University of California Merced
2024
16- Gallardo A., Dutagaci B., Binding of Small Molecule Inhibitors to RNA Polymerase-Spt5 Complex Impacts RNA and DNA Stability, J. Comput.-Aided Mol. Des., 2024
15- Amith W. D., Dutagaci B., Complex Conformational Space of RNA Polymerase II C-Terminal Domain upon Phosphorylation, J. Phys. Chem. B127, 43, 9223–9235
2022
14- Gallardo A., Bogart B., Dutagaci B., Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations, J. Chem. Inf. Model., 2022, 62(12), 3079-3089.
Postdoctoral training at Michigan State University (2015-2020):
13- Lin G., Barnes C.O., Weiss S., Dutagaci B., Qiu C., Feig M., Lyubimov A., Song J., Cohen A. E., Kaplan C. D., Calero G., Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser, bioRxiv, doi:
12- Dutagaci B.*, Duan B., Qiu Chenxi, Kaplan C.D., Feig M.*, Characterization of RNA Polymerase II Trigger Loop Mutations using Molecular Dynamics Simulations and Machine Learning, PLoS Comput Biol 2023, 19(3): e1010999.
11- Walhout P. K., He Z., Dutagaci B., Nawrocki G., Feig M., Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions, J. Phys. Chem. B 2022, 126, 48, 10256–10272.
10- Dutagaci B., Nawrocki G., Lapidus L., Goodluck J., Ashkarran A.A., Hoogstraten C.G., Feig M., Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments, eLife 2021;10:e64004.
9- Brocke, S. A., Degen, A., MacKerell, A. D., Dutagaci, B.*, Feig, M.*, Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. J. Chem. Inf. Model., 2019, 59(3), 1147-1162. *co-corresponding authors
8- Dutagaci, B., Heo, L., Feig, M., Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations, 2018, 86, 738-750.
7- Dutagaci, B., Feig, M., Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model, J. Chem. Inf. Model., 2017, 57, 3032-3042.
6- Dutagaci, B., Wittayanarakul K., Mori T., Feig M., Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions, J. Chem. Theory Comput., 2017, 13, 3049-3059.
5- Dutagaci, B., Sayadi M., Feig M., Heterogeneous Dielectric Generalized Born Model with a van der Waals Term Provides Improved Association Energetics of Membrane-Embedded Transmembrane Helices, J. Comput. Chem., 2017, 38, 1308-1320.
Postdoctoral training at Bogazici University (2014-2015):
4- Haslak, Z. P., Bozkurt, E., Dutagaci, B, De Proft F., Aviyente, V., De Vleeschouwer, F. A DFT Approach to Discriminate the Antagonist and Partial Agonist Activity of Ligands Binding to the NMDA Receptor, Mol. Phys., 2018, 116, 323-337.
Graduate Studies at Johann Wolfgang Goethe University (2008-2013)
3- Jakdetchai, O., Denysenkov V., Becker-Baldus J., Dutagaci B., Prisner T., Glaubitz C., DNP-enhanced NMR on aligned lipid bilayers at ambient temperature. J. Am. Chem. Soc., 2014, 136, 15533-15536.
2- Dutagaci, B., Becker-Baldus J., Faraldo-Gómez J. D., Glaubitz C., Ceramide-lipid interactions studied by MD simulations and solid-state NMR . Biochim. Biophys. Acta, 2014, 1838, 2511-2519.
1- Huesch, J., Dutagaci B., Glaubitz C., Geppert T., Schneider G., Harms M., Mueller-Goymann C. C., Fink L., Schmidt M. U., Setzer C., Zirkel J., Rebmann, H., Schubert-Zsilavecz, M., Abdel-Tawab M., Structural properties of so-called NSAID-phospholipid-complexes. Eur. J. Pharm. Sci. 2011, 44, 103-116
*co-corresponding authors