Short Description

The Laboratory of Biomolecular Structure and Biophysical Analysis was founded in 2015, and supports the educational and research work of the Department of Molecular Biology and Genetics in the fields of Structural Biology (determination of the 3D structure of proteins and nucleoprotein complexes using X-ray crystallography), Protein Biochemistry (overexpression and purification of biomolecules using chromatographic methods), Study and characterization of enzyme structure-function relationships, Structural Bioinformatics (structure-function analysis using computational methods), and Biophysics. The research is conducted in facilities located on the 2nd floor of the Department of Molecular Biology and Genetics building, comprising a laboratory appropriately equipped for protein overexpression in bacterial systems, chromatographic purification, and biomolecular crystallization.

The lab research focuses on studying the structure-function relationship of proteins, uncovering the atomic details that drive life’s processes and exploring how subtle changes—like a single mutation or a small displacement of a structural element—can dramatically alter protein function and contribute to health and disease.
Key Questions We Investigate:
(1) How do mutations or chemical modifications (i.e. post translational) impact protein activity? (2) What are the molecular mechanisms of macromolecular interactions and communication? (3) What is the atomic basis of molecular recognition? (4) What is the significance of protein dynamics? (5) How are structural changes in proteins linked to biochemical mechanisms? (6) What is the biological significance of pseudoenzymes, moonlighting and metamorphic proteins? (7) How proteins adapt to extreme conditions?
Our approach combines a wide array of experimental and computational techniques including Protein biochemistry and liquid chromatography, Molecular biology and enzymology, X-ray crystallography and other biophysical methods, Structural bioinformatics and molecular docking

(1) Overexpression and purification of proteins,

(2) Biophysical characterization of proteins and their complexes,

(3) Determination of protein structures and their complexes using X-ray crystallography

1. InTechThrace: Integrated Technologies in biomedical research: multilevel biomarker analysis in Thrace. Operational Program “Competitiveness, Entrepreneurship & Innovation, 2014-2020 (EPAnEK)”. (member, 2022-2023).
2. POLYPEPPHARM: Improved generic polypeptide drugs with innovative pharmaceutical forms. Operational Programme “Competitiveness, Entrepreneurship and Innovation,2014-2020 (EPAnEK)”. (member, 2021-2023).

  1. Molfetas AS, Boutris N, Tomatsidou A, Kokkinidis M, Fadouloglou VE. Variations of the NodB Architecture Are Attuned to Functional Specificities into and beyond the Carbohydrate Esterase Family 4. Biomolecules. 2024 Mar 8;14(3):325. doi: 10.3390/biom14030325. PMID: 38540745; PMCID: PMC10967932.
  2. Litso I, Plaitakis A, Fadouloglou VE, Providaki M, Kokkinidis M, Zaganas I. Structural Evolution of Primate Glutamate Dehydrogenase 2 as Revealed by In Silico Predictions and Experimentally Determined Structures. Biomolecules. 2023 Dec 23;14(1):22. doi: 10.3390/biom14010022. PMID: 38254622; PMCID: PMC10812971.
  3. Xanthis V, Mantso T, Dimtsi A, Pappa A, Fadouloglou VE. Human Aldehyde Dehydrogenases: A Superfamily of Similar Yet Different Proteins Highly Related to Cancer. Cancers (Basel). 2023 Sep 4;15(17):4419. doi: 10.3390/cancers15174419. PMID: 37686694; PMCID: PMC10650815.
  4. Makraki E, Miliara S, Pagkalos M, Kokkinidis M, Mylonas E, Fadouloglou VE. Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA. Front Mol Biosci. 2023 Jul 17;10:1219668. doi: 10.3389/fmolb.2023.1219668. PMID: 37555016; PMCID: PMC10406553.
  5. Voulgaridou GP, Theologidis V, Xanthis V, Papagiannaki E, Tsochantaridis I, Fadouloglou VE, Pappa A. Identification of a peptide ligand for human ALDH3A1 through peptide phage display: Prediction and characterization of protein interaction sites and inhibition of ALDH3A1 enzymatic activity. Front Mol Biosci. 2023 Mar 20;10:1161111. doi: 10.3389/fmolb.2023.1161111. PMID: 37021113; PMCID: PMC10067601.
  6. Gazi AD, Kokkinidis M, Fadouloglou VE. α-Helices in the Type III Secretion Effectors: A Prevalent Feature with Versatile Roles. Int J Mol Sci. 2021 May 21;22(11):5412. doi: 10.3390/ijms22115412. PMID: 34063760; PMCID: PMC8196651.
  7. Amprazi M, Tomatsidou A, Paliogianni D and Fadouloglou VE. Post-Translational Modifications: Host Defence Mechanism, Pathogenic Weapon, and Emerged Target of Anti-Infective Drugs, in book: Frontiers in Anti-Infective Drug Discovery, Volume 9, pp: 25-122 (98), doi: 10.2174/9781681088297121090004.
  8. Dimovasili C, Fadouloglou VE, Kefala A, Providaki M, Kotsifaki D, Kanavouras K, Sarrou I, Plaitakis A, Zaganas I, Kokkinidis M. Crystal structure of glutamate dehydrogenase 2, a positively selected novel human enzyme involved in brain biology and cancer pathophysiology. J Neurochem. 2021 May;157(3):802-815. doi: 10.1111/jnc.15296. Epub 2021 Jan 23. PMID: 33421122.
  9. Kokkinidis M, Glykos NM, Fadouloglou VE. Catalytic activity regulation through post-translational modification: the expanding universe of protein diversity. Adv Protein Chem Struct Biol. 2020;122:97-125. doi: 10.1016/bs.apcsb.2020.05.001. Epub 2020 Jun 27. PMID: 32951817; PMCID: PMC7320668.
  10. Khalid RR, Maryam A, Fadouloglou VE, Siddiqi AR, Zhang Y. Cryo-EM density map fitting driven in-silico structure of human soluble guanylate cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding. J Mol Graph Model. 2019 Jul;90:109-119. doi: 10.1016/j.jmgm.2019.04.009. Epub 2019 Apr 24. PMID: 31055154; PMCID: PMC7956049.
  11. 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. 2017 Apr 19;139(15):5330-5337. doi: 10.1021/jacs.6b12209. Epub 2017 Apr 5. PMID: 28333455.
  12. Fadouloglou VE, Lin HT, Tria G, Hernández H, Robinson CV, Svergun DI, Luisi BF. Maturation of 6S regulatory RNA to a highly elongated structure. FEBS J. 2015 Dec;282(23):4548-64. doi: 10.1111/febs.13516. Epub 2015 Oct 13. PMID: 26367381; PMCID: PMC7610929.
  13. Balomenou S, Arnaouteli S, Koutsioulis D, Fadouloglou VE and Bouriotis V. Deacetylases: New Antibacterial Drug Targets. in book: Frontiers in Anti-Infective Drug Discovery , pp: 68-130 (63), doi: 10.2174/9781681080826115040005.
  14. Fadouloglou VE. Electroelution of nucleic acids from polyacrylamide gels: a custom-made, agarose-based electroeluter. Anal Biochem. 2013 Jun 1;437(1):49-51. doi: 10.1016/j.ab.2013.02.021. Epub 2013 Mar 7. PMID: 23499972.
  15. 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 Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):276-83. doi: 10.1107/S0907444912045829. Epub 2013 Jan 19. PMID: 23385463.
  16. Charova SN, Gazi AD, Kotzabasaki M, Sarris PF, Fadouloglou VE, Panopoulos NJ and Kokkinidis M. Protein Flexibility and Coiled-Coil Propensity: New Insights Into Type III and Other Bacterial Secretion Systems. In book: Biochemistry, Edited by Deniz Ekinci, 2012 March. doi: 10.5772/32582.
  17. 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 Microbiol. 2012 Sep 2;12:188. doi: 10.1186/1471-2180-12-188. PMID: 22937899; PMCID: PMC3574062.
  18. Kokkinidis M, Glykos NM, Fadouloglou VE. Protein flexibility and enzymatic catalysis. Adv Protein Chem Struct Biol. 2012;87:181-218. doi: 10.1016/B978-0-12-398312-1.00007-X. PMID: 22607756.
  19. Deli A, Koutsioulis D, Fadouloglou VE, Spiliotopoulou P, Balomenou S, Arnaouteli S, Tzanodaskalaki M, Mavromatis K, Kokkinidis M and Bouriotis V (2010) LmbE proteins from Bacillus cereus are de-N-acetylases with broad substrate specificity and are highly similar to proteins in Bacillus anthracis, FEBS J. 277, 2740-2753.
  20. Fadouloglou VE, Stavrakoudis A, Bouriotis V, Kokkinidis M and Glykos NM (2009) 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.
  21. Fadouloglou VE, Bastaki MN, Ashcroft AE, Phillips SEV, Panopoulos NJ, Glykos NM and Kokkinidis M (2009) On the quaternary association of the type III secretion system HrcQB-C protein: Experimental evidence differentiates among the various oligomerization models J. Struct. Biol. 166, 214-25.
  22. Fadouloglou VE, Kokkinidis M & Glykos NM (2008) Determination of protein oligomerization state: Two approaches based on glutaraldehyde crosslinking Anal. Biochem 373, 404-406.
  23. Fadouloglou VE, Deli A, Glykos NM, Psylinakis E, Bouriotis V & Kokkinidis M (2007) Crystal structure of the BcZBP, a zinc-binding protein from Bacillus cereus: functional insights from structural data, FEBS J. 274, 3044-3054.
  24. Fadouloglou VE, Kotsifaki D, Gazi AD, Fellas G, Meramveliotaki C, Deli A, Psylinakis E, Bouriotis V & Kokkinidis M (2006) Purification, crystallization and preliminary characterization of a putative LmbE-like deacetylase from Bacillus cereus, Acta Cryst. F62, 261-264.
  25. Tampakaki AP, Fadouloglou VE, Gazi A.D., Panopoulos N.J. & Kokkinidis M. (2004) Conserved features of type III secretion, Cell. Microbiol., 6, 805-816.
  26. Papanikolaou Y, Kotsifaki D, Gazi AD, Fadouloglou VE, Glykos NM, Cesareni G & Kokkinidis M (2004) Ionic strength reducers: an efficient approach to protein purification and crystallization. Application to two Rop variants, Acta Cryst. D60, 1334-1337.
  27. Fadouloglou VE, Tampakaki A, Glykos NM, Bastaki MN, Hadden J, Phillips SEV, Panopoulos N & Kokkinidis M (2004) Structure of HrcQB-C, a conserved component of the bacterial type III secretion systems, Proc. Natl. Acad. Sci. USA 101, 70-75.
  28. Fadouloglou VE, Tampakaki A, Panopoulos N & Kokkinidis M (2001) Structural studies of the Hrp secretion system: expression, purification, crystallization and preliminary X-ray analysis of the C-terminal domain of the HrcQBprotein from Pseudomonas syringae pv. phaseolicola, Acta Cryst., D57, 1689-1691.
  29. Fadouloglou VE, Glykos NM & Kokkinidis M (2001) Side-chain conformations in 4-a-helical bundles, Protein Eng., 14 (5), 321-328.
  30. Fadouloglou VE, Glykos NM & Kokkinidis M (2000) A fast and inexpensive procedure for drying polyacrylamide gels, Anαl. Biochem., 287, 185-186.
  31. Spyridaki A, Glykos NM, Kotsifaki D, Fadouloglou VE & Kokkinidis M (2000) Crystallization and diffraction to ultrahigh resolution (0.8Å) of a designed variant of the Rop protein, Acta Cryst., D56, 1015-1016.

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Στογιαννούδη Μαρκέλλα Μεταπτυχιακή Φοιτήτρια
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Director

Fadouloglou Vasiliki, Associate Professor

+30 25510 30660

fadoulog@mbg.duth.gr

Τμήμα Μοριακής Βιολογίας και Γενετικής, ΔΠΘ, Kτίριο Φώτης Καφάτος, Πανεπιστημιούπολη, περιοχή Δραγάνα, 68100 Αλεξανδρούπολη