Viši naučni saradnik

 

 

 

 

 

Adresa:

IHTM, Centar za hemiju, Studentski trg 12-16, 11000 Beograd
Laboratorija za teorijsku hemiju
Telefon: +381 11 3336 610
Faks: +381 11 2636 061
Elektronska pošta: dpopovic@chem.bg.ac.rs

Obrazovanje:

1993. Diplomirani hemičar, Hemijski fakultet, Univerzitet u Beogradu.
2002. Doktor hemijskih nauka, Freie Universität, Berlin, Nemačka.

Zvanja:

2007. Assistant Specialist, step III, (Naučni saradnik) na University of California, Davis
2013. Istraživač saradnik
2015. Viši naučni saradnik

Članstva u društvima:

Srpsko hemijsko društvo, Američko hemijsko društvo

Profesionalno iskustvo:

1994 – 1998 Istraživač u Institutu za istraživanje i razvoj – Farmaceutska kompanija Zdravlje Leskovac
1998 – 2002 Doktorske studije na Freie Universität, Berlin, Nemačka
2002 – 2006 Postdoktorske studije na University of California, Davis, SAD
2006 – 2008 Naučni saradnik (Assistant Specialist) na University of California, Davis, SAD
2009 – 2010 Studijski boravak na City College of New York, SAD
2011 – 2012 Naučni saradnik na University of California, Davis, SAD
2013 – IHTM – Centar za hemiju

Oblasti interesovanja:

• Teorijska i računarska hemija
• Komjuterske simulacije bioloških makromolekulekula
• Molekulsko modelovanje
• Molekulska mehanika i molekulska dinamika
• Kombinovani kvantno-mehanički/kontinuum elektrostatički proračuni (QM/MM)
• Pretraga proteinske baze podataka
• Proračuni pKa vrednosti amino-kiselinskih ostataka i redoks potencijala kofaktora u proteinima
• Reakcioni mehanizami enzima
• Sprezanje reakcija transfera elektrona i protona
• Bioenergetika hemijskih procesa u proteinima
• Kinetika hemijskih reakcija
• Membranski proteini i protonske pumpe
• Respiratorni electron-transportni niz

Znanje jezika: Engleski i Nemački

Najznačajniji projekti:

Međunarodni:
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).
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).

Osnovna istraživanja:
2013 – 2015 "Racionalni dizajn i sinteza biološki aktivnih i koordinacionih jedinjenja i funkcionalnih materijala, relevantnih u (bio)nanotehnologiji" (projekat br. OI/172035, Mistarstvo za nauku i tehnološki razvoj Republike Srbije). Rukovodilac projekta: Dr. Aleksandar Nikolić.

Primenjena istraživanja:
1994 – 1998 "Istraživanje novih postupaka sinteze i polusinteze i karakterizacija bioaktivnih molekula" (projekat br. 02M34PT3, Ministarsvo za nauku i tehnologiju Republike Srbije). Rukovodilac projekta: Dr. Vlastimir Stamenković.

Izabrane publikacije:

Poglavlja u istaknutnim monografijama međunarodnog značaja:

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]

Publikovani radovi:

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. Citohrom c oksidaza - Molekulskа proton pumpa i njen reakcioni mehanizam. 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. Saopštenja:

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. 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.