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Michael Kokkinidis

Michael Kokkinidis

IMBB Group Leader (Full Professor, Univ. of Crete)
Email address
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Phone
+30-2810-394351
Fax
+30-2810-391101
Lab web page

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.

  •  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 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.

Schierling B, Noël AJ, Wende W, Hien le T, Volkov E, Kubareva E, Oretskaya T, Kokkinidis M, Römpp A, Spengler B, Pingoud A. (2010) Controlling the enzymatic activity of a restriction enzyme by light. Proc. Natl. Acad. Sci. USA 107:1361-1366.

Gazi AD, Bastaki M, Charova SN, Gkougkoulia EA, Kapellios EA, Panopoulos NJ, Kokkinidis M. (2008) Evidence for a coiled-coil interaction mode of disordered proteins from bacterial type III secretion systems. J. Biol. Chemistry 283:34062 - 34068.

Fadouloglou VE, Tampakaki AP, Glykos NM, Bastaki MN, Hadden JM, Phillips SE, Panopoulos NJ, Kokkinidis M. (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 JA, Jin J, Wan H, Kokkinidis M, Kafatos FC. (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 PA, Wilson KS, Kokkinidis M. (1994) The crystal structure of Pvu II endonuclease reveals extensive structural homologies to Eco RV. Nature, Struct. Biol. 1:469-475.

LIST OF PUBLICATIONS

Kokkinidis, M., Roentgenstrukturuntersuchungen an nikotinischen and muskarinischen Agonisten des natuerlichen Neurotransmitters Acetylcholin zur Aufklaerung der Struktur- Wirkungsbeziehungen, PhD Thesis, TU Munich, Germany (1981)

RESEARCH PAPERS

Voelkl, J., Bauer, H.C., Freudenberg, U., Kokkinidis M., Land, G., Steinhauser, K.A., and Alefeld, G., Isotope and Structure Dependence of the Diffusion Coefficient of Hydrogen in Metals, Proceedings of the 6th Intern. Conference on Internal Friction and Ultrasonic Attenuation in Solids, Tokyo (1977), pp. 485-489

Gieren A., and Kokkinidis M., "Activity Triangles" in Crystal Structures of Cholinergic Agonists, Naturwissenschaften 68 , 482-483 (1981)

Gieren, A., and Kokkinidis, M., X-Ray Structure Analysis of Trimethyl(4-oxopentyl)ammonium-chloride, Z. Naturforsch. 37c , 282-288 (1982)

Gieren, A., and Kokkinidis, M., X-Ray Structure Analysis of (2-Ethoxyethyl)trimethylammonium Chloride, Z. Naturforsch. 37c , 977-984 (1982)

Neidlein, R., Tran-Viet, D., Gieren, A., Kokkinidis, M., Wilckens, R., Geserich, H.P., and Ruppel, W., Synthesen, Konstitutionsaufklaerung und elektrische Eigenschaften von Di- und Polychalkogendiimiden (Syntheses, Structures, X-ray Structure Analyses, and Electric Properties of Di- and Polychalkogen Diimides, Part 1), Chemische Berichte 115 , 2898-2904 (1982)

Anninos, P., and Kokkinidis, M. , Dynamics of Neural Nets Constructed of Cells with Chemical Affinity, Biophysical Journal 41 , 388a (1983)

Anninos, P., and Kokkinidis, M. , A Mathematical Model for Multiple Memory Domains, Neurosc. 196.16 , 645 (1983)

Neidlein, R., Droste-T.-Viet, D., Gieren, A., Kokkinidis, M. , Wilckens, R., Geserich, H.P., and Ruppel, W., Synthesen, chemische und elektrische Eigenschaften von Tetrathiafulvalen mit 1,6-Methano[10]annulen-Partialstruktur und von Chalcogendiimid-Derivaten, Helvetica Chimica Acta 67 , 574-582 (1984)

Anninos, P., and Kokkinidis, M. , The Behavior of Noisy Neural Nets, Biophysical Journal 45 , 175a (1984)

Anninos, P., and Kokkinidis, M. , A Neural Net Model for Multiple Memory Domains, J. Theor. Biol . 109 , 95-110 (1984)

Anninos, P., Kokkinidis, M. , and Skouras, A., Noisy Neural Nets Exhibiting Memory Domains, J. Theor. Biol. 109 , 581-594 (1984)

Kokkinidis, M. , and Anninos, P., A Neural Net Model for Epileptic Disturbances, Proceedings of the Intern. AMSE Conference “Modelling and Simulation”, Athens (1984), vol. 4.2 , pp. 1-15

Kokkinidis, M. , and Gieren A., Cholinergic Neurotransmitter - Receptor Interactions, Trends Pharm. Sci. , 369-370 (1984)

Kokkinidis, M. , and Anninos, P., Noisy Neural Nets Exhibiting Epileptic Features, J. Theor. Biol. 113 , 559-588 (1985)

Gieren, A., and Kokkinidis, M. , X-Ray Structure Analysis of Trimethylpentylammonium-chloride and (4-Acetoxybutyl) trimethylammonium-iodide, Z. Naturforsch. 41c , 618-626 (1986)

Gieren, A., and Kokkinidis, M. , Structure-Activity Correlations for cholinergic Stimulants Derived from Crystal Structures of their Halides, Z. Naturforsch. 41c , 627-640 (1986)

Gieren, A., and Kokkinidis, M. , X-Ray Structure Analysis of Trimethyl[2-(propionyloxy)ethyl]ammonium-iodide Z. Naturforsch. 41c , 641-646 (1986)

Kokkinidis, M. , Tsernoglou, D., and Brueckner, H., Crystal Structure of Z-Aib-Aib-Aib-Ala-Ala-Aib-OtBu, a Hexapeptide Fragment of Trichotoxin, Biochem. Biophys. Res. Commun. 136 , 870-875 (1986)

Anninos, P., Kokkinidis M. , Hoke, M., Pantev, Ch., Lehnertz, K., and Luetkenhoener, B., MEG Measurements with a SQUID to Determine Structure and Function of the Human Brain, Brain Research Bulletin 16 , 549-551 (1986)

Kokkinidis, M. , Banner, D.W., Tsernoglou, D., and Brueckner, H., Crystal Structure of L-Pro-L-Leu-Aib-Aib-L-Glu-L-Valol, the C-Terminal Hexapeptide Fragment of Trichotoxin, Biochem. Biophys. Res. Commun. 139 , 590-595 (1986)

Kokkinidis, M. , Tsernoglou, D., and Brueckner, H., Synthesis and X-Ray Analysis of Oligopeptides Containing á-Aminoisobutyric Acid (Aib), in: Peptides86 pp.319-322, (D. Theodoropoulos ed.), Walter de Gruyter , Berlin-New York (1987)

Kokkinidis, M. , Cesareni, G., Helmer Citterich, M., Castagnoli, L., Scarpa, M., Tsernoglou, D., and Banner, D.W., A Data Base for Protein Design: the Structures of ROP and its Mutants, Prot. Engineering 1 , 244 (1987)

Banner, D.W., Kokkinidis, M. , and Tsernoglou, D., The Structure of the ColEl Rop Protein at 1.7 Angstroem resolution, J. Mol. Biol. 196 , 657-675 (1987)

Castagnoli, L., Scarpa, M., Kokkinidis, M. , Banner, D.W., Tsernoglou, D., and Cesareni, G., Genetic and Structural Analysis of the ColEl Rom (Rop) Protein, EMBO J. 8 , 621-629 (1989)

Kokkinidis M. and Vlassi, M., Analysis of Sequence/Structure Relationships in 4 - a -Helix Bundles, Acta Cryst. A46 , C-97-98 (1990)

Kokkinidis M. , Gessmann R., Vlassi M. and Brueckner, H., Structures of Model Peptides containing á-Aminoisobutyric acid (Aib), Acta Cryst. A46 , C-140 (1990)

Bereziat, G., Etienne, J., Kokkinidis, M. , Olivier, J.L. and Parnas, P., New trends in mammalian non-pancreatic phospholipase A 2 research, Journal of Lipid Mediators 2 , 159-172 (1990)

Athanasiadis, A., Gregoriu, M., Thanos, D., Kokkinidis, M. and Papamatheakis, J., Complete nucleotide sequence of the Pvu II restriction enzyme gene from Proteus vulgaris , Nucl. Acid Res. 18 , 6434 (1990)

Gessmann, R., Brueckner, H. and Kokkinidis, M. , Structural Flexibility of Aib-containing Peptides: The N-terminal Tripeptide of Trichotoxin, Biochem. Biophys. Res. Commun. 174 , 878-884 (1991)

Gessmann, R., Brueckner, H. and Kokkinidis, M. , The crystal structure of Z-Aib-Gly-Aib-Leu-Aib-OtBu, the synthetic, protected N-terminal pentapeptide of trichotoxin, Peptide Research 4 , 239-244 (1991)

Paliakasis, C.D. and Kokkinidis, M. , The stability of 4-alpha-helix bundles, Prot. Engineering 4 , 849-850 (1991)

Athanasiadis, A. and Kokkinidis, M. , Purification, crystallization and preliminary X-ray diffraction studies of the Pvu II endonuclease, J. Mol. Biol. 222 , 451-453 (1991)

Vlassi, M., Brueckner, H. and Kokkinidis, M. , Peptides with built-in conformational constraints: The crystal structure of Z-(Aib) 6 -OtBu t (Z. Kristall. 202 , 89-98 (1992)

Vlassi, M., Brueckner, H. and Kokkinidis, M., Peptides with built-in conformational constraints: The crystal structure of Z-(Aib) 7 -OtBu t (Acta Cryst. B49 , 560-564 (1993)

Paliakasis, C.D. and Kokkinidis, M., Relationships between sequence and structure for the four- a -helix bundle tertiary motif in proteins ( Prot. Engineering 5 , 739-749 (1992)

Gessmann, R., Vlassi, M., Brueckner, H. and Kokkinidis, M. , Folding and intermolecular interactions of Aib-containing peptides ( in “Peptides 1992”, pp. 491-492, C.H. Schneider and A.N. Eberle, Eds., Escom Science, Leiden, The Netherlands (1993))

Kokkinidis, M., Vlassi, Papanikolaou, Y., Kotsifaki, D., M., Kingswell, A., Tsernoglou, D. and Hinz, H.-J., Correlation between protein stability and crystal properties of designed ROP variants ( PROTEINS 16, 214-217 (1993))

Steif , Ch. , Weber, P., Hinz, H.-J., Flossdorf, J., Cesareni, G. and Kokkinidis, M. , Subunit interactions provide a significant contribution to the stability of the dimeric four-á-helical bundle protein ROP ( Biochemistry 32 , 3867-3876 (1993))

Fotinou, C., Kokkinidis, M ., Fritzsch, G, Haase, W., Michel, H. and Ghanotakis, D.F., Characterization of a Photosystem II core and its three-dimensional crystals . (Photosynthesis Research 37, 41-48 (1993))

Gessman, H. Brueckner and M. Kokkinidis, The crystal structures of two Aib-containing tripeptides ( Amino Acids 5 , 108 (1993))

Gessmann, R., Brueckner, H. and Kokkinidis, M. , The crystal structure of Z-Leu-Aib-Pro-Leuol, the synthetic, protected C-terminal tetrapeptide of trichovirin ( Z. Kristallographie 209, 587-603 (1994))

Athanasiadis, A., Vlassi, M., Kotsifaki, D., Tucker, P., Wilson, K.S. and M. Kokkinidis , The crystal structure of Pvu II endonuclease reveals extensive structural homologies to Eco RV. ( Nature, Struct. Biol. 1 , 469-475 (1994))

Vlassi, M., Ch. Steif, P. Weber, Tsernoglou, D., Wilson, K.S., H.-J. Hinz and Kokkinidis, M. , Restored heptad pattern continuity does not alter the folding of a 4- a -helix bundle ( Nature, Struct. Biol. 1 , 706-714 (1994))

Gogos, J., Jin Jingmin, Wan, H., Kokkinidis, M. and Kafatos, F.C., 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 (1996)

Paliakasis, K., Routsias, J., Petratos, K., Ouzounis, Ch., Kokkinidis, M. and Papadopoulos, G., Novel structural features of the Human Histocompatibility Molecules HLA-DQ as revealed by modeling based on the published structure of the related molecule HLA-DR, J. Struct. Biol. 117 , 145-163 (1996)

Athanasiadis, A., Papanikolaou, Y., Rina, M., Z. Dauter, K. Petratos, Bouriotis, V. and Kokkinidis, M. , Purification , crystallization and preliminary X-ray analysis of the M. Bse CI methyltransferase from Bacillus stearothermophilus ( Acta Cryst. D53 , 477-479 (1997))

Y. Papanikolau and M. Kokkinidis , The solubility, chromatographic properties and crystallization of macromolecules strongly depend on substances that reduce the ionic strength of the solution, Prot. Engineering 10 , 847-850 (1997).

R. Gessmann, M. Currle, H. Brueckner and M. Kokkinidis , Unusual conformations adopted by standard amino acids in Aib containing oligopeptides, Z. Kristall. 212 , 819-825 (1997)

M. Rina, F. Caufrier, M. Markaki, K. Mavromatis, M. Kokkinidis and V. Bouriotis, Cloning and characterization of the gene encoding PspPI methyltransferase from the Antarctic psychrotroph Psychrobacter sp. strain TA137. Predicted interactions with DNA and organization of the variable region, Gene 197 , 353-360 (1997)

M.W. Lassalle, H-J. Hinz, H. Wenzel, M. Vlassi, M. Kokkinidis and G. Cesareni, Dimer-to-Tetramer Transformation: Loop Excision Dramatically alters Structure and Stability of the ROP Four a - Helix Bundle Protein, J. Mol. Biol. 279 , 987-1000 (1998)

R. Gessmann, H. Brueckner and M. Kokkinidis , The Crystal Structure of Z-(Aib) 9 - Ot Bu , Acta Cryst. B54, 300-307 (1998)

M. Vlassi, K.S. Wilson and M. Kokkinidis , Structural Parameters for Proteins Derived from the Atomic-Resolution (1.09 Angstroem) Structure of a Designed Variant of the ColE1 ROP Protein, Acta Cryst. D54, 1245-1260 (1998)

R. Gessmann, P. Benos, H. Brueckner and M. Kokkinidis , The Crystal Structures of the Synthetic C-terminal Octo- and Dodecapeptides of Trichovirin, J. Pept. Sci. 5 , 83-95 (1999)

M. Vlassi, G. Cesareni and M. Kokkinidis , A correlation between the loss of hydrophobic core packing interactions and protein stability, J. Mol. Biol. 285, 817-827 (1999)

Glykos, N.M., Cesareni, G. and Kokkinidis, M ., Protein plasticity to the extreme: Changing the topology of a 4- a -helix bundle with a single amino-acid substitution. Structure7 , 597-603 (1999)

Glykos, N.M. and Kokkinidis, M ., Meaningful refinement of polyalanine models using rigid-body simulated annealing: application to the structure determination of the A31P Rop mutant, Acta Cryst. D55, 1301-1308 (1999)

N.M. Glykos and M. Kokkinidis , A Stochastic Approach to Molecular Replacement, Acta Cryst. D56, 169-174 (2000)

A.E. Andreeva, B.E. Borissova, R. Mironova, N.M. Glykos, D. Kotsifaki, I. Ivanov, M. Krysteva and M. Kokkinidis , Crystallization of type I chloramphenicol acetyltransferase: An approach based on the concept of ionic strength reducers, Acta Cryst. D56 , 101-103 (2000)

M.D.Rina, Ch. Pozidis, K. Mavromatis, M. Tzanodaskalaki, M. Kokkinidis and V. Bouriotis: An Alkaline Phosphatase from the Antarctic Strain TAB5: Enzymatic Properties and Psychrophilic Adaptations, Eur. J. Biochem ., 267, 1230-1238 (2000)

Y. Papanikolau, R. Gessmann, K. Petratos, K. Igarashi and M. Kokkinidis : Crystallization of the E.coli polyamine-induced protein: a novel procedure based on the concept of ionic strength reducers ( J. Crystal Growth 210, 761-766 (2000)

N.M. Glykos and M. Kokkinidis , GraphEnt : a maximum entropy program with graphics capabilities J. Appl. Cryst . 33, 982-985 (2000)

A. Spyridaki, N.M. Glykos, D. Kotsifaki, V. Fadouloglou and M. Kokkinidis , Crystallization and diffraction to ultrahigh resolution (0.8 Angstroem) of a designed variant of the Rop protein ( Acta Cryst. D 56, 1015-1016 (2000)

N.M. Glykos and M. Kokkinidis , On the distribution of the bulk solvent correction parameters, Acta Cryst. D56, 1070-1072 (2000)

F. Fountoulaki, R. Gessmann, H. Bruckner and M. Kokkinidis , The Crystal Structure of the Peptide Z-Pro-Leuol, Acta Cryst. C56, E578-e579 (2000)

V. Fadouloglou, N. Gl7ykos and M. Kokkinidis , A fast and inexpensive procedure for drying polyacrylamide gels, Anal. Biochem. 287, 185-186 (2000)

N.M. Glykos and M. Kokkinidis , Practical maximum entropy (in: Methods in Macromolecular Crystallography (2001), D. Turk & L. Johnson eds., Series I, Vol. 325, pp.136-141, IOS Press, Amsterdam)

V. Fadoulogou, N.M. Glykos and M. Kokkinidis , Side-chain conformations in 4-alpha-helical bundles, Prot. Engng. 14, 321-328 (2001)

R. Gessmann, H. Bruckner and M. Kokkinidis , The Crystal Structure of the Tripeptide Z-Aib-Aib-L-Hyp-Ome Acta Cryst. E57, 1-3 (2001)

N. M. Glykos and M. Kokkinidis , Multidimensional Molecular Replacement (Acta Cryst. D57, 1462-1473 (2001)

V.E. Fadouloglou, A.P. Tampakaki, N.J. Panopoulos and M. Kokkinidis , Structural studies of the Hrp secretion system: expression, purification, crystallization and preliminary X-ray analysis of the C-terminal domain of the HrcQ B protein from Pseudomonas syringae pv. Phaseolicola , Acta Cryst. D57, 1689-1691 9 (2001)

I. Tsigos, K. Mavromatis, M. Tzanodaskalaki, Ch. Pozidis, M. Kokkinidis and V. Bouriotis, Engineering the properties of a cold active enzyme through rational redesign of the active site, Eur. J. Biochem. 208, 1-8 (2001)

? . Mavromatis, I. Tsigos, M. Tzanodaskalaki, M. Kokkinidis and V. Bouriotis, Exploring the role of a glycine cluster in cold adaptation of an alkaline phosphatase, Eur. J. Biochem. 269, 1230-1238 (2002)

N.M.Glykos and M. Kokkinidis , Structure determination of a small protein through a 23-dimensional molecular-replacement search, Acta. Cryst. D59, 709-718 (2003)

Mavromatis, K., Feller, G., Kokkinidis, M . and Bouriotis, V., Cold adaptation of a psychrophilic chitinase: a mutagenesis study, Prot. Engng. 16 , 497-503 (2003)

A. Spyridaki, C. Matzen, Th. Lanio, A. Jeltsch, A. Simoncsits, A. Athanasiadis, E. Scheuring-Vanamee, M. Kokkinidis and A. Pingoud, Structural and biochemical characterization of a new Mg 2+ binding site near Tyr94 in the restriction endonuclease Pvu II, J. Mol. Biol. 331, 395-406 (2003)

V.E. Fadouloglou, A.P. Tampakaki, N.M. Glykos, M.N. Bastaki, J.M. Hadden, S.E. Phillips, N.J. Panopoulos and M. Kokkinidis , Structure of HrcQ B -C, a conserved component of the bacterial type III secretion systems, Proc. Natl. Acad. Sci. USA 101 , 70-75 (2004)

N.M. Glykos and M. Kokkinidis, Molecular replacement with multiple different models, J. Appl. Cryst. 37, 159-161 (2004)

N.M. Glykos and M. Kokkinidis , Structural polymorphism of a marginally stable 4- a -helix bundle. Images of a molten globule? (Proteins: Structure, Function and Bioinformatics 56, 420-425 (2004)

Y. Papanikolau, D. Kotsifaki, V.E. Fadouloglou, A.D.Gazi, N.M. Glykos, G.Cesareni and  M.Kokkinidis , Ionic strength reducers: an efficient approach to protein purification and crystallization. Application to two Rop variants (Acta Cryst. D 60. 1334-1337 (2004)

A. P. Tampakaki, V.E. Fadouloglou , A.D. Gazi, N. J. Panopoulos and M. Kokkinidis , Conserved Features of Type III Secretion ( Cellular Microbiology 6, 805-816 (2004 ))

V . E . Fadouloglou , D. Kotsifaki , A. Gazi , G. Fellas , C. Meramveliotaki , A. Deli , E. Psylinakis , V. Bouriotis and M. Kokkinidis , Purification , crystallization and preliminary characterization of a putative , LmbE - like deacetylase from Bacillus cereus , ?cta Cryst. F62, 261-264 (2006)

N.M. Glykos, Y. Papanikolau, M. Vlassi, D. Kotsifaki, G. Cesareni and M. Kokkinidis , Loopless Rop: structure and dynamics of an engineered homotetrameric variant of the Repressor of Primer protein, Biochemistry 45 , 10905-10919 (2006)

E. Kapetaniou, D. Kotsifaki, M. Providaki, M. Rina, V. Bouriotis and M. Kokkinidis, Purification, crystallization and preliminary X-ray analysis of the BseCI DNA methyltransferase from Bacillus stearothermophilus in complex with its cognate DNA, Acta Cryst. F 63, 12-14 (2007)

V.E. Fadouloglou, A. Deli, N.M, Glykos, E. Psylinakis, V. Bouriotis and M. Kokkinidis , Crystal structure of the Bc ZBP, a zinc-binding protein from Bacillus cereus : Functional insights from structural data, FEBS Journal 274 , 3044-3054 (2007)

Ch. Meramveliotaki , D. Kotsifaki, M. Androulaki, A. Hountas, E. Eliopoulos and M. Kokkinidis, Purification, crystallization, X-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease, Acta Cryst. F 63, 836-838 (2007)

M. Ambrazi, G. Fellas, E.G. Kapetaniou, D. Kotsifaki, M. Providaki, and M. Kokkinidis , Purification, crystallization, X-ray diffraction analysis and phasing of a loop variant of the ColE1 Rop protein, Acta Cryst. F 64, 432-434 (2008)

V . E. Fadouloglou, M . Kokkinidis and N . M. Glykos , Determination of the protein oligomerization state: two approaches based on glutaraldehyde cross-linking , Anal. Biochem. 373, 404-406 (2008)

 A. Tsalafoutas, E. G. Kapetaniou, D. Kotsifaki, A. Deli, E. Psylinakis, V. Bouriotis and M. Kokkinidis , Purification, crystallization and preliminary X-ray analysis of the GlcNAc deacetylase PDA4 from Bacillus Cereus in complex with (GlcNAc) 6 ?cta Cryst. F64, 203-205 (2008)

A. Gazi , M. Bastaki, S.N. Charova, E.A. Gkougkoulia, E.A. Kapellios, N.J. Panopoulos and M. Kokkinidis , Evidence for a coiled-coil interaction mode of disordered proteins from bacterial type III secretion systems, J. Biol. Chemistry , 283: 34062 – 34068 (2008)

A . Gazi , S . N . Charova , N . J . Panopoulos and M . Kokkinidis , (2009) Coiled - Coils in Type III Secretion Systems : Structural Flexibility , Disorder and Biological Implications . Cell . Microbiol . 11 : 719–729

V . E . Fadouloglou , M . N . Bastaki , A . E . Ashcroft , S . E . V . Phillips , N . J . Panopoulos , N . M . Glykos and M . Kokkinidis , (2009) On the quaternary association of the type III secretion system HrcQ B - C protein : Experimental evidence differentiates among the various oligomerization models , J . Structural Biol . 166 :214-225.

T . M . Geel , G . Meiss , B . T . F . van der Gun , B . J . Kroesen , L . F . M . H . de Leij , V . Siksnys , A . Š ilanskas , M . Kokkinidis , A . Pingoud , M . H . J . Ruiters and P . M . J . McLaughlin , Endonucleases as tool to induce apoptosis in TRAIL - insensitive ovarian carcinoma cell Exp . Cell Res . 315, 2487-2495 ( 2009 )

N . M . Glykos , Stavrakoudis , A ., Bouriotis , V . and Kokkinidis , M ., Molecular dynamics simulations of BcZBP , a deacetylase from Bacillus cereus : Active site loops determine substrate accessibility and specificity , J . Chem . Theory Comput . 5, 3299-3311 (2009)

B. Schierling, A.-J. Noël, W. Wende, H.L. Tie, E. Kubareva, T. Oretskaya, M. Kokkinidis and A. Pingoud, Controlling the enzymatic activity of a restriction enzyme by light, Proc. Natl. Acad. Sci. USA 107:1361-1366 (2010).

A.D. Gazi, V.E. Fadouloglou, S.N. Charova, N. Mathioudakis, P. Sarris, N.J. Panopoulos and Michael Kokkinidis , Pseudomonas syringae pv phaseolicola 1448A: Bioinformatics analysis of a second Type III Secretion System and evolutionary implications. (submitted)

A. Roidis and M. Kokkinidis , Crystal structure of Chloramphenicol acetyltransferase I in the apoenzyme form and in complex with fusidic acid: new insights into steroid recognition by enzymes (submitted)

A.P. Tampakaki, N.Skandalis, A.D. Gazi, M.N. Bastaki, P.F. Sarris, S.N. Charova, M. Kokkinidis, and N.J. Panopoulos, Playing the “Harp”: Evolution of Our Understanding of hrp/hrc Genes , Ann. Rev. Phytopath. 48 , 347-370 (2010)

Deli A, Koutsioulis D, Fadouloglou VE, Spiliotopoulou P, Balomenou S, Arnaouteli S, Tzanodaskalaki M, Mavromatis K, Kokkinidis M, Bouriotis V, LmbE proteins from Bacillus cereus are de-N-acetylases with broad substrate specificity and are highly similar to proteins in Bacillus anthracis, FEBS JOURNAL, 277(13): 2740-2753 (2010)

Sarris PF, Skandalis N, Kokkinidis M, Panopoulos NJ, In silico analysis reveals multiple putative type VI secretion systems and effector proteins in Pseudomonas syringae pathovars, MOLECULAR PLANT PATHOLOGY, 11(6): 795-804 (2010)

Kokkinidis, M; Glykos, NM; Fadouloglou, VE, PROTEIN FLEXIBILITY AND ENZYMATIC CATALYSIS, STRUCTURAL AND MECHANISTIC ENZYMOLOGY: BRINGING TOGETHER EXPERIMENTS AND COMPUTING, Book Series: Advances in Protein Chemistry and Structural Biology, Volume: 87  Pages: 181-218 (2012)

Dikić J, Menges C, Clarke S, Kokkinidis M, Pingoud A, Wende W, Desbiolles P. The rotation-coupled sliding of EcoRV. Nucleic Acids Research. 40(9):4064-4070 (2012)

Kefala K, Kotsifaki D, Providaki M, Kapetaniou EG, Rahme L, Kokkinidis M. Purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal fragment of the MvfR protein from Pseudomonas aeruginosa. ACTA Crystallographica Section F-Structural Biology And Crystallization Communications. 68(Pt 6):695-697 (2012)

Gazi AD, Sarris PF, Fadouloglou VE, Charova SN, Mathioudakis N, Panopoulos NJ, Kokkinidis M. Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains. BMC Microbiology. 2;12:188 (2012)

Fadouloglou VE, Kapanidou M, Agiomirgianaki A, Arnaouteli S, Bouriotis V, Glykos NM, Kokkinidis M., Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus. Acta Crystallographica Section D-Biological Crystallography, 69(Pt 2):276-283 (2013)

Barrier E, Braz Fernandes FM, Bujan M, Feiters MC, Froideval A, Ghijsen J, Hase T, Hough MA, Jergel M, Jimenez I, Kajander T, Kikas A, Kokkinidis M, Kover L, Larsen HB, Lawson DM, Lawniczak-Jablonska K, Mariani C, Mikulik P, Monnier J, Morera S, McGuinness C, Müller-Buschbaum P, Meedom Nielson M, Pietsch U, Tromp M, Simon M, Stangl J, Zanotti G, The benefit of the European User Community from transnational access to national radiation facilities., JOURNAL OF SYNCHROTRON RADIATION, 21: 638-639  Part: 3 (2014)

Amprazi, M; Kotsifaki, D; Providaki, M; Kapetaniou, EG; Fellas, G; Kyriazidis, I; Perez, J; Kokkinidis, M, Structural plasticity of 4-alpha-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(30): 11049-11054 (2014)

Gazi AD, Charova S, Aivaliotis M, Panopoulos NJ, Kokkinidis M. HrpG and HrpV proteins from the Type III secretion system of Erwinia amylovora form a stable heterodimer, Fems Microbiology Letters, ;362(1):1-8 (2015) 

Kefala A, Kotsifaki D, Providaki M, Amprazi M, Kokkinidis M. Expression, purification and crystallization of a protein resulting from the inversion of the amino-acid sequence of a helical bundle, Acta Crystallogr F Struct Biol Commun. ;73(Pt 1):51-53 (2017)

Fadouloglou VE, Balomenou S, Aivaliotis M, Kotsifaki D, Arnaouteli S, Tomatsidou A, Efstathiou G, Kountourakis N, Miliara S, Griniezaki M, Tsalafouta A, Pergantis SA, Boneca IG, Glykos NM, Bouriotis V, Kokkinidis M. Unusual α-Carbon Hydroxylation of Proline Promotes Active-Site Maturation, J Am Chem Soc.;139(15):5330-5337 (2017)

CONFERENCE ABSTRACTS/PROCEEDINGS

 Gieren, A., and Kokkinidis, M ., Struktur and Aktivitaet Zweier Nikotinischer Agonisten des Neurotransmitters Acetylcholin, Abstracts of the 18th Hauptversammlung der Gesellschaft Deutscher Chemiker, Berlin, Germany, p. 148 (1979)

Gieren, A., and Kokkinidis, M. , Struktur- Wirkungsbeziehungen beim natuerlichen Neurotransmitter Acetylcholin und seinen Agonisten, Referate der Chemiedozententagung Tuebingen, Germany, p. 12A (1981)

Gieren, A., and Kokkinidis, M., Structure and Function of the Natural Neurotransmitter Acetylcholine and its Agonists, Abstracts of the Seventh European Crystallographic Meeting, Jerusalem, Israel, p. 146 (1982)

Anninos, P., and Kokkinidis, M., Neuronal Systems with Multiple Memory Domains, Abstracts of the III. Intern. Soc. of Greek Neurosc. Symp., p. 1 (1984)

Anninos, P., Kokkinidis, M., and Thomas, G., Higher Order Difference Equation in Neural Nets with Chemical Markers, Abstracts of the 14th Ann. Meeting Soc. for Neuroscience 37.16, p. 130 (1984)

Kokkinidis, M. , X-Ray Diffraction Studies of the ColEl ROP Protein, Abstracts of the CEC Meeting, Rijswijk, Holland, p. 27m (1984)

Kokkinidis, M., Banner, D.W., and Tsernoglou, D., X-Ray Structure Analysis of the ROP Protein, Abstracts of the CEC/BEP Meeting Cambridge, U.K., p. 50 (1986)

Kokkinidis, M., The Structure of the ColEl Rop Protein and of one of its Mutants, Abstracts of the 1987 BAP Meeting on Enzyme Engineering, Capri, Italy (1987)

Kokkinidis, M ., Cesareni, G., Tsernoglou, D. and Banner, D.W., The ROP Protein and its Mutants: Structure/Sequence Relationships, Abstracts of the 9th Annual Conference of the Greek Society of Biological Sciences, p.158 (1987)

Kokkinidis, M., Tsernoglou, D. and Cesareni, G., Structural/genetic analysis of the 4-á-helix motif, Abstracts of the 10th Annual Conference of the Greek Society of Biological Sciences, p. 93 (1988)

K.P. Kuehn, R. Schwarzwald, K.O. Greulich, Ludwig, H., D.W. Banner, G. Cesareni, A. Kingswell, M. Kokkinidis , Abstracts of the 1 st Intern. Symposium of Laser Photobiology, Univ. Luebeck, Germany, Sept. 30 th -Oct. 1 st (1988)

K.P. Kuehn, D.W. Banner, G. Cesareni, A. Kingswell, M. Kokkinidis , R. Schwarzwald, K.O. Greulich & H. Ludwig, Fluorescence measurements on the rop-protein and some mutants: the orientation of arginine for quenching tyrosine fluorescence & the position of the non-crystallizing part in solution, Abstracts of the Intern. Symposium on thermodynamics applied to biological systems, St. Margherita Ligure, Italy, 11-17 Sept. (1988)

Kokkinidis, M., Genetic and Structural Analysis of the 4-alpha-helix motif in Proteins, Abstracts of the ICGEB European Affiliated Centres Colloquium, Trieste, Italy, p. 3 (1989)

Kokkinidis, M., ROP: a model system for the analysis of the 4-alpha-helix bundle motif in proteins, BAP meeting on “Metalloproteins: Biocatalysis, protein folding and stability”, Heraklion, Crete, Greece 16-18 April 1989

Kavounis, K.A., Kokkinidis, M. and Tsernoglou, D., X-ray Structure of a Mutant of the ROP Protein, Abstracts of the 11th annual Conference of the Greek Society of Biological Sciences (1989)

Weber, P., Hinz HJ, Cesareni, G., Kokkinidis, M . Mutations And Protein Stability - Thermodynamic a nd Structural Studies ? n Rop Protein , Biological Chemistry (formerly Biological Chemistry Hoppe-Seyler) 370, 971 (1989)

Kokkinidis, M. and Paliakasis, C.D., Four-alpha-helix Bundle Proteins: Structures and Sequences, Abstracts of the CAPE Symposium “Prediction and Experiment: Three-dimensional Structures of Homologous Proteins”, GBF, Braunschweig, Germany, p.61 (1991)

Gessmann, R., Vlassi, M., Brueckner, H. and Kokkinidis, M., Folding and intermolecular interactions of Aib-containing peptides, Abstracts of the European Peptide Symposium, EPS22, Interlaken , Switzerland, P166 (1992)

M. Kokkinidis , M. Vlassi and C. Paliakasis, Structural changes in ROP resulting from point mutations: Relationships between sequence and structure/stability in 4- a -helical bundles, EC Workshop on Protein Folding, stability and design, Heraklion/Crete (Greece) 30. March-1.April 1993

Miller, W., M. N. Mindrinos, L. G. Rahme, R. D. Frederick, C. Grimm, R. Gressman, X. Kyriakides, M. Kokkinidis , and N. J. Panopoulos. Pseudomonas syringae pv. phaseolicola-plant interactions: host-pathogen signalling through cascade control of hrp gene expression. p. 267-274. In Proc. 6th Internat. Sympos. on Molecular Plan t- Microbe Interactions. Klewer Academic Publishers, Dordrecht , The Netherlands (1993).

Paliakasis, C.D. and Kokkinidis, M ., Relationships between sequence and structure for the four- a -helix bundle tertiary motif in proteins, pp. 33-42, Proceedings of the China-EC Workshop on Protein Engineering, Beijing (China) 22-27 August, 1994

M. Kokkinidis , Rop, a small RNA-binding protein, Proceedings of the BIOMEDI meeting on the Structure-Function and Dynamics of HIV Regulatory Proteins, Bayreuth (Germany), 30. April-4.May, 1994

M. Kokkinidis , Structure-function relationships of Type II Restriction Endonucleases deduced from the crystal structure of PvuII, Proceedings of the 4 th European Workshop on the Crystallography of Biological Macromolecules, pp. O22-O23 Como (Italy) May 21-25, 1995

M. Kokkinidis and A. Athanasiadis, Restriction Endonucleases: Sequence-Structure-Function Relationships, EMBO Workshop: Nucleotidyl and Phosphoryl Transfer in the Protein and RNA World, 29. September-3. October 1996, Xanten, Germany

E. Scheuring Vanamee, D. Kotsifaki, N.M. Glykos and M. Kokkinidis , Metal binding sites in R. Pvu II. E258, Abstρacts of the 1997 Annual Meeting of the Αmerican Crystallographic Association, St. Louis, Missouri, July 19-25, 1997 

M. Vlassi and M. Kokkinidis , Structural parameters for proteins derived from the atomic resolution (1.09 Å) structure of designed variants of the ColE1 ROP protein. Abstracts of the 18 th European Crystallographic Meeting, Aug. 15-20, 1998, Praha, Praha, Czech Republic. D4-P5, Bull. of the Czech & Slovak Association, vol 5, special issue B 

M. Kokkinidis , G. Cesareni, H.J. Hinz, Y. Papanikolau and M. Vlassi, A five-residue deletion alters completely the folding and increases drastically the stability of ROP . Abstracts of the 18 th European Crystallographic Meeting, Aug. 15-20, 1998, Praha, Czech Republic. D4-P13, Bull. of the Czech & Slovak Association, vol 5, special issue B 

M. Kokkinidis , Recurrent tertiary motifs in proteins: Basic principles of their folding and stability, Abstracts of the TEMPUS workshop, Lesidren, Bulgaria, May 17-20, 1999.

A.Roidis and M. Kokkinidis , Type II restriction endonucleases: Structure, function and engineering of novel properties. Abstracts of the International Union of Crystallography XVII Congress, Aug. 4-13, 1999 Glasgow, Scotland. P07.04.035, Acta Cryst. A55 Supplement p. 306 (also available at http://www.iucr.org/iucr-top/cong/18/poster/posters.html )

M. Vlassi, G. Cesareni and M. Kokkinidis , The loss of hydrophobic core packing interactions is strongly correlated to the loss of protein stability. Abstracts of the International Union of Crystallography XVII Congress, Aug. 4-13, 1999 Glasgow, Scotland. P08.04.002, Acta Cryst. A55 Supplement p. 314 (also available at http://www.iucr.org/iucr top/cong/18/poster/posters.html )

K. Mavromatis, T. Lonhienne, C. Gerday, M. Kokkinidis and V. Bouriotis , Cold adapted chitinases from the Antarctic bacterium Arthrobacter str. TAD 20. , Proceedings of the 3 rd International Meeting on Chitin Enzymology, Senigalia, Italy pp 249-256 (2001)

I. Tsigos; K. Mavromatis; M. Tzanodaskalaki; C. Pozidis; M. Kokkinidis and V. Bouriotis, Engineering the properties of a cold active enzyme through rational redesign of the active site. 27 th FEBS meeting”, Lisbon, Portugal (2001)

Glykos , N.M. , & Kokkinidis, M. (2001), ``GraphEnt : A maximum entropy program with graphics capabilities'', in Methods in Macromolecular Crystallography, Turk, D. and Johnson, L. (eds.), Vol. 325, pp. 136-141.

Glykos, N.M., & Kokkinidis, M.   (2001), ``Multidimensional Molecular Replacement'', Abstracts of the 20th European Crystallographic Meeting, Krakow, Poland, August 25th-31st.

 Fadouloglou , V . E ., Tampakaki A ., Panopoulos , N & Kokkinidis , M ., “ Structural studies of the Hrp secretion system : expression , purification , crystallization and MAD data collection of the C - terminal domain of the HrcQ B protein from the Pseudomonas syringae pv . phaseolicola ”, Proceedings of the 1 st meeting of the Greek Crystallographic Association, 17-18 ?ai, 2002.

M. Kokkinidis , Development of highly specific enzymes for genome modification, Proceedings of the 1 st International Conference on Clinical Gene Therapy, p.27 Groningen, The Netherlands, 24-26 Jamuary 2002

 Fadouloglou , V . E ., Glykos , N . M . , Panopoulos , N & Kokkinidis , M ., “ Crystal structure of the HrcQ B - C protein from Pseudomonas syringae Hrp secretion system ”, proceedings of the meeting Finding the way out: protein traffic in bacteria , A.P.Pugsley and V. de Lorenzo eds, 20-22 October, 2003, p 57.

Glykos, N.M., & Kokkinidis, M.  (2004), ``Unfolding the complexities of protein folding'', 4th Hellenic Forum on Bioactive Peptides, April 22--24, 2004, University of Patras

A. Gazi … and M. Kokkinidis , in “Evolving Methods of Macromolecular Crystallography”, International School of Crystallography - 37th Course, Erice, Sicily, Italy May 13 – 22, 2005

C. Meramveliotaki, E. Eliopoulos and M. Kokkinidis , Structure Determination of scPvuII by crystallographic and SAXS methods, Conference proceedings Acta Cryst. A.61, C226 (2005), XX Congress of the International Union of Crystallography, Florence, Italy, 23-31 August (2005)

 Fadouloglou , V . E ., Glykos , N . M . & Kokkinidis , M ., “ HrcQ B -C and FliN-C proteins: A conserved component of type III secretion system and the bacterial flagellum. A comparative analysis of crystallographic and molecular dynamic simulations' data”, Proceedings of the International School of Crystallography “Evolving methods for macromolecular crystallography”, Sir Tom Blundell, Randy Read, Joel Sussman, eds., 12-22 May, 2005, pp 194.

V.E. Fadouloglou, N.M. Glykos and M. Kokkinidis , Self-association of a conserved component of the Type III secretion system: A molecular dynamics study of the HrcQb and FliN protein. p. 46, Proceedings of the ASM conference “Protein Traffic in Prokaryotes”, May 6-10, Iraklion, Crete, Greece (2006)

M. Kokkinidis , N.M. Glykos, Ch. Meramveliotaki, M. Androulaki, E. Kapetaniou, D. Kotsifaki and M. Providaki, Structural studies of nucleic acid-binding proteins, Meeting of the Asia-Link programme, Sept. 15-20, 2006, Bangalore, India

Gazi, A. D., Charova, S. N., Panopoulos N.J. , Kokkinidis , M., HrpG protein from the Hrp1 family of type III secretion injectisomes participates in substrate export regulation, FEBS J. 275, 202 (2008).       

OTHER PUBLICATIONS, EDITING OF CONFERENCE PROCEEDINGS

Biotechnology Action Programme of the Commission of the European Communities, Progress Report 1988, pp. 571-576

Biotechnology Action Programme of the Commission of the European Communities, Progress Report and Final Meeting of Contractors 1989, pp. 137-141

Biotechnology R&D in the EC, A. Vassarotti and E. Magnien eds. ELSEVIER 1990, pp. 150-156

Metalloproteins: Biocatalysis, Protein Folding and Stability (workshop in the framework of the EU BAP programme). Heraklion, Crete 16-18/4/1989 (Book of Abstracts)

Practical Course: Protein Design 90. Heraklion, Crete, 23. Sep-7. Oct 1990 (Book of Abstracts)

Practical Course: Protein Design 91 Heraklion, Crete, 1. Sep.-15. Sep. 1991 (Book of Abstracts)

Workshop on Protein Folding, Stability & Design, 30. March-1. April 1993, Heraklion, Crete, Greece (Book of Abstracts)

European Science Foundation (?SF) Course on Macromolecular Crystallography, 28. November-3. December 1994, Heraklion, Crete, Greece (Course Manual)

Computer Applications in Structural Biology and Sequence Analysis, ICSU/COBIOTECH Practical Course, 2-6 September 1996, Heraklion, Crete, Greece (Course Manual & Book of Abstracts)

Branden & Tooze (Greek translation, 2006)

 

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