Adıgüzel, Yekbun
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Name Variants
A.,Yekbun
Adiguzel,Y.
Y.,Adıgüzel
Adlguzel Y.
Yekbun Adıgüzel
Adıgüzel, Yekbun
Yekbun, Adiguzel
Adiguzel,Yekbun
A., Yekbun
Adiguzel, Yekbun
Yekbun, Adıgüzel
Adiguzel Y.
Y.,Adiguzel
Adıgüzel Y.
Y., Adıgüzel
Y., Adiguzel
Adıgüzel,Y.
Adiguzel,Y.
Y.,Adıgüzel
Adlguzel Y.
Yekbun Adıgüzel
Adıgüzel, Yekbun
Yekbun, Adiguzel
Adiguzel,Yekbun
A., Yekbun
Adiguzel, Yekbun
Yekbun, Adıgüzel
Adiguzel Y.
Y.,Adiguzel
Adıgüzel Y.
Y., Adıgüzel
Y., Adiguzel
Adıgüzel,Y.
Job Title
Profesör Doktor
Email Address
yekbun.adiguzel@atilim.edu.tr
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Scholarly Output
7
Articles
3
Citation Count
3
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0
7 results
Scholarly Output Search Results
Now showing 1 - 7 of 7
Book Part Citation Count: 0In silico study of molecular mimicry between SARS-CoV-2 and neutrophil extracellular traps composition in granulocyte-rich supernatants of patients with systemic lupus erythematosus and lupus nephritis(Elsevier, 2022) Adiguzel,Y.; Shoenfeld,Y.; Basic SciencesNeutrophil extracellular traps (NETs) are detected in both COVID-19 and autoimmune disorders. Molecular mimicry between NETs-related proteins and SARS-CoV-2 proteins may be the mechanism that can lead to an autoimmune response. Accordingly, similar sequences were searched with blastp, between SARS-CoV-2 proteins and 148 proteins that were reported in the NETs composition induced in neutrophils of supernatants from patients with systemic lupus erythematosus and lupus nephritis. Query-subject epitope pairs with strong-binding affinities to 12 HLA supertype representative alleles were predicted for the aligned sequences with at least 50% identities. According to the prediction results, all HLA alleles under study have affinities to the similar SARS-CoV-2 and NETs' proteins. These affinities can bring molecular mimicry-based autoimmunity risk with NETs-pathology, in susceptible individuals, upon infection with SARS-CoV-2. However, HLA-A∗01:01 carriers can be at a higher risk due to the association of this allele with the highest number of NETs-related human proteins, and similar (unique) query-subject epitope pairs of those proteins and SARS-CoV-2. Additionally, HLA-A∗02:01 carriers may specifically be prone to higher risk than expected, if infected with SARS-CoV-2. Furthermore, HLA-A∗24:02 was predicted to bind strongly to an elevated number of unique SARS-CoV-2 subject sequences while the number of both associated human proteins, and unique queries of those, are rather low. It may be indicative of a pertaining pathology despite viral evolution. © 2023 Elsevier Inc. All rights reserved.Article Citation Count: 2Shared 6mer Peptides of Human and Omicron (21K and 21L) at SARS-CoV-2 Mutation Sites(Mdpi, 2022) Adiguzel, Yekbun; Shoenfeld, Yehuda; Basic SciencesWe investigated the short sequences involving Omicron 21K and Omicron 21L variants to reveal any possible molecular mimicry-associated autoimmunity risks and changes in those. We first identified common 6mers of the viral and human protein sequences present for both the mutant (Omicron) and nonmutant (SARS-CoV-2) versions of the same viral sequence and then predicted the binding affinities of those sequences to the HLA supertype representatives. We evaluated change in the potential autoimmunity risk, through comparative assessment of the nonmutant and mutant viral sequences and their similar human peptides with common 6mers and affinities to the same HLA allele. This change is the lost and the new, or de novo, autoimmunity risk, associated with the mutations in the Omicron 21K and Omicron 21L variants. Accordingly, e.g., the affinity of virus-similar sequences of the Ig heavy chain junction regions shifted from the HLA-B*15:01 to the HLA-A*01:01 allele at the mutant sequences. Additionally, peptides of different human proteins sharing 6mers with SARS-CoV-2 proteins at the mutation sites of interest and with affinities to the HLA-B*07:02 allele, such as the respective SARS-CoV-2 sequences, were lost. Among all, any possible molecular mimicry-associated novel risk appeared to be prominent in HLA-A*24:02 and HLA-B*27:05 serotypes upon infection with Omicron 21L. Associated disease, pathway, and tissue expression data supported possible new risks for the HLA-B*27:05 and HLA-A*01:01 serotypes, while the risks for the HLA-B*07:02 serotypes could have been lost or diminished, and those for the HLA-A*03:01 serotypes could have been retained, for the individuals infected with Omicron variants under study. These are likely to affect the complications related to cross-reactions influencing the relevant HLA serotypes upon infection with Omicron 21K and Omicron 21L.Review Citation Count: 1Shared Pathogenicity Features and Sequences between EBV, SARS-CoV-2, and HLA Class I Molecule-binding Motifs with a Potential Role in Autoimmunity(Humana Press inc, 2023) Adiguzel, Yekbun; Mahroum, Naim; Muller, Sylviane; Blank, Miri; Halpert, Gilad; Shoenfeld, Yehuda; Basic SciencesEpstein-Barr virus (EBV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are extraordinary in their ability to activate autoimmunity as well as to induce diverse autoimmune diseases. Here we reviewed the current knowledge on their relation. Further, we suggested that molecular mimicry could be a possible common mechanism of autoimmunity induction in the susceptible individuals infected with SARS-CoV-2. Molecular mimicry between SARS-CoV-2 and human proteins, and EBV and human proteins, are present. Besides, relation of the pathogenicity associated with both coronavirus diseases and EBV supports the notion. As a proof-of-the-concept, we investigated 8mer sequences with shared 5mers of SARS-CoV-2, EBV, and human proteins, which were predicted as epitopes binding to the same human leukocyte antigen (HLA) supertype representatives. We identified significant number of human peptide sequences with predicted-affinities to the HLA-A*02:01 allele. Rest of the peptide sequences had predicted-affinities to the HLA-A*02:01, HLA-B*40:01, HLA-B*27:05, HLA-A*01:01, and HLA-B*39:01 alleles. Carriers of these serotypes can be under a higher risk of autoimmune response induction upon getting infected, through molecular mimicry-based mechanisms common to SARS-CoV-2 and EBV infections. We additionally reviewed established associations of the identified proteins with the EBV-related pathogenicity and with the autoimmune diseases.Book Part Citation Count: 0Molecular Mimicry Study Between Peptides of SARS-CoV-2 and Neutrophil Extracellular Traps-Related Proteins(Elsevier, 2024) Adiguzel,Y.; Shoenfeld,Y.; Basic SciencesBackground Neutrophil extracellular traps (NETs) are observed in both COVID-19 pathology and autoimmune disorders, and molecular mimicry is a mechanism that can lead to an autoimmune response. Methods Similar sequences between SARS-CoV-2 proteins and 5 proteins (plasminogen receptor KT: PLRKT, myeloperoxidase: MPO, proteinase 3: PR-3, neutrophil elastase: NE, matrix metalloproteinase 9: MMP-9) that are present in NETs were searched. Human and SARS-CoV-2 sequence pairs were identified. Those among the identified sequence pairs, which are predicted as strong-binding peptides or epitopes of the same selected MHC class I and class II alleles, were predicted. Results In the case of MHC class I alleles, similar PLRKT and SARS-CoV-2 peptide sequences with high predicted-affinities to HLA-A*24:02, HLA-B*08:01, and HLA-B*15:01; similar MPO and SARS-CoV-2 peptide sequences with strong predicted-affinities to HLA-A*01:01, HLA-A*26:01, and HLA-B*15:01; and similar MMP-9 and SARS-CoV-2 peptide sequences with elevated predicted-affinities to HLA-B*39:01 were predicted. In the case of MHC class II alleles, similar PLRKT and SARS-CoV-2 peptide sequences with high predicted-affinities to HLA-DPA1*02:01/DPB1*01:01 were predicted. Conclusion This work is a proof-of-concept study, which revealed the potential involvement of molecular mimicry in NET pathology within susceptible individuals, in the case of being infected with SARS-CoV-2, leading to autoimmunity. © 2024 Elsevier B.V. All rights reserved.Article Citation Count: 0Web Server-based structure prediction as a supplementary tool for basic and acidic FGF secondary structure analysis using FTIR spectroscopy and a case study comparing curve-fit with the model-based structure inspection of the FTIR data(DergiPark, 2023) Korkmaz,F.; Mollaoglu,A.; Adiguzel,Y.; Basic SciencesFourier Transform Infrared (FTIR) spectroscopy can provide relative proportion of secondary structure elements in a protein. However, extracting this information from the Amide I band area of an FTIR spectrum is difficult. In addition to experimental methods, several protein secondary structure prediction algorithms serving on the Web can be used as supplementary tools requiring only protein amino acid sequences as inputs. In addition, web-server based docking tools can provide structure information when proteins are mixed and potentially interacting. Accordingly, we aimed to utilize web-server based structure predictors in fibroblast growth factor (FGF) protein structure determination through the FTIR data. Seven such predictors were selected and tested on basic FGF (bFGF) protein, to predict FGF secondary structure. Results were compared to available structure-files deposited in the Protein Data Bank (PDB). Then, FTIR spectra of bFGF and the acidic form of the protein with 50 folds more bovine serum albumin as carrier protein (1FGFA/50BSA) were collected. Optimized Amide I curve-fit parameters of bFGF with low (<5) root mean square deviation (RMSD) in the PDB data and the predictions were obtained. Those parameters were applied in curve-fitting of 1FGFA/50BSA data. Secondary structure was inspected also through applying models derived from the previously established methods. Results of model-based secondary structure estimation from FTIR data were compared with secondary structure calculated as 1 part contribution from 1FGFA/1BSA complex and 49 parts contribution from BSA. Complex structure was obtained through docking. RMSD in the PDB data and the predictions were respectively 3.05 and 2.39 with the optimized parameters. Those parameters did not work well for the 1FGFA/50BSA data. Models are better in this case, wherein one model (Model-1’) with the lowest average RMSD has 8.38 RMSD in the bFGF and 4.78 RMSD in the 1FGFA/50BSA structures. Model-based secondary structure predictions are better for determining bFGF and 1FGFA/50BSA secondary structures through the curve-fit approach that we followed, under non-optimal conditions like protein/BSA mixtures. Web servers can assist experimental studies investigating structures with unknown structures. Any web-based structure prediction supporting the experimental results would be enforcing the findings, but the unsupported results would not necessarily falsify the experimental data. © (2023), (DergiPark). All rights reserved.Book Part Citation Count: 0Perspectives on Molecular Mimicry Between Human, SARS-CoV-2, and Plasmodium Species Through a Probabilistic and Evolutionary Insight(Elsevier, 2024) Adiguzel,Y.; Shoenfeld,Y.; Basic SciencesThis chapter examines potential molecular mimicry between similar peptide sequences and shared 6mers of five selected proteins and the proteomes of both SARS-CoV-2 and five Plasmodium species that infect humans (P. falciparum, P. malariae, P. vivax, P. knowlesi, and P. ovale). Human proteins are plasminogen receptor (KT), neutrophil collagenase (neutrophil collagenase isoform 2), myeloperoxidase precursor, mitochondrial peptide methionine sulfoxide reductase isoform a precursor, and myeloblastin precursor. The chapter eventually focuses on a probabilistic and evolutionary insight into molecular mimicry. © 2024 Elsevier B.V. All rights reserved.Article Citation Count: 0Information-theoretic approach in allometric scaling relations of DNA and proteins(Wiley, 2022) Adiguzel, Yekbun; Basic SciencesAllometric scaling relations can be observed in between molecular parameters. Hence, we looked for presence of such relation among sizes (i.e., lengths) of proteins and genes. Protein lengths exist in the literature as the number of amino acids. They can also be derived from the mRNA lengths. Here, we looked for allometric scaling relation by using such data and simultaneously, the data was compared with the sizes of genes and proteins that were obtained from our modified information-theoretic approach. Results implied presence of scaling relation in the calculated results. This was expected due to the implemented modification in the information-theoretic calculation. Relation in the literature-based data was lacking high goodness of fit value. It could be due to physical factors and selective pressures, which ended up in deviations of the literature-sourced values from those in the model. Genome size is correlated with cell size. Intracellular volume, which is related to the DNA size, would require certain number of proteins, the sizes of which can therefore be correlated with the protein sizes. Cell sizes, genome sizes, and average protein and gene sizes, along with the number of proteins, namely the expression levels of the genes, are the physical factors, and the molecular factors influence those physical factors. The selective pressures on those can act through the connection between those physical factors and limit the dynamic ranges. Biological measures could be prone to such forces and are likely to deviate from expected models, regardless of the validity of assumptions, unless those are also implemented in the models. Yet, present discrepancies could be pointing at the need for model improvement, data imperfection, invalid assumptions, etc. Still, current work highlights possible use of information-theoretic approach in allometric scaling relations' studies.
