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Kyriacos Petratos

Kyriacos Petratos

Principal Researcher
Email address
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Phone
+30-2810-394353
Fax
+30-2810-394408
Lab web page
www.imbb.forth.gr/petratos

The primary interest of my laboratory is the understanding of the function of proteins by determination and analysis of the crystal structures of these macromolecules at high resolution. In particular, our main focus is the elucidation of the catalytic mechanisms of enzymes. In order to achieve this we try to co-crystallize the enzyme under study in different chemical states along its reaction coordinate and analyze the structures of the Michaelis complex(-es) and other possible intermediates. Moreover, in combination with X-ray crystallography, we employ biochemical methods, e.g. site directed mutagenesis targeting to analysis of the role of selected amino-acid residues in the active sites of enzymes. Another area of interest is the development of rational crystallization methods for proteins and their complexes with partner molecules with the usage of ionic strength reducing agents, e.g. polyethylene glycols (PEGs). We extensively employ synchrotron radiation for our macromolecular crystallography experiments, particularly the energy tunability of the latter that allows the application of anomalous diffraction methods for phasing of the Bragg reflections. Finally, we are interested in the biotechnological applications of the structural analyses, e.g. design and production of more stable and faster biocatalysts in selected ranges of pH and temperature.

R. Gessmann, C. Kyvelidou, M. Papadovasilaki and K. Petratos (2011) The crystal structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis. Biopolymers 95: 202-207.

R. Gessmann, H. Bruckner and K. Petratos (2003) Three Complete Turns of a 3(10)-Helix at Atomic Resolution: The Crystal Structure of Z-(Aib)11-O t Bu. J. Pept. Sci. 9: 753-762.

Y. Papanikolau, G. Prag, G. Tavlas, C. E. Vorgias, A. B. Oppenheim and K. Petratos (2001) High Resolution Structural Analyses of Mutant Chitinase A Complexes with Substrates Provide New Insight into the Mechanism of Catalysis. Biochemistry 40: 11338-11343.

F. K. Winkler, D. W. Banner, Ch. Oefner, D. Tsernoglou, R. S. Brown, S. P. Heathman, R. K. Bryan, P. D. Martin, K. Petratos and K. S. Wilson (1993) The crystal structure of Eco RV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12: 1781-1795.

K. Petratos, Z. Dauter and K. S. Wilson (1988) Refinement of the Structure of Pseudoazurin fromAlcaligenes faecalis S-6 at 1.55 A Resolution. Acta Crystallogr. B 44: 628-636.

Publications since 2000

Georgilis E, Gessmann R, Mitraki A, Petratos K.
"Diphenylalanine in tetrahydrofuran: a highly potent candidate for the development of novel nanomaterials"
Acta Crystallogr C Struct Chem. 73(Pt 6):447-450. [doi: 10.1107/S2053229617006830] (2017)

Gessmann R, Axford D, Brückner H, Berg A, Petratos K.
"A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution"
Acta Crystallogr F Struct Biol Commun. 73(Pt 2):95-100. [doi: 10.1107/S2053230X17001236] (2017)

Papageorgiou AC, Adam PS, Stavros P, Nounesis G, Meijers R, Petratos K, Vorgias CE.
"HU histone-like DNA-binding protein from Thermus thermophilus: structural and evolutionary analyses"
Extremophiles. 20(5):695-709. [doi: 10.1007/s00792-016-0859-1] (2016)

R. Gessmann, H. Brückner, K. Petratos
"The crystal structure of Z-(Aib)10-OH at 0.65 Å resolution: three complete turns of 310-helix"
J. Pept. Sci.  22: 76-81. [doi: 10.1002/psc.2842] (2016)

R. Gessmann, H. Brückner, K. Petratos
"The first N-terminal unprotected (Gly-Aib)n peptide: H-Gly-Aib-Gly-Aib-OtBu"
Acta Crystallogr.  C71: 1114-1117. [doi: 10.1107/S2053229615022597] (2015)

M. Papadovasilaki, D. Oberthür, R. Gessmann, I. Sarrou, C. Betzel, E. Scoulica, K. Petratos
“Biophysical and enzymatic properties of aminoglycoside adenylyltransferase AadA6 from Pseudomonas aeruginosa”
Biochem. Biophys. Rep.  4: 152-157. [doi: 10.1016/j.bbrep.2015.09.011] (2015)

R. Gessmann, H. Brückner, M. Aivaliotis, K. Petratos
“The crystal structure of Z-Gly-Aib-Gly-Aib-OtBu”
J Pept Sci 21(6):476-9 [doi: 10.1002/psc.2764] (2015)

R. Gessmann, M. Papadovasilaki, E. Drougkas, K. Petratos
“Zinc-substituted pseudoazurin solved by S/Zn-SAD phasing”
Acta Crystallogr. F71, 19-23 (2015)

R. Gessmann, H. Bruckner, K. Petratos
"The achiral tetrapeptide Z-Aib-Aib-Aib-Gly-OtBu"
Acta Crystallogr. C70, 1046-1049  [doi:10.1107/S2053229614022165] (2014)

R. Gessmann, H. Bruckner, K. Petratos
"The peptide Z-Aib-Aib-Aib-L-Ala-OtBu"
Acta Crystallogr C Struct Chem. 70(Pt 4), 405-407 (2014)

R. Gessmann, D. Axford, G. Evans, H. Brückner, K. Petratos 
“The crystal structure of samarosporin I at atomic resolution” 
J. Pept. Sci. 18, 678-84 (2012)

R. Gessmann, D. Axford, R. L. Owen, H. Brückner and K. Petratos 
“Four complete turns of a curved 3(10)-helix at atomic resolution: The crystal structure of the peptaibol trichovirin I‑4A in polar environment suggests a transition to aplha-helix for membrane function” 
Acta Crystallogr. D68, 109-116 (2012)

R. Gessmann, C. Kyvelidou, M. Papadovasilaki and K. Petratos
“The crystal structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis” 
Biopolymers, 95, 202-207 (2011)

R. Gessmann, N. Kourtis, K. Petratos and N. Tavernarakis
“Molecular modeling of mechanosensory ion channel structural and functional features” 
PLoS ONE 5(9), e12814 (2010)

V. Prokova, S. Mavridou, P. Papakosta, K. Petratos and D. Kardassis 
"Novel Mutations in Smad Proteins That Inhibit Signaling by the  Transforming Growth Factor ß in Mammalian Cells"
Biochemistry 46, 13775-13786 (2007)

Y. Papanikolau, M. Papadovasilaki, R. B. G. Ravelli, A. A. McCarthy, S. Cusack, A. Economou and K. Petratos 
“Structure of dimeric SecA, the Escherichia coli preprotein translocase motor” 
J. Mol. Biol. 366, 1545-1557 (2007)

E. Touloupakis, R. Gessmann, K. Kavelaki, E. Christofakis, K. Petratos and D. F. Ghanotakis 
“Isolation, characterization, sequencing and crystal structure of charybdin, a type 1 ribosome-inactivating protein from C. maritima agg.”
FEBS J. 273, 2684-2692 (2006)

S. Pyrpassopoulos, M. Vlassi, A. Tsortos, Y. Papanikolau, K. Petratos, C. E. Vorgias and G. Nounesis 
“Equilibrium heat-induced denaturation of chitinase 40 from S. thermoviolaceus” 
Proteins  64, 513-523 (2006)

Y. Papanikolau, I. Tsigos, M. Papadovasilaki, V. Bouriotis and K. Petratos
“Crystallization and preliminary X-ray diffraction studies of an alcohol dehydrogenase from the Antarctic psychrophile Moraxella sp. TAE123”
Acta Crystallogr. F61 , 246-248 (2005)

R. Gessmann, H. Brückner and K. Petratos
“Three Complete Turns of a 3 10 -Helix at Atomic Resolution: The Crystal Structure of Z-(Aib) 11 -OtBu”
J. Pept. Sci. 9, 753-762 (2003)

R. Gessmann, N. Schiemann, H. Brückner and K. Petratos
“The tetrapeptide Z-Leu-Aib-Pro-Val-OBg monohydrate”
Acta Crystallogr. C59, o413-o415 (2003)

Y. Papanikolau, G. Tavlas, C. E. Vorgias and K. Petratos
“ De novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin”
Acta Crystallogr. D59, 400-403 (2003)

Y. Papanikolau and K. Petratos
“Application of the effects of ionic strength reducing agents in the purification and crystallization of chitinase A”
Acta Crystallogr. D58, 1593-1596 (2002)

Y. Papanikolau, G. Prag, G. Tavlas, C. E. Vorgias, A. B. Oppenheim and K. Petratos
“High Resolution Structural Analyses of Mutant Chitinase A Complexes with Substrates Provide New Insight into the Mechanism of Catalysis”
Biochemistry 40, 11338-11343 (2001)

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. Cryst. Growth 210, 761-766 (2000)

G. Prag, Y. Papanikolau, G. Tavlas, C. E. Vorgias, K. Petratos and A. B. Oppenheim
“Structures of chitobiase mutants complexed with the substrate di-N-acetyl-D-glucosamine: the catalytic role of the conserved acidic pair, aspartate 539 and glutamate 540”
J. Mol. Biol. 300, 611-617 (2000)

 

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