TY  - CONF
AU  - Popović, Dragan
PY  - 2024
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7459
AB  - The interactions between the enclosed protein environment and cofactors are crucial in understanding redox protein systems. The redox potential (Em) is a key parameter of all redox active proteins and is easily accessible in experimental and computational studies. By advanced computational methods, this research examined in-depth the complex relationship between a confined protein system and its cofactor within a bioinspired protein scaffold and found multiple contributing factors. The Em values were dissected to identify interactions in heme proteins that contribute to various energy terms.
PB  - COST Action CA21101 "COSY"
C3  - The 1st Virtual meeting WG2 of COST action CA21101 COSY "From quantum to classical dynamics of isolated molecules and 3D materials", February 6, 2024, Belgrade, Serbia
T1  - Protein environment – cofactor interactions in redox protein systems
SP  - 15
EP  - 15
UR  - https://hdl.handle.net/21.15107/rcub_cer_7459
ER  - 

@conference{
author = "Popović, Dragan",
year = "2024",
abstract = "The interactions between the enclosed protein environment and cofactors are crucial in understanding redox protein systems. The redox potential (Em) is a key parameter of all redox active proteins and is easily accessible in experimental and computational studies. By advanced computational methods, this research examined in-depth the complex relationship between a confined protein system and its cofactor within a bioinspired protein scaffold and found multiple contributing factors. The Em values were dissected to identify interactions in heme proteins that contribute to various energy terms.",
publisher = "COST Action CA21101 "COSY"",
journal = "The 1st Virtual meeting WG2 of COST action CA21101 COSY "From quantum to classical dynamics of isolated molecules and 3D materials", February 6, 2024, Belgrade, Serbia",
title = "Protein environment – cofactor interactions in redox protein systems",
pages = "15-15",
url = "https://hdl.handle.net/21.15107/rcub_cer_7459"
}

Popović, D.. (2024). Protein environment – cofactor interactions in redox protein systems. in The 1st Virtual meeting WG2 of COST action CA21101 COSY "From quantum to classical dynamics of isolated molecules and 3D materials", February 6, 2024, Belgrade, Serbia
COST Action CA21101 "COSY"., 15-15.
https://hdl.handle.net/21.15107/rcub_cer_7459

Popović D. Protein environment – cofactor interactions in redox protein systems. in The 1st Virtual meeting WG2 of COST action CA21101 COSY "From quantum to classical dynamics of isolated molecules and 3D materials", February 6, 2024, Belgrade, Serbia. 2024;:15-15.
https://hdl.handle.net/21.15107/rcub_cer_7459 .

Popović, Dragan, "Protein environment – cofactor interactions in redox protein systems" in The 1st Virtual meeting WG2 of COST action CA21101 COSY "From quantum to classical dynamics of isolated molecules and 3D materials", February 6, 2024, Belgrade, Serbia (2024):15-15,
https://hdl.handle.net/21.15107/rcub_cer_7459 .

TY  - JOUR
AU  - Protić-Rosić, Isidora
AU  - Lopandić, Zorana
AU  - Popović, Dragan
AU  - Blagojević, Gordan
AU  - Gavrović-Jankulović, Marija
PY  - 2024
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7457
AB  - Novel allergen immunotherapy (AIT) approaches necessitate the use of more effective and safe therapeutics, which can be accomplished by employing novel adjuvants for improved innate immune cell activation, as well as hypoallergenic allergen forms. In this study, we investigate the immunomodulatory effects of a chimera rBet v 1a-BanLecwt (rBv1a-BLwt; Cwt) composed of the major birch pollen allergen Bet v 1a and banana lectin (BanLecwt; BLwt) and two novel chimeras, rBv1l-BLH84T (rBet v 1l-BanLecH84T; C1) and rBLH84T-Bv1l (rBanLecH84T-Bet v 1l; C2), both composed of BLH84T and hypoallergenic birch pollen allergen Bv1l in the co-culture model Caco-2/THP-1, and PBMCs from donors with birch pollen allergy. The chimeric molecules rBv1l-BLH84T (C1) and rBLH84T-Bv1l (C2) were created in silico and then produced in E. coli using recombinant DNA technology. Real-time PCR analysis of gene expression following compound treatment in the co-culture model revealed that all three chimeras have the potential to induce the anti-inflammatory cytokine IL-10 gene expression in Caco-2 cells and IFN-γ gene expression in THP-1 cells. Sandwich ELISA revealed that Cwt increased IL-10 secretion and IFN-/IL-4 levels in PBMCs from birch pollen allergic donors, whereas C1 and C2 were less effective. The findings suggest that Cwt should be analyzed further due to its potential benefit in AIT.
PB  - Elsevier
T2  - International Immunopharmacology
T1  - rBet v 1a-BanLec_wt induce upregulation of IL-10 and IFN-γ gene expression in Caco-2/THP-1 co-culture and secretion of IL-10 and IFN-γ/IL-4 levels in PBMCs of birch pollen allergic donors
VL  - 129
SP  - 111607
DO  - 10.1016/j.intimp.2024.111607
ER  - 

@article{
author = "Protić-Rosić, Isidora and Lopandić, Zorana and Popović, Dragan and Blagojević, Gordan and Gavrović-Jankulović, Marija",
year = "2024",
abstract = "Novel allergen immunotherapy (AIT) approaches necessitate the use of more effective and safe therapeutics, which can be accomplished by employing novel adjuvants for improved innate immune cell activation, as well as hypoallergenic allergen forms. In this study, we investigate the immunomodulatory effects of a chimera rBet v 1a-BanLecwt (rBv1a-BLwt; Cwt) composed of the major birch pollen allergen Bet v 1a and banana lectin (BanLecwt; BLwt) and two novel chimeras, rBv1l-BLH84T (rBet v 1l-BanLecH84T; C1) and rBLH84T-Bv1l (rBanLecH84T-Bet v 1l; C2), both composed of BLH84T and hypoallergenic birch pollen allergen Bv1l in the co-culture model Caco-2/THP-1, and PBMCs from donors with birch pollen allergy. The chimeric molecules rBv1l-BLH84T (C1) and rBLH84T-Bv1l (C2) were created in silico and then produced in E. coli using recombinant DNA technology. Real-time PCR analysis of gene expression following compound treatment in the co-culture model revealed that all three chimeras have the potential to induce the anti-inflammatory cytokine IL-10 gene expression in Caco-2 cells and IFN-γ gene expression in THP-1 cells. Sandwich ELISA revealed that Cwt increased IL-10 secretion and IFN-/IL-4 levels in PBMCs from birch pollen allergic donors, whereas C1 and C2 were less effective. The findings suggest that Cwt should be analyzed further due to its potential benefit in AIT.",
publisher = "Elsevier",
journal = "International Immunopharmacology",
title = "rBet v 1a-BanLec_wt induce upregulation of IL-10 and IFN-γ gene expression in Caco-2/THP-1 co-culture and secretion of IL-10 and IFN-γ/IL-4 levels in PBMCs of birch pollen allergic donors",
volume = "129",
pages = "111607",
doi = "10.1016/j.intimp.2024.111607"
}

Protić-Rosić, I., Lopandić, Z., Popović, D., Blagojević, G.,& Gavrović-Jankulović, M.. (2024). rBet v 1a-BanLec_wt induce upregulation of IL-10 and IFN-γ gene expression in Caco-2/THP-1 co-culture and secretion of IL-10 and IFN-γ/IL-4 levels in PBMCs of birch pollen allergic donors. in International Immunopharmacology
Elsevier., 129, 111607.
https://doi.org/10.1016/j.intimp.2024.111607

Protić-Rosić I, Lopandić Z, Popović D, Blagojević G, Gavrović-Jankulović M. rBet v 1a-BanLec_wt induce upregulation of IL-10 and IFN-γ gene expression in Caco-2/THP-1 co-culture and secretion of IL-10 and IFN-γ/IL-4 levels in PBMCs of birch pollen allergic donors. in International Immunopharmacology. 2024;129:111607.
doi:10.1016/j.intimp.2024.111607 .

Protić-Rosić, Isidora, Lopandić, Zorana, Popović, Dragan, Blagojević, Gordan, Gavrović-Jankulović, Marija, "rBet v 1a-BanLec_wt induce upregulation of IL-10 and IFN-γ gene expression in Caco-2/THP-1 co-culture and secretion of IL-10 and IFN-γ/IL-4 levels in PBMCs of birch pollen allergic donors" in International Immunopharmacology, 129 (2024):111607,
https://doi.org/10.1016/j.intimp.2024.111607 . .

TY  - CONF
AU  - Protić-Rosić, Isidora
AU  - Lopandić, Zorana
AU  - Popović, Dragan
AU  - Blagojević, Gordan
AU  - Gavrović-Jankulović, Marija
PY  - 2023
UR  - http://intor.torlakinstitut.com/handle/123456789/714
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6817
AB  - Allergen immunotherapy (AIT) is currently the only disease-modifying treatment forallergies. Pre-clinical models for the evaluation of novel therapeutics are crucial forensuring their efficacy and safety. While cell culture models are cost-effective andefficient, they cannot fully replicate the cellular interactions in vivo. Therefore, it isessential to use more sophisticated model systems, such as co-cultures, to assess thepotential of new therapeutics more accurately. Immunomodulatory protein banana lectin(BLwt) is an attractive candidate for adjuvant in AIT. Its mutant BLH84T was developed toreduce its potential mitogenicity. The aim of this study was the development of the coculture model system for testing the immunomodulatory effect of chimeras composed ofthe major birch pollen allergen (Bv1a) and BLwt (Bv1a-BLwt, Cwt), the hypoallergenicisoform of Bv1a (Bv1l) and BLH84T (Bv1l-BLH84T, C1 and BLH84T-Bv1l, C2). Chimericstructures were designed in silico, fully minimized, and relaxed without van der Waalsatomic clashes. Afterward, proteins were successfully expressed in Escherichia coli andpurified by IMAC yielding around 0.4 mg per 1L of expression medium. The IgE bindingcapacity was assessed using ELISA inhibition with birch pollen allergic patients’ sera.Caco-2 intestinal epithelial cells and THP-1 differentiated macrophages were used for theco-culture model system development. After protein application on the apical side of theco-culture, the integrity of the epithelial monolayer was not disturbed. Theimmunomodulatory potential of antigens was tested by measuring the gene expressionlevels for pro- and anti-inflammatory cytokines in both cell lines from co-culture. Theobtained results indicate that the best anti-inflammatory response was favored aftertreatment with Cwt. Additionally, to further confirm the immunomodulatory effect of therecombinant chimeras, PBMCs obtained from individuals allergic to birch pollen wereemployed and treated with recombinant proteins. Only after treatment with Cwt, PBMCssecreted the anti-inflammatory cytokine IL-10. Obtained results suggest that Cwt chimeracould have a therapeutic effect in AIT in birch pollen allergy.
PB  - Faculty of Chemistry
PB  - Serbian Biochemical Society
C3  - Serbian Biochemical Society Twelfth Conference International scientific meeting September 21-23, 2023, Belgrade, Serbia “Biochemistry in Biotechnology”
T1  - Evaluation of the immunomodulatory potential of chimera Bv1a-BLwt and its mutants on the co-culture model system
SP  - 71
EP  - 72
UR  - https://hdl.handle.net/21.15107/rcub_cer_6817
ER  - 

@conference{
author = "Protić-Rosić, Isidora and Lopandić, Zorana and Popović, Dragan and Blagojević, Gordan and Gavrović-Jankulović, Marija",
year = "2023",
abstract = "Allergen immunotherapy (AIT) is currently the only disease-modifying treatment forallergies. Pre-clinical models for the evaluation of novel therapeutics are crucial forensuring their efficacy and safety. While cell culture models are cost-effective andefficient, they cannot fully replicate the cellular interactions in vivo. Therefore, it isessential to use more sophisticated model systems, such as co-cultures, to assess thepotential of new therapeutics more accurately. Immunomodulatory protein banana lectin(BLwt) is an attractive candidate for adjuvant in AIT. Its mutant BLH84T was developed toreduce its potential mitogenicity. The aim of this study was the development of the coculture model system for testing the immunomodulatory effect of chimeras composed ofthe major birch pollen allergen (Bv1a) and BLwt (Bv1a-BLwt, Cwt), the hypoallergenicisoform of Bv1a (Bv1l) and BLH84T (Bv1l-BLH84T, C1 and BLH84T-Bv1l, C2). Chimericstructures were designed in silico, fully minimized, and relaxed without van der Waalsatomic clashes. Afterward, proteins were successfully expressed in Escherichia coli andpurified by IMAC yielding around 0.4 mg per 1L of expression medium. The IgE bindingcapacity was assessed using ELISA inhibition with birch pollen allergic patients’ sera.Caco-2 intestinal epithelial cells and THP-1 differentiated macrophages were used for theco-culture model system development. After protein application on the apical side of theco-culture, the integrity of the epithelial monolayer was not disturbed. Theimmunomodulatory potential of antigens was tested by measuring the gene expressionlevels for pro- and anti-inflammatory cytokines in both cell lines from co-culture. Theobtained results indicate that the best anti-inflammatory response was favored aftertreatment with Cwt. Additionally, to further confirm the immunomodulatory effect of therecombinant chimeras, PBMCs obtained from individuals allergic to birch pollen wereemployed and treated with recombinant proteins. Only after treatment with Cwt, PBMCssecreted the anti-inflammatory cytokine IL-10. Obtained results suggest that Cwt chimeracould have a therapeutic effect in AIT in birch pollen allergy.",
publisher = "Faculty of Chemistry, Serbian Biochemical Society",
journal = "Serbian Biochemical Society Twelfth Conference International scientific meeting September 21-23, 2023, Belgrade, Serbia “Biochemistry in Biotechnology”",
title = "Evaluation of the immunomodulatory potential of chimera Bv1a-BLwt and its mutants on the co-culture model system",
pages = "71-72",
url = "https://hdl.handle.net/21.15107/rcub_cer_6817"
}

Protić-Rosić, I., Lopandić, Z., Popović, D., Blagojević, G.,& Gavrović-Jankulović, M.. (2023). Evaluation of the immunomodulatory potential of chimera Bv1a-BLwt and its mutants on the co-culture model system. in Serbian Biochemical Society Twelfth Conference International scientific meeting September 21-23, 2023, Belgrade, Serbia “Biochemistry in Biotechnology”
Faculty of Chemistry., 71-72.
https://hdl.handle.net/21.15107/rcub_cer_6817

Protić-Rosić I, Lopandić Z, Popović D, Blagojević G, Gavrović-Jankulović M. Evaluation of the immunomodulatory potential of chimera Bv1a-BLwt and its mutants on the co-culture model system. in Serbian Biochemical Society Twelfth Conference International scientific meeting September 21-23, 2023, Belgrade, Serbia “Biochemistry in Biotechnology”. 2023;:71-72.
https://hdl.handle.net/21.15107/rcub_cer_6817 .

Protić-Rosić, Isidora, Lopandić, Zorana, Popović, Dragan, Blagojević, Gordan, Gavrović-Jankulović, Marija, "Evaluation of the immunomodulatory potential of chimera Bv1a-BLwt and its mutants on the co-culture model system" in Serbian Biochemical Society Twelfth Conference International scientific meeting September 21-23, 2023, Belgrade, Serbia “Biochemistry in Biotechnology” (2023):71-72,
https://hdl.handle.net/21.15107/rcub_cer_6817 .

TY  - CONF
AU  - Đorđević, Ivana
AU  - Popović, Dragan
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6815
AB  - Here we have included the conformational gating by Glu242 into a framework of the proposed  His291 pumping model [4]. DFT/electrostatic calculations are employed to obtain energetics of  the proton and electron transfer reaction steps during the O→E transition [2, 3, 5–7]. In addition,  transition state theory estimates activation energies and kinetic barriers from the rate constant of  transitions. The energy profile of the reaction mechanism is studied by exploring how the redox  state of the metal centers, dielectric solvation effects, and membrane potential gradient affect the  energy levels and possible leakage of the protein pump through the Glu242 gating site. Particular  emphasis is made on side reactions that may short-circuit the pump, resulting in a loss of proton  pumping, and how this may be avoided in natural biological systems [2, 3]. CcO employs several  control mechanisms and gating situations to ensure the proton translocation unidirectionality and  prevent proton leak in the opposite direction
PB  - COST Action CA21101 "COSY"
C3  - Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade
T1  - Energetics and Kinetics of Steps in Proton Pumping Mechanism of Mammalian Cytochrome c Oxidase
SP  - 43
EP  - 43
UR  - https://hdl.handle.net/21.15107/rcub_cer_6815
ER  - 

@conference{
author = "Đorđević, Ivana and Popović, Dragan",
year = "2023",
abstract = "Here we have included the conformational gating by Glu242 into a framework of the proposed  His291 pumping model [4]. DFT/electrostatic calculations are employed to obtain energetics of  the proton and electron transfer reaction steps during the O→E transition [2, 3, 5–7]. In addition,  transition state theory estimates activation energies and kinetic barriers from the rate constant of  transitions. The energy profile of the reaction mechanism is studied by exploring how the redox  state of the metal centers, dielectric solvation effects, and membrane potential gradient affect the  energy levels and possible leakage of the protein pump through the Glu242 gating site. Particular  emphasis is made on side reactions that may short-circuit the pump, resulting in a loss of proton  pumping, and how this may be avoided in natural biological systems [2, 3]. CcO employs several  control mechanisms and gating situations to ensure the proton translocation unidirectionality and  prevent proton leak in the opposite direction",
publisher = "COST Action CA21101 "COSY"",
journal = "Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade",
title = "Energetics and Kinetics of Steps in Proton Pumping Mechanism of Mammalian Cytochrome c Oxidase",
pages = "43-43",
url = "https://hdl.handle.net/21.15107/rcub_cer_6815"
}

Đorđević, I.,& Popović, D.. (2023). Energetics and Kinetics of Steps in Proton Pumping Mechanism of Mammalian Cytochrome c Oxidase. in Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade
COST Action CA21101 "COSY"., 43-43.
https://hdl.handle.net/21.15107/rcub_cer_6815

Đorđević I, Popović D. Energetics and Kinetics of Steps in Proton Pumping Mechanism of Mammalian Cytochrome c Oxidase. in Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade. 2023;:43-43.
https://hdl.handle.net/21.15107/rcub_cer_6815 .

Đorđević, Ivana, Popović, Dragan, "Energetics and Kinetics of Steps in Proton Pumping Mechanism of Mammalian Cytochrome c Oxidase" in Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade (2023):43-43,
https://hdl.handle.net/21.15107/rcub_cer_6815 .

TY  - CONF
AU  - Popović, Dragan
AU  - Đorđević, Ivana
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6814
AB  - With computer simulations that assess pKas of critical residues, explore electron and proton pathways, and evaluate the energetics of PT and ET processes, we can provide a more in-depth understanding of the molecular mechanism and catalytic cycle of CcO. Combining the DFT electronic structure and energy calculations with reaction and protein field contributions allows self-consistent solvation energy calculations to be iteratively performed. Moreover, valuable insights into mechanistic details and energetics of proton pumping and coupled ET/PT reactions are gained at the atomic level.
PB  - COST Action CA21101 "COSY"
C3  - Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade
T1  - DFT/Solvation Continuum Electrostatic Calculations of Proton  Pumping in Mammalian Cytochrome c Oxidase
SP  - 32
EP  - 32
UR  - https://hdl.handle.net/21.15107/rcub_cer_6814
ER  - 

@conference{
author = "Popović, Dragan and Đorđević, Ivana",
year = "2023",
abstract = "With computer simulations that assess pKas of critical residues, explore electron and proton pathways, and evaluate the energetics of PT and ET processes, we can provide a more in-depth understanding of the molecular mechanism and catalytic cycle of CcO. Combining the DFT electronic structure and energy calculations with reaction and protein field contributions allows self-consistent solvation energy calculations to be iteratively performed. Moreover, valuable insights into mechanistic details and energetics of proton pumping and coupled ET/PT reactions are gained at the atomic level.",
publisher = "COST Action CA21101 "COSY"",
journal = "Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade",
title = "DFT/Solvation Continuum Electrostatic Calculations of Proton  Pumping in Mammalian Cytochrome c Oxidase",
pages = "32-32",
url = "https://hdl.handle.net/21.15107/rcub_cer_6814"
}

Popović, D.,& Đorđević, I.. (2023). DFT/Solvation Continuum Electrostatic Calculations of Proton  Pumping in Mammalian Cytochrome c Oxidase. in Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade
COST Action CA21101 "COSY"., 32-32.
https://hdl.handle.net/21.15107/rcub_cer_6814

Popović D, Đorđević I. DFT/Solvation Continuum Electrostatic Calculations of Proton  Pumping in Mammalian Cytochrome c Oxidase. in Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade. 2023;:32-32.
https://hdl.handle.net/21.15107/rcub_cer_6814 .

Popović, Dragan, Đorđević, Ivana, "DFT/Solvation Continuum Electrostatic Calculations of Proton  Pumping in Mammalian Cytochrome c Oxidase" in Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade (2023):32-32,
https://hdl.handle.net/21.15107/rcub_cer_6814 .

TY  - CONF
AU  - Lazić, Anita
AU  - Đorđević, Ivana
AU  - Radovanović, Lidija
AU  - Popović, Dragan
AU  - Rogan, Jelena
AU  - Trišović, Nemanja
AU  - Janjić, Goran
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6816
AB  - The hierarchical development of the crystal structure of racemic 3-(4-methoxybenzyl)-6,7- benzo-1,3-diazaspiro[4.5]decane-2,4-dione was analyzed through cooperativity of various homo  and heterochiral dimeric motifs associated with the presence of different intermolecular  interactions, namely strong N–H···O and weaker C–H···O, C–H···π and PILOs.1 Although a  bigger number of the contacts in the environment of the tetralin unit results from its larger  contact surface, the 4-methoxybenzyl unit provides a greater contribution to the overall  stabilization. In addition, the investigated compound is identified as a potential inhibitor of  kinase enzymes and AG protein-coupled receptors, with a slightly higher affinity for the later  enzyme. An analysis of the nature of the amino acid residues around the tetralin and 4-methoxy  benzyl units revealed that interactions with nonpolar groups are the most prevalent and even  more numerous than interactions with other amino acid residues (polar, positive and negative).
PB  - COST Action CA21101 "COSY"
C3  - Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade
T1  - Self-discriminating assembly and biorecognition of a spirohydantoin derived from α-tetralone
SP  - 47
EP  - 47
UR  - https://hdl.handle.net/21.15107/rcub_cer_6816
ER  - 

@conference{
author = "Lazić, Anita and Đorđević, Ivana and Radovanović, Lidija and Popović, Dragan and Rogan, Jelena and Trišović, Nemanja and Janjić, Goran",
year = "2023",
abstract = "The hierarchical development of the crystal structure of racemic 3-(4-methoxybenzyl)-6,7- benzo-1,3-diazaspiro[4.5]decane-2,4-dione was analyzed through cooperativity of various homo  and heterochiral dimeric motifs associated with the presence of different intermolecular  interactions, namely strong N–H···O and weaker C–H···O, C–H···π and PILOs.1 Although a  bigger number of the contacts in the environment of the tetralin unit results from its larger  contact surface, the 4-methoxybenzyl unit provides a greater contribution to the overall  stabilization. In addition, the investigated compound is identified as a potential inhibitor of  kinase enzymes and AG protein-coupled receptors, with a slightly higher affinity for the later  enzyme. An analysis of the nature of the amino acid residues around the tetralin and 4-methoxy  benzyl units revealed that interactions with nonpolar groups are the most prevalent and even  more numerous than interactions with other amino acid residues (polar, positive and negative).",
publisher = "COST Action CA21101 "COSY"",
journal = "Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade",
title = "Self-discriminating assembly and biorecognition of a spirohydantoin derived from α-tetralone",
pages = "47-47",
url = "https://hdl.handle.net/21.15107/rcub_cer_6816"
}

Lazić, A., Đorđević, I., Radovanović, L., Popović, D., Rogan, J., Trišović, N.,& Janjić, G.. (2023). Self-discriminating assembly and biorecognition of a spirohydantoin derived from α-tetralone. in Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade
COST Action CA21101 "COSY"., 47-47.
https://hdl.handle.net/21.15107/rcub_cer_6816

Lazić A, Đorđević I, Radovanović L, Popović D, Rogan J, Trišović N, Janjić G. Self-discriminating assembly and biorecognition of a spirohydantoin derived from α-tetralone. in Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade. 2023;:47-47.
https://hdl.handle.net/21.15107/rcub_cer_6816 .

Lazić, Anita, Đorđević, Ivana, Radovanović, Lidija, Popović, Dragan, Rogan, Jelena, Trišović, Nemanja, Janjić, Goran, "Self-discriminating assembly and biorecognition of a spirohydantoin derived from α-tetralone" in Book of abstracts - COST Training School, COST action CA21101 COSY, "Multiscale modeling of the properties of compounds: From isolated molecules to 3D materials relevant for industrial and astrophysical applications," 19th - 22nd September, 2023, Belgrade (2023):47-47,
https://hdl.handle.net/21.15107/rcub_cer_6816 .

TY  - JOUR
AU  - Lopandić, Zorana
AU  - Dragačević, Luka
AU  - Popović, Dragan M.
AU  - Anđelković, Uroš
AU  - Minić, Rajna
AU  - Gavrović-Jankulović, Marija
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4629
AB  - Fluorescently labeled lectins are useful tools for in vivo and in vitro studies of the structure and function of tissues and various pathogens such as viruses, bacteria, and fungi. For the evaluation of high-mannose glycans present on various glycoproteins, a three-dimensional (3D) model of the chimera was designed from the crystal structures of recombinant banana lectin (BanLec, Protein Data Bank entry (PDB): 5EXG) and an enhanced green fluorescent protein (eGFP, PDB 4EUL) by applying molecular modeling and molecular mechanics and expressed in Escherichia coli. BanLec-eGFP, produced as a soluble cytosolic protein of about 42 kDa, revealed β-sheets (41%) as the predominant secondary structures, with the emission peak maximum detected at 509 nm (excitation wavelength 488 nm). More than 65% of the primary structure was confirmed by mass spectrometry. Competitive BanLec-eGFP binding to high mannose glycans of the influenza vaccine (Vaxigrip®) was shown in a fluorescence-linked lectin sorbent assay (FLLSA) with monosaccharides (mannose and glucose) and wild type BanLec and H84T BanLec mutant. BanLec-eGFP exhibited binding to mannose residues on different strains of Salmonella in flow cytometry, with especially pronounced binding to a Salmonella Typhi clinical isolate. BanLec-eGFP can be a useful tool for screening high-mannose glycosylation sites on different microorganisms.
PB  - MDPI
T2  - Biomolecules
T1  - BanLec-eGFP Chimera as a Tool for Evaluation of Lectin Binding to High-Mannose Glycans on Microorganisms
VL  - 11
IS  - 2
SP  - 180
DO  - 10.3390/biom11020180
ER  - 

@article{
author = "Lopandić, Zorana and Dragačević, Luka and Popović, Dragan M. and Anđelković, Uroš and Minić, Rajna and Gavrović-Jankulović, Marija",
year = "2021",
abstract = "Fluorescently labeled lectins are useful tools for in vivo and in vitro studies of the structure and function of tissues and various pathogens such as viruses, bacteria, and fungi. For the evaluation of high-mannose glycans present on various glycoproteins, a three-dimensional (3D) model of the chimera was designed from the crystal structures of recombinant banana lectin (BanLec, Protein Data Bank entry (PDB): 5EXG) and an enhanced green fluorescent protein (eGFP, PDB 4EUL) by applying molecular modeling and molecular mechanics and expressed in Escherichia coli. BanLec-eGFP, produced as a soluble cytosolic protein of about 42 kDa, revealed β-sheets (41%) as the predominant secondary structures, with the emission peak maximum detected at 509 nm (excitation wavelength 488 nm). More than 65% of the primary structure was confirmed by mass spectrometry. Competitive BanLec-eGFP binding to high mannose glycans of the influenza vaccine (Vaxigrip®) was shown in a fluorescence-linked lectin sorbent assay (FLLSA) with monosaccharides (mannose and glucose) and wild type BanLec and H84T BanLec mutant. BanLec-eGFP exhibited binding to mannose residues on different strains of Salmonella in flow cytometry, with especially pronounced binding to a Salmonella Typhi clinical isolate. BanLec-eGFP can be a useful tool for screening high-mannose glycosylation sites on different microorganisms.",
publisher = "MDPI",
journal = "Biomolecules",
title = "BanLec-eGFP Chimera as a Tool for Evaluation of Lectin Binding to High-Mannose Glycans on Microorganisms",
volume = "11",
number = "2",
pages = "180",
doi = "10.3390/biom11020180"
}

Lopandić, Z., Dragačević, L., Popović, D. M., Anđelković, U., Minić, R.,& Gavrović-Jankulović, M.. (2021). BanLec-eGFP Chimera as a Tool for Evaluation of Lectin Binding to High-Mannose Glycans on Microorganisms. in Biomolecules
MDPI., 11(2), 180.
https://doi.org/10.3390/biom11020180

Lopandić Z, Dragačević L, Popović DM, Anđelković U, Minić R, Gavrović-Jankulović M. BanLec-eGFP Chimera as a Tool for Evaluation of Lectin Binding to High-Mannose Glycans on Microorganisms. in Biomolecules. 2021;11(2):180.
doi:10.3390/biom11020180 .

Lopandić, Zorana, Dragačević, Luka, Popović, Dragan M., Anđelković, Uroš, Minić, Rajna, Gavrović-Jankulović, Marija, "BanLec-eGFP Chimera as a Tool for Evaluation of Lectin Binding to High-Mannose Glycans on Microorganisms" in Biomolecules, 11, no. 2 (2021):180,
https://doi.org/10.3390/biom11020180 . .

TY  - CONF
AU  - Lazić, Anita
AU  - Đorđević, Ivana
AU  - Radovanović, Lidija
AU  - Popović, Dragan
AU  - Rogan, Jelena
AU  - Janjić, Goran
AU  - Trišović, Nemanja
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7124
AB  - A racemic spirohydantoin derivative bearing a tetralin and 4-methoxybenzyl group was synthesized
and its crystal structure was determined. The hierarchical development of the crystal packing was
discussed through cooperativity of various homo and heterohiral dimeric motifs associated with the
presence of different intermolecular interactions. A hallmark structural feature of the investigated
compound was alternation of double layers. A larger number of the contact fragments in the
environment of the tetralin unit results from its larger contact surface, while the 4-methoxybenzyl
unit provides a slightly greater contribution to the overall stabilization. Regarding the
pharmacological potential of the investigated compound, we performed a docking study on the
dopamine D3 receptor and IRAK 4 (Interleukin-1 Receptor-Associated Kinase 4) enzyme. The total
number of amino acid, which interact with the 4-methoxybenzyl unit, was slightly larger than the
number of amino acids in the neighborhood of the tetralin unit as a result of its greater flexibility. It
made the 4-methoxybenzyl unit more adaptable for interactions with the biological targets.
PB  - Belgrade : Serbian Chemical Society
C3  - Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia
T1  - Role of intermolecular interactions in the self-assembly and biorecognition of a spirohydantoin derivative
T1  - Улога интермолекулских интеракција у супрамолекулској организацији и биолошком препознавању деривата спирохидантоина
SP  - 93
EP  - 93
UR  - https://hdl.handle.net/21.15107/rcub_cer_7124
ER  - 

@conference{
author = "Lazić, Anita and Đorđević, Ivana and Radovanović, Lidija and Popović, Dragan and Rogan, Jelena and Janjić, Goran and Trišović, Nemanja",
year = "2021",
abstract = "A racemic spirohydantoin derivative bearing a tetralin and 4-methoxybenzyl group was synthesized
and its crystal structure was determined. The hierarchical development of the crystal packing was
discussed through cooperativity of various homo and heterohiral dimeric motifs associated with the
presence of different intermolecular interactions. A hallmark structural feature of the investigated
compound was alternation of double layers. A larger number of the contact fragments in the
environment of the tetralin unit results from its larger contact surface, while the 4-methoxybenzyl
unit provides a slightly greater contribution to the overall stabilization. Regarding the
pharmacological potential of the investigated compound, we performed a docking study on the
dopamine D3 receptor and IRAK 4 (Interleukin-1 Receptor-Associated Kinase 4) enzyme. The total
number of amino acid, which interact with the 4-methoxybenzyl unit, was slightly larger than the
number of amino acids in the neighborhood of the tetralin unit as a result of its greater flexibility. It
made the 4-methoxybenzyl unit more adaptable for interactions with the biological targets.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia",
title = "Role of intermolecular interactions in the self-assembly and biorecognition of a spirohydantoin derivative, Улога интермолекулских интеракција у супрамолекулској организацији и биолошком препознавању деривата спирохидантоина",
pages = "93-93",
url = "https://hdl.handle.net/21.15107/rcub_cer_7124"
}

Lazić, A., Đorđević, I., Radovanović, L., Popović, D., Rogan, J., Janjić, G.,& Trišović, N.. (2021). Role of intermolecular interactions in the self-assembly and biorecognition of a spirohydantoin derivative. in Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia
Belgrade : Serbian Chemical Society., 93-93.
https://hdl.handle.net/21.15107/rcub_cer_7124

Lazić A, Đorđević I, Radovanović L, Popović D, Rogan J, Janjić G, Trišović N. Role of intermolecular interactions in the self-assembly and biorecognition of a spirohydantoin derivative. in Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia. 2021;:93-93.
https://hdl.handle.net/21.15107/rcub_cer_7124 .

Lazić, Anita, Đorđević, Ivana, Radovanović, Lidija, Popović, Dragan, Rogan, Jelena, Janjić, Goran, Trišović, Nemanja, "Role of intermolecular interactions in the self-assembly and biorecognition of a spirohydantoin derivative" in Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia (2021):93-93,
https://hdl.handle.net/21.15107/rcub_cer_7124 .

TY  - JOUR
AU  - Protić-Rosić, Isidora
AU  - Nešić, Andrijana
AU  - Lukić, Ivana
AU  - Miljković, Radmila
AU  - Popović, Dragan M.
AU  - Atanasković-Marković, Marina
AU  - Stojanović, Marijana
AU  - Gavrović -Jankulović, Marija
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4777
AB  - Allergen-specific immunotherapy (AIT) is a desensitizing treatment for allergic diseases that corrects the underlined pathological immune response to innocuous protein antigens, called allergens. Recombinant allergens employed in the AIT allowed the production of well-defined formulations that possessed consistent quality but were often less efficient than natural allergen extracts. Combining recombinant allergens with an adjuvant or immunomodulatory agent could improve AIT efficacy. This study aimed to perform structural and functional characterization of newly designed recombinant chimera composed of the Bet v 1, the major birch pollen allergen, and Banana Lectin (BanLec), TLR2, and CD14 binding protein, for the application in AIT. rBet v 1-BanLec chimera was designed in silico and expressed as a soluble fraction in Escherichia coli. Purified rBet v 1-BanLec (33.4 kDa) retained BanLec-associated biological activity of carbohydrate-binding and preserved IgE reactive epitopes of Bet v 1. The chimera revealed secondary structures with predominant β sheets. The immunomodulatory capacity of rBet v 1-BanLec tested on macrophages showed changes in myeloperoxidase activity, reduced NO production, and significant alterations in the production of cytokines when compared to both rBanLec and rBet v 1. Comparing to rBet v 1, rBet v 1-BanLec was demonstrated to be more efficient promoter of IL-10 production as well as weaker inducer of NO production and secretion of pro-inflammatory cytokines TNFα, and IL-6. The ability of rBet v 1-BanLec to promote IL-10 in together with the preserved 3D structure of Bet v 1 part implies that the construct might exert a beneficial effect in the allergen-specific immunotherapy.
PB  - Elsevier
T2  - Molecular Immunology
T1  - Recombinant Bet v 1-BanLec chimera modulates functional characteristics of peritoneal murine macrophages by promoting IL-10 secretion
VL  - 138
SP  - 58
EP  - 67
DO  - 10.1016/j.molimm.2021.06.015
ER  - 

@article{
author = "Protić-Rosić, Isidora and Nešić, Andrijana and Lukić, Ivana and Miljković, Radmila and Popović, Dragan M. and Atanasković-Marković, Marina and Stojanović, Marijana and Gavrović -Jankulović, Marija",
year = "2021",
abstract = "Allergen-specific immunotherapy (AIT) is a desensitizing treatment for allergic diseases that corrects the underlined pathological immune response to innocuous protein antigens, called allergens. Recombinant allergens employed in the AIT allowed the production of well-defined formulations that possessed consistent quality but were often less efficient than natural allergen extracts. Combining recombinant allergens with an adjuvant or immunomodulatory agent could improve AIT efficacy. This study aimed to perform structural and functional characterization of newly designed recombinant chimera composed of the Bet v 1, the major birch pollen allergen, and Banana Lectin (BanLec), TLR2, and CD14 binding protein, for the application in AIT. rBet v 1-BanLec chimera was designed in silico and expressed as a soluble fraction in Escherichia coli. Purified rBet v 1-BanLec (33.4 kDa) retained BanLec-associated biological activity of carbohydrate-binding and preserved IgE reactive epitopes of Bet v 1. The chimera revealed secondary structures with predominant β sheets. The immunomodulatory capacity of rBet v 1-BanLec tested on macrophages showed changes in myeloperoxidase activity, reduced NO production, and significant alterations in the production of cytokines when compared to both rBanLec and rBet v 1. Comparing to rBet v 1, rBet v 1-BanLec was demonstrated to be more efficient promoter of IL-10 production as well as weaker inducer of NO production and secretion of pro-inflammatory cytokines TNFα, and IL-6. The ability of rBet v 1-BanLec to promote IL-10 in together with the preserved 3D structure of Bet v 1 part implies that the construct might exert a beneficial effect in the allergen-specific immunotherapy.",
publisher = "Elsevier",
journal = "Molecular Immunology",
title = "Recombinant Bet v 1-BanLec chimera modulates functional characteristics of peritoneal murine macrophages by promoting IL-10 secretion",
volume = "138",
pages = "58-67",
doi = "10.1016/j.molimm.2021.06.015"
}

Protić-Rosić, I., Nešić, A., Lukić, I., Miljković, R., Popović, D. M., Atanasković-Marković, M., Stojanović, M.,& Gavrović -Jankulović, M.. (2021). Recombinant Bet v 1-BanLec chimera modulates functional characteristics of peritoneal murine macrophages by promoting IL-10 secretion. in Molecular Immunology
Elsevier., 138, 58-67.
https://doi.org/10.1016/j.molimm.2021.06.015

Protić-Rosić I, Nešić A, Lukić I, Miljković R, Popović DM, Atanasković-Marković M, Stojanović M, Gavrović -Jankulović M. Recombinant Bet v 1-BanLec chimera modulates functional characteristics of peritoneal murine macrophages by promoting IL-10 secretion. in Molecular Immunology. 2021;138:58-67.
doi:10.1016/j.molimm.2021.06.015 .

Protić-Rosić, Isidora, Nešić, Andrijana, Lukić, Ivana, Miljković, Radmila, Popović, Dragan M., Atanasković-Marković, Marina, Stojanović, Marijana, Gavrović -Jankulović, Marija, "Recombinant Bet v 1-BanLec chimera modulates functional characteristics of peritoneal murine macrophages by promoting IL-10 secretion" in Molecular Immunology, 138 (2021):58-67,
https://doi.org/10.1016/j.molimm.2021.06.015 . .

TY  - CONF
AU  - Popović, Dragan
AU  - Stuchebrukhov, Alexei
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/5877
AB  - Damages in DNA structure are often caused by UV light, ionizing radiation, toxic substances and 
environmental pollution. To maintain genetic stability, cells protect themselves against these kinds 
of lesions. Moreover, the main DNA repair processes in prokaryotic and eukaryotic cells are quite 
similar. Photolyases repair the major DNA defects-cyclobutane pyrimidine dimers (CPD) and 
(6-4)-photoproducts. The enzyme contains two photoactive cofactors: folate-the photon antenna 
molecule and catalytically active FADH-form. Photolyase repairs UV (200-300 nm) induced damage in DNA by splitting the ring of CPD dimer into pyrimidine monomers. If not repaired the CPD lesions are highly cytotoxic, mutagenic, and carcinogenic. In the present theoretical/computational study of photolyase from E. coli, continuum electrostatic and electron tunneling currents methods are employed to get a full insight into photoactivation and 
photorepair mechanism of the enzyme and the structure-function interrelation. Protonation state 
of titratable residues, redox potentials of the conserved tryptophan triad, the energetics and kinetic 
reaction rates are calculated comparing well with available experimental data. The free energies of 
all potentially relevant enzyme states during the photoreactivation mechanism are evaluated. This presentation also addresses a several long-time controversial questions about the biological 
relevance of unusual U-shape of FADH cofactor; hopping vs. super-exchange mechanism of the ET pathway; the shortest FADH- to CPD distance, after flipping out the CPD damage to the active site, in the CPD-protein complex or presence of radical FADH* state in the resting state of photolyase. The study could be relevant for other types of photolyases and cryptochromes, which all share the same structural features.
PB  - USA, CA : UC Davis
C3  - 6th Postdoctoral Research Symposium, March 30, 2021, Davis, CA, USA, Web symposium
T1  - DNA Photolyase: Molecular Machinery for Repair of UV-Induced Damage in DNA
SP  - 33
UR  - https://hdl.handle.net/21.15107/rcub_cer_5877
ER  - 

@conference{
author = "Popović, Dragan and Stuchebrukhov, Alexei",
year = "2021",
abstract = "Damages in DNA structure are often caused by UV light, ionizing radiation, toxic substances and 
environmental pollution. To maintain genetic stability, cells protect themselves against these kinds 
of lesions. Moreover, the main DNA repair processes in prokaryotic and eukaryotic cells are quite 
similar. Photolyases repair the major DNA defects-cyclobutane pyrimidine dimers (CPD) and 
(6-4)-photoproducts. The enzyme contains two photoactive cofactors: folate-the photon antenna 
molecule and catalytically active FADH-form. Photolyase repairs UV (200-300 nm) induced damage in DNA by splitting the ring of CPD dimer into pyrimidine monomers. If not repaired the CPD lesions are highly cytotoxic, mutagenic, and carcinogenic. In the present theoretical/computational study of photolyase from E. coli, continuum electrostatic and electron tunneling currents methods are employed to get a full insight into photoactivation and 
photorepair mechanism of the enzyme and the structure-function interrelation. Protonation state 
of titratable residues, redox potentials of the conserved tryptophan triad, the energetics and kinetic 
reaction rates are calculated comparing well with available experimental data. The free energies of 
all potentially relevant enzyme states during the photoreactivation mechanism are evaluated. This presentation also addresses a several long-time controversial questions about the biological 
relevance of unusual U-shape of FADH cofactor; hopping vs. super-exchange mechanism of the ET pathway; the shortest FADH- to CPD distance, after flipping out the CPD damage to the active site, in the CPD-protein complex or presence of radical FADH* state in the resting state of photolyase. The study could be relevant for other types of photolyases and cryptochromes, which all share the same structural features.",
publisher = "USA, CA : UC Davis",
journal = "6th Postdoctoral Research Symposium, March 30, 2021, Davis, CA, USA, Web symposium",
title = "DNA Photolyase: Molecular Machinery for Repair of UV-Induced Damage in DNA",
pages = "33",
url = "https://hdl.handle.net/21.15107/rcub_cer_5877"
}

Popović, D.,& Stuchebrukhov, A.. (2021). DNA Photolyase: Molecular Machinery for Repair of UV-Induced Damage in DNA. in 6th Postdoctoral Research Symposium, March 30, 2021, Davis, CA, USA, Web symposium
USA, CA : UC Davis., 33.
https://hdl.handle.net/21.15107/rcub_cer_5877

Popović D, Stuchebrukhov A. DNA Photolyase: Molecular Machinery for Repair of UV-Induced Damage in DNA. in 6th Postdoctoral Research Symposium, March 30, 2021, Davis, CA, USA, Web symposium. 2021;:33.
https://hdl.handle.net/21.15107/rcub_cer_5877 .

Popović, Dragan, Stuchebrukhov, Alexei, "DNA Photolyase: Molecular Machinery for Repair of UV-Induced Damage in DNA" in 6th Postdoctoral Research Symposium, March 30, 2021, Davis, CA, USA, Web symposium (2021):33,
https://hdl.handle.net/21.15107/rcub_cer_5877 .

TY  - JOUR
AU  - Popović, Dragan
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/5876
AB  - Оштећења на ДНК структури, као што су одсецања и модификације азотних бaзa или промене на шећерно-фосфатним групама, често су изаsвана UV светлошћу, јонизационим зрачењем, токсичним и канцерогеним супстанцама, као и загађењима из животне средине. Да би се одржала генетичка стабилност ћепије, развили су се заштитии механизми који оправљају различите врсте оштећења. Многи ДНК репарациони процеси код прокариотских и еукариотских ћeлuja cy веома слични. Фотолиаза отклања најчешће ДНК дефекте, настале UV (200-300 нм) зрачењем — циклобутан пиримидиске димере (CPD) u (6-4)-фотопродукте, тако што катализује цепање циклобутанског прстена CPD димера на пиримидинске мономере у ретро-Дилс-Алдеровој реакцији иницираној блиском UV или видљивом плавом светлошliу (UV/VIS, 300-500 nm). CPD оштећења ДНК која нису поправљена и отклоњена су високо цитотоксична, изазивајући мутагене и канцерогене промене у ћелији и на нивоу ДНК и одговарајућих протеина. Механизам рада овог ензима је познат и у доброј мери експериментално истажен. Ипак, многи термодинамички и кинетички параметри могу бити одређени само путем теоријско-рачунарских студија на чије резултате ћe овде такође бити бачен акценат. Поред тога, у овом тексту је понуђен одговор на неколико контраверзних детаља и питања, која су дуго времена била неразјашњена.
AB  - Damages in the DNA structure, such as, excision and modification of bases or alternation of sugar-phosphate groups are often caused by UV light, ionizing radiation, toxic and carcinogenic substances, and environmental pollution. To maintain genetic stability, cells protect themselves against these kinds of lesions. Moreover, the main DNA repair processes in prokaryotic and eukaryotic cells are quite similar. Photolyases catalyze the repair of the most common DNA defects caused by UV (200-300 nm) radiation - cyclobutane pyrimidine (CPD) dimers and (6-4)-photoproducts. The DNA repair is achieved by splitting the ring of CPD dimer into pyrimidine monomers in retro-Diels-Alder reaction induced by near UV/ visible blue light (UV/VIS, 300-500 nm). If not repaired the CPD lesions are highly cytotoxic, mutagenic, and carcinogenic. Molecular mechanism of the enzyme is yet known and pretty well experimentally examined. However, many thermodynamic and kinetic parameters are not easy accessible and could be only obtained by theoretical/computational studies, which results are also discussed here. Beside a general introduction to the photoreactivation mechanism and the structure-function interrelation in the DNA photolyase, this text also addresses a several long-time controversial questions.
PB  - Serbian Chemical Society
T2  - Hemijski pregled
T1  - Фотолиаза - молекулски механизам оправке uv-индукованих днк лезија
T1  - Photolyase - molecular mechanism for repair of UV-damaged DNA
VL  - 62
IS  - 3
SP  - 50
EP  - 62
UR  - https://hdl.handle.net/21.15107/rcub_cer_5876
ER  - 

@article{
author = "Popović, Dragan",
year = "2021",
abstract = "Оштећења на ДНК структури, као што су одсецања и модификације азотних бaзa или промене на шећерно-фосфатним групама, често су изаsвана UV светлошћу, јонизационим зрачењем, токсичним и канцерогеним супстанцама, као и загађењима из животне средине. Да би се одржала генетичка стабилност ћепије, развили су се заштитии механизми који оправљају различите врсте оштећења. Многи ДНК репарациони процеси код прокариотских и еукариотских ћeлuja cy веома слични. Фотолиаза отклања најчешће ДНК дефекте, настале UV (200-300 нм) зрачењем — циклобутан пиримидиске димере (CPD) u (6-4)-фотопродукте, тако што катализује цепање циклобутанског прстена CPD димера на пиримидинске мономере у ретро-Дилс-Алдеровој реакцији иницираној блиском UV или видљивом плавом светлошliу (UV/VIS, 300-500 nm). CPD оштећења ДНК која нису поправљена и отклоњена су високо цитотоксична, изазивајући мутагене и канцерогене промене у ћелији и на нивоу ДНК и одговарајућих протеина. Механизам рада овог ензима је познат и у доброј мери експериментално истажен. Ипак, многи термодинамички и кинетички параметри могу бити одређени само путем теоријско-рачунарских студија на чије резултате ћe овде такође бити бачен акценат. Поред тога, у овом тексту је понуђен одговор на неколико контраверзних детаља и питања, која су дуго времена била неразјашњена., Damages in the DNA structure, such as, excision and modification of bases or alternation of sugar-phosphate groups are often caused by UV light, ionizing radiation, toxic and carcinogenic substances, and environmental pollution. To maintain genetic stability, cells protect themselves against these kinds of lesions. Moreover, the main DNA repair processes in prokaryotic and eukaryotic cells are quite similar. Photolyases catalyze the repair of the most common DNA defects caused by UV (200-300 nm) radiation - cyclobutane pyrimidine (CPD) dimers and (6-4)-photoproducts. The DNA repair is achieved by splitting the ring of CPD dimer into pyrimidine monomers in retro-Diels-Alder reaction induced by near UV/ visible blue light (UV/VIS, 300-500 nm). If not repaired the CPD lesions are highly cytotoxic, mutagenic, and carcinogenic. Molecular mechanism of the enzyme is yet known and pretty well experimentally examined. However, many thermodynamic and kinetic parameters are not easy accessible and could be only obtained by theoretical/computational studies, which results are also discussed here. Beside a general introduction to the photoreactivation mechanism and the structure-function interrelation in the DNA photolyase, this text also addresses a several long-time controversial questions.",
publisher = "Serbian Chemical Society",
journal = "Hemijski pregled",
title = "Фотолиаза - молекулски механизам оправке uv-индукованих днк лезија, Photolyase - molecular mechanism for repair of UV-damaged DNA",
volume = "62",
number = "3",
pages = "50-62",
url = "https://hdl.handle.net/21.15107/rcub_cer_5876"
}

Popović, D.. (2021). Фотолиаза - молекулски механизам оправке uv-индукованих днк лезија. in Hemijski pregled
Serbian Chemical Society., 62(3), 50-62.
https://hdl.handle.net/21.15107/rcub_cer_5876

Popović D. Фотолиаза - молекулски механизам оправке uv-индукованих днк лезија. in Hemijski pregled. 2021;62(3):50-62.
https://hdl.handle.net/21.15107/rcub_cer_5876 .

Popović, Dragan, "Фотолиаза - молекулски механизам оправке uv-индукованих днк лезија" in Hemijski pregled, 62, no. 3 (2021):50-62,
https://hdl.handle.net/21.15107/rcub_cer_5876 .

TY  - JOUR
AU  - Lazić, Anita M.
AU  - Đorđević, Ivana
AU  - Radovanović, Lidija
AU  - Popović, Dragan
AU  - Rogan, Jelena R.
AU  - Janjić, Goran
AU  - Trišović, Nemanja
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3638
AB  - A racemic spirohydantoin derivative with two aromatic substituents, a tetralin and a 4-methoxybenzyl unit, was synthesized and its crystal structure was determined. To define the relationship between molecular stereochemistry and spatial association modes, development of the crystal packing was analyzed through cooperativity of intermolecular interactions. Homo and heterochiral dimeric motifs were stabilized by intermolecular N−H⋅⋅⋅O, C−H⋅⋅⋅O, C−H⋅⋅⋅π interactions and parallel interactions at large offsets (PILO), thus forming alternating double layers. The greatest contribution to the total stabilization came from a motif of opposite enantiomers linked by N−H⋅⋅⋅O bonds (interaction energy=−13.72 kcal/mol), followed by a homochiral motif where the 4-methoxybenzyl units allowed C−H⋅⋅⋅π, C−H⋅⋅⋅O interactions and PILO (interaction energy=−11.56 kcal/mol). The number of the contact fragments in the environment of the tetralin unit was larger, but the 4-methoxybenzyl unit had greater contribution to the total stabilization. The statistical analysis of the data from the Cambridge Structural Database (CSD) showed that this is a general trend. The compound is a potential inhibitor of kinase enzymes and antigen protein-coupled receptors. A correlation between the docking study and the results of the CSD analysis can be drawn. Due to a greater flexibility, the 4-methoxybenzyl unit is more adaptable for interactions with the biological targets than the tetralin unit.
PB  - John Wiley and Sons Inc
T2  - ChemPlusChem
T1  - Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions
VL  - 85
IS  - 6
SP  - 1220
EP  - 1232
DO  - 10.1002/cplu.202000273
ER  - 

@article{
author = "Lazić, Anita M. and Đorđević, Ivana and Radovanović, Lidija and Popović, Dragan and Rogan, Jelena R. and Janjić, Goran and Trišović, Nemanja",
year = "2020",
abstract = "A racemic spirohydantoin derivative with two aromatic substituents, a tetralin and a 4-methoxybenzyl unit, was synthesized and its crystal structure was determined. To define the relationship between molecular stereochemistry and spatial association modes, development of the crystal packing was analyzed through cooperativity of intermolecular interactions. Homo and heterochiral dimeric motifs were stabilized by intermolecular N−H⋅⋅⋅O, C−H⋅⋅⋅O, C−H⋅⋅⋅π interactions and parallel interactions at large offsets (PILO), thus forming alternating double layers. The greatest contribution to the total stabilization came from a motif of opposite enantiomers linked by N−H⋅⋅⋅O bonds (interaction energy=−13.72 kcal/mol), followed by a homochiral motif where the 4-methoxybenzyl units allowed C−H⋅⋅⋅π, C−H⋅⋅⋅O interactions and PILO (interaction energy=−11.56 kcal/mol). The number of the contact fragments in the environment of the tetralin unit was larger, but the 4-methoxybenzyl unit had greater contribution to the total stabilization. The statistical analysis of the data from the Cambridge Structural Database (CSD) showed that this is a general trend. The compound is a potential inhibitor of kinase enzymes and antigen protein-coupled receptors. A correlation between the docking study and the results of the CSD analysis can be drawn. Due to a greater flexibility, the 4-methoxybenzyl unit is more adaptable for interactions with the biological targets than the tetralin unit.",
publisher = "John Wiley and Sons Inc",
journal = "ChemPlusChem",
title = "Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions",
volume = "85",
number = "6",
pages = "1220-1232",
doi = "10.1002/cplu.202000273"
}

Lazić, A. M., Đorđević, I., Radovanović, L., Popović, D., Rogan, J. R., Janjić, G.,& Trišović, N.. (2020). Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions. in ChemPlusChem
John Wiley and Sons Inc., 85(6), 1220-1232.
https://doi.org/10.1002/cplu.202000273

Lazić AM, Đorđević I, Radovanović L, Popović D, Rogan JR, Janjić G, Trišović N. Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions. in ChemPlusChem. 2020;85(6):1220-1232.
doi:10.1002/cplu.202000273 .

Lazić, Anita M., Đorđević, Ivana, Radovanović, Lidija, Popović, Dragan, Rogan, Jelena R., Janjić, Goran, Trišović, Nemanja, "Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions" in ChemPlusChem, 85, no. 6 (2020):1220-1232,
https://doi.org/10.1002/cplu.202000273 . .

TY  - JOUR
AU  - Lazić, Anita M.
AU  - Đorđević, Ivana
AU  - Radovanović, Lidija
AU  - Popović, Dragan
AU  - Rogan, Jelena R.
AU  - Janjić, Goran
AU  - Trišović, Nemanja
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3716
AB  - A racemic spirohydantoin derivative with two aromatic substituents, a tetralin and a 4-methoxybenzyl unit, was synthesized and its crystal structure was determined. To define the relationship between molecular stereochemistry and spatial association modes, development of the crystal packing was analyzed through cooperativity of intermolecular interactions. Homo and heterochiral dimeric motifs were stabilized by intermolecular N−H⋅⋅⋅O, C−H⋅⋅⋅O, C−H⋅⋅⋅π interactions and parallel interactions at large offsets (PILO), thus forming alternating double layers. The greatest contribution to the total stabilization came from a motif of opposite enantiomers linked by N−H⋅⋅⋅O bonds (interaction energy=−13.72 kcal/mol), followed by a homochiral motif where the 4-methoxybenzyl units allowed C−H⋅⋅⋅π, C−H⋅⋅⋅O interactions and PILO (interaction energy=−11.56 kcal/mol). The number of the contact fragments in the environment of the tetralin unit was larger, but the 4-methoxybenzyl unit had greater contribution to the total stabilization. The statistical analysis of the data from the Cambridge Structural Database (CSD) showed that this is a general trend. The compound is a potential inhibitor of kinase enzymes and antigen protein-coupled receptors. A correlation between the docking study and the results of the CSD analysis can be drawn. Due to a greater flexibility, the 4-methoxybenzyl unit is more adaptable for interactions with the biological targets than the tetralin unit.
PB  - John Wiley and Sons Inc.
T2  - ChemPlusChem
T1  - Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions
VL  - 85
IS  - 6
SP  - 1220
EP  - 1232
DO  - 10.1002/cplu.202000273
ER  - 

@article{
author = "Lazić, Anita M. and Đorđević, Ivana and Radovanović, Lidija and Popović, Dragan and Rogan, Jelena R. and Janjić, Goran and Trišović, Nemanja",
year = "2020",
abstract = "A racemic spirohydantoin derivative with two aromatic substituents, a tetralin and a 4-methoxybenzyl unit, was synthesized and its crystal structure was determined. To define the relationship between molecular stereochemistry and spatial association modes, development of the crystal packing was analyzed through cooperativity of intermolecular interactions. Homo and heterochiral dimeric motifs were stabilized by intermolecular N−H⋅⋅⋅O, C−H⋅⋅⋅O, C−H⋅⋅⋅π interactions and parallel interactions at large offsets (PILO), thus forming alternating double layers. The greatest contribution to the total stabilization came from a motif of opposite enantiomers linked by N−H⋅⋅⋅O bonds (interaction energy=−13.72 kcal/mol), followed by a homochiral motif where the 4-methoxybenzyl units allowed C−H⋅⋅⋅π, C−H⋅⋅⋅O interactions and PILO (interaction energy=−11.56 kcal/mol). The number of the contact fragments in the environment of the tetralin unit was larger, but the 4-methoxybenzyl unit had greater contribution to the total stabilization. The statistical analysis of the data from the Cambridge Structural Database (CSD) showed that this is a general trend. The compound is a potential inhibitor of kinase enzymes and antigen protein-coupled receptors. A correlation between the docking study and the results of the CSD analysis can be drawn. Due to a greater flexibility, the 4-methoxybenzyl unit is more adaptable for interactions with the biological targets than the tetralin unit.",
publisher = "John Wiley and Sons Inc.",
journal = "ChemPlusChem",
title = "Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions",
volume = "85",
number = "6",
pages = "1220-1232",
doi = "10.1002/cplu.202000273"
}

Lazić, A. M., Đorđević, I., Radovanović, L., Popović, D., Rogan, J. R., Janjić, G.,& Trišović, N.. (2020). Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions. in ChemPlusChem
John Wiley and Sons Inc.., 85(6), 1220-1232.
https://doi.org/10.1002/cplu.202000273

Lazić AM, Đorđević I, Radovanović L, Popović D, Rogan JR, Janjić G, Trišović N. Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions. in ChemPlusChem. 2020;85(6):1220-1232.
doi:10.1002/cplu.202000273 .

Lazić, Anita M., Đorđević, Ivana, Radovanović, Lidija, Popović, Dragan, Rogan, Jelena R., Janjić, Goran, Trišović, Nemanja, "Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions" in ChemPlusChem, 85, no. 6 (2020):1220-1232,
https://doi.org/10.1002/cplu.202000273 . .

TY  - JOUR
AU  - Janjić, Goran
AU  - Jelić, Stefan
AU  - Trišović, Nemanja
AU  - Popović, Dragan
AU  - Đorđević, Ivana
AU  - Milčić, Miloš
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3882
AB  - Fluorination of compounds causes an increase in the proton-donating ability and a decrease in the proton-accepting capacity of groups in their vicinity. The formation of F···F interactions is followed by the shift of the electron density in the area of F···F contact, which creates a new region with a larger surface area, a higher negative potential, and, hence, a more pronounced accepting ability. The new region also has a greater ability to form multiple (simultaneous) interactions with species from the environment, thus compensating for the reduction of the accepting capacity of the groups in the vicinity. This phenomenon explains not only the abundance of F···F interactions in crystal structures, but also a large number of structures with F···O interactions. Only C–H···F interactions are more numerous than F···F interactions in crystal structures, which indicates a high affinity of fluorinated compounds for nonpolar groups.
PB  - American Chemical Society (ACS)
T2  - Crystal Growth and Design
T1  - New Theoretical Insight into Fluorination and Fluorine–Fluorine Interactions as a Driving Force in Crystal Structures
VL  - 20
IS  - 5
SP  - 2943
EP  - 2951
DO  - 10.1021/acs.cgd.9b01565
ER  - 

@article{
author = "Janjić, Goran and Jelić, Stefan and Trišović, Nemanja and Popović, Dragan and Đorđević, Ivana and Milčić, Miloš",
year = "2020",
abstract = "Fluorination of compounds causes an increase in the proton-donating ability and a decrease in the proton-accepting capacity of groups in their vicinity. The formation of F···F interactions is followed by the shift of the electron density in the area of F···F contact, which creates a new region with a larger surface area, a higher negative potential, and, hence, a more pronounced accepting ability. The new region also has a greater ability to form multiple (simultaneous) interactions with species from the environment, thus compensating for the reduction of the accepting capacity of the groups in the vicinity. This phenomenon explains not only the abundance of F···F interactions in crystal structures, but also a large number of structures with F···O interactions. Only C–H···F interactions are more numerous than F···F interactions in crystal structures, which indicates a high affinity of fluorinated compounds for nonpolar groups.",
publisher = "American Chemical Society (ACS)",
journal = "Crystal Growth and Design",
title = "New Theoretical Insight into Fluorination and Fluorine–Fluorine Interactions as a Driving Force in Crystal Structures",
volume = "20",
number = "5",
pages = "2943-2951",
doi = "10.1021/acs.cgd.9b01565"
}

Janjić, G., Jelić, S., Trišović, N., Popović, D., Đorđević, I.,& Milčić, M.. (2020). New Theoretical Insight into Fluorination and Fluorine–Fluorine Interactions as a Driving Force in Crystal Structures. in Crystal Growth and Design
American Chemical Society (ACS)., 20(5), 2943-2951.
https://doi.org/10.1021/acs.cgd.9b01565

Janjić G, Jelić S, Trišović N, Popović D, Đorđević I, Milčić M. New Theoretical Insight into Fluorination and Fluorine–Fluorine Interactions as a Driving Force in Crystal Structures. in Crystal Growth and Design. 2020;20(5):2943-2951.
doi:10.1021/acs.cgd.9b01565 .

Janjić, Goran, Jelić, Stefan, Trišović, Nemanja, Popović, Dragan, Đorđević, Ivana, Milčić, Miloš, "New Theoretical Insight into Fluorination and Fluorine–Fluorine Interactions as a Driving Force in Crystal Structures" in Crystal Growth and Design, 20, no. 5 (2020):2943-2951,
https://doi.org/10.1021/acs.cgd.9b01565 . .

TY  - CONF
AU  - Trišović, Nemanja
AU  - Jelić, Stefan
AU  - Popović, Dragan
AU  - Đorđević, Ivana
AU  - Milčić, Miloš
AU  - Janjić, Goran
PY  - 2020
UR  - https://qcrom2020.cs-campus.fr/event/
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4032
AB  - The results of the crystallographic analysis in combination with quantum chemical calculations have
shown that fluorination of organic compounds causes an increase in the proton-donating ability and a
decrease in the proton-accepting capacity of the groups in their neighbourhood1
. The establishment of
F∙∙∙F interactions causes the electron density to shift towards the area of F∙∙∙F contact, thus creating a
new region with a higher negative potential and the more pronounced accepting ability. This new
region has a larger surface area and it is able to form simultaneous interactions with species from the
crystal environment. This compensates the reduction of the accepting capacity of the groups in the
neigbourhood of the interacting F atoms. Taking into account the formation of this new region, not
only the abundance of F∙∙∙F interactions in the crystal structures (the second largest group of
interactions), but also a large number of structures with F∙∙∙O interactions (third largest group of
interactions) can be explained. Only the C–H∙∙∙F interactions are more numerous than F∙∙∙F
interactions, indicating an increased affinity of fluorinated compounds for non-polar groups.
PB  - Commission on Quantum Crystallography of IUCr
C3  - Book of Abstracts - Quantum Crystallography Online Meeting 2020, QCrOM2020
T1  - Fluorination as a Driving Force in Crystal Structures
SP  - 35
UR  - https://hdl.handle.net/21.15107/rcub_cer_4032
ER  - 

@conference{
author = "Trišović, Nemanja and Jelić, Stefan and Popović, Dragan and Đorđević, Ivana and Milčić, Miloš and Janjić, Goran",
year = "2020",
abstract = "The results of the crystallographic analysis in combination with quantum chemical calculations have
shown that fluorination of organic compounds causes an increase in the proton-donating ability and a
decrease in the proton-accepting capacity of the groups in their neighbourhood1
. The establishment of
F∙∙∙F interactions causes the electron density to shift towards the area of F∙∙∙F contact, thus creating a
new region with a higher negative potential and the more pronounced accepting ability. This new
region has a larger surface area and it is able to form simultaneous interactions with species from the
crystal environment. This compensates the reduction of the accepting capacity of the groups in the
neigbourhood of the interacting F atoms. Taking into account the formation of this new region, not
only the abundance of F∙∙∙F interactions in the crystal structures (the second largest group of
interactions), but also a large number of structures with F∙∙∙O interactions (third largest group of
interactions) can be explained. Only the C–H∙∙∙F interactions are more numerous than F∙∙∙F
interactions, indicating an increased affinity of fluorinated compounds for non-polar groups.",
publisher = "Commission on Quantum Crystallography of IUCr",
journal = "Book of Abstracts - Quantum Crystallography Online Meeting 2020, QCrOM2020",
title = "Fluorination as a Driving Force in Crystal Structures",
pages = "35",
url = "https://hdl.handle.net/21.15107/rcub_cer_4032"
}

Trišović, N., Jelić, S., Popović, D., Đorđević, I., Milčić, M.,& Janjić, G.. (2020). Fluorination as a Driving Force in Crystal Structures. in Book of Abstracts - Quantum Crystallography Online Meeting 2020, QCrOM2020
Commission on Quantum Crystallography of IUCr., 35.
https://hdl.handle.net/21.15107/rcub_cer_4032

Trišović N, Jelić S, Popović D, Đorđević I, Milčić M, Janjić G. Fluorination as a Driving Force in Crystal Structures. in Book of Abstracts - Quantum Crystallography Online Meeting 2020, QCrOM2020. 2020;:35.
https://hdl.handle.net/21.15107/rcub_cer_4032 .

Trišović, Nemanja, Jelić, Stefan, Popović, Dragan, Đorđević, Ivana, Milčić, Miloš, Janjić, Goran, "Fluorination as a Driving Force in Crystal Structures" in Book of Abstracts - Quantum Crystallography Online Meeting 2020, QCrOM2020 (2020):35,
https://hdl.handle.net/21.15107/rcub_cer_4032 .

TY  - JOUR
AU  - Popović, Dragan
AU  - Đorđević, Ivana
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4031
AB  - The molecular mechanism by which electron transfer (ET) is coupled to proton pumping in cytochrome oxidase is one of the main unsolved problems in biochemistry. Particularly, the nature and position of the proton-loading site is under dispute. The CuB complex has three ligated histidines, whereas only His290 and His291 are ionizable sites with the same pKa values in aqueous solution, but apparently quite different ones within the enzyme. Earlier, a model of proton pumping with the central role of His290 was proposed. Recent calculations indicate that the His291 ligand of the CuB center might play the role of the pumping element, since its protonation state depends on the oxidation state of the binuclear complex (BNC). The present electrostatic study was applied to assess the role of the protein environment on the acidity of the two histidines. Their pKa values and effects of different energy terms were evaluated to discover the nature of their diverse behavior in the enzyme. Here, a new set of pKa values for the non-standard model compounds within the BNC was applied. The enhanced results are compared with results of previous studies in the light of the plausible proton pumping mechanism. The obtained microscopic and apparent pKa values in the oxidized state of BNC are virtually the same, indicating that deprotonated form of His291 accounts for the large pKa increase of His290, since then both titratable sites on then CuB center cannot simultaneously be in the charged state. The present results support the underlined His291 pumping model.
AB  - Молекулски механизам помоћу којег је пренос електрона спрегнут са протонском пумпом у цитохром c оксидази (CcО) представља један од главних нерешених проблема у биохемији. Посебно, природа и положај места везивања протона за пумпање (PLS) су главне тачке спорења. CuB комплекс има три хистидинска лиганда, при чему су само His290 и His291 титратибилни и међусобно слични са истим pKa вредностима у воденом раствору, али су очигледно сасвим различити унутар CcО ензима. Раније је био предложен модел протонске пумпе у CcО са централном улогом His290, али недавни прорачуни наше групе показују да би His291, лиганд CuB центра, могао имати улогу PLS елемента, јер његово стање протоновања зависи од оксидационог стања бинуклеарног комплекса (BNC). Ова електростатичка студија примењена је за процену утицаја протеинског окружења на киселост два хистидина. Израчунали смо њихове pKa вредности и раздвојили јачине ефеката различитих енергетских доприноса како бисмо открили природу њиховог различитог понашања у ензиму. Овде смо за нестандардна модел једињења унутар бинуклеарног комплекса користили нови сет са pKa вредностима у воденом раствору. Побољшани резултати су упоређени са резултатима из претходних студија са бацањем акцента на могући механизам пумпања протона. Добиjене микроскопске и макроскопске pKa вредности у оксидованом стању BNC су практично исте, што индицира да депротоновани облик His291 изазива велики пoраст pKa вредности His290, јер оба титрациона места у CuB центру не могу истовремено бити у наелектрисаном стању. Приказани резултати подржавају предложени хистидински (His291) модел протонске пумпе.
PB  - Belgrade : Serbian Chemical Society
T2  - Journal of the Serbian Chemical Society
T1  - Catalytic center of cytochrome c oxidase: Effects of protein environment on pKa values of Cub histidine ligands
T1  - Каталитички центар цитохром оксидазе: утицај протеинског окружења на pka вредности хистидинских лиганада Cub центра
VL  - 85
IS  - 11
SP  - 1429
EP  - 1444
DO  - 10.2298/JSC200720047P
ER  - 

@article{
author = "Popović, Dragan and Đorđević, Ivana",
year = "2020",
abstract = "The molecular mechanism by which electron transfer (ET) is coupled to proton pumping in cytochrome oxidase is one of the main unsolved problems in biochemistry. Particularly, the nature and position of the proton-loading site is under dispute. The CuB complex has three ligated histidines, whereas only His290 and His291 are ionizable sites with the same pKa values in aqueous solution, but apparently quite different ones within the enzyme. Earlier, a model of proton pumping with the central role of His290 was proposed. Recent calculations indicate that the His291 ligand of the CuB center might play the role of the pumping element, since its protonation state depends on the oxidation state of the binuclear complex (BNC). The present electrostatic study was applied to assess the role of the protein environment on the acidity of the two histidines. Their pKa values and effects of different energy terms were evaluated to discover the nature of their diverse behavior in the enzyme. Here, a new set of pKa values for the non-standard model compounds within the BNC was applied. The enhanced results are compared with results of previous studies in the light of the plausible proton pumping mechanism. The obtained microscopic and apparent pKa values in the oxidized state of BNC are virtually the same, indicating that deprotonated form of His291 accounts for the large pKa increase of His290, since then both titratable sites on then CuB center cannot simultaneously be in the charged state. The present results support the underlined His291 pumping model., Молекулски механизам помоћу којег је пренос електрона спрегнут са протонском пумпом у цитохром c оксидази (CcО) представља један од главних нерешених проблема у биохемији. Посебно, природа и положај места везивања протона за пумпање (PLS) су главне тачке спорења. CuB комплекс има три хистидинска лиганда, при чему су само His290 и His291 титратибилни и међусобно слични са истим pKa вредностима у воденом раствору, али су очигледно сасвим различити унутар CcО ензима. Раније је био предложен модел протонске пумпе у CcО са централном улогом His290, али недавни прорачуни наше групе показују да би His291, лиганд CuB центра, могао имати улогу PLS елемента, јер његово стање протоновања зависи од оксидационог стања бинуклеарног комплекса (BNC). Ова електростатичка студија примењена је за процену утицаја протеинског окружења на киселост два хистидина. Израчунали смо њихове pKa вредности и раздвојили јачине ефеката различитих енергетских доприноса како бисмо открили природу њиховог различитог понашања у ензиму. Овде смо за нестандардна модел једињења унутар бинуклеарног комплекса користили нови сет са pKa вредностима у воденом раствору. Побољшани резултати су упоређени са резултатима из претходних студија са бацањем акцента на могући механизам пумпања протона. Добиjене микроскопске и макроскопске pKa вредности у оксидованом стању BNC су практично исте, што индицира да депротоновани облик His291 изазива велики пoраст pKa вредности His290, јер оба титрациона места у CuB центру не могу истовремено бити у наелектрисаном стању. Приказани резултати подржавају предложени хистидински (His291) модел протонске пумпе.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Journal of the Serbian Chemical Society",
title = "Catalytic center of cytochrome c oxidase: Effects of protein environment on pKa values of Cub histidine ligands, Каталитички центар цитохром оксидазе: утицај протеинског окружења на pka вредности хистидинских лиганада Cub центра",
volume = "85",
number = "11",
pages = "1429-1444",
doi = "10.2298/JSC200720047P"
}

Popović, D.,& Đorđević, I.. (2020). Catalytic center of cytochrome c oxidase: Effects of protein environment on pKa values of Cub histidine ligands. in Journal of the Serbian Chemical Society
Belgrade : Serbian Chemical Society., 85(11), 1429-1444.
https://doi.org/10.2298/JSC200720047P

Popović D, Đorđević I. Catalytic center of cytochrome c oxidase: Effects of protein environment on pKa values of Cub histidine ligands. in Journal of the Serbian Chemical Society. 2020;85(11):1429-1444.
doi:10.2298/JSC200720047P .

Popović, Dragan, Đorđević, Ivana, "Catalytic center of cytochrome c oxidase: Effects of protein environment on pKa values of Cub histidine ligands" in Journal of the Serbian Chemical Society, 85, no. 11 (2020):1429-1444,
https://doi.org/10.2298/JSC200720047P . .

TY  - JOUR
AU  - Mrkić, Ivan
AU  - Minić, Rajna
AU  - Popović, Dragan
AU  - Zivkovic, Irena
AU  - Gavrović-Jankulović, Marija
PY  - 2018
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2380
AB  - Aim To investigate the immunomodulatory potential of a chimera composed of the receptor-binding domain of hemagglutinin 1 (H1s) from Influenza virus and Der p 2 (D2) allergen for allergen-specific immunotherapy of house-dust mite allergy (HDM). Main methods: H1sD2 chimera and D2 allergen were produced by genetic engineering in E. coli. Recombinant antigens were extracted from inclusion bodies by urea, then refolded and purified by immobilized-metal affinity chromatography (IMAC). Purity was verified by 2D-PAGE and secondary structures were assessed by CD spectroscopy. IgE reactivity of H1sD2 and D2 was tested in western blot with sera from 8 persons with clinical history of HDM allergy. Immunogenicity of H1sD2 and D2 were analyzed in Balb/c mice. Cytokine profile was analyzed by ELISA after stimulation of mouse spleen cells with H1sD2 and D2. Leukocyte population abundance of cells isolated from spleen and lymph node was assessed by flow cytometry. Key findings: Purified recombinant proteins H1sD2 (42 kDa) and D2 (15 kDa) revealed well defined secondary structures, and preserved IgE reactive epitopes. Analysis of supernatants of mouse spleen cells after stimulation with H1sD2 and D2, revealed a qualitatively different cytokine profile from H1sD2 immunized mouse cells (increase in IL10). CD8+ cells were decreased in the lymph node of D2 immunized mice, whereas H1sD2 immunization led to an increase of CD8+ cells in both the lymph node and the spleen. Significance: H1sD2 chimera attenuates Der p 2-inherent Th2 response and directs the immune response toward Th1 and Treg phenotype.
PB  - Oxford : Pergamon-Elsevier Science Ltd
T2  - Life Sciences
T1  - Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy
VL  - 213
SP  - 158
EP  - 165
DO  - 10.1016/j.lfs.2018.10.036
ER  - 

@article{
author = "Mrkić, Ivan and Minić, Rajna and Popović, Dragan and Zivkovic, Irena and Gavrović-Jankulović, Marija",
year = "2018",
abstract = "Aim To investigate the immunomodulatory potential of a chimera composed of the receptor-binding domain of hemagglutinin 1 (H1s) from Influenza virus and Der p 2 (D2) allergen for allergen-specific immunotherapy of house-dust mite allergy (HDM). Main methods: H1sD2 chimera and D2 allergen were produced by genetic engineering in E. coli. Recombinant antigens were extracted from inclusion bodies by urea, then refolded and purified by immobilized-metal affinity chromatography (IMAC). Purity was verified by 2D-PAGE and secondary structures were assessed by CD spectroscopy. IgE reactivity of H1sD2 and D2 was tested in western blot with sera from 8 persons with clinical history of HDM allergy. Immunogenicity of H1sD2 and D2 were analyzed in Balb/c mice. Cytokine profile was analyzed by ELISA after stimulation of mouse spleen cells with H1sD2 and D2. Leukocyte population abundance of cells isolated from spleen and lymph node was assessed by flow cytometry. Key findings: Purified recombinant proteins H1sD2 (42 kDa) and D2 (15 kDa) revealed well defined secondary structures, and preserved IgE reactive epitopes. Analysis of supernatants of mouse spleen cells after stimulation with H1sD2 and D2, revealed a qualitatively different cytokine profile from H1sD2 immunized mouse cells (increase in IL10). CD8+ cells were decreased in the lymph node of D2 immunized mice, whereas H1sD2 immunization led to an increase of CD8+ cells in both the lymph node and the spleen. Significance: H1sD2 chimera attenuates Der p 2-inherent Th2 response and directs the immune response toward Th1 and Treg phenotype.",
publisher = "Oxford : Pergamon-Elsevier Science Ltd",
journal = "Life Sciences",
title = "Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy",
volume = "213",
pages = "158-165",
doi = "10.1016/j.lfs.2018.10.036"
}

Mrkić, I., Minić, R., Popović, D., Zivkovic, I.,& Gavrović-Jankulović, M.. (2018). Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy. in Life Sciences
Oxford : Pergamon-Elsevier Science Ltd., 213, 158-165.
https://doi.org/10.1016/j.lfs.2018.10.036

Mrkić I, Minić R, Popović D, Zivkovic I, Gavrović-Jankulović M. Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy. in Life Sciences. 2018;213:158-165.
doi:10.1016/j.lfs.2018.10.036 .

Mrkić, Ivan, Minić, Rajna, Popović, Dragan, Zivkovic, Irena, Gavrović-Jankulović, Marija, "Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy" in Life Sciences, 213 (2018):158-165,
https://doi.org/10.1016/j.lfs.2018.10.036 . .

TY  - JOUR
AU  - Mrkić, Ivan
AU  - Minić, Rajna
AU  - Popović, Dragan
AU  - Zivkovic, Irena
AU  - Gavrović-Jankulović, Marija
PY  - 2018
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4288
AB  - Aim To investigate the immunomodulatory potential of a chimera composed of the receptor-binding domain of hemagglutinin 1 (H1s) from Influenza virus and Der p 2 (D2) allergen for allergen-specific immunotherapy of house-dust mite allergy (HDM). Main methods: H1sD2 chimera and D2 allergen were produced by genetic engineering in E. coli. Recombinant antigens were extracted from inclusion bodies by urea, then refolded and purified by immobilized-metal affinity chromatography (IMAC). Purity was verified by 2D-PAGE and secondary structures were assessed by CD spectroscopy. IgE reactivity of H1sD2 and D2 was tested in western blot with sera from 8 persons with clinical history of HDM allergy. Immunogenicity of H1sD2 and D2 were analyzed in Balb/c mice. Cytokine profile was analyzed by ELISA after stimulation of mouse spleen cells with H1sD2 and D2. Leukocyte population abundance of cells isolated from spleen and lymph node was assessed by flow cytometry. Key findings: Purified recombinant proteins H1sD2 (42 kDa) and D2 (15 kDa) revealed well defined secondary structures, and preserved IgE reactive epitopes. Analysis of supernatants of mouse spleen cells after stimulation with H1sD2 and D2, revealed a qualitatively different cytokine profile from H1sD2 immunized mouse cells (increase in IL10). CD8+ cells were decreased in the lymph node of D2 immunized mice, whereas H1sD2 immunization led to an increase of CD8+ cells in both the lymph node and the spleen. Significance: H1sD2 chimera attenuates Der p 2-inherent Th2 response and directs the immune response toward Th1 and Treg phenotype.
PB  - Oxford : Pergamon-Elsevier Science Ltd
T2  - Life Sciences
T1  - Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy
VL  - 213
SP  - 158
EP  - 165
DO  - 10.1016/j.lfs.2018.10.036
ER  - 

@article{
author = "Mrkić, Ivan and Minić, Rajna and Popović, Dragan and Zivkovic, Irena and Gavrović-Jankulović, Marija",
year = "2018",
abstract = "Aim To investigate the immunomodulatory potential of a chimera composed of the receptor-binding domain of hemagglutinin 1 (H1s) from Influenza virus and Der p 2 (D2) allergen for allergen-specific immunotherapy of house-dust mite allergy (HDM). Main methods: H1sD2 chimera and D2 allergen were produced by genetic engineering in E. coli. Recombinant antigens were extracted from inclusion bodies by urea, then refolded and purified by immobilized-metal affinity chromatography (IMAC). Purity was verified by 2D-PAGE and secondary structures were assessed by CD spectroscopy. IgE reactivity of H1sD2 and D2 was tested in western blot with sera from 8 persons with clinical history of HDM allergy. Immunogenicity of H1sD2 and D2 were analyzed in Balb/c mice. Cytokine profile was analyzed by ELISA after stimulation of mouse spleen cells with H1sD2 and D2. Leukocyte population abundance of cells isolated from spleen and lymph node was assessed by flow cytometry. Key findings: Purified recombinant proteins H1sD2 (42 kDa) and D2 (15 kDa) revealed well defined secondary structures, and preserved IgE reactive epitopes. Analysis of supernatants of mouse spleen cells after stimulation with H1sD2 and D2, revealed a qualitatively different cytokine profile from H1sD2 immunized mouse cells (increase in IL10). CD8+ cells were decreased in the lymph node of D2 immunized mice, whereas H1sD2 immunization led to an increase of CD8+ cells in both the lymph node and the spleen. Significance: H1sD2 chimera attenuates Der p 2-inherent Th2 response and directs the immune response toward Th1 and Treg phenotype.",
publisher = "Oxford : Pergamon-Elsevier Science Ltd",
journal = "Life Sciences",
title = "Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy",
volume = "213",
pages = "158-165",
doi = "10.1016/j.lfs.2018.10.036"
}

Mrkić, I., Minić, R., Popović, D., Zivkovic, I.,& Gavrović-Jankulović, M.. (2018). Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy. in Life Sciences
Oxford : Pergamon-Elsevier Science Ltd., 213, 158-165.
https://doi.org/10.1016/j.lfs.2018.10.036

Mrkić I, Minić R, Popović D, Zivkovic I, Gavrović-Jankulović M. Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy. in Life Sciences. 2018;213:158-165.
doi:10.1016/j.lfs.2018.10.036 .

Mrkić, Ivan, Minić, Rajna, Popović, Dragan, Zivkovic, Irena, Gavrović-Jankulović, Marija, "Newly designed hemagglutinin-Der p 2 chimera is a potential candidate for allergen specific immunotherapy" in Life Sciences, 213 (2018):158-165,
https://doi.org/10.1016/j.lfs.2018.10.036 . .

TY  - CONF
AU  - Popović, Dragan
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/5879
AB  - Cytochrome c oxidase (CcO) is the terminal enzyme of aerobic respiration, which is  responsible for processing most of the biological oxygen and generating electrochemical  proton gradient in aerobic cells [1]. The energy released from the reduction of molecular  oxygen to water is used to pump protons across the mitochondrial or bacterial membrane.  The structure of the enzyme has been solved for several organisms; however details of its  molecular mechanism of proton pumping still remain elusive.  Recent time-resolved optical and electrometric experiments on the O E transition have  suggested a sequence of reaction steps for the proton-translocation mechanism of CcO  [2]. The pump function introduces a mechanistic requirement of a valve that prevents  protons from flowing backwards during the process. It was recently found that Glu242, a  key amino acid in transferring protons to be pumped across the membrane and to the site  of oxygen reduction, fulfills the function of such a valve by preventing simultaneous  contact to the pump site and to the proton-conducting D-channel [3, 4]. Here we have  included the conformational gating by Glu242 into the framework of the proposed His291  pumping model [5]. DFT/electrostatic calculations are employed to obtain energetics of  proton and electron transfer reaction steps during the O E transition, while transition  state theory is used for estimating activation energies and kinetic barriers from the rate  constant of transitions. The energy profile of the reaction mechanism is studied by  exploring how the redox state of the adjacent metal centers, dielectric effects, and  membrane potential gradient, affect the energy levels and the leaks of the Glu-valve.  Special emphasis is made on side-reactions that may short-circuit the pump, and the  means by which these may be avoided. The state with the proton on the pump site  (His291) is especially vulnerable to leak back to Glu instead of being released to the P- side of the membrane, what would result in a loss of proton-pumping.  Obviously, there are more different control mechanisms and gating situations employed  by the enzyme to ensure the unidirectionality of the proton translocation and to prevent  proton leak in the opposite direction.
PB  - Serbian Chemical Society
C3  - Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia
T1  - Energetics of the steps in proton pumping mechanism and preventing of  backflow reactions in cytochrome c oxidase
SP  - 103
UR  - https://hdl.handle.net/21.15107/rcub_cer_5879
ER  - 

@conference{
author = "Popović, Dragan",
year = "2013",
abstract = "Cytochrome c oxidase (CcO) is the terminal enzyme of aerobic respiration, which is  responsible for processing most of the biological oxygen and generating electrochemical  proton gradient in aerobic cells [1]. The energy released from the reduction of molecular  oxygen to water is used to pump protons across the mitochondrial or bacterial membrane.  The structure of the enzyme has been solved for several organisms; however details of its  molecular mechanism of proton pumping still remain elusive.  Recent time-resolved optical and electrometric experiments on the O E transition have  suggested a sequence of reaction steps for the proton-translocation mechanism of CcO  [2]. The pump function introduces a mechanistic requirement of a valve that prevents  protons from flowing backwards during the process. It was recently found that Glu242, a  key amino acid in transferring protons to be pumped across the membrane and to the site  of oxygen reduction, fulfills the function of such a valve by preventing simultaneous  contact to the pump site and to the proton-conducting D-channel [3, 4]. Here we have  included the conformational gating by Glu242 into the framework of the proposed His291  pumping model [5]. DFT/electrostatic calculations are employed to obtain energetics of  proton and electron transfer reaction steps during the O E transition, while transition  state theory is used for estimating activation energies and kinetic barriers from the rate  constant of transitions. The energy profile of the reaction mechanism is studied by  exploring how the redox state of the adjacent metal centers, dielectric effects, and  membrane potential gradient, affect the energy levels and the leaks of the Glu-valve.  Special emphasis is made on side-reactions that may short-circuit the pump, and the  means by which these may be avoided. The state with the proton on the pump site  (His291) is especially vulnerable to leak back to Glu instead of being released to the P- side of the membrane, what would result in a loss of proton-pumping.  Obviously, there are more different control mechanisms and gating situations employed  by the enzyme to ensure the unidirectionality of the proton translocation and to prevent  proton leak in the opposite direction.",
publisher = "Serbian Chemical Society",
journal = "Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia",
title = "Energetics of the steps in proton pumping mechanism and preventing of  backflow reactions in cytochrome c oxidase",
pages = "103",
url = "https://hdl.handle.net/21.15107/rcub_cer_5879"
}

Popović, D.. (2013). Energetics of the steps in proton pumping mechanism and preventing of  backflow reactions in cytochrome c oxidase. in Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia
Serbian Chemical Society., 103.
https://hdl.handle.net/21.15107/rcub_cer_5879

Popović D. Energetics of the steps in proton pumping mechanism and preventing of  backflow reactions in cytochrome c oxidase. in Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia. 2013;:103.
https://hdl.handle.net/21.15107/rcub_cer_5879 .

Popović, Dragan, "Energetics of the steps in proton pumping mechanism and preventing of  backflow reactions in cytochrome c oxidase" in Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia (2013):103,
https://hdl.handle.net/21.15107/rcub_cer_5879 .

TY  - CONF
AU  - Popović, Dragan
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/5878
AB  - This presentation is on the theoretical computational study of the DNA photolyase from E. coli. Continuum electrostatic method [4] is employed to get a full insight into the photoactivation mechanism of the enzyme. Protonation state of titratable residues, the redox potentials of tryptophan triad, energetics and the reaction rates are calculated and compared with available experimental data. The free energies of all potentially relevant states for the radical transfer during the photoactivation process are evaluated.
PB  - Serbian Chemical Society
C3  - Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia
T1  - Photoactivation mechanism of DNA photolyase
SP  - 102
UR  - https://hdl.handle.net/21.15107/rcub_cer_5878
ER  - 

@conference{
author = "Popović, Dragan",
year = "2013",
abstract = "This presentation is on the theoretical computational study of the DNA photolyase from E. coli. Continuum electrostatic method [4] is employed to get a full insight into the photoactivation mechanism of the enzyme. Protonation state of titratable residues, the redox potentials of tryptophan triad, energetics and the reaction rates are calculated and compared with available experimental data. The free energies of all potentially relevant states for the radical transfer during the photoactivation process are evaluated.",
publisher = "Serbian Chemical Society",
journal = "Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia",
title = "Photoactivation mechanism of DNA photolyase",
pages = "102",
url = "https://hdl.handle.net/21.15107/rcub_cer_5878"
}

Popović, D.. (2013). Photoactivation mechanism of DNA photolyase. in Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia
Serbian Chemical Society., 102.
https://hdl.handle.net/21.15107/rcub_cer_5878

Popović D. Photoactivation mechanism of DNA photolyase. in Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia. 2013;:102.
https://hdl.handle.net/21.15107/rcub_cer_5878 .

Popović, Dragan, "Photoactivation mechanism of DNA photolyase" in Book of abstracts - 8th International Conference of the Chemical Societies of the South-East European Countries (ICOSEC 8), June 27-29, 2013, Belgrade, Serbia (2013):102,
https://hdl.handle.net/21.15107/rcub_cer_5878 .

TY  - JOUR
AU  - Popović, Dragan
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1171
AB  - Nobel Prize 2013 for chemistry is awarded to three American scientists in the field of theoretical and computational chemistry. Awarded are: Prof. Martin Karplus (Université de Strasbourg, France and Harvard University, USA), Prof. Michael Levitt (Stanford University, Los Angeles, USA) and Prof. Arieh Warshel (University of Southern California, Los Angeles, USA) for development of the multi-scale models for the complex chemical systems. A brief overview of contributions, for which they have been awarded, is presented here.
AB  - 'Nobelova nagrada za hemiju za 2013. godinu je dodeljena trojici naturalizovanih američkih naučnika iz oblasti teorijske i računarske hemije. Nagrađeni su: prof. Martin Karplus (Martin Karplus) sa Univerziteta u Strazburu, Francuska i Univerziteta Harvard, SAD, prof. Majkl Levit (Michael Levitt) sa Univerziteta Stenford, Los Anđeles, SAD i prof. Arieh Voršel (Arieh Warshel) sa Univerziteta Južna Kalifornija (USC), Los Anđeles, SAD i to za razvoj multi-scale modela za kompleksne hemijske sisteme' kaže se, između ostalog, u saopštenju Nobelovog komiteta za dodelu ovogodišnjih nagrada. Trojica naučnika su dobila Nobelovu nagradu za razvoj kompjuterskih modela za simuliranje hemijskih procesa, čime je ponuđen revolucionaran i univerzalan alat istraživačima u hemiji, dizajnerima novih lekova i inženjerima u različitim oblastima istraživanja. Dobitnici su prepoznati po tome što su 'preneli izvođenje eksperimenata u sajber prostor,' kaže se dalje u saopštenju.
PB  - Srpsko hemijsko društvo, Beograd
T2  - Hemijski pregled
T1  - Nobel prize 2013 for chemistry from the cyber space
T1  - Iz sajber prostora - Nobelova nagrada za hemiju 2013
VL  - 54
IS  - 6
SP  - 142
EP  - 147
UR  - https://hdl.handle.net/21.15107/rcub_cer_1171
ER  - 

@article{
author = "Popović, Dragan",
year = "2013",
abstract = "Nobel Prize 2013 for chemistry is awarded to three American scientists in the field of theoretical and computational chemistry. Awarded are: Prof. Martin Karplus (Université de Strasbourg, France and Harvard University, USA), Prof. Michael Levitt (Stanford University, Los Angeles, USA) and Prof. Arieh Warshel (University of Southern California, Los Angeles, USA) for development of the multi-scale models for the complex chemical systems. A brief overview of contributions, for which they have been awarded, is presented here., 'Nobelova nagrada za hemiju za 2013. godinu je dodeljena trojici naturalizovanih američkih naučnika iz oblasti teorijske i računarske hemije. Nagrađeni su: prof. Martin Karplus (Martin Karplus) sa Univerziteta u Strazburu, Francuska i Univerziteta Harvard, SAD, prof. Majkl Levit (Michael Levitt) sa Univerziteta Stenford, Los Anđeles, SAD i prof. Arieh Voršel (Arieh Warshel) sa Univerziteta Južna Kalifornija (USC), Los Anđeles, SAD i to za razvoj multi-scale modela za kompleksne hemijske sisteme' kaže se, između ostalog, u saopštenju Nobelovog komiteta za dodelu ovogodišnjih nagrada. Trojica naučnika su dobila Nobelovu nagradu za razvoj kompjuterskih modela za simuliranje hemijskih procesa, čime je ponuđen revolucionaran i univerzalan alat istraživačima u hemiji, dizajnerima novih lekova i inženjerima u različitim oblastima istraživanja. Dobitnici su prepoznati po tome što su 'preneli izvođenje eksperimenata u sajber prostor,' kaže se dalje u saopštenju.",
publisher = "Srpsko hemijsko društvo, Beograd",
journal = "Hemijski pregled",
title = "Nobel prize 2013 for chemistry from the cyber space, Iz sajber prostora - Nobelova nagrada za hemiju 2013",
volume = "54",
number = "6",
pages = "142-147",
url = "https://hdl.handle.net/21.15107/rcub_cer_1171"
}

Popović, D.. (2013). Nobel prize 2013 for chemistry from the cyber space. in Hemijski pregled
Srpsko hemijsko društvo, Beograd., 54(6), 142-147.
https://hdl.handle.net/21.15107/rcub_cer_1171

Popović D. Nobel prize 2013 for chemistry from the cyber space. in Hemijski pregled. 2013;54(6):142-147.
https://hdl.handle.net/21.15107/rcub_cer_1171 .

Popović, Dragan, "Nobel prize 2013 for chemistry from the cyber space" in Hemijski pregled, 54, no. 6 (2013):142-147,
https://hdl.handle.net/21.15107/rcub_cer_1171 .

TY  - JOUR
AU  - Popović, Dragan
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1195
AB  - The function of cytochrome c oxidase as a biomolecular nanomachine that transforms energy of redox reaction into protonmotive force across a biological membrane has been subject of intense research, debate, and controversy. The structure of the enzyme has been solved for several organisms; however details of its molecular mechanism of proton pumping still remain elusive. Particularly, the identity of the proton pumping site, the key element of the mechanism, is still open to dispute. The pumping mechanism has been for a long time one of the key unsolved issues of bioenergetics and biochemistry, but with the accelerating progress in this field many important details and principles have emerged. Current advances in cytochrome oxidase research are reviewed here, along with a brief discussion of the most complete proton pumping mechanism proposed to date, and a molecular basis for control of its efficiency.
PB  - Springer Wien, Wien
T2  - Amino Acids
T1  - Current advances in research of cytochrome c oxidase
VL  - 45
IS  - 5
SP  - 1073
EP  - 1087
DO  - 10.1007/s00726-013-1585-y
ER  - 

@article{
author = "Popović, Dragan",
year = "2013",
abstract = "The function of cytochrome c oxidase as a biomolecular nanomachine that transforms energy of redox reaction into protonmotive force across a biological membrane has been subject of intense research, debate, and controversy. The structure of the enzyme has been solved for several organisms; however details of its molecular mechanism of proton pumping still remain elusive. Particularly, the identity of the proton pumping site, the key element of the mechanism, is still open to dispute. The pumping mechanism has been for a long time one of the key unsolved issues of bioenergetics and biochemistry, but with the accelerating progress in this field many important details and principles have emerged. Current advances in cytochrome oxidase research are reviewed here, along with a brief discussion of the most complete proton pumping mechanism proposed to date, and a molecular basis for control of its efficiency.",
publisher = "Springer Wien, Wien",
journal = "Amino Acids",
title = "Current advances in research of cytochrome c oxidase",
volume = "45",
number = "5",
pages = "1073-1087",
doi = "10.1007/s00726-013-1585-y"
}

Popović, D.. (2013). Current advances in research of cytochrome c oxidase. in Amino Acids
Springer Wien, Wien., 45(5), 1073-1087.
https://doi.org/10.1007/s00726-013-1585-y

Popović D. Current advances in research of cytochrome c oxidase. in Amino Acids. 2013;45(5):1073-1087.
doi:10.1007/s00726-013-1585-y .

Popović, Dragan, "Current advances in research of cytochrome c oxidase" in Amino Acids, 45, no. 5 (2013):1073-1087,
https://doi.org/10.1007/s00726-013-1585-y . .

TY  - JOUR
AU  - Popović, Dragan M.
AU  - Stuchebrukhov, Alexei A.
PY  - 2004
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7100
AB  - Cytochrome c oxidase (CcO) is the terminal enzyme of the cell respiratory chain in mitochondria and aerobic bacteria. It catalyzes the reduction of oxygen to water and utilizes the free energy of the reduction reaction for proton pumping across the inner-mitochondrial membrane, a process that results in a membrane electrochemical proton gradient. Although the structure of the enzyme has been solved for several organisms, the molecular mechanism of proton pumping remains unknown. In the present paper, continuum electrostatic calculations were employed to evaluate the electrostatic potential, energies, and protonation state of bovine heart cytochrome c oxidase for different redox states of the enzyme along its catalytic cycle. Three different computational models of the enzyme were employed to test the stability of the results. The energetics and pH dependence of the P→F, F→O, and O→E steps of the cycle have been investigated. On the basis of electrostatic calculations, two possible schemes of redox-linked proton pumping are discussed. The first scheme involves His291 as a pump element, whereas the second scheme involves a group linked to propionate D of heme a3. In both schemes, loading of the pump site is coupled to ET between the two hemes of the enzyme, while transfer of a chemical proton is accompanied by ejection of the pumped H+. The two models, as well as the energetics results are compared with recent experimental kinetic data. The proton pumping across the membrane is an endergonic process, which requires a sufficient amount of energy to be provided by the chemical reaction in the active site. In our calculations, the conversion of OH- to H2O provides 520 meV of energy to displace pump protons from a loading site and overall about 635 meV for each electron passing through the system. Assuming that the two charges are translocated per electron against the membrane potential of 200 meV, the model predicts an overall efficiency of 63%.
PB  - American Chemical Society (ACS)
T2  - Journal of the American Chemical Society
T1  - Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome                    c                    Oxidase
VL  - 126
IS  - 6
SP  - 1858
EP  - 1871
DO  - 10.1021/ja038267w
ER  - 

@article{
author = "Popović, Dragan M. and Stuchebrukhov, Alexei A.",
year = "2004",
abstract = "Cytochrome c oxidase (CcO) is the terminal enzyme of the cell respiratory chain in mitochondria and aerobic bacteria. It catalyzes the reduction of oxygen to water and utilizes the free energy of the reduction reaction for proton pumping across the inner-mitochondrial membrane, a process that results in a membrane electrochemical proton gradient. Although the structure of the enzyme has been solved for several organisms, the molecular mechanism of proton pumping remains unknown. In the present paper, continuum electrostatic calculations were employed to evaluate the electrostatic potential, energies, and protonation state of bovine heart cytochrome c oxidase for different redox states of the enzyme along its catalytic cycle. Three different computational models of the enzyme were employed to test the stability of the results. The energetics and pH dependence of the P→F, F→O, and O→E steps of the cycle have been investigated. On the basis of electrostatic calculations, two possible schemes of redox-linked proton pumping are discussed. The first scheme involves His291 as a pump element, whereas the second scheme involves a group linked to propionate D of heme a3. In both schemes, loading of the pump site is coupled to ET between the two hemes of the enzyme, while transfer of a chemical proton is accompanied by ejection of the pumped H+. The two models, as well as the energetics results are compared with recent experimental kinetic data. The proton pumping across the membrane is an endergonic process, which requires a sufficient amount of energy to be provided by the chemical reaction in the active site. In our calculations, the conversion of OH- to H2O provides 520 meV of energy to displace pump protons from a loading site and overall about 635 meV for each electron passing through the system. Assuming that the two charges are translocated per electron against the membrane potential of 200 meV, the model predicts an overall efficiency of 63%.",
publisher = "American Chemical Society (ACS)",
journal = "Journal of the American Chemical Society",
title = "Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome                    c                    Oxidase",
volume = "126",
number = "6",
pages = "1858-1871",
doi = "10.1021/ja038267w"
}

Popović, D. M.,& Stuchebrukhov, A. A.. (2004). Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome                    c                    Oxidase. in Journal of the American Chemical Society
American Chemical Society (ACS)., 126(6), 1858-1871.
https://doi.org/10.1021/ja038267w

Popović DM, Stuchebrukhov AA. Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome                    c                    Oxidase. in Journal of the American Chemical Society. 2004;126(6):1858-1871.
doi:10.1021/ja038267w .

Popović, Dragan M., Stuchebrukhov, Alexei A., "Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome                    c                    Oxidase" in Journal of the American Chemical Society, 126, no. 6 (2004):1858-1871,
https://doi.org/10.1021/ja038267w . .