Microsoft word - cv popovic _may 2007_ 3.doc

DRAGAN POPOVIC
Department of Chemistry, University of California, Davis One Shields Avenue, Davis, California 95616, USA (530)754-8695 (office); (530)752-8995 (fax) EDUCATION
Ph.D. Chemistry magna cum laude, Freie Universität Berlin in Germany, 2002
Dissertation: “Modeling of Conformation and Redox Potentials of Hemes and Other
Cofactors in Proteins”, available online: http://www.diss.fu-berlin.de/2002/12/
Advisor: Prof. Ernst-Walter Knapp
B.S. Chemistry (GPA: 9.78 on a 10.0 scale), University of Belgrade in Serbia, 1993
Diploma thesis: “The ligand field analysis of NxO6-x chromophores”; Diploma exam grade: 10
AREAS OF SPECIALIZATION
• continuum electrostatic and pKa calculations in proteins • ab initio and DFT calculations • combined quantum/classical treatment of biological macromolecular systems • coupled electron and proton transfer reactions • proton pumping and DNA repair • molecular dynamics simulations • organic synthesis of active compounds for lowering high blood pressure RESEARCH EXPERIENCE
Assistant Specialist, University of California, Davis, 02/2007 – present
Postdoctoral Research, University of California, Davis, 08/2002 – 02/2007
DFT/continuum electrostatic method; solvation energy and pKa calculations; mitochondrial
respiratory electron transport chain; coupled electron and proton transfer reactions; oxygen
reduction and proton pumping in cytochrome c oxidase; redox-dependent acidity of copper-
histidine ligand in proton pumping mechanism; Coulomb pump model with kinetic gating;
kinetics of pump (loaded) and chemical (substrate) protons – fast vs. slow proton transfer
phase; proton translocation along the proton-conducting (entrance and exit) channels by
Grotthus mechanism; catalytic cycle of cytochrome c oxidase
Professor Alexei A. Stuchebrukhov, Department of Chemistry

Doctoral Research, Free University of Berlin, 10/1998 – 01/2002
(employed after graduation as Guest Researcher, until 08/2002)
PDB data mining of heme-proteins; molecular modeling of the artificial cyt b – four-helix
bundle attached to cyclic decapeptide as a template; ab initio quantum chemistry; classical
molecular dynamics simulations; continuum electrostatic method solving the Poisson-
Boltzmann eq.; pKa and redox potential evaluation; Monte Carlo acid-base titration; method extended to perform redox titration; protonation and redox behavior of different residues and redox-active groups; redox-Bohr effect; energetics of the photoactivation process in DNA photolyse; influence of different structural parts analyzed to understand how protein environment tunes the redox potential of cofactors and pKa’s of protonatable groups; cation-π interactions
Professor Ernst-Walter Knapp, Department of Chemistry
Undergraduate Research, University of Belgrade, 02/1993 – 11/1993
Angular overlap method (AOM); ligand field analysis of different six-coordinated
metal-ligand complexes containing nitrogen and oxygen as ligated atoms
Professor Svetozar Niketic, Department of Chemistry
TEACHING EXPERIENCE
Teaching Assistant, Department of Chemistry, Free University of Berlin
Computational Biochemistry Practicum, two-week course “Computer simulations of biological macromolecules“, six times between Fall 1999 – Spring 2002 Teaching Assistant, Department of Chemistry, University of Belgrade
Theory of Chemical Bonds, Spring 1993 Organic Chemistry Laboratory, Fall 1992 General Chemistry, Spring 1992 INDUSTRIAL EXPERIENCE
Research Associate, Zdravlje Pharmaceutical Comp., Leskovac, Serbia, 05/1994 – 09/1998
novel procedures developed for synthesis of the active compounds for lowering
high blood pressure; synthetic organic chemistry and product analytical control
Institute for Research and Development of Zdravlje Pharmaceutical Company
COMPUTER EXPERIENCE
• Programming: code development with C • Computational chemistry packages: Gaussian, CHARMM, MEAD, Karlsberg • Operating Systems: Windows Vista/XP/2000, Linux, UNIX (SGI, DEC), Macintosh OS • Software: MS Office, EndNote, MathType, Adobe Photoshop, Illustrator, Canvas, Origin, XMGR, VMD, WebLab Viewer, RasMol, MDL ISIS Draw • Website design, construction: http://stuchebrukhov.ucdavis.edu/ LANGUAGE SKILLS
Serbian (native), English (fluent), German (intermediate level), understand several Slavic languages PROFESSIONAL AFFILIATIONS, AWARDS, HONORS
Member of American Chemical Society, 2003 – present Department of Bioinformatics Research Fellowship, Charité, Berlin, 2002 “Dynamik und Evolution zellulärer und makromolekularer Prozesse” (GRK 268) Graduate Fellowship, Humboldt University, Berlin, 1998 – 2001 Serbian Chemical Society Award for the Best Graduated Student, 1994 “Galenika–ICN” Undergraduate Scholarship, University of Belgrade, 1989 – 1993 PUBLICATIONS
Journal Articles:
Zaric, S.D., Popovic, D.M. & Knapp, E.W. Metal ligand aromatic cation-π interactions in metalloproteins: Ligands coordinated to metal interact with aromatic residues. Chemistry – A European Journal 6: 3935. Popovic, D.M., Zaric, S.D., Rabenstein, B. & Knapp, E.W. Artificial cytochrome b: Computer modeling and evaluation of redox potentials. Journal of the American Chemical Society 123: 6040. Zaric, S.D., Popovic, D.M. & Knapp, E.W. Factors determining the orientation of axially coordinated imidazoles in heme proteins. Biochemistry 40: 7914. Popovic, D.M., Zmiric, A., Zaric, S.D. & Knapp, E.W. Energetics of radical transfer in DNA photolyase. Journal of the American Chemical Society 124: 3775. Knapp, E.W., Popovic, D.M. & Zaric, S.D. Synthetic cytochrome b: Computer modeling and evaluation of redox potentials. Abstracts of Papers of the American Chemical Society 223: C52. Popovic, D., Zheng, X., Quenneville, J. & Stuchebrukhov, A. Computer simulations of cytochrome c oxidase. Biophysical Journal 84: 458A. Popovic, D.M. & Stuchebrukhov, A.A. Electrostatic study of the proton pumping mechanism in bovine heart cytochrome c oxidase. Journal of the American Chemical Society 126: 1858. Popovic, D.M. & Stuchebrukhov, A.A. Proton pumping mechanism and catalytic cycle of cytochrome c oxidase: Coulomb pump model with kinetic gating. FEBS Letters 566: 126. Popovic, D. & Stuchebrukhov, A. Computational study of proton pumping mechanism of bovine heart cytochrome c oxidase. Biophysical Journal 86: 258A. Quenneville, J., Popovic, D.M. & Stuchebrukhov, A.A. Redox-dependent pKa of CuB histidine ligand in cytochrome c oxidase. Journal of Physical Chemistry B 108: 18383. Popovic, D.M. & Stuchebrukhov, A.A. Proton exit channels in bovine cytochrome c oxidase. Journal of Physical Chemistry B 109: 1999. Popovic, D.M., Quenneville, J. & Stuchebrukhov, A.A. DFT/electrostatic calculations of pKa values in cytochrome c oxidase. Journal of Physical Chemistry B 109: 3616. Popovic, D.M. & Stuchebrukhov, A.A. Two conformational states of Glu242 and pKa’s in bovine cytochrome c oxidase. Photochemical & Photobiological Sciences 5: 611. Quenneville, J., Popovic, D.M. & Stuchebrukhov, A.A. Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase. Biochimica Et Biophysica Acta-Bioenergetics 1757: 1035. Makhov, D.V., Popovic, D.M. & Stuchebrukhov, A.A. Improved density functional theory/electrostatic calculation of the His291 protonation state in cytochrome c oxidase: Self-consistent charges for solvation energy calculation. Journal of Physical Chemistry B 110: 12162. Stuchebrukhov, A.A. & Popovic, D.M. Comment on "acidity of a Cu-bound histidine in the binuclear center of cytochrome c oxidase". Journal of Physical Chemistry B 110: 17286. Popovic, D.M., Quenneville, J. & Stuchebrukhov, A.A. Combined DFT and Electrostatic Calculations of pKa’s in proteins: Study of Cytochrome c Oxidase. Review chapter for the book: "Modern Methods for Theoretical Physical Chemistry of Biopolymers", Editors: E.B. Starikow, J.P. Lewis, S. Tanaka, Elsevier 2006, [ISBN:0-444-52220-4]. Medvedev, E.S., Kotelnikov, A.I., Barinov, A.V., Psikha, B.L., Ortega, J.M., Popovic, D.M. & Stuchebrukhov, A.A. Protein dynamics control of electron transfer in Photosynthetic Reaction Center from Rps. Sulfoviridis. Accepted to Journal of Physical Chemistry B. Popovic, D.M., Makhov, D.V., & Stuchebrukhov, A.A. Energetics of an Excess Proton in D-channel of Cytochrome c Oxidase. Submitted to Journal of the American Chemical Society. YU Patents:
Stankovic, S.; Stojanovic, N.; Stojanovic, D.; Stanojevic, C.; Popovic, D. Procedure For Synthesis Of
Atenolol (ATENOLOL). Application number P-394/98, submitted on 09/07/1998, published on
08/12/2002. Patent number YU 49569 B, issued date 04/10/2007; AD Zdravlje, Center for Research and
Development, Vlajkova 199, 16000 Leskovac, Yugoslavia. (Int. Cl.: C 07 C 233/22; A 61 K 31/165).
Stankovic, S.; Stojanovic, N.; Stojicic, S.; Mitov, S.; Popovic, D. Procedure For Synthesis Of 1,4-
Dihydropyridine Derivatives (NIFELAT, NITRENDIPIN, NISOLDIPIN). Application number P-250/99,
submitted on 06/04/1999, published on 08/12/2002; AD Zdravlje, Center for Research and Development,
Vlajkova 199, 16000 Leskovac, Yugoslavia. (Int. Cl.: C 07 D 211/80; A 61 K 31/44).
Ph.D. Thesis:
D. M. Popovic. “Modeling of Conformation and Redox Potentials of Hemes and Other Cofactors in Proteins”, available online: http://www.diss.fu-berlin.de/2002/12/. (Free University, Berlin, Jan. 2002). PRESENTATIONS
D. Popovic and A. Stuchebrukhov, “Coupled Electron and Proton Transfer Reactions and Proton
Pumping Mechanism of Cytochrome c Oxidase.” Talk, Symposium in honor of Rudy Marcus at 232nd
American Chemical Society National Meeting, San Francisco, CA, USA, September 10-14, 2006.
D. Popovic and E.W. Knapp, “Electrostatics of Native and Artificial Cytochrome b.” Talk & Poster,
Workshop “Biophysics and Bioinformatics” – 2001, Berlin, Germany, August 22-25, 2001.

D. Popovic and E.W. Knapp, “Calculating Redox Potential in Native and Artificial Cytochrome b.” Talk
& Poster, Evaluation of the Graduiertenkolleg (GRK 268) by the German Research Society (DFG),
Humboldt University, Berlin, Germany, July 14-15, 1999.

D. Popovic and E.W. Knapp, “Artificial Metallo-Proteins – A Model of Cytochrome b.” Talk & Poster,
Workshop 1999 of the Graduate Programme ''Dynamics and Evolution of Cellular and Macromolecular
Processes'', Hiddensee, Germany, March 17-19, 1999.
D. Popovic and A. Stuchebrukhov, “Proton Pumping Mechanism of Cytochrome c Oxidase: Electron-
Coupled Proton Transfer Reactions.” Poster, 232nd American Chemical Society National Meeting, San
Francisco, CA, USA, September 10-14, 2006.
D. Popovic and E.W. Knapp, “Artificial Metallo-Proteins – A Model of Cytochrome b.” Poster, 5th
World Congress of Theoretically Oriented Chemists, WATOC-99, London, August 1-6, 1999.
D. Popovic and A. Stuchebrukhov, “Computational Studies of Proton Pumping Mechanism of
Cytochrome c Oxidase.” Poster, 13th European Bioenergetics Conference (EBEC 2004), Pisa, Italy,
August 21-26, 2004.
D. Popovic and A. Stuchebrukhov, “Computational Study of Proton Pumping Mechanism of Bovine
Heart Cytochrome c Oxidase.” Poster, Biophysical Society 48th Annual Meeting (BPS2004), Baltimore,
MD, USA, February 14-18, 2004.
D. Popovic, X. Zheng, and A. Stuchebrukhov, “Coupled Electron and Proton Transfer Reactions, Proton
Pumps, and Cytochrome c Oxidase: A Computational Study.” Poster, Hawaii Int. Conference, Honolulu,
Hawaii, USA, January 15-18, 2004.

D. Popovic and E.W. Knapp, “Electrostatic Calculations of Native and Artificial Cytochrome b: Redox
Potential Evaluation.” Poster, European Biophysics Conference 2000, München, Germany, September 9-
13, 2000.
D. Popovic and E.W. Knapp, “Factors Determining the Orientation of Axially Coordinated Imidazoles in
Heme-Proteins” Poster, European Biophysics Conference 2000, München, Germany, September 9-13,
2000.
REFERENCES
Davis, CA 95616 Prof. Robert B. Gennis, Ph.D. Urbana, IL 61801 Prof. Alexander M. Kuznetsov, Ph.D. A. N. Frumkin Institute of Electrochemistry, Russian Acad. of Sciences, Moscow 117071, Russia Prof. Emile S. Medvedev, Ph.D. Institute of Chemical Physics in Chernogolovka, Russian Acad. of Sciences, Chernogolovka 142432, Russia

Source: http://stuchebrukhov.ucdavis.edu/members/DP_CV.pdf