Michael Kokkinidis

Our laboratory uses macromolecular crystallography and other structural biology and biocomputing techniques in the study of biological processes. We have published more than 110 research papers and coordinated several transnational and national research projects. Our research activities include:

• Structural studies of DNA binding proteins, e.g. restriction endonucleases (R. Pvu II), mammalian (DNMT1, DNMT3) and bacterial (Bse CI) 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 T3SS protein complexes are in progress. We also elucidated recently the link between T3SS protein expression and secretion, realized through protein complex formation and component migration.
• 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.
• Recently we discovered a new and highly atypical post translational modification in proteins which hydroxylates the Cα atom in proline or glycine residues. In polysaccharide deacetylases this modification enhances enzymatic activity by an order of magnitute. Its significance in other enzyme families is presently under investigation.