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PubMed2004

Dynamic identification of phosphopeptides using immobilized metal ion affinity chromatography enrichment, subsequent partial beta-elimination/chemical tagging and matrix-assisted laser desorption/ionization mass spectrometric analysis.

The enrichment of phosphopeptides using immobilized metal ion affinity chromatography (IMAC) and subsequent mass spectrometric analysis is a powerful protocol for detecting phosphopeptides and analyzing their phosphorylation state. However, nonspecific binding peptides, such as acidic, nonphosphorylated peptides, often coelute and make analyses of mass spectra difficult. This study used a partial chemical tagging reaction of a phosphopeptide mixture, enriched by IMAC and contaminated with nonspecific binding peptides, following a modified beta-elimination/Michael addition method, and dynamic mass analysis of the resulting peptide pool. Mercaptoethanol was used as a chemical tag and nitrilotriacetic acid (NTA) immobilized on Sepharose beads was used for IMAC enrichment. The time-dependent dynamic mass analysis of the partially tagged reaction mixture detected intact phosphopeptides and their mercaptoethanol-tagged derivatives simultaneously by their mass difference (-20 Da for each phosphorylation site). The number of new peaks appearing with the mass shift gave the number of multiply phosphorylated sites in a phosphopeptide. Therefore, this partial chemical tagging/dynamic mass analysis method can be a powerful tool for rapid and efficient phosphopeptide identification and analysis of the phosphorylation state concurrently using only MS analysis data.

Adsorption↗
PubMed1975

Phosphopeptide and phosphoprotein metabolism in brain.

Phosphopeptide and phosphoprotein phosphorylation was studied in rat brain microsomes and rat brain slices which were incubated in the presence of [gamma-32 P] ATP under various experimental conditions. Radioactive phosphoserine was isolated from phosphopeptides and phosphoproteins. Naplus, K+, Mg2+ and cyclic AMP had a stimulating effect on the labelling of phosphopeptides. Ouabain and Ca2+ lowered the level of 32P incorporation into the phosphopeptides. The phosphoproteins behaved similarly to the phosphopeptides except for the potassium effect. Chase experiments showed a faster decrease in the labelling of phosphopeptides than in phosphoproteins. We suggest that both compounds may be involved in active transport phenomena.

Adenosine Triphosphate↗
PubMed2006

Two-dimensional HPLC on-line analysis of phosphopeptides using titania and monolithic columns.

Conventional and comprehensive two-dimensional (2D) HPLC systems using the combination of titania and monolithic columns were established for the on-line analysis of phosphopeptides. Compared with immobilized metal affinity chromatography of a general method for the analysis of phosphopeptides, the use of titania columns in the analysis permits the specific isolation of phosphopeptides in a higher yield. Using the current 2D HPLC systems, phosphopeptides were specifically isolated from nonphosphorylated peptides by the first-dimension titania column, followed by the high-speed separation of the phosphopeptides by the second-dimension monolithic column. Proteolytic digests of beta-casein were analyzed within 30 min using the comprehensive 2D HPLC system; all phosphopeptides from beta-casein could be efficiently isolated and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The comprehensive 2D HPLC system coupled with mass spectrometry will be useful for high-throughput and on-line phosphoproteome analyses.

Caseins↗
PubMed2002

Factors governing the solubilization of phosphopeptides retained on ferric NTA IMAC beads and their analysis by MALDI TOFMS.

We have revisited the direct analysis experiments reported by Tomer and co-workers in the MALDI-TOFMS analysis of phosphopeptide-loaded immobilized metal ion affinity chromatography (IMAC) beads (Zhou, W.; Merrick, B. A.; Khaledi, M. G.; Tomer, K. B. J. Am. Soc. Mass Spectrom. 2000, 11, 273-282). The results described herein provide no evidence to support a laser-induced direct desorption of phosphopeptides chelated on IMAC beads. However, we have established that solubilization of mono-phosphopeptides from their immobilized Fe3+-NTA chelates does occur effectively in solutions containing certain MALDI matrices. Particularly effective is 2,5-dihydroxybenzoic acid (2,5-DHB), which apparently forms a stronger chelation complex with Fe3+-NTA than mono-phosphopeptides. With regard to the disparity observed between the low pH value of MALDI matrices (saturated 2,5-DHB(aq) approximately pH 2) and the high pH values of conventional IMAC eluents (typically above pH 7), we have also investigated the influence of eluent pH on the recovery of phosphopeptides from IMAC media. Finally, we have confirmed the importance of employing ammonium dihydrogen phosphate as buffer to achieve effective liberation of mono- and all poly-phosphopeptide species from Fe3+-NTA IMAC resin.

Amino Acid Sequence↗
PubMed2002

Improved sensitivity for phosphopeptide mapping using capillary column HPLC and microionspray mass spectrometry: comparative phosphorylation site mapping from gel-derived proteins.

Reversible protein phosphorylation regulates many cellular processes. Understanding how phosphorylation controls a given pathway usually involves specific knowledge of which amino acid residues are phosphorylated on a given protein. This is often a nontrivial task. In addition to the difficulties involved in purifying sufficient amounts of any given protein, most phosphoproteins contain multiple, substoichiometric sites of phosphorylation. In this paper, we describe substantial improvements made to our previously reported multidimensional electrospray MS-based phosphopeptide mapping technique that have resulted in a 20-fold increase in sensitivity for the overall process. Chief among these improvements are the incorporation of capillary chromatography and a microionspray source for the mass spectrometer into the first dimension of the analysis. In the first dimension of the process, phosphopeptides present in the proteolytic digest of a protein are selectively detected and collected into fractions during on-line LC/ESMS, which monitors for phosphopeptide specific marker ions. The phosphopeptide containing fractions are then analyzed in the second dimension by either MALDI-PSD or nano-ES with precursor ion scanning. The relative merits and limitations of these two techniques for phosphopeptide detection are demonstrated. The enhancement in sensitivity of the method under the new experimental conditions makes it suitable for phosphorylation mapping (from selective detection through sequencing) on gel-separated phosphoproteins where the level of phosphorylation at any given site is <200 fmol. Furthermore, this method detects serine, threonine, and tyrosine phosphorylation equally well. We have successfully employed this new configuration to map 11 in vivo sites of phosphorylation on the Saccharomyces cerevisiae protein kinase YAK1. YAK1 peptides containing all five YAK1 PKA consensus sites are phosphorylated, suggesting that YAK1 is an in vivo substrate for PKA. In addition, four peptides containing cdk sites and the autophosphorylation site at Tyr530 were found to be phosphorylated. Because the first dimension of this method generates a phosphorylation profile that can be used for a semiquantitative evaluation of site specific phosphoxylation, we evaluated its ability to detect site-specific changes in the phosphorylation profile of a protein in response to altered cellular conditions. This comparative phosphopeptide mapping strategy allowed us to detect a change in phosphorylation stoichiometry on the motor protein myosin-V in response to treatment with either mitotic or interphase Xenopus egg extracts and to identify the single functionally significant phosphorylation site that regulates myosin-V cargo binding.

Chromatography, High Pressure Liquid↗
PubMed2004

Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns.

Selective detection of phosphopeptides from proteolytic digests is a challenging and highly relevant task in many proteomics applications. Often phosphopeptides are present in small amounts and need selective isolation or enrichment before identification. Here we report a novel automated method for the enrichment of phosphopeptides from complex mixtures. The method employs a two-dimensional column setup, with titanium oxide-based solid-phase material (Titansphere) as the first dimension and reversed-phase material as the second dimension. Phosphopeptides are separated from nonphosphorylated peptides by trapping them under acidic conditions on a TiO(2) precolumn. Nonphosphorylated peptides break through and are trapped on a reversed-phase precolumn after which they are analyzed by nanoflow LC-ESI-MS/MS. Subsequently, phosphopeptides are desorbed from the TiO(2) column under alkaline conditions, reconcentrated onto the reversed-phase precolumn, and analyzed by nanoflow LC-ESI-MS/MS. The selectivity and practicality of using TiO(2) precolumns for trapping phosphopeptides are demonstrated via the analysis of a model peptide RKISASEF, in a 1:1 mixture of a non- and a monophosphorylated form. A sample of 125 fmol of the phosphorylated peptide could easily be isolated from the nonphosphorylated peptide with a recovery above 90%. In addition, proteolytic digests of three different autophosphorylation forms of the 153-kDa homodimeric cGMP-dependent protein kinase are analyzed. From proteolytic digests of the fully autophosphorylated protein at least eight phosphorylation sites are identified, including two previously uncharacterized sites, namely, Ser-26 and Ser-44. Ser-26 is characterized as a minor phosphorylation site in purified PKG samples, while Ser-44 is identified as a novel in vitro autophosphorylation target. These results clearly show that TiO(2) has strong affinity for phosphorylated peptides, and thus, we conclude that this material has a high potential in the field of phosphoproteomics.

Automation↗
PubMed2005

Mapping of phosphorylation sites by a multi-protease approach with specific phosphopeptide enrichment and NanoLC-MS/MS analysis.

We have developed a multi-protease approach that allows sensitive and comprehensive mapping of protein phosphorylation sites. The combined application of the low-specificity proteases elastase, proteinase K, and thermolysin in addition to trypsin results in high sequence coverage, a prerequisite for comprehensive phosphorylation site mapping. Phosphopeptide enrichment is performed with the recently introduced phosphopeptide affinity material titansphere. We have optimized the selectivity of the phosphopeptide enrichment with titansphere, without compromising the high recovery rate of approximately 90%. Phosphopeptide-enriched fractions are analyzed with a highly sensitive nanoLC-MS/MS system using a 25-microm-i.d. reversed-phase column, operated at a flow rate of 25 nL/min. The new approach was applied to the murine circadian protein period 2 (mPER2). A total of 21 phosphorylation sites of mPER2 have been detected by the multi-protease approach, whereas only 6 phosphorylation sites were identified using solely trypsin. Titansphere proved to be well suited for the enrichment of a large variety of phosphopeptides, including peptides carrying two, three, or four phosphorylated residues, as well as phosphopeptides containing more basic than acidic amino acids.

Amino Acid Sequence↗
PubMed2006

Phosphate group-driven fragmentation of multiply charged phosphopeptide anions. Improved recognition of peptides phosphorylated at serine, threonine, or tyrosine by negative ion electrospray tandem mass spectrometry.

The nanoelectrospray product ion spectra of multiply charged phosphopeptide anions reveal the occurrence of phosphate-specific high-mass fragment ions of the type [M - nH - 79](n-1)-. These so far unrecognized fragments, which are observed for phosphoserine-, phosphothreonine-, and phosphotyrosine-containing peptides, are the counterparts of the established inorganic phosphopeptide marker ion found at m/z 79 = [PO3]-. The high-mass marker ions are formed with high efficiency at moderate collision offset values and are particularly useful for sensitive recognition of pSer-, pThr-, and pTyr-peptides due to the low background level in MS/MS spectra at m/z values above those of the precursor ions. By virtue of this feature, the detection of the new phosphorylation-specific fragment ions appears to be more sensitive than the detection of the low-mass phosphate marker ion at m/z 79, where a higher interference by nonspecific background signals is generally observed. The number of phosphate groups within a phosphopeptide can also be estimated on the basis of the [M - nH - 79](n-1)- ions, since these exhibit an effective, sequential neutral loss of H3PO4 of the residing phosphate groups. A mechanistic explanation for the formation of the [M - nH - 79](n-1)- ions from multiply charged phosphopeptides is given. The high-mass marker ions are proposed to originate from phosphopeptide anions, which carry two negative charges located at the phosphate group. A new search tool denominated "variable m/z gain analysis", which utilizes these newly recognized high-mass fragments for spotting of phosphopeptides in a negative ion parent scan, is proposed. The findings strengthen the value of negative ion ESI-MS/MS for analysis of protein phosphorylation.

Amino Acid Sequence↗
PubMed1988

The presence and origin of phosphopeptides in human saliva.

The presence of phosphopeptides in whole saliva (saliva expectorated from the mouth) was demonstrated and their origin was evaluated. Whole saliva contained much larger numbers of small phosphopeptides than are found in the glandular secretions. Most of these originated from the acidic proline-rich proteins (PRPs) in the major salivary glands and were formed, after secretion into the oral cavity, as a result of rapid degradation by proteolytic enzymes from extraglandular sources contained in sediment from whole saliva. Some peptides may have been formed by cleavage of basic PRPs, but other phosphoproteins apparently contributed little to the observed phosphopeptides. Most of the enzymes that produced phosphopeptides are serine proteinases. The gel-electrophoretic band patterns of the phosphopeptides obtained from 26 individuals of various acidic-PRP phenotypes were remarkably similar, demonstrating that the enzymes responsible were generally present in the population surveyed and that similar cleavages occur regardless of the nature of the acidic PRPs. Many of these peptides were N-terminal proteolytic cleavage products of acidic PRPs. The N-terminal phosphorylated region of acidic PRPs contains various biological activities, such as inhibition of hydroxyapatite formation, calcium binding and binding to hydroxyapatite, the major mineral of teeth. The demonstration of these phosphopeptides in the saliva that is in contact with the oral surface may therefore be of biological importance.

Electrophoresis, Polyacrylamide Gel↗
PubMed1990

Phosphopeptides derived from human salivary acidic proline-rich proteins. Biological activities and concentration in saliva.

Human saliva contains a large number of phosphopeptides derived by cleavage of acidic proline-rich proteins (APRPs). These peptides were purified by column chromatography and they constituted 0.5% of APRPs in parotid saliva, but 11% of APRPs in saliva expectorated from the mouth (whole saliva), indicating that there is considerable cleavage of APRPs after secretion from the gland. Similarly to APRP, the phosphopeptides bind Ca2+, but they accounted for only 4% of protein-bound Ca2+ in whole saliva. APRPs as well as the phosphopeptides inhibited formation of hydroxyapatite, but, whereas 19-20 micrograms of APRP was needed for 50% inhibition, only 0.7-3.3 micrograms of purified peptides was needed for the same degree of activity, and the phosphopeptides accounted for 18% of total inhibitory activity in whole saliva. All phosphopeptides adsorbed on hydroxyapatite in vitro, and adsorption of phosphopeptides on tooth surfaces in vivo could also be demonstrated, indicating that they would be able to inhibit unwanted mineral formation on the tooth surface in vivo. Degradation of APRPs after secretion therefore does not lead to a loss of their biological activities.

Adsorption↗
PubMed1998

Transcriptional activation of heat shock factor HSF1 probed by phosphopeptide analysis of factor 32P-labeled in vivo.

Mapping of tryptic phosphopeptides of heat shock factor 1 (HSF1) from non-stressed or moderately heat-stressed HeLa cells, labeled in vivo by [32P]orthophosphate, revealed four major phosphopeptides A to D. Heat stress drastically increased phosphopeptide signals. To identify target peptides and amino acids and to correlate phosphorylation and transactivation function, phosphopeptide maps were produced of LexA-human HSF1 chimeras and mutant derivatives thereof, and transactivation activities of original and mutant chimeras were compared. LexA-HSF1 chimeras were previously shown to be regulated identically to HSF1, except that they transactivate promoters with LexA-binding sites instead of hsp promoters. The patterns of phosphopeptides of LexA-HSF1 and endogenous HSF1 were similar. Analysis of single residue substitutions suggested that phosphopeptide C is peptide VKEEPPSPPQSPR (297-309) phosphorylated on Ser-307 but not Ser-303. Substitution of Ser-307 but not Ser-303 caused deregulation of factor activity. Mapping of several constitutively active chimeras associated unphosphorylated peptide C with the transcriptionally active HSF1 conformation, suggesting that dephosphorylation of this peptide (at Ser-307) may either be an integral step in the activation process or serve to maintain the active conformation of HSF1. Exploiting this correlation, indirect evidence was obtained that activation domains of HSF1 interact with the distantly located regulatory domain to maintain the factor in an inactive state.

Amino Acid Sequence↗
PubMed2004

Transducible heat shock protein 20 (HSP20) phosphopeptide alters cytoskeletal dynamics.

Activation of cyclic nucleotide dependent signaling pathways leads to relaxation of smooth muscle, alterations in the cytoskeleton of cultured cells, and increases in the phosphorylation of HSP20. To determine the effects of phosphorylated HSP20 on the actin cytoskeleton, phosphopeptide analogs of HSP20 were synthesized. These peptides contained 1) the amino acid sequence surrounding the phosphorylation site of HSP20, 2) a phosphoserine, and 3) a protein transduction domain. Treatment of Swiss 3T3 cells with phosphopeptide analogs of HSP20 led to loss of actin stress fibers and focal adhesion complexes as demonstrated by immunocytochemistry, interference reflection microscopy, and biochemical quantitation of globular-actin. Treatment with phosphopeptide analogs of HSP20 also led to dephosphorylation of the actin depolymerizing protein cofilin. Pull-down assays demonstrated that 14-3-3 proteins associated with phosphopeptide analogs of HSP20 (but not peptide analogs in which the serine was not phosphorylated). The binding of 14-3-3 protein to phosphopeptide analogs of HSP20 prevented the association of cofilin with 14-3-3. These data suggest that HSP20 may modulate actin cytoskeletal dynamics by competing with the actin depolymerizing protein cofilin for binding to the scaffolding protein 14-3-3. Interestingly, the entire protein was not needed for this effect, suggesting that the association is modulated by phosphopeptide motifs of HSP20. These data also suggest the possibility that cyclic nucleotide dependent relaxation of smooth muscle may be mediated by a thin filament (actin) regulatory process. Finally, these data suggest that protein transduction can be used as a tool to elucidate the specific function of peptide motifs of proteins.

14-3-3 Proteins↗
PubMed2004

A computational method for the analysis and prediction of protein:phosphopeptide-binding sites.

Phosphopeptide-binding domains, including the FHA, SH2, WW, WD40, MH2, and Polo-box domains, as well as the 14-3-3 proteins, exert control functions in important processes such as cell growth, division, differentiation, and apoptosis. Structures and mechanisms of phosphopeptide binding are generally diverse, revealing few general principles. A computational method for analysis of phosphopeptide-binding domains was therefore developed to elucidate the physical and chemical nature of phosphopeptide binding, given this lack of structural similarity. The surfaces of nine phosphopeptide-binding proteins, representing seven distinct classes of phosphopeptide-binding modules, were discretized, and encoded with information about amino acid identity, surface curvature, and electrostatic potential at every point on the surface in order to identify local surface properties enriched in phosphoresidue contact sites. Cross-validation indicated that propensities corresponding to this enrichment calculated from a subset of the training data could be used to predict the phosphoresidue contact site on proteins not used in training with no false negative results, and with few unconfirmed positive predictions. The locations of phosphoresidue contact sites were then predicted on the surfaces of the checkpoint kinase Chk1 and the BRCA1 BRCT repeat domain, and these predictions are consistent with recent experimental evidence.

Binding Sites↗
PubMed1986

Depolarization-dependent protein phosphorylation in rat cortical synaptosomes: characterization of active protein kinases by phosphopeptide analysis of substrates.

Depolarization of synaptosomes is known to cause a calcium-dependent increase in the phosphorylation of a number of proteins. It was the aim of this study to determine which protein kinases are activated on depolarization by analyzing the incorporation of 32Pi into synaptosomal phosphoproteins and phosphopeptides. The following well-characterized phosphoproteins were chosen for study: phosphoprotein "87K," synapsin Ia and Ib, phosphoproteins IIIa and IIIb, the catalytic subunits of calmodulin kinase II, and the B-50 protein. Each was initially identified as a phosphoprotein in lysed synaptosomes after incubation with [gamma-32P]ATP. Mobility on two-dimensional polyacrylamide gels and phosphorylation by specific protein kinases were the primary criteria used for identification. A technique was developed that allowed simultaneous analysis of the phosphopeptides derived from all of these proteins. Phosphopeptides were characterized in lysed synaptosomes after activating cyclic AMP-, calmodulin-, and phospholipid-stimulated protein kinases in the presence of [gamma-32P]ATP. Phosphoproteins labelled in intact synaptosomes after incubation with 32Pi were then compared with those seen after ATP-labelling of lysed synaptosomes. As expected from previous work, phosphoprotein "87K," and synapsin Ia and Ib were labelled, but for the first time, phosphoproteins IIIa, IIIb, and the B-50 protein were identified as being labelled in intact synaptosomes; the calmodulin kinase II subunits were hardly phosphorylated. From a comparison of the phosphopeptide profiles it was found that cyclic AMP-, calmodulin-, and phospholipid-stimulated protein kinases are all active in intact synaptosomes and their activity is dependent on extrasynaptosomal calcium. The activation of cyclic AMP-stimulated protein kinases in intact synaptosomes was confirmed by the addition of dibutyryl cyclic AMP and theophylline which specifically increased the labelling of phosphopeptides in synapsin Ia and Ib and in phosphoproteins IIIa and IIIb. On depolarization of intact synaptosomes, a number of phosphopeptides showed increased labelling and the pattern suggested that cyclic AMP-, calmodulin-, and phospholipid-stimulated protein kinases were all activated. No new peptides were phosphorylated, suggesting that depolarization simply increased the activity of already active protein kinases and that there was no depolarization-specific increase in protein phosphorylation.

Adenosine Triphosphate↗
PubMed1998

Calcium binding of phosphopeptides derived from hydrolysis of alpha s-casein or beta-casein using immobilized trypsin.

Calcium binding to casein phosphopeptides that were derived from alpha s-CN or beta-CN was studied. Purified alpha s-CN or beta-CN was prepared from fresh skim milk using an anion-exchange column. Peptides were prepared by casein hydrolysis using a fluidized bed bioreactor containing 2 ml of immobilized trypsin (activity: 49.4 U/g of beads). The disappearance of intact protein and the appearance of products of low molecular mass were monitored by SDS-PAGE. alpha s-Casein and beta-CN hydrolysates were loaded on an anion-exchange column, followed by stepwise elution with 0, 0.1, 0.2, 0.4, and 0.5 M KCl in equilibration buffer to separate the phosphopeptides from the other casein peptides. Protein and P were measured in the elution peaks. Calcium binding to each fraction was determined with a Ca-selective electrode. Electrophoresis showed that intact proteins were hydrolyzed rapidly, and peptides appeared on the gel in greater concentrations as the incubation time increased. The major products were a main band with a molecular mass of 6.2 kDa from beta-CN hydrolysates and a series of bands from 4.0 to 12.8 kDa from alpha s-CN hydrolysate. The greatest yield and concentration of phosphate from beta-CN hydrolysate were found in the peak that eluted with 0.4 M KCl in equilibration buffer and for alpha s-CN in the peak that eluted with 0.1 M KCl. The alpha s-CN phosphopeptides showed greater Ca2+ binding than the phosphopeptides from beta-CN. Separation of casein phosphopeptides using anion exchange was not specific. However, results showed that each peak containing high concentrations of phosphate had Ca(2+)-binding ability. Further characterization of these casein phosphopeptides might result in a Ca-complexing food ingredient.

Amino Acid Sequence↗
PubMed1998

Preparation of phosphopeptides derived from alpha s-casein and beta-casein using immobilized glutamic acid-specific endopeptidase and characterization of their calcium binding.

Phosphopeptides that were derived from alpha s-CN or beta-CN were prepared with immobilized glutamic acid-specific endopeptidase, and their Ca2+ binding was characterized. alpha s-Casein or beta-CN was hydrolyzed in a fluidized bed bioreactor containing 2 ml of immobilized glutamic acid-specific endopeptidase by recirculating 20 ml of alpha s-CN or beta-CN solution (10 mg/ml in 50 mM Tris.HCl and 0.02% NaN3, pH 8.0) for 3 h at 20 degrees C. The molecular masses of casein peptides were monitored by SDS-PAGE. Each hydrolysate was applied to an anion-exchange column using stepwise elution with various concentrations of KCl to separate peptides. The casein phosphopeptide content of the elution profile was monitored by analysis of protein and P concentrations. Calcium binding in phosphopeptide-enriched fractions was determined by CaCl2 titration and measurement of free Ca2+ with a Ca-selective electrode. The electrophoresis patterns showed four major peptides having molecular masses of 10.8, 9.0, 6.6, and 3.6 kDa in the alpha s-CN hydrolysate and 9.3, 8.2, and 6.2 kDa in the beta-CN hydrolysate. The highest concentrations of P were detected in the fractions that eluted with 0.4 and 0.5 M KCl for the alpha s-CN hydrolysate and with 0.4 M KCl for the beta-CN hydrolysate. The calcium-binding ability was found only in the fraction that was eluted with 0.4 M KCl; the maximum Ca2+ binding and the apparent binding constant were 0.24 mmol/mg of protein and 75 M-1, and 0.14 mmol/mg of protein and 148 M-1, respectively. alpha s-Casein phosphopeptides had different patterns for Ca2+ binding than did beta-CN phosphopeptides as the total Ca concentration was increased. Calcium binding to these casein phosphopeptides differed from that previously characterized for the tryptic peptides.

Amino Acid Sequence↗
PubMed2002

Design and characterization of non-phosphopeptide inhibitors for Src family SH2 domains.

The development of novel non-phosphopeptide inhibitors for the Src family SH2 domain is described. Several commercially available hydroxyl aromatic acids have been appended off the N-terminus of pYEEIE and the potent phosphopeptide inhibitors of GST-Lck-SH2 were identified via ELISA. The most potent inhibitor, caffeic acid-pYEEIE, exhibited approximately 30-fold more binding activity than Ac-pYEEIE. Non-phosphopeptides were synthesized by replacing phosphotyrosine of caffeic acid-pYEEIE with tyrosine or 3,4-dihydroxyphenylalanine (DOPA). Caffeic acid-DOPA-EEIE that did not contain phosphotyrosine and its isosteres exhibited less than 20 times decreased binding affinity for GST-Lck-SH2 than Ac-pYEEIE. Moreover, it had a similar binding affinity for the GST-Lck-SH2, GST-Src-SH2, and GST-Fyn-SH2 domains. This study showed that the pY-1 positions of the phosphopeptide inhibitors and of the non-phosphopeptide inhibitors played an important role in the binding for the SH2 domain and that the non-phosphopeptide inhibitor must be a new lead in the development of SH2 inhibitors.

Caffeic Acids↗
PubMed2006

On-bead chemical synthesis and display of phosphopeptides for affinity pull-down proteomics.

We describe a new method for phosphopeptide proteomics based on the solid-phase synthesis of phosphopeptides on beads suitable for affinity pull-down experiments. Peptide sequences containing the Bad Ser112 and Ser136 phosphorylation motifs were used as bait in affinity pull-down experiments to determine their ability to bind 14-3-3 proteins. Support-bound peptides were assembled directly on the solid support (PEGA) by standard solid-phase synthesis through a BAL-type handle. The peptides were varied in length and sequence. This synthetic strategy also allowed introduction of a soft electrophile (aldehyde) at the C terminus for potential activity-based proteomics. The synthetic support-bound Bad phosphopeptides were able to pull down 14-3-3zeta. Furthermore, Bad phosphopeptides bound endogenous 14-3-3 proteins, and all seven members of the 14-3-3 family were identified by mass spectrometry. In control experiments, none of the unphosphorylated Bad peptides bound transfected 14-3-3zeta or endogenous 14-3-3. We conclude that the combined synthesis and display of phosphopeptides on-bead is a fast and efficient method for affinity pull-down proteomics.

Molecular Structure↗