Selected Publications

• Sugihara, M., and A.-N. Bondar. On the influence of the retinal methyl groups on retinal structure and dynamics. Current Physical Chemistry (Special issue on Quantum Nanobiology and Biophysical Chemistry), Accepted (2013).

• 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.