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: 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: 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: 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.