Selected Publications

 

      • Lukas Kemmler, Mohamed Ibrahim, Holger Dobbek, Athina Zouni, and Ana-Nicoleta Bondar. Dynamic water bridging and proton transfer at a surface carboxylate cluster of photosystem II. PhysChemChemPhys , 21, 25449-25466 (2019). doi: 10.1039/c9cp03926
       
      • Malte Siemers, Michalis Lazaratos, Konstantina Karathanou, Federico Guerra, Leonid Brown, and Ana-Nicoleta Bondar. Bridge: A graph-based algorithm to analyze dynamic H-bond networks in membrane proteins, Journal of Chemical Theory and Computation .  (2019). doi: 10.1093/femsle/fny124

 

      • Ana-Nicoleta Bondar. Introduction to topical issue on Biomembrane Structure, Dynamics, and Reactions. Chemical Reviews , 119, 5535-5536 (2019). doi: 10.1021/acs.chemrev.9b00093

 

      • Ana-Nicoleta Bondar and Joanne M. Lemieux. Reactions at membrane interfaces. Chemical Reviews , 119, 6162-6182 (2019). doi: 10.1021/acs.chemrev.8b00596

 

      • Ana-Nicoleta Bondar. Mechanisms by which lipids influence conformational dynamics of the GlpG intramembrane protease. Journal of Physical Chemistry B , 123, 4159-4172 (2019). doi: 10.1021/acs.jpcb.8b11291

 

      • Konstantina Karathanou and Ana-Nicoleta Bondar. Using graphs of dynamic hydrogen-bond networks to dissect conformational coupling in a protein motor. Journal of Chemical Information and Modeling , 59, 1882-1896 (2019). doi: 10.1021/acs.jcim.b800979

 

      • Konstantina Karathanou and Ana-Nicoleta Bondar. Dynamic hydrogen-bond networks in bacterial protein secretion. FEMS Microbiology Letters . 365, fny124 (2018), Invited mini review. doi: 10.1093/femsle/fny124

 

      • Federico Guerra, Malte Siemers, Christopher Mielack, and Ana-Nicoleta Bondar. Dynamics of long-distance hydrogen-bond networks in photosystem II. Journal of Physical Chemistry B , 122, 4625-4641 (2018). Selected for ACS Editor's choice. doi: 10.1021/acs.jpcb.8b00649

 

      • Nadia Elghobashi-Meinhardt, Prasad Phatak, Ana-Nicoleta Bondar, Marcus Elstner, and Jeremy C. Smith. Catalysis of ground-state cis-trans isomerization of bacteriorhodopsin's retinal chromophore by a hydrogen bond network. Journal of Membrane Biology, 251, 315-327 (2018). doi: 10.1007/s00232-018-0027-x

 

      • Konstantina Karathanou and Ana-Nicoleta Bondar. Dynamic water hydrogen-bond networks at the interface of a lipid membrane containing palmitoyloleoyl phosphatidylglycerol. Journal of Membrane Biology, 251, 461-473 (2018). doi: 10.1007/s00232-018-0023-1

 

      • Stefan Milenkovic and Ana-Nicoleta Bondar. Motions of the SecA protein motor bound to signal peptide: Insights from molecular dynamics simulations. BBA - Biomembranes 1860, 416-427 (2018), doi: 10.1016/j.bbamem.2017.11.004

 

      • Andrew Harris, Matia Saita, Tom Resler, Alexandra Hughes-Visentin, Raiza Maia, Franziska Sellnau, Ana-Nicoleta Bondar, Joachim Heberle, Leonid Brown. Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin. Physical Chemistry Chemical Physics 20, 3184-3199 (2018). doi: 10.1039/C7CP06068H

 

      • Suliman Adam, Michaela Knapp-Mohammady, Jun Yi, and Ana-Nicoleta Bondar. Revised CHARMM force-field parameters for iron-containing cofactors of photosystem II. Journal of Computational Chemistry 39, 7-20 (2018). Cover Image of the Issue. doi: 10.1002/jcc.24918.

 

      • A.-N. Bondar and J. C. Smith. Protonation-state coupled conformational dynamics in reaction mechanisms of channel and pump rhodopsins. Photochemistry and Photobiology 93, 1336-1344 (2017). Invited Review, Cover Image of the Issue . doi: 10.1111/php.12790

 

      • C. del Val and A.-N. Bondar. Charged groups at binding interfaces of the PsbO subunit of photosystem II: a combined bioinformatics and simulation study. BBA Bioenergetics, 1858, 432-441 (2017). doi: j.bbabio.2017.03.004

 

      • A.-N. Bondar. Biophysical mechanism of rhomboid proteolysis: setting a foundation for therapeutics. Seminars in Cell and Developmental Biology 60, 46-51 (2016). doi: 10.1016/j.semcdb.2016.09.006

 

      • E. Nango, A. Royant, M. Kubo, T. Nakane, C. Wickstrand, T. Kimura, T. Tanaka, K. Tono, C. Song, R. Tanaka, T. Arima, A. Yamashita, J. Kobayashi, T. Hosaka, E. Mizohata, P. Nogly, M. Sugahara, D. Nam, T. Nomura, T. Shimamura, D. Im, T. Fujiwara, Y. Yamanaka, B. Jeon, T. Nishizawa, K. Oda, M. Fukuda, R. Andersson, P. Båth, R. Dods, J. Davidsson, S. Matsuoka, S. Kawatake, M. Murata, O. Nureki, S. Owada, T. Kameshima, T. Hatsui, Y. Joti, G. Schertler, M. Yabashi, A.-N. Bondar, J. Standfuss, R. Neutze, S. Iwata. A three-dimensional movie of structural changes in bacteriorhodopsin. Science 354, 1552-1557 (2016), doi:10.1021/acs.biochem.6b00441

 

      • 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 55, 4626-4635 (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 1847, 1518-1529 (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. Proceedings of the National Academy of Sciences 112, 9016-9021 (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. Journal of Membrane Biology 248, 611-640 (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 1837, 1964-1972 (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 248, 443-453 (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 Journal of Physical Chemistry B 119, 2229-2240(2014), doi:10.1021/jp505818r 

 

      • Minoru Sugihara, Makiko Suwa and Ana-Nicoleta Bondar. Dynamics of bovine opsin bound to G-protein fragments. Journal of Structural Biology 188, 79-86 (2014), 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. Physical Chemistry Chemical Physics, 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. Current Physical Chemistry 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. Journal of Membrane Biology 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 Letters. 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. Theoretical Chemistry Accounts 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. Journal of Physical Chemistry B 115 (21), 7129-7135 (2011).doi:10.1021/jp201865k.

 

      • Bondar, A.-N., S. Fischer, and J. C. Smith. Water pathways in bacteriorhodopsin. Journal of Membrane Biology (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). Journal of Membrane Biology (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. Theoretical Chemistry Accounts 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. Biophysical Journal 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. Biophysical Journal 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. Journal of the American Chemical Society 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. Journal of Physical Chemistry 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. Journal of Structural Biology 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. Photochemical & Photobiological Sciences (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. Journal of Physical Chemistry 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. Journal of Molecular Biology 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. Philosophical Transactions of the Royal Society 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.Journal of the American Chemical Society 126 (44), 14668-14677 (2004). doi:10.1021/ja047982i.