Selected Publications

  • Martin Bommer, Ana-Nicoleta Bondar, Athina Zouni, Holger Dobbek, and Holger Dau. Crystallograhic and computational analysis of the barrel part of the PsbO protein of photosystem II: carboxylate-water clusters as putative proton transfer relays and structural switches. Biochemistry (2016) , doi:10.1021/acs.biochem.6b00441


  • Stefan Milenkovic and Ana-Nicoleta Bondar. Mechanism of conformational coupling in SecA: Key role of hydrogen bonding networks and water interactions. BBA Bioenergetics 1858, 374-385 (2016), doi:10.1016/j.bbamem.2015.11.010


  • Sebastian Lorch, Sara Capponi, Florian Pieront, and Ana-Nicoleta Bondar. Dynamic carboxylate/water networks on the surface of the PsbO subunit of photosystem II. Journal of Physical Chemistry B 119, 12172-12181 (2015), doi:10.1016/j.bbamem.2015.11.010


  • Federico Guerra, Suliman Adam, and Ana-Nicoleta Bondar. Revised force-field parameters for chlorophyll-a, pheophytin-a, and plastoquinone-9. Journal of Molecular Graphics and Modelling 58, 30-39 (2015), doi:10.1016/j.jmgm.2015.03.001


  • Andrew Harris, Milena Ljumovic, Ana-Nicoleta Bondar, Yohei Shibata, Shota Ito, Keiichi Inoue, Hideki Kandori, Leonid Brown. A new group of eubacterial light-driven retinal-binding proton pumps with an unusual cytoplasmic proton donor. BBA Bioenergetics (2015) doi:10.1016/j.bbabio.2015.08.003


  • Sara Capponi, Matthias Heyden, Ana-Nicoleta Bondar, Douglas J. Tobias, Stephen H. White. Anomalous behavior of water inside the SecY translocon. Proc. Natl Acad Sci USA (2015) doi:10.1016/j.jmgm.2015.03.001


  • Zoe Cournia, Toby W. Allen, Ioan Andricioaei, Bruno Antonny, Daniel Baum, Grace Brannigan, Nicolae-Viorel Buchete, Jason T. Deckman, Lucie Delemotte, Coral del Val, Ran Friedman, Paraskevi Gkeka, Hans-Christian Hege, Jerome Henin, Marina A. Kasimova, Antonios Kolocouris, Michael L. Klein, Syma Khalid, M. Joanne Lemieux, Norbert Lindow, Mahua Roy, Jana Selent, Mounir Tarek, Florentina Tofoleanu, Stefano Vanni, Sinisa Urban, David J. Wales, Jeremy C. Smith, Ana-Nicoleta Bondar. Membrane Protein Structure, function, and dynamics: a perspective from experiments and theory.J. Membr. Biol. 2015, doi:10.1007/s00232-015-9802-0


  • Eduardo Jardon-Valdez, Ana-Nicoleta Bondar and Douglas J. Tobias. Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin. BBA-Bioenergetics 2014 doi:10.1016/j.bbabio.2014.09.006


  • Federico Guerra and Ana-Nicoleta Bondar. Dynamics of the plasma membrane proton pump. Journal of Membrane Biology 2014, doi:10.1007/s00232-014-9732-2


  • Tino Wolter, Marcus Elstner, Stefan Fischer, Jeremy C. Smith, and Ana-Nicoleta Bondar. Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States J. Phys. Chem. B (2014) In Press, doi:10.1021/jp505818r


  • Minoru Sugihara, Makiko Suwa and Ana-Nicoleta Bondar. Dynamics of bovine opsin bound to G-protein fragments. J. Struct. Biol. (2014) In Press, doi:10.1016/j.jsb.2014.08.001


  • Oliver Karge, Ana-Nicoleta Bondar and Holger Dau. Cationic screening of charged surface groups (carboxylates) affects electron transfer steps in photosystem-II water oxidation and quinone reduction. BBA Bioenergetics 1837, 1625-1634 (2014), doi:10.1016/j.bbabio.2014.07.012


  • Coral del Val, Luiza Bondar and Ana-Nicoleta Bondar. Coupling between inter-helical hydrogen bonding and water dynamics in a proton transporter. Journal of Structural Biology 186 95-111 (2014), doi:10.1016/j.jsb.2014.02.010

 

  • Coral del Val, Jose Rouyela-Flor, Stefan Milenkovic, and Ana-Nicoleta Bondar, Channelrhodopsins: a bioinformatics perspective. BBA Bioenergetics 1837, 643-655 (2014) doi:10.1016/j.bbabio.2013.11.005

 

  • Norbert Lindow, Daniel Baum, Ana-Nicoleta Bondar, and Hans-Christian Hege. Exploration of cavity dynamics in biomolecular systems. BMC Bioinformatics, 2013, 14 (Suppl 19):S5 doi:10.1186/1471-2105-14-S19-S5

 

  • Wolter, T., K. Welke, P. Phatak, A.-N. Bondar, and M. Elstner. Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation. Phys. Chem. Chem. Phys., 15, 12582-12590 (2013). doi:10.1039/C3CP44280B.

 

  • Sugihara, M., and A.-N. Bondar. Influence of the Retinal Methyl Groups on Retinal Structure and Dynamics. Curr. Phys. Chem. 3 (2), 211-218 (2013). doi:10.2174/1877946811303020011.

 

  • Lindow, N., D. Baum, A.-N. Bondar, and H.-C. Hege. Dynamic channels in biomolecular systems: Path analysis and visualization. In 2012 IEEE Symposium on Biological Data Visualization (BioVis), 14-15 Oct, 2012, Seattle, WA, USA, 99-106 (2012). doi:10.1109/BioVis.2012.6378599.

 

  • Andersson, M., A.-N. Bondar, and J. A. Freites, D. J. Tobias, H. R. Kaback, and S. H. White. Proton-Coupled Dynamics in Lactose Permease. Structure 20 (11), 1893-1904 (2012). doi:10.1016/j.str.2012.08.021.

 

  • Del Val, C., S. H. White, and A.-N. Bondar. Ser/Thr Motifs in Transmembrane Proteins: Conservation Patterns and Effects on Local Protein Structure and Dynamics. J. Membr. Biol. 245 (11), 717-730 (2012). doi:10.1007/s00232-012-9452-4.

 

  • Bondar, A.-N., and H. Dau. Extended protein/water H-bond networks in photosynthetic water oxidation. BBA Bioenergetics 1817 (8), 1177-1190 (2012).doi:10.1016/j.bbabio.2012.03.031.

 

  • Nack, M., I. Radu, B.-J. Schultz, T. Resler, R. Schlesinger, A.-N. Bondar, C. del Val, S. Abbruzzetti, C. Viappiani, C. Bamann, E. Bamberg, and J. Heberle. Kinetics of proton release and uptake by channelrhodopsin-2. FEBS Lett. 586 (9), 1344-1348 (2012). doi:10.1016/j.febslet.2012.03.047. Supplementary Information: Sequence analysis

 

  • Bondar, A.-N., and S. H. White. Hydrogen bond dynamics in membrane protein function. BBA Biomembranes 1818 (4), 942-950 (2012). doi:10.1016/j.bbamem.2011.11.035.

 

  • Bondar, A.-N., M. Knapp-Mohammady, S. Suhai, S. Fischer, and J. C. Smith. Ground-state properties of the retinal molecule: from quantum mechanical to classical mechanical computations of retinal proteins. Theor. Chem. Acc. 130 (4-6), 1169-1183 (2011). doi:10.1007/s00214-011-1054-1.

 

  • Clemens, M., P. Phatak, Q. Cui, A.-N. Bondar, and M. Elstner. Role of Arg 82 in the Early Steps of the Bacteriorhodopsin Proton-Pumping Cycle. J. Phys. Chem. B 115 (21), 7129-7135 (2011).doi:10.1021/jp201865k.

 

  • Bondar, A.-N., S. Fischer, and J. C. Smith. Water pathways in bacteriorhodopsin. J. Membr. Biol. (S.H. White Festschrift) 239 (1-2), 73-84 (2011). doi:10.1007/s00232-010-9329-3.

 

  • Bondar, A.-N., T. B. Woolf, and D. J. Tobias. Festschrift in the Honor of Stephen H. White’s 70th Birthday. (Editorial). J. Membr. Biol. (S.H. White Festschrift) 239 (1-2), 1-3 (2011). doi:10.1007/s00232-010-9337-3.

1-2

 

  • Bondar, A.-N., M. Elstner, and J. C. Smith. Mechanism of a proton pump analyzed with computer simulations. Theor. Chem. Acc. 125 (3-6), 353-363 (2010). doi:10.1007/s00214-009-0565-5.

 

  • Bondar, A.-N., C. del Val, J. A. Freites, D. J. Tobias, and S. H. White. Dynamics of SecY Translocons with Translocation-Defective Mutations. Structure 18 (7), 847-857 (2010). doi:10.1016/j.str.2010.04.010.

 

  • Jardón-Valadez, E., A.-N. Bondar, and D. J. Tobias. Coupling of Retinal, Protein, and Water Dynamics in Squid Rhodopsin. Biophys. J. 99 (7), 2200-2207 (2010). doi:10.1016/j.bpj.2010.06.067.

 

  • Jardón-Valadez, E., A.-N. Bondar, and D. J. Tobias. Dynamics of the Internal Water Molecules in Squid Rhodopsin. Biophys. J. 96 (7), 2572-2576 (2009). doi:10.1016/j.bpj.2008.12.3927.

 

  • Bondar, A.-N., C. del Val, and S. H. White. Rhomboid Protease Dynamics and Lipid Interactions. Structure 17 (3), 395-405 (2009). doi:10.1016/j.str.2008.12.017.

 

  • Phatak, P., J. Frahmcke, M. Wanko, M. Hoffmann, P. Strodel, J. C. Smith, S. Suhai, A.-N. Bondar, and M. Elstner. Long-Distance Proton Transfer with a Break in the Bacteriorhodopsin Active Site. J. Am. Chem. Soc. 131 (20), 7064-7078 (2009). doi:10.1021/ja809767v.

 

  • Bondar, A.-N., J. Baudry, S. Suhai, S. Fischer, and J. C. Smith. Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions. J. Phys. Chem. B 112 (47), 14729-14741 (2008). doi:10.1021/jp801916f.

 

  • Bondar, A.-N., S. Suhai, S. Fischer, J. C. Smith, and M. Elstner. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements. J. Struct. Biol. 157 (3), 454-469 (2007). doi:10.1016/j.jsb.2006.10.007.

 

  • Bondar, A.-N., J. C. Smith, and S. Fischer. Structural and energetic determinants of primary proton transfer in bacteriorhodopsin. Photochem. Photobiol. Sci. (Themed issue Proton Transfer in Biological Systems) 5 (6), 547-552 (2006). doi:10.1039/b516451f.

 

  • Gruia, A. D., A.-N. Bondar, J. C. Smith, and S. Fischer. Mechanism of a Molecular Valve in the Halorhodopsin Chloride Pump. Structure 13 (4), 617-627 (2005). doi:10.1016/j.str.2005.01.021.

 

  • Bondar, A.-N., S. Fischer, S. Suhai, and J. C. Smith. Tuning of Retinal Twisting in Bacteriorhodopsin Controls the Directionality of the Early Photocycle Steps. J. Phys. Chem. B 109 (31), 14786-14788 (2005). doi:10.1021/jp0531255.

 

  • Okada, T., M. Sugihara, A.-N. Bondar, M. Elstner, P. Entel, and V. Buss. The Retinal Conformation and its Environment in Light of a New 2.2 Å Crystal Structure. J. Mol. Biol. 342 (2), 571-583 (2004). doi:10.1016/j.jmb.2004.07.044.

 

  • Bondar, A.-N., M. Elstner, S. Suhai, J. C. Smith, and S. Fischer. Mechanism of Primary Proton Transfer in Bacteriorhodopsin. Structure 12 (7), 1281-1288 (2004). doi:10.1016/j.str.2004.04.016.

 

  • Smith, J. C., F. Merzel, A.-N. Bondar, A. Tournier, and S. Fischer. Structure, dynamics and reactions of protein hydration water. Phil. Trans. Royal Soc. B 359 (1448), 1181-1190 (2004). doi:10.1098/rstb.2004.1497.

 

  • Bondar, A.-N., S. Fischer, J. C. Smith, M. Elstner, and S. Suhai. Key Role of Electrostatic Interactions in Bacteriorhodopsin Proton Transfer.J. Am. Chem. Soc. 126 (44), 14668-14677 (2004). doi:10.1021/ja047982i.