Protein crystallography lab.

Gallery: Protein crystallography lab.

Facility manager: Dr. Veronika Harmat

Members: Dr. Veronika Harmat, Dr. Zsolt Dürvanger, Dr. Dóra K. Menyhárd , Anna J. Kiss-Szemán, Máté Sulyok-Eiler , Gergő Hegedűs, István Bódy, /en/members/students/109

For a better understanding of function and interactions of biological macromolecules, 3D-structure is required at an atomic resolution, typically determined by protein crystallography; a perfect method of choice. On the other hand, small molecular crystallographic studies explore the structural basis of physical-chemical characteristics of the compound. In 2018. new X-ray crystallographic instruments were installed in the EU 2020 framework (Széchenyi 2020*). The aim of these consortial projects is to establish an infrastructure serving as an open lab for a wider range of research groups (ELTE-CrystalLAB). The Rigaku XtaLAB Synergy-R X-ray diffractometer is capable for small molecular and protein crystallographic data collection as well as in situ crystal testing. A TTP Labtech Mosquito-LCP is available for automated crystallization, and monitoring crystal growth is carried out by a Formulatrix Rock Imager 2 system.

*The research within project No. VEKOP-2.3.3-15-2017-00018 and VEKOP-2-3-2-16-2017-00014 was supported by the European Union and the State of Hungary, co-financed by the European Regional Development Fund.

Laboratory News

  • Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation

    A group of hormone peptides is stored in the form of functional amyloid fibers in acid secretion vesicles before they reassemble their biologically active helical spatial structure when they enter the blood circulation. In the article published in Nature Communications, we explain the molecular basis of pH-dependent reversible amyloid formation in the case of gastrointestinal peptides belonging to the glucagon family. The article is presented on the website of the MTA by several Hungarian online newspapers. [1, 2, 3]

  • High affinity binding in a flexible protein-protein complex: structural studies on the calmodulin – melittin complex

    Interaction of calmodulin and melittin is widely used as a test system for method development, and as a reference in studies of calmodulin interactions. However, results on the interaction pattern of this complex were non-conclusive so far. Our aim was to explore the fine details of this interaction. Our crystallographic study revealed multiple different binding modes, and our succeeding MD simulations concluded that these could transform to each other: the nanomolar affinity binding of this complex is realized by a ‘slippery’ binding way and interchanging interactions.
    Our publication has been selected as one of "Editors' Picks," of the Journal of Biological Chemistry.

  • X-Ray diffraction data collection at synchrotron sources


    We visited European microfocus synchrotron sources at ESRF and BESSY.

    Szink2

Publications

  • Veronika Harmat , Klarissza Domokos , Dóra K. Menyhárd , Anna Palló , Zoltán Szeltner , Ilona Szamosi , Tamás Beke , Gábor Náray-Szabó , László Polgár
    Structure and catalysis of acylamonoacyl peptidase: closed and open subunits of a dimer oligopeptidase
    Journal of Biological Chemistry 286:1987-1998. PMID: 21084296 | DOI: 10.1074/jbc.M110.169862 (2011) Kivonat
  • József Dobó , Veronika Harmat , László Beinrohr , Edina Sebestyén , Péter Závodszky , Péter Gál
    MASP-1, a Promiscuous Complement Protease: Structure of Its Catalytic Region Reveals the Basis of Its Broad Specificity
    J. Immunol. 183:1207-1214. (2009) Kivonat
  • József Kardos , Péter Závodszky , Yuji Goto , Gábor Náray-Szabó , László Gráf , Katalin Szilágyi , Orsolya Barabás , Anna Palló , Veronika Harmat , Péter Gál
    Revisiting the mechanism of the autoactivation of the complement protease C1r in the C1 complex: Structure of the active catalytic region of C1r
    Mol. Immunol. 45(6):1752-1760 (2008) Kivonat
  • András L. Kiss , Balázs Hornung , Krisztina Rádi , Zsolt Gengeliczki , Bálint Sztáray , Tünde Juhász , Zoltán Szeltner , Veronika Harmat , László Polgár
    The acylaminoacyl peptidase from Aeropyrum pernix K1 thought to be an exopeptidase displays endopeptidase activity
    J. Mol. Biol. 368: 509-520. (2007) Kivonat
  • László Beinrohr , Veronika Harmat , József Dobó , Zsolt Lörincz , Péter Gál , Péter Závodszky
    C1 inhibitor serpin domain structure reveals the likely mechanism of heparin potentiation and conformational disease
    J. Biol. Chem. 282: 21100-21109. (2007) Kivonat
  • Krisztián Fodor , Veronika Harmat , Csaba Hetényi , József Kardos , József Antal , András Perczel , András Patthy , Gergely Katona , László Gráf
    Extended intermolecular interactions in a serine protease canonical inhibitor complex account for strong and highly specific inhibition
    J. Mol. Biol. 350:156-169. (2005) Kivonat
  • István Horváth , Veronika Harmat , András Perczel , Villő Pálfi , László Nyitray , Attila Nagy , Emma Hlavanda , Gábor Náray-Szabó , Judit Ovádi
    The structure of the complex of calmodulin with KAR-2: a novel mode of binding explains the unique pharmacology of the drug
    J. Biol. Chem. 280(9):8266-8274. | PMID: 15596444 (2005) Kivonat
  • Márton Megyeri , Veronika Harmat , Balázs Major , Ádám Végh , Júlia Balczer , Dávid Héja , Katalin Szilágyi , Dániel Datz , Gábor Pál , Péter Závodszky , Péter Gál , József Dobó
    Quantitative characterization of the activation steps of Mannan-Binding Lectin (MBL)-Associated Serine Proteases (MASPs) points to the central role of MASP-1 in the initiation of the complement lectin pathway
    J Biol Chem 288(13):8922-8934. | DOI: 10.1074/jbc.M112.446500 | PMID: 23386610 (2013) Kivonat
  • Ibolya Leveles , Veronika Németh , Judit E. Szabó , Veronika Harmat , Kinga Nyíri , Ábris Ádám Bendes , Veronika Papp-Kádár , Imre Zagyva , Gergely Róna , Olivér Ozohanics , Károly Vékey , Judit Tóth , Beáta G. Vértessy
    Structure and enzymatic mechanism of a moonlighting dUTPase
    Acta Crystallogr D Biol Crystallogr. D69:2298-2308. | DOI: 10.1107/S0907444913021136 | PMID: 24311572 (2013) Kivonat
  • Péter Rapali , László Radnai , Dániel Süveges , Veronika Harmat , Ferenc Tölgyesi , Weixiao Y. Wahlgren , Gábor Pál
    Directed evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome
    PLoS One 6(4):e18818. | DOI: 10.1371/journal.pone.0018818 | PMID: 21533121 (2011) Kivonat
  • Ildikó Pécsi , Ibolya Leveles , Veronika Harmat , Beáta G. Vértessy , Judit Tóth
    Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase
    Nucleic Acids Res. 38(20):7179-7186. | DOI: 10.1093/nar/gkq584 | PMID: 20601405 (2010) Kivonat
  • Károly Kánai , Péter Arányi , Zsolt Böcskei , György Ferenczy , Veronika Harmat , Kálmán Simon , Sándor Bátori , Gábor Náray-Szabó , István Hermecz
    Prolyl oligopeptidase inhibition by N-acyl-pro-pyrrolidine-type molecules
    J Med Chem. 51(23):7514-7522. | DOI: 10.1021/jm800944x | PMID: 19006380 (2008) Kivonat
  • Krisztián Fodor , Veronika Harmat , Richard Neutze , László Szilágyi , László Gráf , Gergely Katona
    Enzyme:substrate hydrogen bond shortening during the acylation phase of serine protease catalysis
    Biochemistry 45(7):2114-2121. | 10.1021/bi0517133 | PMID: 16475800 (2006) Kivonat
  • Péter Gál , Andrea Kocsis , Tünde Bián , Veronika Harmat , László Barna , Géza Ambrus , Barbara Végh , Robert B. Sim , Péter Závodszky , Gábor Náray-Szabó
    A true autoactivating enzyme. Structural insight into mannose-binding lectin-associated serine protease-2 activations
    J. Biol. Chem. 280(39):33435-33444. | PMID: 16040602 (2005) Kivonat
  • Veronika Harmat , Péter Gál , József Kardos , Katalin Szilágyi , Géza Ambrus , Gábor Náray-Szabó , Péter Závodszky
    The structure of MBL-associated serine protease-2 reveals that identical substrate specificities of C1s and MASP-2 are realized through different sets of enzyme-substrate interactions
    J. Mol. Biol. 342(5):1533-1546. | PMID: 15364579 (2004) Kivonat
  • Veronika Harmat , Zsolt Böcskei , Gábor Náray-Szabó , Imre Bata , Andrea S. Csutor , István Hermecz , Péter Arányi , Beáta Szabó , Károly Liliom , Beáta G. Vértessy
    A new potent calmodulin antagonist with arylalkylamine structure: crystallographic, spectroscopic and functional studies
    J. Mol. Biol. 297(3):747-755. | DOI: 10.1006/jmbi.2000.3607 | PMID: 10731425 (2000) Kivonat
  • Beáta G. Vértessy , Veronika Harmat , Gábor Náray-Szabó , Zsolt Böcskei , Ferenc Orosz , Judit Ovádi
    Simultaneous binding of drugs with different chemical structures to Ca2+-calmodulin: crystallographic and spectroscopic studies
    Biochemistry 37(44):15300-15310. | DOI: 10.1021/bi980795a | PMID: 9799490 (1998) Kivonat
  • Dóra K. Menyhárd , Zoltán Orgován , Zoltán Szeltner , Ilona Szamosi , Veronika Harmat
    Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality
    Acta Crystallogr D Biol Crystallogr. 71(Pt 3):461-472. | DOI: 10.1107/S1399004714026819 | PMID: 25760596 (2015) Kivonat
  • Viktória Goldschmidt Gőz , István Pintér , Veronika Harmat , András Perczel
    Approaches to Pyranuronic beta-Sugar Amino Acid Building Blocks of Peptidosaccharide Foldamers
    Eur. J. Org. Chem. 355-361. DOI: 10.1002/ejoc.201701612 (2018) Kivonat
  • Tibor Pasinszki , Dániel Dzsotján , Győző György Lajgut , Veronika Harmat , Antal Csámpai , Andrea Bor , István Zupkó
    Synthesis, spectral- and theoretical study, x-ray analysis, and antiproliferative activity of 4,5-dihydrobenzoferroceno[1,2-d][1,2,3]selenadiazole and its benzo-fused analogue
    Journal of Organometallic Chemistry 863:70-76. | DOI: 10.1016/j.jorganchem.2018.03.031 (2018) Kivonat
  • Roland Szalay , Veronika Harmat , János Eőri , Gábor Pongor
    Strong influence of intramolecular Si⋯O proximity on reactivity: Systematic molecular structure, solvolysis, and mechanistic study of cyclic N-trimethylsilyl carboxamide derivatives
    Tetrahedron Letters 58(23):2186-2192. | DOI: 10.1016/j.tetlet.2017.04.057 (2017) Kivonat
  • V. Bugris , Cs. Dudás , B. Kutus , V. Harmat , K. Csankó , S. Brockhauser , I. Pálinkó , Peter Turner , P. Sipos
    Crystal and solution structures of calcium complexes relevant to problematic waste disposal: calcium gluconate and calcium isosaccharinate
    Acta Crystallographica Section B 598-609 | doi.org/10.1107/S2052520618013720 (2018) Kivonat
  • Anikó Angyal , András Demjén , Veronika Harmat , János Wölfling , László G. Puskás , Iván Kanizsai
    1,3-Dipolar Cycloaddition of Isatin-Derived Azomethine Ylides with 2H‐Azirines: Stereoselective Synthesis of 1,3- Diazaspiro[bicyclo[3.1.0]hexane]oxindoles
    The Journal of Organic Chemistry 4273-4281 DOI: 10.1021/acs.joc.9b00242 (2019) Kivonat
  • Valéria Bugris , Veronika Harmat , Györgyi Ferenc , Sándor Brockhauser , Ian Carmichael , Elspeth F. Garman
    Radiation-damage investigation of a DNA 16-mer
    Journal of Synchrotron Radiation 998-1009 doi.org/10.1107/S160057751900763X (2019) Kivonat
  • Zsolt Dürvanger , Veronika Harmat
    Structural Diversity in Calmodulin - Peptide Interactions
    Current Protein & Peptide Science 1102 - 1111 doi.org/10.2174/1389203720666190925101937 (2019) Kivonat
  • Anna J. Kiss-Szemán , Veronika Harmat , Dóra K. Menyhárd
    Achieving Functionality Through Modular Build-up: Structure and Size Selection of Serine Oligopeptidases
    Current Protein & Peptide Science 1089 - 1101 DOI:10.2174/1389203720666190925103339 (2019) Kivonat
  • Kinga Judit Fodor , Dániel Hutai , Tamás Jernei , Angéla Takács , Zsófia Szász , Máté Sulyok-Eiler , Veronika Harmat , Rita Oláh Szabó , Gitta Schlosser , Ferenc Hudecz , László Kőhidai , Antal Csámpai
    Novel Polycondensed Partly Saturated β-Carbolines Including Ferrocene Derivatives: Synthesis, DFT-Supported Structural Analysis, Mechanism of Some Diastereoselective Transformations and a Preliminary Study of their In Vitro Antiproliferative Effects
    Molecules 25(7), 1599 | doi: 10.3390/molecules25071599 (2020) Kivonat
  • Anita Kapros , Attila Balázs , Veronika Harmat , Adrienn Háló , Lívia Budai , István Pintér , Dóra K. Menyhárd , András Perczel
    Configuration‐Controlled Crystal and/or Gel Formation of Protected d‐Glucosamines Supported by Promiscuous Interaction Surfaces and a Conformationally Heterogeneous Solution State
    Chemistry—A European Journal 26 | doi.org/10.1002/chem.202000882 (2020) Kivonat
  • Anna J. Kiss-Szemán , Pál Stráner , Imre Jákli , Naoki Hosogi , Veronika Harmat , Dóra K. Menyhárd , András Perczel
    Cryo-EM structure of acylpeptide hydrolase reveals substrate selection by multimerization and a multi-state serine-protease triad
    Chemical Science DOI: 10.1039/d2sc02276a (2022) Kivonat
  • Anna J. Kiss-Szemán , Luca Takács , Zoltán Orgován , Pál Stráner , Imre Jákli , Gitta Schlosser , Simonas Masiulis , Veronika Harmat , Dóra K. Menyhárd , András Perczel
    A carbapenem antibiotic inhibiting a mammalian serine protease: structure of the acylaminoacyl peptidase–meropenem complex
    Chemical Science 13, 14264 - 14276 I DOI: 10.1039/D2SC05520A (2022) Kivonat
  • Zsolt Dürvanger , Eszter Boros , Zoltán Attila Nagy , Rózsa Hegedüs , Márton Megyeri , József Dobó , Péter Gál , Gitta Schlosser , Annamária F. Ángyán , Zoltán Gáspári , András Perczel , Veronika Harmat , Gábor Mező , Dóra K. Menyhárd , Gábor Pál
    Directed Evolution-Driven Increase of Structural Plasticity Is a Prerequisite for Binding the Complement Lectin Pathway Blocking MASP-Inhibitor Peptides
    ACS Chem. Biol. 17(4), 969–986 I DOI: 10.1021/acschembio.2c00114 (2022) Kivonat
  • Zoltán Attila Nagy , Dávid Héja , Dániel Bencze , Bence Kiss , Eszter Boros , Dávid Szakács , Krisztián Fodor , Matthias Wilmanns , Andrea Kocsis , József Dobó , Péter Gál , Veronika Harmat , Gábor Pál
    Synergy of protease-binding sites within the ecotin homodimer is crucial for inhibition of MASP enzymes and for blocking lectin pathway activation
    J. Biol. Chem. 298(6) 101985 I DOI: 10.1016/j.jbc.2022.101985 (2022) Kivonat
  • Kende Attila Béres , Zoltán Homonnay , Libor Kvitek , Zsolt Dürvanger , Martina Kubikova , Veronika Harmat , Fanni Szilágyi , Zsuzsanna Czégény , Péter Németh , Laura Bereczki , Vladimir M. Petruševski , Mátyás Pápai , Attila Farkas , László Kótai
    Thermally Induced Solid-Phase Quasi-Intramolecular Redox Reactions of [Hexakis(urea-O)iron(III)] Permanganate: An Easy Reaction Route to Prepare Potential (Fe,Mn)Ox Catalysts for CO2 Hydrogenation
    Inorg. Chem. 61(36), 14403–14418 I DOI: 10.1021/acs.inorgchem.2c02265 (2022) Kivonat
  • Kende Attila Béres , Zoltán Homonnay , Berta Barta Holló , Maria Gracheva , Vladimir M. Petruševski , Attila Farkas , Zsolt Dürvanger , László Kótai
    Synthesis, structure, and Mössbauer spectroscopic studies on the heat‑induced solid‑phase redox reactions of hexakis(urea‑O)iron(III) peroxodisulfate
    Journal of Materials Research 38, 1102–1118 I DOI: 10.1557/s43578-022-00794-w (2022) Kivonat
  • Zsolt Dürvanger , Tünde Juhász , Károly Liliom , Veronika Harmat
    Structures of calmodulin–melittin complexes show multiple binding modes lacking classical anchoring interactions
    J. Biol. Chem. 299(4): 104596 I DOI: 10.1016/j.jbc.2023.104596 (2023) Kivonat
  • Dániel Horváth , Zsolt Dürvanger , Dóra K. Menyhárd , Máté Sulyok-Eiler , Fruzsina Bencs , Gergő Gyulai , Péter Horváth , Nóra Taricska , András Perczel
    Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation
    Nature Communications 14, 4621 I https://doi.org/10.1038/s41467-023-40294-x (2023) Kivonat
  • Kende Attila Béres , Zoltán Homonnay , Laura Bereczki , Zsolt Dürvanger , Vladimir M. Petruševski , Attila Farkas , László Kótai
    Crystal Nanoarchitectonics and Characterization of the Octahedral Iron(III)–Nitrate Complexes with Isomer Dimethylurea Ligands
    Crystals 13(7), 1019 I DOI: https://doi.org/10.3390/cryst13071019 I ISSN 2073-4352 (2023) Kivonat
  • Kende Attila Béres , Fanni Szilágyi , Zoltán Homonnay , Zsolt Dürvanger , Laura Bereczki , László Trif , Vladimir M. Petruševski , Attila Farkas , Niloofar Bayat , László Kótai
    Structural, Spectroscopic, and Thermal Decomposition Features of [Carbonatotetraamminecobalt(III)] Iodide—Insight into the Simultaneous Solid-Phase Quasi-Intramolecular Redox Reactions
    Inorganics 11(2):68. I DOI: https://doi.org/10.3390/inorganics11020068 (2023) Kivonat

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