Biochemistry & Biophysics | Structural & Computational Biology
Structural Biology of the Cytoskeleton
We investigate the molecular mechanisms underlying the actin-based cytoskeleton of striated muscle. A striking feature of muscle proteins, and particularly of the specialised striated muscle sarcomere compartment Z-disk, is the high frequency of multiple protein-protein interactions. We aim to generate detailed structural information on the protein-protein interaction network in the Z-disk, from its basic components - α-actinin and filamin C - to macromolecular complexes and...more
We investigate the molecular mechanisms underlying the actin-based cytoskeleton of striated muscle. A striking feature of muscle proteins, and particularly of the specialised striated muscle sarcomere compartment Z-disk, is the high frequency of multiple protein-protein interactions. We aim to generate detailed structural information on the protein-protein interaction network in the Z-disk, from its basic components - α-actinin and filamin C - to macromolecular complexes and the adaptor and regulatory Z-disk proteins centred on them.
Several of the components required for the generation of Z-disk complexes are already available in quantities and quality required for structural studies: alpha-actinin, several segments of filamin C, myotilin, FATZ, myopodin and ZASP. We are proceeding with generation of binary and higher complexes and their biochemical, biophysical and structural characterisation combining high resolution studies (X-ray diffraction, NMR) with lower resolution approaches that can either yield molecular envelopes (SAXS, SANS, EM) or specific distance information (mass-spectrometry, NMR). These activities are complemented by the development of bioinformatics tools for results and fine tuning of the protein constructs to be structurally analyzed. New bioinformatics strategies are being designed to extend our prediction capabilities.
With other groups and faculties we are working on structural studies of the RNA chaperone Hfq and its interactions with RNA (Bläsi), yeast magnesium channel Mrs2 (Schweyen), and trypasonomal cytoskeletal protein MORN1 (Warren). In collaboration with M. Wagner (Faculty for Life Sciences, Univ. Vienna) and C. Obinger (University of Natural Resources and Life Sciences, Vienna) we are studying the family of bacterial chlorite dismutases.
Elucidation of chlorite dismutase reaction mechanism has been performed by analysis of the structures of wild-type, active site mutants and complexes combined with biochemical studies to elucidate the catalytic mechanism. To study Hfq:RNA interactions at the molecular level we used bioinformatics and biophysical methods combined with molecular and structural biology to provide novel insights into the conformation and dynamic properties of the C-terminal extension of Hfq from E. coli. We showed that the C-terminal extensions are intrinsically disordered and protrude away from the hexameric core. Such regions provide conformational fluctuations, which can facilitate intermolecular interactions. We showed that only RNA fragments exceeding a certain length interact with the intrinsically disordered C-termini of Hfq residing in the C-terminal extension, the minimal portion supporting the interactions with longer RNA.
In order to overcome the major bottlenecks in structural and functional studies of proteins, which are availability of milligram amounts of active, chemically and conformationally pure protein and crystallization, an FFG funded Laura Bassi Centre for Optimized Structural Studies (COSS) was established as a joint venture of IMP, Intercell and UNIVIE-MFPL with the goal to set-up an efficient platform to combine the recent advances in automated expression screening of protein targets employing nested constructs design and cell-free protein expression systems followed by biophysical characterization to find conditions best suited for structural and functional studies.
Seminar Series "Modern Concepts in Structural Biology"
Crystals from bacterium “Candidatus Nitrospira defluvii” in action
Lectures by Kristina Djinovic
Ribeiro, Euripedes de Almeida; Pinotsis, Nikos; Ghisleni, Andrea; Salmazo, Anita; Konarev, Petr V; Kostan, Julius; Sjöblom, Björn; Schreiner, Claudia; Polyansky, Anton A; Gkougkoulia, Eirini A; Holt, Mark R; Aachmann, Finn L; Zagrović, Bojan; Bordignon, Enrica; Pirker, Katharina F; Svergun, Dmitri I; Gautel, Mathias; Djinović-Carugo, Kristina (2014). The Structure and Regulation of Human Muscle α-Actinin. CELL;159(6):1447-60. PMID: 25433700
Song, Jae-Geun; Kostan, Julius; Drepper, Friedel; Knapp, Bettina; de Almeida Ribeiro, Euripedes; Konarev, Petr V; Grishkovskaya, Irina; Wiche, Gerhard; Gregor, Martin; Svergun, Dmitri I; Warscheid, Bettina; Djinović-Carugo, Kristina (2015). Structural Insights into Ca(2+)-Calmodulin Regulation of Plectin 1a-Integrin β4 Interaction in Hemidesmosomes. STRUCTURE;23(3):558-70. PMID: 25703379
Kostan J, Salzer U, Orlova A, Toeroe I, Hodnik V, Senju Y, Zou J, Schreiner C, Steiner J, Meriläinen J, Nikki M, Virtanen I, Carugo O, Rappsilber J, Lappalainen P, Lehto VP, Anderluh G, Egelman EH, Djinović-Carugo K (2014). Direct Interaction of Actin Filaments with F-BAR Protein Pacsin2. EMBO REP;15(11):1154-62. PMID: 25216944
Doctoral Program "Integrative Structural Biology"
2016-2019: The Group Djinovic participates in the special Doctoral Program "Integrative Structural Biology" reviewed and funded by the Austrian Science Fund FWF. Kristina Djinovic-Carugo is Vice Speaker of the program.
Doctoral Program "Structure and Interaction of Biological Macromolecules"
2009-2013: Doctoral Program "Structure and Interaction of Biological Macromolecules" reviewed and funded by the Austrian Science Fund FWF.
COSS - Center for Optimized Structural Studies
2010-2013: Laura-Bassi Center of Expertise "COSS - Center for Optimized Structural Studies" funded by the Austrian Research Promotion Agency FFG (Co-ordinator)
Bioinformatics Integration Network III
2009-2013: Research Network funded by the GEN-AU Genome Research Program of the Federal Ministry of Science and Research
DFG/FWF Research Unit
2010-2014: Researc Unit 'Alpha Actinin, Filamin C and their Complexes with Binding Partners' funded by the German Research Foundation and the Austrian Science Fund
Marie Curie Initial Training Network
2009-2013: FP7 Marie-Curie Action ITN Muscle Z-disk Protein Complexes: from atomic structure to physiological function (MUZIC)
FWF Stand Alone Projects
2010-2013: MORN repeat proteins and the Trypanosoma brucei bilobe (with G. Warren)
2010-2013: Structural Aspects of RAF-1:Rok-alpha Interaction (with M. Baccarini)