Proteomics, Human Gut Microbiome, and Stress Granules
My laboratory performs research in the following three areas:
- Supramolecular structure of RNA-rich stress granules and function of stress granules in neurodegeneration. Currently, we are focused on the role of non-canonical DNA structures, G quadruplexes, in the initiation of cytoplasmic stress granule assembly.
- Function of human gut microbiota in chronic kidney disease. We are interested in the human gut microbiome as both, a potential source of prognostic biomarkers and as a therapeutic target for the chronic kidney disease. Currently, we are investigating the effect of resistant starch supplementation on the human gut microbiome and its potential to slow the progression of chronic kidney disease.
- Development of mass spectrometry-based proteomics tools for the analysis of protein-protein interaction networks and for metaproteomics. We have designed experimental methods and computational tools to analyze pairwise protein-protein interactions using short non-specific cross-linkers and currently are advancing these methods to large scale. In addition, we are developing metaproteomics data processing pipe-line for the analysis of microbiome-derived proteins labeled with tandem mass tags.
Zybailov, B. L.; Byrd, A. K.; Glazko, G. V.; Rahmatallah, Y.; Raney, K. D., Protein-protein interaction analysis for functional characterization of helicases. Methods 2016.
Gao, J.; Zybailov, B. L.; Byrd, A. K.; Griffin, W. C.; Chib, S.; Mackintosh, S. G.; Tackett, A. J.; Raney, K. D., Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA. Chem Commun (Camb) 2015, 51 (33), 7242-4.
Jaiswal, M.; Washburn, M.; Zybailov, B., Mass Spectrometry-Based Methods of Proteome Analysis. In Reviews in Cell Biology and Molecular Medicine, Meyers, R. A., Ed. Wiley-VCH Verlag GmbH & Co. KGaA: 2015; pp 51-103.
Zybailov, B.; Gokulan, K.; Wiese, J.; Ramanagoudr-Bhojappa, R.; Byrd, A. K.; Glazko, G.; Jaiswal, M.; Mackintosh, S.; Varughese, K. I.; Raney, K. D., Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry. J Proteomics Bioinform 2015, 8 (11), 243-252.
Jaiswal, M.; Crabtree, N.; Bauer, M. A.; Hall, R.; Raney, K. D.; Zybailov, B. L., XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry. BMC Bioinformatics 2014, 15 Suppl 11, S16.
Zybailov, B. L.; Glazko, G. V.; Jaiswal, M.; Raney, K. D., Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. J Proteomics Bioinform 2013, 6(Suppl 2), 001.
Zybaĭlov, B. L.; Sherpa, M. D.; Glazko, G. V.; Raney, K. D.; Glazko, V. I., [G4-quadruplexes and genome instability]. Mol Biol (Mosk) 2013, 47 (2), 224-31.
Glazko, G. V.; Zybailov, B. L.; Rogozin, I. B., Computational prediction of polycomb-associated long non-coding RNAs. PLoS One 2012, 7 (9), e44878.