Associate Research Professor
(Senior Research Associate)

 

 

 

 

Address:

Department of Chemistry, Institute of Chemistry, Technology and Metallurgy,
University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia Telephone: +381 11 3336 610
Fax: +381 11 2636 061
E-mail: dpopovic@chem.bg.ac.rs

Country of Birth: Serbia

Academic Degree:

1993 B.Sc. Chemistry (GPA: 9.87 on a 10.0 scale), Faculty of Chemistry, University of Belgrade
2002 Ph.D. Chemistry (magna cum laude), Free University (Freie Universität) of Berlin, Department of Chemistry, Biology and Pharmacy, Germany
dissertation: Modeling of conformation and redox potentials of hemes and other cofactors in proteins

Research Rank: 2015 Associate Research Professor – University of Belgrade, Institute of Chemistry, Technology and Metallurgy

Memberships:

ACS Member (American Chemical Society)
SCS Member (Serbian Chemical Society)

Professional Experience:

1994 – 1998 Industrial experience, researcher in the Institute for R&D (Lab: Organic synthesis) – Pharmaceutical company Zdravlje, Leskovac, Serbia
1998 – 2002 Doctoral studies at the Freie Universität, Berlin, Germany
2002 – 2006 Postdoctoral studies at the University of California, Davis, USA
2006 – 2008 Assistant Specialist at the University of California, Davis, USA
2009 – 2010 Study visit at the City College of New York, USA
2011 – 2012 University of California, Davis, USA
2013 – Present IChTM – Department of Chemistry

Awards and Honors:

1989 – 1993 Scholarship of ICN-Galenika, pharmaceutical company
1994 Award and diploma of Serbian Chemical Society for the best graduated student in 1992/93 at the Faculty of Chemistry, University of Belgrade
1998 – 2001 Graduate Fellowship, Humboldt University Berlin and German Research Society (DFG)
2001 – 2002 Research Fellowship, Department of Biochemistry - Charité Berlin and DFG (as visiting researcher)

Research Interests:

• Theoretical and computational chemistry
• Computer simulations of biological macromolecules
• Molecular modelling of synthetic proteins
• Protein data base mining
• Molecular mechanics (MM) and molecular dynamics (MD)
• Combined quantum-mechanical/continuum electrostatic approach (QM/MM)
• pKa and redox-potential calculations
• Reaction mechanisms in enzymes
• Coupling of electron and proton transfer reactions
• Bioenergetics of chemical processes in proteins
• Kinetics of chemical reactions
• Proton pumping
• Membrane proteins and respiratory electron-transport chain

Professional Achievements:

• Patented new methods of synthesis and characterization of bioactive molecules for treating cardiovascular diseases and scale up for pharmaceutical industrial production
• Introduced new computational method in research field of computational and theoretical biochemistry and biophysics of biopolymers, such as enzymes, proteins, DNA, polysaccharides, etc. by combining quantum-chemical and electrostatic calculations
• Proposed mechanism of proton pumping and catalytic cycle of cytochrome c oxidase – Coulomb pump model with kinetic gating, including gating through conformational states of Glu242 side-chain

Citations: 659 (586 without self-citations), Jan. 2016; h-index = 13

Language Skills: Serbian (native), English (proficiency), German (advanced), Russian (basic)

Major Projects:

International:
2002 – 2012 "Theoretical and computational studies of biological electron transfer", National Institute of Health (NIH grant project, No. GM 054052). Project Director: Prof. Dr. Alexei Stuchebrukhov (UC Davis).
2002 – 2012 "Electron tunneling in proteins", National Science Foundation (NSF grant project, No. PHY 0646273). Project Director: Prof. Dr. Alexei Stuchebrukhov (UC Davis).
2009 – 2010 "Importance of buried charges in proteins", National Science Foundation (NSF grant project, No. MCB 1022208). Project Director: Prof. Dr. Marilyn Gunner (CUNY).
2001 – 2002 "Protein-Kofaktor Wechselwirkungen in biologischen Prozessen", Deutsche Forschungs-gemeinschaft (SFB 498). Project Director: Prof. Dr. Dietmar Stehlik (Freie Universität Berlin).
1998 – 2001 "Dynamik und Evolution zellulärer und makromolekularer Prozesse", Deutsche Forschungs-gemeinschaft (GRK 268). Project Director: Prof. Dr. Reinhart Heinrich (Humboldt Universität Berlin).

National:
2013 – 2015 "Rational design and synthesis of biologically active and coordinated compounds and functional materials, relevant in (bio)nanotechnology" (project No. OI/172035, Ministry of Education, Science and Technological Development of the Republic of Serbia). Project Director: Dr. Aleksandar Nikolić.
1994 – 1998 " "Exploring new methods of synthesis and semi-synthesis and characterization of bioactive molecules" (project No. 02M34PT3, Ministry of Science and Technology of the Republic of Serbia). Project Director: Dr. Vlastimir Stamenković.

Major Publications:

Chapters in distinguished International Monographs:

1. Popović, D.M., Quenneville, J., Stuchebrukhov, A.A. Chapter 3/ Combined DFT and Electrostatic Calculations of pKa’s in proteins: Study of Cytochrome c Oxidase. In "Modern Methods for Theoretical Physical Chemistry of Biopolymers", Eds.: E.B. Starikow, J.P. Lewis, S. Tanaka. Elsevier, 53-78, 2006.  [ISBN: 978-0-444-52220-4]
2. Popović, D.M., Quenneville, J., Stuchebrukhov, A.A. Chapter 26/ Combined Density Functional Theory (DFT) and Electrostatics Study of the Proton Pumping Mechanism in Cytochrome c Oxidase. In "Computational Inorganic and Bioinorganic Chemistry", Eds.: Edward I. Solomon, Robert A. Scott, Bruce R. King. John Wiley & Sons, Ltd., 353-362, 2009. [ISBN: 978-0-470-69997-3]

Jouranal Papers:

1. Zarić, S.D., Popović, 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 (2000) 3935-3942.
2. Popović, D.M., Zarić, S.D., Rabenstein, B., Knapp, E.W. Artificial cytochrome b: Computer modeling and evaluation of redox potentials. Journal of the American Chemical Society 123 (2001) 6040-6053.
3. Popović, D.M., Zarić, S.D., Knapp, E.W. Factors determining the orientation of axially coordinated imidazoles in heme proteins. Biochemistry 40 (2001) 7914-7928.
4. Popović, D.M., Zmirić, A., Zarić, S.D., Knapp, E.W. Energetics of radical transfer in DNA photolyase. Journal of the American Chemical Society 124 (2002) 3775-3782.
5. Popović, 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 (2004) 1858-1871.
6. Popović, D.M., Stuchebrukhov, A.A. Proton pumping mechanism and catalytic cycle of cytochrome c oxidase: Coulomb pump model with kinetic gating. FEBS Letters 566 (2004) 126-130.
7. Popović, D.M., Stuchebrukhov, A.A. Proton exit channels in bovine cytochrome c oxidase. Journal of Physical Chemistry B 109 (2005) 1999-2006.
8. Quenneville, J., Popović, D.M., Stuchebrukhov, A.A. Redox-dependent pKa of CuB histidine ligand in cytochrome c oxidase. Journal of Physical Chemistry B 108 (2004) 18383-18389.
9. Popović, D.M., Quenneville, J., Stuchebrukhov, A.A. DFT/electrostatic calculations of pKa values in cytochrome c oxidase. Journal of Physical Chemistry B 109 (2005) 3616-3626.
10. Popović, D.M., Stuchebrukhov, A.A. Two conformational states of Glu242 and pKa’s in bovine cytochrome c oxidase. Photochemical & Photobiological Sciences 5 (2006) 611-620.
11. Makhov, D.V., Popović, D.M., Stuchebrukhov, A.A. Improved density functional theory/electrostatic calculation of the His291 protonation state in cytochrome c oxidase: Self-consistent charges for salvation energy calculation. Journal of Physical Chemistry B 110 (2006) 12162-12166.
12. Popović, D.M., Quenneville, J., Stuchebrukhov, A.A. Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase. Biochim. Biophys.Acta-Bioenergetics 1757 (2006) 1035-1046.
13. Medvedev, E.S., Kotelnikov, A.I., Barinov, A.V., Psikha, B.L., Ortega, J.M., Popović, D.M., Stuchebrukhov, A.A. Protein dynamics control of electron transfer in Photosynthetic Reaction Center from Rps. Sulfoviridis. Journal of Physical Chemistry B 112 (2008) 3208-3216.
14. Popović, D.M., Leontyev, I.V., Beech, D.G., Stuchebrukhov, A.A. Similarity of cytochrome c oxidases in different organisms. Proteins: Structure, Function, and Bioinformatics 78 (2010) 2691-2698.
15. Couch, V., Popović, D., Stuchebrukhov, A. Redox-Coupled Protonation of Respiratory Complex I: The Hydrophilic Domain. Biophys J. 101 (2011) 431-438.
16. Popović, D.M., Stuchebrukhov, A.A. Coupled electron and proton transfer reactions during the O→E transition in bovine cytochrome c oxidase. Biochim. Biophys. Acta-Bioenergetics 1817 (2012) 506-517.
17. Popović, D.M. Citochrome c oxidase - Molecular proton pump and its reaction mechanism. Hemijski Pregled  53, br.3 (2013) 58-66.
18. Popović, D.M. Nobel Prize 2013 for Chemistry from the cyber space. Hemijski Pregled 53, br.6 (2013) 142-147.
19. Popović, D.M. Current Advances in Research of Cytochrome c Oxidase. Invited review article, Amino Acids, 45 (2013) 1073-1087.

Selected presentations and conferencepapers:

1. D. Popović, A. Stuchebrukhov, "Coupled electron transfer: Proton transfer reactions and proton pumping mechanism of cytochrome c oxidase." Invited Talk, ACS Symposium in honor of Rudolph Marcus "Fifty Years of Electron Transfer and RRKM Theories" at 232nd American Chemical Society National Meeting, San Francisco, CA, USA, September 10-14, 2006.
2. D. Popović, "Proton pumping mechanism of cytochrome c oxidase: Electron-coupled proton transfer reactions." Invited Talk, Gordon Research Conference "Protons & Membrane Reactions", Ventura, CA, USA, February 22-27, 2009.
3. D. Popović, E.W. Knapp, "Artificial Metallo-Proteins – A Model of Cytochrome b." 5th World Congress of Theoretically Oriented Chemists, WATOC-99, London, UK, August 1-6, 1999.
4. D. Popović, E.W. Knapp, "Calculating redox potential in native and artificial cytochrome b." 3rd European Biophysics Conference 2000, München, Germany, September 9-13, 2000.
5. D. Popović, "Photoactivation mechanism of DNA photolyase." Talk, 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), Belgrade, Serbia, June 27-29, 2013.
6. D. Popović, “Energetics of the steps in proton pumping mechanism and preventing of backflow reactions in cytochrome c oxidase.” Talk, 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), Belgrade, Serbia, June 27-29, 2013.
7. 7.    D. Popović, I. Juranić, “Influence of protein environment on redox properties of cofactors: Redox potentials of artificial cytochrome b.” Conference paper & Talk, Vol: Proceedings, pp. 96-100 (TH O 1), 52nd Meeting of the Serbian Chemical Society, Novi Sad, Serbia, May 29-30, 2015.