• Molecules and Cells
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• v.23 no.3
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• pp.340-348
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• 2007

Although considerable effort has been devoted in the mass spectrometric analysis of phosphorylated peptides, successful identification of multi-phosphorylated peptides in enzymatically digested protein samples still remains challenging. The ionization behavior of multi-phosphorylated peptides appears to be somewhat different from that of mono- or di-phosphorylated peptides. In this study, we demonstrate increased sensitivity of detection of multi-phosphorylated peptides of beta casein without using phosphopeptide enrichment techniques. Proteinase K digestion alone increased the detection limit of beta casein multi-phosphorylated peptides in the LC-MS analysis almost 500 fold, compared to conventional trypsin digestion (~50 pmol). In order to understand this effect, various factors affecting the ionization of phosphopeptides were investigated. Unlike ionizations of phosphopeptides with minor modifications, those of multi-phosphorylated peptides appeared to be subject to effects such as selectively suppressed ionization by more ionizable peptides and decreased ionization efficiency by multi-phosphorylation. The enhanced detection limit of multi-phosphorylated peptides resulting from proteinase K digestion was validated using a complex protein sample, namely a lysate of HEK 293 cells. Compared to trypsin digestion, the numbers of phosphopeptides identified and modification sites per peptide were noticeably increased by proteinase K digestion. Non-specific proteases such as proteinase K and elastase have been used in the past to increase detection of phosphorylation sites but the effectiveness of proteinase K digestion for multi-phosphorylated peptides has not been reported.

• Bulletin of the Korean Chemical Society
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• v.33 no.10
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• pp.3298-3302
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• 2012

Although offline enrichment of phosphorylated peptides is widely used, enrichment for phosphopeptides using $TiO_2$ is often performed manually, which is labor-intensive and can lead to irreproducible results. To address the problems associated with offline enrichment and to improve the effectiveness of phosphopeptide detection, we developed an automated online enrichment system for phosphopeptide analysis. A standard protein mixture comprising BSA, fetuin, crystalline, ${\alpha}$-casein and ${\beta}$-casein, and ovalbumin was assessed using our new system. Our multidimensional system has four main parts: a sample pump, a 20-mm $TiO_2$-based column, a weak anion-exchange, and a strong cation-exchange (2:1 WAX:SCX) separation column with LC/MS. Phosphorylated peptides were successfully detected using the $TiO_2$-based online system with little interference from nonphosphorylated peptides. Our results confirmed that our online enrichment system is a simple and efficient method for detecting phosphorylated peptides.

• Molecules and Cells
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• v.44 no.7
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• pp.500-516
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• 2021

Cardiac hypertrophic signaling cascades resulting in heart failure diseases are mediated by protein phosphorylation. Recent developments in mass spectrometry-based phosphoproteomics have led to the identification of thousands of differentially phosphorylated proteins and their phosphorylation sites. However, functional studies of these differentially phosphorylated proteins have not been conducted in a large-scale or high-throughput manner due to a lack of methods capable of revealing the functional relevance of each phosphorylation site. In this study, an integrated approach combining quantitative phosphoproteomics and cell-based functional screening using phosphorylation competition peptides was developed. A pathological cardiac hypertrophy model, junctate-1 transgenic mice and control mice, were analyzed using label-free quantitative phosphoproteomics to identify differentially phosphorylated proteins and sites. A cell-based functional assay system measuring hypertrophic cell growth of neonatal rat ventricle cardiomyocytes (NRVMs) following phenylephrine treatment was applied, and changes in phosphorylation of individual differentially phosphorylated sites were induced by incorporation of phosphorylation competition peptides conjugated with cell-penetrating peptides. Cell-based functional screening against 18 selected phosphorylation sites identified three phosphorylation sites (Ser-98, Ser-179 of Ldb3, and Ser-1146 of palladin) displaying near-complete inhibition of cardiac hypertrophic growth of NRVMs. Changes in phosphorylation levels of Ser-98 and Ser-179 in Ldb3 were further confirmed in NRVMs and other pathological/physiological hypertrophy models, including transverse aortic constriction and swimming models, using site-specific phospho-antibodies. Our integrated approach can be used to identify functionally important phosphorylation sites among differentially phosphorylated sites, and unlike conventional approaches, it is easily applicable for large-scale and/or high-throughput analyses.

• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.607-611
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• 2004

Glycinin, one of the predominant storage proteins in soybeans, was examined as to whether it could be used as a calcium-binding mediator after chemical phosphorylation and enzymatic hydrolysis. Glycinin is composed of six subunits. One of the proglycinin subunits $(A_{la}B_{lb})$ was overexpressed in E. coli to obtain nonphosphorylated proteins with homogeneity. To investigate the enhanced calcium-binding properties of the phosphopeptides, the proglycinin was purified, phosphorylated, and hydrolyzed with trypsin. The proglycinin expressed in E. coli was purified by ammonium sulfate precipitation, ion-exchange chromatography, and cryoprecipitation. Chemical phosphorylation by sodium trimetaphosphate was performed to obtain phosphorylated proglycinin. After the phosphorylation, one-dimensional isoelectric focusing gel electroanalysis confirmed the phosphorylation of the proglycinin. The phosphorylated peptides were then hydrolyzed with trypsin, followed by a binding reaction with calcium chloride. The calcium-bound phosphopeptides were finally separated using immobilized metal $(Ca^{2+})$ chromatography. Consequently, a limited tryptic hydrolysate of the isolated phosphopeptides exhibited an enhanced calcium-binding ability, suggesting the potential of glycinin phosphopeptides as a calcium-binding mediator with greater availability.

• Journal of the Korean Chemical Society
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• v.41 no.4
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• pp.205-209
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• 1997

The site specificity of dephosphorylation of myelin basic protein(MBP) was studied in vitro. To assign amino acid site of dephosphorylation, MBP was phosphorylated by protein kinase C(PKC) and dephosphorylated by protein phosphatase PP2A. The phosphorylated MBP was digested by trypsine and the digested peptides were separated by a reverse phase HPLC chromatography. The radioactivity of each fraction was counted and partially sequenced. Seven radioactive peptides were observed and $Ser^{55}$ in the second peak($P_2$) shows the best susceptibility for the phosphorylation. However in the dephosphorylation, the fifth peak($P_5$) appeared to release it's phosphate group most rapidly. This result demonstrates that MBP is a suitable substrate for protein phosphatase.

• Mass Spectrometry Letters
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• v.3 no.2
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• pp.39-42
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• 2012

Phosphorylation and glycosylation are two of the most important and widespread post-translational modifications (PTMs) in an organism. Proteomics analysis of the PTMs has been challenged by low stoichiometry of the modified proteins and suppression effects by high abundance proteins, typically no-functional house-keeping proteins. In this study, a novel method was applied for not only isolating PTM peptides from intact peptides but also concurrently characterizing of glyco- and phosphoproteome using electrostatic repulsion hydrophilic interaction chromatography (ERLIC) packed with silica coated by crosslinked polyethyleneimine. For 2 mg tryptic digest of mouse proteome of epicardial adipose tissue with fat diet, 802 N-glycosylated peptides of 316 glycoproteins and 159 phosphorylated peptides of 75 phosphoproteins were identified using HPLC chip/quadrupole time-of-flight (Q-OF) tandem mass spectrometer.

• BMB Reports
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• v.29 no.4
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• pp.386-392
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• 1996

A Saccharomyces cerevisiae Protein Tyrosine Phosphatase, PTP1, was expressed from an Escherichia coli expression system and milligram quantities of active PTP1 were purified chromatographically. The substrate specificity of the recombinant PTP1 was probed using synthetic phosphotyrosine-containing peptides corresponding to the regulatory phosphorylation sites of the yeast MAP kinase homologues $Fus3_{176-186}$, $Kss1_{179-189}$, and $Hog1_{170-180}$. Peptide sequences derived from the MAP kinase homologues were chosen arbitrarily as starting points for sequence variation studies even though they are not likely to be candidates for physiological substrates of PTP1. Phosphotyrosyl-$Hog1_{170-180}$ peptide showed a $K_M$ value of 877 ${\mu}M$ and phosphorylated $Kss1_{179-189}$ and $Fus3_{176-186}$ peptides showed lower $K_M$ values of 74 ${\mu}M$ and 51 ${\mu}M$ each. To study the effect of sequence variations of the peptide, amino acids of the undecapeptide $Hog1_{170-180}$ (DPQMTGpYVSTR) were sequentially substituted by an alanine residue. More extensive variations of each amino acid revealed positional importance of each amino acid residue. Based on these results, we derived a peptide sequence (DADEpYDA) that is recognized by PTP1 with an affinity ($K_M$ is 4 ${\mu}M$) significantly higher than that of the peptides derived from the phosphorylation sites of Fus3, Kss1, and Hog1.

• Journal of Life Science
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• v.8 no.6
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• pp.654-659
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• 1998

The 2B subunit of N-methyl-D-aspartate (NMDA) receptors (NR2B) is the major phosphotyrosine-containing pro-tein in the postsynaptic density (PSD). In order to identify the site for tyrosine phosphorylation on NR2B, a mass spectrometry was applied on tryptic and endolys-C peptides. The NR2B subunit was isolated from N-octyl glucoside (NOG)-insoluble PSD fraction through SDS-PAGE and electroelution. The eluted protein was confirmed to be NR2B and phosphorylated on tyrosine by its cognate antibody and phosphotyrosine-specific antibody. By matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry of the peptides generated by digesting the eluted NR2B with trysin or endolys-C, a potential site for tyrosine phosphorylation could be identified as Tyr-1304.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.32 no.6
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• pp.713-717
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• 1999

In order to utilize protein hydrolysate produced from hoki (Johnius Belengeri) frame among many different fish processing wastes, hoki frame peptide (PHFP) and phosphorylated hoki frame peptide (PHFP) were prepared, and their calcium absorption accelerating effects were investigated in comparison to control and casein phosphopeptide (CPP). In in vitro experiment, HFP and PHFP inhibited calcium phosphate formation as high as 1.5-fold and 2.5-fold, respectively, comparing to control, In addition, the inhibition rate of calcium phosphate precipitation as increasing concentrations of HFP and PHFP was risen and was similar to that of CPP at 2.0 mg/ml of PHFP concentration, In in vivo experiment using the rats, the groups fed HFP and PHFP indicated significantly increased calcium content in the femur. In particular, the calcium content in the small intestine of the rat fed PHFP was higher than that of control group by approximately $60\%$.

• Animal cells and systems
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• v.9 no.3
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• pp.161-171
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• 2005

Integrin-linked kinase 1 (ILK1) regulates several protein kinases, including PKB/Akt kinase and glycogen synthase kinase ${\beta}$. ILK1 is also involved distinctively in the cell morphological and structural functions by interacting with the components of the extracellular matrix or integrin. According to the information of serum- and glucocorticoid-induced kinase 1 (SGK1) substrate specificity (R-X-R-X-X(S/T)-${\phi};{\phi}$ indicates a hydrophobic amino acid), two putative phosphorylation sites, $Thr^{181}\;and\;Ser^{246}$, were found in ILK1. We showed that ILK1 fusion protein and two fluorescein-labeled ILK1 peptides, $FITC-^{174}RTRPRNGTLN^{183}$ and $FITC-^{239}CPRLRIFSHP^{248}$, were phosphorylated by SGK1 in vitro. We also identified that 14-3-3 ${\theta}\;{\varepsilon}\;and\;{\xi}$, among several 143-3 isotypes $({\beta},\;{\gamma},\;{\varepsilon},\;{\eta},\;{\sigma},\;{\theta},\;{\tau}\;and\;{\xi})$ formed protein complex with ILK1 in COS-1 cells. Furthermore, the phosphorylation of $Ser^{246}$ by SGK1 induced the binding with 14-3-3. It was also demonstrated that 14-3-3-bound ILK1 has reduced kinase activity. Thus, these data suggest that SGK1 phosphorylates $Thr^{181}\;and\;Ser^{246}$ of ILK1 and the phosphorylation of its $Ser^{246}$ makes ILK1 bind to 14-3-3, resulting in the inhibition of ILK1 kinase activity.