Ana-Nicoleta Bondar
Assistant Project Scientist
Department of Physiology and Biophysics
University of California at Irvine
Med. Sci. I, D-347
Irvine, CA 92697-4560
Voice: 949-824-6993
FAX: 949-824-8540
E-Mail:
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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).
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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).
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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).
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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)).
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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).
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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).
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Ana-Nicoleta Bondar.
Active ion transport across cellular membranes: The
mechanism of the bacteriorhodopsin proton pump.
PhD Thesis. University of Heidelberg (2004).
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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).
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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).
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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).
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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).
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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).
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Ana-Nicoleta Bondar.
Pathways for retinal deprotonation in bacteriorhodopsin.
Romanian Reports in Physics 57, 971-977 (2005).
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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).
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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).
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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, In Press.
A Brief Curriculum Vitae
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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.
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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).
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Advanced studies in Nonlinearity and self-organization within complex
systems, Faculty of Physics, ‘Al. I. Cuza’ University Iasi,
Romania (1997-1999, three semesters).
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B. S. Physics, ‘Al. I. Cuza’ University of Iasi, Romania
(1992-1997). Research advisor for the diploma thesis: Prof.
Petre T. Frangopol.
Fellowships
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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
