Yalçın, Talat
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Yalcin, Talat
Yalçın, T.
Yalçın, T
Yalcin, T.
Yalcin, T
Yalçın, T.
Yalçın, T
Yalcin, T.
Yalcin, T
Job Title
Email Address
talatyalcin@iyte.edu.tr
Main Affiliation
04.01. Department of Chemistry
Status
Current Staff
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Sustainable Development Goals
1NO POVERTY
0
Research Products
2ZERO HUNGER
4
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3GOOD HEALTH AND WELL-BEING
2
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4QUALITY EDUCATION
3
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5GENDER EQUALITY
0
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6CLEAN WATER AND SANITATION
8
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7AFFORDABLE AND CLEAN ENERGY
9
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8DECENT WORK AND ECONOMIC GROWTH
1
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9INDUSTRY, INNOVATION AND INFRASTRUCTURE
14
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10REDUCED INEQUALITIES
0
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11SUSTAINABLE CITIES AND COMMUNITIES
0
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
6
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13CLIMATE ACTION
11
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14LIFE BELOW WATER
3
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15LIFE ON LAND
1
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
0
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17PARTNERSHIPS FOR THE GOALS
0
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Documents
48
Citations
2389
h-index
23
Documents
28
Citations
1547
Scholarly Output
38
Articles
18
Views / Downloads
84018/16668
Supervised MSc Theses
13
Supervised PhD Theses
4
WoS Citation Count
163
Scopus Citation Count
173
Patents
0
Projects
12
WoS Citations per Publication
4.29
Scopus Citations per Publication
4.55
Open Access Source
33
Supervised Theses
17
| Journal | Count |
|---|---|
| Journal of the American Society for Mass Spectrometry | 4 |
| International Journal of Mass Spectrometry | 4 |
| Journal of Mass Spectrometry | 2 |
| Bilecik Şeyh Edebali Üniversitesi Fen Bilimleri Dergisi | 1 |
| Doga, Turkish Journal of Botany | 1 |
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38 results
Scholarly Output Search Results
Now showing 1 - 10 of 38
Article Residue-Specific Pathways in Peptide Fragmentation: the Role of Aromatic Side Chain in A3 Ion Formation From B3 Ion(Elsevier, 2025) Atik, A. Emin; Yalçın, Talat; Karaca, Sila; Yalcin, TalatPeptide fragmentation chemistry is essential for the sequence elucidation of proteins through tandem mass spectrometry (MS/MS). In this study, we examine the gas-phase fragmentation of b3 ions from model tripeptides under low-energy CID conditions, focusing on the pathway leading to the stable formation of a3 ions from b3 ions. The study utilized C-terminal amidated model tripeptides, including YGG-NH2, GYG-NH2, and GGX-NH2, where X represents D, E, H, Q, C, S, F, and Y. Our results reveal that only tripeptides with phenylalanine (F) and tyrosine (Y) as the third residue yield a3 ions upon b3 ion fragmentation under the applied experimental conditions, suggesting a unique stabilizing role of aromatic side chains in facilitating this pathway. Our theoretical studies indicate that the a3 ions from GGF-NH2 and GGY-NH2 preferentially adopt an energetically favored linear imineprotonated isomer, which is lower in energy by 3.29 kcal/mol and 4.17 kcal/mol, respectively, compared to their 7-membered ring isomers protonated at the ring imine. The latter structure has been previously assigned for the GGG sequence as a predominant structure, supported by IR spectroscopy and DFT calculations (JACS, 2010, 132, 14,766-14779). We proposed a plausible fragmentation mechanism for the a3 ions based on the linear imineprotonated structure. These findings provide insights into residue-specific fragmentation mechanisms and enhance our understanding of peptide ion dissociation, particularly in small peptides.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: 5Citation - Scopus: 4Comparative Proteomic Analysis of Leishmania Parasites Isolated From Visceral and Cutaneous Leishmaniasis Patients(Cambridge University Press, 2021) Dinç, Melike; Yalçın, Talat; Çavuş, İbrahim; Özbilgin, AhmetLeishmaniasis is an infectious disease in which different clinical manifestations are classified into three main forms as visceral, cutaneous, and mucocutaneous. These disease forms are associated with parasite species of protozoan genus, Leishmania. For instance, Leishmania infantum and Leishmania tropica are typically linked with visceral (VL) and cutaneous (CL) leishmaniasis respectively, however these two species can also cause other form to a lesser extent. What is more alarming is this characteristic, which threatens classic diagnoses and therapies, is started to be acquired by other species. To address this issue, gel-based and gel-free proteomic analyses were carried out on the species, Leishmania infantum to determine the proteins differentiating between the parasites caused visceral and cutaneous leishmaniasis. In addition, Leishmania tropica parasites representing the typical cases for cutaneous leishmaniasis were included. Electrophoresis gels of parasites caused to visceral leishmaniasis were distinguishable from the others in terms of repetitive down-regulation on some specific locations. In addition, a distinct spot of an antioxidant enzyme, superoxide dismutase was shown up only on the gels of cutaneous leishmaniasis samples regardless of the species. In the gel-free approach, 37 proteins which were verified with a second database search using a different search engine, were distinguished from the comparison between VL and CL samples. Among them, 31 proteins for the CL group and 6 proteins for the VL group were determined differentially abundant. Two proteins from the gel-based analysis namely pyruvate kinase and succinly-coA:3-ketoacid-coenzyme A transferase analysis were encountered in the protein list of the CL group.Master Thesis Mass Spectrometry-Based Comparative Proteomic Analysis of Drug Resistant and Nonresistant Strains of Parasite Trichomonas Vaginalis(Izmir Institute of Technology, 2018) Özyağcı, Begüm; Yalçın, TalatTrichomonas vaginalis (T. vaginalis) causes sexually transmitted disease, trichomoniasis. Acute infections can result in cervical cancer, pelvic inflammatory disease, HIV-1 infection, preterm births, and low birth weight. Metronidazole, an antibiotic, is the standard treatment of the disease. However, in some cases T. vaginalis shows resistance to metronidazole thus treatment fails. Nevertheless, resistance mechanism of the parasite is not fully understood. Mass spectrometry has become an important tool in proteomic analysis with the emergence of soft ionization techniques instead of traditional protein identification and sequencing methods. In this study, a comparative gel-free proteomic analysis based on mass spectrometry with soft ionization technology was performed in two sets for resistant and non-resistant strains of T. vaginalis parasite isolated from clinical cases. Total proteins were digested by in solution digestion method and separated with high pH reversed-phase liquid chromatography. After fractions were concatenated, each fraction of sample was analyzed by reversed-phase liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) and proteins were identified by database search. Common and differential proteins between resistant and two sensitive trichomoniasis samples were compared according to their molecular function. Results indicate that ferredoxin 5 and hydroxyl amine reductase are differential proteins with iron-sulfur cluster binding activity identified for only resistant strain. Thioredoxin reductase, alcohol dehydrogenase, superoxide dismutase, pyruvate:ferredoxin oxidoreductase are studied proteins in the literature and also identified as common proteins in all strains for this study. These proteins might have a role in drug resistance mechanism of T. vaginalis.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.Master Thesis Importance of Database Normalization for Reliable Protein Identification in Mass Spectrometry-Based Proteomics(Izmir Institute of Technology, 2016) Mungan, Mehmet Direnç; Allmer, Jens; Yalçın, TalatOne of the revolutionary steps towards proteomics, was introducing mass spectrometry to protein inference analysis. Its powerful aspects such as speed, and accuracy towards identifying and quantifying proteins have made it the first choice to obtain highthroughput data. Due to development of a variety of fragmentation techniques, mass spectrometry-based analysis even made it possible to acquire knowledge about single polymorphisms and modifications of amino acids of a peptide. Although this technology provides enormous amounts of data, identification of the proteins is still a hard challenge to overcome due to the shortcomings of computational methods. Herein a novel methodology is offered to better analyze mass spectrometry data and overcome the deficiency of protein identification algorithms in terms of speed and accuracy. When the spectral data is acquired from an organism by mass spectrometry, database search algorithms are used for protein identification if the protein sequences of the organism are known. These algorithms compare the experimental data from mass spectrometry analysis to theoretical data gathered from known databases of organism to try and find the best match by ranking the PSMs via scoring functions. Since the databases can be too large to search and multiple databases with different sizes can contain the peptides of experimental data, database search algorithms may fail to produce fair, fast or complete results. In this work a methodology is presented to overcome unfair scoring of peptides in different size databases and enable database search algorithms to utilize relatively big sized entries such as human chromosome six frame translations. In terms of speed and accuracy the method is found to be better than some of the existing methods.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.Doctoral Thesis Gas-Phase Fragmentation Mechanisms of Protonated Peptides Via Tandem Mass Spectrometry(Izmir Institute of Technology, 2013) Taşoğlu, Çağdaş; Yalçın, TalatProtein identification based on enzymatic digestion of proteins and tandem mass spectrometric (MS/MS) analysis of peptide fragments has become a more popular method than classical approaches like Edman degradation. However, today’s protein sequencing tools have been constructed on a limited basis of peptide fragmentation chemistry such that some peptides can fragment in unusual ways that may not be predicted by the current bioinformatics software. Thus, erroneous assignments can be done in protein identification, which can lead to vital problems. Herein, it was aimed to reveal the rich chemistry lying behind the gas-phase fragmentation of peptides containing specific residues using MS/MS and collision induced dissociation (CID) analysis. As a result, the implementation of more detailed peptide fragmentation mechanisms into bioinformatics algorithms will no doubt help to improve database search tools. Results clearly indicate that b6 and b7 ions have higher tendency towards macrocyclization when compared to b5 ions. Besides it was observed that neighboring amino acid influences the selective opening of the macrocyclic structure and no preferential cleavage order can be specified depending on the amino acid residue. Next study showed that proline-containing peptides have high tendency to place the proline residue in the N-terminal position during the ring opening of macrocyclic structure. This is then followed by dipeptide elimination of proline with its adjacent C-terminal residue. Moreover, we demonstrated that sequence-scrambling exists for all histidine-containing peptides whatever the residue position and neighbor residue is. Additionally, we suggest that α-amino-ε-caprolactam formation at the side chain of lysine prevents macrocyclization reaction of b7 when K is positioned at the C-terminus. Finally, it was observed that macrocyclization reaction proceeds for peptides containing arginine when arginine gets closer to the C-terminus. Besides arginine was found to behave like lysine and forms ornithine when located at the C-terminus.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: 20Citation - Scopus: 20Genome-Wide Identification of Genes That Play a Role in Boron Stress Response in Yeast(Elsevier Ltd., 2011) Uluışık, İrem; Kaya, Alaattin; Ünlü, Ercan Selçuk; Avşar, Kadir; Karakaya, Hüseyin Çağlar; Yalçın, Talat; Koç, AhmetBoron is an essential micronutrient for plants and it is either necessary or beneficial for animals. Studies identified only few genes related to boron metabolism thus far and details of how boron is imported into cells and used in cell metabolism are largely unknown. In order to identify genes that play roles in boron metabolism, we screened the entire set of yeast haploid deletion mutants and identified 6 mutants that were resistant to toxic levels of boron, and 21 mutants that were highly sensitive to boron treatment. Furthermore, we performed a proteomic approach to identify additional proteins that are significantly up-regulated by boron treatment. Our results revealed many genes and pathways related to boron stress response and suggest a possible link between boron toxicity and translational control.