facilitate the plants survival during the unfavorable conditions. Well before plants are able to synthesize nascent proteins in response to stress, proteins which already exist in the cell can be subjected to an array of posttranslation modifications (PTMs) that permit a rapid response. These activated proteins can, in turn, aid in further stress responses. Different PTMs have different functions in growth and development of plants. Protein phosphorylation, a reversible form of modification has been well elucidated, and its role in signaling cascades is well documented. In this mini-review, we discuss the integration of protein phosphorylation with other components of abiotic stress-responsive pathways including phytohormones and ion homeostasis. Overall, this review demonstrates the high interconnectivity of the stress response system in plants and how readily plants are able to toggle between various signaling pathways in order to survive harsh conditions. Most notably, fluctuations of the cytosolic calcium levels seem to be a linking component of the various signaling pathways.

Aberrant Protein Phosphorylation in Cancer by Using Raman Biomarkers

(1) Background: Novel methods are required for analysing post-translational modifications of protein phosphorylation by visualizing biochemical landscapes of proteins in human normal and cancerous tissues and cells. (2) Methods: A label-free Raman method is presented for detecting spectral changes that arise in proteins due to phosphorylation in the tissue of human breasts, small intestines, and brain tumours, as well as in the normal human astrocytes and primary glioblastoma U-87 MG cell lines. Raman spectroscopy and Raman imaging are effective tools for monitoring and analysing the vibrations of functional groups involved in aberrant phosphorylation in cancer without any phosphorecognition of tag molecules. (3) Results: Our results based on 35 fresh human cancer and normal tissues prove that the aberrant tyrosine phosphorylation monitored by the unique spectral signatures of Raman vibrations is a universal characteristic in the metabolic regulation in different types of cancers. Overexpressed tyrosine phosphorylation in the human breast, small intestine and brain tissues and in the human primary glioblastoma U-87 MG cell line was monitored by using Raman biomarkers. (4) We showed that the bands at 1586 cm-1 and 829 cm-1, corresponding to phosphorylated tyrosine, play a pivotal role as a Raman biomarker of the phosphorylation status in aggressive cancers. We found that the best Raman biomarker of phosphorylation is the 1586/829 ratio showing the statistical significance at p Values of ≤ 0.05. (5) Conclusions: Raman spectroscopy and imaging have the potential to be used as screening functional assays to detect phosphorylated target proteins and will help researchers to understand the role of phosphorylation in cellular processes and cancer progression. The abnormal and excessive high level of tyrosine phosphorylation in cancer samples compared with normal samples was found in the cancerous human tissue of breasts, small intestines and brain tumours, as well as in the mitochondria and lipid droplets of the glioblastoma U-87 MG cell line. Detailed insights are presented into the intracellular oncogenic metabolic pathways mediated by phosphorylated tyrosine.

Analysis and identification of tyrosine phosphorylated proteins in hemocytes of Litopenaeus vannamei infected with WSSV

Previous studies have demonstrated that protein tyrosine phosphorylation plays an important role in WSSV infection. In the present work, in order to further elucidate the potential role of protein tyrosine phosphorylation in white spot syndrome virus (WSSV) infection. The expression variation of tyrosine phosphorylated proteins in hemocytes of shrimp (Litopenaeus vannamei) after WSSV infection were examined by flow cytometric immunofluorescence assay (FCIFA) and enzyme linked immunosorbent assay (ELISA), and results showed that the level of protein tyrosine phosphorylation in hemocytes fluctuated significantly after WSSV infection and exhibited two peaks at 6 and 24 h post infection (hpi). Meanwhile, tyrosine phosphorylated proteins in hemocytes after WSSV infection were also detected by cell immunofluorescence, and results showed that the fluorescence intensity in hemocytes was altered with the course of WSSV infection and showed stronger fluorescent signals at 6 and 24 hpi compared to other time points. Furthermore, two dimensional gel electrophoresis (2-DE) and 2-DE western blotting were applied to identify the differentially expressed tyrosine phosphorylated proteins in hemocytes before and after WSSV infection. The result of 2-DE western blotting showed that there were nine tyrosine phosphorylated proteins in the hemocytes of healthy shrimp, whereas twenty-one tyrosine phosphorylated proteins were detected in the hemocytes of shrimp at 6hpi. Then, the differential tyrosine phosphorylated proteins were analyzed by Mass Spectrometry (MS), and eight of them were identified to be sodium/potassium-transporting ATPase subunit alpha, ubiquitin/ribosomal L40 fusion protein, actin-D, phosphopyruvate hydratase, beta-actin, ATP synthase subunit beta, receptor for activated protein kinase c1 and protein disulfide-isomerase. Moreover, the expression levels of sodium/potassium-transporting ATPase subunit alpha, ubiquitin/ribosomal L40 fusion protein, phosphopyruvate hydratase, ATP synthase subunit beta, receptor for activated protein kinase c1 and protein disulfide-isomerase were examined to be up-regulated post WSSV infection by quantitative real-time RT-PCR. Taken together, these results demonstrated that protein tyrosine phosphorylation was involved in the process of WSSV infection, which might play an important role in the immune response to WSSV infection in shrimp.

Detection of peptides with intact phosphate groups using MALDI TOF/TOF and comparison with the ESI-MS/MS

A wide variety of post-translational modifications such as oxidation, phosphorylation, glycosylation, methylation, and acetylation play critical roles in cellular functions. Detection of post-translational modifications in proteins is important to understand their crucial roles in cellular functions. Identifying each modification requires special attention in mass spectral acquisition and analysis. Here, we report a mass spectral method for the detection of multiple phosphorylations in peptides by analyzing their products after fragmentation. Synthetic peptides were used to identify these modifications by matrix-assisted laser desorption/ionization (MALDI) TOF/TOF. Peptides with serine, threonine, and tyrosine were used with mono- to tetra-phosphorylation sites in different combinations to get insights into their fragmentation and identify the location of these sites. The y-ion series were observed without the loss of phosphate groups and were thus very useful in determining the localization and sequence of the phosphate residues. Acetylation of the peptides was found to be useful in detecting the b1-ion and helped in identifying the N-terminus. When a mixture of the phosphorylated peptides (from mouse protein sequences) were analyzed by LC-MS/MS on a Velos Orbitrap Mass Spectrometer and the data subjected to analysis by Sequest using the mouse database, the peptides were identified along with the parent proteins. A comparison of MALDI TOF/TOF spectra with ESI MS/MS helped in eliminating falsely discovered peptides using the database search.

Conformational Clusters of Phosphorylated Tyrosine

Tyrosine phosphorylation plays an important role in many cellular and intercellular processes including signal transduction, subcellular localization, and regulation of enzymatic activity. In 1999, Blom et al., using the limited number of protein data bank (PDB) structures available at that time, reported that the side chain structures of phosphorylated tyrosine (pY) are partitioned into two conserved conformational clusters ( Blom, N.; Gammeltoft, S.; Brunak, S. J. Mol. Biol. 1999 , 294 , 1351 - 1362 ). We have used the spectral clustering algorithm to cluster the increasingly growing number of protein structures with pY sites, and have found that the pY residues cluster into three distinct side chain conformations. Two of these pY conformational clusters associate strongly with a narrow range of tyrosine backbone conformation. The novel cluster also highly correlates with the identity of the n + 1 residue, and is strongly associated with a sequential pYpY conformation which places two adjacent pY side chains in a specific relative orientation. Further analysis shows that the three pY clusters are associated with distinct distributions of cognate protein kinases.

Identification of a p53-based portable degron based on the MDM2-p53 binding region

In recent years the ubiquitin proteasome system (UPS) has garnered increasing interest as a target for chemotherapeutics. Due to the success of the proteasome inhibitors Bortezomib and Carfilzomib in the treatment of multiple myeloma, several new compounds have been developed to target E3 ubiquitin ligases and the proteasome in numerous human cancers. This has increased the need for new analytical methods to precisely measure intracellular enzyme activity in cells. A key component of a desired analytical method is a substrate that is capable of rapid intracellular ubiquitination yet easily incorporated into the next generation of more sophisticated UPS reporters. Portable degradation sequences, or degrons, have the ability to bind to E3 ligases and promote substrate ubiquitination when the sequence is presented in isolation or appended to other entities such as fluorescent peptide-based reporters. Previous work identified an E3 ligase (MDM2)-binding element at p53 amino acids 92-112, which was later demonstrated to be rapidly ubiquitinated in cytosolic lysates effectively functioning as a transportable degron. In this work, a shortened p53 sequence within amino acids 92-112 that displayed rapid ubiquitination kinetics was identified. A nine-member peptide library was synthesized using sequence elements of various sizes and lengths, all based on the initial 22 amino acid long sequence, containing a single ubiquitination site lysine. The ubiquitination kinetics were determined using a combination of gel electrophoresis and analytical high performance liquid chromatography (HPLC) to rank the members of the library and identify the optimal ubiquitination sequence. This analysis identified the five amino acid sequence, KGSYG, corresponding to residues 105-108 with an added N-terminal lysine, as a portable degron since this sequence demonstrated the most rapid ubiquitination kinetics.

Focused Proteomics Revealed a Novel Rho-kinase Signaling Pathway in the Heart

Protein phosphorylation plays an important role in the physiological regulation of cardiac function. Myocardial contraction and pathogenesis of cardiac diseases have been reported to be associated with adaptive or maladaptive protein phosphorylation; however, phosphorylation signaling in the heart is not fully elucidated. We recently developed a novel kinase-interacting substrate screening (KISS) method for exhaustive screening of protein kinase substrates, using mass spectrometry and affinity chromatography. First, we examined protein phosphorylation by extracellular signal-regulated kinase (ERK) and protein kinase A (PKA), which has been relatively well studied in cardiomyocytes. The KISS method showed that ERK and PKA mediated the phosphorylation of known cardiac-substrates of each kinase such as Rps6ka1 and cTnI, respectively. Using this method, we found about 330 proteins as Rho-kinase-mediated substrates, whose substrate in cardiomyocytes is unknown. Among them, CARP/Ankrd1, a muscle ankyrin repeat protein, was confirmed as a novel Rho-kinase-mediated substrate. We also found that non-phosphorylatable form of CARP repressed cardiac hypertrophy-related gene Myosin light chain-2v (MLC-2v) promoter activity, and decreased cell size of heart derived H9c2 myoblasts more efficiently than wild type-CARP. Thus, focused proteomics enable us to reveal a novel signaling pathway in the heart.

Mass spectrometric real-time monitoring of an enzymatic phosphorylation assay using internal standards and data-handling freeware

RATIONALE

Continuous-flow reaction detection systems (monitoring enzymatic reactions with mass spectrometry (MS)) lack quantitative values so far. Therefore, two independent internal standards (IS) are implemented in a way that the online system stability can be observed, quantitative conversion values for substrate and product can be obtained and they can be used as mass calibration standards for high MS accuracy.

METHODS

An application previously developed for the MS detection of peptide phosphorylation by cAMP-dependent protein kinase A (PKA) (De Boer et al., Anal. Bioanal. Chem. 2005, 381, 647-655) was transferred to a continuous-flow reaction detection system. This enzymatic reaction, involving enzyme activation as well as the transfer of a phosphate group from ATP to a peptide substrate, was used to prove the compatibility of a quantitative enzymatic assay in a continuous-flow real-time system (connected to MS).

RESULTS

Moreover (using internal standards), the critical parameter reaction temperature (including solution density variations depending on temperature) was studied in the continuous-flow mixing system. Furthermore, two substrates (malantide and kemptide), two enzyme types (catalytic subunit of PKA and complete PKA) and one inhibitor were tested to determine system robustness and long-term availability. Even spraying solutions that contained significant amount of MS contaminants (e.g. the polluted catalytic subunit) resulted in quantifiable MS signal intensities. Subsequent recalculations using the internal standards led to results representing the power of this application.

CONCLUSIONS

The presented methodology and the data evaluation with available Achroma freeware enable the direct coupling of biochemical assays with quantitative MS detection. Monitoring changes such as temperature, reaction time, inhibition, or compound concentrations can be observed quantitatively and thus enzymatic activity can be calculated.

Identification of putative phosphoproteins in wheat spikes induced by Fusarium graminearum

Phosphorylation and dephosphorylation events were initiated in wheat scab resistance. The putative FHB-responsive phosphoproteins are mainly involved in three functional groups and contain at least one tyrosine, serine, or threonine phosphorylation site. Fusarium head blight (FHB), caused by Fusarium graminearum, is a severe disease in wheat. Protein phosphorylation plays an important role in plant-pathogen interactions, however, a global analysis of protein phosphorylation in response to FHB infection remains to be explored. To study the effect of FHB on the phosphorylation state of wheat proteins, proteins extracted from spikes of a resistant wheat cultivar after 6 h of inoculation with F. graminearum or sterile H2O were separated by two-dimensional gel electrophoresis, and then the immunodetection of putative phosphoproteins was conducted by Western blotting using specific anti-phosphotyrosine antibody, anti-phosphothreonine antibody and anti-phosphoserine antibody. A total of 35 phosphorylated signals was detected and protein identities of 28 spots were determined. Functional categorization showed that the putative FHB-responsive phosphoproteins were mainly involved in defense/stress response, signal transduction, and metabolism. The phosphorylation status of proteins associated with signaling pathways mediated by salicylic acid, calcium ions, small GTPase, as well as with detoxification, reactive oxygen species scavenging, antimicrobial compound synthesis, and cell wall fortification was regulated in wheat spikes in response to F. graminearum infection. The present study reveals dynamics of wheat phosphoproteome in response to F. graminearum infection and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of wheat scab resistance.

Identification of IDUA and WNT16 Phosphorylation-Related Non-Synonymous Polymorphisms for Bone Mineral Density in Meta-Analyses of Genome-Wide Association Studies

Protein phosphorylation regulates a wide variety of cellular processes. Thus, we hypothesize that single-nucleotide polymorphisms (SNPs) that may modulate protein phosphorylation could affect osteoporosis risk. Based on a previous conventional genome-wide association (GWA) study, we conducted a three-stage meta-analysis targeting phosphorylation-related SNPs (phosSNPs) for femoral neck (FN)-bone mineral density (BMD), total hip (HIP)-BMD, and lumbar spine (LS)-BMD phenotypes. In stage 1, 9593 phosSNPs were meta-analyzed in 11,140 individuals of various ancestries. Genome-wide significance (GWS) and suggestive significance were defined by α = 5.21 × 10(-6) (0.05/9593) and 1.00 × 10(-4), respectively. In stage 2, nine stage 1-discovered phosSNPs (based on α = 1.00 × 10(-4)) were in silico meta-analyzed in Dutch, Korean, and Australian cohorts. In stage 3, four phosSNPs that replicated in stage 2 (based on α = 5.56 × 10(-3), 0.05/9) were de novo genotyped in two independent cohorts. IDUA rs3755955 and rs6831280, and WNT16 rs2707466 were associated with BMD phenotypes in each respective stage, and in three stages combined, achieving GWS for both FN-BMD (p = 8.36 × 10(-10), p = 5.26 × 10(-10), and p = 3.01 × 10(-10), respectively) and HIP-BMD (p = 3.26 × 10(-6), p = 1.97 × 10(-6), and p = 1.63 × 10(-12), respectively). Although in vitro studies demonstrated no differences in expressions of wild-type and mutant forms of IDUA and WNT16B proteins, in silico analyses predicts that WNT16 rs2707466 directly abolishes a phosphorylation site, which could cause a deleterious effect on WNT16 protein, and that IDUA phosSNPs rs3755955 and rs6831280 could exert indirect effects on nearby phosphorylation sites. Further studies will be required to determine the detailed and specific molecular effects of these BMD-associated non-synonymous variants.

Variable Digestion Strategies for Phosphoproteomics Analysis

In recent years, mass spectrometry-based phosphoproteomics has propelled our knowledge about the regulation of cellular pathways. Nevertheless, typically applied bottom-up strategies have several limitations. Trypsin, the preferentially used proteolytic enzyme shows impaired cleavage efficiency in the vicinity of phosphorylation sites. Moreover, depending on the frequency and distribution of tryptic cleavage sites (Arg/Lys), generated peptides can be either too short or too long for confident identification using standard LC-MS approaches. To overcome these limitations, we introduce an alternative and simple approach based on the usage of the nonspecific serine protease subtilisin, which enables a fast and reproducible digestion and provides access to "hidden" areas of the proteome. Thus, in a single LC-MS experiment >1800 phosphopeptides were confidently identified and localized from 125 μg of HeLa digest, compared to >2100 sites after tryptic digestion. While the overlap was less than 20 %, subtilisin allowed the identification of many phosphorylation sites that are theoretically not accessible via tryptic digestion, thus considerably increasing the coverage of the phosphoproteome.

Detection of low-abundance protein phosphorylation by selective 18O labeling and mass spectrometry

Reversible phosphorylation regulates the majority of intracellular networking and pathways. The study of this widely explored post-translational modification is usually challenged by low stoichiometric levels of modification. Many approaches have been developed to overcome this problem and to achieve rigorous characterization of protein phosphorylation. We describe a method for enhanced detection of low-abundance protein phosphorylation that uses selective introduction of (18)O label into phosphorylation sites with H(2)(18)O and mass spectrometric detection. The method was applied to introduce (18)O label into bacterially expressed Aurora A kinase phosphorylation sites and resulted in the representation of phosphorylated peptides as doublets or triplets according to the number of phosphate groups. A total of 28 phosphopeptides were observed by this method.

Inductively coupled plasma-mass spectrometry (ICP-MS) for quantitative analysis in environmental and life sciences: a review of challenges, solutions, and trends

This focal point review provides an overview of recent developments and capabilities of inductively coupled plasma mass spectrometry (ICP-MS) coupled with different separation techniques for applications in the fields of quantitative environmental and bio-analysis. Over the past years numerous technical improvements, which are highlighted in this review, have helped to promote the evolution of ICP-MS to one of the most versatile tools for elemental quantification. In particular, the benefits and possibilities of using state-of-the-art hyphenated ICP-MS approaches for quantitative analysis are demonstrated with a focus on environmental and bio-analytical applications.

Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses

A multifunctional liquid chromatography system that performs 1-dimensional, 2-dimensional (strong cation exchange/reverse phase liquid chromatography or SCX/RPLC) separations and online phosphopeptide enrichment using a single binary nanoflow pump has been developed. With a simple operation of a function selection valve equipped with a SCX column and a TiO2 (titanium dioxide) column, a fully automated selection of three different experiment modes was achieved. Because the current system uses essentially the same solvent flow paths, the same trap column, and the same separation column for reverse-phase separation of 1D, 2D, and online phosphopeptides enrichment experiments, the elution time information obtained from these experiments is in excellent agreement, which facilitates correlating peptide information from different experiments. The final reverse-phase separation of the three experiments is completely decoupled from all of the function selection processes; thereby salts or acids from SCX or TiO2 column do not affect the efficiency of the reverse-phase separation.

Comparative proteomics and phosphoproteomics analyses of DHEA-induced on hepatic lipid metabolism in broiler chickens

Dehydroepiandrosterone (DHEA) is a precursor of the adrenocorticosteroid hormones that are common to all animals, including poultry. The study described herein was undertaken to investigate the effect of DHEA on lipid metabolism in broiler chickens during embryonic development and to determine the regulatory mechanisms involved in its physiological action. Treatment group eggs were injected with 50mg DHEA diluted in 50 μL dimethyl sulfoxide (DMSO) per kg, while control group eggs (arbor acres [AA] fertilized) were injected with 50 μL DMSO per kg prior to incubation. Liver samples were collected on days 9, 14 and 19 of embryonic development as well as at hatching. Extracted proteins were analyzed by two dimensional gel electrophoresis (2-DE) in combination with western blotting for specific anti-phosphotyrosine. The differential spots were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) or MALDI-TOF-TOF-MS. Peptide mass fingerprinting (PMF) of the differentially-expressed proteins were performed using the MASCOT, Prospector or proFound server. Thirty-seven proteins and twenty-two tyrosine phosphorylation proteins were successfully identified. All 37 proteins and 22 tyrosine phosphorylation proteins exhibited a significant volume difference from the control group. These results demonstrated that DHEA increased the expression and level of tyrosine phosphorylation and sulfotransferase proteins in broilers (at pI 5.9), therefore promoting the biotransformation of DHEA. The expression of apolipoproteinA-I was increased in the DHEA treatment group, which facilitated the conversion of cholesterol to cholesterol esters. Also, DHEA increased the expression of peroxiredoxin-6 and its tyrosine phosphorylation protein levels, thus enhancing its anti-oxidative activity. Furthermore, pyruvate dehydrogenase expression was decreased and the level of its tyrosine phosphorylation proteins increased in the DHEA treatment group. Take together, those data indicate that DHEA reduces the supply of acetyl-CoA by inhibiting the activity of its target enzyme (i.e., pyruvate dehydrogenase), thus affecting both protein synthesis and phosphorylation level and decreasing fat deposition in broiler chickens during embryonic development, which could reflect a physiologically-relevant DHEA fat-reduction mechanism in the broiler chicken.

Phosphorylation events during viral infections provide potential therapeutic targets

For many medically relevant viruses, there is now considerable evidence that both viral and cellular kinases play important roles in viral infection. Ultimately, these kinases, and the cellular signaling pathways that they exploit, may serve as therapeutic targets for treating patients. Currently, small molecule inhibitors of kinases are under investigation as therapy for herpes viral infections. Additionally, a number of cellular or host-directed tyrosine kinase inhibitors that have been previously FDA approved for cancer treatment are under study in animal models and clinical trials, as they have shown promise for the treatment of various viral infections as well. This review will highlight the wide range of viral proteins phosphorylated by viral and cellular kinases, and the potential for variability of kinase recognition sites within viral substrates to impact phosphorylation and kinase prediction. Research studying kinase-targeting prophylactic and therapeutic treatments for a number of viral infections will also be discussed.

Peptide mapping using capillary electrophoresis offline coupled to matrix-assisted laser desorption ionization time of flight mass spectrometry

This article reports the results of a study carried out to evaluate the offline hyphenation of capillary zone electrophoresis with matrix-assisted lased desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) for the analysis of low-abundant complex samples, represented by the tryptic phosphorylated peptides of phosphoproteins, such as α-casein, β-casein, and fetuin. The proposed method employs a latex-coated capillary and consists in the online preconcentration of the tryptic peptides by a pH-mediated stacking method, their separation by capillary zone electrophoresis, and subsequent deposition of the separated analytes onto a MALDI target for their MS analysis. The online preconcentration method allows loading a large sample volume (∼150 nL), which is introduced into the capillary after the hydrodynamic injection of a short plug of 1.0 M ammonium hydroxide solution and is sandwiched between two plugs of the acidic background electrolyte solution (BGE) filling the capillary. The sample spotting of the separated analytes onto the MALDI target is performed either during or postseparation using an automatic spotting device connected to the exit of the separation capillary. The proposed method allows the separation and identification of multiphosphorylated peptides from other peptides and enables their identification at femtomole level with improved efficiency compared with LC approaches hyphenated to MS.

Phosphorylation of Ser-80 of VP1 and Ser-254 of VP2 is essential for human BK virus propagation in tissue culture

BK virus (BKV) infection may cause polyomavirus-associated nephropathy in patients with renal transplantation. Recently, the phosphorylated amino acids on the structural proteins VP1, VP2 and VP3 of BKV have been identified by liquid chromatography-tandem mass spectrometry in our laboratory. In this study, we further analysed the biological effects of these phosphorylation events. Phosphorylation of the BKV structural proteins was demonstrated by [(32)P]orthophosphate labelling in vivo. Site-directed mutagenesis was performed to replace all of the phosphorylated amino acids. The mutated BKV genomes were transfected into Vero cells for propagation analysis. The results showed that expression of the early protein LT and of the late protein VP1 by the mutants VP1-S80A, VP1-S80-133A, VP1-S80-327A, VP1-S80-133-327A and VP2-S254A was abolished. However, propagation of other mutants was similar to that of wild-type BKV. The results suggest that phosphorylation of Ser-80 of VP1 and Ser-254 of VP2 is crucial for BKV propagation.

A manual sequence method of peptides and phosphopeptides using 4-(1'-cyanoisoindolyl)phenylisothiocyanate

A method for sequence analysis and identification of phosphoamino acids in peptides based on high performance liquid chromatography (HPLC) is described. The peptides were derivatized with an Edman type reagent, 4-(1'-cyanoisoindolyl)phenylisothiocyanate (CIPIC) and subsequently cleaved to generate stable and fluorescent 4-(1'-cyanoisoindolyl)phenylthiazolinone (CIP-TZ)-amino acids. Several experimental factors that affected derivatization on membranes were examined. Under the optimized conditions, the CIP-TZ derivatives of Try(p), Thr(p) and Ser(p) were obtained and separated from their parent amino acids with baseline resolution using an isocratic elution system. Up to the 4th residue of phosphorylated pentapeptides was successfully identified, whereas phosphoamino acid residues could not be detected by the conventional procedure using phenylisothiocyanate (PITC). The results demonstrated the potential of CIPIC as a derivatization reagent for peptide sequencing and the applicability of the method for the study and identification of phosphoamino acids in peptides.

Comparison of 2 cell-based phosphoprotein assays to support screening and development of an ALK inhibitor

Anaplastic lymphoma kinase (ALK) when expressed as a fusion protein with nucleophosmin (NPM) has been implicated as a driving oncogene in a subset of lymphomas. Recent reports of ALK expression in a number of other cancers have raised the possibility that an ALK inhibitor may benefit patients with these diseases as well. In a campaign to identify and develop a selective ALK inhibitor, 2 assays were devised to measure the phosphorylation of tyrosine residue 1604 of ALK (pY(1604) ALK). Amplified Luminescent Proximity Homogeneous Assay (AlphaScreen(®)) and phosflow platforms were used to detect modulation of pY(1604) ALK to determine the relative potency of a set of small-molecule inhibitors. Prior to making use of these assays in diverse settings, the authors attempted to ensure their equivalence with a direct comparison of their performance. The pY(1604) ALK assays correlated well both with each other and with assays of ALK enzyme activity or ALK-dependent cell proliferation. The AlphaScreen(®) assay was amenable to automation and enabled rapid, high-throughput compound assessment in an NPM-ALK-driven cell line, whereas the phosflow assay enabled the authors to characterize the activity of compounds with respect to their impact on targeted enzymes and pathways. Results show that both AlphaScreen(®) and phosflow ALK assays exhibited diverse characteristics that made them desirable for different applications but were determined to be equally sensitive and robust in the detection of inhibition of pY(1604) ALK.

Electron capture dissociation mass spectrometric analysis of lysine-phosphorylated peptides

Phosphorylation of proteins is an essential signalling mechanism in eukaryotic and prokaryotic cells. Although N-phosphorylation of basic amino acid is known for its importance in biological systems, it is still poorly explored in terms of products and mechanisms. In the present study, two MS fragmentation methods, ECD (electron-capture dissociation) and CID (collision-induced dissociation), were tested as tools for analysis of N-phosphorylation of three model peptides, RKRSRAE, RKRARKE and PLSRTLSVAAKK. The peptides were phosphorylated by reaction with monopotassium phosphoramidate. The results were confirmed by ¹H NMR and ³¹P NMR studies. The ECD method was found useful for the localization of phosphorylation sites in unstable lysine-phosphorylated peptides. Its main advantage is a significant reduction of the neutral losses related to the phosphoramidate moiety. Moreover, the results indicate that the ECD–MS may be useful for analysis of regioselectivity of the N-phosphorylation reaction. Stabilities of the obtained lysine-phosphorylated peptides under various conditions were also tested.

Capillary electrophoresis-mass spectrometry for the analysis of amino acids

In this review, the recent contribution of CE-MS technology to the analysis of amino acids, as well as the advantages of the hyphenation and the technologies involved in the instrumental coupling are reported. Different sections are dedicated to the recent contributions of CE-MS to the analysis of protein amino acids and their post-translational modifications, such as phosphorylation and sulfation. CE-MS analysis of some amino acid derivatives, such as the free methylated-derivatives of arginine is also discussed. A section is specifically devoted to the CE-MS applications in the field of chiral separation of D- and L-amino acid enantiomers.

Progress and possible applications of miniaturised separation techniques and elemental mass spectrometry for quantitative, heteroatom-tagged proteomics

The application of miniaturised separation techniques such as capillary LC, nano LC or capillary electrophoresis offers a number of advantages in terms of analytical performance, solvent consumption and the ability to analyse very small sample amounts. These features make them attractive for various bioanalytical tasks, in particular those related to the analysis of proteins and peptides. The skillful combination of such techniques with inductively coupled plasma mass spectrometry (ICP-MS) has recently permitted the design of combined analytical approaches utilising either elemental or molecule-specific detection techniques such as electrospray ionisation (ESI) or matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry in a highly complementary manner for, as an example, proteomics-orientated research (heteroatom-tagged proteomics). Such hybrid approaches are, in particular, providing promising new options for the fast screening of complex samples for specific metal-containing or--more generally speaking--heteroatom-containing biomolecules, as well as the accurate absolute quantification of biomolecules, which is still an unsolved problem in bioanalysis. Here, progress in as well as the potential and the special requirements of hyphenating miniaturised separation techniques with ICP-MS are reviewed and critically discussed. In addition, selected applications are highlighted to indicate current and possible future trends within this emerging area of research.

Identification of novel variants in the TMIE gene of patients with nonsyndromic hearing loss

OBJECTIVE

To determine whether variants of the TMIE gene are causes of nonsyndromic deafness in Taiwan.

METHODS

A genetic survey was made from 370 individuals, with 250 nonsyndromic hearing loss and 120 normal hearing individuals. Genomic DNA was extracted from peripheral blood leukocytes and then subjected to PCR to amplify selected exons and flanking introns of the TMIE gene; the amplified products were screened for base variants by autosequence. Data from the two groups were then compared using Fisher's two-tailed exact test and Armitage's trend test.

RESULTS

The analysis revealed 7 novel variants in the TMIE gene. Of the 7 variants, 5 variants were found in both nonsyndromic hearing loss and normal hearing group. Both allelic and genotype frequencies of these sequence changes did not differ significantly between patients and controls (P>0.05). However, a missense variant (c.257G>A) and one promoter variant (g.1-219A>T) were found in two patients with nonsyndromic hearing loss. Family study and microsatellite analysis found that c.257G>A variant is not inherited from his parents. The c.257G>A variant encodes a protein with glutamine at position 86 instead of arginine (p.R86Q), a residue that is conserved in mammals but different in fish, and predicted to be extracellular.

CONCLUSIONS

Despite the fact that the frequency of TMIE variants in our study subjects was low, we suggested that c.257G>A (p.R86Q) variant is a de novo and may be as a risk factor for the development of hearing loss in Taiwanese.

Facile identification and quantitation of protein phosphorylation via beta-elimination and Michael addition with natural abundance and stable isotope labeled thiocholine

Herein, we employ the unique chemical properties of the quaternary amine present in thiocholine (2-mercapto-N,N,N-trimethyl-ethanaminium) in conjunction with alkaline beta-elimination and Michael addition (BEMA) reactions for the specific detection, identification, and quantitation of phosphorylated serine/threonine containing peptides. Through replacement of the phosphate with thiocholine, the negative charge on the phosphopeptide is switched to a quaternary amine containing a permanent positive charge. This strategy resulted in a 100-fold increase in ionization sensitivity during ESI (sub-500 amol/microL detection limit) accompanied by a markedly enhanced production of informative peptidic fragment ions during CID that dramatically increase sequence coverage. Moreover, the definitive localization of phosphorylated residues is greatly facilitated through the generation of diagnostic triads of fragmentation ions resulting from peptide bond cleavage and further neutral loss of either trimethylamine (-59 Da) or thiocholine thiolate (-119 Da) during collision induced dissociation (CID) in tandem mass spectrometry (MS(2) and MS(3)). Synthesis of stable isotope labeled thiocholine enabled the quantitation of protein phosphorylation with high precision by ratiometric comparisons using heavy and light thiocholine. Collectively, this study demonstrates a sensitive and efficient strategy for mapping of phosphopeptides by BEMA using thiocholine through the production of a diagnostic repertoire of unique fragment ions during liquid chromatography-tandem mass spectrometry (LC-MS(2)/MS(3)) analyses, facilitating phosphosite identification and quantitative phosphoproteomics.

2D-DIGE: comparative proteomics of cellular signalling pathways

Two-dimensional (2-D) gel electrophoresis concerted with protein identification by mass spectrometry (MS) is an extremely powerful method for comparative expression profiling of complex protein samples such as cell lysates. The highly resolutive 2-D electrophoresis allows the separation of heterogeneous protein samples on the basis of isoelectric point (pI), molecular mass (Mr), solubility, and relative abundance ((1) J Biol Chem 250: 4007-4021, 1975; (2) Electrophoresis 14: 1067-1073, 1993). Consequently, it provides a comprehensive view of a proteome state ((3) Electrophoresis 21: 1037-1053, 2000), where variations in protein expression levels, isoforms, or post-translational modifications (e.g. phosphorylation) can be highlighted and investigated ((4) Electrophoresis 21: 2196-2208, 2000). Furthermore, this allows the identification of biological markers that characterize a specific physiological or pathological background of a cell or a tissue ((5) Proteomics 1: 397-408, 2001; (6) J Bacteriol 179: 7595-7599, 1997). In this way one can compare the effects of a stimulus or drug on cells or tissue, or more importantly, analyse the effects of disease on the expression level of proteins. Relatively recently, conventional 2-D gel electrophoresis has been combined with protein labelling strategies using up to three different fluorescent dyes to allow comparative analysis of different protein samples within a single 2-D gel platform. In this technique, termed differential in-gel electrophoresis (DIGE), samples are labelled separately then combined and run on the same 2D gel minimizing experimental variation and greatly facilitating spot matching. When three CyDyes (Cy2, Cy3, and Cy5) have been used, three images of the gel are captured then superposed to localize the differentially regulated spots on the 2-D gel using image analysis software. This is an extremely powerful tool in comparative proteomics as these dyes provide a linear response to protein concentration up to five orders of magnitude and great sensitivity with detection down to 125 pg of a single protein, which is less than needed for MS identification. In this chapter, we describe the basic methods for protein labelling, optimization of the isoelectrofocusing parameters for the first dimension (where proteins are separated according to their isoelectric point (pI)), sodium-dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) separation for the second dimension (based on molecular weight (MW)), and different post-staining protocols of the 2-D gel and protein preparation for mass spectrometry identification.

Microscale characterization of the binding specificity and affinity of a monoclonal antisulfotyrosyl IgG antibody

Sulfation is a potentially important post-translational modification of proteins and has been demonstrated in a number of polypeptides, notably in gastrointestinal hormones. In contrast to phosphorylation, however, the investigation of sulfation patterns in tissues and on purified proteins has been complicated by the absence of specific immunoreagents (antibodies) for this modification as well as the chemical lability of the sulfate group. Here, we investigate the properties of a novel mAb against sulfated tyrosyl groups (anti-Tyr(SO(3)H) antibody) using CE and a panel of sulfated and nonsulfated peptides and proteins. The data show that the anti-Tyr(SO(3)H) antibody is completely specific for compounds containing sulfated tyrosyls. Affinity electrophoresis experiments allowed us to estimate dissociation constants for sulfated hirudin fragment (56-65), gastrin-17, and cholecystokinin octapeptide (CCK8) in the 1-3 microM range. The affinity of the antibody toward complement 4 protein that contains three sulfotyrosines was analyzed by surface plasmon resonance technology and modeled according to a bivalent-binding model which yielded a K(d1) of 20.1 microM for the monovalent complex. The same binding was studied by CE and found to be in the micromolar scale albeit with some uncertainty due to complex separation patterns. The work illustrates the amount of information on antibody-antigen interactions that may be obtained with microelectrophoretic methods consuming minute quantities of material. Furthermore the specificity of this antibody could be confirmed in one operation using an array of sulfated and nonsulfated compounds.

Detecting the site of phosphorylation in phosphopeptides without loss of phosphate group using MALDI TOF mass spectrometry

Phosphopeptides with one and four phosphate groups were characterized by MALDI mass spectrometry. The molecular ion of monophosphopeptide could be detected both as positive and negative ions by MALDI TOF with delayed extraction (DE) and in the reflector mode. The tetraphospho peptide could be detected in linear mode. When MS/MS spectra of the monophospho peptides were obtained in a MALDI TOF TOF instrument by CID, b and y ions with the intact phosphate group were observed, in addition the b and y ions without the phosphate group. Our study indicates that it is possible to detect phosphorylated peptides with out the loss of phosphate group by MALDI TOF as well as MALDI TOF TOF instruments with delayed extraction and in the reflector mode.

Non-disruptive release of Pseudomonas putida proteins by in situ electric breakdown of intact cells

Analysis of the native proteome of bacterial cells typically involves physical procedures (sonication, French press) and/or biochemical methods (treatment with lysozyme, osmotic shock etc.) to break open the bacteria to yield a soluble protein fraction. Such procedures are not only time consuming, but they change bacterial physiology during manipulation and affect labile post-translational modifications such as His-P bonds. In this work, we document the efficacy of the dielectric breakdown of live bacteria for releasing and delivering the protein contents of intact cells directly into a non-denaturing gel system. By means of such an in situ electrophoresis, the protein pool enters the separation medium without any manipulation of the cells other than being exposed to a moderate electric voltage. To validate the method we have followed the fate of the two forms of the PtsN (EIIA(Ntr)) protein of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) of Pseudomonas putida through the various stages of the procedure. Apart of detecting the corresponding polypeptides, we show that this procedure releases the bulk of the proteome while keeping unharmed the phosphorylation state of EIIA(Ntr) as it was present in the cells prior to applying the electric field. The method is applicable to other bacteria as well.

Liquid chromatographic analysis of phosphoamino acids at femtomole level using chemical derivatization with N-hydroxysuccinimidyl fluorescein-O-acetate

Phosphorylation of amino acid residues in proteins plays a major role in biological systems. In this paper, a reversed-phase high performance liquid chromatographic (HPLC) method based on chemical derivatization has been described for the separation and quantification of phosphoamino acids at femtomole level, using fluorimetric detection (FLD). The protocol involved pre-column derivatization of phosphoamino acids with N-hydroxysuccinimidyl fluorescein-O-acetate (SIFA) and subsequent separation on ZORBAX Eclipse XDB-C8 column. Several experimental factors that influenced derivatization and separation were carefully investigated. The derivatization was performed at 40 degrees C for 40 min in borate buffer (pH 8.5). Under the optimum conditions, phosphoserine (P-Ser), phosphothreonine (P-Thr) and phosphotyrosine (P-Tyr) were satisfactorily separated in 8 min. The detection limits (signal-to-noise ratio=3) for the phosphoamino acids could reach 10-20 fmol, which was the lowest value reported for HPLC methods and comparable to those obtained by capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection methods. The proposed method has been validated and used to characterize the phosphoamino acids in the hydrolyzed phosphorylated protein samples. The results clearly demonstrated the potential of this technique to study phosphoamino acids as well as provided a new analytical methodology that should be applicable to the study of phosphorylation of protein in biological system.

Capillary electrophoresis of phosphorylated amino acids with fluorescence detection

A rapid and sensitive capillary electrophoresis (CE) method coupled with fluorescence detection was developed for identification of protein phosphorylation by determination of phosphoamino acids. Naphthalene-2,3-dicarboxaldehyde (NDA), a fluorescence derivatization reagent, was used to label protein hydrolysate. The optimal derivatization reaction was performed with 3.5mM NDA, 40 mM NaCN and 20mM borate buffer (pH 10.0) for 15 min. The baseline separation of three phosphorylated amino acids could be obtained in less than 180 s with good repeatability by using 30 mM borate (pH 9.2) containing 2.0mM beta-cyclodextrin (beta-CD) as the running buffer. The detection limits for phosphothreonine, phosphotyrosine and phosphoserine were 7.0 x 10(-9)M, 5.6 x 10(-9)M and 7.2 x 10(-9)M, respectively (S/N=3). Also, the interference from other protein amino acids with large molar excess over that of phosphoamino acids was studied. With beta-casein as the analysis protein, this method was successfully validated.

Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry

Proteins from biological samples are often identified by mass spectrometry (MS) with the two following "bottom-up" approaches: peptide mass fingerprinting or peptide sequence tag. Nevertheless, these strategies are time-consuming (digestion, liquid chromatography step, desalting step), the N- (or C-) terminal information often lacks and post-translational modifications (PTMs) are hardly observed. The in-source decay (ISD) occurring in a matrix assisted laser desorption/ionization (MALDI) source appears an interesting analytical tool to obtain N-terminal sequence, to identify proteins and to characterize PTMs by a "top-down" strategy. The goal of this review deals with the usefulness of the ISD technique in MALDI source in proteomics fields. In the first part, the ISD principle is explained and in the second part, the use of ISD in proteomic studies is discussed for protein identification and sequence characterization.

Identification of phosphoproteins and determination of phosphorylation sites by zirconium dioxide enrichment and SELDI-MS/MS

Reversible protein phosphorylation mediated by protein kinases and phosphatases is the most studied post-translational modification. Efficient characterization of phosphoproteomes is hampered by (1) low stoechiometry, (2) the dynamic nature of the phosphorylation process and (3) the difficulties of mass spectrometry to identify phosphoproteins from complex mixtures and to determine their sites of phosphorylation. Combination of the phosphopeptide enrichment method with MALDI-TOFMS, or alternatively, with HPLC-ESI-MS/MS and MS(3) analysis was shown to be a step forward for the successful application of MS in the study of protein phosphorylation. In our study we used phosphopeptide enrichment performed in a simple single-tube experiment using zirconium dioxide (ZrO(2)). A simple protein mixture containing precipitated bovine milk caseins was enzymatically digested and the mixture of tryptic fragments was analysed before and after enrichment using nanoflow HPLC-ESI-MS/MS and surface-enhanced laser desorption/ionization (SELDI)-MS/MS on QqTOF instruments to compare the efficiency of the two methods in the determination of phosphorylation sites. Both approaches confirm the high selectivity obtained by the use of batch-wise, ZrO(2)-based protocol using di-ammonium phosphate as the eluting buffer. More phosphorylation sites (five for beta-casein and three for alpha(S1)-casein) were characterized by SELDI-MS/MS than by nanoflow HPLC-ESI-MS/MS. Therefore, ZrO(2)-based phosphopeptide enrichment combined with SELDI-MS/MS is an attractive alternative to previously reported approaches for the study of protein phosphorylation in mixtures of low complexity with the advance of fast in situ peptide purification. The method was limited to successful analysis of high-abundance proteins. Only one phosphorylation site was determined for the minor casein component alpha(S2)-casein by ESI-MS/MS and none for kappa-casein. Therefore an improvement in enrichment efficiency, especially for successful phosphoproteomic applications, is needed.

Highly efficient and selective enrichment of phosphopeptides using porous anodic alumina membrane for MALDI-TOF MS analysis

Because of its good biocompatibility, high surface-to-volume ratio, and distinct surface electrical properties, porous anodic alumina (PAA) membrane has been used to selectively enrich phosphopeptides from a mixture of synthetic peptides and tryptic digest product of beta-casein by a direct MALDI-TOF MS analysis. As we reported previously, PAA membrane has strong incorporation ability to the phosphate anion. Herein, we describe the application of PAA membrane as a selective sampling absorbent for phosphopeptides. The PAA membrane could enrich phosphopeptides with high efficiency and selectivity; for example, the tryptic digest product of beta-casein at a concentration as low as 4 x 10(-9) M can be satisfactorily detected. Compared to that from the nonenriching peptide mixture, the MS signal of the phosphorylated peptides enriched by the PAA membrane is remarkably improved. In addition, acidic peptides have insignificant influence on the enriching process. Results show that the adsorption of phosphate anions on the PAA membrane plays a determining role in achieving highly selective enriching capacity toward phosphopeptides. The feasibility of PAA membranes as specific absorbents for phosphopeptides is also demonstrated.