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  1. Article ; Online: Molecular mimicry between SARS-CoV-2 and human proteins.

    Adiguzel, Yekbun

    Autoimmunity reviews

    2021  Volume 20, Issue 4, Page(s) 102791

    MeSH term(s) COVID-19 ; Humans ; Molecular Mimicry ; SARS-CoV-2 ; Viral Proteins
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2021-02-18
    Publishing country Netherlands
    Document type Letter
    ZDB-ID 2144145-5
    ISSN 1873-0183 ; 1568-9972
    ISSN (online) 1873-0183
    ISSN 1568-9972
    DOI 10.1016/j.autrev.2021.102791
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  2. Article ; Online: Information-theoretic approach in allometric scaling relations of DNA and proteins.

    Adiguzel, Yekbun

    Chemical biology & drug design

    2021  Volume 99, Issue 2, Page(s) 331–343

    Abstract: Allometric 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 ...

    Abstract Allometric 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.
    MeSH term(s) DNA/chemistry ; Information Theory ; Nucleic Acid Conformation ; Pharmaceutical Preparations/chemistry ; Protein Conformation ; Proteins/chemistry ; Thermodynamics
    Chemical Substances Pharmaceutical Preparations ; Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2021-12-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 2216600-2
    ISSN 1747-0285 ; 1747-0277
    ISSN (online) 1747-0285
    ISSN 1747-0277
    DOI 10.1111/cbdd.13988
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  3. Article ; Online: Peptides of H. sapiens and P. falciparum that are predicted to bind strongly to HLA-A*24:02 and homologous to a SARS-CoV-2 peptide.

    Adiguzel, Yekbun

    Acta tropica

    2021  Volume 221, Page(s) 106013

    Abstract: Aim: This study is looking for a common pathogenicity between SARS-CoV-2 and Plasmodium species, in individuals with certain HLA serotypes.: Methods: 1. Tblastx searches of SARS-CoV-2 are performed by limiting searches to five Plasmodium species that ...

    Abstract Aim: This study is looking for a common pathogenicity between SARS-CoV-2 and Plasmodium species, in individuals with certain HLA serotypes.
    Methods: 1. Tblastx searches of SARS-CoV-2 are performed by limiting searches to five Plasmodium species that infect humans. 2. Aligned sequences in the respective organisms' proteomes are searched with blastp. 3. Binding predictions of the identified SARS-CoV-2 peptide to HLA supertype representatives are performed. 4. Blastp searches of predicted epitopes that bind strongly to the identified HLA allele are performed by limiting searches to H. sapiens and Plasmodium species, separately. 5. Peptides with minimum 60% identity to the predicted epitopes are found in results. 6. Peptides among those, which bind strongly to the same HLA allele, are predicted. 7. Step-4 is repeated by limiting searches to H. sapiens, followed by the remaining steps until step-7, for peptides sourced by Plasmodium species after step-6.
    Results: SARS-CoV-2 peptide with single letter amino acid code CFLGYFCTCYFGLFC has the highest identity to P. vivax. Its YFCTCYFGLF part is predicted to bind strongly to HLA-A*24:02. Peptides in the human proteome both homologous to YFCTCYFGLF and with a strong binding affinity to HLA-A*24:02 are YYCARRFGLF, YYCHCPFGVF, and YYCQQYFFLF. Such peptides in the Plasmodium species' proteomes are FFYTFYFELF, YFVACLFILF, and YFPTITFHLF. The first one belonging to P. falciparum has a homologous peptide (YFYLFSLELF) in the human proteome, which also has a strong binding affinity to the same HLA allele.
    Conclusion: Immune responses to the identified-peptides with similar sequences and strong binding affinities to HLA-A*24:02 can be related to autoimmune response risk in individuals with HLA-A*24:02 serotypes, upon getting infected with SARS-CoV-2 or P. falciparum.
    MeSH term(s) COVID-19 ; Epitopes, T-Lymphocyte ; HLA-A24 Antigen ; Humans ; Malaria, Vivax ; Peptides/genetics ; SARS-CoV-2
    Chemical Substances Epitopes, T-Lymphocyte ; HLA-A*24:02 antigen ; HLA-A24 Antigen ; Peptides
    Language English
    Publishing date 2021-06-17
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 210415-5
    ISSN 1873-6254 ; 0001-706X
    ISSN (online) 1873-6254
    ISSN 0001-706X
    DOI 10.1016/j.actatropica.2021.106013
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  4. Book ; Online: Peptides of H. sapiens and P. falciparum that are predicted to bind strongly to HLA-A*24:02 and homologous to a SARS-CoV-2 peptide

    Adıgüzel, Yekbun

    2021  

    Abstract: Aim: This study is looking for a common pathogenicity between SARS-CoV-2 and plasmodium species, in individuals with certain HLA serotypes. Methods: 1-) Tblastx searches of SARS-CoV-2 are performed by limiting searches to plasmodium species that infect ... ...

    Abstract Aim: This study is looking for a common pathogenicity between SARS-CoV-2 and plasmodium species, in individuals with certain HLA serotypes. Methods: 1-) Tblastx searches of SARS-CoV-2 are performed by limiting searches to plasmodium species that infect human. 2-) Aligned sequences in the respective organisms' proteomes are searched with blastp. 3-) Binding predictions of the identified SARS-CoV-2 peptide to MHC class I supertype representatives are performed. 4-) Blastp searches of predicted-epitopes that bind strongly to the identified HLA allele are performed by limiting searches to human and to the plasmodium species. 5-) Peptides with minimum 60 % identity to the predicted-epitopes are found in results. 6-) Peptides among those, which bind strongly to the same HLA allele, are predicted. 7-) Step-4 is repeated by limiting searches to human, for peptides sourced by limiting searches to plasmodium species at step-4. 8-) Step-5 and 6 are performed with results of 7. Results: CFLGYFCTCYFGLFC peptide of SARS-CoV-2 has the highest identity to P. vivax. Its GYFCTCYFGLF and YFCTCYFGLF parts are predicted to bind strongly to HLA-A*24:02. Results obtained only for peptides homologous to YFCTCYFGLF, as follows: YYCARRFGLF, YYCHCPFGVF, and YYCQQYFFLF are potential HLA-A*24:02 epitopes in the human proteome. Among FFYTFYFELF, YFVACLFILF, and YFPTITFHLF peptides in the plasmodium species' proteomes with strong binding affinity to HLA-A*24:02, only FFYTFYFELF of P. falciparum is homologous to the potential HLA-A*24:02 epitope YFYLFSLELF in the human proteome. Conclusion: Immune responses to the identified-peptides with similar sequences and strong binding affinities to HLA-A*24:02 may lead to autoimmune response risk in individuals with HLA-A*24:02 serotypes, upon getting infected with SARS-CoV-2 or P. falciparum.

    Comment: 29 pages, 4 figures
    Keywords Quantitative Biology - Other Quantitative Biology
    Subject code 570
    Publishing date 2021-01-18
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Coronavirus associated molecular mimicry common to SARS-CoV-2 peptide

    Adiguzel, Yekbun

    bioRxiv

    Abstract: Relationship of COVID-19 and immunity is complex and can involve autoimmune reactions through molecular mimicry. We investigated autoimmunity related pathological mechanisms involving molecular mimicry that are common to certain coronaviruses, including ... ...

    Abstract Relationship of COVID-19 and immunity is complex and can involve autoimmune reactions through molecular mimicry. We investigated autoimmunity related pathological mechanisms involving molecular mimicry that are common to certain coronaviruses, including SARS-CoV-2, by means of a selected peptide sequence (CFLGYFCTCYFGLFC). Accordingly, coronavirus-associated sequences that are homologous to that 15mer sequence in the SARS-CoV-2 proteome are attained first. Then, homologous human and coronavirus sequences are obtained, wherein the coronavirus sequences are homologous to the 15mer SARS-CoV-2 peptide. All the identified query-subject sequences contained at least 7 residue matches in the aligned regions. Finally, parts of those coronavirus and host sequences, which are predicted to have high affinity to the same human leukocyte antigen (HLA) alleles as that of the SARS-CoV-2 sequence, are selected among the query and subject epitope-pairs that were both (predicted to be) strongly binding to the same HLA alleles. The proteins or the protein regions with those predicted epitopes include, but not limited to, immunoglobulin heavy chain junction regions, phospholipid phosphatase-related protein type 2, slit homolog 2 protein, and CRB1 isoform I precursor. These proteins are potentially associated with certain pathologies, but especially the possible CRB1 related coronavirus pathogenicity could be furthered by autoimmunity risk in HLA*A24:02 serotypes. Overall, results imply autoimmunity risk in COVID-19 patients with HLA*A02:01 and HLA*A24:02 serotypes in general, through molecular mimicry. This is also common to other coronaviruses than SARS-CoV-2. These results are indicative at the current stage, they need to be validated. Yet, they can pave the way to autoimmunity treatment options to be used in COVID-19 and its associated diseases.
    Keywords covid19
    Language English
    Publishing date 2021-01-28
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.01.28.428642
    Database COVID19

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  6. Article: Peptides of H. sapiens and P. falciparum that are predicted to bind strongly to HLA-A*24:02 and homologous to a SARS-CoV-2 peptide

    Adiguzel, Yekbun

    Acta tropica. 2021 Sept., v. 221

    2021  

    Abstract: This study is looking for a common pathogenicity between SARS-CoV-2 and Plasmodium species, in individuals with certain HLA serotypes.1. Tblastx searches of SARS-CoV-2 are performed by limiting searches to five Plasmodium species that infect humans. 2. ... ...

    Abstract This study is looking for a common pathogenicity between SARS-CoV-2 and Plasmodium species, in individuals with certain HLA serotypes.1. Tblastx searches of SARS-CoV-2 are performed by limiting searches to five Plasmodium species that infect humans. 2. Aligned sequences in the respective organisms’ proteomes are searched with blastp. 3. Binding predictions of the identified SARS-CoV-2 peptide to HLA supertype representatives are performed. 4. Blastp searches of predicted epitopes that bind strongly to the identified HLA allele are performed by limiting searches to H. sapiens and Plasmodium species, separately. 5. Peptides with minimum 60% identity to the predicted epitopes are found in results. 6. Peptides among those, which bind strongly to the same HLA allele, are predicted. 7. Step-4 is repeated by limiting searches to H. sapiens, followed by the remaining steps until step-7, for peptides sourced by Plasmodium species after step-6.SARS-CoV-2 peptide with single letter amino acid code CFLGYFCTCYFGLFC has the highest identity to P. vivax. Its YFCTCYFGLF part is predicted to bind strongly to HLA-A*24:02. Peptides in the human proteome both homologous to YFCTCYFGLF and with a strong binding affinity to HLA-A*24:02 are YYCARRFGLF, YYCHCPFGVF, and YYCQQYFFLF. Such peptides in the Plasmodium species’ proteomes are FFYTFYFELF, YFVACLFILF, and YFPTITFHLF. The first one belonging to P. falciparum has a homologous peptide (YFYLFSLELF) in the human proteome, which also has a strong binding affinity to the same HLA allele.Immune responses to the identified-peptides with similar sequences and strong binding affinities to HLA-A*24:02 can be related to autoimmune response risk in individuals with HLA-A*24:02 serotypes, upon getting infected with SARS-CoV-2 or P. falciparum.
    Keywords Plasmodium falciparum ; Severe acute respiratory syndrome coronavirus 2 ; alleles ; amino acids ; autoimmunity ; epitopes ; humans ; pathogenicity ; peptides ; proteome ; risk ; serotypes
    Language English
    Dates of publication 2021-09
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 210415-5
    ISSN 1873-6254 ; 0001-706X
    ISSN (online) 1873-6254
    ISSN 0001-706X
    DOI 10.1016/j.actatropica.2021.106013
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  7. Article ; Online: Shared 6mer Peptides of Human and Omicron (21K and 21L) at SARS-CoV-2 Mutation Sites.

    Adiguzel, Yekbun / Shoenfeld, Yehuda

    Antibodies (Basel, Switzerland)

    2022  Volume 11, Issue 4

    Abstract: We 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 ... ...

    Abstract We 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.
    Language English
    Publishing date 2022-10-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2661514-9
    ISSN 2073-4468 ; 2073-4468
    ISSN (online) 2073-4468
    ISSN 2073-4468
    DOI 10.3390/antib11040068
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  8. Article ; Online: Biophysical and biological perspective in biosemiotics.

    Adiguzel, Yekbun

    Progress in biophysics and molecular biology

    2016  Volume 121, Issue 3, Page(s) 245–254

    Abstract: The cell and its basic constituents are introduced here through a biophysical and information communication theoretic approach in biology and biosemiotics. With this purpose, the requirements of primordial cellular structures, single binding events, and ... ...

    Abstract The cell and its basic constituents are introduced here through a biophysical and information communication theoretic approach in biology and biosemiotics. With this purpose, the requirements of primordial cellular structures, single binding events, and signalling cascades are first mentioned stepwise, in relation to the model of the cellular sensing mechanism. This is followed by the concepts of cross reactions in sensing and pattern recognitions, wherein an information theoretic approach is addressed and the features of multicellularity are discussed along. Multicellularity is introduced as the path that leads to the loss of the direct causal relations. The loss of true causal relation is considered as a form of translation that enables meaning-encoded communication over the informative processes. In this sense, semiosis may not be exclusive. Synthetic biology is exemplified as a form of artificial selection mechanisms for the generation of 'self-reproducing' systems with information coding and processing machineries. These discussions are summarised at the end.
    MeSH term(s) Animals ; Biology/methods ; Biophysics/methods ; Humans ; Signal Transduction
    Language English
    Publishing date 2016-09
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 209302-9
    ISSN 1873-1732 ; 0079-6107
    ISSN (online) 1873-1732
    ISSN 0079-6107
    DOI 10.1016/j.pbiomolbio.2016.06.008
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  9. Article ; Online: Shared Pathogenicity Features and Sequences between EBV, SARS-CoV-2, and HLA Class I Molecule-binding Motifs with a Potential Role in Autoimmunity.

    Adiguzel, Yekbun / Mahroum, Naim / Muller, Sylviane / Blank, Miri / Halpert, Gilad / Shoenfeld, Yehuda

    Clinical reviews in allergy & immunology

    2023  Volume 65, Issue 2, Page(s) 206–230

    Abstract: Epstein-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 ... ...

    Abstract Epstein-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.
    MeSH term(s) Humans ; SARS-CoV-2 ; Herpesvirus 4, Human ; Autoimmunity ; COVID-19 ; Epstein-Barr Virus Infections ; Virulence ; HLA-B Antigens ; Autoimmune Diseases ; Peptides ; HLA-A Antigens
    Chemical Substances HLA-B Antigens ; Peptides ; HLA-A Antigens
    Language English
    Publishing date 2023-07-28
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1239045-8
    ISSN 1559-0267 ; 1080-0549
    ISSN (online) 1559-0267
    ISSN 1080-0549
    DOI 10.1007/s12016-023-08962-4
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  10. Book ; Online ; Thesis: ATR-FTIR spectroscopy of membrane-bound Ras protein

    Adigüzel, Yekbun

    2008  

    Author's details written by Yekbun Adigüzel
    Language English
    Size Online-Ressource (PDF-Datei: 162 S., 4307 KB)
    Publisher Univ.-Bibliothek
    Publishing place Bochum
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Bochum, 2008
    Database Former special subject collection: coastal and deep sea fishing

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