Dr. Metaxia Vlassi holds a B.Sc in Physics (University of Patras, Greece) and a Ph.D. in X-ray Crystallography ( University of Patras, Greece in collaboration with the Université Catholique de LLN, Belgium). M.V. is heading the “Protein Structure & Molecular Modeling” laboratory of the Institute of Biosciences & Applications (ΙΒ-Α) of NCSR “Demokritos”. In 1998, MV was actively involved in the establishment of the “Centre for Crystallographic Studies of Macromolecules” (CCM) facility of NCSR “D” and since 2013 she is in charge of the Circular Dichroism (CD) Lab at IB-A/NCSR "D". MV’s current research activities focus on in silico structural studies (with emphasis on molecular dynamics simulations) of proteins aiming at unraveling sequence/structure/function relationships. She has published 50 peer reviewed articles. Person in charge of the in sillico structural studies of NCSR Demokritos node.

STAMATIOS (AKIS) LIOKATIS

Address: Sikelianou 3a, 45221 Ioannina Tel: +30 6976615407
Email: aliokatis@gmail.com

Research positions / experience

Faculty of Medicine, University of Ioannina (Post-Doc - Group leader: Prof. A. Politou)           2023-todate

Leibniz Institute of Molecular Pharmacology (FMP Berlin) Principal Investigator                     2014 - 2019

Leibniz Institute of Molecular Pharmacology (FMP Berlin) Post-Doc - In-Cell NMR group (Group leader: Dr. P.Selenko) 2008 – 2013

EMBL-Heidelberg Visiting Ph.D. student – Biomolecular NMR group (Group leader: Prof. M.Sattler) 2005-6-5 months

• Biocenter, University of Basel, Switzerland (Visiting Ph.D. student – M.E. Müller Institute for Struct. Biol. (Group leader: Prof. U.Aebi)  2004

Higher Education

University of Ioannina, Greece (Medical School), Ph.D. in Biochemistry/Structural Biology. Thesis: Structural and functional characterization of the LBR Tudor domain (Supervisor: Anastasia Politou) 2008

University of Ioannina, Greece (Chemistry Department) M.Sc. in Biochemistry Thesis: The impact of intravenous lipid administration in patients with acute lung injury (Supervisor: Marilena Lekka) 2002

University of Ioannina, Greece (Chemistry Department) B.Sc. in Chemistry 1999

Skills - Techniques

• Protein biochemistry/Molecular biology
Bacteria and mammalian cell culture
Cell extracts preparation
Recombinant DNA technology (cloning, PCR, protein overexpression, isotope-labeling)
Protein purification with chromatographic methods (affinity, ion exchange, size exclusion) in batch or automated setup (FPLC/HPLC, AKTA systems)

In vitro reconstitution of nucleosomes
Enzymatic assays (western blotting)
Protein-protein interactions – PPIs (IPs, pull-down assays, analytical gel filtration)
• Protein biophysics/Structural biology
CD spectroscopy (low-resolution structural characterization of proteins)
Electron microscopy – negative staining (Structural characterization of proteins)
ITC (studying PPIs)
Fluorescence spectroscopy (studying PPIs)
NMR spectroscopy (atomic-resolution protein structure, dynamic characterization, enzymatic activities, studying PPIs)
• Software tools
NMR spectroscopy (TopSpin, iNMR, Sparky,CcpNmr)
Molecular graphics (Pymol)
Bionformatic tools (Expasy portal)
Scientific graphing (GraphPad Prism)
Adobe suites (Photoshop, Illustrator)
Office suites (Powerpoint, Word, Excel)

Fellowships / Grants Year

Research grant for a principal investigator from the German Research Foundation (DFG) 2017 Title: Cross-regulation of post-translational protein modifications and effects on the histone H3tail conformations/dynamics: A structural and mechanistic study on whole nucleosomes by NMR spectroscopy – Part Two (240.000 € for 2.5 years).

Research grant for a principal investigator from the German Research Foundation (DFG) 2013 Title: Cross-regulation of post-translational protein modifications and effects on the histone H3tail conformations/dynamics: A structural and mechanistic study on whole nucleosomes by NMR spectroscopy – Part One (295.300 € for 3 years).

FEBS fellowship Jun 2006 Attending the young scientist forum and FEBS congress in Istanbul, Turkey

EMBO short-term Sep-Dec 2004 Training on electron microscopy and analytical ultracentrifugation at the Biocenter of University of Basel, studying the oligomerization state of Lamin B Receptor.

Original publications (full list)

1. Liokatis S. Reconstitution of nucleosomes with differentially isotope-labeled sister histones. J Vis Exp (2017); 121:55349

2. Liokatis S*, Klingberg R, Tan S, Schwarzer D. Differentially Isotope-Labeled Nucleosomes to Study Asymmetric Histone Modification Crosstalk by Time-Resolved NMR Spectroscopy. Angew Chem Int Ed (2016); 55(29):8262-5
3. Stuetzer A*, Liokatis S*, Kiesel A, Schwarzer D, Sprangers R, Soeding J, Selenko P, Fischle W.  Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails. Molecular Cell (2016); 61(2):247-59

4. Theillet FX, Rose HM, Liokatis S, Binolfi A, Thongwichian R, Stuiver M, Selenko P. Site-specific mapping and time-resolved NMR monitoring of serine and threonine phosphorylation in reconstituted kinase reaction mixtures or mammalian cell extracts. Nature Protocols (2013);8(7):1416-32

5. Liokatis S, Stuetzer A, Elsaesser SJ, Theillet FX, Klingberg R, van Rossum B, Schwarzer D, Allis CD, Fischle W, Selenko P. Phosphorylation of histone H3 Ser10 establishes a hierarchy for subsequent intramolecular modification events. Nature Struct Mol Biol (2012);19(8):819-23

6. Theillet FX, Liokatis S, Jost JO, Bekei B, Rose HM, Binolfi A, Schwarzer D, Selenko P. Site-specific mapping and time-resolved monitoring of lysine methylation by high-resolution NMR spectroscopy. J Am Chem Soc (2012);134(18):7616-9
7. Theillet FX, Smet-Nocca C, Liokatis S, Thongwichian R, Kosten J, Yoon MK, Kriwacki RW,  Landrieu I, Lippens G, Selenko P. Cell signaling, post-translational protein modifications and NMR  spectroscopy. J Biomol NMR (2012);54(3):217-36
8. Liokatis S, Edlich C, Soupsana K, Giannios I, Panagiotidou P, Tripsianes K, Sattler M, Georgatos SD,  Politou AS. Solution structure and molecular interactions of the Lamin B Receptor Tudor domain. J Biol Chem (2012);287(2):1032-1042 

9. Theillet FX, Binolfi A, Liokatis S, Verzini S, Selenko P. Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins. J Biomol NMR (2011);51(4):487-95

10. Dose A*, Liokatis S*, Theillet FX, Schwarzer D, Selenko P. NMR profiling of histone deacetylase and acetyl-transferase activities in real time. ACS Chem Biol (2011);6(5):419

11. Liokatis S, Dose A, Schwarzer D, Selenko P. Simultaneous detection of protein phosphorylation and  acetylation by high-resolution NMR spectroscopy. J Am Chem Soc (2010);132(42):14704
12. Karetsou Z, Emmanouilidou A, Sanidas I, Liokatis S, Nikolakaki E, Politou AS, Papamarcaki T.  Identification of distinct SET/TAF-Ibeta domains required for core histone binding and quantitative  characterisation of the interaction. BMC Biochem (2009):10
13. Lekka ME, Liokatis S, Nathanail C, Galani V, Nakos G. The impact of intravenous fat emulsion  administration in acute lung injury. Am J Respir Crit Care Med (2004);169(5):638-44
14. Nakos G, Tsangaris H, Liokatis S, Kitsiouli E, Lekka ME. Ventilator-associated pneumonia and  atelectasis: evaluation through bronchoalveolar lavage fluid analysis. Intensive Care Med (2003);29(4):555-63

Conferences (selected)

Liokatis S, Selenko P. Independent observation of sister histones and readout of asymmetric post- translational modifications (PTM) patterns in nucleosomes by high-resolution Nuclear Magnetic Resonance (NMR) spectroscopy (Poster presentation). EMBO Conference: Chromatins and Epigenetics, 2015 – Heidelberg (DE).

Liokatis S, Selenko P. NMR-monitoring of asymmetric post-translational modification patterns in nucleosomes (Oral presentation). 6th Conference of the Hellenic Society of Biochemistry and Molecular Biology: 2015 – Athens (GR).

Liokatis S. Reading asymmetric post-translational modification (PTM) patterns in nucleosomes by high-resolution NMR spectroscopy (Oral presentation). SEE-DRUG Conference- NMR applications in life sciences: 2015 – Patras (GR).

Liokatis S, Stuetzer A, Sprangers R, Schwarzer D, Fischle W, Selenko P. Modulation of transient histone-tail/DNA interactions by post-translational modifications determine the nucleosomal histone H3 code (Poster presentation). EMBO Workshop on Magnetic resonance for cellular structural biology: 2014 – Grosseto (IT).

Liokatis S, Stuetzer A, Elsaesser SJ, Allis CD, Sprangers R, Fischle W, Selenko P. A ta(i)le of post- translational modifications and dynamics (Oral presentation). Chromatin and Systems Biology, Summer School: 2011 – Spetses (GR).

Liokatis S, Edlich C, Sattler M, Georgatos SD, Politou AS. Structural and functional characterization of Lamin B Receptor (LBR) Tudor domain (Poster presentation). FEBS Biochemistry Congress: 2006 – Istanbul (TR).

Liokatis S, Makatsori D, Sattler M, Georgatos SD, Politou AS. Structural-functional studies of the Lamin B Receptor (LBR) (Poster presentation). EMBL Conference- Structures in Biology: 2004 – Istanbul (TR).

Languages

Greek (Mother tongue)

English (Fluent writing and spoken) – Proficiency from University of Michigan

German (B2 level communication skills)

EDUCATION

2019: PhD in Structural Biology and Protein Biomaterials (UoC, IMBB-FORTH - Greece)

2012: M.Sc. in Protein Biotechnology (UoC-Greece)

2009: Diploma Degree in Biology (UoC-Greece)

WORKING EXPERIENCE

Oct 2019 – Now: Post-Doctoral Researcher at I.M.B.B.-F.O.R.TH, Greece
                                (Laboratory of Structural Biology)

Sep 2020 – Now: Autonomous teaching and exam organizing of the under-graduate courses
                                "Enzymatic Biotechnology" and “Protein Engineering” at the Dept. of
                                 Biology of the Uni. of Crete

2014 – 2020:  Experienced scientist position at I.M.B.B.-F.O.R.TH, Greece (InnovCrete project /FP7-Regpot  program) and at University of Crete

Oct. 2010 –Jan. 2011: Laboratory Teaching Assistant of Microbiology Teaching Lab

                                        at the Dept. of Biology, Uni. of Crete

SELECTED PUBLICATIONS

*Kefala K., Kotsifaki D., Providaki M., Kapetaniou E., Rahme L. and Kokkinidis M. Purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal fragment of the MvfR protein of  Pseudomonas aeruginosa. (2012). Acta. Cryst F, 68, 695-697

*Kefala A., Kotsifaki D., Providaki M., Amprazi M. and Kokkinidis M. Expression, purification and crystallization of a protein resulting from the inversion of the aminoacid sequence of a helical bundle. (2017). ). Acta. Cryst F, 73, 51-53

 Dimovasili C., Fadouloglou V.E.,  Kefala A.,  Providaki M., Kotsifaki D,  Sarrou I.,  Plaitakis A.,  Zaganas I. and Kokkinidis M. Crystal structure of glutamate dehydrogenase 2, a positively selected novel human enzyme involved in brain biology and cancer pathophysiology. Journal of Neurochemistry (accepted) 

RESEARCH PROFILE

Being in a Structural Biology group since 2011, Dr. Kefala A. has studied deeply the protein folding problem, elucidating the relation between amino acid sequence and structural properties of α-helical bundles. The knowledge obtained was used for protein design leading to bio-derived materials for bio-medical applications and basic research through structural studies of protein folding through reverse sequences.

Notable achievements include: 

The elucidation of the protein folding of mutants of the α-helical protein Rop that is used as a canonical paradigm of this structural motif.

Protein design of novel protein-based biomaterials with specific engineered properties.

EDUCATION

2019: International Diploma in Business Administration (ELKEDIM. Lifelong LC, Greece)

2012: PhD in Structural Biology and Protein Biomaterials (UoC, IMBB-FORTH - Greece)

2007: M.Sc. in Protein Biotechnology (UoC-Greece)

2005: Diploma Degree in Biochemistry and Biotechnology (UoT-Greece)

WORKING EXPERIENCE

May 2016 – Now: Post-Doctoral Researcher at I.M.B.B.-F.O.R.TH, Greece
                                (Laboratory of Structural Biology)

Nov. 2012 – Apr. 2016:  Experienced scientist position at I.M.B.B.-F.O.R.TH, Greece

                                          (InnovCrete project /FP7-Regpot program)

Sept 2019 – Now: Autonomous teaching and exam organizing of the under-graduate courses
                                "Enzymatic Biotechnology" and “Protein Engineering” at the Dept. of
                                 Biology of the Uni. of Crete
Oct. 2006 –Jan. 2007: Laboratory Teaching Assistant of Microbiology Teaching Lab

                                        at the Dept. of Biology, Uni. of Crete

SELECTED PUBLICATIONS

Mermigka G, Amprazi M, Mentzelopoulou A, Amartolou A, Sarris PF (2020) Plant and Animal Innate Immunity Complexes: Fighting Different Enemies with Similar Weapons. Trends Plant Sci. 2020 Jan;25(1):80-91

Kefala K., Kotsifaki D., Providaki M., Amprazi M. and Kokkinidis M. (2017) Expression, purification and crystallization of a protein resulting from the  inversion of the amino-acid sequence of a helical bundle. Acta. Cryst F, 73(1), 51-53

Amprazi M., Kotsifaki D., Providaki M.,  Kapetaniou EG., Fellas G., Kyriazidis I.,Perez J.and Kokkinidis M. (2014) Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein. PNAS. 111(30): 11049-54

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

SCΗOLARSHIPS, AWARDS and GRANTS

Grant "Support for Researchers, with Emphasis on Young Researchers" of the Ministry of Education's Education and Lifelong Learning Program (40.600 euro) (2018)

Short-Term Fellowship by FEBS (2.000 euro) (2012) and Short-Term Fellowship by EMBO (9.000 euro)(2011)

Scholarship “HRAKLEITOS II” for perusing a PhD of the Hellenic Ministry of Education, co-funded by (ESF) & National Source (45.000 euro) (2009-2012)

RESEARCH PROFILE

Being in a Structural Biology group since 2006, Maria Amprazi has studied deeply the protein folding problem, elucidating the relation between amino acid sequence and structural properties of α-helical bundles. The knowledge obtained was used for protein design leading to bio-derived materials for bio-medical applications.

Notable achievements include: 

The elucidation of the protein folding pathway of the α-helical protein Rop that is used as a canonical paradigm of this structural motif.

Protein design of novel protein-based biomaterials with specific engineered properties.

Design and production of protein scaffolds that lead to restriction enzymes with new specificities, finding great application in gene therapy.