Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 2Citation - Scopus: 2Gas Phase Fragmentation Behavior of Proline in Macrocyclic B7 Ions(American Chemical Society, 2023) Taşoğlu, Çağdaş; Arslanoğlu, Alper; Yalçın, TalatThefragmentation characteristics of b (7) ionsproduced from proline-containing heptapeptides have been studiedin detail. The study has utilized the following C-terminally amidatedmodel peptides: PA(6), APA(5), A(2)PA(4), A(3)PA(3), A(4)PA(2), A(5)PA, A(6)P, PYAGFLV, PAGFLVY, PGFLVYA, PFLVYAG,PLVYAGF, PVYAGFL, YPAGFLV, YAPGFLV, YAGPFLV, YAGFPLV, YAGFLPV, YAGFLVP,PYAFLVG, PVLFYAG, A(2)PXA(3), and A(2)XPA(3) (where X = C, D, F, G, L, V, and Y, respectively). The resultshave shown that b (7) ions undergo head-to-tailcyclization and form a macrocyclic structure. Under the collision-induceddissociation (CID) condition, it generates nondirect sequence ionsregardless of the position of the proline and the neighboring aminoacid residues. This study highlights the unusual and unique fragmentationbehavior of proline-containing heptapeptides. Following the head-to-tailcyclization, the ring opens up and places the proline residue in theN-terminal position while forming a regular oxazolone form of b (2) ions for all peptide series. Then, the fragmentationreaction pathway is followed by the elimination of proline with itsC-terminal neighbor residue as an oxazolone (e.g., PXoxa) for all proline-containing peptide series.Book Part Citation - Scopus: 1Mass Spectroscopy in Polymer Research(John Wiley and Sons Inc., 2012) Hacaloğlu, Jale; Yalçın, TalatMass spectrometers are currently available in numerous confi gurations with various ionization techniques and mass analyzers. For a specifi c polymer sample, an optimal choice should be done depending on the information sought. In practice, no single mass spectrometric technique can provide all necessary information for structural, compositional, and thermal and oxidative degradation characteristics of polymeric samples. The analyzer used determines the limits of the sensitivity and resolution and the mass range, whereas the type of ionization source specifi es the information that can be gained.Article Citation - WoS: 2Citation - Scopus: 2Observation of the Side Chain O-Methylation of Glutamic Acid or Aspartic Acid Containing Model Peptides by Electrospray Ionization-Mass Spectrometry(Elsevier Ltd., 2017) Atik, Ahmet Emin; Güray, Melda Zeynep; Yalçın, TalatO-methylation of the side chains of glutamic acid (E) and aspartic acid (D) residues is generally observed modification when an acidified methanol/water (MeOH/dH2O) mixture is used as a solvent system during sample preparation for proteomic research. This chemical modification may result misidentification with endogenous protein methylation; therefore, a special care should be taken during sample handling prior to mass spectrometric analysis. In the current study, we systematically examined the extent of E/D methylation and C-terminus carboxyl group of synthetic model peptides in terms of different incubation temperatures, storage times, and added acid types as well as its percentages. To monitor these effects, C-terminus amidated and free acid forms of synthetic model peptides comprised of E or D residue(s) have been analyzed by electrospray ionization-mass spectrometry (ESI-MS). Additionally, LC–MS/MS experiments were performed to confirm the formation of methylated peptide product. The results showed that the rate of methylation was increased as the temperature increases along with prolong incubation times. Moreover, the extent of methylation was remarkably high when formic acid (FA) used as a protonation agent instead of acetic acid (AA). In addition, it was found that the degree of methylation was significantly decreased by lowering acid percentages in ESI solution. More than one acidic residue containing model peptides have been also used to explore the extent of multiple methylation reaction. Lastly, the ethanol (EtOH) and isopropanol (iPrOH) have been substituted separately with MeOH in sample preparation step to investigate the extent of esterification reaction under the same experimental conditions. However, in the positive perspective of view, this method can be used as a simple, rapid and cheap method for methylation of acidic residues under normal laboratory conditions.Article Citation - WoS: 4Citation - Scopus: 4Gas-Phase Structures and Proton Affinities of N-Terminal Proline Containing B2 + Ions From Protonated Model Peptides(Elsevier Ltd., 2015) Karaca, Sıla; Atik, Ahmet Emin; Elmacı, Nuran; Yalçın, TalatIn this study, we investigated the effect of the second amino acid identity of hexapeptides on gas-phase structures and the proton affinities of N-terminal proline containing b2 + ions produced from the fragmentation of b6 + ions under low-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). It should be noted that, among all other fragments, the b2 + and nominally b4 + (AAAA) ions ([M+H]+ → b6 + → b2 + (PX+) + b4 + (AAAA+) were mainly considered in this study. This is a unique example of consecutive cleavage of b6 + ions which fragments to b2 + and nominal b4 + ions. All structural and proton affinity calculations for b2 + ions were carried out with the B3LYP/6-31+G(d,p) level of theory. The study utilized C-terminal amidated model peptides consisting of PAAAAA-NH2 and PXAAAA-NH2 where X is phenylalanine (F), glutamic acid (E), tryptophan (W), and histidine (H) residue. Two main structural isomers of b2 + ions, namely oxazolone and diketopiperazine, have been considered for the computations. The results demonstrated that the proton affinities of oxazolone isomers of PX are greater than its diketopiperazine isomers. Higher correlation coefficient is calculated if the structure of PX is considered as oxazolone rather than diketopiperazine isomer. Additionally, a linear fit is observed between intensity ratio (PX/AAAA) and calculated proton affinities of PX ions. Additionally, MS/MS results revealed that the relative intensities of b2 +-PA, PF, and PE- ions are lower compared to the relative intensity of AAAA fragment ion. In contrast, b2 +-PW and PH- ions have higher relative intensities compared to the AAAA ion. This behavior is explained by the proton affinities of fragment ions computationally.Article Citation - WoS: 1Citation - Scopus: 1Specific Rearrangement Reactions of Acetylated Lysine Containing Peptide Bn (n=4-7) Ion Series(John Wiley and Sons Inc., 2014) Atik, Ahmet Emin; Hernandez, Oscar; Maitre, Philippe; Yalçın, TalatCharacterization of ε-N-acetylated lysine containing peptides, one of the most prominent post-translational modifications of proteins, is an important goal for tandem mass spectrometry experiments. A systematic study for the fragmentation reactions of b ions derived from ε-N-acetyllysine containing model octapeptides (KAcYAGFLVG and YAKAcGFLVG) has been examined in detail. Collision-induced dissociation (CID) mass spectra of bn (n=4-7) fragments of ε-N-acetylated lysine containing peptides are compared with those of N-terminal acetylated and doubly acetylated (both ε-N and N-terminal) peptides, as well as acetyl-free peptides. Both direct and nondirect fragments are observed for acetyl-free and singly acetylated (ε-N or N-terminal) peptides. In the case of ε-N-acetylated lysine containing peptides, however, specific fragment ions (m/z 309, 456, 569 and 668) are observed in CID mass spectra of bn (n=4-7) ions. The CID mass spectra of these four ions are shown to be identical to those of selected protonated C-terminal amidated peptides. On this basis, a new type of rearrangement chemistry is proposed to account for the formation of these fragment ions,which are specific for ε-N-acetylated lysine containing peptides. Consistent with the observation of nondirect fragments, it is proposed that the b ions undergo head-to-tail macrocyclization followed by ring opening. The proposed reaction pathway assumes that bn (n=4-7) of ε-N-acetylated lysine containing peptides has a tendency to place the KAc residue at the C-terminal position after macrocyclization/reopening mechanism. Then, following the loss of CO, it is proposed that the marker ions are the result of the loss of an acetyllysine imine as a neutral fragment.Article Citation - WoS: 9Citation - Scopus: 9The Role of Lysine ?-Amine Group on the Macrocyclization of B Ions(Elsevier Ltd., 2012) Atik, Ahmet Emin; Görgülü, Güvenç; Yalçın, TalatA study was carried out to examine if the amine (NH 2) group located on the side chains of lysine (K), glutamine (Q), or asparagine (N) residue has any effect on the macrocyclization of b ions even though the N-terminals of the peptides were acetylated. The work utilized the model peptides Ac-KYAGFLVG, Ac-QYAGFLV-NH 2, and Ac-NYAGFLV-NH 2. The CID mass spectra of b 7 ions originated from these three peptides exhibited that the macrocyclization still occurred for the lysine containing peptide in spite of the N-terminal of the peptide was acetylated, but was failed to be observed for glutamine and asparagine containing peptides. These current results reveal that the lysine side chain ε-amine group has been involved in the macrocyclization of the peptide b ions for the N-terminal acetylated peptides and consequently, non-direct sequence b ions were observed in the CID mass spectra. However, due to the amide group on the side chains of the glutamine and asparagine residues, the nucleophilicity of their groups greatly reduced; therefore the scrambling b ions were not detected in their b 7 ion CID mass spectra. In addition, the effect of the lysine position was also studied for series of six isomeric octapeptides such as, Ac-KYAGFLVG, Ac-YKAGFLVG, Ac-YAKGFLVG, Ac-YAGKFLVG, Ac-YAGFKLVG and Ac-YAGFLKVG in order to examine the relationship between the intensities of non-direct sequence b ions and the lysine position in the octapeptide series. The results clearly demonstrated that the most abundant non-direct sequence b ions were observed for the first position of lysine residue in the N-terminal acetylated octapeptide, however, when the lysine residue gets closer to the C-terminal position the relative intensities of the scrambled b ions were greatly decreased.Article Citation - WoS: 7Citation - Scopus: 7Investigation of Peptide Size, Residue Position, Neighbor Amino Acid and Side Chain Effect on Macrocyclization of B N (n = 5-7) Ions(Elsevier Ltd., 2012) Taşoğlu, Çağdaş; Görgülü, Güvenç; Yalçın, TalatA systematic study was carried out to examine the effects of the side chain, peptide size, residue position, and neighboring amino acid on the macrocyclization of b ions. The work utilized isomeric model peptides YAGFLV-NH 2, AGFLVY-NH 2, GFLVYA-NH 2, FLVYAG-NH 2, LVYAGF-NH 2, VYAGFL-NH 2, which all have the same amino acid sequence in cyclic form. The b 6 ions derived from all these isomeric peptides form the same macrocyclic structure due to the generation of the same amino acid sequence order upon cyclization. Hence, the MS/MS spectra and breakdown graphs of b 6 ions derived from these peptides are similar to each other. However, the relative intensities of the non-direct sequence ions in both the MS/MS spectra and breakdown graphs of the b 6 ions derived from FAYVGL-NH 2, GVYALF-NH 2 and VFYLAG-NH 2 show a different distribution from each other and the first series, even though they are all isomeric peptides. This could be due to the different amino acid sequence order in the cyclic forms of these peptides. It is clearly shown that the neighboring amino acid influences the selective opening of the macrocyclic form. Additionally, XYAGFLV-NH 2 and YAGXFLV-NH 2 (where X = C, D, E, H, K, M, N, P, Q, S, T, and W are amino acid residues) were also studied in order to examine the influence of the peptide size, amino acid side chain, and position on the ring formation and cleavage of macrocyclic b 5, b 6 and b 7 ions. The results have clearly shown that b 6 and b 7 ions have a higher tendency of macrocyclization compared to b 5 ions with the exception of QYAGFLV-NH 2. Additionally, it was observed that selective ring opening is also dependent on the size of the b ions and the position of the amino acid residue. From our study of the macrocyclic b 6 ions of our model peptides, the Q, W, K, and M residues were found to be more favorable eliminations when compared to C, D, E, H, N, P, S, and T. Based on the results, no preferential cleavage order can be specified depending on the nature of amino acid side chain.Article Citation - WoS: 5Citation - Scopus: 5Non-Direct Sequence Ions in the Tandem Mass Spectrometry of Protonated Peptide Amides - an Energy-Resolved Study(American Chemical Society, 2013) Harrison, Alex G.; Taşoğlu, Çağdaş; Yalçın, TalatThe fragmentation reactions of the MH+ ions of Leu-enkephalin amide and a variety of heptapeptide amides have been studied in detail as a function of collision energy using a QqToF beam type mass spectrometer. The initial fragmentation of the protonated amides involves primarily formation of bn ions, including significant loss of NH3 from the MH+ ions. Further fragmentation of these bn ions occurs following macrocyclization/ring opening leading in many cases to bn ions with permuted sequences and, thus, to formation of non-direct sequence ions. The importance of these non-direct sequence ions increases markedly with increasing collision energy, making peptide sequence determination difficult, if not impossible, at higher collision energies. [Figure not available: see fulltext.]Article Citation - WoS: 1Citation - Scopus: 1Protonated Dipeptide Losses From B 5 and B 4 Ions of Side Chain Hydroxyl Group Containing Pentapeptides(American Chemical Society, 2013) Atik, Ahmet Emin; Yalçın, TalatIn this study, C-terminal protonated dipeptide eliminations were reported for both b 5 and b 4 ions of side chain hydroxyl group (-OH) containing pentapeptides. The study utilized the model C-terminal amidated pentapeptides having sequences of XGGFL and AXVYI, where X represents serine (S), threonine (T), glutamic acid (E), aspartic acid (D), or tyrosine (Y) residue. Upon low-energy collision-induced dissociation (CID) of XGGFL (where X = S, T, E, D, and Y) model peptide series, the ions at m/z 279 and 223 were observed as common fragments in all b 5 and b 4 ion (except b 4 ion of YGGFL) mass spectra, respectively. By contrast, peptides, namely SMeGGFL-NH2 and EOMeGGFL- NH2, did not show either the ion at m/z 279 or the ion at m/z 223. It is shown that the side chain hydroxyl group is required for the possible mechanism to take place that furnishes the protonated dipeptide loss from b 5 and b 4 ions. In addition, the ions at m/z 295 and 281 were detected as common fragments in all b 5 and b 4 ion (except b 4 ion of AYVYI) mass spectra, respectively, for AXVYI model peptide series. The MS4 experiments exhibited that the fragment ions at m/z 279, 223, 295, and 281 entirely reflect the same fragmentation behavior of [M + H]+ ion generated from commercial dipeptides FL-OH, GF-OH, YI-OH, and VY-OH. These novel eliminations reported here for b 5 and b 4 ions can be useful in assigning the correct and reliable peptide sequences for high-throughput proteomic studies. [Figure not available: see fulltext.]Article Citation - WoS: 11Citation - Scopus: 14Proteomic Changes During Boron Tolerance in Barley (hordeum Vulgare) and the Role of Vacuolar Proton-Translocating Atpase Subunit E(Türkiye Klinikleri Journal of Medical Sciences, 2011) Atik, Ahmet Emin; Bozdağ, Gönensin Ozan; Akıncı, Ersin; Kaya, Alaattin; Koç, Ahmet; Yalçın, Talat; Karakaya, Hüseyin ÇağlarBoron is an essential micronutrient for plants and animals; however, it can be toxic when present at high concentrations. The purpose of this study was to understand the mechanisms of boron tolerance in the Turkish barley (Hordeum vulgare) Anadolu cultivar. For this purpose, 2-dimensional electrophoresis (2-DE) was used to screen differentially expressed proteins for both control and boron-stressed Anadolu barley genotypes. Seven proteins were revealed by 2-DE: 1) ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo large chain), 2) TLP5, a thaumatin-like protein, 3) PR5, a basic pathogenesis-related protein, 4) a RNase S-like protein, 5) a PSI type III chlorophyll a/b-binding protein, 6) a light-harvesting complex I LHC I, and 7) the vacuolar proton-translocating ATPase subunit E protein. These were found to be upregulated in response to boron treatment. Even though the protein encoded by the V-ATPase subunit E gene was overexpressed, its transcript level was downregulated by boron treatment. Heterologous expression of the barley V-ATPase subunit E gene in yeast provided boron resistance to yeast cells. These results indicated that the V-ATPase subunit E gene was functional and conferred tolerance to toxic boron levels in yeast and might play a role in the overall boron tolerance of barley. © TÜBITAK.