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  1. AU="Akberova, N I"
  2. AU="Bolouki Moghaddam, Farzaneh"
  3. AU="Rajeshkannan, Nadarajah"
  4. AU="Noda, Judith"
  5. AU=Loucks Catrina M.
  6. AU="Lachérade, J-C"
  7. AU=Jalali Subhadra AU=Jalali Subhadra
  8. AU="Yang, Yung"
  9. AU="Belt, Brian"
  10. AU="Beckley, Akinpelumi A"
  11. AU="Adams, Tempe"
  12. AU=Wahidi Momen M
  13. AU="Pardis C. Sabeti"
  14. AU=Arkowitz Robert A
  15. AU="Sempoux, Christine"
  16. AU="Selebatso, Moses"
  17. AU=Sountoulides Petros
  18. AU="Huachun Zou"
  19. AU=SHENG Nan AU=SHENG Nan
  20. AU="Gascon, Pierre"
  21. AU="Hoa Phong, Pham Huu Thien"
  22. AU="Guiyan Ni"

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  1. Buch ; Konferenzbeitrag: Bioinformatika i molekuljarnoe modelirovanie

    Akberova, N. I

    I meždunarodnaja internet-konferencija, Kazanʹ, 25 - 26 sentjabrja 2012 goda ; sbornik trudov

    2012  

    Titelvarianten Sbornik trudov Meždunarodnoj Naučnoj Konferencii Bioinformatika i Molekuljarnoe Modelirovanie
    Körperschaft Kazanskij (Privolʹžskij) Federalʹnyj Universitet
    Veranstaltung/Kongress Meždunarodnaja Internet-Konferencija Bioinformatika i Molekuljarnoe Modelirovanie (1, 2012.09.25-26, Kazanʹ)
    Verfasserangabe FGAOU VPO "Kazanskij (Privolžskij) Federalʹnyj Universitet ... [Red.: N. I. Akberova]
    Sprache Russisch
    Umfang 77 S.
    Verlag Kazanskij Univ
    Erscheinungsort Kazanʹ
    Dokumenttyp Buch ; Konferenzbeitrag
    Anmerkung In kyrill. Schr.
    ISBN 9785990341760 ; 5990341768
    Datenquelle Katalog der Technische Informationsbibliothek Hannover

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  2. Artikel ; Online: An anti-DNA antibody prefers damaged dsDNA over native.

    Akberova, N I / Zhmurov, A A / Nevzorova, T A / Litvinov, R I

    Journal of biomolecular structure & dynamics

    2017  Band 35, Heft 1, Seite(n) 219–232

    Abstract: DNA-protein interactions, including DNA-antibody complexes, have both fundamental and practical significance. In particular, antibodies against double-stranded DNA play an important role in the pathogenesis of autoimmune diseases. Elucidation of ... ...

    Abstract DNA-protein interactions, including DNA-antibody complexes, have both fundamental and practical significance. In particular, antibodies against double-stranded DNA play an important role in the pathogenesis of autoimmune diseases. Elucidation of structural mechanisms of an antigen recognition and interaction of anti-DNA antibodies provides a basis for understanding the role of DNA-containing immune complexes in human pathologies and for new treatments. Here we used Molecular Dynamic simulations of bimolecular complexes of a segment of dsDNA with a monoclonal anti-DNA antibody's Fab-fragment to obtain detailed structural and physical characteristics of the dynamic intermolecular interactions. Using a computationally modified crystal structure of a Fab-DNA complex (PDB: 3VW3), we studied in silico equilibrium Molecular Dynamics of the Fab-fragment associated with two homologous dsDNA fragments, containing or not containing dimerized thymine, a product of DNA photodamage. The Fab-fragment interactions with the thymine dimer-containing DNA was thermodynamically more stable than with the native DNA. The amino acid residues constituting a paratope and the complementary nucleotide epitopes for both Fab-DNA constructs were identified. Stacking and electrostatic interactions were shown to play the main role in the antibody-dsDNA contacts, while hydrogen bonds were less significant. The aggregate of data show that the chemically modified dsDNA (containing a covalent thymine dimer) has a higher affinity toward the antibody and forms a stronger immune complex. These findings provide a mechanistic insight into formation and properties of the pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus, associated with skin photosensibilization and DNA photodamage.
    Mesh-Begriff(e) Antibodies, Antinuclear/chemistry ; Antibodies, Antinuclear/metabolism ; Antigen-Antibody Complex ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Damage ; Humans ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin Fab Fragments/metabolism ; Models, Molecular ; Molecular Conformation ; Protein Binding ; Pyrimidine Dimers/chemistry ; Thermodynamics
    Chemische Substanzen Antibodies, Antinuclear ; Antigen-Antibody Complex ; Immunoglobulin Fab Fragments ; Pyrimidine Dimers ; DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2017-01
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2015.1128979
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: [Molecular dynamics of immune complex of photoadduct-containing DNA with Fab-Anti-DNA antibody fragment].

    Akberova, N I / Zhmurov, A A / Nevzorova, T A / Litvinov, R I

    Molekuliarnaia biologiia

    2016  Band 50, Heft 3, Seite(n) 509–519

    Abstract: Antibodies to DNA play an important role in the pathogenesis of autoimmune diseases. The elucidation of structural mechanisms of both the antigen recognition and the interaction of anti-DNA antibodies with DNA will help to understand the role of DNA- ... ...

    Abstract Antibodies to DNA play an important role in the pathogenesis of autoimmune diseases. The elucidation of structural mechanisms of both the antigen recognition and the interaction of anti-DNA antibodies with DNA will help to understand the role of DNA-containing immune complexes in various pathologies and can provide a basis for new treatment modalities. Moreover, the DNA-antibody complex is an analog of specific intracellular DNA-protein interactions. In this work, we used in silico molecular dynamic simulations of bimolecular complexes of the dsDNA segment containing the Fab fragment of an anti-DNA antibody to obtain the detailed thermodynamic and structural characteristics of dynamic intermolecular interactions. Using computationally modified crystal structure of the Fab-DNA complex (PDB ID: 3VW3), we studied the equilibrium molecular dynamics of the 64M-5 antibody Fab fragment associated with the dsDNA fragment containing the thymine dimer, the product of DNA photodamage. Amino acid residues that constitute paratopes and the complementary nucleotide epitopes for the Fab-DNA construct were identified. Stacking and electrostatic interactions were found to play the main role in mediating the most specific antibody-dsDNA contacts, while hydrogen bonds were less significant. These findings may shed light on the formation and properties of pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus associated with skin photosensitivity and DNA photodamage.
    Mesh-Begriff(e) Antibodies, Antinuclear/chemistry ; Antibodies, Antinuclear/metabolism ; Antigen-Antibody Complex/chemistry ; Antigen-Antibody Complex/metabolism ; Binding Sites, Antibody ; DNA/chemistry ; DNA/metabolism ; Humans ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin Fab Fragments/metabolism ; Light ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Photochemical Processes ; Protein Binding ; Protein Conformation ; Pyrimidine Dimers/chemistry ; Pyrimidine Dimers/metabolism ; Static Electricity ; Thermodynamics
    Chemische Substanzen Antibodies, Antinuclear ; Antigen-Antibody Complex ; Immunoglobulin Fab Fragments ; Pyrimidine Dimers ; DNA (9007-49-2)
    Sprache Russisch
    Erscheinungsdatum 2016-05
    Erscheinungsland Russia (Federation)
    Dokumenttyp Journal Article
    ZDB-ID 213542-5
    ISSN 0026-8984
    ISSN 0026-8984
    DOI 10.7868/S0026898416020026
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

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  4. Artikel: Molecular dynamics and free energy of binding of oleic acid to DNA in aqueous solutions.

    Tarasov, D S / Ibragimova, M Y / Izotova, E D / Akberova, N I / Zhdanov, R I

    Doklady. Biochemistry and biophysics

    2012  Band 446, Seite(n) 223–228

    Mesh-Begriff(e) Binding Sites ; Computer Simulation ; DNA/chemistry ; DNA/ultrastructure ; Energy Transfer ; Models, Chemical ; Molecular Dynamics Simulation ; Oleic Acid/chemistry ; Solutions ; Thermodynamics ; Water/chemistry
    Chemische Substanzen Solutions ; Water (059QF0KO0R) ; Oleic Acid (2UMI9U37CP) ; DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2012-11-07
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2062390-2
    ISSN 1608-3091 ; 1607-6729
    ISSN (online) 1608-3091
    ISSN 1607-6729
    DOI 10.1134/S1607672912050043
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Volltext online

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  5. Artikel: [Peculiarities of genotype distribution of interleukins (IL-1 and IL-10) in patients with peptic ulcer disease and their associations with persistence of Mycoplasma hyorhinis and Helicobacter pylori genotypes].

    Abuzarova, E R / Gorshkov, O V / Chernova, O A / Chernov, V M / Akberova, N I / Abdulkhakov, R A

    Eksperimental'naia i klinicheskaia gastroenterologiia = Experimental & clinical gastroenterology

    2008  , Heft 6, Seite(n) 27–31

    Abstract: It was found for the first time in our study that there is a significant prevalence of combinations of IL-1 and IL-10 genotypes--IL-1B-511C/C, IL-1B+3954C/C, IL-1RN1/1, IL-10-1082A/A and IL-1B-511T/C, IL-1B+3954C/C, IL-1RN1/2, IL-10- 1082A/G--in the ... ...

    Abstract It was found for the first time in our study that there is a significant prevalence of combinations of IL-1 and IL-10 genotypes--IL-1B-511C/C, IL-1B+3954C/C, IL-1RN1/1, IL-10-1082A/A and IL-1B-511T/C, IL-1B+3954C/C, IL-1RN1/2, IL-10- 1082A/G--in the group of patients with gastric and duodenal ulcer disease and control one, respectively. The correlation between the Tox- (cagA- vacAs1-) strains of H. pylori and the combinations of genotypes IL-1B-511T/C, IL-1B +3954C/C, IL-1RN1/1, IL-10-1082G/G was shown (p <0,05). Co-infection with H. pylori and M. hyorhinis was detected in 19% of patients. The association between combinations of genotypes IL-1B-511T/T IL-1B+3954C/C, IL-1RN2/2, IL-10-1082A/G and co-infection with H. pylori and M. hyorhinis was also found (p <0,05).
    Mesh-Begriff(e) Adult ; Aged ; Case-Control Studies ; Female ; Genetic Predisposition to Disease ; Genotype ; Helicobacter Infections/epidemiology ; Helicobacter Infections/genetics ; Helicobacter Infections/immunology ; Helicobacter Infections/microbiology ; Helicobacter pylori/genetics ; Helicobacter pylori/pathogenicity ; Host-Pathogen Interactions/genetics ; Humans ; Interleukin 1 Receptor Antagonist Protein/genetics ; Interleukin-10/genetics ; Interleukin-1beta/genetics ; Male ; Middle Aged ; Mycoplasma Infections/epidemiology ; Mycoplasma Infections/genetics ; Mycoplasma Infections/immunology ; Mycoplasma Infections/microbiology ; Mycoplasma hyorhinis/genetics ; Mycoplasma hyorhinis/pathogenicity ; Peptic Ulcer/epidemiology ; Peptic Ulcer/genetics ; Peptic Ulcer/immunology ; Peptic Ulcer/microbiology ; Polymorphism, Single Nucleotide ; Prevalence ; Virulence ; Virulence Factors/genetics ; Young Adult
    Chemische Substanzen IL10 protein, human ; IL1RN protein, human ; Interleukin 1 Receptor Antagonist Protein ; Interleukin-1beta ; Virulence Factors ; Interleukin-10 (130068-27-8)
    Sprache Russisch
    Erscheinungsdatum 2008
    Erscheinungsland Russia (Federation)
    Dokumenttyp English Abstract ; Journal Article
    ISSN 1682-8658
    ISSN 1682-8658
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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