Keywords
Last Name
Institution

Boris L Zybailov

TitleAssistant Professor
InstitutionUniversity of Arkansas for Medical Sciences
DepartmentBiochemistry & Molecular Biology, College of Medicine
DivisionBiochemistry & Molecular Faculty
Address433-2 Biomedical Research II
1120 Marshall Street
Mail Slot # 516
Little Rock AR 72202
Phone501-686-7254
vCardDownload vCard

    Collapse Overview 
    Collapse overview
    The current focus of my laboratory is investigation of protein-protein and protein-nucleic acid interactions in the context of stress granule assembly. Specifically, we are interested in the role of G4 DNA structures and their protein interactors in mediating intracellular stress during aging. Over the past 12 years I worked in the area of quantitative mass spectrometry developing label-free and stable isotope-based proteomics methods and applying them to various bio-analytical problems. First, during my post-doctoral training with Mike Washburn at Stowers Institute (Kansas City, MO) I developed the statistical framework for the spectral counting methods and applied it to the study of differential accumulation of yeast membrane proteins. During my second post-doc with Klaas van Wijk at Cornell University (Ithaca, NY) I used spectral counting to study organelle proteome dynamics and protein homeostasis in Arabidopsis. In addition to the large-scale proteomics studies I also was involved in targeted analysis of protein complexes: mammalian mediator complex (at Stowers) and Clp protease complex (at Cornell). During my work as a Research Associate with David Goldfarb, as a part of newly formed company - Calorics Pharmaceuticals - I designed proteomics screens to identify targets of caloric restriction mimetics – small molecules extending replicative lifespan in yeast. We routinely use methods of systems biology, mass-spectrometry based proteomics, large-scale OMICS data integration and big data mining.


    Collapse Affiliation 
    Collapse member of
    American Society for Mass Spectrometry
    Collapse collaborator
    Kevin D Raney
    Galina Glazko

    Collapse Biography 
    Collapse awards and honors
    2003Frederick C.Wedler Outstanding Doctoral Dissertation Award , Penn State University

    Collapse Bibliographic 
    Collapse additional bibliographic sources
    The links below are provided by the researcher to provide access to external online bibliographies that they keep independently from the Profiles System.


    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Rahmatallah Y, Zybailov B, Emmert-Streib F, Glazko G. GSAR: Bioconductor package for Gene Set analysis in R. BMC Bioinformatics. 2017 Jan 24; 18(1):61. PMID: 28118818.
      View in: PubMed
    2. Byrd AK, Zybailov BL, Maddukuri L, Gao J, Marecki JC, Jaiswal M, Bell MR, Griffin WC, Reed MR, Chib S, Mackintosh SG, MacNicol AM, Baldini G, Eoff RL, Raney KD. Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress. J Biol Chem. 2016 Aug 19; 291(34):18041-57. PMID: 27369081; PMCID: PMC5016190 [Available on 08/19/17].
    3. Zybailov BL, Byrd AK, Glazko GV, Rahmatallah Y, Raney KD. Protein-protein interaction analysis for functional characterization of helicases. Methods. 2016 Oct 01; 108:56-64. PMID: 27090004; PMCID: PMC5035562 [Available on 10/01/17].
    4. Zybailov B, Gokulan K, Wiese J, Ramanagoudr-Bhojappa R, Byrd AK, Glazko G, Jaiswal M, Mackintosh S, Varughese KI, Raney KD. Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry. J Proteomics Bioinform. 2015 Nov; 8(11):243-252. PMID: 26807012.
      View in: PubMed
    5. Gao J, Zybailov BL, Byrd AK, Griffin WC, Chib S, Mackintosh SG, Tackett AJ, Raney KD. Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA. Chem Commun (Camb). 2015 Apr 28; 51(33):7242-4. PMID: 25813861; PMCID: PMC4465349.
    6. Jaiswal M, Crabtree N, Bauer MA, Hall R, Raney KD, Zybailov BL. XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry. BMC Bioinformatics. 2014; 15 Suppl 11:S16. PMID: 25350700; PMCID: PMC4251045.
    7. Zybailov BL, Sherpa MD, Glazko GV, Raney KD, Glazko VI. [G4-quadruplexes and genome instability]. Mol Biol (Mosk). 2013 Mar-Apr; 47(2):224-31. PMID: 23808155.
      View in: PubMed
    8. Zybailov BL, Glazko GV, Jaiswal M, Raney KD. Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. J Proteomics Bioinform. 2013 Feb 08; 6(Suppl 2):001. PMID: 25045217.
      View in: PubMed
    9. Glazko GV, Zybailov BL, Rogozin IB. Computational prediction of polycomb-associated long non-coding RNAs. PLoS One. 2012; 7(9):e44878. PMID: 23028655; PMCID: PMC3441527.
    10. Lundquist PK, Poliakov A, Bhuiyan NH, Zybailov B, Sun Q, van Wijk KJ. The functional network of the Arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis. Plant Physiol. 2012 Mar; 158(3):1172-92. PMID: 22274653; PMCID: PMC3291262.
    11. Zybailov B, Sun Q, van Wijk KJ. Workflow for large scale detection and validation of peptide modifications by RPLC-LTQ-Orbitrap: application to the Arabidopsis thaliana leaf proteome and an online modified peptide library. Anal Chem. 2009 Oct 01; 81(19):8015-24. PMID: 19725545.
      View in: PubMed
    12. Zybailov B, Friso G, Kim J, Rudella A, Rodríguez VR, Asakura Y, Sun Q, van Wijk KJ. Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism. Mol Cell Proteomics. 2009 Aug; 8(8):1789-1810. PMID: 19423572; PMCID: PMC2722778.
    13. Kim J, Rudella A, Ramirez Rodriguez V, Zybailov B, Olinares PD, van Wijk KJ. Subunits of the plastid ClpPR protease complex have differential contributions to embryogenesis, plastid biogenesis, and plant development in Arabidopsis. Plant Cell. 2009 Jun; 21(6):1669-92. PMID: 19525416; PMCID: PMC2714938.
    14. Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ. PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res. 2009 Jan; 37(Database issue):D969-74. PMID: 18832363; PMCID: PMC2686560.
    15. Majeran W, Zybailov B, Ytterberg AJ, Dunsmore J, Sun Q, van Wijk KJ. Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol Cell Proteomics. 2008 Sep; 7(9):1609-38. PMID: 18453340; PMCID: PMC2556027.
    16. Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, Sun Q, van Wijk KJ. Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One. 2008 Apr 23; 3(4):e1994. PMID: 18431481; PMCID: PMC2291561.
    17. Chen X, Wurtmann EJ, Van Batavia J, Zybailov B, Washburn MP, Wolin SL. An ortholog of the Ro autoantigen functions in 23S rRNA maturation in D. radiodurans. Genes Dev. 2007 Jun 01; 21(11):1328-39. PMID: 17510283; PMCID: PMC1877746.
    18. Zybailov BL, Florens L, Washburn MP. Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. Mol Biosyst. 2007 May; 3(5):354-60. PMID: 17460794.
      View in: PubMed
    19. Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res. 2006 Sep; 5(9):2339-47. PMID: 16944946.
      View in: PubMed
    20. Zybailov B, Coleman MK, Florens L, Washburn MP. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem. 2005 Oct 01; 77(19):6218-24. PMID: 16194081.
      View in: PubMed
    21. Sakuragi Y, Zybailov B, Shen G, Bryant DA, Golbeck JH, Diner BA, Karygina I, Pushkar Y, Stehlik D. Recruitment of a foreign quinone into the A1 site of photosystem I. Characterization of a menB rubA double deletion mutant in Synechococcus sp. PCC 7002 devoid of FX, FA, and FB and containing plastoquinone or exchanged 9,10-anthraquinone. J Biol Chem. 2005 Apr 01; 280(13):12371-81. PMID: 15681848.
      View in: PubMed
    22. Paoletti AC, Zybailov B, Washburn MP. Principles and applications of multidimensional protein identification technology. Expert Rev Proteomics. 2004 Oct; 1(3):275-82. PMID: 15966824.
      View in: PubMed
    23. Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, Swanson SK, Banks CA, Jin J, Cai Y, Washburn MP, Conaway JW, Conaway RC. A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol Cell. 2004 Jun 04; 14(5):685-91. PMID: 15175163.
      View in: PubMed
    24. Tomomori-Sato C, Sato S, Parmely TJ, Banks CA, Sorokina I, Florens L, Zybailov B, Washburn MP, Brower CS, Conaway RC, Conaway JW. A mammalian mediator subunit that shares properties with Saccharomyces cerevisiae mediator subunit Cse2. J Biol Chem. 2004 Feb 13; 279(7):5846-51. PMID: 14638676.
      View in: PubMed
    25. Xu W, Chitnis P, Valieva A, van der Est A, Pushkar YN, Krzystyniak M, Teutloff C, Zech SG, Bittl R, Stehlik D, Zybailov B, Shen G, Golbeck JH. Electron transfer in cyanobacterial photosystem I: I. Physiological and spectroscopic characterization of site-directed mutants in a putative electron transfer pathway from A0 through A1 to FX. J Biol Chem. 2003 Jul 25; 278(30):27864-75. PMID: 12721305.
      View in: PubMed
    26. Xu W, Chitnis PR, Valieva A, van der Est A, Brettel K, Guergova-Kuras M, Pushkar YN, Zech SG, Stehlik D, Shen G, Zybailov B, Golbeck JH. Electron transfer in cyanobacterial photosystem I: II. Determination of forward electron transfer rates of site-directed mutants in a putative electron transfer pathway from A0 through A1 to FX. J Biol Chem. 2003 Jul 25; 278(30):27876-87. PMID: 12721306.
      View in: PubMed
    27. Wade Johnson T, Naithani S, Stewart C, Zybailov B, Daniel Jones A, Golbeck JH, Chitnis PR. The menD and menE homologs code for 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylate synthase and O-succinylbenzoic acid-CoA synthase in the phylloquinone biosynthetic pathway of Synechocystis sp. PCC 6803. Biochim Biophys Acta. 2003 Mar 06; 1557(1-3):67-76. PMID: 12615349.
      View in: PubMed
    28. Shinkarev VP, Zybailov B, Vassiliev IR, Golbeck JH. Modeling of the P700+ charge recombination kinetics with phylloquinone and plastoquinone-9 in the A1 site of photosystem I. Biophys J. 2002 Dec; 83(6):2885-97. PMID: 12496065; PMCID: PMC1302373.
    29. Sakuragi Y, Zybailov B, Shen G, Jones AD, Chitnis PR, van der Est A, Bittl R, Zech S, Stehlik D, Golbeck JH, Bryant DA. Insertional inactivation of the menG gene, encoding 2-phytyl-1,4-naphthoquinone methyltransferase of Synechocystis sp. PCC 6803, results in the incorporation of 2-phytyl-1,4-naphthoquinone into the A(1) site and alteration of the equilibrium constant between A(1) and F(X) in photosystem I. Biochemistry. 2002 Jan 08; 41(1):394-405. PMID: 11772039.
      View in: PubMed
    30. Johnson TW, Zybailov B, Jones AD, Bittl R, Zech S, Stehlik D, Golbeck JH, Chitnis PR. Recruitment of a foreign quinone into the A1 site of photosystem I. In vivo replacement of plastoquinone-9 by media-supplemented naphthoquinones in phylloquinone biosynthetic pathway mutants of Synechocystis sp. PCC 6803. J Biol Chem. 2001 Oct 26; 276(43):39512-21. PMID: 11470786.
      View in: PubMed
    31. Vassilieva EV, Antonkine ML, Zybailov BL, Yang F, Jakobs CU, Golbeck JH, Bryant DA. Electron transfer may occur in the chlorosome envelope: the CsmI and CsmJ proteins of chlorosomes are 2Fe-2S ferredoxins. Biochemistry. 2001 Jan 16; 40(2):464-73. PMID: 11148041.
      View in: PubMed
    32. Semenov AY, Vassiliev IR, van Der Est A, Mamedov MD, Zybailov B, Shen G, Stehlik D, Diner BA, Chitnis PR, Golbeck JH. Recruitment of a foreign quinone into the A1 site of photosystem I. Altered kinetics of electron transfer in phylloquinone biosynthetic pathway mutants studied by time-resolved optical, EPR, and electrometric techniques. J Biol Chem. 2000 Aug 04; 275(31):23429-38. PMID: 10801789.
      View in: PubMed
    33. Zybailov B, van der Est A, Zech SG, Teutloff C, Johnson TW, Shen G, Bittl R, Stehlik D, Chitnis PR, Golbeck JH. Recruitment of a foreign quinone into the A(1) site of photosystem I. II. Structural and functional characterization of phylloquinone biosynthetic pathway mutants by electron paramagnetic resonance and electron-nuclear double resonance spectroscopy. J Biol Chem. 2000 Mar 24; 275(12):8531-9. PMID: 10722691.
      View in: PubMed
    34. Johnson TW, Shen G, Zybailov B, Kolling D, Reategui R, Beauparlant S, Vassiliev IR, Bryant DA, Jones AD, Golbeck JH, Chitnis PR. Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. pcc 6803. J Biol Chem. 2000 Mar 24; 275(12):8523-30. PMID: 10722690.
      View in: PubMed
    35. Kjaer B, Frigaard NU, Yang F, Zybailov B, Miller M, Golbeck JH, Scheller HV. Menaquinone-7 in the reaction center complex of the green sulfur bacterium Chlorobium vibrioforme functions as the electron acceptor A1. Biochemistry. 1998 Mar 10; 37(10):3237-42. PMID: 9536963.
      View in: PubMed
    Zybailov's Networks
    Click the "See All" links for more information and interactive visualizations!
    Concepts Expand Description
    _
    Co-Authors Expand Description
    _
    Similar People Expand Description
    _
    Same Department Expand Description
    Physical Neighbors Expand Description
    _