Karaca Lab. on Computational Structural Biology

OVERVIEW

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.

RESEARCH INTERESTS

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.

Group Members

Karaca Lab. on Computational Structural Biology

Group Leader

EZGI KARACA
ezgi.karaca@ibg.edu.tr
+90 232 299 41 00 (5041)
+9 02322994154

BURCU ÖZDEN Researcher  burcu.ozden@ibg.edu.tr


AYŞE BERÇIN BARLAS Ph.D. Student  aysebercin.barlas@msfr.ibg.edu.tr


EDA ŞAMİLOĞLU MSc Student  eda.samiloglu@msfr.ibg.edu.tr


MEHDI KOŞACA MSc Student  mehdi.kosaca@msfr.ibg.edu.tr


Selected Publications

Azbazdar Y, Ozalp O, Sezgin E, Veerapathiran S, Duncan AL, Sansom MSP, Eggeling C, Wohland T, Karaca E, Ozhan G. More Favorable Palmitic Acid Over Palmitoleic Acid Modification of Wnt3 Ensures Its Localization and Activity in Plasma Membrane Domains. Frontiers in cell and developmental biology. 2019 November; 7: 281. doi:10.3389/fcell.2019.00281.

Pavlopoulou A, Karaca E, Balestrazzi A, Georgakilas AG. In Silico Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress. Oxidative medicine and cellular longevity. 2019 July; 2019: 8683054. doi:10.1155/2019/8683054.

Dafsari HS, Sprute R, Wunderlich G, Daimagüler HS, Karaca E, Contreras A, Becker K, Schulze-Rhonhof M, Kiening K, Karakulak T, Kloss M, Horn A, Pauls A, Nürnberg P, Altmüller J, Thiele H, Assmann B, Koy A, Cirak S. Novel mutations in KMT2B offer pathophysiological insights into childhood-onset progressive dystonia.. Journal of human genetics. 2019 August; 64 (8): 803-813. doi:10.1038/s10038-019-0625-1.

Bonvin AMJJ, Karaca E, Kastritis PL, Rodrigues JPGLM. Defining distance restraints in HADDOCK. Nature Protocols. 2018 June; 13: 1503. doi:10.1038/s41596-018-0017-6.

Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O. Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance. Cell. 2018 March; 173 (1): 208-220.e220. doi:10.1016/j.cell.2018.02.032.

Ercan I, Tufekci KU, Karaca E, Genc S, Genc K. Peptide Derivatives of Erythropoietin in the Treatment of Neuroinflammation and Neurodegeneration. Advances in Protein Chemistry and Structural Biology. 2018 February; 112: 309-357. doi:10.1016/bs.apcsb.2018.01.007.

Karaca E, Rodrigues JPGLM, Graziadei A, Bonvin AMJJ, Carlomagno T. M3: an integrative framework for structure determination of molecular machines. Nature methods. 2017 August; 14 (9): 897-902. doi:10.1038/nmeth.4392.

Vangone A, Rodrigues JP, Xue LC, van Zundert GC, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond AS, Visscher KM, Trellet M, Kastritis PL, Bonvin AM. Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1.. Proteins. 2017 March; 85 (3): 417-423. doi:10.1002/prot.25198.

Bebel A, Karaca E, Kumar B, Stark WM, Barabas O. Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending.. eLife. 2016 December; 5. doi:10.7554/eLife.19706.

van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.. Journal of molecular biology. 2016 February; 428 (4): 720-725. doi:10.1016/j.jmb.2015.09.014.

Rodrigues JP, Karaca E, Bonvin AM. Information-driven structural modelling of protein-protein interactions.. Methods in molecular biology (Clifton, N.J.). 2015 January; 1215: 399-424. doi:10.1007/978-1-4939-1465-4_18.

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ. Blind prediction of interfacial water positions in CAPRI.. Proteins. 2014 April; 82 (4): 620-32. doi:10.1002/prot.24439.

Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.. Proteins. 2014 December; 87 (12): 1200-1221. doi:10.1002/prot.25838.

Rodrigues JP, Melquiond AS, Karaca E, Trellet M, van Dijk M, van Zundert GC, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AM. Defining the limits of homology modeling in information-driven protein docking.. Proteins. 2013 December; 81 (12): 2119-28. doi:10.1002/prot.24382.

Karaca E, Bonvin AM. On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys.. Acta crystallographica. Section D, Biological crystallography. 2013 May; 69 (Pt 5): 683-94. doi:10.1107/S0907444913007063.

Karaca E, Bonvin AM. Advances in integrative modeling of biomolecular complexes.. Methods. 2013 March; 59 (3): 372-81. doi:10.1016/j.ymeth.2012.12.004.

Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM. Clustering biomolecular complexes by residue contacts similarity.. Proteins. 2012 July; 80 (7): 1810-7. doi:10.1002/prot.24078.

Karaca E, Bonvin AM. A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes.. Structure. 2011 April; 19 (4): 555-65. doi:10.1016/j.str.2011.01.014.

Karaca E, Tozluoğlu M, Nussinov R, Haliloğlu T. Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation.. Journal of molecular biology. 2011 March; 406 (4): 620-30. doi:10.1016/j.jmb.2010.12.044.

Adrien S.J. Melquiond, Ezgi Karaca, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin. Next challenges in protein–protein docking: from proteome to interactome and beyond. WIREs Computational Molecular Science. 2011 January. doi:10.1002/wcms.91.

de Vries SJ, Melquiond AS, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JP, Bonvin AM. Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.. Proteins. 2010 November; 78 (15): 3242-9. doi:10.1002/prot.22814.

Karaca E, Melquiond AS, de Vries SJ, Kastritis PL, Bonvin AM. Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.. Molecular and Cellular proteomics. 2010 August; 9 (8): 1784-94. doi:10.1074/mcp.M000051-MCP201.

Nicastro G, Todi SV, Karaca E, Bonvin AM, Paulson HL, Pastore A. Understanding the role of the Josephin domain in the PolyUb binding and cleavage properties of ataxin-3.. PloS one. 2010 August; 5 (8): e12430. doi:10.1371/journal.pone.0012430.

Tozluoğlu M, Karaca E, Nussinov R, Haliloğlu T. A mechanistic view of the role of E3 in sumoylation.. PLoS computational biology. 2010 August; 6 (8). doi:10.1371/journal.pcbi.1000913.

Tozluoğlu M, Karaca E, Haliloglu T, Nussinov R. Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis.. Nucleic acids research. 2008 September; 36 (15): 5033-49. doi:10.1093/nar/gkn481.

Total: 25

Contact

Karaca Lab. on Computational Structural Biology

Group Leader

EZGI KARACA
ezgi.karaca@ibg.edu.tr
+90 232 299 41 00 (5041)
+9 02322994154