Evolutionary Biochemistry of Cellular Stress Response
In our laboratory, we study how proteins differentiate in order to perform specialized functions. In particular, we are using theoretical and experimental approaches to investigate:
a) The origin, long-term evolution, and functional differentiation of molecules involved in the innate and adaptive immune systems. We are studying the Immunoglobulin (Ig)-like domains, which play a pivotal role in the immune response of vertebrates. We are using bioinformatics and phylogenetic methods to study the evolutionary relationships of the Ig-like domains. On the basis of these studies we generate hypotheses, which we test by molecular biology and biochemistry techniques.
b) The functional diversification of stress response proteins. We are studying the heat shock proteins (hsps), which as a major component of the stress response pathway are important for cell survival and homeostasis. We are using comparative genomics/proteomics to reveal conserved and new functional partners of the hsps in evolutionarily key species. We test the physiological importance of these interactions by examining how environmental or molecular perturbations affect the cellular response, adaptation, and survival.
Selected publications (Click for full list)
Das S, Nikolaidis N, Goto H, McCallister C, Li J, Hirano M, Cooper MD. Comparative genomics and evolution of the alpha-defensin multigene family in primates. Mol Biol Evol. 2010 27: 2333-2343
Das S, U Mohamedy, M Hirano, M Nei, N Nikolaidis. Analysis of immunoglobulin light chain genes in Zebra finch: Genomic and evolutionary implications. Molecular Biology and Evolution 2010 (1):113-120
Roca AL, Y Ishida, N Nikolaidis, SO Kolokotronis, S Fratpietro, K Stewardson , S Hensley, M Tisdale, G Boeskorov, AD Greenwood. Characterization of the mammalian hair length gene FGF5 in living elephants and the extinct woolly mammoth. BMC Evolutionary Biology 2009 9:232
van Rossum DB, Oberdick D, Rbaibi Y, Bhardwaj G, Barrow RK, Nikolaidis N, Snyder SH, Kiselyov K, Patterson RL.TRP_2, a lipid/trafficking domain that mediates diacylglycerol-induced vesicle fusion. Journal of Biological Chemistry 2008 283:34384-34392
Kerff F, R Herman, E Sauvage, S Petrella, P Filee, P Charlier, B Joris, A Amoroso, A Tabuchi, N Nikolaidis, DJ Cosgrove. Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a cell wall binding protein with expansin structure. Proceedings of the National Academy of Sciences USA 2008 105:16876-16881
Lai Z-C, X Wei, T Shimizu, E Ramos, M Rohrbaugh, N Nikolaidis, L-L Ho, and Y Li. Control of cell proliferation and apoptosis by mob as tumor suppressor, mats. Cell 2005 120:675-685