Computational Structural Biology of Biomolecular Interactions
Tülay Karakulak, Msc Student
Deniz Doğan, Msc Student
Life is operated at the nanometer scale through orchestrated communications of biomolecules. By dissecting this nanoworld, we can acquire a fundamental understanding of how biological macromolecules function, how they are related to disease-linked pathways and how to design drugs targeting them. This understanding led to the birth and rise of Structural Biology, the study of the structures of biomolecules and their complexes at atomic resolution.
Experimental structure determination techniques, X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy, have solved tens of thousands of structures of biomolecules and their complexes. Still, the field cannot keep pace with the speed at which data are generated in other disciplines, such as genetics, biochemistry and various associated “omics” technologies. Computational structural biology emerged to help overcome this bottleneck and has evolved to generate high-accuracy models of biological macromolecules rapidly.
As a computational structural biology group, we are interested in unveiling the physical principles of biomolecular interactions through determining and/or dissecting the structures of biomolecular complexes. In order to do so, we develop and apply various computational tools, such as docking, homology modelling and molecular dynamics. We also integrate experimental and evolutionary information in to our calculations, which we obtain through our collaborations.
Lately, we have been concentrated on (i) understanding the molecular basis of a number of nucleic acid modifications, (ii) developing therapeutics to inhibit over-activation of tyrosine kinases in cancer and (iii) exploring the structural principles of epigenetic modifications.
If you are interested in solving molecular puzzles of biology through computation – while working in a dynamic and highly collaborative environment, please contact us by e-mail!
|May 17 – present||Assistant Professor, Dokuz Eylul University, Izmir Biomedicine and Genome Institute|
|2013 – 2016||Postdoctoral fellow, EMBL Heidelberg (Carlomagno and Barabas Labs)|
|2008 – 2013||PhD, Computational Structural Biology, Utrecht University (Bonvin Lab)|
|2002 – 2008||MSc and BSc, Chemical Engineering, Boğaziçi University (Haliloğlu and Nussinov Labs)|
AWARDS AND RECOGNITION
• Return Fellowship of TÜBİTAK – 2017-2018
• Return Fellowship of the Alexander von Humbolt Foundation – 2017-2018
• Long term Alexander von Humbolt Postdoctoral Research Fellowship – 2014-2016
• PhD student of the year – 2012
Full list and citations can be reached here.
• Karaca E, Rodrigues JPGLM, Graziadei A, Bonvin AMJJ, Carlomagno T (2017): M3: an integrative framework for structure determination of molecular machines. Nature Methods, 2017, doi: 10.1038/nmeth.4392
• Bebel B, Karaca E, Kumar B, Stark WM, Barabas O (2016): Pre- and post-cleavage synaptic complexes of Helicobacter pylori Xer recombination, eLIFE, doi: 10.7554/eLife.19706
• van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E et al. (2015): The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes. J. Mol. Biol., 428(4):720-5.
• Karaca E, Bonvin AMJJ (2013): On the usefulness of Ion Mobility Mass Spectrometry and SAXS data in scoring docking decoys, Acta Cryst. D, 69, 683–694.
• Karaca E, Bonvin AMJJ (2013): Advances in Integrative Modeling of Biomolecular Complexes, Methods, 1;59(3):372-81.
• Karaca E, Bonvin AMJJ. (2011): A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes, Structure, 19-4, 555-565.
• Karaca E, Tozluoglu M, Nussinov R, Haliloglu T. (2011) Alternative Allosteric Mechanisms Can Regulate the Substrate and E2 in SUMO Conjugation, J. Mol. Biol., 406-4, 620-630.
• Karaca E*, Melquiond ASJ*, de Vries SJ*,Kastritis PL, Bonvin AMJJ. (2010): Building Macromolecular Assemblies by Information-driven Docking, Mol.Cell. Prot., 9-8, 1784-1794.
• Nicastro G*, Todi SV*, Karaca, E, Bonvin AMJJ, Paulson HL, Pastore A. (2010) Understanding the role of the Josephin domain in the PolyUb binding and cleavage properties of ataxin-3, PloS one, 5-8, e12430.
• Tozluoglu M*, Karaca E*, Haliloglu T, Nussinov R. (2008): Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis, Nucleic Acids Res., 36-15, 5033-49.
• Rodrigues JPGLM, Karaca E, Bonvin AMJJ. (2015): Information-driven structural modeling of protein-protein interactions, in: Methods in Molecular Biology: Molecular Modelling of Proteins, Edited by Andreas Kukol, 399-424.
• Schmitz C, Melquiond ASJ, de Vries SJ, Karaca E, van Dijk M, Kastritis PL, Bonvin AMJJ. (2012): Protein-protein docking with HADDOCK, in: NMR of Biomolecules: Towards Mechanistic Systems Biology, Edited by I. Bertini, K.S. McGreevy and G. Parigi, Wiley-VCH, 512–535.