Publications

• Nicoleta Bondar, Roy Daniel, John Finney, Stefan Fischer, Mikio Kataoka, Andrei Petrescu and Jeremy Smith. Protein Folding and Dynamics- New insights from Computer Simulation and Scattering Experiments. J. Phys. Soc. Jpn. 70 Suppl. A pp. 392-395 (2001).
• Nicoleta Bondar, M. Elstner, S. Fischer, J. C. Smith and S. Suhai. Can coordinate driving describe proton transfer coupled to complex protein motions? Phase Transitions 77(1-2): 47-52 (2004).
• Minoru Sugihara, Volker Buss, Peter Entel, Jürgen Hafner, Ana-Nicoleta Bondar, Marcus Elstner and Thomas Frauenheim. Ab Initio, Tight-Binding and QM/MM calculations of the rhodopsin chromophore in its binding pocket. Phase Transitions 77(1-2) 31-45 (2004).
• Ana-Nicoleta Bondar, Marcus Elstner, Sándor Suhai, Jeremy C. Smith and Stefan Fischer. Mechanism of primary proton transfer in bacteriorhodopsin. Structure 12: 1281-1288 (2004). (with a Preview by Menachem Gutman in Structure 12: 1123-1125 (2004)).
• Jeremy C. Smith, Franci Merzel, Ana-Nicoleta Bondar, Alexander Tournier and Stefan Fischer. Structure, dynamics and reactions of protein hydration water. Phil. Trans. Roy. Soc. B 359, 1181-1190 (2004).
• Ana-Nicoleta Bondar, Stefan Fischer, Jeremy C. Smith, Marcus Elstner, and Sándor Suhai. The key role of electrostatic interactions in bacteriorhodopsin proton transfer. J. Am. Chem. Soc. 126, 14668-14677 (2004).
• Ana-Nicoleta Bondar. Active ion transport across cellular membranes: The mechanism of the bacteriorhodopsin proton pump. PhD Thesis. University of Heidelberg (2004).
• Tetsuji Okada, Minoru Sugihara, Ana-Nicoleta Bondar, Marcus Elstner, Peter Entel and Volker Buss. The retinal conformation and its environment in light of a new 2.2 Å crystal structure. J. Mol. Biol. 342, 571-583 (2004).
• Andreea D. Gruia, Ana-Nicoleta Bondar, Jeremy C. Smith and Stefan Fischer. Mechanism of a molecular valve in the halorhodopsin chloride pump. Structure 13, 617-627 (2005).
• Ana-Nicoleta Bondar, Marcus Elstner, Sándor Suhai, Stefan Fischer and Jeremy C. Smith. Direct proton transfer in a putative L-state intermediate of the bacteriorhodopsin photocycle. Phase Transitions 78, 5-9 (2005).
• Ana-Nicoleta Bondar, Stefan Fischer, Sándor Suhai, and Jeremy C. Smith. Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps. J. Phys. Chem. B 109, 14786-14788 (2005).
• Ana-Nicoleta Bondar, Jeremy C. Smith, and Stefan Fischer. QM/MM investigation of the hydrogen bonding interactions in putative K and early-M intermediates of the bacteriorhodopsin photocycle. Phase Transitions 78, 671-675 (2005).
• Ana-Nicoleta Bondar. Pathways for retinal deprotonation in bacteriorhodopsin. Romanian Reports in Physics 57, 971-977 (2005).
• Ana-Nicoleta Bondar, Jeremy C. Smith, and Stefan Fischer. Structural and energetic determinants of primary proton transfer in bacteriorhodopsin. Photochem. Photobiol. Sci., Special Issue on Proton Transfer in Biological Systems, 5, 547-552 (2006).
• Ana-Nicoleta Bondar, Sándor Suhai, Stefan Fischer, Jeremy C. Smith, and Marcus 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, 454-469 (2007).
• Ana-Nicoleta Bondar, Sándor Suhai, Jeremy C. Smith, and Petre T. Frangopol. Computer simulations of local anesthetics mechanism: Quantum chemical investigation of procaine. Romanian Reports in Physics, 59:289-299 (2007).
• Ana-Nicoleta Bondar, Jerome Baudry, Sándor Suhai, Stefan Fisher, and Jeremy C. Smith. Key role of water molecules in bacteriorhodopsin proton-transfer reactions. J. Phys. Chem. B 112, 14729-14741 (2008).
• Ana-Nicoleta Bondar and Minoru Sugihara. Theoretical analysis of hydrogen-bonding in the active site of bovine rhodopsin. Revista de Chimie 59, 1260-1262 (2008).
• Ana-Nicoleta Bondar, Coral del Val, and Stephan H. White. Rhomboid protease dynamics and lipid interactions. Structure 17, 395-405 (2009).
• Ana-Nicoleta Bondar and Jeremy C. Smith. Water molecules in short- and long-distance proton transfer in bacteriorhodopsin. Israel J. Chem. 2009 49: 155-161.
• Ana-Nicoleta Bondar, Jeremy C. Smith, and Mercus Elstner. Mechanism of a proton pump analyzed with computer simulations. Theor. Chem. Acc. 2010, 125: 353-363.
• Prasad Phatak, Jan S. Frähmcke, Marius Wanko, Michael Hoffmann, Paul Strodel, Jeremy C. Smith, Sándor Suhai, Ana-Nicoleta Bondar, and Marcus Elstner. Long-distance proton transfer with a break in the bacteriorhodopsin active site. J. Am. Chem. Soc. 2009, doi 10.1021/ja809767v.
• Eduardo Jardón-Veladez, Ana-Nicoleta Bondar, and Douglas J. Tobias. Dynamics of the internal water molecules in squid rhodopsin. Biophys. J. 2009, 96: 2572-2576.
• Ana-Nicoleta Bondar, Coral del Val, J. Alfredo Freites, Douglas J. Tobias, and Stephen H. White. Dynamics of SecY translocons with translocation-defective mutations. Structure, 2010, In Press.
• Eduardo Jardon-Veladez, Ana-Nicoleta Bondar, and Douglas J. Tobias. Coupling of retinal, protein, and water dynamics in squid rhodopsin. Biophys. J., 2010, Accepted.

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A Brief Curriculum Vitae

• Postdoctoral studies (2004-2006), Computational Biophysics Group, University of Heidelberg, Germany (and ongoing collaboration with the Department of Molecular Biophysics, German Cancer Research Center Heidelberg.
• PhD magna cum laudae from the University of Heidelberg, Germany (2004). PhD studies (2000-2004) carried out jointly at the University of Heidelberg (with Prof. Jeremy C. Smith and Dr. Stefan Fischer) and the German Cancer Research Center (DKFZ) Heidelberg (with Prof. Sandor Suhai and Dr. Marcus Elstner).
• Advanced studies in Nonlinearity and self-organization within complex systems, Faculty of Physics, ‘Al. I. Cuza’ University Iasi, Romania (1997-1999, three semesters).
• B. S. Physics, ‘Al. I. Cuza’ University of Iasi, Romania (1992-1997). Research advisor for the diploma thesis: Prof. Petre T. Frangopol.

Fellowships

• Short-term fellowship from the Japan Society for the Promotion of Science. Host: Prof. Tsutomu Kouyama, Nagoya University, Japan (June 1-20, 2006).

Research Interests

Computer simulations of proteins and lipid membranes

Protein:protein and protein:lipid interactions

Intramembrane proteolysis

Ion pumping

Retinal proteins

QM/MM computations of proton transfer reactions

Mechanism of local anesthetics action

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