Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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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: 7Citation - Scopus: 6Visceral Leishmaniasis Caused by Leishmania Tropica(Springer, 2023) Özbilgin, Ahmet; Tunalı, Varol; Çavuş, İbrahim; Vardarlı Tetik, Aslı; Dinç, Melike; Yalçın, Talat; Gündüz, Cumhur; Beyaz, Merve; Köse, ŞükranPurposeIn Turkey, the main causative agent of visceral leishmaniasis (VL) is Leishmania. infantum and the main causative agent of cutaneous leishmaniasis (CL) is Leishmania tropica. In this study, we aimed to discuss the possible mechanisms, clinical aspects, and threat of visceralizing L. tropica.MethodsThis study includes seven cases of VL caused by L. tropica.Five patients were male (71%) and four were adults (57%).ResultsAll the VL patients complained of fever and splenomegaly. Fatigue, pancytopenia, and hepatomegaly were present in six patients each (86%), while weight loss and gastrointestinal system (GIS) symptoms were present in 5 patients (71%).ConclusionsIn this study, we have evaluated seven cases of visceralized L. tropica (VLT) in the context of the changing leishmaniasis epidemiology in Turkey. We have evaluated the possible mechanisms of visceralization; inter- and intraspecies genetic exchange with all the old world leishmaniasis agents present in the region, stress induced by inappropriate use of drugs, and possible ongoing adaptation mechanisms of Leishmania spp. The threat posed by VLT is significant as L. tropica is the most widespread and most common cause of leishmaniasis in Turkey. We do not know the vectorial capacity of the sand flies for the transmission of VLT strains or if these strains are in circulation in Turkey. Future studies should be carried out to investigate these issues as the transition of L. tropica from a mild disease-causing agent to a mortal one poses a significant public health concern for Turkey and Europe.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.