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Research Interests
My laboratory uses macromolecular crystallography and other structural biology
techniques in the study of biological processes. We have published approx. 100
research papers and coordinated several transnational research projects.
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Structural studies of DNA binding proteins, e.g. restriction endonucleases
(Pvu II), mammalian (DNMT1, DNMT3) and bacterial ( BseCI) DNA
methyltransferases and of RNA-binding proteins (Rop) have been performed.
Applications resulting from this work include the engineering of
"programmable" endonucleases and novel DNA specificities for gene therapy
and endonucleases which are controllable by light.
Gram negative bacteria deploy various secretion systems for exporting
proteins to eukaryotic hosts. We study the Type III secretion systems (T3SS)
which are directly related to pathogenicity and essential mediators of the
interactions between bacteria and eukaryotes . We have determined the first
crystal structure of a conserved core T3SS protein (HrcQ B ) and performed
the first characterization by SAXS of an intrinsically disordered, highly
interactive protein (HrpO). Numerous studies of TTSS protein complexes are
in progress.
We have made fundamental contributions to protein folding/stability with a
focus on helical bundle proteins and applications resulting in the development
of innovative, bio-inspired materials.
Other crystallographic projects target bacterial resistance to antibiotics,
deacetylases, etc.
Selected Publications
B. Schierling, A.-J. Noel, W. Wende, H.L. Tie, E. Kubareva, T. Oretskaya, M. Kokkinidis
and A. Pingoud (2010) Controlling the enzymatic activity of a restriction enzyme by light.
Proc. Natl. Acad. Sci. USA 107: 1361-1366.
A. Gazi , M. Bastaki, S.N. Charova, E.A. Gkougkoulia, E.A. Kapellios, N.J. Panopoulos and
M. Kokkinidis (2008) Evidence for a coiled-coil interaction mode of disordered proteins from
bacterial type III secretion systems. J. Biol. Chemistry 283: 34062 - 34068.
V.E. Fadouloglou, A.P. Tampakaki, N.M. Glykos, M.N. Bastaki, J.M. Hadden, S.E. Phillips,
N.J. Panopoulos and M. Kokkinidis (2004) Structure of HrcQ B -C, a conserved component
of the bacterial type III secretion systems. Proc. Natl. Acad. Sci. USA 101: 70-75.
Gogos, J., Jin Jingmin, Wan, H., Kokkinidis, M. and Kafatos, F.C. (1996) Recognition of
diverse Sequences by Class I Zinc Fingers: Asymmetries and indirect effects on specificity in
the interaction between CF2II and A+T-rich sequence elements.Proc. Natl. Acad. Sci. USA
93: 2159-2164.
Athanasiadis, A., Vlassi, M., Kotsifaki, D., Tucker, P., Wilson , K.S. and M. Kokkinidis
(1994) The crystal structure of Pvu II endonuclease reveals extensive structural homologies to
Eco RV. Nature, Struct. Biol. 1: 469-475.