Ömür Çelikbıçak

Novel short peptides isolated from phage display library inhibit vascular endothelial growth factor activity

Signal transduction through the vascular endothelial growth factor (VEGF)-VEGF receptor (VEGFR) pathway has a pivotal importance in angiogenesis, and has therefore become a prime target in antitumor therapy. In search for peptides antagonizing VEGF binding to its receptors, we screened a random heptamer library displayed on phage for peptides that bind the whole VEGF165 molecule and inhibit VEGF dependent human umbilical vein endothelial cell (HUVEC) proliferation. Two selected peptides with sequences WHLPFKC and WHKPFRF were synthesized. Biacore and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis indicated that these peptides bind the VEGF homodimer in a concentration-dependent manner, with micromolar affinity, and with a 2:1 peptide: VEGF stoichiometry. They inhibited HUVEC proliferation in vitro by 77 and 55%, respectively. Taken together, our results indicate that these peptides could be potent inhibitors of angiogenesis. Furthermore, we show that the peptide-VEGF binding properties can be quantified, a prerequisite for the further optimization of binders.

Ti(IV) carrying polydopamine-coated, monodisperse-porous SiO2 microspheres with stable magnetic properties for highly selective enrichment of phosphopeptides

A marked decrease in the saturation magnetization by the formation of functional shells around the magnetic core is an important disadvantage of magnetic core-shell nanoparticles. Another drawback of Ti(IV)-functionalized immobilized metal affinity chromatography (IMAC) sorbents is the acidic character of the binding medium used for Ti4+ attachment onto composite magnetic nanoparticles, which causes an additional decrease in the saturation magnetization owing to the chemical interaction between the acidic moiety and the magnetic core. An IMAC sorbent in the form of magnetic microspheres with superior and stable magnetic properties with respect to magnetic core-shell nanoparticles was designed for phosphopeptide enrichment. Magnetic, monodisperse-porous silica microspheres (MagSiO2) 6μm in size were synthesized by a new staged-shape template hydrolysis-condensation protocol. A porous-silica shell layer was generated around the microspheres to protect the magnetic core from the acidic medium during Ti4+ attachment (MagSiO2@SiO2). The MagSiO2@SiO2 microspheres were coated with a polydopamine shell (MagSiO2@SiO2@PDA) and Ti4+ was attached onto the composite microspheres (MagSiO2@SiO2@PDA@Ti(IV)). Formation of the PDA layer and Ti4+ attachment did not cause any significant decrease in the saturation magnetization. The platform exhibited excellent performance for phosphopeptide enrichment from the digests of phosphorylated proteins. Selectivity was investigated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The detection limit for phosphopeptide enrichment by the MagSiO2@SiO2@PDA@Ti(IV) microspheres from the tryptic digests of β-casein was 50 fmol/mL. Usability of the proposed magnetic sorbent with complex biological samples was demonstrated by successful enrichment of four phosphopeptides from human serum. The proposed sorbent showed stable performance over five repeated uses.

Comparison of two methods for purification of enterocin B, a bacteriocin produced by Enterococcus faecium W3.

This study aimed to compare two different approaches for the purification of enterocin B from Enterococcus faecium strain W3 based on the observation that the bacteriocin was found both in cell associated form and in culture supernatant. The first approach employed ammonium sulfate precipitation, cation-exchange chromatography, and sequential reverse-phase high-performance liquid chromatography. The latter approach exploited a pH-mediated cell adsorption–desorption method to extract cell-bound bacteriocin, and one run of reverse-phase chromatography. The first method resulted in purification of enterocin B with a recovery of 4% of the initial bacteriocin activity found in culture supernatant. MALDI-TOF MS analysis and de novo peptide sequencing of the purified bacteriocin confirmed that the active peptide was enterocin B. The second method achieved the purification of enterocin B with a higher recovery (16%) and enabled us to achieve pure bacteriocin within a shorter period of time by avoiding time consuming purification protocols. The purity and identity of the active peptide were confirmed again by matrix-assisted laser desorption/ionization time-of flight (MALDI-TOF) mass spectrometry (MS) analysis. Although both approaches were satisfactory to obtain a sufficient amount of enterocin B for use in MS and amino acid sequence analysis, the latter was proved to be applicable in large-scale and rapid purification of enterocin B.

A Trypsin Immobilized Sol-Gel for Protein Indentification in MALDI-MS Applications

The proteolytic enzyme trypsin was chemically immobilized to an amine-functionalized sol-gel using adipoyl chloride under nonaqueous conditions and a nitrogen atmosphere. In the synthesis of the sol-gel, tetraethyl orthosilicate (TEOS), and 3-(2-aminoethylamino) propyldimethoxymethylsilane (AEAPMS) (50:50, v/v) were used, which provided convenient physical and chemical conditions to maintain catalytic activity of immobilized trypsin molecules for the digestion of proteins in proteomics applications. Bovine serum albumin was used as a model protein to perform enzymatic digestion using the trypsin immobilized sol-gel. The resulting peptides were analyzed by matrix-assisted laser desorption/ionization-mass spectrometry to evaluate the digestion performance and specificity of the sol-gel material. The trypsin immobilized sol-gel showed superior enzymatic activity in protein digestion and it was determined that the sol-gel material could be repeatedly used at least 25 times without significant activity loss in long-term use. Additionally, autocatalysis was prevented by immobilization of trypsin. The peptide digest having the highest purity was obtained for protein identification studies.

Highly selective enrichment of phosphopeptides by titanium (IV) attached monodisperse-porous poly(vinylphosphonic acid-co-ethylene dimethacrylate) microspheres

A seeded polymerization protocol was developed for the synthesis of monodisperse-porous poly(vinylphosphonic acid-co-ethylene dimethacrylate), [poly(VPA-co-EDMA)] microspheres with superior porous properties. The protocol allowed the direct synthesis of phosphonic acid functionalized porous microspheres with the mean size of ∼4μm and the specific surface area of 420m2g-1 without applying any complicated post-derivatization protocol for the attachment of phosphonic acid group. The phosphonic acid content of poly(VPA-co-EDMA) microspheres was determined as 1.5mmol H2PO3g-1 microspheres. Ti(IV) ions were attached onto the microspheres via metal-chelate complex formation by phosphonate-groups and Ti(IV) carrying monodisperse-porous poly(vinylphosphonic acid-co-ethylene dimethacrylate), [Ti(IV)@poly(VPA-co-EDMA)] microspheres were obtained as a new sorbent for phosphopeptide enrichment via immobilized metal affinity chromatography. The phosphopeptides in the enriched samples were identified by matrix-assited laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Four different phosphopeptides were detected with extremely high intensity by the treatment of β-casein digest prepared with the concentration of 10 fmol/mL with Ti(IV)@poly(VPA-co-EDMA) microspheres. Highly selective enrichment of phosphopeptides was also successfully carried out even at trace amounts in a complex mixture of digested proteins (molar ratio of β-casein to BSA, 1:1000) and eight different phosphorylated peptides from BSA digest were successfully identified. Moreover, four highly intense signals of the phosphopeptides in human serum were observed with high S/N ratio and clear background after enrichment by using Ti(IV)@poly(VPA-co-EDMA) microspheres.

Specific enrichment and direct detection of phosphopeptides on insoluble transition metal oxide particles in matrix-assisted laser desorption/ionization mass spectrometry applications.

Several transition metal oxides, such as iron (III), nickel (II) and zirconium (IV) oxides, were examined in detail for the specific enrichment and the purification of phosphopeptides from a digested peptide mixture solution. Phosphopeptide enrichment was performed on the metal oxide particles using a peptide mixture obtained by tryptic digestion of β-casein. The mixture of protein digests containing bovine serum albumin (BSA):β-casein digests (100: 1 mole ratio) was also used for the phosphopeptide enrichment. Furthermore, non-fat milk digest was examined as a complex biological sample. In each phosphopeptide enrichment process, phosphopeptides were specifically enriched and separated from the non-phosphopeptides. The phosphopeptides were adsorbed onto the metal oxide surface at acidic pH values between 1.0 and 2.0 and, for desorption of phosphopeptides from metal oxide particles, pH values were examined and optimized in the enrichment studies. The analysis of phosphopeptides were carried out by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using 2,5-dihydroxybenzoic acid matrix containing 1.0% phosphoric acid to obtain intense protonated signals and to overcome degradation of the phosphopeptides by phosphate group loss in mass spectrometric conditions. Moreover, it was demonstrated that the direct detection of phosphopeptides from the surface of the metal oxide particles was possible using MALDI-MS by mixing the phosphopeptide–adsorbed metal oxide particles with MALDI matrix solution in slurry form before the analysis. Thus, the effects of interferences arising from chemical species used in the desorption process was successfully eliminated for the fast and sensitive detection of phosphopeptides in MALDI-MS applications.

Monitoring protein glycation by electrospray ionization (ESI) quadrupole time-of-flight (Q-TOF) mass spectrometer

In this study electrospray ionization quadrupole time-of-flight (ESI-Q-TOF) mass spectrometry was used to investigate protein glycation. The glycated species of cytochrome C, lysozyme, and β-casein formed during glycation with d-glucose were identified and monitored in binary systems heated at 70°C under dry and aqueous conditions. Cytochrome C had multiple charges in non-glycated state, primarily changing from +13 to +17 positive charges, whereas β-casein had charge states up to +30. Upon heating with glucose at 70°C in aqueous state, attachment of one glucose molecule onto proteins was observed in each charge state. However, heating in dry state caused much more glucose attachment, leading to the formation of multiple glycoforms of proteins. By using ESI-QTOF-MS technique, formation of glycated cytochrome C containing up to 12 glucose moieties were observed, while glycated species containing 6 and 8 glucose moieties were observed for lysozyme and β-casein, respectively in various heating conditions.

Use of Sulfonates as Desorption Agents for Phosphopeptide Elution from an Anion-exchange Material

ABSTRACT In general, phosphopeptides are specifically adsorbed to the surface of the material at the initial step of phosphopeptide enrichment methods. Thus, nonphosphopeptides can be removed from the media by following the appropriate washing steps. After sufficient washing, the phosphopeptides are eluted from the surface of the material completely for further analysis. Performing the elution of phosphopeptides fully in the enrichment step is very important in terms of determining the whole phosphoproteome profile of a sample by subsequent mass spectrometric analysis. Materials containing anion exchanger groups such as amines on the surface can be used as a selective stationary phase in phosphopeptide enrichment methods. Positively charged groups on the surface of this type of material interact with the phosphate groups of phosphopeptides through electrostatic interactions. Such interactions can be basically manipulated by changing the pH of the medium or replacing the salts present in the solution. Phosphopeptides attached to the surface of anion-exchange materials may be displaced with the addition of highly acidic compounds such as sulfonates to the enrichment medium. Here, we used various sulfonates as desorption agents for the elution of retained phosphopeptides from the surface of an anion-exchange material. We found that differences in the chemical structures and properties of the sulfonates remarkably affected phosphopeptide retrieval from the anion-exchange material.